Applications of a global nuclear-structure model to studies of the heaviest elements

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

Moeller, P.; Nix, J.R.

1993-10-01

We present some new results on heavy-element nuclear-structure properties calculated on the basis of the finite-range droplet model and folded-Yukawa single-particle potential. Specifically, we discuss calculations of nuclear ground-state masses and microscopic corrections, {alpha}-decay properties, {beta}-decay properties, fission potential-energy surfaces, and spontaneous-fission half-lives. These results, obtained in a global nuclear-structure approach, are particularly reliable for describing the stability properties of the heaviest elements.

Stability of mechanical joints in launching vehicles: Local and global stationary values of energy density

NASA Astrophysics Data System (ADS)

Chue, Ching-Hwei

A method was developed for predicting the behavior of mechanical joints in launch vehicles with particular emphasis placed on how the combined effects of loading, geometry, and materials could be optimized in terms of structure instability and/or integrity. What was considered to be essential is the fluctuation of the volume energy density with time in the structure. The peaks and valleys of the volume energy density function will be associated with failure by fracture and/or yielding while the distance between their local and global stationary values govern the structure instability. The Solid Rocket Booster (SRB) of the space shuttle was analyzed under axisymmetric and non-axisymmetric loadings. A semi-analytical finite element program was developed for solving the case of non-axisymmetric loading. Following a dynamic stress analysis, contours of the volume energy density in the structure were obtained as a function of time. The magnitudes and locations of these stationary values were then calculated locally and globally and related to possible failure by fracture. In the case of axisymmetric flight, the local and global instability behavior do not change appreciably. Fluctuations in the energy density and the dynamic stability length parameter become appreciable when the non-axisymmetric loads are considered. The magnitude of the energy in the shell structure is sensitive to alterations in the gas pressure induced by the solid propellant.

Dual mechanisms regulate ecosystem stability under decade-long warming and hay harvest

PubMed Central

Shi, Zheng; Xu, Xia; Souza, Lara; Wilcox, Kevin; Jiang, Lifen; Liang, Junyi; Xia, Jianyang; García-Palacios, Pablo; Luo, Yiqi

2016-01-01

Past global change studies have identified changes in species diversity as a major mechanism regulating temporal stability of production, measured as the ratio of the mean to the standard deviation of community biomass. However, the dominant plant functional group can also strongly determine the temporal stability. Here, in a grassland ecosystem subject to 15 years of experimental warming and hay harvest, we reveal that warming increases while hay harvest decreases temporal stability. This corresponds with the biomass of the dominant C4 functional group being higher under warming and lower under hay harvest. As a secondary mechanism, biodiversity also explains part of the variation in temporal stability of production. Structural equation modelling further shows that warming and hay harvest regulate temporal stability through influencing both temporal mean and variation of production. Our findings demonstrate the joint roles that dominant plant functional group and biodiversity play in regulating the temporal stability of an ecosystem under global change. PMID:27302085

Glassy nature and glass-to-crystal transition in the binary metallic glass CuZr

NASA Astrophysics Data System (ADS)

Wei, Zi-Yang; Shang, Cheng; Zhang, Xiao-Jie; Liu, Zhi-Pan

2017-06-01

The prediction for the stability of glassy material is a key challenge in physical science. Here, we report a theoretical framework to predict the glass stability based on stochastic surface walking global optimization and reaction pathway sampling. This is demonstrated by revealing for the first time the global potential energy surface (PES) of two systems, CuZr binary metallic glass and nonglassy pure Cu systems, and establishing the lowest energy pathways linking glassy/amorphous structures with crystalline structures. The CuZr system has a significant number of glassy structures on PES that are ˜0.045 eV /atom above the crystal structure. Two clear trends are identified from global PES in the glass-to-crystal transition of the CuZr system: (i) the local Zr-Cu coordination (nearest neighbor) increases, and (ii) the local Zr bonding environment becomes homogeneous. This allows us to introduce quantitative structural and energetics conditions to distinguish the glassy structures from the crystalline structures. Because of the local Zr-Cu exchange in the glass-to-crystal transition, a high reaction barrier (>0.048 eV /atom ) is present to separate the glassy structures and the crystals in CuZr. By contrast, the Cu system, although it does possess amorphous structures that appear at much higher energy (˜0.075 eV /atom ) with respect to the crystal structure, has very low reaction barriers for the crystallization of amorphous structures, i.e. <0.011 eV /atom . The quantitative data on PES now available from global optimization techniques deepens our understanding on the microscopic nature of glassy material and might eventually facilitate the design of stable glassy materials.

The Network of Global Corporate Control

PubMed Central

Vitali, Stefania; Glattfelder, James B.; Battiston, Stefano

2011-01-01

The structure of the control network of transnational corporations affects global market competition and financial stability. So far, only small national samples were studied and there was no appropriate methodology to assess control globally. We present the first investigation of the architecture of the international ownership network, along with the computation of the control held by each global player. We find that transnational corporations form a giant bow-tie structure and that a large portion of control flows to a small tightly-knit core of financial institutions. This core can be seen as an economic “super-entity” that raises new important issues both for researchers and policy makers. PMID:22046252

Application of a parallel genetic algorithm to the global optimization of medium-sized Au-Pd sub-nanometre clusters

NASA Astrophysics Data System (ADS)

Hussein, Heider A.; Demiroglu, Ilker; Johnston, Roy L.

2018-02-01

To contribute to the discussion of the high activity and reactivity of Au-Pd system, we have adopted the BPGA-DFT approach to study the structural and energetic properties of medium-sized Au-Pd sub-nanometre clusters with 11-18 atoms. We have examined the structural behaviour and stability as a function of cluster size and composition. The study suggests 2D-3D crossover points for pure Au clusters at 14 and 16 atoms, whereas pure Pd clusters are all found to be 3D. For Au-Pd nanoalloys, the role of cluster size and the influence of doping were found to be extensive and non-monotonic in altering cluster structures. Various stability criteria (e.g. binding energies, second differences in energy, and mixing energies) are used to evaluate the energetics, structures, and tendency of segregation in sub-nanometre Au-Pd clusters. HOMO-LUMO gaps were calculated to give additional information on cluster stability and a systematic homotop search was used to evaluate the energies of the generated global minima of mono-substituted clusters and the preferred doping sites, as well as confirming the validity of the BPGA-DFT approach.

High-Level ab initio electronic structure calculations of Water Clusters (H2O)16 and (H2O)17: a new global minimum for (H2O)16

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

Yoo, Soohaeng; Apra, Edoardo; Zeng, Xiao Cheng

The lowest-energy structures of water clusters (H2O)16 and (H2O)17 were revisited at the MP2 and CCSD(T) levels of theory. A new global minimum structure for (H2O)16 was found at the MP2 and CCSD(T) levels of theory and the effect of zero-point energy corrections on the relative stability of the low-lying minimum energy structures was assessed. For (H2O)17 the CCSD(T) calculations confirm the previously found at the MP2 level of theory "interior" arrangement (fully coordinated water molecule inside a spherical cluster) as the global minimum.

High-Level ab-initio Electronic Structure Calculations of Water Clusters (H2O)16 and (H2O)17 : a New Global Minimum for (H2O)16

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

Yoo, Soohaeng; Apra, Edoardo; Zeng, X.C.

The lowest-energy structures of water clusters (H2O)16 and (H2O)17 were revisited at the MP2 and CCSD(T) levels of theory. A new global minimum structure for (H2O)16 was found at both the MP2 and CCSD(T) levels of theory, and the effect of zero-point energy corrections on the relative stability of the low-lying minimum energy structures was assessed. For (H2O)17, the CCSD(T) calculations confirm the previously found at the MP2 level of theory interior arrangement (fully coordinated water molecule inside a spherical cluster) as the global minimum

Salt bridge as a gatekeeper against partial unfolding.

PubMed

Hinzman, Mark W; Essex, Morgan E; Park, Chiwook

2016-05-01

Salt bridges are frequently observed in protein structures. Because the energetic contribution of salt bridges is strongly dependent on the environmental context, salt bridges are believed to contribute to the structural specificity rather than the stability. To test the role of salt bridges in enhancing structural specificity, we investigated the contribution of a salt bridge to the energetics of native-state partial unfolding in a cysteine-free version of Escherichia coli ribonuclease H (RNase H*). Thermolysin cleaves a protruding loop of RNase H(*) through transient partial unfolding under native conditions. Lys86 and Asp108 in RNase H(*) form a partially buried salt bridge that tethers the protruding loop. Investigation of the global stability of K86Q/D108N RNase H(*) showed that the salt bridge does not significantly contribute to the global stability. However, K86Q/D108N RNase H(*) is greatly more susceptible to proteolysis by thermolysin than wild-type RNase H(*) is. The free energy for partial unfolding determined by native-state proteolysis indicates that the salt bridge significantly increases the energy for partial unfolding by destabilizing the partially unfolded form. Double mutant cycles with single and double mutations of the salt bridge suggest that the partially unfolded form is destabilized due to a significant decrease in the interaction energy between Lys86 and Asp108 upon partial unfolding. This study demonstrates that, even in the case that a salt bridge does not contribute to the global stability, the salt bridge may function as a gatekeeper against partial unfolding that disturbs the optimal geometry of the salt bridge. © 2016 The Protein Society.

Quantification of the Thermodynamically Linked Quaternary and Tertiary Structural Stabilities of Transthyretin and its Disease-Associated Variants–the Relationship between Stability and Amyloidosis†

PubMed Central

Hurshman Babbes, Amy R.; Powers, Evan T.; Kelly, Jeffery W.

2009-01-01

Urea denaturation studies were carried out as a function of transthyretin (TTR) concentration to quantify the thermodynamically linked quaternary and tertiary structural stability and to better understand the relationship between mutant folding energetics and amyloid disease phenotype. Urea denaturation of TTR involves at least two equilibria—dissociation of tetramers into folded monomers, and monomer unfolding. To deal with the thermodynamic linkage of these equilibria, we analyzed concentration-dependent denaturation data by global fitting to an equation that simultaneously accounts for the two-step denaturation process. Using this method, the quaternary and tertiary structural stabilities of well-behaved TTR sequences, wild type (WT) TTR and the disease-associated variant V122I, were scrutinized. The V122I variant is linked to late onset familial amyloid cardiomyopathy, the most common familial TTR amyloid disease. V122I TTR exhibits a destabilized quaternary structure and a stable tertiary structure relative to WT TTR. Three other variants of TTR were also examined, L55P, V30M, and A25T TTR. The L55P mutation is associated with the most aggressive familial TTR amyloid disease. L55P TTR has a complicated denaturation pathway that includes dimers and trimers, and so globally fitting its concentration-dependent urea denaturation data yielded error-laden estimates of stability parameters. Nevertheless, it is clear that L55P TTR is substantially less stable than WT TTR, primarily because its tertiary structure is unstable, although its quaternary structure is destabilized as well. V30M is the most common mutation associated with neuropathic forms of TTR amyloid disease. V30M TTR is certainly destabilized relative to WT TTR, but like L55P TTR it has a complex denaturation pathway that cannot be fit to the aforementioned two-step denaturation model. Literature data suggest that V30M TTR has stable quaternary structure but unstable tertiary structure. The A25T mutant, associated with central nervous system amyloidosis, is highly aggregation-prone and exhibits drastically reduced quaternary and tertiary structural stability. The observed differences in stability amongst the disease-associated TTR variants highlight the complexity and the heterogeneity of TTR amyloid disease, an observation having important implications for the treatment of these diseases. PMID:18537267

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.

Disentangling Stability, Variability and Adaptability in Human Performance: Focus on the Interplay between Local Variance and Serial Correlation

ERIC Educational Resources Information Center

Torre, Kjerstin; Balasubramaniam, Ramesh

2011-01-01

We address the complex relationship between the stability, variability, and adaptability of psychological systems by decomposing the global variance of serial performance into two independent parts: the local variance (LV) and the serial correlation structure. For two time series with equal LV, the presence of persistent long-range correlations…

Multi-stability in folded shells: non-Euclidean origami

NASA Astrophysics Data System (ADS)

Evans, Arthur

2015-03-01

Both natural and man-made structures benefit from having multiple mechanically stable states, from the quick snapping motion of hummingbird beaks to micro-textured surfaces with tunable roughness. Rather than discuss special fabrication techniques for creating bi-stability through material anisotropy, in this talk I will present several examples of how folding a structure can modify the energy landscape and thus lead to multiple stable states. Using ideas from origami and differential geometry, I will discuss how deforming a non-Euclidean surface can be done either continuously or discontinuously, and explore the effects that global constraints have on the ultimate stability of the surface.

Disruption of a hydrogen bond network in human versus spider monkey cytochrome c affects heme crevice stability.

PubMed

Goldes, Matthew E; Jeakins-Cooley, Margaret E; McClelland, Levi J; Mou, Tung-Chung; Bowler, Bruce E

2016-05-01

The hypothesis that the recent rapid evolution of primate cytochromes c, which primarily involves residues in the least stable Ω-loop (Ω-loop C, residues 40-57), stabilizes the heme crevice of cytochrome c relative to other mammals, is tested. To accomplish this goal, we have compared the properties of human and spider monkey cytochrome c and a set of four variants produced in the process of converting human cytochrome c into spider monkey cytochrome c. The global stability of all variants has been measured by guanidine hydrochloride denaturation. The stability of the heme crevice has been assessed with the alkaline conformational transition. Structural insight into the effects of the five amino acid substitutions needed to convert human cytochrome c into spider monkey cytochrome c is provided by a 1.15Å resolution structure of spider monkey cytochrome c. The global stability for all variants is near 9.0kcal/mol at 25°C and pH7, which is higher than that observed for other mammalian cytochromes c. The heme crevice stability is more sensitive to the substitutions required to produce spider monkey cytochrome c with decreases of up to 0.5 units in the apparent pKa of the alkaline conformational transition relative to human cytochrome c. The structure of spider monkey cytochrome c indicates that the Y46F substitution destabilizes the heme crevice by disrupting an extensive hydrogen bond network that connects three surface loops including Ω-loop D (residues 70-85), which contains the Met80 heme ligand. Copyright © 2015 Elsevier Inc. All rights reserved.

A decentralized approach to vibration suppression in segmented reflector telescopes. [large spaceborne

NASA Technical Reports Server (NTRS)

Ryaciotaki-Boussalis, Helen A.; Wang, Shyh Jong

1989-01-01

The problem of vibration suppression in segmented reflector telescopes is considered. The decomposition of the structure into smaller components is discussed, and control laws for vibration suppression as well as conditions for stability at the local level are derived. These conditions and the properties of the interconnecting patterns are then utilized to obtain sufficient conditions for global stability.

Imitation dynamics of vaccine decision-making behaviours based on the game theory.

PubMed

Yang, Junyuan; Martcheva, Maia; Chen, Yuming

2016-01-01

Based on game theory, we propose an age-structured model to investigate the imitation dynamics of vaccine uptake. We first obtain the existence and local stability of equilibria. We show that Hopf bifurcation can occur. We also establish the global stability of the boundary equilibria and persistence of the disease. The theoretical results are supported by numerical simulations.

Global Sentry: NASA/USRA high altitude reconnaissance aircraft design, volume 2

NASA Technical Reports Server (NTRS)

Alexandru, Mona-Lisa; Martinez, Frank; Tsou, Jim; Do, Henry; Peters, Ashish; Chatsworth, Tom; Yu, YE; Dhillon, Jaskiran

1990-01-01

The Global Sentry is a high altitude reconnaissance aircraft design for the NASA/USRA design project. The Global Sentry uses proven technologies, light-weight composites, and meets the R.F.P. requirements. The mission requirements for the Global Sentry are described. The configuration option is discussed and a description of the final design is given. Preliminary sizing analyses and the mass properties of the design are presented. The aerodynamic features of the Global Sentry are described along with the stability and control characteristics designed into the flight control system. The performance characteristics are discussed as is the propulsion installation and system layout. The Global Sentry structural design is examined, including a wing structural analysis. The cockpit, controls and display layouts are covered. Manufacturing is covered and the life cost estimation. Reliability is discussed. Conclusions about the current Global Sentry design are presented, along with suggested areas for future engineering work.

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

Stabilisation of discrete-time polynomial fuzzy systems via a polynomial lyapunov approach

NASA Astrophysics Data System (ADS)

Nasiri, Alireza; Nguang, Sing Kiong; Swain, Akshya; Almakhles, Dhafer

2018-02-01

This paper deals with the problem of designing a controller for a class of discrete-time nonlinear systems which is represented by discrete-time polynomial fuzzy model. Most of the existing control design methods for discrete-time fuzzy polynomial systems cannot guarantee their Lyapunov function to be a radially unbounded polynomial function, hence the global stability cannot be assured. The proposed control design in this paper guarantees a radially unbounded polynomial Lyapunov functions which ensures global stability. In the proposed design, state feedback structure is considered and non-convexity problem is solved by incorporating an integrator into the controller. Sufficient conditions of stability are derived in terms of polynomial matrix inequalities which are solved via SOSTOOLS in MATLAB. A numerical example is presented to illustrate the effectiveness of the proposed controller.

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

Effects of spanwise rotation on the structure of two-dimensional fully developed turbulent channel flow.

NASA Technical Reports Server (NTRS)

Johnston, J. P.; Halleen, R. M.; Lezius, D. K.

1972-01-01

Experiments on fully developed turbulent flow in a channel which is rotating at a steady rate about a spanwise axis are described. The Coriolis force components in the region of two-dimensional mean flow affect both local and global stability. Three stability-related phenomena were observed or inferred: (1) the reduction (increase) of the rate of wall-layer streak bursting in locally stabilized (destabilized) wall layers; (2) the total suppression of transition to turbulence in a stabilized layer; (3) the development of large-scale roll cells on the destabilized side of the channel by growth of a Taylor-Gortler vortex instability. Local effects of rotational stabilization, such as reduction of the turbulent stress in wall layers, can be related to the local Richardson number in a simple way. This paper not only investigates this effect, but also, by methods of flow visualization, exposes some of the underlying structure changes caused by rotation.-

Positional effects of monofluorinated phenylalanines on histone acetyltransferase stability and activity.

PubMed

Voloshchuk, Natalya; Zhu, Anita Y; Snydacker, David; Montclare, Jin Kim

2009-09-15

To explore the impact of global incorporation of fluorinated aromatic amino acids on protein function, we investigated the effects of three monofluorinated phenylalanine analogs para-fluorophenylalanine (pFF), meta-fluorophenylalanine (mFF), and ortho-fluorophenylalanine (oFF) on the stability and enzymatic activity of the histone acetyltransferase (HAT), tGCN5. We selected this set of fluorinated amino acids because they bear the same size and overall polarity but alter in side chain shape and dipole direction. Our experiments showed that among three fluorinated amino acids, the global incorporation of pFF affords the smallest perturbation to the structure and function of tGCN5.

Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models

DOE PAGES

Wieder, William R.; Hartman, Melannie D.; Sulman, Benjamin N.; ...

2017-11-09

Emerging insights into factors responsible for soil organic matter stabilization and decomposition are being applied in a variety of contexts, but new tools are needed to facilitate the understanding, evaluation, and improvement of soil biogeochemical theory and models at regional to global scales. To isolate the effects of model structural uncertainty on the global distribution of soil carbon stocks and turnover times we developed a soil biogeochemical testbed that forces three different soil models with consistent climate and plant productivity inputs. The models tested here include a first-order, microbial implicit approach (CASA-CNP), and two recently developed microbially explicit models thatmore » can be run at global scales (MIMICS and CORPSE). When forced with common environmental drivers, the soil models generated similar estimates of initial soil carbon stocks (roughly 1,400 Pg C globally, 0–100 cm), but each model shows a different functional relationship between mean annual temperature and inferred turnover times. Subsequently, the models made divergent projections about the fate of these soil carbon stocks over the 20th century, with models either gaining or losing over 20 Pg C globally between 1901 and 2010. Single-forcing experiments with changed inputs, tem- perature, and moisture suggest that uncertainty associated with freeze-thaw processes as well as soil textural effects on soil carbon stabilization were larger than direct temper- ature uncertainties among models. Finally, the models generated distinct projections about the timing and magnitude of seasonal heterotrophic respiration rates, again reflecting structural uncertainties that were related to environmental sensitivities and assumptions about physicochemical stabilization of soil organic matter. Here, by providing a computationally tractable and numerically consistent framework to evaluate models we aim to better understand uncertainties among models and generate insights about fac- tors regulating the turnover of soil organic matter.« less

Carbon cycle confidence and uncertainty: Exploring variation among soil biogeochemical models

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

Wieder, William R.; Hartman, Melannie D.; Sulman, Benjamin N.

Emerging insights into factors responsible for soil organic matter stabilization and decomposition are being applied in a variety of contexts, but new tools are needed to facilitate the understanding, evaluation, and improvement of soil biogeochemical theory and models at regional to global scales. To isolate the effects of model structural uncertainty on the global distribution of soil carbon stocks and turnover times we developed a soil biogeochemical testbed that forces three different soil models with consistent climate and plant productivity inputs. The models tested here include a first-order, microbial implicit approach (CASA-CNP), and two recently developed microbially explicit models thatmore » can be run at global scales (MIMICS and CORPSE). When forced with common environmental drivers, the soil models generated similar estimates of initial soil carbon stocks (roughly 1,400 Pg C globally, 0–100 cm), but each model shows a different functional relationship between mean annual temperature and inferred turnover times. Subsequently, the models made divergent projections about the fate of these soil carbon stocks over the 20th century, with models either gaining or losing over 20 Pg C globally between 1901 and 2010. Single-forcing experiments with changed inputs, tem- perature, and moisture suggest that uncertainty associated with freeze-thaw processes as well as soil textural effects on soil carbon stabilization were larger than direct temper- ature uncertainties among models. Finally, the models generated distinct projections about the timing and magnitude of seasonal heterotrophic respiration rates, again reflecting structural uncertainties that were related to environmental sensitivities and assumptions about physicochemical stabilization of soil organic matter. Here, by providing a computationally tractable and numerically consistent framework to evaluate models we aim to better understand uncertainties among models and generate insights about fac- tors regulating the turnover of soil organic matter.« less

Mathematics, thermodynamics, and modeling to address ten common misconceptions about protein structure, folding, and stability.

PubMed

Robic, Srebrenka

2010-01-01

To fully understand the roles proteins play in cellular processes, students need to grasp complex ideas about protein structure, folding, and stability. Our current understanding of these topics is based on mathematical models and experimental data. However, protein structure, folding, and stability are often introduced as descriptive, qualitative phenomena in undergraduate classes. In the process of learning about these topics, students often form incorrect ideas. For example, by learning about protein folding in the context of protein synthesis, students may come to an incorrect conclusion that once synthesized on the ribosome, a protein spends its entire cellular life time in its fully folded native confirmation. This is clearly not true; proteins are dynamic structures that undergo both local fluctuations and global unfolding events. To prevent and address such misconceptions, basic concepts of protein science can be introduced in the context of simple mathematical models and hands-on explorations of publicly available data sets. Ten common misconceptions about proteins are presented, along with suggestions for using equations, models, sequence, structure, and thermodynamic data to help students gain a deeper understanding of basic concepts relating to protein structure, folding, and stability.

United time-frequency spectroscopy for dynamics and global structure.

PubMed

Marian, Adela; Stowe, Matthew C; Lawall, John R; Felinto, Daniel; Ye, Jun

2004-12-17

Ultrashort laser pulses have thus far been used in two distinct modes. In the time domain, the pulses have allowed probing and manipulation of dynamics on a subpicosecond time scale. More recently, phase stabilization has produced optical frequency combs with absolute frequency reference across a broad bandwidth. Here we combine these two applications in a spectroscopic study of rubidium atoms. A wide-bandwidth, phase-stabilized femtosecond laser is used to monitor the real-time dynamic evolution of population transfer. Coherent pulse accumulation and quantum interference effects are observed and well modeled by theory. At the same time, the narrow linewidth of individual comb lines permits a precise and efficient determination of the global energy-level structure, providing a direct connection among the optical, terahertz, and radio-frequency domains. The mechanical action of the optical frequency comb on the atomic sample is explored and controlled, leading to precision spectroscopy with an appreciable reduction in systematic errors.

Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components

PubMed Central

Fagerlund, Robert D.; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S.

2015-01-01

Ribonuclease (RNase) P and RNase MRP are closely related catalytic ribonucleoproteins involved in the metabolism of a wide range of RNA molecules, including tRNA, rRNA, and some mRNAs. The catalytic RNA component of eukaryotic RNase P retains the core elements of the bacterial RNase P ribozyme; however, the peripheral RNA elements responsible for the stabilization of the global architecture are largely absent in the eukaryotic enzyme. At the same time, the protein makeup of eukaryotic RNase P is considerably more complex than that of the bacterial RNase P. RNase MRP, an essential and ubiquitous eukaryotic enzyme, has a structural organization resembling that of eukaryotic RNase P, and the two enzymes share most of their protein components. Here, we present the results of the analysis of interactions between the largest protein component of yeast RNases P/MRP, Pop1, and the RNA moieties of the enzymes, discuss structural implications of the results, and suggest that Pop1 plays the role of a scaffold for the stabilization of the global architecture of eukaryotic RNase P RNA, substituting for the network of RNA–RNA tertiary interactions that maintain the global RNA structure in bacterial RNase P. PMID:26135751

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

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins.

PubMed

Perez, Romel B; Tischer, Alexander; Auton, Matthew; Whitten, Steven T

2014-12-01

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins (IDPs), mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline (PRO) and alanine (ALA) to glycine (GLY) substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (R(h)) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the GLY substitutions decreased polyproline II (PP(II)) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in R(h) were not associated with folding. The experiments showed that changes in local PP(II) structure cause changes in R(h) that are variable and that depend on the intrinsic chain propensities of PRO and ALA residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed PRO and alanine effects on the structures of IDPs. © 2014 Wiley Periodicals, Inc.

Alanine and proline content modulate global sensitivity to discrete perturbations in disordered proteins

PubMed Central

Perez, Romel B.; Tischer, Alexander; Auton, Matthew; Whitten, Steven T.

2014-01-01

Molecular transduction of biological signals is understood primarily in terms of the cooperative structural transitions of protein macromolecules, providing a mechanism through which discrete local structure perturbations affect global macromolecular properties. The recognition that proteins lacking tertiary stability, commonly referred to as intrinsically disordered proteins, mediate key signaling pathways suggests that protein structures without cooperative intramolecular interactions may also have the ability to couple local and global structure changes. Presented here are results from experiments that measured and tested the ability of disordered proteins to couple local changes in structure to global changes in structure. Using the intrinsically disordered N-terminal region of the p53 protein as an experimental model, a set of proline and alanine to glycine substitution variants were designed to modulate backbone conformational propensities without introducing non-native intramolecular interactions. The hydrodynamic radius (Rh) was used to monitor changes in global structure. Circular dichroism spectroscopy showed that the glycine substitutions decreased polyproline II (PPII) propensities relative to the wild type, as expected, and fluorescence methods indicated that substitution-induced changes in Rh were not associated with folding. The experiments showed that changes in local PPII structure cause changes in Rh that are variable and that depend on the intrinsic chain propensities of proline and alanine residues, demonstrating a mechanism for coupling local and global structure changes. Molecular simulations that model our results were used to extend the analysis to other proteins and illustrate the generality of the observed proline and alanine effects on the structures of intrinsically disordered proteins. PMID:25244701

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.

Human Neuronal Calcium Sensor-1 Protein Avoids Histidine Residues To Decrease pH Sensitivity.

PubMed

Gong, Yehong; Zhu, Yuzhen; Zou, Yu; Ma, Buyong; Nussinov, Ruth; Zhang, Qingwen

2017-01-26

pH is highly regulated in mammalian central nervous systems. Neuronal calcium sensor-1 (NCS-1) can interact with numerous target proteins. Compared to that in the NCS-1 protein of Caenorhabditis elegans, evolution has avoided the placement of histidine residues at positions 102 and 83 in the NCS-1 protein of humans and Xenopus laevis, possibly to decrease the conformational sensitivity to pH gradients in synaptic processes. We used all-atom molecular dynamics simulations to investigate the effects of amino acid substitutions between species on human NCS-1 by substituting Arg102 and Ser83 for histidine at neutral (R102H and S83H) and acidic pHs (R102H p and S83H p ). Our cumulative 5 μs simulations revealed that the R102H mutation slightly increases the structural flexibility of loop L2 and the R102H p mutation decreases protein stability. Community network analysis illustrates that the R102H and S83H mutations weaken the interdomain and strengthen the intradomain communications. Secondary structure contents in the S83H and S83H p mutants are similar to those in the wild type, whereas the global structural stabilities and salt-bridge probabilities decrease. This study highlights the conformational dynamics effects of the R102H and S83H mutations on the local structural flexibility and global stability of NCS-1, whereas protonated histidine decreases the stability of NCS-1. Thus, histidines at positions 102 and 83 may not be compatible with the function of NCS-1 whether in the neutral or protonated state.

Global optimization of small bimetallic Pd-Co binary nanoalloy clusters: a genetic algorithm approach at the DFT level.

PubMed

Aslan, Mikail; Davis, Jack B A; Johnston, Roy L

2016-03-07

The global optimisation of small bimetallic PdCo binary nanoalloys are systematically investigated using the Birmingham Cluster Genetic Algorithm (BCGA). The effect of size and composition on the structures, stability, magnetic and electronic properties including the binding energies, second finite difference energies and mixing energies of Pd-Co binary nanoalloys are discussed. A detailed analysis of Pd-Co structural motifs and segregation effects is also presented. The maximal mixing energy corresponds to Pd atom compositions for which the number of mixed Pd-Co bonds is maximised. Global minimum clusters are distinguished from transition states by vibrational frequency analysis. HOMO-LUMO gap, electric dipole moment and vibrational frequency analyses are made to enable correlation with future experiments.

The HSOB GAIA: a cryogenic high stability cesic optical bench for missions requiring sub-nanometric optical stability

NASA Astrophysics Data System (ADS)

Courteau, Pascal; Poupinet, Anne; Kroedel, Mathias; Sarri, Giuseppe

2017-11-01

Global astrometry, very demanding in term of stability, requires extremely stable material for optical bench. CeSiC developed by ECM and Alcatel Alenia Space for mirrors and high stability structures, offers the best compromise in term of structural strength, stability and very high lightweight capability, with characteristics leading to be insensitive to thermo-elastic at cryogenic T°. The HSOB GAIA study realised by Alcatel Alenia Space under ESA contract aimed to design, develop and test a full scale representative High Stability Optical Bench in CeSiC. The bench has been equipped with SAGEIS-CSO laser metrology system MOUSE1, Michelson interferometer composed of integrated optics with a nm resolution. The HSOB bench has been submitted to an homogeneous T° step under vacuum to characterise the homothetic behaviour of its two arms. The quite negligible inter-arms differential measured with a nm range reproducibility, demonstrates that a complete 3D structure in CeSiC has the same CTE homogeneity as characterisation samples, fully in line with the GAIA need (1pm at 120K). This participates to the demonstration that CeSiC properties at cryogenic T° is fully appropriate to the manufacturing of complex highly stable optical structures. This successful study confirms ECM and Alcatel Alenia Space ability to define and manufacture monolithic lightweight highly stable optical structures, based on inner cells triangular design made only possible by the unique CeSiC manufacturing process.

Global stability of an age-structure epidemic model with imperfect vaccination and relapse

NASA Astrophysics Data System (ADS)

Cao, Bin; Huo, Hai-Feng; Xiang, Hong

2017-11-01

A new age-structured epidemic model with imperfect vaccination and relapse is proposed. The total population of our model is partitioned into five subclasses: susceptible class S, vaccinated class V, exposed class E, infectious class I and removed class R. Age-structures are equipped with in exposed and recovered classes. Furthermore, imperfect vaccination is also introduced in our model. The basic reproduction number R0 is defined and proved as a threshold parameter of the model. Asymptotic smoothness of solutions and uniform persistence of the system are showed via reformulating the system as a system of Volterra integral equation. Furthermore, by constructing proper Volterra-type Lyapunov functional we get when R0 < 1, the disease-free equilibrium is globally asymptotically stable. When R0 > 1, the endemic equilibrium is globally stable. Our results show that to increase the efficiency of vaccination and reduce influence of relapse are vital essential for controlling epidemic.

Plutonium Metallurgy

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

Freibert, Franz J.

2012-08-09

Due to its nuclear properties, Pu will remain a material of global interest well into the future. Processing, Structure, Properties and Performance remains a good framework for discussion of Pu materials science Self-irradiation and aging effects continue to be central in discussions of Pu metallurgy Pu in its elemental form is extremely unstable, but alloying helps to stabilize Pu; but, questions remain as to how and why this stabilization occurs. Which is true Pu-Ga binary phase diagram: US or Russian? Metallurgical issues such as solute coring, phase instability, crystallographic texture, etc. result in challenges to casting, processing, and properties modelingmore » and experiments. For Ga alloyed FCC stabilized Pu, temperature and pressure remain as variables impacting phase stability.« less

Reliability assessment of slender concrete columns at the stability failure

NASA Astrophysics Data System (ADS)

Valašík, Adrián; Benko, Vladimír; Strauss, Alfred; Täubling, Benjamin

2018-01-01

The European Standard for designing concrete columns within the use of non-linear methods shows deficiencies in terms of global reliability, in case that the concrete columns fail by the loss of stability. The buckling failure is a brittle failure which occurs without warning and the probability of its formation depends on the columns slenderness. Experiments with slender concrete columns were carried out in cooperation with STRABAG Bratislava LTD in Central Laboratory of Faculty of Civil Engineering SUT in Bratislava. The following article aims to compare the global reliability of slender concrete columns with slenderness of 90 and higher. The columns were designed according to methods offered by EN 1992-1-1 [1]. The mentioned experiments were used as basis for deterministic nonlinear modelling of the columns and subsequent the probabilistic evaluation of structural response variability. Final results may be utilized as thresholds for loading of produced structural elements and they aim to present probabilistic design as less conservative compared to classic partial safety factor based design and alternative ECOV method.

Footprinting analysis of interactions between the largest eukaryotic RNase P/MRP protein Pop1 and RNase P/MRP RNA components.

PubMed

Fagerlund, Robert D; Perederina, Anna; Berezin, Igor; Krasilnikov, Andrey S

2015-09-01

Ribonuclease (RNase) P and RNase MRP are closely related catalytic ribonucleoproteins involved in the metabolism of a wide range of RNA molecules, including tRNA, rRNA, and some mRNAs. The catalytic RNA component of eukaryotic RNase P retains the core elements of the bacterial RNase P ribozyme; however, the peripheral RNA elements responsible for the stabilization of the global architecture are largely absent in the eukaryotic enzyme. At the same time, the protein makeup of eukaryotic RNase P is considerably more complex than that of the bacterial RNase P. RNase MRP, an essential and ubiquitous eukaryotic enzyme, has a structural organization resembling that of eukaryotic RNase P, and the two enzymes share most of their protein components. Here, we present the results of the analysis of interactions between the largest protein component of yeast RNases P/MRP, Pop1, and the RNA moieties of the enzymes, discuss structural implications of the results, and suggest that Pop1 plays the role of a scaffold for the stabilization of the global architecture of eukaryotic RNase P RNA, substituting for the network of RNA-RNA tertiary interactions that maintain the global RNA structure in bacterial RNase P. © 2015 Fagerlund et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Interactive effects of warming, eutrophication and size structure: impacts on biodiversity and food-web structure.

PubMed

Binzer, Amrei; Guill, Christian; Rall, Björn C; Brose, Ulrich

2016-01-01

Warming and eutrophication are two of the most important global change stressors for natural ecosystems, but their interaction is poorly understood. We used a dynamic model of complex, size-structured food webs to assess interactive effects on diversity and network structure. We found antagonistic impacts: Warming increases diversity in eutrophic systems and decreases it in oligotrophic systems. These effects interact with the community size structure: Communities of similarly sized species such as parasitoid-host systems are stabilized by warming and destabilized by eutrophication, whereas the diversity of size-structured predator-prey networks decreases strongly with warming, but decreases only weakly with eutrophication. Nonrandom extinction risks for generalists and specialists lead to higher connectance in networks without size structure and lower connectance in size-structured communities. Overall, our results unravel interactive impacts of warming and eutrophication and suggest that size structure may serve as an important proxy for predicting the community sensitivity to these global change stressors. © 2015 John Wiley & Sons Ltd.

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.

Global optimization of cholic acid aggregates

NASA Astrophysics Data System (ADS)

Jójárt, Balázs; Viskolcz, Béla; Poša, Mihalj; Fejer, Szilard N.

2014-04-01

In spite of recent investigations into the potential pharmaceutical importance of bile acids as drug carriers, the structure of bile acid aggregates is largely unknown. Here, we used global optimization techniques to find the lowest energy configurations for clusters composed between 2 and 10 cholate molecules, and evaluated the relative stabilities of the global minima. We found that the energetically most preferred geometries for small aggregates are in fact reverse micellar arrangements, and the classical micellar behaviour (efficient burial of hydrophobic parts) is achieved only in systems containing more than five cholate units. Hydrogen bonding plays a very important part in keeping together the monomers, and among the size range considered, the most stable structure was found to be the decamer, having 17 hydrogen bonds. Molecular dynamics simulations showed that the decamer has the lowest dissociation propensity among the studied aggregation numbers.

Thermostability in rubredoxin and its relationship to mechanical rigidity

NASA Astrophysics Data System (ADS)

Rader, A. J.

2010-03-01

The source of increased stability in proteins from organisms that thrive in extreme thermal environments is not well understood. Previous experimental and theoretical studies have suggested many different features possibly responsible for such thermostability. Many of these thermostabilizing mechanisms can be accounted for in terms of structural rigidity. Thus a plausible hypothesis accounting for this remarkable stability in thermophilic enzymes states that these enzymes have enhanced conformational rigidity at temperatures below their native, functioning temperature. Experimental evidence exists to both support and contradict this supposition. We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum using the FIRST software. A global increase in structural rigidity (equivalently a decrease in flexibility) corresponds to an increase in thermostability. Locally, rigidity differences (between mesophilic and thermophilic structures) agree with differences in protection factors.

Solid phase stability of molybdenum under compression: Sound velocity measurements and first-principles calculations

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

Zhang, Xiulu; Laboratory for Extreme Conditions Matter Properties, Southwest University of Science and Technology, 621010 Mianyang, Sichuan; Liu, Zhongli

2015-02-07

The high-pressure solid phase stability of molybdenum (Mo) has been the center of a long-standing controversy on its high-pressure melting. In this work, experimental and theoretical researches have been conducted to check its solid phase stability under compression. First, we performed sound velocity measurements from 38 to 160 GPa using the two-stage light gas gun and explosive loading in backward- and forward-impact geometries, along with the high-precision velocity interferometry. From the sound velocities, we found no solid-solid phase transition in Mo before shock melting, which does not support the previous solid-solid phase transition conclusion inferred from the sharp drops of themore » longitudinal sound velocity [Hixson et al., Phys. Rev. Lett. 62, 637 (1989)]. Then, we searched its structures globally using the multi-algorithm collaborative crystal structure prediction technique combined with the density functional theory. By comparing the enthalpies of body centered cubic structure with those of the metastable structures, we found that bcc is the most stable structure in the range of 0–300 GPa. The present theoretical results together with previous ones greatly support our experimental conclusions.« less

Stabilization of Small Boron Cage by Transition Metal Encapsulation

NASA Astrophysics Data System (ADS)

Zhang, Lijun; Lv, Jian; Wang, Yanchao; Ma, Yanming

2015-03-01

The discovery of chemically stable fullerene-like structures formed by elements other than carbon has been long-standing desired. On this aspect significant efforts have centered around boron, only one electron deficient compared with carbon. However, during the past decade a large number of experimental and theoretical studies have established that small boron clusters are either planar/quasi-planar or forming double-ring tubular structures. Until recently, two all-boron fullerenes have been independently discovered: B38 proposed by our structure searching calculations and B40 observed in a joint experimental and theoretical study. Here we extend our work to the even smaller boron clusters and propose an effective routine to stabilize them by transition metal encapsulation. By combining swarm-intelligence structure searching and first-principles calculations, we have systematically investigated the energy landscapes of transition-metal-doped MB24 clusters (M = Ti, Zr, Hf, Cr, Mo, W, Fe, Ru and Os). Two stable symmetric endohedral boron cages, MoB24 and WB24 are identified. The stability of them can be rationalized in terms of their unique 18-electron closed-shell electronic structures. Funded by Recruitment Program of Global Experts of China and China Postdoctoral Science Foundation.

Modulation of the multistate folding of designed TPR proteins through intrinsic and extrinsic factors

PubMed Central

Phillips, J J; Javadi, Y; Millership, C; Main, E R G

2012-01-01

Tetratricopeptide repeats (TPRs) are a class of all alpha-helical repeat proteins that are comprised of 34-aa helix-turn-helix motifs. These stack together to form nonglobular structures that are stabilized by short-range interactions from residues close in primary sequence. Unlike globular proteins, they have few, if any, long-range nonlocal stabilizing interactions. Several studies on designed TPR proteins have shown that this modular structure is reflected in their folding, that is, modular multistate folding is observed as opposed to two-state folding. Here we show that TPR multistate folding can be suppressed to approximate two-state folding through modulation of intrinsic stability or extrinsic environmental variables. This modulation was investigated by comparing the thermodynamic unfolding under differing buffer regimes of two distinct series of consensus-designed TPR proteins, which possess different intrinsic stabilities. A total of nine proteins of differing sizes and differing consensus TPR motifs were each thermally and chemically denatured and their unfolding monitored using differential scanning calorimetry (DSC) and CD/fluorescence, respectively. Analyses of both the DSC and chemical denaturation data show that reducing the total stability of each protein and repeat units leads to observable two-state unfolding. These data highlight the intimate link between global and intrinsic repeat stability that governs whether folding proceeds by an observably two-state mechanism, or whether partial unfolding yields stable intermediate structures which retain sufficient stability to be populated at equilibrium. PMID:22170589

Structure-based energetics of protein interfaces guide Foot-and-Mouth Disease virus vaccine design

PubMed Central

Scott, Katherine; Burman, Alison; Loureiro, Silvia; Ren, Jingshan; Porta, Claudine; Ginn, Helen M.; Jackson, Terry; Perez-Martin, Eva; Siebert, C. Alistair; Paul, Guntram; Huiskonen, Juha T.; Jones, Ian M.; Esnouf, Robert M.; Fry, Elizabeth E.; Maree, Francois F.; Charleston, Bryan; Stuart, David I.

2018-01-01

Summary Virus capsids are primed for disassembly yet capsid integrity is key to generating a protective immune response. Here we devise a computational method to assess relative stability of protein-protein interfaces and use it to design improved candidate vaccines for two of the least stable, but globally important, serotypes of Foot-and-Mouth Disease virus (FMDV), O and SAT2. FMDV capsids comprise identical pentameric protein subunits held together by tenuous non-covalent interactions, and are often unstable. Chemically inactivated or recombinant empty capsids, which could form the basis of future vaccines, are even less stable than live virus. We use a novel restrained molecular dynamics strategy, to rank mutations predicted to strengthen the pentamer interfaces to produce stabilized capsids. Structural analyses and stability assays confirmed the predictions, and vaccinated animals generated improved neutralising antibody responses to stabilised particles over parental viruses and wild-type capsids. PMID:26389739

Effects of manganese doping on the structure evolution of small-sized boron clusters

NASA Astrophysics Data System (ADS)

Zhao, Lingquan; Qu, Xin; Wang, Yanchao; Lv, Jian; Zhang, Lijun; Hu, Ziyu; Gu, Guangrui; Ma, Yanming

2017-07-01

Atomic doping of clusters is known as an effective approach to stabilize or modify the structures and properties of resulting doped clusters. We herein report the effect of manganese (Mn) doping on the structure evolution of small-sized boron (B) clusters. The global minimum structures of both neutral and charged Mn doped B cluster \\text{MnB}nQ (n  =  10-20 and Q  =  0, ±1) have been proposed through extensive first-principles swarm-intelligence based structure searches. It is found that Mn doping has significantly modified the grow behaviors of B clusters, leading to two novel structural transitions from planar to tubular and then to cage-like B structures in both neutral and charged species. Half-sandwich-type structures are most favorable for small \\text{MnB}n-/0/+ (n  ⩽  13) clusters and gradually transform to Mn-centered double-ring tubular structures at \\text{MnB}16-/0/+ clusters with superior thermodynamic stabilities compared with their neighbors. Most strikingly, endohedral cages become the ground-state structures for larger \\text{MnB}n-/0/+ (n  ⩾  19) clusters, among which \\text{MnB}20+ adopts a highly symmetric structure with superior thermodynamic stability and a large HOMO-LUMO gap of 4.53 eV. The unique stability of the endohedral \\text{MnB}\\text{20}+ cage is attributed to the geometric fit and formation of 18-electron closed-shell configuration. The results significantly advance our understanding about the structure and bonding of B-based clusters and strongly suggest transition-metal doping as a viable route to synthesize intriguing B-based nanomaterials.

Global adaptive control for uncertain nonaffine nonlinear hysteretic systems.

PubMed

Liu, Yong-Hua; Huang, Liangpei; Xiao, Dongming; Guo, Yong

2015-09-01

In this paper, the global output tracking is investigated for a class of uncertain nonlinear hysteretic systems with nonaffine structures. By combining the solution properties of the hysteresis model with the novel backstepping approach, a robust adaptive control algorithm is developed without constructing a hysteresis inverse. The proposed control scheme is further modified to tackle the bounded disturbances by adaptively estimating their bounds. It is rigorously proven that the designed adaptive controllers can guarantee global stability of the closed-loop system. Two numerical examples are provided to show the effectiveness of the proposed control schemes. Copyright © 2015 ISA. Published by Elsevier Ltd. All rights reserved.

Dynamics differentiate between active and inactive inteins

PubMed Central

Cronin, Melissa; Coolbaugh, Michael J; Nellis, David; Zhu, Jianwei; Wood, David W.; Nussinov, Ruth; Ma, Buyong

2014-01-01

The balance between stability and dynamics for active enzymes can be somewhat quantified by studies of intein splicing and cleaving reactions. Inteins catalyze the ligation of flanking host exteins while excising themselves. The potential for applications led to engineering of a mini-intein splicing domain, where the homing endonuclease domain of the Mycobacterium tuberculosis RecA (Mtu recA) intein was removed. The remaining domains were linked by several short peptides, but splicing activity in all was substantially lower than the full-length intein. Native splicing activity was restored in some cases by a V67L mutation. Using computations and experiments, we examine the impact of this mutation on the stability and conformational dynamics of the mini-intein splicing domain. Molecular dynamics simulations were used to delineate the factors that determine the active state, including the V67L mini-intein mutant, and peptide linker. We found that (1) the V67L mutation lowers the global fluctuations in all modeled mini-inteins, stabilizing the mini-intein constructs; (2) the connecting linker length affects intein dynamics; and (3) the flexibilities of the linker and intein core are higher in the active structure. We have observed that the interaction of the linker region and a turn region around residues 35-41 provides the pathway for the allostery interaction. Our experiments reveal that intein catalysis is characterized by non-linear Arrhenius plot, confirming the significant contribution of protein conformational dynamics to intein function. We conclude that while the V67L mutation stabilizes the global structure, cooperative dynamics of all intein regions appear more important for intein function than high stability. Our studies suggest that effectively quenching the conformational dynamics of an intein through engineered allosteric interactions could deactivate intein splicing or cleaving. PMID:25087201

Felder-Soloman's Index of Learning Styles: internal consistency, temporal stability, and factor structure.

PubMed

Hosford, Charles C; Siders, William A

2010-10-01

Strategies to facilitate learning include using knowledge of students' learning style preferences to inform students and their teachers. Aims of this study were to evaluate the factor structure, internal consistency, and temporal stability of medical student responses to the Index of Learning Styles (ILS) and determine its appropriateness as an instrument for medical education. The ILS assesses preferences on four dimensions: sensing/intuitive information perceiving, visual/verbal information receiving, active/reflective information processing, and sequential/global information understanding. Students entering the 2002-2007 classes completed the ILS; some completed the ILS again after 2 and 4 years. Analyses of responses supported the ILS's intended structure and moderate reliability. Students had moderate preferences for sensing and visual learning. This study provides evidence supporting the appropriateness of the ILS for assessing learning style preferences in medical students.

Unraveling the Planar-Globular Transition in Gold Nanoclusters through Evolutionary Search

DOE PAGES

Kinaci, Alper; Narayanan, Badri; Sen, Fatih G.; ...

2016-11-28

Au nanoclusters are of technological relevance for catalysis, photonics, sensors, and of fundamental scientific interest owing to planar to globular structural transformation at an anomalously high number of atoms i.e. in the range 12-14. The nature and causes of this transition remain a mystery. In order to unravel this conundrum, high throughput density functional theory (DFT) calculations, coupled with a global structural optimization scheme based on a modified genetic algorithm (GA) are conducted. Furthermore, more than 20,000 Au 12, Au 13, and Au 14 nanoclusters are evaluated. With any DFT functional, globular and planar structures coexist across the size rangemore » of interest. Contrary to what was previously believed, the planar-globular transition is gradual at room temperature rather than a sharp transition. The effects of anionicity, s-d band hybridization and long range interactions on the dimensional transition are quantified by using the structures adjacent to minima. Anionicity marginally changes the relative stability of the clusters. The degree of s-d hybridization is varied via changing the Hubbard U value which corroborate that s-d hybridization alone does not stabilize planar structures. van der Waals interactions, on the other hand, stabilize globular structures. Our results elucidate the balance between the different reasons of the dimensional transition in gold nanoclusters.« less

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.

The Potential and Flux Landscape Theory of Ecology

PubMed Central

Zhang, Kun; Wang, Erkang; Wang, Jin

2014-01-01

The species in ecosystems are mutually interacting and self sustainable stable for a certain period. Stability and dynamics are crucial for understanding the structure and the function of ecosystems. We developed a potential and flux landscape theory of ecosystems to address these issues. We show that the driving force of the ecological dynamics can be decomposed to the gradient of the potential landscape and the curl probability flux measuring the degree of the breaking down of the detailed balance (due to in or out flow of the energy to the ecosystems). We found that the underlying intrinsic potential landscape is a global Lyapunov function monotonically going down in time and the topology of the landscape provides a quantitative measure for the global stability of the ecosystems. We also quantified the intrinsic energy, the entropy, the free energy and constructed the non-equilibrium thermodynamics for the ecosystems. We studied several typical and important ecological systems: the predation, competition, mutualism and a realistic lynx-snowshoe hare model. Single attractor, multiple attractors and limit cycle attractors emerge from these studies. We studied the stability and robustness of the ecosystems against the perturbations in parameters and the environmental fluctuations. We also found that the kinetic paths between the multiple attractors do not follow the gradient paths of the underlying landscape and are irreversible because of the non-zero flux. This theory provides a novel way for exploring the global stability, function and the robustness of ecosystems. PMID:24497975

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

Semi-Metallic Be5C2 Monolayer Global Minimum with Quasi-Planar Pentacoordinate Carbons and Negative Poissons Ratio (Open Access Publisher’s Version)

DTIC Science & Technology

2016-05-03

ARTICLE Received 25 Nov 2015 | Accepted 1 Apr 2016 | Published 3 May 2016 Semi-metallic Be5C2 monolayer global minimum with quasi -planar...forming a quasi -planar pentacoordinate carbon moiety. Be5C2 monolayer appears to have good stability as revealed by its moderate cohesive energy...some promise to be realized experimentally . Be5C2 monolayer is a gapless semiconductor with a Dirac-like point in the band structure and also has an

Regulation, Competition and Network Evolution in Aviation

NASA Technical Reports Server (NTRS)

Gillen, David; Morrison, William

2003-01-01

Our focus is the evolution of business strategies and network structure decisions in the commercial passenger aviation industry. The paper reviews the growth of hub-and-spoke networks as the dominant business model following deregulation in the latter part of the 20 century, followed by the emergence of value-based airlines as a global phenomenon at the end of the century. The paper highlights the link between airline business strategies and network structures, and examines the resulting competition between divergent network structure business models. In this context we discuss issues of market structure stability and the role played by competition policy.

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.

Nuclear transmutation in steels

NASA Astrophysics Data System (ADS)

Belozerova, A. R.; Shimanskii, G. A.; Belozerov, S. V.

2009-05-01

The investigations of the effects of nuclear transmutation in steels that are widely used in nuclear power and research reactors and in steels that are planned for the application in thermonuclear fusion plants, which are employed under the conditions of a prolonged action of neutron irradiation with different spectra, made it possible to study the effects of changes in the isotopic and chemical composition on the tendency of changes in the structural stability of these steels. For the computations of nuclear transmutation in steels, we used a program complex we have previously developed on the basis of algorithms for constructing branched block-type diagrams of nuclide transformations and for locally and globally optimizing these diagrams with the purpose of minimizing systematic errors in the calculation of nuclear transmutation. The dependences obtained were applied onto a Schaeffler diagram for steels used for structural elements of reactors. For the irradiation in fission reactors, we observed only a weak influence of the effects of nuclear transmutation in steels on their structural stability. On the contrary, in the case of irradiation with fusion neutrons, a strong influence of the effects of nuclear transmutation in steels on their structural stability has been noted.

Cerium-based, intermetallic-strengthened aluminum casting alloy: High-volume co-product development

DOE PAGES

Sims, Zachary C.; Weiss, David; McCall, S. K.; ...

2016-05-23

Here, several rare earth elements are considered by-products to rare earth mining efforts. By using one of these by-product elements in a high-volume application such as aluminum casting alloys, the supply of more valuable rare earths can be globally stabilized. Stabilizing the global rare earth market will decrease the long-term criticality of other rare earth elements. The low demand for Ce, the most abundant rare earth, contributes to the instability of rare earth extraction. In this article, we discuss a series of intermetallic-strengthened Al alloys that exhibit the potential for new high-volume use of Ce. The castability, structure, and mechanicalmore » properties of binary, ternary, and quaternary Al-Ce based alloys are discussed. We have determined Al-Ce based alloys to be highly castable across a broad range of compositions. Nanoscale intermetallics dominate the microstructure and are the theorized source of the high ductility. In addition, room-temperature physical properties appear to be competitive with existing aluminum alloys with extended high-temperature stability of the nanostructured intermetallic.« less

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.

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.

D3h [A-CE3-A]- (E = Al and Ga, A = Si, Ge, Sn, and Pb): A new class of hexatomic mono-anionic species with trigonal bipyramidal carbon

NASA Astrophysics Data System (ADS)

Wu, Yan-Bo; Li, Yan-Qin; Bai, Hui; Lu, Hai-Gang; Li, Si-Dian; Zhai, Hua-Jin; Wang, Zhi-Xiang

2014-03-01

The non-classical trigonal bipyramidal carbon (TBPC) arrangement generally exists as transition states (TSs) in nucleophilic bimolecular substitution (SN2) reactions. Nevertheless, chemists have been curious about whether such a carbon bonding could be stable in equilibrium structures for decades. As the TBPC arrangement was normally realized as cationic species theoretically and experimentally, only one anionic example ([At-C(CN)3-At]-) was computationally devised. Herein, we report the design of a new class of anionic TBPC species by using the strategy similar to that for stabilizing the non-classical planar hypercoordinate carbon. When electron deficient Al and Ga were used as the equatorial ligands, eight D3h [A-CE3-A]- (E = Al and Ga, A = Si, Ge, Sn, and Pb) TBPC structures were found to be the energy minima rather than TSs at both the B3LYP and MP2 levels. Remarkably, the energetic results at the CCSD(T) optimization level further identify [Ge-CAl3-Ge]- and [Sn-CGa3-Sn]- even to be the global minima and [Si-CAl3-Si]- and [Ge-CGa3-Ge]- to be the local minima, only slightly higher than their global minima. The electronic structure analyses reveal that the substantial ionic C-E bonding, the peripheral E-A covalent bonding, and the axial mc-2e (multi center-two electrons) bonding play roles in stabilizing these TBPC structures. The structural simplicity and the high thermodynamic stability suggest that some of these species may be generated and captured in the gas phase. Furthermore, as mono-anionic species, their first vertical detachment energies are differentiable from those of their nearest isomers, which would facilitate their characterization via experiments such as the negative ion photoelectron spectroscopy.

Local and global stability for Lotka-Volterra systems with distributed delays and instantaneous negative feedbacks

NASA Astrophysics Data System (ADS)

Faria, Teresa; Oliveira, José J.

This paper addresses the local and global stability of n-dimensional Lotka-Volterra systems with distributed delays and instantaneous negative feedbacks. Necessary and sufficient conditions for local stability independent of the choice of the delay functions are given, by imposing a weak nondelayed diagonal dominance which cancels the delayed competition effect. The global asymptotic stability of positive equilibria is established under conditions slightly stronger than the ones required for the linear stability. For the case of monotone interactions, however, sharper conditions are presented. This paper generalizes known results for discrete delays to systems with distributed delays. Several applications illustrate the results.

Stability analysis for stochastic BAM nonlinear neural network with delays

NASA Astrophysics Data System (ADS)

Lv, Z. W.; Shu, H. S.; Wei, G. L.

2008-02-01

In this paper, stochastic bidirectional associative memory neural networks with constant or time-varying delays is considered. Based on a Lyapunov-Krasovskii functional and the stochastic stability analysis theory, we derive several sufficient conditions in order to guarantee the global asymptotically stable in the mean square. Our investigation shows that the stochastic bidirectional associative memory neural networks are globally asymptotically stable in the mean square if there are solutions to some linear matrix inequalities(LMIs). Hence, the global asymptotic stability of the stochastic bidirectional associative memory neural networks can be easily checked by the Matlab LMI toolbox. A numerical example is given to demonstrate the usefulness of the proposed global asymptotic stability criteria.

Structural study of gold clusters.

PubMed

Xiao, Li; Tollberg, Bethany; Hu, Xiankui; Wang, Lichang

2006-03-21

Density functional theory (DFT) calculations were carried out to study gold clusters of up to 55 atoms. Between the linear and zigzag monoatomic Au nanowires, the zigzag nanowires were found to be more stable. Furthermore, the linear Au nanowires of up to 2 nm are formed by slightly stretched Au dimers. These suggest that a substantial Peierls distortion exists in those structures. Planar geometries of Au clusters were found to be the global minima till the cluster size of 13. A quantitative correlation is provided between various properties of Au clusters and the structure and size. The relative stability of selected clusters was also estimated by the Sutton-Chen potential, and the result disagrees with that obtained from the DFT calculations. This suggests that a modification of the Sutton-Chen potential has to be made, such as obtaining new parameters, in order to use it to search the global minima for bigger Au clusters.

Ideal MHD stability of double transport barrier plasmas in DIII-D

NASA Astrophysics Data System (ADS)

Li, G. Q.; Wang, S. J.; Lao, L. L.; Turnbull, A. D.; Chu, M. S.; Brennan, D. P.; Groebner, R. J.; Zhao, L.

2008-01-01

The ideal MHD stability for double transport barrier (DTB or DB) plasmas with varying edge and internal barrier width and height was investigated, using the ideal MHD stability code GATO. A moderate ratio of edge transport barriers (ETB) height to internal transport barriers (ITBs) height is found to be beneficial to MHD stability and the βN is limited by global low n instabilities. For moderate ITB width DB plasmas, if the ETB is weak, the stability is limited by n = 1 (n is the toroidal mode number) global mode; whereas if the ETB is strong it is limited by intermediate-n edge peeling-ballooning modes. Broadening the ITB can improve stability if the ITB half width wi lsim 0.3. For very broad ITB width plasmas the stability is limited by stability to a low n (n > 1) global mode.

Induction of a Tier-1-Like Phenotype in Diverse Tier-2 Isolates by Agents That Guide HIV-1 Env to Perturbation-Sensitive, Nonnative States.

PubMed

Johnson, Jacklyn; Zhai, Yinjie; Salimi, Hamid; Espy, Nicole; Eichelberger, Noah; DeLeon, Orlando; O'Malley, Yunxia; Courter, Joel; Smith, Amos B; Madani, Navid; Sodroski, Joseph; Haim, Hillel

2017-08-01

The envelope glycoproteins (Envs) on the surfaces of HIV-1 particles are targeted by host antibodies. Primary HIV-1 isolates demonstrate different global sensitivities to antibody neutralization; tier-1 isolates are sensitive, whereas tier-2 isolates are more resistant. Single-site mutations in Env can convert tier-2 into tier-1-like viruses. We hypothesized that such global change in neutralization sensitivity results from weakening of intramolecular interactions that maintain Env integrity. Three strategies commonly applied to perturb protein structure were tested for their effects on global neutralization sensitivity: exposure to low temperature, Env-activating ligands, and a chaotropic agent. A large panel of diverse tier-2 isolates from clades B and C was analyzed. Incubation at 0°C, which globally weakens hydrophobic interactions, causes gradual and reversible exposure of the coreceptor-binding site. In the cold-induced state, Envs progress at isolate-specific rates to unstable forms that are sensitive to antibody neutralization and then gradually lose function. Agents that mimic the effects of CD4 (CD4Ms) also induce reversible structural changes to states that exhibit isolate-specific stabilities. The chaotropic agent urea (at low concentrations) does not affect the structure or function of native Env. However, urea efficiently perturbs metastable states induced by cold and CD4Ms and increases their sensitivity to antibody neutralization and their inactivation rates Therefore, chemical and physical agents can guide Env from the stable native state to perturbation-sensitive forms and modulate their stability to bestow tier-1-like properties on primary tier-2 strains. These concepts can be applied to enhance the potency of vaccine-elicited antibodies and microbicides at mucosal sites of HIV-1 transmission. IMPORTANCE An effective vaccine to prevent transmission of HIV-1 is a primary goal of the scientific and health care communities. Vaccine-elicited antibodies target the viral envelope glycoproteins (Envs) and can potentially inhibit infection. However, the potency of such antibodies is generally low. Single-site mutations in Env can enhance the global sensitivity of HIV-1 to neutralization by antibodies. We found that such a hypersensitivity phenotype can also be induced by agents that destabilize protein structure. Exposure to 0°C or low concentrations of Env-activating ligands gradually guides Env to metastable forms that expose cryptic epitopes and that are highly sensitive to neutralization. Low concentrations of the chaotropic agent urea do not affect native Env but destabilize perturbed states induced by cold or CD4Ms and increase their neutralization. The concept of enhancing antibody sensitivity by chemical agents that affect the structural stability of proteins can be applied to increase the potency of topical microbicides and vaccine-elicited antibodies. Copyright © 2017 American Society for Microbiology.

Sum-of-squares of polynomials approach to nonlinear stability of fluid flows: an example of application

PubMed Central

Tutty, O.

2015-01-01

With the goal of providing the first example of application of a recently proposed method, thus demonstrating its ability to give results in principle, global stability of a version of the rotating Couette flow is examined. The flow depends on the Reynolds number and a parameter characterizing the magnitude of the Coriolis force. By converting the original Navier–Stokes equations to a finite-dimensional uncertain dynamical system using a partial Galerkin expansion, high-degree polynomial Lyapunov functionals were found by sum-of-squares of polynomials optimization. It is demonstrated that the proposed method allows obtaining the exact global stability limit for this flow in a range of values of the parameter characterizing the Coriolis force. Outside this range a lower bound for the global stability limit was obtained, which is still better than the energy stability limit. In the course of the study, several results meaningful in the context of the method used were also obtained. Overall, the results obtained demonstrate the applicability of the recently proposed approach to global stability of the fluid flows. To the best of our knowledge, it is the first case in which global stability of a fluid flow has been proved by a generic method for the value of a Reynolds number greater than that which could be achieved with the energy stability approach. PMID:26730219

From intuition to statistics in building subsurface structural models

USGS Publications Warehouse

Brandenburg, J.P.; Alpak, F.O.; Naruk, S.; Solum, J.

2011-01-01

Experts associated with the oil and gas exploration industry suggest that combining forward trishear models with stochastic global optimization algorithms allows a quantitative assessment of the uncertainty associated with a given structural model. The methodology is applied to incompletely imaged structures related to deepwater hydrocarbon reservoirs and results are compared to prior manual palinspastic restorations and borehole data. This methodology is also useful for extending structural interpretations into other areas of limited resolution, such as subsalt in addition to extrapolating existing data into seismic data gaps. This technique can be used for rapid reservoir appraisal and potentially have other applications for seismic processing, well planning, and borehole stability analysis.

NH2-terminal sequence truncation decreases the stability of bovine rhodanese, minimally perturbs its crystal structure, and enhances interaction with GroEL under native conditions.

PubMed

Trevino, R J; Gliubich, F; Berni, R; Cianci, M; Chirgwin, J M; Zanotti, G; Horowitz, P M

1999-05-14

The NH2-terminal sequence of rhodanese influences many of its properties, ranging from mitochondrial import to folding. Rhodanese truncated by >9 residues is degraded in Escherichia coli. Mutant enzymes with lesser truncations are recoverable and active, but they show altered active site reactivities (Trevino, R. J., Tsalkova, T., Dramer, G., Hardesty, B., Chirgwin, J. M., and Horowitz, P. M. (1998) J. Biol. Chem. 273, 27841-27847), suggesting that the NH2-terminal sequence stabilizes the overall structure. We tested aspects of the conformations of these shortened species. Intrinsic and probe fluorescence showed that truncation decreased stability and increased hydrophobic exposure, while near UV CD suggested altered tertiary structure. Under native conditions, truncated rhodanese bound to GroEL and was released and reactivated by adding ATP and GroES, suggesting equilibrium between native and non-native conformers. Furthermore, GroEL assisted folding of denatured mutants to the same extent as wild type, although at a reduced rate. X-ray crystallography showed that Delta1-7 crystallized isomorphously with wild type in polyethyleneglycol, and the structure was highly conserved. Thus, the missing NH2-terminal residues that contribute to global stability of the native structure in solution do not significantly alter contacts at the atomic level of the crystallized protein. The two-domain structure of rhodanese was not significantly altered by drastically different crystallization conditions or crystal packing suggesting rigidity of the native rhodanese domains and the stabilization of the interdomain interactions by the crystal environment. The results support a model in which loss of interactions near the rhodanese NH2 terminus does not distort the folded native structure but does facilitate the transition in solution to a molten globule state, which among other things, can interact with molecular chaperones.

Decentralization, stabilization, and estimation of large-scale linear systems

NASA Technical Reports Server (NTRS)

Siljak, D. D.; Vukcevic, M. B.

1976-01-01

In this short paper we consider three closely related aspects of large-scale systems: decentralization, stabilization, and estimation. A method is proposed to decompose a large linear system into a number of interconnected subsystems with decentralized (scalar) inputs or outputs. The procedure is preliminary to the hierarchic stabilization and estimation of linear systems and is performed on the subsystem level. A multilevel control scheme based upon the decomposition-aggregation method is developed for stabilization of input-decentralized linear systems Local linear feedback controllers are used to stabilize each decoupled subsystem, while global linear feedback controllers are utilized to minimize the coupling effect among the subsystems. Systems stabilized by the method have a tolerance to a wide class of nonlinearities in subsystem coupling and high reliability with respect to structural perturbations. The proposed output-decentralization and stabilization schemes can be used directly to construct asymptotic state estimators for large linear systems on the subsystem level. The problem of dimensionality is resolved by constructing a number of low-order estimators, thus avoiding a design of a single estimator for the overall system.

Persistence of soil organic matter as an ecosystem property.

PubMed

Schmidt, Michael W I; Torn, Margaret S; Abiven, Samuel; Dittmar, Thorsten; Guggenberger, Georg; Janssens, Ivan A; Kleber, Markus; Kögel-Knabner, Ingrid; Lehmann, Johannes; Manning, David A C; Nannipieri, Paolo; Rasse, Daniel P; Weiner, Steve; Trumbore, Susan E

2011-10-05

Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily--and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

Persistence of soil organic matter as an ecosystem property

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

Schmidt, M.W.; Torn, M. S.; Abiven, S.

2011-08-15

Globally, soil organic matter (SOM) contains more than three times as much carbon as either the atmosphere or terrestrial vegetation. Yet it remains largely unknown why some SOM persists for millennia whereas other SOM decomposes readily—and this limits our ability to predict how soils will respond to climate change. Recent analytical and experimental advances have demonstrated that molecular structure alone does not control SOM stability: in fact, environmental and biological controls predominate. Here we propose ways to include this understanding in a new generation of experiments and soil carbon models, thereby improving predictions of the SOM response to global warming.

Robust distributed model predictive control of linear systems with structured time-varying uncertainties

NASA Astrophysics Data System (ADS)

Zhang, Langwen; Xie, Wei; Wang, Jingcheng

2017-11-01

In this work, synthesis of robust distributed model predictive control (MPC) is presented for a class of linear systems subject to structured time-varying uncertainties. By decomposing a global system into smaller dimensional subsystems, a set of distributed MPC controllers, instead of a centralised controller, are designed. To ensure the robust stability of the closed-loop system with respect to model uncertainties, distributed state feedback laws are obtained by solving a min-max optimisation problem. The design of robust distributed MPC is then transformed into solving a minimisation optimisation problem with linear matrix inequality constraints. An iterative online algorithm with adjustable maximum iteration is proposed to coordinate the distributed controllers to achieve a global performance. The simulation results show the effectiveness of the proposed robust distributed MPC algorithm.

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

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

Coherent structures in interacting vortex rings

NASA Astrophysics Data System (ADS)

Deng, Jian; Xue, Jingyu; Mao, Xuerui; Caulfield, C. P.

2017-02-01

We investigate experimentally the nonlinear structures that develop from interacting vortex rings induced by a sinusoidally oscillating ellipsoidal disk in fluid at rest. We vary the scaled amplitude or Keulegan-Carpenter number 0.3

Unifying mechanical and thermodynamic descriptions across the thioredoxin protein family.

PubMed

Mottonen, James M; Xu, Minli; Jacobs, Donald J; Livesay, Dennis R

2009-05-15

We compare various predicted mechanical and thermodynamic properties of nine oxidized thioredoxins (TRX) using a Distance Constraint Model (DCM). The DCM is based on a nonadditive free energy decomposition scheme, where entropic contributions are determined from rigidity and flexibility of structure based on distance constraints. We perform averages over an ensemble of constraint topologies to calculate several thermodynamic and mechanical response functions that together yield quantitative stability/flexibility relationships (QSFR). Applied to the TRX protein family, QSFR metrics display a rich variety of similarities and differences. In particular, backbone flexibility is well conserved across the family, whereas cooperativity correlation describing mechanical and thermodynamic couplings between the residue pairs exhibit distinctive features that readily standout. The diversity in predicted QSFR metrics that describe cooperativity correlation between pairs of residues is largely explained by a global flexibility order parameter describing the amount of intrinsic flexibility within the protein. A free energy landscape is calculated as a function of the flexibility order parameter, and key values are determined where the native-state, transition-state, and unfolded-state are located. Another key value identifies a mechanical transition where the global nature of the protein changes from flexible to rigid. The key values of the flexibility order parameter help characterize how mechanical and thermodynamic response is linked. Variation in QSFR metrics and key characteristics of global flexibility are related to the native state X-ray crystal structure primarily through the hydrogen bond network. Furthermore, comparison of three TRX redox pairs reveals differences in thermodynamic response (i.e., relative melting point) and mechanical properties (i.e., backbone flexibility and cooperativity correlation) that are consistent with experimental data on thermal stabilities and NMR dynamical profiles. The results taken together demonstrate that small-scale structural variations are amplified into discernible global differences by propagating mechanical couplings through the H-bond network.

Doping-stabilized two-dimensional black phosphorus.

PubMed

Xuan, Xiaoyu; Zhang, Zhuhua; Guo, Wanlin

2018-05-03

Two-dimensional (2D) black phosphorus (BP) has attracted broad interests but remains to be synthesized. One of the issues lies in its large number of 2D allotropes with highly degenerate energies, especially 2D blue phosphorus. Here, we show that both nitrogen and hole-carrier doping can lift the energy degeneracy and locate 2D BP in a deep global energy minimum, while arsenic doping favours the formation of 2D blue phosphorus, attributed to a delicate interplay between s-p overlapping and repulsion of lone pairs. Chemically inert substrates, e.g. graphene and hexagonal boron nitride, can be synergic with carrier doping to stabilize the BP further over other 2D allotropes, while frequently used metal substrates severely reduce the stability of 2D BP. These results not only offer new insight into the structural stability of 2D phosphorus but also suggest a promising pathway towards the chemical synthesis of 2D BP.

STRUM: structure-based prediction of protein stability changes upon single-point mutation.

PubMed

Quan, Lijun; Lv, Qiang; Zhang, Yang

2016-10-01

Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several methods have been proposed to predict the effect of mutations on protein stability; but most require features from experimental structure. Given the fast progress in protein structure prediction, this work explores the possibility to improve the mutation-induced stability change prediction using low-resolution structure modeling. We developed a new method (STRUM) for predicting stability change caused by single-point mutations. Starting from wild-type sequences, 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, where physics- and knowledge-based energy functions are derived on the I-TASSER models and used to train STRUM models through gradient boosting regression. STRUM was assessed by 5-fold cross validation on 3421 experimentally determined mutations from 150 proteins. The Pearson correlation coefficient (PCC) between predicted and measured changes of Gibbs free-energy gap, ΔΔG, upon mutation reaches 0.79 with a root-mean-square error 1.2 kcal/mol in the mutation-based cross-validations. The PCC reduces if separating training and test mutations from non-homologous proteins, which reflects inherent correlations in the current mutation sample. Nevertheless, the results significantly outperform other state-of-the-art methods, including those built on experimental protein structures. Detailed analyses show that the most sensitive features in STRUM are the physics-based energy terms on I-TASSER models and the conservation scores from multiple-threading template alignments. However, the ΔΔG prediction accuracy has only a marginal dependence on the accuracy of protein structure models as long as the global fold is correct. These data demonstrate the feasibility to use low-resolution structure modeling for high-accuracy stability change prediction upon point mutations. http://zhanglab.ccmb.med.umich.edu/STRUM/ CONTACT: qiang@suda.edu.cn and zhng@umich.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

STRUM: structure-based prediction of protein stability changes upon single-point mutation

PubMed Central

Quan, Lijun; Lv, Qiang; Zhang, Yang

2016-01-01

Motivation: Mutations in human genome are mainly through single nucleotide polymorphism, some of which can affect stability and function of proteins, causing human diseases. Several methods have been proposed to predict the effect of mutations on protein stability; but most require features from experimental structure. Given the fast progress in protein structure prediction, this work explores the possibility to improve the mutation-induced stability change prediction using low-resolution structure modeling. Results: We developed a new method (STRUM) for predicting stability change caused by single-point mutations. Starting from wild-type sequences, 3D models are constructed by the iterative threading assembly refinement (I-TASSER) simulations, where physics- and knowledge-based energy functions are derived on the I-TASSER models and used to train STRUM models through gradient boosting regression. STRUM was assessed by 5-fold cross validation on 3421 experimentally determined mutations from 150 proteins. The Pearson correlation coefficient (PCC) between predicted and measured changes of Gibbs free-energy gap, ΔΔG, upon mutation reaches 0.79 with a root-mean-square error 1.2 kcal/mol in the mutation-based cross-validations. The PCC reduces if separating training and test mutations from non-homologous proteins, which reflects inherent correlations in the current mutation sample. Nevertheless, the results significantly outperform other state-of-the-art methods, including those built on experimental protein structures. Detailed analyses show that the most sensitive features in STRUM are the physics-based energy terms on I-TASSER models and the conservation scores from multiple-threading template alignments. However, the ΔΔG prediction accuracy has only a marginal dependence on the accuracy of protein structure models as long as the global fold is correct. These data demonstrate the feasibility to use low-resolution structure modeling for high-accuracy stability change prediction upon point mutations. Availability and Implementation: http://zhanglab.ccmb.med.umich.edu/STRUM/ Contact: qiang@suda.edu.cn and zhng@umich.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27318206

Cross-border Portfolio Investment Networks and Indicators for Financial Crises

PubMed Central

Joseph, Andreas C.; Joseph, Stephan E.; Chen, Guanrong

2014-01-01

Cross-border equity and long-term debt securities portfolio investment networks are analysed from 2002 to 2012, covering the 2008 global financial crisis. They serve as network-proxies for measuring the robustness of the global financial system and the interdependence of financial markets, respectively. Two early-warning indicators for financial crises are identified: First, the algebraic connectivity of the equity securities network, as a measure for structural robustness, drops close to zero already in 2005, while there is an over-representation of high-degree off-shore financial centres among the countries most-related to this observation, suggesting an investigation of such nodes with respect to the structural stability of the global financial system. Second, using a phenomenological model, the edge density of the debt securities network is found to describe, and even forecast, the proliferation of several over-the-counter-traded financial derivatives, most prominently credit default swaps, enabling one to detect potentially dangerous levels of market interdependence and systemic risk. PMID:24510060

Cross-border Portfolio Investment Networks and Indicators for Financial Crises

NASA Astrophysics Data System (ADS)

Joseph, Andreas C.; Joseph, Stephan E.; Chen, Guanrong

2014-02-01

Cross-border equity and long-term debt securities portfolio investment networks are analysed from 2002 to 2012, covering the 2008 global financial crisis. They serve as network-proxies for measuring the robustness of the global financial system and the interdependence of financial markets, respectively. Two early-warning indicators for financial crises are identified: First, the algebraic connectivity of the equity securities network, as a measure for structural robustness, drops close to zero already in 2005, while there is an over-representation of high-degree off-shore financial centres among the countries most-related to this observation, suggesting an investigation of such nodes with respect to the structural stability of the global financial system. Second, using a phenomenological model, the edge density of the debt securities network is found to describe, and even forecast, the proliferation of several over-the-counter-traded financial derivatives, most prominently credit default swaps, enabling one to detect potentially dangerous levels of market interdependence and systemic risk.

Cross-border portfolio investment networks and indicators for financial crises.

PubMed

Joseph, Andreas C; Joseph, Stephan E; Chen, Guanrong

2014-02-10

Cross-border equity and long-term debt securities portfolio investment networks are analysed from 2002 to 2012, covering the 2008 global financial crisis. They serve as network-proxies for measuring the robustness of the global financial system and the interdependence of financial markets, respectively. Two early-warning indicators for financial crises are identified: First, the algebraic connectivity of the equity securities network, as a measure for structural robustness, drops close to zero already in 2005, while there is an over-representation of high-degree off-shore financial centres among the countries most-related to this observation, suggesting an investigation of such nodes with respect to the structural stability of the global financial system. Second, using a phenomenological model, the edge density of the debt securities network is found to describe, and even forecast, the proliferation of several over-the-counter-traded financial derivatives, most prominently credit default swaps, enabling one to detect potentially dangerous levels of market interdependence and systemic risk.

Assessment of the DORIS network monumentation

NASA Astrophysics Data System (ADS)

Saunier, J.

2016-12-01

Stability of the monumentation is essential for precise positioning applications to minimize velocity uncertainties and noises in the position data. In charge of the DORIS global tracking network deployment since the beginning, IGN, in consultation with CNES, designed three standard monuments compliant with the DORIS system requirements and general geodetic specifications, and suitable for various site configurations: building roofs, concrete pedestals or pillars. This paper describes the monument types in use in the DORIS network according to the current required specifications and provides a comparative assessment of the stability of the monuments over the network based on three methods: a theoretical study of the mechanical behavior of the metallic structures, a misclosure analysis taken during ground surveys and a qualitative approach taking into account different factors. This overview of the network monumentation gives new key numbers following the previous network assessment performed by Fagard (2006). Significant improvements have been made following the continuous efforts to renovate the network monumentation. These results are relevant for the Global Geodetic Observing System (GGOS) goals of measurement stability for the geodetic techniques. Today, two-thirds of the DORIS network monuments are compliant with the standards aiming at stability of 0.1 mm/y. This stability result has been measured for 16 of the 58 stations more than 10 y after its installation while monuments with more than 1 mm antenna tilts are over 10 y old when specifications were less stringent. The grading and scoring grid drawn up for each monument led to the mapping of the stability of the current DORIS network. Finally, we present a number of further actions to monitor the monument stability and provide new elements for the network monumentation assessment, exploring two different approaches: analysis of the time series and direct measurements using devices placed on each monument.

Modeling resistive wall modes and disruptive instabilities with M3D-C1

NASA Astrophysics Data System (ADS)

Ferraro, Nm; Jardin, Sc; Pfefferle, D.

2016-10-01

Disruptive instabilities pose a significant challenge to the tokamak approach to magnetic fusion energy, and must be reliably avoided in a successful reactor. These instabilities generally involve rapid, global changes to the magnetic field, and electromagnetic interaction with surrounding conducting structures. Here we apply the extended-MHD code M3D-C1 to calculate the stability and evolution of disruptive modes, including their interaction with external conducting structures. The M3D-C1 model includes the effects of resistivity, equilibrium rotation, and resistive walls of arbitrary thickness, each of which may play important roles in the stability and evolution of disruptive modes. The strong stabilizing effect of rotation on resistive wall modes is explored and compared with analytic theory. The nonlinear evolution of vertical displacement events is also considered, including the evolution of non-axisymmetric instabilities that may arise during the current-quench phase of the disruption. It is found that the non-axisymmetric stability of the plasma during a VDE depends strongly on the thermal history of the plasma. This work is supported by US DOE Grant DE-AC02-09CH11466 and the SciDAC Center for Extended MHD Modeling.

Modeling and Analysis of a Nonlinear Age-Structured Model for Tumor Cell Populations with Quiescence

NASA Astrophysics Data System (ADS)

Liu, Zijian; Chen, Jing; Pang, Jianhua; Bi, Ping; Ruan, Shigui

2018-05-01

We present a nonlinear first-order hyperbolic partial differential equation model to describe age-structured tumor cell populations with proliferating and quiescent phases at the avascular stage in vitro. The division rate of the proliferating cells is assumed to be nonlinear due to the limitation of the nutrient and space. The model includes a proportion of newborn cells that enter directly the quiescent phase with age zero. This proportion can reflect the effect of treatment by drugs such as erlotinib. The existence and uniqueness of solutions are established. The local and global stabilities of the trivial steady state are investigated. The existence and local stability of the positive steady state are also analyzed. Numerical simulations are performed to verify the results and to examine the impacts of parameters on the nonlinear dynamics of the model.

Short-term responses and resistance of soil microbial community structure to elevated CO2 and N addition in grassland mesocosms.

PubMed

Simonin, Marie; Nunan, Naoise; Bloor, Juliette M G; Pouteau, Valérie; Niboyet, Audrey

2017-05-01

Nitrogen (N) addition is known to affect soil microbial communities, but the interactive effects of N addition with other drivers of global change remain unclear. The impacts of multiple global changes on the structure of microbial communities may be mediated by specific microbial groups with different life-history strategies. Here, we investigated the combined effects of elevated CO2 and N addition on soil microbial communities using PLFA profiling in a short-term grassland mesocosm experiment. We also examined the linkages between the relative abundance of r- and K-strategist microorganisms and resistance of the microbial community structure to experimental treatments. N addition had a significant effect on microbial community structure, likely driven by concurrent increases in plant biomass and in soil labile C and N. In contrast, microbial community structure did not change under elevated CO2 or show significant CO2 × N interactions. Resistance of soil microbial community structure decreased with increasing fungal/bacterial ratio, but showed a positive relationship with the Gram-positive/Gram-negative bacterial ratio. Our findings suggest that the Gram-positive/Gram-negative bacteria ratio may be a useful indicator of microbial community resistance and that K-strategist abundance may play a role in the short-term stability of microbial communities under global change. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Composite Structure Optimization with Genetic Algorithm

NASA Astrophysics Data System (ADS)

Deslandes, Olivier

2014-06-01

In the frame of optimization studies in CNES launcher directorate structure, thermic and material department, the need of an optimization tool based on metaheuristic and finite element models for composite structural dimensioning was underlined.Indeed, composite structures need complex optimization methodologies in order to be really compared to metallic structures with regard to mass, static strength and stiffness constraints (metallic structures using optimization methods better known).After some bibliography research, the use of a genetic algorithm coupled with design of experiment to generate the initial population was chosen. Academic functions were used to validate the optimization process and then it was applied to an industrial study aiming to optimize an interstage skirt with regard to its mass, stiffness and stability (global buckling).

Stability Results, Almost Global Generalized Beltrami Fields and Applications to Vortex Structures in the Euler Equations

NASA Astrophysics Data System (ADS)

Enciso, Alberto; Poyato, David; Soler, Juan

2018-05-01

Strong Beltrami fields, that is, vector fields in three dimensions whose curl is the product of the field itself by a constant factor, have long played a key role in fluid mechanics and magnetohydrodynamics. In particular, they are the kind of stationary solutions of the Euler equations where one has been able to show the existence of vortex structures (vortex tubes and vortex lines) of arbitrarily complicated topology. On the contrary, there are very few results about the existence of generalized Beltrami fields, that is, divergence-free fields whose curl is the field times a non-constant function. In fact, generalized Beltrami fields (which are also stationary solutions to the Euler equations) have been recently shown to be rare, in the sense that for "most" proportionality factors there are no nontrivial Beltrami fields of high enough regularity (e.g., of class {C^{6,α}}), not even locally. Our objective in this work is to show that, nevertheless, there are "many" Beltrami fields with non-constant factor, even realizing arbitrarily complicated vortex structures. This fact is relevant in the study of turbulent configurations. The core results are an "almost global" stability theorem for strong Beltrami fields, which ensures that a global strong Beltrami field with suitable decay at infinity can be perturbed to get "many" Beltrami fields with non-constant factor of arbitrarily high regularity and defined in the exterior of an arbitrarily small ball, and a "local" stability theorem for generalized Beltrami fields, which is an analogous perturbative result which is valid for any kind of Beltrami field (not just with a constant factor) but only applies to small enough domains. The proof relies on an iterative scheme of Grad-Rubin type. For this purpose, we study the Neumann problem for the inhomogeneous Beltrami equation in exterior domains via a boundary integral equation method and we obtain Hölder estimates, a sharp decay at infinity and some compactness properties for these sequences of approximate solutions. Some of the parts of the proof are of independent interest.

Engineering spin-orbit torque in Co/Pt multilayers with perpendicular magnetic anisotropy

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

Huang, Kuo-Feng; Wang, Ding-Shuo; Lai, Chih-Huang, E-mail: chlai@mx.nthu.edu.tw

To address thermal stability issues for spintronic devices with a reduced size, we investigate spin-orbit torque in Co/Pt multilayers with strong perpendicular magnetic anisotropy. Note that the spin-orbit torque arises from the global imbalance of the spin currents from the top and bottom interfaces for each Co layer. By inserting Ta or Cu layers to strengthen the top-down asymmetry, the spin-orbit torque efficiency can be greatly modified without compromised perpendicular magnetic anisotropy. Above all, the efficiency builds up as the number of layers increases, realizing robust thermal stability and high spin-orbit-torque efficiency simultaneously in the multilayers structure.

Allosteric Regulation of the Hsp90 Dynamics and Stability by Client Recruiter Cochaperones: Protein Structure Network Modeling

PubMed Central

Blacklock, Kristin; Verkhivker, Gennady M.

2014-01-01

The fundamental role of the Hsp90 chaperone in supporting functional activity of diverse protein clients is anchored by specific cochaperones. A family of immune sensing client proteins is delivered to the Hsp90 system with the aid of cochaperones Sgt1 and Rar1 that act cooperatively with Hsp90 to form allosterically regulated dynamic complexes. In this work, functional dynamics and protein structure network modeling are combined to dissect molecular mechanisms of Hsp90 regulation by the client recruiter cochaperones. Dynamic signatures of the Hsp90-cochaperone complexes are manifested in differential modulation of the conformational mobility in the Hsp90 lid motif. Consistent with the experiments, we have determined that targeted reorganization of the lid dynamics is a unifying characteristic of the client recruiter cochaperones. Protein network analysis of the essential conformational space of the Hsp90-cochaperone motions has identified structurally stable interaction communities, interfacial hubs and key mediating residues of allosteric communication pathways that act concertedly with the shifts in conformational equilibrium. The results have shown that client recruiter cochaperones can orchestrate global changes in the dynamics and stability of the interaction networks that could enhance the ATPase activity and assist in the client recruitment. The network analysis has recapitulated a broad range of structural and mutagenesis experiments, particularly clarifying the elusive role of Rar1 as a regulator of the Hsp90 interactions and a stability enhancer of the Hsp90-cochaperone complexes. Small-world organization of the interaction networks in the Hsp90 regulatory complexes gives rise to a strong correspondence between highly connected local interfacial hubs, global mediator residues of allosteric interactions and key functional hot spots of the Hsp90 activity. We have found that cochaperone-induced conformational changes in Hsp90 may be determined by specific interaction networks that can inhibit or promote progression of the ATPase cycle and thus control the recruitment of client proteins. PMID:24466147

Allosteric regulation of the Hsp90 dynamics and stability by client recruiter cochaperones: protein structure network modeling.

PubMed

Blacklock, Kristin; Verkhivker, Gennady M

2014-01-01

The fundamental role of the Hsp90 chaperone in supporting functional activity of diverse protein clients is anchored by specific cochaperones. A family of immune sensing client proteins is delivered to the Hsp90 system with the aid of cochaperones Sgt1 and Rar1 that act cooperatively with Hsp90 to form allosterically regulated dynamic complexes. In this work, functional dynamics and protein structure network modeling are combined to dissect molecular mechanisms of Hsp90 regulation by the client recruiter cochaperones. Dynamic signatures of the Hsp90-cochaperone complexes are manifested in differential modulation of the conformational mobility in the Hsp90 lid motif. Consistent with the experiments, we have determined that targeted reorganization of the lid dynamics is a unifying characteristic of the client recruiter cochaperones. Protein network analysis of the essential conformational space of the Hsp90-cochaperone motions has identified structurally stable interaction communities, interfacial hubs and key mediating residues of allosteric communication pathways that act concertedly with the shifts in conformational equilibrium. The results have shown that client recruiter cochaperones can orchestrate global changes in the dynamics and stability of the interaction networks that could enhance the ATPase activity and assist in the client recruitment. The network analysis has recapitulated a broad range of structural and mutagenesis experiments, particularly clarifying the elusive role of Rar1 as a regulator of the Hsp90 interactions and a stability enhancer of the Hsp90-cochaperone complexes. Small-world organization of the interaction networks in the Hsp90 regulatory complexes gives rise to a strong correspondence between highly connected local interfacial hubs, global mediator residues of allosteric interactions and key functional hot spots of the Hsp90 activity. We have found that cochaperone-induced conformational changes in Hsp90 may be determined by specific interaction networks that can inhibit or promote progression of the ATPase cycle and thus control the recruitment of client proteins.

Decentralized control of large flexible structures by joint decoupling

NASA Technical Reports Server (NTRS)

Su, Tzu-Jeng; Juang, Jer-Nan

1992-01-01

A decentralized control design method is presented for large complex flexible structures by using the idea of joint decoupling. The derivation is based on a coupled substructure state-space model, which is obtained from enforcing conditions of interface compatibility and equilibrium to the substructure state-space models. It is shown that by restricting the control law to be localized state feedback and by setting the joint actuator input commands to decouple joint 'degrees of freedom' (dof) from interior dof, the global structure control design problem can be decomposed into several substructure control design problems. The substructure control gains and substructure observers are designed based on modified substructure state-space models. The controllers produced by the proposed method can operate successfully at the individual substructure level as well as at the global structure level. Therefore, not only control design but also control implementation is decentralized. Stability and performance requirement of the closed-loop system can be achieved by using any existing state feedback control design method. A two-component mass-spring damper system and a three-truss structure are used as examples to demonstrate the proposed method.

How to measure ecosystem stability? An evaluation of the reliability of stability metrics based on remote sensing time series across the major global ecosystems.

PubMed

De Keersmaecker, Wanda; Lhermitte, Stef; Honnay, Olivier; Farifteh, Jamshid; Somers, Ben; Coppin, Pol

2014-07-01

Increasing frequency of extreme climate events is likely to impose increased stress on ecosystems and to jeopardize the services that ecosystems provide. Therefore, it is of major importance to assess the effects of extreme climate events on the temporal stability (i.e., the resistance, the resilience, and the variance) of ecosystem properties. Most time series of ecosystem properties are, however, affected by varying data characteristics, uncertainties, and noise, which complicate the comparison of ecosystem stability metrics (ESMs) between locations. Therefore, there is a strong need for a more comprehensive understanding regarding the reliability of stability metrics and how they can be used to compare ecosystem stability globally. The objective of this study was to evaluate the performance of temporal ESMs based on time series of the Moderate Resolution Imaging Spectroradiometer derived Normalized Difference Vegetation Index of 15 global land-cover types. We provide a framework (i) to assess the reliability of ESMs in function of data characteristics, uncertainties and noise and (ii) to integrate reliability estimates in future global ecosystem stability studies against climate disturbances. The performance of our framework was tested through (i) a global ecosystem comparison and (ii) an comparison of ecosystem stability in response to the 2003 drought. The results show the influence of data quality on the accuracy of ecosystem stability. White noise, biased noise, and trends have a stronger effect on the accuracy of stability metrics than the length of the time series, temporal resolution, or amount of missing values. Moreover, we demonstrate the importance of integrating reliability estimates to interpret stability metrics within confidence limits. Based on these confidence limits, other studies dealing with specific ecosystem types or locations can be put into context, and a more reliable assessment of ecosystem stability against environmental disturbances can be obtained. © 2013 John Wiley & Sons Ltd.

Shaking table experimentation on adjacent structures controlled by passive and semi-active MR dampers

NASA Astrophysics Data System (ADS)

Basili, M.; De Angelis, M.; Fraraccio, G.

2013-06-01

This paper presents the results of shaking table tests on adjacent structures controlled by passive and semi-active MR dampers. The aim was to demonstrate experimentally the effectiveness of passive and semi-active strategies in reducing structural vibrations due to seismic excitation. The physical model at issue was represented by two adjacent steel structures, respectively of 4 and 2 levels, connected at the second level by a MR damper. When the device operated in semi-active mode, an ON-OFF control algorithm, derived by the Lyapunov stability theory, was implemented and experimentally validated. Since the experimentation concerned adjacent structures, two control objectives have been reached: global and selective protection. In case of global protection, the attention was focused on protecting both structures, whereas, in case of selective protection, the attention was focused on protecting only one structure. For each objective the effectiveness of passive control has been compared with the situation of no control and then the effectiveness of semi-active control has been compared with the passive one. The quantities directly compared have been: measured displacements, accelerations and force-displacement of the MR damper, moreover some global response quantities have been estimated from experimental measures, which are the base share force and the base bending moment, the input energy and the energy dissipated by the device. In order to evaluate the effectiveness of the control action in both passive and semi-active case, an energy index EDI, previously defined and already often applied numerically, has been utilized. The aspects investigated in the experimentation have been: the implementation and validation of the control algorithm for selective and global protection, the MR damper input voltage influence, the kind of seismic input and its intensity.

Structures and stabilities of Al(n) (+), Al(n), and Al(n) (-) (n=13-34) clusters.

PubMed

Aguado, Andrés; López, José M

2009-02-14

Putative global minima of neutral (Al(n)) and singly charged (Al(n) (+) and Al(n) (-)) aluminum clusters with n=13-34 have been located from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ the generalized gradient approximation of Perdew, Burke, and Ernzerhof to describe exchange-correlation electronic effects. Our results show that icosahedral growth dominates the structures of aluminum clusters for n=13-22. For n=23-34, there is a strong competition between decahedral structures, relaxed fragments of a fcc crystalline lattice (some of them including stacking faults), and hexagonal prismatic structures. For such small cluster sizes, there is no evidence yet for a clear establishment of the fcc atomic packing prevalent in bulk aluminum. The global minimum structure for a given number of atoms depends significantly on the cluster charge for most cluster sizes. An explicit comparison is made with previous theoretical results in the range n=13-30: for n=19, 22, 24, 25, 26, 29, 30 we locate a lower energy structure than previously reported. Sizes n=32, 33 are studied here for the first time by an ab initio technique.

GAIA payload module mechanical development

NASA Astrophysics Data System (ADS)

Touzeau, S.; Sein, E.; Lebranchu, C.

2017-11-01

Gaia is the European Space Agency's cornerstone mission for global space astrometry. Its goal is to make the largest, most precise three-dimensional map of our Galaxy by surveying an unprecedented number of stars. This paper gives an overview of the mechanical system engineering and verification of the payload module. This development includes several technical challenges. First of all, the very high stability performance as required for the mission is a key driver for the design, which incurs a high degree of stability. This is achieved through the extensive use of Silicon Carbide (Boostec® SiC) for both structures and mirrors, a high mechanical and thermal decoupling between payload and service modules, and the use of high-performance engineering tools. Compliance of payload mass and volume with launcher capability is another key challenge, as well as the development and manufacturing of the 3.2-meter diameter toroidal primary structure. The spacecraft mechanical verification follows an innovative approach, with direct testing on the flight model, without any dedicated structural model.

X-ray crystallographic studies of RNase A variants engineered at the most destabilizing positions of the main hydrophobic core: further insight into protein stability.

PubMed

Kurpiewska, Katarzyna; Font, Josep; Ribó, Marc; Vilanova, Maria; Lewiński, Krzysztof

2009-11-15

To investigate the structural origin of decreased pressure and temperature stability, the crystal structure of bovine pancreatic ribonuclease A variants V47A, V54A, V57A, I81A, I106A, and V108A was solved at 1.4-2.0 A resolution and compared with the structure of wild-type protein. The introduced mutations had only minor influence on the global structure of ribonuclease A. The structural changes had individual character that depends on the localization of mutated residue, however, they seemed to expand from mutation site to the rest of the structure. Several different parameters have been evaluated to find correlation with decrease of free energy of unfolding DeltaDeltaG(T), and the most significant correlation was found for main cavity volume change. Analysis of the difference distance matrices revealed that the ribonuclease A molecule is organized into five relatively rigid subdomains with individual response to mutation. This behavior consistent with results of unfolding experiments is an intrinsic feature of ribonuclease A that might be surviving remnants of folding intermediates and reflects the dynamic nature of the molecule. 2009 Wiley-Liss, Inc.

Stability Operations: Getting It Right in the Global War on Terrorism

DTIC Science & Technology

2005-03-18

the United States of America (Washington, D.C.: The White House, September 2002), 1 " John Pike, "Where are the Legions? [ SPQR ] Global Deployments of...for a Postconflict Stability Force. Washington, D.C.: United States Institute of Peace Press, 2004. Pike, John. "Where Are the Legions? [ SPQR ] Global

Maximum Lyapunov exponents as predictors of global gait stability: a modelling approach.

PubMed

Bruijn, Sjoerd M; Bregman, Daan J J; Meijer, Onno G; Beek, Peter J; van Dieën, Jaap H

2012-05-01

To examine the stability of human walking, methods such as local dynamic stability have been adopted from dynamical systems theory. Local dynamic stability is calculated by estimating maximal finite time Lyapunov exponents (λ(S) and λ(L)), which quantify how a system responds continuously to very small (i.e. "local") perturbations. However, it is unknown if, and to what extent, these measures are correlated to global stability, defined operationally as the probability of falling. We studied whether changes in probability of falling of a simple model of human walking (a so-called dynamic walker) could be predicted from maximum finite time Lyapunov exponents. We used an extended version of the simplest walking model with arced feet and a hip spring. This allowed us to change the probability of falling of the model by changing either the foot radius, the slope at which the model walks, the stiffness of the hip spring, or a combination of these factors. Results showed that λ(S) correlated fairly well with global stability, although this relationship was dependent upon differences in the distance between initial nearest neighbours on the divergence curve. A measure independent of such changes (the log(distance between initially nearest neighbours after 50 samples)) correlated better with global stability, and, more importantly, showed a more consistent relationship across conditions. In contrast, λ(L) showed either weak correlations, or correlations opposite to expected, thus casting doubt on the use of this measure as a predictor of global gait stability. Our findings support the use of λ(S), but not of λ(L), as measure of human gait stability. Copyright © 2011 IPEM. Published by Elsevier Ltd. All rights reserved.

A Study of Impact Point Detecting Method Based on Seismic Signal

NASA Astrophysics Data System (ADS)

Huo, Pengju; Zhang, Yu; Xu, Lina; Huang, Yong

The projectile landing position has to be determined for its recovery and range in the targeting test. In this paper, a global search method based on the velocity variance is proposed. In order to verify the applicability of this method, simulation analysis within the scope of four million square meters has been conducted in the same array structure of the commonly used linear positioning method, and MATLAB was used to compare and analyze the two methods. The compared simulation results show that the global search method based on the speed of variance has high positioning accuracy and stability, which can meet the needs of impact point location.

A robot control architecture supported on contraction theory

NASA Astrophysics Data System (ADS)

Silva, Jorge; Sequeira, João; Santos, Cristina

2017-01-01

This paper proposes fundamentals for stability and success of a global system composed by a mobile robot, a real environment and a navigation architecture with time constraints. Contraction theory is a typical framework that provides tools and properties to prove the stability and convergence of the global system to a unique fixed point that identifies the mission success. A stability indicator based on the combination contraction property is developed to identify the mission success as a stability measure. The architecture is fully designed through C1 nonlinear dynamical systems and feedthrough maps, which makes it amenable for contraction analysis. Experiments in a realistic and uncontrolled environment are realised to verify if inherent perturbations of the sensory information and of the environment affect the stability and success of the global system.

Vibrational and structural study of onopordopicrin based on the FTIR spectrum and DFT calculations.

PubMed

Chain, Fernando E; Romano, Elida; Leyton, Patricio; Paipa, Carolina; Catalán, César A N; Fortuna, Mario; Brandán, Silvia Antonia

2015-01-01

In the present work, the structural and vibrational properties of the sesquiterpene lactone onopordopicrin (OP) were studied by using infrared spectroscopy and density functional theory (DFT) calculations together with the 6-31G(∗) basis set. The harmonic vibrational wavenumbers for the optimized geometry were calculated at the same level of theory. The complete assignment of the observed bands in the infrared spectrum was performed by combining the DFT calculations with Pulay's scaled quantum mechanical force field (SQMFF) methodology. The comparison between the theoretical and experimental infrared spectrum demonstrated good agreement. Then, the results were used to predict the Raman spectrum. Additionally, the structural properties of OP, such as atomic charges, bond orders, molecular electrostatic potentials, characteristics of electronic delocalization and topological properties of the electronic charge density were evaluated by natural bond orbital (NBO), atoms in molecules (AIM) and frontier orbitals studies. The calculated energy band gap and the chemical potential (μ), electronegativity (χ), global hardness (η), global softness (S) and global electrophilicity index (ω) descriptors predicted for OP low reactivity, higher stability and lower electrophilicity index as compared with the sesquiterpene lactone cnicin containing similar rings. Copyright © 2015 Elsevier B.V. All rights reserved.

Global exponential stability of BAM neural networks with time-varying delays and diffusion terms

NASA Astrophysics Data System (ADS)

Wan, Li; Zhou, Qinghua

2007-11-01

The stability property of bidirectional associate memory (BAM) neural networks with time-varying delays and diffusion terms are considered. By using the method of variation parameter and inequality technique, the delay-independent sufficient conditions to guarantee the uniqueness and global exponential stability of the equilibrium solution of such networks are established.

Workshop on Closed System Ecology

NASA Technical Reports Server (NTRS)

1982-01-01

Self maintaining laboratory scale ecological systems completely isolated from exchanges of matter with external systems were demonstrated. These research tools are discussed in terms of their anticipated value in understanding (1) global ecological material and energy balances, (2) the dynamics of stability and instability in ecosystems, (3) the effects of man-made substances and structures on ecosystems, and (4) the precise requirements for dynamic control of controlled ecology life support systems (CELSS).

Measuring Quality in Rural Kindergarten Classrooms: Reliability and Validity Evidence for the Classroom Assessment Scoring System, Kindergarten-Third Grade (CLASS K-3)

ERIC Educational Resources Information Center

Sandilos, Lia E.

2012-01-01

The purpose of the current study was to evaluate the structural validity and stability of scores on a measure of global classroom quality, the Classroom Assessment Scoring System, Kindergarten-Third Grade (CLASS K-3; Pianta, La Paro, & Hamre, 2008). Using data from a sample of 417 kindergarten classrooms in the rural Southern and Mid-Atlantic…

Tropical cyclones in a stabilized 1.5 and 2 degree warmer world.

NASA Astrophysics Data System (ADS)

Wehner, M. F.; Stone, D. A.; Loring, B.; Krishnan, H.

2017-12-01

We present an ensemble of very high resolution global climate model simulations of a stabilized 1.5oC and 2oC warmer climate as envisioned by the Paris COP21 agreement. The resolution of this global climate model (25km) permits simulated tropical cyclones up to Category Five on the Saffir-Simpson scale Projected changes in tropical cyclones are significant. Tropical cyclones in the two stabilization scenarios are less frequent but more intense than in simulations of the present. Output data from these simulations is freely available to all interested parties and should prove a useful resource to those interested in studying the impacts of stabilized global warming.

Localized structural frustration for evaluating the impact of sequence variants

PubMed Central

Kumar, Sushant; Clarke, Declan; Gerstein, Mark

2016-01-01

Population-scale sequencing is increasingly uncovering large numbers of rare single-nucleotide variants (SNVs) in coding regions of the genome. The rarity of these variants makes it challenging to evaluate their deleteriousness with conventional phenotype–genotype associations. Protein structures provide a way of addressing this challenge. Previous efforts have focused on globally quantifying the impact of SNVs on protein stability. However, local perturbations may severely impact protein functionality without strongly disrupting global stability (e.g. in relation to catalysis or allostery). Here, we describe a workflow in which localized frustration, quantifying unfavorable local interactions, is employed as a metric to investigate such effects. Using this workflow on the Protein Databank, we find that frustration produces many immediately intuitive results: for instance, disease-related SNVs create stronger changes in localized frustration than non-disease related variants, and rare SNVs tend to disrupt local interactions to a larger extent than common variants. Less obviously, we observe that somatic SNVs associated with oncogenes and tumor suppressor genes (TSGs) induce very different changes in frustration. In particular, those associated with TSGs change the frustration more in the core than the surface (by introducing loss-of-function events), whereas those associated with oncogenes manifest the opposite pattern, creating gain-of-function events. PMID:27915290

Assessment of Global Wind Energy Resource Utilization Potential

NASA Astrophysics Data System (ADS)

Ma, M.; He, B.; Guan, Y.; Zhang, H.; Song, S.

2017-09-01

Development of wind energy resource (WER) is a key to deal with climate change and energy structure adjustment. A crucial issue is to obtain the distribution and variability of WER, and mine the suitable location to exploit it. In this paper, a multicriteria evaluation (MCE) model is constructed by integrating resource richness and stability, utilization value and trend of resource, natural environment with weights. The global resource richness is assessed through wind power density (WPD) and multi-level wind speed. The utilizable value of resource is assessed by the frequency of effective wind. The resource stability is assessed by the coefficient of variation of WPD and the frequency of prevailing wind direction. Regression slope of long time series WPD is used to assess the trend of WER. All of the resource evaluation indicators are derived from the atmospheric reanalysis data ERA-Interim with spatial resolution 0.125°. The natural environment factors mainly refer to slope and land-use suitability, which are derived from multi-resolution terrain elevation data 2010 (GMTED 2010) and GlobalCover2009. Besides, the global WER utilization potential map is produced, which shows most high potential regions are located in north of Africa. Additionally, by verifying that 22.22 % and 48.8 9% operational wind farms fall on medium-high and high potential regions respectively, the result can provide a basis for the macroscopic siting of wind farm.

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.

Crystal structure, stability and spectroscopic properties of methane and CO2 hydrates.

PubMed

Martos-Villa, Ruben; Francisco-Márquez, Misaela; Mata, M Pilar; Sainz-Díaz, C Ignacio

2013-07-01

Methane hydrates are highly present in sea-floors and in other planets and their moons. Hence, these compounds are of great interest for environment, global climate change, energy resources, and Cosmochemistry. The knowledge of stability and physical-chemical properties of methane hydrate crystal structure is important for evaluating some new green becoming technologies such as, strategies to produce natural gas from marine methane hydrates and simultaneously store CO2 as hydrates. However, some aspects related with their stability, spectroscopic and other chemical-physical properties of both hydrates are not well understood yet. The structure and stability of crystal structure of methane and CO2 hydrates have been investigated by means of calculations with empirical interatomic potentials and quantum-mechanical methods based on Hartree-Fock and Density Functional Theory (DFT) approximations. Molecular Dynamic simulations have been also performed exploring different configurations reproducing the experimental crystallographic properties. Spectroscopic properties have also been studied. Frequency shifts of the main vibration modes were observed upon the formation of these hydrates, confirming that vibration stretching peaks of C-H at 2915cm(-1) and 2905cm(-1) are due to methane in small and large cages, respectively. Similar effect is observed in the CO2 clathrates. The guest-host binding energy in these clathrates calculated with different methods are compared and discussed in terms of adequacy of empirical potentials and DFT methods for describing the interactions between gas guest and the host water cage, proving an exothermic nature of methane and CO2 hydrates formation process. Copyright © 2013 Elsevier Inc. All rights reserved.

Functional Trait Changes, Productivity Shifts and Vegetation Stability in Mountain Grasslands during a Short-Term Warming.

PubMed

Debouk, Haifa; de Bello, Francesco; Sebastià, Maria-Teresa

2015-01-01

Plant functional traits underlie vegetation responses to environmental changes such as global warming, and consequently influence ecosystem processes. While most of the existing studies focus on the effect of warming only on species diversity and productivity, we further investigated (i) how the structure of community plant functional traits in temperate grasslands respond to experimental warming, and (ii) whether species and functional diversity contribute to a greater stability of grasslands, in terms of vegetation composition and productivity. Intact vegetation turves were extracted from temperate subalpine grassland (highland) in the Eastern Pyrenees and transplanted into a warm continental, experimental site in Lleida, in Western Catalonia (lowland). The impacts of simulated warming on plant production and diversity, functional trait structure, and vegetation compositional stability were assessed. We observed an increase in biomass and a reduction in species and functional diversity under short-term warming. The functional structure of the grassland communities changed significantly, in terms of functional diversity and community-weighted means (CWM) for several traits. Acquisitive and fast-growing species with higher SLA, early flowering, erect growth habit, and rhizomatous strategy became dominant in the lowland. Productivity was significantly positively related to species, and to a lower extent, functional diversity, but productivity and stability after warming were more dependent on trait composition (CWM) than on diversity. The turves with more acquisitive species before warming changed less in composition after warming. Results suggest that (i) the short-term warming can lead to the dominance of acquisitive fast growing species over conservative species, thus reducing species richness, and (ii) the functional traits structure in grassland communities had a greater influence on the productivity and stability of the community under short-term warming, compared to diversity effects. In summary, short-term climate warming can greatly alter vegetation functional structure and its relation to productivity.

Functional Trait Changes, Productivity Shifts and Vegetation Stability in Mountain Grasslands during a Short-Term Warming

PubMed Central

Debouk, Haifa; de Bello, Francesco; Sebastià, Maria-Teresa

2015-01-01

Plant functional traits underlie vegetation responses to environmental changes such as global warming, and consequently influence ecosystem processes. While most of the existing studies focus on the effect of warming only on species diversity and productivity, we further investigated (i) how the structure of community plant functional traits in temperate grasslands respond to experimental warming, and (ii) whether species and functional diversity contribute to a greater stability of grasslands, in terms of vegetation composition and productivity. Intact vegetation turves were extracted from temperate subalpine grassland (highland) in the Eastern Pyrenees and transplanted into a warm continental, experimental site in Lleida, in Western Catalonia (lowland). The impacts of simulated warming on plant production and diversity, functional trait structure, and vegetation compositional stability were assessed. We observed an increase in biomass and a reduction in species and functional diversity under short-term warming. The functional structure of the grassland communities changed significantly, in terms of functional diversity and community-weighted means (CWM) for several traits. Acquisitive and fast-growing species with higher SLA, early flowering, erect growth habit, and rhizomatous strategy became dominant in the lowland. Productivity was significantly positively related to species, and to a lower extent, functional diversity, but productivity and stability after warming were more dependent on trait composition (CWM) than on diversity. The turves with more acquisitive species before warming changed less in composition after warming. Results suggest that (i) the short-term warming can lead to the dominance of acquisitive fast growing species over conservative species, thus reducing species richness, and (ii) the functional traits structure in grassland communities had a greater influence on the productivity and stability of the community under short-term warming, compared to diversity effects. In summary, short-term climate warming can greatly alter vegetation functional structure and its relation to productivity. PMID:26513148

L{sup 2}-stability of the Vlasov-Maxwell-Boltzmann system near global Maxwellians

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

Ha, Seung-Yeal, E-mail: syha@snu.ac.kr; Xiao, Qinghua, E-mail: pdexqh@hotmail.com; Xiong, Linjie, E-mail: xlj@whu.edu.cn

2013-12-15

We present a L{sup 2}-stability theory of the Vlasov-Maxwell-Boltzmann system for the two-species collisional plasma. We show that in a perturbative regime of a global Maxwellian, the L{sup 2}-distance between two strong solutions can be controlled by that between initial data in a Lipschitz manner. Our stability result extends earlier results [Ha, S.-Y. and Xiao, Q.-H., “A revisiting to the L{sup 2}-stability theory of the Boltzmann equation near global Maxwellians,” (submitted) and Ha, S.-Y., Yang, X.-F., and Yun, S.-B., “L{sup 2} stability theory of the Boltzmann equation near a global Maxwellian,” Arch. Ration. Mech. Anal. 197, 657–688 (2010)] on themore » L{sup 2}-stability of the Boltzmann equation to the Boltzmann equation coupled with self-consistent external forces. As a direct application of our stability result, we show that classical solutions in Duan et al. [“Optimal large-time behavior of the Vlasov-Maxwell-Boltzmann system in the whole space,” Commun. Pure Appl. Math. 24, 1497–1546 (2011)] and Guo [“The Vlasov-Maxwell-Boltzmann system near Maxwellians,” Invent. Math. 153(3), 593–630 (2003)] satisfy a uniform L{sup 2}-stability estimate. This is the first result on the L{sup 2}-stability of the Boltzmann equation coupled with self-consistent field equations in three dimensions.« less

Magnetorotational instability: nonmodal growth and the relationship of global modes to the shearing box

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

Squire, J.; Bhattacharjee, A.

2014-12-10

We study magnetorotational instability (MRI) using nonmodal stability techniques. Despite the spectral instability of many forms of MRI, this proves to be a natural method of analysis that is well-suited to deal with the non-self-adjoint nature of the linear MRI equations. We find that the fastest growing linear MRI structures on both local and global domains can look very different from the eigenmodes, invariably resembling waves shearing with the background flow (shear waves). In addition, such structures can grow many times faster than the least stable eigenmode over long time periods, and be localized in a completely different region ofmore » space. These ideas lead—for both axisymmetric and non-axisymmetric modes—to a natural connection between the global MRI and the local shearing box approximation. By illustrating that the fastest growing global structure is well described by the ordinary differential equations (ODEs) governing a single shear wave, we find that the shearing box is a very sensible approximation for the linear MRI, contrary to many previous claims. Since the shear wave ODEs are most naturally understood using nonmodal analysis techniques, we conclude by analyzing local MRI growth over finite timescales using these methods. The strong growth over a wide range of wave-numbers suggests that nonmodal linear physics could be of fundamental importance in MRI turbulence.« less

Relative stability of major types of beta-turns as a function of amino acid composition: a study based on Ab initio energetic and natural abundance data.

PubMed

Perczel, András; Jákli, Imre; McAllister, Michael A; Csizmadia, Imre G

2003-06-06

Folding properties of small globular proteins are determined by their amino acid sequence (primary structure). This holds both for local (secondary structure) and for global conformational features of linear polypeptides and proteins composed from natural amino acid derivatives. It thus provides the rational basis of structure prediction algorithms. The shortest secondary structure element, the beta-turn, most typically adopts either a type I or a type II form, depending on the amino acid composition. Herein we investigate the sequence-dependent folding stability of both major types of beta-turns using simple dipeptide models (-Xxx-Yyy-). Gas-phase ab initio properties of 16 carefully selected and suitably protected dipeptide models (for example Val-Ser, Ala-Gly, Ser-Ser) were studied. For each backbone fold most probable side-chain conformers were considered. Fully optimized 321G RHF molecular structures were employed in medium level [B3LYP/6-311++G(d,p)//RHF/3-21G] energy calculations to estimate relative populations of the different backbone conformers. Our results show that the preference for beta-turn forms as calculated by quantum mechanics and observed in Xray determined proteins correlates significantly.

Multiscale simulations on conformational dynamics and membrane interactions of the non-structural 2 (NS2) transmembrane domain.

PubMed

Hung, Huynh Minh; Hang, Tran Dieu; Nguyen, Minh Tho

2016-09-09

Hepatitis C virus (HCV) is one of the most crucial global health issues, in which the HCV non-structural protein 2 (NS2), particularly its three transmembrane segments, plays a crucial role in HCV assembly. In this context, multiscale MD simulations have been applied to investigate the preferred orientation of transmembrane domain of NS2 protein (TNS2) in a POPC bilayer, structural stability and characteristic of intramembrane protein-lipid and protein-protein interaction. Our study indicates that NS2 protein adopts three trans-membrane segments with highly stable α-helix structure in a POPC bilayer and a short helical luminal segment. While the first and second TM segment involved in continuous helical domain, the third TM segment is however cleaved into two sub-segments with different tilt angles via a kink at L87G88. Salt bridges K81-E45, R32-PO4 and R43-PO4 are determined as the key factor to stabilize the structure of TM2 and TM3 which consist of charged residues located in the hydrophobic region of the membrane. Copyright © 2016 Elsevier Inc. All rights reserved.

Analysis of an age structured model for tick populations subject to seasonal effects

NASA Astrophysics Data System (ADS)

Liu, Kaihui; Lou, Yijun; Wu, Jianhong

2017-08-01

We investigate an age-structured hyperbolic equation model by allowing the birth and death functions to be density dependent and periodic in time with the consideration of seasonal effects. By studying the integral form solution of this general hyperbolic equation obtained through the method of integration along characteristics, we give a detailed proof of the uniqueness and existence of the solution in light of the contraction mapping theorem. With additional biologically natural assumptions, using the tick population growth as a motivating example, we derive an age-structured model with time-dependent periodic maturation delays, which is quite different from the existing population models with time-independent maturation delays. For this periodic differential system with seasonal delays, the basic reproduction number R0 is defined as the spectral radius of the next generation operator. Then, we show the tick population tends to die out when R0 < 1 while remains persistent if R0 > 1. When there is no intra-specific competition among immature individuals due to the sufficient availability of immature tick hosts, the global stability of the positive periodic state for the whole model system of four delay differential equations can be obtained with the observation that a scalar subsystem for the adult stage size can be decoupled. The challenge for the proof of such a global stability result can be overcome by introducing a new phase space, based on which, a periodic solution semiflow can be defined which is eventually strongly monotone and strictly subhomogeneous.

Conformational switching upon phosphorylation: a predictive framework based on energy landscape principles.

PubMed

Lätzer, Joachim; Shen, Tongye; Wolynes, Peter G

2008-02-19

We investigate how post-translational phosphorylation modifies the global conformation of a protein by changing its free energy landscape using two test proteins, cystatin and NtrC. We first examine the changes in a free energy landscape caused by phosphorylation using a model containing information about both structural forms. For cystatin the free energy cost is fairly large indicating a low probability of sampling the phosphorylated conformation in a perfectly funneled landscape. The predicted barrier for NtrC conformational transition is several times larger than the barrier for cystatin, indicating that the switch protein NtrC most probably follows a partial unfolding mechanism to move from one basin to the other. Principal component analysis and linear response theory show how the naturally occurring conformational changes in unmodified proteins are captured and stabilized by the change of interaction potential. We also develop a partially guided structure prediction Hamiltonian which is capable of predicting the global structure of a phosphorylated protein using only knowledge of the structure of the unphosphorylated protein or vice versa. This algorithm makes use of a generic transferable long-range residue contact potential along with details of structure short range in sequence. By comparing the results obtained with this guided transferable potential to those from the native-only, perfectly funneled Hamiltonians, we show that the transferable Hamiltonian correctly captures the nature of the global conformational changes induced by phosphorylation and can sample substantially correct structures for the modified protein with high probability.

Numerical simulation of a two-sex human papillomavirus (HPV) vaccination model

NASA Astrophysics Data System (ADS)

Suryani, I.; Adi-Kusumo, F.

2014-02-01

Human Papillomavirus (HPV) is a major cause of cervical cancer, precancerous lesions, cancer and other disease. HPV is the most common sexually transmitted infection. Although HPV virus primarily affects woman but it can also affects man because it cause of cancer of the anus, vulva, vagina, penis and some other cancers. HPV vaccines now used to prevent cervical cancer and genital warts because the vaccine protect against four types of HPV that most commonly cause disease are types 6, 11, 16, and 18. This paper is sequel work of Elbasha (2008). Difference with Elbasha (2008) are give alternative proof global stability, numerical simulation and interpretation. Global stability of the equilibrium on the model of a two-sex HPV vaccination were explored by using Lyapunov. Although we use the same lyapunov function, we use the largest invariant set to proof the global stability. The result show that the global stability of the equilibrium depends on the effective reproduction number (R). If R < 1 then the infection-free equilibrium is asymptotically stable globally. If R > 1 then endemic equilibrium have globally asymptotically stable properties. Then equilibrium proceed with the interpretation of numerical simulation.

Protein stability and dynamics influenced by ligands in extremophilic complexes - a molecular dynamics investigation.

PubMed

Khan, Sara; Farooq, Umar; Kurnikova, Maria

2017-08-22

In this study, we explore the structural and dynamic adaptations of the Tryptophan synthase α-subunit in a ligand bound state in psychrophilic, mesophilic and hyperthermophilic organisms at different temperatures by MD simulations. We quantify the global and local fluctuations in the 40 ns time scale by analyzing the root mean square deviation/fluctuations. The distinct behavior of the active site and loop 6 is observed with the elevation of temperature. Protein stability relies more on electrostatic interactions, and these interactions might be responsible for the stability of varying temperature evolved proteins. The paper also focuses on the effect of temperature on protein dynamics and stability governed by the distinct behavior of the ligand associated with its retention, binding and dissociation over the course of time. The integration of principle component analysis and a free energy landscape was useful in identifying the conformational space accessible to ligand bound homologues and how the presence of the ligand alters the conformational and dynamic properties of the protein.

Theoretical and Experimental Approaches towards study of Methane Occupation Dynamics within Gas Hydrates

NASA Astrophysics Data System (ADS)

Mendonca, P.; Shemella, P.; Nayak, S.; Sharma, A.

2006-12-01

Hydrate structures of hydrocarbon (commonly methane hydrates) within the continental shelf regions are considered a huge energy resource since they are a significant reservoir for terrestrial carbon. Any changes, abrupt or continual, will have an impact on the carbon (as well as water) cycle. However, tapping into this reservoir for energy resource has been challenging from both technical and scientific fronts primarily because any rapid release of methane (CH4) will likely have serious impact on the global climate of Earth as well as the stability of the continental shelf. While fossil fuel combustion derived CO2 in the atmosphere is considered a major contributor to global warming, the massive amounts of methane release from the gas hydrates has been a point of debate for its impact on the global climate. Due to the lack of a clear physical mechanism for such structural destabilization, environmental changes within the ocean setting (viz. temperature, salinity or biology) are typically assigned as possible causes. A good kinetic model that ties into structural instability of these essentially non-stoichiometric compounds at both the macromolecular (thermodynamic) and nanometric scale is essential. Preliminary experiments on single crystal methane hydrate high pressure phase (~1.0GPa) indicate a measurable kinetics of methane diffusion upon bringing structural disorder to the single crystal. Although there have been several kinetic studies of gas-hydrate nucleation and dissociation, systematic study of kinetics (and dynamics) of diffusion based changes within the gas hydrates has been lacking. In addition to experimental data on single crystal methane hydrates, we will present a first principle study on the structure, energetic, and dynamics of sI phase methane hydrate. We use density functional theory to study the energetic effect of the occupancy of neighboring cages in a cluster model system consisting of two sI gas hydrates. In this situation there can be two, one, or no methane, and we find that the binding for the first methane is exothermic. The second methane binding is endothermic, suggesting that the stability of a methane molecule is determined by the occupancy of adjacent cages. Using these results, we will present the calculated binding energies of a periodic system based on crystal structure data and compare them to the cluster method. This combined experimental and theoretical investigation is aimed at generating fundamental dataset that can be tested for the broader impact of such processes on the global carbon cycle.

Community living long before man: fossil and living microbial mats and early life

NASA Technical Reports Server (NTRS)

Margulis, L.; Lopez Baluja, L.; Awramik, S. M.; Sagan, D.

1986-01-01

Microbial mats are layered communities of bacteria that form cohesive structures, some of which are preserved in sedimentary rocks as stromatolites. Certain rocks, approximately three and a half thousand million years old and representing the oldest known fossils, are interpreted to derive from microbial mats and to contain fossils of microorganisms. Modern microbial mats (such as the one described here from Matanzas, Cuba) and their fossil counterparts are of great interest in the interpretation of early life on Earth. Since examination of microbial mats and stromatolites increases our understanding of long-term stability and change, within the global environment, such structures should be protected wherever possible as natural science preserves. Furthermore, since they have existed virtually from the time of life's origin, microbial mats have developed exemplary mechanisms of local community persistence and may even play roles in the larger global environment that we do not understand.

Determination of Global Stability of the Slosh Motion in a Spacecraft via Num Erical Experiment

NASA Astrophysics Data System (ADS)

Kang, Ja-Young

2003-12-01

The global stability of the attitude motion of a spin-stabilized space vehicle is investigated by performing numerical experiment. In the previous study, a stationary solution and a particular resonant condition for a given model were found by using analytical method but failed to represent the system stability over parameter values near and off the stationary points. Accordingly, as an extension of the previous work, this study performs numerical experiment to investigate the stability of the system across the parameter space and determines stable and unstable regions of the design parameters of the system.

On-the-Fly Machine Learning of Atomic Potential in Density Functional Theory Structure Optimization

NASA Astrophysics Data System (ADS)

Jacobsen, T. L.; Jørgensen, M. S.; Hammer, B.

2018-01-01

Machine learning (ML) is used to derive local stability information for density functional theory calculations of systems in relation to the recently discovered SnO2 (110 )-(4 ×1 ) reconstruction. The ML model is trained on (structure, total energy) relations collected during global minimum energy search runs with an evolutionary algorithm (EA). While being built, the ML model is used to guide the EA, thereby speeding up the overall rate by which the EA succeeds. Inspection of the local atomic potentials emerging from the model further shows chemically intuitive patterns.

The Rubidium Atomic Clock and Basic Research

DTIC Science & Technology

2007-12-10

from orbiting GPS (global positioning system) satellites. Thankfully, you make it home without an exciting but har- rowing story to tell family...the vapor-cell atomic clock, -i\\till is elec- tronically tied to an atomic resonance, thereby transferring the stability of atomic structure to the...are applied to the resonance cell, there is a net transfer of atoms from F = 1 back into F = 2 and a decrease in transmitted light intensity. The

Scale-Limited Lagrange Stability and Finite-Time Synchronization for Memristive Recurrent Neural Networks on Time Scales.

PubMed

Xiao, Qiang; Zeng, Zhigang

2017-10-01

The existed results of Lagrange stability and finite-time synchronization for memristive recurrent neural networks (MRNNs) are scale-free on time evolvement, and some restrictions appear naturally. In this paper, two novel scale-limited comparison principles are established by means of inequality techniques and induction principle on time scales. Then the results concerning Lagrange stability and global finite-time synchronization of MRNNs on time scales are obtained. Scaled-limited Lagrange stability criteria are derived, in detail, via nonsmooth analysis and theory of time scales. Moreover, novel criteria for achieving the global finite-time synchronization are acquired. In addition, the derived method can also be used to study global finite-time stabilization. The proposed results extend or improve the existed ones in the literatures. Two numerical examples are chosen to show the effectiveness of the obtained results.

Stabilization of global temperature at 1.5°C and 2.0°C: implications for coastal areas

PubMed Central

Brown, Sally; Wolff, Claudia; Merkens, Jan-Ludolf

2018-01-01

The effectiveness of stringent climate stabilization scenarios for coastal areas in terms of reduction of impacts/adaptation needs and wider policy implications has received little attention. Here we use the Warming Acidification and Sea Level Projector Earth systems model to calculate large ensembles of global sea-level rise (SLR) and ocean pH projections to 2300 for 1.5°C and 2.0°C stabilization scenarios, and a reference unmitigated RCP8.5 scenario. The potential consequences of these projections are then considered for global coastal flooding, small islands, deltas, coastal cities and coastal ecology. Under both stabilization scenarios, global mean ocean pH (and temperature) stabilize within a century. This implies significant ecosystem impacts are avoided, but detailed quantification is lacking, reflecting scientific uncertainty. By contrast, SLR is only slowed and continues to 2300 (and beyond). Hence, while coastal impacts due to SLR are reduced significantly by climate stabilization, especially after 2100, potential impacts continue to grow for centuries. SLR in 2300 under both stabilization scenarios exceeds unmitigated SLR in 2100. Therefore, adaptation remains essential in densely populated and economically important coastal areas under climate stabilization. Given the multiple adaptation steps that this will require, an adaptation pathways approach has merits for coastal areas. This article is part of the theme issue ‘The Paris Agreement: understanding the physical and social challenges for a warming world of 1.5°C above pre-industrial levels’. PMID:29610380

Stabilization of global temperature at 1.5°C and 2.0°C: implications for coastal areas.

PubMed

Nicholls, Robert J; Brown, Sally; Goodwin, Philip; Wahl, Thomas; Lowe, Jason; Solan, Martin; Godbold, Jasmin A; Haigh, Ivan D; Lincke, Daniel; Hinkel, Jochen; Wolff, Claudia; Merkens, Jan-Ludolf

2018-05-13

The effectiveness of stringent climate stabilization scenarios for coastal areas in terms of reduction of impacts/adaptation needs and wider policy implications has received little attention. Here we use the Warming Acidification and Sea Level Projector Earth systems model to calculate large ensembles of global sea-level rise (SLR) and ocean pH projections to 2300 for 1.5°C and 2.0°C stabilization scenarios, and a reference unmitigated RCP8.5 scenario. The potential consequences of these projections are then considered for global coastal flooding, small islands, deltas, coastal cities and coastal ecology. Under both stabilization scenarios, global mean ocean pH (and temperature) stabilize within a century. This implies significant ecosystem impacts are avoided, but detailed quantification is lacking, reflecting scientific uncertainty. By contrast, SLR is only slowed and continues to 2300 (and beyond). Hence, while coastal impacts due to SLR are reduced significantly by climate stabilization, especially after 2100, potential impacts continue to grow for centuries. SLR in 2300 under both stabilization scenarios exceeds unmitigated SLR in 2100. Therefore, adaptation remains essential in densely populated and economically important coastal areas under climate stabilization. Given the multiple adaptation steps that this will require, an adaptation pathways approach has merits for coastal areas.This article is part of the theme issue 'The Paris Agreement: understanding the physical and social challenges for a warming world of 1.5°C above pre-industrial levels'. © 2018 The Authors.

Stabilization of global temperature at 1.5°C and 2.0°C: implications for coastal areas

NASA Astrophysics Data System (ADS)

Nicholls, Robert J.; Brown, Sally; Goodwin, Philip; Wahl, Thomas; Lowe, Jason; Solan, Martin; Godbold, Jasmin A.; Haigh, Ivan D.; Lincke, Daniel; Hinkel, Jochen; Wolff, Claudia; Merkens, Jan-Ludolf

2018-05-01

The effectiveness of stringent climate stabilization scenarios for coastal areas in terms of reduction of impacts/adaptation needs and wider policy implications has received little attention. Here we use the Warming Acidification and Sea Level Projector Earth systems model to calculate large ensembles of global sea-level rise (SLR) and ocean pH projections to 2300 for 1.5°C and 2.0°C stabilization scenarios, and a reference unmitigated RCP8.5 scenario. The potential consequences of these projections are then considered for global coastal flooding, small islands, deltas, coastal cities and coastal ecology. Under both stabilization scenarios, global mean ocean pH (and temperature) stabilize within a century. This implies significant ecosystem impacts are avoided, but detailed quantification is lacking, reflecting scientific uncertainty. By contrast, SLR is only slowed and continues to 2300 (and beyond). Hence, while coastal impacts due to SLR are reduced significantly by climate stabilization, especially after 2100, potential impacts continue to grow for centuries. SLR in 2300 under both stabilization scenarios exceeds unmitigated SLR in 2100. Therefore, adaptation remains essential in densely populated and economically important coastal areas under climate stabilization. Given the multiple adaptation steps that this will require, an adaptation pathways approach has merits for coastal areas. This article is part of the theme issue `The Paris Agreement: understanding the physical and social challenges for a warming world of 1.5°C above pre-industrial levels'.

A quantum network of clocks

NASA Astrophysics Data System (ADS)

Kómár, P.; Kessler, E. M.; Bishof, M.; Jiang, L.; Sørensen, A. S.; Ye, J.; Lukin, M. D.

2014-08-01

The development of precise atomic clocks plays an increasingly important role in modern society. Shared timing information constitutes a key resource for navigation with a direct correspondence between timing accuracy and precision in applications such as the Global Positioning System. By combining precision metrology and quantum networks, we propose a quantum, cooperative protocol for operating a network of geographically remote optical atomic clocks. Using nonlocal entangled states, we demonstrate an optimal utilization of global resources, and show that such a network can be operated near the fundamental precision limit set by quantum theory. Furthermore, the internal structure of the network, combined with quantum communication techniques, guarantees security both from internal and external threats. Realization of such a global quantum network of clocks may allow construction of a real-time single international time scale (world clock) with unprecedented stability and accuracy.

The E. coli thioredoxin folding mechanism: the key role of the C-terminal helix.

PubMed

Vazquez, Diego S; Sánchez, Ignacio E; Garrote, Ana; Sica, Mauricio P; Santos, Javier

2015-02-01

In this work, the unfolding mechanism of oxidized Escherichia coli thioredoxin (EcTRX) was investigated experimentally and computationally. We characterized seven point mutants distributed along the C-terminal α-helix (CTH) and the preceding loop. The mutations destabilized the protein against global unfolding while leaving the native structure unchanged. Global analysis of the unfolding kinetics of all variants revealed a linear unfolding route with a high-energy on-pathway intermediate state flanked by two transition state ensembles TSE1 and TSE2. The experiments show that CTH is mainly unfolded in TSE1 and the intermediate and becomes structured in TSE2. Structure-based molecular dynamics are in agreement with these experiments and provide protein-wide structural information on transient states. In our model, EcTRX folding starts with structure formation in the β-sheet, while the protein helices coalesce later. As a whole, our results indicate that the CTH is a critical module in the folding process, restraining a heterogeneous intermediate ensemble into a biologically active native state and providing the native protein with thermodynamic and kinetic stability. Copyright © 2014 Elsevier B.V. All rights reserved.

Climate Change, Instability and a Full Spectrum Approach to Conflict Prevention in Africa

DTIC Science & Technology

2009-10-23

commander to follow. 15. SUBJECT TERMS Climate Change, Global Warming , Security Cooperation, Stability, Instability, Stabilization, Security...note that global warming could also create similar impacts on resources.19 In modern times disputes over natural resources have erupted into conflict...16. Center for Naval Analysis, National Security and the Threat of Climate Change, 18. 17. Michael T. Klare, ― Global Warming Battlefields: How

Global-change effects on early-stage decomposition processes in tidal wetlands - implications from a global survey using standardized litter

NASA Astrophysics Data System (ADS)

Mueller, Peter; Schile-Beers, Lisa M.; Mozdzer, Thomas J.; Chmura, Gail L.; Dinter, Thomas; Kuzyakov, Yakov; de Groot, Alma V.; Esselink, Peter; Smit, Christian; D'Alpaos, Andrea; Ibáñez, Carles; Lazarus, Magdalena; Neumeier, Urs; Johnson, Beverly J.; Baldwin, Andrew H.; Yarwood, Stephanie A.; Montemayor, Diana I.; Yang, Zaichao; Wu, Jihua; Jensen, Kai; Nolte, Stefanie

2018-05-01

Tidal wetlands, such as tidal marshes and mangroves, are hotspots for carbon sequestration. The preservation of organic matter (OM) is a critical process by which tidal wetlands exert influence over the global carbon cycle and at the same time gain elevation to keep pace with sea-level rise (SLR). The present study assessed the effects of temperature and relative sea level on the decomposition rate and stabilization of OM in tidal wetlands worldwide, utilizing commercially available standardized litter. While effects on decomposition rate per se were minor, we show strong negative effects of temperature and relative sea level on stabilization, as based on the fraction of labile, rapidly hydrolyzable OM that becomes stabilized during deployment. Across study sites, OM stabilization was 29 % lower in low, more frequently flooded vs. high, less frequently flooded zones. Stabilization declined by ˜ 75 % over the studied temperature gradient from 10.9 to 28.5 °C. Additionally, data from the Plum Island long-term ecological research site in Massachusetts, USA, show a pronounced reduction in OM stabilization by > 70 % in response to simulated coastal eutrophication, confirming the potentially high sensitivity of OM stabilization to global change. We therefore provide evidence that rising temperature, accelerated SLR, and coastal eutrophication may decrease the future capacity of tidal wetlands to sequester carbon by affecting the initial transformations of recent OM inputs to soil OM.

Short-Range-Order Mineral Physical Protection On Black Carbon Stabilization

NASA Astrophysics Data System (ADS)

Liang, B.; Weng, Y. T.; Wang, C. C.; Song, Y. F.; Lehmann, J.; Wang, C. H.

2015-12-01

Soil organic matter is one of the largest reservoirs in global carbon cycle, and black carbon (BC) represents a chemical resistant component. Black C plays an important role in global climate change. Generally considered recalcitrant due to high aromaticity, the reactive surface and functional groups of BC are crucial for carbon sequestration in soils. Mineral sorption and physical protection is an important mechanism for BC long term stabilization and sequestration in environments. Previous studies on mineral protection of BC were limited to analysis techniques in two-dimensions, for example, by SEM, TEM, and NanoSIMS. Little is known about the scope of organo-mineral association, the in-situ distribution and forms of minerals, and the ultimate interplay of BC and minerals. The aim of this study is to investigate the three-dimensional interaction of organic C and minerals in submicron scale using synchrotron-based Transmission X-ray Microcopy (TXM) and Fourier-Transform Infrared Spectroscopy (FTIR). Abundant poorly-crystallined nano-minerals particles were observed. These short-range-order (SRO) minerals also aggregate into clusters and sheets, and form envelops-like structures on the surface of BC. On top of large surface contact area, the intimate interplay between BC and minerals reinforces the stability of both organic C and minerals, resulting from chemical bonding through cation bridging and ligand exchange. The mineral protection enhances BC stabilization and sequestration and lowers its bioavailability in environment. The results suggest that mineral physical protection for BC sequestration may be more important than previous understanding.

Altered native stability is the dominant basis for susceptibility of α1-antitrypsin mutants to polymerization

PubMed Central

Irving, James A.; Haq, Imran; Dickens, Jennifer A.; Faull, Sarah V.; Lomas, David A.

2014-01-01

Serpins are protease inhibitors whose most stable state is achieved upon transition of a central 5-stranded β-sheet to a 6-stranded form. Mutations, low pH, denaturants and elevated temperatures promote this transition, which can result in a growing polymer chain of inactive molecules. Different types of polymer are possible, but, experimentally only heat has been shown to generate polymers in vitro consistent with ex vivo pathological specimens. Many mutations that alter the rate of heat-induced polymerization have been described, but interpretation is problematic because discrimination is lacking between the effect of global changes in native stability and specific effects on structural mechanism. We show that the temperature midpoint (Tm) of thermal denaturation reflects the transition of α1-antitrypsin to the polymerization intermediate, and determine the relationship with fixed-temperature polymerization half-times (t0.5) in the presence of stabilizing additives [TMAO (trimethylamine N-oxide), sucrose and sodium sulfate], point mutations and disulfide bonds. Combined with a retrospective analysis of 31 mutants characterized in the literature, the results of the present study show that global changes to native state stability are the predominant basis for the effects of mutations and osmolytes on heat-induced polymerization, summarized by the equation: ln(t0.5,mutant/t0.5,wild-type)=0.34×ΔTm. It is deviations from this relationship that hold key information about the polymerization process. PMID:24552432

Observed correlation between the depth to base and top of gas hydrate occurrence from review of global drilling data

NASA Astrophysics Data System (ADS)

Riedel, M.; Collett, T. S.

2017-07-01

A global inventory of data from gas hydrate drilling expeditions is used to develop relationships between the base of structure I gas hydrate stability, top of gas hydrate occurrence, sulfate-methane transition depth, pressure (water depth), and geothermal gradients. The motivation of this study is to provide first-order estimates of the top of gas hydrate occurrence and associated thickness of the gas hydrate occurrence zone for climate-change scenarios, global carbon budget analyses, or gas hydrate resource assessments. Results from publically available drilling campaigns (21 expeditions and 52 drill sites) off Cascadia, Blake Ridge, India, Korea, South China Sea, Japan, Chile, Peru, Costa Rica, Gulf of Mexico, and Borneo reveal a first-order linear relationship between the depth to the top and base of gas hydrate occurrence. The reason for these nearly linear relationships is believed to be the strong pressure and temperature dependence of methane solubility in the absence of large difference in thermal gradients between the various sites assessed. In addition, a statistically robust relationship was defined between the thickness of the gas hydrate occurrence zone and the base of gas hydrate stability (in meters below seafloor). The relationship developed is able to predict the depth of the top of gas hydrate occurrence zone using observed depths of the base of gas hydrate stability within less than 50 m at most locations examined in this study. No clear correlation of the depth to the top and base of gas hydrate occurrences with geothermal gradient and sulfate-methane transition depth was identified.

Observed correlation between the depth to base and top of gas hydrate occurrence from review of global drilling data

USGS Publications Warehouse

Riedel, Michael; Collett, Timothy S.

2017-01-01

A global inventory of data from gas hydrate drilling expeditions is used to develop relationships between the base of structure I gas hydrate stability, top of gas hydrate occurrence, sulfate-methane transition depth, pressure (water depth), and geothermal gradients. The motivation of this study is to provide first-order estimates of the top of gas hydrate occurrence and associated thickness of the gas hydrate occurrence zone for climate-change scenarios, global carbon budget analyses, or gas hydrate resource assessments. Results from publically available drilling campaigns (21 expeditions and 52 drill sites) off Cascadia, Blake Ridge, India, Korea, South China Sea, Japan, Chile, Peru, Costa Rica, Gulf of Mexico, and Borneo reveal a first-order linear relationship between the depth to the top and base of gas hydrate occurrence. The reason for these nearly linear relationships is believed to be the strong pressure and temperature dependence of methane solubility in the absence of large difference in thermal gradients between the various sites assessed. In addition, a statistically robust relationship was defined between the thickness of the gas hydrate occurrence zone and the base of gas hydrate stability (in meters below seafloor). The relationship developed is able to predict the depth of the top of gas hydrate occurrence zone using observed depths of the base of gas hydrate stability within less than 50 m at most locations examined in this study. No clear correlation of the depth to the top and base of gas hydrate occurrences with geothermal gradient and sulfate-methane transition depth was identified.

Probing the Structures and Electronic Properties of Dual-Phosphorus-Doped Gold Cluster Anions (AunP-2, n = 1–8): A Density functional Theory Investigation

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

Xu, Kang-Ming; Huang, Teng; Liu, Yi-Rong

2015-07-29

The geometries of gold clusters doped with two phosphorus atoms, (AunP-2, n = 1–8) were investigated using density functional theory (DFT) methods. Various two-dimensional (2D) and three-dimensional (3D) structures of the doped clusters were studied. The results indicate that the structures of dual-phosphorus-doped gold clusters exhibit large differences from those of pure gold clusters with small cluster sizes. In our study, as for Au6P-2, two cis–trans isomers were found. The global minimum of Au8P-2 presents a similar configuration to that of Au-20, a pyramid-shaped unit, and the potential novel optical and catalytic properties of this structure warrant further attention. Themore » higher stability of AunP-2 clusters relative to Au-n+2 (n = 1–8) clusters was verified based on various energy parameters, and the results indicate that the phosphorus atom can improve the stabilities of the gold clusters. We then explored the evolutionary path of (n = 1–8) clusters. We found that AunP-2 clusters exhibit the 2D–3D structural transition at n = 6, which is much clearer and faster than that of pure gold clusters and single-phosphorus-doped clusters. The electronic properties of AunP-2 (n = 1–8) were then investigated. The photoelectron spectra provide additional fundamental information on the structures and molecular orbitals shed light on the evolution of AunP-2 (n = 1–8). Natural bond orbital (NBO) described the charge distribution in stabilizing structures and revealed the strong relativistic effects of the gold atoms.« less

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

Fluvial gravel stabilization by net-spinning Hydropsychid caddisflies: exploring the magnitude and geographic scope of ecosystem engineering effect and evaluating resistance to anthropogenic stresses

NASA Astrophysics Data System (ADS)

Daniels, M.; Albertson, L.; Sklar, L. S.; Tumolo, B.; Mclaughlin, M. K.

2017-12-01

Several studies have demonstrated the substantial effects that organisms can have on earth surface processes. Known as ecosystem engineers, in streams these organisms maintain, modify, or create physical habitat structure by influencing fluvial processes such as gravel movement, fine sediment deposition and bank erosion. However, the ecology of ecosystem engineers and the magnitude of ecosystem engineering effects in a world increasingly influence by anthropogenically-driven changes is not well understood. Here we present a synthesis of research findings on the potential gravel stabilization effects of Hydropsychid caddisflies, a globally distributed group of net-spinning insects that live in the benthic substrate of most freshwater streams. Hydropsychid caddisflies act as ecosystem engineers because these silk structures can fundamentally alter sediment transport conditions, including sediment stability and flow currents. The silk nets spun by these insects attach gravel grains to one another, increasing the shear stress required to initiate grain entrainment. In a series of independent laboratory experiments, we investigate the gravel size fractions most affected by these silk attachments. We also investigate the role of anthropogenic environmental stresses on ecosystem engineering potential by assessing the impact of two common stressors, high fine sediment loads and stream drying, on silk structures. Finally, an extensive field survey of grain size and Hydropsychid caddisfly population densities informs a watershed-scale network model of Hydropsychid caddisfly gravel stabilizing potential. Our findings provide some of the first evidence that caddisfly silk may be a biological structure that is resilient to various forms of human-mediated stress and that the effects of animal ecosystem engineers are underappreciated as an agent of resistance and recovery for aquatic communities experiencing changes in sediment loads and hydrologic regimes.

Al6H18: A baby crystal of γ-AlH3

NASA Astrophysics Data System (ADS)

Kiran, B.; Kandalam, Anil K.; Xu, Jing; Ding, Y. H.; Sierka, M.; Bowen, K. H.; Schnöckel, H.

2012-10-01

Using global-minima search methods based on the density functional theory calculations of (AlH3)n (n = 1-8) clusters, we show that the growth pattern of alanes for n ≥ 4 is dominated by structures containing hexa-coordinated Al atoms. This is in contrast to the earlier studies where either linear or ring structures of AlH3 were predicted to be the preferred structures in which the Al atoms can have a maximum of five-fold coordination. Our calculations also reveal that the Al6H18 cluster, with its hexa-coordination of the Al atoms, resembles the unit-cell of γ-AlH3, thus Al6H18 is designated as the "baby crystal." The fragmentation energies of the (AlH3)n (n = 2-8) along with the dimerization energies for even n clusters indicate an enhanced stability of the Al6H18 cluster. Both covalent (hybridization) and ionic (charge) contribution to the bonding are the driving factors in stabilizing the isomers containing hexa-coordinated Al atoms.

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

A novel control algorithm for interaction between surface waves and a permeable floating structure

NASA Astrophysics Data System (ADS)

Tsai, Pei-Wei; Alsaedi, A.; Hayat, T.; Chen, Cheng-Wu

2016-04-01

An analytical solution is undertaken to describe the wave-induced flow field and the surge motion of a permeable platform structure with fuzzy controllers in an oceanic environment. In the design procedure of the controller, a parallel distributed compensation (PDC) scheme is utilized to construct a global fuzzy logic controller by blending all local state feedback controllers. A stability analysis is carried out for a real structure system by using Lyapunov method. The corresponding boundary value problems are then incorporated into scattering and radiation problems. They are analytically solved, based on separation of variables, to obtain series solutions in terms of the harmonic incident wave motion and surge motion. The dependence of the wave-induced flow field and its resonant frequency on wave characteristics and structure properties including platform width, thickness and mass has been thus drawn with a parametric approach. From which mathematical models are applied for the wave-induced displacement of the surge motion. A nonlinearly inverted pendulum system is employed to demonstrate that the controller tuned by swarm intelligence method can not only stabilize the nonlinear system, but has the robustness against external disturbance.

Global stability results for a generalized Lotka-Volterra system with distributed delays. Applications to predator-prey and to epidemic systems.

PubMed

Beretta, E; Capasso, V; Rinaldi, F

1988-01-01

The paper contains an extension of the general ODE system proposed in previous papers by the same authors, to include distributed time delays in the interaction terms. The new system describes a large class of Lotka-Volterra like population models and epidemic models with continuous time delays. Sufficient conditions for the boundedness of solutions and for the global asymptotic stability of nontrivial equilibrium solutions are given. A detailed analysis of the epidemic system is given with respect to the conditions for global stability. For a relevant subclass of these systems an existence criterion for steady states is also given.

Global stability analysis of axisymmetric boundary layer over a circular cylinder

NASA Astrophysics Data System (ADS)

Bhoraniya, Ramesh; Vinod, Narayanan

2018-05-01

This paper presents a linear global stability analysis of the incompressible axisymmetric boundary layer on a circular cylinder. The base flow is parallel to the axis of the cylinder at inflow boundary. The pressure gradient is zero in the streamwise direction. The base flow velocity profile is fully non-parallel and non-similar in nature. The boundary layer grows continuously in the spatial directions. Linearized Navier-Stokes (LNS) equations are derived for the disturbance flow quantities in the cylindrical polar coordinates. The LNS equations along with homogeneous boundary conditions forms a generalized eigenvalues problem. Since the base flow is axisymmetric, the disturbances are periodic in azimuthal direction. Chebyshev spectral collocation method and Arnoldi's iterative algorithm is used for the solution of the general eigenvalues problem. The global temporal modes are computed for the range of Reynolds numbers and different azimuthal wave numbers. The largest imaginary part of the computed eigenmodes is negative, and hence, the flow is temporally stable. The spatial structure of the eigenmodes shows that the disturbance amplitudes grow in size and magnitude while they are moving towards downstream. The global modes of axisymmetric boundary layer are more stable than that of 2D flat-plate boundary layer at low Reynolds number. However, at higher Reynolds number they approach 2D flat-plate boundary layer. Thus, the damping effect of transverse curvature is significant at low Reynolds number. The wave-like nature of the disturbance amplitudes is found in the streamwise direction for the least stable eigenmodes.

Bifurcations and degenerate periodic points in a three dimensional chaotic fluid flow

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

Smith, L. D., E-mail: lachlan.smith@monash.edu; CSIRO Mineral Resources, Clayton, Victoria 3800; Rudman, M.

2016-05-15

Analysis of the periodic points of a conservative periodic dynamical system uncovers the basic kinematic structure of the transport dynamics and identifies regions of local stability or chaos. While elliptic and hyperbolic points typically govern such behaviour in 3D systems, degenerate (parabolic) points also play an important role. These points represent a bifurcation in local stability and Lagrangian topology. In this study, we consider the ramifications of the two types of degenerate periodic points that occur in a model 3D fluid flow. (1) Period-tripling bifurcations occur when the local rotation angle associated with elliptic points is reversed, creating a reversalmore » in the orientation of associated Lagrangian structures. Even though a single unstable point is created, the bifurcation in local stability has a large influence on local transport and the global arrangement of manifolds as the unstable degenerate point has three stable and three unstable directions, similar to hyperbolic points, and occurs at the intersection of three hyperbolic periodic lines. The presence of period-tripling bifurcation points indicates regions of both chaos and confinement, with the extent of each depending on the nature of the associated manifold intersections. (2) The second type of bifurcation occurs when periodic lines become tangent to local or global invariant surfaces. This bifurcation creates both saddle–centre bifurcations which can create both chaotic and stable regions, and period-doubling bifurcations which are a common route to chaos in 2D systems. We provide conditions for the occurrence of these tangent bifurcations in 3D conservative systems, as well as constraints on the possible types of tangent bifurcation that can occur based on topological considerations.« less

Cavity-Creating Mutations in Pseudomonas aeruginosa Azurin: Effects on Protein Dynamics and Stability

PubMed Central

Gabellieri, Edi; Balestreri, Ettore; Galli, Alvaro; Cioni, Patrizia

2008-01-01

Changes in flexibility and structural stability of Pseudomonas aeruginosa azurin in response to cavity-creating mutations were probed by the phosphorescence emission of Trp-48, which was deeply buried in the compact hydrophobic core of the macromolecule, and by measurements of guanidinum hydrochloride unfolding, respectively. Replacement of the bulky side chains Phe-110, Phe-29, and Tyr-108 with the smaller Ala introduced cavities at different distances from the hydrophobic core. The phosphorescence lifetime (τ0) of Trp-48, buried inside the protein core, and the acrylamide quenching rate constant (kq) were used to monitor local and global flexibility changes induced by the introduction of the cavity. The results of this work demonstrate the following: 1), the effect on core flexibility of the insertion of cavities is not correlated readily to the distance of the cavity from the core; 2), the protein global flexibility results are related to the cavity distance from the packed core of the macromolecule; and 3), the increase in protein flexibility does not correspond necessarily to a comparable destabilizing effect of some mutations. PMID:18424505

The Trilateral Force: The Atlantic Alliance and the Future of Nuclear Weapons Strategy

DTIC Science & Technology

2013-01-01

2010), 10. 4 Robert Manning, Envisioning 2030: U.S. Strategy for a Post-Western World, Atlantic Council (2013), 46. 5 Paul Bracken, The Second...Strategic Stability: Contending Interpretations, U.S. Army War College Strategic Studies Institute (2013); Paul Bracken, “The Bomb Returns for a Second...U.S. Nuclear Strategy, Force Structure and Posture, Global Zero (2012), 6. 27 Dana Johnson, et al., “Triad, Dyad, Monad? Shaping the U.S. Force of

INDIA’S GROWING INFLUENCE IN STABILIZING REGIONAL SECURITY IN SOUTHEAST ASIA

DTIC Science & Technology

2016-02-16

in this academic research paper are those of the author and do not reflect the official policy or position of the US government , the Department of...Defense, or Air University. In accordance with Air Force Instruction 51-303, it is not copyrighted but is the property of the United States government ...Change in the global political and economic structure, unstable Indian government from the end of 1989 till mid-1991, internal political crisis

Polymorphism in the two-locus Levene model with nonepistatic directional selection.

PubMed

Bürger, Reinhard

2009-11-01

For the Levene model with soft selection in two demes, the maintenance of polymorphism at two diallelic loci is studied. Selection is nonepistatic and dominance is intermediate. Thus, there is directional selection in every deme and at every locus. We assume that selection is in opposite directions in the two demes because otherwise no polymorphism is possible. If at one locus there is no dominance, then a complete analysis of the dynamical and equilibrium properties is performed. In particular, a simple necessary and sufficient condition for the existence of an internal equilibrium and sufficient conditions for global asymptotic stability are obtained. These results are extended to deme-independent degree of dominance at one locus. A perturbation analysis establishes structural stability within the full parameter space. In the absence of genotype-environment interaction, which requires deme-independent dominance at both loci, nongeneric equilibrium behavior occurs, and the introduction of arbitrarily small genotype-environment interaction changes the equilibrium structure and may destroy stable polymorphism. The volume of the parameter space for which a (stable) two-locus polymorphism is maintained is computed numerically. It is investigated how this volume depends on the strength of selection and on the dominance relations. If the favorable allele is (partially) dominant in its deme, more than 20% of all parameter combinations lead to a globally asymptotically stable, fully polymorphic equilibrium.

Stability in a changing world - palm community dynamics in the hyperdiverse western Amazon over 17 years.

PubMed

Olivares, Ingrid; Svenning, Jens-Christian; van Bodegom, Peter M; Valencia, Renato; Balslev, Henrik

2017-03-01

Are the hyperdiverse local forests of the western Amazon undergoing changes linked to global and local drivers such as climate change, or successional dynamics? We analyzed local climatic records to assess potential climatic changes in Yasuní National Park, Ecuador, and compared two censuses (1995, 2012) of a palm community to assess changes in community structure and composition. Over 17 years, the structure and composition of this palm community remained remarkably stable. Soil humidity was significantly lower and canopy conditions were significantly more open in 2012 compared to 1995, but local climatic records showed that no significant changes in precipitation, temperature or river level have occurred during the last decade. Thus, we found no evidence of recent directional shifts in climate or the palm community in Yasuní. The absence of changes in local climate and plant community dynamics in Yasuní contrasts with recent findings from eastern Amazon, where environmental change is driving significant changes in ecosystem dynamics. Our findings suggest that until now, local forests in the northwest Amazon may have escaped pressure from climate change. The stability of this rich palm community embedded in the hyperdiverse Yasuní National Park underlines its uniqueness as a sanctuary for the protection of Amazonian diversity from global change impacts. © 2016 John Wiley & Sons Ltd.

Localized structural frustration for evaluating the impact of sequence variants.

PubMed

Kumar, Sushant; Clarke, Declan; Gerstein, Mark

2016-12-01

Population-scale sequencing is increasingly uncovering large numbers of rare single-nucleotide variants (SNVs) in coding regions of the genome. The rarity of these variants makes it challenging to evaluate their deleteriousness with conventional phenotype-genotype associations. Protein structures provide a way of addressing this challenge. Previous efforts have focused on globally quantifying the impact of SNVs on protein stability. However, local perturbations may severely impact protein functionality without strongly disrupting global stability (e.g. in relation to catalysis or allostery). Here, we describe a workflow in which localized frustration, quantifying unfavorable local interactions, is employed as a metric to investigate such effects. Using this workflow on the Protein Databank, we find that frustration produces many immediately intuitive results: for instance, disease-related SNVs create stronger changes in localized frustration than non-disease related variants, and rare SNVs tend to disrupt local interactions to a larger extent than common variants. Less obviously, we observe that somatic SNVs associated with oncogenes and tumor suppressor genes (TSGs) induce very different changes in frustration. In particular, those associated with TSGs change the frustration more in the core than the surface (by introducing loss-of-function events), whereas those associated with oncogenes manifest the opposite pattern, creating gain-of-function events. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Magnetorotational Instability: Nonmodal Growth and the Relationship of Global Modes to the Shearing Box

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

J Squire, A Bhattacharjee

We study the magnetorotational instability (MRI) (Balbus & Hawley 1998) using non-modal stability techniques.Despite the spectral instability of many forms of the MRI, this proves to be a natural method of analysis that is well-suited to deal with the non-self-adjoint nature of the linear MRI equations. We find that the fastest growing linear MRI structures on both local and global domains can look very diff erent to the eigenmodes, invariably resembling waves shearing with the background flow (shear waves). In addition, such structures can grow many times faster than the least stable eigenmode over long time periods, and be localizedmore » in a completely di fferent region of space. These ideas lead – for both axisymmetric and non-axisymmetric modes – to a natural connection between the global MRI and the local shearing box approximation. By illustrating that the fastest growing global structure is well described by the ordinary diff erential equations (ODEs) governing a single shear wave, we find that the shearing box is a very sensible approximation for the linear MRI, contrary to many previous claims. Since the shear wave ODEs are most naturally understood using non-modal analysis techniques, we conclude by analyzing local MRI growth over finite time-scales using these methods. The strong growth over a wide range of wave-numbers suggests that non-modal linear physics could be of fundamental importance in MRI turbulence (Squire & Bhattacharjee 2014).« less

Molecular mobility in amorphous state: Implications on physical stability

NASA Astrophysics Data System (ADS)

Bhardwaj, Sunny Piyush

Amorphous pharmaceuticals are desirable in drug development due to their advantageous biopharmaceutical properties of higher apparent aqueous solubility and dissolution rate. The main obstacle in their widespread use, however, is their higher physicochemical instability than their crystalline counterparts. The goal of the present research project was to investigate correlations between the molecular mobility and physical stability in model amorphous compounds. The objective was to identify the specific mobility which is responsible for the physical instability in each case. This will potentially enable the development of effective strategies for the stabilization of amorphous pharmaceuticals. Moreover, these correlations can be used to develop predictive models for the stability at the pharmaceutically relevant storage conditions. Subtraction of dc conductivity enabled the comprehensive characterization of molecular mobility in amorphous trehalose. This was followed by investigation of correlation between crystallization behavior and different relaxations. Global mobility was found to be strongly coupled to both crystallization onset time and rate. Different preparation methods imparted different mobility states to amorphous trehalose which was postulated to be the reason for the significant physical stability differences. Predictive models were developed and a good agreement was found between the predicted and the experimental crystallization onset times at temperatures around and below the glass transition temperature (Tg). Effect of annealing was investigated on water sorption, enthalpic recovery and dielectric relaxation times in amorphous trehalose. Global mobility was found to be linearly correlated to the water sorption potential which enabled the development of predictive models. Global mobility was also found to be strongly correlated to physical instability in amorphous itraconazole. Effect of polymer (PVP and HPMCAS) on itraconazole mobility and stability was also evaluated. Global mobility was found to be correlated to stability in both the solid dispersions. HPMCAS was found to be a better stabilizer than PVP due to its pronounced effect on global mobility.

The Global Economy--Policy Issues and Prospects.

ERIC Educational Resources Information Center

Laden, Ben E.

Economic policies of the industrial nations are on a dangerous course, constituting a threat to worldwide growth and to financial and economic stability. The results of inappropriate policies throughout the industrial countries are (1) financial strains which endanger global economic stability, (2) extraordinary imbalances of trade, and (3)…

Global exponential stability of inertial memristor-based neural networks with time-varying delays and impulses.

PubMed

Zhang, Wei; Huang, Tingwen; He, Xing; Li, Chuandong

2017-11-01

In this study, we investigate the global exponential stability of inertial memristor-based neural networks with impulses and time-varying delays. We construct inertial memristor-based neural networks based on the characteristics of the inertial neural networks and memristor. Impulses with and without delays are considered when modeling the inertial neural networks simultaneously, which are of great practical significance in the current study. Some sufficient conditions are derived under the framework of the Lyapunov stability method, as well as an extended Halanay differential inequality and a new delay impulsive differential inequality, which depend on impulses with and without delays, in order to guarantee the global exponential stability of the inertial memristor-based neural networks. Finally, two numerical examples are provided to illustrate the efficiency of the proposed methods. Copyright © 2017 Elsevier Ltd. All rights reserved.

Magnetohydrodynamic Simulations of the Wiggle Instability in Spiral Galaxies

NASA Astrophysics Data System (ADS)

Tanaka, Minoru; Wada, Keiichi; Machida, Mami; Matsumoto, Ryoji; Miyaji, Shigeki

2005-09-01

We studied the stability of galactic spiral shocks through two dimensional global magnetohydrodynamic simulations. Recently, Wada & Koda (2003) showed, using global hydrodynamic simulations, that galactic gas flows behind a spiral shock becomes unstable against a perturbation parallel to the shock front and form spur-like density structures. They attributed the origin of this wiggle instability to the Kelvin-Helmholtz (K-H) instability triggered by the acceleration of the gas behind the shock. We carried out global simulations including galactic magnetic fields. The initial magnetic field is assumed to be either uniform or purely toroidal. We found that although the magnetic field reduces the growth rate of the K-H instability, wiggle instability develops even in galaxies with μG magnetic fields. We also present the results of local simulations to demonstrate the dependence of the growth rate of the instability with the wavelength. The interval of spurs is determined by the most unstable wavelength of the wiggle instability.

A quantum network of clocks

NASA Astrophysics Data System (ADS)

Komar, Peter; Kessler, Eric; Bishof, Michael; Jiang, Liang; Sorensen, Anders; Ye, Jun; Lukin, Mikhail

2014-05-01

Shared timing information constitutes a key resource for positioning and navigation with a direct correspondence between timing accuracy and precision in applications such as the Global Positioning System (GPS). By combining precision metrology and quantum networks, we propose here a quantum, cooperative protocol for the operation of a network consisting of geographically remote optical atomic clocks. Using non-local entangled states, we demonstrate an optimal utilization of the global network resources, and show that such a network can be operated near the fundamental limit set by quantum theory yielding an ultra-precise clock signal. Furthermore, the internal structure of the network, combined with basic techniques from quantum communication, guarantees security both from internal and external threats. Realization of such a global quantum network of clocks may allow construction of a real-time single international time scale (world clock) with unprecedented stability and accuracy. See also: Komar et al. arXiv:1310.6045 (2013) and Kessler et al. arXiv:1310.6043 (2013).

Dynamic/Jitter Assessment of Multiple Potential HabEx Structural Designs

NASA Technical Reports Server (NTRS)

Knight, J. Brent; Stahl, H. Philip; Singleton, Andy; Hunt, Ron; Therrell, Melissa; Caldwell, Kate; Garcia, Jay; Baysinger, Mike

2017-01-01

One of the driving structural requirements of the Habitable Exo-Planet (HabEx) telescope is to maintain Line Of Sight (LOS) stability between the Primary Mirror (PM) and Secondary Mirror (SM) of = 5 mas. Dynamic analyses of two configurations of a proposed (HabEx) 4 meter off-axis telescope structure were performed to predict effects of jitter on primary/secondary mirror alignment. The dynamic disturbance used as the forcing function was the James Webb Space Telescope reaction wheel assembly vibration emission specification level. The objective of these analyses was to predict "order-of-magnitude" performance for various structural configurations which will roll into efforts to define the HabEx structural design's global architecture. Two variations of the basic architectural design were analyzed. Relative motion between the PM and the SM for each design configuration are reported.

Dynamic/jitter assessment of multiple potential HabEx structural designs

NASA Astrophysics Data System (ADS)

Knight, J. Brent; Stahl, H. Philip; Singleton, Andy; Hunt, Ron; Therrell, Melissa; Caldwell, Kate; Garcia, Jay; Baysinger, Mike

2017-09-01

One of the driving structural requirements of the Habitable Exo-Planet (HabEx) telescope is to maintain Line Of Sight (LOS) stability between the Primary Mirror (PM) and Secondary Mirror (SM) of <= 5 milli-arc seconds (mas). Dynamic analyses of two configurations of a proposed HabEx 4 meter off-axis telescope structure were performed to predict effects of a vibration input on primary/secondary mirror alignment. The dynamic disturbance used as the forcing function was the James Webb Space Telescope reaction wheel assembly vibration emission specification level. The objective of these analyses was to predict "order-of-magnitude" performance for various structural configurations which contribute to efforts in defining the HabEx structural design's global architecture. Two variations of the basic architectural design were analyzed. Relative motion between the PM and the SM for each design configuration are reported.

Human Impacts and Climate Change Influence Nestedness and Modularity in Food-Web and Mutualistic Networks.

PubMed

Takemoto, Kazuhiro; Kajihara, Kosuke

2016-01-01

Theoretical studies have indicated that nestedness and modularity-non-random structural patterns of ecological networks-influence the stability of ecosystems against perturbations; as such, climate change and human activity, as well as other sources of environmental perturbations, affect the nestedness and modularity of ecological networks. However, the effects of climate change and human activities on ecological networks are poorly understood. Here, we used a spatial analysis approach to examine the effects of climate change and human activities on the structural patterns of food webs and mutualistic networks, and found that ecological network structure is globally affected by climate change and human impacts, in addition to current climate. In pollination networks, for instance, nestedness increased and modularity decreased in response to increased human impacts. Modularity in seed-dispersal networks decreased with temperature change (i.e., warming), whereas food web nestedness increased and modularity declined in response to global warming. Although our findings are preliminary owing to data-analysis limitations, they enhance our understanding of the effects of environmental change on ecological communities.

Global stability of a multiple delayed viral infection model with general incidence rate and an application to HIV infection.

PubMed

Ji, Yu

2015-06-01

In this paper, the dynamical behavior of a viral infection model with general incidence rate and two time delays is studied. By using the Lyapunov functional and LaSalle invariance principle, the global stabilities of the infection-free equilibrium and the endemic equilibrium are obtained. We obtain a threshold of the global stability for the uninfected equilibrium, which means the disease will be under control eventually. These results can be applied to a variety of viral infections of disease that would make it possible to devise optimal treatment strategies. Numerical simulations with application to HIV infection are given to verify the analytical results.

Allometric scaling enhances stability in complex food webs.

PubMed

Brose, Ulrich; Williams, Richard J; Martinez, Neo D

2006-11-01

Classic local stability theory predicts that complex ecological networks are unstable and are unlikely to persist despite empiricists' abundant documentation of such complexity in nature. This contradiction has puzzled biologists for decades. While some have explored how stability may be achieved in small modules of a few interacting species, rigorous demonstrations of how large complex and ecologically realistic networks dynamically persist remain scarce and inadequately understood. Here, we help fill this void by combining structural models of complex food webs with nonlinear bioenergetic models of population dynamics parameterized by biological rates that are allometrically scaled to populations' average body masses. Increasing predator-prey body mass ratios increase population persistence up to a saturation level that is reached by invertebrate and ectotherm vertebrate predators when being 10 or 100 times larger than their prey respectively. These values are corroborated by empirical predator-prey body mass ratios from a global data base. Moreover, negative effects of diversity (i.e. species richness) on stability (i.e. population persistence) become neutral or positive relationships at these empirical ratios. These results demonstrate that the predator-prey body mass ratios found in nature may be key to enabling persistence of populations in complex food webs and stabilizing the diversity of natural ecosystems.

Synthesis and biology of cyclic imine toxins, an emerging class of potent, globally distributed marine toxins.

PubMed

Stivala, Craig E; Benoit, Evelyne; Aráoz, Rómulo; Servent, Denis; Novikov, Alexei; Molgó, Jordi; Zakarian, Armen

2015-03-01

From a small group of exotic compounds isolated only two decades ago, Cyclic Imine (CI) toxins have become a major class of marine toxins with global distribution. Their distinct chemical structure, biological mechanism of action, and intricate chemistry ensures that CI toxins will continue to be the subject of fascinating fundamental studies in the broad fields of chemistry, chemical biology, and toxicology. The worldwide occurrence of potent CI toxins in marine environments, their accumulation in shellfish, and chemical stability are important considerations in assessing risk factors for human health. This review article aims to provide an account of chemistry, biology, and toxicology of CI toxins from their discovery to the present day.

Stability metrics for multi-source biomedical data based on simplicial projections from probability distribution distances.

PubMed

Sáez, Carlos; Robles, Montserrat; García-Gómez, Juan M

2017-02-01

Biomedical data may be composed of individuals generated from distinct, meaningful sources. Due to possible contextual biases in the processes that generate data, there may exist an undesirable and unexpected variability among the probability distribution functions (PDFs) of the source subsamples, which, when uncontrolled, may lead to inaccurate or unreproducible research results. Classical statistical methods may have difficulties to undercover such variabilities when dealing with multi-modal, multi-type, multi-variate data. This work proposes two metrics for the analysis of stability among multiple data sources, robust to the aforementioned conditions, and defined in the context of data quality assessment. Specifically, a global probabilistic deviation and a source probabilistic outlyingness metrics are proposed. The first provides a bounded degree of the global multi-source variability, designed as an estimator equivalent to the notion of normalized standard deviation of PDFs. The second provides a bounded degree of the dissimilarity of each source to a latent central distribution. The metrics are based on the projection of a simplex geometrical structure constructed from the Jensen-Shannon distances among the sources PDFs. The metrics have been evaluated and demonstrated their correct behaviour on a simulated benchmark and with real multi-source biomedical data using the UCI Heart Disease data set. The biomedical data quality assessment based on the proposed stability metrics may improve the efficiency and effectiveness of biomedical data exploitation and research.

Fully three-dimensional ideal magnetohydrodynamic stability analysis of low- n modes and Mercier modes in stellarators

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

Fu, G.Y.; Cooper, W.A.; Gruber, R.

1992-06-01

The TERPSICHORE three-dimensional linear ideal magnetohydrodynamic (MHD) stability code ({ital Theory} {ital of} {ital Fusion} {ital Plasmas}, Proceedings of the Joint Varenna--Lausanne International Workshop, Chexbres, Switzerland, 1988 (Editrice Compositori, Bologna, Italy, 1989), p. 93; {ital Controlled} {ital Fusion} {ital and} {ital Plasma} {ital Heating}, Proceedings of the 17th European Conference, Amsterdam, The Netherlands (European Physical Society, Petit-Lancy, Switzerland, 1990), Vol. 14B, Part II, p. 931; {ital Theory} {ital of} {ital Fusion} {ital Plasmas}, Proceedings of the Joint Varenna--Lausanne International Workshop, Valla Monastero, Varenna, Italy, 1990 (Editrice Compositori, Bologna, Italy, 1990), p. 655) has been extended to the full MHD equations.more » The new code is used to calculate the physical growth rates of nonlocal low-{ital n} modes for {ital l}=2 torsatron configurations. A comprehensive investigation of the relation between the Mercier modes and the low-{ital n} modes has been performed. The unstable localized low-{ital n} modes are found to be correlated with the Mercier criterion. Finite growth rates of the low-{ital n} modes correspond to finite values of the Mercier criterion parameter. Near the Mercier marginal stability boundary, the low-{ital n} modes tend to be weakly unstable with very small growth rates. However, the stability of global-type low-{ital n} modes is found to be decorrelated from that of Mercier modes. The low-{ital n} modes with global radial structures can be more stable or more unstable than Mercier modes.« less

Global Output-Feedback Control for Simultaneous Tracking and Stabilization of Wheeled Mobile Robots

NASA Astrophysics Data System (ADS)

Chang, J.; Zhang, L. J.; Xue, D.

A time-varying global output-feedback controller is presented that solves both tracking and stabilization for wheeled mobile robots simultaneously at the torque level. The controller synthesis is based on a coordinate transformation, Lyapunov direct method and backstepping technique. The performance of the proposed controller is demonstrated by simulation.

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.

A class of stabilizing controllers for flexible multibody systems

NASA Technical Reports Server (NTRS)

Joshi, Suresh M.; Kelkar, Atul G.; Maghami, Peiman G.

1995-01-01

The problem of controlling a class of nonlinear multibody flexible space systems consisting of a flexible central body to which a number of articulated appendages are attached is considered. Collocated actuators and sensors are assumed, and global asymptotic stability of such systems is established under a nonlinear dissipative control law. The stability is shown to be robust to unmodeled dynamics and parametric uncertainties. For a special case in which the attitude motion of the central body is small, the system, although still nonlinear, is shown to be stabilized by linear dissipative control laws. Two types of linear controllers are considered: static dissipative (constant gain) and dynamic dissipative. The static dissipative control law is also shown to provide robust stability in the presence of certain classes of actuator and sensor nonlinearities and actuator dynamics. The results obtained for this special case can also be readily applied for controlling single-body linear flexible space structures. For this case, a synthesis technique for the design of a suboptimal dynamic dissipative controller is also presented. The results obtained in this paper are applicable to a broad class of multibody and single-body systems such as flexible multilink manipulators, multipayload space platforms, and space antennas. The stability proofs use the Lyapunov approach and exploit the inherent passivity of such systems.

Development of a very small telescope for a milli-arcsec space astrometry

NASA Astrophysics Data System (ADS)

Suganuma, M.; Kobayashi, Y.; Gouda, N.; Yano, T.; Yamada, Y.; Takato, N.; Yamauchi, M.

2008-07-01

We are preparing a reflecting telescope for Nano-JASMINE, a very small satellite for global space astrometry of milli-arcsecond accuracy. The telescope has a 5-cm diameter primary mirror and a beam-combiner in front of it. It occupies only about 12x12x17cm and is entirely made out of aluminum alloy. The telescope and its surrounding structures are carefully designed for thermal stability of the optics, especially to control changes in the relative angle of the beam-combiner.

Destabilizing Effects of Impulse in Delayed Bam Neural Networks

NASA Astrophysics Data System (ADS)

Li, Chuandong; Li, Chaojie; Liu, Chao

This paper further studies the global exponential stability of the equilibrium point of the delayed bidirectional associative memory (DBAM) neural networks with impulse effects. Several results characterizing the aggregated effects of impulse and dynamical property of the impulse-free DBAM on the exponential stability of the considered DBAM have been established. It is shown that the impulsive DBAM will preserve the global exponential stability of the impulse-free DBAM even if the impulses have enlarging effects on the states of neurons.

Global robust stability of bidirectional associative memory neural networks with multiple time delays.

PubMed

Senan, Sibel; Arik, Sabri

2007-10-01

This correspondence presents a sufficient condition for the existence, uniqueness, and global robust asymptotic stability of the equilibrium point for bidirectional associative memory neural networks with discrete time delays. The results impose constraint conditions on the network parameters of the neural system independently of the delay parameter, and they are applicable to all bounded continuous nonmonotonic neuron activation functions. Some numerical examples are given to compare our results with the previous robust stability results derived in the literature.

Global exponential stability of BAM neural networks with time-varying delays: The discrete-time case

NASA Astrophysics Data System (ADS)

Raja, R.; Marshal Anthoni, S.

2011-02-01

This paper deals with the problem of stability analysis for a class of discrete-time bidirectional associative memory (BAM) neural networks with time-varying delays. By employing the Lyapunov functional and linear matrix inequality (LMI) approach, a new sufficient conditions is proposed for the global exponential stability of discrete-time BAM neural networks. The proposed LMI based results can be easily checked by LMI control toolbox. Moreover, an example is also provided to demonstrate the effectiveness of the proposed method.

Non Lyapunov stability of a constant spatially developing 2-D gas flow

NASA Astrophysics Data System (ADS)

Balint, Agneta M.; Balint, Stefan; Tanasie, Loredana

2017-01-01

Different types of stabilities (global, local) and instabilities (global absolute, local convective) of the constant spatially developing 2-D gas flow are analyzed in a particular phase space of continuously differentiable functions, endowed with the usual algebraic operations and the topology generated by the uniform convergence on the plane. For this purpose the Euler equations linearized at the constant flow are used. The Lyapunov stability analysis was presented in [1] and this paper is a continuation of [1].

Superspace and global stability in general relativity

NASA Astrophysics Data System (ADS)

Gurzadyan, A. V.; Kocharyan, A. A.

A framework is developed enabling the global analysis of the stability of cosmological models using the local geometric characteristics of the infinite-dimensional superspace, i.e. using the generalized Jacobi equation reformulated for pseudo-Riemannian manifolds. We give a direct formalism for dynamical analysis in the superspace, the requisite equation pertinent for stability analysis of the universe by means of generalized covariant and Fermi derivative is derived. Then, the relevant definitions and formulae are retrieved for cosmological models with a scalar field.

Stability and change in political conservatism following the global financial crisis.

PubMed

Milojev, Petar; Greaves, Lara; Osborne, Danny; Sibley, Chris G

2015-01-01

The current study analyzes data from a national probability panel sample of New Zealanders (N = 5,091) to examine stability and change in political orientation over four consecutive yearly assessments (2009-2012) following the 2007/2008 global financial crisis. Bayesian Latent Growth Modeling identified systematic variation in the growth trajectory of conservatism that was predicted by age and socio-economic status. Younger people (ages 25-45) did not change in their political orientation. Older people, however, became more conservative over time. Likewise, people with lower socio-economic status showed a marked increase in political conservatism. In addition, tests of rank-order stability showed that age had a cubic relationship with the stability of political orientation over our four annual assessments. Our findings provide strong support for System Justification Theory by showing that increases in conservatism in the wake of the recent global financial crisis occurred primarily among the poorest and most disadvantaged.

Changes in tropical cyclones under stabilized 1.5 and 2.0°C global warming scenarios as simulated by the Community Atmospheric Model under the HAPPI protocols

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

Wehner, Michael F.; Reed, Kevin A.; Loring, Burlen

The United Nations Framework Convention on Climate Change (UNFCCC) invited the scientific community to explore the impacts of a world in which anthropogenic global warming is stabilized at only 1.5°C above preindustrial average temperatures. In this paper, we present a projection of future tropical cyclone statistics for both 1.5 and 2.0°C stabilized warming scenarios with direct numerical simulation using a high-resolution global climate model. As in similar projections at higher warming levels, we find that even at these low warming levels the most intense tropical cyclones become more frequent and more intense, while simultaneously the frequency of weaker tropical stormsmore » is decreased. We also conclude that in the 1.5°C stabilization, the effect of aerosol forcing changes complicates the interpretation of greenhouse gas forcing changes.« less

Changes in tropical cyclones under stabilized 1.5 and 2.0 °C global warming scenarios as simulated by the Community Atmospheric Model under the HAPPI protocols

NASA Astrophysics Data System (ADS)

Wehner, Michael F.; Reed, Kevin A.; Loring, Burlen; Stone, Dáithí; Krishnan, Harinarayan

2018-02-01

The United Nations Framework Convention on Climate Change (UNFCCC) invited the scientific community to explore the impacts of a world in which anthropogenic global warming is stabilized at only 1.5 °C above preindustrial average temperatures. We present a projection of future tropical cyclone statistics for both 1.5 and 2.0 °C stabilized warming scenarios with direct numerical simulation using a high-resolution global climate model. As in similar projections at higher warming levels, we find that even at these low warming levels the most intense tropical cyclones become more frequent and more intense, while simultaneously the frequency of weaker tropical storms is decreased. We also conclude that in the 1.5 °C stabilization, the effect of aerosol forcing changes complicates the interpretation of greenhouse gas forcing changes.

Changes in tropical cyclones under stabilized 1.5 and 2.0°C global warming scenarios as simulated by the Community Atmospheric Model under the HAPPI protocols

DOE PAGES

Wehner, Michael F.; Reed, Kevin A.; Loring, Burlen; ...

2018-02-28

The United Nations Framework Convention on Climate Change (UNFCCC) invited the scientific community to explore the impacts of a world in which anthropogenic global warming is stabilized at only 1.5°C above preindustrial average temperatures. In this paper, we present a projection of future tropical cyclone statistics for both 1.5 and 2.0°C stabilized warming scenarios with direct numerical simulation using a high-resolution global climate model. As in similar projections at higher warming levels, we find that even at these low warming levels the most intense tropical cyclones become more frequent and more intense, while simultaneously the frequency of weaker tropical stormsmore » is decreased. We also conclude that in the 1.5°C stabilization, the effect of aerosol forcing changes complicates the interpretation of greenhouse gas forcing changes.« less

Boundary layers and global stability of laboratory quasi-Keplerian flow

NASA Astrophysics Data System (ADS)

Edlund, E. M.; Ji, H.

2013-11-01

Studies in the HTX device at PPPL, a modified Taylor-Couette experiment, have demonstrated a robust stability of astrophysically relevant, quasi-Keplerian flows. Independent rings on the axial boundary can be used to fine tune the rotation profile, allowing ideal Couette rotation to be achieved over nearly the entire radial gap. Fluctuation levels in these flows are observed to be at nearly the noise floor of the laser Doppler velocimetry (LDV) diagnostic, in agreement with prior studies under similar conditions. Deviations from optimal operating parameters illustrate the importance of centrifugally unstable boundary layers in Taylor-Couette devices of the classical configuration where the axial boundaries rotate with the outer cylinder. The global stability of nearly ideal-Couette flows, with implications for astrophysical systems, will be discussed in light of the global stability of these flows with respect to externally applied perturbations of large magnitude.

Spontaneous Unfolding-Refolding of Fibronectin Type III Domains Assayed by Thiol Exchange

PubMed Central

Shah, Riddhi; Ohashi, Tomoo; Erickson, Harold P.; Oas, Terrence G.

2017-01-01

Globular proteins are not permanently folded but spontaneously unfold and refold on time scales that can span orders of magnitude for different proteins. A longstanding debate in the protein-folding field is whether unfolding rates or folding rates correlate to the stability of a protein. In the present study, we have determined the unfolding and folding kinetics of 10 FNIII domains. FNIII domains are one of the most common protein folds and are present in 2% of animal proteins. FNIII domains are ideal for this study because they have an identical seven-strand β-sandwich structure, but they vary widely in sequence and thermodynamic stability. We assayed thermodynamic stability of each domain by equilibrium denaturation in urea. We then assayed the kinetics of domain opening and closing by a technique known as thiol exchange. For this we introduced a buried Cys at the identical location in each FNIII domain and measured the kinetics of labeling with DTNB over a range of urea concentrations. A global fit of the kinetics data gave the kinetics of spontaneous unfolding and refolding in zero urea. We found that the folding rates were relatively similar, ∼0.1–1 s−1, for the different domains. The unfolding rates varied widely and correlated with thermodynamic stability. Our study is the first to address this question using a set of domains that are structurally homologous but evolved with widely varying sequence identity and thermodynamic stability. These data add new evidence that thermodynamic stability correlates primarily with unfolding rate rather than folding rate. The study also has implications for the question of whether opening of FNIII domains contributes to the stretching of fibronectin matrix fibrils. PMID:27909052

Probing the structural evolution of ruthenium doped germanium clusters: Photoelectron spectroscopy and density functional theory calculations

PubMed Central

Jin, Yuanyuan; Lu, Shengjie; Hermann, Andreas; Kuang, Xiaoyu; Zhang, Chuanzhao; Lu, Cheng; Xu, Hongguang; Zheng, Weijun

2016-01-01

We present a combined experimental and theoretical study of ruthenium doped germanium clusters, RuGen− (n = 3–12), and their corresponding neutral species. Photoelectron spectra of RuGen− clusters are measured at 266 nm. The vertical detachment energies (VDEs) and adiabatic detachment energies (ADEs) are obtained. Unbiased CALYPSO structure searches confirm the low-lying structures of anionic and neutral ruthenium doped germanium clusters in the size range of 3 ≤ n ≤ 12. Subsequent geometry optimizations using density functional theory (DFT) at PW91/LANL2DZ level are carried out to determine the relative stability and electronic properties of ruthenium doped germanium clusters. It is found that most of the anionic and neutral clusters have very similar global features. Although the global minimum structures of the anionic and neutral clusters are different, their respective geometries are observed as the low-lying isomers in either case. In addition, for n > 8, the Ru atom in RuGen−/0 clusters is absorbed endohedrally in the Ge cage. The theoretically predicted vertical and adiabatic detachment energies are in good agreement with the experimental measurements. The excellent agreement between DFT calculations and experiment enables a comprehensive evaluation of the geometrical and electronic structures of ruthenium doped germanium clusters. PMID:27439955

Stability investigations of airfoil flow by global analysis

NASA Technical Reports Server (NTRS)

Morzynski, Marek; Thiele, Frank

1992-01-01

As the result of global, non-parallel flow stability analysis the single value of the disturbance growth-rate and respective frequency is obtained. This complex value characterizes the stability of the whole flow configuration and is not referred to any particular flow pattern. The global analysis assures that all the flow elements (wake, boundary and shear layer) are taken into account. The physical phenomena connected with the wake instability are properly reproduced by the global analysis. This enhances the investigations of instability of any 2-D flows, including ones in which the boundary layer instability effects are known to be of dominating importance. Assuming fully 2-D disturbance form, the global linear stability problem is formulated. The system of partial differential equations is solved for the eigenvalues and eigenvectors. The equations, written in the pure stream function formulation, are discretized via FDM using a curvilinear coordinate system. The complex eigenvalues and corresponding eigenvectors are evaluated by an iterative method. The investigations performed for various Reynolds numbers emphasize that the wake instability develops into the Karman vortex street. This phenomenon is shown to be connected with the first mode obtained from the non-parallel flow stability analysis. The higher modes are reflecting different physical phenomena as for example Tollmien-Schlichting waves, originating in the boundary layer and having the tendency to emerge as instabilities for the growing Reynolds number. The investigations are carried out for a circular cylinder, oblong ellipsis and airfoil. It is shown that the onset of the wake instability, the waves in the boundary layer, the shear layer instability are different solutions of the same eigenvalue problem, formulated using the non-parallel theory. The analysis offers large potential possibilities as the generalization of methods used till now for the stability analysis.

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication

PubMed Central

Stetz, Gabrielle; Verkhivker, Gennady M.

2017-01-01

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms. PMID:28095400

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

PubMed

Stetz, Gabrielle; Verkhivker, Gennady M

2017-01-01

Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of allostery, we introduced a community-hopping model of allosteric communication. Atomistic reconstruction of signaling pathways in the DnaK structures captured a direction-specific mechanism and molecular details of signal transmission that are fully consistent with the mutagenesis experiments. The results of our study reconciled structural and functional experiments from a network-centric perspective by showing that global properties of the residue interaction networks and coevolutionary signatures may be linked with specificity and diversity of allosteric regulation mechanisms.

Boundedness and global stability of the two-predator and one-prey models with nonlinear prey-taxis

NASA Astrophysics Data System (ADS)

Wang, Jianping; Wang, Mingxin

2018-06-01

This paper concerns the reaction-diffusion systems modeling the population dynamics of two predators and one prey with nonlinear prey-taxis. We first investigate the global existence and boundedness of the unique classical solution for the general model. Then, we study the global stabilities of nonnegative spatially homogeneous equilibria for an explicit system with type I functional responses and density-dependent death rates for the predators and logistic growth for the prey. Moreover, the convergence rates are also established.

Analysis of stock prices of mining business

NASA Astrophysics Data System (ADS)

Ahn, Sanghyun; Lim, G. C.; Kim, S. H.; Kim, Soo Yong; Yoon, Kwon Youb; Stanfield, Joseph Lee; Kim, Kyungsik

2011-06-01

Stock exchanges have a diversity of so-called business groups and much evidence has been presented by covariance matrix analysis (Laloux et al. (1999) [6], Plerou et al. (2002) [7], Plerou et al. (1999) [8], Mantegna (1999) [9], Utsugi et al. (2004) [21] and Lim et al. (2009) [26]). A market-wide effect plays a crucial role in shifting the correlation structure from random to non-random. In this work, we study the structural properties of stocks related to the mining industry, especially rare earth minerals, listed on two exchanges, namely the TSX (Toronto stock exchange) and the TSX-V (Toronto stock exchange-ventures). In general, raw-material businesses are sensitively affected by the global economy while each firm has its own cycle. We prove that the global crisis during 2006-2009 affected the mineral market considerably. These two aspects compete to control price fluctuations. We show that the internal cycle overwhelms the global economic environment in terms of random matrix theory and overlapping matrices. However, during the period of 2006-2009, the effect of the global economic environment emerges. This result is well explained by the recent global financial/economic crisis. For comparison, we analyze the time stability of business clusters of the KOSPI, that is, the electric/electronic business, using an overlapping matrix. A clear difference in behavior is confirmed. Consequently, rare earth minerals in the raw-material business should be classified not by standard business classifications but by the internal cycle of business.

Altered LINE-1 Methylation in Mothers of Children with Down Syndrome

PubMed Central

Babić Božović, Ivana; Stanković, Aleksandra; Živković, Maja; Vraneković, Jadranka; Kapović, Miljenko; Brajenović-Milić, Bojana

2015-01-01

Down syndrome (DS, also known as trisomy 21) most often results from chromosomal nondisjunction during oogenesis. Numerous studies sustain a causal link between global DNA hypomethylation and genetic instability. It has been suggested that DNA hypomethylation might affect the structure and dynamics of chromatin regions that are critical for chromosome stability and segregation, thus favouring chromosomal nondisjunction during meiosis. Maternal global DNA hypomethylation has not yet been analyzed as a potential risk factor for chromosome 21 nondisjunction. This study aimed to asses the risk for DS in association with maternal global DNA methylation and the impact of endogenous and exogenous factors that reportedly influence DNA methylation status. Global DNA methylation was analyzed in peripheral blood lymphocytes by quantifying LINE-1 methylation using the MethyLight method. Levels of global DNA methylation were significantly lower among mothers of children with maternally derived trisomy 21 than among control mothers (P = 0.000). The combination of MTHFR C677T genotype and diet significantly influenced global DNA methylation (R2 = 4.5%, P = 0.046). The lowest values of global DNA methylation were observed in mothers with MTHFR 677 CT+TT genotype and low dietary folate. Although our findings revealed an association between maternal global DNA hypomethylation and trisomy 21 of maternal origin, further progress and final conclusions regarding the role of global DNA methylation and the occurrence of trisomy 21 are facing major challenges. PMID:26017139

Stability-activity tradeoffs constrain the adaptive evolution of RubisCO.

PubMed

Studer, Romain A; Christin, Pascal-Antoine; Williams, Mark A; Orengo, Christine A

2014-02-11

A well-known case of evolutionary adaptation is that of ribulose-1,5-bisphosphate carboxylase (RubisCO), the enzyme responsible for fixation of CO2 during photosynthesis. Although the majority of plants use the ancestral C3 photosynthetic pathway, many flowering plants have evolved a derived pathway named C4 photosynthesis. The latter concentrates CO2, and C4 RubisCOs consequently have lower specificity for, and faster turnover of, CO2. The C4 forms result from convergent evolution in multiple clades, with substitutions at a small number of sites under positive selection. To understand the physical constraints on these evolutionary changes, we reconstructed in silico ancestral sequences and 3D structures of RubisCO from a large group of related C3 and C4 species. We were able to precisely track their past evolutionary trajectories, identify mutations on each branch of the phylogeny, and evaluate their stability effect. We show that RubisCO evolution has been constrained by stability-activity tradeoffs similar in character to those previously identified in laboratory-based experiments. The C4 properties require a subset of several ancestral destabilizing mutations, which from their location in the structure are inferred to mainly be involved in enhancing conformational flexibility of the open-closed transition in the catalytic cycle. These mutations are near, but not in, the active site or at intersubunit interfaces. The C3 to C4 transition is preceded by a sustained period in which stability of the enzyme is increased, creating the capacity to accept the functionally necessary destabilizing mutations, and is immediately followed by compensatory mutations that restore global stability.

RNA 3D Structural Motifs: Definition, Identification, Annotation, and Database Searching

NASA Astrophysics Data System (ADS)

Nasalean, Lorena; Stombaugh, Jesse; Zirbel, Craig L.; Leontis, Neocles B.

Structured RNA molecules resemble proteins in the hierarchical organization of their global structures, folding and broad range of functions. Structured RNAs are composed of recurrent modular motifs that play specific functional roles. Some motifs direct the folding of the RNA or stabilize the folded structure through tertiary interactions. Others bind ligands or proteins or catalyze chemical reactions. Therefore, it is desirable, starting from the RNA sequence, to be able to predict the locations of recurrent motifs in RNA molecules. Conversely, the potential occurrence of one or more known 3D RNA motifs may indicate that a genomic sequence codes for a structured RNA molecule. To identify known RNA structural motifs in new RNA sequences, precise structure-based definitions are needed that specify the core nucleotides of each motif and their conserved interactions. By comparing instances of each recurrent motif and applying base pair isosteriCity relations, one can identify neutral mutations that preserve its structure and function in the contexts in which it occurs.

Bifurcation Analysis of a Predator-Prey System with Ratio-Dependent Functional Response

NASA Astrophysics Data System (ADS)

Jiang, Xin; She, Zhikun; Feng, Zhaosheng; Zheng, Xiuliang

2017-12-01

In this paper, we are concerned with the structural stability of a density dependent predator-prey system with ratio-dependent functional response. Starting with the geometrical analysis of hyperbolic curves, we obtain that the system has one or two positive equilibria under various conditions. Inspired by the S-procedure and semi-definite programming, we use the sum of squares decomposition based method to ensure the global asymptotic stability of the positive equilibrium through the associated polynomial Lyapunov functions. By exploring the monotonic property of the trace of the Jacobian matrix with respect to r under the given different conditions, we analytically verify that there is a corresponding unique r∗ such that the trace is equal to zero and prove the existence of Hopf bifurcation, respectively.

Dynamics of Galaxies

NASA Astrophysics Data System (ADS)

Bertin, Giuseppe

2000-08-01

Part I. Basic Phenomenology: 1. Scales; 2. Observational windows; 3. Classifications; 4. Photometry, kinematics, dark matter; 5. Basic questions, semi-empirical approach, dynamical window; Part II. Physical Models: 6. Self-gravity and relation with plasma physics; 7. Relaxation times, absence of thermodynamical equilibrium; 8. Models; 9. Equilibrium and stability: symmetry and symmetry breaking; 10. Classical ellipsoids; 11. Introduction to dispersive waves; 12. Jeans instability; Part III. Spiral Galaxies: 13. Orbits; 14. The basic state: vertical and horizontal equilibrium in the disk; 15. Density waves; 16. Role of gas; 17. Global spiral modes; 18. Spiral structure in galaxies; 19. Bending waves; 20. Dark matter in spiral galaxies; Part IV. Elliptical Galaxies: 21. Orbits; 22. Stellar dynamical approach; 23. Stability; 24. Dark matter in elliptical galaxies; Part V. In Perspective: 25. Selected aspects of formation and evolution; Notes; Index.

Global exponential stability and lag synchronization for delayed memristive fuzzy Cohen-Grossberg BAM neural networks with impulses.

PubMed

Yang, Wengui; Yu, Wenwu; Cao, Jinde; Alsaadi, Fuad E; Hayat, Tasawar

2018-02-01

This paper investigates the stability and lag synchronization for memristor-based fuzzy Cohen-Grossberg bidirectional associative memory (BAM) neural networks with mixed delays (asynchronous time delays and continuously distributed delays) and impulses. By applying the inequality analysis technique, homeomorphism theory and some suitable Lyapunov-Krasovskii functionals, some new sufficient conditions for the uniqueness and global exponential stability of equilibrium point are established. Furthermore, we obtain several sufficient criteria concerning globally exponential lag synchronization for the proposed system based on the framework of Filippov solution, differential inclusion theory and control theory. In addition, some examples with numerical simulations are given to illustrate the feasibility and validity of obtained results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Evaluation of the Thermodynamic Consistency of Closure Approximations in Several Models Proposed for the Description of Liquid Crystalline Dynamics

NASA Astrophysics Data System (ADS)

Edwards, Brian J.

2002-05-01

Given the premise that a set of dynamical equations must possess a definite, underlying mathematical structure to ensure local and global thermodynamic stability, as has been well documented, several different models for describing liquid crystalline dynamics are examined with respect to said structure. These models, each derived during the past several years using a specific closure approximation for the fourth moment of the distribution function in Doi's rigid rod theory, are all shown to be inconsistent with this basic mathematical structure. The source of this inconsistency lies in Doi's expressions for the extra stress tensor and temporal evolution of the order parameter, which are rederived herein using a transformation that allows for internal compatibility with the underlying mathematical structure that is present on the distribution function level of description.

Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily

PubMed Central

Ohnishi, Satoshi; Tochio, Naoya; Tomizawa, Tadashi; Akasaka, Ryogo; Harada, Takushi; Seki, Eiko; Sato, Manami; Watanabe, Satoru; Fujikura, Yukiko; Koshiba, Seizo; Terada, Takaho; Shirouzu, Mikako; Tanaka, Akiko; Kigawa, Takanori; Yokoyama, Shigeyuki

2008-01-01

The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a β-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) (MAGI1 WW2) shares high sequence similarity with SAV1 WW2, suggesting comparable dimerization. However, an analytical ultracentrifugation study revealed that MAGI1 WW2 (Leu355–Pro390) chiefly exists as a monomer at low protein concentrations, with an association constant of 1.3 × 102 M−1. We determined its solution structure, and a structural comparison with the dimeric SAV1 WW2 suggested that an Asp residue is crucial for the inhibition of the dimerization. The substitution of this acidic residue with Ser resulted in the dimerization of MAGI1 WW2. The spin-relaxation data suggested that the MAGI1 WW2 undergoes a dynamic process of transient dimerization that is limited by the charge repulsion. Additionally, we characterized a longer construct of this WW domain with a C-terminal extension (Leu355–Glu401), as the formation of an extra α-helix was predicted. An NMR structural determination confirmed the formation of an α-helix in the extended C-terminal region, which appears to be independent from the dimerization regulation. A thermal denaturation study revealed that the dimerized MAGI1 WW2 with the Asp-to-Ser mutation gained apparent stability in a protein concentration-dependent manner. A structural comparison between the two constructs with different lengths suggested that the formation of the C-terminal α-helix stabilized the global fold by facilitating contacts between the N-terminal linker region and the main body of the WW domain. PMID:18562638

Structural basis for controlling the dimerization and stability of the WW domains of an atypical subfamily.

PubMed

Ohnishi, Satoshi; Tochio, Naoya; Tomizawa, Tadashi; Akasaka, Ryogo; Harada, Takushi; Seki, Eiko; Sato, Manami; Watanabe, Satoru; Fujikura, Yukiko; Koshiba, Seizo; Terada, Takaho; Shirouzu, Mikako; Tanaka, Akiko; Kigawa, Takanori; Yokoyama, Shigeyuki

2008-09-01

The second WW domain in mammalian Salvador protein (SAV1 WW2) is quite atypical, as it forms a beta-clam-like homodimer. The second WW domain in human MAGI1 (membrane associated guanylate kinase, WW and PDZ domain containing 1) (MAGI1 WW2) shares high sequence similarity with SAV1 WW2, suggesting comparable dimerization. However, an analytical ultracentrifugation study revealed that MAGI1 WW2 (Leu355-Pro390) chiefly exists as a monomer at low protein concentrations, with an association constant of 1.3 x 10(2) M(-1). We determined its solution structure, and a structural comparison with the dimeric SAV1 WW2 suggested that an Asp residue is crucial for the inhibition of the dimerization. The substitution of this acidic residue with Ser resulted in the dimerization of MAGI1 WW2. The spin-relaxation data suggested that the MAGI1 WW2 undergoes a dynamic process of transient dimerization that is limited by the charge repulsion. Additionally, we characterized a longer construct of this WW domain with a C-terminal extension (Leu355-Glu401), as the formation of an extra alpha-helix was predicted. An NMR structural determination confirmed the formation of an alpha-helix in the extended C-terminal region, which appears to be independent from the dimerization regulation. A thermal denaturation study revealed that the dimerized MAGI1 WW2 with the Asp-to-Ser mutation gained apparent stability in a protein concentration-dependent manner. A structural comparison between the two constructs with different lengths suggested that the formation of the C-terminal alpha-helix stabilized the global fold by facilitating contacts between the N-terminal linker region and the main body of the WW domain.

The oxidation of methionine-54 of epoetinum alfa does not affect molecular structure or stability, but does decrease biological activity.

PubMed

Labrenz, Steven R; Calmann, Melissa A; Heavner, George A; Tolman, Glen

2008-01-01

Erythropoietin therapy is used to treat severe anemia in renal failure and chemotherapy patients. One of these therapies based on recombinant human erythropoietin is marketed under the trade name of EPREX and utilizes epoetinum alfa as the active pharmaceutical ingredient. The effect of oxidation of methionine-54 on the structure and stability of the erythropoietin molecule has not been directly tested. We have observed partial and full chemical oxidation of methionine-54 to methionine-54 sulfoxide, accomplished using tert-Butylhydroperoxide and hydrogen peroxide, respectively. A blue shift in the fluorescence center of spectral mass wavelength was observed as a linear response to the level of methionine sulfoxide in the epoetinum alfa molecule, presumably arising from a local change in the environment near tryptophan-51, as supported by potassium iodide quenching studies. Circular dichroism studies demonstrated no change in the folded structure of the molecule with methionine oxidation. The thermal unfolding profiles of partial and completely oxidized epoetinum alfa overlap, with a T(m) of 49.5 degrees C across all levels of methionine sulfoxide content. When the protein was tested for activity, a decrease in biological activity was observed, correlating with methionine sulfoxide levels. An allosteric effect between Met54, Trp51, and residues involved in receptor binding is proposed. These results indicate that methionine oxidation has no effect on the folded structure and global thermodynamic stability of the recombinant human erythropoietin molecule. Oxidation can affect potency, but only at levels significantly in excess of those seen in EPREX.

The role of plastic β-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein

NASA Astrophysics Data System (ADS)

Lei, Hongxing; Duan, Yong

2004-12-01

In this study, the thermal stability of a designed α/β protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7-9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (α helix and β hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix.

The role of plastic beta-hairpin and weak hydrophobic core in the stability and unfolding of a full sequence design protein.

PubMed

Lei, Hongxing; Duan, Yong

2004-12-15

In this study, the thermal stability of a designed alpha/beta protein FSD (full sequence design) was studied by explicit solvent simulations at three moderate temperatures, 273 K, 300 K, and 330 K. The average properties of the ten trajectories at each temperature were analyzed. The thermal unfolding, as judged by backbone root-mean-square deviation and percentage of native contacts, was displayed with increased sampling outside of the native basin as the temperature was raised. The positional fluctuation of the hairpin residues was significantly higher than that of the helix residues at all three temperatures. The hairpin segment displayed certain plasticity even at 273 K. Apart from the terminal residues, the highest fluctuation was shown in the turn residues 7-9. Secondary structure analysis manifested the structural heterogeneity of the hairpin segment. It was also revealed by the simulation that the hydrophobic core was vulnerable to thermal denaturation. Consistent with the experiment, the I7Y mutation in the double mutant FSD-EY (FSD with mutations Q1E and I7Y) dramatically increased the protein stability in the simulation, suggesting that the plasticity of the hairpin can be partially compensated by a stronger hydrophobic core. As for the unfolding pathway, the breathing of the hydrophobic core and the separation of the two secondary structure elements (alpha helix and beta hairpin) was the initiation step of the unfolding. The loss of global contacts from the separation further destabilized the hairpin structure and also led to the unwinding of the helix. (c) 2004 American Institute of Physics

Low frequency azimuthal stability of the ionization region of the Hall thruster discharge. II. Global analysis

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

Escobar, D.; Ahedo, E., E-mail: eduardo.ahedo@uc3m.es

2015-10-15

The linear stability of the Hall thruster discharge is analysed against axial-azimuthal perturbations in the low frequency range using a time-dependent 2D code of the discharge. This azimuthal stability analysis is spatially global, as opposed to the more common local stability analyses, already afforded previously (D. Escobar and E. Ahedo, Phys. Plasmas 21(4), 043505 (2014)). The study covers both axial and axial-azimuthal oscillations, known as breathing mode and spoke, respectively. The influence on the spoke instability of different operation parameters such as discharge voltage, mass flow, and thruster size is assessed by means of different parametric variations and compared againstmore » experimental results. Additionally, simplified models are used to unveil and characterize the mechanisms driving the spoke. The results indicate that the spoke is linked to azimuthal oscillations of the ionization process and to the Bohm condition in the transition to the anode sheath. Finally, results obtained from local and global stability analyses are compared in order to explain the discrepancies between both methods.« less

Design of the RWM Feedback Control System for NSTX

NASA Astrophysics Data System (ADS)

Bialek, James; Sabbagh, Steven; Paoletti, Franco

2002-11-01

The National Spherical Torus Experiment ( NSTX ) has been designed to investigate the physics of global mode stabilization at low aspect ratio. Present experiments are now probing performance limits determined by machine configuration and passive stabilization. For example, the ideal no-wall normalized beta limit has already been exceeded by greater than 20stabilized by a nearby perfectly conducting wall are observed to grow at a rate determined by nearby resistive structure. Sustained performance improvements may be obtained by using active feedback to suppress such long wavelength pressure driven instabilities, known as resistive wall modes (RWM). We report on the performance of several design options for an NSTX - RWM feedback control system. The VALEN feedback analysis code has been used to evaluate the performance of these configurations. We explicitly model the vacuum vessel, center stack casing, the 48 copper passive plates, their mounts, active feedback coils and sensor arrays. The highest performance system has both control coils and sensors inside the vacuum vessel. In this case it is possible to reach 94beta limit.

The stability of aluminium oxide monolayer and its interface with two-dimensional materials

NASA Astrophysics Data System (ADS)

Song, Ting Ting; Yang, Ming; Chai, Jian Wei; Callsen, Martin; Zhou, Jun; Yang, Tong; Zhang, Zheng; Pan, Ji Sheng; Chi, Dong Zhi; Feng, Yuan Ping; Wang, Shi Jie

2016-07-01

The miniaturization of future electronic devices requires the knowledge of interfacial properties between two-dimensional channel materials and high-κ dielectrics in the limit of one atomic layer thickness. In this report, by combining particle-swarm optimization method with first-principles calculations, we present a detailed study of structural, electronic, mechanical, and dielectric properties of Al2O3 monolayer. We predict that planar Al2O3 monolayer is globally stable with a direct band gap of 5.99 eV and thermal stability up to 1100 K. The stability of this high-κ oxide monolayer can be enhanced by substrates such as graphene, for which the interfacial interaction is found to be weak. The band offsets between the Al2O3 monolayer and graphene are large enough for electronic applications. Our results not only predict a stable high-κ oxide monolayer, but also improve the understanding of interfacial properties between a high-κ dielectric monolayer and two-dimensional material.

Balancing the stability and the catalytic specificities of OP hydrolases with enhanced V-agent activities.

PubMed

Reeves, T E; Wales, M E; Grimsley, J K; Li, P; Cerasoli, D M; Wild, J R

2008-06-01

Rational site-directed mutagenesis and biophysical analyses have been used to explore the thermodynamic stability and catalytic capabilities of organophosphorus hydrolase (OPH) and its genetically modified variants. There are clear trade-offs in the stability of modifications that enhance catalytic activities. For example, the H254R/H257L variant has higher turnover numbers for the chemical warfare agents VX (144 versus 14 s(-1) for the native enzyme (wild type) and VR (Russian VX, 465 versus 12 s(-1) for wild type). These increases are accompanied by a loss in stability in which the total Gibb's free energy for unfolding is 19.6 kcal/mol, which is 5.7 kcal/mol less than that of the wild-type enzyme. X-ray crystallographic studies support biophysical data that suggest amino acid residues near the active site contribute to the chemical and thermal stability through hydrophobic and cation-pi interactions. The cation-pi interactions appear to contribute an additional 7 kcal/mol to the overall global stability of the enzyme. Using rational design, it has been possible to make amino acid changes in this region that restored the stability, yet maintained effective V-agent activities, with turnover numbers of 68 and 36 s(-1) for VX and VR, respectively. This study describes the first rationally designed, stability/activity balance for an OPH enzyme with a legitimate V-agent activity, and its crystal structure.

A Climatic Stability Approach to Prioritizing Global Conservation Investments

PubMed Central

Iwamura, Takuya; Wilson, Kerrie A.; Venter, Oscar; Possingham, Hugh P.

2010-01-01

Climate change is impacting species and ecosystems globally. Many existing templates to identify the most important areas to conserve terrestrial biodiversity at the global scale neglect the future impacts of climate change. Unstable climatic conditions are predicted to undermine conservation investments in the future. This paper presents an approach to developing a resource allocation algorithm for conservation investment that incorporates the ecological stability of ecoregions under climate change. We discover that allocating funds in this way changes the optimal schedule of global investments both spatially and temporally. This allocation reduces the biodiversity loss of terrestrial endemic species from protected areas due to climate change by 22% for the period of 2002–2052, when compared to allocations that do not consider climate change. To maximize the resilience of global biodiversity to climate change we recommend that funding be increased in ecoregions located in the tropics and/or mid-elevation habitats, where climatic conditions are predicted to remain relatively stable. Accounting for the ecological stability of ecoregions provides a realistic approach to incorporating climate change into global conservation planning, with potential to save more species from extinction in the long term. PMID:21152095

p53 R175H hydrophobic patch and H-bond reorganization observed by MD simulation.

PubMed

Thayer, Kelly M; Quinn, Taylor R

2016-03-01

Molecular dynamics simulations probe the origins of aberrant functionality of R175H p53, which normally prevent tumorigenesis. This hotspot mutation exhibits loss of its essential zinc cofactor, aggregation, and activation of gain of function promoters, characteristics contributing to the loss of normal p53 activity. This study provided molecular level insight into the reorganization of the hydrogen bonding network and the formation of a hydrophobic patch on the surface of the protein. The hydrogen bonding network globally redistributes at the expense of the stability of the β-sandwich structure, and surface residues reorganize to expose a 250 Å(2) hydrophobic patch of residues covering approximately 2% of the solvent accessible surface. These changes could both stabilize the protein in the conformation exposing the patch to solvent to mediate the reported aggregation, and cause a destabilization in the area associated with DNA binding residues to affect the specificity. The development of the patch prior to loss of zinc indicates that stabilizing the patch quickly may prevent zinc loss. Considerations for rational design of small molecule therapeutics in light of the structural insight has been discussed and it suggest the positive ring around the hydrophobic patch and conserved residues may constitute a druggable site. © 2015 Wiley Periodicals, Inc.

Titin domains progressively unfolded by force are homogenously distributed along the molecule.

PubMed

Bianco, Pasquale; Mártonfalvi, Zsolt; Naftz, Katalin; Kőszegi, Dorina; Kellermayer, Miklós

2015-07-21

Titin is a giant filamentous protein of the muscle sarcomere in which stretch induces the unfolding of its globular domains. However, the mechanisms of how domains are progressively selected for unfolding and which domains eventually unfold have for long been elusive. Based on force-clamp optical tweezers experiments we report here that, in a paradoxical violation of mechanically driven activation kinetics, neither the global domain unfolding rate, nor the folded-state lifetime distributions of full-length titin are sensitive to force. This paradox is reconciled by a gradient of mechanical stability so that domains are gradually selected for unfolding as the magnitude of the force field increases. Atomic force microscopic screening of extended titin molecules revealed that the unfolded domains are distributed homogenously along the entire length of titin, and this homogeneity is maintained with increasing overstretch. Although the unfolding of domains with progressively increasing mechanical stability makes titin a variable viscosity damper, the spatially randomized variation of domain stability ensures that the induced structural changes are not localized but are distributed along the molecule's length. Titin may thereby provide complex safety mechanims for protecting the sarcomere against structural disintegration under excessive mechanical conditions. Copyright © 2015 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Limits to Stability

ERIC Educational Resources Information Center

Cottey, Alan

2012-01-01

The author reflects briefly on what limited degree of global ecological stability and human cultural stability may be achieved, provided that humanity retains hope and does not give way to despair or hide in denial. These thoughts were triggered by a recent conference on International Stability and Systems Engineering. (Contains 5 notes.)

Host-guest complex of N-(2-chloroethyl), N-nitroso, N‧, N‧ -dicyclohexylsulfamid with β-cyclodextrin: Fluorescence, QTAIM analysis and structure-chemical reactivity

NASA Astrophysics Data System (ADS)

Bensouilah, Nadjia; Fisli, Hassina; Bensouilah, Hamza; Zaater, Sihem; Abdaoui, Mohamed; Boutemeur-Kheddis, Baya

2017-10-01

In this work, the inclusion complex of DCY/CENS: N-(2-chloroethyl), N-nitroso, N‧, N‧-dicyclohexylsulfamid and β-cyclodextrin (β-CD) is investigated using the fluorescence spectroscopy, PM3, ONIOM2 and DFT methods. The experimental part reveals that DCY/CENS forms a 1:1 stoichiometric ratio inclusion complex with β-CD. The constant of stability is evaluated using the Benesi-Hildebrand equation. The results of the theoretical optimization showed that the lipophilic fraction of molecule (cyclohexyl group) is inside of β-CD. Accordingly, the Nitroso-Chloroethyl moiety is situated outside the cavity of the macromolecule host. The favorable structure of the optimized complex indicates the existence of weak intermolecular hydrogen bonds and the most important van der Waals (vdW) interactions which are studied on the basis of Natural Bonding Orbital (NBO) analysis. The NBO is employed to compute the electronic donor-acceptor exchanges between drug and β-CD. Furthermore, a detailed topological charge density analysis based on the quantum theory of atoms in molecules (QTAIM), has been accomplished on the most favorable complex using B3LYP/6-31G(d) method. The presence of stabilizing intermolecular hydrogen bonds and van der Waals interactions in the most favorable complex is predicted. Also, the energies of these interactions are estimated with Espinosa's formula. The findings of this investigation reveal that the correlation between the structural parameters and the electronic density is good. Finally, and based on DFT calculations, the reactivity of the interesting molecule in free state was studied and compared with that in the complexed state using chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors.

Structures and electron affinities of the di-arsenic fluorides As2Fn/As2Fn- (n=1-8).

PubMed

Kasalová, Veronika; Schaefer, Henry F

2005-04-15

Developments in the preparation of new materials for microelectronics are focusing new attention on molecular systems incorporating several arsenic atoms. A systematic investigation of the As2Fn/As2Fn- systems was carried out using Density Functional Theory methods and a DZP++ quality basis set. Global and low-lying local geometric minima and relative energies are discussed and compared. The three types of neutral-anion separations reported in this work are: the adiabatic electron affinity (EAad), the vertical electron affinity (EAvert), and the vertical detachment energy (VDE). Harmonic vibrational frequencies pertaining to the global minimum for each compound are reported. From the first four studied species (As2Fn, n=1-4), all neutral molecules and their anions are shown to be stable with respect to As-As bond breaking. The neutral As2F molecule and its anion are predicted to have Cs symmetry. We find the trans F-As-As-F isomer of C2h symmetry and a pyramidalized vinylidene-like As-As-F2- isomer of Cs symmetry to be the global minima for the As2F2 and As2F2- species, respectively. The lowest lying minima of As2F3 and As2F3- are vinyl radical-like structures F-As-As-F2 of Cs symmetry. The neutral As2F4 global minimum is a trans-bent (like Si2H4) F2-As-As-F2 isomer of C2 symmetry, while its anion is predicted to have an unusual fluorine-bridged (C(1)) structure. The global minima of the neutral As2Fn species, n=5-8, are weakly bound complexes, held together by dipole-dipole interactions. All such structures have the AsFm-AsFn form, where (m,n) is (2,3) for As2F5, (3,3) for As2F6, (4,3) for As2F7), and (5,3) for As2F8. For As2F8 the beautiful pentavalent F4As-AsF4 structure (analogous to the stable AsF5 molecule) lies about 30 kcal/mol above the AsF3 . . . AsF5 complex. The stability of AsF(5) depends crucially on the strong As-F bonds, and replacing one of these with an As-As bond (in F4As-AsF4) has a very negative impact on the molecule's stability. The anions As2Fn-, n=5-8, are shown to be stable with respect to the As-As bond breaking, and we predict that all of them have fluorine-bridged or fluorine-linked structures. The zero-point vibrational energy corrected adiabatic electron affinities are predicted to be 2.28 eV (As2F), 1.95 eV (As2F2), 2.39 eV (As2F3), 1.71 eV (As2F4), 2.72 eV (As2F5), 1.79 eV (As2F6), 5.26 eV (As2F7), and 3.40 eV (As2F8) from the BHLYP method. Vertical detachment energies are rather large, especially for species with fluorine-bridged global minima, having values up to 6.45 eV (As2F7, BHLYP).

Non Lyapunov stability of the constant spatially developing 1-D gas flow in presence of solutions having strictly positive exponential growth rate

NASA Astrophysics Data System (ADS)

Balint, Stefan; Balint, Agneta M.

2017-01-01

Different types of stabilities (global, local) and instabilities (global absolute, local convective) of the constant spatially developing 1-D gas flow are analyzed in the phase space of continuously differentiable functions, endowed with the usual algebraic operations and the topology generated by the uniform convergence on the real axis. For this purpose the Euler equations linearized at the constant flow are used. The Lyapunov stability analysis was presented in [1] and this paper is a continuation of [1].

Regional Climate Impacts of Stabilizing Global Warming at 1.5 K Using Solar Geoengineering

NASA Astrophysics Data System (ADS)

Jones, Anthony C.; Hawcroft, Matthew K.; Haywood, James M.; Jones, Andy; Guo, Xiaoran; Moore, John C.

2018-02-01

The 2015 Paris Agreement aims to limit global warming to well below 2 K above preindustrial levels, and to pursue efforts to limit global warming to 1.5 K, in order to avert dangerous climate change. However, current greenhouse gas emissions targets are more compatible with scenarios exhibiting end-of-century global warming of 2.6-3.1 K, in clear contradiction to the 1.5 K target. In this study, we use a global climate model to investigate the climatic impacts of using solar geoengineering by stratospheric aerosol injection to stabilize global-mean temperature at 1.5 K for the duration of the 21st century against three scenarios spanning the range of plausible greenhouse gas mitigation pathways (RCP2.6, RCP4.5, and RCP8.5). In addition to stabilizing global mean temperature and offsetting both Arctic sea-ice loss and thermosteric sea-level rise, we find that solar geoengineering could effectively counteract enhancements to the frequency of extreme storms in the North Atlantic and heatwaves in Europe, but would be less effective at counteracting hydrological changes in the Amazon basin and North Atlantic storm track displacement. In summary, solar geoengineering may reduce global mean impacts but is an imperfect solution at the regional level, where the effects of climate change are experienced. Our results should galvanize research into the regionality of climate responses to solar geoengineering.

Stability of streamwise vortices

NASA Technical Reports Server (NTRS)

Khorrami, M. K.; Grosch, C. E.; Ash, R. L.

1987-01-01

A brief overview of some theoretical and computational studies of the stability of streamwise vortices is given. The local induction model and classical hydrodynamic vortex stability theories are discussed in some detail. The importance of the three-dimensionality of the mean velocity profile to the results of stability calculations is discussed briefly. The mean velocity profile is provided by employing the similarity solution of Donaldson and Sullivan. The global method of Bridges and Morris was chosen for the spatial stability calculations for the nonlinear eigenvalue problem. In order to test the numerical method, a second order accurate central difference scheme was used to obtain the coefficient matrices. It was shown that a second order finite difference method lacks the required accuracy for global eigenvalue calculations. Finally the problem was formulated using spectral methods and a truncated Chebyshev series.

Adaptive correlation filter-based video stabilization without accumulative global motion estimation

NASA Astrophysics Data System (ADS)

Koh, Eunjin; Lee, Chanyong; Jeong, Dong Gil

2014-12-01

We present a digital video stabilization approach that provides both robustness and efficiency for practical applications. In this approach, we adopt a stabilization model that maintains spatio-temporal information of past input frames efficiently and can track original stabilization position. Because of the stabilization model, the proposed method does not need accumulative global motion estimation and can recover the original position even if there is a failure in interframe motion estimation. It can also intelligently overcome the situation of damaged or interrupted video sequences. Moreover, because it is simple and suitable to parallel scheme, we implement it on a commercial field programmable gate array and a graphics processing unit board with compute unified device architecture in a breeze. Experimental results show that the proposed approach is both fast and robust.

A density functional global optimisation study of neutral 8-atom Cu-Ag and Cu-Au clusters

NASA Astrophysics Data System (ADS)

Heard, Christopher J.; Johnston, Roy L.

2013-02-01

The effect of doping on the energetics and dimensionality of eight atom coinage metal subnanometre particles is fully resolved using a genetic algorithm in tandem with on the fly density functional theory calculations to determine the global minima (GM) for Cu n Ag(8- n) and Cu n Au(8- n) clusters. Comparisons are made to previous ab initio work on mono- and bimetallic clusters, with excellent agreement found. Charge transfer and geometric arguments are considered to rationalise the stability of the particular permutational isomers found. An interesting transition between three dimensional and two dimensional GM structures is observed for copper-gold clusters, which is sharper and appears earlier in the doping series than is known for gold-silver particles.

Multiple model self-tuning control for a class of nonlinear systems

NASA Astrophysics Data System (ADS)

Huang, Miao; Wang, Xin; Wang, Zhenlei

2015-10-01

This study develops a novel nonlinear multiple model self-tuning control method for a class of nonlinear discrete-time systems. An increment system model and a modified robust adaptive law are proposed to expand the application range, thus eliminating the assumption that either the nonlinear term of the nonlinear system or its differential term is global-bounded. The nonlinear self-tuning control method can address the situation wherein the nonlinear system is not subject to a globally uniformly asymptotically stable zero dynamics by incorporating the pole-placement scheme. A novel, nonlinear control structure based on this scheme is presented to improve control precision. Stability and convergence can be confirmed when the proposed multiple model self-tuning control method is applied. Furthermore, simulation results demonstrate the effectiveness of the proposed method.

Thermodynamic Effects on Phase Stabilities and Structural Properties of TiO2 from the First-principles

NASA Astrophysics Data System (ADS)

Aoki, Yuta; Saito, Susumu

2013-03-01

Titanium dioxide (TiO2) is one of the most representative photocatalytic materials and much attention is focused on understanding and improvement of its photocatalytic activity. At the same time, TiO2 is known to be a highly polymorphic material and as many as eleven crystal phases have been identified so far. It is expected that TiO2 show various photocatalytic properties depending on crystal phases. However, relative stabilities of these identified phases are still controversial. In order to clarify the thermodynamic phase stabilities of TiO2, we obtain the free energies of its several representative phases, rutile, anatase, brookite, and TiO2-II within the framework of the density-functional theory using the pseudopotential method. We calculate both the static energy and the contribution of phonons to the free energy through the quasiharmonic approximation for each phase. It is found that treatment of semicore electrons in constructing the pseudopotential of the Ti atom significantly affects the relative phase stabilities. From the phase diagram obtained, we find that the anatase phase is the most stable at lower temperature and pressure. We also discuss the thermodynamic effects on structural properties such as thermal expansion. We acknowledge the financial supports from the Global Center-of-Excellence Program by MEXT, Japan through the Nanoscience and Quantum Physics Project of Tokyo Institute of Technology, and the Elements Science and Technology Project by MEXT.

Global stability of plane Couette flow beyond the energy stability limit

NASA Astrophysics Data System (ADS)

Fuentes, Federico; Goluskin, David

2017-11-01

This talk will present computations verifying that the laminar state of plane Couette flow is nonlinearly stable to all perturbations. The Reynolds numbers up to which this globally stability is verified are larger than those at which stability can be proven by the energy method, which is the typical method for demonstrating nonlinear stability of a fluid flow. This improvement is achieved by constructing Lyapunov functions that are more general than the energy. These functions are not restricted to being quadratic, and they are allowed to depend explicitly on the spectrum of the velocity field in the eigenbasis of the energy stability operator. The optimal choice of such a Lyapunov function is a convex optimization problem, and it can be constructed with computer assistance by solving a semidefinite program. This general method will be described in a companion talk by David Goluskin; the present talk focuses on its application to plane Couette flow.

Effects of alcohols on the stability and low-frequency local motions that control the slow changes in structural dynamics of ferrocytochrome c.

PubMed

Jain, Rishu; Sharma, Deepak; Kumar, Rajesh

2013-10-01

To determine the effects of alcohols on the low-frequency local motions that control slow changes in structural dynamics of native-like compact states of proteins, we have studied the effects of alcohols on structural fluctuation of M80-containing Ω-loop by measuring the rate of thermally driven CO dissociation from a natively folded carbonmonoxycytochrome c under varying concentrations of alcohols (methanol, ethanol, 1-propanol, 2-propanol, 3°-butanol, 2,2,2-trifluoroethanol). As alcohol is increased, the rate coefficient of CO dissociation (k(diss)) first decreases in subdenaturing region and then increases on going from subdenaturing to denaturing milieu. This decrease in k(diss) is more for 2,2,2-trifluroethanol and 1-propanol and least for methanol, indicating that the first phase of motional constraint is due to the hydrophobicity of alcohols and intramolecular protein cross-linking effect of alcohols, which results in conformational entropy loss of protein. The thermal denaturation midpoint for ferrocytochrome c decreases with increase in alcohol, indicating that alcohol decrease the global stability of protein. The stabilization free energy (ΔΔG) in alcohols' solution was calculated from the slope of the Wyman-Tanford plot and water activity. The m-values obtained from the slope of ΔΔG versus alcohols plot were found to be more negative for longer and linear chain alcohols, indicating destabilization of proteins by alcohols through disturbance of hydrophobic interactions and hydrogen bonding.

Boundedness and global robust stability analysis of delayed complex-valued neural networks with interval parameter uncertainties.

PubMed

Song, Qiankun; Yu, Qinqin; Zhao, Zhenjiang; Liu, Yurong; Alsaadi, Fuad E

2018-07-01

In this paper, the boundedness and robust stability for a class of delayed complex-valued neural networks with interval parameter uncertainties are investigated. By using Homomorphic mapping theorem, Lyapunov method and inequality techniques, sufficient condition to guarantee the boundedness of networks and the existence, uniqueness and global robust stability of equilibrium point is derived for the considered uncertain neural networks. The obtained robust stability criterion is expressed in complex-valued LMI, which can be calculated numerically using YALMIP with solver of SDPT3 in MATLAB. An example with simulations is supplied to show the applicability and advantages of the acquired result. Copyright © 2018 Elsevier Ltd. All rights reserved.

Global asymptotic stability to a generalized Cohen-Grossberg BAM neural networks of neutral type delays.

PubMed

Zhang, Zhengqiu; Liu, Wenbin; Zhou, Dongming

2012-01-01

In this paper, we first discuss the existence of a unique equilibrium point of a generalized Cohen-Grossberg BAM neural networks of neutral type delays by means of the Homeomorphism theory and inequality technique. Then, by applying the existence result of an equilibrium point and constructing a Lyapunov functional, we study the global asymptotic stability of the equilibrium solution to the above Cohen-Grossberg BAM neural networks of neutral type. In our results, the hypothesis for boundedness in the existing paper, which discussed Cohen-Grossberg neural networks of neutral type on the activation functions, are removed. Finally, we give an example to demonstrate the validity of our global asymptotic stability result for the above neural networks. Copyright © 2011 Elsevier Ltd. All rights reserved.

On the structure of climate variability near the tropopause and its relationship to equatorial planetary waves

NASA Astrophysics Data System (ADS)

Grise, Kevin M.

The tropopause is an important interface in the climate system, separating the unique dynamical, chemical, and radiative regimes of the troposphere and stratosphere. Previous studies have demonstrated that the long-term mean structure and variability of the tropopause results from a complex interaction of stratospheric and tropospheric processes. This project provides new insight into the processes involved in the global tropopause region through two perspectives: (1) a high vertical resolution climatology of static stability and (2) an observational analysis of equatorial planetary waves. High vertical resolution global positioning system radio occultation profiles are used to document fine-scale features of the global static stability field near the tropopause. Consistent with previous studies, a region of enhanced static stability, known as the tropopause inversion layer (TIL), exists in a narrow layer above the extratropical tropopause and is strongest over polar regions during summer. However, in the tropics, the TIL possesses a unique horizontally and vertically varying structure with maxima located at ˜17 and ˜19 km. The upper feature peaks during boreal winter and has its largest magnitude between 10º and 15º latitude in both hemispheres; the lower feature exhibits a weaker seasonal cycle and is centered at the Equator. The spatial structure of both features resembles the equatorial planetary wave response to the climatological distribution of deep convection. Equatorial planetary waves not only dominate the climatological-mean general circulation near the tropical tropopause but also play an important role in its intraseasonal and interannual variability. The structure of the equatorial planetary waves emerges as the leading pattern of variability of the zonally asymmetric tropical atmospheric circulation. Regressions on an index of the equatorial planetary waves reveal that they are associated with a distinct pattern of equatorially symmetric climate variability characterized by variations in: (1) the distribution of convection in the deep tropics; (2) the eddy momentum flux convergence and the zonal-mean zonal wind in the tropical upper troposphere; (3) the mean meridional circulation of the tropical and subtropical troposphere; (4) temperatures in the tropical upper troposphere, the tropical lower stratosphere, and the subtropical troposphere of both hemispheres; and (5) the amplitude of the upper tropospheric anticyclones that straddle the Equator over the western tropical Pacific Ocean. The pulsation of the equatorial planetary waves in time provides a framework for interpreting a broad range of climate phenomena. Variability in the equatorial planetary waves is associated with variability in the tropical TIL and is linked to both the El Nino-Southern Oscillation and the Madden-Julian Oscillation (MJO). Evidence is presented that suggests that the MJO can be viewed as the linear superposition of: (1) the pulsation of the equatorial planetary waves at a fixed location and (2) a propagating component. Variability in the equatorial planetary waves may also contribute to variability in troposphere/stratosphere exchange and the width of the tropical belt.

Stability and instability of a neuron network with excitatory and inhibitory small-world connections.

PubMed

Yu, Dongyuan; Xu, Xu; Zhou, Jing; Li, Eric

2017-05-01

This study considers a delayed neural network with excitatory and inhibitory shortcuts. The global stability of the trivial equilibrium is investigated based on Lyapunov's direct method and the delay-dependent criteria are obtained. It is shown that both the excitatory and inhibitory shortcuts decrease the stability interval, but a time delay can be employed as a global stabilizer. In addition, we analyze the bounds of the eigenvalues of the adjacent matrix using matrix perturbation theory and then obtain the generalized sufficient conditions for local stability. The possibility of small inhibitory shortcuts is helpful for maintaining stability. The mechanisms of instability, bifurcation modes, and chaos are also investigated. Compared with methods based on mean-field theory, the proposed method can guarantee the stability of the system in most cases with random events. The proposed method is effective for cases where excitatory and inhibitory shortcuts exist simultaneously in the network. Copyright © 2017 Elsevier Ltd. All rights reserved.

The progression of paraspinal muscle recruitment intensity in localized and global strength training exercises is not based on instability alone.

PubMed

Colado, Juan C; Pablos, Carlos; Chulvi-Medrano, Ivan; Garcia-Masso, Xavier; Flandez, Jorgez; Behm, David G

2011-11-01

To evaluate electromyographic activity of several paraspinal muscles during localized stabilizing exercises and multijoint or global stabilizing exercises. Cross-sectional counterbalanced repeated measures. Research laboratory. Volunteers (N=25) without low-back pain. Subjects performed (1) localized stabilizing exercises (callisthenic exercises with only body weight as resistance): static lumbar extension, stable (on floor) and unstable static unipedal forward flexion, stable dynamic unipedal forward flexion, and unstable supine bridge; and (2) global stabilizing exercises (70% of maximum voluntary isometric contraction [MVIC]): dead lift and lunge. Mean and maximum amplitude of the electromyographic RMS of the lumbar and thoracic multifidus spinae and erector spinae. Electromyographic signals were normalized to the MVIC achieved during a back-extension exercise. Normalizing to the MVIC, paraspinal muscles were significantly (P<.05) most active, with mean and peak amplitudes of 88.1% and 113.4% during the dynamic stable dead lift at 70% of MVIC, respectively. The supine bridge on the unstable surface obtained the significantly lowest values of 29.03% and 30.3%, respectively. The other exercises showed intermediate values that ranged from 35.4% to 61.6%. Findings from this study may be helpful to strength trainers and physical therapists in their choice of exercises for strengthening paraspinal muscles. Our results suggest that in asymptomatic young experienced subjects, the dead lift at 70% of MVIC provides higher levels of mean and peak electromyographic signals than localized stabilizing exercises and other types of global stabilizing exercises. Copyright © 2011 American Congress of Rehabilitation Medicine. Published by Elsevier Inc. All rights reserved.

Development of Modal Analysis for the Study of Global Modes in High Speed Boundary Layer Flows

NASA Astrophysics Data System (ADS)

Brock, Joseph Michael

Boundary layer transition for compressible flows remains a challenging and unsolved problem. In the context of high-speed compressible flow, transitional and turbulent boundary-layers produce significantly higher surface heating caused by an increase in skin-friction. The higher heating associated with transitional and turbulent boundary layers drives thermal protection systems (TPS) and mission trajectory bounds. Proper understanding of the mechanisms that drive transition is crucial to the successful design and operation of the next generation spacecraft. Currently, prediction of boundary-layer transition is based on experimental efforts and computational stability analysis. Computational analysis, anchored by experimental correlations, offers an avenue to assess/predict stability at a reduced cost. Classical methods of Linearized Stability Theory (LST) and Parabolized Stability Equations (PSE) have proven to be very useful for simple geometries/base flows. Under certain conditions the assumptions that are inherent to classical methods become invalid and the use of LST/PSE is inaccurate. In these situations, a global approach must be considered. A TriGlobal stability analysis code, Global Mode Analysis in US3D (GMAUS3D), has been developed and implemented into the unstructured solver US3D. A discussion of the methodology and implementation will be presented. Two flow configurations are presented in an effort to validate/verify the approach. First, stability analysis for a subsonic cylinder wake is performed and results compared to literature. Second, a supersonic blunt cone is considered to directly compare LST/PSE analysis and results generated by GMAUS3D.

Evaluating the stability of DSM-5 PTSD symptom network structure in a national sample of U.S. military veterans.

PubMed

von Stockert, Sophia H H; Fried, Eiko I; Armour, Cherie; Pietrzak, Robert H

2018-03-15

Previous studies have used network models to investigate how PTSD symptoms associate with each other. However, analyses examining the degree to which these networks are stable over time, which are critical to identifying symptoms that may contribute to the chronicity of this disorder, are scarce. In the current study, we evaluated the temporal stability of DSM-5 PTSD symptom networks over a three-year period in a nationally representative sample of trauma-exposed U.S. military veterans. Data were analyzed from 611 trauma-exposed U.S. military veterans who participated in the National Health and Resilience in Veterans Study (NHRVS). We estimated regularized partial correlation networks of DSM-5 PTSD symptoms at baseline (Time 1) and at three-year follow-up (Time 2), and examined their temporal stability. Evaluation of the network structure of PTSD symptoms at Time 1 and Time 2 using a formal network comparison indicated that the Time 1 network did not differ significantly from the Time 2 network with regard to network structure (p = 0.12) or global strength (sum of all absolute associations, i.e. connectivity; p = 0.25). Centrality estimates of both networks (r = 0.86) and adjacency matrices (r = 0.69) were highly correlated. In both networks, avoidance, intrusive, and negative cognition and mood symptoms were among the more central nodes. This study is limited by the use of a self-report instrument to assess PTSD symptoms and recruitment of a relatively homogeneous sample of predominantly older, Caucasian veterans. Results of this study demonstrate the three-year stability of DSM-5 PTSD symptom network structure in a nationally representative sample of trauma-exposed U.S. military veterans. They further suggest that trauma-related avoidance, intrusive, and dysphoric symptoms may contribute to the chronicity of PTSD symptoms in this population. Published by Elsevier B.V.

MHD stability analysis and global mode identification preparing for high beta operation in KSTAR

NASA Astrophysics Data System (ADS)

Park, Y. S.; Sabbagh, S. A.; Berkery, J. W.; Jiang, Y.; Ahn, J. H.; Han, H. S.; Bak, J. G.; Park, B. H.; Jeon, Y. M.; Kim, J.; Hahn, S. H.; Lee, J. H.; Ko, J. S.; in, Y. K.; Yoon, S. W.; Oh, Y. K.; Wang, Z.; Glasser, A. H.

2017-10-01

H-mode plasma operation in KSTAR has surpassed the computed n = 1 ideal no-wall stability limit in discharges exceeding several seconds in duration. The achieved high normalized beta plasmas are presently limited by resistive tearing instabilities rather than global kink/ballooning or RWMs. The ideal and resistive stability of these plasmas is examined by using different physics models. The observed m/ n = 2/1 tearing stability is computed by using the M3D-C1 code, and by the resistive DCON code. The global MHD stability modified by kinetic effects is examined using the MISK code. Results from the analysis explain the stabilization of the plasma above the ideal MHD no-wall limit. Equilibrium reconstructions used include the measured kinetic profiles and MSE data. In preparation for plasma operation at higher beta utilizing the planned second NBI system, three sets of 3D magnetic field sensors have been installed and will be used for RWM active feedback control. To accurately determine the dominant n-component produced by low frequency unstable RWMs, an algorithm has been developed that includes magnetic sensor compensation of the prompt applied field and the field from the induced current on the passive conductors. Supported by US DOE Contracts DE-FG02-99ER54524 and DE-SC0016614.

Evolutionary Strategies for Protein Folding

NASA Astrophysics Data System (ADS)

Murthy Gopal, Srinivasa; Wenzel, Wolfgang

2006-03-01

The free energy approach for predicting the protein tertiary structure describes the native state of a protein as the global minimum of an appropriate free-energy forcefield. The low-energy region of the free-energy landscape of a protein is extremely rugged. Efficient optimization methods must therefore speed up the search for the global optimum by avoiding high energy transition states, adapt large scale moves or accept unphysical intermediates. Here we investigate an evolutionary strategies(ES) for optimizing a protein conformation in our all-atom free-energy force field([1],[2]). A set of random conformations is evolved using an ES to get a diverse population containing low energy structure. The ES is shown to balance energy improvement and yet maintain diversity in structures. The ES is implemented as a master-client model for distributed computing. Starting from random structures and by using this optimization technique, we were able to fold a 20 amino-acid helical protein and 16 amino-acid beta hairpin[3]. We compare ES to basin hopping method. [1]T. Herges and W. Wenzel,Biophys.J. 87,3100(2004) [2] A. Verma and W. Wenzel Stabilization and folding of beta-sheet and alpha-helical proteins in an all-atom free energy model(submitted)(2005) [3] S. M. Gopal and W. Wenzel Evolutionary Strategies for Protein Folding (in preparation)

Detailed design of a lattice composite fuselage structure by a mixed optimization method

NASA Astrophysics Data System (ADS)

Liu, D.; Lohse-Busch, H.; Toropov, V.; Hühne, C.; Armani, U.

2016-10-01

In this article, a procedure for designing a lattice fuselage barrel is developed. It comprises three stages: first, topology optimization of an aircraft fuselage barrel is performed with respect to weight and structural performance to obtain the conceptual design. The interpretation of the optimal result is given to demonstrate the development of this new lattice airframe concept for the fuselage barrel. Subsequently, parametric optimization of the lattice aircraft fuselage barrel is carried out using genetic algorithms on metamodels generated with genetic programming from a 101-point optimal Latin hypercube design of experiments. The optimal design is achieved in terms of weight savings subject to stability, global stiffness and strain requirements, and then verified by the fine mesh finite element simulation of the lattice fuselage barrel. Finally, a practical design of the composite skin complying with the aircraft industry lay-up rules is presented. It is concluded that the mixed optimization method, combining topology optimization with the global metamodel-based approach, allows the problem to be solved with sufficient accuracy and provides the designers with a wealth of information on the structural behaviour of the novel anisogrid composite fuselage design.

Potential and flux field landscape theory. I. Global stability and dynamics of spatially dependent non-equilibrium systems.

PubMed

Wu, Wei; Wang, Jin

2013-09-28

We established a potential and flux field landscape theory to quantify the global stability and dynamics of general spatially dependent non-equilibrium deterministic and stochastic systems. We extended our potential and flux landscape theory for spatially independent non-equilibrium stochastic systems described by Fokker-Planck equations to spatially dependent stochastic systems governed by general functional Fokker-Planck equations as well as functional Kramers-Moyal equations derived from master equations. Our general theory is applied to reaction-diffusion systems. For equilibrium spatially dependent systems with detailed balance, the potential field landscape alone, defined in terms of the steady state probability distribution functional, determines the global stability and dynamics of the system. The global stability of the system is closely related to the topography of the potential field landscape in terms of the basins of attraction and barrier heights in the field configuration state space. The effective driving force of the system is generated by the functional gradient of the potential field alone. For non-equilibrium spatially dependent systems, the curl probability flux field is indispensable in breaking detailed balance and creating non-equilibrium condition for the system. A complete characterization of the non-equilibrium dynamics of the spatially dependent system requires both the potential field and the curl probability flux field. While the non-equilibrium potential field landscape attracts the system down along the functional gradient similar to an electron moving in an electric field, the non-equilibrium flux field drives the system in a curly way similar to an electron moving in a magnetic field. In the small fluctuation limit, the intrinsic potential field as the small fluctuation limit of the potential field for spatially dependent non-equilibrium systems, which is closely related to the steady state probability distribution functional, is found to be a Lyapunov functional of the deterministic spatially dependent system. Therefore, the intrinsic potential landscape can characterize the global stability of the deterministic system. The relative entropy functional of the stochastic spatially dependent non-equilibrium system is found to be the Lyapunov functional of the stochastic dynamics of the system. Therefore, the relative entropy functional quantifies the global stability of the stochastic system with finite fluctuations. Our theory offers an alternative general approach to other field-theoretic techniques, to study the global stability and dynamics of spatially dependent non-equilibrium field systems. It can be applied to many physical, chemical, and biological spatially dependent non-equilibrium systems.

Free energy profile of RNA hairpins: a molecular dynamics simulation study.

PubMed

Deng, Nan-Jie; Cieplak, Piotr

2010-02-17

RNA hairpin loops are one of the most abundant secondary structure elements and participate in RNA folding and protein-RNA recognition. To characterize the free energy surface of RNA hairpin folding at an atomic level, we calculated the potential of mean force (PMF) as a function of the end-to-end distance, by using umbrella sampling simulations in explicit solvent. Two RNA hairpins containing tetraloop cUUCGg and cUUUUg are studied with AMBER ff99 and CHARMM27 force fields. Experimentally, the UUCG hairpin is known to be significantly more stable than UUUU. In this study, the calculations using AMBER force field give a qualitatively correct description for the folding of two RNA hairpins, as the calculated PMF confirms the global stability of the folded structures and the resulting relative folding free energy is in quantitative agreement with the experimental result. The hairpin stabilities are also correctly differentiated by the more rapid molecular mechanics-Poisson Boltzmann-surface area approach, but the relative free energy estimated from this method is overestimated. The free energy profile shows that the native state basin and the unfolded state plateau are separated by a wide shoulder region, which samples a variety of native-like structures with frayed terminal basepair. The calculated PMF lacks major barriers that are expected near the transition regions, and this is attributed to the limitation of the 1-D reaction coordinate. The PMF results are compared with other studies of small RNA hairpins using kinetics method and coarse grained models. The two RNA hairpins described by CHARMM27 are significantly more deformable than those represented by AMBER. Compared with the AMBER results, the CHARMM27 calculated DeltaG(fold) for the UUUU tetraloop is in better agreement with the experimental results. However, the CHARMM27 calculation does not confirm the global stability of the experimental UUCG structure; instead, the extended conformations are predicted to be thermodynamically stable in solution. This finding is further supported by separate unrestrained CHARMM27 simulations, in which the UUCG hairpin unfolds spontaneously within 10 ns. The instability of the UUCG hairpin originates from the loop region, and propagates to the stem. The results of this study provide a molecular picture of RNA hairpin unfolding and reveal problems in the force field descriptions for the conformational energy of certain RNA hairpin. Copyright 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Slope stability and rockfall assessment of volcanic tuffs using RPAS with 2-D FEM slope modelling

NASA Astrophysics Data System (ADS)

Török, Ákos; Barsi, Árpád; Bögöly, Gyula; Lovas, Tamás; Somogyi, Árpád; Görög, Péter

2018-02-01

Steep, hardly accessible cliffs of rhyolite tuff in NE Hungary are prone to rockfalls, endangering visitors of a castle. Remote sensing techniques were employed to obtain data on terrain morphology and to provide slope geometry for assessing the stability of these rock walls. A RPAS (Remotely Piloted Aircraft System) was used to collect images which were processed by Pix4D mapper (structure from motion technology) to generate a point cloud and mesh. The georeferencing was made by Global Navigation Satellite System (GNSS) with the use of seven ground control points. The obtained digital surface model (DSM) was processed (vegetation removal) and the derived digital terrain model (DTM) allowed cross sections to be drawn and a joint system to be detected. Joint and discontinuity system was also verified by field measurements. On-site tests as well as laboratory tests provided additional engineering geological data for slope modelling. Stability of cliffs was assessed by 2-D FEM (finite element method). Global analyses of cross sections show that weak intercalating tuff layers may serve as potential slip surfaces. However, at present the greatest hazard is related to planar failure along ENE-WSW joints and to wedge failure. The paper demonstrates that RPAS is a rapid and useful tool for generating a reliable terrain model of hardly accessible cliff faces. It also emphasizes the efficiency of RPAS in rockfall hazard assessment in comparison with other remote sensing techniques such as terrestrial laser scanning (TLS).

Sharp conditions for global stability of Lotka-Volterra systems with distributed delays

NASA Astrophysics Data System (ADS)

Faria, Teresa

We give a criterion for the global attractivity of a positive equilibrium of n-dimensional non-autonomous Lotka-Volterra systems with distributed delays. For a class of autonomous Lotka-Volterra systems, we show that such a criterion is sharp, in the sense that it provides necessary and sufficient conditions for the global asymptotic stability independently of the choice of the delay functions. The global attractivity of positive equilibria is established by imposing a diagonal dominance of the instantaneous negative feedback terms, and relies on auxiliary results showing the boundedness of all positive solutions. The paper improves and generalizes known results in the literature, namely by considering systems with distributed delays rather than discrete delays.

Global Stability and Dynamics of Strongly Nonlinear Systems Using Koopman Operator Theory

DTIC Science & Technology

2017-03-01

calculus, applied mathematics, Director’s Research Initiative 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT UU 18... research of Svenkeson et al.4 Section 2 is Accomplishments and Section 3 is the Conclusion. 2. Accomplishments 2.1 Prescribed External Forcing To study ...ARL-TR-7959 MAR 2017 US Army Research Laboratory Global Stability and Dynamics of Strongly Nonlinear Systems Using Koopman

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.

Biocrusts in the context of global change

USGS Publications Warehouse

Reed, Sasha C.; Maestre, Fernando T.; Ochoa-Hueso, Raul; Kuske, Cheryl; Darrouzet-Nardi, Anthony N.; Darby, Brian; Sinsabaugh, Bob; Oliver, Mel; Sancho, Leo; Belnap, Jayne

2016-01-01

A wide range of studies show global environmental change will profoundly affect the structure, function, and dynamics of terrestrial ecosystems. The research synthesized here underscores that biocrust communities are also likely to respond significantly to global change drivers, with a large potential for modification to their abundance, composition, and function. We examine how elevated atmospheric CO2 concentrations, climate change (increased temperature and altered precipitation), and nitrogen deposition affect biocrusts and the ecosystems they inhabit. We integrate experimental and observational data, as well as physiological, community ecology, and biogeochemical perspectives. Taken together, these data highlight the potential for biocrust organisms to respond dramatically to environmental change and show how changes to biocrust community composition translate into effects on ecosystem function (e.g., carbon and nutrient cycling, soil stability, energy balance). Due to the importance of biocrusts in regulating dryland ecosystem processes and the potential for large modifications to biocrust communities, an improved understanding and predictive capacity regarding biocrust responses to environmental change are of scientific and societal relevance.

OAST Space Theme Workshop. Volume 2: Theme summary. 5: Global service (no. 11). A. Statement. B. 26 April 1976 presentation. C. Summary

NASA Technical Reports Server (NTRS)

1976-01-01

The benefits to be obtained from cost-effective global observation of the earth, its environment, and its natural and man-made features are examined using typical spacecraft and missions which could enhance the benefits of space operations. The technology needs and areas of interest include: (1) a ten-fold increase in the dimensions of deployable and erectable structures to provide booms, antennas, and platforms for global sensor systems; (2) control and stabilization systems capable of pointing accuracies of 1 arc second or less to locate targets of interest and maintain platform or sensor orientation during operations; (3) a factor of five improvements in spacecraft power capacity to support payloads and supporting electronics; (4) auxiliary propulsion systems capable of 5 to 10 years on orbit operation; (5) multipurpose sensors; and (6) end-to-end data management and an information system configured to accept new components or concepts as they develop.

Marshall N. Rosenbluth Outstanding Doctoral Thesis Award Talk: Control of Non-Axisymmetric Fields With Static and Dynamic Boundary Conditions

NASA Astrophysics Data System (ADS)

Paz-Soldan, C.

2013-10-01

Small deformations of the otherwise axisymmetric field, known as ``error fields'' (EFs), lead to large changes in global MHD stability. This talk will compare results from both 1) a line-tied screw-pinch with rotating conducting walls and 2) the DIII-D tokamak to illustrate that in both devices the EF has greatest effect where it overlaps with the spatial structure of its global kink mode. In both configurations the kink structure in the symmetry direction is well described by a single mode number (azimuthal m = 1 , toroidal n = 1 , respectively) and EF ordering is clear. In the asymmetric direction (axial and poloidal, respectively) the harmonics of the kink are coupled (by line-tying and toroidicity, respectively) and thus EF ordering is not straightforward. In the pinch, the kink is axially localized to the anode region and consequently the anode EF dominates the MHD stability. In DIII-D, the poloidal harmonics of the n = 1 EF whose pitch is smaller than the local field-line pitch are empirically shown to be dominant across a wide breadth of EF optimization experiments. In analogy with the pinch, these harmonics are also where overlap with the kink is greatest and thus where the largest plasma kink response is found. The robustness of the kink structure further enables vacuum-field cost-function minimization techniques to accurately predict optimal EF correction coil currents by strongly weighting the kink-like poloidal harmonics in the minimization. To test the limits of this paradigm recent experiments in DIII-D imposed field structures that lack kink-overlapping harmonics, yielding ~10X less sensitivity. The very different plasmas of the pinch and tokamak thus both demonstrate the dominance of the kink mode in determining optimal EF correction. Supported by US DOE under DE-AC05-06OR23100, DE-FG02-00ER54603, DE-FC02-04ER54698, and NSF 0903900.

Structure of hydrogen-rich transverse jets in a vitiated turbulent flow

DOE PAGES

Lyra, Sgouria; Wilde, Benjamin; Kolla, Hemanth; ...

2014-11-24

Our paper reports the results of a joint experimental and numerical study of the flow characteristics and flame structure of a hydrogen rich jet injected normal to a turbulent, vitiated crossflow of lean methane combustion products. Simultaneous high-speed stereoscopic PIV and OH PLIF measurements were obtained and analyzed alongside three-dimensional direct numerical simulations of inert and reacting JICF with detailed H2/COH2/CO chemistry. Both the experiment and the simulation reveal that, contrary to most previous studies of reacting JICF stabilized in low-to-moderate temperature air crossflow, the present conditions lead to a burner-attached flame that initiates uniformly around the burner edge. Significantmore » asymmetry is observed, however, between the reaction zones located on the windward and leeward sides of the jet, due to the substantially different scalar dissipation rates. The windward reaction zone is much thinner in the near field, while also exhibiting significantly higher local and global heat release than the much broader reaction zone found on the leeward side of the jet. The unsteady dynamics of the windward shear layer, which largely control the important jet/crossflow mixing processes in that region, are explored in order to elucidate the important flow stability implications arising in the inert and reacting JICF. The paper concludes with an analysis of the ignition, flame characteristics, and global structure of the burner-attached flame. FurthermoreChemical explosive mode analysis (CEMA) shows that the entire windward shear layer, and a large region on the leeward side of the jet, are highly explosive prior to ignition and are dominated by non-premixed flame structures after ignition. The predominantly mixing limited nature of the flow after ignition is examined by computing the Takeno flame index, which shows that ~70% of the heat release occurs in non-premixed regions.« less

ARO 1.2: Solid Mechanics: Augmented Finite Element Method for High-Fidelity Analysis of Structural Composites

DTIC Science & Technology

2017-10-03

Physics of Solids, 78 (314-332). 2014. 6. C . X. Zhang, J . Z. Song, Q. D. Yang, “Periodic buckling patterns of graphene/hexagonal boron nitride...Mechanics, 139 (78-97), 2015. 9. Y. C . Gu, J . Jung, Q. D. Yang, and W. Q. Chen, “A New Stabilizing Method for Numerical Analyses with Severe...Local and Global Instability”, ASME Journal of Applied Mechanics, 82 (101010-1, -12), 2015 10. J . Jung, B. C . Do, and Q. D. Yang, “A-FEM for Arbitrary

Application of Improved APO Algorithm in Vulnerability Assessment and Reconstruction of Microgrid

NASA Astrophysics Data System (ADS)

Xie, Jili; Ma, Hailing

2018-01-01

Artificial Physics Optimization (APO) has good global search ability and can avoid the premature convergence phenomenon in PSO algorithm, which has good stability of fast convergence and robustness. On the basis of APO of the vector model, a reactive power optimization algorithm based on improved APO algorithm is proposed for the static structure and dynamic operation characteristics of microgrid. The simulation test is carried out through the IEEE 30-bus system and the result shows that the algorithm has better efficiency and accuracy compared with other optimization algorithms.

Dynamics of a New 5D Hyperchaotic System of Lorenz Type

NASA Astrophysics Data System (ADS)

Zhang, Fuchen; Chen, Rui; Wang, Xingyuan; Chen, Xiusu; Mu, Chunlai; Liao, Xiaofeng

Ultimate boundedness of chaotic dynamical systems is one of the fundamental concepts in dynamical systems, which plays an important role in investigating the stability of the equilibrium, estimating the Lyapunov dimension of attractors and the Hausdorff dimension of attractors, the existence of periodic solutions, chaos control, chaos synchronization. However, it is often difficult to obtain the bounds of the hyperchaotic systems due to the complex algebraic structure of the hyperchaotic systems. This paper has investigated the boundedness of solutions of a nonlinear hyperchaotic system. We have obtained the global exponential attractive set and the ultimate bound set for this system. To obtain the ellipsoidal ultimate bound, the ultimate bound of the proposed system is theoretically estimated using Lagrange multiplier method, Lyapunov stability theory and optimization theory. To show the ultimate bound region, numerical simulations are provided.

First-principle study of structural, electronic and magnetic properties of (FeC)n (n = 1-8) and (FeC)8TM (TM = V, Cr, Mn and Co) clusters.

PubMed

Li, Cheng-Gang; Zhang, Jie; Zhang, Wu-Qin; Tang, Ya-Nan; Ren, Bao-Zeng; Hu, Yan-Fei

2017-12-13

The structural, electronic and magnetic properties of the (FeC) n (n = 1-8) clusters are studied using the unbiased CALYPSO structure search method and density functional theory. A combination of the PBE functional and 6-311 + G* basis set is used for determining global minima on potential energy surfaces of (FeC) n clusters. Relatively stabilities are analyzed via computing their binding energies, second order difference and HOMO-LUMO gaps. In addition, the origin of magnetic properties, spin density and density of states are discussed in detail, respectively. At last, based on the same computational method, the structures, magnetic properties and density of states are systemically investigated for the 3d (V, Cr, Mn and Co) atom doped (FeC) 8 cluster.

A Particle Swarm Optimization-Based Approach with Local Search for Predicting Protein Folding.

PubMed

Yang, Cheng-Hong; Lin, Yu-Shiun; Chuang, Li-Yeh; Chang, Hsueh-Wei

2017-10-01

The hydrophobic-polar (HP) model is commonly used for predicting protein folding structures and hydrophobic interactions. This study developed a particle swarm optimization (PSO)-based algorithm combined with local search algorithms; specifically, the high exploration PSO (HEPSO) algorithm (which can execute global search processes) was combined with three local search algorithms (hill-climbing algorithm, greedy algorithm, and Tabu table), yielding the proposed HE-L-PSO algorithm. By using 20 known protein structures, we evaluated the performance of the HE-L-PSO algorithm in predicting protein folding in the HP model. The proposed HE-L-PSO algorithm exhibited favorable performance in predicting both short and long amino acid sequences with high reproducibility and stability, compared with seven reported algorithms. The HE-L-PSO algorithm yielded optimal solutions for all predicted protein folding structures. All HE-L-PSO-predicted protein folding structures possessed a hydrophobic core that is similar to normal protein folding.

CD-loop Extension in Zika Virus Envelope Protein Key for Stability and Pathogenesis.

PubMed

Gallichotte, Emily N; Dinnon, Kenneth H; Lim, Xin-Ni; Ng, Thiam-Seng; Lim, Elisa X Y; Menachery, Vineet D; Lok, Shee-Mei; Baric, Ralph S

2017-12-05

With severe disease manifestations including microcephaly, congenital malformation, and Guillain-Barré syndrome, Zika virus (ZIKV) remains a persistent global public health threat. Despite antigenic similarities with dengue viruses, structural studies have suggested the extended CD-loop and hydrogen-bonding interaction network within the ZIKV envelope protein contribute to stability differences between the viral families. This enhanced stability may lead to the augmented infection, disease manifestation, and persistence in body fluids seen following ZIKV infection. To examine the role of these motifs in infection, we generated a series of ZIKV recombinant viruses that disrupted the hydrogen-bonding network (350A, 351A, and 350A/351A) or the CD-loop extension (Δ346). Our results demonstrate a key role for the ZIKV extended CD-loop in cell-type-dependent replication, virion stability, and in vivo pathogenesis. Importantly, the Δ346 mutant maintains similar antigenicity to wild-type virus, opening the possibility for its use as a live-attenuated vaccine platform for ZIKV and other clinically relevant flaviviruses. © The Author(s) 2017. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.

Mechanical Failure in Colloidal Gels

NASA Astrophysics Data System (ADS)

Kodger, Thomas Edward

When colloidal particles in a dispersion are made attractive, they aggregate into fractal clusters which grow to form a space-spanning network, or gel, even at low volume fractions. These gels are crucial to the rheological behavior of many personal care, food products and dispersion-based paints. The mechanical stability of these products relies on the stability of the colloidal gel network which acts as a scaffold to provide these products with desired mechanical properties and to prevent gravitational sedimentation of the dispersed components. Understanding the mechanical stability of such colloidal gels is thus of crucial importance to predict and control the properties of many soft solids. Once a colloidal gel forms, the heterogeneous structure bonded through weak physical interactions, is immediately subject to body forces, such as gravity, surface forces, such as adhesion to a container walls and shear forces; the interplay of these forces acting on the gel determines its stability. Even in the absence of external stresses, colloidal gels undergo internal rearrangements within the network that may cause the network structure to evolve gradually, in processes known as aging or coarsening or fail catastrophically, in a mechanical instability known as syneresis. Studying gel stability in the laboratory requires model colloidal system which may be tuned to eliminate these body or endogenous forces systematically. Using existing chemistry, I developed several systems to study delayed yielding by eliminating gravitational stresses through density matching and cyclic heating to induce attraction; and to study syneresis by eliminating adhesion to the container walls, altering the contact forces between colloids, and again, inducing gelation through heating. These results elucidate the varied yet concomitant mechanisms by which colloidal gels may locally or globally yield, but then reform due to the nature of the physical, or non-covalent, interactions which form them.

Global Maps of ProQ Binding In Vivo Reveal Target Recognition via RNA Structure and Stability Control at mRNA 3' Ends.

PubMed

Holmqvist, Erik; Li, Lei; Bischler, Thorsten; Barquist, Lars; Vogel, Jörg

2018-05-15

The conserved RNA-binding protein ProQ has emerged as the centerpiece of a previously unknown third large network of post-transcriptional control in enterobacteria. Here, we have used in vivo UV crosslinking and RNA sequencing (CLIP-seq) to map hundreds of ProQ binding sites in Salmonella enterica and Escherichia coli. Our analysis of these binding sites, many of which are conserved, suggests that ProQ recognizes its cellular targets through RNA structural motifs found in small RNAs (sRNAs) and at the 3' end of mRNAs. Using the cspE mRNA as a model for 3' end targeting, we reveal a function for ProQ in protecting mRNA against exoribonucleolytic activity. Taken together, our results underpin the notion that ProQ governs a post-transcriptional network distinct from those of the well-characterized sRNA-binding proteins, CsrA and Hfq, and suggest a previously unrecognized, sRNA-independent role of ProQ in stabilizing mRNAs. Copyright © 2018 Elsevier Inc. All rights reserved.

Predictive modeling of pedestal structure in KSTAR using EPED model

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

Han, Hyunsun; Kim, J. Y.; Kwon, Ohjin

2013-10-15

A predictive calculation is given for the structure of edge pedestal in the H-mode plasma of the KSTAR (Korea Superconducting Tokamak Advanced Research) device using the EPED model. Particularly, the dependence of pedestal width and height on various plasma parameters is studied in detail. The two codes, ELITE and HELENA, are utilized for the stability analysis of the peeling-ballooning and kinetic ballooning modes, respectively. Summarizing the main results, the pedestal slope and height have a strong dependence on plasma current, rapidly increasing with it, while the pedestal width is almost independent of it. The plasma density or collisionality gives initiallymore » a mild stabilization, increasing the pedestal slope and height, but above some threshold value its effect turns to a destabilization, reducing the pedestal width and height. Among several plasma shape parameters, the triangularity gives the most dominant effect, rapidly increasing the pedestal width and height, while the effect of elongation and squareness appears to be relatively weak. Implication of these edge results, particularly in relation to the global plasma performance, is discussed.« less

Is it efficient to co-compost and co-vermicompost green waste with biochar and/or clay to reduce CO2 emissions? A short-term laboratory experiment on (vermi)composts with additives.

NASA Astrophysics Data System (ADS)

Barthod, Justine; Rumpel, Cornélia; Paradelo, Remigio; Dignac, Marie-France

2016-04-01

Intensive farming practices can lead to a depletion of soil organic matter, negatively impacting important soil properties such as structural stability, fertility and C storage. The addition of organic amendments such as compost and vermicompost, rich in carbon, helps maintaining soil organic matter levels or restoring degraded soils. Composting and vermicomposting are based on stabilization of organic matter through the mineralization of easily decomposable organic matter compounds, therefore releasing greenhouse gases, including CO2. The aim of this study was to evaluate the global potential reduction of such emissions by the use of additives (2:1 clay and/or biochar): during (vermi)composting processes and after use of the final products as soil amendments. We hypothesized that the interactions between the additives and organic matter may lead to carbon stabilization and that such interactions may be enhanced by the presence of worms (Eisenia). We added in different proportions clay (25% or 50%), biochar (10%) and a mixture of biochar (10%) with clay (25%) to pre-composted green waste. The CO2 emissions of the composting and vermicomposting processes were measured during 21 days. After that, the amendments were added to a loamy cambisol soil and the CO2 emissions were monitored during 30 days of a laboratory experiment. The most efficient treatments in terms of reducing global CO2 emissions were the co-vermicomposting process with 25% clay followed by co-composting with 50% clay and with 10% biochar plus 25% clay. In this treatment (vermicompost with 25% clay), the carbon emissions were decreased by up to 44% compared to regular compost. Addition of biochar reduced CO2 emissions only during composting. Co-composting with biochar could be a promising avenue to limit global CO2 emissions whereas in presence of worms clay additions are better suited. These findings suggest that the presence of worms increased the formation of organo-mineral associations and thus C protection up to a certain clay/organic matter ratio. This strategy could be used to enhance the stability of organic amendments and increase soil carbon sequestration.

Crystal Structures of the Reduced, Sulfenic Acid, and Mixed Disulfide Forms of SarZ, a Redox Active Global Regulator in Staphylococcus aureus

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

Poor, Catherine B.; Chen, Peng R.; Duguid, Erica

2010-01-20

SarZ is a global transcriptional regulator that uses a single cysteine residue, Cys{sup 13}, to sense peroxide stress and control metabolic switching and virulence in Staphylococcus aureus. SarZ belongs to the single-cysteine class of OhrR-MgrA proteins that play key roles in oxidative resistance and virulence regulation in various bacteria. We present the crystal structures of the reduced form, sulfenic acid form, and mixed disulfide form of SarZ. Both the sulfenic acid and mixed disulfide forms are structurally characterized for the first time for this class of proteins. The Cys{sup 13} sulfenic acid modification is stabilized through two hydrogen bonds withmore » surrounding residues, and the overall DNA-binding conformation is retained. A further reaction of the Cys{sup 13} sulfenic acid with an external thiol leads to formation of a mixed disulfide bond, which results in an allosteric change in the DNA-binding domains, disrupting DNA binding. Thus, the crystal structures of SarZ in three different states provide molecular level pictures delineating the mechanism by which this class of redox active regulators undergoes activation. These structures help to understand redox-mediated virulence regulation in S. aureus and activation of the MarR family proteins in general.« less

Eutrophication weakens stabilizing effects of diversity in natural grasslands.

PubMed

Hautier, Yann; Seabloom, Eric W; Borer, Elizabeth T; Adler, Peter B; Harpole, W Stanley; Hillebrand, Helmut; Lind, Eric M; MacDougall, Andrew S; Stevens, Carly J; Bakker, Jonathan D; Buckley, Yvonne M; Chu, Chengjin; Collins, Scott L; Daleo, Pedro; Damschen, Ellen I; Davies, Kendi F; Fay, Philip A; Firn, Jennifer; Gruner, Daniel S; Jin, Virginia L; Klein, Julia A; Knops, Johannes M H; La Pierre, Kimberly J; Li, Wei; McCulley, Rebecca L; Melbourne, Brett A; Moore, Joslin L; O'Halloran, Lydia R; Prober, Suzanne M; Risch, Anita C; Sankaran, Mahesh; Schuetz, Martin; Hector, Andy

2014-04-24

Studies of experimental grassland communities have demonstrated that plant diversity can stabilize productivity through species asynchrony, in which decreases in the biomass of some species are compensated for by increases in others. However, it remains unknown whether these findings are relevant to natural ecosystems, especially those for which species diversity is threatened by anthropogenic global change. Here we analyse diversity-stability relationships from 41 grasslands on five continents and examine how these relationships are affected by chronic fertilization, one of the strongest drivers of species loss globally. Unmanipulated communities with more species had greater species asynchrony, resulting in more stable biomass production, generalizing a result from biodiversity experiments to real-world grasslands. However, fertilization weakened the positive effect of diversity on stability. Contrary to expectations, this was not due to species loss after eutrophication but rather to an increase in the temporal variation of productivity in combination with a decrease in species asynchrony in diverse communities. Our results demonstrate separate and synergistic effects of diversity and eutrophication on stability, emphasizing the need to understand how drivers of global change interactively affect the reliable provisioning of ecosystem services in real-world systems.

Global exponential stability analysis on impulsive BAM neural networks with distributed delays

NASA Astrophysics Data System (ADS)

Li, Yao-Tang; Yang, Chang-Bo

2006-12-01

Using M-matrix and topological degree tool, sufficient conditions are obtained for the existence, uniqueness and global exponential stability of the equilibrium point of bidirectional associative memory (BAM) neural networks with distributed delays and subjected to impulsive state displacements at fixed instants of time by constructing a suitable Lyapunov functional. The results remove the usual assumptions that the boundedness, monotonicity, and differentiability of the activation functions. It is shown that in some cases, the stability criteria can be easily checked. Finally, an illustrative example is given to show the effectiveness of the presented criteria.

Global asymptotic stability analysis of bidirectional associative memory neural networks with time delays.

PubMed

Arik, Sabri

2005-05-01

This paper presents a sufficient condition for the existence, uniqueness and global asymptotic stability of the equilibrium point for bidirectional associative memory (BAM) neural networks with distributed time delays. The results impose constraint conditions on the network parameters of neural system independently of the delay parameter, and they are applicable to all continuous nonmonotonic neuron activation functions. It is shown that in some special cases of the results, the stability criteria can be easily checked. Some examples are also given to compare the results with the previous results derived in the literature.

A Lie algebraic condition for exponential stability of discrete hybrid systems and application to hybrid synchronization.

PubMed

Zhao, Shouwei

2011-06-01

A Lie algebraic condition for global exponential stability of linear discrete switched impulsive systems is presented in this paper. By considering a Lie algebra generated by all subsystem matrices and impulsive matrices, when not all of these matrices are Schur stable, we derive new criteria for global exponential stability of linear discrete switched impulsive systems. Moreover, simple sufficient conditions in terms of Lie algebra are established for the synchronization of nonlinear discrete systems using a hybrid switching and impulsive control. As an application, discrete chaotic system's synchronization is investigated by the proposed method.

Effect of antibodies on pathogen dynamics with delays and two routes of infection

NASA Astrophysics Data System (ADS)

Elaiw, A. M.; Almatrafi, A. A.; Hobiny, A. D.

2018-06-01

We study the global stability of pathogen dynamics models with saturated pathogen-susceptible and infected-susceptible incidence. The models incorporate antibody immune response and three types of discrete or distributed time delays. We first show that the solutions of the model are nonnegative and ultimately bounded. We determine two threshold parameters, the basic reproduction number and antibody response activation number. We establish the existence and stability of the steady states. We study the global stability analysis of models using Lyapunov method. The numerical simulations have shown that antibodies can reduce the pathogen progression.

The Three-Dimensional (3D) Numerical Stability Analysis of Hyttemalmen Open-Pit

NASA Astrophysics Data System (ADS)

Cała, Marek; Kowalski, Michał; Stopkowicz, Agnieszka

2014-10-01

The purpose of this paper was to perform the 3D numerical calculations allowing slope stability analysis of Hyttemalmen open pit (location Kirkenes, Finnmark Province, Norway). After a ramp rock slide, which took place in December 2010, as well as some other small-scale rock slope stability problems, it proved necessary to perform a serious stability analyses. The Hyttemalmen open pit was designed with a depth up to 100 m, a bench height of 24 m and a ramp width of 10 m. The rock formation in the iron mining district of Kirkenes is called the Bjornevaten Group. This is the most structurally complicated area connected with tectonic process such as folding, faults and metamorphosis. The Bjornevaten Group is a volcano-sedimentary sequence. Rock slope stability depends on the mechanical properties of the rock, hydro-geological conditions, slope topography, joint set systems and seismic activity. However, rock slope stability is mainly connected with joint sets. Joints, or general discontinuities, are regarded as weak planes within rock which have strength reducing consequences with regard to rock strength. Discontinuities within the rock mass lead to very low tensile strength. Several simulations were performed utilising the RocLab (2007) software to estimate the gneiss cohesion for slopes of different height. The RocLab code is dedicated to estimate rock mass strength using the Hoek-Brown failure criterion. Utilising both the GSI index and the Hoek-Brown strength criterion the equivalent Mohr-Coulomb parameters (cohesion and angle of internal friction) can be calculated. The results of 3D numerical calculations (with FLA3D code) show that it is necessary to redesign the slope-bench system in the Hyttemalmen open pit. Changing slope inclination for lower stages is recommended. The minimum factor of safety should be equal 1.3. At the final planned stage of excavation, the factor of safety drops to 1.06 with failure surface ranging through all of the slopes. In the case of a slope angle 70° for lower stages, FS = 1.26, which is not enough to provide slope stability. Another series of calculations were therefore performed taking water table lowering into consideration, which increases the global safety factor. It was finally evaluated, that for a water table level of 72 m the factor of safety equals 1.3, which is enough to assure global open-pit stability.

Finite-difference solution of the compressible stability eigenvalue problem

NASA Technical Reports Server (NTRS)

Malik, M. R.

1982-01-01

A compressible stability analysis computer code is developed. The code uses a matrix finite difference method for local eigenvalue solution when a good guess for the eigenvalue is available and is significantly more computationally efficient than the commonly used initial value approach. The local eigenvalue search procedure also results in eigenfunctions and, at little extra work, group velocities. A globally convergent eigenvalue procedure is also developed which may be used when no guess for the eigenvalue is available. The global problem is formulated in such a way that no unstable spurious modes appear so that the method is suitable for use in a black box stability code. Sample stability calculations are presented for the boundary layer profiles of a Laminar Flow Control (LFC) swept wing.

A new delay-independent condition for global robust stability of neural networks with time delays.

PubMed

Samli, Ruya

2015-06-01

This paper studies the problem of robust stability of dynamical neural networks with discrete time delays under the assumptions that the network parameters of the neural system are uncertain and norm-bounded, and the activation functions are slope-bounded. By employing the results of Lyapunov stability theory and matrix theory, new sufficient conditions for the existence, uniqueness and global asymptotic stability of the equilibrium point for delayed neural networks are presented. The results reported in this paper can be easily tested by checking some special properties of symmetric matrices associated with the parameter uncertainties of neural networks. We also present a numerical example to show the effectiveness of the proposed theoretical results. Copyright © 2015 Elsevier Ltd. All rights reserved.

Revealing the hidden structural phases of FeRh

NASA Astrophysics Data System (ADS)

Kim, Jinwoong; Ramesh, R.; Kioussis, Nicholas

2016-11-01

Ab initio electronic structure calculations reveal that tetragonal distortion has a dramatic effect on the relative stability of the various magnetic structures (C-, A-, G-, A'-AFM, and FM) of FeRh giving rise to a wide range of novel stable/metastable structures and magnetic phase transitions between these states. We predict that the cubic G-AFM structure, which was believed thus far to be the ground state, is metastable and that the tetragonally expanded G-AFM is the stable structure. The low energy barrier separating these states suggests phase coexistence at room temperature. We propose an A'-AFM phase to be the global ground state among all magnetic phases which arises from the strain-induced tuning of the exchange interactions. The results elucidate the underlying mechanism for the recent experimental findings of electric-field control of magnetic phase transition driven via tetragonal strain. The magnetic phase transitions open interesting prospects for exploiting strain engineering for the next-generation memory devices.

Tropospheric Delay from VLBI and GNSS Measurements

NASA Astrophysics Data System (ADS)

Gubanov, V. S.

2018-02-01

Using an updated version of the QUASAR software package developed at the Institute of Applied Astronomy of the Russian Academy of Sciences, we have processed the VLBI observations within the international CONT14 program (May 6-20, 2014), in which a global network of 17 stations was involved (a total of 250 000 observations). The package update concerned the optimization of data structure and the refinement of stochastic models for the random variations in wet tropospheric delay and atomic clock difference. The main goal of this paper is to compare the VLBI determinations of the tropospheric delay with its independent determinations using global navigation satellite systems (GNSS). We show that both these determinations agree well between themselves only in the case of a global analysis of the VLBI observations, where the VLBI station coordinates are also refined, along with the tropospheric delay and the clock synchronization and Earth orientation parameters. If, alternatively, the station coordinates are insufficiently accurate and are not refined from VLBI observations, then it is appropriate not to determine the tropospheric delay from these observations, but to take it from the publicly accessible independent GNSS data. However, this requires that the VLBI and GNSS techniques operate simultaneously at a common observing site. We have established the shortcomings of the universally accepted method of stabilizing the global solution associated with the absence of a criterion for choosing reference stations and radio sources. Two ways of their elimination are proposed: (i) introducing a coordinated list of weight factors for the errors in the coordinates of such stations and sources into the stabilization algorithm and (ii) adopting a coordinated list of stations and sources the refinement of whose coordinates is not required at all for a certain time.

Assistant Secretary of Defense for Homeland Defense and Global Security

Science.gov Websites

Defense for Policy ASD for Asian and Pacific Security Affairs ASD for Homeland Defense Global Security Special Operations/Low-Intensity Conflict Counternarcotics and Global Threats Stability and Humanitarian HomeOUSDP OfficesASD for Homeland Defense Global Security Assistant Secretary of Defense for Homeland

Adaptive tracking control for a class of stochastic switched systems

NASA Astrophysics Data System (ADS)

Zhang, Hui; Xia, Yuanqing

2018-02-01

The problem of adaptive tracking is considered for a class of stochastic switched systems, in this paper. As preliminaries, the criterion of global asymptotical practical stability in probability is first presented by the aid of common Lyapunov function method. Based on the Lyapunov stability criterion, adaptive backstepping controllers are designed to guarantee that the closed-loop system has a unique global solution, which is globally asymptotically practically stable in probability, and the tracking error in the fourth moment converges to an arbitrarily small neighbourhood of zero. Simulation examples are given to demonstrate the efficiency of the proposed schemes.

A Comprehensive Strategy to Evaluate Compatible Stability of Chinese Medicine Injection and Infusion Solutions Based on Chemical Analysis and Bioactivity Assay.

PubMed

Li, Jian-Ping; Liu, Yang; Guo, Jian-Ming; Shang, Er-Xin; Zhu, Zhen-Hua; Zhu, Kevin Y; Tang, Yu-Ping; Zhao, Bu-Chang; Tang, Zhi-Shu; Duan, Jin-Ao

2017-01-01

Stability of traditional Chinese medicine injection (TCMI) is an important issue related with its clinical application. TCMI is composed of multi-components, therefore, when evaluating TCMI stability, several marker compounds cannot represent global components or biological activities of TCMI. Till now, when evaluating TCMI stability, method involving the global components or biological activities has not been reported. In this paper, we established a comprehensive strategy composed of three different methods to evaluate the chemical and biological stability of a typical TCMI, Danhong injection (DHI). UHPLC-TQ/MS was used to analyze the stability of marker compounds (SaA, SaB, RA, DSS, PA, CA, and SG) in DHI, UHPLC-QTOF/MS was used to analyze the stability of global components (MW 80-1000 Da) in DHI, and cell based antioxidant capability assay was used to evaluate the bioactivity of DHI. We applied this strategy to assess the compatible stability of DHI and six infusion solutions (GS, NS, GNS, FI, XI, and DGI), which were commonly used in combination with DHI in clinic. GS was the best infusion solution for DHI, and DGI was the worst one based on marker compounds analysis. Based on global components analysis, XI and DGI were the worst infusion solutions for DHI. And based on bioactivity assay, GS was the best infusion solution for DHI, and XI was the worst one. In conclusion, as evaluated by the established comprehensive strategy, GS was the best infusion solution, however, XI and DGI were the worst infusion solutions for DHI. In the compatibility of DHI and XI or DGI, salvianolic acids in DHI would be degraded, resulting in the reduction of original composition and generation of new components, and leading to the changes of biological activities. This is the essence of instability compatibility of DHI and some infusion solutions. Our study provided references for choosing the reasonable infusion solutions for DHI, which could contribute the improvement of safety and efficacy of DHI. Moreover, the established strategy may be applied for the compatible stability evaluation of other TCMIs.

Global growth and stability of agricultural yield decrease with pollinator dependence

PubMed Central

Garibaldi, Lucas A.; Aizen, Marcelo A.; Klein, Alexandra M.; Cunningham, Saul A.; Harder, Lawrence D.

2011-01-01

Human welfare depends on the amount and stability of agricultural production, as determined by crop yield and cultivated area. Yield increases asymptotically with the resources provided by farmers’ inputs and environmentally sensitive ecosystem services. Declining yield growth with increased inputs prompts conversion of more land to cultivation, but at the risk of eroding ecosystem services. To explore the interdependence of agricultural production and its stability on ecosystem services, we present and test a general graphical model, based on Jensen's inequality, of yield–resource relations and consider implications for land conversion. For the case of animal pollination as a resource influencing crop yield, this model predicts that incomplete and variable pollen delivery reduces yield mean and stability (inverse of variability) more for crops with greater dependence on pollinators. Data collected by the Food and Agriculture Organization of the United Nations during 1961–2008 support these predictions. Specifically, crops with greater pollinator dependence had lower mean and stability in relative yield and yield growth, despite global yield increases for most crops. Lower yield growth was compensated by increased land cultivation to enhance production of pollinator-dependent crops. Area stability also decreased with pollinator dependence, as it correlated positively with yield stability among crops. These results reveal that pollen limitation hinders yield growth of pollinator-dependent crops, decreasing temporal stability of global agricultural production, while promoting compensatory land conversion to agriculture. Although we examined crop pollination, our model applies to other ecosystem services for which the benefits to human welfare decelerate as the maximum is approached. PMID:21422295

Continental drift and climate change drive instability in insect assemblages

NASA Astrophysics Data System (ADS)

Li, Fengqing; Tierno de Figueroa, José Manuel; Lek, Sovan; Park, Young-Seuk

2015-06-01

Global change has already had observable effects on ecosystems worldwide, and the accelerated rate of global change is predicted in the future. However, the impacts of global change on the stability of biodiversity have not been systematically studied in terms of both large spatial (continental drift) and temporal (from the last inter-glacial period to the next century) scales. Therefore, we analyzed the current geographical distribution pattern of Plecoptera, a thermally sensitive insect group, and evaluated its stability when coping with global change across both space and time throughout the Mediterranean region—one of the first 25 global biodiversity hotspots. Regional biodiversity of Plecoptera reflected the geography in both the historical movements of continents and the current environmental conditions in the western Mediterranean region. The similarity of Plecoptera assemblages between areas in this region indicated that the uplift of new land and continental drift were the primary determinants of the stability of regional biodiversity. Our results revealed that climate change caused the biodiversity of Plecoptera to slowly diminish in the past and will cause remarkably accelerated biodiversity loss in the future. These findings support the theory that climate change has had its greatest impact on biodiversity over a long temporal scale.

Continental drift and climate change drive instability in insect assemblages

PubMed Central

Li, Fengqing; Tierno de Figueroa, José Manuel; Lek, Sovan; Park, Young-Seuk

2015-01-01

Global change has already had observable effects on ecosystems worldwide, and the accelerated rate of global change is predicted in the future. However, the impacts of global change on the stability of biodiversity have not been systematically studied in terms of both large spatial (continental drift) and temporal (from the last inter-glacial period to the next century) scales. Therefore, we analyzed the current geographical distribution pattern of Plecoptera, a thermally sensitive insect group, and evaluated its stability when coping with global change across both space and time throughout the Mediterranean region—one of the first 25 global biodiversity hotspots. Regional biodiversity of Plecoptera reflected the geography in both the historical movements of continents and the current environmental conditions in the western Mediterranean region. The similarity of Plecoptera assemblages between areas in this region indicated that the uplift of new land and continental drift were the primary determinants of the stability of regional biodiversity. Our results revealed that climate change caused the biodiversity of Plecoptera to slowly diminish in the past and will cause remarkably accelerated biodiversity loss in the future. These findings support the theory that climate change has had its greatest impact on biodiversity over a long temporal scale. PMID:26081036

Continental drift and climate change drive instability in insect assemblages.

PubMed

Li, Fengqing; Tierno de Figueroa, José Manuel; Lek, Sovan; Park, Young-Seuk

2015-06-17

Global change has already had observable effects on ecosystems worldwide, and the accelerated rate of global change is predicted in the future. However, the impacts of global change on the stability of biodiversity have not been systematically studied in terms of both large spatial (continental drift) and temporal (from the last inter-glacial period to the next century) scales. Therefore, we analyzed the current geographical distribution pattern of Plecoptera, a thermally sensitive insect group, and evaluated its stability when coping with global change across both space and time throughout the Mediterranean region--one of the first 25 global biodiversity hotspots. Regional biodiversity of Plecoptera reflected the geography in both the historical movements of continents and the current environmental conditions in the western Mediterranean region. The similarity of Plecoptera assemblages between areas in this region indicated that the uplift of new land and continental drift were the primary determinants of the stability of regional biodiversity. Our results revealed that climate change caused the biodiversity of Plecoptera to slowly diminish in the past and will cause remarkably accelerated biodiversity loss in the future. These findings support the theory that climate change has had its greatest impact on biodiversity over a long temporal scale.

General properties of magnetic CP stars

NASA Astrophysics Data System (ADS)

Glagolevskij, Yu. V.

2017-07-01

We present the review of our previous studies related to observational evidence of the fossil field hypothesis of formation and evolution of magnetic and non-magnetic chemically peculiar stars. Analysis of the observed data shows that these stars acquire their main properties in the process of gravitational collapse. In the non-stationary Hayashi phase, a magnetic field becomes weakened and its configuration complicated, but the fossil field global orientation remains. After a non-stationary phase, relaxation of young star's tangled field takes place and by the time of joining ZAMS (Zero Age Main Sequence) it is generally restored to a dipole structure. Stability of dipole structures allows them to remain unchanged up to the end of their life on the Main Sequence which is 109 years at most.

Continuous uniformly finite time exact disturbance observer based control for fixed-time stabilization of nonlinear systems with mismatched disturbances

PubMed Central

Liu, Chongxin; Liu, Hang

2017-01-01

This paper presents a continuous composite control scheme to achieve fixed-time stabilization for nonlinear systems with mismatched disturbances. The composite controller is constructed in two steps: First, uniformly finite time exact disturbance observers are proposed to estimate and compensate the disturbances. Then, based on adding a power integrator technique and fixed-time stability theory, continuous fixed-time stable state feedback controller and Lyapunov functions are constructed to achieve global fixed-time system stabilization. The proposed control method extends the existing fixed-time stable control results to high order nonlinear systems with mismatched disturbances and achieves global fixed-time system stabilization. Besides, the proposed control scheme improves the disturbance rejection performance and achieves performance recovery of nominal system. Simulation results are provided to show the effectiveness, the superiority and the applicability of the proposed control scheme. PMID:28406966

Solution structure of a lipid transfer protein extracted from rice seeds. Comparison with homologous proteins.

PubMed

Poznanski, J; Sodano, P; Suh, S W; Lee, J Y; Ptak, M; Vovelle, F

1999-02-01

Nuclear magnetic resonance (NMR) spectroscopy was used to determine the three dimensional structure of rice nonspecific lipid transfer protein (ns-LTP), a 91 amino acid residue protein belonging to the broad family of plant ns-LTP. Sequence specific assignment was obtained for all but three HN backbone 1H resonances and for more than 95% of the 1H side-chain resonances using a combination of 1H 2D NOESY; TOCSY and COSY experiments at 293 K. The structure was calculated on the basis of four disulfide bridge restraints, 1259 distance constraints derived from 1H-1H Overhauser effects, 72 phi angle restraints and 32 hydrogen-bond restraints. The final solution structure involves four helices (H1: Cys3-Arg18, H2: Ala25-Ala37, H3: Thr41-Ala54 and H4: Ala66-Cys73) followed by a long C-terminal tail (T) with no observable regular structure. N-capping residues (Thr2, Ser24, Thr40), whose side-chain oxygen atoms are involved in hydrogen bonds with i + 3 amide proton additionally stabilize the N termini of the first three helices. The fourth helix involving Pro residues display a mixture of alpha and 3(10) conformation. The rms deviation of 14 final structures with respect to the average structure is 1.14 +/- 0.16 A for all heavy atoms (C, N, O and S) and 0.72 +/- 0.01 A for the backbone atoms. The global fold of rice ns-LTP is close to the previously published structures of wheat, barley and maize ns-LTPs exhibiting nearly identical pattern of the numerous sequence specific interactions. As reported previously for different four-helix topology proteins, hydrophobic, hydrogen bonding and electrostatic mechanisms of fold stabilization were found for the rice ns-LTP. The sequential alignment of 36 ns-LTP primary structures strongly suggests that there is a uniform pattern of specific long-range interactions (in terms of sequence), which stabilize the fold of all plant ns-LTPs.

Dynamic Analysis of the Melanoma Model: From Cancer Persistence to Its Eradication

NASA Astrophysics Data System (ADS)

Starkov, Konstantin E.; Jimenez Beristain, Laura

In this paper, we study the global dynamics of the five-dimensional melanoma model developed by Kronik et al. This model describes interactions of tumor cells with cytotoxic T cells and respective cytokines under cellular immunotherapy. We get the ultimate upper and lower bounds for variables of this model, provide formulas for equilibrium points and present local asymptotic stability/hyperbolic instability conditions. Next, we prove the existence of the attracting set. Based on these results we come to global asymptotic melanoma eradication conditions via global stability analysis. Finally, we provide bounds for a locus of the melanoma persistence equilibrium point, study the case of melanoma persistence and describe conditions under which we observe global attractivity to the unique melanoma persistence equilibrium point.

Structure and Connectivity Analysis of Financial Complex System Based on G-Causality Network

NASA Astrophysics Data System (ADS)

Xu, Chuan-Ming; Yan, Yan; Zhu, Xiao-Wu; Li, Xiao-Teng; Chen, Xiao-Song

2013-11-01

The recent financial crisis highlights the inherent weaknesses of the financial market. To explore the mechanism that maintains the financial market as a system, we study the interactions of U.S. financial market from the network perspective. Applied with conditional Granger causality network analysis, network density, in-degree and out-degree rankings are important indicators to analyze the conditional causal relationships among financial agents, and further to assess the stability of U.S. financial systems. It is found that the topological structure of G-causality network in U.S. financial market changed in different stages over the last decade, especially during the recent global financial crisis. Network density of the G-causality model is much higher during the period of 2007-2009 crisis stage, and it reaches the peak value in 2008, the most turbulent time in the crisis. Ranked by in-degrees and out-degrees, insurance companies are listed in the top of 68 financial institutions during the crisis. They act as the hubs which are more easily influenced by other financial institutions and simultaneously influence others during the global financial disturbance.

Composite Study Of Aerosol Long-Range Transport Events From East Asia And North America

NASA Astrophysics Data System (ADS)

Jiang, X.; Waliser, D. E.; Guan, B.; Xavier, P.; Petch, J.; Klingaman, N. P.; Woolnough, S.

2011-12-01

While the Madden-Julian Oscillation (MJO) exerts pronounced influences on global climate and weather systems, current general circulation models (GCMs) exhibit rather limited capability in representing this prominent tropical variability mode. Meanwhile, the fundamental physics of the MJO are still elusive. Given the central role of the diabatic heating for prevailing MJO theories and demands for reducing the model deficiencies in simulating the MJO, a global model inter-comparison project on diabatic processes and vertical heating structure associated with the MJO has been coordinated through a joint effort by the WCRP-WWRP/THORPEX YOTC MJO Task Force and GEWEX GASS Program. In this presentation, progress of this model inter-comparison project will be reported, with main focus on climate simulations from about 27 atmosphere-only and coupled GCMs. Vertical structures of heating and diabatic processes associated with the MJO based on multi-model simulations will be presented along with their reanalysis and satellite estimate counterparts. Key processes possibly responsible for a realistic simulation of the MJO, including moisture-convection interaction, gross moist stability, ocean coupling, and surface heat flux, will be discussed.

Gyrokinetic global three-dimensional simulations of linear ion-temperature-gradient modes in Wendelstein 7-X

NASA Astrophysics Data System (ADS)

Kornilov, V.; Kleiber, R.; Hatzky, R.; Villard, L.; Jost, G.

2004-06-01

Using a global approach for solving an ion gyrokinetic model in three-dimensional geometry the linear stability and structure of ion-temperature-gradient (ITG) modes in the configuration of the stellarator Wendelstein 7-X (W7-X) [G. Grieger et al., in Plasma Physics and Controlled Nuclear Fusion Research 1990 (International Atomic Energy Agency, Vienna, 1991), Vol. 3, p. 525.] is studied. The time evolution of electrostatic perturbations is solved as an initial value problem with a particle-in-cell δf method. The vacuum magnetohydrodynamic equilibrium is calculated by the code VMEC [S. P. Hirshman and D. K. Lee, Comput. Phys. Commun. 39, 161 (1986)]. In this work the most unstable ITG mode in W7-X is presented. This mode has a pronounced ballooning-type structure; however, it is not tokamak-like. A driving mechanism analysis using the energy transfer shows that the contribution of curvature effects is non-negligible. The growth rate and the mixing-length estimate for transport are compared with those for ITG modes found in axisymmetric geometries.

Dimensions of global population projections: what do we know about future population trends and structures?

PubMed Central

Lutz, Wolfgang; KC, Samir

2010-01-01

The total size of the world population is likely to increase from its current 7 billion to 8–10 billion by 2050. This uncertainty is because of unknown future fertility and mortality trends in different parts of the world. But the young age structure of the population and the fact that in much of Africa and Western Asia, fertility is still very high makes an increase by at least one more billion almost certain. Virtually, all the increase will happen in the developing world. For the second half of the century, population stabilization and the onset of a decline are likely. In addition to the future size of the population, its distribution by age, sex, level of educational attainment and place of residence are of specific importance for studying future food security. The paper provides a detailed discussion of different relevant dimensions in population projections and an evaluation of the methods and assumptions used in current global population projections and in particular those produced by the United Nations and by IIASA. PMID:20713384

Stability and nonlinear adjustment of vortices in Keplerian flows

NASA Astrophysics Data System (ADS)

Bodo, G.; Tevzadze, A.; Chagelishvili, G.; Mignone, A.; Rossi, P.; Ferrari, A.

2007-11-01

Aims:We investigate the stability, nonlinear development and equilibrium structure of vortices in a background shearing Keplerian flow Methods: We make use of high-resolution global two-dimensional compressible hydrodynamic simulations. We introduce the concept of nonlinear adjustment to describe the transition of unbalanced vortical fields to a long-lived configuration. Results: We discuss the conditions under which vortical perturbations evolve into long-lived persistent structures and we describe the properties of these equilibrium vortices. The properties of equilibrium vortices appear to be independent from the initial conditions and depend only on the local disk parameters. In particular we find that the ratio of the vortex size to the local disk scale height increases with the decrease of the sound speed, reaching values well above the unity. The process of spiral density wave generation by the vortex, discussed in our previous work, appear to maintain its efficiency also at nonlinear amplitudes and we observe the formation of spiral shocks attached to the vortex. The shocks may have important consequences on the long term vortex evolution and possibly on the global disk dynamics. Conclusions: Our study strengthens the arguments in favor of anticyclonic vortices as the candidates for the promotion of planetary formation. Hydrodynamic shocks that are an intrinsic property of persistent vortices in compressible Keplerian flows are an important contributor to the overall balance. These shocks support vortices against viscous dissipation by generating local potential vorticity and should be responsible for the eventual fate of the persistent anticyclonic vortices. Numerical codes have be able to resolve shock waves to describe the vortex dynamics correctly.

Ice-free Arctic projections under the Paris Agreement

NASA Astrophysics Data System (ADS)

Sigmond, Michael; Fyfe, John C.; Swart, Neil C.

2018-05-01

Under the Paris Agreement, emissions scenarios are pursued that would stabilize the global mean temperature at 1.5-2.0 °C above pre-industrial levels, but current emission reduction policies are expected to limit warming by 2100 to approximately 3.0 °C. Whether such emissions scenarios would prevent a summer sea-ice-free Arctic is unknown. Here we employ stabilized warming simulations with an Earth System Model to obtain sea-ice projections under stabilized global warming, and correct biases in mean sea-ice coverage by constraining with observations. Although there is some sensitivity to details in the constraining method, the observationally constrained projections suggest that the benefits of going from 2.0 °C to 1.5 °C stabilized warming are substantial; an eightfold decrease in the frequency of ice-free conditions is expected, from once in every five to once in every forty years. Under 3.0 °C global mean warming, however, permanent summer ice-free conditions are likely, which emphasizes the need for nations to increase their commitments to the Paris Agreement.

Redistribution of flexibility in stabilizing antibody fragment mutants follows Le Châtelier's principle.

PubMed

Li, Tong; Tracka, Malgorzata B; Uddin, Shahid; Casas-Finet, Jose; Jacobs, Donald J; Livesay, Dennis R

2014-01-01

Le Châtelier's principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier's principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect.

Redistribution of Flexibility in Stabilizing Antibody Fragment Mutants Follows Le Châtelier’s Principle

PubMed Central

Li, Tong; Tracka, Malgorzata B.; Uddin, Shahid; Casas-Finet, Jose; Jacobs, Donald J.; Livesay, Dennis R.

2014-01-01

Le Châtelier’s principle is the cornerstone of our understanding of chemical equilibria. When a system at equilibrium undergoes a change in concentration or thermodynamic state (i.e., temperature, pressure, etc.), La Châtelier’s principle states that an equilibrium shift will occur to offset the perturbation and a new equilibrium is established. We demonstrate that the effects of stabilizing mutations on the rigidity ⇔ flexibility equilibrium within the native state ensemble manifest themselves through enthalpy-entropy compensation as the protein structure adjusts to restore the global balance between the two. Specifically, we characterize the effects of mutation to single chain fragments of the anti-lymphotoxin-β receptor antibody using a computational Distance Constraint Model. Statistically significant changes in the distribution of both rigidity and flexibility within the molecular structure is typically observed, where the local perturbations often lead to distal shifts in flexibility and rigidity profiles. Nevertheless, the net gain or loss in flexibility of individual mutants can be skewed. Despite all mutants being exclusively stabilizing in this dataset, increased flexibility is slightly more common than increased rigidity. Mechanistically the redistribution of flexibility is largely controlled by changes in the H-bond network. For example, a stabilizing mutation can induce an increase in rigidity locally due to the formation of new H-bonds, and simultaneously break H-bonds elsewhere leading to increased flexibility distant from the mutation site via Le Châtelier. Increased flexibility within the VH β4/β5 loop is a noteworthy illustration of this long-range effect. PMID:24671209

Socio-ecological dynamics and challenges to the governance of Neglected Tropical Disease control.

PubMed

Michael, Edwin; Madon, Shirin

2017-02-06

The current global attempts to control the so-called "Neglected Tropical Diseases (NTDs)" have the potential to significantly reduce the morbidity suffered by some of the world's poorest communities. However, the governance of these control programmes is driven by a managerial rationality that assumes predictability of proposed interventions, and which thus primarily seeks to improve the cost-effectiveness of implementation by measuring performance in terms of pre-determined outputs. Here, we argue that this approach has reinforced the narrow normal-science model for controlling parasitic diseases, and in doing so fails to address the complex dynamics, uncertainty and socio-ecological context-specificity that invariably underlie parasite transmission. We suggest that a new governance approach is required that draws on a combination of non-equilibrium thinking about the operation of complex, adaptive, systems from the natural sciences and constructivist social science perspectives that view the accumulation of scientific knowledge as contingent on historical interests and norms, if more effective control approaches sufficiently sensitive to local disease contexts are to be devised, applied and managed. At the core of this approach is an emphasis on the need for a process that assists with the inclusion of diverse perspectives, social learning and deliberation, and a reflexive approach to addressing system complexity and incertitude, while balancing this flexibility with stability-focused structures. We derive and discuss a possible governance framework and outline an organizational structure that could be used to effectively deal with the complexity of accomplishing global NTD control. We also point to examples of complexity-based management structures that have been used in parasite control previously, which could serve as practical templates for developing similar governance structures to better manage global NTD control. Our results hold important wider implications for global health policy aiming to effectively control and eradicate parasitic diseases across the world.

The Lunar Crust: Global Structure and Signature of Major Basins

NASA Technical Reports Server (NTRS)

Neumann, Gregory A.; Zuber, Maria T.; Smith, David E.; Lemoine, Frank G.

1996-01-01

New lunar gravity and topography data from the Clementine Mission provide a global Bouguer anomaly map corrected for the gravitational attraction of mare fill in mascon basins. Most of the gravity signal remaining after corrections for the attraction of topography and mare fill can be attributed to variations in depth to the lunar Moho and therefore crustal thickness. The large range of global crustal thickness (approx. 20-120 km) is indicative of major spatial variations in melting of the lunar exterior and/or significant impact-related redistribution. The 6l-km average crustal thickness, constrained by a depth-to-Moho measured during the Apollo 12 and 14 missions, is preferentially distributed toward the farside, accounting for much of the offset in center-of-figure from the center-of-mass. While the average farside thickness is 12 km greater than the nearside, the distribution is nonuniform, with dramatic thinning beneath the farside, South Pole-Aitken basin. With the global crustal thickness map as a constraint, regional inversions of gravity and topography resolve the crustal structure of major mascon basins to half wavelengths of 150 km. In order to yield crustal thickness maps with the maximum horizontal resolution permitted by the data, the downward continuation of the Bouguer gravity is stabilized by a three- dimensional, minimum-slope and curvature algorithm. Both mare and non-mare basins are characterized by a central upwarped moho that is surrounded by rings of thickened crust lying mainly within the basin rims. The inferred relief at this density interface suggests a deep structural component to the surficial features of multiring lunar impact basins. For large (greater than 300 km diameter) basins, moho relief appears uncorrelated with diameter, but is negatively correlated with basin age. In several cases, it appears that the multiring structures were out of isostatic equilibrium prior to mare emplacement, suggesting that the lithosphere was strong enough to maintain their state of stress to the present.

Molecular-Dynamics Simulations of ELIC a Prokaryotic Homologue of the Nicotinic Acetylcholine Receptor

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

Cheng, Xiaolin; Ivanov, Ivaylo N; Wang, Hailong

2009-01-01

The ligand-gated ion channel from Erwinia chrysanthemi (ELIC) is a prokaryotic homolog of the eukaryotic nicotinic acetylcholine receptor (nAChR) that responds to the binding of neurotransmitter acetylcholine and mediates fast signal transmission. ELIC is similar to the nAChR in its primary sequence and overall subunit organization, but despite their structural similarity, it is not clear whether these two ligand-gated ion channels operate in a similar manner. Further, it is not known to what extent mechanistic insights gleaned from the ELIC structure translate to eukaryotic counterparts such as the nAChR. Here we use molecular-dynamics simulations to probe the conformational dynamics andmore » hydration of the transmembrane pore of ELIC. The results are compared with those from our previous simulation of the human ?7 nAChR. Overall, ELIC displays increased stability compared to the nAChR, whereas the two proteins exhibit remarkable similarity in their global motion and flexibility patterns. The majority of the increased stability of ELIC does not stem from the deficiency of the models used in the simulations, and but rather seems to have a structural basis. Slightly altered dynamical correlation features are also observed among several loops within the membrane region. In sharp contrast to the nAChR, ELIC is completely dehydrated from the pore center to the extracellular end throughout the simulation. Finally, the simulation of an ELIC mutant substantiates the important role of F246 on the stability, hydration and possibly function of the ELIC channel.« less

Stability and bifurcation analysis on a ratio-dependent predator-prey model with time delay

NASA Astrophysics Data System (ADS)

Xu, Rui; Gan, Qintao; Ma, Zhien

2009-08-01

A ratio-dependent predator-prey model with time delay due to the gestation of the predator is investigated. By analyzing the corresponding characteristic equations, the local stability of a positive equilibrium and a semi-trivial boundary equilibrium is discussed, respectively. Further, it is proved that the system undergoes a Hopf bifurcation at the positive equilibrium. Using the normal form theory and the center manifold reduction, explicit formulae are derived to determine the direction of bifurcations and the stability and other properties of bifurcating periodic solutions. By means of an iteration technique, sufficient conditions are obtained for the global attractiveness of the positive equilibrium. By comparison arguments, the global stability of the semi-trivial equilibrium is also addressed. Numerical simulations are carried out to illustrate the main results.

Local vs. global redundancy - trade-offs between resilience against cascading failures and frequency stability

NASA Astrophysics Data System (ADS)

Plietzsch, A.; Schultz, P.; Heitzig, J.; Kurths, J.

2016-05-01

When designing or extending electricity grids, both frequency stability and resilience against cascading failures have to be considered amongst other aspects of energy security and economics such as construction costs due to total line length. Here, we compare an improved simulation model for cascading failures with state-of-the-art simulation models for short-term grid dynamics. Random ensembles of realistic power grid topologies are generated using a recent model that allows for a tuning of global vs local redundancy. The former can be measured by the algebraic connectivity of the network, whereas the latter can be measured by the networks transitivity. We show that, while frequency stability of an electricity grid benefits from a global form of redundancy, resilience against cascading failures rather requires a more local form of redundancy and further analyse the corresponding trade-off.

Stability of differential susceptibility and infectivity epidemic models

PubMed Central

Bonzi, B.; Fall, A. A.; Iggidr, Abderrahman; Sallet, Gauthier

2011-01-01

We introduce classes of differential susceptibility and infectivity epidemic models. These models address the problem of flows between the different susceptible, infectious and infected compartments and differential death rates as well. We prove the global stability of the disease free equilibrium when the basic reproduction ratio ≤ 1 and the existence and uniqueness of an endemic equilibrium when > 1. We also prove the global asymptotic stability of the endemic equilibrium for a differential susceptibility and staged progression infectivity model, when > 1. Our results encompass and generalize those of [18, 22]. AMS Subject Classification : 34A34,34D23,34D40,92D30 PMID:20148330

Global Mittag-Leffler stability analysis of fractional-order impulsive neural networks with one-side Lipschitz condition.

PubMed

Zhang, Xinxin; Niu, Peifeng; Ma, Yunpeng; Wei, Yanqiao; Li, Guoqiang

2017-10-01

This paper is concerned with the stability analysis issue of fractional-order impulsive neural networks. Under the one-side Lipschitz condition or the linear growth condition of activation function, the existence of solution is analyzed respectively. In addition, the existence, uniqueness and global Mittag-Leffler stability of equilibrium point of the fractional-order impulsive neural networks with one-side Lipschitz condition are investigated by the means of contraction mapping principle and Lyapunov direct method. Finally, an example with numerical simulation is given to illustrate the validity and feasibility of the proposed results. Copyright © 2017 Elsevier Ltd. All rights reserved.

Postaragonite phases of CaCO3 at lower mantle pressures

NASA Astrophysics Data System (ADS)

Smith, Dean; Lawler, Keith V.; Martinez-Canales, Miguel; Daykin, Austin W.; Fussell, Zachary; Smith, G. Alexander; Childs, Christian; Smith, Jesse S.; Pickard, Chris J.; Salamat, Ashkan

2018-01-01

The stability, structure, and properties of carbonate minerals at lower mantle conditions have significant impact on our understanding of the global carbon cycle and the composition of the interior of the Earth. In recent years there has been significant interest in the behavior of carbonates at lower mantle conditions, specifically in their carbon hybridization, which has relevance for the storage of carbon within the deep mantle. Using high-pressure synchrotron x-ray diffraction in a diamond anvil cell coupled with direct laser heating of CaCO3 using a CO2 laser, we identify a crystalline phase of the material above 40 GPa—corresponding to a lower mantle depth of around 1000 km—which has first been predicted by ab initio structure predictions. The observed s p2 carbon hybridized species at 40 GPa is monoclinic with P 21/c symmetry and is stable up to 50 GPa, above which it transforms into a structure which cannot be indexed by existing known phases. A combination of ab initio random structure search (AIRSS) and quasiharmonic approximation (QHA) calculations are used to re-explore the relative phase stabilities of the rich phase diagram of CaCO3. Nudged elastic band (NEB) calculations are used to investigate the reaction mechanisms between relevant crystal phases of CaCO3 and we postulate that the mineral is capable of undergoing s p2-s p3 hybridization change purely in the P 21/c structure—forgoing the accepted postaragonite P m m n structure.

Stabilization of golden cages by encapsulation of a single transition metal atom

PubMed Central

Li, Hui-Fang

2018-01-01

Golden cage-doped nanoclusters have attracted great attention in the past decade due to their remarkable electronic, optical and catalytic properties. However, the structures of large golden cage doped with Mo and Tc are still not well known because of the challenges in global structural searches. Here, we report anionic and neutral golden cage doped with a transition metal atom MAu16 (M = Mo and Tc) using Saunders ‘Kick' stochastic automation search method associated with density-functional theory (DFT) calculation (SK-DFT). The geometric structures and electronic properties of the doped clusters, MAu16q (M = Mo and Tc; q = 0 and −1), are investigated by means of DFT theoretical calculations. Our calculations confirm that the 4d transition metals Mo and Tc can be stably encapsulated in the Au16− cage, forming three different configurations, i.e. endohedral cages, planar structures and exohedral derivatives. The ground-state structures of endohedral cages C2v Mo@Au16−-(a) and C1 Tc@Au16−-(b) exhibit a marked stability, as judged by their high binding energy per atom (greater than 2.46 eV), doping energy (0.29 eV) as well as a large HOMO–LUMO gap (greater than 0.40 eV). The predicted photoelectron spectra should aid in future experimental characterization of MAu16− (M = Mo and Tc). PMID:29410813

β-Boomerang Antimicrobial and Antiendotoxic Peptides: Lipidation and Disulfide Bond Effects on Activity and Structure.

PubMed

Mohanram, Harini; Bhattacharjya, Surajit

2014-04-21

Drug-resistant Gram-negative bacterial pathogens and endotoxin- or lipopolysaccharide (LPS)-mediated inflammations are among some of the most  prominent health issues globally. Antimicrobial peptides (AMPs) are eminent molecules that can kill drug-resistant strains and neutralize LPS toxicity. LPS, the outer layer of the outer membrane of Gram-negative bacteria safeguards cell integrity against hydrophobic compounds, including antibiotics and AMPs. Apart from maintaining structural integrity, LPS, when released into the blood stream, also induces inflammatory pathways leading to septic shock. In previous works, we have reported the de novo design of a set of 12-amino acid long cationic/hydrophobic peptides for LPS binding and activity. These peptides adopt β-boomerang like conformations in complex with LPS. Structure-activity studies demonstrated some critical features of the β-boomerang scaffold that may be utilized for the further development of potent analogs. In this work, β-boomerang lipopeptides were designed and structure-activity correlation studies were carried out. These lipopeptides were homo-dimerized through a disulfide bridge to stabilize conformations and for improved activity. The designed peptides exhibited potent antibacterial activity and efficiently neutralized LPS toxicity under in vitro assays. NMR structure of C4YI13C in aqueous solution demonstrated the conserved folding of the lipopeptide with a boomerang aromatic lock stabilized with disulfide bond at the C-terminus and acylation at the N-terminus. These lipo-peptides displaying bacterial sterilization and low hemolytic activity may be useful for future applications as antimicrobial and antiendotoxin molecules.

Prediction of protein tertiary structure to low resolution: performance for a large and structurally diverse test set.

PubMed

Eyrich, V A; Standley, D M; Friesner, R A

1999-05-14

We report the tertiary structure predictions for 95 proteins ranging in size from 17 to 160 residues starting from known secondary structure. Predictions are obtained from global minimization of an empirical potential function followed by the application of a refined atomic overlap potential. The minimization strategy employed represents a variant of the Monte Carlo plus minimization scheme of Li and Scheraga applied to a reduced model of the protein chain. For all of the cases except beta-proteins larger than 75 residues, a native-like structure, usually 4-6 A root-mean-square deviation from the native, is located. For beta-proteins larger than 75 residues, the energy gap between native-like structures and the lowest energy structures produced in the simulation is large, so that low RMSD structures are not generated starting from an unfolded state. This is attributed to the lack of an explicit hydrogen bond term in the potential function, which we hypothesize is necessary to stabilize large assemblies of beta-strands. Copyright 1999 Academic Press.

M3D-K Simulations of Beam-Driven Alfven Eigenmodes in ASDEX-U

NASA Astrophysics Data System (ADS)

Wang, Ge; Fu, Guoyong; Lauber, Philipp; Schneller, Mirjam

2013-10-01

Core-localized Alfven eigenmodes are often observed in neutral beam-heated plasma in ASDEX-U tokamak. In this work, hybrid simulations with the global kinetic/MHD hybrid code M3D-K have been carried out to investigate the linear stability and nonlinear dynamics of beam-driven Alfven eigenmodes using experimental parameters and profiles of an ASDEX-U discharge. The safety factor q profile is weakly reversed with minimum q value about qmin = 3.0. The simulation results show that the n = 3 mode transits from a reversed shear Alfven eigenmode (RSAE) to a core-localized toroidal Alfven eigenmode (TAE) as qmin drops from 3.0 to 2.79, consistent with results from the stability code NOVA as well as the experimental measurement. The M3D-K results are being compared with those of the linear gyrokinetic stability code LIGKA for benchmark. The simulation results will also be compared with the measured mode frequency and mode structure. This work was funded by the Max-Planck/Princeton Center for Plasma Physics.

New climatic targets against global warming: will the maximum 2 °C temperature rise affect estuarine benthic communities?

PubMed

Crespo, Daniel; Grilo, Tiago Fernandes; Baptista, Joana; Coelho, João Pedro; Lillebø, Ana Isabel; Cássio, Fernanda; Fernandes, Isabel; Pascoal, Cláudia; Pardal, Miguel Ângelo; Dolbeth, Marina

2017-06-20

The Paris Agreement signed by 195 countries in 2015 sets out a global action plan to avoid dangerous climate change by limiting global warming to remain below 2 °C. Under that premise, in situ experiments were run to test the effects of 2 °C temperature increase on the benthic communities in a seagrass bed and adjacent bare sediment, from a temperate European estuary. Temperature was artificially increased in situ and diversity and ecosystem functioning components measured after 10 and 30 days. Despite some warmness effects on the analysed components, significant impacts were not verified on macro and microfauna structure, bioturbation or in the fluxes of nutrients. The effect of site/habitat seemed more important than the effects of the warmness, with the seagrass habitat providing more homogenous results and being less impacted by warmness than the adjacent bare sediment. The results reinforce that most ecological responses to global changes are context dependent and that ecosystem stability depends not only on biological diversity but also on the availability of different habitats and niches, highlighting the role of coastal wetlands. In the context of the Paris Agreement it seems that estuarine benthic ecosystems will be able to cope if global warming remains below 2 °C.

Changes in extremely hot days under stabilized 1.5 and 2.0 °C global warming scenarios as simulated by the HAPPI multi-model ensemble

NASA Astrophysics Data System (ADS)

Wehner, Michael; Stone, Dáithí; Mitchell, Dann; Shiogama, Hideo; Fischer, Erich; Graff, Lise S.; Kharin, Viatcheslav V.; Lierhammer, Ludwig; Sanderson, Benjamin; Krishnan, Harinarayan

2018-03-01

The half a degree additional warming, prognosis and projected impacts (HAPPI) experimental protocol provides a multi-model database to compare the effects of stabilizing anthropogenic global warming of 1.5 °C over preindustrial levels to 2.0 °C over these levels. The HAPPI experiment is based upon large ensembles of global atmospheric models forced by sea surface temperature and sea ice concentrations plausible for these stabilization levels. This paper examines changes in extremes of high temperatures averaged over three consecutive days. Changes in this measure of extreme temperature are also compared to changes in hot season temperatures. We find that over land this measure of extreme high temperature increases from about 0.5 to 1.5 °C over present-day values in the 1.5 °C stabilization scenario, depending on location and model. We further find an additional 0.25 to 1.0 °C increase in extreme high temperatures over land in the 2.0 °C stabilization scenario. Results from the HAPPI models are consistent with similar results from the one available fully coupled climate model. However, a complicating factor in interpreting extreme temperature changes across the HAPPI models is their diversity of aerosol forcing changes.

Coastal flood implications of 1.5°C, 2°C and 2.5°C global mean temperature stabilization targets for small island nations

NASA Astrophysics Data System (ADS)

Rasmussen, D.; Buchanan, M. K.; Kopp, R. E.; Oppenheimer, M.

2017-12-01

Sea-level rise (SLR) is magnifying the frequency and severity of flooding in coastal regions. The rate and amount of global-mean SLR is a function of the trajectory of the global mean surface temperature (GMST). Therefore, temperature stabilization targets (e.g., 1.5°C or 2°C, as from the Paris Agreement) have important implications for regulating coastal flood risk. Quantifying the differences in the impact from SLR between these and other GMST stabilization targets is necessary for assessing the benefits and harms of mitigation goals. Low-lying small island nations are particularly vulnerable to inundation and coastal flooding from SLR because building protective and resilient infrastructure may not be physically or economically feasible. For small island nations, keeping GMST below a specified threshold may be the only option for maintaining habitability. Here, we assess differences in the return levels of coastal floods for small island nations between 1.5°C, 2.0°C, and 2.5°C GMST stabilization. We employ probabilistic, localized SLR projections and long-term hourly tide gauge records to construct estimates of local flood risk. We then estimate the number of small island nations' inhabitants at risk for permanent inundation under different GMST stabilization targets.

Experimental and density functional theory studies on benzalkonium ibuprofenate, a double active pharmaceutical ingredient.

PubMed

Safna Hussan, K P; Thayyil, M Shahin; Rajan, Vijisha K; Muraleedharan, K

2018-02-01

Molecular aspects of a double active pharmaceutical ingredient in ionic liquid form, benzalkonium ibuprofenate (BaIb), were studied using density functional theory (DFT/B3LYP/6-31+G (d, p)). A detailed discussion on optimized geometry, energy, heat and the enthalpy of BaIb was carried out. The computed vibrational results agree well with the experimental results. The stability and biological activity were compared to the parent drugs on the basis of global descriptive parameters. The electrophilic and nucleophilic sites were pointed out in the MESP structures well evidently. NBO analysis was also done to predict the relative aromaticity, delocalization effects and the contribution towards stabilization energy of the title compound. The information about non-covalent, non-ionic weak interaction between the cation and anion was obtained from the list of Mulliken charges and NBO analysis. Copyright © 2017 Elsevier Ltd. All rights reserved.

Using Hamiltonian control to desynchronize Kuramoto oscillators

NASA Astrophysics Data System (ADS)

Gjata, Oltiana; Asllani, Malbor; Barletti, Luigi; Carletti, Timoteo

2017-02-01

Many coordination phenomena are based on a synchronization process, whose global behavior emerges from the interactions among the individual parts. Often in nature, such self-organized mechanism allows the system to behave as a whole and thus grounding its very first existence, or expected functioning, on such process. There are, however, cases where synchronization acts against the stability of the system; for instance in some neurodegenerative diseases or epilepsy or the famous case of Millennium Bridge where the crowd synchronization of the pedestrians seriously endangered the stability of the structure. In this paper we propose an innovative control method to tackle the synchronization process based on the application of the Hamiltonian control theory, by adding a small control term to the system we are able to impede the onset of the synchronization. We present our results on a generalized class of the paradigmatic Kuramoto model.

Stabilizing effect of cannibalism in a two stages population model.

PubMed

Rault, Jonathan; Benoît, Eric; Gouzé, Jean-Luc

2013-03-01

In this paper we build a prey-predator model with discrete weight structure for the predator. This model will conserve the number of individuals and the biomass and both growth and reproduction of the predator will depend on the food ingested. Moreover the model allows cannibalism which means that the predator can eat the prey but also other predators. We will focus on a simple version with two weight classes or stage (larvae and adults) and present some general mathematical results. In the last part, we will assume that the dynamics of the prey is fast compared to the predator's one to go further in the results and eventually conclude that under some conditions, cannibalism can stabilize the system: more precisely, an unstable equilibrium without cannibalism will become almost globally stable with some cannibalism. Some numerical simulations are done to illustrate this result.

New explicit global asymptotic stability criteria for higher order difference equations

NASA Astrophysics Data System (ADS)

El-Morshedy, Hassan A.

2007-12-01

New explicit sufficient conditions for the asymptotic stability of the zero solution of higher order difference equations are obtained. These criteria can be applied to autonomous and nonautonomous equations. The celebrated Clark asymptotic stability criterion is improved. Also, applications to models from mathematical biology and macroeconomics are given.

Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange

PubMed Central

Yu, Wookyung; Baxa, Michael C.; Gagnon, Isabelle; Freed, Karl F.; Sosnick, Tobin R.

2016-01-01

The relationship between folding cooperativity and downhill, or barrier-free, folding of proteins under highly stabilizing conditions remains an unresolved topic, especially for proteins such as λ-repressor that fold on the microsecond timescale. Under aqueous conditions where downhill folding is most likely to occur, we measure the stability of multiple H bonds, using hydrogen exchange (HX) in a λYA variant that is suggested to be an incipient downhill folder having an extrapolated folding rate constant of 2 × 105 s−1 and a stability of 7.4 kcal·mol−1 at 298 K. At least one H bond on each of the three largest helices (α1, α3, and α4) breaks during a common unfolding event that reflects global denaturation. The use of HX enables us to both examine folding under highly stabilizing, native-like conditions and probe the pretransition state region for stable species without the need to initiate the folding reaction. The equivalence of the stability determined at zero and high denaturant indicates that any residual denatured state structure minimally affects the stability even under native conditions. Using our ψ analysis method along with mutational ϕ analysis, we find that the three aforementioned helices are all present in the folding transition state. Hence, the free energy surface has a sufficiently high barrier separating the denatured and native states that folding appears cooperative even under extremely stable and fast folding conditions. PMID:27078098

Receptivity of a precessing vortex core to open-loop forcing in a swirling jet and its predictability by linear stability adjoint theory

NASA Astrophysics Data System (ADS)

Müller, Jens; Lückoff, Finn; Oberleithner, Kilian

2017-11-01

The precessing vortex core (PVC) is a dominant coherent structure which occurs in swirling jets such as in swirl-stabilised gas turbine combustors. It stems from a global hydrodynamic instability caused by an internal feedback mechanism within the jet core. In this work, open-loop forcing is applied to a generic non-reacting swirling jet to investigate its receptivity to external actuation regarding lock-in behaviour of the PVC for different streamwise positions and Reynolds numbers. The forcing is periodically exerted by zero net mass flux synthetic jets which are introduced radially through slits inside the duct walls upstream of the swirling jet's exit plane. Time-resolved pressure measurements are conducted to identify the PVC frequency and stereo PIV combined with proper orthogonal decomposition in the duct and free field is used to extract the mean flow and the PVC mode. The data is used in a global linear stability framework to gain the adjoint of the PVC which reveals the regions of highest receptivity to periodic forcing based on mean flow input only. This theoretical receptivity model is compared with the experimentally obtained receptivity results and the validity and applicability of the adjoint model for the prediction of optimal forcing positions is discussed.

Global optimization of additive potential energy functions: Predicting binary Lennard-Jones clusters

NASA Astrophysics Data System (ADS)

Kolossváry, István; Bowers, Kevin J.

2010-11-01

We present a method for minimizing additive potential-energy functions. Our hidden-force algorithm can be described as an intricate multiplayer tug-of-war game in which teams try to break an impasse by randomly assigning some players to drop their ropes while the others are still tugging until a partial impasse is reached, then, instructing the dropouts to resume tugging, for all teams to come to a new overall impasse. Utilizing our algorithm in a non-Markovian parallel Monte Carlo search, we found 17 new putative global minima for binary Lennard-Jones clusters in the size range of 90-100 particles. The method is efficient enough that an unbiased search was possible; no potential-energy surface symmetries were exploited. All new minima are comprised of three nested polyicosahedral or polytetrahedral shells when viewed as a nested set of Connolly surfaces (though the shell structure has previously gone unscrutinized, known minima are often qualitatively similar). Unlike known minima, in which the outer and inner shells are comprised of the larger and smaller atoms, respectively, in 13 of the new minima, the atoms are not as clearly separated by size. Furthermore, while some known minima have inner shells stabilized by larger atoms, four of the new minima have outer shells stabilized by smaller atoms.

Global stability of a multiple infected compartments model for waterborne diseases

NASA Astrophysics Data System (ADS)

Wang, Yi; Cao, Jinde

2014-10-01

In this paper, mathematical analysis is carried out for a multiple infected compartments model for waterborne diseases, such as cholera, giardia, and rotavirus. The model accounts for both person-to-person and water-to-person transmission routes. Global stability of the equilibria is studied. In terms of the basic reproduction number R0, we prove that, if R0⩽1, then the disease-free equilibrium is globally asymptotically stable and the infection always disappears; whereas if R0>1, there exists a unique endemic equilibrium which is globally asymptotically stable for the corresponding fast-slow system. Numerical simulations verify our theoretical results and present that the decay rate of waterborne pathogens has a significant impact on the epidemic growth rate. Also, we observe numerically that the unique endemic equilibrium is globally asymptotically stable for the whole system. This statement indicates that the present method need to be improved by other techniques.

Robustness of hydrological indicators for transient and stabilized climate states

NASA Astrophysics Data System (ADS)

Boulange, J. E.; Hanasaki, N.

2017-12-01

By signing the Paris agreement, countries have committed to pursue efforts to limit global warming to +1.5 °C relative to pre-industrial levels. Consequently, there is a growing interest in better understanding the impacts of a +1.5°C world. Previous analyses were conducted by considering a time slice period, centered on the year when the global mean temperature (GMT) crosses the +1.5°C threshold (Fig. 1). This time slice period is characterized by a transient state which may influence the reported results (transient climate state). Ideally, analyses should be carried under the condition the GMT is stabilized at +1.5°C (stabilized climate state) but, such targeted simulations do not exist for most GCMs.1A global hydrological model, the H08 model,2 and hydrological indicators (HI) obtained for the transient and stabilized states, are used to answer the following questions: (1) are there quantifiable differences between the HI computed for the transient and stabilized states? (2) can relations be derived between the HI computed for the transient and stabilized states? (3) what are the potential impacts induced by the differences in HI computed for the transient and stabilized states? Signal to noise ratios (S/N) obtained for the transient and stabilized states, in an identical warmer world (+1.7°C), are compared (Fig. 2). The S/N ratio computed for the stabilized state were significantly lower than those of the transient state for most regions and HI. However, at higher latitude, the S/N ratios computed for the two states were similar whereas for medium and low latitudes, the differences were more pronounced. For most regions and HI (except for surface temperature), the S/N ratios of the stabilized state were 10 to 20% weaker than those of the transient state. References:1 Knutti, R., Rogelj, J., Sedlacek, J. & Fischer, E. M. Nature Geosci (2016). 2 Hanasaki, N. et al. Hydrol. Earth Syst. Sci. (2008).

A vehicle stability control strategy with adaptive neural network sliding mode theory based on system uncertainty approximation

NASA Astrophysics Data System (ADS)

Ji, Xuewu; He, Xiangkun; Lv, Chen; Liu, Yahui; Wu, Jian

2018-06-01

Modelling uncertainty, parameter variation and unknown external disturbance are the major concerns in the development of an advanced controller for vehicle stability at the limits of handling. Sliding mode control (SMC) method has proved to be robust against parameter variation and unknown external disturbance with satisfactory tracking performance. But modelling uncertainty, such as errors caused in model simplification, is inevitable in model-based controller design, resulting in lowered control quality. The adaptive radial basis function network (ARBFN) can effectively improve the control performance against large system uncertainty by learning to approximate arbitrary nonlinear functions and ensure the global asymptotic stability of the closed-loop system. In this paper, a novel vehicle dynamics stability control strategy is proposed using the adaptive radial basis function network sliding mode control (ARBFN-SMC) to learn system uncertainty and eliminate its adverse effects. This strategy adopts a hierarchical control structure which consists of reference model layer, yaw moment control layer, braking torque allocation layer and executive layer. Co-simulation using MATLAB/Simulink and AMESim is conducted on a verified 15-DOF nonlinear vehicle system model with the integrated-electro-hydraulic brake system (I-EHB) actuator in a Sine With Dwell manoeuvre. The simulation results show that ARBFN-SMC scheme exhibits superior stability and tracking performance in different running conditions compared with SMC scheme.

Re-Structuring of Marine Communities Exposed to Environmental Change: A Global Study on the Interactive Effects of Species and Functional Richness

PubMed Central

Wahl, Martin; Link, Heike; Alexandridis, Nicolaos; Thomason, Jeremy C.; Cifuentes, Mauricio; Costello, Mark J.; da Gama, Bernardo A. P.; Hillock, Kristina; Hobday, Alistair J.; Kaufmann, Manfred J.; Keller, Stefanie; Kraufvelin, Patrik; Krüger, Ina; Lauterbach, Lars; Antunes, Bruno L.; Molis, Markus; Nakaoka, Masahiro; Nyström, Julia; bin Radzi, Zulkamal; Stockhausen, Björn; Thiel, Martin; Vance, Thomas; Weseloh, Annika; Whittle, Mark; Wiesmann, Lisa; Wunderer, Laura; Yamakita, Takehisa; Lenz, Mark

2011-01-01

Species richness is the most commonly used but controversial biodiversity metric in studies on aspects of community stability such as structural composition or productivity. The apparent ambiguity of theoretical and experimental findings may in part be due to experimental shortcomings and/or heterogeneity of scales and methods in earlier studies. This has led to an urgent call for improved and more realistic experiments. In a series of experiments replicated at a global scale we translocated several hundred marine hard bottom communities to new environments simulating a rapid but moderate environmental change. Subsequently, we measured their rate of compositional change (re-structuring) which in the great majority of cases represented a compositional convergence towards local communities. Re-structuring is driven by mortality of community components (original species) and establishment of new species in the changed environmental context. The rate of this re-structuring was then related to various system properties. We show that availability of free substratum relates negatively while taxon richness relates positively to structural persistence (i.e., no or slow re-structuring). Thus, when faced with environmental change, taxon-rich communities retain their original composition longer than taxon-poor communities. The effect of taxon richness, however, interacts with another aspect of diversity, functional richness. Indeed, taxon richness relates positively to persistence in functionally depauperate communities, but not in functionally diverse communities. The interaction between taxonomic and functional diversity with regard to the behaviour of communities exposed to environmental stress may help understand some of the seemingly contrasting findings of past research. PMID:21611170

Hierarchical Biomolecular Dynamics: Picosecond Hydrogen Bonding Regulates Microsecond Conformational Transitions.

PubMed

Buchenberg, Sebastian; Schaudinnus, Norbert; Stock, Gerhard

2015-03-10

Biomolecules exhibit structural dynamics on a number of time scales, including picosecond (ps) motions of a few atoms, nanosecond (ns) local conformational transitions, and microsecond (μs) global conformational rearrangements. Despite this substantial separation of time scales, fast and slow degrees of freedom appear to be coupled in a nonlinear manner; for example, there is theoretical and experimental evidence that fast structural fluctuations are required for slow functional motion to happen. To elucidate a microscopic mechanism of this multiscale behavior, Aib peptide is adopted as a simple model system. Combining extensive molecular dynamics simulations with principal component analysis techniques, a hierarchy of (at least) three tiers of the molecule's free energy landscape is discovered. They correspond to chiral left- to right-handed transitions of the entire peptide that happen on a μs time scale, conformational transitions of individual residues that take about 1 ns, and the opening and closing of structure-stabilizing hydrogen bonds that occur within tens of ps and are triggered by sub-ps structural fluctuations. Providing a simple mechanism of hierarchical dynamics, fast hydrogen bond dynamics is found to be a prerequisite for the ns local conformational transitions, which in turn are a prerequisite for the slow global conformational rearrangement of the peptide. As a consequence of the hierarchical coupling, the various processes exhibit a similar temperature behavior which may be interpreted as a dynamic transition.

NL(q) Theory: A Neural Control Framework with Global Asymptotic Stability Criteria.

PubMed

Vandewalle, Joos; De Moor, Bart L.R.; Suykens, Johan A.K.

1997-06-01

In this paper a framework for model-based neural control design is presented, consisting of nonlinear state space models and controllers, parametrized by multilayer feedforward neural networks. The models and closed-loop systems are transformed into so-called NL(q) system form. NL(q) systems represent a large class of nonlinear dynamical systems consisting of q layers with alternating linear and static nonlinear operators that satisfy a sector condition. For such NL(q)s sufficient conditions for global asymptotic stability, input/output stability (dissipativity with finite L(2)-gain) and robust stability and performance are presented. The stability criteria are expressed as linear matrix inequalities. In the analysis problem it is shown how stability of a given controller can be checked. In the synthesis problem two methods for neural control design are discussed. In the first method Narendra's dynamic backpropagation for tracking on a set of specific reference inputs is modified with an NL(q) stability constraint in order to ensure, e.g., closed-loop stability. In a second method control design is done without tracking on specific reference inputs, but based on the input/output stability criteria itself, within a standard plant framework as this is done, for example, in H( infinity ) control theory and &mgr; theory. Copyright 1997 Elsevier Science Ltd.

Global asymptotic stability of hybrid bidirectional associative memory neural networks with time delays

NASA Astrophysics Data System (ADS)

Arik, Sabri

2006-02-01

This Letter presents a sufficient condition for the existence, uniqueness and global asymptotic stability of the equilibrium point for bidirectional associative memory (BAM) neural networks with distributed time delays. The results impose constraint conditions on the network parameters of neural system independently of the delay parameter, and they are applicable to all bounded continuous non-monotonic neuron activation functions. The results are also compared with the previous results derived in the literature.

A qualitative content analysis of global health engagements in Peacekeeping and Stability Operations Institute's stability operations lessons learned and information management system.

PubMed

Nang, Roberto N; Monahan, Felicia; Diehl, Glendon B; French, Daniel

2015-04-01

Many institutions collect reports in databases to make important lessons-learned available to their members. The Uniformed Services University of the Health Sciences collaborated with the Peacekeeping and Stability Operations Institute to conduct a descriptive and qualitative analysis of global health engagements (GHEs) contained in the Stability Operations Lessons Learned and Information Management System (SOLLIMS). This study used a summative qualitative content analysis approach involving six steps: (1) a comprehensive search; (2) two-stage reading and screening process to identify first-hand, health-related records; (3) qualitative and quantitative data analysis using MAXQDA, a software program; (4) a word cloud to illustrate word frequencies and interrelationships; (5) coding of individual themes and validation of the coding scheme; and (6) identification of relationships in the data and overarching lessons-learned. The individual codes with the most number of text segments coded included: planning, personnel, interorganizational coordination, communication/information sharing, and resources/supplies. When compared to the Department of Defense's (DoD's) evolving GHE principles and capabilities, the SOLLIMS coding scheme appeared to align well with the list of GHE capabilities developed by the Department of Defense Global Health Working Group. The results of this study will inform practitioners of global health and encourage additional qualitative analysis of other lessons-learned databases. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

Global and segmental kinematic changes following sequential resection of posterior osteoligamentous structures in the lumbar spine: An in vitro biomechanical investigation using pure moment testing protocols.

PubMed

Chamoli, Uphar; Korkusuz, Mert H; Sabnis, Ashutosh B; Manolescu, Andrei R; Tsafnat, Naomi; Diwan, Ashish D

2015-11-01

Lumbar spinal surgeries may compromise the integrity of posterior osteoligamentous structures implicating mechanical stability. Circumstances necessitating a concomitant surgery to achieve restabilisation are not well understood. The main objective of this in vitro study was to quantify global and segmental (index and adjacent levels) kinematic changes in the lumbar spine following sequential resection of the posterior osteoligamentous structures using pure moment testing protocols. Six fresh frozen cadaveric kangaroo lumbar spines (T12-S1) were tested under a bending moment in flexion-extension, bilateral bending, and axial torsion in a 6-degree-of-freedom Kinematic Spine Simulator. Specimens were tested in the following order: intact state (D0), after interspinous and supraspinous ligaments transection between L4 and L5 (D1), further after a total bilateral facetectomy between L4 and L5 (D2). Segmental motions at the cephalad, damaged, and caudal levels were recorded using an infrared-based motion tracking device. Following D1, no significant change in the global range of motion was observed in any of the bending planes. Following D2, a significant increase in the global range of motion from the baseline (D0) was observed in axial torsion (median normalised change +20%). At the damaged level, D2 resulted in a significant increase in the segmental range of motion in flexion-extension (+77%) and axial torsion (+492%). Additionally, a significant decrease in the segmental range of motion in axial torsion (-35%) was observed at the caudal level following D2. These results suggest that a multi-segment lumbar spine acts as a mechanism for transmitting motions, and that a compromised joint may significantly alter motion transfer to adjacent segments. We conclude that the interspinous and supraspinous ligaments play a modest role in restricting global spinal motions within physiologic limits. Following interspinous and supraspinous ligaments transection, a total bilateral facetectomy resulted in a significant increase in axial torsion motion, both at global and damaged levels, accompanied with a compensatory decrease in motion at the caudal level. © IMechE 2015.

Loss of conformational stability in calmodulin upon methionine oxidation.

PubMed Central

Gao, J; Yin, D H; Yao, Y; Sun, H; Qin, Z; Schöneich, C; Williams, T D; Squier, T C

1998-01-01

We have used electrospray ionization mass spectrometry (ESI-MS), circular dichroism (CD), and fluorescence spectroscopy to investigate the secondary and tertiary structural consequences that result from oxidative modification of methionine residues in wheat germ calmodulin (CaM), and prevent activation of the plasma membrane Ca-ATPase. Using ESI-MS, we have measured rates of modification and molecular mass distributions of oxidatively modified CaM species (CaMox) resulting from exposure to H2O2. From these rates, we find that oxidative modification of methionine to the corresponding methionine sulfoxide does not predispose CaM to further oxidative modification. These results indicate that methionine oxidation results in no large-scale alterations in the tertiary structure of CaMox, because the rates of oxidative modification of individual methionines are directly related to their solvent exposure. Likewise, CD measurements indicate that methionine oxidation results in little change in the apparent alpha-helical content at 28 degrees C, and only a small (0.3 +/- 0.1 kcal mol(-1)) decrease in thermal stability, suggesting the disruption of a limited number of specific noncovalent interactions. Fluorescence lifetime, anisotropy, and quenching measurements of N-(1-pyrenyl)-maleimide (PMal) covalently bound to Cys26 indicate local structural changes around PMal in the amino-terminal domain in response to oxidative modification of methionine residues in the carboxyl-terminal domain. Because the opposing globular domains remain spatially distant in both native and oxidatively modified CaM, the oxidative modification of methionines in the carboxyl-terminal domain are suggested to modify the conformation of the amino-terminal domain through alterations in the structural features involving the interdomain central helix. The structural basis for the linkage between oxidative modification and these global conformational changes is discussed in terms of possible alterations in specific noncovalent interactions that have previously been suggested to stabilize the central helix in CaM. PMID:9512014

Structural and immunologic correlates of chemically stabilized HIV-1 envelope glycoproteins

PubMed Central

de Val, Natalia; Montefiori, David; Tomaras, Georgia D.; Shen, Xiaoying; Kalyuzhniy, Oleksandr; Sanders, Rogier W.; McCoy, Laura E.; Moore, John P.; Ward, Andrew B.

2018-01-01

Inducing broad spectrum neutralizing antibodies against challenging pathogens such as HIV-1 is a major vaccine design goal, but may be hindered by conformational instability within viral envelope glycoproteins (Env). Chemical cross-linking is widely used for vaccine antigen stabilization, but how this process affects structure, antigenicity and immunogenicity is poorly understood and its use remains entirely empirical. We have solved the first cryo-EM structure of a cross-linked vaccine antigen. The 4.2 Å structure of HIV-1 BG505 SOSIP soluble recombinant Env in complex with a CD4 binding site-specific broadly neutralizing antibody (bNAb) Fab fragment reveals how cross-linking affects key properties of the trimer. We observed density corresponding to highly specific glutaraldehyde (GLA) cross-links between gp120 monomers at the trimer apex and between gp120 and gp41 at the trimer interface that had strikingly little impact on overall trimer conformation, but critically enhanced trimer stability and improved Env antigenicity. Cross-links were also observed within gp120 at sites associated with the N241/N289 glycan hole that locally modified trimer antigenicity. In immunogenicity studies, the neutralizing antibody response to cross-linked trimers showed modest but significantly greater breadth against a global panel of difficult-to-neutralize Tier-2 heterologous viruses. Moreover, the specificity of autologous Tier-2 neutralization was modified away from the N241/N289 glycan hole, implying a novel specificity. Finally, we have investigated for the first time T helper cell responses to next-generation soluble trimers, and report on vaccine-relevant immunodominant responses to epitopes within BG505 that are modified by cross-linking. Elucidation of the structural correlates of a cross-linked viral glycoprotein will allow more rational use of this methodology for vaccine design, and reveals a strategy with promise for eliciting neutralizing antibodies needed for an effective HIV-1 vaccine. PMID:29746590

Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.

PubMed

Sripathi, Kamali N; Banáš, Pavel; Réblová, Kamila; Šponer, Jiří; Otyepka, Michal; Walter, Nils G

2015-02-28

The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5') hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5') general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5') hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs.

Wobble Pairs of the HDV Ribozyme Play Specific Roles in Stabilization of Active Site Dynamics

PubMed Central

Sripathi, Kamali N.; Banáš, Pavel; Reblova, Kamila; Šponer, Jiři; Otyepka, Michal

2015-01-01

The hepatitis delta virus (HDV) is the only known human pathogen whose genome contains a catalytic RNA motif (ribozyme). The overall architecture of the HDV ribozyme is that of a double-nested pseudoknot, with two GU pairs flanking the active site. Although extensive studies have shown that mutation of either wobble results in decreased catalytic activity, little work has focused on linking these mutations to specific structural effects on catalytic fitness. Here we use molecular dynamics simulations based on an activated structure to probe the active site dynamics as a result of wobble pair mutations. In both wild-type and mutant ribozymes, the in-line fitness of the active site (as a measure of catalytic proficiency) strongly depends on the presence of a C75(N3H3+)N1(O5′) hydrogen bond, which positions C75 as the general acid for the reaction. Our mutational analyses show that each GU wobble supports catalytically fit conformations in distinct ways; the reverse G25U20 wobble promotes high in-line fitness, high occupancy of the C75(N3H3+)G1(O5′) general-acid hydrogen bond and stabilization of the G1U37 wobble, while the G1U37 wobble acts more locally by stabilizing high in-line fitness and the C75(N3H3+)G1(O5′) hydrogen bond. We also find that stable type I A-minor and P1.1 hydrogen bonding above and below the active site, respectively, prevent local structural disorder from spreading and disrupting global conformation. Taken together, our results define specific, often redundant architectural roles for several structural motifs of the HDV ribozyme active site, expanding the known roles of these motifs within all HDV-like ribozymes and other structured RNAs. PMID:25631765

Bubble and skyrmion crystals in frustrated magnets with easy-axis anisotropy

DOE PAGES

Hayami, Satoru; Lin, Shi-Zeng; Batista, Cristian D.

2016-05-12

We clarify the conditions for the emergence of multiple-Q structures out of lattice and easy-axis spin anisotropy in frustrated magnets. By considering magnets whose exchange interaction has multiple global minima in momentum space, we find that both types of anisotropy stabilize triple-Q orderings. Moderate anisotropy leads to a magnetic field-induced skyrmion crystal, which evolves into a bubble crystal for increasing spatial and spin anisotropy. Finally, the bubble crystal exhibits a quasi-continuous (devil’s staircase) temperature dependent ordering wave-vector, characteristic of the competition between frustrated exchange and strong easy-axis anisotropy.

The cetaceopteryx: A global range military transport aircraft

NASA Technical Reports Server (NTRS)

Brivkalns, Chad; English, Nicole; Kazemi, Tahmineh; Kopel, Kim; Kroger, Seth; Ortega, ED

1993-01-01

This paper presents a design of a military transport aircraft capable of carrying 800,000 lbs of payload from any point in the United States to any other point in the world. Such massive airlift requires aggressive use of advanced technology and a unique configuration. The Cetaceopteyx features a joined wing, canard and six turbofan engines. The aircraft has a cost 1.07 billion (1993) dollars each. This paper presents in detail the mission description, preliminary sizing, aircraft configuration, wing design, fuselage design, empennage design, propulsion system, landing gear design, structures, drag, stability and control, systems layout, and cost analysis of the aircraft.

EIT: Solar corona synoptic observations from SOHO with an Extreme-ultraviolet Imaging Telescope

NASA Technical Reports Server (NTRS)

Delaboudiniere, J. P.; Gabriel, A. H.; Artzner, G. E.; Michels, D. J.; Dere, K. P.; Howard, R. A.; Catura, R.; Stern, R.; Lemen, J.; Neupert, W.

1988-01-01

The Extreme-ultraviolet Imaging Telescope (EIT) of SOHO (solar and heliospheric observatory) will provide full disk images in emission lines formed at temperatures that map solar structures ranging from the chromospheric network to the hot magnetically confined plasma in the corona. Images in four narrow bandpasses will be obtained using normal incidence multilayered optics deposited on quadrants of a Ritchey-Chretien telescope. The EIT is capable of providing a uniform one arc second resolution over its entire 50 by 50 arc min field of view. Data from the EIT will be extremely valuable for identifying and interpreting the spatial and temperature fine structures of the solar atmosphere. Temporal analysis will provide information on the stability of these structures and identify dynamical processes. EIT images, issued daily, will provide the global corona context for aid in unifying the investigations and in forming the observing plans for SOHO coronal instruments.

Stability Analysis of Continuous-Time and Discrete-Time Quaternion-Valued Neural Networks With Linear Threshold Neurons.

PubMed

Chen, Xiaofeng; Song, Qiankun; Li, Zhongshan; Zhao, Zhenjiang; Liu, Yurong

2018-07-01

This paper addresses the problem of stability for continuous-time and discrete-time quaternion-valued neural networks (QVNNs) with linear threshold neurons. Applying the semidiscretization technique to the continuous-time QVNNs, the discrete-time analogs are obtained, which preserve the dynamical characteristics of their continuous-time counterparts. Via the plural decomposition method of quaternion, homeomorphic mapping theorem, as well as Lyapunov theorem, some sufficient conditions on the existence, uniqueness, and global asymptotical stability of the equilibrium point are derived for the continuous-time QVNNs and their discrete-time analogs, respectively. Furthermore, a uniform sufficient condition on the existence, uniqueness, and global asymptotical stability of the equilibrium point is obtained for both continuous-time QVNNs and their discrete-time version. Finally, two numerical examples are provided to substantiate the effectiveness of the proposed results.

Under Secretary of Defense for Policy > OUSDP Offices > ASD for Homeland

Science.gov Websites

Defense Global Security > Defense Critical Infrastructure Program > Roles Skip to main for Asian and Pacific Security Affairs ASD for Homeland Defense Global Security DASD Defense -Intensity Conflict Counternarcotics and Global Threats Stability and Humanitarian Affairs Special Operations

Improving the Long-Term Stability of Atmospheric Surface Deformation Predictions by Mitigating the Effects of Orography Updates in Operational Weather Forecast Models

NASA Astrophysics Data System (ADS)

Dill, Robert; Bergmann-Wolf, Inga; Thomas, Maik; Dobslaw, Henryk

2016-04-01

The global numerical weather prediction model routinely operated at the European Centre for Medium-Range Weather Forecasts (ECMWF) is typically updated about two times a year to incorporate the most recent improvements in the numerical scheme, the physical model or the data assimilation procedures into the system for steadily improving daily weather forecasting quality. Even though such changes frequently affect the long-term stability of meteorological quantities, data from the ECMWF deterministic model is often preferred over alternatively available atmospheric re-analyses due to both the availability of the data in near real-time and the substantially higher spatial resolution. However, global surface pressure time-series, which are crucial for the interpretation of geodetic observables, such as Earth rotation, surface deformation, and the Earth's gravity field, are in particular affected by changes in the surface orography of the model associated with every major change in horizontal resolution happened, e.g., in February 2006, January 2010, and May 2015 in case of the ECMWF operational model. In this contribution, we present an algorithm to harmonize surface pressure time-series from the operational ECMWF model by projecting them onto a time-invariant reference topography under consideration of the time-variable atmospheric density structure. The effectiveness of the method will be assessed globally in terms of pressure anomalies. In addition, we will discuss the impact of the method on predictions of crustal deformations based on ECMWF input, which have been recently made available by GFZ Potsdam.

Stability of nanocrystalline Ni-based alloys: coupling Monte Carlo and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Waseda, O.; Goldenstein, H.; Silva, G. F. B. Lenz e.; Neiva, A.; Chantrenne, P.; Morthomas, J.; Perez, M.; Becquart, C. S.; Veiga, R. G. A.

2017-10-01

The thermal stability of nanocrystalline Ni due to small additions of Mo or W (up to 1 at%) was investigated in computer simulations by means of a combined Monte Carlo (MC)/molecular dynamics (MD) two-steps approach. In the first step, energy-biased on-lattice MC revealed segregation of the alloying elements to grain boundaries. However, the condition for the thermodynamic stability of these nanocrystalline Ni alloys (zero grain boundary energy) was not fulfilled. Subsequently, MD simulations were carried out for up to 0.5 μs at 1000 K. At this temperature, grain growth was hindered for minimum global concentrations of 0.5 at% W and 0.7 at% Mo, thus preserving most of the nanocrystalline structure. This is in clear contrast to a pure Ni model system, for which the transformation into a monocrystal was observed in MD simulations within 0.2 μs at the same temperature. These results suggest that grain boundary segregation of low-soluble alloying elements in low-alloyed systems can produce high-temperature metastable nanocrystalline materials. MD simulations carried out at 1200 K for 1 at% Mo/W showed significant grain boundary migration accompanied by some degree of solute diffusion, thus providing additional evidence that solute drag mostly contributed to the nanostructure stability observed at lower temperature.

Modeling global changes induced by local perturbations to the HIV-1 capsid.

PubMed

Bergman, Shana; Lezon, Timothy R

2017-01-01

The HIV-1 capsid is a conical protein shell made up of hexamers and pentamers of the capsid protein. The capsid houses the viral genome and replication machinery, and its opening, or uncoating, within the host cell marks a critical step in the HIV-1 lifecycle. Binding of host factors such as TRIM5α and cyclophilin A (CypA) can alter the capsid's stability, accelerating or delaying the onset of uncoating and disrupting infectivity. We employ coarse-grained computational modeling to investigate the effects of point mutations and host factor binding on HIV-1 capsid stability. We find that the largest fluctuations occur in the low-curvature regions of the capsid, and that its structural dynamics are affected by perturbations at the inter-hexamer interfaces and near the CypA binding loop, suggesting roles for these features in capsid stability. Our models show that linking capsid proteins across hexamers attenuates vibration in the low-curvature regions of the capsid, but that linking within hexamers does not. These results indicate a possible mechanism through which CypA binding alters capsid stability and highlight the utility of coarse-grained network modeling for understanding capsid mechanics. Copyright © 2016 The Authors. Published by Elsevier Inc. All rights reserved.

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.

The tropical tropopause inversion layer: variability and modulation by equatorial waves

NASA Astrophysics Data System (ADS)

Pilch Kedzierski, Robin; Matthes, Katja; Bumke, Karl

2016-09-01

The tropical tropopause layer (TTL) acts as a transition layer between the troposphere and the stratosphere over several kilometers, where air has both tropospheric and stratospheric properties. Within this region, a fine-scale feature is located: the tropopause inversion layer (TIL), which consists of a sharp temperature inversion at the tropopause and the corresponding high static stability values right above, which theoretically affect the dispersion relations of atmospheric waves like Rossby or inertia-gravity waves and hamper stratosphere-troposphere exchange (STE). Therefore, the TIL receives increasing attention from the scientific community, mainly in the extratropics so far. Our goal is to give a detailed picture of the properties, variability and forcings of the tropical TIL, with special emphasis on small-scale equatorial waves and the quasi-biennial oscillation (QBO).We use high-resolution temperature profiles from the COSMIC satellite mission, i.e., ˜ 2000 measurements per day globally, between 2007 and 2013, to derive TIL properties and to study the fine-scale structures of static stability in the tropics. The situation at near tropopause level is described by the 100 hPa horizontal wind divergence fields, and the vertical structure of the QBO is provided by the equatorial winds at all levels, both from the ERA-Interim reanalysis.We describe a new feature of the equatorial static stability profile: a secondary stability maximum below the zero wind line within the easterly QBO wind regime at about 20-25 km altitude, which is forced by the descending westerly QBO phase and gives a double-TIL-like structure. In the lowermost stratosphere, the TIL is stronger with westerly winds. We provide the first evidence of a relationship between the tropical TIL strength and near-tropopause divergence, with stronger (weaker) TIL with near-tropopause divergent (convergent) flow, a relationship analogous to that of TIL strength with relative vorticity in the extratropics.To elucidate possible enhancing mechanisms of the tropical TIL, we quantify the signature of the different equatorial waves on the vertical structure of static stability in the tropics. All waves show, on average, maximum cold anomalies at the thermal tropopause, warm anomalies above and a net TIL enhancement close to the tropopause. The main drivers are Kelvin, inertia-gravity and Rossby waves. We suggest that a similar wave modulation will exist at mid- and polar latitudes from the extratropical wave modes.

A scanning radar altimeter for mapping continental topography

NASA Technical Reports Server (NTRS)

Dixon, T. H.

1986-01-01

Topographic information constitutes a fundamental data set for the Earth sciences. In the geological and geophysical sciences, topography combined with gravitational information provides an important constraint on the structure and rheologic properties of the crust and lithosphere. Detailed topography data can also be used to map offsets associated with faulting and to reveal the effects of tectonic deformation. In the polar regions, elevation data form a crucial but as yet largely unavailable resource for studying ice sheet mass balance and ice flow dynamics. The vast Antarctic ice sheet is the largest fresh water reservoir on Earth and is an important influence on ocean circulation and global climate. However, our knowledge of its stability is so limited that we cannot even specify whether the Antarctic ice sheet is growing or shrinking. It is clear that there is need for high quality global topography data. A summary of potential applications with their resolution requirements is shown.

A spectral multi-domain technique applied to high-speed chemically reacting flows

NASA Technical Reports Server (NTRS)

Macaraeg, Michele G.; Streett, Craig L.; Hussaini, M. Yousuff

1989-01-01

The first applications of a spectral multidomain method for viscous compressible flow is presented. The method imposes a global flux balance condition at the interface so that high-order continuity of the solution is preserved. The global flux balance is imposed in terms of a spectral integral of the discrete equations across adjoining domains. Since the discretized equations interior to each domain solved are uncoupled from each other, and since the interface relation has a block structure, the solution scheme can be adapted to the particular requirements of each subdomain. The spectral multidomain technique presented is well-suited for the multiple scales associated with the chemically reacting and transition flows in hypersonic research. A nonstaggered multidomain discretization is used for the chemically reacting flow calculation, and the first implementation of a staggered multidomain mesh is presented for accurately solving the stability equation for a viscous compressible fluid.

Global stability and periodic solution of the viral dynamics

NASA Astrophysics Data System (ADS)

Song, Xinyu; Neumann, Avidan U.

2007-05-01

It is well known that the mathematical models provide very important information for the research of human immunodeficiency virus-type 1 and hepatitis C virus (HCV). However, the infection rate of almost all mathematical models is linear. The linearity shows the simple interaction between the T cells and the viral particles. In this paper, we consider the classical mathematical model with saturation response of the infection rate. By stability analysis we obtain sufficient conditions on the parameters for the global stability of the infected steady state and the infection-free steady state. We also obtain the conditions for the existence of an orbitally asymptotically stable periodic solution. Numerical simulations are presented to illustrate the results.

Examination of Csr regulatory circuitry using epistasis analysis with RNA-seq (Epi-seq) confirms that CsrD affects gene expression via CsrA, CsrB and CsrC.

PubMed

Potts, Anastasia H; Leng, Yuanyuan; Babitzke, Paul; Romeo, Tony

2018-03-29

The Csr global regulatory system coordinates gene expression in response to metabolic status. This system utilizes the RNA binding protein CsrA to regulate gene expression by binding to transcripts of structural and regulatory genes, thus affecting their structure, stability, translation, and/or transcription elongation. CsrA activity is controlled by sRNAs, CsrB and CsrC, which sequester CsrA away from other transcripts. CsrB/C levels are partly determined by their rates of turnover, which requires CsrD to render them susceptible to RNase E cleavage. Previous epistasis analysis suggested that CsrD affects gene expression through the other Csr components, CsrB/C and CsrA. However, those conclusions were based on a limited analysis of reporters. Here, we reassessed the global behavior of the Csr circuitry using epistasis analysis with RNA seq (Epi-seq). Because CsrD effects on mRNA levels were entirely lost in the csrA mutant and largely eliminated in a csrB/C mutant under our experimental conditions, while the majority of CsrA effects persisted in the absence of csrD, the original model accounts for the global behavior of the Csr system. Our present results also reflect a more nuanced role of CsrA as terminal regulator of the Csr system than has been recognized.

Electronic structure and reactivity of cobalt oxide dimers and their hexacarbonyl complexes: a density functional study.

PubMed

Uzunova, Ellie L; Mikosch, Hans

2012-03-29

The dimers of cobalt oxide (CoO)(2) with cyclic and open bent structure are studied with the B1LYP density functional; the ordering of states is validated by the CCSD(T) method. The D(2h)-symmetry rhombic dioxide Co(2)O(2) with antiferromagnetically ordered electrons on cobalt centers is the global minimum. The cyclic peroxide Co(2)(O(2)) with side-on-bonded dioxygen in (7)B(2) ground state is separated from the global minimum by an energy gap of 3.15 eV. The dioxide is highly reactive as indicated by the high value of proton affinity and chemical reactivity indices. The four-member ring structures are more stable than those with three-member ring or chain configuration. The thermodynamic stability toward dissociation to CoO increases upon carbonylation, whereas proton affinity and reactivity with release of molecular oxygen also increase. The global minimum of Co(2)O(2)(CO)(6) corresponds to a triplet state (3)A" with oxygen atoms shifted above the molecular plane of the rhombic dioxide Co(2)O(2). The SOMO-LUMO gap in the ground-state carbonylated dioxide is wider, compared to the same gap in the bare dicobalt dioxide. The peroxo-isomer Co(2)(O(2))(CO)(6) retains the planar Co(2)(O(2)) ring and is only stable in a high-spin state (7)A". The carbonylated clusters have increased reactivity in both redox and nucleophilic reactions, as a result of the increased electron density in the Co(2)O(2)-ring area.

Hierarchical Type Stability Criteria for Delayed Neural Networks via Canonical Bessel-Legendre Inequalities.

PubMed

Zhang, Xian-Ming; Han, Qing-Long; Zeng, Zhigang

2018-05-01

This paper is concerned with global asymptotic stability of delayed neural networks. Notice that a Bessel-Legendre inequality plays a key role in deriving less conservative stability criteria for delayed neural networks. However, this inequality is in the form of Legendre polynomials and the integral interval is fixed on . As a result, the application scope of the Bessel-Legendre inequality is limited. This paper aims to develop the Bessel-Legendre inequality method so that less conservative stability criteria are expected. First, by introducing a canonical orthogonal polynomial sequel, a canonical Bessel-Legendre inequality and its affine version are established, which are not explicitly in the form of Legendre polynomials. Moreover, the integral interval is shifted to a general one . Second, by introducing a proper augmented Lyapunov-Krasovskii functional, which is tailored for the canonical Bessel-Legendre inequality, some sufficient conditions on global asymptotic stability are formulated for neural networks with constant delays and neural networks with time-varying delays, respectively. These conditions are proven to have a hierarchical feature: the higher level of hierarchy, the less conservatism of the stability criterion. Finally, three numerical examples are given to illustrate the efficiency of the proposed stability criteria.

Improvement of Global and Regional Mean Sea Level Trends Derived from all Altimetry Missions.

NASA Astrophysics Data System (ADS)

Ablain, Michael; Benveniste, Jérôme; Faugere, Yannice; Larnicol, Gilles; Cazenave, Anny; Johannessen, Johnny A.; Stammer, Detlef; Timms, Gary

2012-07-01

The global mean sea level (GMSL) has been calculated on a continual basis since January 1993 using data from satellite altimetry missions. The global mean sea level (MSL) deduced from TOPEX/Poseidon, Jason-1 and Jason-2 is increasing with a global trend of 3.2 mm from 1993 to 2010 applying the post glacial rebound (MSL Aviso website http://www.jason.oceanobs.com/msl). Besides, the regional sea level trends bring out an inhomogeneous repartition of the ocean elevation with local MSL slopes ranging from +/- 8 mm/year. A study published in 2009 [Ablain et al., 2009] has shown that the global MSL trend uncertainty was estimated at +/-0.6 mm/year with a confidence interval of 90%. The main sources of errors at global and regional scales are due to the orbit calculation and the wet troposphere correction. But others sea-level components have also a significant impact on the long-term stability of MSL as for instance the stability of instrumental parameters and the atmospheric corrections. Thanks to recent studies performed in Sea Level Essential Climate Variable Project in the frame of the Climate Change Initiative, an ESA Programme, in addition to activities performed within the SALP/CNES, strong improvements have been provided for the estimation of the global and regional MSL trends. In this paper, we propose to describe them; they concern the orbit calculation thanks to new gravity fields, the atmospheric corrections thanks to ERA-interim reanalyses, the wet troposphere corrections thanks to the stability improvement, and also empirical corrections allowing us to link regional time series together better. These improvements are described at global and regional scale for all the altimetry missions.

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...

Atomistic simulations and network-based modeling of the Hsp90-Cdc37 chaperone binding with Cdk4 client protein: A mechanism of chaperoning kinase clients by exploiting weak spots of intrinsically dynamic kinase domains

PubMed Central

Czemeres, Josh; Buse, Kurt

2017-01-01

A fundamental role of the Hsp90 and Cdc37 chaperones in mediating conformational development and activation of diverse protein kinase clients is essential in signal transduction. There has been increasing evidence that the Hsp90-Cdc37 system executes its chaperoning duties by recognizing conformational instability of kinase clients and modulating their folding landscapes. The recent cryo-electron microscopy structure of the Hsp90-Cdc37-Cdk4 kinase complex has provided a framework for dissecting regulatory principles underlying differentiation and recruitment of protein kinase clients to the chaperone machinery. In this work, we have combined atomistic simulations with protein stability and network-based rigidity decomposition analyses to characterize dynamic factors underlying allosteric mechanism of the chaperone-kinase cycle and identify regulatory hotspots that control client recognition. Through comprehensive characterization of conformational dynamics and systematic identification of stabilization centers in the unbound and client- bound Hsp90 forms, we have simulated key stages of the allosteric mechanism, in which Hsp90 binding can induce instability and partial unfolding of Cdk4 client. Conformational landscapes of the Hsp90 and Cdk4 structures suggested that client binding can trigger coordinated dynamic changes and induce global rigidification of the Hsp90 inter-domain regions that is coupled with a concomitant increase in conformational flexibility of the kinase client. This process is allosteric in nature and can involve reciprocal dynamic exchanges that exert global effect on stability of the Hsp90 dimer, while promoting client instability. The network-based rigidity analysis and emulation of thermal unfolding of the Cdk4-cyclin D complex and Hsp90-Cdc37-Cdk4 complex revealed weak spots of kinase instability that are present in the native Cdk4 structure and are targeted by the chaperone during client recruitment. Our findings suggested that this mechanism may be exploited by the Hsp90-Cdc37 chaperone to recruit and protect intrinsically dynamic kinase clients from degradation. The results of this investigation are discussed and interpreted in the context of diverse experimental data, offering new insights into mechanisms of chaperone regulation and binding. PMID:29267381

Global exponential stability of positive periodic solution of the n-species impulsive Gilpin-Ayala competition model with discrete and distributed time delays.

PubMed

Zhao, Kaihong

2018-12-01

In this paper, we study the n-species impulsive Gilpin-Ayala competition model with discrete and distributed time delays. The existence of positive periodic solution is proved by employing the fixed point theorem on cones. By constructing appropriate Lyapunov functional, we also obtain the global exponential stability of the positive periodic solution of this system. As an application, an interesting example is provided to illustrate the validity of our main results.

International Agreements and Cooperation in Environmental Conservation and Resource Management.

ERIC Educational Resources Information Center

Thacher, Peter S.

1991-01-01

Considerations regarding stabilizing the greenhouse effect (global warming) emphasize the difficulties in launching a comprehensive plan to deal with aspects of global change. Experience gained in dealing with atmospheric issues will help in developing a process that links management and research in solving global problems. (SLD)

AEERL (AIR AND ENERGY ENGINEERING RESEARCH LABORATORY) RESEARCH PLAN ON THE GLOBAL CLIMATE EMISSIONS ASSESSMENT AND STABILIZATION PROGRAM

EPA Science Inventory

The paper discusses the Environmental Protection Agency's (EPA) Air and Energy Engineering Research Laboratory (AEERL) research plan for work in the global climate area. The plan, written for discussion with senior scientists and program managers at EPA's Global Climate Change Re...

The Army’s Carbon Bootprint

DTIC Science & Technology

2009-05-06

GWP relative to CO2 • GWP is determined by stability of the chemical in the atmosphere and its capacity to influence global warming Global Warming Potential...GWP) Mr. Larry Webber/(410)436-1231/ Lawrence.webber.us.army.mil 06MAY2009 The Army’s Carbon Bootprint Greenhouse Gas (GHG) Global Warming Potential

July: "Soils are living: Overview of soil biodiversity, global issues, and new resources"

USDA-ARS?s Scientific Manuscript database

The July poster will provide an overview of soil biology and the many ecosystem functions that soil organisms drive including their impact on global biodiversity, climate regulation, soil health/stability, and plant growth. Five main global issues related to soil biodiversity will be presented such ...

Impact of genetic variation on three dimensional structure and function of proteins

PubMed Central

Bhattacharya, Roshni; Rose, Peter W.; Burley, Stephen K.

2017-01-01

The Protein Data Bank (PDB; http://wwpdb.org) was established in 1971 as the first open access digital data resource in biology with seven protein structures as its initial holdings. The global PDB archive now contains more than 126,000 experimentally determined atomic level three-dimensional (3D) structures of biological macromolecules (proteins, DNA, RNA), all of which are freely accessible via the Internet. Knowledge of the 3D structure of the gene product can help in understanding its function and role in disease. Of particular interest in the PDB archive are proteins for which 3D structures of genetic variant proteins have been determined, thus revealing atomic-level structural differences caused by the variation at the DNA level. Herein, we present a systematic and qualitative analysis of such cases. We observe a wide range of structural and functional changes caused by single amino acid differences, including changes in enzyme activity, aggregation propensity, structural stability, binding, and dissociation, some in the context of large assemblies. Structural comparison of wild type and mutated proteins, when both are available, provide insights into atomic-level structural differences caused by the genetic variation. PMID:28296894

Convective and global stability analysis of a Mach 5.8 boundary layer grazing a compliant surface

NASA Astrophysics Data System (ADS)

Dettenrieder, Fabian; Bodony, Daniel

2016-11-01

Boundary layer transition on high-speed vehicles is expected to be affected by unsteady surface compliance. The stability properties of a Mach 5.8 zero-pressure-gradient laminar boundary layer grazing a nominally-flat thermo-mechanically compliant panel is considered. The linearized compressible Navier-Stokes equations describe small amplitude disturbances in the fluid while the panel deformations are described by the Kirchhoff-Love plate equation and its thermal state by the transient heat equation. Compatibility conditions that couple disturbances in the fluid to those in the solid yield simple algebraic and robin boundary conditions for the velocity and thermal states, respectively. A local convective stability analysis shows that the panel can modify both the first and second Mack modes when, for metallic-like panels, the panel thickness exceeds the lengthscale δ99 Rex- 0 . 5 . A global stability analysis, which permits finite panel lengths with clamped-clamped boundary conditions, shows a rich eigenvalue spectrum with several branches. Unstable modes are found with streamwise-growing panel deformations leading to Mach wave-type radiation. Stable global modes are also found and have distinctly different panel modes but similar radiation patterns. Air Force Office of Scientific Research.

Differential Modulation of Functional Dynamics and Allosteric Interactions in the Hsp90-Cochaperone Complexes with p23 and Aha1: A Computational Study

PubMed Central

Blacklock, Kristin; Verkhivker, Gennady M.

2013-01-01

Allosteric interactions of the molecular chaperone Hsp90 with a large cohort of cochaperones and client proteins allow for molecular communication and event coupling in signal transduction networks. The integration of cochaperones into the Hsp90 system is driven by the regulatory mechanisms that modulate the progression of the ATPase cycle and control the recruitment of the Hsp90 clientele. In this work, we report the results of computational modeling of allosteric regulation in the Hsp90 complexes with the cochaperones p23 and Aha1. By integrating protein docking, biophysical simulations, modeling of allosteric communications, protein structure network analysis and the energy landscape theory we have investigated dynamics and stability of the Hsp90-p23 and Hsp90-Aha1 interactions in direct comparison with the extensive body of structural and functional experiments. The results have revealed that functional dynamics and allosteric interactions of Hsp90 can be selectively modulated by these cochaperones via specific targeting of the regulatory hinge regions that could restrict collective motions and stabilize specific chaperone conformations. The protein structure network parameters have quantified the effects of cochaperones on conformational stability of the Hsp90 complexes and identified dynamically stable communities of residues that can contribute to the strengthening of allosteric interactions. According to our results, p23-mediated changes in the Hsp90 interactions may provide “molecular brakes” that could slow down an efficient transmission of the inter-domain allosteric signals, consistent with the functional role of p23 in partially inhibiting the ATPase cycle. Unlike p23, Aha1-mediated acceleration of the Hsp90-ATPase cycle may be achieved via modulation of the equilibrium motions that facilitate allosteric changes favoring a closed dimerized form of Hsp90. The results of our study have shown that Aha1 and p23 can modulate the Hsp90-ATPase activity and direct the chaperone cycle by exerting the precise control over structural stability, global movements and allosteric communications in Hsp90. PMID:23977182

Synthetic Biology of Proteins: Tuning GFPs Folding and Stability with Fluoroproline

PubMed Central

Steiner, Thomas; Hess, Petra; Bae, Jae Hyun; Wiltschi, Birgit; Moroder, Luis; Budisa, Nediljko

2008-01-01

Background Proline residues affect protein folding and stability via cis/trans isomerization of peptide bonds and by the Cγ-exo or -endo puckering of their pyrrolidine rings. Peptide bond conformation as well as puckering propensity can be manipulated by proper choice of ring substituents, e.g. Cγ-fluorination. Synthetic chemistry has routinely exploited ring-substituted proline analogs in order to change, modulate or control folding and stability of peptides. Methodology/Principal Findings In order to transmit this synthetic strategy to complex proteins, the ten proline residues of enhanced green fluorescent protein (EGFP) were globally replaced by (4R)- and (4S)-fluoroprolines (FPro). By this approach, we expected to affect the cis/trans peptidyl-proline bond isomerization and pyrrolidine ring puckering, which are responsible for the slow folding of this protein. Expression of both protein variants occurred at levels comparable to the parent protein, but the (4R)-FPro-EGFP resulted in irreversibly unfolded inclusion bodies, whereas the (4S)-FPro-EGFP led to a soluble fluorescent protein. Upon thermal denaturation, refolding of this variant occurs at significantly higher rates than the parent EGFP. Comparative inspection of the X-ray structures of EGFP and (4S)-FPro-EGFP allowed to correlate the significantly improved refolding with the Cγ-endo puckering of the pyrrolidine rings, which is favored by 4S-fluorination, and to lesser extents with the cis/trans isomerization of the prolines. Conclusions/Significance We discovered that the folding rates and stability of GFP are affected to a lesser extent by cis/trans isomerization of the proline bonds than by the puckering of pyrrolidine rings. In the Cγ-endo conformation the fluorine atoms are positioned in the structural context of the GFP such that a network of favorable local interactions is established. From these results the combined use of synthetic amino acids along with detailed structural knowledge and existing protein engineering methods can be envisioned as a promising strategy for the design of complex tailor-made proteins and even cellular structures of superior properties compared to the native forms. PMID:18301757

Structural dynamics of Casein Kinase I (CKI) from malarial parasite Plasmodium falciparum (Isolate 3D7): Insights from theoretical modelling and molecular simulations.

PubMed

Dehury, Budheswar; Behera, Santosh Kumar; Mahapatra, Namita

2017-01-01

The protein kinases (PKs), belonging to serine/threonine kinase (STKs), are important drug targets for a wide spectrum of diseases in human. Among protein kinases, the Casein Kinases (CKs) are vastly expanded in various organisms, where, the malarial parasite Plasmodium falciparum possesses a single member i.e., PfCKI, which can phosphorylate various proteins in parasite extracts in vitro condition. But, the structure-function relationship of PfCKI and dynamics of ATP binding is yet to be understood. Henceforth, an attempt was made to study the dynamics, stability, and ATP binding mechanisms of PfCKI through computational modelling, docking, molecular dynamics (MD) simulations, and MM/PBSA binding free energy estimation. Bi-lobed catalytic domain of PfCKI shares a high degree of secondary structure topology with CKI domains of rice, human, and mouse indicating co-evolution of these kinases. Molecular docking study revealed that ATP binds to the active site where the glycine-rich ATP-binding motif (G16-X-G18-X-X-G21) along with few conserved residues plays a crucial role maintaining stability of the complex. Structural superposition of PfCKI with close structural homologs depicted that the location and length of important loops are different, indicating the dynamic properties of these loops among CKIs, which is consistent with principal component analysis (PCA). PCA displayed that the overall global motion of ATP-bound form is comparatively higher than that of apo form. The present study provides insights into the structural features of PfCKI, which could contribute towards further understanding of related protein structures, dynamics of catalysis and phosphorylation mechanism in these important STKs from malarial parasite in near future. Copyright © 2016 Elsevier Inc. All rights reserved.

Simulating protein folding initiation sites using an alpha-carbon-only knowledge-based force field

PubMed Central

Buck, Patrick M.; Bystroff, Christopher

2015-01-01

Protein folding is a hierarchical process where structure forms locally first, then globally. Some short sequence segments initiate folding through strong structural preferences that are independent of their three-dimensional context in proteins. We have constructed a knowledge-based force field in which the energy functions are conditional on local sequence patterns, as expressed in the hidden Markov model for local structure (HMMSTR). Carbon-alpha force field (CALF) builds sequence specific statistical potentials based on database frequencies for α-carbon virtual bond opening and dihedral angles, pairwise contacts and hydrogen bond donor-acceptor pairs, and simulates folding via Brownian dynamics. We introduce hydrogen bond donor and acceptor potentials as α-carbon probability fields that are conditional on the predicted local sequence. Constant temperature simulations were carried out using 27 peptides selected as putative folding initiation sites, each 12 residues in length, representing several different local structure motifs. Each 0.6 μs trajectory was clustered based on structure. Simulation convergence or representativeness was assessed by subdividing trajectories and comparing clusters. For 21 of the 27 sequences, the largest cluster made up more than half of the total trajectory. Of these 21 sequences, 14 had cluster centers that were at most 2.6 Å root mean square deviation (RMSD) from their native structure in the corresponding full-length protein. To assess the adequacy of the energy function on nonlocal interactions, 11 full length native structures were relaxed using Brownian dynamics simulations. Equilibrated structures deviated from their native states but retained their overall topology and compactness. A simple potential that folds proteins locally and stabilizes proteins globally may enable a more realistic understanding of hierarchical folding pathways. PMID:19137613

Stability and global Hopf bifurcation in a delayed food web consisting of a prey and two predators

NASA Astrophysics Data System (ADS)

Meng, Xin-You; Huo, Hai-Feng; Zhang, Xiao-Bing

2011-11-01

This paper is concerned with a predator-prey system with Holling II functional response and hunting delay and gestation. By regarding the sum of delays as the bifurcation parameter, the local stability of the positive equilibrium and the existence of Hopf bifurcation are investigated. We obtained explicit formulas to determine the properties of Hopf bifurcation by using the normal form method and center manifold theorem. Special attention is paid to the global continuation of local Hopf bifurcation. Using a global Hopf bifurcation result of Wu [Wu JH. Symmetric functional differential equations and neural networks with memory, Trans Amer Math Soc 1998;350:4799-4838] for functional differential equations, we may show the global existence of the periodic solutions. Finally, several numerical simulations illustrating the theoretical analysis are also given.

Conformational changes in the expression domain of the Escherichia coli thiM riboswitch

PubMed Central

Rentmeister, Andrea; Mayer, Günter; Kuhn, Nicole; Famulok, Michael

2007-01-01

The thiM riboswitch contains an aptamer domain that adaptively binds the coenzyme thiamine pyrophosphate (TPP). The binding of TPP to the aptamer domain induces structural rearrangements that are relayed to a second domain, the so-called expression domain, thereby interfering with gene expression. The recently solved crystal structures of the aptamer domains of the thiM riboswitches in complex with TPP revealed how TPP stabilizes secondary and tertiary structures in the RNA ligand complex. To understand the global modes of reorganization between the two domains upon metabolite binding the structure of the entire riboswitch in presence and absence of TPP needs to be determined. Here we report the secondary structure of the entire thiM riboswitch from Escherichia coli in its TPP-free form and its transition into the TPP-bound variant, thereby depicting domains of the riboswitch that serve as communication links between the aptamer and the expression domain. Furthermore, structural probing provides an explanation for the lack of genetic control exerted by a riboswitch variant with mutations in the expression domain that still binds TPP. PMID:17517779

Structural Rearrangement in an RsmA/CsrA Ortholog of Pseudomonas aeruginosa Creates a Dimeric RNA-Binding Protein, RsmN

PubMed Central

Morris, Elizabeth R.; Hall, Gareth; Li, Chan; Heeb, Stephan; Kulkarni, Rahul V.; Lovelock, Laura; Silistre, Hazel; Messina, Marco; Cámara, Miguel; Emsley, Jonas; Williams, Paul; Searle, Mark S.

2013-01-01

Summary In bacteria, the highly conserved RsmA/CsrA family of RNA-binding proteins functions as global posttranscriptional regulators acting on mRNA translation and stability. Through phenotypic complementation of an rsmA mutant in Pseudomonas aeruginosa, we discovered a family member, termed RsmN. Elucidation of the RsmN crystal structure and that of the complex with a hairpin from the sRNA, RsmZ, reveals a uniquely inserted α helix, which redirects the polypeptide chain to form a distinctly different protein fold to the domain-swapped dimeric structure of RsmA homologs. The overall β sheet structure required for RNA recognition is, however, preserved with compensatory sequence and structure differences, allowing the RsmN dimer to target binding motifs in both structured hairpin loops and flexible disordered RNAs. Phylogenetic analysis indicates that, although RsmN appears unique to P. aeruginosa, homologous proteins with the inserted α helix are more widespread and arose as a consequence of a gene duplication event. PMID:23954502

Neutral and charged gallium clusters: structures, physical properties and implications for the melting features

NASA Astrophysics Data System (ADS)

Núñez, Sara; López, José M.; Aguado, Andrés

2012-09-01

We report the putative Global Minimum (GM) structures and electronic properties of GaN+, GaN and GaN- clusters with N = 13-37 atoms, obtained from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ an exchange-correlation functional which accounts for van der Waals dispersion interactions (vdW-DFT). We find a wide diversity of structural motifs within the located GM, including decahedral, polyicosahedral, polytetrahedral and layered structures. The GM structures are also extremely sensitive to the number of electrons in the cluster, so that the structures of neutral and charged clusters differ for most sizes. The main magic numbers (clusters with an enhanced stability) are identified and interpreted in terms of electronic and geometric shell closings. The theoretical results are consistent with experimental abundance mass spectra of GaN+ and with photoelectron spectra of GaN-. The size dependence of the latent heats of melting, the shape of the heat capacity peaks, and the temperature dependence of the collision cross-sections, all measured for GaN+ clusters, are properly interpreted in terms of the calculated cohesive energies, spectra of configurational excitations, and cluster shapes, respectively. The transition from ``non-melter'' to ``magic-melter'' behaviour, experimentally observed between Ga30+ and Ga31+, is traced back to a strong geometry change. Finally, the higher-than-bulk melting temperatures of gallium clusters are correlated with a more typically metallic behaviour of the clusters as compared to the bulk, contrary to previous theoretical claims.We report the putative Global Minimum (GM) structures and electronic properties of GaN+, GaN and GaN- clusters with N = 13-37 atoms, obtained from first-principles density functional theory structural optimizations. The calculations include spin polarization and employ an exchange-correlation functional which accounts for van der Waals dispersion interactions (vdW-DFT). We find a wide diversity of structural motifs within the located GM, including decahedral, polyicosahedral, polytetrahedral and layered structures. The GM structures are also extremely sensitive to the number of electrons in the cluster, so that the structures of neutral and charged clusters differ for most sizes. The main magic numbers (clusters with an enhanced stability) are identified and interpreted in terms of electronic and geometric shell closings. The theoretical results are consistent with experimental abundance mass spectra of GaN+ and with photoelectron spectra of GaN-. The size dependence of the latent heats of melting, the shape of the heat capacity peaks, and the temperature dependence of the collision cross-sections, all measured for GaN+ clusters, are properly interpreted in terms of the calculated cohesive energies, spectra of configurational excitations, and cluster shapes, respectively. The transition from ``non-melter'' to ``magic-melter'' behaviour, experimentally observed between Ga30+ and Ga31+, is traced back to a strong geometry change. Finally, the higher-than-bulk melting temperatures of gallium clusters are correlated with a more typically metallic behaviour of the clusters as compared to the bulk, contrary to previous theoretical claims. Electronic supplementary information (ESI) available: Atomic coordinates (in xyz format and Å units) and point group symmetries for the global minimum structures reported in this paper. See DOI: 10.1039/c2nr31222k

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

NASA Astrophysics Data System (ADS)

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

2018-05-01

We report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experiments and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Finally, the observed frequencies of the Nsbnd H and Osbnd H stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

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

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

Here, we report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experimentsmore » and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Lastly, the observed frequencies of the NH and OH stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.« less

Revealing the structure of isolated peptides: IR-IR predissociation spectroscopy of protonated triglycine isomers

DOE PAGES

Voss, Jonathan M.; Fischer, Kaitlyn C.; Garand, Etienne

2018-03-08

Here, we report an isomer specific IR-IR double resonance study of the mass-selected protonated triglycine peptide. Comparison of experimental spectra with calculations reveals the presence of two isomers, with protonation occurring at either the terminal amine site or one of the amide oxygen sites. The amine protonated isomer identified in our experiment contains an atypical cis amide configuration as well as a more typical trans amide. The amide protonated peptide, on the other hand, contains two trans amide moieties. Both isomers are found to be the lowest energy structures for their respective protonation site, but it is unclear, from experimentsmore » and calculations, which one is the global minimum. The presence of both in our experiments likely points to kinetic trapping of a higher energy structure. Lastly, the observed frequencies of the NH and OH stretch vibrations are used to estimate the hydrogen-bond strengths present in each isomer, accounting for the relative stabilities of these structures.« less

High-throughput search of ternary chalcogenides for p-type transparent electrodes

PubMed Central

Shi, Jingming; Cerqueira, Tiago F. T.; Cui, Wenwen; Nogueira, Fernando; Botti, Silvana; Marques, Miguel A. L.

2017-01-01

Delafossite crystals are fascinating ternary oxides that have demonstrated transparent conductivity and ambipolar doping. Here we use a high-throughput approach based on density functional theory to find delafossite and related layered phases of composition ABX2, where A and B are elements of the periodic table, and X is a chalcogen (O, S, Se, and Te). From the 15 624 compounds studied in the trigonal delafossite prototype structure, 285 are within 50 meV/atom from the convex hull of stability. These compounds are further investigated using global structural prediction methods to obtain their lowest-energy crystal structure. We find 79 systems not present in the materials project database that are thermodynamically stable and crystallize in the delafossite or in closely related structures. These novel phases are then characterized by calculating their band gaps and hole effective masses. This characterization unveils a large diversity of properties, ranging from normal metals, magnetic metals, and some candidate compounds for p-type transparent electrodes. PMID:28266587

An effective immunization strategy for airborne epidemics in modular and hierarchical social contact network

NASA Astrophysics Data System (ADS)

Song, Zhichao; Ge, Yuanzheng; Luo, Lei; Duan, Hong; Qiu, Xiaogang

2015-12-01

Social contact between individuals is the chief factor for airborne epidemic transmission among the crowd. Social contact networks, which describe the contact relationships among individuals, always exhibit overlapping qualities of communities, hierarchical structure and spatial-correlated. We find that traditional global targeted immunization strategy would lose its superiority in controlling the epidemic propagation in the social contact networks with modular and hierarchical structure. Therefore, we propose a hierarchical targeted immunization strategy to settle this problem. In this novel strategy, importance of the hierarchical structure is considered. Transmission control experiments of influenza H1N1 are carried out based on a modular and hierarchical network model. Results obtained indicate that hierarchical structure of the network is more critical than the degrees of the immunized targets and the modular network layer is the most important for the epidemic propagation control. Finally, the efficacy and stability of this novel immunization strategy have been validated as well.

The impact of laser irradiation on global stability in patients with vertebrobasilar insufficiency: A clinical report

PubMed Central

Lukowicz, Malgorzata; Zalewski, Pawel; Bulatowicz, Irena; Buszko, Katarzyna; Klawe, Jacek J.

2011-01-01

Summary Background The purpose of our experiment was to determine whether laser stimulation can improve microcirculation in the posterior regions of the brain in patients with vertebrobasilar insufficiency (VBI). Material/Methods We studied 25 patients (20 female, 5 male, mean age 64) diagnosed with chronic VBI. All were evaluated using the De Klyn test, followed by qualitative assessment of stability using a Berg Balance Scale and evaluation of global stability using an electronic balance platform. A CTL-1100 low power laser was used with standard parameters. We established a protocol for laser irradiation at 5 points along the vertebral artery in the cervical region bilaterally. Irradiation was performed 10 times over two weeks. Results Significant improvement occurred after therapy in headache (p=0.0005), vertigo (p<0.0000), and tinnitus (p=0.0387). No significant differences were observed in nausea or nystagmus caused by head rotation. The Berg Balance Scale results showed significant differences in almost all features. There was a tendency towards improved stability in all parameters, and statistically significant differences in the total surface of support and the spread surface of support for the left foot. Conclusions Laser stimulation as applied in this study can be useful in the treatment of patients with VBI. The main reason for improvement in global stability, balance, and other VBI symptoms is better blood perfusion. PMID:21873949

Satellite Instrument Calibration for Measuring Global Climate Change. Report of a Workshop at the University of Maryland Inn and Conference Center, College Park, MD. , November 12-14, 2002

NASA Technical Reports Server (NTRS)

Ohring, G.; Wielicki, B.; Spencer, R.; Emery, B.; Datla, R.

2004-01-01

Measuring the small changes associated with long-term global climate change from space is a daunting task. To address these problems and recommend directions for improvements in satellite instrument calibration some 75 scientists, including researchers who develop and analyze long-term data sets from satellites, experts in the field of satellite instrument calibration, and physicists working on state of the art calibration sources and standards met November 12 - 14, 2002 and discussed the issues. The workshop defined the absolute accuracies and long-term stabilities of global climate data sets that are needed to detect expected trends, translated these data set accuracies and stabilities to required satellite instrument accuracies and stabilities, and evaluated the ability of current observing systems to meet these requirements. The workshop's recommendations include a set of basic axioms or overarching principles that must guide high quality climate observations in general, and a roadmap for improving satellite instrument characterization, calibration, inter-calibration, and associated activities to meet the challenge of measuring global climate change. It is also recommended that a follow-up workshop be conducted to discuss implementation of the roadmap developed at this workshop.

Discovery of a Superconducting High-Entropy Alloy

NASA Astrophysics Data System (ADS)

Koželj, P.; Vrtnik, S.; Jelen, A.; Jazbec, S.; Jagličić, Z.; Maiti, S.; Feuerbacher, M.; Steurer, W.; Dolinšek, J.

2014-09-01

High-entropy alloys (HEAs) are multicomponent mixtures of elements in similar concentrations, where the high entropy of mixing can stabilize disordered solid-solution phases with simple structures like a body-centered cubic or a face-centered cubic, in competition with ordered crystalline intermetallic phases. We have synthesized an HEA with the composition Ta34Nb33Hf8Zr14Ti11 (in at. %), which possesses an average body-centered cubic structure of lattice parameter a =3.36 Å. The measurements of the electrical resistivity, the magnetization and magnetic susceptibility, and the specific heat revealed that the Ta34Nb33Hf8Zr14Ti11 HEA is a type II superconductor with a transition temperature Tc≈7.3 K, an upper critical field μ0Hc2≈8.2 T, a lower critical field μ0Hc1≈32 mT, and an energy gap in the electronic density of states (DOS) at the Fermi level of 2Δ ≈2.2 meV. The investigated HEA is close to a BCS-type phonon-mediated superconductor in the weak electron-phonon coupling limit, classifying it as a "dirty" superconductor. We show that the lattice degrees of freedom obey Vegard's rule of mixtures, indicating completely random mixing of the elements on the HEA lattice, whereas the electronic degrees of freedom do not obey this rule even approximately so that the electronic properties of a HEA are not a "cocktail" of properties of the constituent elements. The formation of a superconducting gap contributes to the electronic stabilization of the HEA state at low temperatures, where the entropic stabilization is ineffective, but the electronic energy gain due to the superconducting transition is too small for the global stabilization of the disordered state, which remains metastable.

Effect of varying polyglutamate chain length on the structure and stability of ferricytochrome c.

PubMed

Antalík, Marián; Bágel'ová, Jaroslava; Gazová, Zuzana; Musatov, Andrej; Fedunová, Diana

2003-03-21

The effect of varying polyglutamate chain length on local and global stability of horse heart ferricytochrome c was studied using scanning calorimetry and spectroscopy methods. Spectral data indicate that polyglutamate chain lengths equal or greater than eight monomer units significantly change the apparent pK(a) for the alkaline transition of cytochrome c. The change in pK(a) is comparable to the value when cytochrome c is complexed with cytochrome bc(1). Glutamate and diglutamate do not significantly alter the temperature transition for cleavage of the Met(80)-heme iron bond of cytochrome c. At low ionic strength, polyglutamates consisting of eight or more glutamate monomers increase midpoint of the temperature transition from 57.3+/-0.2 to 66.9+/-0.2 degrees C. On the other hand, the denaturation temperature of cytochrome c decreases from 85.2+/-0.2 to 68.8+/-0.2 degrees C in the presence of polyglutamates with number of glutamate monomers n >or approximately equal 8. The rate constant for cyanide binding to the heme iron of cytochrome c of cytochrome c-polyglutamate complex also decreases by approximately 42.5% with n>or approximately equal 8. The binding constant for the binding of octaglutamate (m.w. approximately 1000) to cyt c was found to be 1.15 x 10(5) M(-1) at pH 8.0 and low ionic strength. The results indicate that the polyglutamate (n>or approximately equal 8) is able to increase the stability of the methionine sulfur-heme iron bond of cytochrome c in spite of structural differences that weaken the overall stability of the cyt c at neutral and slightly alkaline pH.

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

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

Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

DNA sequence determinants controlling affinity, stability and shape of DNA complexes bound by the nucleoid protein Fis

DOE PAGES

Hancock, Stephen P.; Stella, Stefano; Cascio, Duilio; ...

2016-03-09

The abundant Fis nucleoid protein selectively binds poorly related DNA sequences with high affinities to regulate diverse DNA reactions. Fis binds DNA primarily through DNA backbone contacts and selects target sites by reading conformational properties of DNA sequences, most prominently intrinsic minor groove widths. High-affinity binding requires Fis-stabilized DNA conformational changes that vary depending on DNA sequence. In order to better understand the molecular basis for high affinity site recognition, we analyzed the effects of DNA sequence within and flanking the core Fis binding site on binding affinity and DNA structure. X-ray crystal structures of Fis-DNA complexes containing variable sequencesmore » in the noncontacted center of the binding site or variations within the major groove interfaces show that the DNA can adapt to the Fis dimer surface asymmetrically. We show that the presence and position of pyrimidine-purine base steps within the major groove interfaces affect both local DNA bending and minor groove compression to modulate affinities and lifetimes of Fis-DNA complexes. Sequences flanking the core binding site also modulate complex affinities, lifetimes, and the degree of local and global Fis-induced DNA bending. In particular, a G immediately upstream of the 15 bp core sequence inhibits binding and bending, and A-tracts within the flanking base pairs increase both complex lifetimes and global DNA curvatures. Taken together, our observations support a revised DNA motif specifying high-affinity Fis binding and highlight the range of conformations that Fis-bound DNA can adopt. Lastly, the affinities and DNA conformations of individual Fis-DNA complexes are likely to be tailored to their context-specific biological functions.« less

Title: Chimeras in small, globally coupled networks: Experiments and stability analysis

NASA Astrophysics Data System (ADS)

Hart, Joseph D.; Bansal, Kanika; Murphy, Thomas E.; Roy, Rajarshi

Since the initial observation of chimera states, there has been much discussion of the conditions under which these states emerge. The emphasis thus far has mainly been to analyze large networks of coupled oscillators; however, recent studies have begun to focus on the opposite limit: what is the smallest system of coupled oscillators in which chimeras can exist? We experimentally observe chimeras and other partially synchronous patterns in a network of four globally-coupled chaotic opto-electronic oscillators. By examining the equations of motion, we demonstrate that symmetries in the network topology allow a variety of synchronous states to exist, including cluster synchronous states and a chimera state. Using the group theoretical approach recently developed for analyzing cluster synchronization, we show how to derive the variational equations for these synchronous patterns and calculate their linear stability. The stability analysis gives good agreement with our experimental results. Both experiments and simulations suggest that these chimera states often appear in regions of multistability between global, cluster, and desynchronized states.

A parasitism-mutualism-predation model consisting of crows, cuckoos and cats with stage-structure and maturation delays on crows and cuckoos

USGS Publications Warehouse

Luo, Yantao; Zhang, Long; Teng, Zhidong; DeAngelis, Donald L.

2018-01-01

In this paper, a parasitism-mutualism-predation model is proposed to investigate the dynamics of multi-interactions among cuckoos, crows and cats with stage-structure and maturation time delays on cuckoos and crows. The crows permit the cuckoos to parasitize their nestlings (eggs) on the crow chicks (eggs). In return, the cuckoo nestlings produce a malodorous cloacal secretion to protect the crow chicks from predation by the cats, which is apparently beneficial to both the crow and cuckoo population. The multi-interactions, i.e., parasitism and mutualism between the cuckoos (nestlings) and crows (chicks), predation between the cats and crow chicks are modeled both by Holling-type II and Beddington-DeAngelis-type functional responses. The existence of positive equilibria of three subsystems of the model are discussed. The criteria for the global stability of the trivial equilibrium are established by the Krein-Rutman Theorem and other analysis methods. Moreover, the threshold dynamics for the coexistence and weak persistence of the model are obtained, and we show, both analytically and numerically, that the stabilities of the interior equilibria may change with the increasing maturation time delays. We find there exists an evident difference in the dynamical properties of the parasitism-mutualism-predation model based on whether or not we consider the effects of stage-structure and maturation time delays on cuckoos and crows. Inclusion of stage structure results in many varied dynamical complexities which are difficult to encompass without this inclusion.

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

Du, Mao -Hua; Singh, David J.; Zhang, Lijun

Oxides with good p-type conductivity have been long sought after to achieve high performance all-oxide optoelectronic devices. Divalent Sn(II) based oxides are promising candidates because of their rather dispersive upper valence bands caused by the Sn-5s/O-2p anti-bonding hybridization. There are so far few known Sn(II) oxides being p-type conductive suitable for device applications. Here, we present via first-principles global optimization structure searches a material design study for a hitherto unexplored Sn(II)-based system, ternary alkaline-earth metal Sn(II) oxides in the stoichiometry of MSn 2O 3 (M = Mg, Ca, Sr, Ba). We identify two stable compounds of SrSn 2O 3 andmore » BaSn 2O 3, which can be stabilized by Sn-rich conditions in phase stability diagrams. Their structures follow the Zintl behaviour and consist of basic structural motifs of SnO 3 tetrahedra. Unexpectedly they show distinct electronic properties with band gaps ranging from 1.90 (BaSn 2O 3) to 3.15 (SrSn 2O 3) eV, and hole effective masses ranging from 0.87 (BaSn 2O 3) to above 6.0 (SrSn 2O 3) m0. Further exploration of metastable phases indicates a wide tunability of electronic properties controlled by the details of the bonding between the basic structural motifs. Lastly, this suggests further exploration of alkaline-earth metal Sn(II) oxides for potential applications requiring good p-type conductivity such as transparent conductors and photovoltaic absorbers.« less

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.

Biodiversity and ecosystem stability across scales in metacommunities

PubMed Central

Wang, Shaopeng; Loreau, Michel

2016-01-01

Although diversity-stability relationships have been extensively studied in local ecosystems, the global biodiversity crisis calls for an improved understanding of these relationships in a spatial context. Here we use a dynamical model of competitive metacommunities to study the relationships between species diversity and ecosystem variability across scales. We derive analytic relationships under a limiting case; these results are extended to more general cases with numerical simulations. Our model shows that, while alpha diversity decreases local ecosystem variability, beta diversity generally contributes to increasing spatial asynchrony among local ecosystems. Consequently, both alpha and beta diversity provide stabilizing effects for regional ecosystems, through local and spatial insurance effects, respectively. We further show that at the regional scale, the stabilizing effect of biodiversity increases as spatial environmental correlation increases. Our findings have important implications for understanding the interactive effects of global environmental changes (e.g. environmental homogenization) and biodiversity loss on ecosystem sustainability at large scales. PMID:26918536

Surrogate models for efficient stability analysis of brake systems

NASA Astrophysics Data System (ADS)

Nechak, Lyes; Gillot, Frédéric; Besset, Sébastien; Sinou, Jean-Jacques

2015-07-01

This study assesses capacities of the global sensitivity analysis combined together with the kriging formalism to be useful in the robust stability analysis of brake systems, which is too costly when performed with the classical complex eigenvalues analysis (CEA) based on finite element models (FEMs). By considering a simplified brake system, the global sensitivity analysis is first shown very helpful for understanding the effects of design parameters on the brake system's stability. This is allowed by the so-called Sobol indices which discriminate design parameters with respect to their influence on the stability. Consequently, only uncertainty of influent parameters is taken into account in the following step, namely, the surrogate modelling based on kriging. The latter is then demonstrated to be an interesting alternative to FEMs since it allowed, with a lower cost, an accurate estimation of the system's proportions of instability corresponding to the influent parameters.

β-Boomerang Antimicrobial and Antiendotoxic Peptides: Lipidation and Disulfide Bond Effects on Activity and Structure

PubMed Central

Mohanram, Harini; Bhattacharjya, Surajit

2014-01-01

Drug-resistant Gram-negative bacterial pathogens and endotoxin- or lipopolysaccharide (LPS)-mediated inflammations are among some of the most prominent health issues globally. Antimicrobial peptides (AMPs) are eminent molecules that can kill drug-resistant strains and neutralize LPS toxicity. LPS, the outer layer of the outer membrane of Gram-negative bacteria safeguards cell integrity against hydrophobic compounds, including antibiotics and AMPs. Apart from maintaining structural integrity, LPS, when released into the blood stream, also induces inflammatory pathways leading to septic shock. In previous works, we have reported the de novo design of a set of 12-amino acid long cationic/hydrophobic peptides for LPS binding and activity. These peptides adopt β-boomerang like conformations in complex with LPS. Structure-activity studies demonstrated some critical features of the β-boomerang scaffold that may be utilized for the further development of potent analogs. In this work, β-boomerang lipopeptides were designed and structure-activity correlation studies were carried out. These lipopeptides were homo-dimerized through a disulfide bridge to stabilize conformations and for improved activity. The designed peptides exhibited potent antibacterial activity and efficiently neutralized LPS toxicity under in vitro assays. NMR structure of C4YI13C in aqueous solution demonstrated the conserved folding of the lipopeptide with a boomerang aromatic lock stabilized with disulfide bond at the C-terminus and acylation at the N-terminus. These lipo-peptides displaying bacterial sterilization and low hemolytic activity may be useful for future applications as antimicrobial and antiendotoxin molecules. PMID:24756162

Explosive Remnants of War in Stability Operations

DTIC Science & Technology

2012-09-01

strategic partner capacity building, global ERW and Counter-IED (C-IED) efforts, while adhering to global Mine /UXO awareness efforts. 15. NUMBER OF...PAGES 139 14. SUBJECT TERMS Explosive Remnants of War—Collection Point (ERW - CP), Landmine, Anti- Personnel Mine , Mine Action, Cluster Munitions...strategic partner capacity building, global ERW and Counter- IED (C-IED) efforts, while adhering to global Mine /UXO awareness efforts. vi THIS PAGE

CBe5Hn((n-4)) (n = 2-5): Hydrogen-Stabilized CBe5 Pentagons Containing Planar or Quasi-Planar Pentacoordinate Carbons.

PubMed

Guo, Jin-Chang; Ren, Guang-Ming; Miao, Chang-Qing; Tian, Wen-Juan; Wu, Yan-Bo; Wang, Xiaotai

2015-12-31

The diagonal relationship between beryllium and aluminum and the isoelectronic relationship between BeH unit and Al atom were utilized to design a new series ppC- or quasi-ppC-containing species C5v CBe5H5(+), Cs CBe5H4, C2v CBe5H3(-), and C2v CBe5H2(2-) by replacing the Al atoms in previously reported global minima planar pentacoordinate carbon (ppC) species D5h CAl5(+), C2v CAl4Be, C2v CAl3Be2(-), and C2v CAl2Be3(2-) with BeH units. The three-center two-electron (3c-2e) bonds formed between Be and bridging H atoms were crucial for the stabilization of these ppC species. The natural bond orbital (NBO) and adaptive natural density partitioning (AdNDP) analyses revealed that the central ppCs or quasi-ppCs possess the stable eight electron-shell structures. The AdNDP analyses also disclosed that these species are all 6σ+2π double-aromatic in nature. The aromaticity was proved by the calculated negative nucleus-independent chemical shifts (NICS) values. DFT and high-level CCSD(T) calculations revealed that these ppC- or quasi-ppC species are the global minimum or competitive low-lying local minimum (Cs CBe5H4) on their potential energy surfaces. The Born-Oppenheimer molecular dynamic (BOMD) simulations revealed that the H atoms in C2v CBe5H3(-) and C2v CBe5H2(2-) can easily rotate around the CBe5 cores and the structure of quasi-planar C5v CBe5H5(+) will become the planar structure at room temperature; however, these interesting dynamic behaviors did not indicate the kinetic instability as the basic ppC structures were maintained during the simulations. Therefore, it would be potentially possible to realize these interesting ppC- or quasi-ppc-species in future experiments.

GPS-Only Terrestrial Reference Frame Based on a Global Reprocessing

NASA Astrophysics Data System (ADS)

Dietrich, R.; Rothacher, M.; Ruelke, A.; Fritsche, M.; Steigenberger, P.

2007-12-01

The realization of the International Terrestrial Reference System (ITRS) with highest accuracy and stability is fundamental and crucial for applications in geodesy, geodynamics, geophysics and global change. In a joint effort TU Dresden and TU Munich/GFZ Potsdam reprocessed a global GPS network of more than 200 stations. As a contribution to an ITRS realization daily normal equations from 1994 to 2005 were rigorously combined in order to determine a global GPS-only reference frame (PDR05/Potsdam-Dresden-Reprocessing Reference Frame). We present a realization of the global terrestrial reference system which follows the center of mass approach in consideration of the load-induced deformation of the Earth's crust due to the redistribution of surface masses. The stability of our reference frame will be evaluated based on the obtained long-term trends of station coordinates, the load-induced deformation estimates and the homogeneous time series of station positions. We will compare our solution with other recent terrestrial reference system realizations and give some conclusions for future realizations of the ITRS.

A Conceptual Framework for Integrated STEM Education

ERIC Educational Resources Information Center

Kelley, Todd R.; Knowles, J. Geoff

2016-01-01

The global urgency to improve STEM education may be driven by environmental and social impacts of the twenty-first century which in turn jeopardizes global security and economic stability. The complexity of these global factors reach beyond just helping students achieve high scores in math and science assessments. Friedman (The world is flat: A…

Robust flow stability: Theory, computations and experiments in near wall turbulence

NASA Astrophysics Data System (ADS)

Bobba, Kumar Manoj

Helmholtz established the field of hydrodynamic stability with his pioneering work in 1868. From then on, hydrodynamic stability became an important tool in understanding various fundamental fluid flow phenomena in engineering (mechanical, aeronautics, chemical, materials, civil, etc.) and science (astrophysics, geophysics, biophysics, etc.), and turbulence in particular. However, there are many discrepancies between classical hydrodynamic stability theory and experiments. In this thesis, the limitations of traditional hydrodynamic stability theory are shown and a framework for robust flow stability theory is formulated. A host of new techniques like gramians, singular values, operator norms, etc. are introduced to understand the role of various kinds of uncertainty. An interesting feature of this framework is the close interplay between theory and computations. It is shown that a subset of Navier-Stokes equations are globally, non-nonlinearly stable for all Reynolds number. Yet, invoking this new theory, it is shown that these equations produce structures (vortices and streaks) as seen in the experiments. The experiments are done in zero pressure gradient transiting boundary layer on a flat plate in free surface tunnel. Digital particle image velocimetry, and MEMS based laser Doppler velocimeter and shear stress sensors have been used to make quantitative measurements of the flow. Various theoretical and computational predictions are in excellent agreement with the experimental data. A closely related topic of modeling, simulation and complexity reduction of large mechanics problems with multiple spatial and temporal scales is also studied. A nice method that rigorously quantifies the important scales and automatically gives models of the problem to various levels of accuracy is introduced. Computations done using spectral methods are presented.

New exponential stability criteria for stochastic BAM neural networks with impulses

NASA Astrophysics Data System (ADS)

Sakthivel, R.; Samidurai, R.; Anthoni, S. M.

2010-10-01

In this paper, we study the global exponential stability of time-delayed stochastic bidirectional associative memory neural networks with impulses and Markovian jumping parameters. A generalized activation function is considered, and traditional assumptions on the boundedness, monotony and differentiability of activation functions are removed. We obtain a new set of sufficient conditions in terms of linear matrix inequalities, which ensures the global exponential stability of the unique equilibrium point for stochastic BAM neural networks with impulses. The Lyapunov function method with the Itô differential rule is employed for achieving the required result. Moreover, a numerical example is provided to show that the proposed result improves the allowable upper bound of delays over some existing results in the literature.

Global exponential stability of neutral high-order stochastic Hopfield neural networks with Markovian jump parameters and mixed time delays.

PubMed

Huang, Haiying; Du, Qiaosheng; Kang, Xibing

2013-11-01

In this paper, a class of neutral high-order stochastic Hopfield neural networks with Markovian jump parameters and mixed time delays is investigated. The jumping parameters are modeled as a continuous-time finite-state Markov chain. At first, the existence of equilibrium point for the addressed neural networks is studied. By utilizing the Lyapunov stability theory, stochastic analysis theory and linear matrix inequality (LMI) technique, new delay-dependent stability criteria are presented in terms of linear matrix inequalities to guarantee the neural networks to be globally exponentially stable in the mean square. Numerical simulations are carried out to illustrate the main results. © 2013 ISA. Published by ISA. All rights reserved.

The intervening domain from MeCP2 enhances the DNA affinity of the methyl binding domain and provides an independent DNA interaction site.

PubMed

Claveria-Gimeno, Rafael; Lanuza, Pilar M; Morales-Chueca, Ignacio; Jorge-Torres, Olga C; Vega, Sonia; Abian, Olga; Esteller, Manel; Velazquez-Campoy, Adrian

2017-01-31

Methyl-CpG binding protein 2 (MeCP2) preferentially interacts with methylated DNA and it is involved in epigenetic regulation and chromatin remodelling. Mutations in MeCP2 are linked to Rett syndrome, the leading cause of intellectual retardation in girls and causing mental, motor and growth impairment. Unstructured regions in MeCP2 provide the plasticity for establishing interactions with multiple binding partners. We present a biophysical characterization of the methyl binding domain (MBD) from MeCP2 reporting the contribution of flanking domains to its structural stability and dsDNA interaction. The flanking disordered intervening domain (ID) increased the structural stability of MBD, modified its dsDNA binding profile from an entropically-driven moderate-affinity binding to an overwhelmingly enthalpically-driven high-affinity binding. Additionally, ID provided an additional site for simultaneously and autonomously binding an independent dsDNA molecule, which is a key feature linked to the chromatin remodelling and looping activity of MeCP2, as well as its ability to interact with nucleosomes replacing histone H1. The dsDNA interaction is characterized by an unusually large heat capacity linked to a cluster of water molecules trapped within the binding interface. The dynamics of disordered regions together with extrinsic factors are key determinants of MeCP2 global structural properties and functional capabilities.

The intervening domain from MeCP2 enhances the DNA affinity of the methyl binding domain and provides an independent DNA interaction site

PubMed Central

Claveria-Gimeno, Rafael; Lanuza, Pilar M.; Morales-Chueca, Ignacio; Jorge-Torres, Olga C.; Vega, Sonia; Abian, Olga; Esteller, Manel; Velazquez-Campoy, Adrian

2017-01-01

Methyl-CpG binding protein 2 (MeCP2) preferentially interacts with methylated DNA and it is involved in epigenetic regulation and chromatin remodelling. Mutations in MeCP2 are linked to Rett syndrome, the leading cause of intellectual retardation in girls and causing mental, motor and growth impairment. Unstructured regions in MeCP2 provide the plasticity for establishing interactions with multiple binding partners. We present a biophysical characterization of the methyl binding domain (MBD) from MeCP2 reporting the contribution of flanking domains to its structural stability and dsDNA interaction. The flanking disordered intervening domain (ID) increased the structural stability of MBD, modified its dsDNA binding profile from an entropically-driven moderate-affinity binding to an overwhelmingly enthalpically-driven high-affinity binding. Additionally, ID provided an additional site for simultaneously and autonomously binding an independent dsDNA molecule, which is a key feature linked to the chromatin remodelling and looping activity of MeCP2, as well as its ability to interact with nucleosomes replacing histone H1. The dsDNA interaction is characterized by an unusually large heat capacity linked to a cluster of water molecules trapped within the binding interface. The dynamics of disordered regions together with extrinsic factors are key determinants of MeCP2 global structural properties and functional capabilities. PMID:28139759

The GCOS Reference Upper-Air Network (GRUAN)

NASA Astrophysics Data System (ADS)

Vömel, H.; Berger, F. H.; Immler, F. J.; Seidel, D.; Thorne, P.

2009-04-01

While the global upper-air observing network has provided useful observations for operational weather forecasting for decades, its measurements lack the accuracy and long-term continuity needed for understanding climate change. Consequently, the scientific community faces uncertainty on such key issues as the trends of temperature in the upper troposphere and stratosphere or the variability and trends of stratospheric water vapour. To address these shortcomings, and to ensure that future climate records will be more useful than the records to date, the Global Climate Observing System (GCOS) program initiated the GCOS Reference Upper Air Network (GRUAN). GRUAN will be a network of about 30-40 observatories with a representative sampling of geographic regions and surface types. These stations will provide upper-air reference observations of the essential climate variables, i.e. temperature, geopotential, humidity, wind, radiation and cloud properties using specialized radiosondes and complementary remote sensing profiling instrumentation. Long-term stability, quality assurance / quality control, and a detailed assessment of measurement uncertainties will be the key aspects of GRUAN observations. The network will not be globally complete but will serve to constrain and adjust data from more spatially comprehensive global observing systems including satellites and the current radiosonde networks. This paper outlines the scientific rationale for GRUAN, its role in the Global Earth Observation System of Systems, network requirements and likely instrumentation, management structure, current status and future plans.

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.

Correlations between Transition Metal Chemistry, Local Structure and Global Structure in Li 2Ru 0.5Mn 0.5O 3 Investigated in a Wide Voltage Window

DOE PAGES

Lyu, Yingchun; Hu, Enyuan; Xiao, Dongdong; ...

2017-10-20

Li 2Ru 0.5Mn 0.5O 3, a high capacity lithium rich layered cathode material for lithium-ion batteries, was subject to comprehen-sive diagnostic studies including in situ/ex situ X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), pair distribu-tion function (PDF) and high resolution scanning transmission electron microscopy (STEM) analysis, to understand the cor-relations between transition metal chemistry, structure and lithium storage electrochemical behavior. Ru-Ru dimers have been identified in the as-prepared sample and found to be preserved upon prolonged cycling. Presence of these dimers, which are likely caused by the delocalized nature of 4d electrons, is found to favor the stabilization of themore » structure in a lay-ered phase. The in situ XAS results confirm the participation of oxygen redox into the charge compensation at high charge voltage, and the great flexibility of the covalent bond between Ru and O may provide great reversibility of the global struc-ture despite of the significant local distortion around Ru. In contrast, the local distortion around Mn occurs at low discharge voltage and is accompanied by a “layered to 1T” phase transformation, which is found to be detrimental to the cycle per-formances. It is clear that the changes of local structure around individual transition metal cations respond separately and differently to lithium intercalation/deintercalation. Here, cations with the capability to tolerate the lattice distortion will benefit for maintaining the integrality of the crystal structure and therefore is able to enhance the long-term cycling performance of the electrode materials.« less

Correlations between Transition Metal Chemistry, Local Structure and Global Structure in Li 2Ru 0.5Mn 0.5O 3 Investigated in a Wide Voltage Window

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

Lyu, Yingchun; Hu, Enyuan; Xiao, Dongdong

Li 2Ru 0.5Mn 0.5O 3, a high capacity lithium rich layered cathode material for lithium-ion batteries, was subject to comprehen-sive diagnostic studies including in situ/ex situ X-ray diffraction (XRD), X-ray absorption spectroscopy (XAS), pair distribu-tion function (PDF) and high resolution scanning transmission electron microscopy (STEM) analysis, to understand the cor-relations between transition metal chemistry, structure and lithium storage electrochemical behavior. Ru-Ru dimers have been identified in the as-prepared sample and found to be preserved upon prolonged cycling. Presence of these dimers, which are likely caused by the delocalized nature of 4d electrons, is found to favor the stabilization of themore » structure in a lay-ered phase. The in situ XAS results confirm the participation of oxygen redox into the charge compensation at high charge voltage, and the great flexibility of the covalent bond between Ru and O may provide great reversibility of the global struc-ture despite of the significant local distortion around Ru. In contrast, the local distortion around Mn occurs at low discharge voltage and is accompanied by a “layered to 1T” phase transformation, which is found to be detrimental to the cycle per-formances. It is clear that the changes of local structure around individual transition metal cations respond separately and differently to lithium intercalation/deintercalation. Here, cations with the capability to tolerate the lattice distortion will benefit for maintaining the integrality of the crystal structure and therefore is able to enhance the long-term cycling performance of the electrode materials.« less

Origin of polymorphism of the two-dimensional group-IV monochalcogenides

NASA Astrophysics Data System (ADS)

Wu, Minghui; Wei, Su-Huai; Huang, Li

2017-11-01

Unlike other two-dimensional (2D) isovalent materials, the 2D group IV monochalcogenides, M X (M =Si , Ge, Sn, and Pb; X =S , Se, and Te), are found to be either in a black phosphorene-derived distorted NaCl-type (d -NaCl) structure or a recently predicted P m a 2 structure. Both M and X atoms in the d -NaCl structure are threefold coordinated, whereas M and X in the P m a 2 structure are fourfold and twofold coordinated, respectively. Using first-principles total energy and electronic structure calculations and a global structural search technique, we systematically investigated the mechanism underlying the polymorphism of the 2D group-IV monochalcogenides. Our analysis show that the relative stability of the two distinct crystallographic phases depends on the strength of the M -M covalent bond and the electronegativity difference between the constituent elements M and X . For small cations, the covalency plays more important role, whereas for large cations the Coulomb interaction becomes more dominant. Therefore, the Si X and Ge X compounds assume the P m a 2 structure, whereas the M X compounds with heavy cation elements (M =Sn and Pb) tend to adopt the d -NaCl structure.

Photoinduced intramolecular charge transfer (ICT) reaction in trans-methyl p-(dimethylamino) cinnamate: A combined fluorescence measurement and quantum chemical calculations

NASA Astrophysics Data System (ADS)

Chakraborty, Amrita; Kar, Samiran; Guchhait, Nikhil

2006-01-01

The photophysical behaviour of trans-methyl p-(dimethylamino) cinnamate ( t-MDMAC) donor-acceptor system has been investigated by steady-state absorption and emission spectroscopy and quantum chemical calculations. The molecule t-MDMAC shows an emission from the locally excited state in non-polar solvents. In addition to weak local emission, a strong solvent dependent red shifted fluorescence in polar aprotic solvents is attributed to highly polar intramolecular charge transfer state. However, the formation of hydrogen-bonded clusters with polar protic solvents has been suggested from a linear correlation between the observed red shifted fluorescence band maxima with hydrogen bonding parameters ( α). Calculations by ab initio and density functional theory show that the lone pair electron at nitrogen center is out of plane of the benzene ring in the global minimum ground state structure. In the gas phase, a potential energy surface along the twist coordinate at the donor (-NMe 2) and acceptor (-CH = CHCOOMe) sites shows stabilization of S 1 state and destabilization S 2 and S 0 states. A similar potential energy calculation along the twist coordinate in acetonitrile solvent using non-equilibrium polarized continuum model also shows more stabilization of S 1 state relative to other states and supports solvent dependent red shifted emission properties. In all types of calculations it is found that the nitrogen lone pair is delocalized over the benzene ring in the global minimum ground state and is localized on the nitrogen centre at the 90° twisted configuration. The S 1 energy state stabilization along the twist coordinate at the donor site and localized nitrogen lone pair at the perpendicular configuration support well the observed dual fluorescence in terms of proposed twisted intramolecular charge transfer (TICT) model.

Assessment of Rock Slope Stability in Limestone Quarries in the Tournai's Region (Belgium) Using Structural Data

NASA Astrophysics Data System (ADS)

Tshibangu, Jean-Pierre; Deloge, K. Pierre-Alexandre; Deschamps, Benoît; Coudyzer, Christophe

The Tournais region is characterised by famous outcrops of carboniferous limestone which is mined out for cement and raw material production. The four main quarries found in the Region, i.e. Gaurain-Ramecroix, Milieu, Antoing and Lemay; are owned by the three main cement producers in Belgium: Italcimenti, Holcim and CBR. The global production of limestone is about 20 millions tons per year, giving big pits with depths up to 150 m. With the growth of the pits, the quarries are approaching each other leading to the problem of managing the reserves contained in the separating walls and their mechanical stability. The limestone deposit is composed of different seams having varying thickness, chemical com- position and even mechanical properties. The deposit has an overall horizontal dip and is intersected by two main sets of discontinuities with a spacing of about 10 m or less. It is also crossed by a set of east to west faults but the quarries are implanted in the in between areas, so to not be crossed by these faults. The layers and specially the shallow ones are characterised by a typical karstic weathering giving open or filled cavities. This paper presents the global work quarried out in order to study the stability of the Lemays quarry. First a description of the orientation and spacing of discontinuities is presented, and an attempt made to correlate to the development of weathering. Mechanical laboratory tests have been performed and a qualification of the rock mass assessed. A coupled approach is then presented using a mining planning analysis and mechanical simulation (i.e. Finite Element method).

Optimizing molecular properties using a relative index of thermodynamic stability and global optimization techniques

NASA Astrophysics Data System (ADS)

Fournier, René; Mohareb, Amir

2016-01-01

We devised a global optimization (GO) strategy for optimizing molecular properties with respect to both geometry and chemical composition. A relative index of thermodynamic stability (RITS) is introduced to allow meaningful energy comparisons between different chemical species. We use the RITS by itself, or in combination with another calculated property, to create an objective function F to be minimized. Including the RITS in the definition of F ensures that the solutions have some degree of thermodynamic stability. We illustrate how the GO strategy works with three test applications, with F calculated in the framework of Kohn-Sham Density Functional Theory (KS-DFT) with the Perdew-Burke-Ernzerhof exchange-correlation. First, we searched the composition and configuration space of CmHnNpOq (m = 0-4, n = 0-10, p = 0-2, q = 0-2, and 2 ≤ m + n + p + q ≤ 12) for stable molecules. The GO discovered familiar molecules like N2, CO2, acetic acid, acetonitrile, ethane, and many others, after a small number (5000) of KS-DFT energy evaluations. Second, we carried out a GO of the geometry of Cu m Snn + (m = 1, 2 and n = 9-12). A single GO run produced the same low-energy structures found in an earlier study where each Cu m S nn + species had been optimized separately. Finally, we searched bimetallic clusters AmBn (3 ≤ m + n ≤ 6, A,B= Li, Na, Al, Cu, Ag, In, Sn, Pb) for species and configurations having a low RITS and large highest occupied Molecular Orbital (MO) to lowest unoccupied MO energy gap (Eg). We found seven bimetallic clusters with Eg > 1.5 eV.

Structural diagnostics of the tropopause inversion layer and its evolution

NASA Astrophysics Data System (ADS)

Gettelman, A.; Wang, T.

2015-01-01

The Tropopause Inversion Layer (TIL) is marked by a peak in static stability directly above the tropopause. The TIL is quantitatively defined with new diagnostics using Global Positioning System Radio Occultation temperature soundings and reanalysis data. A climatology of the TIL is developed from reanalysis data (1980-2011) using diagnostics for the position, depth, and strength of the TIL based on the TIL peak in static stability. TIL diagnostics have defined relationships to the synoptic situation in the Upper Troposphere and Lower Stratosphere. The TIL is present nearly all the time. The TIL becomes hard to define in the subtropics where tropical air overlies midlatitude air, in a region of complex static stability profiles. The mean position of the subtropical TIL gradient is sharp and is co-located with the subtropical tropopause break. Over the period 1980-2011 the TIL depth below the tropopause has decreased by 5% per decade and increased above the tropical tropopause by a similar percentage. Furthermore, the latitude of the abrupt change in the TIL from tropical to extratropical in the lower stratosphere appears to have shifted poleward in each hemisphere by ˜1° latitude per decade, depending on the diagnostic examined. Reanalysis trends should be treated with caution.

Inherent robustness of discrete-time adaptive control systems

NASA Technical Reports Server (NTRS)

Ma, C. C. H.

1986-01-01

Global stability robustness with respect to unmodeled dynamics, arbitrary bounded internal noise, as well as external disturbance is shown to exist for a class of discrete-time adaptive control systems when the regressor vectors of these systems are persistently exciting. Although fast adaptation is definitely undesirable, so far as attaining the greatest amount of global stability robustness is concerned, slow adaptation is shown to be not necessarily beneficial. The entire analysis in this paper holds for systems with slowly varying return difference matrices; the plants in these systems need not be slowly varying.

Global stability for an HIV-1 infection model with Beddington-DeAngelis incidence rate and CTL immune response

NASA Astrophysics Data System (ADS)

Lv, Cuifang; Huang, Lihong; Yuan, Zhaohui

2014-01-01

In this paper, an HIV-1 infection model with Beddington-DeAngelis incidence rate and CTL immune response is investigated. One main feature of this model is that an eclipse stage for the infected cells is included and a portion of these cells is reverted to uninfected cells. We derive the basic reproduction number R1 and the immune response reproduction number R2 for the HIV-1 infection model. By constructing Lyapunov functions, the global stabilities for the equilibria have been analyzed.

Stabilizing benzene-like planar N6 rings to form a single atomic honeycomb BeN3 sheet with high carrier mobility.

PubMed

Li, Xiaoyin; Zhang, Shunhong; Zhang, Cunzhi; Wang, Qian

2018-01-18

It is a longstanding quest to use the planar N 6 ring as a structural unit to build stable atomic sheets. However, unlike C 6 H 6 , the neutral N 6 ring is unstable due to the strong repulsion of the lone-pair of electrons. Using first-principles calculations and the global structure search method, we show that the N 6 unit can be stabilized by the linkage of Be atoms, forming a h-BeN 3 honeycomb monolayer, in which the geometry and the π-molecular orbitals of the N 6 rings are well kept. This sheet is not only energetically, dynamically and thermally stable, but also can withstand high temperatures up to 1000 K. Band structure calculation combined with a group theory analysis and a tight-binding model uncover that h-BeN 3 has a π-band dominated band structure with an indirect band gap of 1.67 eV. While it possesses a direct band gap of 2.07 eV at the Γ point lying in the photon energy region of visual light, its interband dipole transition is symmetrically allowed so that electrons can be excited by photons free of phonons. Based on deformation potential theory, a systematic study of the transport properties reveals that the h-BeN 3 sheet possesses a high carrier mobility of ∼10 3 cm 2 V -1 s -1 , superior to the extensively studied transition metal dichalcogenide monolayers. We further demonstrate that this sheet can be rolled up into either zigzag or armchair nanotubes. These nanotubes are also dynamically stable, and are all direct band gap semiconductors with carrier mobility comparable to that of their 2D counterparts, regardless of their chirality and diameter. The robust stability and novel electronic and transport properties of the h-BeN 3 sheet and its tubular derivatives endow them with great potential for applications in nanoelectronic devices.

Dual, differential isotope labeling shows the preferential movement of labile plant constituents into mineral-bonded soil organic matter.

PubMed

Haddix, Michelle L; Paul, Eldor A; Cotrufo, M Francesca

2016-06-01

The formation and stabilization of soil organic matter (SOM) are major concerns in the context of global change for carbon sequestration and soil health. It is presently believed that lignin is not selectively preserved in soil and that chemically labile compounds bonding to minerals comprise a large fraction of the SOM. Labile plant inputs have been suggested to be the main precursor of the mineral-bonded SOM. Litter decomposition and SOM formation are expected to have temperature sensitivity varying with the lability of plant inputs. We tested this framework using dual (13) C and (15) N differentially labeled plant material to distinguish the metabolic and structural components within a single plant material. Big Bluestem (Andropogon gerardii) seedlings were grown in an enriched (13) C and (15) N environment and then prior to harvest, removed from the enriched environment and allowed to incorporate natural abundance (13) C-CO2 and (15) N fertilizer into the metabolic plant components. This enabled us to achieve a greater than one atom % difference in (13) C between the metabolic and structural components within the plant litter. This differentially labeled litter was incubated in soil at 15 and 35 °C, for 386 days with CO2 measured throughout the incubation. After 14, 28, 147, and 386 days of incubation, the soil was subsequently fractionated. There was no difference in temperature sensitivity of the metabolic and structural components with regard to how much was respired or in the amount of litter biomass stabilized. Only the metabolic litter component was found in the sand, silt, or clay fraction while the structural component was exclusively found in the light fraction. These results support the stabilization framework that labile plant components are the main precursor of mineral-associated organic matter. © 2016 John Wiley & Sons Ltd.

Global Failure Modes in High Temperature Composite Structures

NASA Technical Reports Server (NTRS)

Knauss, W. G.

1998-01-01

Composite materials have been considered for many years as the major advance in the construction of energy efficient aerospace structures. Notable advances have been made in understanding the special design considerations that set composites apart from the usual "isotropic" engineering materials such as the metals. As a result, a number of significant engineering designs have been accomplished. However, one shortcoming of the currently favored composites is their relatively unforgiving behavior with respect to failure (brittleness) under seemingly mild impact conditions and large efforts are underway to rectify that situation, much along the lines of introducing thermoplastic matrix materials. Because of their relatively more pronounced (thermo) viscoelastic behavior these materials respond with "toughness" in fracture situations. From the point of view of applications requiring material strength, this property is highly desirable. This feature impacts several important and distinct engineering problems which have been' considered under this grant and cover the 1) effect of impact damage on structural (buckling) stability of composite panels, the 2) effect of time dependence on the progression of buckling instabilities, and the 3) evolution of damage and fracture at generic thickness discontinuities in structures. The latter topic has serious implications for structural stability problems (buckling failure in reinforced shell structures) as well as failure progression in stringer-reinforced shell structures. This grant has dealt with these issues. Polymer "toughness" is usually associated with uncrosslinked or thermo-plastic polymers. But, by comparison with their thermoset counterparts they tend to exhibit more pronounced time dependent material behavior; also, that time dependence can occur at lower temperatures which places restriction in the high temperature use of these "newer and tougher" materials that are not quite so serious with the thermoset matrix materials. From a structural point of view the implications of this material behavior are potentially severe in that structural failure characteristics are no longer readily observed in short term qualification tests so characteristic for aerospace structures built from typical engineering metals.

The quantum structure of anionic hydrogen clusters

NASA Astrophysics Data System (ADS)

Calvo, F.; Yurtsever, E.

2018-03-01

A flexible and polarizable interatomic potential has been developed to model hydrogen clusters interacting with one hydrogen anion, (H2)nH-, in a broad range of sizes n = 1-54 and parametrized against coupled cluster quantum chemical calculations. Using path-integral molecular dynamics simulations at 1 K initiated from the putative classical global minima, the equilibrium structures are found to generally rely on icosahedral shells with the hydrogen molecules pointing toward the anion, producing geometric magic numbers at sizes n = 12, 32, and 44 that are in agreement with recent mass spectrometry measurements. The energetic stability of the clusters is also connected with the extent of vibrational delocalization, measured here by the fluctuations among inherent structures hidden in the vibrational wave function. As the clusters grow, the outer molecules become increasingly free to rotate, and strong finite size effects are also found between magic numbers, associated with more prominent vibrational delocalization. The effective icosahedral structure of the 44-molecule cluster is found to originate from quantum nuclear effects as well, the classical structure showing no particular symmetry.

A Distal Disulfide Bridge in OXA-1 β-Lactamase Stabilizes the Catalytic Center and Alters the Dynamics of the Specificity Determining Ω Loop

DOE PAGES

Simakov, Nikolay; Leonard, David A.; Smith, Jeremy C.; ...

2016-09-26

Widespread antibiotic resistance, particularly when mediated by broad-spectrum β-lactamases, has major implications for public health. Substitutions in the active site often allow broad-spectrum enzymes to accommodate diverse types of β-lactams. Substitutions observed outside the active site are thought to compensate for the loss of thermal stability. The OXA-1 clade of class D β-lactamases contains a pair of conserved cysteines located outside the active site that forms a disulfide bond in the periplasm. In this paper, the effect of the distal disulfide bond on the structure and dynamics of OXA-1 was investigated via 4 μs molecular dynamics simulations. The results revealmore » that the disulfide promotes the preorganized orientation of the catalytic residues and affects the conformation of the functionally important Ω loop. Furthermore, principal component analysis reveals differences in the global dynamics between the oxidized and reduced forms, especially in the motions involving the Ω loop. A dynamical network analysis indicates that, in the oxidized form, in addition to its role in ligand binding, the KTG family motif is a central hub of the global dynamics. Finally, as activity of OXA-1 has been measured only in the reduced form, we suggest that accurate assessment of its functional profile would require oxidative conditions mimicking periplasm.« less

Climate, ocean circulation, and sea level changes under stabilization and overshoot pathways to 1.5 K warming

NASA Astrophysics Data System (ADS)

Palter, Jaime B.; Frölicher, Thomas L.; Paynter, David; John, Jasmin G.

2018-06-01

The Paris Agreement has initiated a scientific debate on the role that carbon removal - or net negative emissions - might play in achieving less than 1.5 K of global mean surface warming by 2100. Here, we probe the sensitivity of a comprehensive Earth system model (GFDL-ESM2M) to three different atmospheric CO2 concentration pathways, two of which arrive at 1.5 K of warming in 2100 by very different pathways. We run five ensemble members of each of these simulations: (1) a standard Representative Concentration Pathway (RCP4.5) scenario, which produces 2 K of surface warming by 2100 in our model; (2) a stabilization pathway in which atmospheric CO2 concentration never exceeds 440 ppm and the global mean temperature rise is approximately 1.5 K by 2100; and (3) an overshoot pathway that passes through 2 K of warming at mid-century, before ramping down atmospheric CO2 concentrations, as if using carbon removal, to end at 1.5 K of warming at 2100. Although the global mean surface temperature change in response to the overshoot pathway is similar to the stabilization pathway in 2100, this similarity belies several important differences in other climate metrics, such as warming over land masses, the strength of the Atlantic Meridional Overturning Circulation (AMOC), ocean acidification, sea ice coverage, and the global mean sea level change and its regional expressions. In 2100, the overshoot ensemble shows a greater global steric sea level rise and weaker AMOC mass transport than in the stabilization scenario, with both of these metrics close to the ensemble mean of RCP4.5. There is strong ocean surface cooling in the North Atlantic Ocean and Southern Ocean in response to overshoot forcing due to perturbations in the ocean circulation. Thus, overshoot forcing in this model reduces the rate of sea ice loss in the Labrador, Nordic, Ross, and Weddell seas relative to the stabilized pathway, suggesting a negative radiative feedback in response to the early rapid warming. Finally, the ocean perturbation in response to warming leads to strong pathway dependence of sea level rise in northern North American cities, with overshoot forcing producing up to 10 cm of additional sea level rise by 2100 relative to stabilization forcing.

Magnetotail Reconnection

NASA Astrophysics Data System (ADS)

Petrukovich, A.; Artemyev, A.; Nakamura, R.

Reconnection is the key process responsible for the magnetotail dynamics. Driven reconnection in the distant tail is not sufficient to support global magnetospheric convection and the near Earth neutral line spontaneously forms to restore the balance. Mechanisms of initiation of such near-Earth magnetotail reconnection still represent one of major unresolved issues in space physics. We review the progress in this topic during the last decade. Recent theoretical advances suggest several variants of overcoming the famous tearing stability problem. Multipoint spacecraft observations reveal detailed structure of pre-onset current sheet of and reconnection zone down to ion larmor scale, supporting the importance of unstable state development through internal magnetotail reconfiguration.

Free energy landscapes of small peptides in an implicit solvent model determined by force-biased multicanonical molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Watanabe, Yukihisa S.; Kim, Jae Gil; Fukunishi, Yoshifumi; Nakamura, Haruki

2004-12-01

In order to investigate whether the implicit solvent (GB/SA) model could reproduce the free energy landscapes of peptides, the potential of mean forces (PMFs) of eight tripeptides was examined and compared with the PMFs of the explicit water model. The force-biased multicanonical molecular dynamics method was used for the enhanced conformational sampling. Consequently, the GB/SA model reproduced almost all the global and local minima in the PMFs observed with the explicit water model. However, the GB/SA model overestimated frequencies of the structures that are stabilized by intra-peptide hydrogen bonds.

Beneficial utilization of lime sludge for subgrade stabilization, a pilot study : executive summary report.

DOT National Transportation Integrated Search

2010-06-01

A global chemical stabilization design is recently : adopted by the Ohio Department of Transportation : (ODOT). This produces performance and economic : benefits in providing pavement with a rugged base : supporting. Given the large quantities of lim...

Beneficial Utilization of Lime Sludge for Subgrade Stabilization : a Pilot study : Executive Summary Report

DOT National Transportation Integrated Search

2010-06-01

A global chemical stabilization design is recently : adopted by the Ohio Department of Transportation : (ODOT). This produces performance and economic : benefits in providing pavement with a rugged base : supporting. Given the large quantities of lim...

An analysis of yield stability in a conservation agriculture system

USDA-ARS?s Scientific Manuscript database

Climate models predict increasing growing-season weather variability, with negative consequences for crop production. Maintaining agricultural productivity despite variability in weather (i.e., crop yield stability) will be critical to meeting growing global demand. Conservation agriculture is an ...

Passivity-Based Control for Two-Wheeled Robot Stabilization

NASA Astrophysics Data System (ADS)

Uddin, Nur; Aryo Nugroho, Teguh; Agung Pramudito, Wahyu

2018-04-01

A passivity-based control system design for two-wheeled robot (TWR) stabilization is presented. A TWR is a statically-unstable non-linear system. A control system is applied to actively stabilize the TWR. Passivity-based control method is applied to design the control system. The design results in a state feedback control law that makes the TWR closed loop system globally asymptotically stable (GAS). The GAS is proven mathematically. The TWR stabilization is demonstrated through computer simulation. The simulation results show that the designed control system is able to stabilize the TWR.

Psychrophiles

NASA Astrophysics Data System (ADS)

Siddiqui, Khawar S.; Williams, Timothy J.; Wilkins, David; Yau, Sheree; Allen, Michelle A.; Brown, Mark V.; Lauro, Federico M.; Cavicchioli, Ricardo

2013-05-01

Psychrophilic (cold-adapted) microorganisms make a major contribution to Earth's biomass and perform critical roles in global biogeochemical cycles. The vast extent and environmental diversity of Earth's cold biosphere has selected for equally diverse microbial assemblages that can include archaea, bacteria, eucarya, and viruses. Underpinning the important ecological roles of psychrophiles are exquisite mechanisms of physiological adaptation. Evolution has also selected for cold-active traits at the level of molecular adaptation, and enzymes from psychrophiles are characterized by specific structural, functional, and stability properties. These characteristics of enzymes from psychrophiles not only manifest in efficient low-temperature activity, but also result in a flexible protein structure that enables biocatalysis in nonaqueous solvents. In this review, we examine the ecology of Antarctic psychrophiles, physiological adaptation of psychrophiles, and properties of cold-adapted proteins, and we provide a view of how these characteristics inform studies of astrobiology.

Theoretical study of the structures and chemical ordering of CoPd nanoalloys supported on MgO(001)

NASA Astrophysics Data System (ADS)

Taran, Songul; Garip, Ali Kemal; Arslan, Haydar

2016-06-01

Metal nanoalloys on oxide surface are a widely studied topic in surface science and technology. In this study, the structures of CoPd nanoalloys adsorbed on MgO(001) have been searched by basin-hopping global optimization method within an atomistic model. Two different sizes (34 and 38 atom) have been considered for all compositions of CoPd/MgO(001) nanoalloys. Co and Pd atoms, for all the compositions, have cube-on-cube (001) epitaxy with substrate at interface. For both sizes, we have found that Pd rich composition nanoalloys have three layers, Co rich composition nanoalloys have four layers in morphology. Excess energy and second difference in energy analyzes have been performed to investigate the relative stability of nanoalloys with respect to their size and composition.

Glossary of AWS Acrinabs. Acronyms, Initialisms, and Abbreviations Commonly Used in Air Weather Service

DTIC Science & Technology

1991-01-01

Foundation FYDP ......... Five Year Defense Plan FSI ............ Fog Stability Index 17 G G ................ gravity, giga- GISM ......... Gridded ...Global Circulation Model GOES-TAP GOES imagery processing & dissemination system GCS .......... grid course GOFS ........ Global Ocean Flux Study GD...Analysis Support System Complex Systems GRID .......... Global Resource Information Data -Base GEMAG ..... geomagnetic GRIST..... grazing-incidence solar

Symmetry, Hopf bifurcation, and the emergence of cluster solutions in time delayed neural networks.

PubMed

Wang, Zhen; Campbell, Sue Ann

2017-11-01

We consider the networks of N identical oscillators with time delayed, global circulant coupling, modeled by a system of delay differential equations with Z N symmetry. We first study the existence of Hopf bifurcations induced by the coupling time delay and then use symmetric Hopf bifurcation theory to determine how these bifurcations lead to different patterns of symmetric cluster oscillations. We apply our results to a case study: a network of FitzHugh-Nagumo neurons with diffusive coupling. For this model, we derive the asymptotic stability, global asymptotic stability, absolute instability, and stability switches of the equilibrium point in the plane of coupling time delay (τ) and excitability parameter (a). We investigate the patterns of cluster oscillations induced by the time delay and determine the direction and stability of the bifurcating periodic orbits by employing the multiple timescales method and normal form theory. We find that in the region where stability switching occurs, the dynamics of the system can be switched from the equilibrium point to any symmetric cluster oscillation, and back to equilibrium point as the time delay is increased.

Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics

NASA Astrophysics Data System (ADS)

Wang, Bin; Shao, Yanchun; Chen, Tao; Chen, Wanping; Chen, Fusheng

2015-12-01

Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains.

Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics.

PubMed

Wang, Bin; Shao, Yanchun; Chen, Tao; Chen, Wanping; Chen, Fusheng

2015-12-22

Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains.

Pyrrole multimers and pyrrole-acetylene hydrogen bonded complexes studied in N2 and para-H2 matrixes using matrix isolation infrared spectroscopy and ab initio computations

NASA Astrophysics Data System (ADS)

Sarkar, Shubhra; Ramanathan, N.; Gopi, R.; Sundararajan, K.

2017-12-01

Hydrogen bonded interaction of pyrrole multimer and acetylene-pyrrole complexes were studied in N2 and p-H2 matrixes. DFT computations showed T-shaped geometry for the pyrrole dimer and cyclic complex for the trimer and tetramer were the most stable structures, stabilized by Nsbnd H⋯π interactions. The experimental vibrational wavenumbers observed in N2 and p-H2 matrixes for the pyrrole multimers were correlated with the computed wavenumbers. Computations performed at MP2/aug-cc-pVDZ level of theory showed that C2H2 and C4H5N forms 1:1 hydrogen-bonded complexes stabilized by Csbnd H⋯π interaction (Complex A), Nsbnd H⋯π interaction (Complex B) and π⋯π interaction (Complex C), where the former complex is the global minimum and latter two complexes were the first and second local minima, respectively. Experimentally, 1:1 C2H2sbnd C4H5N complexes A (global minimum) and B (first local minimum) were identified from the shifts in the Nsbnd H stretching, Nsbnd H bending, Csbnd H bending region of pyrrole and Csbnd H asymmetric stretching and bending region of C2H2 in N2 and p-H2 matrixes. Computations were also performed for the higher complexes and found two minima corresponding to the 1:2 C2H2sbnd C4H5N and three minima for the 2:1 C2H2sbnd C4H5N complexes. Experimentally the global minimum 1:2 and 2:1 C2H2sbnd C4H5N complexes were identified in N2 and p-H2 matrixes.

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

Invariants, Attractors and Bifurcation in Two Dimensional Maps with Polynomial Interaction

NASA Astrophysics Data System (ADS)

Hacinliyan, Avadis Simon; Aybar, Orhan Ozgur; Aybar, Ilknur Kusbeyzi

This work will present an extended discrete-time analysis on maps and their generalizations including iteration in order to better understand the resulting enrichment of the bifurcation properties. The standard concepts of stability analysis and bifurcation theory for maps will be used. Both iterated maps and flows are used as models for chaotic behavior. It is well known that when flows are converted to maps by discretization, the equilibrium points remain the same but a richer bifurcation scheme is observed. For example, the logistic map has a very simple behavior as a differential equation but as a map fold and period doubling bifurcations are observed. A way to gain information about the global structure of the state space of a dynamical system is investigating invariant manifolds of saddle equilibrium points. Studying the intersections of the stable and unstable manifolds are essential for understanding the structure of a dynamical system. It has been known that the Lotka-Volterra map and systems that can be reduced to it or its generalizations in special cases involving local and polynomial interactions admit invariant manifolds. Bifurcation analysis of this map and its higher iterates can be done to understand the global structure of the system and the artifacts of the discretization by comparing with the corresponding results from the differential equation on which they are based.

Unfolding stabilities of two structurally similar proteins as probed by temperature-induced and force-induced molecular dynamics simulations.

PubMed

Gorai, Biswajit; Prabhavadhni, Arasu; Sivaraman, Thirunavukkarasu

2015-09-01

Unfolding stabilities of two homologous proteins, cardiotoxin III and short-neurotoxin (SNTX) belonging to three-finger toxin (TFT) superfamily, have been probed by means of molecular dynamics (MD) simulations. Combined analysis of data obtained from steered MD and all-atom MD simulations at various temperatures in near physiological conditions on the proteins suggested that overall structural stabilities of the two proteins were different from each other and the MD results are consistent with experimental data of the proteins reported in the literature. Rationalization for the differential structural stabilities of the structurally similar proteins has been chiefly attributed to the differences in the structural contacts between C- and N-termini regions in their three-dimensional structures, and the findings endorse the 'CN network' hypothesis proposed to qualitatively analyse the thermodynamic stabilities of proteins belonging to TFT superfamily of snake venoms. Moreover, the 'CN network' hypothesis has been revisited and the present study suggested that 'CN network' should be accounted in terms of 'structural contacts' and 'structural strengths' in order to precisely describe order of structural stabilities of TFTs.

Self-organizing map analysis using multivariate data from theophylline tablets predicted by a thin-plate spline interpolation.

PubMed

Yasuda, Akihito; Onuki, Yoshinori; Obata, Yasuko; Yamamoto, Rie; Takayama, Kozo

2013-01-01

The "quality by design" concept in pharmaceutical formulation development requires the establishment of a science-based rationale and a design space. We integrated thin-plate spline (TPS) interpolation and Kohonen's self-organizing map (SOM) to visualize the latent structure underlying causal factors and pharmaceutical responses. As a model pharmaceutical product, theophylline tablets were prepared based on a standard formulation. The tensile strength, disintegration time, and stability of these variables were measured as response variables. These responses were predicted quantitatively based on nonlinear TPS. A large amount of data on these tablets was generated and classified into several clusters using an SOM. The experimental values of the responses were predicted with high accuracy, and the data generated for the tablets were classified into several distinct clusters. The SOM feature map allowed us to analyze the global and local correlations between causal factors and tablet characteristics. The results of this study suggest that increasing the proportion of microcrystalline cellulose (MCC) improved the tensile strength and the stability of tensile strength of these theophylline tablets. In addition, the proportion of MCC has an optimum value for disintegration time and stability of disintegration. Increasing the proportion of magnesium stearate extended disintegration time. Increasing the compression force improved tensile strength, but degraded the stability of disintegration. This technique provides a better understanding of the relationships between causal factors and pharmaceutical responses in theophylline tablet formulations.

Azasugar inhibitors as pharmacological chaperones for Krabbe disease

DOE PAGES

Hill, Chris H.; Viuff, Agnete H.; Spratley, Samantha J.; ...

2015-03-23

Krabbe disease is a devastating neurodegenerative disorder characterized by rapid demyelination of nerve fibers. This disease is caused by defects in the lysosomal enzyme β-galactocerebrosidase (GALC), which hydrolyzes the terminal galactose from glycosphingolipids. These lipids are essential components of eukaryotic cell membranes: substrates of GALC include galactocerebroside, the primary lipid component of myelin, and psychosine, a cytotoxic metabolite. Mutations of GALC that cause misfolding of the protein may be responsive to pharmacological chaperone therapy (PCT), whereby small molecules are used to stabilize these mutant proteins, thus correcting trafficking defects and increasing residual catabolic activity in cells. Here we describe amore » new approach for the synthesis of galacto-configured azasugars and the characterization of their interaction with GALC using biophysical, biochemical and crystallographic methods. We identify that the global stabilization of GALC conferred by azasugar derivatives, measured by fluorescence-based thermal shift assays, is directly related to their binding affinity, measured by enzyme inhibition. X-ray crystal structures of these molecules bound in the GALC active site reveal which residues participate in stabilizing interactions, show how potency is achieved and illustrate the penalties of aza/iminosugar ring distortion. The structure–activity relationships described here identify the key physical properties required of pharmacological chaperones for Krabbe disease and highlight the potential of azasugars as stabilizing agents for future enzyme replacement therapies. This work lays the foundation for new drug-based treatments of Krabbe disease.« less

Eutrophication weakens stabilizing effects of diversity in natural grasslands

USDA-ARS?s Scientific Manuscript database

Experimental manipulations have demonstrated that plant diversity can stabilize ecosystem functioning through population asynchrony, with decreases in the functions of some species compensated by increases in others. However, the relevance to natural ecosystems is debated. We use a global study of...

Final Technical Report: Vibrational Spectroscopy of Transient Combustion Intermediates Trapped in Helium Nanodroplets

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

Douberly, Gary Elliott

The objective of our experimental research program is to isolate and stabilize transient intermediates and products of prototype combustion reactions. This will be accomplished by Helium Nanodroplet Isolation, a novel technique where liquid helium droplets freeze out high energy metastable configurations of a reacting system, permitting infrared spectroscopic characterizations of products and intermediates that result from hydrocarbon radical reactions with molecular oxygen and other small molecules relevant to combustion environments. The low temperature (0.4 K) and rapid cooling associated with He droplets provides a perfectly suited medium to isolate and probe a broad range of molecular radical and carbene systemsmore » important to combustion chemistry. The sequential addition of molecular species to He droplets often leads to the stabilization of high-energy, metastable cluster configurations that represent regions of the potential energy surface far from the global minimum. Single and double resonance IR laser spectroscopy techniques, along with Stark and Zeeman capabilities, are being used to probe the structural and dynamical properties of these systems.« less

Spatial arrangement of organic compounds on a model mineral surface: implications for soil organic matter stabilization.

PubMed

Petridis, Loukas; Ambaye, Haile; Jagadamma, Sindhu; Kilbey, S Michael; Lokitz, Bradley S; Lauter, Valeria; Mayes, Melanie A

2014-01-01

The complexity of the mineral-organic carbon interface may influence the extent of stabilization of organic carbon compounds in soils, which is important for global climate futures. The nanoscale structure of a model interface was examined here by depositing films of organic carbon compounds of contrasting chemical character, hydrophilic glucose and amphiphilic stearic acid, onto a soil mineral analogue (Al2O3). Neutron reflectometry, a technique which provides depth-sensitive insight into the organization of the thin films, indicates that glucose molecules reside in a layer between Al2O3 and stearic acid, a result that was verified by water contact angle measurements. Molecular dynamics simulations reveal the thermodynamic driving force behind glucose partitioning on the mineral interface: The entropic penalty of confining the less mobile glucose on the mineral surface is lower than for stearic acid. The fundamental information obtained here helps rationalize how complex arrangements of organic carbon on soil mineral surfaces may arise.

Design of high-strength refractory complex solid-solution alloys

DOE PAGES

Singh, Prashant; Sharma, Aayush; Smirnov, A. V.; ...

2018-03-28

Nickel-based superalloys and near-equiatomic high-entropy alloys containing molybdenum are known for higher temperature strength and corrosion resistance. Yet, complex solid-solution alloys offer a huge design space to tune for optimal properties at slightly reduced entropy. For refractory Mo-W-Ta-Ti-Zr, we showcase KKR electronic structure methods via the coherent-potential approximation to identify alloys over five-dimensional design space with improved mechanical properties and necessary global (formation enthalpy) and local (short-range order) stability. Deformation is modeled with classical molecular dynamic simulations, validated from our first-principle data. We predict complex solid-solution alloys of improved stability with greatly enhanced modulus of elasticity (3× at 300 K)more » over near-equiatomic cases, as validated experimentally, and with higher moduli above 500 K over commercial alloys (2.3× at 2000 K). We also show that optimal complex solid-solution alloys are not described well by classical potentials due to critical electronic effects.« less

Grain boundary phase transformations in PtAu and relevance to thermal stabilization of bulk nanocrystalline metals

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

O’Brien, C. J.; Barr, C. M.; Price, P. M.

There has recently been a great deal of interest in employing immiscible solutes to stabilize nanocrystalline microstructures. Existing modeling efforts largely rely on mesoscale Monte Carlo approaches that employ a simplified model of the microstructure and result in highly homogeneous segregation to grain boundaries. However, there is ample evidence from experimental and modeling studies that demonstrates segregation to grain boundaries is highly non-uniform and sensitive to boundary character. This work employs a realistic nanocrystalline microstructure with experimentally relevant global solute concentrations to illustrate inhomogeneous boundary segregation. Furthermore, experiments quantifying segregation in thin films are reported that corroborate the prediction thatmore » grain boundary segregation is highly inhomogeneous. In addition to grain boundary structure modifying the degree of segregation, the existence of a phase transformation between low and high solute content grain boundaries is predicted. In order to conduct this study, new embedded atom method interatomic potentials are developed for Pt, Au, and the PtAu binary alloy.« less

Design of high-strength refractory complex solid-solution alloys

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

Singh, Prashant; Sharma, Aayush; Smirnov, A. V.

Nickel-based superalloys and near-equiatomic high-entropy alloys containing molybdenum are known for higher temperature strength and corrosion resistance. Yet, complex solid-solution alloys offer a huge design space to tune for optimal properties at slightly reduced entropy. For refractory Mo-W-Ta-Ti-Zr, we showcase KKR electronic structure methods via the coherent-potential approximation to identify alloys over five-dimensional design space with improved mechanical properties and necessary global (formation enthalpy) and local (short-range order) stability. Deformation is modeled with classical molecular dynamic simulations, validated from our first-principle data. We predict complex solid-solution alloys of improved stability with greatly enhanced modulus of elasticity (3× at 300 K)more » over near-equiatomic cases, as validated experimentally, and with higher moduli above 500 K over commercial alloys (2.3× at 2000 K). We also show that optimal complex solid-solution alloys are not described well by classical potentials due to critical electronic effects.« less

Dynamic effects of memory in a cobweb model with competing technologies

NASA Astrophysics Data System (ADS)

Agliari, Anna; Naimzada, Ahmad; Pecora, Nicolò

2017-02-01

We analyze a simple model based on the cobweb demand-supply framework with costly innovators and free imitators and study the endogenous dynamics of price and firms' fractions in a homogeneous good market. The evolutionary selection between technologies depends on a performance measure in which a memory parameter is introduced. The resulting dynamics is then described by a two-dimensional map. In addition to the locally stabilizing effect due to the presence of memory, we show the existence of a double stability threshold which entails for different dynamic scenarios occurring when the memory parameter takes extreme values (i.e. when consideration of the last profit realization prevails or it is too much neglected). The eventuality of different coexisting attractors as well as the structure of the basins of attraction that characterizes the path dependence property of the model with memory is shown. In particular, through global analysis we also illustrate particular bifurcations sequences that may increase the complexity of the related basins of attraction.

Grain boundary phase transformations in PtAu and relevance to thermal stabilization of bulk nanocrystalline metals

DOE PAGES

O’Brien, C. J.; Barr, C. M.; Price, P. M.; ...

2017-10-31

There has recently been a great deal of interest in employing immiscible solutes to stabilize nanocrystalline microstructures. Existing modeling efforts largely rely on mesoscale Monte Carlo approaches that employ a simplified model of the microstructure and result in highly homogeneous segregation to grain boundaries. However, there is ample evidence from experimental and modeling studies that demonstrates segregation to grain boundaries is highly non-uniform and sensitive to boundary character. This work employs a realistic nanocrystalline microstructure with experimentally relevant global solute concentrations to illustrate inhomogeneous boundary segregation. Furthermore, experiments quantifying segregation in thin films are reported that corroborate the prediction thatmore » grain boundary segregation is highly inhomogeneous. In addition to grain boundary structure modifying the degree of segregation, the existence of a phase transformation between low and high solute content grain boundaries is predicted. In order to conduct this study, new embedded atom method interatomic potentials are developed for Pt, Au, and the PtAu binary alloy.« less

Symmetry breaking in the planar configurations of disilicon tetrahalides: Pseudo-Jahn-Teller effect parameters, hardness and electronegativity.

PubMed

Kouchakzadeh, Ghazaleh; Nori-Shargh, Davood

2015-11-21

CCSD(T), MP2, LC-BLYP, LC-ωPBE and B3LYP methods with the Def2-TZVPP basis set and natural bond orbital (NBO) interpretations were performed to investigate the correlations between the Pseudo-Jahn-Teller Effect (PJTE) parameters [i.e. vibronic coupling constant values (F), energy gaps between reference states (Δ) and the primary force constant (K0)], structural and configurational properties, global hardness, global electronegativity, natural bond orders, stabilization energies associated with electron delocalizations and natural atomic charges of disilicon tetrafluoride (1), disilicon tetrachloride (2), disilicon tetrabromide (3) and disilicon tetraiodide (4). All levels of theory showed the trans-bent (C2h) configurations as the energy minimum structures of compounds 1-4, and the flap angles between the X2Si planes and the Si=Si bonds in the distorted (C2h) configurations decrease from compound 1 to compound 4. The negative curvatures of the ground state electronic configurations and the positive curvatures of the excited states of the adiabatic potential energy surfaces (APESs) which resulted from the mixing of the ground Ag and excited B2g states are due to the PJTE (i.e. PJT(Ag + B2g) ⊗ b2g problem). Contrary to the usual expectation, with the decrease of the energy gaps between reference states (Δ), the PJTE stabilization energy, E(PJT), decreases from compound 1 to compound 4. The canonical molecular orbital (CMO) analysis revealed that the contributions of the ψ(HOMO)(b3u) and ψL(UMO)(b1u) molecular orbitals in the vibronic coupling constant (F) decrease from compound 1 to compound 4. This fact clearly justifies the decrease of the vibronic coupling constant (F) and the primary force constant (the force constant without the PJTE) values on going from compound 1 to compound 4, leading to the decrease of the negative curvatures of the ground state electronic configuration curves of their corresponding APESs. The results obtained showed that the stabilization energies associated with the mixing of the distorted donor π(Si-Si)(b(u)) bonding and acceptor σ(Si-Si)*(b(u)) antibonding orbitals along the b2g bending distortions decrease from compound 1 to compound 4. This fact reasonably explains the increase of the Si-Si natural bond orders (nbo) on going from compound 1 to compound 4. With the increase of the Si-Si natural bond orders, the corresponding E(PJT) decreases from compound 1 to compound 4. Importantly, the variations of the global hardness (η) differences (Δ[η(C2h) - η(D2h)]) do not correlate with the trend observed for their corresponding total energy differences, justifying that the configurational properties of compounds 1-4 do not obey the maximum hardness principle. Interestingly, the trans-bent (C2h) configurations of compounds 1-4 are more electronegative than their corresponding planar (D2h) forms and the variations of their global electronegativity (χ) differences (Δ[χ(C2h) - χ(D2h)]) succeed in accounting for the decrease of the E(PJT) stabilization energies for the D2h → C2h conversion processes on going from compound 1 to compound 4.

Picosecond to nanosecond dynamics provide a source of conformational entropy for protein folding.

PubMed

Stadler, Andreas M; Demmel, Franz; Ollivier, Jacques; Seydel, Tilo

2016-08-03

Myoglobin can be trapped in fully folded structures, partially folded molten globules, and unfolded states under stable equilibrium conditions. Here, we report an experimental study on the conformational dynamics of different folded conformational states of apo- and holomyoglobin in solution. Global protein diffusion and internal molecular motions were probed by neutron time-of-flight and neutron backscattering spectroscopy on the picosecond and nanosecond time scales. Global protein diffusion was found to depend on the α-helical content of the protein suggesting that charges on the macromolecule increase the short-time diffusion of protein. With regard to the molten globules, a gel-like phase due to protein entanglement and interactions with neighbouring macromolecules was visible due to a reduction of the global diffusion coefficients on the nanosecond time scale. Diffusion coefficients, residence and relaxation times of internal protein dynamics and root mean square displacements of localised internal motions were determined for the investigated structural states. The difference in conformational entropy ΔSconf of the protein between the unfolded and the partially or fully folded conformations was extracted from the measured root mean square displacements. Using thermodynamic parameters from the literature and the experimentally determined ΔSconf values we could identify the entropic contribution of the hydration shell ΔShydr of the different folded states. Our results point out the relevance of conformational entropy of the protein and the hydration shell for stability and folding of myoglobin.

An RNA-binding compound that stabilizes the HIV-1 gRNA packaging signal structure and specifically blocks HIV-1 RNA encapsidation.

PubMed

Ingemarsdotter, Carin K; Zeng, Jingwei; Long, Ziqi; Lever, Andrew M L; Kenyon, Julia C

2018-03-14

NSC260594, a quinolinium derivative from the NCI diversity set II compound library, was previously identified in a target-based assay as an inhibitor of the interaction between the HIV-1 (ψ) stem-loop 3 (SL3) RNA and Gag. This compound was shown to exhibit potent antiviral activity. Here, the effects of this compound on individual stages of the viral lifecycle were examined by qRT-PCR, ELISA and Western blot, to see if its actions were specific to the viral packaging stage. The structural effects of NSC260594 binding to the HIV-1 gRNA were also examined by SHAPE and dimerization assays. Treatment of cells with NSC260594 did not reduce the number of integration events of incoming virus, and treatment of virus producing cells did not affect the level of intracellular Gag protein or viral particle release as determined by immunoblot. However, NSC260594 reduced the incorporation of gRNA into virions by up to 82%, without affecting levels of gRNA inside the cell. This reduction in packaging correlated closely with the reduction in infectivity of the released viral particles. To establish the structural effects of NSC260594 on the HIV-1 gRNA, we performed SHAPE analyses to pinpoint RNA structural changes. NSC260594 had a stabilizing effect on the wild type RNA that was not confined to SL3, but that was propagated across the structure. A packaging mutant lacking SL3 did not show this effect. NSC260594 acts as a specific inhibitor of HIV-1 RNA packaging. No other viral functions are affected. Its action involves preventing the interaction of Gag with SL3 by stabilizing this small RNA stem-loop which then leads to stabilization of the global packaging signal region (psi or ψ). This confirms data, previously only shown in analyses of isolated SL3 oligonucleotides, that SL3 is structurally labile in the presence of Gag and that this is critical for the complete psi region to be able to adopt different conformations. Since replication is otherwise unaffected by NSC260594 the flexibility of SL3 appears to be a unique requirement for genome encapsidation and identifies this process as a highly specific drug target. This study is proof of principle that development of a new class of antiretroviral drugs that specifically target viral packaging by binding to the viral genomic RNA is achievable.

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

Delay-Dependent Stability Criterion for Bidirectional Associative Memory Neural Networks with Interval Time-Varying Delays

NASA Astrophysics Data System (ADS)

Park, Ju H.; Kwon, O. M.

In the letter, the global asymptotic stability of bidirectional associative memory (BAM) neural networks with delays is investigated. The delay is assumed to be time-varying and belongs to a given interval. A novel stability criterion for the stability is presented based on the Lyapunov method. The criterion is represented in terms of linear matrix inequality (LMI), which can be solved easily by various optimization algorithms. Two numerical examples are illustrated to show the effectiveness of our new result.

Regional-Scale Forcing and Feedbacks from Alternative Scenarios of Global-Scale Land Use Change

NASA Astrophysics Data System (ADS)

Jones, A. D.; Chini, L. P.; Collins, W.; Janetos, A. C.; Mao, J.; Shi, X.; Thomson, A. M.; Torn, M. S.

2011-12-01

Future patterns of land use change depend critically on the degree to which terrestrial carbon management strategies, such as biological carbon sequestration and biofuels, are utilized in order to mitigate global climate change. Furthermore, land use change associated with terrestrial carbon management induces biogeophysical changes to surface energy budgets that perturb climate at regional and possibly global scales, activating different feedback processes depending on the nature and location of the land use change. As a first step in a broader effort to create an integrated earth system model, we examine two scenarios of future anthropogenic activity generated by the Global Change Assessment Model (GCAM) within the full-coupled Community Earth System Model (CESM). Each scenario stabilizes radiative forcing from greenhouse gases and aerosols at 4.5 W/m^2. In the first, stabilization is achieved through a universal carbon tax that values terrestrial carbon equally with fossil carbon, leading to modest afforestation globally and low biofuel utilization. In the second scenario, stabilization is achieved with a tax on fossil fuel and industrial carbon alone. In this case, biofuel utilization increases dramatically and crop area expands to claim approximately 50% of forest cover globally. By design, these scenarios exhibit identical climate forcing from atmospheric constituents. Thus, differences among them can be attributed to the biogeophysical effects of land use change. In addition, we utilize offline radiative transfer and offline land model simulations to identify forcing and feedback mechanisms operating in different regions. We find that boreal deforestation has a strong climatic signature due to significant albedo change coupled with a regional-scale water vapor feedback. Tropical deforestation, on the other hand, has more subtle effects on climate. Globally, the two scenarios yield warming trends over the 21st century that differ by 0.5 degrees Celsius. This work demonstrates the importance of land use in shaping future patterns of climate change, both globally and regionally.

Local and global Hopf bifurcation analysis in a neutral-type neuron system with two delays

NASA Astrophysics Data System (ADS)

Lv, Qiuyu; Liao, Xiaofeng

2018-03-01

In recent years, neutral-type differential-difference equations have been applied extensively in the field of engineering, and their dynamical behaviors are more complex than that of the delay differential-difference equations. In this paper, the equations used to describe a neutral-type neural network system of differential difference equation with two delays are studied (i.e. neutral-type differential equations). Firstly, by selecting τ1, τ2 respectively as a parameter, we provide an analysis about the local stability of the zero equilibrium point of the equations, and sufficient conditions of asymptotic stability for the system are derived. Secondly, by using the theory of normal form and applying the theorem of center manifold introduced by Hassard et al., the Hopf bifurcation is found and some formulas for deciding the stability of periodic solutions and the direction of Hopf bifurcation are given. Moreover, by applying the theorem of global Hopf bifurcation, the existence of global periodic solution of the system is studied. Finally, an example is given, and some computer numerical simulations are taken to demonstrate and certify the correctness of the presented results.

Global Mittag-Leffler stability and synchronization analysis of fractional-order quaternion-valued neural networks with linear threshold neurons.

PubMed

Yang, Xujun; Li, Chuandong; Song, Qiankun; Chen, Jiyang; Huang, Junjian

2018-05-04

This paper talks about the stability and synchronization problems of fractional-order quaternion-valued neural networks (FQVNNs) with linear threshold neurons. On account of the non-commutativity of quaternion multiplication resulting from Hamilton rules, the FQVNN models are separated into four real-valued neural network (RVNN) models. Consequently, the dynamic analysis of FQVNNs can be realized by investigating the real-valued ones. Based on the method of M-matrix, the existence and uniqueness of the equilibrium point of the FQVNNs are obtained without detailed proof. Afterwards, several sufficient criteria ensuring the global Mittag-Leffler stability for the unique equilibrium point of the FQVNNs are derived by applying the Lyapunov direct method, the theory of fractional differential equation, the theory of matrix eigenvalue, and some inequality techniques. In the meanwhile, global Mittag-Leffler synchronization for the drive-response models of the addressed FQVNNs are investigated explicitly. Finally, simulation examples are designed to verify the feasibility and availability of the theoretical results. Copyright © 2018 Elsevier Ltd. All rights reserved.

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

Estimation of the global climate effect of brown carbon

NASA Astrophysics Data System (ADS)

Zhang, A.; Wang, Y.; Zhang, Y.; Weber, R. J.; Song, Y.

2017-12-01

Carbonaceous aerosols significantly affect global radiative forcing and climate through absorption and scattering of sunlight. Black carbon (BC) and brown carbon (BrC) are light-absorbing carbonaceous aerosols. The global distribution and climate effect of BrC is uncertain. A recent study suggests that BrC absorption is comparable to BC in the upper troposphere over biomass burning region and that the resulting heating tends to stabilize the atmosphere. Yet current climate models do not include proper treatments of BrC. In this study, we derived a BrC global biomass burning emission inventory from Global Fire Emissions Database 4 (GFED4) and developed a BrC module in the Community Atmosphere Model version 5 (CAM5) of Community Earth System Model (CESM) model. The model simulations compared well to BrC observations of the Studies of Emissions, Atmospheric Composition, Clouds and Climate Coupling by Regional Surveys (SEAC4RS) and Deep Convective Clouds and Chemistry Project (DC-3) campaigns and includes BrC bleaching. Model results suggested that BrC in the upper troposphere due to convective transport is as important an absorber as BC globally. Upper tropospheric BrC radiative forcing is particularly significant over the tropics, affecting the atmosphere stability and Hadley circulation.

Robust Kalman filtering cooperated Elman neural network learning for vision-sensing-based robotic manipulation with global stability.

PubMed

Zhong, Xungao; Zhong, Xunyu; Peng, Xiafu

2013-10-08

In this paper, a global-state-space visual servoing scheme is proposed for uncalibrated model-independent robotic manipulation. The scheme is based on robust Kalman filtering (KF), in conjunction with Elman neural network (ENN) learning techniques. The global map relationship between the vision space and the robotic workspace is learned using an ENN. This learned mapping is shown to be an approximate estimate of the Jacobian in global space. In the testing phase, the desired Jacobian is arrived at using a robust KF to improve the ENN learning result so as to achieve robotic precise convergence of the desired pose. Meanwhile, the ENN weights are updated (re-trained) using a new input-output data pair vector (obtained from the KF cycle) to ensure robot global stability manipulation. Thus, our method, without requiring either camera or model parameters, avoids the corrupted performances caused by camera calibration and modeling errors. To demonstrate the proposed scheme's performance, various simulation and experimental results have been presented using a six-degree-of-freedom robotic manipulator with eye-in-hand configurations.

Design of ternary alkaline-earth metal Sn(II) oxides with potential good p-type conductivity

DOE PAGES

Du, Mao -Hua; Singh, David J.; Zhang, Lijun; ...

2016-04-19

Oxides with good p-type conductivity have been long sought after to achieve high performance all-oxide optoelectronic devices. Divalent Sn(II) based oxides are promising candidates because of their rather dispersive upper valence bands caused by the Sn-5s/O-2p anti-bonding hybridization. There are so far few known Sn(II) oxides being p-type conductive suitable for device applications. Here, we present via first-principles global optimization structure searches a material design study for a hitherto unexplored Sn(II)-based system, ternary alkaline-earth metal Sn(II) oxides in the stoichiometry of MSn 2O 3 (M = Mg, Ca, Sr, Ba). We identify two stable compounds of SrSn 2O 3 andmore » BaSn 2O 3, which can be stabilized by Sn-rich conditions in phase stability diagrams. Their structures follow the Zintl behaviour and consist of basic structural motifs of SnO 3 tetrahedra. Unexpectedly they show distinct electronic properties with band gaps ranging from 1.90 (BaSn 2O 3) to 3.15 (SrSn 2O 3) eV, and hole effective masses ranging from 0.87 (BaSn 2O 3) to above 6.0 (SrSn 2O 3) m0. Further exploration of metastable phases indicates a wide tunability of electronic properties controlled by the details of the bonding between the basic structural motifs. Lastly, this suggests further exploration of alkaline-earth metal Sn(II) oxides for potential applications requiring good p-type conductivity such as transparent conductors and photovoltaic absorbers.« less

Accepting the Invitation to Open Innovation in Malaria Drug Discovery: Synthesis, Biological Evaluation, and Investigation on the Structure-Activity Relationships of Benzo[b]thiophene-2-carboxamides as Antimalarial Agents.

PubMed

Pieroni, Marco; Azzali, Elisa; Basilico, Nicoletta; Parapini, Silvia; Zolkiewski, Michal; Beato, Claudia; Annunziato, Giannamaria; Bruno, Agostino; Vacondio, Federica; Costantino, Gabriele

2017-03-09

Malaria eradication is a global health priority, but current therapies are not always suitable for providing a radical cure. Artemisinin has paved the way for the current malaria treatment, the so-called Artemisinin-based Combination Therapy (ACT). However, with the detection of resistance to ACT, innovative compounds active against multiple parasite species and at multiple life stages are needed. GlaxoSmithKline has recently disclosed the results of a phenotypic screening of an internal library, publishing a collection of 400 antimalarial chemotypes, termed the "Malaria Box". After analysis of the data set, we have carried out a medicinal chemistry campaign in order to define the structure-activity relationships for one of the released compounds, which embodies a benzothiophene-2-carboxamide core. Thirty-five compounds were prepared, and a description of the structural features responsible for the in vitro activity against different strains of P. falciparum, the toxicity, and the metabolic stability is herein reported.

Environmental-stress-induced Chromatin Regulation and its Heritability

PubMed Central

Fang, Lei; Wuptra, Kenly; Chen, Danqi; Li, Hongjie; Huang, Shau-Ku; Jin, Chunyuan; Yokoyama, Kazunari K

2014-01-01

Chromatin is subject to proofreading and repair mechanisms during the process of DNA replication, as well as repair to maintain genetic and epigenetic information and genome stability. The dynamic structure of chromatin modulates various nuclear processes, including transcription and replication, by altering the accessibility of the DNA to regulatory factors. Structural changes in chromatin are affected by the chemical modification of histone proteins and DNA, remodeling of nucleosomes, incorporation of variant histones, noncoding RNAs, and nonhistone DNA-binding proteins. Phenotypic diversity and fidelity can be balanced by controlling stochastic switching of chromatin structure and dynamics in response to the environmental disruptors and endogenous stresses. The dynamic chromatin remodeling can, therefore, serve as a sensor, through which environmental and/or metabolic agents can alter gene expression, leading to global cellular changes involving multiple interactive networks. Furthermore its recent evidence also suggests that the epigenetic changes are heritable during the development. This review will discuss the environmental sensing system for chromatin regulation and genetic and epigenetic controls from developmental perspectives. PMID:25045581

Global optimization of ionic Mg(n)F(2n) (n=1-30) clusters.

PubMed

Francisco, E; Martín Pendás, A; Blanco, M A

2005-12-15

The global optimization basin-hopping (BH) method has been used to locate the global minima (GM) of Mg(n)F(2n) (n=1-30) clusters using a Born-Mayer-type potential. Some of the GM were particularly difficult to find, requiring more than 1.5 x 10(4) BH steps. We have found that both the binding energy per MgF2 unit and the effective volume of the GM isomers increase almost linearly with n, and that cluster symmetry decreases with cluster size. The data derived from the BH runs reveal a growing density of local minima just above the GM as n increases. Despite this, the attraction basin around each GM is relatively large, since after all their atomic coordinates are randomly displaced by values as high as 2.0 bohrs, the perturbed structures, upon reoptimization, relax back to the GM in more than 50% of the cases (except for n=10 and 11). The relative stabilities derived from energy second differences suggest that n=8,10,13,15, and 20 are probably the magic numbers for these systems. Mass spectrum experiments would be very useful to clarify this issue.

Effects of Near Infrared Radiation on DNA. DLS and ATR-FTIR Study

NASA Astrophysics Data System (ADS)

Szymborska-Małek, Katarzyna; Komorowska, Małgorzata; Gąsior-Głogowska, Marlena

2018-01-01

We presume that the primary effect of Near Infrared (NIR) radiation on aqueous solutions of biological molecules concerns modification of hydrogen bonded structures mainly the global and the hydration shell water molecules. Since water has a significant influence on the DNA structure, we expect that the thermal stability of DNA could be modified by NIR radiation. The herring sperm DNA was exposed to NIR radiation (700-1100 nm) for 5, 10, and 20 min periods. The temperature dependent infrared measurements were done for the thin films formed on the diamond ATR crystal from evaporated DNA solutions exposed and unexposed to NIR radiation. For the NIR-treated samples (at room temperature) the B form was better conserved than in the control sample independently of the irradiation period. Above 50 °C a considerable increase in the A form was only observed for 10 min NIR exposed samples. The hydrodynamic radius, (Rh), studied by the dynamic light scattering, showed drastic decrease with the increasing irradiation time. Principal components analysis (PCA) allowed to detect the spectral features correlated with the NIR effect and thermal stability of the DNA films. Obtained results strongly support the idea that the photoionization of water by NIR radiation in presence of DNA molecules is the main factor influencing on its physicochemical properties.

Functional and Biochemical Characterization of Three Recombinant Human Glucose-6-Phosphate Dehydrogenase Mutants: Zacatecas, Vanua-Lava and Viangchan.

PubMed

Gómez-Manzo, Saúl; Marcial-Quino, Jaime; Vanoye-Carlo, America; Serrano-Posada, Hugo; González-Valdez, Abigail; Martínez-Rosas, Víctor; Hernández-Ochoa, Beatriz; Sierra-Palacios, Edgar; Castillo-Rodríguez, Rosa Angélica; Cuevas-Cruz, Miguel; Rodríguez-Bustamante, Eduardo; Arreguin-Espinosa, Roberto

2016-05-21

Glucose-6-phosphate dehydrogenase (G6PD) deficiency in humans causes severe disease, varying from mostly asymptomatic individuals to patients showing neonatal jaundice, acute hemolysis episodes or chronic nonspherocytic hemolytic anemia. In order to understand the effect of the mutations in G6PD gene function and its relation with G6PD deficiency severity, we report the construction, cloning and expression as well as the detailed kinetic and stability characterization of three purified clinical variants of G6PD that present in the Mexican population: G6PD Zacatecas (Class I), Vanua-Lava (Class II) and Viangchan (Class II). For all the G6PD mutants, we obtained low purification yield and altered kinetic parameters compared with Wild Type (WT). Our results show that the mutations, regardless of the distance from the active site where they are located, affect the catalytic properties and structural parameters and that these changes could be associated with the clinical presentation of the deficiency. Specifically, the structural characterization of the G6PD Zacatecas mutant suggests that the R257L mutation have a strong effect on the global stability of G6PD favoring an unstable active site. Using computational analysis, we offer a molecular explanation of the effects of these mutations on the active site.

Recommendations on: internal standard criteria, stability, incurred sample reanalysis and recent 483s by the Global CRO Council for Bioanalysis.

PubMed

Lowes, Steve; Jersey, Jim; Shoup, Ronald; Garofolo, Fabio; Savoie, Natasha; Mortz, Ejvind; Needham, Shane; Caturla, Maria Cruz; Steffen, Ray; Sheldon, Curtis; Hayes, Roger; Samuels, Tim; Di Donato, Lorella; Kamerud, John; Michael, Steve; Lin, Zhongping John; Hillier, Jim; Moussallie, Marc; de Souza Teixeira, Leonardo; Rocci, Mario; Buonarati, Mike; Truog, James; Hussain, Saleh; Lundberg, Richard; Breau, Alan; Zhang, Tianyi; Jonker, Jianine; Berger, Neil; Gagnon-Carignan, Sofi; Nehls, Corey; Nicholson, Robert; Hilhorst, Martijn; Karnik, Shane; de Boer, Theo; Houghton, Richard; Smith, Kirk; Cojocaru, Laura; Allen, Mike; Harter, Tammy; Fatmi, Saadya; Sayyarpour, Farhad; Vija, Jenifer; Malone, Michele; Heller, Dennis

2011-06-01

"The Global CRO Council (GCC) for Bioanalysis was formed in an effort to bring together many CRO leaders to openly discuss bioanalysis and the regulatory challenges unique to the outsourcing industry"

Allostery in the ferredoxin protein motif does not involve a conformational switch.

PubMed

Nechushtai, Rachel; Lammert, Heiko; Michaeli, Dorit; Eisenberg-Domovich, Yael; Zuris, John A; Luca, Maria A; Capraro, Dominique T; Fish, Alex; Shimshon, Odelia; Roy, Melinda; Schug, Alexander; Whitford, Paul C; Livnah, Oded; Onuchic, José N; Jennings, Patricia A

2011-02-08

Regulation of protein function via cracking, or local unfolding and refolding of substructures, is becoming a widely recognized mechanism of functional control. Oftentimes, cracking events are localized to secondary and tertiary structure interactions between domains that control the optimal position for catalysis and/or the formation of protein complexes. Small changes in free energy associated with ligand binding, phosphorylation, etc., can tip the balance and provide a regulatory functional switch. However, understanding the factors controlling function in single-domain proteins is still a significant challenge to structural biologists. We investigated the functional landscape of a single-domain plant-type ferredoxin protein and the effect of a distal loop on the electron-transfer center. We find the global stability and structure are minimally perturbed with mutation, whereas the functional properties are altered. Specifically, truncating the L1,2 loop does not lead to large-scale changes in the structure, determined via X-ray crystallography. Further, the overall thermal stability of the protein is only marginally perturbed by the mutation. However, even though the mutation is distal to the iron-sulfur cluster (∼20 Å), it leads to a significant change in the redox potential of the iron-sulfur cluster (57 mV). Structure-based all-atom simulations indicate correlated dynamical changes between the surface-exposed loop and the iron-sulfur cluster-binding region. Our results suggest intrinsic communication channels within the ferredoxin fold, composed of many short-range interactions, lead to the propagation of long-range signals. Accordingly, protein interface interactions that involve L1,2 could potentially signal functional changes in distal regions, similar to what is observed in other allosteric systems.

Revisiting the Stability of Spatially Heterogeneous Predator-Prey Systems Under Eutrophication.

PubMed

Farkas, J Z; Morozov, A Yu; Arashkevich, E G; Nikishina, A

2015-10-01

We employ partial integro-differential equations to model trophic interaction in a spatially extended heterogeneous environment. Compared to classical reaction-diffusion models, this framework allows us to more realistically describe the situation where movement of individuals occurs on a faster time scale than on the demographic (population) time scale, and we cannot determine population growth based on local density. However, most of the results reported so far for such systems have only been verified numerically and for a particular choice of model functions, which obviously casts doubts about these findings. In this paper, we analyse a class of integro-differential predator-prey models with a highly mobile predator in a heterogeneous environment, and we reveal the main factors stabilizing such systems. In particular, we explore an ecologically relevant case of interactions in a highly eutrophic environment, where the prey carrying capacity can be formally set to 'infinity'. We investigate two main scenarios: (1) the spatial gradient of the growth rate is due to abiotic factors only, and (2) the local growth rate depends on the global density distribution across the environment (e.g. due to non-local self-shading). For an arbitrary spatial gradient of the prey growth rate, we analytically investigate the possibility of the predator-prey equilibrium in such systems and we explore the conditions of stability of this equilibrium. In particular, we demonstrate that for a Holling type I (linear) functional response, the predator can stabilize the system at low prey density even for an 'unlimited' carrying capacity. We conclude that the interplay between spatial heterogeneity in the prey growth and fast displacement of the predator across the habitat works as an efficient stabilizing mechanism. These results highlight the generality of the stabilization mechanisms we find in spatially structured predator-prey ecological systems in a heterogeneous environment.

Existence and global exponential stability of periodic solution to BAM neural networks with periodic coefficients and continuously distributed delays

NASA Astrophysics Data System (ADS)

Zhou, distributed delays [rapid communication] T.; Chen, A.; Zhou, Y.

2005-08-01

By using the continuation theorem of coincidence degree theory and Liapunov function, we obtain some sufficient criteria to ensure the existence and global exponential stability of periodic solution to the bidirectional associative memory (BAM) neural networks with periodic coefficients and continuously distributed delays. These results improve and generalize the works of papers [J. Cao, L. Wang, Phys. Rev. E 61 (2000) 1825] and [Z. Liu, A. Chen, J. Cao, L. Huang, IEEE Trans. Circuits Systems I 50 (2003) 1162]. An example is given to illustrate that the criteria are feasible.

Boundedness, Mittag-Leffler stability and asymptotical ω-periodicity of fractional-order fuzzy neural networks.

PubMed

Wu, Ailong; Zeng, Zhigang

2016-02-01

We show that the ω-periodic fractional-order fuzzy neural networks cannot generate non-constant ω-periodic signals. In addition, several sufficient conditions are obtained to ascertain the boundedness and global Mittag-Leffler stability of fractional-order fuzzy neural networks. Furthermore, S-asymptotical ω-periodicity and global asymptotical ω-periodicity of fractional-order fuzzy neural networks is also characterized. The obtained criteria improve and extend the existing related results. To illustrate and compare the theoretical criteria, some numerical examples with simulation results are discussed in detail. Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.

Applied radiation physics: The use of x-rays for the structural characterization of aqueous emulsions and the development of new insect sterilization protocols

NASA Astrophysics Data System (ADS)

Brar, Ramaninder K.

X-rays have great potential of applications in a wide variety of fields. This dissertation presents the use of x-rays for the structural characterization of aqueous emulsions and for insect sterilization. The stabilization of hydrophobic colloids, such as oil droplets, in water has attracted scientist for a variety of scientific, pharmaceutical and industrial applications. Several studies have been done to understand the stability of oil-in-water emulsions. The work of Pashley and his coworkers has demonstrated that the removal of dissolved gasses from water enhances the dispersion of hydrophobic oil in water and these surfactant-free emulsions do not lose their stability when the previously removed gasses are reintroduced. However, very little is known about the structure and stability of these emulsions over time or even to what extent they form. The formation of a stable emulsion in the complete absence of a surfactant could provide an alternative approach to a physiologically safe drug carrier. In this dissertation we demonstrate the formation of stabilized surfactant-free degassed emulsions of hydrocarbons - hexane, heptane and octane and silicone oil in ultra-pure water. The enhancement of dispersion of oil droplets by degassing was large for highly hydrophobic silicone oil. Turbidity measurements and small angle x-ray scattering results show that the uniformly dispersed oil droplets weakly aggregate over a period of several hours. Gentle perturbation re-generates the dispersion to nearly initial conditions. The control of insect species for the protection of crops, livestock, and prevention of disease, such as dengue fever and malaria, is a high priority in today's global economy. Sterile Insect Technique (SIT), a method of insect extermination without the use of pesticides, has proven very effective in eradicating certain dipteran insect populations. However, when standard sterilization methods developed for dipterans are applied to mosquito populations significant complications arise, such as an inability to compete with non-irradiated males and high mortality rates. To improve mosquito SIT, we have developed new radiation protocols for insect sterilization using long wavelength x-rays. Our results have demonstrated that longer wavelength x-rays have a significant effect on the outcome of the sterile males' longevity as well as on the efficacy of sterilization while employing a substantially lower dose.

Different Mechanisms of Soil Microbial Response to Global Change Result in Different Outcomes in the MIMICS-CN Model

NASA Astrophysics Data System (ADS)

Kyker-Snowman, E.; Wieder, W. R.; Grandy, S.

2017-12-01

Microbial-explicit models of soil carbon (C) and nitrogen (N) cycling have improved upon simulations of C and N stocks and flows at site-to-global scales relative to traditional first-order linear models. However, the response of microbial-explicit soil models to global change factors depends upon which parameters and processes in a model are altered by those factors. We used the MIcrobial-MIneral Carbon Stabilization Model with coupled N cycling (MIMICS-CN) to compare modeled responses to changes in temperature and plant inputs at two previously-modeled sites (Harvard Forest and Kellogg Biological Station). We spun the model up to equilibrium, applied each perturbation, and evaluated 15 years of post-perturbation C and N pools and fluxes. To model the effect of increasing temperatures, we independently examined the impact of decreasing microbial C use efficiency (CUE), increasing the rate of microbial turnover, and increasing Michaelis-Menten kinetic rates of litter decomposition, plus several combinations of the three. For plant inputs, we ran simulations with stepwise increases in metabolic litter, structural litter, whole litter (structural and metabolic), or labile soil C. The cumulative change in soil C or N varied in both sign and magnitude across simulations. For example, increasing kinetic rates of litter decomposition resulted in net releases of both C and N from soil pools, while decreasing CUE produced short-term increases in respiration but long-term accumulation of C in litter pools and shifts in soil C:N as microbial demand for C increased and biomass declined. Given that soil N cycling constrains the response of plant productivity to global change and that soils generate a large amount of uncertainty in current earth system models, microbial-explicit models are a critical opportunity to advance the modeled representation of soils. However, microbial-explicit models must be improved by experiments to isolate the physiological and stoichiometric parameters of soil microbes that shift under global change.

Soil Carbon Chemistry and Greenhouse Gas Production in Global Peatlands

NASA Astrophysics Data System (ADS)

Normand, A. E.; Turner, B. L.; Lamit, L. J.; Smith, A. N.; Baiser, B.; Clark, M. W.; Hazlett, C.; Lilleskov, E.; Long, J.; Grover, S.; Reddy, K. R.

2017-12-01

Peatlands play a critical role in the global carbon cycle because they contain approximately 30% of the 1500 Pg of carbon stored in soils worldwide. However, the stability of these vast stores of carbon is under threat from climate and land-use change, with important consequences for global climate. Ecosystem models predict the impact of peatland perturbation on carbon fluxes based on total soil carbon pools, but responses could vary markedly depending on the chemical composition of soil organic matter. Here we combine experimental and observational studies to quantify the chemical nature and response to perturbation of soil organic matter in peatlands worldwide. We quantified carbon functional groups in a global sample of 125 freshwater peatlands using solid-state 13C nuclear magnetic resonance (NMR) spectroscopy to determine the drivers of molecular composition of soil organic matter. We then incubated a representative subset of the soils under aerobic and anaerobic conditions to determine how organic matter composition influences carbon dioxide (CO2) and methane (CH4) emissions following drainage or flooding. The functional chemistry of peat varied markedly at large and small spatial scales, due to long-term land use change, mean annual temperature, nutrient status, and vegetation, but not pH. Despite this variation, we found predictable responses of greenhouse gas production following drainage based on soil carbon chemistry, defined by a novel Global Peat Stability Index, with greater CO2 and CH4 fluxes from soils enriched in oxygen-containing organic carbon (O-alkyl C) and depleted in aromatic and hydrophobic compounds. Incorporation of the Global Peat Stability Index of peatland organic matter into earth system models and management strategies, which will improve estimates of GHG fluxes from peatlands and ultimately advance management to reduce carbon loss from these sensitive ecosystems.

[Environmental behavior and effect of biomass-derived black carbon in soil: a review].

PubMed

Liu, Yu-Xue; Liu, Wei; Wu, Wei-Xiang; Zhong, Zhe-Ke; Chen, Ying-Xu

2009-04-01

Biomass-derived black carbon, also named biochar, has the characteristics of high stability against decay and high capability of adsorption, and can affect the environment through its interactions with climate and geology, playing a significant role in global climate change, carbon biogeochemical cycle, and environmental system. In recent years, more and more researchers in the fields of atmospheric sciences, geology, and environmental science focused on the environmental behavior and effect of biochar. As one possible source of the components with high aromatic structure in soil humus, biochar is of great importance in increasing soil carbon storage and improving soil fertility, and in maintaining the balance of soil ecosystem. This paper offered the latest information regarding the characteristics and biotic and abiotic oxidation mechanisms of biochar, its effects on global climate change, and the environmental effect of biochar in soil. Research prospects were briefly discussed on the environmental behavior and effect of biochar in soil ecosystem.

Global asymptotic stability of plant-seed bank models.

PubMed

Eager, Eric Alan; Rebarber, Richard; Tenhumberg, Brigitte

2014-07-01

Many plant populations have persistent seed banks, which consist of viable seeds that remain dormant in the soil for many years. Seed banks are important for plant population dynamics because they buffer against environmental perturbations and reduce the probability of extinction. Viability of the seeds in the seed bank can depend on the seed's age, hence it is important to keep track of the age distribution of seeds in the seed bank. In this paper we construct a general density-dependent plant-seed bank model where the seed bank is age-structured. We consider density dependence in both seedling establishment and seed production, since previous work has highlighted that overcrowding can suppress both of these processes. Under certain assumptions on the density dependence, we prove that there is a globally stable equilibrium population vector which is independent of the initial state. We derive an analytical formula for the equilibrium population using methods from feedback control theory. We apply these results to a model for the plant species Cirsium palustre and its seed bank.

Full-f XGC1 gyrokinetic study of improved ion energy confinement from impurity stabilization of ITG turbulence

NASA Astrophysics Data System (ADS)

Kim, Kyuho; Kwon, Jae-Min; Chang, C. S.; Seo, Janghoon; Ku, S.; Choe, W.

2017-06-01

Flux-driven full-f gyrokinetic simulations are performed to study carbon impurity effects on the ion temperature gradient (ITG) turbulence and ion thermal transport in a toroidal geometry. Employing the full-f gyrokinetic code XGC1, both main ions and impurities are evolved self-consistently including turbulence and neoclassical physics. It is found that the carbon impurity profile self-organizes to form an inwardly peaked density profile, which weakens the ITG instabilities and reduces the overall fluctuations and ion thermal transport. A stronger reduction appears in the low frequency components of the fluctuations. The global structure of E × B flow also changes, resulting in the reduction of global avalanche like transport events in the impure plasma. Detailed properties of impurity transport are also studied, and it is revealed that both the inward neoclassical pinch and the outward turbulent transport are equally important in the formation of the steady state impurity profile.

Global asymptotic stability and hopf bifurcation for a blood cell production model.

PubMed

Crauste, Fabien

2006-04-01

We analyze the asymptotic stability of a nonlinear system of two differential equations with delay, describing the dynamics of blood cell produc- tion. This process takes place in the bone marrow, where stem cells differen- tiate throughout division in blood cells. Taking into account an explicit role of the total population of hematopoietic stem cells in the introduction of cells in cycle, we are led to study a characteristic equation with delay-dependent coefficients. We determine a necessary and sufficient condition for the global stability of the first steady state of our model, which describes the popula- tion's dying out, and we obtain the existence of a Hopf bifurcation for the only nontrivial positive steady state, leading to the existence of periodic solutions. These latter are related to dynamical diseases affecting blood cells known for their cyclic nature.

Bimodal pair f-KdV dynamics in star-forming clouds

NASA Astrophysics Data System (ADS)

Karmakar, Pralay Kumar; Haloi, Archana; Roy, Supriya

2018-04-01

A theoretical formalism for investigating the bimodal conjugational mode dynamics of hybrid source, dictated by a unique pair of forced Korteweg-de Vries (f-KdV) equations in a complex turbo-magnetized star-forming cloud, is reported. It uses a standard multi-scale analysis executed over the cloud-governing equations in a closure form to derive the conjugated pair f-KdV system. We numerically see the structural features of two distinctive classes of eigenmode patterns stemming from the conjoint gravito-electrostatic interplay. The electrostatic compressive monotonic aperiodic shock-like patterns and gravitational compressive non-monotonic oscillatory shock-like structures are excitable. It is specifically revealed that the constitutive grain-charge (grain-mass) acts as electrostatic stabilizer (gravitational destabilizer) against the global cloud collapse dynamics. The basic features of the nonlinear coherent structures are confirmed in systematic phase-plane landscapes, indicating electrostatic irregular non-homoclinic open trajectories and gravitational atypical non-chaotic homoclinic fixed-point attractors. The relevance in the real astro-cosmic scenarios of the early phases of structure formation via wave-driven fluid-accretive transport processes is summarily emphasized.

Locating structures and evolution pathways of reconstructed rutile TiO2(011) using genetic algorithm aided density functional theory calculations.

PubMed

Ding, Pan; Gong, Xue-Qing

2016-05-01

Titanium dioxide (TiO2) is an important metal oxide that has been used in many different applications. TiO2 has also been widely employed as a model system to study basic processes and reactions in surface chemistry and heterogeneous catalysis. In this work, we investigated the (011) surface of rutile TiO2 by focusing on its reconstruction. Density functional theory calculations aided by a genetic algorithm based optimization scheme were performed to extensively sample the potential energy surfaces of reconstructed rutile TiO2 structures that obey (2 × 1) periodicity. A lot of stable surface configurations were located, including the global-minimum configuration that was proposed previously. The wide variety of surface structures determined through the calculations performed in this work provide insight into the relationship between the atomic configuration of a surface and its stability. More importantly, several analytical schemes were proposed and tested to gauge the differences and similarities among various surface structures, aiding the construction of the complete pathway for the reconstruction process.

A trade off between catalytic activity and protein stability determines the clinical manifestations of glucose-6-phosphate dehydrogenase (G6PD) deficiency.

PubMed

Boonyuen, Usa; Chamchoy, Kamonwan; Swangsri, Thitiluck; Junkree, Thanyaphorn; Day, Nicholas P J; White, Nicholas J; Imwong, Mallika

2017-11-01

Glucose-6-phosphate dehydrogenase (G6PD) deficiency is the most common polymorphism and enzymopathy in humans, affecting approximately 400 million people worldwide. It is responsible for various clinical manifestations, including favism, hemolytic anemia, chronic non-spherocytic hemolytic anemia, spontaneous abortion, and neonatal hyperbilirubinemia. Understanding the molecular mechanisms underlying the severity of G6PD deficiency is of great importance but that of many G6PD variants are still unknown. In this study, we report the construction, expression, purification, and biochemical characterization in terms of kinetic properties and stability of five clinical G6PD variants-G6PD Bangkok, G6PD Bangkok noi, G6PD Songklanagarind, G6PD Canton+Bangkok noi, and G6PD Union+Viangchan. G6PD Bangkok and G6PD Canton+Bangkok noi showed a complete loss of catalytic activity and moderate reduction in thermal stability when compared with the native G6PD. G6PD Bangkok noi and G6PD Union+Viangchan showed a significant reduction in catalytic efficiency, whereas G6PD Songklanagarind showed a catalytic activity comparable to the wild-type enzyme. The Union+Viangchan mutation showed a remarkable effect on the global stability of the enzyme. In addition, our results indicate that the location of mutations in G6PD variants affects their catalytic activity, stability, and structure. Hence, our results provide a molecular explanation for clinical manifestations observed in individuals with G6PD deficiency. Copyright © 2017 The Authors. Published by Elsevier B.V. All rights reserved.

Stability and Scalability of the CMS Global Pool: Pushing HTCondor and GlideinWMS to New Limits

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

Balcas, J.; Bockelman, B.; Hufnagel, D.

The CMS Global Pool, based on HTCondor and glideinWMS, is the main computing resource provisioning system for all CMS workflows, including analysis, Monte Carlo production, and detector data reprocessing activities. The total resources at Tier-1 and Tier-2 grid sites pledged to CMS exceed 100,000 CPU cores, while another 50,000 to 100,000 CPU cores are available opportunistically, pushing the needs of the Global Pool to higher scales each year. These resources are becoming more diverse in their accessibility and configuration over time. Furthermore, the challenge of stably running at higher and higher scales while introducing new modes of operation such asmore » multi-core pilots, as well as the chaotic nature of physics analysis workflows, places huge strains on the submission infrastructure. This paper details some of the most important challenges to scalability and stability that the CMS Global Pool has faced since the beginning of the LHC Run II and how they were overcome.« less

Global alliances effect in coalition forming

NASA Astrophysics Data System (ADS)

Vinogradova, Galina; Galam, Serge

2014-11-01

Coalition forming is investigated among countries, which are coupled with short range interactions, under the influence of externally-set opposing global alliances. The model extends a recent Natural Model of coalition forming inspired from Statistical Physics, where instabilities are a consequence of decentralized maximization of the individual benefits of actors. In contrast to physics where spins can only evaluate the immediate cost/benefit of a flip of orientation, countries have a long horizon of rationality, which associates with the ability to envision a way up to a better configuration even at the cost of passing through intermediate loosing states. The stabilizing effect is produced through polarization by the global alliances of either a particular unique global interest factor or multiple simultaneous ones. This model provides a versatile theoretical tool for the analysis of real cases and design of novel strategies. Such analysis is provided for several real cases including the Eurozone. The results shed a new light on the understanding of the complex phenomena of planned stabilization in the coalition forming.

Stability and scalability of the CMS Global Pool: Pushing HTCondor and glideinWMS to new limits

NASA Astrophysics Data System (ADS)

Balcas, J.; Bockelman, B.; Hufnagel, D.; Hurtado Anampa, K.; Aftab Khan, F.; Larson, K.; Letts, J.; Marra da Silva, J.; Mascheroni, M.; Mason, D.; Perez-Calero Yzquierdo, A.; Tiradani, A.

2017-10-01

The CMS Global Pool, based on HTCondor and glideinWMS, is the main computing resource provisioning system for all CMS workflows, including analysis, Monte Carlo production, and detector data reprocessing activities. The total resources at Tier-1 and Tier-2 grid sites pledged to CMS exceed 100,000 CPU cores, while another 50,000 to 100,000 CPU cores are available opportunistically, pushing the needs of the Global Pool to higher scales each year. These resources are becoming more diverse in their accessibility and configuration over time. Furthermore, the challenge of stably running at higher and higher scales while introducing new modes of operation such as multi-core pilots, as well as the chaotic nature of physics analysis workflows, places huge strains on the submission infrastructure. This paper details some of the most important challenges to scalability and stability that the CMS Global Pool has faced since the beginning of the LHC Run II and how they were overcome.

Effect of Resting-State fNIRS Scanning Duration on Functional Brain Connectivity and Graph Theory Metrics of Brain Network.

PubMed

Geng, Shujie; Liu, Xiangyu; Biswal, Bharat B; Niu, Haijing

2017-01-01

As an emerging brain imaging technique, functional near infrared spectroscopy (fNIRS) has attracted widespread attention for advancing resting-state functional connectivity (FC) and graph theoretical analyses of brain networks. However, it remains largely unknown how the duration of the fNIRS signal scanning is related to stable and reproducible functional brain network features. To answer this question, we collected resting-state fNIRS signals (10-min duration, two runs) from 18 participants and then truncated the hemodynamic time series into 30-s time bins that ranged from 1 to 10 min. Measures of nodal efficiency, nodal betweenness, network local efficiency, global efficiency, and clustering coefficient were computed for each subject at each fNIRS signal acquisition duration. Analyses of the stability and between-run reproducibility were performed to identify optimal time length for each measure. We found that the FC, nodal efficiency and nodal betweenness stabilized and were reproducible after 1 min of fNIRS signal acquisition, whereas network clustering coefficient, local and global efficiencies stabilized after 1 min and were reproducible after 5 min of fNIRS signal acquisition for only local and global efficiencies. These quantitative results provide direct evidence regarding the choice of the resting-state fNIRS scanning duration for functional brain connectivity and topological metric stability of brain network connectivity.

Zwitterionization of glycine in water environment: Stabilization mechanism and NMR spectral signatures

NASA Astrophysics Data System (ADS)

Valverde, Danillo; da Costa Ludwig, Zélia Maria; da Costa, Célia Regina; Ludwig, Valdemir; Georg, Herbert C.

2018-01-01

At physiological conditions, myriads of biomolecules (e.g., amino acids, peptides, and proteins) exist predominantly in the zwitterionic structural form and their biological functions will result in these conditions. However these geometrical structures are inaccessible energetically in the gas phase, and at this point, stabilization of amino-acids in physiological conditions is still under debate. In this paper, the electronic properties of a glycine molecule in the liquid environment were studied by performing a relaxation of the glycine geometry in liquid water using the free energy gradient method combined with a sequential quantum mechanics/molecular mechanics approach. A series of Monte Carlo Metropolis simulations of the glycine molecule embedded in liquid water, followed by only a quantum mechanical calculation in each of them were carried out. Both the local and global liquid environments were emphasized to obtain nuclear magnetic resonance (NMR) parameters for the glycine molecule in liquid water. The results of the equilibrium structure in solution and the systematic study of the hydrogen bonds were used to discard the direct proton transfer from the carboxyl group to the ammonium group of the glycine molecule in water solution. The calculations of the Density Functional Theory (DFT) were performed to study the polarization of the solvent in the parameters of nuclear magnetic resonance of the glycine molecule in liquid water. DFT calculations predicted isotropic chemical changes on the H, C, N, and O atoms of glycine in liquid water solution which agree with the available experimental data.

Synchronisation and stability in river metapopulation networks.

PubMed

Yeakel, J D; Moore, J W; Guimarães, P R; de Aguiar, M A M

2014-03-01

Spatial structure in landscapes impacts population stability. Two linked components of stability have large consequences for persistence: first, statistical stability as the lack of temporal fluctuations; second, synchronisation as an aspect of dynamic stability, which erodes metapopulation rescue effects. Here, we determine the influence of river network structure on the stability of riverine metapopulations. We introduce an approach that converts river networks to metapopulation networks, and analytically show how fluctuation magnitude is influenced by interaction structure. We show that river metapopulation complexity (in terms of branching prevalence) has nonlinear dampening effects on population fluctuations, and can also buffer against synchronisation. We conclude by showing that river transects generally increase synchronisation, while the spatial scale of interaction has nonlinear effects on synchronised dynamics. Our results indicate that this dual stability - conferred by fluctuation and synchronisation dampening - emerges from interaction structure in rivers, and this may strongly influence the persistence of river metapopulations. © 2013 John Wiley & Sons Ltd/CNRS.

Topology of three-dimensional separated flows

NASA Technical Reports Server (NTRS)

Tobak, M.; Peake, D. J.

1981-01-01

Based on the hypothesis that patterns of skin-friction lines and external streamlines reflect the properties of continuous vector fields, topology rules define a small number of singular points (nodes, saddle points, and foci) that characterize the patterns on the surface and on particular projections of the flow (e.g., the crossflow plane). The restricted number of singular points and the rules that they obey are considered as an organizing principle whose finite number of elements can be combined in various ways to connect together the properties common to all steady three dimensional viscous flows. Introduction of a distinction between local and global properties of the flow resolves an ambiguity in the proper definition of a three dimensional separated flow. Adoption of the notions of topological structure, structural stability, and bifurcation provides a framework to describe how three dimensional separated flows originate and succeed each other as the relevant parameters of the problem are varied.

Observational constraints on black hole accretion disks

NASA Technical Reports Server (NTRS)

Liang, Edison P.

1994-01-01

We review the empirical constraints on accretion disk models of stellar-mass black holes based on recent multiwavelength observational results. In addition to time-averaged emission spectra, the time evolutions of the intensity and spectrum provide critical information about the structure, stability, and dynamics of the disk. Using the basic thermal Keplerian disk paradigm, we consider in particular generalizations of the standard optically thin disk models needed to accommodate the extremely rich variety of dynamical phenomena exhibited by black hole candidates ranging from flares of electron-positron annihilations and quasiperiodic oscillations in the X-ray intensity to X-ray novae activity. These in turn provide probes of the disk structure and global geometry. The goal is to construct a single unified framework to interpret a large variety of black hole phenomena. This paper will concentrate on the interface between basic theory and observational data modeling.

Mathematical analysis of an age-structured population model with space-limited recruitment.

PubMed

Kamioka, Katumi

2005-11-01

In this paper, we investigate structured population model of marine invertebrate whose life stage is composed of sessile adults and pelagic larvae, such as barnacles contained in a local habitat. First we formulate the basic model as an Cauchy problem on a Banach space to discuss the existence and uniqueness of non-negative solution. Next we define the basic reproduction number R0 to formulate the invasion condition under which the larvae can successfully settle down in the completely vacant habitat. Subsequently we examine existence and stability of steady states. We show that the trivial steady state is globally asymptotically stable if R0 < or = 1, whereas it is unstable if R0 > 1. Furthermore, we show that a positive (non-trivial) steady state uniquely exists if R0 > 1 and it is locally asymptotically stable as far as absolute value of R0 - 1 is small enough.

Recent variability of the tropical tropopause inversion layer

NASA Astrophysics Data System (ADS)

Wang, Wuke; Matthes, Katja; Schmidt, Torsten; Neef, Lisa

2013-12-01

The recent variability of the tropopause temperature and the tropopause inversion layer (TIL) are investigated with Global Positioning System Radio Occultation data and simulations with the National Center for Atmospheric Research's Whole Atmosphere Community Climate Model (WACCM). Over the past decade (2001-2011) the data show an increase of 0.8 K in the tropopause temperature and a decrease of 0.4 K in the strength of the tropopause inversion layer in the tropics, meaning that the vertical temperature gradient has declined, and therefore that the stability above the tropopause has weakened. WACCM simulations with finer vertical resolution show a more realistic TIL structure and variability. Model simulations show that the increased tropopause temperature and the weaker tropopause inversion layer are related to weakened upwelling in the tropics. Such changes in the thermal structure of the upper troposphere and lower stratosphere may have important implications for climate, such as a possible rise in water vapor in the lower stratosphere.

Comparison of two non-convex mixed-integer nonlinear programming algorithms applied to autoregressive moving average model structure and parameter estimation

NASA Astrophysics Data System (ADS)

Uilhoorn, F. E.

2016-10-01

In this article, the stochastic modelling approach proposed by Box and Jenkins is treated as a mixed-integer nonlinear programming (MINLP) problem solved with a mesh adaptive direct search and a real-coded genetic class of algorithms. The aim is to estimate the real-valued parameters and non-negative integer, correlated structure of stationary autoregressive moving average (ARMA) processes. The maximum likelihood function of the stationary ARMA process is embedded in Akaike's information criterion and the Bayesian information criterion, whereas the estimation procedure is based on Kalman filter recursions. The constraints imposed on the objective function enforce stability and invertibility. The best ARMA model is regarded as the global minimum of the non-convex MINLP problem. The robustness and computational performance of the MINLP solvers are compared with brute-force enumeration. Numerical experiments are done for existing time series and one new data set.

Competitive Exclusion and Coexistence of Pathogens in a Homosexually-Transmitted Disease Model

PubMed Central

Chai, Caichun; Jiang, Jifa

2011-01-01

A sexually-transmitted disease model for two strains of pathogen in a one-sex, heterogeneously-mixing population has been studied completely by Jiang and Chai in (J Math Biol 56:373–390, 2008). In this paper, we give a analysis for a SIS STD with two competing strains, where populations are divided into three differential groups based on their susceptibility to two distinct pathogenic strains. We investigate the existence and stability of the boundary equilibria that characterizes competitive exclusion of the two competing strains; we also investigate the existence and stability of the positive coexistence equilibrium, which characterizes the possibility of coexistence of the two strains. We obtain sufficient and necessary conditions for the existence and global stability about these equilibria under some assumptions. We verify that there is a strong connection between the stability of the boundary equilibria and the existence of the coexistence equilibrium, that is, there exists a unique coexistence equilibrium if and only if the boundary equilibria both exist and have the same stability, the coexistence equilibrium is globally stable or unstable if and only if the two boundary equilibria are both unstable or both stable. PMID:21347222

Global insights into acetic acid resistance mechanisms and genetic stability of Acetobacter pasteurianus strains by comparative genomics

PubMed Central

Wang, Bin; Shao, Yanchun; Chen, Tao; Chen, Wanping; Chen, Fusheng

2015-01-01

Acetobacter pasteurianus (Ap) CICC 20001 and CGMCC 1.41 are two acetic acid bacteria strains that, because of their strong abilities to produce and tolerate high concentrations of acetic acid, have been widely used to brew vinegar in China. To globally understand the fermentation characteristics, acid-tolerant mechanisms and genetic stabilities, their genomes were sequenced. Genomic comparisons with 9 other sequenced Ap strains revealed that their chromosomes were evolutionarily conserved, whereas the plasmids were unique compared with other Ap strains. Analysis of the acid-tolerant metabolic pathway at the genomic level indicated that the metabolism of some amino acids and the known mechanisms of acetic acid tolerance, might collaboratively contribute to acetic acid resistance in Ap strains. The balance of instability factors and stability factors in the genomes of Ap CICC 20001 and CGMCC 1.41 strains might be the basis for their genetic stability, consistent with their stable industrial performances. These observations provide important insights into the acid resistance mechanism and the genetic stability of Ap strains and lay a foundation for future genetic manipulation and engineering of these two strains. PMID:26691589

Adjusting Mitigation Pathways to Stabilize Climate at 1.5°C and 2.0°C Rise in Global Temperatures to Year 2300

NASA Astrophysics Data System (ADS)

Goodwin, Philip; Brown, Sally; Haigh, Ivan David; Nicholls, Robert James; Matter, Juerg M.

2018-03-01

To avoid the most dangerous consequences of anthropogenic climate change, the Paris Agreement provides a clear and agreed climate mitigation target of stabilizing global surface warming to under 2.0°C above preindustrial, and preferably closer to 1.5°C. However, policy makers do not currently know exactly what carbon emissions pathways to follow to stabilize warming below these agreed targets, because there is large uncertainty in future temperature rise for any given pathway. This large uncertainty makes it difficult for a cautious policy maker to avoid either: (1) allowing warming to exceed the agreed target or (2) cutting global emissions more than is required to satisfy the agreed target, and their associated societal costs. This study presents a novel Adjusting Mitigation Pathway (AMP) approach to restrict future warming to policy-driven targets, in which future emissions reductions are not fully determined now but respond to future surface warming each decade in a self-adjusting manner. A large ensemble of Earth system model simulations, constrained by geological and historical observations of past climate change, demonstrates our self-adjusting mitigation approach for a range of climate stabilization targets ranging from 1.5°C to 4.5°C, and generates AMP scenarios up to year 2300 for surface warming, carbon emissions, atmospheric CO2, global mean sea level, and surface ocean acidification. We find that lower 21st century warming targets will significantly reduce ocean acidification this century, and will avoid up to 4 m of sea-level rise by year 2300 relative to a high-end scenario.

Stabilization Wedges and the Management of Global Carbon for the next 50 years

ScienceCinema

Socolow, Robert

2018-05-24

More than 40 years after receiving a Ph.D. in physics, I am still working on problems where conservation laws matter. In particular, for the problems I work on now, the conservation of the carbon atom matters. I will tell the saga of an annual flow of 8 billion tons of carbon associated with the global extraction of fossil fuels from underground. Until recently, it was taken for granted that virtually all of this carbon will move within weeks through engines of various kinds and then into the atmosphere. For compelling environmental reasons, I and many others are challenging this complacent view, asking whether the carbon might wisely be directed elsewhere. To frame this and similar discussions, Steve Pacala and I introduced the 'stabilization wedge' in 2004 as a useful unit for discussing climate stabilization. Updating the definition, a wedge is the reduction of CO2 emissions by one billion tons of carbon per year in 2057, achieved by any strategy generated as a result of deliberate attention to global carbon. Each strategy uses already commercialized technology, generally at much larger scale than today. Implementing seven wedges should enable the world to achieve the interim goal of emitting no more CO2 globally in 2057 than today. This would place humanity, approximately, on a path to stabilizing CO2 at less than double the pre-industrial concentration, and it would put those at the helm in the following 50 years in a position to drive CO2 emissions to a net of zero in the following 50 years. Arguably, the tasks of the two half-centuries are comparably difficult.

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile.

PubMed

Arjunan, V; Thillai Govindaraja, S; Jose, Sujin P; Mohan, S

2014-07-15

The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm(-1) respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G(**), high level 6-311++G(**) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The (1)H (400 MHz; CDCl3) and (13)C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors. Copyright © 2014 Elsevier B.V. All rights reserved.

Energy balance and stability. [in stellar coronae

NASA Technical Reports Server (NTRS)

Hammer, R.

1982-01-01

The energy balance of the outer atmospheres of solarlike stars is discussed. The energy balance of open coronal regions is considered, discussing the construction and characteristics of models of such regions in some detail. In particular, the temperature as a function of height is considered, as are the damping length dependence of the global energy balance in the region between the base of the transition region and the critical point, and the effects of changing the amount of coronal heating, the stellar mass, and the stellar radius. Models of coronal loops are more briefly discussed. The chromosphere is then included in the discussion of the energy balance, and the connection between global energy balance and global thermal stability is addressed. The observed positive correlations between the chromospheric and coronal energy losses and the pressure of the transition region is qualitatively explained.

The Use of Plant Antimicrobial Compounds for Food Preservation

PubMed Central

Hintz, Tana; Matthews, Karl K.

2015-01-01

Foodborne disease is a global issue with significant impact on human health. With the growing consumer demand for natural preservatives to replace chemical compounds, plant antimicrobial compounds must be thoroughly investigated for their potential to serve as biopreservatives. This review paper will focus on the plant-derived products as antimicrobial agents for use in food preservation and to control foodborne pathogens in foods. Structure, modes of action, stability, and resistance to these plant compounds will be discussed as well as their application in food industries and possible technologies by which they can be delivered. Benefits as well as challenges, such as the need for further research for implementation and governmental regulation, will be highlighted. PMID:26539472

Effects of radial electric fields on linear ITG instabilities in W7-X and LHD

NASA Astrophysics Data System (ADS)

Riemann, J.; Kleiber, R.; Borchardt, M.

2016-07-01

The impact of radial electric fields on the properties of linear ion-temperature-gradient (ITG) modes in stellarators is studied. Numerical simulations have been carried out with the global particle-in-cell (PIC) code EUTERPE, modelling the behaviour of ITG modes in Wendelstein 7-X and an LHD-like configuration. In general, radial electric fields seem to lead to a reduction of ITG instability growth, which can be related to the action of an induced E× B -drift. Focus is set on the modification of mode properties (frequencies, power spectrum, spatial structure and localization) to understand the observed growth rates as the result of competing stabilizing mechanisms.

A review of some problems in global-local stress analysis

NASA Technical Reports Server (NTRS)

Nelson, Richard B.

1989-01-01

The various types of local-global finite-element problems point out the need to develop a new generation of software. First, this new software needs to have a complete analysis capability, encompassing linear and nonlinear analysis of 1-, 2-, and 3-dimensional finite-element models, as well as mixed dimensional models. The software must be capable of treating static and dynamic (vibration and transient response) problems, including the stability effects of initial stress, and the software should be able to treat both elastic and elasto-plastic materials. The software should carry a set of optional diagnostics to assist the program user during model generation in order to help avoid obvious structural modeling errors. In addition, the program software should be well documented so the user has a complete technical reference for each type of element contained in the program library, including information on such topics as the type of numerical integration, use of underintegration, and inclusion of incompatible modes, etc. Some packaged information should also be available to assist the user in building mixed-dimensional models. An important advancement in finite-element software should be in the development of program modularity, so that the user can select from a menu various basic operations in matrix structural analysis.

The Impact of Globalization on African Conflicts

DTIC Science & Technology

2003-01-01

There is no region of this world that not experienced wars, but while many parts of the world have moved towards greater political and economic ... stability and co-operation, sub-Saharan Africa remains a cauldron of instability and economic deprivation. Globalization, which in simple terms means a