Robust stability of fractional order polynomials with complicated uncertainty structure

PubMed Central

Şenol, Bilal; Pekař, Libor

2017-01-01

The main aim of this article is to present a graphical approach to robust stability analysis for families of fractional order (quasi-)polynomials with complicated uncertainty structure. More specifically, the work emphasizes the multilinear, polynomial and general structures of uncertainty and, moreover, the retarded quasi-polynomials with parametric uncertainty are studied. Since the families with these complex uncertainty structures suffer from the lack of analytical tools, their robust stability is investigated by numerical calculation and depiction of the value sets and subsequent application of the zero exclusion condition. PMID:28662173

Unstalled flutter stability predictions and comparisons to test data for a composite prop-fan model

NASA Technical Reports Server (NTRS)

Turnberg, J. E.

1986-01-01

The aeroelastic stability analyses for three graphite/epoxy composite Prop-Fan designs and post-test stability analysis for one of the designs, the SR-3C-X2 are presented. It was shown that Prop-Fan stability can be effectively analyzed using the F203 modal aeroelastic stability analysis developed at Hamilton Standard and that first mode torsion-bending coupling has a direct effect on blade stability. Positive first mode torsion-bending coupling is a destabilizing factor and the minimization of this parameter will increase Prop-Fan stability. It was also shown that Prop-Fan stability analysis using F203 is sensitive to the blade modal data used as input. Calculated blade modal properties varied significantly with the structural analysis used, and these variations are reflected in the F203 calculations.

Recent Advances in Heliogyro Solar Sail Structural Dynamics, Stability, and Control Research

NASA Technical Reports Server (NTRS)

Wilkie, W. Keats; Warren, Jerry E.; Horta, Lucas G.; Lyle, Karen H.; Juang, Jer-Nan; Gibbs, S. Chad; Dowell, Earl H.; Guerrant, Daniel V.; Lawrence, Dale

2015-01-01

Results from recent NASA sponsored research on the structural dynamics, stability, and control characteristics of heliogyro solar sails are summarized. Specific areas under investigation include coupled nonlinear finite element analysis of heliogyro membrane blade with solar radiation pressure effects, system identification of spinning membrane structures, and solarelastic stability analysis of heliogyro solar sails, including stability during blade deployment. Recent results from terrestrial 1-g blade dynamics and control experiments on "rope ladder" membrane blade analogs, and small-scale in vacuo system identification experiments with hanging and spinning high-aspect ratio membranes will also be presented. A low-cost, rideshare payload heliogyro technology demonstration mission concept is used as a mission context for these heliogyro structural dynamics and solarelasticity investigations, and is also described. Blade torsional dynamic response and control are also shown to be significantly improved through the use of edge stiffening structural features or inclusion of modest tip masses to increase centrifugal stiffening of the blade structure. An output-only system identification procedure suitable for on-orbit blade dynamics investigations is also developed and validated using ground tests of spinning sub-scale heliogyro blade models. Overall, analytical and experimental investigations to date indicate no intractable stability or control issues for the heliogyro solar sail concept.

Constraint Network Analysis (CNA): a Python software package for efficiently linking biomacromolecular structure, flexibility, (thermo-)stability, and function.

PubMed

Pfleger, Christopher; Rathi, Prakash Chandra; Klein, Doris L; Radestock, Sebastian; Gohlke, Holger

2013-04-22

For deriving maximal advantage from information on biomacromolecular flexibility and rigidity, results from rigidity analyses must be linked to biologically relevant characteristics of a structure. Here, we describe the Python-based software package Constraint Network Analysis (CNA) developed for this task. CNA functions as a front- and backend to the graph-based rigidity analysis software FIRST. CNA goes beyond the mere identification of flexible and rigid regions in a biomacromolecule in that it (I) provides a refined modeling of thermal unfolding simulations that also considers the temperature-dependence of hydrophobic tethers, (II) allows performing rigidity analyses on ensembles of network topologies, either generated from structural ensembles or by using the concept of fuzzy noncovalent constraints, and (III) computes a set of global and local indices for quantifying biomacromolecular stability. This leads to more robust results from rigidity analyses and extends the application domain of rigidity analyses in that phase transition points ("melting points") and unfolding nuclei ("structural weak spots") are determined automatically. Furthermore, CNA robustly handles small-molecule ligands in general. Such advancements are important for applying rigidity analysis to data-driven protein engineering and for estimating the influence of ligand molecules on biomacromolecular stability. CNA maintains the efficiency of FIRST such that the analysis of a single protein structure takes a few seconds for systems of several hundred residues on a single core. These features make CNA an interesting tool for linking biomacromolecular structure, flexibility, (thermo-)stability, and function. CNA is available from http://cpclab.uni-duesseldorf.de/software for nonprofit organizations.

Computational Analysis Reveals the Association of Threonine 118 Methionine Mutation in PMP22 Resulting in CMT-1A

PubMed Central

Swetha, Rayapadi G.

2014-01-01

The T118M mutation in PMP22 gene is associated with Charcot Marie Tooth, type 1A (CMT1A). CMT1A is a form of Charcot-Marie-Tooth disease, the most common inherited disorder of the peripheral nervous system. Mutations in CMT related disorder are seen to increase the stability of the protein resulting in the diseased state. We performed SNP analysis for all the nsSNPs of PMP22 protein and carried out molecular dynamics simulation for T118M mutation to compare the stability difference between the wild type protein structure and the mutant protein structure. The mutation T118M resulted in the overall increase in the stability of the mutant protein. The superimposed structure shows marked structural variation between the wild type and the mutant protein structures. PMID:25400662

Recent Progress in Heliogyro Solar Sail Structural Dynamics

NASA Technical Reports Server (NTRS)

Wilkie, William K.; Warren, Jerry E.; Horta, Lucas G.; Juang, Jer-Nan; Gibbs, Samuel C.; Dowell, E.; Guerrant, Daniel; Lawrence Dale

2014-01-01

Results from recent National Aeronautics and Space Administration (NASA) research on the structural dynamics and control characteristics of heliogyro solar sails are summarized. Specific areas under investigation include coupled nonlinear finite element analysis of heliogyro membrane blade with solar radiation pressure effects, system identification of spinning membrane structures, solarelastic stability analysis of heliogyro solar sails, including stability during blade deployment, and results from small-scale in vacuo dynamics experiments with spinning high-aspect ratio membranes. A low-cost, rideshare payload heliogyro technology demonstration mission concept, used as a mission context for these heliogyro structural dynamics and solarelasticity investigations, is also described.

Floquet analysis of Kuznetsov-Ma breathers: A path towards spectral stability of rogue waves.

PubMed

Cuevas-Maraver, J; Kevrekidis, P G; Frantzeskakis, D J; Karachalios, N I; Haragus, M; James, G

2017-07-01

In the present work, we aim at taking a step towards the spectral stability analysis of Peregrine solitons, i.e., wave structures that are used to emulate extreme wave events. Given the space-time localized nature of Peregrine solitons, this is a priori a nontrivial task. Our main tool in this effort will be the study of the spectral stability of the periodic generalization of the Peregrine soliton in the evolution variable, namely the Kuznetsov-Ma breather. Given the periodic structure of the latter, we compute the corresponding Floquet multipliers, and examine them in the limit where the period of the orbit tends to infinity. This way, we extrapolate towards the stability of the limiting structure, namely the Peregrine soliton. We find that multiple unstable modes of the background are enhanced, yet no additional unstable eigenmodes arise as the Peregrine limit is approached. We explore the instability evolution also in direct numerical simulations.

Benchmarking the stability of human detergent-solubilised voltage-gated sodium channels for structural studies using eel as a reference

PubMed Central

Slowik, Daria; Henderson, Richard

2015-01-01

With the ultimate goal of detailed structural analysis of mammalian and particularly human voltage-gated sodium channels (VGSCs), we have investigated the relative stability of human and rat VGSCs and compared them with electric eel VGSC. We found that NaV1.3 from rat was the most stable after detergent solubilisation. The order of stability was rNaV1.3 > hNaV1.2 > hNaV1.1 > hNaV1.6 > hNaV1.3 > hNaV1.4. However, a comparison with the VGSC from Electrophorus electricus, which is most similar to NaV1.4, shows that the eel VGSC is considerably more stable in detergent than the human VGSCs examined. We conclude that current methods of structural analysis, such as single particle electron cryomicroscopy (cryoEM), may be most usefully targeted to eel VGSC or rNaV1.3, but that structural analysis on the full spectrum of VGSCs, by methods that require greater stability such as crystallisation and X-ray crystallography, will require further stabilisation of the channel. PMID:25838126

The role of stabilization centers in protein thermal stability

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

Magyar, Csaba; Gromiha, M. Michael; Sávoly, Zoltán

2016-02-26

The definition of stabilization centers was introduced almost two decades ago. They are centers of noncovalent long range interaction clusters, believed to have a role in maintaining the three-dimensional structure of proteins by preventing their decay due to their cooperative long range interactions. Here, this hypothesis is investigated from the viewpoint of thermal stability for the first time, using a large protein thermodynamics database. The positions of amino acids belonging to stabilization centers are correlated with available experimental thermodynamic data on protein thermal stability. Our analysis suggests that stabilization centers, especially solvent exposed ones, do contribute to the thermal stabilizationmore » of proteins. - Highlights: • Stabilization centers contribute to thermal stabilization of protein structures. • Stabilization center content correlates with melting temperature of proteins. • Exposed stabilization center content correlates with stability even in hyperthermophiles. • Stability changing mutations are frequently found at stabilization centers.« less

Stability of elastic bending and torsion of uniform cantilever rotor blades in hover with variable structural coupling

NASA Technical Reports Server (NTRS)

Hodges, D. H., Roberta.

1976-01-01

The stability of elastic flap bending, lead-lag bending, and torsion of uniform, untwisted, cantilever rotor blades without chordwise offsets between the elastic, mass, tension, and areodynamic center axes is investigated for the hovering flight condition. The equations of motion are obtained by simplifying the general, nonlinear, partial differential equations of motion of an elastic rotating cantilever blade. The equations are adapted for a linearized stability analysis in the hovering flight condition by prescribing aerodynamic forces, applying Galerkin's method, and linearizing the resulting ordinary differential equations about the equilibrium operating condition. The aerodynamic forces are obtained from strip theory based on a quasi-steady approximation of two-dimensional unsteady airfoil theory. Six coupled mode shapes, calculated from free vibration about the equilibrium operating condition, are used in the linearized stability analysis. The study emphasizes the effects of two types of structural coupling that strongly influence the stability of hingeless rotor blades. The first structural coupling is the linear coupling between flap and lead-lag bending of the rotor blade. The second structural coupling is a nonlinear coupling between flap bending, lead-lag bending, and torsion deflections. Results are obtained for a wide variety of hingeless rotor configurations and operating conditions in order to provide a reasonably complete picture of hingeless rotor blade stability characteristics.

Substructure analysis using NICE/SPAR and applications of force to linear and nonlinear structures. [spacecraft masts

NASA Technical Reports Server (NTRS)

Razzaq, Zia; Prasad, Venkatesh; Darbhamulla, Siva Prasad; Bhati, Ravinder; Lin, Cai

1987-01-01

Parallel computing studies are presented for a variety of structural analysis problems. Included are the substructure planar analysis of rectangular panels with and without a hole, the static analysis of space mast, using NICE/SPAR and FORCE, and substructure analysis of plane rigid-jointed frames using FORCE. The computations are carried out on the Flex/32 MultiComputer using one to eighteen processors. The NICE/SPAR runstream samples are documented for the panel problem. For the substructure analysis of plane frames, a computer program is developed to demonstrate the effectiveness of a substructuring technique when FORCE is enforced. Ongoing research activities for an elasto-plastic stability analysis problem using FORCE, and stability analysis of the focus problem using NICE/SPAR are briefly summarized. Speedup curves for the panel, the mast, and the frame problems provide a basic understanding of the effectiveness of parallel computing procedures utilized or developed, within the domain of the parameters considered. Although the speedup curves obtained exhibit various levels of computational efficiency, they clearly demonstrate the excellent promise which parallel computing holds for the structural analysis problem. Source code is given for the elasto-plastic stability problem and the FORCE program.

Flight-determined stability analysis of multiple-input-multiple-output control systems

NASA Technical Reports Server (NTRS)

Burken, John J.

1992-01-01

Singular value analysis can give conservative stability margin results. Applying structure to the uncertainty can reduce this conservatism. This paper presents flight-determined stability margins for the X-29A lateral-directional, multiloop control system. These margins are compared with the predicted unscaled singular values and scaled structured singular values. The algorithm was further evaluated with flight data by changing the roll-rate-to-aileron command-feedback gain by +/- 20 percent. Minimum eigenvalues of the return difference matrix which bound the singular values are also presented. Extracting multiloop singular values from flight data and analyzing the feedback gain variations validates this technique as a measure of robustness. This analysis can be used for near-real-time flight monitoring and safety testing.

Flight-determined stability analysis of multiple-input-multiple-output control systems

NASA Technical Reports Server (NTRS)

Burken, John J.

1992-01-01

Singular value analysis can give conservative stability margin results. Applying structure to the uncertainty can reduce this conservatism. This paper presents flight-determined stability margins for the X-29A lateral-directional, multiloop control system. These margins are compared with the predicted unscaled singular values and scaled structured singular values. The algorithm was further evaluated with flight data by changing the roll-rate-to-aileron-command-feedback gain by +/- 20 percent. Also presented are the minimum eigenvalues of the return difference matrix which bound the singular values. Extracting multiloop singular values from flight data and analyzing the feedback gain variations validates this technique as a measure of robustness. This analysis can be used for near-real-time flight monitoring and safety testing.

Modelling, design and stability analysis of an improved SEPIC converter for renewable energy systems

NASA Astrophysics Data System (ADS)

G, Dileep; Singh, S. N.; Singh, G. K.

2017-09-01

In this paper, a detailed modelling and analysis of a switched inductor (SI)-based improved single-ended primary inductor converter (SEPIC) has been presented. To increase the gain of conventional SEPIC converter, input and output side inductors are replaced with SI structures. Design and stability analysis for continuous conduction mode operation of the proposed SI-SEPIC converter has also been presented in this paper. State space averaging technique is used to model the converter and carry out the stability analysis. Performance and stability analysis of closed loop configuration is predicted by observing the open loop behaviour using Nyquist diagram and Nichols chart. System was found to stable and critically damped.

Elastic stability of biaxially loaded longitudinally stiffened composite structures.

NASA Technical Reports Server (NTRS)

Viswanathan, A. V.; Tamekuni, M.; Tripp, L. L.

1973-01-01

A linear analysis method is presented for the elastic stability of structures of uniform cross section, that may be idealized as an assemblage of laminated plate-strips, flat and curved, and beams. Each plate-strip and beam covers the entire length of the structure and is simply supported on the edges normal to the longitudinal axis. Arbitrary boundary conditions may be specified on any external longitudinal side of plate-strips. The structure or selected plate-strips may be loaded in any desired combination of inplane biaxial loads. The analysis simultaneously considers all modes of instability and is applicable for the buckling of laminated composite structures. Some numerical results are presented to indicate possible applications.

Advanced composite vertical stabilizer for DC-10 transport aircraft

NASA Technical Reports Server (NTRS)

Stephens, C. O.

1978-01-01

The structural design configuration for the Composite Vertical Stabilizer is described and the structural design, analysis, and weight activities are presented. The status of fabrication and test activities for the development test portion of the program is described. Test results are presented for the skin panels, spar web, spar cap to cover, and laminate properties specimens. Engineering drawings of vertification test panels and root fittings, rudder support specimens, titanium fittings, and rear spar specimen analysis models are included.

Aging effects on vertical graphene nanosheets and their thermal stability

NASA Astrophysics Data System (ADS)

Ghosh, S.; Polaki, S. R.; Ajikumar, P. K.; Krishna, N. G.; Kamruddin, M.

2018-03-01

The present study investigates environmental aging effects and thermal stability of vertical graphene nanosheets (VGN). Self-organized VGN is synthesized by plasma enhanced chemical vapor deposition and exposed to ambient conditions over 6-month period to examine its aging behavior. A systematic inspection is carried out on morphology, chemical structure, wettability and electrical property by scanning electron microscopy, Raman spectroscopy, X-ray photoelectron spectroscopy, water contact angle and four-probe resistivity measurements at regular intervals, respectively. Detailed microscopic and spectroscopic analysis substantiated the retention of graphitic quality and surface chemistry of VGN over the test period. An unchanged sheet resistance and hydrophobicity reveals its electrical and wetting stability over the time, respectively. Thermogravimetric analysis ensures an excellent thermal stability of VGN up to 575 °C in ambient atmosphere. These findings of long-term morphological, structural, wetting, electrical and thermal stability of VGN validate their potential utilization for the next-generation device applications.

NASTRAN/FLEXSTAB procedure for static aeroelastic analysis

NASA Technical Reports Server (NTRS)

Schuster, L. S.

1984-01-01

Presented is a procedure for using the FLEXSTAB External Structural Influence Coefficients (ESIC) computer program to produce the structural data necessary for the FLEXSTAB Stability Derivatives and Static Stability (SD&SS) program. The SD&SS program computes trim state, stability derivatives, and pressure and deflection data for a flexible airplane having a plane of symmetry. The procedure used a NASTRAN finite-element structural model as the source of structural data in the form of flexibility matrices. Selection of a set of degrees of freedom, definition of structural nodes and panels, reordering and reformatting of the flexibility matrix, and redistribution of existing point mass data are among the topics discussed. Also discussed are boundary conditions and the NASTRAN substructuring technique.

ASTROP2 Users Manual: A Program for Aeroelastic Stability Analysis of Propfans

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Lucero, John M.

1996-01-01

This manual describes the input data required for using the second version of the ASTROP2 (Aeroelastic STability and Response Of Propulsion systems - 2 dimensional analysis) computer code. In ASTROP2, version 2.0, the program is divided into two modules: 2DSTRIP, which calculates the structural dynamic information; and 2DASTROP, which calculates the unsteady aerodynamic force coefficients from which the aeroelastic stability can be determined. In the original version of ASTROP2, these two aspects were performed in a single program. The improvements to version 2.0 include an option to account for counter rotation, improved numerical integration, accommodation for non-uniform inflow distribution, and an iterative scheme to flutter frequency convergence. ASTROP2 can be used for flutter analysis of multi-bladed structures such as those found in compressors, turbines, counter rotating propellers or propfans. The analysis combines a two-dimensional, unsteady cascade aerodynamics model and a three dimensional, normal mode structural model using strip theory. The flutter analysis is formulated in the frequency domain resulting in an eigenvalue determinant. The flutter frequency and damping can be inferred from the eigenvalues.

Determination of the oxidative stability of perfluoropolyalkyl ethers and correlation with chemical structure

NASA Technical Reports Server (NTRS)

Helmick, Larry S.; Jones, William R., Jr.

1992-01-01

The oxidative stabilities of several perfluoropolyalkyl ethers (PFPAE) with related chemical structures were determined by thermal gravimetric analysis and correlated with their chemical structures. These results show that oxidative stability increases as the number of difluoroformal groups decreases and as trifluoromethyl substituents are added. They are also consistent with a recently proposed intramolecular disproportionation reaction mechanism involving coordination of successive ether oxygens to a Lewis acid. Since polytetrafluoroethylene contains no oxygen, it provides an indication of the upper limit to oxidative stability of PFPAE fluids. These results also show that oxidative decomposition of PFPAE fluids requires the presence of an active metal as well as air. Consequently, it may be possible to minimize decomposition and thus improve oxidative stability by passivating reactive metal surfaces.

Enhancing synchronization stability in a multi-area power grid

PubMed Central

Wang, Bing; Suzuki, Hideyuki; Aihara, Kazuyuki

2016-01-01

Maintaining a synchronous state of generators is of central importance to the normal operation of power grids, in which many networks are generally interconnected. In order to understand the condition under which the stability can be optimized, it is important to relate network stability with feedback control strategies as well as network structure. Here, we present a stability analysis on a multi-area power grid by relating it with several control strategies and topological design of network structure. We clarify the minimal feedback gain in the self-feedback control, and build the optimal communication network for the local and global control strategies. Finally, we consider relationship between the interconnection pattern and the synchronization stability; by optimizing the network interlinks, the obtained network shows better synchronization stability than the original network does, in particular, at a high power demand. Our analysis shows that interlinks between spatially distant nodes will improve the synchronization stability. The results seem unfeasible to be implemented in real systems but provide a potential guide for the design of stable power systems. PMID:27225708

On the linear stability of sheared and magnetized jets without current sheets - relativistic case

NASA Astrophysics Data System (ADS)

Kim, Jinho; Balsara, Dinshaw S.; Lyutikov, Maxim; Komissarov, Serguei S.

2018-03-01

In our prior series of papers, we studied the non-relativistic and relativistic linear stability analysis of magnetized jets that do not have current sheets. In this paper, we extend our analysis to relativistic jets with a velocity shear and a similar current sheet free structure. The jets that we study are realistic because we include a velocity shear, a current sheet free magnetic structure, a relativistic velocity and a realistic thermal pressure so as to achieve overall pressure balance in the unperturbed jet. In order to parametrize the velocity shear, we apply a parabolic profile to the jets' 4-velocity. We find that the velocity shear significantly improves the stability of relativistic magnetized jets. This fact is completely consistent with our prior stability analysis of non-relativistic, sheared jets. The velocity shear mainly plays a role in stabilizing the short wavelength unstable modes for the pinch as well as the kink instability modes. In addition, it also stabilizes the long wavelength fundamental pinch instability mode. We also visualize the pressure fluctuations of each unstable mode to provide a better physical understanding of the enhanced stabilization by the velocity shear. Our overall conclusion is that combining velocity shear with a strong and realistic magnetic field makes relativistic jets even more stable.

The ring residue proline 8 is crucial for the thermal stability of the lasso peptide caulosegnin II.

PubMed

Hegemann, Julian D; Fage, Christopher D; Zhu, Shaozhou; Harms, Klaus; Di Leva, Francesco Saverio; Novellino, Ettore; Marinelli, Luciana; Marahiel, Mohamed A

2016-04-01

Lasso peptides are fascinating natural products with a unique structural fold that can exhibit tremendous thermal stability. Here, we investigate factors responsible for the thermal stability of caulosegnin II. By employing X-ray crystallography, mutational analysis and molecular dynamics simulations, the ring residue proline 8 was proven to be crucial for thermal stability.

Design, ancillary testing, analysis and fabrication data for the advanced composite stabilizer for Boeing 737 aircraft, volume 2

NASA Technical Reports Server (NTRS)

Aniversario, R. B.; Harvey, S. T.; Mccarty, J. E.; Parsons, J. T.; Peterson, D. C.; Pritchett, L. D.; Wilson, D. R.; Wogulis, E. R.

1982-01-01

Results of tests conducted to demonstrate that composite structures save weight, possess long term durability, and can be fabricated at costs competitive with conventional metal structures are presented with focus on the use of graphite-epoxy in the design of a stabilizer for the Boeing 737 aircraft. Component definition, materials evaluation, material design properties, and structural elements tests are discussed. Fabrication development, as well as structural repair and inspection are also examined.

Stability of Nonlinear Principal Components Analysis: An Empirical Study Using the Balanced Bootstrap

ERIC Educational Resources Information Center

Linting, Marielle; Meulman, Jacqueline J.; Groenen, Patrick J. F.; van der Kooij, Anita J.

2007-01-01

Principal components analysis (PCA) is used to explore the structure of data sets containing linearly related numeric variables. Alternatively, nonlinear PCA can handle possibly nonlinearly related numeric as well as nonnumeric variables. For linear PCA, the stability of its solution can be established under the assumption of multivariate…

Aeroelastic stability analyses of two counter rotating propfan designs for a cruise missile model

NASA Technical Reports Server (NTRS)

Mahajan, Aparajit J.; Lucero, John M.; Mehmed, Oral; Stefko, George L.

1992-01-01

Aeroelastic stability analyses were performed to insure structural integrity of two counterrotating propfan blade designs for a NAVY/Air Force/NASA cruise missile model wind tunnel test. This analysis predicted if the propfan designs would be flutter free at the operating conditions of the wind tunnel test. Calculated stability results are presented for the two blade designs with rotational speed and Mach number as the parameters. A aeroelastic analysis code ASTROP2 (Aeroelastic Stability and Response of Propulsion Systems - 2 Dimensional Analysis), developed at LeRC, was used in this project. The aeroelastic analysis is a modal method and uses the combination of a finite element structural model and two dimensional steady and unsteady cascade aerodynamic models. This code was developed to analyze single rotation propfans but was modified and applied to counterrotating propfans for the present work. Modifications were made to transform the geometry and rotation of the aft rotor to the same reference frame as the forward rotor, to input a non-uniform inflow into the rotor being analyzed, and to automatically converge to the least stable aeroelastic mode.

Stability analysis of fractional-order Hopfield neural networks with time delays.

PubMed

Wang, Hu; Yu, Yongguang; Wen, Guoguang

2014-07-01

This paper investigates the stability for fractional-order Hopfield neural networks with time delays. Firstly, the fractional-order Hopfield neural networks with hub structure and time delays are studied. Some sufficient conditions for stability of the systems are obtained. Next, two fractional-order Hopfield neural networks with different ring structures and time delays are developed. By studying the developed neural networks, the corresponding sufficient conditions for stability of the systems are also derived. It is shown that the stability conditions are independent of time delays. Finally, numerical simulations are given to illustrate the effectiveness of the theoretical results obtained in this paper. Copyright © 2014 Elsevier Ltd. All rights reserved.

Conformation and Stability of Intramolecular Telomeric G-Quadruplexes: Sequence Effects in the Loops

PubMed Central

Sattin, Giovanna; Artese, Anna; Nadai, Matteo; Costa, Giosuè; Parrotta, Lucia; Alcaro, Stefano; Palumbo, Manlio; Richter, Sara N.

2013-01-01

Telomeres are guanine-rich sequences that protect the ends of chromosomes. These regions can fold into G-quadruplex structures and their stabilization by G-quadruplex ligands has been employed as an anticancer strategy. Genetic analysis in human telomeres revealed extensive allelic variation restricted to loop bases, indicating that the variant telomeric sequences maintain the ability to fold into G-quadruplex. To assess the effect of mutations in loop bases on G-quadruplex folding and stability, we performed a comprehensive analysis of mutant telomeric sequences by spectroscopic techniques, molecular dynamics simulations and gel electrophoresis. We found that when the first position in the loop was mutated from T to C or A the resulting structure adopted a less stable antiparallel topology; when the second position was mutated to C or A, lower thermal stability and no evident conformational change were observed; in contrast, substitution of the third position from A to C induced a more stable and original hybrid conformation, while mutation to T did not significantly affect G-quadruplex topology and stability. Our results indicate that allelic variations generate G-quadruplex telomeric structures with variable conformation and stability. This aspect needs to be taken into account when designing new potential anticancer molecules. PMID:24367632

Structural and Functional Analysis of an mRNP Complex That Mediates the High Stability of Human β-Globin mRNA

PubMed Central

Yu, Jia; Russell, J. Eric

2001-01-01

Human globins are encoded by mRNAs exhibiting high stabilities in transcriptionally silenced erythrocyte progenitors. Unlike α-globin mRNA, whose stability is enhanced by assembly of a specific messenger RNP (mRNP) α complex on its 3′ untranslated region (UTR), neither the structure(s) nor the mechanism(s) that effects the high-level stability of human β-globin mRNA has been identified. The present work describes an mRNP complex assembling on the 3′ UTR of the β-globin mRNA that exhibits many of the properties of the stability-enhancing α complex. The β-globin mRNP complex is shown to contain one or more factors homologous to αCP, a 39-kDa RNA-binding protein that is integral to α-complex assembly. Sequence analysis implicates a specific 14-nucleotide pyrimidine-rich track within its 3′ UTR as the site of β-globin mRNP assembly. The importance of this track to mRNA stability is subsequently verified in vivo using mice expressing human β-globin transgenes that contain informative mutations in this region. In combination, the in vitro and in vivo analyses indicate that the high stabilities of the α- and β-globin mRNAs are maintained through related mRNP complexes that may share a common regulatory pathway. PMID:11486027

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

Accumulated experimental observations demonstrate that protein stability is often preserved upon conservative point mutation. In contrast, less is known about the effects of large sequence or structure changes on the stability of a particular fold. Almost completely unknown is the degree to which stability of different regions of a protein is generally preserved throughout evolution. In this work, these questions are addressed through thermodynamic analysis of a large representative sample of protein fold space based on remote, yet accepted, homology. More than 3,000 proteins were computationally analyzed using the structural-thermodynamic algorithm COREX/BEST. Estimated position-specific stability (i.e., local Gibbs free energy of folding) and its component enthalpy and entropy were quantitatively compared between all proteins in the sample according to all-vs.-all pairwise structural alignment. It was discovered that the local stabilities of homologous pairs were significantly more correlated than those of non-homologous pairs, indicating that local stability was indeed generally conserved throughout evolution. However, the position-specific enthalpy and entropy underlying stability were less correlated, suggesting that the overall regional stability of a protein was more important than the thermodynamic mechanism utilized to achieve that stability. Finally, two different types of statistically exceptional evolutionary structure-thermodynamic relationships were noted. First, many homologous proteins contained regions of similar thermodynamics despite localized structure change, suggesting a thermodynamic mechanism enabling evolutionary fold change. Second, some homologous proteins with extremely similar structures nonetheless exhibited different local stabilities, a phenomenon previously observed experimentally in this laboratory. These two observations, in conjunction with the principal conclusion that homologous proteins generally conserved local stability, may provide guidance for a future thermodynamically informed classification of protein homology.

Correlating the Impact of Well-Defined Oligosaccharide Structures on Physical Stability Profiles of IgG1-Fc Glycoforms.

PubMed

More, Apurva S; Toprani, Vishal M; Okbazghi, Solomon Z; Kim, Jae H; Joshi, Sangeeta B; Middaugh, C Russell; Tolbert, Thomas J; Volkin, David B

2016-02-01

As part of a series of articles in this special issue describing 4 well-defined IgG1-Fc glycoforms as a model system for biosimilarity analysis (high mannose-Fc, Man5-Fc, GlcNAc-Fc and N297Q-Fc aglycosylated), the focus of this work is comparisons of their physical properties. A trend of decreasing apparent solubility (thermodynamic activity) by polyethylene glycol precipitation (pH 4.5, 6.0) and lower conformational stability by differential scanning calorimetry (pH 4.5) was observed with reducing size of the N297-linked oligosaccharide structures. Using multiple high-throughput biophysical techniques, the physical stability of the Fc glycoproteins was then measured in 2 formulations (NaCl and sucrose) across a wide range of temperatures (10°C-90°C) and pH (4.0-7.5) conditions. The data sets were used to construct 3-index empirical phase diagrams and radar charts to visualize the regions of protein structural stability. Each glycoform showed improved stability in the sucrose (vs. salt) formulation. The HM-Fc and Man5-Fc displayed the highest relative stability, followed by GlcNAc-Fc, with N297Q-Fc being the least stable. Thus, the overall physical stability profiles of the 4 IgG1-Fc glycoforms also show a correlation with oligosaccharide structure. These data sets are used to develop a mathematical model for biosimilarity analysis (as described in a companion article by Kim et al. in this issue). Copyright © 2016 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

The Structure and Temporal Stability of the Child and Adolescent Perfectionism Scale

ERIC Educational Resources Information Center

O'Connor, Rory C.; Dixon, Diane; Rasmussen, Susan

2009-01-01

In this study, the authors examined the factor structure and temporal stability of the Child and Adolescent Perfectionism Scale (CAPS; G. L. Flett, P. L. Hewitt, D. J. Boucher, L. A. Davidson, & Y. Munro, 1997) in 2 samples of adolescents (15-16 years old). In Sample 1 (n = 624), confirmatory factor analysis did not support a 2-factor structure…

Structural and physical properties of collagen extracted from moon jellyfish under neutral pH conditions.

PubMed

Miki, Ayako; Inaba, Satomi; Baba, Takayuki; Kihira, Koji; Fukada, Harumi; Oda, Masayuki

2015-01-01

We extracted collagen from moon jellyfish under neutral pH conditions and analyzed its amino acid composition, secondary structure, and thermal stability. The content of hydroxyproline was 4.3%, which is lower than that of other collagens. Secondary structure analysis using circular dichroism (CD) showed a typical collagen helix. The thermal stability of this collagen at pH 3.0 was lower than those from fish scale and pig skin, which also correlates closely with jellyfish collagen having lower hydroxyproline content. Because the solubility of jellyfish collagen used in this study at neutral pH was quite high, it was possible to analyze its structural and physical properties under physiological conditions. Thermodynamic analysis using CD and differential scanning calorimetry showed that the thermal stability at pH 7.5 was higher than at pH 3.0, possibly due to electrostatic interactions. During the process of unfolding, fibrillation would occur only at neutral pH.

Thermostability of In Vitro Evolved Bacillus subtilis Lipase A: A Network and Dynamics Perspective

PubMed Central

Srivastava, Ashutosh; Sinha, Somdatta

2014-01-01

Proteins in thermophilic organisms remain stable and function optimally at high temperatures. Owing to their important applicability in many industrial processes, such thermostable proteins have been studied extensively, and several structural factors attributed to their enhanced stability. How these factors render the emergent property of thermostability to proteins, even in situations where no significant changes occur in their three-dimensional structures in comparison to their mesophilic counter-parts, has remained an intriguing question. In this study we treat Lipase A from Bacillus subtilis and its six thermostable mutants in a unified manner and address the problem with a combined complex network-based analysis and molecular dynamic studies to find commonality in their properties. The Protein Contact Networks (PCN) of the wild-type and six mutant Lipase A structures developed at a mesoscopic scale were analyzed at global network and local node (residue) level using network parameters and community structure analysis. The comparative PCN analysis of all proteins pointed towards important role of specific residues in the enhanced thermostability. Network analysis results were corroborated with finer-scale molecular dynamics simulations at both room and high temperatures. Our results show that this combined approach at two scales can uncover small but important changes in the local conformations that add up to stabilize the protein structure in thermostable mutants, even when overall conformation differences among them are negligible. Our analysis not only supports the experimentally determined stabilizing factors, but also unveils the important role of contacts, distributed throughout the protein, that lead to thermostability. We propose that this combined mesoscopic-network and fine-grained molecular dynamics approach is a convenient and useful scheme not only to study allosteric changes leading to protein stability in the face of negligible over-all conformational changes due to mutations, but also in other molecular networks where change in function does not accompany significant change in the network structure. PMID:25122499

Stability and Control Analysis of the F-15B Quiet SpikeTM Aircraft

NASA Technical Reports Server (NTRS)

McWherter, Shaun C.; Moua, Cheng M.; Gera, Joseph; Cox, Timothy H.

2009-01-01

The primary purpose of the Quiet Spike(TradeMark) flight research program was to analyze the aerodynamic, structural, and mechanical proof-of-concept of a large multi-stage telescoping nose spike installed on the National Aeronautics and Space Administration Dryden Flight Research Center (Edwards, California) F-15B airplane. This report describes the preflight stability and control analysis performed to assess the effect of the spike on the stability, controllability, and handling qualities of the airplane; and to develop an envelope expansion approach to maintain safety of flight. The overall flight test objective was to collect flight data to validate the spike structural dynamics and loads model up to Mach 1.8. Other objectives included validating the mechanical feasibility of a morphing fuselage at operational conditions and determining the near-field shock wave characterization. The two main issues relevant to the stability and control objectives were the effects of the spike-influenced aerodynamics on the F-15B airplane flight dynamics, and the air data and angle-of-attack sensors. The analysis covered the sensitivity of the stability margins, and the handling qualities due to aerodynamic variation and the maneuvering limitations of the F-15B Quiet Spike configuration. The results of the analysis and the implications for the flight test program are also presented.

Stability analysis of magnetized neutron stars - a semi-analytic approach

NASA Astrophysics Data System (ADS)

Herbrik, Marlene; Kokkotas, Kostas D.

2017-04-01

We implement a semi-analytic approach for stability analysis, addressing the ongoing uncertainty about stability and structure of neutron star magnetic fields. Applying the energy variational principle, a model system is displaced from its equilibrium state. The related energy density variation is set up analytically, whereas its volume integration is carried out numerically. This facilitates the consideration of more realistic neutron star characteristics within the model compared to analytical treatments. At the same time, our method retains the possibility to yield general information about neutron star magnetic field and composition structures that are likely to be stable. In contrast to numerical studies, classes of parametrized systems can be studied at once, finally constraining realistic configurations for interior neutron star magnetic fields. We apply the stability analysis scheme on polytropic and non-barotropic neutron stars with toroidal, poloidal and mixed fields testing their stability in a Newtonian framework. Furthermore, we provide the analytical scheme for dropping the Cowling approximation in an axisymmetric system and investigate its impact. Our results confirm the instability of simple magnetized neutron star models as well as a stabilization tendency in the case of mixed fields and stratification. These findings agree with analytical studies whose spectrum of model systems we extend by lifting former simplifications.

[The functional state classification and evaluation of the stability level in mental loads based on the factor structure of heart rate variability parameters].

PubMed

Mashin, V A; Mashina, M N

2004-12-01

In the paper, outcomes of the researches devoted to factor analysis of heart rate variability parameters and definition of the most informative parameters for diagnostics of functional states and an evaluation of level of stability to mental loads, are presented. The factor structure of parameters, which unclude integral level of heart rate variability (1), balance between activity of vagus and brain cortical-limbic systems (2), integrated level of cardiovascular system functioning (3), is substantiated. Factor analysis outcomes have been used for construction of functional state classification, for their differential diagnostics, and for development and check of algorithm for evaluation of the stability level in mental loads.

Assessment of physical stability of an antibody drug conjugate by higher order structure analysis: impact of thiol- maleimide chemistry.

PubMed

Guo, Jianxin; Kumar, Sandeep; Prashad, Amarnauth; Starkey, Jason; Singh, Satish K

2014-07-01

To provide a systematic biophysical approach towards a better understanding of impact of conjugation chemistry on higher order structure and physical stability of an antibody drug conjugate (ADC). ADC was prepared using thiol-maleimide chemistry. Physical stabilities of ADC and its parent IgG1 mAb were compared using calorimetric, spectroscopic and molecular modeling techniques. ADC and mAb respond differently to thermal stress. Both the melting temperatures and heat capacities are substantially lower for the ADC. Spectroscopic experiments show that ADC and mAb have similar secondary and tertiary structures, but these are more easily destabilized by thermal stress on the ADC indicating reduced conformational stability. Molecular modeling calculations suggest a substantial decrease in the conformational energy of the mAb upon conjugation. The local surface around the conjugation sites also becomes more hydrophobic in the ADC, explaining the lower colloidal stability and greater tendency of the ADC to aggregate. Computational and biophysical analyses of an ADC and its parent mAb have provided insights into impact of conjugation on physical stability and pinpointed reasons behind lower structural stability and increased aggregation propensity of the ADC. This knowledge can be used to design appropriate formulations to stabilize the ADC.

Soluble fullerene derivatives: The effect of electronic structure on transistor performance and air stability

NASA Astrophysics Data System (ADS)

Ball, James M.; Bouwer, Ricardo K. M.; Kooistra, Floris B.; Frost, Jarvist M.; Qi, Yabing; Domingo, Ester Buchaca; Smith, Jeremy; de Leeuw, Dago M.; Hummelen, Jan C.; Nelson, Jenny; Kahn, Antoine; Stingelin, Natalie; Bradley, Donal D. C.; Anthopoulos, Thomas D.

2011-07-01

The family of soluble fullerene derivatives comprises a widely studied group of electron transporting molecules for use in organic electronic and optoelectronic devices. For electronic applications, electron transporting (n-channel) materials are required for implementation into organic complementary logic circuit architectures. To date, few soluble candidate materials have been studied that fulfill the stringent requirements of high carrier mobility and air stability. Here we present a study of three soluble fullerenes with varying electron affinity to assess the impact of electronic structure on device performance and air stability. Through theoretical and experimental analysis of the electronic structure, characterization of thin-film structure, and characterization of transistor device properties we find that the air stability of the present series of fullerenes not only depends on the absolute electron affinity of the semiconductor but also on the disorder within the thin-film.

Static and dynamic stability analysis of the space shuttle vehicle-orbiter

NASA Technical Reports Server (NTRS)

Chyu, W. J.; Cavin, R. K.; Erickson, L. L.

1978-01-01

The longitudinal static and dynamic stability of a Space Shuttle Vehicle-Orbiter (SSV Orbiter) model is analyzed using the FLEXSTAB computer program. Nonlinear effects are accounted for by application of a correction technique in the FLEXSTAB system; the technique incorporates experimental force and pressure data into the linear aerodynamic theory. A flexible Orbiter model is treated in the static stability analysis for the flight conditions of Mach number 0.9 for rectilinear flight (1 g) and for a pull-up maneuver (2.5 g) at an altitude of 15.24 km. Static stability parameters and structural deformations of the Orbiter are calculated at trim conditions for the dynamic stability analysis, and the characteristics of damping in pitch are investigated for a Mach number range of 0.3 to 1.2. The calculated results for both the static and dynamic stabilities are compared with the available experimental data.

Thermochemical Stability Study of Alkyl-Tethered Quaternary Ammonium Cations for Anion Exchange Membrane Fuel Cells

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

Mohanty, Angela D.; Tignor, Steven E.; Sturgeon, Matthew R.

2017-01-01

The increased interest in the use of anion exchange membranes (AEMs) for applications in electrochemical devices has prompted significant efforts in designing materials with robust stability in alkaline media. Most reported AEMs suffer from polymer backbone degradation as well as cation functional group degradation. In this report, we provide comprehensive experimental investigations for the analysis of cation functional group stability under alkaline media. A silver oxide-mediated ion exchange method and an accelerated stability test in aqueous KOH solutions at elevated temperatures using a Parr reactor were used to evaluate a broad scope of quaternary ammonium (QA) cationic model compound structures,more » particularly focusing on alkyl-tethered cations. Additionally, byproduct analysis was employed to gain better understanding of degradation pathways and trends of alkaline stability. Experimental results under different conditions gave consistent trends in the order of cation stability of various QA small molecule model compounds. Overall, cations that are benzyl-substituted or that are near to electronegative atoms (such as oxygen) degrade faster in alkaline media in comparison to alkyl-tethered QAs. These comprehensive model compound stability studies provide valuable information regarding the relative stability of various cation structures and can help guide researchers towards designing new and promising candidates for AEM materials.« less

Large-scale systems: Complexity, stability, reliability

NASA Technical Reports Server (NTRS)

Siljak, D. D.

1975-01-01

After showing that a complex dynamic system with a competitive structure has highly reliable stability, a class of noncompetitive dynamic systems for which competitive models can be constructed is defined. It is shown that such a construction is possible in the context of the hierarchic stability analysis. The scheme is based on the comparison principle and vector Liapunov functions.

Polyhydroxy surfactants for the formulation of lipid nanoparticles (SLN and NLC): effects on size, physical stability and particle matrix structure.

PubMed

Kovacevic, A; Savic, S; Vuleta, G; Müller, R H; Keck, C M

2011-03-15

The two polyhydroxy surfactants polyglycerol 6-distearate (Plurol(®)Stearique WL1009 - (PS)) and caprylyl/capryl glucoside (Plantacare(®) 810 - (PL)) are a class of PEG-free stabilizers, made from renewable resources. They were investigated for stabilization of aqueous solid lipid nanoparticle (SLN) and nanostructured lipid carrier (NLC) dispersions. Production was performed by high pressure homogenization, analysis by photon correlation spectroscopy (PCS), laser diffraction (LD), zeta potential measurements and differential scanning calorimetry (DSC). Particles were made from Cutina CP as solid lipid only (SLN) and its blends with Miglyol 812 (NLC, the blends containing increasing amounts of oil from 20% to 60%). The obtained particle sizes were identical for both surfactants, about 200 nm with polydispersity indices below 0.20 (PCS), and unimodal size distribution (LD). All dispersions with both surfactants were physically stable for 3 months at room temperature, but Plantacare (PL) showing a superior stability. The melting behaviour and crystallinity of bulk lipids/lipid blends were compared to the nanoparticles. Both were lower for the nanoparticles. The crystallinity of dispersions stabilized with PS was higher, the zeta potential decreased with storage time associated with this higher crystallinity, and leading to a few, but negligible larger particles. The lower crystallinity particles stabilized with PL remained unchanged in zeta potential (about -50 mV) and in size. These data show that surfactants have a distinct influence on the particle matrix structure (and related stability and drug loading), to which too little attention was given by now. Despite being from the same surfactant class, the differences on the structure are pronounced. They are attributed to the hydrophobic-lipophilic tail structure with one-point anchoring in the interface (PL), and the loop conformation of PS with two hydrophobic anchor points, i.e. their molecular structure and its interaction with the matrix surface and matrix bulk. Analysis of the effects of the surfactants on the particle matrix structure could potentially be used to further optimization of stability, drug loading and may be drug release. Copyright © 2011 Elsevier B.V. All rights reserved.

Experimental techniques for studying the structure of foams and froths.

PubMed

Pugh, R J

2005-06-30

Several techniques are described in this review to study the structure and the stability of froths and foams. Image analysis proved useful for detecting structure changes in 2-D foams and has enabled the drainage process and the gradients in bubble size distribution to be determined. However, studies on 3-D foams require more complex techniques such as Multiple-Light Scattering Methods, Microphones and Optical Tomography. Under dynamic foaming conditions, the Foam Scan Column enables the water content of foams to be determined by conductivity analysis. It is clear that the same factors, which play a role in foam stability (film thickness, elasticity, etc.) also have a decisive influence on the stability of isolated froth or foam films. Therefore, the experimental thin film balance (developed by the Bulgarian Researchers) to study thinning of microfilms formed by a concave liquid drop suspended in a short vertical capillary tube has proved useful. Direct measurement of the thickness of the aqueous microfilm is determined by a micro-reflectance method and can give fundamental information on drainage and thin film stability. It is also important to consider the influence of the mineral particles on the stability of the froth and it have been shown that particles of well defined size and hydrophobicity can be introduced into the thin film enabling stabilization/destabilization mechanisms to be proposed. It has also been shown that the dynamic and static stability can be increased by a reduction in particle size and an increase in particle concentration.

Stability region maximization by decomposition-aggregation method. [Skylab stability

NASA Technical Reports Server (NTRS)

Siljak, D. D.; Cuk, S. M.

1974-01-01

This work is to improve the estimates of the stability regions by formulating and resolving a proper maximization problem. The solution of the problem provides the best estimate of the maximal value of the structural parameter and at the same time yields the optimum comparison system, which can be used to determine the degree of stability of the Skylab. The analysis procedure is completely computerized, resulting in a flexible and powerful tool for stability considerations of large-scale linear as well as nonlinear systems.

Highly Dynamic Anion-Quadrupole Networks in Proteins.

PubMed

Kapoor, Karan; Duff, Michael R; Upadhyay, Amit; Bucci, Joel C; Saxton, Arnold M; Hinde, Robert J; Howell, Elizabeth E; Baudry, Jerome

2016-11-01

The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.

Thermal Stability of RNA Structures with Bulky Cations in Mixed Aqueous Solutions.

PubMed

Nakano, Shu-Ichi; Tanino, Yuichi; Hirayama, Hidenobu; Sugimoto, Naoki

2016-10-04

Bulky cations are used to develop nucleic-acid-based technologies for medical and technological applications in which nucleic acids function under nonaqueous conditions. In this study, the thermal stability of RNA structures was measured in the presence of various bulky cations in aqueous mixtures with organic solvents or polymer additives. The stability of oligonucleotide, transfer RNA, and polynucleotide structures was decreased in the presence of salts of tetrabutylammonium and tetrapentylammonium ions, and the stability and salt concentration dependences were dependent on cation sizes. The degree to which stability was dependent on salt concentration was correlated with reciprocals of the dielectric constants of mixed solutions, regardless of interactions between the cosolutes and RNA. Our results show that organic solvents affect the strength of electrostatic interactions between RNA and cations. Analysis of ion binding to RNA indicated greater enhancement of cation binding to RNA single strands than to duplexes in media with low dielectric constants. Furthermore, background bulky ions changed the dependence of RNA duplex stability on the concentration of metal ion salts. These unique properties of large tetraalkylammonium ions are useful for controlling the stability of RNA structures and its sensitivity to metal ion salts. Copyright © 2016 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Projection-based stabilization of interface Lagrange multipliers in immersogeometric fluid-thin structure interaction analysis, with application to heart valve modeling.

PubMed

Kamensky, David; Evans, John A; Hsu, Ming-Chen; Bazilevs, Yuri

2017-11-01

This paper discusses a method of stabilizing Lagrange multiplier fields used to couple thin immersed shell structures and surrounding fluids. The method retains essential conservation properties by stabilizing only the portion of the constraint orthogonal to a coarse multiplier space. This stabilization can easily be applied within iterative methods or semi-implicit time integrators that avoid directly solving a saddle point problem for the Lagrange multiplier field. Heart valve simulations demonstrate applicability of the proposed method to 3D unsteady simulations. An appendix sketches the relation between the proposed method and a high-order-accurate approach for simpler model problems.

Influence of different metal ions on the ultrastructure, biochemical properties, and protein localization of the K562 cell nuclear matrix.

PubMed

Neri, L M; Bortul, R; Zweyer, M; Tabellini, G; Borgatti, P; Marchisio, M; Bareggi, R; Capitani, S; Martelli, A M

1999-06-01

The higher order of chromatin organization is thought to be determined by the nuclear matrix, a mainly proteinaceous structure that would act as a nucleoskeleton. The matrix is obtained from isolated nuclei by a series of extraction steps involving the use of high salt and nonspecific nucleases, which remove chromatin and other loosely bound components. It is currently under debate whether these structures, isolated in vitro by unphysiological extraction buffers, correspond to a nucleoskeleton existing in vivo. In most cell types investigated, the nuclear matrix does not spontaneously resist these extractions steps; rather, it must be stabilized before the application of extracting agents. In this study nuclei, isolated from K562 human erythroleukemia cells, were stabilized by incubation with different metal ions (Ca2+, Cu2+, Zn2+, Cd2+), and the matrix was obtained by extraction with 2 M NaCl. By means of ultrastructural analysis of the resulting structures, we determined that, except for Ca2+, all the other metals induced a stabilization of the matrix, which retained the inner fibrogranular network and residual nucleoli. The biochemical composition, analyzed by two-dimensional gel electrophoresis separation, exhibited a distinct matrix polypeptide pattern, characteristic of each type of stabilizing ion employed. We also investigated to what extent metal ions could maintain in the final structures the original distribution of three inner matrix components, i.e. NuMA, topoisomerase IIalpha, and RNP. Confocal microscopy analysis showed that only NuMa, and, to a lesser extent, topoisomerase IIalpha, were unaffected by stabilization with divalent ions. On the contrary, the fluorescent RNP patterns detected in the resulting matrices were always disarranged, irrespective of the stabilization procedure. These results indicate that several metal ions are powerful stabilizing agents of the nuclear matrix prepared from K562 erythroleukemia cells and also strengthen the concept that NuMA and topoisomerase IIalpha may act as structural components of the nuclear matrix.

X-ray source assembly having enhanced output stability, and fluid stream analysis applications thereof

DOEpatents

Radley, Ian [Glenmont, NY; Bievenue, Thomas J [Delmar, NY; Burdett, John H [Charlton, NY; Gallagher, Brian W [Guilderland, NY; Shakshober, Stuart M [Hudson, NY; Chen, Zewu [Schenectady, NY; Moore, Michael D [Alplaus, NY

2008-06-08

An x-ray source assembly and method of operation are provided having enhanced output stability. The assembly includes an anode having a source spot upon which electrons impinge and a control system for controlling position of the anode source spot relative to an output structure. The control system can maintain the anode source spot location relative to the output structure notwithstanding a change in one or more operating conditions of the x-ray source assembly. One aspect of the disclosed invention is most amenable to the analysis of sulfur in petroleum-based fuels.

Stability of mixed time integration schemes for transient thermal analysis

NASA Technical Reports Server (NTRS)

Liu, W. K.; Lin, J. I.

1982-01-01

A current research topic in coupled-field problems is the development of effective transient algorithms that permit different time integration methods with different time steps to be used simultaneously in various regions of the problems. The implicit-explicit approach seems to be very successful in structural, fluid, and fluid-structure problems. This paper summarizes this research direction. A family of mixed time integration schemes, with the capabilities mentioned above, is also introduced for transient thermal analysis. A stability analysis and the computer implementation of this technique are also presented. In particular, it is shown that the mixed time implicit-explicit methods provide a natural framework for the further development of efficient, clean, modularized computer codes.

Thermodynamics-hydration relationships within loops that affect G-quadruplexes under molecular crowding conditions.

PubMed

Fujimoto, Takeshi; Nakano, Shu-ichi; Sugimoto, Naoki; Miyoshi, Daisuke

2013-01-31

We systematically investigated the effects of loop length on the conformation, thermodynamic stability, and hydration of DNA G-quadruplexes under dilute and molecular crowding conditions in the presence of Na(+). Structural analysis showed that molecular crowding induced conformational switches of oligonucleotides with the longer guanine stretch and the shorter thymine loop. Thermodynamic parameters further demonstrated that the thermodynamic stability of G-quadruplexes increased by increasing the loop length from two to four, whereas it decreased by increasing the loop length from four to six. Interestingly, we found by osmotic pressure analysis that the number of water molecules released from the G-quadruplex decreased with increasing thermodynamic stability. We assumed that base-stacking interactions within the loops not only stabilized the whole G-quadruplex structure but also created hydration sites by accumulating nucleotide functional groups. The molecular crowding effects on the stability of G-quadruplexes composed of abasic sites, which reduce the stacking interactions at the loops, further demonstrated that G-quadruplexes with fewer stacking interactions within the loops released a larger number of water molecules upon folding. These results showed that the stacking interactions within the loops determined the thermodynamic stability and hydration of the whole G-quadruplex.

Predicting the Influence of Nano-Scale Material Structure on the In-Plane Buckling of Orthotropic Plates

NASA Technical Reports Server (NTRS)

Gates, Thomas S.; Odegard, Gregory M.; Nemeth, Michael P.; Frankland, Sarah-Jane V.

2004-01-01

A multi-scale analysis of the structural stability of a carbon nanotube-polymer composite material is developed. The influence of intrinsic molecular structure, such as nanotube length, volume fraction, orientation and chemical functionalization, is investigated by assessing the relative change in critical, in-plane buckling loads. The analysis method relies on elastic properties predicted using the hierarchical, constitutive equations developed from the equivalent-continuum modeling technique applied to the buckling analysis of an orthotropic plate. The results indicate that for the specific composite materials considered in this study, a composite with randomly orientated carbon nanotubes consistently provides the highest values of critical buckling load and that for low volume fraction composites, the non-functionalized nanotube material provides an increase in critical buckling stability with respect to the functionalized system.

Computational analysis of histidine mutations on the structural stability of human tyrosinases leading to albinism insurgence.

PubMed

Hassan, Mubashir; Abbas, Qamar; Raza, Hussain; Moustafa, Ahmed A; Seo, Sung-Yum

2017-07-25

Misfolding and structural alteration in proteins lead to serious malfunctions and cause various diseases in humans. Mutations at the active binding site in tyrosinase impair structural stability and cause lethal albinism by abolishing copper binding. To evaluate the histidine mutational effect, all mutated structures were built using homology modelling. The protein sequence was retrieved from the UniProt database, and 3D models of original and mutated human tyrosinase sequences were predicted by changing the residual positions within the target sequence separately. Structural and mutational analyses were performed to interpret the significance of mutated residues (N 180 , R 202 , Q 202 , R 211 , Y 363 , R 367 , Y 367 and D 390 ) at the active binding site of tyrosinases. CSpritz analysis depicted that 23.25% residues actively participate in the instability of tyrosinase. The accuracy of predicted models was confirmed through online servers ProSA-web, ERRAT score and VERIFY 3D values. The theoretical pI and GRAVY generated results also showed the accuracy of the predicted models. The CCA negative correlation results depicted that the replacement of mutated residues at His within the active binding site disturbs the structural stability of tyrosinases. The predicted CCA scores of Tyr 367 (-0.079) and Q/R 202 (0.032) revealed that both mutations have more potential to disturb the structural stability. MD simulation analyses of all predicted models justified that Gln 202 , Arg 202 , Tyr 367 and D 390 replacement made the protein structures more susceptible to destabilization. Mutational results showed that the replacement of His with Q/R 202 and Y/R 363 has a lethal effect and may cause melanin associated diseases such as OCA1. Taken together, our computational analysis depicts that the mutated residues such as Q/R 202 and Y/R 363 actively participate in instability and misfolding of tyrosinases, which may govern OCA1 through disturbing the melanin biosynthetic pathway.

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

Theisen, Matthew K.; Lafontaine Rivera, Jimmy G.; Liao, James C.

Stability in a metabolic system may not be obtained if incorrect amounts of enzymes are used. Without stability, some metabolites may accumulate or deplete leading to the irreversible loss of the desired operating point. Even if initial enzyme amounts achieve a stable steady state, changes in enzyme amount due to stochastic variations or environmental changes may move the system to the unstable region and lose the steady-state or quasi-steady-state flux. This situation is distinct from the phenomenon characterized by typical sensitivity analysis, which focuses on the smooth change before loss of stability. Here we show that metabolic networks differ significantlymore » in their intrinsic ability to attain stability due to the network structure and kinetic forms, and that after achieving stability, some enzymes are prone to cause instability upon changes in enzyme amounts. We use Ensemble Modelling for Robustness Analysis (EMRA) to analyze stability in four cell-free enzymatic systems when enzyme amounts are changed. Loss of stability in continuous systems can lead to lower production even when the system is tested experimentally in batch experiments. The predictions of instability by EMRA are supported by the lower productivity in batch experimental tests. Finally, the EMRA method incorporates properties of network structure, including stoichiometry and kinetic form, but does not require specific parameter values of the enzymes.« less

Residue-residue contacts: application to analysis of secondary structure interactions.

PubMed

Potapov, Vladimir; Edelman, Marvin; Sobolev, Vladimir

2013-01-01

Protein structures and their complexes are formed and stabilized by interactions, both inside and outside of the protein. Analysis of such interactions helps in understanding different levels of structures (secondary, super-secondary, and oligomeric states). It can also assist molecular biologists in understanding structural consequences of modifying proteins and/or ligands. In this chapter, our definition of atom-atom and residue-residue contacts is described and applied to analysis of protein-protein interactions in dimeric β-sandwich proteins.

Hamiltonian dynamics for complex food webs

NASA Astrophysics Data System (ADS)

Kozlov, Vladimir; Vakulenko, Sergey; Wennergren, Uno

2016-03-01

We investigate stability and dynamics of large ecological networks by introducing classical methods of dynamical system theory from physics, including Hamiltonian and averaging methods. Our analysis exploits the topological structure of the network, namely the existence of strongly connected nodes (hubs) in the networks. We reveal new relations between topology, interaction structure, and network dynamics. We describe mechanisms of catastrophic phenomena leading to sharp changes of dynamics and hence completely altering the ecosystem. We also show how these phenomena depend on the structure of interaction between species. We can conclude that a Hamiltonian structure of biological interactions leads to stability and large biodiversity.

Dynamic Stability of Uncertain Laminated Beams Under Subtangential Loads

NASA Technical Reports Server (NTRS)

Goyal, Vijay K.; Kapania, Rakesh K.; Adelman, Howard (Technical Monitor); Horta, Lucas (Technical Monitor)

2002-01-01

Because of the inherent complexity of fiber-reinforced laminated composites, it can be challenging to manufacture composite structures according to their exact design specifications, resulting in unwanted material and geometric uncertainties. In this research, we focus on the deterministic and probabilistic stability analysis of laminated structures subject to subtangential loading, a combination of conservative and nonconservative tangential loads, using the dynamic criterion. Thus a shear-deformable laminated beam element, including warping effects, is derived to study the deterministic and probabilistic response of laminated beams. This twenty-one degrees of freedom element can be used for solving both static and dynamic problems. In the first-order shear deformable model used here we have employed a more accurate method to obtain the transverse shear correction factor. The dynamic version of the principle of virtual work for laminated composites is expressed in its nondimensional form and the element tangent stiffness and mass matrices are obtained using analytical integration The stability is studied by giving the structure a small disturbance about an equilibrium configuration, and observing if the resulting response remains small. In order to study the dynamic behavior by including uncertainties into the problem, three models were developed: Exact Monte Carlo Simulation, Sensitivity Based Monte Carlo Simulation, and Probabilistic FEA. These methods were integrated into the developed finite element analysis. Also, perturbation and sensitivity analysis have been used to study nonconservative problems, as well as to study the stability analysis, using the dynamic criterion.

Influence of the type of aqueous sodium silicate on the stabilization and rheology of kaolin clay suspensions

NASA Astrophysics Data System (ADS)

Izak, Piotr; Ogłaza, Longin; Mozgawa, Włodzimierz; Mastalska-Popławska, Joanna; Stempkowska, Agata

2018-05-01

To avoid agglomeration and sedimentation of grains, ceramic slurries should be modified by stabilizers in order to increase the electrostatic interactions between the dispersed particles. In this study we present the spectral analysis of aqueous sodium silicates obtained by different synthesis methods and their influence on the rheological properties of kaolin based slurries. Infrared and Raman spectra can be used to describe the structure of silicate structural units present in aqueous sodium silicates. It was confirmed that the best stabilization results possess aqueous sodium silicates of the silicate moduli of about 2 and the optimal concentration of the used fluidizer is 0.3 wt% to the kaolin clay dry mass. One of the most important conclusions is that the synthesis method of the fluidizer has no significant effect on its stabilization properties but used medium does create adequate stabilization mechanism depending on the silicate structures present in the sodium silicate solution.

Structural design and analysis for an ultra low CTE optical bench for the Hubble Space Telescope corrective optics

NASA Technical Reports Server (NTRS)

Neam, Douglas C.; Gerber, John D.

1992-01-01

The stringent stability requirements of the Corrective Optics Space Telescope Axial Replacement (COSTAR) necessitates a Deployable Optical Bench (DOB) with both a low CTE and high resonant frequency. The DOB design consists of a monocoque thin shell structure which marries metallic machined parts with graphite epoxy formed structure. Structural analysis of the DOB has been integrated into the laminate design and optimization process. Also, the structural analytical results are compared with vibration and thermal test data to assess the reliability of the analysis.

Stability of the iterative solutions of integral equations as one phase freezing criterion.

PubMed

Fantoni, R; Pastore, G

2003-10-01

A recently proposed connection between the threshold for the stability of the iterative solution of integral equations for the pair correlation functions of a classical fluid and the structural instability of the corresponding real fluid is carefully analyzed. Direct calculation of the Lyapunov exponent of the standard iterative solution of hypernetted chain and Percus-Yevick integral equations for the one-dimensional (1D) hard rods fluid shows the same behavior observed in 3D systems. Since no phase transition is allowed in such 1D system, our analysis shows that the proposed one phase criterion, at least in this case, fails. We argue that the observed proximity between the numerical and the structural instability in 3D originates from the enhanced structure present in the fluid but, in view of the arbitrary dependence on the iteration scheme, it seems uneasy to relate the numerical stability analysis to a robust one-phase criterion for predicting a thermodynamic phase transition.

Correlation of analytical and experimental hot structure vibration results

NASA Technical Reports Server (NTRS)

Kehoe, Michael W.; Deaton, Vivian C.

1993-01-01

High surface temperatures and temperature gradients can affect the vibratory characteristics and stability of aircraft structures. Aircraft designers are relying more on finite-element model analysis methods to ensure sufficient vehicle structural dynamic stability throughout the desired flight envelope. Analysis codes that predict these thermal effects must be correlated and verified with experimental data. Experimental modal data for aluminum, titanium, and fiberglass plates heated at uniform, nonuniform, and transient heating conditions are presented. The data show the effect of heat on each plate's modal characteristics, a comparison of predicted and measured plate vibration frequencies, the measured modal damping, and the effect of modeling material property changes and thermal stresses on the accuracy of the analytical results at nonuniform and transient heating conditions.

Stability of Ensemble Models Predicts Productivity of Enzymatic Systems

DOE PAGES

Theisen, Matthew K.; Lafontaine Rivera, Jimmy G.; Liao, James C.

2016-03-10

Stability in a metabolic system may not be obtained if incorrect amounts of enzymes are used. Without stability, some metabolites may accumulate or deplete leading to the irreversible loss of the desired operating point. Even if initial enzyme amounts achieve a stable steady state, changes in enzyme amount due to stochastic variations or environmental changes may move the system to the unstable region and lose the steady-state or quasi-steady-state flux. This situation is distinct from the phenomenon characterized by typical sensitivity analysis, which focuses on the smooth change before loss of stability. Here we show that metabolic networks differ significantlymore » in their intrinsic ability to attain stability due to the network structure and kinetic forms, and that after achieving stability, some enzymes are prone to cause instability upon changes in enzyme amounts. We use Ensemble Modelling for Robustness Analysis (EMRA) to analyze stability in four cell-free enzymatic systems when enzyme amounts are changed. Loss of stability in continuous systems can lead to lower production even when the system is tested experimentally in batch experiments. The predictions of instability by EMRA are supported by the lower productivity in batch experimental tests. Finally, the EMRA method incorporates properties of network structure, including stoichiometry and kinetic form, but does not require specific parameter values of the enzymes.« less

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.

Spanwise effects on instabilities of compressible flow over a long rectangular cavity

NASA Astrophysics Data System (ADS)

Sun, Y.; Taira, K.; Cattafesta, L. N.; Ukeiley, L. S.

2017-12-01

The stability properties of two-dimensional (2D) and three-dimensional (3D) compressible flows over a rectangular cavity with length-to-depth ratio of L/D=6 are analyzed at a free-stream Mach number of M_∞ =0.6 and depth-based Reynolds number of Re_D=502. In this study, we closely examine the influence of three-dimensionality on the wake mode that has been reported to exhibit high-amplitude fluctuations from the formation and ejection of large-scale spanwise vortices. Direct numerical simulation (DNS) and bi-global stability analysis are utilized to study the stability characteristics of the wake mode. Using the bi-global stability analysis with the time-averaged flow as the base state, we capture the global stability properties of the wake mode at a spanwise wavenumber of β =0. To uncover spanwise effects on the 2D wake mode, 3D DNS are performed with cavity width-to-depth ratio of W/D=1 and 2. We find that the 2D wake mode is not present in the 3D cavity flow with W/D=2, in which spanwise structures are observed near the rear region of the cavity. These 3D instabilities are further investigated via bi-global stability analysis for spanwise wavelengths of λ /D=0.5{-}2.0 to reveal the eigenspectra of the 3D eigenmodes. Based on the findings of 2D and 3D global stability analysis, we conclude that the absence of the wake mode in 3D rectangular cavity flows is due to the release of kinetic energy from the spanwise vortices to the streamwise vortical structures that develops from the spanwise instabilities.

Colour stability of aesthetic brackets: ceramic and plastic.

PubMed

Filho, Hibernon Lopes; Maia, Lúcio Henrique; Araújo, Marcus V; Eliast, Carlos Nelson; Ruellas, Antônio Carlos O

2013-05-01

The colour stability of aesthetic brackets may differ according to their composition, morphology and surface property, which may consequently influence their aesthetic performance. To assess the colour stability of aesthetic brackets (ceramic and plastic) after simulating aging and staining. Twelve commercially manufactured ceramic brackets and four different plastic brackets were assessed. To determine possible colour change (change of E*(ab)) and the value of the NBS (National Bureau of Standards) unit system, spectrophotometric colour measurements for CIE L*, a* and b* were taken before and after the brackets were aged and stained. Statistical analysis was undertaken using a one-way ANOVA analysis of variance and a Tukey multiple comparison test (alpha = 0.05). The colour change between the various (ceramic and plastic) materials was not significant (p > 0.05), but still varied significantly (p < 0.001) between the brackets of the same composition or crystalline structure and among commercial brands. Colour stability cannot be confirmed simply by knowing the type of material and crystalline composition or structure.

Structural stability of rubble-pile asteroids

NASA Astrophysics Data System (ADS)

Sharma, Ishan

2013-03-01

Granular aggregates, like fluids, do not admit all manners of shapes and rotation rates. It is hoped that an analysis of a suspected granular asteroid’s equilibrium shape and its structural stability will help confirm its rubble-pile nature, and, perhaps, even constrain the asteroid’s material parameters. Equilibrium shapes have been analyzed in the past by several investigators (Holsapple, K.A. [2001]. Icarus 154, 432-448; Harris, A.W., Fahnestock, E.G., Pravec, P. [2009]. Icarus 199, 310-318; Sharma, I., Jenkins, J.T., Burns, J.A. [2009]. Icarus 200, 304-322). Here, we extend the classical Lagrange-Dirichlet stability theorem to the case of self-gravitating granular aggregates. This stability test is then applied to probe the stability of several near-Earth asteroids, and explore the influence of material parameters such as internal friction angle and plastic bulk modulus. Finally, we consider their structural stability to close planetary encounters. We find that it is possible for asteroids to be stable to small perturbations, but unstable to strong and/or extended perturbations as experienced during close flybys. Conversely, assuming stability in certain situations, it is possible to estimate material properties of some asteroids like, for example, 1943 Anteros.

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

Moczydlowski, Edward G.

Ion channel proteins regulate complex patterns of cellular electrical activity and ionic signaling. Certain K+ channels play an important role in immunological biodefense mechanisms of adaptive and innate immunity. Most ion channel proteins are oligomeric complexes with the conductive pore located at the central subunit interface. The long-term activity of many K+ channel proteins is dependent on the concentration of extracellular K+; however, the mechanism is unclear. Thus, this project focused on mechanisms underlying structural stability of tetrameric K+ channels. Using KcsA of Streptomyces lividans as a model K+ channel of known structure, the molecular basis of tetramer stability wasmore » investigated by: 1. Bioinformatic analysis of the tetramer interface. 2. Effect of two local anesthetics (lidocaine, tetracaine) on tetramer stability. 3. Molecular simulation of drug docking to the ion conduction pore. The results provide new insights regarding the structural stability of K+ channels and its possible role in cell physiology.« less

Active vibration suppression of helicopter horizontal stabilizers

NASA Astrophysics Data System (ADS)

Cinquemani, Simone; Cazzulani, Gabriele; Resta, Ferruccio

2017-04-01

Helicopters are among the most complex machines ever made. While ensuring high performance from the aeronautical point of view, they are not very comfortable due to vibration mainly created by the main rotor and by the interaction with the surrounding air. One of the most solicited structural elements of the vehicle are the horizontal stabilizers. These elements are particularly stressed because of their composite structure which, while guaranteeing lightness and strength, is characterized by a low damping. This work makes a preliminary analysis on the dynamics of the structure and proposes different solutions to actively suppress vibrations. Among them, the best in terms of the relationship between performance and weight / complexity of the system is that based on inertial actuators mounted on the inside of the horizontal stabilizers. The work addresses the issue of the design of the device and its use in the stabilizer from both the numerical and the experimental points of view.

Study on antibacterial alginate-stabilized copper nanoparticles by FT-IR and 2D-IR correlation spectroscopy

PubMed Central

Díaz-Visurraga, Judith; Daza, Carla; Pozo, Claudio; Becerra, Abraham; von Plessing, Carlos; García, Apolinaria

2012-01-01

Background The objective of this study was to clarify the intermolecular interaction between antibacterial copper nanoparticles (Cu NPs) and sodium alginate (NaAlg) by Fourier transform infrared spectroscopy (FT-IR) and to process the spectra applying two-dimensional infrared (2D-IR) correlation analysis. To our knowledge, the addition of NaAlg as a stabilizer of copper nanoparticles has not been previously reported. It is expected that the obtained results will provide valuable additional information on: (1) the influence of reducing agent ratio on the formation of copper nanoparticles in order to design functional nanomaterials with increased antibacterial activity, and (2) structural changes related to the incorporation of Cu NPs into the polymer matrix. Methods Cu NPs were prepared by microwave heating using ascorbic acid as reducing agent and NaAlg as stabilizing agent. The characterization of synthesized Cu NPs by ultraviolet visible spectroscopy, transmission electron microscopy (TEM), electron diffraction analysis, X-ray diffraction (XRD), and semiquantitative analysis of the weight percentage composition indicated that the average particle sizes of Cu NPs are about 3–10 nm, they are spherical in shape, and consist of zerovalent Cu and Cu2O. Also, crystallite size and relative particle size of stabilized Cu NPs were calculated by XRD using Scherrer’s formula and FT from the X-ray diffraction data. Thermogravimetric analysis, differential thermal analysis, differential scanning calorimetry (DSC), FT-IR, second-derivative spectra, and 2D-IR correlation analysis were applied to studying the stabilization mechanism of Cu NPs by NaAlg molecules. The minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of stabilized Cu NPs against five bacterial strains (Staphylococccus aureus ATCC 6538P, Escherichia coli ATCC 25922 and O157: H7, and Salmonella enterica serovar Typhimurium ATCC 13311 and 14028) were evaluated with macrodilution, agar dilution plate count, and well-diffusion methods. Results On the basis of the semiquantitative analysis, there was a direct correlation between the reducing agent ratio and the percentage of zerovalent Cu. This was confirmed with the statistical analysis of population of Cu NPs from TEM micrographs. At lower reducing agent ratios, two phases coexist (Cu2O and zerovalent Cu) due to incomplete reduction of copper ions by the reducing agent; however, at higher reducing agent ratios, the Cu NPs consist mainly of zerovalent Cu. Crystallite size and relative particle size of stabilized Cu NPs showed considerable differences in results and tendencies in respect to TEM analysis. However, the relative particle size values obtained from FT of XRD data agreed well with the histograms from the TEM observations. From FT results, the relative particle size and reducing agent ratio of stabilized Cu NPs showed an inverse correlation. The incomplete reduction of copper ions at lower reducing agent ratios was also confirmed by DSC studies. FT-IR and 2D-IR correlation spectra analysis suggested the first event involved in the stabilization of Cu NPs is their electrostatic interaction with –C=O of carboxylate groups of NaAlg, followed by the interaction with the available O–C–O−, and finally with the –OH groups. Bacterial susceptibility to stabilized nanoparticles was found to vary depending on the bacterial strains. The lowest MIC and MBC of stabilized Cu NPs ranged between 2 mg/L and 8 mg/L for all studied strains. Disk-diffusion studies with both E. coli strains revealed greater effectiveness of the stabilized Cu NPs compared to the positive controls (cloxacillin, amoxicillin, and nitrofurantoin). S. aureus showed the highest sensitivity to stabilized Cu NPs compared to the other studied strains. Conclusion Cu NPs were successfully synthesized via chemical reduction assisted with microwave heating. Average particle size, polydispersity, and phase composition of Cu NPs depended mainly on the reducing agent ratio. Likewise, thermal stability and antibacterial activity of stabilized Cu NPs were affected by their phase composition. Because of the carboxylate groups in polymer chains, the structural changes of stabilized Cu NPs are different from those of NaAlg. NaAlg acted as a size controller and stabilizing agent of Cu NPs, due to their ability to bind strongly to the metal surface. Our study on the stabilizing agent–dependent structural changes of stabilized NPs is helpful for wide application of NaAlg as an important biopolymer. PMID:22848180

Structural adaptation of cold-active RTX lipase from Pseudomonas sp. strain AMS8 revealed via homology and molecular dynamics simulation approaches.

PubMed

Mohamad Ali, Mohd Shukuri; Mohd Fuzi, Siti Farhanie; Ganasen, Menega; Abdul Rahman, Raja Noor Zaliha Raja; Basri, Mahiran; Salleh, Abu Bakar

2013-01-01

The psychrophilic enzyme is an interesting subject to study due to its special ability to adapt to extreme temperatures, unlike typical enzymes. Utilizing computer-aided software, the predicted structure and function of the enzyme lipase AMS8 (LipAMS8) (isolated from the psychrophilic Pseudomonas sp., obtained from the Antarctic soil) are studied. The enzyme shows significant sequence similarities with lipases from Pseudomonas sp. MIS38 and Serratia marcescens. These similarities aid in the prediction of the 3D molecular structure of the enzyme. In this study, 12 ns MD simulation is performed at different temperatures for structural flexibility and stability analysis. The results show that the enzyme is most stable at 0°C and 5°C. In terms of stability and flexibility, the catalytic domain (N-terminus) maintained its stability more than the noncatalytic domain (C-terminus), but the non-catalytic domain showed higher flexibility than the catalytic domain. The analysis of the structure and function of LipAMS8 provides new insights into the structural adaptation of this protein at low temperatures. The information obtained could be a useful tool for low temperature industrial applications and molecular engineering purposes, in the near future.

Lyapunov exponents, covariant vectors and shadowing sensitivity analysis of 3D wakes: from laminar to chaotic regimes

NASA Astrophysics Data System (ADS)

Wang, Qiqi; Rigas, Georgios; Esclapez, Lucas; Magri, Luca; Blonigan, Patrick

2016-11-01

Bluff body flows are of fundamental importance to many engineering applications involving massive flow separation and in particular the transport industry. Coherent flow structures emanating in the wake of three-dimensional bluff bodies, such as cars, trucks and lorries, are directly linked to increased aerodynamic drag, noise and structural fatigue. For low Reynolds laminar and transitional regimes, hydrodynamic stability theory has aided the understanding and prediction of the unstable dynamics. In the same framework, sensitivity analysis provides the means for efficient and optimal control, provided the unstable modes can be accurately predicted. However, these methodologies are limited to laminar regimes where only a few unstable modes manifest. Here we extend the stability analysis to low-dimensional chaotic regimes by computing the Lyapunov covariant vectors and their associated Lyapunov exponents. We compare them to eigenvectors and eigenvalues computed in traditional hydrodynamic stability analysis. Computing Lyapunov covariant vectors and Lyapunov exponents also enables the extension of sensitivity analysis to chaotic flows via the shadowing method. We compare the computed shadowing sensitivities to traditional sensitivity analysis. These Lyapunov based methodologies do not rely on mean flow assumptions, and are mathematically rigorous for calculating sensitivities of fully unsteady flow simulations.

Computational Modeling of Allosteric Regulation in the Hsp90 Chaperones: A Statistical Ensemble Analysis of Protein Structure Networks and Allosteric Communications

PubMed Central

Blacklock, Kristin; Verkhivker, Gennady M.

2014-01-01

A fundamental role of the Hsp90 chaperone in regulating functional activity of diverse protein clients is essential for the integrity of signaling networks. In this work we have combined biophysical simulations of the Hsp90 crystal structures with the protein structure network analysis to characterize the statistical ensemble of allosteric interaction networks and communication pathways in the Hsp90 chaperones. We have found that principal structurally stable communities could be preserved during dynamic changes in the conformational ensemble. The dominant contribution of the inter-domain rigidity to the interaction networks has emerged as a common factor responsible for the thermodynamic stability of the active chaperone form during the ATPase cycle. Structural stability analysis using force constant profiling of the inter-residue fluctuation distances has identified a network of conserved structurally rigid residues that could serve as global mediating sites of allosteric communication. Mapping of the conformational landscape with the network centrality parameters has demonstrated that stable communities and mediating residues may act concertedly with the shifts in the conformational equilibrium and could describe the majority of functionally significant chaperone residues. The network analysis has revealed a relationship between structural stability, global centrality and functional significance of hotspot residues involved in chaperone regulation. We have found that allosteric interactions in the Hsp90 chaperone may be mediated by modules of structurally stable residues that display high betweenness in the global interaction network. The results of this study have suggested that allosteric interactions in the Hsp90 chaperone may operate via a mechanism that combines rapid and efficient communication by a single optimal pathway of structurally rigid residues and more robust signal transmission using an ensemble of suboptimal multiple communication routes. This may be a universal requirement encoded in protein structures to balance the inherent tension between resilience and efficiency of the residue interaction networks. PMID:24922508

Computational modeling of allosteric regulation in the hsp90 chaperones: a statistical ensemble analysis of protein structure networks and allosteric communications.

PubMed

Blacklock, Kristin; Verkhivker, Gennady M

2014-06-01

A fundamental role of the Hsp90 chaperone in regulating functional activity of diverse protein clients is essential for the integrity of signaling networks. In this work we have combined biophysical simulations of the Hsp90 crystal structures with the protein structure network analysis to characterize the statistical ensemble of allosteric interaction networks and communication pathways in the Hsp90 chaperones. We have found that principal structurally stable communities could be preserved during dynamic changes in the conformational ensemble. The dominant contribution of the inter-domain rigidity to the interaction networks has emerged as a common factor responsible for the thermodynamic stability of the active chaperone form during the ATPase cycle. Structural stability analysis using force constant profiling of the inter-residue fluctuation distances has identified a network of conserved structurally rigid residues that could serve as global mediating sites of allosteric communication. Mapping of the conformational landscape with the network centrality parameters has demonstrated that stable communities and mediating residues may act concertedly with the shifts in the conformational equilibrium and could describe the majority of functionally significant chaperone residues. The network analysis has revealed a relationship between structural stability, global centrality and functional significance of hotspot residues involved in chaperone regulation. We have found that allosteric interactions in the Hsp90 chaperone may be mediated by modules of structurally stable residues that display high betweenness in the global interaction network. The results of this study have suggested that allosteric interactions in the Hsp90 chaperone may operate via a mechanism that combines rapid and efficient communication by a single optimal pathway of structurally rigid residues and more robust signal transmission using an ensemble of suboptimal multiple communication routes. This may be a universal requirement encoded in protein structures to balance the inherent tension between resilience and efficiency of the residue interaction networks.

Space construction system analysis. Part 2: Space construction experiments concepts

NASA Technical Reports Server (NTRS)

Boddy, J. A.; Wiley, L. F.; Gimlich, G. W.; Greenberg, H. S.; Hart, R. J.; Lefever, A. E.; Lillenas, A. N.; Totah, R. S.

1980-01-01

Technology areas in the orbital assembly of large space structures are addressed. The areas included structures, remotely operated assembly techniques, and control and stabilization. Various large space structure design concepts are reviewed and their construction procedures and requirements are identified.

Efficient, Multi-Scale Designs Take Flight

NASA Technical Reports Server (NTRS)

2003-01-01

Engineers can solve aerospace design problems faster and more efficiently with a versatile software product that performs automated structural analysis and sizing optimization. Collier Research Corporation's HyperSizer Structural Sizing Software is a design, analysis, and documentation tool that increases productivity and standardization for a design team. Based on established aerospace structural methods for strength, stability, and stiffness, HyperSizer can be used all the way from the conceptual design to in service support. The software originated from NASA s efforts to automate its capability to perform aircraft strength analyses, structural sizing, and weight prediction and reduction. With a strategy to combine finite element analysis with an automated design procedure, NASA s Langley Research Center led the development of a software code known as ST-SIZE from 1988 to 1995. Collier Research employees were principal developers of the code along with Langley researchers. The code evolved into one that could analyze the strength and stability of stiffened panels constructed of any material, including light-weight, fiber-reinforced composites.

Stability analysis via the concept of Lyapunov exponents: a case study in optimal controlled biped standing

NASA Astrophysics Data System (ADS)

Sun, Yuming; Wu, Christine Qiong

2012-12-01

Balancing control is important for biped standing. In spite of large efforts, it is very difficult to design balancing control strategies satisfying three requirements simultaneously: maintaining postural stability, improving energy efficiency and satisfying the constraints between the biped feet and the ground. In this article, a proportional-derivative (PD) controller is proposed for a standing biped, which is simplified as a two-link inverted pendulum with one additional rigid foot-link. The genetic algorithm (GA) is used to search for the control gain meeting all three requirements. The stability analysis of such a deterministic biped control system is carried out using the concept of Lyapunov exponents (LEs), based on which, the system stability, where the disturbance comes from the initial states, and the structural stability, where the disturbance comes from the PD gains, are examined quantitively in terms of stability region. This article contributes to the biped balancing control, more significantly, the method shown in the studied case of biped provides a general framework of systematic stability analysis for certain deterministic nonlinear dynamical systems.

Linear stability analysis of scramjet unstart

NASA Astrophysics Data System (ADS)

Jang, Ik; Nichols, Joseph; Moin, Parviz

2015-11-01

We investigate the bifurcation structure of unstart and restart events in a dual-mode scramjet using the Reynolds-averaged Navier-Stokes equations. The scramjet of interest (HyShot II, Laurence et al., AIAA2011-2310) operates at a free-stream Mach number of approximately 8, and the length of the combustor chamber is 300mm. A heat-release model is applied to mimic the combustion process. Pseudo-arclength continuation with Newton-Raphson iteration is used to calculate multiple solution branches. Stability analysis based on linearized dynamics about the solution curves reveals a metric that optimally forewarns unstart. By combining direct and adjoint eigenmodes, structural sensitivity analysis suggests strategies for unstart mitigation, including changing the isolator length. This work is supported by DOE/NNSA and AFOSR.

SiC-dopped MCM-41 materials with enhanced thermal and hydrothermal stabilities

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

Wang, Yingyong; Jin, Guoqiang; Tong, Xili

2011-11-15

Graphical abstract: Novel SiC-dopped MCM-41 materials were synthesized by adding silicon carbide suspension in the molecular sieve precursor solvent followed by in situ hydrothermal synthesis. The dopped materials have a wormhole-like mesoporous structure and exhibit enhanced thermal and hydrothermal stabilities. Highlights: {yields} SiC-dopped MCM-41 was synthesized by in situ hydrothermal synthesis of molecular sieve precursor combined with SiC. {yields} The dopped MCM-41 materials show a wormhole-like mesoporous structure. {yields} The thermal stability of the dopped materials have an increment of almost 100 {sup o}C compared with the pure MCM-41. {yields} The hydrothermal stability of the dopped materials is also bettermore » than that of the pure MCM-41. -- Abstract: SiC-dopped MCM-41 mesoporous materials were synthesized by the in situ hydrothermal synthesis, in which a small amount of SiC was added in the precursor solvent of molecular sieve before the hydrothermal treatment. The materials were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, N{sub 2} physical adsorption and thermogravimetric analysis, respectively. The results show that the thermal and hydrothermal stabilities of MCM-41 materials can be improved obviously by incorporating a small amount of SiC. The structure collapse temperature of SiC-dopped MCM-41 materials is 100 {sup o}C higher than that of pure MCM-41 according to the differential scanning calorimetry analysis. Hydrothermal treatment experiments also show that the pure MCM-41 will losses it's ordered mesoporous structure in boiling water for 24 h while the SiC-dopped MCM-41 materials still keep partial porous structure.« less

X-ray source assembly having enhanced output stability, and fluid stream analysis applications thereof

DOEpatents

Radley, Ian; Bievenue, Thomas J.; Burdett Jr., John H.; Gallagher, Brian W.; Shakshober, Stuart M.; Chen, Zewu; Moore, Michael D.

2007-04-24

An x-ray source assembly (2700) and method of operation are provided having enhanced output stability. The assembly includes an anode (2125) having a source spot upon which electrons (2120) impinge and a control system (2715/2720) for controlling position of the anode source spot relative to an output structure. The control system can maintain the anode source spot location relative to the output structure (2710) notwithstanding a change in one or more operating conditions of the x-ray source assembly. One aspect of the disclosed invention is most amenable to the analysis of sulfur in petroleum-based fuels.

Role of conformational sampling in computing mutation-induced changes in protein structure and stability.

PubMed

Kellogg, Elizabeth H; Leaver-Fay, Andrew; Baker, David

2011-03-01

The prediction of changes in protein stability and structure resulting from single amino acid substitutions is both a fundamental test of macromolecular modeling methodology and an important current problem as high throughput sequencing reveals sequence polymorphisms at an increasing rate. In principle, given the structure of a wild-type protein and a point mutation whose effects are to be predicted, an accurate method should recapitulate both the structural changes and the change in the folding-free energy. Here, we explore the performance of protocols which sample an increasing diversity of conformations. We find that surprisingly similar performances in predicting changes in stability are achieved using protocols that involve very different amounts of conformational sampling, provided that the resolution of the force field is matched to the resolution of the sampling method. Methods involving backbone sampling can in some cases closely recapitulate the structural changes accompanying mutations but not surprisingly tend to do more harm than good in cases where structural changes are negligible. Analysis of the outliers in the stability change calculations suggests areas needing particular improvement; these include the balance between desolvation and the formation of favorable buried polar interactions, and unfolded state modeling. Copyright © 2010 Wiley-Liss, Inc.

Protein secondary structure and stability determined by combining exoproteolysis and matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Villanueva, Josep; Villegas, Virtudes; Querol, Enrique; Avilés, Francesc X; Serrano, Luis

2002-09-01

In the post-genomic era, several projects focused on the massive experimental resolution of the three-dimensional structures of all the proteins of different organisms have been initiated. Simultaneously, significant progress has been made in the ab initio prediction of protein three-dimensional structure. One of the keys to the success of such a prediction is the use of local information (i.e. secondary structure). Here we describe a new limited proteolysis methodology, based on the use of unspecific exoproteases coupled with matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), to map quickly secondary structure elements of a protein from both ends, the N- and C-termini. We show that the proteolytic patterns (mass spectra series) obtained can be interpreted in the light of the conformation and local stability of the analyzed proteins, a direct correlation being observed between the predicted and the experimentally derived protein secondary structure. Further, this methodology can be easily applied to check rapidly the folding state of a protein and characterize mutational effects on protein conformation and stability. Moreover, given global stability information, this methodology allows one to locate the protein regions of increased or decreased conformational stability. All of this can be done with a small fraction of the amount of protein required by most of the other methods for conformational analysis. Thus limited exoproteolysis, together with MALDI-TOF MS, can be a useful tool to achieve quickly the elucidation of protein structure and stability. Copyright 2002 John Wiley & Sons, Ltd.

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.

PubMed

Wei, Dengguo; Parkinson, Gary N; Reszka, Anthony P; Neidle, Stephen

2012-05-01

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.

The Structure of the Mouse Serotonin 5-HT3 Receptor in Lipid Vesicles.

PubMed

Kudryashev, Mikhail; Castaño-Díez, Daniel; Deluz, Cédric; Hassaine, Gherici; Grasso, Luigino; Graf-Meyer, Alexandra; Vogel, Horst; Stahlberg, Henning

2016-01-05

The function of membrane proteins is best understood if their structure in the lipid membrane is known. Here, we determined the structure of the mouse serotonin 5-HT3 receptor inserted in lipid bilayers to a resolution of 12 Å without stabilizing antibodies by cryo electron tomography and subtomogram averaging. The reconstruction reveals protein secondary structure elements in the transmembrane region, the extracellular pore, and the transmembrane channel pathway, showing an overall similarity to the available X-ray model of the truncated 5-HT3 receptor determined in the presence of a stabilizing nanobody. Structural analysis of the 5-HT3 receptor embedded in a lipid bilayer allowed the position of the membrane to be determined. Interactions between the densely packed receptors in lipids were visualized, revealing that the interactions were maintained by the short horizontal helices. In combination with methodological improvements, our approach enables the structural analysis of membrane proteins in response to voltage and ligand gating. Copyright © 2016 Elsevier Ltd. All rights reserved.

NASA/Howard University Large Space Structures Institute

NASA Technical Reports Server (NTRS)

Broome, T. H., Jr.

1984-01-01

Basic research on the engineering behavior of large space structures is presented. Methods of structural analysis, control, and optimization of large flexible systems are examined. Topics of investigation include the Load Correction Method (LCM) modeling technique, stabilization of flexible bodies by feedback control, mathematical refinement of analysis equations, optimization of the design of structural components, deployment dynamics, and the use of microprocessors in attitude and shape control of large space structures. Information on key personnel, budgeting, support plans and conferences is included.

Structural design/margin assessment

NASA Technical Reports Server (NTRS)

Ryan, R. S.

1993-01-01

Determining structural design inputs and the structural margins following design completion is one of the major activities in space exploration. The end result is a statement of these margins as stability, safety factors on ultimate and yield stresses, fracture limits (fracture control), fatigue lifetime, reuse criteria, operational criteria and procedures, stability factors, deflections, clearance, handling criteria, etc. The process is normally called a load cycle and is time consuming, very complex, and involves much more than structures. The key to successful structural design is the proper implementation of the process. It depends on many factors: leadership and management of the process, adequate analysis and testing tools, data basing, communications, people skills, and training. This process and the various factors involved are discussed.

Dynamics of a gravity-gradient stabilized flexible spacecraft

NASA Technical Reports Server (NTRS)

Meirovitch, L.; Juang, J. N.

1974-01-01

The dynamics of gravity-gradient stabilized flexible satellite in the neighborhood of a deformed equilibrium configuration are discussed. First the equilibrium configuration was determined by solving a set of nonlinear differential equations. Then stability of motion about the deformed equilibrium was tested by means of the Liapunov direct method. The natural frequencies of oscillation of the complete structure were calculated. The analysis is applicable to the RAE/B satellite.

Structure-Based Network Analysis of Activation Mechanisms in the ErbB Family of Receptor Tyrosine Kinases: The Regulatory Spine Residues Are Global Mediators of Structural Stability and Allosteric Interactions

PubMed Central

James, Kevin A.; Verkhivker, Gennady M.

2014-01-01

The ErbB protein tyrosine kinases are among the most important cell signaling families and mutation-induced modulation of their activity is associated with diverse functions in biological networks and human disease. We have combined molecular dynamics simulations of the ErbB kinases with the protein structure network modeling to characterize the reorganization of the residue interaction networks during conformational equilibrium changes in the normal and oncogenic forms. Structural stability and network analyses have identified local communities integrated around high centrality sites that correspond to the regulatory spine residues. This analysis has provided a quantitative insight to the mechanism of mutation-induced “superacceptor” activity in oncogenic EGFR dimers. We have found that kinase activation may be determined by allosteric interactions between modules of structurally stable residues that synchronize the dynamics in the nucleotide binding site and the αC-helix with the collective motions of the integrating αF-helix and the substrate binding site. The results of this study have pointed to a central role of the conserved His-Arg-Asp (HRD) motif in the catalytic loop and the Asp-Phe-Gly (DFG) motif as key mediators of structural stability and allosteric communications in the ErbB kinases. We have determined that residues that are indispensable for kinase regulation and catalysis often corresponded to the high centrality nodes within the protein structure network and could be distinguished by their unique network signatures. The optimal communication pathways are also controlled by these nodes and may ensure efficient allosteric signaling in the functional kinase state. Structure-based network analysis has quantified subtle effects of ATP binding on conformational dynamics and stability of the EGFR structures. Consistent with the NMR studies, we have found that nucleotide-induced modulation of the residue interaction networks is not limited to the ATP site, and may enhance allosteric cooperativity with the substrate binding region by increasing communication capabilities of mediating residues. PMID:25427151

Instability risk analysis and risk assessment system establishment of underground storage caverns in bedded salt rock

NASA Astrophysics Data System (ADS)

Jing, Wenjun; Zhao, Yan

2018-02-01

Stability is an important part of geotechnical engineering research. The operating experiences of underground storage caverns in salt rock all around the world show that the stability of the caverns is the key problem of safe operation. Currently, the combination of theoretical analysis and numerical simulation are the mainly adopts method of reserve stability analysis. This paper introduces the concept of risk into the stability analysis of underground geotechnical structure, and studies the instability of underground storage cavern in salt rock from the perspective of risk analysis. Firstly, the definition and classification of cavern instability risk is proposed, and the damage mechanism is analyzed from the mechanical angle. Then the main stability evaluating indicators of cavern instability risk are proposed, and an evaluation method of cavern instability risk is put forward. Finally, the established cavern instability risk assessment system is applied to the analysis and prediction of cavern instability risk after 30 years of operation in a proposed storage cavern group in the Huai’an salt mine. This research can provide a useful theoretical base for the safe operation and management of underground storage caverns in salt rock.

Theoretical Study on Structural Stability of Fully Filled p-Type Skutterudites RETM4Sb12 ( RE = Rare Earth; TM = Fe, Ru)

NASA Astrophysics Data System (ADS)

Chen, Zhuo; Yang, Jiong; Liu, Ruiheng; Xi, Lili; Zhang, Wenqing; Yang, Jihui

2013-08-01

The structural stability of filled p-type skutterudites RETM4Sb12 ( RE = rare earth; TM = Fe, Ru) was studied via ab initio calculations. Most of the RE metals (La-Ho and Yb) could be filled into the cages (voids) of Fe4Sb12 to form stable filled skutterudites. However, only a few RE metals (La-Nd and Eu) could be stably filled into the cage of Ru4Sb12-based skutterudites. Systematic analysis of bonding energy showed that the structural stability could be attributed to ionic radius and effective charge state differences of the RE fillers. Resonant rattling frequencies of the fillers in both Fe4Sb12- and Ru4Sb12-based skutterudites were also studied.

Stability analysis of truss type highway sign support structures

DOT National Transportation Integrated Search

2000-12-01

The design of truss type sign support structures is based on the guidelines provided by American Association of State Highway and Transportation Officials Standard Specifications for Highway Signs, Luminaires and Traffic Signals and the American Inst...

Precise structural analysis of α-helical polypeptide by quantum-chemical calculation related to reciprocal side-chain combination of two L-phenylalanine residues

NASA Astrophysics Data System (ADS)

Niimura, Subaru; Kurosu, Hiromichi; Shoji, Akira

2010-04-01

To clarify the positive role of side-chain conformation in the stability of protein secondary structure (main-chain conformation), we successfully calculated the optimization structure of a series of well-defined α-helical octadecapeptides composed of two L-phenylalanine (Phe) and 16 L-alanine (Ala) residues, based on the molecular orbital calculation with density functional theory (DFT/B3LYP/6-31G(d)). From the total energy calculation and the precise secondary structural analysis, we found that the conformational stability of the α-helix is closely related to the reciprocal side-chain combinations (such as positional relation and side-chain conformation) of two Phe residues in this system. Furthermore, we demonstrated that the 1H, 13C, 15N and 17O isotropic chemical shifts of each Phe residue depend on the respective side-chain conformations of the Phe residue.

Analysis of seismic stability of large-sized tank VST-20000 with software package ANSYS

NASA Astrophysics Data System (ADS)

Tarasenko, A. A.; Chepur, P. V.; Gruchenkova, A. A.

2018-05-01

The work is devoted to the study of seismic stability of vertical steel tank VST-20000 with due consideration of the system response “foundation-tank-liquid”, conducted on the basis of the finite element method, modal analysis and linear spectral theory. The calculations are performed for the tank model with a high degree of detailing of metallic structures: shells, a fixed roof, a bottom, a reinforcing ring.

Numerical analysis of stiffened shells of revolution. Volume 1: Theory manual for STARS-2S, 2B, 2V digital computer programs

NASA Technical Reports Server (NTRS)

Svalbonas, V.

1973-01-01

The theoretical analysis background for the STARS-2 (shell theory automated for rotational structures) program is presented. The theory involved in the axisymmetric nonlinear and unsymmetric linear static analyses, and the stability and vibrations (including critical rotation speed) analyses involving axisymmetric prestress are discussed. The theory for nonlinear static, stability, and vibrations analyses, involving shells with unsymmetric loadings are included.

Flames in dusty mixtures: Their structure and stability

NASA Technical Reports Server (NTRS)

Buckmaster, J.; Jackson, T.

1993-01-01

The structure and stability of flames in dusty mixtures is investigated. The presence of the dust leads to significant transport of energy by radiation and the fundamental goal of the analysis is to explore to what extent this displaces the classical non-hydrodynamical stability boundaries of the plane degradation. An approximate description of the radiative transport permits analysis for arbitrary values of both the planck length and the Boltzman number. It is shown that the pulsating/traveling-wave instability usually associated with values of Lewis number (L(sub e)) bigger than 1 is stongly enhanced by the presence of radiation and can be present even if L(sub e) is less than 1. On the other hand radiation tends to supress the cellular instability normally associated with values of L(sub e) less than 1. The latter is consisitent with preliminary experimental observations of Abbud-Madrid and Ronney.

Rotorcraft aeroelastic stability

NASA Technical Reports Server (NTRS)

Ormiston, Robert A.; Warmbrodt, William G.; Hodges, Dewey H.; Peters, David A.

1988-01-01

Theoretical and experimental developments in the aeroelastic and aeromechanical stability of helicopters and tilt-rotor aircraft are addressed. Included are the underlying nonlinear structural mechanics of slender rotating beams, necessary for accurate modeling of elastic cantilever rotor blades, and the development of dynamic inflow, an unsteady aerodynamic theory for low-frequency aeroelastic stability applications. Analytical treatment of isolated rotor stability in hover and forward flight, coupled rotor-fuselage stability in hover and forward flight, and analysis of tilt-rotor dynamic stability are considered. Results of parametric investigations of system behavior are presented, and correlation between theoretical results and experimental data from small and large scale wind tunnel and flight testing are discussed.

Probing the determinants of protein stability: comparison of class A beta-lactamases.

PubMed Central

Vanhove, M; Houba, S; b1motte-Brasseur, J; Frère, J M

1995-01-01

Five class A beta-lactamases produced by various mesophilic bacterial species have been compared. Although closely related in primary and overall structures, these enzymes exhibit very different stabilities. In order to investigate the factors responsible for these differences, several features deduced from the amino acid composition and three-dimensional structures were studied for the five proteins. This analysis revealed that higher stability appeared to correlate with increased numbers of intramolecular hydrogen bonds and of salt bridges. By contrast, the global hydrophobicity of the protein seemed to play a relatively minor role. A strongly unfavourable balance between charged residues and the presence of a cis-peptide bond preceding a non-proline residue might also contribute to the particularly low stability of two of the enzymes. PMID:8948443

Computational analysis of molt-inhibiting hormone from selected crustaceans.

PubMed

C, Kumaraswamy Naidu; Y, Suneetha; P, Sreenivasula Reddy

2013-12-01

Molt-inhibiting hormone (MIH) is a principal endocrine hormone regulating the growth in crustaceans. In total, nine MIH peptide sequences representing members of the family Penaeidae (Penaeus monodon, Litopenaeus vannamei, Marsupenaeus japonicus), Portunidae (Portunus trituberculatus, Charybdis japonica, Charybdis feriata), Cambaridae (Procambarus bouvieri), Parastacidae (Cherax quadricarinatus) and Varunidae (Eriocheir sinensis) were selected for our study. In order to develop a structure based phylogeny, predict functionally important regions and to define stability changes upon single site mutations, the 3D structure of MIH for the crustaceans were built by using homology modeling based on the known structure of MIH from M. japonicus (1J0T). Structure based phylogeny showed a close relationship between P. bouvieri and C. japonica. ConSurf server analysis showed that the residues Cys(8), Arg(15), Cys(25), Asp(27), Cys(28), Asn(30), Arg(33), Cys(41), Cys(45), Phe(51), and Cys(54) may be functionally significant among the MIH of crustaceans. Single amino acid substitutions 'Y' and 'G' at the positions 71 and 72 of the MIH C-terminal region showed an alteration in the stability indicating that a change in this region may alter the function of MIH. In conclusion, we proposed a computational approach to analyze the structure, phylogeny and stability of MIH from crustaceans. © 2013.

X-ray Crystallographic Structure of Thermophilic Rhodopsin: IMPLICATIONS FOR HIGH THERMAL STABILITY AND OPTOGENETIC FUNCTION.

PubMed

Tsukamoto, Takashi; Mizutani, Kenji; Hasegawa, Taisuke; Takahashi, Megumi; Honda, Naoya; Hashimoto, Naoki; Shimono, Kazumi; Yamashita, Keitaro; Yamamoto, Masaki; Miyauchi, Seiji; Takagi, Shin; Hayashi, Shigehiko; Murata, Takeshi; Sudo, Yuki

2016-06-03

Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a "thermal sensor." These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

Acoustic tomography for decay detection in red oak trees

Treesearch

Xiping Wang; R. Bruce Allison; Lihai Wang; Robert J. Ross

2007-01-01

The science of tree stability analysis uses both biological and engineering principles in attempting to rate a tree’s structural soundness and make reasonable predictions of potential for failure. In such analysis, arborists are often challenged by internal structural defects hidden from view within the trunks. This paper reports the results of an investigation using...

Studies on the syntheses, structural Characterization, antimicrobial of the CO-CRYSTAL 1,10-phenanthrolin-1-IUM(1,10-phenH+)-caffeine(caf)-hexafluorophosphate

NASA Astrophysics Data System (ADS)

El Hamdani, H.; El Amane, M.; Duhayon, C.

2018-03-01

Co-crystal of 1,10-phenanthrolin-1-ium-caffeine-hexafluorophosphate was synthesized, studied by FTIR, 1H, 13C NMR, DSC and X-ray structure and crystallized in the monoclinic space group C2/c. The unit cell parameters are a = 19.3761 (3), b = 17.9548 (3), c = 13.8074 (3) with β = 117.8132 (10). The final R value is 0.069 for 29,522 measured reflections. The co-crystal structure analysis indicate the 1,10-phenanthroline is protonated by one nitrogen atom and formed the 1,10-phenanthrolin-1-ium cation, which is stabilized by hydrogen bonds N+-H…Odbnd C interaction with carbonyl and imidazol ring in caffeine molecule. The intermolecular hydrogen bonds: Csbnd H...O, Csbnd H...N, Nsbnd H...O, Csbnd H...F and intramolecular hydrogen bond: C1sbnd H12...O14, together play a vital role in stabilizing the structure of co-crystal. The X-ray structural analysis confirm the assignments of the structure from infrared, 1H, 13C NMR, spectroscopic data DSC and molar conductivity analysis. The antimicrobial activity of the co-crystal was studied.

Nonlinear finite element modeling of vibration control of plane rod-type structural members with integrated piezoelectric patches

NASA Astrophysics Data System (ADS)

Chróścielewski, Jacek; Schmidt, Rüdiger; Eremeyev, Victor A.

2018-05-01

This paper addresses modeling and finite element analysis of the transient large-amplitude vibration response of thin rod-type structures (e.g., plane curved beams, arches, ring shells) and its control by integrated piezoelectric layers. A geometrically nonlinear finite beam element for the analysis of piezolaminated structures is developed that is based on the Bernoulli hypothesis and the assumptions of small strains and finite rotations of the normal. The finite element model can be applied to static, stability, and transient analysis of smart structures consisting of a master structure and integrated piezoelectric actuator layers or patches attached to the upper and lower surfaces. Two problems are studied extensively: (i) FE analyses of a clamped semicircular ring shell that has been used as a benchmark problem for linear vibration control in several recent papers are critically reviewed and extended to account for the effects of structural nonlinearity and (ii) a smart circular arch subjected to a hydrostatic pressure load is investigated statically and dynamically in order to study the shift of bifurcation and limit points, eigenfrequencies, and eigenvectors, as well as vibration control for loading conditions which may lead to dynamic loss of stability.

Design of Launch Vehicle Flight Control Systems Using Ascent Vehicle Stability Analysis Tool

NASA Technical Reports Server (NTRS)

Jang, Jiann-Woei; Alaniz, Abran; Hall, Robert; Bedossian, Nazareth; Hall, Charles; Jackson, Mark

2011-01-01

A launch vehicle represents a complicated flex-body structural environment for flight control system design. The Ascent-vehicle Stability Analysis Tool (ASAT) is developed to address the complicity in design and analysis of a launch vehicle. The design objective for the flight control system of a launch vehicle is to best follow guidance commands while robustly maintaining system stability. A constrained optimization approach takes the advantage of modern computational control techniques to simultaneously design multiple control systems in compliance with required design specs. "Tower Clearance" and "Load Relief" designs have been achieved for liftoff and max dynamic pressure flight regions, respectively, in the presence of large wind disturbances. The robustness of the flight control system designs has been verified in the frequency domain Monte Carlo analysis using ASAT.

Statistical Analysis of High-Cycle Fatigue Behavior of Friction Stir Welded AA5083-H321

DTIC Science & Technology

2011-01-01

durable structures are: (a) FSW is 111being used in a serial production of aluminum alloy -based 112ferryboat deck structures in Finland; (b) Al-Mg- Si -based...and strain-hardened/stabilized Al-Mg-Mn alloy ) are characterized by a relatively large statistical scatter. This scatter is closely related to the...associated with friction stir-welded (FSW) joints of AA5083-H321 (a solid-solution-strengthened and strain-hardened/stabilized Al-Mg-Mn alloy ) are

The stability of coupled renewal-differential equations with econometric applications

NASA Technical Reports Server (NTRS)

Rhoten, R. P.; Aggarwal, J. K.

1969-01-01

Concepts and results are presented in the fields of mathematical modeling, economics, and stability analysis. A coupled renewal-differential equation structure is presented as a modeling form for systems possessing hereditary characteristics, and this structure is applied to a model of the Austrian theory of business cycles. For realistic conditions, the system is shown to have an infinite number of poles, and conditions are presented which are both necessary and sufficient for all poles to lie strictly in the left half plane.

Origin of electrochemical, structural and transport properties in non-aqueous zinc electrolytes

DOE PAGES

Han, Sang -Don; Rajput, Nav Nidhi; Qu, Xiaohui; ...

2016-01-14

Through coupled experimental analysis and computational techniques, we uncover the origin of anodic stability for a range of nonaqueous zinc electrolytes. By examination of electrochemical, structural, and transport properties of nonaqueous zinc electrolytes with varying concentrations, it is demonstrated that the acetonitrile Zn(TFSI) 2, acetonitrile Zn(CF 3SO 3) 2, and propylene carbonate Zn(TFSI) 2 electrolytes can not only support highly reversible Zn deposition behavior on a Zn metal anode (≥99% of Coulombic efficiency), but also provide high anodic stability (up to ~3.8 V). The predicted anodic stability from DFT calculations is well in accordance with experimental results, and elucidates thatmore » the solvents play an important role in anodic stability of most electrolytes. Molecular dynamics (MD) simulations were used to understand the solvation structure (e.g., ion solvation and ionic association) and its effect on dynamics and transport properties (e.g., diffusion coefficient and ionic conductivity) of the electrolytes. Lastly, the combination of these techniques provides unprecedented insight into the origin of the electrochemical, structural, and transport properties in nonaqueous zinc electrolytes« less

Calcium Binding and Disulfide Bonds Regulate the Stability of Secretagogin towards Thermal and Urea Denaturation

PubMed Central

Weiffert, Tanja; Ní Mhurchú, Niamh; O’Connell, David; Linse, Sara

2016-01-01

Secretagogin is a calcium-sensor protein with six EF-hands. It is widely expressed in neurons and neuro-endocrine cells of a broad range of vertebrates including mammals, fishes and amphibia. The protein plays a role in secretion and interacts with several vesicle-associated proteins. In this work, we have studied the contribution of calcium binding and disulfide-bond formation to the stability of the secretagogin structure towards thermal and urea denaturation. SDS-PAGE analysis of secretagogin in reducing and non-reducing conditions identified a tendency of the protein to form dimers in a redox-dependent manner. The denaturation of apo and Calcium-loaded secretagogin was studied by circular dichroism and fluorescence spectroscopy under conditions favoring monomer or dimer or a 1:1 monomer: dimer ratio. This analysis reveals significantly higher stability towards urea denaturation of Calcium-loaded secretagogin compared to the apo protein. The secondary and tertiary structure of the Calcium-loaded form is not completely denatured in the presence of 10 M urea. Reduced and Calcium-loaded secretagogin is found to refold reversibly after heating to 95°C, while both oxidized and reduced apo secretagogin is irreversibly denatured at this temperature. Thus, calcium binding greatly stabilizes the structure of secretagogin towards chemical and heat denaturation. PMID:27812162

[Features of emotional stability in volunteers of gerontology programs].

PubMed

Dolgova, V I

2014-01-01

The paper presents an analysis of the characteristics of emotional stability in volunteers of gerontology programs (among the students of the Faculty of Psychology), depending on the structure of their life meaning and values, personal factors and professional important qualities. It is shown that the emotional stability of volunteers determines the main directions to explore the potential of the psyche of volunteers; modeling appropriate professiogram; organization of volunteer work in a particular program.

Structural stability of interaction networks against negative external fields

NASA Astrophysics Data System (ADS)

Yoon, S.; Goltsev, A. V.; Mendes, J. F. F.

2018-04-01

We explore structural stability of weighted and unweighted networks of positively interacting agents against a negative external field. We study how the agents support the activity of each other to confront the negative field, which suppresses the activity of agents and can lead to collapse of the whole network. The competition between the interactions and the field shape the structure of stable states of the system. In unweighted networks (uniform interactions) the stable states have the structure of k -cores of the interaction network. The interplay between the topology and the distribution of weights (heterogeneous interactions) impacts strongly the structural stability against a negative field, especially in the case of fat-tailed distributions of weights. We show that apart from critical slowing down there is also a critical change in the system structure that precedes the network collapse. The change can serve as an early warning of the critical transition. To characterize changes of network structure we develop a method based on statistical analysis of the k -core organization and so-called "corona" clusters belonging to the k -cores.

Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures.

PubMed

Kellogg, Elizabeth H; Hejab, Nisreen M A; Howes, Stuart; Northcote, Peter; Miller, John H; Díaz, J Fernando; Downing, Kenneth H; Nogales, Eva

2017-03-10

A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. We have obtained high-resolution (3.9-4.2Å) cryo-electron microscopy (cryo-EM) reconstructions of MTs stabilized by the taxane-site binders Taxol and zampanolide, and by peloruside, which targets a distinct, non-taxoid pocket on β-tubulin. We find that each molecule has unique distinct structural effects on the MT lattice structure. Peloruside acts primarily at lateral contacts and has an effect on the "seam" of heterologous interactions, enforcing a conformation more similar to that of homologous (i.e., non-seam) contacts by which it regularizes the MT lattice. In contrast, binding of either Taxol or zampanolide induces MT heterogeneity. In doubly bound MTs, peloruside overrides the heterogeneity induced by Taxol binding. Our structural analysis illustrates distinct mechanisms of these drugs for stabilizing the MT lattice and is of relevance to the possible use of combinations of MSAs to regulate MT activity and improve therapeutic potential. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures

DOE PAGES

Kellogg, Elizabeth H.; Hejab, Nisreen M. A.; Howes, Stuart; ...

2017-01-17

A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. We have obtained high-resolution (3.9–4.2 Å) cryo-electron microscopy (cryo-EM) reconstructions of MTs stabilized by the taxane-site binders Taxol and zampanolide, and by peloruside, which targets a distinct, non-taxoid pocket on β-tubulin. We find that each molecule has unique distinct structural effects on the MT lattice structure. Peloruside acts primarily at lateral contacts and has an effect on the “seam” of heterologous interactions, enforcing a conformation more similar to that of homologous (i.e., non-seam)more » contacts by which it regularizes the MT lattice. In contrast, binding of either Taxol or zampanolide induces MT heterogeneity. In doubly bound MTs, peloruside overrides the heterogeneity induced by Taxol binding. Our structural analysis illustrates distinct mechanisms of these drugs for stabilizing the MT lattice and is of relevance to the possible use of combinations of MSAs to regulate MT activity and improve therapeutic potential.« less

Insights into the Distinct Mechanisms of Action of Taxane and Non-Taxane Microtubule Stabilizers from Cryo-EM Structures

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

Kellogg, Elizabeth H.; Hejab, Nisreen M. A.; Howes, Stuart

A number of microtubule (MT)-stabilizing agents (MSAs) have demonstrated or predicted potential as anticancer agents, but a detailed structural basis for their mechanism of action is still lacking. We have obtained high-resolution (3.9–4.2 Å) cryo-electron microscopy (cryo-EM) reconstructions of MTs stabilized by the taxane-site binders Taxol and zampanolide, and by peloruside, which targets a distinct, non-taxoid pocket on β-tubulin. We find that each molecule has unique distinct structural effects on the MT lattice structure. Peloruside acts primarily at lateral contacts and has an effect on the “seam” of heterologous interactions, enforcing a conformation more similar to that of homologous (i.e., non-seam)more » contacts by which it regularizes the MT lattice. In contrast, binding of either Taxol or zampanolide induces MT heterogeneity. In doubly bound MTs, peloruside overrides the heterogeneity induced by Taxol binding. Our structural analysis illustrates distinct mechanisms of these drugs for stabilizing the MT lattice and is of relevance to the possible use of combinations of MSAs to regulate MT activity and improve therapeutic potential.« less

Comparative analysis of thermal unfolding simulations of RNA recognition motifs (RRMs) of TAR DNA-binding protein 43 (TDP-43).

PubMed

Prakash, Amresh; Kumar, Vijay; Meena, Naveen Kumar; Hassan, Md Imtaiyaz; Lynn, Andrew M

2018-01-10

TAR DNA-binding protein 43 (TDP-43) inclusions have been found in Amyotrophic lateral sclerosis (ALS) and several other neurodegenerative diseases. Many studies suggest the involvement of RNA recognition motifs (RRMs) in TDP-43 proteinopathy. To elucidate the structural stability and the unfolding dynamics of RRMs, we have carried out atomistic molecular dynamics simulations at two different temperatures (300 and 500 K). The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two domains and RRM1 unfolds faster than RRM2 in accordance with the lower thermal stability found experimentally. The unfolding behaviors of secondary structures showed that the α-helix was more stable than β-sheet and structural rearrangements of β-sheets results in formation of additional α-helices. At higher temperature, RRM1 exhibit increased overall flexibility and unfolding than RRM2. The temperature-dependent free energy landscapes consist of multiple metastable states stabilized by non-native contacts and hydrogen bonds in RRM2, thus rendering the RRM2 more prone to misfolding. The structural rearrangements of RRM2 could lead to aberrant protein-protein interactions that may account for enhanced aggregation and toxicity of TDP-43. Our analysis, thus identify the structural and thermodynamic characteristics of the RRMs of TDP-43, which will serve to uncover molecular mechanisms and driving forces in TDP-43 misfolding and aggregation.

Synthesis, electrochemical investigation and structural analysis of doped Li[Ni0.6Mn0.2Co0.2-xMx]O2 (x = 0, 0.05; M = Al, Fe, Sn) cathode materials

NASA Astrophysics Data System (ADS)

Eilers-Rethwisch, Matthias; Winter, Martin; Schappacher, Falko Mark

2018-05-01

Layered Ni-rich Li[Ni0.6Mn0.2Co0.2-xMx]O2 cathode materials (x = 0, 0.05; M = Al, Fe, Sn) are synthesized via a co-precipitation synthesis route and the effect of dopants on the structure and electrochemical performance is investigated. All synthesized materials show a well-defined layered structure of the hexagonal α-NaFeO2 phase investigated by X-ray diffraction (XRD). Undoped LiNi0.6Mn0.2Co0.2O2 exhibits a discharge capacity of 170 mAh g-1 in Li-metal 2032 coin-type cells. Doped materials reach lower capacities between 145 mAh g-1 for Al and 160 mAh g-1 for Sn. However, all doped materials prolong the cycle life by up to 20%. Changes of the lattice parameter before and after delithiation yield information about structural stability. A smaller repulsion of the transition metal layer during delithiation in the Sn-doped material leads to a smaller expansion of the unit cell, which results in enhanced structural stability of the material. The improved structural stability of Sn-doped NMC cathode active material is proven by thermal investigations with the help of Differential Scanning Calorimetry (DSC) and Thermogravimetric Analysis (TGA).

Study of Geometric Porosity on Static Stability and Drag Using Computational Fluid Dynamics for Rigid Parachute Shapes

NASA Technical Reports Server (NTRS)

Greathouse, James S.; Schwing, Alan M.

2015-01-01

This paper explores use of computational fluid dynamics to study the e?ect of geometric porosity on static stability and drag for NASA's Multi-Purpose Crew Vehicle main parachute. Both of these aerodynamic characteristics are of interest to in parachute design, and computational methods promise designers the ability to perform detailed parametric studies and other design iterations with a level of control previously unobtainable using ground or flight testing. The approach presented here uses a canopy structural analysis code to define the inflated parachute shapes on which structured computational grids are generated. These grids are used by the computational fluid dynamics code OVERFLOW and are modeled as rigid, impermeable bodies for this analysis. Comparisons to Apollo drop test data is shown as preliminary validation of the technique. Results include several parametric sweeps through design variables in order to better understand the trade between static stability and drag. Finally, designs that maximize static stability with a minimal loss in drag are suggested for further study in subscale ground and flight testing.

Nuclear magnetic and nuclear quadrupole resonance parameters of β-carboline derivatives calculated using density functional theory

NASA Astrophysics Data System (ADS)

Ahmadinejad, Neda; Tari, Mostafa Talebi

2017-04-01

A density functional theory (DFT) calculations using B3LYP/6-311++G( d,p) method were carried out to investigate the relative stability of the molecules of β-carboline derivatives such as harmaline, harmine, harmalol, harmane and norharmane. Calculated nuclear quadrupole resonance (NQR) parameters were used to determine the 14N nuclear quadrupole coupling constant χ, asymmetry parameter η and EFG tensor ( q zz ). For better understanding of the electronic structure of β-carboline derivatives, natural bond orbital (NBO) analysis, isotropic and anisotropic NMR chemical shieldings were calculated for 14N nuclei using GIAO method for the optimized structures. The NBO analysis shows that pyrrole ring nitrogen (N9) atom has greater tendency than pyridine ring nitrogen (N2) atom to participate in resonance interactions and aromaticity development in the all of these structures. The NMR and NQR parameters were studied in order to find the correlations between electronic structure and the structural stability of the studied molecules.

Bright-dark and dark-dark solitons in coupled nonlinear Schrödinger equation with P T -symmetric potentials

NASA Astrophysics Data System (ADS)

Nath, Debraj; Gao, Yali; Babu Mareeswaran, R.; Kanna, T.; Roy, Barnana

2017-12-01

We explore different nonlinear coherent structures, namely, bright-dark (BD) and dark-dark (DD) solitons in a coupled nonlinear Schrödinger/Gross-Pitaevskii equation with defocusing/repulsive nonlinearity coefficients featuring parity-time ( P T )-symmetric potentials. Especially, for two choices of P T -symmetric potentials, we obtain the exact solutions for BD and DD solitons. We perform the linear stability analysis of the obtained coherent structures. The results of this linear stability analysis are well corroborated by direct numerical simulation incorporating small random noise. It has been found that there exists a parameter regime which can support stable BD and DD solitons.

Testing the factor structure of the Family Quality of Life Survey - 2006.

PubMed

Isaacs, B; Wang, M; Samuel, P; Ajuwon, P; Baum, N; Edwards, M; Rillotta, F

2012-01-01

Although the Family Quality of Life Survey - 2006 (FQOLS-2006) is being used in research, there is little evidence to support its hypothesised domain structure. The purpose of this study was to test the domain structure of the survey using confirmatory factor analysis. Samples from Australia, Canada, Nigeria and the USA were analysed using structural equation modelling. The data from Australia, Canada and the USA were combined on the assumption that these countries are similar, at least to some degree, in economic development, language and culture. The Nigerian data were analysed on its own. The analysis was undertaken in two phases. First, the hypothesis that each of nine domains of the FQOLS-2006 is a unidimensional construct that can reliably measure the dimensions Importance, Stability, Opportunities, Attainment, Stability and Satisfaction was tested. Second, the hypothesis that family quality of life (FQoL) is a single latent construct represented by the nine domains measured in the FQOLS-2006 was tested. In the first phase of the analysis, the Importance dimension was dropped because of skewness and lack of variance. The Stability dimension did not fit well within the individual domain model in both the Nigerian and the combined three countries' data. When Importance and Stability were excluded, the individual domain models showede good or acceptable fit when error variances of some dimensions were allowed to correlate. In the second phase of the analysis, the overall model, FQoL, represented by the nine domains of the FQOLS-2006 showed good fit in both data sets. The conceptual model of the FQOLS-2006 was supported with some qualifications. Each domain on the survey can be reliably measured by four dimensions Opportunities, Initiative, Attainment and Satisfaction. The dimensions of Importance and Stability, however, did not fit. Data reported on these dimensions from past and current studies should be interpreted with caution. The construct of FQoL is also reliably measured by the domains of the FQOLS-2006. Further research into the psychometric properties of the survey, particularly from a cross-cultural perspective, is needed. © 2011 The Authors. Journal of Intellectual Disability Research © 2011 Blackwell Publishing Ltd.

Structures, stability and electronic properties of bimetallic Cun-1Sc and Cun-2Sc2 (n = 2-7) clusters

NASA Astrophysics Data System (ADS)

Li, Zhi; Zhao, Zhen; Zhou, Zhonghao; Wang, Qi

2018-02-01

To investigate the interface between the main phases of Cu-Sc alloys, the structures, stability and electronic properties of bimetallic Cun-1Sc and Cun-2Sc2 (n = 2-7) clusters are systematically calculated by the GGA-PW91 functional. The results reveal that the structures of Cun-1Sc and Cun-2Sc2 (n = 2-7) clusters inherited those of pure Cun (n = 2-7) clusters and they maintained higher symmetry. Cu5Sc cluster possesses more stable than its neighbors while Cu2Sc2 cluster is less stable than its neighbors by binding energy. Cu5Sc cluster possesses the highest kinetic stability of Cun-1Sc clusters and CuSc2, Cu3Sc2 and Cu5Sc2 clusters possess higher kinetic stability than their neighbors by HOMO-LUMO gap. NBO analysis reveals that Cu-Sc atoms have less pd orbital hybridization in the Sc doping Cun (n = 2-7) clusters.

AMTD - Advanced Mirror Technology Development in Mechanical Stability

NASA Technical Reports Server (NTRS)

Knight, J. Brent

2015-01-01

Analytical tools and processes are being developed at NASA Marshal Space Flight Center in support of the Advanced Mirror Technology Development (AMTD) project. One facet of optical performance is mechanical stability with respect to structural dynamics. Pertinent parameters are: (1) the spacecraft structural design, (2) the mechanical disturbances on-board the spacecraft (sources of vibratory/transient motion such as reaction wheels), (3) the vibration isolation systems (invariably required to meet future science needs), and (4) the dynamic characteristics of the optical system itself. With stability requirements of future large aperture space telescopes being in the lower Pico meter regime, it is paramount that all sources of mechanical excitation be considered in both feasibility studies and detailed analyses. The primary objective of this paper is to lay out a path to perform feasibility studies of future large aperture space telescope projects which require extreme stability. To get to that end, a high level overview of a structural dynamic analysis process to assess an integrated spacecraft and optical system is included.

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

Han, Sang -Don; Rajput, Nav Nidhi; Qu, Xiaohui

Through coupled experimental analysis and computational techniques, we uncover the origin of anodic stability for a range of nonaqueous zinc electrolytes. By examination of electrochemical, structural, and transport properties of nonaqueous zinc electrolytes with varying concentrations, it is demonstrated that the acetonitrile Zn(TFSI) 2, acetonitrile Zn(CF 3SO 3) 2, and propylene carbonate Zn(TFSI) 2 electrolytes can not only support highly reversible Zn deposition behavior on a Zn metal anode (≥99% of Coulombic efficiency), but also provide high anodic stability (up to ~3.8 V). The predicted anodic stability from DFT calculations is well in accordance with experimental results, and elucidates thatmore » the solvents play an important role in anodic stability of most electrolytes. Molecular dynamics (MD) simulations were used to understand the solvation structure (e.g., ion solvation and ionic association) and its effect on dynamics and transport properties (e.g., diffusion coefficient and ionic conductivity) of the electrolytes. Lastly, the combination of these techniques provides unprecedented insight into the origin of the electrochemical, structural, and transport properties in nonaqueous zinc electrolytes« less

The research of suspen-dome structure

NASA Astrophysics Data System (ADS)

Gong, Shengyuan

2017-09-01

After overcoming the shortcomings of single-layer latticed shell and cable dome structure, the suspen-dome was developed by inheriting the advantages of them, and it was recognized and applied as a new type of prestressed force large span space structure. Based on the analysis of the background and mechanical principle, the researches of suspen-dome are reviewed, including form-finding analysis, the analysis of static force and stability, the dynamic behaviors and the earthquake resistant behavior, the analysis of prestressing force and optimization design, and the research status of the design of the fir-resistant performance etc. This thesis summarizes the methods of various researches, being a reference for further structural performance research and structural engineering application.

Robust Flutter Margin Analysis that Incorporates Flight Data

NASA Technical Reports Server (NTRS)

Lind, Rick; Brenner, Martin J.

1998-01-01

An approach for computing worst-case flutter margins has been formulated in a robust stability framework. Uncertainty operators are included with a linear model to describe modeling errors and flight variations. The structured singular value, mu, computes a stability margin that directly accounts for these uncertainties. This approach introduces a new method of computing flutter margins and an associated new parameter for describing these margins. The mu margins are robust margins that indicate worst-case stability estimates with respect to the defined uncertainty. Worst-case flutter margins are computed for the F/A-18 Systems Research Aircraft using uncertainty sets generated by flight data analysis. The robust margins demonstrate flight conditions for flutter may lie closer to the flight envelope than previously estimated by p-k analysis.

Structure, reactivity and electronic properties of Mn doped Ni13 clusters

NASA Astrophysics Data System (ADS)

Banerjee, Radhashyam; Datta, Soumendu; Mookerjee, Abhijit

2013-06-01

In this work we have studied the structural and magnetic properties of Ni13 cluster mono- and bi-doped with Mn atoms. We have noted their tendency of being reactive toward the H2 molecule. We have found unusually enhanced stability in the mono-doped cluster (i.e. of the Ni12Mn) and the diminished stability of the corresponding chemisorbed cluster, Ni12MnH2. Our analysis of the stability and HOMO-LUMO gap explains this unusual behavior. Interestingly, we have also seen the quenching in the net magnetic moment upon H2 absorption in the doped NiMnm alloy clusters. This has been reported earlier for smaller Nin clusters [1].

Probing the origin of structural stability of single and double stapled p53 peptide analogs bound to MDM2.

PubMed

Guo, Zuojun; Streu, Kristina; Krilov, Goran; Mohanty, Udayan

2014-06-01

The stabilization of secondary structure is believed to play an important role in the peptide-protein binding interaction. In this study, the α-helical conformation and structural stability of single and double stapled all-hydrocarbon cross-linked p53 peptides when bound and unbound to MDM2 are investigated. We determined the effects of the peptide sequence, the stereochemistry of the cross-linker, the conformation of the double bond in the alkene bridge, and the length of the bridge, to the relative stability of the α-helix structure. The binding affinity calculations by WaterMap provided over one hundred hydration sites in the MDM2 binding pocket where water density is greater than twice that of the bulk, and the relative value of free energy released by displacing these hydration sites. In agreement with the experimental data, potentials of mean force obtained by weighted histogram analysis methods indicated the order of peptides from lowest to highest binding affinity. Our study provides a comprehensive rationalization of the relationship between peptide stapling strategy, the secondary structural stability, and the binding affinity of p53/MDM2 complex. We hope our efforts can help to further the development of a new generation p53/MDM2 inhibitors that can reactivate the function of p53 as tumor suppressor gene. © 2014 John Wiley & Sons A/S.

Stability of Alfvén wings in uniform plasmas

NASA Astrophysics Data System (ADS)

Sallago, P. A.; Platzeck, A. M.

2007-12-01

A conducting source moving uniformly through a magnetized plasma generates, among a variety of perturbations, Alfvén waves. An interesting characteristic of Alfvén waves is that they can build up structures in the plasma called Alfvén wings. These wings have been detected and measured in many solar system bodies, and their existence has also been theoretically proven. However, their stability remains to be studied. The aim of this paper is to analyze the stability of an Alfvén wing developed in a uniform background field, in the presence of an incompressible perturbation that has the same symmetry as the Alfvén wing, in the magnetohydrodynamic approximation. The study of the stability of a magnetohydrodynamic system is often performed by linearizing the equations and using either the normal modes method or the energy method. In spite of being applicable for many problems, both methods become algebraically complicated if the structure under analysis is a highly non-uniform one. Palumbo has developed an analytical method for the study of the stability of static structures with a symmetry in magnetized plasmas, in the presence of incompressible perturbations with the same symmetry as the structure (Palumbo 1998 Thesis, Universidad de Firenze, Italia). In the present paper we extend this method for Alfvén wings that are stationary structures, and conclude that in the presence of this kind of perturbation they are stable.

Flash Nanoprecipitation: Particle Structure and Stability

PubMed Central

Pustulka, Kevin M.; Wohl, Adam R.; Lee, Han Seung; Michel, Andrew R.; Han, Jing; Hoye, Thomas R.; McCormick, Alon V.; Panyam, Jayanth; Macosko, Christopher W.

2013-01-01

Flash nanoprecipitation (FNP) is a process that, through rapid mixing, stabilizes an insoluble low molecular weight compound in a nano-sized, polymer-stabilized delivery vehicle. The polymeric components are typically amphiphilic diblock copolymers (BCPs). In order to fully exploit the potential of FNP, factors affecting particle structure, size, and stability must be understood. Here we show that polymer type, hydrophobicity and crystallinity of the small molecule, and small molecule loading levels all affect particle size and stability. Of the four block copolymers (BCP) that we have studied here, poly(ethylene glycol)-b-poly(lactic-co-glycolic acid) (PEG-b-PLGA) was most suitable for potential drug delivery applications due to its ability to give rise to stable nanoparticles, its biocompatibility, and its degradability. We found little difference in particle size when using PLGA block sizes over the range of 5 to 15kDa. The choice of hydrophobic small molecule was important, as molecules with a calculated water-octanol partition coefficient (clogP) below 6 gave rise to particles that were unstable and underwent rapid Ostwald ripening. Studies probing the internal structure of nanoparticles were also performed. Analysis of differential scanning calorimetry (DSC), cryogenic transmission electron microscopy (cryo-TEM), and 1H-NMR experiments support a three-layer core-shell-corona nanoparticle structure. PMID:24053447

Convergence analysis of directed signed networks via an M-matrix approach

NASA Astrophysics Data System (ADS)

Meng, Deyuan

2018-04-01

This paper aims at solving convergence problems on directed signed networks with multiple nodes, where interactions among nodes are described by signed digraphs. The convergence analysis is achieved by matrix-theoretic and graph-theoretic tools, in which M-matrices play a central role. The fundamental digon sign-symmetry assumption upon signed digraphs can be removed with the proposed analysis approach. Furthermore, necessary and sufficient conditions are established for semi-positive and positive stabilities of Laplacian matrices of signed digraphs, respectively. A benefit of this result is that given strong connectivity, a directed signed network can achieve bipartite consensus (or state stability) if and only if the signed digraph associated with it is structurally balanced (or unbalanced). If the interactions between nodes are described by a signed digraph only with spanning trees, a directed signed network can achieve interval bipartite consensus (or state stability) if and only if the signed digraph contains a structurally balanced (or unbalanced) rooted subgraph. Simulations are given to illustrate the developed results by considering signed networks associated with digon sign-unsymmetric signed digraphs.

Strength Analysis of Coconut Fiber Stabilized Earth for Farm Structures

NASA Astrophysics Data System (ADS)

Enokela, O. S.; P. O, Alada

2012-07-01

Investigation of the strength characteristic of soil from alluvial deposit of River Benue in makurdi stabilized with coconut fiber as a stabilizer was carried as local building material for farm structure. Processed coconut fibers were mixed with the soil at four different mix ratios of 1% fiber, 2% fiber, 3% fiber and 4% fiber by percentage weight with 0% fiber as control. Compaction test and compressive strength were carried out on the various stabilizing ratio. From the compaction test, the correlation between the maximum dry density and optimum moisture content is a second order polynomial with a coefficient of 63% obtained at1.91kg/m3and 20.0% respectively while the compressive strength test shows an optimum failure load of 8.62N/mm2 at 2%fibre:100% soil mix ratio at 2.16 maximum dry density.

The novel support structure design of high stability for space borne primary reflector

NASA Astrophysics Data System (ADS)

Yu, Fei; Ding, Lin; Tan, Ting; Pei, Jing-yang.; Zhao, Xue-min; Bai, Shao-jun

2018-01-01

The novel support structure design of high stability for space borne primary mirror is presented. The structure is supported by a ball head support rod, for statically determinate support of reflector. The ball head assembly includes the supporting rod, nesting, bushing and other important parts. The liner bushing of the resistant material is used to fit for ball head approximated with the reflector material, and then the bad impact of thermal mismatch could be minimized to minimum. In order to ensure that the structure of the support will not be damaged, the glue spots for limitation is added around the reflector, for position stability of reflector. Through analysis and calculation, it can be seen that the novel support structure would not transfer the external stresses to the reflector, and the external stresses usually result from thermal mismatch and assembly misalignment. The novel method is useful for solving the problem of the bad influence form thermal stress and assembly force. In this paper, the supporting structure is introduced and analyzed in detail. The simulation results show that the ball head support reflector works more stably.

Structure and mechanism of maximum stability of isolated alpha-helical protein domains at a critical length scale.

PubMed

Qin, Zhao; Fabre, Andrea; Buehler, Markus J

2013-05-01

The stability of alpha helices is important in protein folding, bioinspired materials design, and controls many biological properties under physiological and disease conditions. Here we show that a naturally favored alpha helix length of 9 to 17 amino acids exists at which the propensity towards the formation of this secondary structure is maximized. We use a combination of thermodynamical analysis, well-tempered metadynamics molecular simulation and statistical analyses of experimental alpha helix length distributions and find that the favored alpha helix length is caused by a competition between alpha helix folding, unfolding into a random coil and formation of higher-order tertiary structures. The theoretical result is suggested to be used to explain the statistical distribution of the length of alpha helices observed in natural protein structures. Our study provides mechanistic insight into fundamental controlling parameters in alpha helix structure formation and potentially other biopolymers or synthetic materials. The result advances our fundamental understanding of size effects in the stability of protein structures and may enable the design of de novo alpha-helical protein materials.

Two worlds collide: Image analysis methods for quantifying structural variation in cluster molecular dynamics

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

Steenbergen, K. G., E-mail: kgsteen@gmail.com; Gaston, N.

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement formore » a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.« less

Two worlds collide: image analysis methods for quantifying structural variation in cluster molecular dynamics.

PubMed

Steenbergen, K G; Gaston, N

2014-02-14

Inspired by methods of remote sensing image analysis, we analyze structural variation in cluster molecular dynamics (MD) simulations through a unique application of the principal component analysis (PCA) and Pearson Correlation Coefficient (PCC). The PCA analysis characterizes the geometric shape of the cluster structure at each time step, yielding a detailed and quantitative measure of structural stability and variation at finite temperature. Our PCC analysis captures bond structure variation in MD, which can be used to both supplement the PCA analysis as well as compare bond patterns between different cluster sizes. Relying only on atomic position data, without requirement for a priori structural input, PCA and PCC can be used to analyze both classical and ab initio MD simulations for any cluster composition or electronic configuration. Taken together, these statistical tools represent powerful new techniques for quantitative structural characterization and isomer identification in cluster MD.

Boundary-Layer Stability Analysis of the Mean Flows Obtained Using Unstructured Grids

NASA Technical Reports Server (NTRS)

Liao, Wei; Malik, Mujeeb R.; Lee-Rausch, Elizabeth M.; Li, Fei; Nielsen, Eric J.; Buning, Pieter G.; Chang, Chau-Lyan; Choudhari, Meelan M.

2012-01-01

Boundary-layer stability analyses of mean flows extracted from unstructured-grid Navier- Stokes solutions have been performed. A procedure has been developed to extract mean flow profiles from the FUN3D unstructured-grid solutions. Extensive code-to-code validations have been performed by comparing the extracted mean ows as well as the corresponding stability characteristics to the predictions based on structured-grid solutions. Comparisons are made on a range of problems from a simple at plate to a full aircraft configuration-a modified Gulfstream-III with a natural laminar flow glove. The future aim of the project is to extend the adjoint-based design capability in FUN3D to include natural laminar flow and laminar flow control by integrating it with boundary-layer stability analysis codes, such as LASTRAC.

X-ray Crystallographic Structure of Thermophilic Rhodopsin

PubMed Central

Tsukamoto, Takashi; Mizutani, Kenji; Hasegawa, Taisuke; Takahashi, Megumi; Honda, Naoya; Hashimoto, Naoki; Shimono, Kazumi; Yamashita, Keitaro; Yamamoto, Masaki; Miyauchi, Seiji; Takagi, Shin; Hayashi, Shigehiko; Murata, Takeshi; Sudo, Yuki

2016-01-01

Thermophilic rhodopsin (TR) is a photoreceptor protein with an extremely high thermal stability and the first characterized light-driven electrogenic proton pump derived from the extreme thermophile Thermus thermophilus JL-18. In this study, we confirmed its high thermal stability compared with other microbial rhodopsins and also report the potential availability of TR for optogenetics as a light-induced neural silencer. The x-ray crystal structure of TR revealed that its overall structure is quite similar to that of xanthorhodopsin, including the presence of a putative binding site for a carotenoid antenna; but several distinct structural characteristics of TR, including a decreased surface charge and a larger number of hydrophobic residues and aromatic-aromatic interactions, were also clarified. Based on the crystal structure, the structural changes of TR upon thermal stimulation were investigated by molecular dynamics simulations. The simulations revealed the presence of a thermally induced structural substate in which an increase of hydrophobic interactions in the extracellular domain, the movement of extracellular domains, the formation of a hydrogen bond, and the tilting of transmembrane helices were observed. From the computational and mutational analysis, we propose that an extracellular LPGG motif between helices F and G plays an important role in the thermal stability, acting as a “thermal sensor.” These findings will be valuable for understanding retinal proteins with regard to high protein stability and high optogenetic performance. PMID:27129243

The Stability of Post Hoc Model Modifications in Covariance Structure Models.

ERIC Educational Resources Information Center

Hutchinson, Susan R.

The work of R. MacCallum et al. (1992) was extended by examining chance modifications through a Monte Carlo simulation. The stability of post hoc model modifications was examined under varying sample size, model complexity, and severity of misspecification using 2- and 4-factor oblique confirmatory factor analysis (CFA) models with four and eight…

A new sensitivity analysis for structural optimization of composite rotor blades

NASA Technical Reports Server (NTRS)

Venkatesan, C.; Friedmann, P. P.; Yuan, Kuo-An

1993-01-01

This paper presents a detailed mathematical derivation of the sensitivity derivatives for the structural dynamic, aeroelastic stability and response characteristics of a rotor blade in hover and forward flight. The formulation is denoted by the term semianalytical approach, because certain derivatives have to be evaluated by a finite difference scheme. Using the present formulation, sensitivity derivatives for the structural dynamic and aeroelastic stability characteristics, were evaluated for both isotropic and composite rotor blades. Based on the results, useful conclusions are obtained regarding the relative merits of the semi-analytical approach, for calculating sensitivity derivatives, when compared to a pure finite difference approach.

Nonketotic hyperglycinemia: Functional assessment of missense variants in GLDC to understand phenotypes of the disease.

PubMed

Bravo-Alonso, Irene; Navarrete, Rosa; Arribas-Carreira, Laura; Perona, Almudena; Abia, David; Couce, María Luz; García-Cazorla, Angels; Morais, Ana; Domingo, Rosario; Ramos, María Antonia; Swanson, Michael A; Van Hove, Johan L K; Ugarte, Magdalena; Pérez, Belén; Pérez-Cerdá, Celia; Rodríguez-Pombo, Pilar

2017-06-01

The rapid analysis of genomic data is providing effective mutational confirmation in patients with clinical and biochemical hallmarks of a specific disease. This is the case for nonketotic hyperglycinemia (NKH), a Mendelian disorder causing seizures in neonates and early-infants, primarily due to mutations in the GLDC gene. However, understanding the impact of missense variants identified in this gene is a major challenge for the application of genomics into clinical practice. Herein, a comprehensive functional and structural analysis of 19 GLDC missense variants identified in a cohort of 26 NKH patients was performed. Mutant cDNA constructs were expressed in COS7 cells followed by enzymatic assays and Western blot analysis of the GCS P-protein to assess the residual activity and mutant protein stability. Structural analysis, based on molecular modeling of the 3D structure of GCS P-protein, was also performed. We identify hypomorphic variants that produce attenuated phenotypes with improved prognosis of the disease. Structural analysis allows us to interpret the effects of mutations on protein stability and catalytic activity, providing molecular evidence for clinical outcome and disease severity. Moreover, we identify an important number of mutants whose loss-of-functionality is associated with instability and, thus, are potential targets for rescue using folding therapeutic approaches. © 2017 Wiley Periodicals, Inc.

Kinetic stability analysis on electromagnetic filamentary structure

NASA Astrophysics Data System (ADS)

Lee, Wonjae; Krasheninnikov, Sergei

2014-10-01

A coherent radial transport of filamentary structures in SOL region is important for its characteristics that can increase unwanted high fluxes to plasma facing components. In the course of propagation in radial direction, the coherency of the filaments is significantly limited by electrostatic resistive drift instability (Angus et al., 2012). Considering higher plasma pressure, which would have more large impact in heat fluxes, electromagnetic effects will reduce the growth rate of the drift wave instability and increase the instabilities from electron inertial effects. According to a linear stability analysis on equations with fluid approximation, the maximum growth rate of the instability from the electron inertia is higher than that of drift-Alfvén wave instability in high beta filaments such as ELMs. However, the analysis on the high beta filaments requires kinetic approach, since the decreased collisionality will make the fluid approximation broken. Therefore, the kinetic analysis will be presented for the electromagnetic effects on the dynamics of filamentary structures. This work was supported by the USDOE Grants DE-FG02-04ER54739 and DE-SC0010413 at UCSD and also by the Kwanjeong Educational Foundation.

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

A Survey of Aspartate Phenylalanine and Glutamate Phenylalanine Interactions in the Protein Data Bank: Searching for Anion Pairs

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

Philip, Vivek M; Harris, Jason B; Adams, Rachel M

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242 8249]. To study the role of anion interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused onmore » identification of Phe Asp or Glu pairs separated by less than 7 in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura Morokuma energy calculations were performed on roughly 19000 benzene formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (2 to 7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion pairs are found throughout protein structures, in helices as well as strands. Numerous pairs also had nearby cation interactions as well as potential stacking. While more than 1000 structures did not contain an anion pair, the 3134 remaining structures contained approximately 2.6 anion pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.« less

A Survey of Aspartate-Phenylalanine and Glutamate-Phenylalanine Interactions in the Protein Data Bank: Searching for Anion-pi Pairs

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

Philip, Vivek M; Harris, Jason B; Adams, Rachel M

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-{pi} pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-{pi} interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification ofmore » Phe-Asp or -Glu pairs separated by less than 7 {angstrom} in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-{pi} pairs are found throughout protein structures, in helices as well as {beta} strands. Numerous pairs also had nearby cation-{pi} interactions as well as potential {pi}-{pi} stacking. While more than 1000 structures did not contain an anion-{pi} pair, the 3134 remaining structures contained approximately 2.6 anion-{pi} pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.« less

A survey of aspartate-phenylalanine and glutamate-phenylalanine interactions in the protein data bank: searching for anion-π pairs.

PubMed

Philip, Vivek; Harris, Jason; Adams, Rachel; Nguyen, Don; Spiers, Jeremy; Baudry, Jerome; Howell, Elizabeth E; Hinde, Robert J

2011-04-12

Protein structures are stabilized using noncovalent interactions. In addition to the traditional noncovalent interactions, newer types of interactions are thought to be present in proteins. One such interaction, an anion-π pair, in which the positively charged edge of an aromatic ring interacts with an anion, forming a favorable anion-quadrupole interaction, has been previously proposed [Jackson, M. R., et al. (2007) J. Phys. Chem. B111, 8242-8249]. To study the role of anion-π interactions in stabilizing protein structure, we analyzed pairwise interactions between phenylalanine (Phe) and the anionic amino acids, aspartate (Asp) and glutamate (Glu). Particular emphasis was focused on identification of Phe-Asp or -Glu pairs separated by less than 7 Å in the high-resolution, nonredundant Protein Data Bank. Simplifying Phe to benzene and Asp or Glu to formate molecules facilitated in silico analysis of the pairs. Kitaura-Morokuma energy calculations were performed on roughly 19000 benzene-formate pairs and the resulting energies analyzed as a function of distance and angle. Edgewise interactions typically produced strongly stabilizing interaction energies (-2 to -7.3 kcal/mol), while interactions involving the ring face resulted in weakly stabilizing to repulsive interaction energies. The strongest, most stabilizing interactions were identified as preferentially occurring in buried residues. Anion-π pairs are found throughout protein structures, in helices as well as β strands. Numerous pairs also had nearby cation-π interactions as well as potential π-π stacking. While more than 1000 structures did not contain an anion-π pair, the 3134 remaining structures contained approximately 2.6 anion-π pairs per protein, suggesting it is a reasonably common motif that could contribute to the overall structural stability of a protein.

On the linear stability of blood flow through model capillary networks.

PubMed

Davis, Jeffrey M

2014-12-01

Under the approximation that blood behaves as a continuum, a numerical implementation is presented to analyze the linear stability of capillary blood flow through model tree and honeycomb networks that are based on the microvascular structures of biological tissues. The tree network is comprised of a cascade of diverging bifurcations, in which a parent vessel bifurcates into two descendent vessels, while the honeycomb network also contains converging bifurcations, in which two parent vessels merge into one descendent vessel. At diverging bifurcations, a cell partitioning law is required to account for the nonuniform distribution of red blood cells as a function of the flow rate of blood into each descendent vessel. A linearization of the governing equations produces a system of delay differential equations involving the discharge hematocrit entering each network vessel and leads to a nonlinear eigenvalue problem. All eigenvalues in a specified region of the complex plane are captured using a transformation based on contour integrals to construct a linear eigenvalue problem with identical eigenvalues, which are then determined using a standard QR algorithm. The predicted value of the dimensionless exponent in the cell partitioning law at the instability threshold corresponds to a supercritical Hopf bifurcation in numerical simulations of the equations governing unsteady blood flow. Excellent agreement is found between the predictions of the linear stability analysis and nonlinear simulations. The relaxation of the assumption of plug flow made in previous stability analyses typically has a small, quantitative effect on the stability results that depends on the specific network structure. This implementation of the stability analysis can be applied to large networks with arbitrary structure provided only that the connectivity among the network segments is known.

Response surface method in geotechnical/structural analysis, phase 1

NASA Astrophysics Data System (ADS)

Wong, F. S.

1981-02-01

In the response surface approach, an approximating function is fit to a long running computer code based on a limited number of code calculations. The approximating function, called the response surface, is then used to replace the code in subsequent repetitive computations required in a statistical analysis. The procedure of the response surface development and feasibility of the method are shown using a sample problem in slop stability which is based on data from centrifuge experiments of model soil slopes and involves five random soil parameters. It is shown that a response surface can be constructed based on as few as four code calculations and that the response surface is computationally extremely efficient compared to the code calculation. Potential applications of this research include probabilistic analysis of dynamic, complex, nonlinear soil/structure systems such as slope stability, liquefaction, and nuclear reactor safety.

Requirements Formulation and Dynamic Jitter Analysis for Fourier-Kelvin Stellar Interferometer

NASA Technical Reports Server (NTRS)

Liu, Kuo-Chia; Hyde, Tristram; Blaurock, Carl; Bolognese, Jeff; Howard, Joseph; Danchi, William

2004-01-01

The Fourier-Kelvin Stellar Interferometer (FKSI) has been proposed to detect and characterize extra solar giant planets. The baseline configuration for FKSI is a two- aperture, structurally connected nulling interferometer, capable of providing null depth less than lo4 in the infrared. The objective of this paper is to summarize the process for setting the top level requirements and the jitter analysis performed on FKSI to date. The first part of the paper discusses the derivation of dynamic stability requirements, necessary for meeting the FKSI nulling demands. An integrated model including structures, optics, and control systems has been developed to support dynamic jitter analysis and requirements verification. The second part of the paper describes how the integrated model is used to investigate the effects of reaction wheel disturbances on pointing and optical path difference stabilities.

The relationship between dental implant stability and trabecular bone structure using cone-beam computed tomography

PubMed Central

2016-01-01

Purpose The objective of this study was to investigate the relationships between primary implant stability as measured by impact response frequency and the structural parameters of trabecular bone using cone-beam computed tomography(CBCT), excluding the effect of cortical bone thickness. Methods We measured the impact response of a dental implant placed into swine bone specimens composed of only trabecular bone without the cortical bone layer using an inductive sensor. The peak frequency of the impact response spectrum was determined as an implant stability criterion (SPF). The 3D microstructural parameters were calculated from CT images of the bone specimens obtained using both micro-CT and CBCT. Results SPF had significant positive correlations with trabecular bone structural parameters (BV/TV, BV, BS, BSD, Tb.Th, Tb.N, FD, and BS/BV) (P<0.01) while SPF demonstrated significant negative correlations with other microstructural parameters (Tb.Sp, Tb.Pf, and SMI) using micro-CT and CBCT (P<0.01). Conclusions There was an increase in implant stability prediction by combining BV/TV and SMI in the stepwise forward regression analysis. Bone with high volume density and low surface density shows high implant stability. Well-connected thick bone with small marrow spaces also shows high implant stability. The combination of bone density and architectural parameters measured using CBCT can predict the implant stability more accurately than the density alone in clinical diagnoses. PMID:27127692

Trade-offs with stability modulate innate and mutationally acquired drug-resistance in bacterial dihydrofolate reductase enzymes.

PubMed

Matange, Nishad; Bodkhe, Swapnil; Patel, Maitri; Shah, Pooja

2018-06-05

Structural stability is a major constraint on the evolution of protein sequences. However, under strong directional selection, mutations that confer novel phenotypes but compromise structural stability of proteins may be permissible. During the evolution of antibiotic resistance, mutations that confer drug resistance often have pleiotropic effects on the structure and function of antibiotic-target proteins, usually essential metabolic enzymes. In this study, we show that trimethoprim-resistant alleles of dihydrofolate reductase from Escherichia coli (EcDHFR) harbouring the Trp30Gly, Trp30Arg or Trp30Cys mutations are significantly less stable than the wild type making them prone to aggregation and proteolysis. This destabilization is associated with lower expression level resulting in a fitness cost and negative epistasis with other TMP-resistant mutations in EcDHFR. Using structure-based mutational analysis we show that perturbation of critical stabilizing hydrophobic interactions in wild type EcDHFR enzyme explains the phenotypes of Trp30 mutants. Surprisingly, though crucial for the stability of EcDHFR, significant sequence variation is found at this site among bacterial DHFRs. Mutational and computational analyses in EcDHFR as well as in DHFR enzymes from Staphylococcus aureus and Mycobacterium tuberculosis demonstrate that natural variation at this site and its interacting hydrophobic residues, modulates TMP-resistance in other bacterial DHFRs as well, and may explain the different susceptibilities of bacterial pathogens to trimethoprim. Our study demonstrates that trade-offs between structural stability and function can influence innate drug resistance as well as the potential for mutationally acquired drug resistance of an enzyme. ©2018 The Author(s).

Physics and evolution of thermophilic adaptation.

PubMed

Berezovsky, Igor N; Shakhnovich, Eugene I

2005-09-06

Analysis of structures and sequences of several hyperthermostable proteins from various sources reveals two major physical mechanisms of their thermostabilization. The first mechanism is "structure-based," whereby some hyperthermostable proteins are significantly more compact than their mesophilic homologues, while no particular interaction type appears to cause stabilization; rather, a sheer number of interactions is responsible for thermostability. Other hyperthermostable proteins employ an alternative, "sequence-based" mechanism of their thermal stabilization. They do not show pronounced structural differences from mesophilic homologues. Rather, a small number of apparently strong interactions is responsible for high thermal stability of these proteins. High-throughput comparative analysis of structures and complete genomes of several hyperthermophilic archaea and bacteria revealed that organisms develop diverse strategies of thermophilic adaptation by using, to a varying degree, two fundamental physical mechanisms of thermostability. The choice of a particular strategy depends on the evolutionary history of an organism. Proteins from organisms that originated in an extreme environment, such as hyperthermophilic archaea (Pyrococcus furiosus), are significantly more compact and more hydrophobic than their mesophilic counterparts. Alternatively, organisms that evolved as mesophiles but later recolonized a hot environment (Thermotoga maritima) relied in their evolutionary strategy of thermophilic adaptation on "sequence-based" mechanism of thermostability. We propose an evolutionary explanation of these differences based on physical concepts of protein designability.

Stabilizing subnanometer Ag(0) nanoclusters by thiolate and diphosphine ligands and their crystal structures

NASA Astrophysics Data System (ADS)

Yang, Huayan; Wang, Yu; Zheng, Nanfeng

2013-03-01

The combined use of thiolate and diphosphine as surface ligands helps to stabilize subnanometer Ag(0) nanoclusters, resulting in the successful crystallization of two Ag(0)-containing nanoclusters (Ag16 and Ag32) for X-ray single crystal analysis. Both clusters have core-shell structures with Ag86+ and Ag2212+ as their cores, which are not simply either fragments of face-centered cubic metals or their five-fold twinned counterparts. The clusters display UV-Vis absorption spectra consisting of molecule-like optical transitions.The combined use of thiolate and diphosphine as surface ligands helps to stabilize subnanometer Ag(0) nanoclusters, resulting in the successful crystallization of two Ag(0)-containing nanoclusters (Ag16 and Ag32) for X-ray single crystal analysis. Both clusters have core-shell structures with Ag86+ and Ag2212+ as their cores, which are not simply either fragments of face-centered cubic metals or their five-fold twinned counterparts. The clusters display UV-Vis absorption spectra consisting of molecule-like optical transitions. Electronic supplementary information (ESI) available: Experimental details, more pictures of the structure and XPS spectra of the clusters. CCDC 916463 and 916464. For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c3nr34328f

A stage structure pest management model with impulsive state feedback control

NASA Astrophysics Data System (ADS)

Pang, Guoping; Chen, Lansun; Xu, Weijian; Fu, Gang

2015-06-01

A stage structure pest management model with impulsive state feedback control is investigated. We get the sufficient condition for the existence of the order-1 periodic solution by differential equation geometry theory and successor function. Further, we obtain a new judgement method for the stability of the order-1 periodic solution of the semi-continuous systems by referencing the stability analysis for limit cycles of continuous systems, which is different from the previous method of analog of Poincarè criterion. Finally, we analyze numerically the theoretical results obtained.

Investigation of biomechanical behavior of lumbar vertebral segments with dynamic stabilization device using finite element approach

NASA Astrophysics Data System (ADS)

Deoghare, Ashish B.; Kashyap, Siddharth; Padole, Pramod M.

2013-03-01

Degenerative disc disease is a major source of lower back pain and significantly alters the biomechanics of the lumbar spine. Dynamic stabilization device is a remedial technique which uses flexible materials to stabilize the affected lumbar region while preserving the natural anatomy of the spine. The main objective of this research work is to investigate the stiffness variation of dynamic stabilization device under various loading conditions under compression, axial rotation and flexion. Three dimensional model of the two segment lumbar spine is developed using computed tomography (CT) scan images. The lumbar structure developed is analyzed in ANSYS workbench. Two types of dynamic stabilization are considered: one with stabilizing device as pedicle instrumentation and second with stabilization device inserted around the inter-vertebral disc. Analysis suggests that proper positioning of the dynamic stabilization device is of paramount significance prior to the surgery. Inserting the device in the posterior region indicates the adverse effects as it shows increase in the deformation of the inter-vertebral disc. Analysis executed by positioning stabilizing device around the inter-vertebral disc yields better result for various stiffness values under compression and other loadings. [Figure not available: see fulltext.

Maximizing detergent stability and functional expression of a GPCR by exhaustive recombination and evolution.

PubMed

Schlinkmann, Karola M; Hillenbrand, Matthias; Rittner, Alexander; Künz, Madeleine; Strohner, Ralf; Plückthun, Andreas

2012-09-21

To identify structural features in a G-protein-coupled receptor (GPCR) crucial for biosynthesis, stability in the membrane and stability in detergent micelles, we developed an evolutionary approach using expression in the inner membrane of Escherichia coli. From the analysis of 800,000 sequences of the rat neurotensin receptor 1, in which every amino acid had been varied to all 64 codons, we uncovered several "shift" positions, where the selected population focuses on a residue different from wild type. Here, we employed in vitro DNA recombination and a comprehensive synthetic binary library made by the Slonomics® technology, allowing us to uncover additive and synergistic effects in the structure that maximize both detergent stability and functional expression. We identified variants with >25,000 functional molecules per E. coli cell, a 50-fold increase over wild type, and observed strong coevolution of detergent stability. We arrived at receptor variants highly stable in short-chain detergents, much more so than those found by alanine scanning on the same receptor. These evolved GPCRs continue to be able to signal through the G-protein. We discuss the structural reasons for these improvements achieved through directed evolution. Copyright © 2012 Elsevier Ltd. All rights reserved.

Theory of buckling and post-buckling behavior of elastic structures

NASA Technical Reports Server (NTRS)

Budiansky, B.

1974-01-01

The present paper provides a unified, general presentation of the basic theory of the buckling and post-buckling behavior of elastic structures in a form suitable for application to a wide variety of special problems. The notation of functional analysis is used for this purpose. Before the general analysis, simple conceptual models are used to elucidate the basic concepts of bifurcation buckling, snap buckling, imperfection sensitivity, load-shortening relations, and stability. The energy approach, the virtual-work approach, and mode interaction are discussed. The derivations and results are applicable to continua and finite-dimensional systems. The virtual-work and energy approaches are given separate treatments, but their equivalence is made explicit. The basic concepts of stability occupy a secondary position in the present approach.

Nonlinear behaviors of FRP-wrapped tall trees subjected to high wind loads

NASA Astrophysics Data System (ADS)

Kang, J.; Yi, Z. Z.; Choi, S. G.

2017-12-01

This study investigated the mechanical stability of historical tall trees wrapped with fiber-reinforced polymer (FRP) laminates using finite element (FE) analysis. High wind loads are considered as external loading conditions as they are one of the major threats on the structural stability of tall old trees. There have been several traditional practices to enhance the stability of tall trees exposed to high windstorms such as tree supporters and anchorages. They, however, have been sometimes causing negative effects with their misuses as the application guidelines for those methods were not adequately studied or documented. Furthermore, the oldest known trees in the country should be protected from the damage of external surface as well as ruin of the landscape. The objective of this study was to evaluate the structural effects of FRP wraps applied to tall trees subjected to high wind loads. The anisotropic material properties of wood and FRP laminates were considered in the analysis in addition to geometrically nonlinear behaviors. This study revealed that FRP wrapping for tall trees could effectively reduce the deflections and maximum stresses of trees, which results in the enhanced stability of tall trees. The optimum geometry and thicknesses of FRP wraps proposed in this study would provide fundemental guidelines for designing and constructing the application of innovative FRP wraps on tall trees, which are structurally unstable or should be preserved nationally and historically.

All-thiol-stabilized Ag44 and Au12Ag32 nanoparticles with single-crystal structures.

PubMed

Yang, Huayan; Wang, Yu; Huang, Huaqi; Gell, Lars; Lehtovaara, Lauri; Malola, Sami; Häkkinen, Hannu; Zheng, Nanfeng

2013-01-01

Noble metal nanoparticles stabilized by organic ligands are important for applications in assembly, site-specific bioconjugate labelling and sensing, drug delivery and medical therapy, molecular recognition and molecular electronics, and catalysis. Here we report crystal structures and theoretical analysis of three Ag44(SR)30 and three Au12Ag32(SR)30 intermetallic nanoclusters stabilized with fluorinated arylthiols (SR=SPhF, SPhF2 or SPhCF3). The nanocluster forms a Keplerate solid of concentric icosahedral and dodecahedral atom shells, protected by six Ag2(SR)5 units. Positive counterions in the crystal indicate a high negative charge of 4(-) per nanoparticle, and density functional theory calculations explain the stability as an 18-electron superatom shell closure in the metal core. Highly featured optical absorption spectra in the ultraviolet-visible region are analysed using time-dependent density functional perturbation theory. This work forms a basis for further understanding, engineering and controlling of stability as well as electronic and optical properties of these novel nanomaterials.

Nonlinear Instability of Hypersonic Flow past a Wedge

NASA Technical Reports Server (NTRS)

Seddougui, Sharon O.; Bassom, Andrew P.

1991-01-01

The nonlinear stability of a compressible flow past a wedge is investigated in the hypersonic limit. The analysis follows the ideas of a weakly nonlinear approach. Interest is focussed on Tollmien-Schlichting waves governed by a triple deck structure and it is found that the attached shock can profoundly affect the stability characteristics of the flow. In particular, it is shown that nonlinearity tends to have a stabilizing influence. The nonlinear evolution of the Tollmien-Schlichting mode is described in a number of asymptotic limits.

Structure and stability of charged colloid-nanoparticle mixtures

NASA Astrophysics Data System (ADS)

Weight, Braden M.; Denton, Alan R.

2018-03-01

Physical properties of colloidal materials can be modified by addition of nanoparticles. Within a model of like-charged mixtures of particles governed by effective electrostatic interactions, we explore the influence of charged nanoparticles on the structure and thermodynamic phase stability of charge-stabilized colloidal suspensions. Focusing on salt-free mixtures of particles of high size and charge asymmetry, interacting via repulsive Yukawa effective pair potentials, we perform molecular dynamics simulations and compute radial distribution functions and static structure factors. Analysis of these structural properties indicates that increasing the charge and concentration of nanoparticles progressively weakens correlations between charged colloids. We show that addition of charged nanoparticles to a suspension of like-charged colloids can induce a colloidal crystal to melt and can facilitate aggregation of a fluid suspension due to attractive van der Waals interactions. We attribute the destabilizing influence of charged nanoparticles to enhanced screening of electrostatic interactions, which weakens repulsion between charged colloids. This interpretation is consistent with recent predictions of an effective interaction theory of charged colloid-nanoparticle mixtures.

Thermal stability analysis of the fine structure of solar prominences

NASA Technical Reports Server (NTRS)

Demoulin, Pascal; Malherbe, Jean-Marie; Schmieder, Brigitte; Raadu, Mickael A.

1986-01-01

The linear thermal stability of a 2D periodic structure (alternatively hot and cold) in a uniform magnetic field is analyzed. The energy equation includes wave heating (assumed proportional to density), radiative cooling and both conduction parallel and orthogonal to magnetic lines. The equilibrium is perturbed at constant gas pressure. With parallel conduction only, it is found to be unstable when the length scale 1// is greater than 45 Mn. In that case, orthogonal conduction becomes important and stabilizes the structure when the length scale is smaller than 5 km. On the other hand, when the length scale is greater than 5 km, the thermal equilibrium is unstable, and the corresponding time scale is about 10,000 s: this result may be compared to observations showing that the lifetime of the fine structure of solar prominences is about one hour; consequently, our computations suggest that the size of the unresolved threads could be of the order of 10 km only.

The NASA Monographs on Shell Stability Design Recommendations: A Review and Suggested Improvements

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.; Starnes, James H., Jr.

1998-01-01

A summary of existing NASA design criteria monographs for the design of buckling-resistant thin-shell structures is presented. Subsequent improvements in the analysis for nonlinear shell response are reviewed, and current issues in shell stability analysis are discussed. Examples of nonlinear shell responses that are not included in the existing shell design monographs are presented, and an approach for including reliability based analysis procedures in the shell design process is discussed. Suggestions for conducting future shell experiments are presented, and proposed improvements to the NASA shell design criteria monographs are discussed.

The NASA Monographs on Shell Stability Design Recommendations: A Review and Suggested Improvements

NASA Technical Reports Server (NTRS)

Nemeth, Michael P.; Starnes, James H., Jr.

1998-01-01

A summary of the existing NASA design criteria monographs for the design of buckling-resistant thin-shell structures is presented. Subsequent improvements in the analysis for nonlinear shell response are reviewed, and current issues in shell stability analysis are discussed. Examples of nonlinear shell responses that are not included in the existing shell design monographs are presented, and an approach for including reliability-based analysis procedures in the shell design process is discussed. Suggestions for conducting future shell experiments are presented, and proposed improvements to the NASA shell design criteria monographs are discussed.

Fractionation and physicochemical characterization of lignin from waste jute bags: Effect of process parameters on yield and thermal degradation.

PubMed

Ahuja, Dheeraj; Kaushik, Anupama; Chauhan, Ghanshyam S

2017-04-01

In this work lignin was extracted from waste jute bags using soda cooking method and effect of varying alkali concentration and pH on yield, purity, structure and thermal degradation of lignin were studied. The Lignin yield, chemical composition and purity were assessed using TAPPI method and UV-vis spectroscopy. Yield and purity of lignin ranged from 27 to 58% and 50-94%, respectively for all the samples and was maximum for 8% alkali concentration and at pH 2 giving higher thermal stability. Chemical structure, thermal stability and elementary analysis of lignin were studied using FTIR, H NMR, thermo gravimetric analysis (TGA) and Elemental analyzer. FTIR and H NMR results showed that core structure of lignin starts breaking beyond 10% alkali concentration. S/G ratio shows the dominance of Syringyl unit over guaiacyl unit. Copyright © 2017 Elsevier B.V. All rights reserved.

An Innovative Structural Mode Selection Methodology: Application for the X-33 Launch Vehicle Finite Element Model

NASA Technical Reports Server (NTRS)

Hidalgo, Homero, Jr.

2000-01-01

An innovative methodology for determining structural target mode selection and mode selection based on a specific criterion is presented. An effective approach to single out modes which interact with specific locations on a structure has been developed for the X-33 Launch Vehicle Finite Element Model (FEM). We presented Root-Sum-Square (RSS) displacement method computes resultant modal displacement for each mode at selected degrees of freedom (DOF) and sorts to locate modes with highest values. This method was used to determine modes, which most influenced specific locations/points on the X-33 flight vehicle such as avionics control components, aero-surface control actuators, propellant valve and engine points for use in flight control stability analysis and for flight POGO stability analysis. Additionally, the modal RSS method allows for primary or global target vehicle modes to also be identified in an accurate and efficient manner.

Insights into the structural stability of Bax from molecular dynamics simulations at high temperatures

PubMed Central

Rosas-Trigueros, Jorge Luis; Correa-Basurto, José; Guadalupe Benítez-Cardoza, Claudia; Zamorano-Carrillo, Absalom

2011-01-01

Bax is a member of the Bcl-2 protein family that participates in mitochondrion-mediated apoptosis. In the early stages of the apoptotic pathway, this protein migrates from the cytosol to the outer mitochondrial membrane, where it is inserted and usually oligomerizes, making cytochrome c-compatible pores. Although several cellular and structural studies have been reported, a description of the stability of Bax at the molecular level remains elusive. This article reports molecular dynamics simulations of monomeric Bax at 300, 400, and 500 K, focusing on the most relevant structural changes and relating them to biological experimental results. Bax gradually loses its α-helices when it is submitted to high temperatures, yet it maintains its globular conformation. The resistance of Bax to adopt an extended conformation could be due to several interactions that were found to be responsible for maintaining the structural stability of this protein. Among these interactions, we found salt bridges, hydrophobic interactions, and hydrogen bonds. Remarkably, salt bridges were the most relevant to prevent the elongation of the structure. In addition, the analysis of our results suggests which conformational movements are implicated in the activation/oligomerization of Bax. This atomistic description might have important implications for understanding the functionality and stability of Bax in vitro as well as within the cellular environment. PMID:21936009

Higher order structural effects stabilizing the reverse Watson–Crick Guanine-Cytosine base pair in functional RNAs

PubMed Central

Chawla, Mohit; Abdel-Azeim, Safwat; Oliva, Romina; Cavallo, Luigi

2014-01-01

The G:C reverse Watson–Crick (W:W trans) base pair, also known as Levitt base pair in the context of tRNAs, is a structurally and functionally important base pair that contributes to tertiary interactions joining distant domains in functional RNA molecules and also participates in metabolite binding in riboswitches. We previously indicated that the isolated G:C W:W trans base pair is a rather unstable geometry, and that dicationic metal binding to the Guanine base or posttranscriptional modification of the Guanine can increase its stability. Herein, we extend our survey and report on other H-bonding interactions that can increase the stability of this base pair. To this aim, we performed a bioinformatics search of the PDB to locate all the occurencies of G:C trans base pairs. Interestingly, 66% of the G:C trans base pairs in the PDB are engaged in additional H-bonding interactions with other bases, the RNA backbone or structured water molecules. High level quantum mechanical calculations on a data set of representative crystal structures were performed to shed light on the structural stability and energetics of the various crystallographic motifs. This analysis was extended to the binding of the preQ1 metabolite to a preQ1-II riboswitch. PMID:24121683

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory

PubMed Central

Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-ichi; Sugimoto, Naoki

2015-01-01

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water–water interactions, (ii) ethylene glycol more effectively disrupted water–water interactions around Watson–Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson–Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. PMID:26538600

Structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 phases from first-principles calculations

NASA Astrophysics Data System (ADS)

Li, X. D.; Li, K.; Wei, C. H.; Han, W. D.; Zhou, N. G.

2018-06-01

The structural, electronic, elastic, and thermodynamic properties of CaSi, Ca2Si, and CaSi2 are systematically investigated by using first-principles calculations method based on density functional theory (DFT). The calculated formation enthalpies and cohesive energies show that CaSi2 possesses the greatest structural stability and CaSi has the strongest alloying ability. The structural stability of the three phases is compared according to electronic structures. Further analysis on electronic structures indicates that the bonding of these phases exhibits the combinations of metallic, covalent, and ionic bonds. The elastic constants are calculated, and the bulk modulus, shear modulus, Young's modulus, Poisson's ratio, and anisotropy factor of polycrystalline materials are deduced. Additionally, the thermodynamic properties were theoretically predicted and discussed.

Vibration control in smart coupled beams subjected to pulse excitations

NASA Astrophysics Data System (ADS)

Pisarski, Dominik; Bajer, Czesław I.; Dyniewicz, Bartłomiej; Bajkowski, Jacek M.

2016-10-01

In this paper, a control method to stabilize the vibration of adjacent structures is presented. The control is realized by changes of the stiffness parameters of the structure's couplers. A pulse excitation applied to the coupled adjacent beams is imposed as the kinematic excitation. For such a representation, the designed control law provides the best rate of energy dissipation. By means of a stability analysis, the performance in different structural settings is studied. The efficiency of the proposed strategy is examined via numerical simulations. In terms of the assumed energy metric, the controlled structure outperforms its passively damped equivalent by over 50 percent. The functionality of the proposed control strategy should attract the attention of practising engineers who seek solutions to upgrade existing damping systems.

Native denaturation differential scanning fluorimetry: Determining the effect of urea using a quantitative real-time thermocycler.

PubMed

Childers, Christine L; Green, Stuart R; Dawson, Neal J; Storey, Kenneth B

2016-09-01

The effect of protein stability on kinetic function is monitored with many techniques that often require large amounts of expensive substrates and specialized equipment not universally available. We present differential scanning fluorimetry (DSF), a simple high-throughput assay performed in real-time thermocyclers, as a technique for analysis of protein unfolding. Furthermore, we demonstrate a correlation between the half-maximal rate of protein unfolding (Knd), and protein unfolding by urea (I50). This demonstrates that DSF methods can determine the structural stability of an enzyme's active site and can compare the relative structural stability of homologous enzymes with a high degree of sequence similarity. Copyright © 2016 Elsevier Inc. All rights reserved.

Simulation studies for surfaces and materials strength

NASA Technical Reports Server (NTRS)

Halicioglu, T.

1985-01-01

From intermolecular force studies, it is now known that the overall non-additive contribution to the lattice enegy is positive so that analysis based on only pairwise additivity suggests a shallower intermolecular potential than the true value. Two body contributions alone are also known to be categorically unable to even qualitatively describe some configurations of molecular clusters in the gas phase or the general relaxation and reconstruction of fcc crystal surfaces. In addition, the many-body contribution was shown to play a key role in the stability of certain crystal structures. In these recent analyses, a relatively simple potential energy function (PEF), comprising only a two-body Mie-type potential plus a three-body Axilrod-Teller-type potential, was found to be extremely effective. This same parametric PEF is applied to describe the bulk stability and surface energy for the diamond cubic structure. To test the stability condition, the FCC, BCC, diamond cubic, graphite and beta-tin structures were considered.

Analysis of thermoelectric properties of high-temperature complex alloys of nickel-base, iron-base and cobalt-base groups

NASA Technical Reports Server (NTRS)

Holanda, R.

1984-01-01

The thermoelectric properties alloys of the nickel-base, iron-base, and cobalt-base groups containing from 1% to 25% 106 chromium were compared and correlated with the following material characteristics: atomic percent of the principle alloy constituent; ratio of concentration of two constituents; alloy physical property (electrical resistivity); alloy phase structure (percent precipitate or percent hardener content); alloy electronic structure (electron concentration). For solid-solution-type alloys the most consistent correlation was obtained with electron concentration, for precipitation-hardenable alloys of the nickel-base superalloy group, the thermoelectric potential correlated with hardener content in the alloy structure. For solid-solution-type alloys, no problems were found with thermoelectric stability to 1000; for precipitation-hardenable alloys, thermoelectric stability was dependent on phase stability. The effects of the compositional range of alloy constituents on temperature measurement uncertainty are discussed.

Thermal stability and electrochemical properties of PVP-protected Ru nanoparticles synthesized at room temperature

NASA Astrophysics Data System (ADS)

Kumar, Manish; Devi, Pooja; Shivling, V. D.

2017-08-01

Stable ruthenium nanoparticles (RuNPs) have been synthesized by the chemical reduction of ruthenium trichloride trihydrate (RuCl3 · 3H2O) using sodium borohydride (NaBH4) as a reductant and polyvinylpyrrolidone (PVP) as a protecting agent in the aqueous medium at room temperature. The nanoparticles thus prepared were characterized by their morphology and structural analysis from transmission electron microscopy (TEM), X-ray powder diffraction (XRD), UV-vis spectroscopy, Fourier transformation infrared and thermogravimetric analysis (TGA) techniques. The TEM image suggested a homogeneous distribution of PVP-protected RuNPs having a small average diameter of 2-4 nm with a chain-like network structure. The XRD pattern also confirmed that a crystallite size is around 2 nm of PVP-protected RuNPs having a single broad peak. The thermal stability studied using TGA, indicated good stability and the electrochemical properties of these nanoparticles revealed that saturation current increases for PVP-protected RuNPs/GC.

Characterizing Environmental Transformation of Multi-walled Carbon Nanotubes and Carbon Nano-Fiber Composites using Thermal Analysis and Related Hyphenated Techniques

EPA Science Inventory

Thermogravimetric analysis (TGA) coupled with gas chromatography and mass spectroscopy (TGA/GCMS), for the evolved gas analysis, has given insight to the stability and kinetics of structural changes and determining adsorbed organics to nanomaterials and nanocomposites. TGA is als...

Rational design for the stability improvement of Armillariella tabescens β-mannanase MAN47 based on N-glycosylation modification.

PubMed

Hu, Weixiong; Liu, Xiaoyun; Li, Yufeng; Liu, Daling; Kuang, Zhihe; Qian, Chuiwen; Yao, Dongsheng

2017-02-01

β-Mannanase has been widely used in industries such as food and feed processing and thus has been a target enzyme for biotechnological development. In this study, we sought to improve the stability and protease resistance of a recombinant β-mannanase, MAN47 from Armillariella tabescens, through rationally designed N-glycosylation. Based on homology modeling, molecular docking, secondary structure analysis and glycosylation feasibility analysis, an enhanced aromatic sequon sequence was introduced into specific MAN47 loop regions to facilitate N-glycosylation. The mutant enzymes were expressed in Pichia pastoris SMD1168, and their thermal stability, pH stability, trypsin resistance and pepsin resistance were determined. Two mutant MAN47 enzymes, g-123 and g-347, were glycosylated as expected when expressed in yeast, and their thermal stability, pH stability, and protease resistance were significantly improved compared to the wild-type enzyme. An enzyme with multiple stability characterizations has broad prospects in practical applications, and the rational design N-glycosylation strategy may have applications in simultaneously improving several properties of other biotechnological targets. Copyright © 2016 Elsevier Inc. All rights reserved.

Efficient first-principles prediction of solid stability: Towards chemical accuracy

NASA Astrophysics Data System (ADS)

Zhang, Yubo; Kitchaev, Daniil A.; Yang, Julia; Chen, Tina; Dacek, Stephen T.; Sarmiento-Pérez, Rafael A.; Marques, Maguel A. L.; Peng, Haowei; Ceder, Gerbrand; Perdew, John P.; Sun, Jianwei

2018-03-01

The question of material stability is of fundamental importance to any analysis of system properties in condensed matter physics and materials science. The ability to evaluate chemical stability, i.e., whether a stoichiometry will persist in some chemical environment, and structure selection, i.e. what crystal structure a stoichiometry will adopt, is critical to the prediction of materials synthesis, reactivity and properties. Here, we demonstrate that density functional theory, with the recently developed strongly constrained and appropriately normed (SCAN) functional, has advanced to a point where both facets of the stability problem can be reliably and efficiently predicted for main group compounds, while transition metal compounds are improved but remain a challenge. SCAN therefore offers a robust model for a significant portion of the periodic table, presenting an opportunity for the development of novel materials and the study of fine phase transformations even in largely unexplored systems with little to no experimental data.

Anharmonic contribution to the stabilization of Mg(OH)2 from first principles.

PubMed

Treviño, P; Garcia-Castro, A C; López-Moreno, S; Bautista-Hernández, A; Bobocioiu, E; Reynard, B; Caracas, R; Romero, A H

2018-06-20

Geometrical and vibrational characterization of magnesium hydroxide was performed using density functional theory. Four possible crystal symmetries were explored: P3[combining macron] (No. 147, point group -3), C2/m (No. 12, point group 2), P3m1 (No. 156, point group 3m) and P3[combining macron]m1 (No. 164, point group -3m) which are the currently accepted geometries found in the literature. While a lot of work has been performed on Mg(OH)2, in particular for the P3[combining macron]m1 phase, there is still a debate on the observed ground state crystal structure and the anharmonic effects of the OH vibrations on the stabilization of the crystal structure. In particular, the stable positions of hydrogen are not yet defined precisely, which have implications in the crystal symmetry, the vibrational excitations, and the thermal stability. Previous work has assigned the P3[combining macron]m1 polymorph as the low energy phase, but it has also proposed that hydrogens are disordered and they could move from their symmetric position in the P3[combining macron]m1 structure towards P3[combining macron]. In this paper, we examine the stability of the proposed phases by using different descriptors. We compare the XRD patterns with reported experimental results, and a fair agreement is found. While harmonic vibrational analysis shows that most phases have imaginary modes at 0 K, anharmonic vibrational analysis indicates that at room temperature only the C2/m phase is stabilized, whereas at higher temperatures, other phases become thermally competitive.

On the design and structural analysis of jet engine fan blade structures

NASA Astrophysics Data System (ADS)

Amoo, Leye M.

2013-07-01

Progress in the design and structural analysis of commercial jet engine fan blades is reviewed and presented. This article is motivated by the key role fan blades play in the performance of advanced gas turbine jet engines. The fundamentals of the associated physics are emphasized. Recent developments and advancements have led to an increase and improvement in fan blade structural durability, stability and reliability. This article is intended as a high level review of the fan blade environment and current state of structural design to aid further research in developing new and innovative fan blade technologies.

How structurally stable are global socioeconomic systems?

PubMed Central

Saavedra, Serguei; Rohr, Rudolf P.; Gilarranz, Luis J.; Bascompte, Jordi

2014-01-01

The stability analysis of socioeconomic systems has been centred on answering whether small perturbations when a system is in a given quantitative state will push the system permanently to a different quantitative state. However, typically the quantitative state of socioeconomic systems is subject to constant change. Therefore, a key stability question that has been under-investigated is how strongly the conditions of a system itself can change before the system moves to a qualitatively different behaviour, i.e. how structurally stable the systems is. Here, we introduce a framework to investigate the structural stability of socioeconomic systems formed by a network of interactions among agents competing for resources. We measure the structural stability of the system as the range of conditions in the distribution and availability of resources compatible with the qualitative behaviour in which all the constituent agents can be self-sustained across time. To illustrate our framework, we study an empirical representation of the global socioeconomic system formed by countries sharing and competing for multinational companies used as proxy for resources. We demonstrate that the structural stability of the system is inversely associated with the level of competition and the level of heterogeneity in the distribution of resources. Importantly, we show that the qualitative behaviour of the observed global socioeconomic system is highly sensitive to changes in the distribution of resources. We believe that this work provides a methodological basis to develop sustainable strategies for socioeconomic systems subject to constantly changing conditions. PMID:25165600

Phase I Metabolic Stability and Electrophilic Reactivity of 2-Phenylaminophenylacetic Acid Derived Compounds.

PubMed

Pang, Yi Yun; Tan, Yee Min; Chan, Eric Chun Yong; Ho, Han Kiat

2016-07-18

Diclofenac and lumiracoxib are two highly analogous 2-phenylaminophenylacetic acid anti-inflammatory drugs exhibiting occasional dose-limiting hepatotoxicities. Prior data indicate that bioactivation and reactive metabolite formation play roles in the observed toxicity, but the exact chemical influence of the substituents remains elusive. In order to elucidate the role of chemical influence on metabolism related toxicity, metabolic stability and electrophilic reactivity were investigated for a series of structurally related analogues and their resulting metabolites. The resulting analogues embody progressive physiochemical changes through varying halogeno- and aliphatic substituents at two positions and were subjected to in vitro human liver microsomal metabolic stability and cell-based GSH depletion assays (to measure electrophilic reactivity). LC-MS/MS analysis of the GSH trapped reactive intermediates derived from the analogues was then used to identify the putative structures of reactive metabolites. We found that chemical modifications of the structural backbone led to noticeable perturbations of metabolic stability, electrophilic reactivity, and structures and composition of reactive metabolites. With the acquired data, the relationships between stability, reactivity, and toxicity were investigated in an attempt to correlate between Phase I metabolism and in vitro toxicity. A positive correlation was identified between reactivity and in vitro toxicity, indicating that electrophilic reactivity can be an indicator for in vitro toxicity. All in all, the effect of substituents on the structures and reactivity of the metabolites, however subtle the changes, should be taken into consideration during future drug design involving similar chemical features.

Computational design of thermostabilizing point mutations for G protein-coupled receptors

PubMed Central

Popov, Petr; Peng, Yao; Shen, Ling; Stevens, Raymond C; Cherezov, Vadim; Liu, Zhi-Jie

2018-01-01

Engineering of GPCR constructs with improved thermostability is a key for successful structural and biochemical studies of this transmembrane protein family, targeted by 40% of all therapeutic drugs. Here we introduce a comprehensive computational approach to effective prediction of stabilizing mutations in GPCRs, named CompoMug, which employs sequence-based analysis, structural information, and a derived machine learning predictor. Tested experimentally on the serotonin 5-HT2C receptor target, CompoMug predictions resulted in 10 new stabilizing mutations, with an apparent thermostability gain ~8.8°C for the best single mutation and ~13°C for a triple mutant. Binding of antagonists confers further stabilization for the triple mutant receptor, with total gains of ~21°C as compared to wild type apo 5-HT2C. The predicted mutations enabled crystallization and structure determination for the 5-HT2C receptor complexes in inactive and active-like states. While CompoMug already shows high 25% hit rate and utility in GPCR structural studies, further improvements are expected with accumulation of structural and mutation data. PMID:29927385

Comprehensive rotorcraft analysis methods

NASA Technical Reports Server (NTRS)

Stephens, Wendell B.; Austin, Edward E.

1988-01-01

The development and application of comprehensive rotorcraft analysis methods in the field of rotorcraft technology are described. These large scale analyses and the resulting computer programs are intended to treat the complex aeromechanical phenomena that describe the behavior of rotorcraft. They may be used to predict rotor aerodynamics, acoustic, performance, stability and control, handling qualities, loads and vibrations, structures, dynamics, and aeroelastic stability characteristics for a variety of applications including research, preliminary and detail design, and evaluation and treatment of field problems. The principal comprehensive methods developed or under development in recent years and generally available to the rotorcraft community because of US Army Aviation Research and Technology Activity (ARTA) sponsorship of all or part of the software systems are the Rotorcraft Flight Simulation (C81), Dynamic System Coupler (DYSCO), Coupled Rotor/Airframe Vibration Analysis Program (SIMVIB), Comprehensive Analytical Model of Rotorcraft Aerodynamics and Dynamics (CAMRAD), General Rotorcraft Aeromechanical Stability Program (GRASP), and Second Generation Comprehensive Helicopter Analysis System (2GCHAS).

Signal frequency distribution and natural-time analyses from acoustic emission monitoring of an arched structure in the Castle of Racconigi

NASA Astrophysics Data System (ADS)

Niccolini, Gianni; Manuello, Amedeo; Marchis, Elena; Carpinteri, Alberto

2017-07-01

The stability of an arch as a structural element in the thermal bath of King Charles Albert (Carlo Alberto) in the Royal Castle of Racconigi (on the UNESCO World Heritage List since 1997) was assessed by the acoustic emission (AE) monitoring technique with application of classical inversion methods to recorded AE data. First, damage source location by means of triangulation techniques and signal frequency analysis were carried out. Then, the recently introduced method of natural-time analysis was preliminarily applied to the AE time series in order to reveal a possible entrance point to a critical state of the monitored structural element. Finally, possible influence of the local seismic and microseismic activity on the stability of the monitored structure was investigated. The criterion for selecting relevant earthquakes was based on the estimation of the size of earthquake preparation zones. The presented results suggest the use of the AE technique as a tool for detecting both ongoing structural damage processes and microseismic activity during preparation stages of seismic events.

Kinetic analysis of the effects of target structure on siRNA efficiency

NASA Astrophysics Data System (ADS)

Chen, Jiawen; Zhang, Wenbing

2012-12-01

RNAi efficiency for target cleavage and protein expression is related to the target structure. Considering the RNA-induced silencing complex (RISC) as a multiple turnover enzyme, we investigated the effect of target mRNA structure on siRNA efficiency with kinetic analysis. The 4-step model was used to study the target cleavage kinetic process: hybridization nucleation at an accessible target site, RISC-mRNA hybrid elongation along with mRNA target structure melting, target cleavage, and enzyme reactivation. At this model, the terms accounting for the target accessibility, stability, and the seed and the nucleation site effects are all included. The results are in good agreement with that of experiments which show different arguments about the structure effects on siRNA efficiency. It shows that the siRNA efficiency is influenced by the integrated factors of target's accessibility, stability, and the seed effects. To study the off-target effects, a simple model of one siRNA binding to two mRNA targets was designed. By using this model, the possibility for diminishing the off-target effects by the concentration of siRNA was discussed.

Overcoming bottlenecks in the membrane protein structural biology pipeline.

PubMed

Hardy, David; Bill, Roslyn M; Jawhari, Anass; Rothnie, Alice J

2016-06-15

Membrane proteins account for a third of the eukaryotic proteome, but are greatly under-represented in the Protein Data Bank. Unfortunately, recent technological advances in X-ray crystallography and EM cannot account for the poor solubility and stability of membrane protein samples. A limitation of conventional detergent-based methods is that detergent molecules destabilize membrane proteins, leading to their aggregation. The use of orthologues, mutants and fusion tags has helped improve protein stability, but at the expense of not working with the sequence of interest. Novel detergents such as glucose neopentyl glycol (GNG), maltose neopentyl glycol (MNG) and calixarene-based detergents can improve protein stability without compromising their solubilizing properties. Styrene maleic acid lipid particles (SMALPs) focus on retaining the native lipid bilayer of a membrane protein during purification and biophysical analysis. Overcoming bottlenecks in the membrane protein structural biology pipeline, primarily by maintaining protein stability, will facilitate the elucidation of many more membrane protein structures in the near future. © 2016 The Author(s). published by Portland Press Limited on behalf of the Biochemical Society.

Robust Fixed-Structure Control

DTIC Science & Technology

1994-10-30

Deterministic Foundation for Statistical Energy Analysis ," J. Sound Vibr., to appear. 1.96 D. S. Bernstein and S. P. Bhat, "Lyapunov Stability, Semistability...S. Bernstein, "Power Flow, Energy Balance, and Statistical Energy Analysis for Large Scale, Interconnected Systems," Proc. Amer. Contr. Conf., pp

Aeroelastic Modeling of X-56A Stiff-Wing Configuration Flight Test Data

NASA Technical Reports Server (NTRS)

Grauer, Jared A.; Boucher, Matthew J.

2017-01-01

Aeroelastic stability and control derivatives for the X-56A Multi-Utility Technology Testbed (MUTT), in the stiff-wing configuration, were estimated from flight test data using the output-error method. Practical aspects of the analysis are discussed. The orthogonal phase-optimized multisine inputs provided excellent data information for aeroelastic modeling. Consistent parameter estimates were determined using output error in both the frequency and time domains. The frequency domain analysis converged faster and was less sensitive to starting values for the model parameters, which was useful for determining the aeroelastic model structure and obtaining starting values for the time domain analysis. Including a modal description of the structure from a finite element model reduced the complexity of the estimation problem and improved the modeling results. Effects of reducing the model order on the short period stability and control derivatives were investigated.

Development of a structural optimization capability for the aeroelastic tailoring of composite rotor blades with straight and swept tips

NASA Technical Reports Server (NTRS)

Friedmann, P. P.; Venkatesan, C.; Yuan, K.

1992-01-01

This paper describes the development of a new structural optimization capability aimed at the aeroelastic tailoring of composite rotor blades with straight and swept tips. The primary objective is to reduce vibration levels in forward flight without diminishing the aeroelastic stability margins of the blade. In the course of this research activity a number of complicated tasks have been addressed: (1) development of a new, aeroelastic stability and response analysis; (2) formulation of a new comprehensive sensitive analysis, which facilitates the generation of the appropriate approximations for the objective and the constraints; (3) physical understanding of the new model and, in particular, determination of its potential for aeroelastic tailoring, and (4) combination of the newly developed analysis capability, the sensitivity derivatives and the optimizer into a comprehensive optimization capability. The first three tasks have been completed and the fourth task is in progress.

Dendronic trimaltoside amphiphiles (DTMs) for membrane protein study† †Electronic supplementary information (ESI) available. See DOI: 10.1039/c7sc03700g

PubMed Central

Sadaf, Aiman; Du, Yang; Santillan, Claudia; Mortensen, Jonas S.; Molist, Iago; Seven, Alpay B.; Hariharan, Parameswaran; Skiniotis, Georgios; Loland, Claus J.; Kobilka, Brian K.; Guan, Lan; Byrne, Bernadette

2017-01-01

The critical contribution of membrane proteins in normal cellular function makes their detailed structure and functional analysis essential. Detergents, amphipathic agents with the ability to maintain membrane proteins in a soluble state in aqueous solution, have key roles in membrane protein manipulation. Structural and functional stability is a prerequisite for biophysical characterization. However, many conventional detergents are limited in their ability to stabilize membrane proteins, making development of novel detergents for membrane protein manipulation an important research area. The architecture of a detergent hydrophobic group, that directly interacts with the hydrophobic segment of membrane proteins, is a key factor in dictating their efficacy for both membrane protein solubilization and stabilization. In the current study, we developed two sets of maltoside-based detergents with four alkyl chains by introducing dendronic hydrophobic groups connected to a trimaltoside head group, designated dendronic trimaltosides (DTMs). Representative DTMs conferred enhanced stabilization to multiple membrane proteins compared to the benchmark conventional detergent, DDM. One DTM (i.e., DTM-A6) clearly outperformed DDM in stabilizing human β2 adrenergic receptor (β2AR) and its complex with Gs protein. A further evaluation of this DTM led to a clear visualization of β2AR-Gs complex via electron microscopic analysis. Thus, the current study not only provides novel detergent tools useful for membrane protein study, but also suggests that the dendronic architecture has a role in governing detergent efficacy for membrane protein stabilization. PMID:29619178

A semi-implicit level set method for multiphase flows and fluid-structure interaction problems

NASA Astrophysics Data System (ADS)

Cottet, Georges-Henri; Maitre, Emmanuel

2016-06-01

In this paper we present a novel semi-implicit time-discretization of the level set method introduced in [8] for fluid-structure interaction problems. The idea stems from a linear stability analysis derived on a simplified one-dimensional problem. The semi-implicit scheme relies on a simple filter operating as a pre-processing on the level set function. It applies to multiphase flows driven by surface tension as well as to fluid-structure interaction problems. The semi-implicit scheme avoids the stability constraints that explicit scheme need to satisfy and reduces significantly the computational cost. It is validated through comparisons with the original explicit scheme and refinement studies on two-dimensional benchmarks.

Sc20C60: a volleyballene

NASA Astrophysics Data System (ADS)

Wang, Jing; Ma, Hong-Man; Liu, Ying

2016-06-01

An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable.An exceptionally stable hollow cage containing 20 scandium atoms and 60 carbon atoms has been identified. This Sc20C60 molecular cluster has a Th point group symmetry and a volleyball-like shape that we refer to below as ``Volleyballene''. Electronic structure analysis shows that the formation of delocalized π bonds between Sc atoms and the neighboring pentagonal rings made of carbon atoms is crucial for stabilizing the cage structure. A relatively large HOMO-LUMO gap (~1.4 eV) was found. The results of vibrational frequency analysis and molecular dynamics simulations both demonstrate that this Volleyballene molecule is exceptionally stable. Electronic supplementary information (ESI) available: Sc20C60: a Volleyballene_SI. See DOI: 10.1039/c5nr07784b

Analysis of inter-residue contacts reveals folding stabilizers in P-loops of potassium, sodium, and TRPV channels.

PubMed

Korkosh, V S; Zhorov, B S; Tikhonov, D B

2016-05-01

The family of P-loop channels includes potassium, sodium, calcium, cyclic nucleotide-gated and TRPV channels, as well as ionotropic glutamate receptors. Despite vastly different physiological and pharmacological properties, the channels have structurally conserved folding of the pore domain. Furthermore, crystallographic data demonstrate surprisingly similar mutual disposition of transmembrane and membrane-diving helices. To understand determinants of this conservation, here we have compared available high-resolution structures of sodium, potassium, and TRPV1 channels. We found that some residues, which are in matching positions of the sequence alignment, occur in different positions in the 3D alignment. Surprisingly, we found 3D mismatches in well-packed P-helices. Analysis of energetics of individual residues in Monte Carlo minimized structures revealed cyclic patterns of energetically favorable inter- and intra-subunit contacts of P-helices with S6 helices. The inter-subunit contacts are rather conserved in all the channels, whereas the intra-subunit contacts are specific for particular types of the channels. Our results suggest that these residue-residue contacts contribute to the folding stabilization. Analysis of such contacts is important for structural and phylogenetic studies of homologous proteins.

STARS: An integrated general-purpose finite element structural, aeroelastic, and aeroservoelastic analysis computer program

NASA Technical Reports Server (NTRS)

Gupta, Kajal K.

1991-01-01

The details of an integrated general-purpose finite element structural analysis computer program which is also capable of solving complex multidisciplinary problems is presented. Thus, the SOLIDS module of the program possesses an extensive finite element library suitable for modeling most practical problems and is capable of solving statics, vibration, buckling, and dynamic response problems of complex structures, including spinning ones. The aerodynamic module, AERO, enables computation of unsteady aerodynamic forces for both subsonic and supersonic flow for subsequent flutter and divergence analysis of the structure. The associated aeroservoelastic analysis module, ASE, effects aero-structural-control stability analysis yielding frequency responses as well as damping characteristics of the structure. The program is written in standard FORTRAN to run on a wide variety of computers. Extensive graphics, preprocessing, and postprocessing routines are also available pertaining to a number of terminals.

Stabilization of Proteins and Noncovalent Protein Complexes during Electrospray Ionization by Amino Acid Additives.

PubMed

Zhang, Hua; Lu, Haiyan; Chingin, Konstantin; Chen, Huanwen

2015-07-21

Ionization of proteins and noncovalent protein complexes with minimal disturbance to their native structure presents a great challenge for biological mass spectrometry (MS). In living organisms, the native structure of intracellular proteins is commonly stabilized by solute amino acids (AAs) accumulated in cells at very high concentrations. Inspired by nature, we hypothesized that AAs could also pose a stabilizing effect on the native structure of proteins and noncovalent protein complexes during ionization. To test this hypothesis, here we explored MS response for various protein complexes upon the addition of free AAs at mM concentrations into the electrospray ionization (ESI) solution. Thermal activation of ESI droplets in the MS inlet capillary was employed as a model destabilizing factor during ionization. Our results indicate that certain AAs, in particular proline (Pro), pose considerable positive effect on the stability of noncovalent protein complexes in ESI-MS without affecting the signal intensity of protein ions and original protein-ligand equilibrium, even when added at the 20 mM concentration. The data suggest that the degree of protein stabilization is primarily determined by the osmolytic and ampholytic characteristics of AA solutes. The highest stability and visibility of noncovalent protein complexes in ESI-MS are achieved using AA additives with neutral isoelectric point, moderate proton affinity, and unfavorable interaction with the native protein state. Overall, our results indicate that the simple addition of free amino acids into the working solution can notably improve the stability and accuracy of protein analysis by native ESI-MS.

Optimum Design of High-Speed Prop-Rotors

NASA Technical Reports Server (NTRS)

Chattopadhyay, Aditi; McCarthy, Thomas Robert

1993-01-01

An integrated multidisciplinary optimization procedure is developed for application to rotary wing aircraft design. The necessary disciplines such as dynamics, aerodynamics, aeroelasticity, and structures are coupled within a closed-loop optimization process. The procedure developed is applied to address two different problems. The first problem considers the optimization of a helicopter rotor blade and the second problem addresses the optimum design of a high-speed tilting proprotor. In the helicopter blade problem, the objective is to reduce the critical vibratory shear forces and moments at the blade root, without degrading rotor aerodynamic performance and aeroelastic stability. In the case of the high-speed proprotor, the goal is to maximize the propulsive efficiency in high-speed cruise without deteriorating the aeroelastic stability in cruise and the aerodynamic performance in hover. The problems studied involve multiple design objectives; therefore, the optimization problems are formulated using multiobjective design procedures. A comprehensive helicopter analysis code is used for the rotary wing aerodynamic, dynamic and aeroelastic stability analyses and an algorithm developed specifically for these purposes is used for the structural analysis. A nonlinear programming technique coupled with an approximate analysis procedure is used to perform the optimization. The optimum blade designs obtained in each case are compared to corresponding reference designs.

LoopX: A Graphical User Interface-Based Database for Comprehensive Analysis and Comparative Evaluation of Loops from Protein Structures.

PubMed

Kadumuri, Rajashekar Varma; Vadrevu, Ramakrishna

2017-10-01

Due to their crucial role in function, folding, and stability, protein loops are being targeted for grafting/designing to create novel or alter existing functionality and improve stability and foldability. With a view to facilitate a thorough analysis and effectual search options for extracting and comparing loops for sequence and structural compatibility, we developed, LoopX a comprehensively compiled library of sequence and conformational features of ∼700,000 loops from protein structures. The database equipped with a graphical user interface is empowered with diverse query tools and search algorithms, with various rendering options to visualize the sequence- and structural-level information along with hydrogen bonding patterns, backbone φ, ψ dihedral angles of both the target and candidate loops. Two new features (i) conservation of the polar/nonpolar environment and (ii) conservation of sequence and conformation of specific residues within the loops have also been incorporated in the search and retrieval of compatible loops for a chosen target loop. Thus, the LoopX server not only serves as a database and visualization tool for sequence and structural analysis of protein loops but also aids in extracting and comparing candidate loops for a given target loop based on user-defined search options.

The stability of monomeric intermediates controls amyloid formation: Abeta25-35 and its N27Q mutant.

PubMed

Ma, Buyong; Nussinov, Ruth

2006-05-15

The structure and stabilities of the intermediates affect protein folding as well as misfolding and amyloid formation. By applying Kramer's theory of barrier crossing and a Morse-function-like energy landscape, we show that intermediates with medium stability dramatically increase the rate of amyloid formation; on the other hand, very stable and very unstable intermediates sharply decrease amyloid formation. Remarkably, extensive molecular dynamics simulations and conformational energy landscape analysis of Abeta25-35 and its N27Q mutant corroborate the mathematical description. Both experimental and current simulation results indicate that the core of the amyloid structure of Abeta25-35 formed from residues 28-35. A single mutation of N27Q of Abeta25-35 makes the Abeta25-35 N27Q amyloid-free. Energy landscape calculations show that Abeta25-35 has extended intermediates with medium stability that are prone to form amyloids, whereas the extended intermediates for Abeta25-35 N27Q split into stable and very unstable species that are not disposed to form amyloids. The results explain the contribution of both alpha-helical and beta-strand intermediates to amyloid formation. The results also indicate that the structure and stability of the intermediates, as well as of the native folded and the amyloid states can be targeted in drug design. One conceivable approach is to stabilize the intermediates to deter amyloid formation.

Arc is a flexible modular protein capable of reversible self-oligomerization

PubMed Central

Myrum, Craig; Baumann, Anne; Bustad, Helene J.; Flydal, Marte Innselset; Mariaule, Vincent; Alvira, Sara; Cuéllar, Jorge; Haavik, Jan; Soulé, Jonathan; Valpuesta, José Maria; Márquez, José Antonio; Martinez, Aurora; Bramham, Clive R.

2015-01-01

The immediate early gene product Arc (activity-regulated cytoskeleton-associated protein) is posited as a master regulator of long-term synaptic plasticity and memory. However, the physicochemical and structural properties of Arc have not been elucidated. In the present study, we expressed and purified recombinant human Arc (hArc) and performed the first biochemical and biophysical analysis of hArc's structure and stability. Limited proteolysis assays and MS analysis indicate that hArc has two major domains on either side of a central more disordered linker region, consistent with in silico structure predictions. hArc's secondary structure was estimated using CD, and stability was analysed by CD-monitored thermal denaturation and differential scanning fluorimetry (DSF). Oligomerization states under different conditions were studied by dynamic light scattering (DLS) and visualized by AFM and EM. Biophysical analyses show that hArc is a modular protein with defined secondary structure and loose tertiary structure. hArc appears to be pyramid-shaped as a monomer and is capable of reversible self-association, forming large soluble oligomers. The N-terminal domain of hArc is highly basic, which may promote interaction with cytoskeletal structures or other polyanionic surfaces, whereas the C-terminal domain is acidic and stabilized by ionic conditions that promote oligomerization. Upon binding of presenilin-1 (PS1) peptide, hArc undergoes a large structural change. A non-synonymous genetic variant of hArc (V231G) showed properties similar to the wild-type (WT) protein. We conclude that hArc is a flexible multi-domain protein that exists in monomeric and oligomeric forms, compatible with a diverse, hub-like role in plasticity-related processes. PMID:25748042

Molecular conformational analysis, vibrational spectra, NBO analysis and first hyperpolarizability of (2E)-3-(3-chlorophenyl)prop-2-enoic anhydride based on density functional theory calculations.

PubMed

Mary, Y Sheena; Raju, K; Panicker, C Yohannan; Al-Saadi, Abdulaziz A; Thiemann, Thies

2014-10-15

The conformational behavior and structural stability of (2E)-3-(3-chlorophenyl)prop-2-enoic anhydride were investigated by using density functional theory. The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of (2E)-3-(3-chlorophenyl)prop-2-enoic anhydride have been investigated experimentally and theoretically. The HOMO and LUMO analysis are used to determine the charge transfer within the molecule. The stability of the molecule arising from hyperconjugative interaction and charge delocalization has been analyzed using NBO analysis. The calculated first hyperpolarizability of the title compound is 15.8×10(-30)esu, and is 121.54 times that of the standard NLO material urea and the title compound is an attractive object for future studies of nonlinear optical properties. MEP was performed by the DFT method and the predicted infrared intensities and Raman activities have also been reported. Copyright © 2014 Elsevier B.V. All rights reserved.

Developing a Data Set and Processing Methodology for Fluid/Structure Interaction Code Validation

DTIC Science & Technology

2007-06-01

50 29. 9-Probe Wake Survey Rake Configurations...structural stability and fatigue in test article components and, in general, in facility support structures and rotating machinery blading . Both T&E... blade analysis and simulations. To ensure the accuracy of the U of CO technology, validation using flight-test data and test data from a wind tunnel

Full-scale testing, production and cost analysis data for the advanced composite stabilizer for Boeing 737 aircraft. Volume 1: Technical summary

NASA Technical Reports Server (NTRS)

Aniversario, R. B.; Harvey, S. T.; Mccarty, J. E.; Parsons, J. T.; Peterson, D. C.; Pritchett, L. D.; Wilson, D. R.; Wogulis, E. R.

1983-01-01

The full scale ground test, ground vibration test, and flight tests conducted to demonstrate a composite structure stabilizer for the Boeing 737 aircraft and obtain FAA certification are described. Detail tools, assembly tools, and overall production are discussed. Cost analyses aspects covered include production costs, composite material usage factors, and cost comparisons.

The Analysis and Modeling of Phase Stability and Multiphase Designs in High Temperature Refractory Metal-Silicon-Boron Alloys

DTIC Science & Technology

2009-01-27

high temperature mechanical properties , it was confirmed that the three phase eutectic structure exhibited exceptionally high strength and creep...microstructurc constituent, offer an attractive property balance of high melting temperature, oxidation resistance and useful high temperature mechanical ...design of new multiphase high-temperature alloys with balanced environmental and mechanical properties . 15. SUBJECT TERMS Phase Stability, Alloying

Extremely strong self-assembly of a bimetallic salen complex visualized at the single-molecule level.

PubMed

Salassa, Giovanni; Coenen, Michiel J J; Wezenberg, Sander J; Hendriksen, Bas L M; Speller, Sylvia; Elemans, Johannes A A W; Kleij, Arjan W

2012-04-25

A bis-Zn(salphen) structure shows extremely strong self-assembly both in solution as well as at the solid-liquid interface as evidenced by scanning tunneling microscopy, competitive UV-vis and fluorescence titrations, dynamic light scattering, and transmission electron microscopy. Density functional theory analysis on the Zn(2) complex rationalizes the very high stability of the self-assembled structures provoked by unusual oligomeric (Zn-O)(n) coordination motifs within the assembly. This coordination mode is strikingly different when compared with mononuclear Zn(salphen) analogues that form dimeric structures having a typical Zn(2)O(2) central unit. The high stability of the multinuclear structure therefore holds great promise for the development of stable self-assembled monolayers with potential for new opto-electronic materials.

Rotordynamic Characteristics of the HPOTP (High Pressure Oxygen Turbopump) of the SSME (Space Shuttle Main Engine)

NASA Technical Reports Server (NTRS)

Childs, D. W.

1984-01-01

Rotational stability of turbopump components in the space shuttle main engine was studied via analysis of component and structural dynamic models. Subsynchronous vibration caused unacceptable migration of the rotor/housing unit with unequal load sharing of the synchronous bearings that resulted in the failure of the High Pressure Oxygen Turbopump. Linear analysis shows that a shrouded inducer eliminates the second critical speed and the stability problem, a stiffened rotor improves the rotordynamic characteristics of the turbopump, and installing damper boost/impeller seals reduces bearing loads. Nonlinear analysis shows that by increasing the "dead band' clearances, a marked reduction in peak bearing loads occurs.

Distinct Structural Elements Govern the Folding, Stability, and Catalysis in the Outer Membrane Enzyme PagP.

PubMed

Iyer, Bharat Ramasubramanian; Mahalakshmi, Radhakrishnan

2016-09-06

The outer membrane enzyme PagP is indispensable for lipid A palmitoylation in Gram-negative bacteria and has been implicated in resistance to host immune defenses. PagP possesses an unusual structure for an integral membrane protein, with a highly dynamic barrel domain that is tilted with respect to the membrane normal. In addition, it contains an N-terminal amphipathic helix. Recent functional and structural studies have shown that these molecular factors are critical for PagP to carry out its function in the challenging environment of the bacterial outer membrane. However, the precise contributions of the N-helix to folding and stability and residues that can influence catalytic rates remain to be addressed. Here, we identify a sequence-dependent stabilizing role for the N-terminal helix of PagP in the measured thermodynamic stability of the barrel. Using chimeric barrel sequences, we show that the Escherichia coli PagP N-terminal helix confers 2-fold greater stability to the Salmonella typhimurium barrel. Further, we find that the W78F substitution in S. typhimurium causes a nearly 20-fold increase in the specific activity in vitro for the phospholipase reaction, compared to that of E. coli PagP. Here, phenylalanine serves as a key regulator of catalysis, possibly by increasing the reaction rate. Through coevolution analysis, we detect an interaction network between seemingly unrelated segments of this membrane protein. Exchanging the structural and functional features between homologous PagP enzymes from E. coli and S. typhimurium has provided us with an understanding of the molecular factors governing PagP stability and function.

Substrate uptake and protein stability relationship in mammalian histidine decarboxylase.

PubMed

Pino-Angeles, A; Morreale, A; Negri, A; Sánchez-Jiménez, F; Moya-García, A A

2010-01-01

There is some evidence linking the substrate entrance in the active site of mammalian histidine decarboxylase and an increased stability against proteolytic degradation. In this work, we study the basis of this relationship by means of protein structure network analysis and molecular dynamics simulations. We find that the substrate binding to the active site influences the conformation of a flexible region sensible to proteolytic degradation and observe how formation of the Michaelis-Menten complex increases stability in the conformation of this region. (c) 2009 Wiley-Liss, Inc.

Materials Examination of the Vertical Stabilizer from American Airlines Flight 587

NASA Technical Reports Server (NTRS)

Fox, Matthew R.; Schultheisz, Carl R.; Reeder, James R.; Jensen, Brian J.

2005-01-01

The first in-flight failure of a primary structural component made from composite material on a commercial airplane led to the crash of American Airlines Flight 587. As part of the National Transportation Safety Board investigation of the accident, the composite materials of the vertical stabilizer were tested, microstructure was analyzed, and fractured composite lugs that attached the vertical stabilizer to the aircraft tail were examined. In this paper the materials testing and analysis is presented, composite fractures are described, and the resulting clues to the failure events are discussed.

Composition and structure of pyrophoric nickel catalysts according to X-ray diffraction data

NASA Astrophysics Data System (ADS)

Osadchaya, T. Yu.; Afineevskii, A. V.; Prozorov, D. A.; Kochetkov, S. P.; Rumyantsev, R. N.; Lukin, M. V.

2017-01-01

The properties of a nickel catalyst obtained by treatment of nickel-aluminum alloy with sodium hydroxide in the presence of H2O2 and additionally stabilized with increased pressure were studied. Additional stabilization decreased the catalyst activity by 25%, but gave a more distinct picture for an XRD analysis of the active catalyst surface and decreased the time of deactivation of the dehydrated catalyst with air oxygen. The catalyst stabilization was explained by the displacement of water, decrease in the pore size, and surface inhomogeneity.

On the influence of tyre and structural properties on the stability of bicycles

NASA Astrophysics Data System (ADS)

Doria, Alberto; Roa Melo, Sergio Daniel

2018-06-01

In recent years the Whipple Carvallo Bicycle Model has been extended to analyse high speed stability of bicycles. Various researchers have developed models taking into account the effects of front frame compliance and tyre properties, nonetheless, a systematic analysis has not been yet carried out. This paper aims at analysing parametrically the influence of front frame compliance and tyre properties on the open loop stability of bicycles. Some indexes based on the eigenvalues of the dynamic system are defined to evaluate quantitatively bicycle stability. The parametric analysis is carried out with a factorial design approach to determine the most influential parameters. A commuting and a racing bicycle are considered and numerical results show different effects of the various parameters on each bicycle. In the commuting bicycle, the tyre properties have greater influence than front frame compliance, and the weave mode has the main effect on stability. Conversely, in the racing bicycle, the front frame compliance parameters have greater influence than tyre properties, and the wobble mode has the main effect on stability.

Structural analysis of oligomeric and protofibrillar Aβ amyloid pair structures considering F20L mutation effects using molecular dynamics simulations.

PubMed

Lee, Myeongsang; Chang, Hyun Joon; Baek, Inchul; Na, Sungsoo

2017-04-01

Aβ amyloid proteins are involved in neuro-degenerative diseases such as Alzheimer's, Parkinson's, and so forth. Because of its structurally stable feature under physiological conditions, Aβ amyloid protein disrupts the normal cell function. Because of these concerns, understanding the structural feature of Aβ amyloid protein in detail is crucial. There have been some efforts on lowering the structural stabilities of Aβ amyloid fibrils by decreasing the aromatic residues characteristic and hydrophobic effect. Yet, there is a lack of understanding of Aβ amyloid pair structures considering those effects. In this study, we provide the structural characteristics of wildtype (WT) and phenylalanine residue mutation to leucine (F20L) Aβ amyloid pair structures using molecular dynamics simulation in detail. We also considered the polymorphic feature of F20L and WT Aβ pair amyloids based on the facing β-strand directions between the amyloid pairs. As a result, we were able to observe the varying effects of mutation, polymorphism, and protofibril lengths on the structural stability of pair amyloids. Furthermore, we have also found that opposite structural stability exists on a certain polymorphic Aβ pair amyloids depending on its oligomeric or protofibrillar state, which can be helpful for understanding the amyloid growth mechanism via repetitive fragmentation and elongation mechanism. Proteins 2017; 85:580-592. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Bounded Linear Stability Analysis - A Time Delay Margin Estimation Approach for Adaptive Control

NASA Technical Reports Server (NTRS)

Nguyen, Nhan T.; Ishihara, Abraham K.; Krishnakumar, Kalmanje Srinlvas; Bakhtiari-Nejad, Maryam

2009-01-01

This paper presents a method for estimating time delay margin for model-reference adaptive control of systems with almost linear structured uncertainty. The bounded linear stability analysis method seeks to represent the conventional model-reference adaptive law by a locally bounded linear approximation within a small time window using the comparison lemma. The locally bounded linear approximation of the combined adaptive system is cast in a form of an input-time-delay differential equation over a small time window. The time delay margin of this system represents a local stability measure and is computed analytically by a matrix measure method, which provides a simple analytical technique for estimating an upper bound of time delay margin. Based on simulation results for a scalar model-reference adaptive control system, both the bounded linear stability method and the matrix measure method are seen to provide a reasonably accurate and yet not too conservative time delay margin estimation.

Thermodynamic properties of water molecules in the presence of cosolute depend on DNA structure: a study using grid inhomogeneous solvation theory.

PubMed

Nakano, Miki; Tateishi-Karimata, Hisae; Tanaka, Shigenori; Tama, Florence; Miyashita, Osamu; Nakano, Shu-Ichi; Sugimoto, Naoki

2015-12-02

In conditions that mimic those of the living cell, where various biomolecules and other components are present, DNA strands can adopt many structures in addition to the canonical B-form duplex. Previous studies in the presence of cosolutes that induce molecular crowding showed that thermal stabilities of DNA structures are associated with the properties of the water molecules around the DNAs. To understand how cosolutes, such as ethylene glycol, affect the thermal stability of DNA structures, we investigated the thermodynamic properties of water molecules around a hairpin duplex and a G-quadruplex using grid inhomogeneous solvation theory (GIST) with or without cosolutes. Our analysis indicated that (i) cosolutes increased the free energy of water molecules around DNA by disrupting water-water interactions, (ii) ethylene glycol more effectively disrupted water-water interactions around Watson-Crick base pairs than those around G-quartets or non-paired bases, (iii) due to the negative electrostatic potential there was a thicker hydration shell around G-quartets than around Watson-Crick-paired bases. Our findings suggest that the thermal stability of the hydration shell around DNAs is one factor that affects the thermal stabilities of DNA structures under the crowding conditions. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Influence of foam structure on the release kinetics of volatiles from espresso coffee prior to consumption.

PubMed

Dold, Susanne; Lindinger, Christian; Kolodziejczyk, Eric; Pollien, Philippe; Ali, Santo; Germain, Juan Carlos; Perin, Sonia Garcia; Pineau, Nicolas; Folmer, Britta; Engel, Karl-Heinz; Barron, Denis; Hartmann, Christoph

2011-10-26

The relationship between the physical structure of espresso coffee foam, called crema, and the above-the-cup aroma release was studied. Espresso coffee samples were produced using the Nespresso extraction system. The samples were extracted with water with different levels of mineral content, which resulted in liquid phases with similar volatile profiles but foams with different structure properties. The structure parameters foam volume, foam drainage, and lamella film thickness at the foam surface were quantified using computer-assisted microscopic image analysis and a digital caliper. The above-the-cup volatile concentration was measured online by using PTR-MS and headspace sampling. A correlation study was done between crema structure parameters and above-the-cup volatile concentration. In the first 2.5 min after the start of the coffee extraction, the presence of foam induced an increase of concentration of selected volatile markers, independently if the crema was of high or low stability. At times longer than 2.5 min, the aroma marker concentration depends on both the stability of the crema and the volatility of the specific aroma compounds. Mechanisms of above-the-cup volatile release involved gas bubble stability, evaporation, and diffusion. It was concluded that after the initial aroma burst (during the first 2-3 min after the beginning of extraction), for the present sample space a crema of high stability provides a stronger aroma barrier over several minutes.

Structure-Based Design of Molecules to Reactivate Tumor-Derived p53 Mutations

DTIC Science & Technology

2007-06-01

cluster in conserved regions or “hot spots” (Hainaut and Hollstein, 2000). Missense mutations leading to amino acid changes are the most common p53...domain stabilization compounds. Analysis of the residue-specific temperature factors of the high resolution core domain structure, coupled with a...second scoring results, 13 compounds (10 from the SPECS database and 3 from the TimTec database) were selected for further analysis using solution

Sampled-data-based vibration control for structural systems with finite-time state constraint and sensor outage.

PubMed

Weng, Falu; Liu, Mingxin; Mao, Weijie; Ding, Yuanchun; Liu, Feifei

2018-05-10

The problem of sampled-data-based vibration control for structural systems with finite-time state constraint and sensor outage is investigated in this paper. The objective of designing controllers is to guarantee the stability and anti-disturbance performance of the closed-loop systems while some sensor outages happen. Firstly, based on matrix transformation, the state-space model of structural systems with sensor outages and uncertainties appearing in the mass, damping and stiffness matrices is established. Secondly, by considering most of those earthquakes or strong winds happen in a very short time, and it is often the peak values make the structures damaged, the finite-time stability analysis method is introduced to constrain the state responses in a given time interval, and the H-infinity stability is adopted in the controller design to make sure that the closed-loop system has a prescribed level of disturbance attenuation performance during the whole control process. Furthermore, all stabilization conditions are expressed in the forms of linear matrix inequalities (LMIs), whose feasibility can be easily checked by using the LMI Toolbox. Finally, numerical examples are given to demonstrate the effectiveness of the proposed theorems. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Subunit association as the stabilizing determinant for archaeal methionine adenosyltransferases.

PubMed

Garrido, Francisco; Alfonso, Carlos; Taylor, John C; Markham, George D; Pajares, María A

2009-07-01

Archaea contain a class of methionine adenosyltransferases (MATs) that exhibit substantially higher stability than their mesophilic counterparts. Their sequences are highly divergent, but preserve the essential active site motifs of the family. We have investigated the origin of this increased stability using chemical denaturation experiments on Methanococcus jannaschii MAT (Mj-MAT) and mutants containing single tryptophans in place of tyrosine residues. The results from fluorescence, circular dichroism, hydrodynamic, and enzyme activity measurements showed that the higher stability of Mj-MAT derives largely from a tighter association of its subunits in the dimer. Local fluorescence changes, interpreted using secondary structure predictions, further identify the least stable structural elements as the C-terminal ends of beta-strands E2 and E6, and the N-terminus of E3. Dimer dissociation however requires a wider perturbation of the molecule. Additional analysis was initially hindered by the lack of crystal structures for archaeal MATs, a limitation that we overcame by construction of a 3D-homology model of Mj-MAT. This model predicts preservation of the chain topology and three-domain organization typical of this family, locates the least stable structural elements at the flat contact surface between monomers, and shows that alterations in all three domains are required for dimer dissociation.

Insight from first principles into the stability and magnetism of alkali-metal superoxide nanoclusters

NASA Astrophysics Data System (ADS)

Arcelus, Oier; Suaud, Nicolas; Katcho, Nebil A.; Carrasco, Javier

2017-05-01

Alkali-metal superoxides are gaining increasing interest as 2p magnetic materials for information and energy storage. Despite significant research efforts on bulk materials, gaps in our knowledge of the electronic and magnetic properties at the nanoscale still remain. Here, we focused on the role that structural details play in determining stability, electronic structure, and magnetic couplings of (MO2)n (M = Li, Na, and K, with n = 2-8) clusters. Using first-principles density functional theory based on the Perdew-Burke-Ernzerhof and Heyd-Scuseria-Ernzerhof functionals, we examined the effect of atomic structure on the relative stability of different polymorphs within each investigated cluster size. We found that small clusters prefer to form planar-ring structures, whereas non-planar geometries become more stable when increasing the cluster size. However, the crossover point depends on the nature of the alkali metal. Our analysis revealed that electrostatic interactions govern the highly ionic M-O2 bonding and ultimately control the relative stability between 2-D and 3-D geometries. In addition, we analyzed the weak magnetic couplings between superoxide molecules in (NaO2)4 clusters comparing model Hamiltonian methods based on Wannier function projections onto πg states with wave function-based multi-reference calculations.

Stabilization of flow past a rounded cylinder

NASA Astrophysics Data System (ADS)

Samtaney, Ravi; Zhang, Wei

2016-11-01

We perform global linear stability analysis on low-Re flow past a rounded cylinder. The cylinder corners are rounded with a radius R, normalized as R+ = R / D where D is the cylinder diameter, and its effect on the flow stability characteristics is investigated. We compute the critical Reynolds number (Recr) for the onset of first instability, and quantify the perturbation growth rate for the super-critical flows. It is found that the flow can be stabilized by partially rounding the cylinder. Compared with the square and circular cylinders, the partially rounded cylinder has a higher Recr , attaining a maximum at around R+ = 0 . 30 , and the perturbation growth rate of the super-critical flows is reduced for Re <= 100 . We perform sensitivity analysis to explore the source of the stabilization. The growth rate sensitivity to base flow modification has two different spatial structures: the growth rate is sensitive to the wake backflow in a large region for square-like cylinders (R+ -> 0 . 00), while only the near-wake backflow is crucial for circular-like cylinders (R+ -> 0 . 50). The stability analysis results are also verified with those of the direct simulations and very good agreement is achieved. Supported by the KAUST Office of Competitive Research Funds under Award No. URF/1/1394-01. The supercomputer Shaheen at KAUST was utilized for the simulations.

REVIEW OF THE STABILITY ANALYSIS FOR THE LANL BSL-3 BUILDING FOUNDATION

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

Heuze, F E; Wagoner, J L

2006-11-30

This work was performed upon request from Dr. Richard Thorpe from NNSA after his review of the LANL report on BSL-3 seismic stability [1]. The authors also reviewed report [1] and concluded, as did Dr. Thorpe, that the stability analysis was inappropriate. There are several reasons for that conclusion: (1) the assumption of a circular failure surface through the combined fill-and-rock foundation does not recognize the geologic structure involved. (2) the assumption of an equivalent static force to an earthquake loading does not represent the multiple cycles of shear loads created by a seismic event that can engender a substantialmore » degradation of shear modulus and shear strength of the soil under the building [2]. (3) there was no credible in-situ strength of the foundation materials (fill and rock mass) available for input into the stability analysis. Following that review, on September 26 the authors made a site visit and held discussions with LANL personnel connected to the BSL-3 building project. No information or evidence was presented to the authors indicating that the static stability of BSL-3 could be an issue. Accordingly, this report focuses on the topic of the BSL-3 site stability under seismic loading.« less

Aeroelastic effects in multirotor vehicles. Part 2: Methods of solution and results illustrating coupled rotor/body aeromechanical stability

NASA Technical Reports Server (NTRS)

Venkatesan, C.; Friedmann, P. P.

1987-01-01

This report is a sequel to the earlier report titled, Aeroelastic Effects in Multi-Rotor Vehicles with Application to Hybrid Heavy Lift System, Part 1: Formulation of Equations of Motion (NASA CR-3822). The trim and stability equations are presented for a twin rotor system with a buoyant envelope and an underslung load attached to a flexible supporting structure. These equations are specialized for the case of hovering flight. A stability analysis, for such a vehicle with 31 degrees of freedom, yields a total of 62 eigenvalues. A careful parametric study is performed to identify the various blade and vehicle modes, as well as the coupling between various modes. Finally, it is shown that the coupled rotor/vehicle stability analysis provides information on both the aeroelastic stability as well as complete vehicle dynamic stability. Also presented are the results of an analytical study aimed at predicting the aeromechanical stability of a single rotor helicopter in ground resonance. The theoretical results are found to be in good agreement with the experimental results, thereby validating the analytical model for the dynamics of the coupled rotor/support system.

Oscillations contribute to memory consolidation by changing criticality and stability in the brain

NASA Astrophysics Data System (ADS)

Wu, Jiaxing; Skilling, Quinton; Ognjanovski, Nicolette; Aton, Sara; Zochowski, Michal

Oscillations are a universal feature of every level of brain dynamics and have been shown to contribute to many brain functions. To investigate the fundamental mechanism underpinning oscillatory activity, the properties of heterogeneous networks are compared in situations with and without oscillations. Our results show that both network criticality and stability are changed in the presence of oscillations. Criticality describes the network state of neuronal avalanche, a cascade of bursts of action potential firing in neural network. Stability measures how stable the spike timing relationship between neuron pairs is over time. Using a detailed spiking model, we found that the branching parameter σ changes relative to oscillation and structural network properties, corresponding to transmission among different critical states. Also, analysis of functional network structures shows that the oscillation helps to stabilize neuronal representation of memory. Further, quantitatively similar results are observed in biological data recorded in vivo. In summary, we have observed that, by regulating the neuronal firing pattern, oscillations affect both criticality and stability properties of the network, and thus contribute to memory formation.

Thermal stability enhancement of modified carboxymethyl cellulose films using SnO2 nanoparticles.

PubMed

Baniasad, Arezou; Ghorbani, Mohsen

2016-05-01

In this study, in-situ and ex-situ hydrothermal synthesis procedures were applied to synthesize novel CMC/porous SnO2 nanocomposites from rice husk extracted carboxymethyl cellulose (CMC) biopolymer. In addition, the effects of SnO2 nanoparticles on thermal stability of the prepared nanocomposite were specifically studied. Products were investigated in terms of morphology, particle size, chemical structure, crystallinity and thermal stability by using field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and thermogravimetric analysis (TGA), respectively. Presence of characteristic bands in the FTIR spectra of samples confirmed the successful formation of CMC and CMC/SnO2 nanocomposites. In addition, FESEM images revealed four different morphologies of porous SnO2 nanoparticles including nanospheres, microcubes, nanoflowers and olive-like nanoparticles with hollow cores which were formed on CMC. These nanoparticles possessed d-spacing values of 3.35Å. Thermal stability measurements revealed that introduction of SnO2 nanoparticles in the structure of CMC enhanced stability of CMC to 85%. Copyright © 2016 Elsevier B.V. All rights reserved.

Buckling analysis of the quadripod structure for the NASA 70-meter antenna

NASA Technical Reports Server (NTRS)

Chian, Chian T.

1987-01-01

As part of the effort to extend the diameter of three Deep Space Network large earth antennas from 64 meters to 70 meters, a slim profiled quadripod structure was designed to support a 7.7 meter diameter subreflector for the 70 meter antenna. The new quadripod design, which particularly emphasizes reduced radio frequency blockage, is achieved by means of a narrow cross sectional profile of the legs. Buckling analysis, using NASTRAN, was conducted in this study to verify the safety margin for the quadripod structural stability.

Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

PubMed Central

Wallentine, Brad D.; Wang, Ying; Tretyachenko-Ladokhina, Vira; Tan, Martha; Senear, Donald F.; Luecke, Hartmut

2013-01-01

To gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53, X-ray crystallographic structures of four p53 core-domain variants were determined. These include an oncogenic mutant, V157F, two single-site suppressor mutants, N235K and N239Y, and the rescued cancer mutant V157F/N235K/N239Y. The V157F mutation substitutes a smaller hydrophobic valine with a larger hydrophobic phenylalanine within strand S4 of the hydrophobic core. The structure of this cancer mutant shows no gross structural changes in the overall fold of the p53 core domain, only minor rearrangements of side chains within the hydrophobic core of the protein. Based on biochemical analysis, these small local perturbations induce instability in the protein, increasing the free energy by 3.6 kcal mol−1 (15.1 kJ mol−1). Further biochemical evidence shows that each suppressor mutation, N235K or N239Y, acts individually to restore thermodynamic stability to V157F and that both together are more effective than either alone. All rescued mutants were found to have wild-type DNA-binding activity when assessed at a permissive temperature, thus pointing to thermodynamic stability as the critical underlying variable. Interestingly, thermodynamic analysis shows that while N239Y demonstrates stabilization of the wild-type p53 core domain, N235K does not. These observations suggest distinct structural mechanisms of rescue. A new salt bridge between Lys235 and Glu198, found in both the N235K and rescued cancer mutant structures, suggests a rescue mechanism that relies on stabilizing the β-sandwich scaffold. On the other hand, the substitution N239Y creates an advantageous hydrophobic contact between the aromatic ring of this tyrosine and the adjacent Leu137. Surprisingly, the rescued cancer mutant shows much larger structural deviations than the cancer mutant alone when compared with wild-type p53. These suppressor mutations appear to rescue p53 function by creating novel intradomain interactions that stabilize the core domain, allowing compensation for the destabilizing V157F mutation. PMID:24100332

Chain length effect on the structure and stability of antimicrobial peptides of the (RW)n series.

PubMed

Phambu, Nsoki; Almarwani, Bashiyar; Garcia, Arlette M; Hamza, Nafisa S; Muhsen, Amira; Baidoo, Jacqueline E; Sunda-Meya, Anderson

2017-08-01

Three peptides containing (RW) n -NH 2 units (where n=4, 6, and 8) have been chosen to study the effect of the chain length on the structure and stability of the peptide using Fourier transform infrared (FTIR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC) techniques. Their interactions with Escherichia coli (E. coli) membrane mimetic vesicles are discussed. Infrared results indicate that addition of (RW) n -NH 2 units increases intermolecular H bonds with antiparallel orientation. TGA and DSC results reveal that (RW) 6 -NH 2 shows the optimal chain length in terms of stability and all three peptides show a preferential interaction with one of the anionic lipids in E. coli membranes. SEM images of (RW) 4 -NH 2 present large aggregates while those of (RW) 6 -NH 2 and (RW) 8 -NH 2 present layers of sheet-like structure. In the presence of model membranes, (RW) n -NH 2 show fibrillar peptide superstructures. This study suggests that repeating structures of (RW) n -NH 2 promotes lateral assembly. Copyright © 2017 Elsevier B.V. All rights reserved.

Three-dimensional Sponges with Super Mechanical Stability: Harnessing True Elasticity of Individual Carbon Nanotubes in Macroscopic Architectures

PubMed Central

Dai, Zhaohe; Liu, Luqi; Qi, Xiaoying; Kuang, Jun; Wei, Yueguang; Zhu, Hongwei; Zhang, Zhong

2016-01-01

Efficient assembly of carbon nanotube (CNT) based cellular solids with appropriate structure is the key to fully realize the potential of individual nanotubes in macroscopic architecture. In this work, the macroscopic CNT sponge consisting of randomly interconnected individual carbon nanotubes was grown by CVD, exhibiting a combination of super-elasticity, high strength to weight ratio, fatigue resistance, thermo-mechanical stability and electro-mechanical stability. To deeply understand such extraordinary mechanical performance compared to that of conventional cellular materials and other nanostructured cellular architectures, a thorough study on the response of this CNT-based spongy structure to compression is conducted based on classic elastic theory. The strong inter-tube bonding between neighboring nanotubes is examined, believed to play a critical role in the reversible deformation such as bending and buckling without structural collapse under compression. Based on in-situ scanning electron microscopy observation and nanotube deformation analysis, structural evolution (completely elastic bending-buckling transition) of the carbon nanotubes sponges to deformation is proposed to clarify their mechanical properties and nonlinear electromechanical coupling behavior. PMID:26732143

Drastic stabilization of parallel DNA hybridizations by a polylysine comb-type copolymer with hydrophilic graft chain.

PubMed

Miyoshi, Daisuke; Ueda, Yu-Mi; Shimada, Naohiko; Nakano, Shu-Ichi; Sugimoto, Naoki; Maruyama, Atsushi

2014-09-01

Electrostatic interactions play a major role in protein-DNA interactions. As a model system of a cationic protein, herein we focused on a comb-type copolymer of a polycation backbone and dextran side chains, poly(L-lysine)-graft-dextran (PLL-g-Dex), which has been reported to form soluble interpolyelectrolyte complexes with DNA strands. We investigated the effects of PLL-g-Dex on the conformation and thermodynamics of DNA oligonucleotides forming various secondary structures. Thermodynamic analysis of the DNA structures showed that the parallel conformations involved in both DNA duplexes and triplexes were significantly and specifically stabilized by PLL-g-Dex. On the basis of thermodynamic parameters, it was further possible to design DNA switches that undergo structural transition responding to PLL-g-Dex from an antiparallel duplex to a parallel triplex even with mismatches in the third strand hybridization. These results suggest that polycationic molecules are able to induce structural polymorphism of DNA oligonucleotides, because of the conformation-selective stabilization effects. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Non-normality and classification of amplification mechanisms in stability and resolvent analysis

NASA Astrophysics Data System (ADS)

Symon, Sean; Rosenberg, Kevin; Dawson, Scott T. M.; McKeon, Beverley J.

2018-05-01

Eigenspectra and pseudospectra of the mean-linearized Navier-Stokes operator are used to characterize amplification mechanisms in laminar and turbulent flows in which linear mechanisms are important. Success of mean flow (linear) stability analysis for a particular frequency is shown to depend on whether two scalar measures of non-normality agree: (1) the product between the resolvent norm and the distance from the imaginary axis to the closest eigenvalue and (2) the inverse of the inner product between the most amplified resolvent forcing and response modes. If they agree, the resolvent operator can be rewritten in its dyadic representation to reveal that the adjoint and forward stability modes are proportional to the forcing and response resolvent modes at that frequency. Hence the real parts of the eigenvalues are important since they are responsible for resonant amplification and the resolvent operator is low rank when the eigenvalues are sufficiently separated in the spectrum. If the amplification is pseudoresonant, then resolvent analysis is more suitable to understand the origin of observed flow structures. Two test cases are studied: low Reynolds number cylinder flow and turbulent channel flow. The first deals mainly with resonant mechanisms, hence the success of both classical and mean stability analysis with respect to predicting the critical Reynolds number and global frequency of the saturated flow. Both scalar measures of non-normality agree for the base and mean flows, and the region where the forcing and response modes overlap scales with the length of the recirculation bubble. In the case of turbulent channel flow, structures result from both resonant and pseudoresonant mechanisms, suggesting that both are necessary elements to sustain turbulence. Mean shear is exploited most efficiently by stationary disturbances while bounds on the pseudospectra illustrate how pseudoresonance is responsible for the most amplified disturbances at spatial wavenumbers and temporal frequencies corresponding to well-known turbulent structures. Some implications for flow control are discussed.

Linear stability analysis of the three-dimensional thermally-driven ocean circulation: application to interdecadal oscillations

NASA Astrophysics Data System (ADS)

Huck, Thierry; Vallis, Geoffrey K.

2001-08-01

What can we learn from performing a linear stability analysis of the large-scale ocean circulation? Can we predict from the basic state the occurrence of interdecadal oscillations, such as might be found in a forward integration of the full equations of motion? If so, do the structure and period of the linearly unstable modes resemble those found in a forward integration? We pursue here a preliminary study of these questions for a case in idealized geometry, in which the full nonlinear behavior can also be explored through forward integrations. Specifically, we perform a three-dimensional linear stability analysis of the thermally-driven circulation of the planetary geostrophic equations. We examine the resulting eigenvalues and eigenfunctions, comparing them with the structure of the interdecadal oscillations found in the fully nonlinear model in various parameter regimes. We obtain a steady state by running the time-dependent, nonlinear model to equilibrium using restoring boundary conditions on surface temperature. If the surface heat fluxes are then diagnosed, and these values applied as constant flux boundary conditions, the nonlinear model switches into a state of perpetual, finite amplitude, interdecadal oscillations. We construct a linearized version of the model by empirically evaluating the tangent linear matrix at the steady state, under both restoring and constant-flux boundary conditions. An eigen-analysis shows there are no unstable eigenmodes of the linearized model with restoring conditions. In contrast, under constant flux conditions, we find a single unstable eigenmode that shows a striking resemblance to the fully-developed oscillations in terms of three-dimensional structure, period and growth rate. The mode may be damped through either surface restoring boundary conditions or sufficiently large horizontal tracer diffusion. The success of this simple numerical method in idealized geometry suggests applications in the study of the stability of the ocean circulation in more realistic configurations, and the possibility of predicting potential oceanic modes, even weakly damped, that might be excited by stochastic atmospheric forcing or mesoscale ocean eddies.

Numerical Modeling of Sliding Stability of RCC dam

NASA Astrophysics Data System (ADS)

Mughieda, O.; Hazirbaba, K.; Bani-Hani, K.; Daoud, W.

2017-06-01

Stability and stress analyses are the most important elements that require rigorous consideration in design of a dam structure. Stability of dams against sliding is crucial due to the substantial horizontal load that requires sufficient and safe resistance to develop by mobilization of adequate shearing forces along the base of the dam foundation. In the current research, the static sliding stability of a roller-compacted-concrete (RCC) dam was modelled using finite element method to investigate the stability against sliding. A commercially available finite element software (SAP 2000) was used to analyze stresses in the body of the dam and foundation. A linear finite element static analysis was performed in which a linear plane strain isoperimetric four node elements was used for modelling the dam-foundation system. The analysis was carried out assuming that no slip will occur at the interface between the dam and the foundation. Usual static loading condition was applied for the static analysis. The greatest tension was found to develop in the rock adjacent to the toe of the upstream slope. The factor of safety against sliding along the entire base of the dam was found to be greater than 1 (FS>1), for static loading conditions.

Space simulation facilities providing a stable thermal vacuum facility

NASA Technical Reports Server (NTRS)

Tellalian, Martin L.

1990-01-01

CBI has recently constructed the Intermediate Thermal Vacuum Facility. Built as a corporate facility, the installation will first be used on the Boost Surveillance and Tracking System (BSTS) program. It will also be used to develop and test other sensor systems. The horizontal chamber has a horseshoe shaped cross section and is supported on pneumatic isolators for vibration isolation. The chamber structure was designed to meet stability and stiffness requirements. The design process included measurement of the ambient ground vibrations, analysis of various foundation test article support configurations, design and analysis of the chamber shell and modal testing of the chamber shell. A detailed 3-D finite element analysis was made in the design stage to predict the lowest three natural frequencies and mode shapes and to identify local vibrating components. The design process is described and the results are compared of the finite element analysis to the results of the field modal testing and analysis for the 3 lowest natural frequencies and mode shapes. Concepts are also presented for stiffening large steel structures along with methods to improve test article stability in large space simulation facilities.

Phystosterols and their derivatives: structural diversity, distribution, metabolism, analysis, and health promoting uses

USDA-ARS?s Scientific Manuscript database

Phytosterols (plant sterols) occur in the cells of all plants. They are important structural components that stabilize the biological membranes of plants. Sterols can occur in the “free” unbound form or they can be covalently bound via an ester or glycosidic bond. Since our previous 2002 review o...

Porosity and water activity effects on stability of crystalline β-carotene in freeze-dried solids.

PubMed

Harnkarnsujarit, Nathdanai; Charoenrein, Sanguansri; Roos, Yrjö H

2012-11-01

Stability of entrapped crystalline β-carotene as affected by water activity, solids microstructure, and composition of freeze-dried systems was investigated. Aliquots (1000 mm(3) , 20% w/w solids) of solutions of maltodextrins of various dextrose equivalents (M040:DE6, M100:DE11, and M250:DE25.5), M100-sugars (1:1 glucose, fructose and sucrose), and agar for gelation with dispersed β-carotene were frozen at -20, -40, or -80 °C and freeze-dried. Glass transition and α-relaxation temperatures were determined with differential scanning calorimetry and dynamic mechanical analysis, respectively. β-Carotene contents were monitored spectrophotometrically. In the glassy solids, pore microstructure had a major effect on β-carotene stability. Small pores with thin walls and large surface area allowed β-carotene exposure to oxygen which led to a higher loss, whereas structural collapse enhanced stability of β-carotene by decreasing exposure to oxygen. As water plasticized matrices, an increase in molecular mobility in the matrix enhanced β-carotene degradation. Stability of dispersed β-carotene was highest at around 0.2 a(w) , but decreasing structural relaxation times above the glass transition correlated well with the rate of β-carotene degradation at higher a(w) . Microstructure, a(w) , and component mobility are important factors in the control of stability of β-carotene in freeze-dried solids. β-Carotene expresses various nutritional benefits; however, it is sensitive to oxygen and the degradation contributes to loss of nutritional values as well as product color. To increase stability of β-carotene in freeze-dried foods, the amount of oxygen penetration need to be limited. The modification of freeze-dried food structures, for example, porosity and structural collapse, components, and humidity effectively enhance the stability of dispersed β-carotene in freeze-dried solids. © 2012 Institute of Food Technologists®

Application of amphipols for structure-functional analysis of TRP channels.

PubMed

Huynh, Kevin W; Cohen, Matthew R; Moiseenkova-Bell, Vera Y

2014-10-01

Amphipathic polymers (amphipols), such as A8-35 and SApol, are a new tool for stabilizing integral membrane proteins in detergent-free conditions for structural and functional studies. Transient receptor potential (TRP) ion channels function as tetrameric protein complexes in a diverse range of cellular processes including sensory transduction. Mammalian TRP channels share ~20 % sequence similarity and are categorized into six subfamilies: TRPC (canonical), TRPV (vanilloid), TRPA (ankyrin), TRPM (melastatin), TRPP (polycystin), and TRPML (mucolipin). Due to the inherent difficulties in purifying eukaryotic membrane proteins, structural studies of TRP channels have been limited. Recently, A8-35 was essential in resolving the molecular architecture of the nociceptor TRPA1 and led to the determination of a high-resolution structure of the thermosensitive TRPV1 channel by cryo-EM. Newly developed maltose-neopentyl glycol (MNG) detergents have also proven to be useful in stabilizing TRP channels for structural analysis. In this review, we will discuss the impacts of amphipols and MNG detergents on structural studies of TRP channels by cryo-EM. We will compare how A8-35 and MNG detergents interact with the hydrophobic transmembrane domains of TRP channels. In addition, we will discuss what these cryo-EM studies reveal on the importance of screening different types of surfactants toward determining high-resolution structures of TRP channels.

Application of amphipols for structure-functional analysis of TRP channels

PubMed Central

Huynh, Kevin W.; Cohen, Matthew R.; Moiseenkova-Bell, Vera Y.

2014-01-01

Amphipathic polymers (amphipols), such as A8-35 and SApol, are a new tool for stabilizing integral membrane proteins in detergent-free conditions for structural and functional studies. Transient receptor potential (TRP) ion channels function as tetrameric protein complexes in a diverse range of cellular processes including sensory transduction. Mammalian TRP channels share ~20% sequence similarity and are categorized into six subfamilies: TRPC (canonical), TRPV (vanilloid), TRPA (ankyrin), TRPM (melastatin), TRPP (polycystin), and TRPML (mucolipin). Due to the inherent difficulties in purifying eukaryotic membrane proteins, structural studies of TRP channels have been limited. Recently, A8-35 was essential in resolving the molecular architecture of the nociceptor TRPA1 and led to the determination of a high resolution structure of the thermosensitive TRPV1 channel by cryo-EM. Newly developed maltose-neopentyl glycol (MNG) detergents have also proven useful in stabilizing TRP channels for structural analysis. In this review, we will discuss the impact of amphipols and MNG detergents on structural studies of TRP channels by cryo-EM. We will compare how A8-35 and MNG detergents interact with the hydrophobic transmembrane (TM) domains of TRP channels. In addition, we will discuss what these cryo-EM studies reveal on the importance of screening different types of surfactants towards determining high resolution structures of TRP channels. PMID:24894720

Patterns induced by super cross-diffusion in a predator-prey system with Michaelis-Menten type harvesting.

PubMed

Liu, Biao; Wu, Ranchao; Chen, Liping

2018-04-01

Turing instability and pattern formation in a super cross-diffusion predator-prey system with Michaelis-Menten type predator harvesting are investigated. Stability of equilibrium points is first explored with or without super cross-diffusion. It is found that cross-diffusion could induce instability of equilibria. To further derive the conditions of Turing instability, the linear stability analysis is carried out. From theoretical analysis, note that cross-diffusion is the key mechanism for the formation of spatial patterns. By taking cross-diffusion rate as bifurcation parameter, we derive amplitude equations near the Turing bifurcation point for the excited modes by means of weakly nonlinear theory. Dynamical analysis of the amplitude equations interprets the structural transitions and stability of various forms of Turing patterns. Furthermore, the theoretical results are illustrated via numerical simulations. Copyright © 2018. Published by Elsevier Inc.

A network analysis of the Chinese stock market

NASA Astrophysics Data System (ADS)

Huang, Wei-Qiang; Zhuang, Xin-Tian; Yao, Shuang

2009-07-01

In many practical important cases, a massive dataset can be represented as a very large network with certain attributes associated with its vertices and edges. Stock markets generate huge amounts of data, which can be use for constructing the network reflecting the market’s behavior. In this paper, we use a threshold method to construct China’s stock correlation network and then study the network’s structural properties and topological stability. We conduct a statistical analysis of this network and show that it follows a power-law model. We also detect components, cliques and independent sets in this network. These analyses allows one to apply a new data mining technique of classifying financial instruments based on stock price data, which provides a deeper insight into the internal structure of the stock market. Moreover, we test the topological stability of this network and find that it displays a topological robustness against random vertex failures, but it is also fragile to intentional attacks. Such a network stability property would be also useful for portfolio investment and risk management.

Synthesis, fluorescence, TGA and crystal structure of thiazolyl-pyrazolines derived from chalcones

NASA Astrophysics Data System (ADS)

Suwunwong, T.; Chantrapromma, S.; Fun, H.-K.

2015-04-01

Thiazolyl-pyrazolines 3a-3d were synthesized in a three step procedure using chalcones as starting materials and characterized by FT-IR, UV-Vis, and 1H NMR techniques. The crystal structure of compound 3a was also determined by X-ray diffraction analysis. Compound 3a crystallized out in the orthorhombic P212121 space group with the unit cell dimensions: a = 5.2106(2) Å, b = 12.4341(5) Å, c = 33.3254(13) Å, α = β = γ = 90°, V = 2159.12(15) Å3, Z = 4, D cald = 1.372 M gm-3 and F(000) = 928. Fluorescence of 3a-3d were studied in solid state and acetonitrile solution. It was found that, these compounds exhibit the green fluorescence light (506-508 nm) in both solid and solution states. The pH stability on fluorescence property and the thermal gravimetric analysis of compound 3a were specifically carried out. It was revealed that 3a shows high thermal stability up to around 250°C and presenting high stability in various pH ranges in the acetonitrilewater matrix.

Evolving nucleotide binding surfaces

NASA Technical Reports Server (NTRS)

Kieber-Emmons, T.; Rein, R.

1981-01-01

An analysis is presented of the stability and nature of binding of a nucleotide to several known dehydrogenases. The employed approach includes calculation of hydrophobic stabilization of the binding motif and its intermolecular interaction with the ligand. The evolutionary changes of the binding motif are studied by calculating the Euclidean deviation of the respective dehydrogenases. Attention is given to the possible structural elements involved in the origin of nucleotide recognition by non-coded primordial polypeptides.

Synthesis and thermal stability of carborane containing phosphazenes

NASA Technical Reports Server (NTRS)

Fewell, L. L.; Basi, R. J.; Parker, J. A.

1983-01-01

Carborane substituted polyphosphazenes were prepared by the thermal polymerization of phenyl-carboranyl penta chlorocyclotriphosphazene. Successive isothermal vacuum pyrolyses were conducted on the polymer and examined for structural changes by infrared spectroscopy. The degradation products were ascertained by gas chromatography-mass spectrometric analysis. It was found that the presence of the carborane group improves the thermal stability of the polymer by retarding the ring chain equilibrium processes of decomposition.

Time-delayed feedback control of breathing localized structures in a three-component reaction-diffusion system.

PubMed

Gurevich, Svetlana V

2014-10-28

The dynamics of a single breathing localized structure in a three-component reaction-diffusion system subjected to time-delayed feedback is investigated. It is shown that variation of the delay time and the feedback strength can lead either to stabilization of the breathing or to delay-induced periodic or quasi-periodic oscillations of the localized structure. A bifurcation analysis of the system in question is provided and an order parameter equation is derived that describes the dynamics of the localized structure in the vicinity of the Andronov-Hopf bifurcation. With the aid of this equation, the boundaries of the stabilization domains as well as the dependence of the oscillation radius on delay parameters can be explicitly derived, providing a robust mechanism to control the behaviour of the breathing localized structure in a straightforward manner. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Synthesis and structural characterization of some trisulfide analoges of thiouracil-based antithyroid drugs

NASA Astrophysics Data System (ADS)

Bhabak, Krishna P.; Bhowmick, Debasish

2012-08-01

Thiourea-based antithyroid drugs are effectively used for the treatment of hyperthyroidism. In this paper, we describe the synthesis of new trisulfides (11-12) from the commonly used thiourea-based antithyroid drugs such as 6-n-propyl-2-thiouracil (PTU) and 6-methyl-2-thiouracil (MTU) in the reaction with I2/KI system. Structural analysis by single crystal X-ray diffraction studies revealed the stabilization of trisulfides by a lactam-lactim tautomerism facilitating effective intramolecular as well as intermolecular non-covalent interactions. Although the structures of both trisulfides were found to be quite similar, a notable difference in the intermolecular interactions was observed between compounds 11 and 12 leading to different structural patterns. Structural stabilization of these trisulfides by tautomerism followed by intramolecular as well as intermolecular H-bonds makes these molecules as perfect examples in molecular recognition with self-complementary donor and acceptor units within a single molecule.

Distinct effects of tubulin isotype mutations on neurite growth in Caenorhabditis elegans

PubMed Central

Zheng, Chaogu; Diaz-Cuadros, Margarete; Nguyen, Ken C. Q.; Hall, David H.; Chalfie, Martin

2017-01-01

Tubulins, the building block of microtubules (MTs), play a critical role in both supporting and regulating neurite growth. Eukaryotic genomes contain multiple tubulin isotypes, and their missense mutations cause a range of neurodevelopmental defects. Using the Caenorhabditis elegans touch receptor neurons, we analyzed the effects of 67 tubulin missense mutations on neurite growth. Three types of mutations emerged: 1) loss-of-function mutations, which cause mild defects in neurite growth; 2) antimorphic mutations, which map to the GTP binding site and intradimer and interdimer interfaces, significantly reduce MT stability, and cause severe neurite growth defects; and 3) neomorphic mutations, which map to the exterior surface, increase MT stability, and cause ectopic neurite growth. Structure-function analysis reveals a causal relationship between tubulin structure and MT stability. This stability affects neuronal morphogenesis. As part of this analysis, we engineered several disease-associated human tubulin mutations into C. elegans genes and examined their impact on neuronal development at the cellular level. We also discovered an α-tubulin (TBA-7) that appears to destabilize MTs. Loss of TBA-7 led to the formation of hyperstable MTs and the generation of ectopic neurites; the lack of potential sites for polyamination and polyglutamination on TBA-7 may be responsible for this destabilization. PMID:28835377

Structural Analysis and Testing of the Inflatable Re-entry Vehicle Experiment (IRVE)

NASA Technical Reports Server (NTRS)

Lindell, Michael C.; Hughes, Stephen J.; Dixon, Megan; Wiley, Cliff E.

2006-01-01

The Inflatable Re-entry Vehicle Experiment (IRVE) is a 3.0 meter, 60 degree half-angle sphere cone, inflatable aeroshell experiment designed to demonstrate various aspects of inflatable technology during Earth re-entry. IRVE will be launched on a Terrier-Improved Orion sounding rocket from NASA s Wallops Flight Facility in the fall of 2006 to an altitude of approximately 164 kilometers and re-enter the Earth s atmosphere. The experiment will demonstrate exo-atmospheric inflation, inflatable structure leak performance throughout the flight regime, structural integrity under aerodynamic pressure and associated deceleration loads, thermal protection system performance, and aerodynamic stability. Structural integrity and dynamic response of the inflatable will be monitored with photogrammetric measurements of the leeward side of the aeroshell during flight. Aerodynamic stability and drag performance will be verified with on-board inertial measurements and radar tracking from multiple ground radar stations. In addition to demonstrating inflatable technology, IRVE will help validate structural, aerothermal, and trajectory modeling and analysis techniques for the inflatable aeroshell system. This paper discusses the structural analysis and testing of the IRVE inflatable structure. Equations are presented for calculating fabric loads in sphere cone aeroshells, and finite element results are presented which validate the equations. Fabric material properties and testing are discussed along with aeroshell fabrication techniques. Stiffness and dynamics tests conducted on a small-scale development unit and a full-scale prototype unit are presented along with correlated finite element models to predict the in-flight fundamental mod

Executive summary: Mod-1 wind turbine generator analysis and design report

NASA Technical Reports Server (NTRS)

1979-01-01

Activities leading to the detail design of a wind turbine generator having a nominal rating of 1.8 megawatts are reported. Topics covered include (1) system description; (2) structural dynamics; (3) stability analysis; (4) mechanical subassemblies design; (5) power generation subsystem; and (6) control and instrumentation subsystem.

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.

Atomistic modeling of La3+ doping segregation effect on nanocrystalline yttria-stabilized zirconia.

PubMed

Zhang, Shenli; Sha, Haoyan; Castro, Ricardo H R; Faller, Roland

2018-05-16

The effect of La3+ doping on the structure and ionic conductivity change in nanocrystalline yttria-stabilized zirconia (YSZ) was studied using a combination of Monte Carlo and molecular dynamics simulations. The simulation revealed the segregation of La3+ at eight tilt grain boundary (GB) structures and predicted an average grain boundary (GB) energy decrease of 0.25 J m-2, which is close to the experimental values reported in the literature. Cation stabilization was found to be the main reason for the GB energy decrease, and energy fluctuations near the grain boundary are smoothed out with La3+ segregation. Both dynamic and energetic analysis on the Σ13(510)/[001] GB structure revealed La3+ doping hinders O2- diffusion in the GB region, where the diffusion coefficient monotonically decreases with increasing La3+ doping concentration. The effect was attributed to the increase in the site-dependent migration barriers for O2- hopping caused by segregated La3+, which also leads to anisotropic diffusion at the GB.

Combined X-ray and NMR Analysis of the Stability of the Cyclotide Cystine Knot Fold That Underpins Its Insecticidal Activity and Potential Use as a Drug Scaffold*S⃞

PubMed Central

Wang, Conan K.; Hu, Shu-Hong; Martin, Jennifer L.; Sjögren, Tove; Hajdu, Janos; Bohlin, Lars; Claeson, Per; Göransson, Ulf; Rosengren, K. Johan; Tang, Jun; Tan, Ning-Hua; Craik, David J.

2009-01-01

Cyclotides are a family of plant defense proteins that are highly resistant to adverse chemical, thermal, and enzymatic treatment. Here, we present the first crystal structure of a cyclotide, varv F, from the European field pansy, Viola arvensis, determined at a resolution of 1.8 Å. The solution state NMR structure was also determined and, combined with measurements of biophysical parameters for several cyclotides, provided an insight into the structural features that account for the remarkable stability of the cyclotide family. The x-ray data confirm the cystine knot topology and the circular backbone, and delineate a conserved network of hydrogen bonds that contribute to the stability of the cyclotide fold. The structural role of a highly conserved Glu residue that has been shown to regulate cyclotide function was also determined, verifying its involvement in a stabilizing hydrogen bond network. We also demonstrate that varv F binds to dodecylphosphocholine micelles, defining the binding orientation and showing that its structure remains unchanged upon binding, further demonstrating that the cyclotide fold is rigid. This study provides a biological insight into the mechanism by which cyclotides maintain their native activity in the unfavorable environment of predator insect guts. It also provides a structural basis for explaining how a cluster of residues important for bioactivity may be involved in self-association interactions in membranes. As well as being important for their bioactivity, the structural rigidity of cyclotides makes them very suitable as a stable template for peptide-based drug design. PMID:19211551

Protein thermal denaturation is modulated by central residues in the protein structure network.

PubMed

Souza, Valquiria P; Ikegami, Cecília M; Arantes, Guilherme M; Marana, Sandro R

2016-03-01

Network structural analysis, known as residue interaction networks or graphs (RIN or RIG, respectively) or protein structural networks or graphs (PSN or PSG, respectively), comprises a useful tool for detecting important residues for protein function, stability, folding and allostery. In RIN, the tertiary structure is represented by a network in which residues (nodes) are connected by interactions (edges). Such structural networks have consistently presented a few central residues that are important for shortening the pathways linking any two residues in a protein structure. To experimentally demonstrate that central residues effectively participate in protein properties, mutations were directed to seven central residues of the β-glucosidase Sfβgly (β-D-glucoside glucohydrolase; EC 3.2.1.21). These mutations reduced the thermal stability of the enzyme, as evaluated by changes in transition temperature (Tm ) and the denaturation rate at 45 °C. Moreover, mutations directed to the vicinity of a central residue also caused significant decreases in the Tm of Sfβgly and clearly increased the unfolding rate constant at 45 °C. However, mutations at noncentral residues or at surrounding residues did not affect the thermal stability of Sfβgly. Therefore, the data reported in the present study suggest that the perturbation of the central residues reduced the stability of the native structure of Sfβgly. These results are in agreement with previous findings showing that networks are robust, whereas attacks on central nodes cause network failure. Finally, the present study demonstrates that central residues underlie the functional properties of proteins. © 2016 Federation of European Biochemical Societies.

Stage Separation Failure: Model Based Diagnostics and Prognostics

NASA Technical Reports Server (NTRS)

Luchinsky, Dmitry; Hafiychuk, Vasyl; Kulikov, Igor; Smelyanskiy, Vadim; Patterson-Hine, Ann; Hanson, John; Hill, Ashley

2010-01-01

Safety of the next-generation space flight vehicles requires development of an in-flight Failure Detection and Prognostic (FD&P) system. Development of such system is challenging task that involves analysis of many hard hitting engineering problems across the board. In this paper we report progress in the development of FD&P for the re-contact fault between upper stage nozzle and the inter-stage caused by the first stage and upper stage separation failure. A high-fidelity models and analytical estimations are applied to analyze the following sequence of events: (i) structural dynamics of the nozzle extension during the impact; (ii) structural stability of the deformed nozzle in the presence of the pressure and temperature loads induced by the hot gas flow during engine start up; and (iii) the fault induced thrust changes in the steady burning regime. The diagnostic is based on the measurements of the impact torque. The prognostic is based on the analysis of the correlation between the actuator signal and fault-induced changes in the nozzle structural stability and thrust.

Electrochemical performance of a thermally rearranged polybenzoxazole nanocomposite membrane as a separator for lithium-ion batteries at elevated temperature

NASA Astrophysics Data System (ADS)

Lee, Moon Joo; Hwang, Jun-Ki; Kim, Ji Hoon; Lim, Hyung-Seok; Sun, Yang-Kook; Suh, Kyung-Do; Lee, Young Moo

2016-02-01

Shape-tunable hydroxyl copolyimide (HPI) nanoparticles are fabricated by a re-precipitation method and are coated onto electrospun HPI membranes, followed by heat treatment to prepare thermally rearranged polybenzoxazole (TR-PBO) composite membranes. The morphology of HPI nanoparticles consisted of sphere and sea-squirt structures, which is controlled by changing the concentration of the stabilizer. The morphological characteristics of TR-PBO nanoparticles convert from HPI nanoparticles by heat treatment and their composite membranes is confirmed by scanning electron microscopy (SEM), transmission electron microscopy (TEM), infrared spectroscopy (ATR-IR), thermogravimetric analysis (TGA) analysis, and contact angle measurements. TGA and DSC measurements confirm the excellent thermal stability compared to Celgard, a commercial PP separator for lithium-ion batteries (LIBs). Further, TR-PBO nano-composite membranes used in coin-cell type LIBs as a separator show excellent high power density performance as compared to Celgard. This is due to the fact that sea-squirt structured nanoparticles have better electrochemical properties than sphere structured nanoparticles at high temperature.

Design and Evaluation of Glass/epoxy Composite Blade and Composite Tower Applied to Wind Turbine

NASA Astrophysics Data System (ADS)

Park, Hyunbum

2018-02-01

In the study, the analysis and manufacturing of small class wind turbine blade was performed. In the structural design, firstly the loading conditions are defined through the load case analysis. The proposed structural configuration of blade has a sandwich type composite structure with the E-glass/Epoxy face sheets and the Urethane foam core for lightness, structural stability, low manufacturing cost and easy manufacturing process. And also, this work proposes a design procedure and results of tower for the small scale wind turbine systems. Structural analysis of blade including load cases, stress, deformation, buckling, vibration and fatigue life was performed using the finite element method, the load spectrum analysis and the Miner rule. Moreover, investigation on structural safety of tower was verified through structural analysis by FEM. The manufacturing of blade and tower was performed based on structural design. In order to investigate the designed structure, the structural tests were conducted and its results were compared with the calculated results. It is confirmed that the final proposed blade and tower meet the design requirements.

Stability assessment of structures under earthquake hazard through GRID technology

NASA Astrophysics Data System (ADS)

Prieto Castrillo, F.; Boton Fernandez, M.

2009-04-01

This work presents a GRID framework to estimate the vulnerability of structures under earthquake hazard. The tool has been designed to cover the needs of a typical earthquake engineering stability analysis; preparation of input data (pre-processing), response computation and stability analysis (post-processing). In order to validate the application over GRID, a simplified model of structure under artificially generated earthquake records has been implemented. To achieve this goal, the proposed scheme exploits the GRID technology and its main advantages (parallel intensive computing, huge storage capacity and collaboration analysis among institutions) through intensive interaction among the GRID elements (Computing Element, Storage Element, LHC File Catalogue, federated database etc.) The dynamical model is described by a set of ordinary differential equations (ODE's) and by a set of parameters. Both elements, along with the integration engine, are encapsulated into Java classes. With this high level design, subsequent improvements/changes of the model can be addressed with little effort. In the procedure, an earthquake record database is prepared and stored (pre-processing) in the GRID Storage Element (SE). The Metadata of these records is also stored in the GRID federated database. This Metadata contains both relevant information about the earthquake (as it is usual in a seismic repository) and also the Logical File Name (LFN) of the record for its later retrieval. Then, from the available set of accelerograms in the SE, the user can specify a range of earthquake parameters to carry out a dynamic analysis. This way, a GRID job is created for each selected accelerogram in the database. At the GRID Computing Element (CE), displacements are then obtained by numerical integration of the ODE's over time. The resulting response for that configuration is stored in the GRID Storage Element (SE) and the maximum structure displacement is computed. Then, the corresponding Metadata containing the response LFN, earthquake magnitude and maximum structure displacement is also stored. Finally, the displacements are post-processed through a statistically-based algorithm from the available Metadata to obtain the probability of collapse of the structure for different earthquake magnitudes. From this study, it is possible to build a vulnerability report for the structure type and seismic data. The proposed methodology can be combined with the on-going initiatives to build a European earthquake record database. In this context, Grid enables collaboration analysis over shared seismic data and results among different institutions.

Investigating the effect of mutation on the thermo stability of GB1 protein

NASA Astrophysics Data System (ADS)

Sawitri, K. N.; Sumaryada, T.; Ambarsari, L.; Wahyudi, S. T.

2018-04-01

The thermo stability of wild-type and mutants of the B1 domain of Protein G (GB1 protein) have been studied using molecular dynamics simulation and free energy perturbation simulation. This research is aimed to examine what residue or what interaction that has a major role in the thermo stability of GB1 protein thermo stability by using the point mutation method. Based on the analysis, the unfolding of wild-type protein occurred in 500 K simulation at 704 ps. The mutations were chosen based on the changes in some analysis parameters and the calculated net solvation free energy change. It was found that a simple replacement of a positively charged residue in the β-sheet (K4S) decreases the stability of GB1 protein (unfolding at 452 ps), while the replacement of a negatively charged residue in the α-helix (E27G) increases the stability (unfolding at 846 ps). It was also found that the K4A mutation will break the α-helix and all β-sheet into the coil and turn. All those results suggest that the non-bonded interaction has the major role in the thermo stability of GB1 protein with the β-sheets were identified as the most important structure in the thermo stability of GB1 protein..

Efficient first-principles prediction of solid stability: Towards chemical accuracy

DOE PAGES

Zhang, Yubo; Kitchaev, Daniil A.; Yang, Julia; ...

2018-03-09

The question of material stability is of fundamental importance to any analysis of system properties in condensed matter physics and materials science. The ability to evaluate chemical stability, i.e., whether a stoichiometry will persist in some chemical environment, and structure selection, i.e. what crystal structure a stoichiometry will adopt, is critical to the prediction of materials synthesis, reactivity and properties. In this paper, we demonstrate that density functional theory, with the recently developed strongly constrained and appropriately normed (SCAN) functional, has advanced to a point where both facets of the stability problem can be reliably and efficiently predicted for mainmore » group compounds, while transition metal compounds are improved but remain a challenge. SCAN therefore offers a robust model for a significant portion of the periodic table, presenting an opportunity for the development of novel materials and the study of fine phase transformations even in largely unexplored systems with little to no experimental data.« less

Efficient first-principles prediction of solid stability: Towards chemical accuracy

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

Zhang, Yubo; Kitchaev, Daniil A.; Yang, Julia

The question of material stability is of fundamental importance to any analysis of system properties in condensed matter physics and materials science. The ability to evaluate chemical stability, i.e., whether a stoichiometry will persist in some chemical environment, and structure selection, i.e. what crystal structure a stoichiometry will adopt, is critical to the prediction of materials synthesis, reactivity and properties. In this paper, we demonstrate that density functional theory, with the recently developed strongly constrained and appropriately normed (SCAN) functional, has advanced to a point where both facets of the stability problem can be reliably and efficiently predicted for mainmore » group compounds, while transition metal compounds are improved but remain a challenge. SCAN therefore offers a robust model for a significant portion of the periodic table, presenting an opportunity for the development of novel materials and the study of fine phase transformations even in largely unexplored systems with little to no experimental data.« less

Passivity/Lyapunov based controller design for trajectory tracking of flexible joint manipulators

NASA Technical Reports Server (NTRS)

Sicard, Pierre; Wen, John T.; Lanari, Leonardo

1992-01-01

A passivity and Lyapunov based approach for the control design for the trajectory tracking problem of flexible joint robots is presented. The basic structure of the proposed controller is the sum of a model-based feedforward and a model-independent feedback. Feedforward selection and solution is analyzed for a general model for flexible joints, and for more specific and practical model structures. Passivity theory is used to design a motor state-based controller in order to input-output stabilize the error system formed by the feedforward. Observability conditions for asymptotic stability are stated and verified. In order to accommodate for modeling uncertainties and to allow for the implementation of a simplified feedforward compensation, the stability of the system is analyzed in presence of approximations in the feedforward by using a Lyapunov based robustness analysis. It is shown that under certain conditions, e.g., the desired trajectory is varying slowly enough, stability is maintained for various approximations of a canonical feedforward.

Theoretical prediction of the energy stability of graphene nanoblisters

NASA Astrophysics Data System (ADS)

Glukhova, O. E.; Slepchenkov, M. M.; Barkov, P. V.

2018-04-01

The paper presents the results of a theoretical prediction of the energy stability of graphene nanoblisters with various geometrical parameters. As a criterion for the evaluation of the stability of investigated carbon objects we propose to consider the value of local stress of the nanoblister atomic grid. Numerical evaluation of stresses experienced by atoms of the graphene blister framework was carried out by means of an original method for calculation of local stresses that is based on energy approach. Atomistic models of graphene nanoblisters corresponding to the natural experiment data were built for the first time in this work. New physical regularities of the influence of topology on the thermodynamic stability of nanoblisters were established as a result of the analysis of the numerical experiment data. We built the distribution of local stresses for graphene blister structures, whose atomic grid contains a variety of structural defects. We have shown how the concentration and location of defects affect the picture of the distribution of the maximum stresses experienced by the atoms of the nanoblisters.

Stability of binaries. Part II: Rubble-pile binaries

NASA Astrophysics Data System (ADS)

Sharma, Ishan

2016-10-01

We consider the stability of the binary asteroids whose members are granular aggregates held together by self-gravity alone. A binary is said to be stable whenever both its members are orbitally and structurally stable to both orbital and structural perturbations. To this end, we extend the stability analysis of Sharma (Sharma [2015] Icarus, 258, 438-453), that is applicable to binaries with rigid members, to the case of binary systems with rubble members. We employ volume averaging (Sharma et al. [2009] Icarus, 200, 304-322), which was inspired by past work on elastic/fluid, rotating and gravitating ellipsoids. This technique has shown promise when applied to rubble-pile ellipsoids, but requires further work to settle some of its underlying assumptions. The stability test is finally applied to some suspected binary systems, viz., 216 Kleopatra, 624 Hektor and 90 Antiope. We also see that equilibrated binaries that are close to mobilizing their maximum friction can sustain only a narrow range of shapes and, generally, congruent shapes are preferred.

Tenth NASTRAN User's Colloquium

NASA Technical Reports Server (NTRS)

1982-01-01

The development of the NASTRAN computer program, a general purpose finite element computer code for structural analysis, was discussed. The application and development of NASTRAN is presented in the following topics: improvements and enhancements; developments of pre and postprocessors; interactive review system; the use of harmonic expansions in magnetic field problems; improving a dynamic model with test data using Linwood; solution of axisymmetric fluid structure interaction problems; large displacements and stability analysis of nonlinear propeller structures; prediction of bead area contact load at the tire wheel interface; elastic plastic analysis of an overloaded breech ring; finite element solution of torsion and other 2-D Poisson equations; new capability for elastic aircraft airloads; usage of substructuring analysis in the get away special program; solving symmetric structures with nonsymmetric loads; evaluation and reduction of errors induced by Guyan transformation.

Nicotinamidase/pyrazinamidase of Mycobacterium tuberculosis forms homo-dimers stabilized by disulfide bonds

PubMed Central

Rueda, Daniel; Sheen, Patricia; Gilman, Robert H.; Bueno, Carlos; Santos, Marco; Pando-Robles, Victoria; Batista, Cesar V.; Zimic, Mirko

2014-01-01

Recombinant wild-pyrazinamidase from H37Rv M. tuberculosis was analyzed by gel electrophoresis under differential reducing conditions to evaluate its quaternary structure. PZAse was fractionated by size exclusion chromatography under non-reducing conditions. PZAse activity was measured and mass spectrometry analysis was performed to determine the identity of proteins by de novo sequencing and to determine the presence of disulfide bonds. This study confirmed that M. tuberculosis wild type PZAse was able to form homo-dimers in vitro. Homo-dimers showed a slightly lower specific PZAse activity compared to monomeric PZAse. PZAse dimers were dissociated into monomers in response to reducing conditions. Mass spectrometry analysis confirmed the existence of disulfide bonds (C72-C138 and C138-C138) stabilizing the quaternary structure of the PZAse homo-dimer. PMID:25199451

Three-dimensional baroclinic instability of a Hadley cell for small Richardson number

NASA Technical Reports Server (NTRS)

Antar, B. N.; Fowlis, W. W.

1983-01-01

For the case of a baroclinic flow whose Richardson number, Ri, is of order unity, a three-dimensional linear stability analysis is conducted on the basis of a model for a thin, horizontal, rotating fluid layer which is subjected to horizontal and vertical temperature gradients. The Hadley cell basic state and stability analysis are both based on the Navier-Stokes and energy equations, and perturbations possessing zonal, meridional, and vertical structures are considered. An attempt is made to extend the previous theoretical work on three-dimensional baroclinic instability for small Ri to a more realistic model involving the Prandtl and Ekman numbers, as well as to finite growth rates and a wider range of the zonal wavenumber. In general, it is found that the symmetric modes of maximum growth are not purely symmetric, but have a weak zonal structure.

Physical stability comparisons of IgG1-Fc variants: effects of N-glycosylation site occupancy and Asp/Gln residues at site Asn 297

PubMed Central

KIM, JAE HYUN; JOSHI, SANGEETA B.; MIDDAUGH, C. RUSSELL; TOLBERT, THOMAS J.; VOLKIN, DAVID B.

2014-01-01

The structural integrity and conformational stability of various IgG1-Fc proteins produced from the yeast Pichia pastoris with different glycosylation site occupancy (di-, mono-, and non- glycosylated) was determined. In addition, the physical stability profiles of three different forms of non-glycosylated Fc molecules (varying amino acid residues at site 297 in the CH2 domain due to point mutations and enzymatic digestion of the Fc glycoforms) were also examined. The physical stability of these IgG1-Fc glycoproteins was examined as a function of pH and temperature by high throughput biophysical analysis using multiple techniques combined with data visualization tools (three index empirical phase diagrams and radar charts). Across the pH range of 4.0 to 6.0, the di- and mono- glycosylated forms of the IgG1-Fc showed the highest and lowest levels of physical stability respectively, with the non-glycosylated forms showing intermediate stability depending on solution pH. In the aglycosylated Fc proteins, the introduction of Asp (D) residues at site 297 (QQ vs. DN vs. DD forms) resulted in more subtle changes in structural integrity and physical stability depending on solution pH. The utility of evaluating the conformational stability profile differences between the various IgG1-Fc glycoproteins is discussed in the context of analytical comparability studies. PMID:24740840

Quantitative Analysis of Nucleic Acid Stability with Ligands Under High Pressure to Design Novel Drugs Targeting G-Quadruplexes.

PubMed

Takahashi, Shuntaro; Sugimoto, Naoki

2017-09-18

Nucleic acids (DNA and RNA) can form various non-canonical structures. Because some serious diseases are caused by the conformational change of G-quadruplex DNA structures, the development of ligands that bind and stabilize G-quadruplex DNA is of interest to the field of nucleic acid chemistry. Volumetric changes (ΔV) in the biomolecular reaction include the structural change of biomolecules and hydration behaviors, which provide information about the tertiary interaction between G-quadruplex DNA and ligands. Thus, it is valuable to investigate ΔV values to understand the mechanism of interaction between non-canonical structures and their ligands. This unit describes methods that can be used to quantitatively analyze the interaction between G-quadruplex DNA and ligands by using high-pressure UV melting. The combination of thermodynamic parameters (ΔG, ΔH, ΔS, and ΔV) is a powerful tool to elucidate the mechanism of ligand binding to G-quadruplex without real structural analysis by NMR and X-ray spectroscopy, and gives useful information to design novel drugs. © 2017 by John Wiley & Sons, Inc. Copyright © 2017 John Wiley & Sons, Inc.

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

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

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza

Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Here, our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm themore » presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.« less

Population-based 3D genome structure analysis reveals driving forces in spatial genome organization

DOE PAGES

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza; ...

2016-03-07

Conformation capture technologies (e.g., Hi-C) chart physical interactions between chromatin regions on a genome-wide scale. However, the structural variability of the genome between cells poses a great challenge to interpreting ensemble-averaged Hi-C data, particularly for long-range and interchromosomal interactions. Here, we present a probabilistic approach for deconvoluting Hi-C data into a model population of distinct diploid 3D genome structures, which facilitates the detection of chromatin interactions likely to co-occur in individual cells. Here, our approach incorporates the stochastic nature of chromosome conformations and allows a detailed analysis of alternative chromatin structure states. For example, we predict and experimentally confirm themore » presence of large centromere clusters with distinct chromosome compositions varying between individual cells. The stability of these clusters varies greatly with their chromosome identities. We show that these chromosome-specific clusters can play a key role in the overall chromosome positioning in the nucleus and stabilizing specific chromatin interactions. By explicitly considering genome structural variability, our population-based method provides an important tool for revealing novel insights into the key factors shaping the spatial genome organization.« less

Structural Characteristics and Function of a New Kind of Thermostable Trehalose Synthase from Thermobaculum terrenum.

PubMed

Wang, Junqing; Ren, Xudong; Wang, Ruiming; Su, Jing; Wang, Feng

2017-09-06

Trehalose has important applications in the food industry and pharmaceutical manufacturing. The thermostable enzyme trehalose synthase from Thermobaculum terrenum (TtTS) catalyzes the reversible interconversion of maltose and trehalose. Here, we investigated the structural characteristics of TtTS in complex with the inhibitor TriS. TtTS exhibits the typical three domain glycoside hydrolase family 13 structure. The catalytic cleft consists of Asp202-Glu244-Asp310 and various conserved substrate-binding residues. However, among trehalose synthases, TtTS demonstrates obvious thermal stability. TtTS has more polar (charged) amino acids distributed on its protein structure surface and more aromatic amino acids buried within than other mesophilic trehalose synthases. Furthermore, TtTS structural analysis revealed four potential metal ion-binding sites rather than the two in a homologous structure. These factors may render TtTS relatively more thermostable among mesophilic trehalose synthases. The detailed thermophilic enzyme structure provided herein may provide guidance for further protein engineering in the design of stabilized enzymes.

The influence of vertical load to the natural vibration of series isolation system

NASA Astrophysics Data System (ADS)

Lin, Z. D.; Shi, H.

2018-02-01

The influence of axial load to the natural vibration of series isolation system is analyzed. The natural frequency of series isolation system is solved by differential quadrature method. According to the vertical load which is the main factor of natural vibration characteristic on the series isolation system, the parameter analysis is carried out. It should provide the basis for the vibration characteristic analysis for the structure of bearing on the top of first story column, and it can also provide evidence for the overall stability analysis of series isolation structure.

Analysis of Structures with Rotating, Flexible Substructures Applied to Rotorcraft Aeroelasticity in GRASP (General Rotorcraft Aeromechanical Stability Program),

DTIC Science & Technology

1987-01-01

two nodes behave identically. In GRASP, these constraints are entirely invisible from the user’s point of view. GRASP (Recall that the Levi - Civita ...virtual rotation GRASP is the first program implementing a new methodWl( = Levi -Ciudta symbol op for dynamic analysis of structures, parts of which may...natural coordinatization of sis for this methodology, which incorporates body flexibility components. with the large discrete motions previously

Sequence swapping does not result in conformation swapping for the beta4/beta5 and beta8/beta9 beta-hairpin turns in human acidic fibroblast growth factor.

PubMed

Kim, Jaewon; Lee, Jihun; Brych, Stephen R; Logan, Timothy M; Blaber, Michael

2005-02-01

The beta-turn is the most common type of nonrepetitive structure in globular proteins, comprising ~25% of all residues; however, a detailed understanding of effects of specific residues upon beta-turn stability and conformation is lacking. Human acidic fibroblast growth factor (FGF-1) is a member of the beta-trefoil superfold and contains a total of five beta-hairpin structures (antiparallel beta-sheets connected by a reverse turn). beta-Turns related by the characteristic threefold structural symmetry of this superfold exhibit different primary structures, and in some cases, different secondary structures. As such, they represent a useful system with which to study the role that turn sequences play in determining structure, stability, and folding of the protein. Two turns related by the threefold structural symmetry, the beta4/beta5 and beta8/beta9 turns, were subjected to both sequence-swapping and poly-glycine substitution mutations, and the effects upon stability, folding, and structure were investigated. In the wild-type protein these turns are of identical length, but exhibit different conformations. These conformations were observed to be retained during sequence-swapping and glycine substitution mutagenesis. The results indicate that the beta-turn structure at these positions is not determined by the turn sequence. Structural analysis suggests that residues flanking the turn are a primary structural determinant of the conformation within the turn.

Thermally stable macromolecules.

NASA Technical Reports Server (NTRS)

Pezdirtz, G. F.; Johnston, N. J.

1972-01-01

Man-made polymers are compared with certain naturally occurring polymers which have long been used at elevated temperatures. The pyrolysis of model compounds is discussed together with aspects of thermogravimetric analysis, torsional braid analysis, and questions of chemical and radiation stability. Some structure-property relationships are examined, giving attention to asbestos, mica, graphite, and diamond. Questions of bond strengths are investigated along with the stability of ladder polymers and some fundamental concepts in the synthesis of aromatic and heteroaromatic polymers. The substances considered include aromatic single-strand polymers, heteroaromatic polymers, polymers obtained by addition polymerizations, and nonhydrogen-containing polymers. Future trends are also explored.

Enhanced enzyme kinetic stability by increasing rigidity within the active site.

PubMed

Xie, Yuan; An, Jiao; Yang, Guangyu; Wu, Geng; Zhang, Yong; Cui, Li; Feng, Yan

2014-03-14

Enzyme stability is an important issue for protein engineers. Understanding how rigidity in the active site affects protein kinetic stability will provide new insight into enzyme stabilization. In this study, we demonstrated enhanced kinetic stability of Candida antarctica lipase B (CalB) by mutating the structurally flexible residues within the active site. Six residues within 10 Å of the catalytic Ser(105) residue with a high B factor were selected for iterative saturation mutagenesis. After screening 2200 colonies, we obtained the D223G/L278M mutant, which exhibited a 13-fold increase in half-life at 48 °C and a 12 °C higher T50(15), the temperature at which enzyme activity is reduced to 50% after a 15-min heat treatment. Further characterization showed that global unfolding resistance against both thermal and chemical denaturation also improved. Analysis of the crystal structures of wild-type CalB and the D223G/L278M mutant revealed that the latter formed an extra main chain hydrogen bond network with seven structurally coupled residues within the flexible α10 helix that are primarily involved in forming the active site. Further investigation of the relative B factor profile and molecular dynamics simulation confirmed that the enhanced rigidity decreased fluctuation of the active site residues at high temperature. These results indicate that enhancing the rigidity of the flexible segment within the active site may provide an efficient method for improving enzyme kinetic stability.

Asymptotic stability and instability of large-scale systems. [using vector Liapunov functions

NASA Technical Reports Server (NTRS)

Grujic, L. T.; Siljak, D. D.

1973-01-01

The purpose of this paper is to develop new methods for constructing vector Lyapunov functions and broaden the application of Lyapunov's theory to stability analysis of large-scale dynamic systems. The application, so far limited by the assumption that the large-scale systems are composed of exponentially stable subsystems, is extended via the general concept of comparison functions to systems which can be decomposed into asymptotically stable subsystems. Asymptotic stability of the composite system is tested by a simple algebraic criterion. By redefining interconnection functions among the subsystems according to interconnection matrices, the same mathematical machinery can be used to determine connective asymptotic stability of large-scale systems under arbitrary structural perturbations.

Micro-Ring Structures Stabilize Microdroplets to Enable Long Term Spheroid Culture in 384 Hanging Drop Array Plates

PubMed Central

Hsiao, Amy Y.; Tung, Yi-Chung; Kuo, Chuan-Hsien; Mosadegh, Bobak; Bedenis, Rachel; Pienta, Kenneth J.; Takayama, Shuichi

2012-01-01

Using stereolithography, 20 different structural variations comprised of millimeter diameter holes surrounded by trenches, plateaus, or micro-ring structures were prepared and tested for their ability to stably hold arrays of microliter sized droplets within the structures over an extended period of time. The micro-ring structures were the most effective in stabilizing droplets against mechanical and chemical perturbations. After confirming the importance of micro-ring structures using rapid prototyping, we developed an injection molding tool for mass production of polystyrene 3D cell culture plates with an array of 384 such micro-ring surrounded through-hole structures. These newly designed and injection molded polystyrene 384 hanging drop array plates with micro-rings were stable and robust against mechanical perturbations as well as surface fouling-facilitated droplet spreading making them capable of long term cell spheroid culture of up to 22 days within the droplet array. This is a significant improvement over previously reported 384 hanging drop array plates which are susceptible to small mechanical shocks and could not reliably maintain hanging drops for longer than a few days. With enhanced droplet stability, the hanging drop array plates with micro-ring structures provide better platforms and open up new opportunities for high-throughput preparation of microscale 3D cell constructs for drug screening and cell analysis. PMID:22057945

Micro-ring structures stabilize microdroplets to enable long term spheroid culture in 384 hanging drop array plates.

PubMed

Hsiao, Amy Y; Tung, Yi-Chung; Kuo, Chuan-Hsien; Mosadegh, Bobak; Bedenis, Rachel; Pienta, Kenneth J; Takayama, Shuichi

2012-04-01

Using stereolithography, 20 different structural variations comprised of millimeter diameter holes surrounded by trenches, plateaus, or micro-ring structures were prepared and tested for their ability to stably hold arrays of microliter sized droplets within the structures over an extended period of time. The micro-ring structures were the most effective in stabilizing droplets against mechanical and chemical perturbations. After confirming the importance of micro-ring structures using rapid prototyping, we developed an injection molding tool for mass production of polystyrene 3D cell culture plates with an array of 384 such micro-ring surrounded through-hole structures. These newly designed and injection molded polystyrene 384 hanging drop array plates with micro-rings were stable and robust against mechanical perturbations as well as surface fouling-facilitated droplet spreading making them capable of long term cell spheroid culture of up to 22 days within the droplet array. This is a significant improvement over previously reported 384 hanging drop array plates which are susceptible to small mechanical shocks and could not reliably maintain hanging drops for longer than a few days. With enhanced droplet stability, the hanging drop array plates with micro-ring structures provide better platforms and open up new opportunities for high-throughput preparation of microscale 3D cell constructs for drug screening and cell analysis.

Worst-Case Flutter Margins from F/A-18 Aircraft Aeroelastic Data

NASA Technical Reports Server (NTRS)

Lind, Rick; Brenner, Marty

1997-01-01

An approach for computing worst-case flutter margins has been formulated in a robust stability framework. Uncertainty operators are included with a linear model to describe modeling errors and flight variations. The structured singular value, micron, computes a stability margin which directly accounts for these uncertainties. This approach introduces a new method of computing flutter margins and an associated new parameter for describing these margins. The micron margins are robust margins which indicate worst-case stability estimates with respect to the defined uncertainty. Worst-case flutter margins are computed for the F/A-18 SRA using uncertainty sets generated by flight data analysis. The robust margins demonstrate flight conditions for flutter may lie closer to the flight envelope than previously estimated by p-k analysis.

SiC/Mg multilayer coatings for SCORE coronagraph: long term stability analysis

NASA Astrophysics Data System (ADS)

Pelizzo, Maria Guglielmina; Fineschi, Silvano; Zuppella, Paola; Corso, Alain Jody; Windt, David L.; Nicolosi, Piergiorgio

2011-10-01

SiC/Mg multilayers have been used as coatings of the Sounding-rocket CORonagraphic Experiment (SCORE) telescope mirrors launched during the NASA HERSCHEL program. This materials couple has been largely studied by researchers since it provides higher performances than a standard Mo/Si multilayer; the SCORE mirrors show in fact a peak reflectance of around 40% at HeII 30.4 nm. Nevertheless, long term stability of this coating is an open problem. A study on the aging and stability of this multilayer has been carried on. SiC/Mg multilayer samples characterized by different structural parameters have been deposited. They have been measured just after deposition and four years later to verify degradation based on natural aging. Experimental results and analysis are presented.

Design and analysis of control system for VCSEL of atomic interference magnetometer

NASA Astrophysics Data System (ADS)

Zhang, Xiao-nan; Sun, Xiao-jie; Kou, Jun; Yang, Feng; Li, Jie; Ren, Zhang; Wei, Zong-kang

2016-11-01

Magnetic field detection is an important means of deep space environment exploration. Benefit from simple structure and low power consumption, atomic interference magnetometer become one of the most potential detector payloads. Vertical Cavity Surface Emitting Laser (VCSEL) is usually used as a light source in atomic interference magnetometer and its frequency stability directly affects the stability and sensitivity of magnetometer. In this paper, closed-loop control strategy of VCSEL was designed and analysis, the controller parameters were selected and the feedback error algorithm was optimized as well. According to the results of experiments that were performed on the hardware-in-the-loop simulation platform, the designed closed-loop control system is reasonable and it is able to effectively improve the laser frequency stability during the actual work of the magnetometer.

Study on Stability Analysis and Monitoring Technology of Deep Concave Open-Pit Mine Slope

NASA Astrophysics Data System (ADS)

Xue, Dinglong; Ren, Fenghua; Li, Yuan

2018-05-01

In this paper, using the FLAC3D software to establish the numerical model of the rock slope in the south of Washan stope and to compare and verify with the monitoring result, reference is made to the original engineering and hydrogeological data of Washan stope. The results show that the stability of the South slope is mainly affected by the dominant structural plane, and the potential slip surface and the dominant structure surface are the same. During the recovery period of -120m platform residual mine, the disturbance stress is increasing but the overall amplitude is small and the slope is relatively stable.

Computational design of a pH stable enzyme: understanding molecular mechanism of penicillin acylase's adaptation to alkaline conditions.

PubMed

Suplatov, Dmitry; Panin, Nikolay; Kirilin, Evgeny; Shcherbakova, Tatyana; Kudryavtsev, Pavel; Svedas, Vytas

2014-01-01

Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. Consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. Thermal stability has been extensively studied in connection with practical application of biocatalysts. However, little work has been done to explore the mechanism of pH-dependent inactivation. In this study, bioinformatic analysis of the Ntn-hydrolase superfamily was performed to identify functionally important subfamily-specific positions in protein structures. Furthermore, the involvement of these positions in pH-induced inactivation was studied. The conformational mobility of penicillin acylase in Escherichia coli was analyzed through molecular modeling in neutral and alkaline conditions. Two functionally important subfamily-specific residues, Gluβ482 and Aspβ484, were found. Ionization of these residues at alkaline pH promoted the collapse of a buried network of stabilizing interactions that consequently disrupted the functional protein conformation. The subfamily-specific position Aspβ484 was selected as a hotspot for mutation to engineer enzyme variant tolerant to alkaline medium. The corresponding Dβ484N mutant was produced and showed 9-fold increase in stability at alkaline conditions. Bioinformatic analysis of subfamily-specific positions can be further explored to study mechanisms of protein inactivation and to design more stable variants for the engineering of homologous Ntn-hydrolases with improved catalytic properties.

Computational Design of a pH Stable Enzyme: Understanding Molecular Mechanism of Penicillin Acylase's Adaptation to Alkaline Conditions

PubMed Central

Suplatov, Dmitry; Panin, Nikolay; Kirilin, Evgeny; Shcherbakova, Tatyana; Kudryavtsev, Pavel; Švedas, Vytas

2014-01-01

Protein stability provides advantageous development of novel properties and can be crucial in affording tolerance to mutations that introduce functionally preferential phenotypes. Consequently, understanding the determining factors for protein stability is important for the study of structure-function relationship and design of novel protein functions. Thermal stability has been extensively studied in connection with practical application of biocatalysts. However, little work has been done to explore the mechanism of pH-dependent inactivation. In this study, bioinformatic analysis of the Ntn-hydrolase superfamily was performed to identify functionally important subfamily-specific positions in protein structures. Furthermore, the involvement of these positions in pH-induced inactivation was studied. The conformational mobility of penicillin acylase in Escherichia coli was analyzed through molecular modeling in neutral and alkaline conditions. Two functionally important subfamily-specific residues, Gluβ482 and Aspβ484, were found. Ionization of these residues at alkaline pH promoted the collapse of a buried network of stabilizing interactions that consequently disrupted the functional protein conformation. The subfamily-specific position Aspβ484 was selected as a hotspot for mutation to engineer enzyme variant tolerant to alkaline medium. The corresponding Dβ484N mutant was produced and showed 9-fold increase in stability at alkaline conditions. Bioinformatic analysis of subfamily-specific positions can be further explored to study mechanisms of protein inactivation and to design more stable variants for the engineering of homologous Ntn-hydrolases with improved catalytic properties. PMID:24959852

Functional and Structural Analysis of the Conserved EFhd2 Protein

PubMed Central

Acosta, Yancy Ferrer; Rodríguez Cruz, Eva N.; Vaquer, Ana del C.; Vega, Irving E.

2013-01-01

EFhd2 is a novel protein conserved from C. elegans to H. sapiens. This novel protein was originally identified in cells of the immune and central nervous systems. However, it is most abundant in the central nervous system, where it has been found associated with pathological forms of the microtubule-associated protein tau. The physiological or pathological roles of EFhd2 are poorly understood. In this study, a functional and structural analysis was carried to characterize the molecular requirements for EFhd2’s calcium binding activity. The results showed that mutations of a conserved aspartate on either EF-hand motif disrupted the calcium binding activity, indicating that these motifs work in pair as a functional calcium binding domain. Furthermore, characterization of an identified single-nucleotide polymorphisms (SNP) that introduced a missense mutation indicates the importance of a conserved phenylalanine on EFhd2 calcium binding activity. Structural analysis revealed that EFhd2 is predominantly composed of alpha helix and random coil structures and that this novel protein is thermostable. EFhd2’s thermo stability depends on its N-terminus. In the absence of the N-terminus, calcium binding restored EFhd2’s thermal stability. Overall, these studies contribute to our understanding on EFhd2 functional and structural properties, and introduce it into the family of canonical EF-hand domain containing proteins. PMID:22973849

PoPMuSiC 2.1: a web server for the estimation of protein stability changes upon mutation and sequence optimality.

PubMed

Dehouck, Yves; Kwasigroch, Jean Marc; Gilis, Dimitri; Rooman, Marianne

2011-05-13

The rational design of modified proteins with controlled stability is of extreme importance in a whole range of applications, notably in the biotechnological and environmental areas, where proteins are used for their catalytic or other functional activities. Future breakthroughs in medical research may also be expected from an improved understanding of the effect of naturally occurring disease-causing mutations on the molecular level. PoPMuSiC-2.1 is a web server that predicts the thermodynamic stability changes caused by single site mutations in proteins, using a linear combination of statistical potentials whose coefficients depend on the solvent accessibility of the mutated residue. PoPMuSiC presents good prediction performances (correlation coefficient of 0.8 between predicted and measured stability changes, in cross validation, after exclusion of 10% outliers). It is moreover very fast, allowing the prediction of the stability changes resulting from all possible mutations in a medium size protein in less than a minute. This unique functionality is user-friendly implemented in PoPMuSiC and is particularly easy to exploit. Another new functionality of our server concerns the estimation of the optimality of each amino acid in the sequence, with respect to the stability of the structure. It may be used to detect structural weaknesses, i.e. clusters of non-optimal residues, which represent particularly interesting sites for introducing targeted mutations. This sequence optimality data is also expected to have significant implications in the prediction and the analysis of particular structural or functional protein regions. To illustrate the interest of this new functionality, we apply it to a dataset of known catalytic sites, and show that a much larger than average concentration of structural weaknesses is detected, quantifying how these sites have been optimized for function rather than stability. The freely available PoPMuSiC-2.1 web server is highly useful for identifying very rapidly a list of possibly relevant mutations with the desired stability properties, on which subsequent experimental studies can be focused. It can also be used to detect sequence regions corresponding to structural weaknesses, which could be functionally important or structurally delicate regions, with obvious applications in rational protein design.

Advanced grid-stiffened composite shells for applications in heavy-lift helicopter rotor blade spars

NASA Astrophysics Data System (ADS)

Narayanan Nampy, Sreenivas

Modern rotor blades are constructed using composite materials to exploit their superior structural performance compared to metals. Helicopter rotor blade spars are conventionally designed as monocoque structures. Blades of the proposed Heavy Lift Helicopter are envisioned to be as heavy as 800 lbs when designed using the monocoque spar design. A new and innovative design is proposed to replace the conventional spar designs with light weight grid-stiffened composite shell. Composite stiffened shells have been known to provide excellent strength to weight ratio and damage tolerance with an excellent potential to reduce weight. Conventional stringer--rib stiffened construction is not suitable for rotor blade spars since they are limited in generating high torsion stiffness that is required for aeroelastic stability of the rotor. As a result, off-axis (helical) stiffeners must be provided. This is a new design space where innovative modeling techniques are needed. The structural behavior of grid-stiffened structures under axial, bending, and torsion loads, typically experienced by rotor blades need to be accurately predicted. The overall objective of the present research is to develop and integrate the necessary design analysis tools to conduct a feasibility study in employing grid-stiffened shells for heavy-lift rotor blade spars. Upon evaluating the limitations in state-of-the-art analytical models in predicting the axial, bending, and torsion stiffness coefficients of grid and grid-stiffened structures, a new analytical model was developed. The new analytical model based on the smeared stiffness approach was developed employing the stiffness matrices of the constituent members of the grid structure such as an arch, helical, or straight beam representing circumferential, helical, and longitudinal stiffeners. This analysis has the capability to model various stiffening configurations such as angle-grid, ortho-grid, and general-grid. Analyses were performed using an existing state-of-the-art and newly developed model to predict the torsion, bending, and axial stiffness of grid and grid-stiffened structures with various stiffening configurations. These predictions were compared to results generated using finite element analysis (FEA) to observe excellent correlation (within 6%) for a range of parameters for grid and grid-stiffened structures such as grid density, stiffener angle, and aspect ratio of the stiffener cross-section. Experimental results from cylindrical grid specimen testing were compared with analytical prediction using the new analysis. The new analysis predicted stiffness coefficients with nearly 7% error compared to FEA results. From the parametric studies conducted, it was observed that the previous state-of-the-art analysis on the other hand exhibited errors of the order of 39% for certain designs. Stability evaluations were also conducted by integrating the new analysis with established stability formulations. A design study was conducted to evaluate the potential weight savings of a simple grid-stiffened rotor blade spar structure compared to a baseline monocoque design. Various design constraints such as stiffness, strength, and stability were imposed. A manual search was conducted for design parameters such as stiffener density, stiffener angle, shell laminate, and stiffener aspect ratio that provide lightweight grid-stiffened designs compared to the baseline. It was found that a weight saving of 9.1% compared to the baseline is possible without violating any of the design constraints.

Feasibility analysis of base compaction specification : [project brief].

DOT National Transportation Integrated Search

2013-02-01

Appropriate design and construction of the aggregate base layer has significant influence on : structural stability and performance of pavements. Controlling the construction quality of : the granular base layer is important to achieve long-lasting p...

Aeroelastic stability and response of rotating structures

NASA Technical Reports Server (NTRS)

Keith, Theo G., Jr.

1993-01-01

A summary of the work performed during the progress period is presented. Analysis methods for predicting loads and instabilities of wind turbines were developed. Three new areas of research to aid the Advanced Turboprop Project (ATP) were initiated and developed. These three areas of research are aeroelastic analysis methods for cascades including blade and disk flexibility; stall flutter analysis; and computational aeroelasticity.

A residue in helical conformation in the native state adopts a β-strand conformation in the folding transition state despite its high and canonical Φ-value.

PubMed

Zarrine-Afsar, Arash; Dahesh, Samira; Davidson, Alan R

2012-05-01

Delineating structures of the transition states in protein folding reactions has provided great insight into the mechanisms by which proteins fold. The most common method for obtaining this information is Φ-value analysis, which is carried out by measuring the changes in the folding and unfolding rates caused by single amino acid substitutions at various positions within a given protein. Canonical Φ-values range between 0 and 1, and residues displaying high values within this range are interpreted to be important in stabilizing the transition state structure, and to elicit this stabilization through native-like interactions. Although very successful in defining the general features of transition state structures, Φ-value analysis can be confounded when non-native interactions stabilize this state. In addition, direct information on backbone conformation within the transition state is not provided. In the work described here, we have investigated structure formation at a conserved β-bulge (with helical conformation) in the Fyn SH3 domain by characterizing the effects of substituting all natural amino acids at one position within this structural motif. By comparing the effects on folding rates of these substitutions with database-derived local structure propensity values, we have determined that this position adopts a non-native backbone conformation in the folding transition state. This result is surprising because this position displays a high and canonical Φ-value of 0.7. This work emphasizes the potential role of non-native conformations in folding pathways and demonstrates that even positions displaying high and canonical Φ-values may, nevertheless, adopt a non-native conformation in the transition state. Copyright © 2012 Wiley Periodicals, Inc.

Structures of oncogenic, suppressor and rescued p53 core-domain variants: mechanisms of mutant p53 rescue

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

Wallentine, Brad D.; Wang, Ying; Tretyachenko-Ladokhina, Vira

2013-10-01

X-ray crystallographic structures of four p53 core-domain variants were determined in order to gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53. To gain insights into the mechanisms by which certain second-site suppressor mutations rescue the function of a significant number of cancer mutations of the tumor suppressor protein p53, X-ray crystallographic structures of four p53 core-domain variants were determined. These include an oncogenic mutant, V157F, two single-site suppressor mutants, N235K and N239Y, and the rescued cancer mutant V157F/N235K/N239Y. The V157F mutationmore » substitutes a smaller hydrophobic valine with a larger hydrophobic phenylalanine within strand S4 of the hydrophobic core. The structure of this cancer mutant shows no gross structural changes in the overall fold of the p53 core domain, only minor rearrangements of side chains within the hydrophobic core of the protein. Based on biochemical analysis, these small local perturbations induce instability in the protein, increasing the free energy by 3.6 kcal mol{sup −1} (15.1 kJ mol{sup −1}). Further biochemical evidence shows that each suppressor mutation, N235K or N239Y, acts individually to restore thermodynamic stability to V157F and that both together are more effective than either alone. All rescued mutants were found to have wild-type DNA-binding activity when assessed at a permissive temperature, thus pointing to thermodynamic stability as the critical underlying variable. Interestingly, thermodynamic analysis shows that while N239Y demonstrates stabilization of the wild-type p53 core domain, N235K does not. These observations suggest distinct structural mechanisms of rescue. A new salt bridge between Lys235 and Glu198, found in both the N235K and rescued cancer mutant structures, suggests a rescue mechanism that relies on stabilizing the β-sandwich scaffold. On the other hand, the substitution N239Y creates an advantageous hydrophobic contact between the aromatic ring of this tyrosine and the adjacent Leu137. Surprisingly, the rescued cancer mutant shows much larger structural deviations than the cancer mutant alone when compared with wild-type p53. These suppressor mutations appear to rescue p53 function by creating novel intradomain interactions that stabilize the core domain, allowing compensation for the destabilizing V157F mutation.« less

Longitudinal structure of MHD perturbations at the boundary of convective stability in the Kruskal-Oberman model

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

Arsenin, V. V.

2010-10-15

It is shown that, in contrast to the MHD model, a perturbation at the boundary of convective stability of a finite-pressure plasma in confinement systems without an averaged minB in the Kruskal-Oberman model is not generally a purely flute one. The reasons for this discrepancy are clarified. The analysis is carried out for axisymmetric configurations formed by a poloidal magnetic field.

Mutational Analysis of the Stability of the H2A and H2B Histone Monomers

PubMed Central

Stump, Matthew R.; Gloss, Lisa M.

2008-01-01

The eukaryotic histone heterodimer H2A-H2B folds through an obligatory dimeric intermediate that forms in a nearly diffusion-limited association reaction in the stopped-flow dead time. It is unclear whether there is partial folding of the isolated monomers before association. To address the possible contributions of structure in the monomers to the rapid association, we characterized H2A and H2B monomers in the absence of their heterodimeric partner. By far-UV circular dichroism, the H2A and H2B monomers are 15% and 31% helical, respectively—significantly less than observed in X-ray crystal structures. Acrylamide quenching of the intrinsic Tyr fluorescence was indicative of tertiary structure. The H2A and H2B monomers exhibit free energies of unfolding of 2.5 and 2.9 kcal mol−1, respectively; at 10 μM, the sum of the stability of the monomers is ~60% of the stability of the native dimer. The helical content, stability and m values indicate that H2B has a more stable, compact structure than H2A. The monomer m values are larger than expected for the extended histone fold motif, suggesting that the monomers adopt an overly-collapsed structure. Stopped-flow refolding—initiated from urea-denatured monomers or the partially folded monomers populated at low denaturant concentrations—yielded essentially identical rates, indicating that monomer folding is productive in the rapid association and folding of the heterodimer. A series of Ala and Gly mutations were introduced into H2A and H2B to probe the importance of helix propensity on the structure and stability of the monomers. The mutational studies show that the central α-helix of the histone fold, which makes extensive inter-monomer contacts, is structured in H2B but only partially folded in H2A. PMID:18976667

Analysis of Slab-column Shearwall Structure of 6000 Tons Cold Storage

NASA Astrophysics Data System (ADS)

He, Dongqing; Song, Pengwei; Jie, Pengyu

2018-05-01

Combining with the functional requirements, the site conditions and the 6000 tons load characteristics of cold storage, so determine its structure system for the slab-column-shear wall structure. The paper recommends the design of foundation, the settings of column cap, the arrangement of shear wall, the punching shear of floor slab and the analysis and calculation results of main structure. By addition shear wall in slab-column structure to increase the overall stiffness of structure and improve the seismic performance of structure. Take the detached form between the main structure and the external wall insulation, while set anchorage beam between in the main floor and the ring beam along the axis of the column grid to enhance the overall stability of the external wall insulation.

46 CFR 45.103 - Structural stress and stability.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 46 Shipping 2 2010-10-01 2010-10-01 false Structural stress and stability. 45.103 Section 45.103... Conditions of Assignment § 45.103 Structural stress and stability. (a) The nature and stowage of the cargo... structural stress. (b) The vessel must meet all applicable stability and subdivision requirements of this...

46 CFR 45.103 - Structural stress and stability.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 46 Shipping 2 2012-10-01 2012-10-01 false Structural stress and stability. 45.103 Section 45.103... Conditions of Assignment § 45.103 Structural stress and stability. (a) The nature and stowage of the cargo... structural stress. (b) The vessel must meet all applicable stability and subdivision requirements of this...

46 CFR 45.103 - Structural stress and stability.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 46 Shipping 2 2013-10-01 2013-10-01 false Structural stress and stability. 45.103 Section 45.103... Conditions of Assignment § 45.103 Structural stress and stability. (a) The nature and stowage of the cargo... structural stress. (b) The vessel must meet all applicable stability and subdivision requirements of this...

46 CFR 45.103 - Structural stress and stability.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 46 Shipping 2 2014-10-01 2014-10-01 false Structural stress and stability. 45.103 Section 45.103... Conditions of Assignment § 45.103 Structural stress and stability. (a) The nature and stowage of the cargo... structural stress. (b) The vessel must meet all applicable stability and subdivision requirements of this...

46 CFR 45.103 - Structural stress and stability.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 46 Shipping 2 2011-10-01 2011-10-01 false Structural stress and stability. 45.103 Section 45.103... Conditions of Assignment § 45.103 Structural stress and stability. (a) The nature and stowage of the cargo... structural stress. (b) The vessel must meet all applicable stability and subdivision requirements of this...

Role of the Disulfide Bond in Prion Protein Amyloid Formation: A Thermodynamic and Kinetic Analysis.

PubMed

Honda, Ryo

2018-02-27

Prion diseases are associated with the structural conversion of prion protein (PrP) to a β-sheet-rich aggregate, PrP Sc . Previous studies have indicated that a reduction of the disulfide bond linking C179 and C214 of PrP yields an amyloidlike β-rich aggregate in vitro. To gain mechanistic insights into the reduction-induced aggregation, here I characterized how disulfide bond reduction modulates the protein folding/misfolding landscape of PrP, by examining 1) the equilibrium stabilities of the native (N) and aggregated states relative to the unfolded (U) state, 2) the transition barrier separating the U and aggregated states, and 3) the final structure of amyloidlike misfolded aggregates. Kinetic and thermodynamic experiments revealed that disulfide bond reduction decreases the equilibrium stabilities of both the N and aggregated states by ∼3 kcal/mol, without changing either the amyloidlike aggregate structure, at least at the secondary structural level, or the transition barrier of aggregation. Therefore, disulfide bond reduction modulates the protein folding/misfolding landscape by entropically stabilizing disordered states, including the U and transition state of aggregation. This also indicates that the equilibrium stability of the N state, but not the transition barrier of aggregation, is the dominant factor determining the reduction-induced aggregation of PrP. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Inducible defenses in food webs: Chapter 3.4

USGS Publications Warehouse

Vos, Matthijs; Kooi, Bob W.; DeAngelis, Donald L.; Mooij, Wolf M.; de Ruiter, Peter; Wolters, Volkmar; Moore, John C.; Melville-Smith, Kimberly

2005-01-01

This chapter reviews the predicted effects of induced defenses on trophic structure and two aspects of stability, “local” stability and persistence, as well as presenting novel results on a third, resilience. Food webs are structures of populations in a given location organized according to their predator–prey interactions. Interaction strengths and, therefore, prey defenses are generally recognized as important ecological factors affecting food webs. Despite this, surprisingly, little light has been shed on the food web-level consequences of inducible defenses. Inducible defenses occur in many taxa in both terrestrial and aquatic food webs. They include refuge use, reduced activity, adaptive life history changes, the production of toxins, synomones and extrafloral nectar, and the formation of colonies, helmets, thorns, or spines. In the chapter, theoretical results for the effects of inducible defenses on trophic structure and the three aspects of stability are reviewed. This is done, in part, using bifurcation analysis—a type of analysis that is applied to nonlinear dynamic systems described by a set of ordinary differential or difference equations. The work presented in the chapter suggests that heterogeneity, as caused by induced defenses in prey species, has major effects on the functioning of food webs. Inducible defenses occur in many species in both aquatic and terrestrial systems, and theoretical work indicates they have major effects on important food web properties such as trophic structure, local stability, persistence, and resilience.

The HPr Proteins from the Thermophile Bacillus stearothermophilus Can Form Domain-swapped Dimers

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

Sridharan, Sudharsan; Razvi, Abbas; Scholtz, J. Martin

2010-07-20

The study of proteins from extremophilic organisms continues to generate interest in the field of protein folding because paradigms explaining the enhanced stability of these proteins still elude us and such studies have the potential to further our knowledge of the forces stabilizing proteins. We have undertaken such a study with our model protein HPr from a mesophile, Bacillus subtilis, and a thermophile, Bacillus stearothermophilus. We report here the high-resolution structures of the wild-type HPr protein from the thermophile and a variant, F29W. The variant proved to crystallize in two forms: a monomeric form with a structure very similar tomore » the wild-type protein as well as a domain-swapped dimer. Interestingly, the structure of the domain-swapped dimer for HPr is very different from that observed for a homologous protein, Crh, from B. subtilis. The existence of a domain-swapped dimer has implications for amyloid formation and is consistent with recent results showing that the HPr proteins can form amyloid fibrils. We also characterized the conformational stability of the thermophilic HPr proteins using thermal and solvent denaturation methods and have used the high-resolution structures in an attempt to explain the differences in stability between the different HPr proteins. Finally, we present a detailed analysis of the solution properties of the HPr proteins using a variety of biochemical and biophysical methods.« less

Aspects of the dimensional changes of jersey structures after knitting process

NASA Astrophysics Data System (ADS)

Szabo, M.; Barbu, I.; Jiaru, L.

2017-08-01

The study proposes a statistical analysis by applying a mathematical model for the study of the dimensional changes of jersey structures made of 100% cotton yarn, with 58/1 metric count of yarn. The Structures are presented as tubular knitted metrage and are designed for underwear and/or outer garments. By analysing the jersey structures, from dimensional stability point of view, there can be observed that values in the limits are within the ±2% interval, values which are considered appropriate. Following the experimental researches, there are proposed solutions for the reduction of dimensional changes on both directions of the knit, on the stich course direction and also on the stich courses in vertical direction, being analyzed the behaviour of the knitted fabrics during relaxation after knitting process. The problem of the dimensional stability of the knitted fabrics is extensive researched. The knitted structures are elastic structures, this being a reason for which dimensional stability will always be a topical theme. The jersey structures, due to the distribution of the platinum loop in the knit plane, due to the relative small number of yarn-yarn contact points that causes the threads to slide into the structure, due to the spiral of the tubular metrage structure, are among those whose dimensional stability is difficult to control. The technical characteristics of the yarns, the technical characteristics of the knitting machines and the technological parameters of the knitting machine are the elements which will be correlated in order to obtain structures with minimum dimensional changes. In order to obtain knitted structures with adequate dimensional stability, this means within ±2%, it is necessary that the dimensional changes during the relaxation periods after knitting and chemical finishing being minimum. For this, all the processes to be applied will be conducted with appropriate and uniform tensions throughout the technological flow. The relaxation periods of 72 hours should be strictly respected, folded and under standard atmospheric conditions, both after knitting and after chemical finishing. The jersey structures are plane structured made on knitting machines equiped with font. There will be analyzed the dimensional changes of the jersey structures made of 100% cotton yarn, Nm 58/1, after the relaxation after knitting process througout the corelation between the technical characteristics of the yarns, of the technological parameter of the knitting operation and of some technical characteristici of the knitting machine.

Rietveld analysis of the cubic crystal structure of Na-stabilized zirconia

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

Fagherazzi, G.; Canton, P.; Benedetti, A.

Using x-ray Rietveld analysis the fcc (fluorite-type) structure of a Na-containing nanocrystalline zirconia powder (9.5 nm estimated of crystallite size) obtained by precipitation and subsequent calcination has been confirmed. The result shows that using conventional x-ray diffraction techniques the cubic crystallographic form of ZrO{sub 2} from the tetragonal one in nanosized powders. These conclusions are supported by the findings of independent Raman scattering experiments. {copyright} {ital 1997 Materials Research Society.}

Structural Analysis Computer Programs for Rigid Multicomponent Pavement Structures with Discontinuities--WESLIQID and WESLAYER. Report 1. Program Development and Numerical Presentations.

DTIC Science & Technology

1981-05-01

represented as a Winkler foundation. The program can treat any number of slabs connected by steel bars or other load trans- fer devices at the joints...dimensional finite element method. The inherent flexibility of such an approach permits the analysis of a rigid pavement with steel bars and stabilized...layers and provides an efficient tool for analyzing stress conditions at the joint. Unfor- tunately, such a procedure would require a tremendously

Using operational and defined fractions to assess soil organic matter stabilization and structure

NASA Astrophysics Data System (ADS)

Horwath, W. R.

2015-12-01

Studies on soil organic matter (SOM) began with alkaline solvents revealing a dark colored substance that could be isolated under low pH. Further studies revealed fulvic and humic acids and humin fractions leading to theories on functional groups and metal-clay bridging mechanisms. The fate of isotopes in these fractions revealed soil carbon pools with varying turnover rates with half the soil carbon (C) in humin and acid hydrolyzed fractions over 1000 years old. These results are the basis of the three pool conceptual framework used in many biogeochemical models. Theories on the role of functional groups and compound classes further elaborated concepts on physical (aggregates) and chemical mechanisms of C stabilization. With the advance of analytical instrumentation, the operational fractions were further defined to the compound and molecular levels. These studies confirmed the majority of soil C is microbially derived. Our observation that all microbial groups contributed nonselectively to soil C maintenance independent of mineralogy suggests that compound characteristics within integrated structures are more important than the source of individual compounds for stabilizing soil C. In dissolved organic C floccing studies using Near Edge X-ray Fine Structure analysis, we found that aromatic compounds interacted first with Fe, however, the majority of direct bonds to Fe were polysaccharides, reinforcing that an integrative chemical structure rather than direct bonds imparted stability in organo-metal interactions. Using a novel differential scanning calorimeter coupled to an isotope ratio mass spectrometer setup, we confirmed that the presence of clays (independent of clay type) increased the microbial utilization of calcium stabilized high versus low temperature compounds, asserting that higher temperature compounds (i.e., phenolics) are likely less tightly bound by clay minerals. The integration of operational and defined fractions of SOM remains a legitimate approach to examine SOM structure and stabilization across scales of soil development and management.

High-Throughput Biophysical Analysis and Data Visualization of Conformational Stability of an IgG1 Monoclonal Antibody (mAb) After Deglycosylation

PubMed Central

Alsenaidy, Mohammad A.; Kim, Jae Hyun; Majumdar, Ranajoy; Weis, David D.; Joshi, Sangeeta B.; Tolbert, Thomas J.; Middaugh, C. Russell; Volkin, David B.

2013-01-01

The structural integrity and conformational stability of an IgG1 monoclonal antibody (mAb), after partial and complete enzymatic removal of the N-linked Fc glycan, was compared to the untreated mAb over a wide range of temperature (10° to 90°C) and solution pH (3 to 8) using circular dichroism, fluorescence spectroscopy, and static light scattering combined with data visualization employing empirical phase diagrams (EPDs). Subtle to larger stability differences between the different glycoforms were observed. Improved detection of physical stability differences was then demonstrated over narrower pH range (4.0-6.0) using smaller temperature increments, especially when combined with an alternative data visualization method (radar plots). Differential scanning calorimetry and differential scanning fluorimetry were then utilized and also showed an improved ability to detect differences in mAb glycoform physical stability. Based on these results, a two-step methodology was used in which mAb glycoform conformational stability is first screened with a wide variety of instruments and environmental stresses, followed by a second evaluation with optimally sensitive experimental conditions, analytical techniques and data visualization methods. With this approach, high-throughput biophysical analysis to assess relatively subtle conformational stability differences in protein glycoforms is demonstrated. PMID:24114789

Improving the Stability of Astaxanthin by Microencapsulation in Calcium Alginate Beads.

PubMed

Lin, Shen-Fu; Chen, Ying-Chen; Chen, Ray-Neng; Chen, Ling-Chun; Ho, Hsiu-O; Tsung, Yu-Han; Sheu, Ming-Thau; Liu, Der-Zen

2016-01-01

There has been considerable interest in the biological functions of astaxanthin and its potential applications in the nutraceutical, cosmetics, food, and feed industries in recent years. However, the unstable structure of astaxanthin considerably limits its application. Therefore, this study reports the encapsulation of astaxanthin in calcium alginate beads using the extrusion method to improve its stability. This study also evaluates the stability of the encapsulated astaxanthin under different storage conditions. The evaluation of astaxanthin stability under various environmental factors reveals that temperature is the most influential environmental factor in astaxanthin degradation. Stability analysis shows that, regardless of the formulation used, the content of astaxanthin encapsulated in alginate beads remains above 90% of the original amount after 21 days of storage at 25°C. These results suggest that the proposed technique is a promising way to enhance the stability of other sensitive compounds.

Improving the Stability of Astaxanthin by Microencapsulation in Calcium Alginate Beads

PubMed Central

Lin, Shen-Fu; Chen, Ying-Chen; Chen, Ray-Neng; Chen, Ling-Chun; Ho, Hsiu-O; Tsung, Yu-Han; Sheu, Ming-Thau; Liu, Der-Zen

2016-01-01

There has been considerable interest in the biological functions of astaxanthin and its potential applications in the nutraceutical, cosmetics, food, and feed industries in recent years. However, the unstable structure of astaxanthin considerably limits its application. Therefore, this study reports the encapsulation of astaxanthin in calcium alginate beads using the extrusion method to improve its stability. This study also evaluates the stability of the encapsulated astaxanthin under different storage conditions. The evaluation of astaxanthin stability under various environmental factors reveals that temperature is the most influential environmental factor in astaxanthin degradation. Stability analysis shows that, regardless of the formulation used, the content of astaxanthin encapsulated in alginate beads remains above 90% of the original amount after 21 days of storage at 25°C. These results suggest that the proposed technique is a promising way to enhance the stability of other sensitive compounds. PMID:27093175

Stability in Real Food Webs: Weak Links in Long Loops

NASA Astrophysics Data System (ADS)

Neutel, Anje-Margriet; Heesterbeek, Johan A. P.; de Ruiter, Peter C.

2002-05-01

Increasing evidence that the strengths of interactions among populations in biological communities form patterns that are crucial for system stability requires clarification of the precise form of these patterns, how they come about, and why they influence stability. We show that in real food webs, interaction strengths are organized in trophic loops in such a way that long loops contain relatively many weak links. We show and explain mathematically that this patterning enhances stability, because it reduces maximum ``loop weight'' and thus reduces the amount of intraspecific interaction needed for matrix stability. The patterns are brought about by biomass pyramids, a feature common to most ecosystems. Incorporation of biomass pyramids in 104 food-web descriptions reveals that the low weight of the long loops stabilizes complex food webs. Loop-weight analysis could be a useful tool for exploring the structure and organization of complex communities.

The Structural Formation and Physical Behaviour of Cross-Linked Epoxy Resins

DTIC Science & Technology

1981-04-01

analysis , at which the heat evolution reaches a maximum, may be used for purposes of characterisation. Aliphatic polyamines react mere quickly than the...DTA, DSC), thermomechanical analysis (TMA), torsional vibration analysis (TVA), deter- mination of the dimensional stability under heat (eq ISO R 75 or...obtained by thermomechanical analysis , taking the temperature of maximum velocity of penetration of a loaded probe (rate of heating - 10°C/min

An Evolutionarily Conserved Family of Virion Tail Needles Related to Bacteriophage P22 gp26: Correlation between Structural Stability and Length of the -Helical Trimeric Coiled Coil

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

Bhardwaj, A.; Walker-Kopp, N; Casjens, S

2009-01-01

Bacteriophages of the Podoviridae family use short noncontractile tails to inject their genetic material into Gram-negative bacteria. In phage P22, the tail contains a thin needle, encoded by the phage gene 26, which is essential both for stabilization and for ejection of the packaged viral genome. Bioinformatic analysis of the N-terminal domain of gp26 (residues 1-60) led us to identify a family of genes encoding putative homologues of the tail needle gp26. To validate this idea experimentally and to explore their diversity, we cloned the gp26-like gene from phages HK620, Sf6 and HS1, and characterized these gene products in solution.more » All gp26-like factors contain an elongated {alpha}-helical coiled-coil core consisting of repeating, adjacent trimerization heptads and form trimeric fibers with length ranging between about 240 to 300 {angstrom}. gp26 tail needles display a high level of structural stability in solution, with Tm (temperature of melting) between 85 and 95 C. To determine how the structural stability of these phage fibers correlates with the length of the {alpha}-helical core, we investigated the effect of insertions and deletions in the helical core. In the P22 tail needle, we identified an 85-residue-long helical domain, termed MiCRU (minimal coiled-coil repeat unit), that can be inserted in-frame inside the gp26 helical core, preserving the straight morphology of the fiber. Likewise, we were able to remove three quarters of the helical core of the HS1 tail needle, minimally decreasing the stability of the fiber. We conclude that in the gp26 family of tail needles, structural stability increases nonlinearly with the length of the {alpha}-helical core. Thus, the overall stability of these bacteriophage fibers is not solely dependent on the number of trimerization repeats in the {alpha}-helical core.« less

Advances and trends in structures and dynamics; Proceedings of the Symposium, Washington, DC, October 22-25, 1984

NASA Technical Reports Server (NTRS)

Noor, A. K. (Editor); Hayduk, R. J. (Editor)

1985-01-01

Among the topics discussed are developments in structural engineering hardware and software, computation for fracture mechanics, trends in numerical analysis and parallel algorithms, mechanics of materials, advances in finite element methods, composite materials and structures, determinations of random motion and dynamic response, optimization theory, automotive tire modeling methods and contact problems, the damping and control of aircraft structures, and advanced structural applications. Specific topics covered include structural design expert systems, the evaluation of finite element system architectures, systolic arrays for finite element analyses, nonlinear finite element computations, hierarchical boundary elements, adaptive substructuring techniques in elastoplastic finite element analyses, automatic tracking of crack propagation, a theory of rate-dependent plasticity, the torsional stability of nonlinear eccentric structures, a computation method for fluid-structure interaction, the seismic analysis of three-dimensional soil-structure interaction, a stress analysis for a composite sandwich panel, toughness criterion identification for unidirectional composite laminates, the modeling of submerged cable dynamics, and damping synthesis for flexible spacecraft structures.

Analysis of aggregate pier systems for stabilization of subgrade settlement.

DOT National Transportation Integrated Search

2014-12-01

Every year, ODOT undertakes numerous pavement patching/resurfacing projects to repair pavement : distress and structural failure due to soft and/or organic soils constituting the subgrade. Other than the : temporary solution of patching/resurfacing, ...

Ares-I Bending Filter Design using a Constrained Optimization Approach

NASA Technical Reports Server (NTRS)

Hall, Charles; Jang, Jiann-Woei; Hall, Robert; Bedrossian, Nazareth

2008-01-01

The Ares-I launch vehicle represents a challenging flex-body structural environment for control system design. Software filtering of the inertial sensor output is required to ensure adequate stable response to guidance commands while minimizing trajectory deviations. This paper presents a design methodology employing numerical optimization to develop the Ares-I bending filters. The design objectives include attitude tracking accuracy and robust stability with respect to rigid body dynamics, propellant slosh, and flex. Under the assumption that the Ares-I time-varying dynamics and control system can be frozen over a short period of time, the bending filters are designed to stabilize all the selected frozen-time launch control systems in the presence of parameter uncertainty. To ensure adequate response to guidance command, step response specifications are introduced as constraints in the optimization problem. Imposing these constrains minimizes performance degradation caused by the addition of the bending filters. The first stage bending filter design achieves stability by adding lag to the first structural frequency to phase stabilize the first flex mode while gain stabilizing the higher modes. The upper stage bending filter design gain stabilizes all the flex bending modes. The bending filter designs provided here have been demonstrated to provide stable first and second stage control systems in both Draper Ares Stability Analysis Tool (ASAT) and the MSFC MAVERIC 6DOF nonlinear time domain simulation.

A search for stability gradients in North American breeding bird communities

USGS Publications Warehouse

Noon, B.R.; Dawson, D.K.; Kelly, J.P.

1985-01-01

To search for the existence of stability gradients in North American breeding land bird communities we operationally defined stability (after Jarvinen 1979) as year-to-year persistence in species composition and distribution of species abundances. From the census data for 174 study plots we derived nine indices that estimate the annual variability of species composition, the species abundance distribution, diversity, and breeding density. The resulting matrix of study plot by stability indices was used to estimate the correlation structure of the stability indices. The correlation matrix was, in turn, subjected to a principal components analysis to derive synthetic gradients of variation. We then searched for patterns of variation in these stability gradients associated with either geographic location or habitat type. Three independent principal component axes reproduced most of the variation in the initial data and were interpreted as gradients of variation in species turnover, diversity, and breeding abundance. Thus, the annual stability of community structure apparently responds independently to species and abundance variation. Despite the clarity of the derived gradients, few patterns emerged when the plots were ordinated by either habitat or geographic location. In general, grasslands showed greater annual variation in diversity than forested habitats, and, for some habitats, northern communities were less stable than more southern communities. However, few of these patterns were very strong, and we interpret them cautiously.

Improved Stability of Tuberculosis Drug Fixed-Dose Combination Using Isoniazid-Caffeic Acid and Vanillic Acid Cocrystal.

PubMed

Battini, Swapna; Mannava, M K Chaitanya; Nangia, Ashwini

2018-06-01

The classic fixed-dose combination (FDC) of 4 tuberculosis drugs, namely rifampicin (RIF), isoniazid (INH), pyrazinamide (PZA), and ethambutol dihydrochloride (EDH) has the twin issues of physical stability and RIF cross-reaction in the 4-FDC. The major reason for these quality issues is the interaction between RIF and INH to yield isonicotinyl hydrazone in drug tablets. Pharmaceutical cocrystals of INH with caffeic acid (CFA) (PZA + EDH + RIF + INH-CFA cocrystal) and vanillic acid (VLA) (PZA + EDH + RIF + INH-VLA cocrystal) are able to stabilize the FDC formulation compared with the reference batch (PZA + EDH + RIF + INH). Stability studies under accelerated humidity and temperature stress conditions of 40°C and 75% relative humidity showed that the physical stability of the cocrystal formulation was superior by powder X-ray diffraction and scanning electron microscopy analysis, and chemical purity was analyzed by high-performance liquid chromatography. Changes in the composition and structure were monitored on samples drawn at 7, 15, 22, and 30 days of storage. FDC-INH-CFA cocrystal batch exhibited greater stability compared with FDC-INH-VLA cocrystal and FDC reference drug batches. The superior stability of INH-CFA cocrystal is attributed to the presence of stronger hydrogen bonds and cyclic O-H⋯O synthon in the crystal structure. Copyright © 2018 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.

Ares I Flight Control System Design

NASA Technical Reports Server (NTRS)

Jang, Jiann-Woei; Alaniz, Abran; Hall, Robert; Bedrossian, Nazareth; Hall, Charles; Ryan, Stephen; Jackson, Mark

2010-01-01

The Ares I launch vehicle represents a challenging flex-body structural environment for flight control system design. This paper presents a design methodology for employing numerical optimization to develop the Ares I flight control system. The design objectives include attitude tracking accuracy and robust stability with respect to rigid body dynamics, propellant slosh, and flex. Under the assumption that the Ares I time-varying dynamics and control system can be frozen over a short period of time, the flight controllers are designed to stabilize all selected frozen-time launch control systems in the presence of parametric uncertainty. Flex filters in the flight control system are designed to minimize the flex components in the error signals before they are sent to the attitude controller. To ensure adequate response to guidance command, step response specifications are introduced as constraints in the optimization problem. Imposing these constraints minimizes performance degradation caused by the addition of the flex filters. The first stage bending filter design achieves stability by adding lag to the first structural frequency to phase stabilize the first flex mode while gain stabilizing the higher modes. The upper stage bending filter design gain stabilizes all the flex bending modes. The flight control system designs provided here have been demonstrated to provide stable first and second stage control systems in both Draper Ares Stability Analysis Tool (ASAT) and the MSFC 6DOF nonlinear time domain simulation.

The effect of radiation on the thermal properties of chitosan/mimosa tenuiflora and chitosan/mimosa tenuiflora/multiwalled carbon nanotubes (MWCNT) composites for bone tissue engineering

NASA Astrophysics Data System (ADS)

Martel-Estrada, S. A.; Santos-Rodríguez, E.; Olivas-Armendáriz, I.; Cruz-Zaragoza, E.; Martínez-Pérez, C. A.

2014-07-01

The purpose of this study is to examine the effect of gamma radiation and UV radiation on the microstructure, chemical structure and thermal stability of Chitosan/Mimosa Tenuiflora and Chitosan/Mimosa Tenuiflora/MWCNT composites scaffolds produced by thermally induced phase separation. The composites were irradiated and observed to undergo radiation-induced degradation through chain scission. Morphology, thermal properties and effects on chemical and semi-crystalline structures were obtained by scanning electronic microscopy (SEM), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), FT-IR analysis and X-ray Diffraction. A relationship between radiation type and the thermal stability of the composites, were also established. This relationship allows a more accurate and precise control of the life span of Chitosan/Mimosa Tenuiflora and Chitosan/Mimosa Tenuiflora/MWCNT composites through the use of radiation in materials for use in tissue engineering.

Immobilization Effect of Morphological, Thermal and Optical Properties in Biotemplate on Zinc Oxide Nanocomposite from Chitosan

NASA Astrophysics Data System (ADS)

Karpuraranjith, M.; Thambidurai, S.

Biotemplate-based zinc oxide nanocomposite was effectively prepared via simple chemical precipitation route. The functional groups of amino (-NH2), hydroxyl (-OH) and O-Zn-O were confirmed and characterized by FTIR spectroscopy. The structural and morphological properties were confirmed by XRD, UV-Vis DRS, HR-SEM and TEM analyses. The elemental composition of carbon, nitrogen, zinc and oxygen was confirmed by energy-dispersive X-ray analysis (EDAX) and Brunauer-Emmett-Teller high surface area of materials was estimated to be 52.49m2/g, respectively. Thermogravimetric analysis (TGA) shows that biotemplate on zinc oxide nanocomposite has higher thermal stability than chitosan matrix. The results demonstrate that biotemplate on zinc oxide matrix causes immobilization effect among the two components. Therefore, chitosan-ZnO nanocomposite has a microcrystalline morphological structure and also good thermal stability, so it can be a promising material for sensors, medical, tissue engineering and wastewater treatment applications.

Optical properties of boron-group (V) hexagonal nanowires: DFT investigation

NASA Astrophysics Data System (ADS)

Santhibhushan, B.; Soni, Mahesh; Srivastava, Anurag

2017-07-01

The paper presents structural, electronic and optical properties of boron-group V hexagonal nanowires (h-NW) within the framework of density functional theory. The h-NW of boron-group V compounds with an analogous diameter of 12 Å have been designed in (1 1 1) plane. Stability analysis performed through formation energies reveal that, the stability of these structures decreases with increasing atomic number of the group V element. The band nature predicts that these nanowires are good electrical conductors. Optical behaviour of the nanowires has been analysed through absorption coefficient, reflectivity, refractive index, optical conductivity and electron energy loss spectrum (EELS), that are computed from the frequency-dependent complex dielectric function. The analysis reveals high reactivity of BP and BAs h-NWs to the incident light especially in the IR and visible ranges, and the optical transparency of BN h-NW in the visible and UV ranges.

Stabilization Effect of Amino Acid Side Chains in Peptide Assemblies on Graphite Studied by Scanning Tunneling Microscopy.

PubMed

Guo, Yuanyuan; Hou, Jingfei; Zhang, Xuemei; Yang, Yanlian; Wang, Chen

2017-04-19

An analysis is presented of the effects of amino acid side chains on peptide assemblies in ambient conditions on a graphite surface. The molecularly resolved assemblies of binary peptides are examined with scanning tunneling microscopy. A comparative analysis of the assembly structures reveals that the lamellae width has an appreciable dependence on the peptide sequence, which could be considered as a manifestation of a stabilizing effect of side-chain moieties of amino acids with high (phenylalanine) and low (alanine, asparagine, histidine and aspartic acid) propensities for aggregation. These amino acids are representative for the chemical structures involving the side chains of charged (histidine and aspartic acid), aromatic (phenylalanine), hydrophobic (alanine), and hydrophilic (asparagine) amino acids. These results might provide useful insight for understanding the effects of sequence on the assembly of surface-bound peptides. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimal Variable-Structure Control Tracking of Spacecraft Maneuvers

NASA Technical Reports Server (NTRS)

Crassidis, John L.; Vadali, Srinivas R.; Markley, F. Landis

1999-01-01

An optimal control approach using variable-structure (sliding-mode) tracking for large angle spacecraft maneuvers is presented. The approach expands upon a previously derived regulation result using a quaternion parameterization for the kinematic equations of motion. This parameterization is used since it is free of singularities. The main contribution of this paper is the utilization of a simple term in the control law that produces a maneuver to the reference attitude trajectory in the shortest distance. Also, a multiplicative error quaternion between the desired and actual attitude is used to derive the control law. Sliding-mode switching surfaces are derived using an optimal-control analysis. Control laws are given using either external torque commands or reaction wheel commands. Global asymptotic stability is shown for both cases using a Lyapunov analysis. Simulation results are shown which use the new control strategy to stabilize the motion of the Microwave Anisotropy Probe spacecraft.

The importance of mRNA structure in determining the pathogenicity of synonymous and non-synonymous mutations in haemophilia

PubMed Central

Hamasaki-Katagiri, Nobuko; Lin, Brian C.; Simon, Jonathan; Hunt, Ryan C.; Schiller, Tal; Russek-Cohen, Estelle; Komar, Anton A.; Bar, Haim; Kimchi-Sarfaty, Chava

2016-01-01

Introduction Mutational analysis is commonly used to support the diagnosis and management of haemophilia. This has allowed for the generation of large mutation databases which provide unparalleled insight into genotype-phenotype relationships. Haemophilia is associated with inversions, deletions, insertions, nonsense and missense mutations. Both synonymous and non-synonymous mutations influence the base pairing of messenger RNA (mRNA), which can alter mRNA structure, cellular half-life and ribosome processivity/elongation. However, the role of mRNA structure in determining the pathogenicity of point mutations in haemophilia has not been evaluated. Aim To evaluate mRNA thermodynamic stability and associated RNA prediction software as a means to distinguish between neutral and disease-associated mutations in haemophilia. Methods Five mRNA structure prediction software programs were used to assess the thermodynamic stability of mRNA fragments carrying neutral vs. disease-associated and synonymous vs. non-synonymous point mutations in F8, F9 and a third X-linked gene, DMD (dystrophin). Results In F8 and DMD, disease-associated mutations tend to occur in more structurally stable mRNA regions, represented by lower MFE (minimum free energy) levels. In comparing multiple software packages for mRNA structure prediction, a 101–151 nucleotide fragment length appears to be a feasible range for structuring future studies. Conclusion mRNA thermodynamic stability is one predictive characteristic, which when combined with other RNA and protein features, may offer significant insight when screening sequencing data for novel disease-associated mutations. Our results also suggest potential utility in evaluating the mRNA thermodynamic stability profile of a gene when determining the viability of interchanging codons for biological and therapeutic applications. PMID:27933712

Exploring protein interiors: the role of a buried histidine in the KH module fold.

PubMed

Fraternali, F; Amodeo, P; Musco, G; Nilges, M; Pastore, A

1999-03-01

The K-homology (KH) module is a novel RNA-binding motif. The structures of a representative KH motif from vigilin (vig-KH6) and of the first KH domain of fmr1 have been recently solved by nuclear magnetic resonance (NMR) and automated assignment-refinement techniques (ARIA). While a hydrophobic residue is found at position 21 in most of the KH modules, a buried His is conserved in all the 15 KH repeats of vigilin. This position must therefore have a key structural role in stabilizing the hydrophobic core. In the present work, we have addressed the following questions in order to obtain a detailed description of the role of His 21: i) what is the exact role of the histidine in the hydrophobic core of vig-KH6? ii) can we define the interactions that allow a conserved buried position to be occupied by a histidine both in vig-KH6 and in the whole vigilin KH sub-family? iii) how is the structure and stability of vig-KH6 influenced by the state of protonation of this histidine? To answer these questions, we have carried out an extensive refinement of the vig-KH6 structure using both an improved ARIA protocol starting from different initial structures and successively running restrained and unrestrained trajectories in water. An analysis of the stability of secondary structural elements, solvent accessibility, and hydrogen bonding patterns allows hypothesis on the structural role of residue His 21 and on the interactions that this residue forms with the environment. The importance of the protonation state of His 21 on the stability of the KH fold was addressed and validated by experimental results.

Variable Structure Control of a Hand-Launched Glider

NASA Technical Reports Server (NTRS)

Anderson, Mark R.; Waszak, Martin R.

2005-01-01

Variable structure control system design methods are applied to the problem of aircraft spin recovery. A variable structure control law typically has two phases of operation. The reaching mode phase uses a nonlinear relay control strategy to drive the system trajectory to a pre-defined switching surface within the motion state space. The sliding mode phase involves motion along the surface as the system moves toward an equilibrium or critical point. Analysis results presented in this paper reveal that the conventional method for spin recovery can be interpreted as a variable structure controller with a switching surface defined at zero yaw rate. Application of Lyapunov stability methods show that deflecting the ailerons in the direction of the spin helps to insure that this switching surface is stable. Flight test results, obtained using an instrumented hand-launched glider, are used to verify stability of the reaching mode dynamics.

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

NASA Astrophysics Data System (ADS)

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; Yang, Jun; Han, Gye Won; Zhao, Suwen; Ishchenko, Andrii; Ye, Lintao; Lin, Xi; Ding, Kang; Dharmarajan, Venkatasubramanian; Griffin, Patrick R.; Gati, Cornelius; Nelson, Garrett; Hunter, Mark S.; Hanson, Michael A.; Cherezov, Vadim; Stevens, Raymond C.; Tan, Wenfu; Tao, Houchao; Xu, Fei

2017-05-01

The Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combining the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.

Dynamic of Change in Pathological Personality Trait Dimensions: A Latent Change Analysis Among at-Risk Women

PubMed Central

Barbot, Baptiste; Hunter, Scott R.; Grigorenko, Elena L.; Luthar, Suniya S.

2012-01-01

This study explores longitudinally a four-factor structure of pathological personality trait dimensions (PPTDs) to examine both its structural stability and intra-individual changes among PPTDs over time. Personality Disorder (PD) scales of the Millon Clinical Multiaxial Inventory-III were administered to 361 low-income women with various psychiatric conditions (drug dependence, depression), who were followed in a two-wave study over 5-years. Cross-sectional and longitudinal factor analyses outlined a robust factorial structure of PPTDs, extrinsically invariant over time, representing Negative Emotionality, Introversion, Antagonism and Impulsivity. Despite moderate rank-order stability in the PPTDs, results also indicated substantial intra-individual variability in the degree and direction of change, consistent with trajectories of change in participants’ clinical diagnoses. Results are discussed in light of current debates on the structure and dynamic of pathological personality. PMID:23710108

Pathways towards instability in financial networks

NASA Astrophysics Data System (ADS)

Bardoscia, Marco; Battiston, Stefano; Caccioli, Fabio; Caldarelli, Guido

2017-02-01

Following the financial crisis of 2007-2008, a deep analogy between the origins of instability in financial systems and complex ecosystems has been pointed out: in both cases, topological features of network structures influence how easily distress can spread within the system. However, in financial network models, the details of how financial institutions interact typically play a decisive role, and a general understanding of precisely how network topology creates instability remains lacking. Here we show how processes that are widely believed to stabilize the financial system, that is, market integration and diversification, can actually drive it towards instability, as they contribute to create cyclical structures which tend to amplify financial distress, thereby undermining systemic stability and making large crises more likely. This result holds irrespective of the details of how institutions interact, showing that policy-relevant analysis of the factors affecting financial stability can be carried out while abstracting away from such details.

Pathways towards instability in financial networks

PubMed Central

Bardoscia, Marco; Battiston, Stefano; Caccioli, Fabio; Caldarelli, Guido

2017-01-01

Following the financial crisis of 2007–2008, a deep analogy between the origins of instability in financial systems and complex ecosystems has been pointed out: in both cases, topological features of network structures influence how easily distress can spread within the system. However, in financial network models, the details of how financial institutions interact typically play a decisive role, and a general understanding of precisely how network topology creates instability remains lacking. Here we show how processes that are widely believed to stabilize the financial system, that is, market integration and diversification, can actually drive it towards instability, as they contribute to create cyclical structures which tend to amplify financial distress, thereby undermining systemic stability and making large crises more likely. This result holds irrespective of the details of how institutions interact, showing that policy-relevant analysis of the factors affecting financial stability can be carried out while abstracting away from such details. PMID:28221338

Control design for robust stability in linear regulators: Application to aerospace flight control

NASA Technical Reports Server (NTRS)

Yedavalli, R. K.

1986-01-01

Time domain stability robustness analysis and design for linear multivariable uncertain systems with bounded uncertainties is the central theme of the research. After reviewing the recently developed upper bounds on the linear elemental (structured), time varying perturbation of an asymptotically stable linear time invariant regulator, it is shown that it is possible to further improve these bounds by employing state transformations. Then introducing a quantitative measure called the stability robustness index, a state feedback conrol design algorithm is presented for a general linear regulator problem and then specialized to the case of modal systems as well as matched systems. The extension of the algorithm to stochastic systems with Kalman filter as the state estimator is presented. Finally an algorithm for robust dynamic compensator design is presented using Parameter Optimization (PO) procedure. Applications in a aircraft control and flexible structure control are presented along with a comparison with other existing methods.

Pathways towards instability in financial networks.

PubMed

Bardoscia, Marco; Battiston, Stefano; Caccioli, Fabio; Caldarelli, Guido

2017-02-21

Following the financial crisis of 2007-2008, a deep analogy between the origins of instability in financial systems and complex ecosystems has been pointed out: in both cases, topological features of network structures influence how easily distress can spread within the system. However, in financial network models, the details of how financial institutions interact typically play a decisive role, and a general understanding of precisely how network topology creates instability remains lacking. Here we show how processes that are widely believed to stabilize the financial system, that is, market integration and diversification, can actually drive it towards instability, as they contribute to create cyclical structures which tend to amplify financial distress, thereby undermining systemic stability and making large crises more likely. This result holds irrespective of the details of how institutions interact, showing that policy-relevant analysis of the factors affecting financial stability can be carried out while abstracting away from such details.

Impact of roots, mycorrhizas and earthworms on soil physical properties as assessed by shrinkage analysis

NASA Astrophysics Data System (ADS)

Milleret, R.; Le Bayon, R.-C.; Lamy, F.; Gobat, J.-M.; Boivin, P.

2009-07-01

SummarySoil biota such as earthworms, arbuscular mycorrhizal fungi (AMF) and plant roots are known to play a major role in engineering the belowground part of the terrestrial ecosystems, thus strongly influencing the water budget and quality on earth. However, the effect of soil organisms and their interactions on the numerous soil physical properties to be considered are still poorly understood. Shrinkage analysis allows quantifying a large spectrum of soil properties in a single experiment, with small standard errors. The objectives of the present study were, therefore, to assess the ability of the method to quantify changes in soil properties as induced by single or combined effects of leek roots ( Allium porrum), AMF ( Glomus intraradices) and earthworms ( Allolobophora chlorotica). The study was performed on homogenised soil microcosms and the experiments lasted 35 weeks. The volume of the root network and the external fungal hyphae was measured at the end, and undisturbed soil cores were collected. Shrinkage analysis allowed calculating the changes in soil hydro-structural stability, soil plasma and structural pore volumes, soil bulk density and plant available water, and structural pore size distributions. Data analysis revealed different impacts of the experimented soil biota on the soil physical properties. At any water content, the presence of A. chlorotica resulted in a decrease of the specific bulk volume and the hydro-structural stability around 25%, and in a significant increase in the bulk soil density. These changes went with a decrease of the structural pore volumes at any pore size, a disappearing of the thinnest structural pores, a decrease in plant available water, and a hardening of the plasma. On the contrary, leek roots decreased the bulk soil density up to 1.23 g cm -3 despite an initial bulk density of 1.15 g cm -3. This increase in volume was accompanied with a enhanced hydro-structural stability, a larger structural pore volume at any pore size, smaller structural pore radii and an increase in plant available water. Interestingly, a synergistic effect of leek roots and AMF in the absence of the earthworms was highlighted, and this synergistic effect was not observed in presence of earthworms. The structural pore volume generated by root and AMF growth was several orders of magnitude larger than the volume of the organisms. Root exudates as well as other AMF secretion have served as carbon source for bacteria that in turn would enhance soil aggregation and porosity, thus supporting the idea of a self-organization of the soil-plant-microbe complex previously described.

Effect of palladium doping on the stability and fragmentation patterns of cationic gold clusters

NASA Astrophysics Data System (ADS)

Ferrari, P.; Hussein, H. A.; Heard, C. J.; Vanbuel, J.; Johnston, R. L.; Lievens, P.; Janssens, E.

2018-05-01

We analyze in detail how the interplay between electronic structure and cluster geometry determines the stability and the fragmentation channels of single Pd-doped cationic Au clusters, PdA uN-1+ (N =2 -20 ). For this purpose, a combination of photofragmentation experiments and density functional theory calculations was employed. A remarkable agreement between the experiment and the calculations is obtained. Pd doping is found to modify the structure of the Au clusters, in particular altering the two-dimensional to three-dimensional transition size, with direct consequences on the stability of the clusters. Analysis of the electronic density of states of the clusters shows that depending on cluster size, Pd delocalizes one 4 d electron, giving an enhanced stability to PdA u6 + , or remains with all 4 d10 electrons localized, closing an electronic shell in PdA u9 + . Furthermore, it is observed that for most clusters, Au evaporation is the lowest-energy decay channel, although for some sizes Pd evaporation competes. In particular, PdA u7 + and PdA u9 + decay by Pd evaporation due to the high stability of the A u7 + and A u9 + fragmentation products.

The structure of non-hierarchical triple system stability regions

NASA Astrophysics Data System (ADS)

Martynova, A. I.; Orlov, V. V.; Rubinov, A. V.

2009-08-01

A detailed study of the two-dimensional initial conditions region section in the planar three-body problem is performed. The initial conditions for the three well-known stable periodic orbits (the Schubart’s orbit, the Broucke’s orbit and the eight-like orbit) belong to this section. Continuous stability regions (for the fixed integration interval) generated by these periodic orbits are found. Zones of the quick stability violation are outlined. The analysis of some concrete trajectories coming from various stability regions is performed. In particular, trajectories possessing varying number of “eights” formed by moving triple system components are discovered. Orbits with librations are also found. The new periodic orbit originated from the zone siding with the Schubart’s orbit region is discovered. This orbit has reversibility points (each of the outer bodies possess a reversibility point) and two points of close double approach of the central body to each of the outer bodies. The influence of the numerical integration accuracy on the results is studied. The stability regions structure is preserved during calculations with different values of the precision parameter, numerical integration methods and regularization algorithms of the equations of motion.

Quantitative percussion diagnostics as an indicator of the level of the structural pathology of teeth: Retrospective follow-up investigation of high-risk sites that remained pathological after restorative treatment.

PubMed

Sheets, Cherilyn G; Wu, Jean C; Earthman, James C

2017-11-29

Structural damage may remain even after a tooth is restored. Conventional diagnostic aids do not quantify the severity of structural damage or allow the monitoring of structural changes after restoration. The purpose of this retrospective clinical study was to provide an in-depth analysis of 9 high-risk sites after restoration. The analysis followed structural defects found upon disassembly, restorative materials used, therapeutic procedures provided, current longevity, and long-term quantitative percussion diagnostics (QPD) to monitor results. The hypothesis was that QPD can be used to quantify positive and negative changes in structural stability. Sixty sites requiring restoration were part of an institutional review board-approved clinical study. Each participant was examined comprehensively, including QPD testing, at each follow-up. Long-term changes in normal fit error (NFE) values after restoration were evaluated according to a pathology rating system established in an earlier publication. Nine highly compromised sites were chosen for further analysis and monitored for an additional 6 years. Of the 9 high-risk sites (NFE>0.04), 7 sites improved and 2 sites deteriorated. Potential causes for each trend were documented. The data support the hypothesis that QPD can be used to monitor changes in structural stability after restoration. Knowledge of changes in advance of any symptoms allows further preventive or therapeutic intervention before serious structural damage can occur. Follow-up QPD indications of site improvement can also assure the clinician of the desired structural outcome. Copyright © 2017 Editorial Council for the Journal of Prosthetic Dentistry. Published by Elsevier Inc. All rights reserved.

Light scattering methods to test inorganic PCMs for application in buildings

NASA Astrophysics Data System (ADS)

De Paola, M. G.; Calabrò, V.; De Simone, M.

2017-10-01

Thermal performance and stability over time are key parameters for the characterization and application of PCMs in the building sector. Generally, inorganic PCMs are dispersions of hydrated salts and additives in water that counteract phase segregation phenomena and subcooling. Traditional methods or in “house” methods can be used for evaluating thermal properties, while stability can be estimated over time by using optical techniques. By considering this double approach, in this work thermal and structural analyses of Glauber salt based composite PCMs are conducted by means of non-conventional equipment: T-history method (thermal analysis) and Turbiscan (stability analysis). Three samples with the same composition (Glauber salt with additives) were prepared by using different sonication times and their thermal performances were compared by testing both the thermal cycling and the thermal properties. The stability of the mixtures was verified by the identification of destabilization phenomena, the evaluation of the migration velocities of particles and the estimation of variation of particle size.

Thermoelectric properties and thermal stability of layered chalcogenides, TlScQ2, Q = Se, Te.

PubMed

Aswathy, Vijayakumar Sajitha; Sankar, Cheriyedath Raj; Varma, Manoj Raama; Assoud, Abdeljalil; Bieringer, Mario; Kleinke, Holger

2017-12-12

A few thallium based layered chalcogenides of α-NaFeO 2 structure-type are known for their excellent thermoelectric properties and interesting topological insulator nature. TlScQ 2 belongs to this structural category. In the present work, we have studied the electronic structure, electrical and thermal transport properties and thermal stability of the title compounds within the temperature range 2-600 K. Density functional theory (DFT) predicts a metallic nature for TlScTe 2 and a semiconducting nature for TlScSe 2 . DFT calculations also show significant lowering of energies of frontier bands upon inclusion of spin-orbit coupling contribution in the calculation. The electronic structure also shows the simultaneous occurrence of holes and electron pockets for the telluride. Experiments reveal that the telluride shows a semi-metallic behaviour whereas the selenide is a semiconductor. The thermoelectric properties for both the materials were also investigated. Both these materials possess very low thermal conductivity which is an attractive feature for thermoelectrics. However, they lack thermal stability and decompose upon warming above room temperature, as evidenced from high temperature powder X-ray diffraction and thermal analysis.

Density-functional theory study of the geometries, stabilities, and electronic properties of Au n Rb (n = 1-10) clusters: comparison with pure gold clusters

NASA Astrophysics Data System (ADS)

Hu, Yan-Fei; Jiang, Gang; Meng, Da-Qiao

2012-01-01

The density functional method with the relativistic effective core potential has been employed to investigate systematically the geometric structures, relative stabilities, growth-pattern behavior, and electronic properties of small bimetallic Au n Rb (n = 1-10) and pure gold Au n (n ≤ 11) clusters. For the geometric structures of the Au n Rb (n = 1-10) clusters, the dominant growth pattern is for a Rb-substituted Au n +1 cluster or one Au atom capped on a Au n -1Rb cluster, and the turnover point from a two-dimensional to a three-dimensional structure occurs at n = 4. Moreover, the stability of the ground-state structures of these clusters has been examined via an analysis of the average atomic binding energies, fragmentation energies, and the second-order difference of energies as a function of cluster size. The results exhibit a pronounced even-odd alternation phenomenon. The same pronounced even-odd alternations are found for the HOMO-LUMO gap, VIPs, VEAs, and the chemical hardness. In addition, about one electron charge transfers from the Au n host to the Rb atom in each corresponding Au n Rb cluster.

Physical stability comparisons of IgG1-Fc variants: effects of N-glycosylation site occupancy and Asp/Gln residues at site Asn 297.

PubMed

Alsenaidy, Mohammad A; Okbazghi, Solomon Z; Kim, Jae Hyun; Joshi, Sangeeta B; Middaugh, C Russell; Tolbert, Thomas J; Volkin, David B

2014-06-01

The structural integrity and conformational stability of various IgG1-Fc proteins produced from the yeast Pichia pastoris with different glycosylation site occupancy (di-, mono-, and nonglycosylated) were determined. In addition, the physical stability profiles of three different forms of nonglycosylated Fc molecules (varying amino-acid residues at site 297 in the CH 2 domain due to the point mutations and enzymatic digestion of the Fc glycoforms) were also examined. The physical stability of these IgG1-Fc glycoproteins was examined as a function of pH and temperature by high-throughput biophysical analysis using multiple techniques combined with data visualization tools (three index empirical phase diagrams and radar charts). Across the pH range of 4.0-6.0, the di- and monoglycosylated forms of the IgG1-Fc showed the highest and lowest levels of physical stability, respectively, with the nonglycosylated forms showing intermediate stability depending on solution pH. In the aglycosylated Fc proteins, the introduction of Asp (D) residues at site 297 (QQ vs. DN vs. DD forms) resulted in more subtle changes in structural integrity and physical stability depending on solution pH. The utility of evaluating the conformational stability profile differences between the various IgG1-Fc glycoproteins is discussed in the context of analytical comparability studies. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

An input-to-state stability approach to verify almost global stability of a synchronous-machine-infinite-bus system.

PubMed

Schiffer, Johannes; Efimov, Denis; Ortega, Romeo; Barabanov, Nikita

2017-08-13

Conditions for almost global stability of an operating point of a realistic model of a synchronous generator with constant field current connected to an infinite bus are derived. The analysis is conducted by employing the recently proposed concept of input-to-state stability (ISS)-Leonov functions, which is an extension of the powerful cell structure principle developed by Leonov and Noldus to the ISS framework. Compared with the original ideas of Leonov and Noldus, the ISS-Leonov approach has the advantage of providing additional robustness guarantees. The efficiency of the derived sufficient conditions is illustrated via numerical experiments.This article is part of the themed issue 'Energy management: flexibility, risk and optimization'. © 2017 The Author(s).

Computer-aided molecular modeling techniques for predicting the stability of drug cyclodextrin inclusion complexes in aqueous solutions

NASA Astrophysics Data System (ADS)

Faucci, Maria Teresa; Melani, Fabrizio; Mura, Paola

2002-06-01

Molecular modeling was used to investigate factors influencing complex formation between cyclodextrins and guest molecules and predict their stability through a theoretical model based on the search for a correlation between experimental stability constants ( Ks) and some theoretical parameters describing complexation (docking energy, host-guest contact surfaces, intermolecular interaction fields) calculated from complex structures at a minimum conformational energy, obtained through stochastic methods based on molecular dynamic simulations. Naproxen, ibuprofen, ketoprofen and ibuproxam were used as model drug molecules. Multiple Regression Analysis allowed identification of the significant factors for the complex stability. A mathematical model ( r=0.897) related log Ks with complex docking energy and lipophilic molecular fields of cyclodextrin and drug.

Influence of heating procedures on the surface structure of stabilized polyacrylonitrile fibers

NASA Astrophysics Data System (ADS)

Zhao, Rui-Xue; Sun, Peng-fei; Liu, Rui-jian; Ding, Zhan-hui; Li, Xiang-shan; Liu, Xiao-yang; Zhao, Xu-dong; Gao, Zhong-min

2018-03-01

The stabilized polyacrylonitrile (PAN) fibers were obtained after heating the precursor PAN fibers under air atmosphere by different procedures. The surface structures and compositions of as-prepared stabilized PAN fibers have been investigated by SEM, SSNMR, XPS and Raman spectroscopy. The results show that 200 °C, 220 °C, 250 °C, and 280 °C are key temperatures for the preparation of stabilized PAN fibers. The effect of heating gradient on the structure of stabilized PAN fibers has been studied. The possible chemical structural formulas for the PAN fibers is provided, which include the stable and unstable structure. The stable structure (α-type) could endure the strong chemical reactions and the unstable structure (β- or γ-type) could mitigate the drastic oxidation reactions. The inferences of chemical formula of stabilized PAN fibers are benefit to the design of appropriate surface structure for the production for high quality carbon fibers.

Calibrating damping rates with LEGACY linewidths

NASA Astrophysics Data System (ADS)

Houdek, Günter

2017-10-01

Linear damping rates of radial oscillation modes in selected Kepler stars are estimated with the help of a nonadiabatic stability analysis. The convective fluxes are obtained from a nonlocal, time-dependent convection model. The mixing-length parameter is calibrated to the surface-convection-zone depth of a stellar model obtained from fitting adiabatic frequencies to the LEGACY* observations, and two of the three nonlocal convection parameters are calibrated to the corresponding LEGACY* linewidth measurements. The atmospheric structure in the 1D stability analysis adopts a temperature-optical-depth relation derived from 3D hydrodynamical simulations. Results from 3D simulations are also used to calibrate the turbulent pressure and to guide the functional form of the depth-dependence of the anisotropy of the turbulent velocity field in the 1D stability computations.

Structured population dynamics: continuous size and discontinuous stage structures.

PubMed

Buffoni, Giuseppe; Pasquali, Sara

2007-04-01

A nonlinear stochastic model for the dynamics of a population with either a continuous size structure or a discontinuous stage structure is formulated in the Eulerian formalism. It takes into account dispersion effects due to stochastic variability of the development process of the individuals. The discrete equations of the numerical approximation are derived, and an analysis of the existence and stability of the equilibrium states is performed. An application to a copepod population is illustrated; numerical results of Eulerian and Lagrangian models are compared.

Self-assembly of Zn(salphen) complexes: steric regulation, stability studies and crystallographic analysis revealing an unexpected dimeric 3,3'-t-Bu-substituted Zn(salphen) complex.

PubMed

Martínez Belmonte, Marta; Wezenberg, Sander J; Haak, Robert M; Anselmo, Daniele; Escudero-Adán, Eduardo C; Benet-Buchholz, Jordi; Kleij, Arjan W

2010-05-21

The self-assembly features of a series of (non)symmetrical Zn(salphen) complexes have been studied in detail by X-ray crystallography, NMR and UV-vis techniques. The combined data demonstrate that the stability of these dimeric assemblies and the relative position of each monomeric unit within the dinuclear structure depend on the location and combination of the aromatic ring substituents.

A compilation and analysis of helicopter handling qualities data. Volume 2: Data analysis

NASA Technical Reports Server (NTRS)

Heffley, R. K.

1979-01-01

A compilation and an analysis of helicopter handling qualities data are presented. Multiloop manual control methods are used to analyze the descriptive data, stability derivatives, and transfer functions for a six degrees of freedom, quasi static model. A compensatory loop structure is applied to coupled longitudinal, lateral and directional equations in such a way that key handling qualities features are examined directly.

Psychometric properties and norms of the German ABC-Community and PAS-ADD Checklist.

PubMed

Zeilinger, Elisabeth L; Weber, Germain; Haveman, Meindert J

2011-01-01

The aim of the present study was to standardize and generate psychometric evidence of the German language versions of two well-established English language mental health instruments: the Aberrant Behavior Checklist-Community (ABC-C) and the Psychiatric Assessment Schedule for Adults with Developmental Disabilities (PAS-ADD) Checklist. New methods in this field were introduced: a simulation method for testing the factor structure and an exploration of long-term stability over two years. The checklists were both administered to a representative sample of 270 individuals with intellectual disability (ID) and, two years later in a second data collection, to 128 participants of the original sample. Principal component analysis and parallel analysis were performed. Reliability measures, long-term stability, subscale intercorrelations, as well as standardized norms were generated. Prevalence of mental health problems was examined. Psychometric properties were mostly excellent, with long-term stability showing moderate to strong effects. The original factor structure of the ABC-C was replicated. PAS-ADD Checklist produced a similar, but still different structure compared with findings from the English language area. The overall prevalence rate of mental health problems in the sample was about 20%. Considering the good results on the measured psychometric properties, the two checklists are recommended for the early detection of mental health problems in persons with ID. Copyright © 2011 Elsevier Ltd. All rights reserved.

Analysis of stability improvement in ZnO thin film transistor with dual-gate structure under negative bias stress

NASA Astrophysics Data System (ADS)

Yun, Ho-Jin; Kim, Young-Su; Jeong, Kwang-Seok; Kim, Yu-Mi; Yang, Seung-dong; Lee, Hi-Deok; Lee, Ga-Won

2014-01-01

In this study, we fabricated dual-gate zinc oxide thin film transistors (ZnO TFTs) without additional processes and analyzed their stability characteristics under a negative gate bias stress (NBS) by comparison with conventional bottom-gate structures. The dual-gate device shows superior electrical parameters, such as subthreshold swing (SS) and on/off current ratio. NBS of VGS = -20 V with VDS = 0 was applied, resulting in a negative threshold voltage (Vth) shift. After applying stress for 1000 s, the Vth shift is 0.60 V in a dual-gate ZnO TFT, while the Vth shift is 2.52 V in a bottom-gate ZnO TFT. The stress immunity of the dual-gate device is caused by the change in field distribution in the ZnO channel by adding another gate as the technology computer aided design (TCAD) simulation shows. Additionally, in flicker noise analysis, a lower noise level with a different mechanism is observed in the dual-gate structure. This can be explained by the top side of the ZnO film having a larger crystal and fewer grain boundaries than the bottom side, which is revealed by the enhanced SS and XRD results. Therefore, the improved stability of the dual-gate ZnO TFT is greatly related to the E-field cancellation effect and crystal quality of the ZnO film.

Mechanical stability analysis of the protein L immunoglobulin-binding domain by full alanine screening using molecular dynamics simulations.

PubMed

Glyakina, Anna V; Likhachev, Ilya V; Balabaev, Nikolay K; Galzitskaya, Oxana V

2015-03-01

This article is the first to study the mechanical properties of the immunoglobulin-binding domain of protein L (referred to as protein L) and its mutants at the atomic level. In the structure of protein L, each amino acid residue (except for alanines and glycines) was replaced sequentially by alanine. Thus, 49 mutants of protein L were obtained. The proteins were stretched at their termini at constant velocity using molecular dynamics simulations in water, i.e. by forced unfolding. 19 out of 49 mutations resulted in a large decrease of mechanical protein stability. These amino acids were affecting either the secondary structure (11 mutations) or loop structures (8 mutations) of protein L. Analysis of mechanical unfolding of the generated protein that has the same topology as protein L but consists of only alanines and glycines allows us to suggest that the mechanical stability of proteins, and specifically protein L, is determined by interactions between certain amino acid residues, although the unfolding pathway depends on the protein topology. This insight can now be used to modulate the mechanical properties of proteins and their unfolding pathways in the desired direction for using them in various biochips, biosensors and biomaterials for medicine, industry, and household purposes. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Manufacturing of mushroom-shaped structures and its hydrophobic robustness analysis based on energy minimization approach

NASA Astrophysics Data System (ADS)

Wang, Li; Yang, Xiaonan; Wang, Quandai; Yang, Zhiqiang; Duan, Hui; Lu, Bingheng

2017-07-01

The construction of stable hydrophobic surfaces has increasingly gained attention owing to its wide range of potential applications. However, these surfaces may become wet and lose their slip effect owing to insufficient hydrophobic stability. Pillars with a mushroom-shaped tip are believed to enhance hydrophobicity stability. This work presents a facile method of manufacturing mushroom-shaped structures, where, compared with the previously used method, the modulation of the cap thickness, cap diameter, and stem height of the structures is more convenient. The effects of the development time on the cap diameter and overhanging angle are investigated and well-defined mushroom-shaped structures are demonstrated. The effect of the microstructure geometry on the contact state of a droplet is predicted by taking an energy minimization approach and is experimentally validated with nonvolatile ultraviolet-curable polymer with a low surface tension by inspecting the profiles of liquid-vapor interface deformation and tracking the trace of the receding contact line after exposure to ultraviolet light. Theoretical and experimental results show that, compared with regular pillar arrays having a vertical sidewall, the mushroom-like structures can effectively enhance hydrophobic stability. The proposed manufacturing method will be useful for fabricating robust hydrophobic surfaces in a cost-effective and convenient manner.

Molecular structure, Normal Coordinate Analysis, harmonic vibrational frequencies, Natural Bond Orbital, TD-DFT calculations and biological activity analysis of antioxidant drug 7-hydroxycoumarin

NASA Astrophysics Data System (ADS)

Sebastian, S.; Sylvestre, S.; Jayarajan, D.; Amalanathan, M.; Oudayakumar, K.; Gnanapoongothai, T.; Jayavarthanan, T.

2013-01-01

In this work, we report harmonic vibrational frequencies, molecular structure, NBO and HOMO, LUMO analysis of Umbelliferone also known as 7-hydroxycoumarin (7HC). The optimized geometric bond lengths and bond angles obtained by computation (monomer and dimmer) shows good agreement with experimental XRD data. Harmonic frequencies of 7HC were determined and analyzed by DFT utilizing 6-311+G(d,p) as basis set. The assignments of the vibrational spectra have been carried out with the help of Normal Coordinate Analysis (NCA) following the Scaled Quantum Mechanical Force Field Methodology (SQMFF). The change in electron density (ED) in the σ* and π* antibonding orbitals and stabilization energies E(2) have been calculated by Natural Bond Orbital (NBO) analysis to give clear evidence of stabilization originating in the hyperconjugation of hydrogen-bonded interaction. The energy and oscillator strength calculated by Time-Dependent Density Functional Theory (TD-DFT) complements with the experimental findings. The simulated spectra satisfactorily coincides with the experimental spectra. Microbial activity of studied compounds was tested against Staphylococcus aureus, Streptococcus pyogenes, Bacillus subtilis, Escherichia coli, Psuedomonas aeruginosa, Klebsiella pneumoniae, Proteus mirabilis, Shigella flexneri, Salmonella typhi and Enterococcus faecalis.

Visualizing nD Point Clouds as Topological Landscape Profiles to Guide Local Data Analysis

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

Oesterling, Patrick; Heine, Christian; Weber, Gunther H.

2012-05-04

Analyzing high-dimensional point clouds is a classical challenge in visual analytics. Traditional techniques, such as projections or axis-based techniques, suffer from projection artifacts, occlusion, and visual complexity.We propose to split data analysis into two parts to address these shortcomings. First, a structural overview phase abstracts data by its density distribution. This phase performs topological analysis to support accurate and non-overlapping presentation of the high-dimensional cluster structure as a topological landscape profile. Utilizing a landscape metaphor, it presents clusters and their nesting as hills whose height, width, and shape reflect cluster coherence, size, and stability, respectively. A second local analysis phasemore » utilizes this global structural knowledge to select individual clusters or point sets for further, localized data analysis. Focusing on structural entities significantly reduces visual clutter in established geometric visualizations and permits a clearer, more thorough data analysis. In conclusion, this analysis complements the global topological perspective and enables the user to study subspaces or geometric properties, such as shape.« less

Effects of ionizing radiation and temperature on uranyl silicates: soddyite (UO2)2(SiO4)(H2O)2 and Uranophane Ca(UO2)2(SiO3OH)2·5H2O.

PubMed

Sureda, R; Casas, I; Giménez, J; de Pablo, J; Quiñones, J; Zhang, J; Ewing, R C

2011-03-15

The stability of soddyite under electron irradiation has been studied over the temperature range of 25-300 °C. At room temperature, soddyite undergoes a crystalline-to-amorphous transformation (amorphization) at a total dose of 6.38 × 10(8) Gy. The electron beam irradiation results suggest that the soddyite structure is susceptible to radiation-induced nanocrystallization of UO(2). The temperature dependence of amorphization dose increases linearly up to 300 °C. A thermogravimetric and calorimetric analysis (TGA-DSC) combined with X-ray diffraction (XRD) indicates that soddyite retains its water groups up to 400 °C, followed by the collapse of the structure. Based on thermal analysis of uranophane, the removal of some water groups at relatively low temperatures provokes the collapse of the uranophane structure. This structural change appears to be the reason for the increase of amorphization dose at 140 °C. According to the results obtained, radiation field of a nuclear waste repository, rather than temperature effects, may cause changes in the crystallinity of soddyite and affect its stability during long-term storage.

Practical aspects of a maximum likelihood estimation method to extract stability and control derivatives from flight data

NASA Technical Reports Server (NTRS)

Iliff, K. W.; Maine, R. E.

1976-01-01

A maximum likelihood estimation method was applied to flight data and procedures to facilitate the routine analysis of a large amount of flight data were described. Techniques that can be used to obtain stability and control derivatives from aircraft maneuvers that are less than ideal for this purpose are described. The techniques involve detecting and correcting the effects of dependent or nearly dependent variables, structural vibration, data drift, inadequate instrumentation, and difficulties with the data acquisition system and the mathematical model. The use of uncertainty levels and multiple maneuver analysis also proved to be useful in improving the quality of the estimated coefficients. The procedures used for editing the data and for overall analysis are also discussed.

Structural domains and main-chain flexibility in prion proteins.

PubMed

Blinov, N; Berjanskii, M; Wishart, D S; Stepanova, M

2009-02-24

In this study we describe a novel approach to define structural domains and to characterize the local flexibility in both human and chicken prion proteins. The approach we use is based on a comprehensive theory of collective dynamics in proteins that was recently developed. This method determines the essential collective coordinates, which can be found from molecular dynamics trajectories via principal component analysis. Under this particular framework, we are able to identify the domains where atoms move coherently while at the same time to determine the local main-chain flexibility for each residue. We have verified this approach by comparing our results for the predicted dynamic domain systems with the computed main-chain flexibility profiles and the NMR-derived random coil indexes for human and chicken prion proteins. The three sets of data show excellent agreement. Additionally, we demonstrate that the dynamic domains calculated in this fashion provide a highly sensitive measure of protein collective structure and dynamics. Furthermore, such an analysis is capable of revealing structural and dynamic properties of proteins that are inaccessible to the conventional assessment of secondary structure. Using the collective dynamic simulation approach described here along with a high-temperature simulations of unfolding of human prion protein, we have explored whether locations of relatively low stability could be identified where the unfolding process could potentially be facilitated. According to our analysis, the locations of relatively low stability may be associated with the beta-sheet formed by strands S1 and S2 and the adjacent loops, whereas helix HC appears to be a relatively stable part of the protein. We suggest that this kind of structural analysis may provide a useful background for a more quantitative assessment of potential routes of spontaneous misfolding in prion proteins.

Water-soluble Au13 clusters protected by binary thiolates: Structural accommodation and the use for chemosensing

NASA Astrophysics Data System (ADS)

Ding, Weihua; Huang, Chuanqi; Guan, Lingmei; Liu, Xianhu; Luo, Zhixun; Li, Weixue

2017-05-01

Here we report a successful synthesis of water-soluble 13-atoms gold clusters under the monolayer protection of binary thiolates, glutathione and penicillamine, under a molecular formula of Au13(SG)5(PA)7. This monolayer-protected cluster (MPC) finds decent stability and is demonstrated to possess an icosahedral geometry pertaining to structural accommodation in contrast to a planar bare Au13 of local minima energy. Natural bond orbital (NBO) analysis depicts the interaction patterns between gold and the ligands, enlightening to understand the origin of enhanced stability of the Au13 MPCs. Further, the water-soluble Au13 MPCs are found to be a decent candidate for chemosensing and bioimaging.

Ribbon structure stabilized by C10 and C12 turns in αγ hybrid peptide.

PubMed

Wani, Naiem Ahmad; Kant, Rajni; Gupta, Vivek Kumar; Aravinda, Subrayashastry; Rai, Rajkishor

2016-04-01

The present study describes the synthesis and crystallographic analysis of αγ hybrid peptides, Boc-Gpn-L-Pro-NHMe (1), Boc-Aib-Gpn-L-Pro-NHMe (2), and Boc-L-Pro-Aib-Gpn-L-Pro-NHMe (3). Peptides 1 and 2 adopt expanded 12-membered (C12 ) helical turn over γα segment. Peptide 3 promotes the ribbon structure stabilized by type II β-turn (C10 ) followed by the expanded C12 helical γα turn. Both right-handed and left-handed helical conformations for Aib residue are observed in peptides 2 and 3, respectively. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Mixed time integration methods for transient thermal analysis of structures

NASA Technical Reports Server (NTRS)

Liu, W. K.

1982-01-01

The computational methods used to predict and optimize the thermal structural behavior of aerospace vehicle structures are reviewed. In general, two classes of algorithms, implicit and explicit, are used in transient thermal analysis of structures. Each of these two methods has its own merits. Due to the different time scales of the mechanical and thermal responses, the selection of a time integration method can be a different yet critical factor in the efficient solution of such problems. Therefore mixed time integration methods for transient thermal analysis of structures are being developed. The computer implementation aspects and numerical evaluation of these mixed time implicit-explicit algorithms in thermal analysis of structures are presented. A computationally useful method of estimating the critical time step for linear quadrilateral element is also given. Numerical tests confirm the stability criterion and accuracy characteristics of the methods. The superiority of these mixed time methods to the fully implicit method or the fully explicit method is also demonstrated.

Mixed time integration methods for transient thermal analysis of structures

NASA Technical Reports Server (NTRS)

Liu, W. K.

1983-01-01

The computational methods used to predict and optimize the thermal-structural behavior of aerospace vehicle structures are reviewed. In general, two classes of algorithms, implicit and explicit, are used in transient thermal analysis of structures. Each of these two methods has its own merits. Due to the different time scales of the mechanical and thermal responses, the selection of a time integration method can be a difficult yet critical factor in the efficient solution of such problems. Therefore mixed time integration methods for transient thermal analysis of structures are being developed. The computer implementation aspects and numerical evaluation of these mixed time implicit-explicit algorithms in thermal analysis of structures are presented. A computationally-useful method of estimating the critical time step for linear quadrilateral element is also given. Numerical tests confirm the stability criterion and accuracy characteristics of the methods. The superiority of these mixed time methods to the fully implicit method or the fully explicit method is also demonstrated.

Aeroservoelastic Uncertainty Model Identification from Flight Data

NASA Technical Reports Server (NTRS)

Brenner, Martin J.

2001-01-01

Uncertainty modeling is a critical element in the estimation of robust stability margins for stability boundary prediction and robust flight control system development. There has been a serious deficiency to date in aeroservoelastic data analysis with attention to uncertainty modeling. Uncertainty can be estimated from flight data using both parametric and nonparametric identification techniques. The model validation problem addressed in this paper is to identify aeroservoelastic models with associated uncertainty structures from a limited amount of controlled excitation inputs over an extensive flight envelope. The challenge to this problem is to update analytical models from flight data estimates while also deriving non-conservative uncertainty descriptions consistent with the flight data. Multisine control surface command inputs and control system feedbacks are used as signals in a wavelet-based modal parameter estimation procedure for model updates. Transfer function estimates are incorporated in a robust minimax estimation scheme to get input-output parameters and error bounds consistent with the data and model structure. Uncertainty estimates derived from the data in this manner provide an appropriate and relevant representation for model development and robust stability analysis. This model-plus-uncertainty identification procedure is applied to aeroservoelastic flight data from the NASA Dryden Flight Research Center F-18 Systems Research Aircraft.

Stability of steady hand force production explored across spaces and methods of analysis.

PubMed

de Freitas, Paulo B; Freitas, Sandra M S F; Lewis, Mechelle M; Huang, Xuemei; Latash, Mark L

2018-06-01

We used the framework of the uncontrolled manifold (UCM) hypothesis and explored the reliability of several outcome variables across different spaces of analysis during a very simple four-finger accurate force production task. Fourteen healthy, young adults performed the accurate force production task with each hand on 3 days. Small spatial finger perturbations were generated by the "inverse piano" device three times per trial (lifting the fingers 1 cm/0.5 s and lowering them). The data were analyzed using the following main methods: (1) computation of indices of the structure of inter-trial variance and motor equivalence in the space of finger forces and finger modes, and (2) analysis of referent coordinates and apparent stiffness values for the hand. Maximal voluntary force and the index of enslaving (unintentional finger force production) showed good to excellent reliability. Strong synergies stabilizing total force were reflected in both structure of variance and motor equivalence indices. Variance within the UCM and the index of motor equivalent motion dropped over the trial duration and showed good to excellent reliability. Variance orthogonal to the UCM and the index of non-motor equivalent motion dropped over the 3 days and showed poor to moderate reliability. Referent coordinate and apparent stiffness indices co-varied strongly and both showed good reliability. In contrast, the computed index of force stabilization showed poor reliability. The findings are interpreted within the scheme of neural control with referent coordinates involving the hierarchy of two basic commands, the r-command and c-command. The data suggest natural drifts in the finger force space, particularly within the UCM. We interpret these drifts as reflections of a trade-off between stability and optimization of action. The implications of these findings for the UCM framework and future clinical applications are explored in the discussion. Indices of the structure of variance and motor equivalence show good reliability and can be recommended for applied studies.

Structure-guided systems-level engineering of oxidation-prone methionine residues in catalytic domain of an alkaline α-amylase from Alkalimonas amylolytica for significant improvement of both oxidative stability and catalytic efficiency.

PubMed

Yang, Haiquan; Liu, Long; Shin, Hyun-dong; Li, Jianghua; Du, Guocheng; Chen, Jian

2013-01-01

High oxidative stability and catalytic efficiency are required for the alkaline α-amylases to keep the enzymatic performance under the harsh conditions in detergent industries. In this work, we attempted to significantly improve both the oxidative stability and catalytic efficiency of an alkaline α-amylase from Alkalimonas amylolytica by engineering the five oxidation-prone methionine residues around the catalytic domain via a systematic approach. Specifically, based on the tertiary structure analysis, five methionines (Met 145, Met 214, Met 229, Met 247 and Met 317) were individually substituted with oxidation-resistant threonine, isoleucine and alaline, respectively. Among the created 15 mutants, 7 mutants M145A, M145I, M214A, M229A, M229T, M247T and M317I showed significantly enhanced oxidative stability or catalytic efficiency. In previous work, we found that the replacement of M247 with leucine could significantly improve the oxidative stability. Thus, these 8 positive mutants (M145A, M145I, M214A, M229A, M229T, M247T, M247L and M317I) were used to conduct the second round of combinational mutations. Among the constructed 85 mutants (25 two-point mutants, 36 three-point mutants, 16 four-point mutants and 8 five-point mutants), the mutant M145I-214A-229T-247T-317I showed a 5.4-fold increase in oxidative stability and a 3.0-fold increase in catalytic efficiency. Interestingly, the specific activity, alkaline stability and thermal stability of this mutant were also increased. The increase of salt bridge and hydrogen bonds around the catalytic domain contributed to the significantly improved catalytic efficiency and stability, as revealed by the three-dimensional structure model of wild-type alkaline α-amylase and its mutant M145I-214A-229T-247T-317I. With the significantly improved oxidative stability and catalytic efficiency, the mutant M145I-214A-229T-247T-317I has a great potential as a detergent additive, and this structure-guided systems engineering strategy may be useful for the protein engineering of the other microbial enzymes to fulfill industrial requirements.

Generation of fatty acids from 1,2-dipalmitoyl-sn-glycero-3-phosphocholine/cardiolipin liposomes that stabilize recombinant human serum albumin.

PubMed

Frahm, Grant E; Cameron, Brooke E; Smith, Jeffrey C; Johnston, Michael J W

2013-06-01

At elevated temperatures, studies have shown that serum albumin undergoes irreversible changes to its secondary structure. Anionic fatty acids and/or anionic surfactants have been shown to stabilize human serum albumin (HSA) against thermal denaturation through bridging hydrophobic domains and cationic amino acids residues of the protein. As albumin can readily interact with a variety of liposomes, this study proposes that cardiolipin delivered via 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) liposomes can improve the thermal stability of recombinant HSA produced in Saccharomyces cerevisiae (ScrHSA) in a similar manner to anionic fatty acids. Thermal stability and structure of ScrHSA in the absence and presence of DPPC/cardiolipin liposomes was assessed with U/V circular dichroism spectropolarimetry and protein thermal stability was confirmed with differential scanning calorimetry. Although freshly prepared DPPC/cardiolipin liposomes did not improve the stability of ScrHSA, DPPC/cardiolipin liposomes incubated at room temperature for 7 d (7dRT) dramatically improved the thermal stability of the protein. Mass spectrometry analysis identified the presence of fatty acids in the 7dRT liposomes, not identified in freshly prepared liposomes, to which the improved stability was attributed. The generation of fatty acids is attributed to either the chemical hydrolysis or oxidative cleavage of the unsaturated acyl chains of cardiolipin. By modulating the lipid composition through the introduction of lipids with higher acyl chain unsaturation, it may be possible to generate the stabilizing fatty acids in a more rapid manner.

Curvilinear Immersed Boundary Method for Simulating Fluid Structure Interaction with Complex 3D Rigid Bodies

PubMed Central

Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

2010-01-01

The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A Numerical Method for Solving the 3D Unsteady Incompressible Navier-Stokes Equations in Curvilinear Domains with Complex Immersed Boundaries, Journal of Computational Physics 225 (2007) 1782–1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions unconditionally unstable iteration schemes result even when strong coupling FSI is employed. For such cases, however, combining the strong-coupling iteration with under-relaxation in conjunction with the Aitken’s acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI algorithm. The stabilizing role of under-relaxation is also clarified and an upper bound of the required for stability under-relaxation coefficient is derived. PMID:20981246

Curvilinear immersed boundary method for simulating fluid structure interaction with complex 3D rigid bodies

NASA Astrophysics Data System (ADS)

Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

2008-08-01

The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A numerical method for solving the 3D unsteady incompressible Navier-Stokes equations in curvilinear domains with complex immersed boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions the FSI algorithm is unconditionally unstable even when strong coupling FSI is employed. For such cases, however, combining the strong coupling iteration with under-relaxation in conjunction with the Aitken's acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI algorithm. The stabilizing role of under-relaxation is also clarified and the upper bound of the under-relaxation coefficient, required for stability, is derived.

Prediction and analysis of structure, stability and unfolding of thermolysin-like proteases

NASA Astrophysics Data System (ADS)

Vriend, Gert; Eijsink, Vincent

1993-08-01

Bacillus neutral proteases (NPs) form a group of well-characterized homologous enzymes, that exhibit large differences in thermostability. The three-dimensional (3D) structures of several of these enzymes have been modelled on the basis of the crystal structures of the NPs of B. thermoproteolyticus (thermolysin) and B. cercus. Several new techniques have been developed to improve the model-building procedures. Also a model-building by mutagenesis' strategy was used, in which mutants were designed just to shed light on parts of the structures that were particularly hard to model. The NP models have been used for the prediction of site-directed mutations aimed at improving the thermostability of the enzymes. Predictions were made using several novel computational techniques, such as position-specific rotamer searching, packing quality analysis and property-profile database searches. Many stabilizing mutations were predicted and produced: improvement of hydrogen bonding, exclusion of buried water molecules, capping helices, improvement of hydrophobic interactions and entropic stabilization have been applied successfully. At elevated temperatures NPs are irreversibly inactivated as a result of autolysis. It has been shown that this denaturation process is independent of the protease activity and concentration and that the inactivation follows first-order kinetics. From this it has been conjectured that local unfolding of (surface) loops, which renders the protein susceptible to autolysis, is the rate-limiting step. Despite the particular nature of the thermal denaturation process, normal rules for protein stability can be applied to NPs. However, rather than stabilizing the whole protein against global unfolding, only a small region has to be protected against local unfolding. In contrast to proteins in general, mutational effects in proteases are not additive and their magnitude is strongly dependent on the location of the mutation. Mutations that alter the stability of the NP by a large amount are located in a relatively weak region (or more precisely, they affect a local unfolding pathway with a relatively low free energy of activation). One weak region, that is supposedly important in the early steps of NP unfolding, has been determined in the NP of B. stearothermophilus. After eliminating this weakest link a drastic increase in thermostability was observed and the search for the second-weakest link, or the second-lowest energy local unfolding pathway is now in progress. Hopefully, this approach can be used to unravel the entire early phase of unfolding.

Analysis of galactosemia-linked mutations of GALT enzyme using a computational biology approach.

PubMed

Facchiano, A; Marabotti, A

2010-02-01

We describe the prediction of the structural and functional effects of mutations on the enzyme galactose-1-phosphate uridyltransferase related to the genetic disease galactosemia, using a fully computational approach. One hundred and seven single-point mutants were simulated starting from the structural model of the enzyme obtained by homology modeling methods. Several bioinformatics programs were then applied to each resulting mutant protein to analyze the effect of the mutations. The mutations have a direct effect on the active site, or on the dimer assembly and stability, or on the monomer stability. We describe how mutations may exert their effect at a molecular level by altering H-bonds, salt bridges, secondary structure or surface features. The alteration of protein stability, at level of monomer and/or dimer, is the main effect observed. We found an agreement between our results and the functional experimental data available in literature for some mutants. The data and analyses for all the mutants are fully available in the web-accessible database hosted at http://bioinformatica.isa.cnr.it/GALT.

Nonlinear Stability and Structure of Compressible Reacting Mixing Layers

NASA Technical Reports Server (NTRS)

Day, M. J.; Mansour, N. N.; Reynolds, W. C.

2000-01-01

The parabolized stability equations (PSE) are used to investigate issues of nonlinear flow development and mixing in compressible reacting shear layers. Particular interest is placed on investigating the change in flow structure that occurs when compressibility and heat release are added to the flow. These conditions allow the 'outer' instability modes- one associated with each of the fast and slow streams-to dominate over the 'central', Kelvin-Helmholtz mode that unaccompanied in incompressible nonreacting mixing layers. Analysis of scalar probability density functions in flows with dominant outer modes demonstrates the ineffective, one-sided nature of mixing that accompany these flow structures. Colayer conditions, where two modes have equal growth rate and the mixing layer is formed by two sets of vortices, offer some opportunity for mixing enhancement. Their extent, however, is found to be limited in the mixing layer's parameter space. Extensive validation of the PSE technique also provides a unique perspective on central- mode vortex pairing, further supporting the view that pairing is primarily governed perspective sheds insight on how linear stability theory is able to provide such an accurate prediction of experimentally-observed, fully nonlinear flow phenomenon.

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

Sharma, Arvind, E-mail: arvindsharma230771@gmail.com; Nagar, A. K., E-mail: ajaya.nagar@gmail.com

We investigate the interaction of optical vector soliton with a symmetric thin-film gallium-silica waveguide structure using the equivalent particle theory. The relevant nonlinear Schrodinger equation has been solved by the method of phase plane analysis. The analysis shows beam break up into transmitted, reflected and nonlinear surface waves at the interface. The stability properties of the solitons so formed have been discussed.

Synthesis, structure, computational and in-silico anticancer studies of N,N-diethyl-N‧-palmitoylthiourea

NASA Astrophysics Data System (ADS)

Asegbeloyin, Jonnie Niyi; Oyeka, Ebube Evaristus; Okpareke, Obinna; Ibezim, Akachukwu

2018-02-01

A new potential ONS donor ligand N,N-diethyl-N‧-palmitoylthiourea (PACDEA) with the molecular formular C21H42N2OS has been synthesized and characterized by ESI-MS, UV, FTIR 1H and 13C NMR spectroscopy and single X-ray crystallography. The asymmetric molecules crystallized in the centrosymmetric structure of monoclinic crystal system with space group P21/c. In the crystal structure of the compound, molecules are linked in a continuous chain by intermolecular Nsbnd H⋯Odbnd C hydrogen bonds, which stabilized the crystal structure. The palmitoyl moiety and N (2)-ethyl group lie on a plane, while the thiocarbonyl moiety is twisted and lying othorgonal to the plane. Non-covalent interaction (NCI) analysis on the hydrogen bonded solid state structure of the molecule revealed the presence of a significant number of non-covalent interactions including intermolecular hydrogen bonding interactions, Csbnd Hsbnd -lone pair interactions, weak Van der Waals interactions, and steric/ring closure interactions. The NCI analysis also showed the presence of intramolecular stabilizing Csbnd H⋯Odbnd C and Csbnd H⋯Sdbnd C interactions. Docking simulation revealed that the compound interacted favourably with ten selected validated anticancer drug targets, which is an indication that the compound could possess some anticancer properties.

Structural Stability of Mathematical Models of National Economy

NASA Astrophysics Data System (ADS)

Ashimov, Abdykappar A.; Sultanov, Bahyt T.; Borovskiy, Yuriy V.; Adilov, Zheksenbek M.; Ashimov, Askar A.

2011-12-01

In the paper we test robustness of particular dynamic systems in a compact regions of a plane and a weak structural stability of one dynamic system of high order in a compact region of its phase space. The test was carried out based on the fundamental theory of dynamical systems on a plane and based on the conditions for weak structural stability of high order dynamic systems. A numerical algorithm for testing the weak structural stability of high order dynamic systems has been proposed. Based on this algorithm we assess the weak structural stability of one computable general equilibrium model.

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method

NASA Astrophysics Data System (ADS)

Miura, Shinichi

2018-03-01

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

Quantum structural fluctuation in para-hydrogen clusters revealed by the variational path integral method.

PubMed

Miura, Shinichi

2018-03-14

In this paper, the ground state of para-hydrogen clusters for size regime N ≤ 40 has been studied by our variational path integral molecular dynamics method. Long molecular dynamics calculations have been performed to accurately evaluate ground state properties. The chemical potential of the hydrogen molecule is found to have a zigzag size dependence, indicating the magic number stability for the clusters of the size N = 13, 26, 29, 34, and 39. One-body density of the hydrogen molecule is demonstrated to have a structured profile, not a melted one. The observed magic number stability is examined using the inherent structure analysis. We also have developed a novel method combining our variational path integral hybrid Monte Carlo method with the replica exchange technique. We introduce replicas of the original system bridging from the structured to the melted cluster, which is realized by scaling the potential energy of the system. Using the enhanced sampling method, the clusters are demonstrated to have the structured density profile in the ground state.

3D confocal Raman imaging of oil-rich emulsion from enzyme-assisted aqueous extraction of extruded soybean powder.

PubMed

Wu, Longkun; Wang, Limin; Qi, Baokun; Zhang, Xiaonan; Chen, Fusheng; Li, Yang; Sui, Xiaonan; Jiang, Lianzhou

2018-05-30

The understanding of the structure morphology of oil-rich emulsion from enzyme-assisted extraction processing (EAEP) was a critical step to break the oil-rich emulsion structure in order to recover oil. Albeit EAEP method has been applied as an alternative way to conventional solvent extraction method, the structure morphology of oil-rich emulsion was still unclear. The current study aimed to investigate the structure morphology of oil-rich emulsion from EAEP using 3D confocal Raman imaging technique. With increasing the enzymatic hydrolysis duration from 1 to 3 h, the stability of oil-rich emulsion was decreased as visualized in the 3D confocal Raman images that the protein and oil were mixed together. The subsequent Raman spectrum analysis further revealed that the decreased stability of oil-rich emulsion was due to the protein aggregations via SS bonds or protein-lipid interactions. The conformational transfer in protein indicated the formation of a compact structure. Copyright © 2017 Elsevier Ltd. All rights reserved.

Chalcone dendrimer stabilized core-shell nanoparticles—a comparative study on Co@TiO2, Ag@TiO2 and Co@AgCl nanoparticles for antibacterial and antifungal activity

NASA Astrophysics Data System (ADS)

Vanathi Vijayalakshmi, R.; Praveen Kumar, P.; Selvarani, S.; Rajakumar, P.; Ravichandran, K.

2017-10-01

A series of core@shell nanoparticles (Co@TiO2, Ag@TiO2 and Co@AgCl) stabilized with zeroth generation triazolylchalcone dendrimer was synthesized using reduction transmetalation method. The coordination of chalcone dendrimer with silver ions was confirmed by UV-vis spectroscopy. The NMR spectrum ensures the number of protons and carbon signals in the chalcone dendrimer. The prepared samples were structurally characterized by XRD, FESEM and HRTEM analysis. The SAED and XRD analyses exhibited the cubic structure with d hkl   =  2.2 Å, 1.9 Å and 1.38 Å. The antibacterial and antifungal activities of the dendrimer stabilized core@shell nanoparticles (DSCSNPs) were tested against the pathogens Bacillus subtilis, Proteus mirabilis, Candida albicans and Aspergillus nigir from which it is identified that the dendrimer stabilized core shell nanoparticles with silver ions at the shell (Co@AgCl) shows effectively high activity against the tested pathogen following the other core@shell nanoparticles viz Ag@TiO2 and Co@TiO2.

Quadruplexes in 'Dicty': crystal structure of a four-quartet G-quadruplex formed by G-rich motif found in the Dictyostelium discoideum genome.

PubMed

Guédin, Aurore; Lin, Linda Yingqi; Armane, Samir; Lacroix, Laurent; Mergny, Jean-Louis; Thore, Stéphane; Yatsunyk, Liliya A

2018-06-01

Guanine-rich DNA has the potential to fold into non-canonical G-quadruplex (G4) structures. Analysis of the genome of the social amoeba Dictyostelium discoideum indicates a low number of sequences with G4-forming potential (249-1055). Therefore, D. discoideum is a perfect model organism to investigate the relationship between the presence of G4s and their biological functions. As a first step in this investigation, we crystallized the dGGGGGAGGGGTACAGGGGTACAGGGG sequence from the putative promoter region of two divergent genes in D. discoideum. According to the crystal structure, this sequence folds into a four-quartet intramolecular antiparallel G4 with two lateral and one diagonal loops. The G-quadruplex core is further stabilized by a G-C Watson-Crick base pair and a A-T-A triad and displays high thermal stability (Tm > 90°C at 100 mM KCl). Biophysical characterization of the native sequence and loop mutants suggests that the DNA adopts the same structure in solution and in crystalline form, and that loop interactions are important for the G4 stability but not for its folding. Four-tetrad G4 structures are sparse. Thus, our work advances understanding of the structural diversity of G-quadruplexes and yields coordinates for in silico drug screening programs and G4 predictive tools.

Role of tryptophan 95 in substrate specificity and structural stability of Sulfolobus solfataricus alcohol dehydrogenase.

PubMed

Pennacchio, Angela; Esposito, Luciana; Zagari, Adriana; Rossi, Mosè; Raia, Carlo A

2009-09-01

A mutant of the thermostable NAD(+)-dependent (S)-stereospecific alcohol dehydrogenase from Sulfolobus solfataricus (SsADH) which has a single substitution, Trp95Leu, located at the substrate binding pocket, was fully characterized to ascertain the role of Trp95 in discriminating between chiral secondary alcohols suggested by the wild-type SsADH crystallographic structure. The Trp95Leu mutant displays no apparent activity with short-chain primary and secondary alcohols and poor activity with aromatic substrates and coenzyme. Moreover, the Trp --> Leu substitution affects the structural stability of the archaeal ADH, decreasing its thermal stability without relevant changes in secondary structure. The double mutant Trp95Leu/Asn249Tyr was also purified to assist in crystallographic analysis. This mutant exhibits higher activity but decreased affinity toward aliphatic alcohols, aldehydes as well as NAD(+) and NADH compared to the wild-type enzyme. The crystal structure of the Trp95Leu/Asn249Tyr mutant apo form, determined at 2.0 A resolution, reveals a large local rearrangement of the substrate site with dramatic consequences. The Leu95 side-chain conformation points away from the catalytic metal center and the widening of the substrate site is partially counteracted by a concomitant change of Trp117 side chain conformation. Structural changes at the active site are consistent with the reduced activity on substrates and decreased coenzyme binding.

Implications of hydrogen/halogen-bond in the stabilization of confined water and anion-water clusters by a cationic receptor

NASA Astrophysics Data System (ADS)

Hoque, Md. Najbul; Das, Gopal

2016-03-01

Anion complexation of benzene capped flexible tripodal receptor and solid state stabilization of discrete hybrid anion-water or infinite water clusters by various supramolecular interactions are reported here. The crystal structure of the receptor in protonated states shows all the three arms projected in one direction. We structurally demonstrate discrete fluoride-water cluster [F2-H2O]2- and square shaped chloride-water cluster [Cl2-(H2O)2]2- inside the cationic channel of the receptor. Structural analysis also reveals that these clusters are stabilized inside the channel through active participation of N/C/Ow‧H⋯Ow, N/C/Ow‧H⋯X- (X- = F-, Cl- and I-) H-bonds and electrostatic interactions. Moreover, C-H⋯π and π⋯π types weak intermolecular interactions appear to play crucial role in supramolecular assembly of receptor. Additionally, on treatment with hydroiodic acid (HI) L resulted zwitterionic iodide complex. Crystal structure reveals the presence of S···I halogen bonded dimer, I2···I halogen bond, 1D infinite water chain and neutral iodine molecules. It is comprehensible that ligand basal structure (benzene capped and N-bridge head in two tripodal) play crucial roles in the formation of diverse halide-water cluster. All structures were well examined by different techniques such as NMR, IR, TGA, DSC, PXRD and XRD.

Structure variations of TBA G-quadruplex induced by 2'-O-methyl nucleotide in K+ and Ca2+ environments.

PubMed

Zhao, Xiaoyang; Liu, Bo; Yan, Jing; Yuan, Ying; An, Liwen; Guan, Yifu

2014-10-01

Thrombin binding aptamer (TBA), a 15-mer oligonucleotide of d(GGTTGGTGTGGTTGG) sequence, folds into a chair-type antiparallel G-quadruplex in the K(+) environment, and each of two G-tetrads is characterized by a syn-anti-syn-anti glycosidic conformation arrangement. To explore its folding topology and structural stability, 2'-O-methyl nucleotide (OMe) with the C3'-endo sugar pucker conformation and anti glycosidic angle was used to selectively substitute for the guanine residues of G-tetrads of TBA, and these substituted TBAs were characterized using a circular dichroism spectrum, thermally differential spectrum, ultraviolet stability analysis, electrophoresis mobility shift assay, and thermodynamic analysis in K(+) and Ca(2+) environments. Results showed that single substitutions for syn-dG residues destabilized the G-quadruplex structure, while single substitutions for anti-dG residues could preserve the G-quadruplex in the K(+) environment. When one or two G-tetrads were modified with OMe, TBA became unstructured. In contrast, in Ca(2+) environment, the native TBA appeared to be unstructured. When two G-tetrads were substituted with OMe, TBA seemed to become a more stable parallel G-4 structure. Further thermodynamic data suggested that OMe-substitutions were an enthalpy-driven event. The results in this study enrich our understanding about the effects of nucleotide derivatives on the G-quadruplex structure stability in different ionic environments, which will help to design G-quadruplex for biological and medical applications. © The Author 2014. Published by ABBS Editorial Office in association with Oxford University Press on behalf of the Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences.

Structure and spectroscopic properties of neutral and cationic tetratomic [C,H,N,Zn] isomers: A theoretical study

NASA Astrophysics Data System (ADS)

Redondo, Pilar; Largo, Antonio; Vega-Vega, Álvaro; Barrientos, Carmen

2015-05-01

The structure and spectroscopic parameters of the most relevant [C,H,N,Zn] isomers have been studied employing high-level quantum chemical methods. For each isomer, we provide predictions for their molecular structure, thermodynamic stabilities as well as vibrational and rotational spectroscopic parameters which could eventually help in their experimental detection. In addition, we have carried out a detailed study of the bonding situations by means of a topological analysis of the electron density in the framework of the Bader's quantum theory of atoms in molecules. The analysis of the relative stabilities and spectroscopic parameters suggests two linear isomers of the neutral [C,H,N,Zn] composition, namely, cyanidehydridezinc HZnCN (1Σ) and hydrideisocyanidezinc HZnNC (1Σ), as possible candidates for experimental detections. For the cationic [C,H,N,Zn]+ composition, the most stable isomers are the ion-molecule complexes arising from the direct interaction of the zinc cation with either the nitrogen or carbon atom of either hydrogen cyanide or hydrogen isocyanide, namely, HCNZn+ (2Σ) and HCNZn+ (2Σ).

Optimization of hydraulic shear parameters and reactor configuration in the aerobic granular sludge process.

PubMed

Zhu, Liang; Zhou, Jiaheng; Yu, Haitian; Xu, Xiangyang

2015-01-01

The hydraulic shear acts as an important selection pressure in aerobic sludge granulation. The effects of the hydraulic shear rate and reactor configuration on structural characteristics of aerobic granule in view of the hydromechanics. The hydraulic shear analysis was proposed to overcome the limitation of using superficial gas velocity (SGV) to express the hydraulic shear stress. Results showed that the stronger hydraulic shear stress with SGV above 2.4 cm s(-1) promoted the microbial aggregation, and favoured the structural stability of the granular sludge. According to the hydraulic shear analysis, the total shear rate reached (0.56-2.31)×10(5) s(-1) in the granular reactor with a larger ratio of height to diameter (H/D), and was higher than that in the reactor with smaller H/D, where the sequencing airlift bioreactor with smaller H/D had a high total shear rate under the same SGV. Results demonstrated that the granular reactor could provide a stronger hydraulic shear stress which promotes the formation and structural stability of aerobic granules.

Determination of the conformation of 2-hydroxy- and 2-aminobenzoic acid dimers using 13C NMR and density functional theory/natural bond order analysis: the central importance of the carboxylic acid carbon.

PubMed

Burnette, Ronald R; Weinhold, Frank

2006-07-20

The 13C chemical shift for the carboxylic acid carbon provides a powerful diagnostic probe to determine the preferred isomeric dimer structures of benzoic acid derivatives undergoing intra- and intermolecular H-bonding in the gas, solution and crystalline phases. We have employed hybrid density functional calculations and natural bond orbital analysis to elucidate the electronic origins of the observed 13C shieldings and their relationship to isomeric stability. We find that delocalizing interactions from the carbonyl oxygen lone pairs (nO) into vicinal carbon-oxygen and carbon-carbon antibonds (sigmaCO*,sigmaCC*) make critical contributions to the 13C shieldings, and these nO --> sigmaCO*, nO --> sigmaCC* interactions are in turn sensitive to the intramolecular interactions that dictate dimer structure and stability. The carboxyl carbon atom can thus serve as a useful detector of subtle structural and conformational features in this pharmacologically important class of carboxylic acid interactions.

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).

Deployable antenna kinematics using tensegrity structure design

NASA Astrophysics Data System (ADS)

Knight, Byron Franklin

With vast changes in spacecraft development over the last decade, a new, cheaper approach was needed for deployable kinematic systems such as parabolic antenna reflectors. Historically, these mesh-surface reflectors have resembled folded umbrellas, with incremental redesigns utilized to save packaging size. These systems are typically over-constrained designs, the assumption being that high reliability necessary for space operations requires this level of conservatism. But with the rapid commercialization of space, smaller launch platforms and satellite buses have demanded much higher efficiency from all space equipment than can be achieved through this incremental approach. This work applies an approach called tensegrity to deployable antenna development. Kenneth Snelson, a student of R. Buckminster Fuller, invented Tensegrity structures in 1948. Such structures use a minimum number of compression members (struts); stability is maintain using tension members (ties). The novelty introduced in this work is that the ties are elastic, allowing the struts to extend or contract, and in this way changing the surface of the antenna. Previously, the University of Florida developed an approach to quantify the stability and motion of parallel manipulators. This approach was applied to deployable, tensegrity, antenna structures. Based on the kinematic analyses for the 3-3 (octahedron) and 4-4 (square anti-prism) structures, the 6-6 (hexagonal anti-prism) analysis was completed which establishes usable structural parameters. The primary objective for this work was to prove the stability of this class of deployable structures, and their potential application to space structures. The secondary objective is to define special motions for tensegrity antennas, to meet the subsystem design requirements, such as addressing multiple antenna-feed locations. This work combines the historical experiences of the artist (Snelson), the mathematician (Ball), and the space systems engineer (Wertz) to develop a new, practical design approach. This kinematic analysis of tensegrity structures blends these differences to provide the design community with a new approach to lightweight, robust, adaptive structures with the high reliability that space demands. Additionally, by applying Screw Theory, a tensegrity structure antenna can be commanded to move along a screw axis, and therefore meeting the requirement to address multiple feed locations.

Molecular Dynamics Simulation Study on the Binding and Stabilization Mechanism of Antiprion Compounds to the "Hot Spot" Region of PrPC.

PubMed

Zhou, Shuangyan; Liu, Xuewei; An, Xiaoli; Yao, Xiaojun; Liu, Huanxiang

2017-11-15

Structural transitions in the prion protein from the cellular form, PrP C , into the pathological isoform, PrP Sc , are regarded as the main cause of the transmissible spongiform encephalopathies, also known as prion diseases. Hence, discovering and designing effective antiprion drugs that can inhibit PrP C to PrP Sc conversion is regarded as a promising way to cure prion disease. Among several strategies to inhibit PrP C to PrP Sc conversion, stabilizing the native PrP C via specific binding is believed to be one of the valuable approaches and many antiprion compounds have been reported based on this strategy. However, the detailed mechanism to stabilize the native PrP C is still unknown. As such, to unravel the stabilizing mechanism of these compounds to PrP C is valuable for the further design and discovery of antiprion compounds. In this study, by molecular dynamics simulation method, we investigated the stabilizing mechanism of several antiprion compounds on PrP C that were previously reported to have specific binding to the "hot spot" region of PrP C . Our simulation results reveal that the stabilization mechanism of specific binding compounds can be summarized as (I) to stabilize both the flexible C-terminal of α2 and the hydrophobic core, such as BMD42-29 and GN8; (II) to stabilize the hydrophobic core, such as J1 and GJP49; (III) to stabilize the overall structure of PrP C by high binding affinity, as NPR-056. In addition, as indicated by the H-bond analysis and decomposition analysis of binding free energy, the residues N159 and Q160 play an important role in the specific binding of the studied compounds and all these compounds interact with PrP C in a similar way with the key interacting residues L130 in the β1 strand, P158, N159, Q160, etc. in the α1-β2 loop, and H187, T190, T191, etc. in the α2 C-terminus although the compounds have large structural difference. As a whole, our obtained results can provide some insights into the specific binding mechanism of main antiprion compounds to the "hot spot" region of PrP C at the molecular level and also provide guidance for effective antiprion drug design in the future.

Improving stability and strength characteristics of framed structures with nonlinear behavior

NASA Technical Reports Server (NTRS)

Pezeshk, Shahram

1990-01-01

In this paper an optimal design procedure is introduced to improve the overall performance of nonlinear framed structures. The design methodology presented here is a multiple-objective optimization procedure whose objective functions involve the buckling eigenvalues and eigenvectors of the structure. A constant volume with bounds on the design variables is used in conjunction with an optimality criterion approach. The method provides a general tool for solving complex design problems and generally leads to structures with better limit strength and stability. Many algorithms have been developed to improve the limit strength of structures. In most applications geometrically linear analysis is employed with the consequence that overall strength of the design is overestimated. Directly optimizing the limit load of the structure would require a full nonlinear analysis at each iteration which would be prohibitively expensive. The objective of this paper is to develop an algorithm that can improve the limit-load of geometrically nonlinear framed structures while avoiding the nonlinear analysis. One of the novelties of the new design methodology is its ability to efficiently model and design structures under multiple loading conditions. These loading conditions can be different factored loads or any kind of loads that can be applied to the structure simultaneously or independently. Attention is focused on optimal design of space framed structures. Three-dimensional design problems are more complicated to carry out, but they yield insight into real behavior of the structure and can help avoiding some of the problems that might appear in planar design procedure such as the need for out-of-plane buckling constraint. Although researchers in the field of structural engineering generally agree that optimum design of three-dimension building frames especially in the seismic regions would be beneficial, methods have been slow to emerge. Most of the research in this area has dealt with the optimization of truss and plane frame structures.

Use of segmented constrained layer damping treatment for improved helicopter aeromechanical stability

NASA Astrophysics Data System (ADS)

Liu, Qiang; Chattopadhyay, Aditi; Gu, Haozhong; Liu, Qiang; Chattopadhyay, Aditi; Zhou, Xu

2000-08-01

The use of a special type of smart material, known as segmented constrained layer (SCL) damping, is investigated for improved rotor aeromechanical stability. The rotor blade load-carrying member is modeled using a composite box beam with arbitrary wall thickness. The SCLs are bonded to the upper and lower surfaces of the box beam to provide passive damping. A finite-element model based on a hybrid displacement theory is used to accurately capture the transverse shear effects in the composite primary structure and the viscoelastic and the piezoelectric layers within the SCL. Detailed numerical studies are presented to assess the influence of the number of actuators and their locations for improved aeromechanical stability. Ground and air resonance analysis models are implemented in the rotor blade built around the composite box beam with segmented SCLs. A classic ground resonance model and an air resonance model are used in the rotor-body coupled stability analysis. The Pitt dynamic inflow model is used in the air resonance analysis under hover condition. Results indicate that the surface bonded SCLs significantly increase rotor lead-lag regressive modal damping in the coupled rotor-body system.

Maltose-neopentyl glycol (MNG) amphiphiles for solubilization, stabilization and crystallization of membrane proteins.

PubMed

Chae, Pil Seok; Rasmussen, Søren G F; Rana, Rohini R; Gotfryd, Kamil; Chandra, Richa; Goren, Michael A; Kruse, Andrew C; Nurva, Shailika; Loland, Claus J; Pierre, Yves; Drew, David; Popot, Jean-Luc; Picot, Daniel; Fox, Brian G; Guan, Lan; Gether, Ulrik; Byrne, Bernadette; Kobilka, Brian; Gellman, Samuel H

2010-12-01

The understanding of integral membrane protein (IMP) structure and function is hampered by the difficulty of handling these proteins. Aqueous solubilization, necessary for many types of biophysical analysis, generally requires a detergent to shield the large lipophilic surfaces of native IMPs. Many proteins remain difficult to study owing to a lack of suitable detergents. We introduce a class of amphiphiles, each built around a central quaternary carbon atom derived from neopentyl glycol, with hydrophilic groups derived from maltose. Representatives of this maltose-neopentyl glycol (MNG) amphiphile family show favorable behavior relative to conventional detergents, as manifested in multiple membrane protein systems, leading to enhanced structural stability and successful crystallization. MNG amphiphiles are promising tools for membrane protein science because of the ease with which they may be prepared and the facility with which their structures may be varied.

[Design and Analysis of CT High-speed Data Transmission Rotating Connector Ring System Retaining Ring].

PubMed

Pan, Li; Cao, Jujiang; Liu, Min; Fu, Weiwei

2017-11-30

High speed data transmission rotating connector system for signal high-speed transmission used in the fixed end and rotating end, it is one of the core component in the CT system. This paper involves structure design and analysis of the retaining ring in the CT high speed data transmission rotating connector system based on the principle of off-axis free space optical transmission. According to the problem of the actual engineering application of space limitations, optical fiber fixed and collimator installation location, we designed the structure of the retaining ring. Using the static analysis function of ANSYS Workbench, it verifies rationality and safety of the strength of retaining ring structure. And based on modal analysis function of ANSYS Workbench, it evaluates the effect of the retaining ring on the stability of the system date transmission, and provides theoretical basis for the feasibility of the structure in practical application.

Two-dimensional infrared spectroscopic study on the thermally induced structural changes of glutaraldehyde-crosslinked collagen

NASA Astrophysics Data System (ADS)

Tian, Zhenhua; Wu, Kun; Liu, Wentao; Shen, Lirui; Li, Guoying

2015-04-01

The thermal stability of collagen solution (5 mg/mL) crosslinked by glutaraldehyde (GTA) [GTA/collagen (w/w) = 0.5] was measured by differential scanning calorimetry and Fourier transform infrared spectroscopy (FTIR), and the thermally induced structural changes were analyzed using two-dimensional (2D) correlation spectra. The denaturation temperature (Td) and enthalpy change (ΔH) of crosslinked collagen were respectively about 27 °C and 88 J/g higher than those of native collagen, illuminating the thermal stability increased. With the increase of temperature, the red-shift of absorption bands and the decreased AIII/A1455 value obtained from FTIR spectra indicated that hydrogen bonds were weakened and the unwinding of triple helix occurred for both native and crosslinked collagens; whereas the less changes in red-shifting and AIII/A1455 values for crosslinked collagen also confirmed the increase in thermal stability. Additionally, the 2D correlation analysis provided information about the thermally induced structural changes. In the 2D synchronous spectra, the intensities of auto-peaks at 1655 and 1555 cm-1, respectively assigned to amide I band (Cdbnd O stretching vibration) and amide II band (combination of Nsbnd H bending and Csbnd N stretching vibrations) in helical conformation were weaker for crosslinked collagen than those for native collagen, indicating that the helical structure of crosslinked collagen was less sensitive to temperature. Moreover, the sequence of the band intensity variations showed that the band at 1555 cm-1 moved backwards owing to the addition of GTA, demonstrating that the response of helical structure of crosslinked collagen to the increased temperature lagged. It was speculated that the stabilization of collagen by GTA was due to the reinforcement of triple helical structure.

Two-dimensional infrared spectroscopic study on the thermally induced structural changes of glutaraldehyde-crosslinked collagen.

PubMed

Tian, Zhenhua; Wu, Kun; Liu, Wentao; Shen, Lirui; Li, Guoying

2015-04-05

The thermal stability of collagen solution (5 mg/mL) crosslinked by glutaraldehyde (GTA) [GTA/collagen (w/w)=0.5] was measured by differential scanning calorimetry and Fourier transform infrared spectroscopy (FTIR), and the thermally induced structural changes were analyzed using two-dimensional (2D) correlation spectra. The denaturation temperature (Td) and enthalpy change (ΔH) of crosslinked collagen were respectively about 27°C and 88 J/g higher than those of native collagen, illuminating the thermal stability increased. With the increase of temperature, the red-shift of absorption bands and the decreased AIII/A1455 value obtained from FTIR spectra indicated that hydrogen bonds were weakened and the unwinding of triple helix occurred for both native and crosslinked collagens; whereas the less changes in red-shifting and AIII/A1455 values for crosslinked collagen also confirmed the increase in thermal stability. Additionally, the 2D correlation analysis provided information about the thermally induced structural changes. In the 2D synchronous spectra, the intensities of auto-peaks at 1655 and 1555 cm(-1), respectively assigned to amide I band (CO stretching vibration) and amide II band (combination of NH bending and CN stretching vibrations) in helical conformation were weaker for crosslinked collagen than those for native collagen, indicating that the helical structure of crosslinked collagen was less sensitive to temperature. Moreover, the sequence of the band intensity variations showed that the band at 1555 cm(-1) moved backwards owing to the addition of GTA, demonstrating that the response of helical structure of crosslinked collagen to the increased temperature lagged. It was speculated that the stabilization of collagen by GTA was due to the reinforcement of triple helical structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Uncovering the role of Nb modification in improving the structure stability and electrochemical performance of LiNi0.6Co0.2Mn0.2O2 cathode charged at higher voltage of 4.5 V

NASA Astrophysics Data System (ADS)

Liu, Siyang; Chen, Xiang; Zhao, Jiayue; Su, Junming; Zhang, Congcong; Huang, Tao; Wu, Jianhua; Yu, Aishui

2018-01-01

Ni-rich cathode materials attract ongoing interest due to their high specific capacity (∼200 mAh g-1). However, these materials suffer rapid capacity fading when charged to a high voltage and cycled at elevated temperature. In this study, we propose a facile method to reconstruct the surface structure of LiNi0.6Co0.2Mn0.2O2 via Nb modification, which integrates the merits of partial Nb5+ doping in the pristine structure and surface Li3NbO4 coating. The obtained results from Rietveld refinement and high resolution transmission electron microscopy confirm that Nb5+ is partially doped into Li+ sites within the surface lattice. Further ex-situ powder X-ray diffraction and kinetic analysis using electrochemical impedance spectroscopy reveal that Nb modification stabilizes the layered structure and facilitates the charge transfer process. Owing to the robust surface structure, 1 mol% Nb modified LiNi0.6Co0.2Mn0.2O2 delivers a discharge capacity of 160.9 mAh g-1 with 91% capacity retention after 100 cycles at 3.0-4.5 V, whereas the discharge capacity of the pristine sample drops to 139.6 mAh g-1, corresponding to 78% of its initial value. The presence of Nb5+ in the Li layer exhibits positive effects on stability of layered structure, and the surface Li3NbO4 coating layer increases interfacial stability, which results in superior electrochemical performance.

Structural variations of single and tandem mismatches in RNA duplexes: a joint MD simulation and crystal structure database analysis.

PubMed

Halder, Sukanya; Bhattacharyya, Dhananjay

2012-10-04

Internal loops within RNA duplex regions are formed by single or tandem basepairing mismatches with flanking canonical Watson-Crick basepairs on both sides. They are the most common motif observed in RNA secondary structures and play integral functional and structural roles. In this report, we have studied the structural features of 1 × 1, 2 × 2, and 3 × 3 internal loops using all-atom molecular dynamics (MD) simulation technique with explicit solvent model. As MD simulation is intricately dependent on the choice of force-field and these are often rather approximate, we have used both the most popular force-fields for nucleic acids-CHARMM27 and AMBER94-for a comparative analysis. We find that tandem noncanonical basepairs forming 2 × 2 and 3 × 3 internal loops are considerably more stable than the single mismatches forming 1 × 1 internal loops, irrespective of the force field. We have also analyzed crystal structure database to study the conservation of these helical fragments in the corresponding sets of RNA structures. We observe that the nature of stability in MD simulations mimic their fluctuating natures in crystal data sets also, probably indicating reliable natures of both the force fields to reproduce experimental results. We also notice significant structural changes in the wobble G:U basepairs present in these double helical stretches, leading to a biphasic stability for these wobble pairs to release the deformational strains introduced by internal loops within duplex regions.

Conformational analysis of glutamic acid: a density functional approach using implicit continuum solvent model.

PubMed

Turan, Başak; Selçuki, Cenk

2014-09-01

Amino acids are constituents of proteins and enzymes which take part almost in all metabolic reactions. Glutamic acid, with an ability to form a negatively charged side chain, plays a major role in intra and intermolecular interactions of proteins, peptides, and enzymes. An exhaustive conformational analysis has been performed for all eight possible forms at B3LYP/cc-pVTZ level. All possible neutral, zwitterionic, protonated, and deprotonated forms of glutamic acid structures have been investigated in solution by using polarizable continuum model mimicking water as the solvent. Nine families based on the dihedral angles have been classified for eight glutamic acid forms. The electrostatic effects included in the solvent model usually stabilize the charged forms more. However, the stability of the zwitterionic form has been underestimated due to the lack of hydrogen bonding between the solute and solvent; therefore, it is observed that compact neutral glutamic acid structures are more stable in solution than they are in vacuum. Our calculations have shown that among all eight possible forms, some are not stable in solution and are immediately converted to other more stable forms. Comparison of isoelectronic glutamic acid forms indicated that one of the structures among possible zwitterionic and anionic forms may dominate over the other possible forms. Additional investigations using explicit solvent models are necessary to determine the stability of charged forms of glutamic acid in solution as our results clearly indicate that hydrogen bonding and its type have a major role in the structure and energy of conformers.

High-throughput analysis of the protein sequence-stability landscape using a quantitative "yeast surface two-hybrid" system and fragment reconstitution

PubMed Central

Dutta, Sanjib; Koide, Akiko; Koide, Shohei

2008-01-01

Stability evaluation of many mutants can lead to a better understanding of the sequence determinants of a structural motif and of factors governing protein stability and protein evolution. The traditional biophysical analysis of protein stability is low throughput, limiting our ability to widely explore the sequence space in a quantitative manner. In this study, we have developed a high-throughput library screening method for quantifying stability changes, which is based on protein fragment reconstitution and yeast surface display. Our method exploits the thermodynamic linkage between protein stability and fragment reconstitution and the ability of the yeast surface display technique to quantitatively evaluate protein-protein interactions. The method was applied to a fibronectin type III (FN3) domain. Characterization of fragment reconstitution was facilitated by the co-expression of two FN3 fragments, thus establishing a "yeast surface two-hybrid" method. Importantly, our method does not rely on competition between clones and thus eliminates a common limitation of high-throughput selection methods in which the most stable variants are predominantly recovered. Thus, it allows for the isolation of sequences that exhibits a desired level of stability. We identified over one hundred unique sequences for a β-bulge motif, which was significantly more informative than natural sequences of the FN3 family in revealing the sequence determinants for the β-bulge. Our method provides a powerful means to rapidly assess stability of many variants, to systematically assess contribution of different factors to protein stability and to enhance protein stability. PMID:18674545

Characteristics of mutants designed to incorporate a new ion pair into the structure of a cold adapted subtilisin-like serine proteinase.

PubMed

Sigurdardóttir, Anna Gudný; Arnórsdóttir, Jóhanna; Thorbjarnardóttir, Sigrídur H; Eggertsson, Gudmundur; Suhre, Karsten; Kristjánsson, Magnús M

2009-03-01

Structural comparisons of VPR, a subtilisin-like serine proteinase from a psychrotrophic Vibrio species and a thermophilic homologue, aqualysin I, have led us to hypothesize about the roles of different residues in the temperature adaptation of the enzymes. Some of these hypotheses are now being examined by analysis of mutants of the enzymes. The selected substitutions are believed to increase the stability of the cold adapted enzyme based on structural analysis of the thermostable structure. We report here on mutants, which were designed to incorporate an ion pair into the structure of VPR. The residues Asp17 and Arg259 are assumed to form an ion pair in aqualysin I. The cold adapted VPR contains Asn (Asn15) and Lys (Lys257) at corresponding sites in its structure. In VPR, Asn 15 is located on a surface loop with its side group pointing towards the side chain of Lys257. By substituting Asn15 by Asp (N15D) it was considered feasible that a salt bridge would form between the oppositely charged groups. To mimic further the putative salt bridge from the thermophile enzyme the corresponding double mutant (N15D/K257R) was also produced. The N15D mutation increased the thermal stability of VPR by approximately 3 degrees C, both in T(50%) and T(m). Addition of the K257R mutation did not however, increase the stability of the double mutant any further. Despite this stabilization of the VPR mutants the catalytic activity (k(cat)) against the substrate Suc-AAPF-NH-Np was increased in the mutants. Molecular dynamics simulations on wild type and the two mutant proteins suggested that indeed a salt bridge was formed in both cases. Furthermore, a truncated form of the N15D mutant (N15DDeltaC) was produced, lacking a 15 residue long C-terminal extended sequence not present in the thermophilic enzyme. In wild type VPR this supposedly moveable, negatively charged arm on the protein molecule might interfere with the new salt bridge introduced as a result of the N15D mutation. Removal of the C-terminal arm improved the thermal stability (T(m) approximately +1.5 degrees C) of the truncated enzyme (VPRDeltaC) as compared to the wild type VPR. Introduction of the N15D substitution into VPRDeltaC improved the thermal stability further by about 3 degrees C, or to about the same extent as in the wild type. However, contrary to what was observed for the wild type, the introduction of the putative salt bridge did not affect the catalytic properties (k(cat)) of the C-terminal truncated enzyme.

An analytical study of the dual mass mechanical system stability

NASA Astrophysics Data System (ADS)

Nikolov, Svetoslav; Sinapov, Petko; Kralov, Ivan; Ignatov, Ignat

2011-12-01

In this paper an autonomous, nonlinear model of five ordinary differential equations modeling the motion of a dual mass mechanical system with universal joint is studied. The model is investigated qualitatively. On the base of the stability analysis performed, we obtain that the system is: i) in an equilibrium state, or ii) in a structurally unstable behavior when equilibrium states disappear. In case (i) the system is in a normal technical condition and in case (ii) hard break-downs take place.

An infinitely-stiff elastic system via a tuned negative-stiffness component stabilized by rotation-produced gyroscopic forces

NASA Astrophysics Data System (ADS)

Kochmann, D. M.; Drugan, W. J.

2016-06-01

An elastic system containing a negative-stiffness element tuned to produce positive-infinite system stiffness, although statically unstable as is any such elastic system if unconstrained, is proved to be stabilized by rotation-produced gyroscopic forces at sufficiently high rotation rates. This is accomplished in possibly the simplest model of a composite structure (or solid) containing a negative-stiffness component that exhibits all these features, facilitating a conceptually and mathematically transparent, completely closed-form analysis.

Ternary Bismuthide SrPtBi 2: Computation and Experiment in Synergism to Explore Solid-State Materials

DOE PAGES

Gui, Xin; Zhao, Xin; Sobczak, Zuzanna; ...

2018-02-14

A combination of theoretical calculation and the experimental synthesis to explore the new ternary compound is demonstrated in the Sr–Pt–Bi system. Because Pt–Bi is considered as a new critical charge-transfer pair for superconductivity, it inspired us to investigate the Sr–Pt–Bi system. With a thorough calculation of all the known stable/metastable compounds in the Sr–Pt–Bi system and crystal structure predictions, the thermodynamic stability of hypothetical stoichiometry, SrPtBi2, is determined. Following the high-temperature synthesis and crystallographic analysis, the first ternary bismuthide in Sr–Pt–Bi, SrPtBi2 was prepared, and the stoichiometry was confirmed experimentally. SrPtBi 2 crystallizes in the space group Pnma (S.G. 62,more » Pearson Symbol oP48), which matches well with theoretical prediction using an adaptive genetic algorithm. Using first-principles calculations, we demonstrate that the orthorhombic structure has lower formation energies than other 112 structure types, such as tetragonal BaMnBi 2 (CuSmP 2) and LaAuBi 2 (CuHfSi 2) structure types. The bonding analysis indicates that the Pt–Bi interactions play a critical role in structural stability. The physical property measurements show the metallic properties at the low temperature, which agrees with the electronic structure assessment.« less

Conceptual design and structural analysis of the spectroscopy of the atmosphere using far infrared emission (SAFIRE) instrument

NASA Technical Reports Server (NTRS)

Moses, Robert W.; Averill, Robert D.

1992-01-01

The conceptual design and structural analysis for the Spectroscopy of the Atmosphere using Far Infrared Emission (SAFIRE) Instrument are provided. SAFIRE, which is an international effort, is proposed for the Earth Observing Systems (EOS) program for atmospheric ozone studies. A concept was developed which meets mission requirements and is the product of numerous parametric studies and design/analysis iterations. Stiffness, thermal stability, and weight constraints led to a graphite/epoxy composite design for the optical bench and supporting struts. The structural configuration was determined by considering various mounting arrangements of the optical, cryo, and electronic components. Quasi-static, thermal, modal, and dynamic response analyses were performed, and the results are presented for the selected configuration.

Solubilization and Stabilization of Isolated Photosystem I Complex with Lipopeptide Detergents

PubMed Central

Wang, Xiaoqiang; Huang, Guihong; Yu, Daoyong; Ge, Baosheng; Wang, Jiqian; Xu, Fengxi; Huang, Fang; Xu, Hai; Lu, Jian R.

2013-01-01

It is difficult to maintain a target membrane protein in a soluble and functional form in aqueous solution without biological membranes. Use of surfactants can improve solubility, but it remains challenging to identify adequate surfactants that can improve solubility without damaging their native structures and biological functions. Here we report the use of a new class of lipopeptides to solubilize photosystem I (PS-I), a well known membrane protein complex. Changes in the molecular structure of these surfactants affected their amphiphilicity and the goal of this work was to exploit a delicate balance between detergency and biomimetic performance in PS-I solubilization via their binding capacity. Meanwhile, the effects of these surfactants on the thermal and structural stability and functionality of PS-I in aqueous solution were investigated by circular dichroism, fluorescence spectroscopy, SDS-PAGE analysis and O2 uptake measurements, respectively. Our studies showed that the solubility of PS-I depended on both the polarity and charge in the hydrophilic head of the lipopeptides and the length of its hydrophobic tail. The best performing lipopeptides in favour of PS-I solubility turned out to be C14DK and C16DK, which were comparable to the optimal amphiphilicity of the conventional chemical surfactants tested. Lipopeptides showed obvious advantages in enhancing PS-I thermostability over sugar surfactant DDM and some full peptide amphiphiles reported previously. Fluorescence spectroscopy along with SDS-PAGE analysis demonstrated that lipopeptides did not undermine the polypeptide composition and conformation of PS-I after solubilization; instead they showed better performance in improving the structural stability and integrity of this multi-subunit membrane protein than conventional detergents. Furthermore, O2 uptake measurements indicated that PS-I solubilized with lipopeptides maintained its functionality. The underlying mechanism for the favorable actions of lipopeptide in PS-I solubilization and stabilization is discussed. PMID:24098786

Fundamental and assessment of concrete structure monitoring by using acoustic emission technique testing: A review

NASA Astrophysics Data System (ADS)

Desa, M. S. M.; Ibrahim, M. H. W.; Shahidan, S.; Ghadzali, N. S.; Misri, Z.

2018-04-01

Acoustic emission (AE) technique is one of the non-destructive (NDT) testing, where it can be used to determine the damage of concrete structures such as crack, corrosion, stability, sensitivity, as structure monitoring and energy formed within cracking opening growth in the concrete structure. This article gives a comprehensive review of the acoustic emission (AE) technique testing due to its application in concrete structure for structural health monitoring (SHM). Assessment of AE technique used for structural are reviewed to give the perception of its structural engineering such as dam, bridge and building, where the previous research has been reviewed based on AE application. The assessment of AE technique focusing on basic fundamental of parametric and signal waveform analysis during analysis process and its capability in structural monitoring. Moreover, the assessment and application of AE due to its function have been summarized and highlighted for future references

Robust enzyme design: bioinformatic tools for improved protein stability.

PubMed

Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas

2015-03-01

The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

LOX/Hydrocarbon Combustion Instability Investigation

NASA Technical Reports Server (NTRS)

Jensen, R. J.; Dodson, H. C.; Claflin, S. E.

1989-01-01

The LOX/Hydrocarbon Combustion Instability Investigation Program was structured to determine if the use of light hydrocarbon combustion fuels with liquid oxygen (LOX) produces combustion performance and stability behavior similar to the LOX/hydrogen propellant combination. In particular methane was investigated to determine if that fuel can be rated for combustion instability using the same techniques as previously used for LOX/hydrogen. These techniques included fuel temperature ramping and stability bomb tests. The hot fire program probed the combustion behavior of methane from ambient to subambient temperatures. Very interesting results were obtained from this program that have potential importance to future LOX/methane development programs. A very thorough and carefully reasoned documentation of the experimental data obtained is contained. The hot fire test logic and the associated tests are discussed. Subscale performance and stability rating testing was accomplished using 40,000 lb. thrust class hardware. Stability rating tests used both bombs and fuel temperature ramping techniques. The test program was successful in generating data for the evaluation of the methane stability characteristics relative to hydrogen and to anchor stability models. Data correlations, performance analysis, stability analyses, and key stability margin enhancement parameters are discussed.

Cervarix, the GSK HPV-16/HPV-18 AS04-adjuvanted cervical cancer vaccine, demonstrates stability upon long-term storage and under simulated cold chain break conditions.

PubMed

Le Tallec, David; Doucet, Diane; Elouahabi, Abdelatif; Harvengt, Pol; Deschuyteneer, Michel; Deschamps, Marguerite

2009-07-01

Cervarix is a recombinant human papillomavirus (HPV)-16 and -18 L1 virus-like-particle (VLP) AS04-adjuvanted vaccine designed to protect against cervical intraepithelial neoplasia and cervical cancer caused by the HPV types 16 and 18. Assessment of the stability of the vaccine during long-term storage and after transient exposure to temperatures out of normal storage range is an integrated part of vaccine quality evaluation. This assessment was done with vaccine samples stored at 2-8 degrees C for up to 36 months, with or without simulated cold chain break (either one week at 37 degrees C, or two or four weeks at 25 degrees C). Among the stability-indicating parameters, antigenicity and immunogenicity were evaluated along with L1 antigen integrity and adsorption to aluminum. Differential scanning calorimetry (DSC) was used to investigate the structural stability of the VLPs before and after vaccine formulation and over time. Cervarix was stable at 2-8 degrees C for at least three years, and the occurrence of cold chain break had no impact, as shown by unchanged product characteristics during the full storage period. DSC analysis demonstrated that the structure of the HPV-16 and -18 L1 proteins and their corresponding VLPs was not affected throughout the manufacturing process. Moreover, the structure of aluminum-adsorbed HPV-16 and -18 L1 VLPs was robust over a 14-month test period. In conclusion, Cervarix was very stable upon long-term storage at 2-8 degrees C with or without transient exposure to higher temperatures (up to 37 degrees C). The observed robust structure of the L1 VLPs contributes to the excellent stability of Cervarix.

Dimensional stability performance of a CFRP sandwich optical bench for microsatellite payload

NASA Astrophysics Data System (ADS)

Desnoyers, N.; Goyette, P.; Leduc, B.; Boucher, M.-A.

2017-09-01

Microsatellite market requires high performance while minimizing mass, volume and cost. Telescopes are specifically targeted by these trade-offs. One of these is to use the optomechanical structure of the telescope to mount electronic devices that may dissipate heat. However, such approach may be problematic in terms of distortions due to the presence of high thermal gradients throughout the telescope structure. To prevent thermal distortions, Carbon Fiber Reinforced Polymer (CFRP) technology can be used for the optomechanical telescope material structure. CFRP is typically about 100 times less sensitive to thermal gradients and its coefficient of thermal expansion (CTE) is about 200 to 600 times lower than standard aluminum alloys according to inhouse measurements. Unfortunately, designing with CFRP material is not as straightforward as with metallic materials. There are many parameters to consider in order to reach the desired dimensional stability under thermal, moisture and vibration exposures. Designing optomechanical structures using CFRP involves many challenges such as interfacing with optics and sometimes dealing with high CTE mounting interface structures like aluminum spacecraft buses. INO has designed a CFRP sandwich telescope structure to demonstrate the achievable performances of such technology. Critical parameters have been optimized to maximize the dimensional stability while meeting the stringent environmental requirements that microsatellite payloads have to comply with. The telescope structure has been tested in vacuum from -40°C to +50°C and has shown a good fit with finite element analysis predictions.

Discriminating between stabilizing and destabilizing protein design mutations via recombination and simulation.

PubMed

Johnson, Lucas B; Gintner, Lucas P; Park, Sehoo; Snow, Christopher D

2015-08-01

Accuracy of current computational protein design (CPD) methods is limited by inherent approximations in energy potentials and sampling. These limitations are often used to qualitatively explain design failures; however, relatively few studies provide specific examples or quantitative details that can be used to improve future CPD methods. Expanding the design method to include a library of sequences provides data that is well suited for discriminating between stabilizing and destabilizing design elements. Using thermophilic endoglucanase E1 from Acidothermus cellulolyticus as a model enzyme, we computationally designed a sequence with 60 mutations. The design sequence was rationally divided into structural blocks and recombined with the wild-type sequence. Resulting chimeras were assessed for activity and thermostability. Surprisingly, unlike previous chimera libraries, regression analysis based on one- and two-body effects was not sufficient for predicting chimera stability. Analysis of molecular dynamics simulations proved helpful in distinguishing stabilizing and destabilizing mutations. Reverting to the wild-type amino acid at destabilized sites partially regained design stability, and introducing predicted stabilizing mutations in wild-type E1 significantly enhanced thermostability. The ability to isolate stabilizing and destabilizing elements in computational design offers an opportunity to interpret previous design failures and improve future CPD methods. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Single layers and multilayers of GaN and AlN in square-octagon structure: Stability, electronic properties, and functionalization

NASA Astrophysics Data System (ADS)

Gürbüz, E.; Cahangirov, S.; Durgun, E.; Ciraci, S.

2017-11-01

Further to planar single-layer hexagonal structures, GaN and AlN can also form free-standing, single-layer structures constructed from squares and octagons. We performed an extensive analysis of dynamical and thermal stability of these structures in terms of ab initio finite-temperature molecular dynamics and phonon calculations together with the analysis of Raman and infrared active modes. These single-layer square-octagon structures of GaN and AlN display directional mechanical properties and have wide, indirect fundamental band gaps, which are smaller than their hexagonal counterparts. These density functional theory band gaps, however, increase and become wider upon correction. Under uniaxial and biaxial tensile strain, the fundamental band gaps decrease and can be closed. The electronic and magnetic properties of these single-layer structures can be modified by adsorption of various adatoms, or by creating neutral cation-anion vacancies. The single-layer structures attain magnetic moment by selected adatoms and neutral vacancies. In particular, localized gap states are strongly dependent on the type of vacancy. The energetics, binding, and resulting electronic structure of bilayer, trilayer, and three-dimensional (3D) layered structures constructed by stacking the single layers are affected by vertical chemical bonds between adjacent layers. In addition to van der Waals interaction, these weak vertical bonds induce buckling in planar geometry and enhance their binding, leading to the formation of stable 3D layered structures. In this respect, these multilayers are intermediate between van der Waals solids and wurtzite crystals, offering a wide range of tunability.

Estimation and Analysis of Nonlinear Stochastic Systems. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Marcus, S. I.

1975-01-01

The algebraic and geometric structures of certain classes of nonlinear stochastic systems were exploited in order to obtain useful stability and estimation results. The class of bilinear stochastic systems (or linear systems with multiplicative noise) was discussed. The stochastic stability of bilinear systems driven by colored noise was considered. Approximate methods for obtaining sufficient conditions for the stochastic stability of bilinear systems evolving on general Lie groups were discussed. Two classes of estimation problems involving bilinear systems were considered. It was proved that, for systems described by certain types of Volterra series expansions or by certain bilinear equations evolving on nilpotent or solvable Lie groups, the optimal conditional mean estimator consists of a finite dimensional nonlinear set of equations. The theory of harmonic analysis was used to derive suboptimal estimators for bilinear systems driven by white noise which evolve on compact Lie groups or homogeneous spaces.

On the effect of Ti on the stability of amorphous indium zinc oxide used in thin film transistor applications

NASA Astrophysics Data System (ADS)

Lee, Sunghwan; Paine, David C.

2011-06-01

In2O3-based amorphous oxide channel materials are of increasing interest for thin film transisitor applications due, in part, to the remarkable stability of this class of materials amorphous structure and electronic properties. We report that this stability is degraded in the presence of Ti, which is widely used as a contact and/or adhesion layer. A cross-sectional transmission electron microscopy analysis, supported by glancing incident angle x-ray and selected area diffraction examination, shows that amorphous indium zinc oxide in contact with Ti undergoes crystallization to the bixbyite phase and reacts to form the rutile phase of TiO2 at a temperature of 200 °C. A basic thermodynamic analysis is presented and forms the basis of a model that describes both the crystallization and the resistivity decrease.

New insights into transcription fidelity: thermal stability of non-canonical structures in template DNA regulates transcriptional arrest, pause, and slippage.

PubMed

Tateishi-Karimata, Hisae; Isono, Noburu; Sugimoto, Naoki

2014-01-01

The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (-ΔG°37) in the presence of 20 wt% PEG was more than 8.2 kcal mol(-1). Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs.

New Insights into Transcription Fidelity: Thermal Stability of Non-Canonical Structures in Template DNA Regulates Transcriptional Arrest, Pause, and Slippage

PubMed Central

Tateishi-Karimata, Hisae; Isono, Noburu; Sugimoto, Naoki

2014-01-01

The thermal stability and topology of non-canonical structures of G-quadruplexes and hairpins in template DNA were investigated, and the effect of non-canonical structures on transcription fidelity was evaluated quantitatively. We designed ten template DNAs: A linear sequence that does not have significant higher-order structure, three sequences that form hairpin structures, and six sequences that form G-quadruplex structures with different stabilities. Templates with non-canonical structures induced the production of an arrested, a slipped, and a full-length transcript, whereas the linear sequence produced only a full-length transcript. The efficiency of production for run-off transcripts (full-length and slipped transcripts) from templates that formed the non-canonical structures was lower than that from the linear. G-quadruplex structures were more effective inhibitors of full-length product formation than were hairpin structure even when the stability of the G-quadruplex in an aqueous solution was the same as that of the hairpin. We considered that intra-polymerase conditions may differentially affect the stability of non-canonical structures. The values of transcription efficiencies of run-off or arrest transcripts were correlated with stabilities of non-canonical structures in the intra-polymerase condition mimicked by 20 wt% polyethylene glycol (PEG). Transcriptional arrest was induced when the stability of the G-quadruplex structure (−ΔGo 37) in the presence of 20 wt% PEG was more than 8.2 kcal mol−1. Thus, values of stability in the presence of 20 wt% PEG are an important indicator of transcription perturbation. Our results further our understanding of the impact of template structure on the transcription process and may guide logical design of transcription-regulating drugs. PMID:24594642

Temporal Stability of the Human Skin Microbiome.

PubMed

Oh, Julia; Byrd, Allyson L; Park, Morgan; Kong, Heidi H; Segre, Julia A

2016-05-05

Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states. Copyright © 2016 Elsevier Inc. All rights reserved.

Improving the Mechanical Performance and Thermal Stability of a PVA-Clay Nanocomposite by Electron Beam Irradiation

NASA Astrophysics Data System (ADS)

Shokuhi Rad, A.; Ebrahimi, D.

2017-07-01

The effects of electron beam irradiation and presence of clay on the mechanical properties and thermal stability of montmorillonite clay-modified polyvinyl alcohol nanocomposites were studied. By using the X-ray diffraction (XRD) and transmission electron microscopy (TEM), the microstructure of the nanocomposites was investigated. The results obtained from TEM and XRD tests showed that montmorillonite clay nanoparticles were located in the polyvinyl alcohol phase. The XRD analysis confirmed the formation of an exfoliated structure in nanocomposites samples. Increasing the amount of clay to 20 wt.% increased the tensile strength and modulus of the nanocomposite. Irradiation up to an absorbed dose of 100 kGy increased its mechanical properties and thermal stability, but at higher irradiation levels, the mechanical strength and thermal stability declined. The sample with 20 wt.% of the nanofiller, exposed to 100 kGy, showed the highest mechanical strength and thermal stability.

Analysis of protein stability and ligand interactions by thermal shift assay.

PubMed

Huynh, Kathy; Partch, Carrie L

2015-02-02

Purification of recombinant proteins for biochemical assays and structural studies is time-consuming and presents inherent difficulties that depend on the optimization of protein stability. The use of dyes to monitor thermal denaturation of proteins with sensitive fluorescence detection enables rapid and inexpensive determination of protein stability using real-time PCR instruments. By screening a wide range of solution conditions and additives in a 96-well format, the thermal shift assay easily identifies conditions that significantly enhance the stability of recombinant proteins. The same approach can be used as an initial low-cost screen to discover new protein-ligand interactions by capitalizing on increases in protein stability that typically occur upon ligand binding. This unit presents a methodological workflow for small-scale, high-throughput thermal denaturation of recombinant proteins in the presence of SYPRO Orange dye. Copyright © 2015 John Wiley & Sons, Inc.

Coupling effect and control strategies of the maglev dual-stage inertially stabilization system based on frequency-domain analysis.

PubMed

Lin, Zhuchong; Liu, Kun; Zhang, Li; Zeng, Delin

2016-09-01

Maglev dual-stage inertially stabilization (MDIS) system is a newly proposed system which combines a conventional two-axis gimbal assembly and a 5-DOF (degree of freedom) magnetic bearing with vernier tilting capacity to perform dual-stage stabilization for the LOS of the suspended optical instrument. Compared with traditional dual-stage system, maglev dual-stage system exhibits different characteristics due to the negative position stiffness of the magnetic forces, which introduces additional coupling in the dual stage control system. In this paper, the coupling effect on the system performance is addressed based on frequency-domain analysis, including disturbance rejection, fine stage saturation and coarse stage structural resonance suppression. The difference between various control strategies is also discussed, including pile-up(PU), stabilize-follow (SF) and stabilize-compensate (SC). A number of principles for the design of a maglev dual stage system are proposed. A general process is also suggested, which leads to a cost-effective design striking a balance between high performance and complexity. At last, a simulation example is presented to illustrate the arguments in the paper. Copyright © 2016 ISA. Published by Elsevier Ltd. All rights reserved.

Composite Structural Analysis of Flat-Back Shaped Blade for Multi-MW Class Wind Turbine

NASA Astrophysics Data System (ADS)

Kim, Soo-Hyun; Bang, Hyung-Joon; Shin, Hyung-Ki; Jang, Moon-Seok

2014-06-01

This paper provides an overview of failure mode estimation based on 3D structural finite element (FE) analysis of the flat-back shaped wind turbine blade. Buckling stability, fiber failure (FF), and inter-fiber failure (IFF) analyses were performed to account for delamination or matrix failure of composite materials and to predict the realistic behavior of the entire blade region. Puck's fracture criteria were used for IFF evaluation. Blade design loads applicable to multi-megawatt (MW) wind turbine systems were calculated according to the Germanischer Lloyd (GL) guideline and the International Electrotechnical Commission (IEC) 61400-1 standard, under Class IIA wind conditions. After the post-processing of final load results, a number of principal load cases were selected and converted into applied forces at the each section along the blade's radius of the FE model. Nonlinear static analyses were performed for laminate failure, FF, and IFF check. For buckling stability, linear eigenvalue analysis was performed. As a result, we were able to estimate the failure mode and locate the major weak point.

Molecular conformational analysis, vibrational spectra, NBO analysis and first hyperpolarizability of (2E)-3-phenylprop-2-enoic anhydride based on density functional theory calculations.

PubMed

Sheena Mary, Y; Raju, K; Panicker, C Yohannan; Al-Saadi, Abdulaziz A; Thiemann, Thies; Van Alsenoy, Christian

2014-07-15

The conformational behavior and structural stability of (2E)-3-phenylprop-2-enoic anhydride were investigated by using density functional theory. Seventeen possible stable conformations of the title compound were determined and verified with their calculated vibrational frequencies being all positive. The optimized molecular structure, vibrational wavenumbers, corresponding vibrational assignments of (2E)-3-phenylprop-2-enoic anhydride have been investigated experimentally and theoretically using Gaussian09 software package. Potential energy distribution of normal modes vibrations was done using GAR2PED program. The HOMO and LUMO analysis are used to determine the charge transfer within the molecule. The stability of the molecule arising from hyper-conjugative interaction and charge delocalization has been analyzed using NBO analysis. The calculated first hyperpolarizability of the title compound is 12×10(-30) esu and is 92.31 times that of the standard NLO material urea and the title compound is an attractive object for future studies of nonlinear optical properties. MEP was performed by the DFT method and the predicted infrared intensities and Raman activities have also been reported. Copyright © 2014 Elsevier B.V. All rights reserved.

The Structural and Rank-Order Stability of Temperament in Young Children Based on a Laboratory-Observational Measure

PubMed Central

Dyson, Margaret W.; Olino, Thomas M.; Durbin, C. Emily; Goldsmith, H. Hill; Bufferd, Sara J.; Miller, Anna R.; Klein, Daniel N.

2015-01-01

It is generally assumed that temperament traits exhibit structural and rank-order stability over time. Most of the research on structural and rank-order stability has relied on parent-report measures. The present study used an alternative approach, a laboratory-observational measure (Laboratory Temperament Assessment Battery [Lab-TAB]), to examine the structural and rank-order stability of temperament traits in a community sample of young children (N = 447). Using structural equation modeling (SEM), we found that a similar five-factor structure consisting of the dimensions of Positive Affect/Interest, Sociability, Dysphoria, Fear/Inhibition, and Impulsivity vs. Constraint provided an adequate fit to the data at both age 3 and 6 years, suggesting good structural stability. Moreover, all five latent factors exhibited significant, albeit modest, rank-order stability from age 3 to 6. In addition, there were significant heterotypic associations of age 3 Sociability with age 6 PA/Interest, and age 3 Impulsivity vs. Constraint with age 6 Fear/Inhibition. PMID:25894709

Global analysis of protein folding using massively parallel design, synthesis and testing

PubMed Central

Rocklin, Gabriel J.; Chidyausiku, Tamuka M.; Goreshnik, Inna; Ford, Alex; Houliston, Scott; Lemak, Alexander; Carter, Lauren; Ravichandran, Rashmi; Mulligan, Vikram K.; Chevalier, Aaron; Arrowsmith, Cheryl H.; Baker, David

2017-01-01

Proteins fold into unique native structures stabilized by thousands of weak interactions that collectively overcome the entropic cost of folding. Though these forces are “encoded” in the thousands of known protein structures, “decoding” them is challenging due to the complexity of natural proteins that have evolved for function, not stability. Here we combine computational protein design, next-generation gene synthesis, and a high-throughput protease susceptibility assay to measure folding and stability for over 15,000 de novo designed miniproteins, 1,000 natural proteins, 10,000 point-mutants, and 30,000 negative control sequences, identifying over 2,500 new stable designed proteins in four basic folds. This scale—three orders of magnitude greater than that of previous studies of design or folding—enabled us to systematically examine how sequence determines folding and stability in uncharted protein space. Iteration between design and experiment increased the design success rate from 6% to 47%, produced stable proteins unlike those found in nature for topologies where design was initially unsuccessful, and revealed subtle contributions to stability as designs became increasingly optimized. Our approach achieves the long-standing goal of a tight feedback cycle between computation and experiment, and promises to transform computational protein design into a data-driven science. PMID:28706065

3D structure of individual nanocrystals in solution by electron microscopy

NASA Astrophysics Data System (ADS)

Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

2015-07-01

Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

Stability of large-scale systems with stable and unstable subsystems.

NASA Technical Reports Server (NTRS)

Grujic, Lj. T.; Siljak, D. D.

1972-01-01

The purpose of this paper is to develop new methods for constructing vector Liapunov functions and broaden the application of Liapunov's theory to stability analysis of large-scale dynamic systems. The application, so far limited by the assumption that the large-scale systems are composed of exponentially stable subsystems, is extended via the general concept of comparison functions to systems which can be decomposed into asymptotically stable subsystems. Asymptotic stability of the composite system is tested by a simple algebraic criterion. With minor technical adjustments, the same criterion can be used to determine connective asymptotic stability of large-scale systems subject to structural perturbations. By redefining the constraints imposed on the interconnections among the subsystems, the considered class of systems is broadened in an essential way to include composite systems with unstable subsystems. In this way, the theory is brought substantially closer to reality since stability of all subsystems is no longer a necessary assumption in establishing stability of the overall composite system.

Fundamental Movement Skills Are More than Run, Throw and Catch: The Role of Stability Skills.

PubMed

Rudd, James R; Barnett, Lisa M; Butson, Michael L; Farrow, Damian; Berry, Jason; Polman, Remco C J

2015-01-01

In motor development literature fundamental movement skills are divided into three constructs: locomotive, object control and stability skills. Most fundamental movement skills research has focused on children's competency in locomotor and object control skills. The first aim of this study was to validate a test battery to assess the construct of stability skills, in children aged 6 to 10 (M age = 8.2, SD = 1.2). Secondly we assessed how the stability skills construct fitted into a model of fundamental movement skill. The Delphi method was used to select the stability skill battery. Confirmatory factor analysis (CFA) was used to assess if the skills loaded onto the same construct and a new model of FMS was developed using structural equation modelling. Three postural control tasks were selected (the log roll, rock and back support) because they had good face and content validity. These skills also demonstrated good predictive validity with gymnasts scoring significantly better than children without gymnastic training and children from a high SES school performing better than those from a mid and low SES schools and the mid SES children scored better than the low SES children (all p < .05). Inter rater reliability tests were excellent for all three skills (ICC = 0.81, 0.87, 0.87) as was test re-test reliability (ICC 0.87-0.95). CFA provided good construct validity, and structural equation modelling revealed stability skills to be an independent factor in an overall FMS model which included locomotor (r = .88), object control (r = .76) and stability skills (r = .81). This study provides a rationale for the inclusion of stability skills in FMS assessment. The stability skills could be used alongside other FMS assessment tools to provide a holistic assessment of children's fundamental movement skills.

Electroless nickel – phosphorus coating on crab shell particles and its characterization

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

Arulvel, S., E-mail: gs.arulvel.research@gmail.com; Elayaperumal, A.; Jagatheeshwaran, M.S.

Being hydrophilic material, crab shell particles have only a limited number of applications. It is, therefore, necessary to modify the surface of the crab shell particles. To make them useful ever for the applications, the main theme we proposed in this article is to utilize crab shell particles (CSP) with the core coated with nickel phosphorus (NiP) as a shell using the electroless coating process. For dealing with serious environmental problems, utilization of waste bio-shells is always an important factor to be considered. Chelating ability of crab shell particles eliminates the surface activation in this work proceeding to the coatingmore » process. The functional group, phase structure, microstructure, chemical composition and thermal analysis of CSP and NiP/CSP were characterized using Fourier transform infra-red spectroscopy (FTIR), x-ray diffraction analyzer (XRD), scanning electron microscope (SEM), energy-dispersive x-ray spectroscopy (EDS), and thermogravimetric analysis (TGA). The combination of an amorphous and crystalline structure was exhibited by CSP and NiP/CSP. NiP/CSP has shown a better thermal stability when compared to uncoated CSP. Stability test, adsorption test, and conductivity test were conducted for the study of adsorption behavior and conductivity of the particles. CSP presented a hydrophilic property in contrast to hydrophobic NiP/CSP. NiP/CSP presented a conductivity of about 44% greater compared to the CSP without any fluctuations. - Highlights: • Utilization of crab shell waste is focused on. • NiP coating on crab shell particle is fabricated using electroless process. • Thermal analysis, stability test, adsorption test and conductivity test were done. • Organic matrix of crab shell particle favors the coating process. • Results demonstrate the characterization of CSP core – NiP shell structure.« less

Phase stabilities at a glance: Stability diagrams of nickel dipnictides

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

Bachhuber, F.; School of Chemical Sciences, The University of Auckland, Private Bag 92019, Auckland; Rothballer, J.

2013-12-07

In the course of the recent advances in chemical structure prediction, a straightforward type of diagram to evaluate phase stabilities is presented based on an expedient example. Crystal structures and energetic stabilities of dipnictides NiPn{sub 2} (Pn = N, P, As, Sb, Bi) are systematically investigated by first principles calculations within the framework of density functional theory using the generalized gradient approximation to treat exchange and correlation. These dipnictides show remarkable polymorphism that is not yet understood systematically and offers room for the discovery of new phases. Relationships between the concerned structures including the marcasite, the pyrite, the arsenopyrite/CoSb{sub 2},more » and the NiAs{sub 2} types are highlighted by means of common structural fragments. Electronic stabilities of experimentally known and related AB{sub 2} structure types are presented graphically in so-called stability diagrams. Additionally, competing binary phases are taken into consideration in the diagrams to evaluate the stabilities of the title compounds with respect to decomposition. The main purpose of the stability diagrams is the introduction of an image that enables the estimation of phase stabilities at a single glance. Beyond that, some of the energetically favored structure types can be identified as potential new phases.« less

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function.

PubMed

Krüger, Dennis M; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-07-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein's (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement.

CNA web server: rigidity theory-based thermal unfolding simulations of proteins for linking structure, (thermo-)stability, and function

PubMed Central

Krüger, Dennis M.; Rathi, Prakash Chandra; Pfleger, Christopher; Gohlke, Holger

2013-01-01

The Constraint Network Analysis (CNA) web server provides a user-friendly interface to the CNA approach developed in our laboratory for linking results from rigidity analyses to biologically relevant characteristics of a biomolecular structure. The CNA web server provides a refined modeling of thermal unfolding simulations that considers the temperature dependence of hydrophobic tethers and computes a set of global and local indices for quantifying biomacromolecular stability. From the global indices, phase transition points are identified where the structure switches from a rigid to a floppy state; these phase transition points can be related to a protein’s (thermo-)stability. Structural weak spots (unfolding nuclei) are automatically identified, too; this knowledge can be exploited in data-driven protein engineering. The local indices are useful in linking flexibility and function and to understand the impact of ligand binding on protein flexibility. The CNA web server robustly handles small-molecule ligands in general. To overcome issues of sensitivity with respect to the input structure, the CNA web server allows performing two ensemble-based variants of thermal unfolding simulations. The web server output is provided as raw data, plots and/or Jmol representations. The CNA web server, accessible at http://cpclab.uni-duesseldorf.de/cna or http://www.cnanalysis.de, is free and open to all users with no login requirement. PMID:23609541

Development of biocomposed material based on zirconium oxide for regeneration of bone tissue

NASA Astrophysics Data System (ADS)

Lytkin, Ivan; Buyakov, Ales; Kurzina, Irina

2017-11-01

Porous ceramic materials based on magnesium oxide stabilized zirconia were studied. The pore structure and thin crystalline structure were studied. The porosity of some of the materials studied was obtained by conducting a pore-forming additive, UHMWPE. It is shown that after impregnation with polylactide, the residual porosity varies from 22.5 to 5.9%. The average pore size was 2 µm. X-Ray diffraction analysis showed that the fine crystal structure of the ceramic is mainly represented by baddeleyite.

ASTROP2-LE: A Mistuned Aeroelastic Analysis System Based on a Two Dimensional Linearized Euler Solver

NASA Technical Reports Server (NTRS)

Reddy, T. S. R.; Srivastava, R.; Mehmed, Oral

2002-01-01

An aeroelastic analysis system for flutter and forced response analysis of turbomachines based on a two-dimensional linearized unsteady Euler solver has been developed. The ASTROP2 code, an aeroelastic stability analysis program for turbomachinery, was used as a basis for this development. The ASTROP2 code uses strip theory to couple a two dimensional aerodynamic model with a three dimensional structural model. The code was modified to include forced response capability. The formulation was also modified to include aeroelastic analysis with mistuning. A linearized unsteady Euler solver, LINFLX2D is added to model the unsteady aerodynamics in ASTROP2. By calculating the unsteady aerodynamic loads using LINFLX2D, it is possible to include the effects of transonic flow on flutter and forced response in the analysis. The stability is inferred from an eigenvalue analysis. The revised code, ASTROP2-LE for ASTROP2 code using Linearized Euler aerodynamics, is validated by comparing the predictions with those obtained using linear unsteady aerodynamic solutions.

Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily.

PubMed

Hou, Guanhua; Cui, Qiang

2013-07-17

The first step for the hydrolysis of a phosphate monoester (pNPP(2-)) in enzymes of the alkaline phosphatase (AP) superfamily, R166S AP and wild-type NPP, is studied using QM/MM simulations based on an approximate density functional theory (SCC-DFTBPR) and a recently introduced QM/MM interaction Hamiltonian. The calculations suggest that similar loose transition states are involved in both enzymes, despite the fact that phosphate monoesters are the cognate substrates for AP but promiscuous substrates for NPP. The computed loose transition states are clearly different from the more synchronous ones previously calculated for diester reactions in the same AP enzymes. Therefore, our results explicitly support the proposal that AP enzymes are able to recognize and stabilize different types of transition states in a single active site. Analysis of the structural features of computed transition states indicates that the plastic nature of the bimetallic site plays a minor role in accommodating multiple types of transition states and that the high degree of solvent accessibility of the AP active site also contributes to its ability to stabilize diverse transition-state structures without the need of causing large structural distortions of the bimetallic motif. The binding mode of the leaving group in the transition state highlights that vanadate may not always be an ideal transition state analog for loose phosphoryl transfer transition states.

Basin stability measure of different steady states in coupled oscillators

NASA Astrophysics Data System (ADS)

Rakshit, Sarbendu; Bera, Bidesh K.; Majhi, Soumen; Hens, Chittaranjan; Ghosh, Dibakar

2017-04-01

In this report, we investigate the stabilization of saddle fixed points in coupled oscillators where individual oscillators exhibit the saddle fixed points. The coupled oscillators may have two structurally different types of suppressed states, namely amplitude death and oscillation death. The stabilization of saddle equilibrium point refers to the amplitude death state where oscillations are ceased and all the oscillators converge to the single stable steady state via inverse pitchfork bifurcation. Due to multistability features of oscillation death states, linear stability theory fails to analyze the stability of such states analytically, so we quantify all the states by basin stability measurement which is an universal nonlocal nonlinear concept and it interplays with the volume of basins of attractions. We also observe multi-clustered oscillation death states in a random network and measure them using basin stability framework. To explore such phenomena we choose a network of coupled Duffing-Holmes and Lorenz oscillators which are interacting through mean-field coupling. We investigate how basin stability for different steady states depends on mean-field density and coupling strength. We also analytically derive stability conditions for different steady states and confirm by rigorous bifurcation analysis.

A conformal approach for the analysis of the non-linear stability of radiation cosmologies

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

Luebbe, Christian, E-mail: c.luebbe@ucl.ac.uk; Department of Mathematics, University of Leicester, University Road, LE1 8RH; Valiente Kroon, Juan Antonio, E-mail: j.a.valiente-kroon@qmul.ac.uk

2013-01-15

The conformal Einstein equations for a trace-free (radiation) perfect fluid are derived in terms of the Levi-Civita connection of a conformally rescaled metric. These equations are used to provide a non-linear stability result for de Sitter-like trace-free (radiation) perfect fluid Friedman-Lemaitre-Robertson-Walker cosmological models. The solutions thus obtained exist globally towards the future and are future geodesically complete. - Highlights: Black-Right-Pointing-Pointer We study the Einstein-Euler system in General Relativity using conformal methods. Black-Right-Pointing-Pointer We analyze the structural properties of the associated evolution equations. Black-Right-Pointing-Pointer We establish the non-linear stability of pure radiation cosmological models.

Proceedings of the Workshop on Identification and Control of Flexible Space Structures, Volume 2

NASA Technical Reports Server (NTRS)

Rodriguez, G. (Editor)

1985-01-01

The results of a workshop on identification and control of flexible space structures held in San Diego, CA, July 4 to 6, 1984 are discussed. The main objectives of the workshop were to provide a forum to exchange ideas in exploring the most advanced modeling, estimation, identification and control methodologies to flexible space structures. The workshop responded to the rapidly growing interest within NASA in large space systems (space station, platforms, antennas, flight experiments) currently under design. Dynamic structural analysis, control theory, structural vibration and stability, and distributed parameter systems are discussed.

Physical Analysis Work for Slope Stability at Shah Alam, Selangor

NASA Astrophysics Data System (ADS)

Ishak, M. F.; Zaini, M. S. I.

2018-04-01

Slope stability analysis is performed to assess the equilibrium conditions and the safe design of a human-made or natural slope to find the endangered areas. Investigation of potential failure and determination of the slope sensitivity with regard to safety, reliability and economics were parts of this study. Ground anchor is designed to support a structure in this study. Ground anchor were implemented at the Mechanically Stabilized Earth (MSE) wall along Anak Persiaran Jubli Perak to overcome the further cracking of pavement parking, concrete deck and building of the Apartments. A result from the laboratory testing of soil sample such as index test and shear strength test were applied to the Slope/W software with regard to the ground anchors that were implemented. The ground anchors were implemented to increase the value of the factor of safety (FOS) of the MSE Wall. The value of the factor of safety (FOS) before implementing the ground anchor was 0.800 and after the ground anchor was implemented the value increase to 1.555. The increase percentage of factor of safety by implementing on stability of slope was 94.38%.

A Coupled Aeroelastic Model for Launch Vehicle Stability Analysis

NASA Technical Reports Server (NTRS)

Orr, Jeb S.

2010-01-01

A technique for incorporating distributed aerodynamic normal forces and aeroelastic coupling effects into a stability analysis model of a launch vehicle is presented. The formulation augments the linear state-space launch vehicle plant dynamics that are compactly derived as a system of coupled linear differential equations representing small angular and translational perturbations of the rigid body, nozzle, and sloshing propellant coupled with normal vibration of a set of orthogonal modes. The interaction of generalized forces due to aeroelastic coupling and thrust can be expressed as a set of augmenting non-diagonal stiffness and damping matrices in modal coordinates with no penalty on system order. While the eigenvalues of the structural response in the presence of thrust and aeroelastic forcing can be predicted at a given flight condition independent of the remaining degrees of freedom, the coupled model provides confidence in closed-loop stability in the presence of rigid-body, slosh, and actuator dynamics. Simulation results are presented that characterize the coupled dynamic response of the Ares I launch vehicle and the impact of aeroelasticity on control system stability margins.

Development of topologically structured membranes of aluminum oxide

NASA Astrophysics Data System (ADS)

Bankova, A.; Videkov, V.; Tzaneva, B.

2014-05-01

In recent years, nanomembranes have become one of the most widely used construction material for ultrasensitive and ultrathin applications in micro-electromechanical systems (MEMS) and other sensor structures due to their remarkable mechanical properties. Among these, the mechanical stability is of particular importance. We present an approach to the analysis of the stability of nanostructured anodic aluminum oxide free membranes subjected to mechanical bending. The membranes tested were with a thickness of 500 nm to 15 urn in various topological shapes; we describe the technological schemes of their preparation. Bends were applied to membranes prepared by using a selective process of etching and anodizing. The results of the preparation of the membranes are discussed, together with the influence of the angle of deflection, and the number of bendings. The results obtained can be used in designing MEMS structures and sensors which use nanostructured anodic aluminum oxide.

Maltose-neopentyl glycol (MNG) amphiphiles for solubilization, stabilization and crystallization of membrane proteins

PubMed Central

Chae, Pil Seok; Rasmussen, Søren G. F.; Rana, Rohini; Gotfryd, Kamil; Chandra, Richa; Goren, Michael A.; Kruse, Andrew C.; Nurva, Shailika; Loland, Claus J.; Pierre, Yves; Drew, David; Popot, Jean-Luc; Picot, Daniel; Fox, Brian G.; Guan, Lan; Gether, Ulrik; Byrne, Bernadette; Kobilka, Brian; Gellman, Samuel H.

2011-01-01

The understanding of integral membrane protein (IMP) structure and function is hampered by the difficulty of handling these proteins. Aqueous solubilization, necessary for many types of biophysical analysis, generally requires a detergent to shield the large lipophilic surfaces displayed by native IMPs. Many proteins remain difficult to study owing to a lack of suitable detergents. We introduce a class of amphiphiles, each of which is built around a central quaternary carbon atom derived from neopentyl glycol, with hydrophilic groups derived from maltose. Representatives of this maltose-neopentyl glycol (MNG) amphiphile family display favorable behavior relative to conventional detergents, as tested on multiple membrane protein systems, leading to enhanced structural stability and successful crystallization. MNG amphiphiles are promising tools for membrane protein science because of the ease with which they may be prepared and the facility with which their structures may be varied. PMID:21037590

The self-concept and conjugal loss: evidence for structural change.

PubMed

Montpetit, Mignon A; Bergeman, C S; Bisconti, Toni L

2010-08-01

The self-concept is often considered to be a personal resource that individuals may use to cope with life stressors, but little is known about how this entity might itself change in response to profound stress. The present study examines structural change in self-concept following conjugal loss in later life. Analyses were conducted on data collected from 57 widows every 4 months over the first 2 years post-loss. The first objective was to explore the adequacy of an operational definition of the self-concept as a latent construct lying at the confluence of self-esteem, perceived environmental mastery, and optimism. Because confirmatory factor analysis (CFA) supported this theoretically based conceptualization, the second objective of the study was to model stability and change in the structure of the self-concept over the 2-year study period. Results suggested that there is both stability and change in the self-system during the adjustment to major life stress.

Structure and stability of M6N8 clusters (M = Si, Ge, Sn, Ti).

PubMed

Davydova, Elena I; Timoshkin, Alexey Y; Frenking, Gernot

2010-06-10

The structures and stabilities of the M(6)N(8) clusters (M = Si, Ge, Sn, Ti) have been theoretically studied at DFT and ab initio levels of theory. Two new isomers have been considered: cage-like molecules and propeller-like molecules. It is shown that only for M = Si are both isomers true minima on the potential energy surface. The thermodynamics of the dissociation process (1/6)M(6)N(8) --> (1/3)M(3)N(4) is discussed. For each M(3)N(4) molecule, four structures with different multiplicity are considered. The thermodynamic analysis shows that independently of the multiplicity of M(3)N(4) nitrides all M(6)N(8) clusters are stable in the gas phase in a wide temperature range and could be potential intermediates in chemical vapor deposition of the nitride materials.

A Euclidean Perspective on the Unfolding of Azurin: Spatial Correlations

PubMed Central

Warren, Jeffrey J.; Gray, Harry B.; Winkler, Jay R.; Kozak, John J.

2013-01-01

We investigate the stability to structural perturbation of Pseudomonas aeruginosa azurin using a previously developed geometric model. Our analysis considers Ru(2,2′,6′,2″-terpyridine)(1,10-phenanthroline)(His83)-labeled wild-type azurin and five variants with mutations to Cu-ligating residues. We find that in the early stages of unfolding, the β-strands exhibit the most structural stability. The conserved residues comprising the hydrophobic core are dislocated only after nearly complete unfolding of the β-barrel. Attachment of the Ru-complex at His83 does not destabilize the protein fold, despite causing some degree of structural rearrangement. Notably, replacing the Cys112 and/or Met121 Cu ligands does not affect the conformational integrity of the protein. Notably, these results are in accord with experimental evidence, as well as molecular dynamics simulations of the denaturation of azurin. PMID:23853392

Characterization of beta-turn and Asx-turns mimicry in a model peptide: stabilization via C--H . . . O interaction.

PubMed

Thakur, A K; Kishore, R

2006-04-15

The chemical synthesis and single-crystal X-ray diffraction analysis of a model peptide, Boc-Thr-Thr-NH2 (1) comprised of proteinogenic residues bearing an amphiphilic Cbeta -stereogenic center, has been described. Interestingly, the analysis of its molecular structure revealed the existence of a distinct conformation that mimics a typical beta-turn and Asx-turns, i.e., the two Thr residues occupy the left- and right-corner positions. The main-chain torsion angles of the N- and C-terminal residues i.e., semiextended: phi = -68.9 degrees , psi = 128.6 degrees ; semifolded: phi = -138.1 degrees , psi = 2.5 degrees conformations, respectively, in conjunction with a gauche- disposition of the obligatory C-terminus Thr CgammaH3 group, characterize the occurrence of the newly described beta-turn- and Asx-turns-like topology. The preferred molecular structure is suggested to be stabilized by an effective nonconventional main-chain to side-chain Ci=O . . . H--Cgamma(i+2)-type intraturn hydrogen bond. Noteworthy, the observed topology of the resulting 10-membered hydrogen-bonded ring is essentially similar to the one perceived for a classical beta-turn and the Asx-turns, stabilized by a conventional intraturn hydrogen bond. Considering the signs as well as magnitudes of the backbone torsion angles and the orientation of the central peptide bond, the overall mimicked topology resembles the type II beta-turn or type II Asx-turns. An analysis of Xaa-Thr sequences in high-resolution X-ray elucidated protein structures revealed the novel topology prevalence in functional proteins (unpublished). In view of indubitable structural as well as functional importance of nonconventional interactions in bioorganic and biomacromolecules, we intend to highlight the participation of Thr CgammaH in the creation of a short-range C=O . . . H--Cgamma -type interaction in peptides and proteins. Copyright 2006 Wiley Periodicals, Inc.

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins.

PubMed

Stetz, Gabrielle; Verkhivker, Gennady M

2015-01-01

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones.

Dancing through Life: Molecular Dynamics Simulations and Network-Centric Modeling of Allosteric Mechanisms in Hsp70 and Hsp110 Chaperone Proteins

PubMed Central

Stetz, Gabrielle; Verkhivker, Gennady M.

2015-01-01

Hsp70 and Hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. Although many aspects of allosteric regulatory mechanisms in Hsp70 and Hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. In this work, we have combined molecular dynamics simulations and protein stability analysis of the chaperone structures with the network modeling of residue interaction networks to characterize molecular determinants of allosteric mechanisms. We have shown that allosteric mechanisms of Hsp70 and Hsp110 chaperones may be primarily determined by nucleotide-induced redistribution of local conformational ensembles in the inter-domain regions and the substrate binding domain. Conformational dynamics and energetics of the peptide substrate binding with the Hsp70 structures has been analyzed using free energy calculations, revealing allosteric hotspots that control negative cooperativity between regulatory sites. The results have indicated that cooperative interactions may promote a population-shift mechanism in Hsp70, in which functional residues are organized in a broad and robust allosteric network that can link the nucleotide-binding site and the substrate-binding regions. A smaller allosteric network in Hsp110 structures may elicit an entropy-driven allostery that occurs in the absence of global structural changes. We have found that global mediating residues with high network centrality may be organized in stable local communities that are indispensable for structural stability and efficient allosteric communications. The network-centric analysis of allosteric interactions has also established that centrality of functional residues could correlate with their sensitivity to mutations across diverse chaperone functions. This study reconciles a wide spectrum of structural and functional experiments by demonstrating how integration of molecular simulations and network-centric modeling may explain thermodynamic and mechanistic aspects of allosteric regulation in chaperones. PMID:26619280

Effect of cobalt doping on crystallinity, stability, magnetic and optical properties of magnetic iron oxide nano-particles

NASA Astrophysics Data System (ADS)

Anjum, Safia; Tufail, Rabia; Rashid, Khalid; Zia, Rehana; Riaz, S.

2017-06-01

This paper is dedicated to investigate the effect of Co2+ ions in magnetite Fe3O4 nano-particles with stoichiometric formula CoxFe3-xO4 where (x = 0, 0.05, 0.1 and 0.15) prepared by co-precipitation method. The structural, thermal, morphological, magnetic and optical properties of magnetite and Co2+ doped magnetite nanoparticles have been carried out using X-ray Diffractometer, Fourier Transform Infrared Spectroscopy, Themogravimetric Analysis, Scanning Electron Microscopy, Vibrating Sample Magnetometer (VSM) and UV-Vis Spectrometer (UV-Vis) respectively. Structural analysis verified the formation of single phase inverse spinel cubic structure with decrease in lattice parameters due to increase in cobalt content. FTIR analysis confirms the single phase of CoxFe3-xO4 nanoparticles with the major band at 887 cm-1, which might be due to the stretching vibrations of metal-oxide bond. The DSC results corroborate the finding of an increase in the maghemite to hematite phase transition temperature with increase in Co2+ content. The decrease in enthalpy with increase in Co2+ concentration attributed to the fact that the degree of conversion from maghemite to hematite decrease which shows that the stability increases with increasing Co2+ content in B-site of Fe3O4 structure. SEM analysis demonstrated the formation of spherical shaped nanoparticles with least agglomeration. The magnetic measurements enlighten that the coercivity and anisotropy of CoxFe3-xO4 nanoparticles are significantly increased. From UV-Vis analysis it is revealed that band gap energy increases with decreasing particle size. This result has a great interest for magnetic fluid hyperthermia application (MPH).

Control-structure interaction in precision pointing servo loops

NASA Technical Reports Server (NTRS)

Spanos, John T.

1989-01-01

The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

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.

Crystal structure of a multi-domain human smoothened receptor in complex with a super stabilizing ligand

DOE PAGES

Zhang, Xianjun; Zhao, Fei; Wu, Yiran; ...

2017-05-17

Here, the Smoothened receptor (SMO) belongs to the Class Frizzled of the G protein-coupled receptor (GPCR) superfamily, constituting a key component of the Hedgehog signalling pathway. Here we report the crystal structure of the multi-domain human SMO, bound and stabilized by a designed tool ligand TC114, using an X-ray free-electron laser source at 2.9 Å. The structure reveals a precise arrangement of three distinct domains: a seven-transmembrane helices domain (TMD), a hinge domain (HD) and an intact extracellular cysteine-rich domain (CRD). This architecture enables allosteric interactions between the domains that are important for ligand recognition and receptor activation. By combiningmore » the structural data, molecular dynamics simulation, and hydrogen-deuterium-exchange analysis, we demonstrate that transmembrane helix VI, extracellular loop 3 and the HD play a central role in transmitting the signal employing a unique GPCR activation mechanism, distinct from other multi-domain GPCRs.« less

A novel integrated framework and improved methodology of computer-aided drug design.

PubMed

Chen, Calvin Yu-Chian

2013-01-01

Computer-aided drug design (CADD) is a critical initiating step of drug development, but a single model capable of covering all designing aspects remains to be elucidated. Hence, we developed a drug design modeling framework that integrates multiple approaches, including machine learning based quantitative structure-activity relationship (QSAR) analysis, 3D-QSAR, Bayesian network, pharmacophore modeling, and structure-based docking algorithm. Restrictions for each model were defined for improved individual and overall accuracy. An integration method was applied to join the results from each model to minimize bias and errors. In addition, the integrated model adopts both static and dynamic analysis to validate the intermolecular stabilities of the receptor-ligand conformation. The proposed protocol was applied to identifying HER2 inhibitors from traditional Chinese medicine (TCM) as an example for validating our new protocol. Eight potent leads were identified from six TCM sources. A joint validation system comprised of comparative molecular field analysis, comparative molecular similarity indices analysis, and molecular dynamics simulation further characterized the candidates into three potential binding conformations and validated the binding stability of each protein-ligand complex. The ligand pathway was also performed to predict the ligand "in" and "exit" from the binding site. In summary, we propose a novel systematic CADD methodology for the identification, analysis, and characterization of drug-like candidates.

Stability analysis of rockmass using a hydrogeologic model of groundwater flow at an underground limestone mine in Korea

NASA Astrophysics Data System (ADS)

Baek, H.; Kim, D.; Kim, G.; Kim, D.; Cheong, S.

2017-12-01

The safety and environmental issues should be addressed for sustainable mining operations. One of the key factors is the groundwater flow into underground mine workings, which will affect the overall workability and efficiency of the mining operation. Prediction of the groundwater inflow requires a detailed knowledge of the geologic conditions, including the presence of major faults and other geologic structures at the mine site. The hydrologic boundaries and depth of the phreatic surface of the mine area, as well as other relevant properties of the rockmass, are also provided. The stability of underground structures, in terms of the maximum stresses and deformations within the rockmass, can be analyzed using either the total stress or the effective stress approaches. Both the dried and saturated conditions should be considered with appropriate safety factors, as the distribution of the water pressure within the rockmass resulted from the groundwater flow directly affects the stability. In some cases, the rockmass rating systems such as the RMR and Q-systems are also applied. Various numerical codes have been used to construct the hydrogeologic models of mine sites, and the MINEDW by Itasca is one of those groundwater flow model codes developed to simulate groundwater flow related to mining. In this study, with a 3D hydrogeologic model constructed using the MINEDW for an underground limestone mine, the rate of mine water inflow and the porewater pressure were estimated. The stability of mine pillars and adits was analyzed adopting the porewater pressure and effective stress developed in the rockmass. The results were also compared with those from other 2D stability analysis procedures.

Structure-based activity prediction of CYP21A2 stability variants: A survey of available gene variations.

PubMed

Bruque, Carlos D; Delea, Marisol; Fernández, Cecilia S; Orza, Juan V; Taboas, Melisa; Buzzalino, Noemí; Espeche, Lucía D; Solari, Andrea; Luccerini, Verónica; Alba, Liliana; Nadra, Alejandro D; Dain, Liliana

2016-12-14

Congenital adrenal hyperplasia due to 21-hydroxylase deficiency accounts for 90-95% of CAH cases. In this work we performed an extensive survey of mutations and SNPs modifying the coding sequence of the CYP21A2 gene. Using bioinformatic tools and two plausible CYP21A2 structures as templates, we initially classified all known mutants (n = 343) according to their putative functional impacts, which were either reported in the literature or inferred from structural models. We then performed a detailed analysis on the subset of mutations believed to exclusively impact protein stability. For those mutants, the predicted stability was calculated and correlated with the variant's expected activity. A high concordance was obtained when comparing our predictions with available in vitro residual activities and/or the patient's phenotype. The predicted stability and derived activity of all reported mutations and SNPs lacking functional assays (n = 108) were assessed. As expected, most of the SNPs (52/76) showed no biological implications. Moreover, this approach was applied to evaluate the putative synergy that could emerge when two mutations occurred in cis. In addition, we propose a putative pathogenic effect of five novel mutations, p.L107Q, p.L122R, p.R132H, p.P335L and p.H466fs, found in 21-hydroxylase deficient patients of our cohort.

Structure-based activity prediction of CYP21A2 stability variants: A survey of available gene variations

PubMed Central

Bruque, Carlos D.; Delea, Marisol; Fernández, Cecilia S.; Orza, Juan V.; Taboas, Melisa; Buzzalino, Noemí; Espeche, Lucía D.; Solari, Andrea; Luccerini, Verónica; Alba, Liliana; Nadra, Alejandro D.; Dain, Liliana

2016-01-01

Congenital adrenal hyperplasia due to 21-hydroxylase deficiency accounts for 90–95% of CAH cases. In this work we performed an extensive survey of mutations and SNPs modifying the coding sequence of the CYP21A2 gene. Using bioinformatic tools and two plausible CYP21A2 structures as templates, we initially classified all known mutants (n = 343) according to their putative functional impacts, which were either reported in the literature or inferred from structural models. We then performed a detailed analysis on the subset of mutations believed to exclusively impact protein stability. For those mutants, the predicted stability was calculated and correlated with the variant’s expected activity. A high concordance was obtained when comparing our predictions with available in vitro residual activities and/or the patient’s phenotype. The predicted stability and derived activity of all reported mutations and SNPs lacking functional assays (n = 108) were assessed. As expected, most of the SNPs (52/76) showed no biological implications. Moreover, this approach was applied to evaluate the putative synergy that could emerge when two mutations occurred in cis. In addition, we propose a putative pathogenic effect of five novel mutations, p.L107Q, p.L122R, p.R132H, p.P335L and p.H466fs, found in 21-hydroxylase deficient patients of our cohort. PMID:27966633

Ceria based inverse opals for thermochemical fuel production: Quantification and prediction of high temperature behavior

NASA Astrophysics Data System (ADS)

Casillas, Danielle Courtney

Solar energy has the potential to supply more than enough energy to meet humanity's energy demands. Here, a method for thermochemical solar energy storage through fuel production is presented. A porous non-stoichiometric oxide, ceria, undergoes partial thermal reduction and oxidation with concentrated solar energy as a heat source, and water as an oxidant. The resulting yields for hydrogen fuel and oxygen are produced in two discrete steps, while the starting material maintains its original phase. Ordered porosity has been shown superior to random porosity for thermochemical fuel production applications, but stability limits for these structures are currently undefined. Ceria-based inverse opals are currently being investigated to assess the architectural influence on thermochemical hydrogen production. Low tortuosity and continuous interconnected pore network allow for facile gas transport and improved reaction kinetics. Ceria-based ordered materials have recently been shown to increase maximum hydrogen production over non-ordered porous ceria. Thermal stability of ordered porosity was quantified using quantitative image analysis. Fourier analysis was applied to SEM images of the material. The algorithm results in an order parameter gamma that describes the degree of long range order maintained by these structures, where gamma>4 signifies ordered porosity. According to this metric, a minimum zirconium content of 20 atomic percent (at%) is necessary for these architectures to survive aggressive annealing up to 1000°C. Zirconium substituted ceria (ZSC) with Zr loadings in excess of 20at% developed undesired tetragonal phases. Through gamma, we were able to find a balance between the benefit of zirconium additions on structural stability and its negative impact on phase. This work demonstrates the stability of seemingly delicate architectures, and the operational limit for ceria based inverse opals to be 1000°C for 1microm pore size. Inverse opals having sub-micron pores did not sustain ordered structures after heating, and those larger than 1microm had reinforced structural stability. Furthermore, this analysis was applied to materials which underwent isothermal hydrogen/water redox cycles. ZDC20 inverse opals having 300, 650 and 1000nm pore sizes maintained ordered porosity at 800°C, indicating a novel opportunity for use at higher temperatures. The mechanism of inverse opal degradation was investigated. Both in situ and ex situ electron microscopy studies were performed on inverse opals subjected to high temperatures. Coarsening by surface diffusion was found to be the dominant grain growth mechanism. The inverse opal grain growth mechanism was found to deviate from that of porous materials due to the high porosity and an upper limit to grain size caused by structural confinement. Furthermore, in situ experiments enabled correlation of nano-scale grain growth to micro-scale feature changes, resulting in an empirical relationship. Lastly, this dissertation presents an investigation of the effect of ordered porosity on hydrogen production rate and quantity. These results differ from those presented in literature, and an opportunity for further investigation is proposed.

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

PubMed

Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

2017-02-15

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala) n n ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala) 2 , as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

The influence of gyroscopic forces on the dynamic behavior and flutter of rotating blades

NASA Technical Reports Server (NTRS)

Sisto, F.; Chang, A. T.

1983-01-01

The structural dynamics of a cantilever turbomachine blade mounted on a spinning and precessing rotor are investigated. Both stability and forced vibration are considered with a blade model that increases in complexity (and verisimilitude) from a spring-restrained point mass, to a uniform cantilever, to a twisted uniform cantilever turbomachine blade mounted on a spinning and precessing rotor are investigated. Both stability and forced vibration are considered with a blade model that increases in complexity (and verisimilitude) from a spring-restrained point mass, to a uniform cantilever, to a twisted uniform cantilever, to a tapered twisted cantilever of arbitrary cross-section. In every instance the formulation is from first principles using a finite element based on beam theory. Both ramp-type and periodic-type precessional angular displacements are considered. In concluding, forced vibrating and flutter are studied using the final and most sophisticated structural model. The analysis of stability is presented and a number of numerical examples are worked out.

Molecular Simulation Uncovers the Conformational Space of the λ Cro Dimer in Solution

PubMed Central

Ahlstrom, Logan S.; Miyashita, Osamu

2011-01-01

The significant variation among solved structures of the λ Cro dimer suggests its flexibility. However, contacts in the crystal lattice could have stabilized a conformation which is unrepresentative of its dominant solution form. Here we report on the conformational space of the Cro dimer in solution using replica exchange molecular dynamics in explicit solvent. The simulated ensemble shows remarkable correlation with available x-ray structures. Network analysis and a free energy surface reveal the predominance of closed and semi-open dimers, with a modest barrier separating these two states. The fully open conformation lies higher in free energy, indicating that it requires stabilization by DNA or crystal contacts. Most NMR models are found to be unstable conformations in solution. Intersubunit salt bridging between Arg4 and Glu53 during simulation stabilizes closed conformations. Because a semi-open state is among the low-energy conformations sampled in simulation, we propose that Cro-DNA binding may not entail a large conformational change relative to the dominant dimer forms in solution. PMID:22098751

GRMHD/RMHD Simulations and Stability of Magnetized Spine-Sheath Relativistic Jets

NASA Technical Reports Server (NTRS)

Hardee, Philip; Mizuno, Yosuke; Nishikawa, Ken-Ichi

2007-01-01

A new general relativistic magnetohydrodynamics (GRMHD ) code "RAISHIN" used to simulate jet generation by rotating and non-rotating black holes with a geometrically thin Keplarian accretion disk finds that the jet develops a spine-sheath structure in the rotating black hole case. Spine-sheath structure and strong magnetic fields significantly modify the Kelvin-Helmholtz (KH) velocity shear driven instability. The RAISHIN code has been used in its relativistic magnetohydrodynamic (RMHD) configuration to study the effects of strong magnetic fields and weakly relativistic sheath motion, cl2, on the KH instability associated with a relativistic, Y = 2.5, jet spine-sheath interaction. In the simulations sound speeds up to ? c/3 and Alfven wave speeds up to ? 0.56 c are considered. Numerical simulation results are compared to theoretical predictions from a new normal mode analysis of the RMHD equations. Increased stability of a weakly magnetized system resulting from c/2 sheath speeds and stabilization of a strongly magnetized system resulting from d 2 sheath speeds is found.

Practical robustness measures in multivariable control system analysis. Ph.D. Thesis

NASA Technical Reports Server (NTRS)

Lehtomaki, N. A.

1981-01-01

The robustness of the stability of multivariable linear time invariant feedback control systems with respect to model uncertainty is considered using frequency domain criteria. Available robustness tests are unified under a common framework based on the nature and structure of model errors. These results are derived using a multivariable version of Nyquist's stability theorem in which the minimum singular value of the return difference transfer matrix is shown to be the multivariable generalization of the distance to the critical point on a single input, single output Nyquist diagram. Using the return difference transfer matrix, a very general robustness theorem is presented from which all of the robustness tests dealing with specific model errors may be derived. The robustness tests that explicitly utilized model error structure are able to guarantee feedback system stability in the face of model errors of larger magnitude than those robustness tests that do not. The robustness of linear quadratic Gaussian control systems are analyzed.

Antioxidant study of quercetin and their metal complex and determination of stability constant by spectrophotometry method.

PubMed

Ravichandran, R; Rajendran, M; Devapiriam, D

2014-03-01

Quercetin found chelate cadmium ions, scavenge free radicals produced by cadmium. Hence new complex, quercetin with cadmium was synthesised, and the synthesised complex structures were determined by UV-vis spectrophotometry, infrared spectroscopy, thermogravimetry and differential thermal analysis techniques (UV-vis, IR, TGA and DTA). The equilibrium stability constants of quercetin-cadmium complex were determined by Job's method. The determined stability constant value of quercetin-cadminum complex at pH 4.4 is 2.27×10(6) and at pH 7.4 is 7.80×10(6). It was found that the quercetin and cadmium ion form 1:1 complex in both pH 4.4 and pH 7.4. The structure of the compounds was elucidated on the basis of obtained results. Furthermore, the antioxidant activity of the free quercetin and quercetin-cadmium complexes were determined by DPPH and ABTS assays. Copyright © 2013 Elsevier Ltd. All rights reserved.

Gamma Group-The Pale Horse: A proposal in response to a commercial air transportation study ort study

NASA Technical Reports Server (NTRS)

Ehler, T.; Hawkins, J.; Newell, J.; Ohara, M.; Schudt, Karl; Soha, G.; Vandenberg, S.

1991-01-01

A conventional remotely piloted vehicle (RPV) was designed to operate in a fictional 'Aeroworld' as a 30 passenger aircraft. The topics addressed include: economic/cost analysis, aerodynamics, weight and structures, propulsion, stability and control, and performance.

Ant Colony Optimization Analysis on Overall Stability of High Arch Dam Basis of Field Monitoring

PubMed Central

Liu, Xiaoli; Chen, Hong-Xin; Kim, Jinxie

2014-01-01

A dam ant colony optimization (D-ACO) analysis of the overall stability of high arch dams on complicated foundations is presented in this paper. A modified ant colony optimization (ACO) model is proposed for obtaining dam concrete and rock mechanical parameters. A typical dam parameter feedback problem is proposed for nonlinear back-analysis numerical model based on field monitoring deformation and ACO. The basic principle of the proposed model is the establishment of the objective function of optimizing real concrete and rock mechanical parameter. The feedback analysis is then implemented with a modified ant colony algorithm. The algorithm performance is satisfactory, and the accuracy is verified. The m groups of feedback parameters, used to run a nonlinear FEM code, and the displacement and stress distribution are discussed. A feedback analysis of the deformation of the Lijiaxia arch dam and based on the modified ant colony optimization method is also conducted. By considering various material parameters obtained using different analysis methods, comparative analyses were conducted on dam displacements, stress distribution characteristics, and overall dam stability. The comparison results show that the proposal model can effectively solve for feedback multiple parameters of dam concrete and rock material and basically satisfy assessment requirements for geotechnical structural engineering discipline. PMID:25025089

Design, analysis, and testing of high frequency passively damped struts

NASA Technical Reports Server (NTRS)

Yiu, Y. C.; Davis, L. Porter; Napolitano, Kevin; Ninneman, R. Rory

1993-01-01

Objectives of the research are: (1) to develop design requirements for damped struts to stabilize control system in the high frequency cross-over and spill-over range; (2) to design, fabricate and test viscously damped strut and viscoelastically damped strut; (3) to verify accuracy of design and analysis methodology of damped struts; and (4) to design and build test apparatus, and develop data reduction algorithm to measure strut complex stiffness. In order to meet the stringent performance requirements of the SPICE experiment, the active control system is used to suppress the dynamic responses of the low order structural modes. However, the control system also inadvertently drives some of the higher order modes unstable in the cross-over and spill-over frequency range. Passive damping is a reliable and effective way to provide damping to stabilize the control system. It also improves the robustness of the control system. Damping is designed into the SPICE testbed as an integral part of the control-structure technology.

Functionalization of Graphene Oxide and its Composite with Poly(3,4-ethylenedioxythiophene) as Electrode Material for Supercapacitors

NASA Astrophysics Data System (ADS)

Wang, Minchao; Jamal, Ruxangul; Wang, Yujie; Yang, Lei; Liu, Fangfang; Abdiryim, Tursun

2015-09-01

In this study, poly(3,4-ethylenedioxythiophene)/thiophene-grafted graphene oxide (PEDOT/Th-GO) composites from covalently linking of Th-GO with PEDOT chains were prepared via in situ chemical polymerization with different weight percentage of Th-GO ranging between 40 and 70 % in reaction medium. The resulting composite materials were characterized using a various analytical techniques. The structural analysis showed that the composites displayed a higher degree of conjugation and thermal stability than pure PEDOT, and the weight percentage of Th-GO could affect the doping level, amount of undesired conjugated segments, and porous structure of composites. Electrochemical analysis suggested that the highest specific capacitance of 320 F g-1 at a current density of 1 A g-1 with good cycling stability (capacitance retention of 80 % at 1 A g-1 after 1000 cycles) was achieved for the composite prepared from 50 wt% Th-GO content in reaction medium.

Functionalization of Graphene Oxide and its Composite with Poly(3,4-ethylenedioxythiophene) as Electrode Material for Supercapacitors.

PubMed

Wang, Minchao; Jamal, Ruxangul; Wang, Yujie; Yang, Lei; Liu, Fangfang; Abdiryim, Tursun

2015-12-01

In this study, poly(3,4-ethylenedioxythiophene)/thiophene-grafted graphene oxide (PEDOT/Th-GO) composites from covalently linking of Th-GO with PEDOT chains were prepared via in situ chemical polymerization with different weight percentage of Th-GO ranging between 40 and 70 % in reaction medium. The resulting composite materials were characterized using a various analytical techniques. The structural analysis showed that the composites displayed a higher degree of conjugation and thermal stability than pure PEDOT, and the weight percentage of Th-GO could affect the doping level, amount of undesired conjugated segments, and porous structure of composites. Electrochemical analysis suggested that the highest specific capacitance of 320 F g(-1) at a current density of 1 A g(-1) with good cycling stability (capacitance retention of 80 % at 1 A g(-1) after 1000 cycles) was achieved for the composite prepared from 50 wt% Th-GO content in reaction medium.

Humidity sensing behavior of tin-loaded 3-D cubic mesoporous silica

NASA Astrophysics Data System (ADS)

Poonia, Ekta; Dahiya, Manjeet S.; Tomer, Vijay K.; Kumar, Krishan; Kumar, Sunil; Duhan, Surender

2018-07-01

The present scientific investigation deals with template synthesis of 3D-cubic mesoporous KIT-6 with in-situ loading of SnO2 to obtain a material with enhanced number of surface active sites. The structural insights have been reported through analysis of XRD, TEM, FESEM, N2 sorption and mid-IR absorption data. X-ray diffraction confirmed 3D-cubic mesoporous structure of silica with Ia 3 bar d symmetry and existence of anatase SnO2 species. A decrease in surface area on loading of SnO2 nanoparticles is revealed via analysis of N2 adsorption-desorption isotherms. Rapid response time of 15 s and super rapid recovery time of 2 s (with response > 100) have been exhibited by sensor based on sample containing 1 wt% of SnO2. Further investigation on sensing performance of nanocomposite with 1 wt% of SnO2 confirmed its ohmic behavior (with negligible V-I hysteresis), excellent cycle stability, outstanding long term stability and very low hysteresis (1.4% at 53% RH).

Synthesis, crystal structure and DFT studies of a dual fluorescent ketamine: Structural changes in the ground and excited states

NASA Astrophysics Data System (ADS)

Latha, V.; Balakrishnan, C.; Neelakantan, M. A.

2015-07-01

A fluorescent probe 2Z,2‧Z-3,3‧-(4,4‧-methylenebis(4,1-phenylene) bis(azanediyl))bis (1,3-diphenylprop-2-en-1-one) (L) was synthesized and characterized by IR, 1H NMR, ESI-mass, UV-visible and fluorescence spectral techniques. The single crystal analysis illustrates the existence of L in ketamine form. The crystal structure is stabilized by intramolecular and intermolecular hydrogen bonding. The thermal stability of L was studied by TG analysis. The fluorescence spectrum of L shows dual emission, and is due to excited state intramolecular proton transfer (ESIPT) process. This is supported by the high Stokes shift value. Electronic structure calculations of L in the ground and excited state have been carried out using DFT and TD-DFT at B3LYP/6-31G (d,p) level, respectively. The vibrational spectrum was computed at this level and compared with experimental values. Major orbital contributions for the electronic transitions were assigned with the help of TD-DFT. The changes in the Mulliken charge, bond lengths and bond angles between the ground and excited states of the tautomers demonstrate that twisted intramolecular charge transfer (TICT) process occurs along with ESIPT in the excited state.

Dynamic stability and bifurcation analysis in fractional thermodynamics

NASA Astrophysics Data System (ADS)

Béda, Péter B.

2018-02-01

In mechanics, viscoelasticity was the first field of applications in studying geomaterials. Further possibilities arise in spatial non-locality. Non-local materials were already studied in the 1960s by several authors as a part of continuum mechanics and are still in focus of interest because of the rising importance of materials with internal micro- and nano-structure. When material instability gained more interest, non-local behavior appeared in a different aspect. The problem was concerned to numerical analysis, because then instability zones exhibited singular properties for local constitutive equations. In dynamic stability analysis, mathematical aspects of non-locality were studied by using the theory of dynamic systems. There the basic set of equations describing the behavior of continua was transformed to an abstract dynamic system consisting of differential operators acting on the perturbation field variables. Such functions should satisfy homogeneous boundary conditions and act as indicators of stability of a selected state of the body under consideration. Dynamic systems approach results in conditions for cases, when the differential operators have critical eigenvalues of zero real parts (dynamic stability or instability conditions). When the critical eigenvalues have non-trivial eigenspace, the way of loss of stability is classified as a typical (or generic) bifurcation. Our experiences show that material non-locality and the generic nature of bifurcation at instability are connected, and the basic functions of the non-trivial eigenspace can be used to determine internal length quantities of non-local mechanics. Fractional calculus is already successfully used in thermo-elasticity. In the paper, non-locality is introduced via fractional strain into the constitutive relations of various conventional types. Then, by defining dynamic systems, stability and bifurcation are studied for states of thermo-mechanical solids. Stability conditions and genericity conditions are presented for constitutive relations under consideration.

Kinematics of Different Components of the Posterolateral Corner of the Knee in the Lateral Collateral Ligament-intact State: A Human Cadaveric Study.

PubMed

Domnick, Christoph; Frosch, Karl-Heinz; Raschke, Michael J; Vogel, Nils; Schulze, Martin; von Glahn, Mathias; Drenck, Tobias C; Herbort, Mirco

2017-10-01

To determine the static stabilizing effects of different anatomical structures of the posterolateral corner (PLC) of the knee in the lateral collateral ligament (LCL)-intact state. Thirteen fresh-frozen human cadaveric knees were dissected and tested using an industrial robot with an optical tracking system. Kinematics were determined for 134 N anterior/posterior loads, 10 N m valgus/varus loads, and 5 N m internal/external rotatory loads in 0°, 20°, 30°, 60°, and 90° of knee flexion. The PLC structures were dissected and consecutively released: (I) intact knee joint, (II) with released posterior cruciate ligament (PCL), (III) popliteomeniscal fibers, (IV) popliteofibular ligament, (V) arcuat and popliteotibial fibers, (VI) popliteus tendon (PLT), and (VII) LCL. Repeated-measures analysis of variance was performed with significance set at P < .05. After releasing the PCL, posterior tibial translation increased by 5.2 mm at 20° to 9.4 mm at 90° of joint flexion (P < .0001). A mild 1.8° varus instability was measured in 0° of flexion (P = .0017). After releasing the PLC structures, posterior tibial translation further increased by 2.9 mm at 20° to 5.9 mm at 90° of flexion (P < .05) and external rotation angle increased by 2.6° at 0° to 7.9° at 90° of flexion (P < .05, vs II). Varus stability did not decrease. Mild differences between states V and VI were found in 60° and 90° external rotation tests (2.1° and 3.1°; P < .05). The connecting ligaments/fibers to the PLT act as a primary static stabilizer against external rotatory loads and a secondary stabilizer against posterior tibial loads (when PCL is injured). After releasing these structures, most static stabilizing function of the intact PLT is lost. The PLC has no varus-stabilizing function in the LCL-intact knee. Anatomy and function of these structures for primary and secondary joint stability should be considered for clinical diagnostics and when performing surgery in the PLC. Copyright © 2017 Arthroscopy Association of North America. Published by Elsevier Inc. All rights reserved.

Crystal Structure and Theoretical Analysis of Green Gold Au 30 (S- t Bu) 18 Nanomolecules and Their Relation to Au 30 S(S- t Bu) 18

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

Dass, Amala; Jones, Tanya; Rambukwella, Milan

We report the complete X-ray crystallographic structure as determined through single crystal X-ray diffraction and a thorough theoretical analysis of the green gold Au30(S-tBu)18. While the structure of Au30S(S-tBu)18 with 19 sulfur atoms has been reported, the crystal structure of Au30(S-tBu)18 without the μ3-sulfur has remained elusive until now, though matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) and electrospray ionization mass spectrometry (ESI-MS) data unequivocally shows its presence in abundance. The Au30(S-tBu)18 nanomolecule is not only distinct in its crystal structure but has unique temperature dependent optical properties. Structure determination allows a rigorous comparison and an excellent agreement with theoreticalmore » predictions of structure, stability, and optical response.« less

Growth and characterization of metal halide perovskite crystals: Benzyltributyl ammonium tetrachloro manganate(II) monohydrate

NASA Astrophysics Data System (ADS)

Dhandapani, M.; Sugandhi, K.; Nithya, S.; Muthuraja, P.; Balachandar, S.; Aranganayagam, K. R.

2018-05-01

The perovskite type organic-inorganic hybrid benzyltributyl ammoniumtetrachloro manganate (II) monohydrates (BTBA-Mn) are synthesized and the single crystals are grown by slow evaporation solution growth technique. The structure of the grown crystals are confirmed by using X-ray diffraction (XRD), unit cell parameter analysis, Fourier transform Infrared (FTIR), elemental analysis and 13C-NMR spectral studies. Thermogravimetry (TG), differential thermal analysis (DTA) and differential scanning colorimetric (DSC) analysis were carried out to understand thermal stability and occurrence of phase transition.

Interdomain Hydrophobic Interactions Modulate the Thermostability of Microbial Esterases from the Hormone-Sensitive Lipase Family*

PubMed Central

Li, Ping-Yi; Chen, Xiu-Lan; Ji, Peng; Li, Chun-Yang; Wang, Peng; Zhang, Yi; Xie, Bin-Bin; Qin, Qi-Long; Su, Hai-Nan; Zhou, Bai-Cheng; Zhang, Yu-Zhong; Zhang, Xi-Ying

2015-01-01

Microbial hormone-sensitive lipases (HSLs) contain a CAP domain and a catalytic domain. However, it remains unclear how the CAP domain interacts with the catalytic domain to maintain the stability of microbial HSLs. Here, we isolated an HSL esterase, E40, from a marine sedimental metagenomic library. E40 exhibited the maximal activity at 45 °C and was quite thermolabile, with a half-life of only 2 min at 40 °C, which may be an adaptation of E40 to the permanently cold sediment environment. The structure of E40 was solved to study its thermolability. Structural analysis showed that E40 lacks the interdomain hydrophobic interactions between loop 1 of the CAP domain and α7 of the catalytic domain compared with its thermostable homologs. Mutational analysis showed that the introduction of hydrophobic residues Trp202 and Phe203 in α7 significantly improved E40 stability and that a further introduction of hydrophobic residues in loop 1 made E40 more thermostable because of the formation of interdomain hydrophobic interactions. Altogether, the results indicate that the absence of interdomain hydrophobic interactions between loop 1 and α7 leads to the thermolability of E40. In addition, a comparative analysis of the structures of E40 and other thermolabile and thermostable HSLs suggests that the interdomain hydrophobic interactions between loop 1 and α7 are a key element for the thermostability of microbial HSLs. Therefore, this study not only illustrates the structural element leading to the thermolability of E40 but also reveals a structural determinant for HSL thermostability. PMID:25771540

Mirror trends of plasticity and stability indicators in primate prefrontal cortex.

PubMed

García-Cabezas, Miguel Á; Joyce, Mary Kate P; John, Yohan J; Zikopoulos, Basilis; Barbas, Helen

2017-10-01

Research on plasticity markers in the cerebral cortex has largely focused on their timing of expression and role in shaping circuits during critical and normal periods. By contrast, little attention has been focused on the spatial dimension of plasticity-stability across cortical areas. The rationale for this analysis is based on the systematic variation in cortical structure that parallels functional specialization and raises the possibility of varying levels of plasticity. Here, we investigated in adult rhesus monkeys the expression of markers related to synaptic plasticity or stability in prefrontal limbic and eulaminate areas that vary in laminar structure. Our findings revealed that limbic areas are impoverished in three markers of stability: intracortical myelin, the lectin Wisteria floribunda agglutinin, which labels perineuronal nets, and parvalbumin, which is expressed in a class of strong inhibitory neurons. By contrast, prefrontal limbic areas were enriched in the enzyme calcium/calmodulin-dependent protein kinase II (CaMKII), known to enhance plasticity. Eulaminate areas have more elaborate laminar architecture than limbic areas and showed the opposite trend: they were enriched in markers of stability and had lower expression of the plasticity-related marker CaMKII. The expression of glial fibrillary acidic protein (GFAP), a marker of activated astrocytes, was also higher in limbic areas, suggesting that cellular stress correlates with the rate of circuit reshaping. Elevated markers of plasticity may endow limbic areas with flexibility necessary for learning and memory within an affective context, but may also render them vulnerable to abnormal structural changes, as seen in neurologic and psychiatric diseases. © 2017 Federation of European Neuroscience Societies and John Wiley & Sons Ltd.

Design of a high altitude long endurance flying-wing solar-powered unmanned air vehicle

NASA Astrophysics Data System (ADS)

Alsahlani, A. A.; Johnston, L. J.; Atcliffe, P. A.

2017-06-01

The low-Reynolds number environment of high-altitude §ight places severe demands on the aerodynamic design and stability and control of a high altitude, long endurance (HALE) unmanned air vehicle (UAV). The aerodynamic efficiency of a §ying-wing configuration makes it an attractive design option for such an application and is investigated in the present work. The proposed configuration has a high-aspect ratio, swept-wing planform, the wing sweep being necessary to provide an adequate moment arm for outboard longitudinal and lateral control surfaces. A design optimization framework is developed under a MATLAB environment, combining aerodynamic, structural, and stability analysis. Low-order analysis tools are employed to facilitate efficient computations, which is important when there are multiple optimization loops for the various engineering analyses. In particular, a vortex-lattice method is used to compute the wing planform aerodynamics, coupled to a twodimensional (2D) panel method to derive aerofoil sectional characteristics. Integral boundary-layer methods are coupled to the panel method in order to predict §ow separation boundaries during the design iterations. A quasi-analytical method is adapted for application to flyingwing con¦gurations to predict the wing weight and a linear finite-beam element approach is used for structural analysis of the wing-box. Stability is a particular concern in the low-density environment of high-altitude flight for flying-wing aircraft and so provision of adequate directional stability and control power forms part of the optimization process. At present, a modified Genetic Algorithm is used in all of the optimization loops. Each of the low-order engineering analysis tools is validated using higher-order methods to provide con¦dence in the use of these computationally-efficient tools in the present design-optimization framework. This paper includes the results of employing the present optimization tools in the design of a HALE, flying-wing UAV to indicate that this is a viable design configuration option.

Structural, quantum chemical, vibrational and thermal studies of a hydrogen bonded zwitterionic co-crystal (nicotinic acid: pyrogallol)

NASA Astrophysics Data System (ADS)

Prabha, E. Arockia Jeya Yasmi; Kumar, S. Suresh; Athimoolam, S.; Sridhar, B.

2017-02-01

In the present work, a new co-crystal of nicotinic acid with pyrogallol (NICPY) has been grown in the zwitterionic form and the corresponding structural, vibrational, thermal, solubility and anti-cancer characteristics have been reported. The single crystal X-ray diffraction analysis confirms that the structural molecular packing of the crystal stabilized through N-H⋯O and O-H⋯O hydrogen bond. The stabilization energy of the hydrogen bond motifs were calculated in the solid state. Vibrational spectral studies such as Fourier transform-infrared (FT-IR) and FT-Raman were adopted to understand the zwitterionic co-crystalline nature of the compound, which has been compared with theoretically calculated vibrational frequencies. The thermal stability of the grown co-crystal was analyzed by TG/DTA study. The solubility of the NICPY co-crystal was investigated in water at different temperature and compared with that of the nicotinic acid, which is the parent compound of NICPY co-crystal. The grown crystals were treated with human cervical cancer cell line (HeLa) to analyze the cytotoxicity of NICPY crystals and compared with the parent compound, which shows that NICPY has moderate activity against human cervical cancer cell line.

Discussing Occupy Wall Street on Twitter: longitudinal network analysis of equality, emotion, and stability of public discussion.

PubMed

Wang, Cheng-Jun; Wang, Pian-Pian; Zhu, Jonathan J H

2013-09-01

To evaluate the quality of public discussion about social movements on Twitter and to understand the structural features and evolution of longitudinal discussion networks, we analyze tweets about the Occupy Wall Street movement posted over the course of 16 days by investigating the relationship between inequality, emotion, and the stability of online discussion. The results reveal that (1) the discussion is highly unequal for both initiating discussions and receiving conversations; (2) the stability of the discussion is much higher for receivers than for initiators; (3) the inequality of online discussions moderates the stability of online discussions; and (4) on an individual level, there is no significant relationship between emotion and political discussion. The implications help evaluate the quality of public discussion, and to understand the relationship between online discussion and social movements.

The structure of the GemC1 coiled coil and its interaction with the Geminin family of coiled-coil proteins

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

Caillat, Christophe; Fish, Alexander; Pefani, Dafni-Eleftheria

The GemC1 coiled-coil structure has subtle differences compared with its homologues Geminin and Idas. Co-expression experiments in cells and biophysical stability analysis of the Geminin-family coiled coils suggest that the GemC1 coiled coil alone is unstable. GemC1, together with Idas and Geminin, an important regulator of DNA-replication licensing and differentiation decisions, constitute a superfamily sharing a homologous central coiled-coil domain. To better understand this family of proteins, the crystal structure of a GemC1 coiled-coil domain variant engineered for better solubility was determined to 2.2 Å resolution. GemC1 shows a less typical coiled coil compared with the Geminin homodimer and themore » Geminin–Idas heterodimer structures. It is also shown that both in vitro and in cells GemC1 interacts with Geminin through its coiled-coil domain, forming a heterodimer that is more stable that the GemC1 homodimer. Comparative analysis of the thermal stability of all of the possible superfamily complexes, using circular dichroism to follow the unfolding of the entire helix of the coiled coil, or intrinsic tryptophan fluorescence of a unique conserved N-terminal tryptophan, shows that the unfolding of the coiled coil is likely to take place from the C-terminus towards the N-terminus. It is also shown that homodimers show a single-state unfolding, while heterodimers show a two-state unfolding, suggesting that the dimer first falls apart and the helices then unfold according to the stability of each protein. The findings argue that Geminin-family members form homodimers and heterodimers between them, and this ability is likely to be important for modulating their function in cycling and differentiating cells.« less

Copper stabilization via spinel formation during the sintering of simulated copper-laden sludge with aluminum-rich ceramic precursors.

PubMed

Tang, Yuanyuan; Chui, Stephen Sin-Yin; Shih, Kaimin; Zhang, Lingru

2011-04-15

The feasibility of incorporating copper-laden sludge into low-cost ceramic products, such as construction ceramics, was investigated by sintering simulated copper-laden sludge with four aluminum-rich ceramic precursors. The results indicated that all of these precursors (γ-Al(2)O(3), corundum, kaolinite, mullite) could crystallochemically stabilize the hazardous copper in the more durable copper aluminate spinel (CuAl(2)O(4)) structure. To simulate the process of copper transformation into a spinel structure, CuO was mixed with the four aluminum-rich precursors, and fired at 650-1150 °C for 3 h. The products were examined using powder X-ray diffraction (XRD) and scanning electron microscopic techniques. The efficiency of copper transformation among crystalline phases was quantitatively determined through Rietveld refinement analysis of the XRD data. The sintering experiment revealed that the optimal sintering temperature for CuAl(2)O(4) formation was around 1000 °C and that the efficiency of copper incorporation into the crystalline CuAl(2)O(4) structure after 3 h of sintering ranged from 40 to 95%, depending on the type of aluminum precursor used. Prolonged leaching tests were carried out by using acetic acid with an initial pH value of 2.9 to leach CuO and CuAl(2)O(4) samples for 22 d. The sample leachability analysis revealed that the CuAl(2)O(4) spinel structure was more superior to stabilize copper, and suggested a promising and reliable technique for incorporating copper-laden sludge or its incineration ash into usable ceramic products. Such results also demonstrated the potential of a waste-to-resource strategy by using waste materials as part of the raw materials with the attainable temperature range used in the production of ceramics.

Optomechanical stability design of space optical mapping camera

NASA Astrophysics Data System (ADS)

Li, Fuqiang; Cai, Weijun; Zhang, Fengqin; Li, Na; Fan, Junjie

2018-01-01

According to the interior orientation elements and imaging quality requirements of mapping application to mapping camera and combined with off-axis three-mirror anastigmat(TMA) system, high optomechanical stability design of a space optical mapping camera is introduced in this paper. The configuration is a coaxial TMA system used in off-axis situation. Firstly, the overall optical arrangement is described., and an overview of the optomechanical packaging is provided. Zerodurglass, carbon fiber composite and carbon-fiber reinforced silicon carbon (C/SiC) are widely used in the optomechanical structure, because their low coefficient of thermal expansion (CTE) can reduce the thermal sensitivity of the mirrors and focal plane. Flexible and unloading support are used in reflector and camera supporting structure. Epoxy structural adhesives is used for bonding optics to metal structure is also introduced in this paper. The primary mirror is mounted by means of three-point ball joint flexures system, which is attach to the back of the mirror. Then, In order to predict flexural displacements due to gravity, static finite element analysis (FEA) is performed on the primary mirror. The optical performance peak-to-valley (PV) and root-mean-square (RMS) wavefront errors are detected before and after assemble. Also, the dynamic finite element analysis(FEA) of the whole optical arrangement is carried out as to investigate the performance of optomechanical. Finally, in order to evaluate the stability of the design, the thermal vacuum test and vibration test are carried out and the Modulation Transfer Function (MTF) and elements of interior orientation are presented as the evaluation index. Before and after the thermal vacuum test and vibration test, the MTF, focal distance and position of the principal point of optical system are measured and the result is as expected.

Effect of urea and alkylureas on the stability and structural fluctuation of the M80-containing Ω-loop of horse cytochrome c.

PubMed

Kumar, Sandeep; Sharma, Deepak; Kumar, Rajesh

2014-03-01

The effect of denaturants on the structural fluctuation of M80-containing Ω-loop of ferrocytochrome c was determined by measuring the rate coefficient of CO-association with ferrocytochrome c under varying concentrations of urea and alkylureas (methylurea (MU), N,N'-dimethylurea (DMU), ethylurea (EU), tetramethylurea (TMU)) at pH7.0, 25°C. As denaturant concentration is increased within the subdenaturing limit, the CO-association reaction is decelerated indicating that subdenaturing concentrations of denaturant reduce the structural fluctuation of the Ω-loop. Structural fluctuation of the Ω-loop is reduced more for urea and least for TMU. Intermolecular docking between horse cytochrome c and denaturant molecule (urea, MU, DMU, EU and TMU) reveals that polyfunctional interactions between the denaturant and different groups of Ω-loop and other part of protein decrease with an increase of alkyl group on urea molecule, which suggests that the decrease in the extent of restricted dynamics of Ω-loop with a corresponding increase of alkyl groups on urea molecule is due to the decrease of denaturant-mediated cross-linking interactions. These denaturant-mediated interactions are expected to reduce the conformational entropy of protein. Analysis of rate-temperature data shows a progressive decrease in conformational entropy of protein in the native to subdenaturing region. Thermodynamic analysis of denaturant (urea, MU, DMU, EU, TMU) effects on the thermal unfolding of ferrocytochrome c reveals that (i) thermodynamic stability of protein decreases with increasing concentration of denaturant or hydrophobicity of urea derivatives, (ii) water activity plays an important role in stabilization of ferrocytochrome c, and (iii) destabilization of ferrocytochrome c by denaturant occurs through the disturbance of hydrophobic interactions and hydrogen-bonding. Copyright © 2014 Elsevier B.V. All rights reserved.

Engineering diverse changes in beta-turn propensities in the N-terminal beta-hairpin of ubiquitin reveals significant effects on stability and kinetics but a robust folding transition state.

PubMed

Simpson, Emma R; Meldrum, Jill K; Searle, Mark S

2006-04-04

Using the N-terminal 17-residue beta-hairpin of ubiquitin as a "host" for mutational studies, we have investigated the influence of the beta-turn sequence on protein stability and folding kinetics by replacing the native G-bulged turn (TLTGK) with more flexible analogues (TG3K and TG5K) and a series of four-residue type I' beta-turn sequences, commonly found in beta-hairpins. Although a statistical analysis of type I' turns demonstrates residue preferences at specific sites, the frequency of occurrence appears to only broadly correlate with experimentally determined protein stabilities. The subsequent engineering of context-dependent non-native tertiary contacts involving turn residues is shown to produce large changes in stability. Relatively few point mutations have been described that probe secondary structure formation in ubiquitin in a manner that is independent of tertiary contacts. To this end, we have used the more rigorous rate-equilibrium free energy relationship (Leffler analysis), rather than the two-point phi value analysis, to show for a family of engineered beta-turn mutants that stability (range of approximately 20 kJ/mol) and folding kinetics (190-fold variation in refolding rate) are linearly correlated (alpha(f) = 0.74 +/- 0.08). The data are consistent with a transition state that is robust with regard to a wide range of statistically favored and disfavored beta-turn mutations and implicate a loosely assembled beta-hairpin as a key template in transition state stabilization with the beta-turn playing a central role.

Macroscopic and microscopic analysis of the thumb carpometacarpal ligaments: a cadaveric study of ligament anatomy and histology.

PubMed

Ladd, Amy L; Lee, Julia; Hagert, Elisabet

2012-08-15

Stability and mobility represent the paradoxical demands of the human thumb carpometacarpal joint, yet the structural origin of each functional demand is poorly defined. As many as sixteen and as few as four ligaments have been described as primary stabilizers, but controversy exists as to which ligaments are most important. We hypothesized that a comparative macroscopic and microscopic analysis of the ligaments of the thumb carpometacarpal joint would further define their role in joint stability. Thirty cadaveric hands (ten fresh-frozen and twenty embalmed) from nineteen cadavers (eight female and eleven male; average age at the time of death, seventy-six years) were dissected, and the supporting ligaments of the thumb carpometacarpal joint were identified. Ligament width, length, and thickness were recorded for morphometric analysis and were compared with use of the Student t test. The dorsal and volar ligaments were excised from the fresh-frozen specimens and were stained with use of a triple-staining immunofluorescent technique and underwent semiquantitative analysis of sensory innervation; half of these specimens were additionally analyzed for histomorphometric data. Mixed-effects linear regression was used to estimate differences between ligaments. Seven principal ligaments of the thumb carpometacarpal joint were identified: three dorsal deltoid-shaped ligaments (dorsal radial, dorsal central, posterior oblique), two volar ligaments (anterior oblique and ulnar collateral), and two ulnar ligaments (dorsal trapeziometacarpal and intermetacarpal). The dorsal ligaments were significantly thicker (p < 0.001) than the volar ligaments, with a significantly greater cellularity and greater sensory innervation compared with the anterior oblique ligament (p < 0.001). The anterior oblique ligament was consistently a thin structure with a histologic appearance of capsular tissue with low cellularity. The dorsal deltoid ligament complex is uniformly stout and robust; this ligament complex is the thickest morphometrically, has the highest cellularity histologically, and shows the greatest degree of sensory nerve endings. The hypocellular anterior oblique ligament is thin, is variable in its location, and is more structurally consistent with a capsular structure than a proper ligament.

Quantum chemical calculations in the structural analysis of phloretin

NASA Astrophysics Data System (ADS)

Gómez-Zavaglia, Andrea

2009-07-01

In this work, a conformational search on the molecule of phloretin [2',4',6'-Trihydroxy-3-(4-hydroxyphenyl)-propiophenone] has been performed. The molecule of phloretin has eight dihedral angles, four of them taking part in the carbon backbone and the other four, related with the orientation of the hydroxyl groups. A systematic search involving a random variation of the dihedral angles has been used to generate input structures for the quantum chemical calculations. Calculations at the DFT(B3LYP)/6-311++G(d,p) level of theory permitted the identification of 58 local minima belonging to the C 1 symmetry point group. The molecular structures of the conformers have been analyzed using hierarchical cluster analysis. This method allowed us to group conformers according to their similarities, and thus, to correlate the conformers' stability with structural parameters. The dendrogram obtained from the hierarchical cluster analysis depicted two main clusters. Cluster I included all the conformers with relative energies lower than 25 kJ mol -1 and cluster II, the remaining conformers. The possibility of forming intramolecular hydrogen bonds resulted the main factor contributing for the stability. Accordingly, all conformers depicting intramolecular H-bonds belong to cluster I. These conformations are clearly favored when the carbon backbone is as planar as possible. The values of the νC dbnd O and νOH vibrational modes were compared among all the conformers of phloretin. The redshifts associated with intramolecular H-bonds were correlated with the H-bonds distances and energies.

A Practice-Oriented Bifurcation Analysis for Pulse Energy Converters: A Stability Margin

NASA Astrophysics Data System (ADS)

Kolokolov, Yury; Monovskaya, Anna

The popularity of systems of pulse energy conversion (PEC-systems) for practical applications is due to the heightened efficiency of energy conversion processes with comparatively simple realizations. Nevertheless, a PEC-system represents a nonlinear object with a variable structure, and the bifurcation analysis remains the basic tool to describe PEC dynamics evolution. The paper is devoted to the discussion on whether the scientific viewpoint on the natural nonlinear dynamics evolution can be involved in practical applications. We focus on the problems connected with stability boundaries of an operating regime. The results of both small-signal analysis and computational bifurcation analysis are considered in the parametrical space in comparison with the results of the experimental identification of the zonal heterogeneity of the operating process. This allows to propose an adapted stability margin as a sufficiently safe distance before the point after which the operating process begins to lose the stability. Such stability margin can extend the permissible operating domain in the parametrical space at the expense of using cause-and-effect relations in the context of natural regularities of nonlinear dynamics. Reasoning and discussion are based on the experimental and computational results for a synchronous buck converter with a pulse-width modulation. The presented results can be useful, first of all, for PEC-systems with significant variation of equivalent inductance and/or capacity. We believe that the discussion supports a viewpoint by which the contemporary methods of the computational and experimental bifurcation analyses possess both analytical abilities and experimental techniques for promising solutions which could be practice-oriented for PEC-systems.