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

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

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

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

PubMed

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

2014-06-01

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

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

PubMed Central

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

2009-01-01

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

Corroded Anchor Structure Stability/Reliability (CAS_Stab-R) Software for Hydraulic Structures

DTIC Science & Technology

2017-12-01

This report describes software that provides a probabilistic estimate of time -to-failure for a corroding anchor strand system. These anchor...stability to the structure. A series of unique pull-test experiments conducted by Ebeling et al. (2016) at the U.S. Army Engineer Research and...Reliability (CAS_Stab-R) produces probabilistic Remaining Anchor Life time estimates for anchor cables based upon the direct corrosion rate for the

Investigating homology between proteins using energetic profiles.

PubMed

Wrabl, James O; Hilser, Vincent J

2010-03-26

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

Influence of 5-N-carboxamide modifications on the thermodynamic stability of oligonucleotides

PubMed Central

Wolk, Steven K.; Shoemaker, Richard K.; Mayfield, Wes S.; Mestdagh, Andrew L.; Janjic, Nebojsa

2015-01-01

We have recently shown that the incorporation of modified nucleotides such as 5-N-carboxamide-deoxyuridines into random nucleic acid libraries improves success rates in SELEX experiments and facilitates the identification of ligands with slow off-rates. Here we report the impact of these modifications on the thermodynamic stability of both duplexes and intramolecular ‘single-stranded’ structures. Within duplexes, large, hydrophobic naphthyl groups were destabilizing relative to the all natural DNA duplex, while the hydrophilic groups exhibited somewhat improved duplex stability. All of the significant changes in stability were driven by opposing contributions from the enthalpic and entropic terms. In contrast, both benzyl and naphthyl modifications stabilized intramolecular single-stranded structures relative to their natural DNA analogs, consistent with the notion that intramolecular folding allows formation of novel, stabilizing hydrophobic interactions. Imino proton NMR data provided evidence that elements of the folded structure form at temperatures well below the Tm, with a melting transition that is distinctly less cooperative when compared to duplex DNA. Although there are no data to suggest that the unmodified DNA sequences fold into structures similar to their modified analogs, this still represents clear evidence that these modifications impart thermodynamic stability to the folded structure not achievable with unmodified DNA. PMID:26438535

Thermal and aqueous stability improvement of graphene oxide enhanced diphenylalanine nanocomposites

NASA Astrophysics Data System (ADS)

Ryan, Kate; Neumayer, Sabine M.; Maraka, Harsha Vardhan R.; Buchete, Nicolae-Viorel; Kholkin, Andrei L.; Rice, James H.; Rodriguez, Brian J.

2017-12-01

Nanocomposites of diphenylalanine (FF) and carbon based materials provide an opportunity to overcome drawbacks associated with using FF micro- and nanostructures in nanobiotechnology applications, in particular their poor structural stability in liquid solutions. In this study, FF/graphene oxide (GO) composites were found to self-assemble into layered micro- and nanostructures, which exhibited improved thermal and aqueous stability. Dependent on the FF/GO ratio, the solubility of these structures was reduced to 35.65% after 30 min as compared to 92.4% for pure FF samples. Such functional nanocomposites may extend the use of FF structures to e.g. biosensing, electrochemical, electromechanical or electronic applications.

Engineering Proteins for Thermostability with iRDP Web Server

PubMed Central

Ghanate, Avinash; Ramasamy, Sureshkumar; Suresh, C. G.

2015-01-01

Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements. PMID:26436543

Engineering Proteins for Thermostability with iRDP Web Server.

PubMed

Panigrahi, Priyabrata; Sule, Manas; Ghanate, Avinash; Ramasamy, Sureshkumar; Suresh, C G

2015-01-01

Engineering protein molecules with desired structure and biological functions has been an elusive goal. Development of industrially viable proteins with improved properties such as stability, catalytic activity and altered specificity by modifying the structure of an existing protein has widely been targeted through rational protein engineering. Although a range of factors contributing to thermal stability have been identified and widely researched, the in silico implementation of these as strategies directed towards enhancement of protein stability has not yet been explored extensively. A wide range of structural analysis tools is currently available for in silico protein engineering. However these tools concentrate on only a limited number of factors or individual protein structures, resulting in cumbersome and time-consuming analysis. The iRDP web server presented here provides a unified platform comprising of iCAPS, iStability and iMutants modules. Each module addresses different facets of effective rational engineering of proteins aiming towards enhanced stability. While iCAPS aids in selection of target protein based on factors contributing to structural stability, iStability uniquely offers in silico implementation of known thermostabilization strategies in proteins for identification and stability prediction of potential stabilizing mutation sites. iMutants aims to assess mutants based on changes in local interaction network and degree of residue conservation at the mutation sites. Each module was validated using an extensively diverse dataset. The server is freely accessible at http://irdp.ncl.res.in and has no login requirements.

On the interaction structure of linear multi-input feedback control systems. M.S. Thesis; [problem solving, lattices (mathematics)

NASA Technical Reports Server (NTRS)

Wong, P. K.

1975-01-01

The closely-related problems of designing reliable feedback stabilization strategy and coordinating decentralized feedbacks are considered. Two approaches are taken. A geometric characterization of the structure of control interaction (and its dual) was first attempted and a concept of structural homomorphism developed based on the idea of 'similarity' of interaction pattern. The idea of finding classes of individual feedback maps that do not 'interfere' with the stabilizing action of each other was developed by identifying the structural properties of nondestabilizing and LQ-optimal feedback maps. Some known stability properties of LQ-feedback were generalized and some partial solutions were provided to the reliable stabilization and decentralized feedback coordination problems. A concept of coordination parametrization was introduced, and a scheme for classifying different modes of decentralization (information, control law computation, on-line control implementation) in control systems was developed.

Influence of putative exopolysaccharide genes on Pseudomonas putida KT2440 biofilm stability.

PubMed

Nilsson, Martin; Chiang, Wen-Chi; Fazli, Mustafa; Gjermansen, Morten; Givskov, Michael; Tolker-Nielsen, Tim

2011-05-01

We report a study of the role of putative exopolysaccharide gene clusters in the formation and stability of Pseudomonas putida KT2440 biofilm. Two novel putative exopolysaccharide gene clusters, pea and peb, were identified, and evidence is provided that they encode products that stabilize P. putida KT2440 biofilm. The gene clusters alg and bcs, which code for proteins mediating alginate and cellulose biosynthesis, were found to play minor roles in P. putida KT2440 biofilm formation and stability under the conditions tested. A P. putida KT2440 derivative devoid of any identifiable exopolysaccharide genes was found to form biofilm with a structure similar to wild-type biofilm, but with a stability lower than that of wild-type biofilm. Based on our data, we suggest that the formation of structured P. putida KT2440 biofilm can occur in the absence of exopolysaccharides; however, exopolysaccharides play a role as structural stabilizers. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Initial Ares I Bending Filter Design

NASA Technical Reports Server (NTRS)

Jang, Jiann-Woei; Bedrossian, Nazareth; Hall, Robert; Norris, H. Lee; Hall, Charles; Jackson, Mark

2007-01-01

The Ares-I launch vehicle represents a challenging flex-body structural environment for control system design. Software filtering of the inertial sensor output will be required to ensure control system stability and adequate performance. This paper presents a design methodology employing numerical optimization to develop the Ares-I bending filters. The filter design methodology was based on a numerical constrained optimization approach to maximize stability margins while meeting performance requirements. The resulting bending filter designs achieved stability by adding lag to the first structural frequency and hence phase stabilizing the first Ares-I flex mode. To minimize rigid body performance impacts, a priority was placed via constraints in the optimization algorithm to minimize bandwidth decrease with the addition of the bending filters. The bending filters provided here have been demonstrated to provide a stable first stage control system in both the frequency domain and the MSFC MAVERIC time domain simulation.

Robust Stabilization Control Based on Guardian Maps Theory for a Longitudinal Model of Hypersonic Vehicle

PubMed Central

Liu, Mengying; Sun, Peihua

2014-01-01

A typical model of hypersonic vehicle has the complicated dynamics such as the unstable states, the nonminimum phases, and the strong coupling input-output relations. As a result, designing a robust stabilization controller is essential to implement the anticipated tasks. This paper presents a robust stabilization controller based on the guardian maps theory for hypersonic vehicle. First, the guardian maps theories are provided to explain the constraint relations between the open subsets of complex plane and the eigenvalues of the state matrix of closed-loop control system. Then, a general control structure in relation to the guardian maps theories is proposed to achieve the respected design demands. Furthermore, the robust stabilization control law depending on the given general control structure is designed for the longitudinal model of hypersonic vehicle. Finally, a simulation example is provided to verify the effectiveness of the proposed methods. PMID:24795535

Chemical denaturation as a tool in the formulation optimization of biologics

PubMed Central

Freire, Ernesto; Schön, Arne; Hutchins, Burleigh M.; Brown, Richard K.

2013-01-01

Biologics have become the fastest growing segment in the pharmaceutical industry. As is the case with all proteins, biologics are susceptible to denature or to aggregate; conditions that, if present, preclude their use as pharmaceuticals. Identifying the solvent conditions that maximize their structural stability is crucial during development. Since the structural stability of a protein is susceptible to different chemical and physical conditions, the use of several complementary techniques can be expected to provide the best answers. Stability measurements that rely on temperature or chemical [urea or guanidine hydrochloride (GuHCl)] denaturation have been the preferred ones in research laboratories and together provide a thorough evaluation of protein stability. In this review, we will discuss chemical denaturation as a tool in the optimization of formulation conditions for biologics, and how chemical denaturation complements the role of thermal denaturation for this purpose. PMID:23796912

Robust stabilization control based on guardian maps theory for a longitudinal model of hypersonic vehicle.

PubMed

Liu, Yanbin; Liu, Mengying; Sun, Peihua

2014-01-01

A typical model of hypersonic vehicle has the complicated dynamics such as the unstable states, the nonminimum phases, and the strong coupling input-output relations. As a result, designing a robust stabilization controller is essential to implement the anticipated tasks. This paper presents a robust stabilization controller based on the guardian maps theory for hypersonic vehicle. First, the guardian maps theories are provided to explain the constraint relations between the open subsets of complex plane and the eigenvalues of the state matrix of closed-loop control system. Then, a general control structure in relation to the guardian maps theories is proposed to achieve the respected design demands. Furthermore, the robust stabilization control law depending on the given general control structure is designed for the longitudinal model of hypersonic vehicle. Finally, a simulation example is provided to verify the effectiveness of the proposed methods.

Coastal protection using topological interlocking blocks

NASA Astrophysics Data System (ADS)

Pasternak, Elena; Dyskin, Arcady; Pattiaratchi, Charitha; Pelinovsky, Efim

2013-04-01

The coastal protection systems mainly rely on the self-weight of armour blocks to ensure its stability. We propose a system of interlocking armour blocks, which form plate-shape assemblies. The shape and the position of the blocks are chosen in such a way as to impose kinematic constraints that prevent the blocks from being removed from the assembly. The topological interlocking shapes include simple convex blocks such as platonic solids, the most practical being tetrahedra, cubes and octahedra. Another class of topological interlocking blocks is so-called osteomorphic blocks, which form plate-like assemblies tolerant to random block removal (almost 25% of blocks need to be removed for the assembly to loose integrity). Both classes require peripheral constraint, which can be provided either by the weight of the blocks or post-tensioned internal cables. The interlocking assemblies provide increased stability because lifting one block involves lifting (and bending) the whole assembly. We model the effect of interlocking by introducing an equivalent additional self-weight of the armour blocks. This additional self-weight is proportional to the critical pressure needed to cause bending of the interlocking assembly when it loses stability. Using beam approximation we find an equivalent stability coefficient for interlocking. It is found to be greater than the stability coefficient of a structure with similar blocks without interlocking. In the case when the peripheral constraint is provided by the weight of the blocks and for the slope angle of 45o, the effective stability coefficient for a structure of 100 blocks is 33% higher than the one for a similar structure without interlocking. Further increase in the stability coefficient can be reached by a specially constructed peripheral constraint system, for instance by using post-tension cables.

Cargo-shell and cargo-cargo couplings govern the mechanics of artificially loaded virus-derived cages

NASA Astrophysics Data System (ADS)

Llauró, Aida; Luque, Daniel; Edwards, Ethan; Trus, Benes L.; Avera, John; Reguera, David; Douglas, Trevor; Pablo, Pedro J. De; Castón, José R.

2016-04-01

Nucleic acids are the natural cargo of viruses and key determinants that affect viral shell stability. In some cases the genome structurally reinforces the shell, whereas in others genome packaging causes internal pressure that can induce destabilization. Although it is possible to pack heterologous cargoes inside virus-derived shells, little is known about the physical determinants of these artificial nanocontainers' stability. Atomic force and three-dimensional cryo-electron microscopy provided mechanical and structural information about the physical mechanisms of viral cage stabilization beyond the mere presence/absence of cargos. We analyzed the effects of cargo-shell and cargo-cargo interactions on shell stability after encapsulating two types of proteinaceous payloads. While bound cargo to the inner capsid surface mechanically reinforced the capsid in a structural manner, unbound cargo diffusing freely within the shell cavity pressurized the cages up to ~30 atm due to steric effects. Strong cargo-cargo coupling reduces the resilience of these nanocompartments in ~20% when bound to the shell. Understanding the stability of artificially loaded nanocages will help to design more robust and durable molecular nanocontainers.Nucleic acids are the natural cargo of viruses and key determinants that affect viral shell stability. In some cases the genome structurally reinforces the shell, whereas in others genome packaging causes internal pressure that can induce destabilization. Although it is possible to pack heterologous cargoes inside virus-derived shells, little is known about the physical determinants of these artificial nanocontainers' stability. Atomic force and three-dimensional cryo-electron microscopy provided mechanical and structural information about the physical mechanisms of viral cage stabilization beyond the mere presence/absence of cargos. We analyzed the effects of cargo-shell and cargo-cargo interactions on shell stability after encapsulating two types of proteinaceous payloads. While bound cargo to the inner capsid surface mechanically reinforced the capsid in a structural manner, unbound cargo diffusing freely within the shell cavity pressurized the cages up to ~30 atm due to steric effects. Strong cargo-cargo coupling reduces the resilience of these nanocompartments in ~20% when bound to the shell. Understanding the stability of artificially loaded nanocages will help to design more robust and durable molecular nanocontainers. Electronic supplementary information (ESI) available: 6 figures, 3 tables and theory. See DOI: 10.1039/c6nr01007e

Spatially dependent responses of a large-river fish assemblage to bank stabilization and side channels

USGS Publications Warehouse

Reinhold, Ann Marie; Bramblett, Robert G.; Zale, Alexander V.; Poole, Geoffrey C.; Roberts, David W.

2017-01-01

The alteration of rivers by anthropogenic bank stabilization to prevent the erosion of economically valuable lands and structures has become commonplace. However, such alteration has ambiguous consequences for fish assemblages, especially in large rivers. Because most large, temperate rivers have impoundments, it can be difficult to separate the influences of bank stabilization structures from those of main-stem impoundments, especially because both stabilization structures and impoundments can cause side-channel loss. Few large rivers are free flowing and retain extensive side channels, but the Yellowstone River (our study area) is one such river. We hypothesized that in this river (1) bank stabilization has changed fish assemblage structure by altering habitats, (2) side-channel availability has influenced fish assemblage structure by providing habitat heterogeneity, and (3) the influences of bank stabilization and side channels on fish assemblages were spatially scale dependent. We developed a spatially explicit framework to test these hypotheses. Fish assemblage structure varied with the extent of bank stabilization and the availability of side channels; however, not all assemblage subsets were influenced. Nevertheless, bank stabilization and side channels had different and sometimes opposite influences on the fish assemblage. The effects of side channels on fish were more consistent and widespread than those of bank stabilization; the catches of more fishes were positively correlated with side-channel availability than with the extent of bank stabilization. The influences of bank stabilization and side channels on the relative abundances of fish also varied, depending on species and river bend geomorphology. The variation in river morphology probably contributed to the assemblage differences between stabilized and reference river bends; stabilized alluvial pools were deeper than reference alluvial pools, but the depths of stabilized and reference bluff pools did not differ. The strengths of the relationships among fish assemblages, bank stabilization, and side channels were spatially scale dependent; optimum spatial scales ranged from less than 200 m to 3,200 m up- and downstream, suggesting that bank stabilization and side channels influenced fish assemblages across multiple spatial scales.

A preliminary study of the metabolic stability of a series of benzoxazinone derivatives as potent neuropeptide Y5 antagonists.

PubMed

Dordal, Alberto; Lipkin, Mike; Macritchie, Jackie; Mas, Josep; Port, Adriana; Rose, Sally; Salgado, Leonardo; Savic, Vladimir; Schmidt, Wolfgang; Serafini, Maria Teresa; Spearing, William; Torrens, Antoni; Yeste, Sandra

2005-08-15

The metabolic stability of benzoxazinone derivatives, a potent series of NPY Y5 antagonists, has been investigated. This study resulted in the identification of the structural moieties prone to metabolic transformations and which strongly influenced the in vitro half-life. This provides opportunities to optimize the structure of this new class of NPY Y5 antagonists.

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

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

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

2017-01-01

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

Network Stability Is a Balancing Act of Personality, Power, and Conflict Dynamics in Rhesus Macaque Societies

PubMed Central

McCowan, Brenda; Beisner, Brianne A.; Capitanio, John P.; Jackson, Megan E.; Cameron, Ashley N.; Seil, Shannon; Atwill, Edward R.; Fushing, Hsieh

2011-01-01

Stability in biological systems requires evolved mechanisms that promote robustness. Cohesive primate social groups represent one example of a stable biological system, which persist in spite of frequent conflict. Multiple sources of stability likely exist for any biological system and such robustness, or lack thereof, should be reflected and thus detectable in the group's network structure, and likely at multiple levels. Here we show how network structure and group stability are linked to the fundamental characteristics of the individual agents in groups and to the environmental and social contexts in which these individuals interact. Both internal factors (e.g., personality, sex) and external factors (e.g., rank dynamics, sex ratio) were considered from the level of the individual to that of the group to examine the effects of network structure on group stability in a nonhuman primate species. The results yielded three main findings. First, successful third-party intervention behavior is a mechanism of group stability in rhesus macaques in that successful interventions resulted in less wounding in social groups. Second, personality is the primary factor that determines which individuals perform the role of key intervener, via its effect on social power and dominance discrepancy. Finally, individuals with high social power are not only key interveners but also key players in grooming networks and receive reconciliations from a higher diversity of individuals. The results from this study provide sound evidence that individual and group characteristics such as personality and sex ratio influence network structures such as patterns of reconciliation, grooming and conflict intervention that are indicators of network robustness and consequent health and well-being in rhesus macaque societies. Utilizing this network approach has provided greater insight into how behavioral and social processes influence social stability in nonhuman primate groups. PMID:21857922

Network stability is a balancing act of personality, power, and conflict dynamics in rhesus macaque societies.

PubMed

McCowan, Brenda; Beisner, Brianne A; Capitanio, John P; Jackson, Megan E; Cameron, Ashley N; Seil, Shannon; Atwill, Edward R; Fushing, Hsieh

2011-01-01

Stability in biological systems requires evolved mechanisms that promote robustness. Cohesive primate social groups represent one example of a stable biological system, which persist in spite of frequent conflict. Multiple sources of stability likely exist for any biological system and such robustness, or lack thereof, should be reflected and thus detectable in the group's network structure, and likely at multiple levels. Here we show how network structure and group stability are linked to the fundamental characteristics of the individual agents in groups and to the environmental and social contexts in which these individuals interact. Both internal factors (e.g., personality, sex) and external factors (e.g., rank dynamics, sex ratio) were considered from the level of the individual to that of the group to examine the effects of network structure on group stability in a nonhuman primate species. The results yielded three main findings. First, successful third-party intervention behavior is a mechanism of group stability in rhesus macaques in that successful interventions resulted in less wounding in social groups. Second, personality is the primary factor that determines which individuals perform the role of key intervener, via its effect on social power and dominance discrepancy. Finally, individuals with high social power are not only key interveners but also key players in grooming networks and receive reconciliations from a higher diversity of individuals. The results from this study provide sound evidence that individual and group characteristics such as personality and sex ratio influence network structures such as patterns of reconciliation, grooming and conflict intervention that are indicators of network robustness and consequent health and well-being in rhesus macaque societies. Utilizing this network approach has provided greater insight into how behavioral and social processes influence social stability in nonhuman primate groups.

Topsoil structure stability in a restored floodplain: Impacts of fluctuating water levels, soil parameters and ecosystem engineers.

PubMed

Schomburg, A; Schilling, O S; Guenat, C; Schirmer, M; Le Bayon, R C; Brunner, P

2018-10-15

Ecosystem services provided by floodplains are strongly controlled by the structural stability of soils. The development of a stable structure in floodplain soils is affected by a complex and poorly understood interplay of hydrological, physico-chemical and biological processes. This paper aims at analysing relations between fluctuating groundwater levels, soil physico-chemical and biological parameters on soil structure stability in a restored floodplain. Water level fluctuations in the soil are modelled using a numerical surface-water-groundwater flow model and correlated to soil physico-chemical parameters and abundances of plants and earthworms. Causal relations and multiple interactions between the investigated parameters are tested through structural equation modelling (SEM). Fluctuating water levels in the soil did not directly affect the topsoil structure stability, but indirectly through affecting plant roots and soil parameters that in turn determine topsoil structure stability. These relations remain significant for mean annual days of complete and partial (>25%) water saturation. Ecosystem functioning of a restored floodplain might already be affected by the fluctuation of groundwater levels alone, and not only through complete flooding by surface water during a flood period. Surprisingly, abundances of earthworms did not show any relation to other variables in the SEM. These findings emphasise that earthworms have efficiently adapted to periodic stress and harsh environmental conditions. Variability of the topsoil structure stability is thus stronger driven by the influence of fluctuating water levels on plants than by the abundance of earthworms. This knowledge about the functional network of soil engineering organisms, soil parameters and fluctuating water levels and how they affect soil structural stability is of fundamental importance to define management strategies of near-natural or restored floodplains in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

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

NASA Technical Reports Server (NTRS)

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

1974-01-01

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

Dual-wavelength nano-engineered Thulium-doped fiber laser via bending of singlemode-multimode-singlemode fiber structure

NASA Astrophysics Data System (ADS)

Zulkifli, A. Z.; Latiff, A. A.; Paul, M. C.; Yasin, M.; Ahmad, H.; Harun, S. W.

2016-12-01

In this paper, a dual-wavelength fiber laser (DWFL) using nano-engineered Thulium-doped fiber as a gain medium with a bent singlemode-multimode-singlemode fiber structure (SMS) is demonstrated. The SMS structure is packaged systematically using Cr-39 polymer plates to provide linear bending via applied load. Experimental results have proved that the bent SMS is capable to provide highly effective wavelength filter and wavelengths stabilizer by balancing the net cavity gain between the two wavelengths. The DWFL provides very narrow spacing of 0.9 nm, narrow 3 dB spectral linewidth of ∼0.07 nm and SNR of ∼42 dB. Based on stability test, very small mode hopping is observed at the two wavelengths having deviations of ±0 nm and ±0.04 nm respectively. In conjunction, the DWFL provides very stable relative wavelength spacing with a deviation of ±0.04 nm.

How do bendy straws bend? A study of re-configurability of multi-stable corrugated shells

NASA Astrophysics Data System (ADS)

Bende, Nakul; Selden, Sarah; Evans, Arthur; Santangelo, Christian; Hayward, Ryan

Shape programmable systems have evolved to allow for reconfiguration of structures through a variety of mechanisms including swelling, stress-relaxation, and thermal expansion. Particularly, there has been a recent interest in systems that exhibit bi-stability or multi-stability to achieve transformation between two or more pre-programmed states. Here, we study the ubiquitous architecture of corrugated shells, such as drinking straws or bellows, which has been well known for centuries. Some of these structures exhibit almost continuous stability amongst a wide range of reconfigurable shapes, but the underlying mechanisms are not well understood. To understand multi-stability in `bendy-straw' structures, we study the unit bi-conical segment using experiments and finite element modeling to elucidate the key geometrical and mechanical factors responsible for its multi-stability. The simple transformations of a unit segment - a change in length or angle can impart complex re-configurability of a structure containing many of these units. The fundamental understanding provided of this simple multi-stable building block could yield improvements in shape re-configurability for a wide array of applications such as corrugated medical tubing, robotics, and deployable structures. NSF EFRI ODISSEI-1240441.

Floating wind turbine system

NASA Technical Reports Server (NTRS)

Viterna, Larry A. (Inventor)

2009-01-01

A floating wind turbine system with a tower structure that includes at least one stability arm extending therefrom and that is anchored to the sea floor with a rotatable position retention device that facilitates deep water installations. Variable buoyancy for the wind turbine system is provided by buoyancy chambers that are integral to the tower itself as well as the stability arm. Pumps are included for adjusting the buoyancy as an aid in system transport, installation, repair and removal. The wind turbine rotor is located downwind of the tower structure to allow the wind turbine to follow the wind direction without an active yaw drive system. The support tower and stability arm structure is designed to balance tension in the tether with buoyancy, gravity and wind forces in such a way that the top of the support tower leans downwind, providing a large clearance between the support tower and the rotor blade tips. This large clearance facilitates the use of articulated rotor hubs to reduced damaging structural dynamic loads. Major components of the turbine can be assembled at the shore and transported to an offshore installation site.

Controlling Plasma Stability of Hydroxamic Acids: A MedChem Toolbox.

PubMed

Hermant, Paul; Bosc, Damien; Piveteau, Catherine; Gealageas, Ronan; Lam, BaoVy; Ronco, Cyril; Roignant, Matthieu; Tolojanahary, Hasina; Jean, Ludovic; Renard, Pierre-Yves; Lemdani, Mohamed; Bourotte, Marilyne; Herledan, Adrien; Bedart, Corentin; Biela, Alexandre; Leroux, Florence; Deprez, Benoit; Deprez-Poulain, Rebecca

2017-11-09

Hydroxamic acids are outstanding zinc chelating groups that can be used to design potent and selective metalloenzyme inhibitors in various therapeutic areas. Some hydroxamic acids display a high plasma clearance resulting in poor in vivo activity, though they may be very potent compounds in vitro. We designed a 57-member library of hydroxamic acids to explore the structure-plasma stability relationships in these series and to identify which enzyme(s) and which pharmacophores are critical for plasma stability. Arylesterases and carboxylesterases were identified as the main metabolic enzymes for hydroxamic acids. Finally, we suggest structural features to be introduced or removed to improve stability. This work thus provides the first medicinal chemistry toolbox (experimental procedures and structural guidance) to assess and control the plasma stability of hydroxamic acids and realize their full potential as in vivo pharmacological probes and therapeutic agents. This study is particularly relevant to preclinical development as it allows obtaining compounds equally stable in human and rodent models.

Fundamental Movement Skills Are More than Run, Throw and Catch: The Role of Stability Skills.

PubMed

Rudd, James R; Barnett, Lisa M; Butson, Michael L; Farrow, Damian; Berry, Jason; Polman, Remco C J

2015-01-01

In motor development literature fundamental movement skills are divided into three constructs: locomotive, object control and stability skills. Most fundamental movement skills research has focused on children's competency in locomotor and object control skills. The first aim of this study was to validate a test battery to assess the construct of stability skills, in children aged 6 to 10 (M age = 8.2, SD = 1.2). Secondly we assessed how the stability skills construct fitted into a model of fundamental movement skill. The Delphi method was used to select the stability skill battery. Confirmatory factor analysis (CFA) was used to assess if the skills loaded onto the same construct and a new model of FMS was developed using structural equation modelling. Three postural control tasks were selected (the log roll, rock and back support) because they had good face and content validity. These skills also demonstrated good predictive validity with gymnasts scoring significantly better than children without gymnastic training and children from a high SES school performing better than those from a mid and low SES schools and the mid SES children scored better than the low SES children (all p < .05). Inter rater reliability tests were excellent for all three skills (ICC = 0.81, 0.87, 0.87) as was test re-test reliability (ICC 0.87-0.95). CFA provided good construct validity, and structural equation modelling revealed stability skills to be an independent factor in an overall FMS model which included locomotor (r = .88), object control (r = .76) and stability skills (r = .81). This study provides a rationale for the inclusion of stability skills in FMS assessment. The stability skills could be used alongside other FMS assessment tools to provide a holistic assessment of children's fundamental movement skills.

The dynamics and control of large flexible space structures. Volume 3, part B: The modelling, dynamics, and stability of large Earth pointing orbiting structures

NASA Technical Reports Server (NTRS)

Bainum, P. M.; Kumar, V. K.

1980-01-01

The dynamics and stability of large orbiting flexible beams, and platforms and dish type structures oriented along the local horizontal are treated both analytically and numerically. It is assumed that such structures could be gravitationally stabilized by attaching a rigid light-weight dumbbell at the center of mass by a spring loaded hinge which also could provide viscous damping. For the beam, the small amplitude inplane pitch motion, dumbbell librational motion, and the anti-symmetric elastic modes are all coupled. The three dimensional equations of motion for a circular flat plate and shallow spherical shell in orbit with a two-degree-of freedom gimballed dumbbell are also developed and show that only those elastic modes described by a single nodal diameter line are influenced by the dumbbell motion. Stability criteria are developed for all the examples and a sensitivity study of the system response characteristics to the key system parameters is carried out.

Engineering Interface Structures and Thermal Stabilities via SPD Processing in Bulk Nanostructured Metals

DOE PAGES

Zheng, Shijian; Carpenter, John S.; McCabe, Rodney J.; ...

2014-02-27

Nanostructured metals achieve extraordinary strength but suffer from low thermal stability, both a consequence of a high fraction of interfaces. Overcoming this tradeoff relies on making the interfaces themselves thermally stable. In this paper, we show that the atomic structures of bi-metal interfaces in macroscale nanomaterials suitable for engineering structures can be significantly altered via changing the severe plastic deformation (SPD) processing pathway. Two types of interfaces are formed, both exhibiting a regular atomic structure and providing for excellent thermal stability, up to more than half the melting temperature of one of the constituents. Most importantly, the thermal stability ofmore » one is found to be significantly better than the other, indicating the exciting potential to control and optimize macroscale robustness via atomic-scale bimetal interface tuning. As a result, we demonstrate an innovative way to engineer pristine bimetal interfaces for a new class of simultaneously strong and thermally stable materials.« less

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

PubMed

Gurevich, Svetlana V

2014-10-28

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

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

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

Helfferich, Julian; Lyubimov, Ivan; Reid, Daniel

Glasses produced via physical vapor deposition can display greater kinetic stability and lower enthalpy than glasses prepared by liquid cooling. While the reduced enthalpy has often been used as a measure of the stability, it is not obvious whether dynamic measures of stability provide the same view. Here, we study dynamics in vapor-deposited and liquid-cooled glass films using molecular simulations of a bead-spring polymer model as well as a Lennard-Jones binary mixture in two and three dimensions. We confirm that the dynamics in vapor-deposited glasses is indeed slower than in ordinary glasses. We further show that the inherent structure energymore » is a good reporter of local dynamics, and that aged systems and glasses prepared by cooling at progressively slower rates exhibit the same behavior as vapor-deposited materials when they both have the same inherent structure energy. These findings suggest that the stability inferred from measurements of the energy is also manifested in dynamic observables, and they strengthen the view that vapor deposition processes provide an effective strategy for creation of stable glasses.« less

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

Moczydlowski, Edward G.

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

FLUT - A program for aeroelastic stability analysis. [of aircraft structures in subsonic flow

NASA Technical Reports Server (NTRS)

Johnson, E. H.

1977-01-01

A computer program (FLUT) that can be used to evaluate the aeroelastic stability of aircraft structures in subsonic flow is described. The algorithm synthesizes data from a structural vibration analysis with an unsteady aerodynamics analysis and then performs a complex eigenvalue analysis to assess the system stability. The theoretical basis of the program is discussed with special emphasis placed on some innovative techniques which improve the efficiency of the analysis. User information needed to efficiently and successfully utilize the program is provided. In addition to identifying the required input, the flow of the program execution and some possible sources of difficulty are included. The use of the program is demonstrated with a listing of the input and output for a simple example.

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

PubMed

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

2017-09-06

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

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.

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

NASA Technical Reports Server (NTRS)

Hodges, D. H., Roberta.

1976-01-01

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

Robust high pressure stability and negative thermal expansion in sodium-rich antiperovskites Na 3OBr and Na 4OI 2

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

Wang, Yonggang; Wen, Ting; Park, Changyong

2016-01-14

The structure stability under high pressure and thermal expansion behavior of Na 3OBr and Na 4OI 2, two prototypes of alkali-metal-rich antiperovskites, were investigated by in situ synchrotron X-ray diffraction techniques under high pressure and low temp. Both are soft materials with bulk modulus of 58.6 GPa and 52.0 GPa for Na 3OBr and Na 4OI 2, resp. The cubic Na 3OBr structure and tetragonal Na 4OI 2 with intergrowth K 2NiF 4 structure are stable under high pressure up to 23 GPa. Although being a characteristic layered structure, Na 4OI 2 exhibits nearly isotropic compressibility. Neg. thermal expansion wasmore » obsd. at low temp. range (20-80 K) in both transition-metal-free antiperovskites for the first time. The robust high pressure structure stability was examined. and confirmed by first-principles calculations. among various possible polymorphisms qualitatively. The results provide in-depth understanding of the neg. thermal expansion and robust crystal structure stability of these antiperovskite systems and their potential applications.« less

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

PubMed

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

2011-03-01

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

Structure and stability of clusters of β-alanine in the gas phase: importance of the nature of intermolecular interactions.

PubMed

Piekarski, Dariusz Grzegorz; Díaz-Tendero, Sergio

2017-02-15

We present a theoretical study of neutral clusters of β-alanine molecules in the gas phase, (β-ala) n n ≤ 5. Classical molecular dynamics simulations carried out with different internal excitation energies provide information on the clusters formation and their thermal decomposition limits. We also present an assessment study performed with different families of density functionals using the dimer, (β-ala) 2 , as a benchmark system. The M06-2X functional provides the best agreement in geometries and relative energies in comparison with the reference values computed with the MP2 and CCSD(T) methods. The structure, stability, dissociation energies and vertical ionization potentials of the studied clusters have been investigated using this functional in combination with the 6-311++G(d,p) basis set. An exhaustive analysis of intermolecular interactions is also presented. These results provide new insights into the stability, interaction nature and formation mechanisms of clusters of amino acids in the gas phase.

Improving Processes of Mechanized Pulsed Arc Welding of Low-Frequency Range Variation of Mode Parameters

NASA Astrophysics Data System (ADS)

Saraev, Yu N.; Solodskiy, S. A.; Ulyanova, O. V.

2016-04-01

A new technology of low-frequency modulation of the arc current in MAG and MIG welding is presented. The technology provides control of thermal and crystallization processes, stabilizes the time of formation and crystallization of the weld pool. Conducting theoretical studies allowed formulating the basic criteria for obtaining strong permanent joints for high-duty structures, providing conditions for more equilibrium structure of the deposited metal and the smaller width of the HAZ. The stabilization of time of the formation and crystallization of the weld pool improves the formation of the weld and increases productivity in welding thin sheet metal.

Applications of Protein Thermodynamic Database for Understanding Protein Mutant Stability and Designing Stable Mutants.

PubMed

Gromiha, M Michael; Anoosha, P; Huang, Liang-Tsung

2016-01-01

Protein stability is the free energy difference between unfolded and folded states of a protein, which lies in the range of 5-25 kcal/mol. Experimentally, protein stability is measured with circular dichroism, differential scanning calorimetry, and fluorescence spectroscopy using thermal and denaturant denaturation methods. These experimental data have been accumulated in the form of a database, ProTherm, thermodynamic database for proteins and mutants. It also contains sequence and structure information of a protein, experimental methods and conditions, and literature information. Different features such as search, display, and sorting options and visualization tools have been incorporated in the database. ProTherm is a valuable resource for understanding/predicting the stability of proteins and it can be accessed at http://www.abren.net/protherm/ . ProTherm has been effectively used to examine the relationship among thermodynamics, structure, and function of proteins. We describe the recent progress on the development of methods for understanding/predicting protein stability, such as (1) general trends on mutational effects on stability, (2) relationship between the stability of protein mutants and amino acid properties, (3) applications of protein three-dimensional structures for predicting their stability upon point mutations, (4) prediction of protein stability upon single mutations from amino acid sequence, and (5) prediction methods for addressing double mutants. A list of online resources for predicting has also been provided.

On a variational approach to some parameter estimation problems

NASA Technical Reports Server (NTRS)

Banks, H. T.

1985-01-01

Examples (1-D seismic, large flexible structures, bioturbation, nonlinear population dispersal) in which a variation setting can provide a convenient framework for convergence and stability arguments in parameter estimation problems are considered. Some of these examples are 1-D seismic, large flexible structures, bioturbation, and nonlinear population dispersal. Arguments for convergence and stability via a variational approach of least squares formulations of parameter estimation problems for partial differential equations is one aspect of the problem considered.

Fungal prion HET-s as a model for structural complexity and self-propagation in prions.

PubMed

Wan, William; Stubbs, Gerald

2014-04-08

The highly ordered and reproducible structure of the fungal prion HET-s makes it an excellent model system for studying the inherent properties of prions, self-propagating infectious proteins that have been implicated in a number of fatal diseases. In particular, the HET-s prion-forming domain readily folds into a relatively complex two-rung β-solenoid amyloid. The faithful self-propagation of this fold involves a diverse array of inter- and intramolecular structural features. These features include a long flexible loop connecting the two rungs, buried polar residues, salt bridges, and asparagine ladders. We have used site-directed mutagenesis and X-ray fiber diffraction to probe the relative importance of these features for the formation of β-solenoid structure, as well as the cumulative effects of multiple mutations. Using fibrillization kinetics and chemical stability assays, we have determined the biophysical effects of our mutations on the assembly and stability of the prion-forming domain. We have found that a diversity of structural features provides a level of redundancy that allows robust folding and stability even in the face of significant sequence alterations and suboptimal environmental conditions. Our findings provide fundamental insights into the structural interactions necessary for self-propagation. Propagation of prion structure seems to require an obligatory level of complexity that may not be reproducible in short peptide models.

3 CFR 13502 - Executive Order 13502 of February 6, 2009. Use of Project Labor Agreements for Federal...

Code of Federal Regulations, 2010 CFR

2010-01-01

... developing by providing structure and stability to large-scale construction projects, thereby promoting the... procurement, producing labor-management stability, and ensuring compliance with laws and regulations governing... construction projects receiving Federal financial assistance, would help to promote the economical, efficient...

Ares-I Bending Filter Design using a Constrained Optimization Approach

NASA Technical Reports Server (NTRS)

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

2008-01-01

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

Ares I Flight Control System Design

NASA Technical Reports Server (NTRS)

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

2010-01-01

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

Stability of Boolean multilevel networks.

PubMed

Cozzo, Emanuele; Arenas, Alex; Moreno, Yamir

2012-09-01

The study of the interplay between the structure and dynamics of complex multilevel systems is a pressing challenge nowadays. In this paper, we use a semiannealed approximation to study the stability properties of random Boolean networks in multiplex (multilayered) graphs. Our main finding is that the multilevel structure provides a mechanism for the stabilization of the dynamics of the whole system even when individual layers work on the chaotic regime, therefore identifying new ways of feedback between the structure and the dynamics of these systems. Our results point out the need for a conceptual transition from the physics of single-layered networks to the physics of multiplex networks. Finally, the fact that the coupling modifies the phase diagram and the critical conditions of the isolated layers suggests that interdependency can be used as a control mechanism.

In Search of Functional Advantages of Knots in Proteins.

PubMed

Dabrowski-Tumanski, Pawel; Stasiak, Andrzej; Sulkowska, Joanna I

2016-01-01

We analysed the structure of deeply knotted proteins representing three unrelated families of knotted proteins. We looked at the correlation between positions of knotted cores in these proteins and such local structural characteristics as the number of intra-chain contacts, structural stability and solvent accessibility. We observed that the knotted cores and especially their borders showed strong enrichment in the number of contacts. These regions showed also increased thermal stability, whereas their solvent accessibility was decreased. Interestingly, the active sites within these knotted proteins preferentially located in the regions with increased number of contacts that also have increased thermal stability and decreased solvent accessibility. Our results suggest that knotting of polypeptide chains provides a favourable environment for the active sites observed in knotted proteins. Some knotted proteins have homologues without a knot. Interestingly, these unknotted homologues form local entanglements that retain structural characteristics of the knotted cores.

Stability analysis of truss type highway sign support structures

DOT National Transportation Integrated Search

2000-12-01

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

Effect of some ultraviolet light absorbers on photo-stabilization of azadirachtin-A.

PubMed

Deota, P T; Upadhyay, P R; Patel, K B; Mehta, K J; Varshney, A K; Mehta, M H

2002-10-01

The effect of photo-stabilization of Azadirachtin-A (Aza-A) was examined when exposed to sunlight and ultraviolet light in the presence of four structurally different ultraviolet stabilizers namely 4-aminobenzoic acid, 2,4-dihydroxybenzophenone, 4,4'-dihydroxybenzophenone and phenyl salicylate. The percentages of Aza-A recovered at different time intervals from slides exposed to different light conditions with and without UV stabilizers as well as kinetic studies indicated that the addition of phenyl salicylate in methanolic solution of Aza-A (in 1:1 mole ratio) provides the best photo-stabilization of Aza-A molecule among the four UV stabilizers studied.

Cargo–shell and cargo–cargo couplings govern the mechanics of artificially loaded virus-derived cages†

PubMed Central

Llauró, Aida; Luque, Daniel; Edwards, Ethan; Trus, Benes L.; Avera, John; Reguera, David; Douglas, Trevor

2016-01-01

Nucleic acids are the natural cargo of viruses and key determinants that affect viral shell stability. In some cases the genome structurally reinforces the shell, whereas in others genome packaging causes internal pressure that can induce destabilization. Although it is possible to pack heterologous cargoes inside virus-derived shells, little is known about the physical determinants of these artificial nanocontainers’ stability. Atomic force and three-dimensional cryo-electron microscopy provided mechanical and structural information about the physical mechanisms of viral cage stabilization beyond the mere presence/absence of cargos. We analyzed the effects of cargo–shell and cargo–cargo interactions on shell stability after encapsulating two types of proteinaceous payloads. While bound cargo to the inner capsid surface mechanically reinforced the capsid in a structural manner, unbound cargo diffusing freely within the shell cavity pressurized the cages up to ~30 atm due to steric effects. Strong cargo–cargo coupling reduces the resilience of these nanocompartments in ~20% when bound to the shell. Understanding the stability of artificially loaded nanocages will help to design more robust and durable molecular nanocontainers. PMID:27091107

Toward a better understanding of helicopter stability derivatives

NASA Technical Reports Server (NTRS)

Hansen, R. S.

1982-01-01

An amended six degree of freedom helicopter stability and control derivative model was developed in which body acceleration and control rate derivatives were included in the Taylor series expansion. These additional derivatives were derived from consideration of the effects of the higher order rotor flapping dynamics, which are known to be inadequately represented in the conventional six degree of freedom, quasistatic stability derivative model. The amended model was a substantial improvement over the conventional model, effectively doubling the unsable bandwidth and providing a more accurate representation of the short period and cross axis characteristics. Further investigations assessed the applicability of the two stability derivative model structures for flight test parameter identification. Parameters were identified using simulation data generated from a higher order base line model having sixth order rotor tip path plane dynamics. Three lower order models were identified: one using the conventional stability derivative model structure, a second using the amended six degree of freedom model structure, and a third model having eight degrees of freedom that included a simplified rotor tip path plane tilt representation.

Fractal markets: Liquidity and investors on different time horizons

NASA Astrophysics Data System (ADS)

Li, Da-Ye; Nishimura, Yusaku; Men, Ming

2014-08-01

In this paper, we propose a new agent-based model to study the source of liquidity and the “emergent” phenomenon in financial market with fractal structure. The model rests on fractal market hypothesis and agents with different time horizons of investments. What is interesting is that though the agent-based model reveals that the interaction between these heterogeneous agents affects the stability and liquidity of the financial market the real world market lacks detailed data to bring it to light since it is difficult to identify and distinguish the investors with different time horizons in the empirical approach. results show that in a relatively short period of time fractal market provides liquidity from investors with different horizons and the market gains stability when the market structure changes from uniformity to diversification. In the real world the fractal structure with the finite of horizons can only stabilize the market within limits. With the finite maximum horizons, the greater diversity of the investors and the fractal structure will not necessarily bring more stability to the market which might come with greater fluctuation in large time scale.

N-terminal aliphatic residues dictate the structure, stability, assembly, and small molecule binding of the coiled-coil region of cartilage oligomeric matrix protein.

PubMed

Gunasekar, Susheel K; Asnani, Mukta; Limbad, Chandani; Haghpanah, Jennifer S; Hom, Wendy; Barra, Hanna; Nanda, Soumya; Lu, Min; Montclare, Jin Kim

2009-09-15

The coiled-coil domain of cartilage oligomeric matrix protein (COMPcc) assembles into a homopentamer that naturally recognizes the small molecule 1,25-dihydroxyvitamin D(3) (vit D). To identify the residues critical for the structure, stability, oligomerization, and binding to vit D as well as two other small molecules, all-trans-retinol (ATR) and curcumin (CCM), here we perform an alanine scanning mutagenesis study. Ten residues lining the hydrophobic pocket of COMPcc were mutated into alanine; of the mutated residues, the N-terminal aliphatic residues L37, L44, V47, and L51 are responsible for maintaining the structure and function. Furthermore, two polar residues, T40 and Q54, within the N-terminal region when converted into alanine improve the alpha-helical structure, stability, and self-assembly behavior. Helical stability, oligomerization, and binding appear to be linked in a manner in which mutations that abolish helical structure and assembly bind poorly to vit D, ATR, and CCM. These results provide not only insight into COMPcc and its functional role but also useful guidelines for the design of stable, pentameric coiled-coils capable of selectively storing and delivering various small molecules.

Structure and Stability of the Spinach Aquaporin SoPIP2;1 in Detergent Micelles and Lipid Membranes

PubMed Central

Plasencia, Inés; Survery, Sabeen; Ibragimova, Sania; Hansen, Jesper S.; Kjellbom, Per; Helix-Nielsen, Claus; Johanson, Urban; Mouritsen, Ole G.

2011-01-01

Background SoPIP2;1 constitutes one of the major integral proteins in spinach leaf plasma membranes and belongs to the aquaporin family. SoPIP2;1 is a highly permeable and selective water channel that has been successfully overexpressed and purified with high yields. In order to optimize reconstitution of the purified protein into biomimetic systems, we have here for the first time characterized the structural stability of SoPIP2;1. Methodology/Principal Finding We have characterized the protein structural stability after purification and after reconstitution into detergent micelles and proteoliposomes using circular dichroism and fluorescence spectroscopy techniques. The structure of SoPIP2;1 was analyzed either with the protein solubilized with octyl-β-D-glucopyranoside (OG) or reconstituted into lipid membranes formed by E. coli lipids, diphytanoylphosphatidylcholine (DPhPC), or reconstituted into lipid membranes formed from mixtures of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPE), 1-palmitoyl-2oleoyl-phosphatidylethanolamine (POPE), 1-palmitoyl-2-oleoyl-phosphatidylserine (POPS), and ergosterol. Generally, SoPIP2;1 secondary structure was found to be predominantly α-helical in accordance with crystallographic data. The protein has a high thermal structural stability in detergent solutions, with an irreversible thermal unfolding occurring at a melting temperature of 58°C. Incorporation of the protein into lipid membranes increases the structural stability as evidenced by an increased melting temperature of up to 70°C. Conclusion/Significance The results of this study provide insights into SoPIP2;1 stability in various host membranes and suggest suitable choices of detergent and lipid composition for reconstitution of SoPIP2;1 into biomimetic membranes for biotechnological applications. PMID:21339815

Structure and stability of the spinach aquaporin SoPIP2;1 in detergent micelles and lipid membranes.

PubMed

Plasencia, Inés; Survery, Sabeen; Ibragimova, Sania; Hansen, Jesper S; Kjellbom, Per; Helix-Nielsen, Claus; Johanson, Urban; Mouritsen, Ole G

2011-02-14

SoPIP2;1 constitutes one of the major integral proteins in spinach leaf plasma membranes and belongs to the aquaporin family. SoPIP2;1 is a highly permeable and selective water channel that has been successfully overexpressed and purified with high yields. In order to optimize reconstitution of the purified protein into biomimetic systems, we have here for the first time characterized the structural stability of SoPIP2;1. We have characterized the protein structural stability after purification and after reconstitution into detergent micelles and proteoliposomes using circular dichroism and fluorescence spectroscopy techniques. The structure of SoPIP2;1 was analyzed either with the protein solubilized with octyl-β-D-glucopyranoside (OG) or reconstituted into lipid membranes formed by E. coli lipids, diphytanoylphosphatidylcholine (DPhPC), or reconstituted into lipid membranes formed from mixtures of 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPE), 1-palmitoyl-2oleoyl-phosphatidylethanolamine (POPE), 1-palmitoyl-2-oleoyl-phosphatidylserine (POPS), and ergosterol. Generally, SoPIP2;1 secondary structure was found to be predominantly α-helical in accordance with crystallographic data. The protein has a high thermal structural stability in detergent solutions, with an irreversible thermal unfolding occurring at a melting temperature of 58°C. Incorporation of the protein into lipid membranes increases the structural stability as evidenced by an increased melting temperature of up to 70°C. The results of this study provide insights into SoPIP2;1 stability in various host membranes and suggest suitable choices of detergent and lipid composition for reconstitution of SoPIP2;1 into biomimetic membranes for biotechnological applications.

Oxygen vacancy-driven evolution of structural and electrical properties in SrFeO 3₋δ thin films and a method of stabilization

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

Enriquez, Erik M.; Chen, Aiping; Harrell, Zachary John

Epitaxial SrFeO 3-δ (SFO) thin films have been grown on various substrates by pulsed laser deposition. The structural and electrical properties of SFO thin films are monitored with time in different atmospheres at room temperature, showing time-dependent crystal structure and electrical conductivity. The increased out-of-plane lattice parameter and resistivity over time are associated with the increased oxygen vacancies density in SFO thin films. The epitaxial strain plays an important role in determining the initial resistivity, and the sample environment determines the trend of resistivity change over time. An amorphous Al 2O 3 passivation layer has been found to be effectivemore » in stabilizing the structure and electrical properties of SFO thin films. Lastly, this work explores time dependent structure and properties variation in oxide films and provides a way to stabilize thin film materials that are sensitive to oxygen vacancies.« less

Oxygen vacancy-driven evolution of structural and electrical properties in SrFeO 3₋δ thin films and a method of stabilization

DOE PAGES

Enriquez, Erik M.; Chen, Aiping; Harrell, Zachary John; ...

2016-10-03

Epitaxial SrFeO 3-δ (SFO) thin films have been grown on various substrates by pulsed laser deposition. The structural and electrical properties of SFO thin films are monitored with time in different atmospheres at room temperature, showing time-dependent crystal structure and electrical conductivity. The increased out-of-plane lattice parameter and resistivity over time are associated with the increased oxygen vacancies density in SFO thin films. The epitaxial strain plays an important role in determining the initial resistivity, and the sample environment determines the trend of resistivity change over time. An amorphous Al 2O 3 passivation layer has been found to be effectivemore » in stabilizing the structure and electrical properties of SFO thin films. Lastly, this work explores time dependent structure and properties variation in oxide films and provides a way to stabilize thin film materials that are sensitive to oxygen vacancies.« less

Nonlinear Stability and Structure of Compressible Reacting Mixing Layers

NASA Technical Reports Server (NTRS)

Day, M. J.; Mansour, N. N.; Reynolds, W. C.

2000-01-01

The parabolized stability equations (PSE) are used to investigate issues of nonlinear flow development and mixing in compressible reacting shear layers. Particular interest is placed on investigating the change in flow structure that occurs when compressibility and heat release are added to the flow. These conditions allow the 'outer' instability modes- one associated with each of the fast and slow streams-to dominate over the 'central', Kelvin-Helmholtz mode that unaccompanied in incompressible nonreacting mixing layers. Analysis of scalar probability density functions in flows with dominant outer modes demonstrates the ineffective, one-sided nature of mixing that accompany these flow structures. Colayer conditions, where two modes have equal growth rate and the mixing layer is formed by two sets of vortices, offer some opportunity for mixing enhancement. Their extent, however, is found to be limited in the mixing layer's parameter space. Extensive validation of the PSE technique also provides a unique perspective on central- mode vortex pairing, further supporting the view that pairing is primarily governed perspective sheds insight on how linear stability theory is able to provide such an accurate prediction of experimentally-observed, fully nonlinear flow phenomenon.

Drastic stability change of X-X mismatch in d(CXG) trinucleotide repeat disorders under molecular crowding condition.

PubMed

Teng, Ye; Pramanik, Smritimoy; Tateishi-Karimata, Hisae; Ohyama, Tatsuya; Sugimoto, Naoki

2018-02-05

The trinucleotide repeat d(CXG) (X = A, C, G or T) is the most common sequence causing repeat expansion disorders. The formation of non-canonical structures, such as hairpin structures with X-X mismatches, has been proposed to affect gene expression and regulation, which are important in pathological studies of these devastating neurological diseases. However, little information is available regarding the thermodynamics of the repeat sequence under crowded cellular conditions where many non-canonical structures such as G-quadruplexes are highly stabilized, while duplexes are destabilised. In this study, we investigated the different stabilities of X-X mismatches in the context of internal d(CXG) self-complementary sequences in an environment with a high concentration of cosolutes to mimic the crowding conditions in cells. The stabilities of full-matched duplexes and duplexes with A-A, G-G, and T-T mismatched base pairs under molecular crowding conditions were notably decreased compared to under dilute conditions. However, the stability of the DNA duplex with a C-C mismatch base pair was only slightly destabilised. Investigating different stabilities of X-X mismatches in d(CXG) sequences is important for improving our understanding of the formation and transition of multiple non-canonical structures in trinucleotide repeat diseases, and may provide insights for pathological studies and drug development. Copyright © 2018 Elsevier Inc. All rights reserved.

The effect of betaine on the foam stability: Molecular simulation

NASA Astrophysics Data System (ADS)

Gao, Fengfeng; Liu, Guokui; Yuan, Shiling

2017-06-01

Zwitterionic betaines are widely used as foam boosters due to these can enhance the stability of foam films. In this paper, mechanistic insights of betaine to improve the stability of alkyl-polyoxyethylene carboxylate (AEC) foam are provided by molecular simulation. In the simulation, we observe the electropositive nitrogen atoms in betaine interact with the electronegative sulfur atoms, an electrostatic structure is formed at the air/water interface. Interaction energies of the mixed surfactants are calculated by the quantum chemistry methods. The calculations show betaine-AEC and betaine-betaine possess attractive interaction, and that AEC-AEC has repulsion to each other. In the other words, the repulsion between the headgroups of anionic surfactants is relaxed by betaine. Additionally, the influence of concentration of betaine on the stability of foam films is also simulated. The RDF and coordination numbers show that the electrostatic structures become denser with the increasing concentration of betaine. Therefore, entry barrier is enhanced accordingly. The SMD simulation also demonstrates the same variation tendency of entry barrier. The simulation details provide vital supplements to experiments.

Deletion of internal structured repeats increases the stability of a leucine-rich repeat protein, YopM

PubMed Central

Barrick, Doug

2011-01-01

Mapping the stability distributions of proteins in their native folded states provides a critical link between structure, thermodynamics, and function. Linear repeat proteins have proven more amenable to this kind of mapping than globular proteins. C-terminal deletion studies of YopM, a large, linear leucine-rich repeat (LRR) protein, show that stability is distributed quite heterogeneously, yet a high level of cooperativity is maintained [1]. Key components of this distribution are three interfaces that strongly stabilize adjacent sequences, thereby maintaining structural integrity and promoting cooperativity. To better understand the distribution of interaction energy around these critical interfaces, we studied internal (rather than terminal) deletions of three LRRs in this region, including one of these stabilizing interfaces. Contrary to our expectation that deletion of structured repeats should be destabilizing, we find that internal deletion of folded repeats can actually stabilize the native state, suggesting that these repeats are destabilizing, although paradoxically, they are folded in the native state. We identified two residues within this destabilizing segment that deviate from the consensus sequence at a position that normally forms a stacked leucine ladder in the hydrophobic core. Replacement of these nonconsensus residues with leucine is stabilizing. This stability enhancement can be reproduced in the context of nonnative interfaces, but it requires an extended hydrophobic core. Our results demonstrate that different LRRs vary widely in their contribution to stability, and that this variation is context-dependent. These two factors are likely to determine the types of rearrangements that lead to folded, functional proteins, and in turn, are likely to restrict the pathways available for the evolution of linear repeat proteins. PMID:21764506

Alloplastic implants for orbital wall reconstruction.

PubMed

Jacono, A A; Moskowitz, B

2000-01-01

Nonabsorbable alloplastic implants for orbital wall reconstruction have been widely accepted by surgeons because of their ready availability, stability, and biocompatability. Many complications have arisen with this class of implants because the lack of host tissue integration allows for implant migration, implant extrusion, recurrent hemorrhage, and infection. Porous polyethylene implants provide a welcome alternative as they have the unique properly of supporting tissue ingrowth in vivo. Their semirigid structure provides structural stability when used around the orbit, and their malleability allows for easy contouring. This paper presents our surgical approach to reconstructing orbital defects with porous polyethylene implants, including orbital floor, and superior, medial, and lateral wall defects, and discusses the advantages/disadvantages of other nonabsorbable alloplasts.

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

Influence of protein fold stability on immunogenicity and its implications for vaccine design

PubMed Central

Scheiblhofer, Sandra; Laimer, Josef; Machado, Yoan; Weiss, Richard; Thalhamer, Josef

2017-01-01

ABSTRACT Introduction: In modern vaccinology and immunotherapy, recombinant proteins more and more replace whole organisms to induce protective or curative immune responses. Structural stability of proteins is of crucial importance for efficient presentation of antigenic peptides on MHC, which plays a decisive role for triggering strong immune reactions. Areas covered: In this review, we discuss structural stability as a key factor for modulating the potency of recombinant vaccines and its importance for antigen proteolysis, presentation, and stimulation of B and T cells. Moreover, the impact of fold stability on downstream events determining the differentiation of T cells into effector cells is reviewed. We summarize studies investigating the impact of protein fold stability on the outcome of the immune response and provide an overview on computational methods to estimate the effects of point mutations on protein stability. Expert commentary: Based on this information, the rational design of up-to-date vaccines is discussed. A model for predicting immunogenicity of proteins based on their conformational stability at different pH values is proposed. PMID:28290225

Fundamental Movement Skills Are More than Run, Throw and Catch: The Role of Stability Skills

PubMed Central

Rudd, James R.; Barnett, Lisa M.; Butson, Michael L.; Farrow, Damian; Berry, Jason; Polman, Remco C. J.

2015-01-01

Introduction In motor development literature fundamental movement skills are divided into three constructs: locomotive, object control and stability skills. Most fundamental movement skills research has focused on children’s competency in locomotor and object control skills. The first aim of this study was to validate a test battery to assess the construct of stability skills, in children aged 6 to 10 (M age = 8.2, SD = 1.2). Secondly we assessed how the stability skills construct fitted into a model of fundamental movement skill. Method The Delphi method was used to select the stability skill battery. Confirmatory factor analysis (CFA) was used to assess if the skills loaded onto the same construct and a new model of FMS was developed using structural equation modelling. Results Three postural control tasks were selected (the log roll, rock and back support) because they had good face and content validity. These skills also demonstrated good predictive validity with gymnasts scoring significantly better than children without gymnastic training and children from a high SES school performing better than those from a mid and low SES schools and the mid SES children scored better than the low SES children (all p < .05). Inter rater reliability tests were excellent for all three skills (ICC = 0.81, 0.87, 0.87) as was test re-test reliability (ICC 0.87–0.95). CFA provided good construct validity, and structural equation modelling revealed stability skills to be an independent factor in an overall FMS model which included locomotor (r = .88), object control (r = .76) and stability skills (r = .81). Discussion This study provides a rationale for the inclusion of stability skills in FMS assessment. The stability skills could be used alongside other FMS assessment tools to provide a holistic assessment of children’s fundamental movement skills. PMID:26468644

Robust high pressure stability and negative thermal expansion in sodium-rich antiperovskites Na{sub 3}OBr and Na{sub 4}OI{sub 2}

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

Wang, Yonggang, E-mail: yyggwang@gmail.com, E-mail: yangwg@hpstar.ac.cn, E-mail: yusheng.zhao@unlv.edu; Institute of Nanostructured Functional Materials, Huanghe Science and Technology College, Zhengzhou, Henan 450006; High Pressure Synergetic Consortium

2016-01-14

The structure stability under high pressure and thermal expansion behavior of Na{sub 3}OBr and Na{sub 4}OI{sub 2}, two prototypes of alkali-metal-rich antiperovskites, were investigated by in situ synchrotron X-ray diffraction techniques under high pressure and low temperature. Both are soft materials with bulk modulus of 58.6 GPa and 52.0 GPa for Na{sub 3}OBr and Na{sub 4}OI{sub 2}, respectively. The cubic Na{sub 3}OBr structure and tetragonal Na{sub 4}OI{sub 2} with intergrowth K{sub 2}NiF{sub 4} structure are stable under high pressure up to 23 GPa. Although being a characteristic layered structure, Na{sub 4}OI{sub 2} exhibits nearly isotropic compressibility. Negative thermal expansion was observed at lowmore » temperature range (20–80 K) in both transition-metal-free antiperovskites for the first time. The robust high pressure structure stability was examined and confirmed by first-principles calculations among various possible polymorphisms qualitatively. The results provide in-depth understanding of the negative thermal expansion and robust crystal structure stability of these antiperovskite systems and their potential applications.« less

Introduction to Using Native Plant Community on Dredge Material Placement Areas

DTIC Science & Technology

2017-05-01

following: • providing wildlife habitat • inhibiting invasive species establishment • enhancing, structural stability of dikes • providing...areas. Typically, a diked structure is constructed and then filled with dredged material over an extended period of time (i.e., 10–50 years) until...Bourne, Tosin Sekoni, and David Price ERDC/TN EWN-17-2 May 2017 2 DMPA/CDF and are more cost effective to establish than other structural

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

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

Genetics Home Reference: early-onset myopathy with fatal cardiomyopathy

MedlinePlus

... they are made of proteins that generate the mechanical force needed for muscles to contract. Titin has several functions within sarcomeres. One of this protein's most important jobs is to provide structure, flexibility, and stability to these cell structures. Titin ...

Robust enzyme design: bioinformatic tools for improved protein stability.

PubMed

Suplatov, Dmitry; Voevodin, Vladimir; Švedas, Vytas

2015-03-01

The ability of proteins and enzymes to maintain a functionally active conformation under adverse environmental conditions is an important feature of biocatalysts, vaccines, and biopharmaceutical proteins. From an evolutionary perspective, robust stability of proteins improves their biological fitness and allows for further optimization. Viewed from an industrial perspective, enzyme stability is crucial for the practical application of enzymes under the required reaction conditions. In this review, we analyze bioinformatic-driven strategies that are used to predict structural changes that can be applied to wild type proteins in order to produce more stable variants. The most commonly employed techniques can be classified into stochastic approaches, empirical or systematic rational design strategies, and design of chimeric proteins. We conclude that bioinformatic analysis can be efficiently used to study large protein superfamilies systematically as well as to predict particular structural changes which increase enzyme stability. Evolution has created a diversity of protein properties that are encoded in genomic sequences and structural data. Bioinformatics has the power to uncover this evolutionary code and provide a reproducible selection of hotspots - key residues to be mutated in order to produce more stable and functionally diverse proteins and enzymes. Further development of systematic bioinformatic procedures is needed to organize and analyze sequences and structures of proteins within large superfamilies and to link them to function, as well as to provide knowledge-based predictions for experimental evaluation. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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

PubMed

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

2013-05-01

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

SPF/DB primary structure for supersonic aircraft (T-38 horizontal stabilizer)

NASA Technical Reports Server (NTRS)

Delmundo, A. R.; Mcquilkin, F. T.; Rivas, R. R.

1981-01-01

The structural integrity and potential cost savings of superplastic forming/diffusion bonding (SPF/DB) titanium structure for future Supersonic Cruise Research (SCR) and military aircraft primary structure applications was demonstrated. Using the horizontal stabilizer of the T-38 aircraft as a baseline, the structure was redesigned to the existing criteria and loads, using SPF/DB titanium technology. The general concept of using a full-depth sandwich structure which is attached to a steel spindle, was retained. Trade studies demonstrated that the optimum design should employ double-truss, sinewave core in the deepest section of the surface, making a transition to single-truss core in the thinner areas at the leading and trailing edges and at the tip. At the extreme thin edges of the surface, the single-truss core was changed to dot core to provide for gas passages during the SPF/DB process. The selected SPF/DB horizontal stabilizer design consisted of a one-piece SPF/DB sinewave truss core panel, a trunnion fitting, and reinforcing straps. The fitting and the straps were mechanically fastened to the SPF/DB panel.

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

Karabacak, Özkan, E-mail: ozkan2917@gmail.com; Department of Electronic Systems, Aalborg University, 9220 Aalborg East; Alikoç, Baran, E-mail: alikoc@itu.edu.tr

Motivated by the chaos suppression methods based on stabilizing an unstable periodic orbit, we study the stability of synchronized periodic orbits of coupled map systems when the period of the orbit is the same as the delay in the information transmission between coupled units. We show that the stability region of a synchronized periodic orbit is determined by the Floquet multiplier of the periodic orbit for the uncoupled map, the coupling constant, the smallest and the largest Laplacian eigenvalue of the adjacency matrix. We prove that the stabilization of an unstable τ-periodic orbit via coupling with delay τ is possiblemore » only when the Floquet multiplier of the orbit is negative and the connection structure is not bipartite. For a given coupling structure, it is possible to find the values of the coupling strength that stabilizes unstable periodic orbits. The most suitable connection topology for stabilization is found to be the all-to-all coupling. On the other hand, a negative coupling constant may lead to destabilization of τ-periodic orbits that are stable for the uncoupled map. We provide examples of coupled logistic maps demonstrating the stabilization and destabilization of synchronized τ-periodic orbits as well as chaos suppression via stabilization of a synchronized τ-periodic orbit.« less

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.

BOMB STABILIZING STRUCTURE

DOEpatents

Kelley, J.L.; Runyan, C.E.

1963-12-10

A stabilizinig structure capable of minimizing deviations of a falling body such as a bomb from desired trajectory is described. The structure comprises a fin or shroud arrangement of double-wedge configuration, the feeding portion being of narrow wedge shape and the after portion being of a wider wedge shape. The structure provides a force component for keeping the body on essentially desired trajectory throughout its fall. (AEC)

Solution structure of a small protein containing a fluorinated side chain in the core

PubMed Central

Cornilescu, Gabriel; Hadley, Erik B.; Woll, Matthew G.; Markley, John L.; Gellman, Samuel H.; Cornilescu, Claudia C.

2007-01-01

We report the first high-resolution structure for a protein containing a fluorinated side chain. Recently we carried out a systematic evaluation of phenylalanine to pentafluorophenylalanine (Phe → F5-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe → F5-Phe mutations are interesting because aryl–perfluoroaryl interactions of optimal geometry are intrinsically more favorable than either aryl–aryl or perfluoroaryl–perfluoroaryl interactions, and because perfluoroaryl units are more hydrophobic than are analogous aryl units. Only one mutation, Phe10 → F5-Phe, was found to provide enhanced tertiary structural stability relative to the native core (by ∼1 kcal/mol, according to guanidinium chloride denaturation studies). The NMR structure of this mutant, described here, reveals very little variation in backbone conformation or side chain packing relative to the wild type. Thus, although Phe → F5-Phe mutations offer the possibility of greater tertiary structural stability from side chain–side chain attraction and/or side chain desolvation, the constraints associated with the native c-VHP fold apparently prevent the modified polypeptide from taking advantage of this possibility. Our findings are important because they complement several studies that have shown that fluorination of saturated side chain carbon atoms can provide enhanced conformational stability. PMID:17123960

Local Conformational Stability of HIV-1 gp120 in Unliganded and CD4-Bound States as Defined by Amide Hydrogen/Deuterium Exchange▿ †

PubMed Central

Kong, Leopold; Huang, Chih-chin; Coales, Stephen J.; Molnar, Kathleen S.; Skinner, Jeff; Hamuro, Yoshitomo; Kwong, Peter D.

2010-01-01

The binding reaction of the HIV-1 gp120 envelope glycoprotein to the CD4 receptor involves exceptional changes in enthalpy and entropy. Crystal structures of gp120 in unliganded and various ligand-bound states, meanwhile, reveal an inner domain able to fold into diverse conformations, a structurally invariant outer domain, and, in the CD4-bound state, a bridging sheet minidomain. These studies, however, provide only hints as to the flexibility of each state. Here we use amide hydrogen/deuterium exchange coupled to mass spectrometry to provide quantifications of local conformational stability for HIV-1 gp120 in unliganded and CD4-bound states. On average, unliganded core gp120 displayed >10,000-fold slower exchange of backbone-amide hydrogens than a theoretically unstructured protein of the same composition, with binding by CD4 reducing the rate of gp120 amide exchange a further 10-fold. For the structurally constant CD4, alterations in exchange correlated well with alterations in binding surface (P value = 0.0004). For the structurally variable gp120, however, reductions in flexibility extended outside the binding surface, and regions of expected high structural diversity (inner domain/bridging sheet) displayed roughly 20-fold more rapid exchange in the unliganded state than regions of low diversity (outer domain). Thus, despite an extraordinary reduction in entropy, neither unliganded gp120 nor free CD4 was substantially unstructured, suggesting that most of the diverse conformations that make up the gp120 unliganded state are reasonably ordered. The results provide a framework for understanding how local conformational stability influences entropic change, conformational diversity, and structural rearrangements in the gp120-CD4 binding reaction. PMID:20660185

Luminescent macrocyclic lanthanide complexes

DOEpatents

Raymond, Kenneth N; Corneillie, Todd M; Xu, Jide

2014-05-20

The present invention provides a novel class of macrocyclic compounds as well as complexes formed between a metal (e.g., lanthanide) ion and the compounds of the invention. Preferred complexes exhibit high stability as well as high quantum yields of lanthanide ion luminescence in aqueous media without the need for secondary activating agents. Preferred compounds incorporate hydroxy-isophthalamide moieties within their macrocyclic structure and are characterized by surprisingly low, non-specific binding to a variety of polypeptides such as antibodies and proteins as well as high kinetic stability. These characteristics distinguish them from known, open-structured ligands.

Communication: Many-body stabilization of non-covalent interactions: Structure, stability, and mechanics of Ag3Co(CN)6 framework.

PubMed

Liu, Xiaofei; Hermann, Jan; Tkatchenko, Alexandre

2016-12-28

Stimuli-responsive metal-organic frameworks (MOFs) and other framework materials exhibit a broad variety of useful properties, which mainly stem from an interplay of strong covalent bonds within the organic linkers with presumably weak van der Waals (vdW) interactions which determine the overall packing of the framework constituents. Using Ag 3 Co(CN) 6 as a fundamental test case-a system with a colossal positive and negative thermal expansion [A. L. Goodwin et al., Science 319, 794 (2008)]-we demonstrate that its structure, stability, dielectric, vibrational, and mechanical properties are critically influenced by many-body electronic correlation contributions to non-covalent vdW interactions. The Ag 3 Co(CN) 6 framework is a remarkable molecular crystal, being visibly stabilized, rather than destabilized, by many-body vdW correlations. A detailed comparison with H 3 Co(CN) 6 highlights the crucial role of strongly polarized metallophilic interactions in dictating the exceptional properties of denser MOFs. Beyond MOFs, our findings indicate that many-body electronic correlations can substantially stabilize polarizable materials, providing a novel mechanism for tuning the properties of nanomaterials with intricate structural motifs.

Synchronization in dynamical networks with unconstrained structure switching

NASA Astrophysics Data System (ADS)

del Genio, Charo I.; Romance, Miguel; Criado, Regino; Boccaletti, Stefano

2015-12-01

We provide a rigorous solution to the problem of constructing a structural evolution for a network of coupled identical dynamical units that switches between specified topologies without constraints on their structure. The evolution of the structure is determined indirectly from a carefully built transformation of the eigenvector matrices of the coupling Laplacians, which are guaranteed to change smoothly in time. In turn, this allows one to extend the master stability function formalism, which can be used to assess the stability of a synchronized state. This approach is independent from the particular topologies that the network visits, and is not restricted to commuting structures. Also, it does not depend on the time scale of the evolution, which can be faster than, comparable to, or even secular with respect to the dynamics of the units.

Discrete-time stability of continuous-time controller designs for large space structures

NASA Technical Reports Server (NTRS)

Balas, M. J.

1982-01-01

In most of the stable control designs for flexible structures, continuous time is assumed. However, in view of the implementation of the controllers by on-line digital computers, the discrete-time stability of such controllers is an important consideration. In the case of direct-velocity feedback (DVFB), involving negative feedback from collocated force actuators and velocity sensors, it is not immediately apparent how much delay due to digital implementation of DVFB can be tolerated without loss of stability. The present investigation is concerned with such questions. A study is conducted of the discrete-time stability of DVFB, taking into account an employment of Euler's method of approximation of the time derivative. The obtained result gives an indication of the acceptable time-step size for stable digital implementation of DVFB. A result derived in connection with the consideration of the discrete-time stability of stable continuous-time systems provides a general condition under which digital implementation of such a system will remain stable.

Thermodynamic database for proteins: features and applications.

PubMed

Gromiha, M Michael; Sarai, Akinori

2010-01-01

We have developed a thermodynamic database for proteins and mutants, ProTherm, which is a collection of a large number of thermodynamic data on protein stability along with the sequence and structure information, experimental methods and conditions, and literature information. This is a valuable resource for understanding/predicting the stability of proteins, and it can be accessible at http://www.gibk26.bse.kyutech.ac.jp/jouhou/Protherm/protherm.html . ProTherm has several features including various search, display, and sorting options and visualization tools. We have analyzed the data in ProTherm to examine the relationship among thermodynamics, structure, and function of proteins. We describe the progress on the development of methods for understanding/predicting protein stability, such as (i) relationship between the stability of protein mutants and amino acid properties, (ii) average assignment method, (iii) empirical energy functions, (iv) torsion, distance, and contact potentials, and (v) machine learning techniques. The list of online resources for predicting protein stability has also been provided.

Accelerated stability studies for moisture-induced aggregation of tetanus toxoid.

PubMed

Jain, Nishant Kumar; Roy, Ipsita

2011-03-01

The study was carried out to evaluate the effect of exposing solid tetanus toxoid to moisture in two different ways on the structure and function of the toxoid. Tetanus toxoid was exposed to moisture by (i) the addition of an optimized amount of buffer and (ii) incubation under an environment provided by a saturated solution of K(2)CrO(4.) The changes in the conformational, structural and antigenic properties of tetanus toxoid were measured and compared. Results show that even at a similar level of moisture-induced aggregation, the amounts of water absorbed by the two preparations of tetanus toxoid are different. Differences in antigenicity and changes in structure of the toxoid at primary, secondary and tertiary structure levels were seen. Although both conditions are used to mimic accelerated stability conditions in the laboratory, the final products are different in the two cases. Thus, conditions for 'accelerated stability studies' for therapeutic proteins need to be selected with care so that they resemble the fate of the actual product.

Kinetic stability and membrane structure of liposomes during in vitro infant intestinal digestion: Effect of cholesterol and lactoferrin.

PubMed

Liu, Weilin; Wei, Fuqiang; Ye, Aiqian; Tian, Mengmeng; Han, Jianzhong

2017-09-01

The effects of cholesterol and lactoferrin on the kinetic stability and membrane structural integrity of negatively charged liposomes under in vitro infant intestinal digestion conditions were elucidated using dynamic light scattering, pH-stat titration, Fourier transform infrared spectroscopy, and pyrene steady state fluorescence probes. The liposomes had a smaller particle diameter, a wider size distribution, and a greater negative charge after digestion. The incorporation of cholesterol into the phospholipid bilayers resulted in a more ordered conformation in the aliphatic tail region and reduced micropolarity, indicating that cholesterol can improve the structural stability of liposomal membranes against intestinal environmental stress. Lactoferrin coverage facilitated the release of free fatty acids and increased the microfluidity of the bilayers, reducing the structural integrity of the liposomes. This study provides useful information on the design of liposomes and other microcapsules with improved and controlled release properties during digestion for particular groups of people. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bio-inspired dewetted surfaces based on SiC/Si interlocked structures for enhanced-underwater stability and regenerative-drag reduction capability

PubMed Central

Lee, By Junghan; Zhang, Zhuo; Baek, Seunghyun; Kim, Sangkuk; Kim, Donghyung; Yong, Kijung

2016-01-01

Drag reduction has become a serious issue in recent years in terms of energy conservation and environmental protection. Among diverse approaches for drag reduction, superhydrophobic surfaces have been mainly researched due to their high drag reducing efficiency. However, due to limited lifetime of plastron (i.e., air pockets) on superhydrophobic surfaces in underwater, the instability of dewetted surfaces has been a sticking point for practical applications. This work presents a breakthrough in improving the underwater stability of superhydrophobic surfaces by optimizing nanoscale surface structures using SiC/Si interlocked structures. These structures have an unequaled stability of underwater superhydrophobicity and enhance drag reduction capabilities,with a lifetime of plastron over 18 days and maximum velocity reduction ratio of 56%. Furthermore, through photoelectrochemical water splitting on a hierarchical SiC/Si nanostructure surface, the limited lifetime problem of air pockets was overcome by refilling the escaping gas layer, which also provides continuous drag reduction effects. PMID:27095674

Structural stability and energetics of grain boundary triple junctions in face centered cubic materials

NASA Astrophysics Data System (ADS)

Adlakha, I.; Solanki, K. N.

2015-03-01

We present a systematic study to elucidate the role of triple junctions (TJs) and their constituent grain boundaries on the structural stability of nanocrystalline materials. Using atomistic simulations along with the nudge elastic band calculations, we explored the atomic structural and thermodynamic properties of TJs in three different fcc materials. We found that the magnitude of excess energy at a TJ was directly related to the atomic density of the metal. Further, the vacancy binding and migration energetics in the vicinity of the TJ were examined as they play a crucial role in the structural stability of NC materials. The resolved line tension which takes into account the stress buildup at the TJ was found to be a good measure in predicting the vacancy binding tendency near the TJ. The activation energy for vacancy migration along the TJ was directly correlated with the measured excess energy. Finally, we show that the resistance for vacancy diffusion increased for TJs with larger excess stored energy and the defect mobility at some TJs is slower than their constituent GBs. Hence, our results have general implications on the diffusional process in NC materials and provide new insight into stabilizing NC materials with tailored TJs.

Short loop length and high thermal stability determine genomic instability induced by G-quadruplex-forming minisatellites

PubMed Central

Piazza, Aurèle; Adrian, Michael; Samazan, Frédéric; Heddi, Brahim; Hamon, Florian; Serero, Alexandre; Lopes, Judith; Teulade-Fichou, Marie-Paule; Phan, Anh Tuân; Nicolas, Alain

2015-01-01

G-quadruplexes (G4) are polymorphic four-stranded structures formed by certain G-rich nucleic acids, with various biological roles. However, structural features dictating their formation and/or functionin vivo are unknown. InS. cerevisiae, the pathological persistency of G4 within the CEB1 minisatellite induces its rearrangement during leading-strand replication. We now show that several other G4-forming sequences remain stable. Extensive mutagenesis of the CEB25 minisatellite motif reveals that only variants with very short (≤ 4 nt) G4 loops preferentially containing pyrimidine bases trigger genomic instability. Parallel biophysical analyses demonstrate that shortening loop length does not change the monomorphic G4 structure of CEB25 variants but drastically increases its thermal stability, in correlation with thein vivo instability. Finally, bioinformatics analyses reveal that the threat for genomic stability posed by G4 bearing short pyrimidine loops is conserved inC. elegans and humans. This work provides a framework explanation for the heterogeneous instability behavior of G4-forming sequencesin vivo, highlights the importance of structure thermal stability, and questions the prevailing assumption that G4 structures with short or longer loops are as likely to formin vivo. PMID:25956747

Flame stabilizer for stagnation flow reactor

DOEpatents

Hahn, David W.; Edwards, Christopher F.

1999-01-01

A method of stabilizing a strained flame in a stagnation flow reactor. By causing a highly strained flame to be divided into a large number of equal size segments it is possible to stablize a highly strained flame that is on the verge of extinction, thereby providing for higher film growth rates. The flame stabilizer is an annular ring mounted coaxially and coplanar with the substrate upon which the film is growing and having a number of vertical pillars mounted on the top surface, thereby increasing the number of azimuthal nodes into which the flame is divided and preserving an axisymmetric structure necessary for stability.

Structure and stability of pyrophyllite edge surfaces: Effect of temperature and water chemical potential

NASA Astrophysics Data System (ADS)

Kwon, Kideok D.; Newton, Aric G.

2016-10-01

The surfaces of clay minerals, which are abundant in atmospheric mineral dust, serve as an important medium to catalyze ice nucleation. The lateral edge surface of 2:1 clay minerals is postulated to be a potential site for ice nucleation. However, experimental investigations of the edge surface structure itself have been limited compared to the basal planes of clay minerals. Density functional theory (DFT) computational studies have provided insights into the pyrophyllite edge surface. Pyrophyllite is an ideal surrogate mineral for the edge surfaces of 2:1 clay minerals as it possesses no or little structural charge. Of the two most-common hydrated edge surfaces, the AC edge, (1 1 0) surface in the monoclinic polytype notation, is predicted to be more stable than the B edge, (0 1 0) surface. These stabilities, however, were determined based on the total energies calculated at 0 K and did not consider environmental effects such as temperature and humidity. In this study, atomistic thermodynamics based on periodic DFT electronic calculations was applied to examine the effects of environmental variables on the structure and thermodynamic stability of the common edge surfaces in equilibrium with bulk pyrophyllite and water vapor. We demonstrate that the temperature-dependent vibrational energy of sorbed water molecules at the edge surface is a significant component of the surface free energy and cannot be neglected when determining the surface stability of pyrophyllite. The surface free energies were calculated as a function of temperature from 240 to 600 K and water chemical potential corresponding to conditions from ultrahigh vacuum to the saturation vapor pressure of water. We show that at lower water chemical potentials (dry conditions), the AC and B edge surfaces possessed similar stabilities; at higher chemical potentials (humid conditions) the AC edge surface was more stable than the B edge surface. At high temperatures, both surfaces showed similar stabilities regardless of the water chemical potential. The equilibrium morphology of pyrophyllite crystals is also expected to be dependent on these two environmental variables. Surface defects may impact the surface reactivity. We discuss the thermodynamic stability of a possible Si cation vacancy defect which provides additional hydroxyl group on the surface.

Vibration control in smart coupled beams subjected to pulse excitations

NASA Astrophysics Data System (ADS)

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

2016-10-01

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

A Review of the Structure, Preparation, and Application of NLCs, PNPs, and PLNs.

PubMed

Li, Qianwen; Cai, Tiange; Huang, Yinghong; Xia, Xi; Cole, Susan P C; Cai, Yu

2017-05-27

Nanostructured lipid carriers (NLCs) are modified solid lipid nanoparticles (SLNs) that retain the characteristics of the SLN, improve drug stability and loading capacity, and prevent drug leakage. Polymer nanoparticles (PNPs) are an important component of drug delivery. These nanoparticles can effectively direct drug delivery to specific targets and improve drug stability and controlled drug release. Lipid-polymer nanoparticles (PLNs), a new type of carrier that combines liposomes and polymers, have been employed in recent years. These nanoparticles possess the complementary advantages of PNPs and liposomes. A PLN is composed of a core-shell structure; the polymer core provides a stable structure, and the phospholipid shell offers good biocompatibility. As such, the two components increase the drug encapsulation efficiency rate, facilitate surface modification, and prevent leakage of water-soluble drugs. Hence, we have reviewed the current state of development for the NLCs', PNPs', and PLNs' structures, preparation, and applications over the past five years, to provide the basis for further study on a controlled release drug delivery system.

A Review of the Structure, Preparation, and Application of NLCs, PNPs, and PLNs

PubMed Central

Li, Qianwen; Cai, Tiange; Huang, Yinghong; Xia, Xi; Cole, Susan P. C.; Cai, Yu

2017-01-01

Nanostructured lipid carriers (NLCs) are modified solid lipid nanoparticles (SLNs) that retain the characteristics of the SLN, improve drug stability and loading capacity, and prevent drug leakage. Polymer nanoparticles (PNPs) are an important component of drug delivery. These nanoparticles can effectively direct drug delivery to specific targets and improve drug stability and controlled drug release. Lipid–polymer nanoparticles (PLNs), a new type of carrier that combines liposomes and polymers, have been employed in recent years. These nanoparticles possess the complementary advantages of PNPs and liposomes. A PLN is composed of a core–shell structure; the polymer core provides a stable structure, and the phospholipid shell offers good biocompatibility. As such, the two components increase the drug encapsulation efficiency rate, facilitate surface modification, and prevent leakage of water-soluble drugs. Hence, we have reviewed the current state of development for the NLCs’, PNPs’, and PLNs’ structures, preparation, and applications over the past five years, to provide the basis for further study on a controlled release drug delivery system. PMID:28554993

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

NASA Astrophysics Data System (ADS)

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

2016-08-01

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

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

PubMed

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

2016-08-19

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

Effects of hydrophobic and dipole-dipole interactions on the conformational transitions of a model polypeptide

NASA Astrophysics Data System (ADS)

Mu, Yan; Gao, Yi Qin

2007-09-01

We studied the effects of hydrophobicity and dipole-dipole interactions between the nearest-neighbor amide planes on the secondary structures of a model polypeptide by calculating the free energy differences between different peptide structures. The free energy calculations were performed with low computational costs using the accelerated Monte Carlo simulation (umbrella sampling) method, with a bias-potential method used earlier in our accelerated molecular dynamics simulations. It was found that the hydrophobic interaction enhances the stability of α helices at both low and high temperatures but stabilizes β structures only at high temperatures at which α helices are not stable. The nearest-neighbor dipole-dipole interaction stabilizes β structures under all conditions, especially in the low temperature region where α helices are the stable structures. Our results indicate clearly that the dipole-dipole interaction between the nearest neighboring amide planes plays an important role in determining the peptide structures. Current research provides a more unified and quantitative picture for understanding the effects of different forms of interactions on polypeptide structures. In addition, the present model can be extended to describe DNA/RNA, polymer, copolymer, and other chain systems.

Physical modeling of river spanning rock structures: Evaluating interstitial flow, local hydraulics, downstream scour development, and structure stability

USGS Publications Warehouse

Collins, K.L.; Thornton, C.I.; Mefford, B.; Holmquist-Johnson, C. L.

2009-01-01

Rock weir and ramp structures uniquely serve a necessary role in river management: to meet water deliveries in an ecologically sound manner. Uses include functioning as low head diversion dams, permitting fish passage, creating habitat diversity, and stabilizing stream banks and profiles. Existing information on design and performance of in-stream rock structures does not provide the guidance necessary to implement repeatable and sustainable construction and retrofit techniques. As widespread use of rock structures increases, the need for reliable design methods with a broad range of applicability at individual sites grows as well. Rigorous laboratory testing programs were implemented at the U.S. Bureau of Reclamation (Reclamation) and at Colorado State University (CSU) as part of a multifaceted research project focused on expanding the current knowledge base and developing design methods to improve the success rate of river spanning rock structures in meeting project goals. Physical modeling at Reclamation is being used to measure, predict, and reduce interstitial flow through rock ramps. CSU is using physical testing to quantify and predict scour development downstream of rock weirs and its impact on the stability of rock structures. ?? 2009 ASCE.

Co-extinction in a host-parasite network: identifying key hosts for network stability.

PubMed

Dallas, Tad; Cornelius, Emily

2015-08-17

Parasites comprise a substantial portion of total biodiversity. Ultimately, this means that host extinction could result in many secondary extinctions of obligate parasites and potentially alter host-parasite network structure. Here, we examined a highly resolved fish-parasite network to determine key hosts responsible for maintaining parasite diversity and network structure (quantified here as nestedness and modularity). We evaluated four possible host extinction orders and compared the resulting co-extinction dynamics to random extinction simulations; including host removal based on estimated extinction risk, parasite species richness and host level contributions to nestedness and modularity. We found that all extinction orders, except the one based on realistic extinction risk, resulted in faster declines in parasite diversity and network structure relative to random biodiversity loss. Further, we determined species-level contributions to network structure were best predicted by parasite species richness and host family. Taken together, we demonstrate that a small proportion of hosts contribute substantially to network structure and that removal of these hosts results in rapid declines in parasite diversity and network structure. As network stability can potentially be inferred through measures of network structure, our findings may provide insight into species traits that confer stability.

Implicit leadership theories in applied settings: factor structure, generalizability, and stability over time.

PubMed

Epitropaki, Olga; Martin, Robin

2004-04-01

The present empirical investigation had a 3-fold purpose: (a) to cross-validate L. R. Offermann, J. K. Kennedy, and P. W. Wirtz's (1994) scale of Implicit Leadership Theories (ILTs) in several organizational settings and to further provide a shorter scale of ILTs in organizations; (b) to assess the generalizability of ILTs across different employee groups, and (c) to evaluate ILTs' change over time. Two independent samples were used for the scale validation (N1 = 500 and N2 = 439). A 6-factor structure (Sensitivity, Intelligence, Dedication, Dynamism, Tyranny, and Masculinity) was found to most accurately represent ELTs in organizational settings. Regarding the generalizability of ILTs, although the 6-factor structure was consistent across different employee groups, there was only partial support for total factorial invariance. Finally, evaluation of gamma, beta, and alpha change provided support for ILTs' stability over time.

Breaking the icosahedra in boron carbide

PubMed Central

Xie, Kelvin Y.; An, Qi; Sato, Takanori; Breen, Andrew J.; Ringer, Simon P.; Goddard, William A.; Cairney, Julie M.; Hemker, Kevin J.

2016-01-01

Findings of laser-assisted atom probe tomography experiments on boron carbide elucidate an approach for characterizing the atomic structure and interatomic bonding of molecules associated with extraordinary structural stability. The discovery of crystallographic planes in these boron carbide datasets substantiates that crystallinity is maintained to the point of field evaporation, and characterization of individual ionization events gives unexpected evidence of the destruction of individual icosahedra. Statistical analyses of the ions created during the field evaporation process have been used to deduce relative atomic bond strengths and show that the icosahedra in boron carbide are not as stable as anticipated. Combined with quantum mechanics simulations, this result provides insight into the structural instability and amorphization of boron carbide. The temporal, spatial, and compositional information provided by atom probe tomography makes it a unique platform for elucidating the relative stability and interactions of primary building blocks in hierarchically crystalline materials. PMID:27790982

Vfold: a web server for RNA structure and folding thermodynamics prediction.

PubMed

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

2014-01-01

The ever increasing discovery of non-coding RNAs leads to unprecedented demand for the accurate modeling of RNA folding, including the predictions of two-dimensional (base pair) and three-dimensional all-atom structures and folding stabilities. Accurate modeling of RNA structure and stability has far-reaching impact on our understanding of RNA functions in human health and our ability to design RNA-based therapeutic strategies. The Vfold server offers a web interface to predict (a) RNA two-dimensional structure from the nucleotide sequence, (b) three-dimensional structure from the two-dimensional structure and the sequence, and (c) folding thermodynamics (heat capacity melting curve) from the sequence. To predict the two-dimensional structure (base pairs), the server generates an ensemble of structures, including loop structures with the different intra-loop mismatches, and evaluates the free energies using the experimental parameters for the base stacks and the loop entropy parameters given by a coarse-grained RNA folding model (the Vfold model) for the loops. To predict the three-dimensional structure, the server assembles the motif scaffolds using structure templates extracted from the known PDB structures and refines the structure using all-atom energy minimization. The Vfold-based web server provides a user friendly tool for the prediction of RNA structure and stability. The web server and the source codes are freely accessible for public use at "http://rna.physics.missouri.edu".

Oriented conductive oxide electrodes on SiO2/Si and glass

DOEpatents

Jia, Quanxi; Arendt, Paul N.

2001-01-01

A thin film structure is provided including a silicon substrate with a layer of silicon dioxide on a surface thereof, and a layer of cubic oxide material deposited upon the layer of silicon dioxide by ion-beam-assisted-deposition, said layer of cubic oxide material characterized as biaxially oriented. Preferably, the cubic oxide material is yttria-stabilized zirconia. Additional thin layers of biaxially oriented ruthenium oxide or lanthanum strontium cobalt oxide are deposited upon the layer of yttria-stabilized zirconia. An intermediate layer of cerium oxide is employed between the yttria-stabilized zirconia layer and the lanthanum strontium cobalt oxide layer. Also, a layer of barium strontium titanium oxide can be upon the layer of biaxially oriented ruthenium oxide or lanthanum strontium cobalt oxide. Also, a method of forming such thin film structures, including a low temperature deposition of a layer of a biaxially oriented cubic oxide material upon the silicon dioxide surface of a silicon dioxide/silicon substrate is provided.

Structure and biocatalytic scope of thermophilic flavin-dependent halogenase and flavin reductase enzymes.

PubMed

Menon, Binuraj R K; Latham, Jonathan; Dunstan, Mark S; Brandenburger, Eileen; Klemstein, Ulrike; Leys, David; Karthikeyan, Chinnan; Greaney, Michael F; Shepherd, Sarah A; Micklefield, Jason

2016-10-04

Flavin-dependent halogenase (Fl-Hal) enzymes have been shown to halogenate a range of synthetic as well as natural aromatic compounds. The exquisite regioselectively of Fl-Hal enzymes can provide halogenated building blocks which are inaccessible using standard halogenation chemistries. Consequently, Fl-Hal are potentially useful biocatalysts for the chemoenzymatic synthesis of pharmaceuticals and other valuable products, which are derived from haloaromatic precursors. However, the application of Fl-Hal enzymes, in vitro, has been hampered by their poor catalytic activity and lack of stability. To overcome these issues, we identified a thermophilic tryptophan halogenase (Th-Hal), which has significantly improved catalytic activity and stability, compared with other Fl-Hal characterised to date. When used in combination with a thermostable flavin reductase, Th-Hal can efficiently halogenate a number of aromatic substrates. X-ray crystal structures of Th-Hal, and the reductase partner (Th-Fre), provide insights into the factors that contribute to enzyme stability, which could guide the discovery and engineering of more robust and productive halogenase biocatalysts.

How structurally stable are global socioeconomic systems?

PubMed Central

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

2014-01-01

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

Targeting G-quadruplex DNA structures in the telomere and oncogene promoter regions by benzimidazole‒carbazole ligands.

PubMed

Kaulage, Mangesh H; Maji, Basudeb; Pasadi, Sanjeev; Ali, Asfa; Bhattacharya, Santanu; Muniyappa, K

2018-03-25

Recent studies support the idea that G-quadruplex structures in the promoter regions of oncogenes and telomere DNA can serve as potential therapeutic targets in the treatment of cancer. Accordingly, several different types of organic small molecules that stabilize G-quadruplex structures and inhibit telomerase activity have been discerned. Here, we describe the binding of benzimidazole-carbazole ligands to G-quadruplex structures formed in G-rich DNA sequences containing the promoter regions of human c-MYC, c-KIT1, c-KIT2, VEGF and BCL2 proto-oncogenes. The fluorescence spectroscopic data indicate that benzimidazole-carbazole ligands bind and stabilize the G-quadruplexes in the promoter region of oncogenes. The molecular docking studies provide insights into the mode and extent of binding of this class of ligands to the G-quadruplexes formed in oncogene promoters. The high stability of these G-quadruplex structures was validated by thermal denaturation and telomerase-catalyzed extension of the 3' end. Notably, benzimidazole-carbazole ligands suppress the expression of oncogenes in cancer cells in a dose-dependent manner. We anticipate that benzimidazole-carbazole ligands, by virtue of their ability to stabilize G-quadruplex structures in the promoter regions of oncogenes, might reduce the risk of cancer through the loss of function in the proteins encoded by these genes. Copyright © 2018 Elsevier Masson SAS. All rights reserved.

Technology development for cryogenic deployable telescope structures and mechanisms

NASA Astrophysics Data System (ADS)

Atkinson, Charles B.; Gilman, Larry; Reynolds, Paul

2003-12-01

At 6-7 meters in diameter, the James Webb Space Telescope (JWST) will require structures that remain stable to levels that are on the order of 10 nanometers under dynamic and thermal loading while operating at cryogenic temperatures. Moreover, the JWST will be the first telescope in space that is deployed, resulting in an aperture that is not only segmented, but has hinge-lines and the associated joining systems or latches in it. In order to understand the behavior and reduce the risk associated with very large, deployed structures and the stability of the associated structure and latches, we developed and tested the largest cryogenic structure ever built and then characterized its stability. This paper presents a description of the design of the Development Optical Telescope Assembly (DOTA), the testing performed, and the results of the testing performed on it. We discuss the material selection and characterization processes, give a description of the test configurations, describe the metrology equipment and the validation process for it, provide the test results, and summarize the conclusions drawn from the results. The testing and associated results include characterization of the thermal stability of the large-scale structure, characterization of the micro-dynamic stability of the latching system, and measurements of the deployment capability of the mechanisms. We also describe how the DOTA design relates to the JWST design and how the test results relate to the JWST requirements.

Micellar and Structural Stability of Nanoscale Amphiphilic Polymers: Implications for Anti-atherosclerotic Bioactivity

PubMed Central

Zhang, Yingyue; Li, Qi; Welsh, William J.; Moghe, Prabhas V.; Uhrich, Kathryn E.

2016-01-01

Atherosclerosis, a leading cause of mortality in developed countries, is characterized by the buildup of oxidized low-density lipoprotein (oxLDL) within the vascular intima, unregulated oxLDL uptake by macrophages, and ensuing formation of arterial plaque. Amphiphilic polymers (AMPs) comprised of a branched hydrophobic domain and a hydrophilic poly(ethylene glycol) (PEG) tail have shown promising anti-atherogenic effects through direct inhibition of oxLDL uptake by macrophages. In this study, five AMPs with controlled variations were evaluated for their micellar and structural stability in the presence of serum and lipase, respectively, to develop underlying structure-atheroprotective activity relations. In parallel, molecular dynamics simulations were performed to explore the AMP conformational preferences within an aqueous environment. Notably, AMPs with ether linkages between the hydrophobic arms and sugar backbones demonstrated enhanced degradation stability and storage stability, and also elicited enhanced anti-atherogenic bioactivity. Additionally, AMPs with increased hydrophobicity elicited increased atheroprotective bioactivity in the presence of serum. These studies provide key insights for designing more serum-stable polymeric micelles as prospective cardiovascular nanotherapies. PMID:26828687

An experimental test of a fundamental food web motif.

PubMed

Rip, Jason M K; McCann, Kevin S; Lynn, Denis H; Fawcett, Sonia

2010-06-07

Large-scale changes to the world's ecosystem are resulting in the deterioration of biostructure-the complex web of species interactions that make up ecological communities. A difficult, yet crucial task is to identify food web structures, or food web motifs, that are the building blocks of this baroque network of interactions. Once identified, these food web motifs can then be examined through experiments and theory to provide mechanistic explanations for how structure governs ecosystem stability. Here, we synthesize recent ecological research to show that generalist consumers coupling resources with different interaction strengths, is one such motif. This motif amazingly occurs across an enormous range of spatial scales, and so acts to distribute coupled weak and strong interactions throughout food webs. We then perform an experiment that illustrates the importance of this motif to ecological stability. We find that weak interactions coupled to strong interactions by generalist consumers dampen strong interaction strengths and increase community stability. This study takes a critical step by isolating a common food web motif and through clear, experimental manipulation, identifies the fundamental stabilizing consequences of this structure for ecological communities.

Micellar and structural stability of nanoscale amphiphilic polymers: Implications for anti-atherosclerotic bioactivity.

PubMed

Zhang, Yingyue; Li, Qi; Welsh, William J; Moghe, Prabhas V; Uhrich, Kathryn E

2016-04-01

Atherosclerosis, a leading cause of mortality in developed countries, is characterized by the buildup of oxidized low-density lipoprotein (oxLDL) within the vascular intima, unregulated oxLDL uptake by macrophages, and ensuing formation of arterial plaque. Amphiphilic polymers (AMPs) comprised of a branched hydrophobic domain and a hydrophilic poly(ethylene glycol) (PEG) tail have shown promising anti-atherogenic effects through direct inhibition of oxLDL uptake by macrophages. In this study, five AMPs with controlled variations were evaluated for their micellar and structural stability in the presence of serum and lipase, respectively, to develop underlying structure-atheroprotective activity relations. In parallel, molecular dynamics simulations were performed to explore the AMP conformational preferences within an aqueous environment. Notably, AMPs with ether linkages between the hydrophobic arms and sugar backbones demonstrated enhanced degradation stability and storage stability, and also elicited enhanced anti-atherogenic bioactivity. Additionally, AMPs with increased hydrophobicity elicited increased atheroprotective bioactivity in the presence of serum. These studies provide key insights for designing more serum-stable polymeric micelles as prospective cardiovascular nanotherapies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Joblessness and Unemployment: A Review of the Literature.

ERIC Educational Resources Information Center

Mason, Patrick L.

This literature review examines evidence on the relationship between African American male economic potential in the formal sector of the economy and transitions in African American family structure and marital stability. This review also provides insight into the crime, unemployment, family structure, and race debate. Competing theoretical…

Stabilization of Glucocerebrosidase by Active Site Occupancy

PubMed Central

2017-01-01

Glucocerebrosidase (GBA) is a lysosomal β-glucosidase that degrades glucosylceramide. Its deficiency results in Gaucher disease (GD). We examined the effects of active site occupancy of GBA on its structural stability. For this, we made use of cyclophellitol-derived activity-based probes (ABPs) that bind irreversibly to the catalytic nucleophile (E340), and for comparison, we used the potent reversible inhibitor isofagomine. We demonstrate that cyclophellitol ABPs improve the stability of GBA in vitro, as revealed by thermodynamic measurements (Tm increase by 21 °C), and introduce resistance to tryptic digestion. The stabilizing effect of cell-permeable cyclophellitol ABPs is also observed in intact cultured cells containing wild-type GBA, N370S GBA (labile in lysosomes), and L444P GBA (exhibits impaired ER folding): all show marked increases in lysosomal forms of GBA molecules upon exposure to ABPs. The same stabilization effect is observed for endogenous GBA in the liver of wild-type mice injected with cyclophellitol ABPs. Stabilization effects similar to those observed with ABPs were also noted at high concentrations of the reversible inhibitor isofagomine. In conclusion, we provide evidence that the increase in cellular levels of GBA by ABPs and by the reversible inhibitor is in part caused by their ability to stabilize GBA folding, which increases the resistance of GBA against breakdown by lysosomal proteases. These effects are more pronounced in the case of the amphiphilic ABPs, presumably due to their high lipophilic potential, which may promote further structural compactness of GBA through hydrophobic interactions. Our study provides further rationale for the design of chaperones for GBA to ameliorate Gaucher disease. PMID:28485919

Permeability and stability of base and subbase materials : research implementation plan.

DOT National Transportation Integrated Search

2000-08-01

The purpose of pavement base and subbase courses is to provide a means for free water to drain from : beneath roadways while providing structural support for the pavement. Problems occur when highway : materials which are assumed to have adequate dra...

Theoretical Investigation of the Structural Stabilities of Ceria Surfaces and Supported Metal Nanocluster in Vapor and Aqueous Phases

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

Ren, Zhibo; Liu, Ning; Chen, Biaohua

Understanding the structural stability and dynamics at the interface between the solid metal oxide and aqueous phase is significant in a variety of industrial applications including heterogeneous catalysis and environmental remediation. In the present work, the stabilities of three low-index ceria (CeO2) surfaces, i.e., (111), (110) and (100) in vapor and aqueous phases were studied using ab initio molecular dynamics simulations and density functional theory (DFT) calculations. Gibbs surface free energies as a function of temperature, water partial pressure, and water coverages were calculated using DFT based atomistic thermodynamic approach. On the basis of surface free energies, the morphology andmore » exposed surface structures of the CeO2 nanoparticle were predicted using Wulff construction principle. It is found that the partially hydroxylated (111) and (100) are two major surface structures of CeO2 nanoparticles in vapor phase at ambient temperature (300 K). As the temperature increases, the fully dehydrated (111) surface gradually becomes the most dominant surface structure. While in aqueous phase, the exposed surface of the CeO2 nanoparticle is dominated by the hydroxylated (110) structure at 393 K. Finally, the morphology and stability of a cuboctahedron Pt13 nanocluster supported on CeO2 surfaces in both gas and aqueous phases were investigated. In gas phase, the supported Pt13 nanocluster has the tendency to wetting the CeO2 surface due to the strong metal-support interaction. The calculated interaction energies suggest the CeO2(110) surface provides the best stability for the Pt13 nanocluster. The CeO2 supported Pt13 nanoclusters are oxidized. Compared to the gas phase, the morphology of the CeO2 supported Pt13 nanocluster is less distorted due to the solvation effect provided by surrounding water molecules in aqueous phase. More electrons are transferred from the Pt13 nanocluster to the CeO2 support, implying the supported Pt13 nanocluster is further oxidized in aqueous phase.« less

Static network structure can stabilize human cooperation.

PubMed

Rand, David G; Nowak, Martin A; Fowler, James H; Christakis, Nicholas A

2014-12-02

The evolution of cooperation in network-structured populations has been a major focus of theoretical work in recent years. When players are embedded in fixed networks, cooperators are more likely to interact with, and benefit from, other cooperators. In theory, this clustering can foster cooperation on fixed networks under certain circumstances. Laboratory experiments with humans, however, have thus far found no evidence that fixed network structure actually promotes cooperation. Here, we provide such evidence and help to explain why others failed to find it. First, we show that static networks can lead to a stable high level of cooperation, outperforming well-mixed populations. We then systematically vary the benefit that cooperating provides to one's neighbors relative to the cost required to cooperate (b/c), as well as the average number of neighbors in the network (k). When b/c > k, we observe high and stable levels of cooperation. Conversely, when b/c ≤ k or players are randomly shuffled, cooperation decays. Our results are consistent with a quantitative evolutionary game theoretic prediction for when cooperation should succeed on networks and, for the first time to our knowledge, provide an experimental demonstration of the power of static network structure for stabilizing human cooperation.

Static network structure can stabilize human cooperation

PubMed Central

Rand, David G.; Nowak, Martin A.; Fowler, James H.; Christakis, Nicholas A.

2014-01-01

The evolution of cooperation in network-structured populations has been a major focus of theoretical work in recent years. When players are embedded in fixed networks, cooperators are more likely to interact with, and benefit from, other cooperators. In theory, this clustering can foster cooperation on fixed networks under certain circumstances. Laboratory experiments with humans, however, have thus far found no evidence that fixed network structure actually promotes cooperation. Here, we provide such evidence and help to explain why others failed to find it. First, we show that static networks can lead to a stable high level of cooperation, outperforming well-mixed populations. We then systematically vary the benefit that cooperating provides to one’s neighbors relative to the cost required to cooperate (b/c), as well as the average number of neighbors in the network (k). When b/c > k, we observe high and stable levels of cooperation. Conversely, when b/c ≤ k or players are randomly shuffled, cooperation decays. Our results are consistent with a quantitative evolutionary game theoretic prediction for when cooperation should succeed on networks and, for the first time to our knowledge, provide an experimental demonstration of the power of static network structure for stabilizing human cooperation. PMID:25404308

Theoretical prediction of a novel inorganic fullerene-like family of silicon-carbon materials

NASA Astrophysics Data System (ADS)

Wang, Ruoxi; Zhang, Dongju; Liu, Chengbu

2005-08-01

In an effort to search for new inorganic fullerene-like structures, we designed a series of novel silicon-carbon cages, (SiC) n ( n = 6-36), based on the uniformly hybrid Si-C four- and six-membered-rings, and researched their geometrical and electronic structures, as well as their relative stabilities using the density function theory. Among these cages, the structures for n = 12, 16, and 36 were found to been energetically more favorable. The calculated disproportionation energy and binding energy per SiC unit show that the (SiC) 12 cage is the most stable one among these designed structures. The present calculations not only indicate that silicon-carbon fullerenes are promised to be synthesized in future, but also provide a new way for stabilizing silicon cages by uniformly doping carbon atoms into silicon structures.

Bimeron nanoconfined design

NASA Astrophysics Data System (ADS)

Iakovlev, I. A.; Sotnikov, O. M.; Mazurenko, V. V.

2018-05-01

We report on the stabilization of the topological bimeron structures in confined geometries. The Monte Carlo simulations for a ferromagnet with a strong Dzyaloshinskii-Moriya interaction revealed the formation of a mixed skyrmion-bimeron phase at finite temperatures. The vacancy grid created in the spin lattice drastically changes the picture of the observed spin configurations and allows one to choose between the formation of a pure bimeron and skyrmion lattice. We found that the rhombic plaquette provides a natural environment for stabilization of the bimeron structures. Such a rhombic geometry can protect the topological state even in the absence of the magnetic field.

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

DOEpatents

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

2008-06-08

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

Structurally stable gel bead containing entrapped enzyme and method for manufacture thereof

DOEpatents

Woodward, J.

1998-12-08

This research provides a structurally stable gel bead containing an entrapped enzyme and a method for its manufacture. The enzyme is covalently cross-linked to gelatin in the presence of glutaraldehyde prior to the formation of the gel bead, to prevent leakage of the enzyme. Propylene glycol alginate is then added to the mixture. Once the gel beads are formed, they are then soaked in glutaraldehyde, which imparts structural stability to the gel beads. This method can be used with many types of enzymes, such as proteases, carbohydrases, proteases, ligases, isomerases, oxidoreductases, and specialty enzymes. These and other enzymes can be immobilized in the gel beads and utilized in a number of enzymatic processes. Exogenously added ions are not required to maintain the structural stability of these gel beads. 7 figs.

Evolving Systems: Adaptive Key Component Control and Inheritance of Passivity and Dissipativity

NASA Technical Reports Server (NTRS)

Frost, S. A.; Balas, M. J.

2010-01-01

We propose a new framework called Evolving Systems to describe the self-assembly, or autonomous assembly, of actively controlled dynamical subsystems into an Evolved System with a higher purpose. Autonomous assembly of large, complex flexible structures in space is a target application for Evolving Systems. A critical requirement for autonomous assembling structures is that they remain stable during and after assembly. The fundamental topic of inheritance of stability, dissipativity, and passivity in Evolving Systems is the primary focus of this research. In this paper, we develop an adaptive key component controller to restore stability in Nonlinear Evolving Systems that would otherwise fail to inherit the stability traits of their components. We provide sufficient conditions for the use of this novel control method and demonstrate its use on an illustrative example.

The role of zinc on the chemistry of complex intermetallic compounds

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

Xie, Weiwei

2014-01-01

Combining experiments and electronic structure theory provides the framework to design and discover new families of complex intermetallic phases and to understand factors that stabilize both new and known phases. Using solid state synthesis and multiple structural determinations, ferromagnetic β-Mn type Co 8+xZn 12–x was analyzed for their crystal and electronic structures.

Remote Performance Monitoring of a Thermoplastic Composite Bridge at Camp Mackall, NC

DTIC Science & Technology

2011-11-01

level, flow, creep, and force for slope stability, subsidence, seismicity studies, structural restoration, or site assessment applications. • Mining ...monitors mine ventilation, slope stability, convergence, and equipment performance. • Machinery testing- provides temperature, pressure, RPM, veloci...Contact an Applications Engineer for help in deter- mining the best antenna for your application. • 21831 0 dBd, ’l.t Wave Dipole Whip Antenna

Magnetic moments of excited states in nuclei far from stability

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

Wolf, A.; Berant, Z.; Gill, R.L.

1985-01-01

Magnetic moments of excited states in nuclei far from stability have been measured by gamma-gamma angular correlation at the output of the fission product separators TRISTAN and JOSEF. The results obtained until now will be reviewed. They provide important nuclear structure information about nuclei around closed shells, and transitional nuclei in the A = 100 and 150 regions. 22 refs., 3 figs., 3 tabs.

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

PubMed

Iyer, Bharat Ramasubramanian; Mahalakshmi, Radhakrishnan

2016-09-06

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

Highly Dynamic Anion-Quadrupole Networks in Proteins.

PubMed

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

2016-11-01

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

Exploiting structure: Introduction and motivation

NASA Technical Reports Server (NTRS)

Xu, Zhong Ling

1993-01-01

Research activities performed during the period of 29 June 1993 through 31 Aug. 1993 are summarized. The Robust Stability of Systems where transfer function or characteristic polynomial are multilinear affine functions of parameters of interest in two directions, Algorithmic and Theoretical, was developed. In the algorithmic direction, a new approach that reduces the computational burden of checking the robust stability of the system with multilinear uncertainty is found. This technique is called 'Stability by linear process.' In fact, the 'Stability by linear process' described gives an algorithm. In analysis, we obtained a robustness criterion for the family of polynomials with coefficients of multilinear affine function in the coefficient space and obtained the result for the robust stability of diamond families of polynomials with complex coefficients also. We obtained the limited results for SPR design and we provide a framework for solving ACS. Finally, copies of the outline of our results are provided in the appendix. Also, there is an administration issue in the appendix.

Sensitivity of Space Station alpha joint robust controller to structural modal parameter variations

NASA Technical Reports Server (NTRS)

Kumar, Renjith R.; Cooper, Paul A.; Lim, Tae W.

1991-01-01

The photovoltaic array sun tracking control system of Space Station Freedom is described. A synthesis procedure for determining optimized values of the design variables of the control system is developed using a constrained optimization technique. The synthesis is performed to provide a given level of stability margin, to achieve the most responsive tracking performance, and to meet other design requirements. Performance of the baseline design, which is synthesized using predicted structural characteristics, is discussed and the sensitivity of the stability margin is examined for variations of the frequencies, mode shapes and damping ratios of dominant structural modes. The design provides enough robustness to tolerate a sizeable error in the predicted modal parameters. A study was made of the sensitivity of performance indicators as the modal parameters of the dominant modes vary. The design variables are resynthesized for varying modal parameters in order to achieve the most responsive tracking performance while satisfying the design requirements. This procedure of reoptimization design parameters would be useful in improving the control system performance if accurate model data are provided.

Asymmetric Preorganization of Inverted Pair Residues in the Sodium-Calcium Exchanger

PubMed Central

Giladi, Moshe; Almagor, Lior; van Dijk, Liat; Hiller, Reuben; Man, Petr; Forest, Eric; Khananshvili, Daniel

2016-01-01

In analogy with many other proteins, Na+/Ca2+ exchangers (NCX) adapt an inverted twofold symmetry of repeated structural elements, while exhibiting a functional asymmetry by stabilizing an outward-facing conformation. Here, structure-based mutant analyses of the Methanococcus jannaschii Na+/Ca2+ exchanger (NCX_Mj) were performed in conjunction with HDX-MS (hydrogen/deuterium exchange mass spectrometry) to identify the structure-dynamic determinants of functional asymmetry. HDX-MS identified hallmark differences in backbone dynamics at ion-coordinating residues of apo-NCX_Mj, whereas Na+or Ca2+ binding to the respective sites induced relatively small, but specific, changes in backbone dynamics. Mutant analysis identified ion-coordinating residues affecting the catalytic capacity (kcat/Km), but not the stability of the outward-facing conformation. In contrast, distinct “noncatalytic” residues (adjacent to the ion-coordinating residues) control the stability of the outward-facing conformation, but not the catalytic capacity. The helix-breaking signature sequences (GTSLPE) on the α1 and α2 repeats (at the ion-binding core) differ in their folding/unfolding dynamics, while providing asymmetric contributions to transport activities. The present data strongly support the idea that asymmetric preorganization of the ligand-free ion-pocket predefines catalytic reorganization of ion-bound residues, where secondary interactions with adjacent residues couple the alternating access. These findings provide a structure-dynamic basis for ion-coupled alternating access in NCX and similar proteins. PMID:26876271

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

PubMed

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

2017-04-01

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

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

PubMed

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

2011-10-26

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

Characterization of Molecular Determinants of the Conformational Stability of Macrophage Migration Inhibitory Factor: Leucine 46 Hydrophobic Pocket

PubMed Central

El-Turk, Farah; Fauvet, Bruno; Ashrafi, Amer; Ouertatani-Sakouhi, Hajer; Cho, Min-Kyu; Neri, Marilisa; Cascella, Michele; Rothlisberger, Ursula; Pojer, Florence; Zweckstetter, Markus; Lashuel, Hilal

2012-01-01

Macrophage Migration Inhibitory Factor (MIF) is a key mediator of inflammatory responses and innate immunity and has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. The oligomerization of MIF, more specifically trimer formation, is essential for its keto-enol tautomerase activity and probably mediates several of its interactions and biological activities, including its binding to its receptor CD74 and activation of certain signaling pathways. Therefore, understanding the molecular factors governing the oligomerization of MIF and the role of quaternary structure in modulating its structural stability and multifunctional properties is crucial for understanding the function of MIF in health and disease. Herein, we describe highly conserved intersubunit interactions involving the hydrophobic packing of the side chain of Leu46 onto the β-strand β3 of one monomer within a hydrophobic pocket from the adjacent monomer constituted by residues Arg11, Val14, Phe18, Leu19, Val39, His40, Val41, Val42, and Pro43. To elucidate the structural significance of these intersubunit interactions and their relative contribution to MIF’s trimerization, structural stability and catalytic activity, we generated three point mutations where Leu46 was replaced by glycine (L46G), alanine (L46A) and phenylalanine (L46F), and their structural properties, stability, oligomerization state, and catalytic activity were characterized using a battery of biophysical methods and X-ray crystallography. Our findings provide new insights into the role of the Leu46 hydrophobic pocket in stabilizing the conformational state of MIF in solution. Disrupting the Leu46 hydrophobic interaction perturbs the secondary and tertiary structure of the protein but has no effect on its oligomerization state. PMID:23028743

Characterization of molecular determinants of the conformational stability of macrophage migration inhibitory factor: leucine 46 hydrophobic pocket.

PubMed

El-Turk, Farah; Fauvet, Bruno; Ashrafi, Amer; Ouertatani-Sakouhi, Hajer; Cho, Min-Kyu; Neri, Marilisa; Cascella, Michele; Rothlisberger, Ursula; Pojer, Florence; Zweckstetter, Markus; Lashuel, Hilal

2012-01-01

Macrophage Migration Inhibitory Factor (MIF) is a key mediator of inflammatory responses and innate immunity and has been implicated in the pathogenesis of several inflammatory and autoimmune diseases. The oligomerization of MIF, more specifically trimer formation, is essential for its keto-enol tautomerase activity and probably mediates several of its interactions and biological activities, including its binding to its receptor CD74 and activation of certain signaling pathways. Therefore, understanding the molecular factors governing the oligomerization of MIF and the role of quaternary structure in modulating its structural stability and multifunctional properties is crucial for understanding the function of MIF in health and disease. Herein, we describe highly conserved intersubunit interactions involving the hydrophobic packing of the side chain of Leu46 onto the β-strand β3 of one monomer within a hydrophobic pocket from the adjacent monomer constituted by residues Arg11, Val14, Phe18, Leu19, Val39, His40, Val41, Val42, and Pro43. To elucidate the structural significance of these intersubunit interactions and their relative contribution to MIF's trimerization, structural stability and catalytic activity, we generated three point mutations where Leu46 was replaced by glycine (L46G), alanine (L46A) and phenylalanine (L46F), and their structural properties, stability, oligomerization state, and catalytic activity were characterized using a battery of biophysical methods and X-ray crystallography. Our findings provide new insights into the role of the Leu46 hydrophobic pocket in stabilizing the conformational state of MIF in solution. Disrupting the Leu46 hydrophobic interaction perturbs the secondary and tertiary structure of the protein but has no effect on its oligomerization state.

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

NASA Technical Reports Server (NTRS)

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

2009-01-01

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

Atomic and electronic structure of a copper/graphene interface as prepared and 1.5 years after

NASA Astrophysics Data System (ADS)

Boukhvalov, D. W.; Bazylewski, P. F.; Kukharenko, A. I.; Zhidkov, I. S.; Ponosov, Yu. S.; Kurmaev, E. Z.; Cholakh, S. O.; Lee, Y. H.; Chang, G. S.

2017-12-01

We report the results of X-ray spectroscopy and Raman measurements of as-prepared graphene on a high quality copper surface and the same materials after 1.5 years under different conditions (ambient and low humidity). The obtained results were compared with density functional theory calculations of the formation energies and electronic structures of various structural defects in graphene/Cu interfaces. For evaluation of the stability of the carbon cover, we propose a two-step model. The first step is oxidation of the graphene, and the second is perforation of graphene with the removal of carbon atoms as part of the carbon dioxide molecule. Results of the modeling and experimental measurements provide evidence that graphene grown on high-quality copper substrate becomes robust and stable in time (1.5 years). However, the stability of this interface depends on the quality of the graphene and the number of native defects in the graphene and substrate. The effect of the presence of a metallic substrate with defects on the stability and electronic structure of graphene is also discussed

Method of manufacturing a heat pipe wick with structural enhancement

DOEpatents

Andraka, Charles E [Albuquerque, NM; Adkins, Douglas R [Albuquerque, NM; Moreno, James B [Albuquerque, NM; Rawlinson, K Scott [Albuquerque, NM; Showalter, Steven K [Albuquerque, NM; Moss, Timothy A [Albuquerque, NM

2006-10-24

Heat pipe wick structure wherein a stout sheet of perforated material overlays a high performance wick material such as stainless steel felt affixed to a substrate. The inventive structure provides a good flow path for working fluid while maintaining durability and structural stability independent of the structure (or lack of structure) associated with the wick material. In one described embodiment, a wick of randomly laid .about.8 micron thickness stainless steel fibers is sintered to a metal substrate and a perforated metal overlay.

Heat pipe wick with structural enhancement

DOEpatents

Andraka, Charles E.; Adkins, Douglas R.; Moreno, James B.; Rawlinson, K. Scott; Showalter, Steven K.; Moss, Timothy A.

2003-11-18

Heat pipe wick structure wherein a stout sheet of perforated material overlays a high performance wick material such as stainless steel felt affixed to a substrate. The inventive structure provides a good flow path for working fluid while maintaining durability and structural stability independent of the structure (or lack of structure) associated with the wick material. In one described embodiment, a wick of randomly laid .about.8 micron thickness stainless steel fibers is sintered to a metal substrate and a perforated metal overlay.

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

NASA Astrophysics Data System (ADS)

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

2018-03-01

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

In What Ways Do Synthetic Nucleotides and Natural Base Lesions Alter the Structural Stability of G-Quadruplex Nucleic Acids?

PubMed Central

2017-01-01

Synthetic analogs of natural nucleotides have long been utilized for structural studies of canonical and noncanonical nucleic acids, including the extensively investigated polymorphic G-quadruplexes (GQs). Dependence on the sequence and nucleotide modifications of the folding landscape of GQs has been reviewed by several recent studies. Here, an overview is compiled on the thermodynamic stability of the modified GQ folds and on how the stereochemical preferences of more than 70 synthetic and natural derivatives of nucleotides substituting for natural ones determine the stability as well as the conformation. Groups of nucleotide analogs only stabilize or only destabilize the GQ, while the majority of analogs alter the GQ stability in both ways. This depends on the preferred syn or anti N-glycosidic linkage of the modified building blocks, the position of substitution, and the folding architecture of the native GQ. Natural base lesions and epigenetic modifications of GQs explored so far also stabilize or destabilize the GQ assemblies. Learning the effect of synthetic nucleotide analogs on the stability of GQs can assist in engineering a required stable GQ topology, and exploring the in vitro action of the single and clustered natural base damage on GQ architectures may provide indications for the cellular events. PMID:29181193

Stream stability at highway structures.

DOT National Transportation Integrated Search

1995-11-01

This document provides guidelines for identifying stream instability problems at highway stream crossings and for the selection and design of appropriate countermeasures to mitigate potential damages to bridges and other highway components at stream ...

Hydrolytic catalysis and structural stabilization in a designed metalloprotein

PubMed Central

Zastrow, Melissa L.; Peacock, Anna F. A.; Stuckey, Jeanne A.; Pecoraro, Vincent L.

2011-01-01

Metal ions are an important part of many natural proteins, providing structural, catalytic and electron transfer functions. Reproducing these functions in a designed protein is the ultimate challenge to our understanding of them. Here, we present an artificial metallohydrolase, which has been shown by X-ray crystallography to contain two different metal ions – a Zn(II) ion which is important for catalytic activity and a Hg(II) ion which provides structural stability. This metallohydrolase displays catalytic activity that compares well with several characteristic reactions of natural enzymes. It catalyses p-nitrophenyl acetate hydrolysis (pNPA) to within ~100-fold of the efficiency of human carbonic anhydrase (CA)II and is at least 550-fold better than comparable synthetic complexes. Similarly, CO2 hydration occurs with an efficiency within ~500-fold of CAII. While histidine residues in the absence of Zn(II) exhibit pNPA hydrolysis, miniscule apopeptide activity is observed for CO2 hydration. The kinetic and structural analysis of this first de novo designed hydrolytic metalloenzyme uncovers necessary design features for future metalloenzymes containing one or more metals. PMID:22270627

Performance of structured lipids incorporating selected phenolic and ascorbic acids.

PubMed

Gruczynska, Eliza; Przybylski, Roman; Aladedunye, Felix

2015-04-15

Conditions applied during frying require antioxidant which is stable at these conditions and provides protection for frying oil and fried food. Novel structured lipids containing nutraceuticals and antioxidants were formed by enzymatic transesterification, exploring canola oil and naturally occurring antioxidants such as ascorbic and selected phenolic acids as substrates. Lipozyme RM IM lipase from Rhizomucor miehei was used as biocatalyst. Frying performance and oxidative stability of the final transesterification products were evaluated. The novel lipids showed significantly improved frying performance compared to canola oil. Oxidative stability assessment of the structured lipids showed significant improvement in resistance to oxidative deterioration compared to original canola oil. Interestingly, the presence of ascorbic acid in an acylglycerol structure protected α-tocopherol against thermal degradation, which was not observed for the phenolic acids. Developed structured lipids containing nutraceuticals and antioxidants may directly affect nutritional properties of lipids also offering nutraceutical ingredients for food formulation. Copyright © 2014 Elsevier Ltd. All rights reserved.

Insights into the structural features and stability of peptide nucleic acid with a D-prolyl-2-aminocyclopentane carboxylic acid backbone that binds to DNA and RNA.

PubMed

Poomsuk, Nattawee; Vilaivan, Tirayut; Siriwong, Khatcharin

2018-06-12

Peptide nucleic acid (PNA) is a powerful biomolecule with a wide variety of important applications. In this work, the molecular structures and binding affinity of PNA with a D-prolyl-2-aminocyclopentane carboxylic acid backbone (acpcPNA) that binds to both DNA and RNA were studied using molecular dynamics simulations. The simulated structures of acpcPNA-DNA and acpcPNA-RNA duplexes more closely resembled the typical structures of B-DNA and A-RNA than the corresponding duplexes of aegPNA. The calculated binding free energies are in good agreement with the experimental results that the acpcPNA-DNA duplex is more stable than the acpcPNA-RNA duplex regardless of the base sequences. The results provide further insights in the relationship between structure and stability of this unique PNA system. Copyright © 2018 Elsevier Inc. All rights reserved.

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

Vijayakumar, M.; Nie, Zimin; Walter, Eric D.

Redox flow battery (RFB) is a promising candidate for energy storage component in designing resilient grid scale power supply due to the advantage of the separation of power and energy. However, poorly understood chemical and thermal stability issues of electrolytes currently limit the performance of RFB. Designing of high performance stable electrolytes requires comprehensive knowledge about the molecular level solvation structure and dynamics of their redox active species. The molecular level understanding of detrimental V2O5 precipitation process led to successful designing of mixed acid based electrolytes for vanadium redox flow batteries (VRFB). The higher stability of mixed acid based electrolytesmore » is attributed to the choice of hydrochloric acid as optimal co-solvent, which provides chloride anions for ligand exchange process in vanadium solvation structure. The role of chloride counter anion on solvation structure and dynamics of vanadium species were studied using combined magnetic resonance spectroscopy and DFT based theoretical methods. Finally, the solvation phenomenon of multiple vanadium species and their impact on VRFB electrolyte chemical stability were discussed.« less

The role of strong electrostatic interactions at the dimer interface of human glutathione synthetase.

PubMed

De Jesus, Margarita C; Ingle, Brandall L; Barakat, Khaldoon A; Shrestha, Bisesh; Slavens, Kerri D; Cundari, Thomas R; Anderson, Mary E

2014-10-01

The obligate homodimer human glutathione synthetase (hGS) provides an ideal system for exploring the role of protein-protein interactions in the structural stability, activity and allostery of enzymes. The two active sites of hGS, which are 40 Å apart, display allosteric modulation by the substrate γ-glutamylcysteine (γ-GC) during the synthesis of glutathione, a key cellular antioxidant. The two subunits interact at a relatively small dimer interface dominated by electrostatic interactions between S42, R221, and D24. Alanine scans of these sites result in enzymes with decreased activity, altered γ-GC affinity, and decreased thermal stability. Molecular dynamics simulations indicate these mutations disrupt interchain bonding and impact the tertiary structure of hGS. While the ionic hydrogen bonds and salt bridges between S42, R221, and D24 do not mediate allosteric communication in hGS, these interactions have a dramatic impact on the activity and structural stability of the enzyme.

Effect of calcium ions on structure and stability of the C1q-like domain of otolin-1 from human and zebrafish.

PubMed

Hołubowicz, Rafał; Wojtas, Magdalena; Taube, Michał; Kozak, Maciej; Ożyhar, Andrzej; Dobryszycki, Piotr

2017-12-01

Otolin-1 is a collagen-like protein expressed in the inner ear of vertebrates. It provides an organic scaffold for otoliths in fish and otoconia in land vertebrates. In this study, the expression and purification procedure of C1q-like domain of otolin-1 from human and zebrafish was developed. The structure and stability of the proteins were investigated. The results of sedimentation velocity analytical ultracentrifugation and small-angle X-ray scattering indicated that the C1q-like domain of otolin-1 forms stable trimers in solution in the presence of calcium ions. It was also observed that calcium ions influenced the secondary structure of the proteins. C1q-like domains were stabilized by the calcium ions. The human variant was especially affected by the calcium ions. The results indicate the importance of the C1q-like domain for the assembly of the organic matrix of otoliths and otoconia. © 2017 Federation of European Biochemical Societies.

Stabilization of Si_60 Cage Structure: The Agony and the Ecstasy

NASA Astrophysics Data System (ADS)

Kawazoe, Y.; Sun, Q.; Wang, Q.; Rao, B. K.; Jena, P.

2003-03-01

The unique role of silicon in the micro-electronics industry has motivated many researchers to find ways to stabilize Si_60 with fullerene structure. In spite of numerous experimental attempts, synthesis of a theoretically predicted C_60-supported Si_60 cluster (C_60@Si_60) has not been possible. Using a state-of-the-art theoretical method, we provide the first answer for this long-standing contradiction between the experimental observation and the theoretical prediction. The flaws in earlier theoretical works are pointed out, and Si_60 is shown to be unstable in the fullerene structure either on its own or when supported on a C_60 fullerene (C_60@Si_60). On the other hand, we show that Si_60 cage can be stabilized by using magic clusters such as Al_12X (X = Si, Ge, Sn, Pb) as endohedral units, which have been identified in recent experiment as stable clusters and as suitable building blocks for cluster-assembled materials.

Stabilization of Lithium Transition Metal Silicates in the Olivine Structure

DOE PAGES

Sun, Xiaoqi; Tripathi, Rajesh; Popov, Guerman; ...

2017-07-28

While olivine LiFePO 4 shows amongst the best electrochemical properties of Li-ion positive electrodes with respect to rate behavior owing to facile Li + migration pathways in the framework, replacing the [PO 4] 3- polyanion with a silicate [SO 4] 4- moitie in olivine is desirable. This would allow additional balancing alkali content and hence electron transfer, and increase the capacity. We demonstrate the first stabilization of a lithium transition-metal silicate (as a pure silicate) in the olivine structure type. Using LiInSiO 4 and LiScSiO 4 as the parent materials, transition metal (Mn, Fe, Co) substitutions on the In/Sc sitemore » were investigated by computational modelling via atomic scale simulation. Transition metal substitution was found to be only favourable for Co, a finding confirmed by the successful solid state synthesis of olivine LixInyCo 2-x-ySiO 4. Finally, the stabilization of the structure was achieved by entropy provided by cation disorder.« less

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

PubMed

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

2015-11-13

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

Exploring advantages/disadvantages and improvements in overcoming gene delivery barriers of amino acid modified trimethylated chitosan.

PubMed

Zheng, Hao; Tang, Cui; Yin, Chunhua

2015-06-01

Present study aimed at exploring advantages/disadvantages of amino acid modified trimethylated chitosan in conquering multiple gene delivery obstacles and thus providing comprehensive understandings for improved transfection efficiency. Arginine, cysteine, and histidine modified trimethyl chitosan were synthesized and employed to self-assemble with plasmid DNA (pDNA) to form nanocomplexes, namely TRNC, TCNC, and THNC, respectively. They were assessed by structural stability, cellular uptake, endosomal escape, release behavior, nuclear localization, and in vitro and in vivo transfection efficiencies. Besides, sodium tripolyphosphate (TPP) was added into TRNC to compromise certain disadvantageous attributes for pDNA delivery. Optimal endosomal escape ability failed to bring in satisfactory transfection efficiency of THNC due to drawbacks in structural stability, cellular uptake, pDNA liberation, and nuclear distribution. TCNC evoked the most potent gene expression owing to multiple advantages including sufficient stability, preferable uptake, efficient pDNA release, and high nucleic accumulation. Undesirable stability and insufficient pDNA release adversely affected TRNC-mediated gene transfer. However, incorporation of TPP could improve such disadvantages and consequently resulted in enhanced transfection efficiencies. Coordination of multiple contributing effects to conquer all delivery obstacles was necessitated for improved transfection efficiency, which would provide insights into rational design of gene delivery vehicles.

X-ray and Neutron Scattering Study of the Formation of Core–Shell-Type Polyoxometalates

DOE PAGES

Yin, Panchao; Wu, Bin; Mamontov, Eugene; ...

2016-02-05

A typical type of core-shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small angle X-ray scattering is used to study the structural features and stability of the core-shell structures in aqueous solutions. Time-resolved small angle X-ray scattering is applied to monitor the synthetic reactions and a three-stage formation mechanism is proposed to describe the synthesis of the core-shell polyoxometalates based on the monitoring results. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core-shell structures and two different types ofmore » water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures. A typical type of core shell polyoxometalates can be obtained through the Keggin-type polyoxometalate-templated growth of a layer of spherical shell structure of {Mo 72Fe 30}. Small-angle X-ray scattering is used to study the structural features and stability of the core shell structures in aqueous solutions. Time-resolved small-angle X-ray scattering is applied to monitor the synthetic reactions, and a three-stage formation mechanism is proposed to describe the synthesis of the core shell polyoxometalates based on the monitoring results. New protocols have been developed by fitting the X-ray data with custom physical models, which provide more convincing, objective, and completed data interpretation. Quasi-elastic and inelastic neutron scattering are used to probe the dynamics of water molecules in the core shell structures, and two different types of water molecules, the confined and structured water, are observed. These water molecules play an important role in bridging core and shell structures and stabilizing the cluster structures.« less

Micromachined silicon acoustic delay line with improved structural stability and acoustic directivity for real-time photoacoustic tomography

NASA Astrophysics Data System (ADS)

Cho, Young; Kumar, Akhil; Xu, Song; Zou, Jun

2017-03-01

Recent studies have shown that micromachined silicon acoustic delay lines can provide a promising solution to achieve real-time photoacoustic tomography without the need for complex transducer arrays and data acquisition electronics. However, as its length increases to provide longer delay time, the delay line becomes more vulnerable to structural instability due to reduced mechanical stiffness. In addition, the small cross-section area of the delay line results in a large acoustic acceptance angle and therefore poor directivity. To address these two issues, this paper reports the design, fabrication, and testing of a new silicon acoustic delay line enhanced with 3D printed polymer micro linker structures. First, mechanical deformation of the silicon acoustic delay line (with and without linker structures) under gravity was simulated by using finite element method. Second, the acoustic crosstalk and acoustic attenuation caused by the polymer micro linker structures were evaluated with both numerical simulation and ultrasound transmission testing. The result shows that the use of the polymer micro linker structures significantly improves the structural stability of the silicon acoustic delay lines without creating additional acoustic attenuation and crosstalk. In addition, a new tapered design for the input terminal of the delay line was also investigate to improve its acoustic directivity by reducing the acoustic acceptance angle. These two improvements are expected to provide an effective solution to eliminate current limitations on the achievable acoustic delay time and out-of-plane imaging resolution of micromachined silicon acoustic delay line arrays.

Cell-based composite materials with programmed structures and functions

DOEpatents

None

2016-03-01

The present invention is directed to the use of silicic acid to transform biological materials, including cellular architecture into inorganic materials to provide biocomposites (nanomaterials) with stabilized structure and function. In the present invention, there has been discovered a means to stabilize the structure and function of biological materials, including cells, biomolecules, peptides, proteins (especially including enzymes), lipids, lipid vesicles, polysaccharides, cytoskeletal filaments, tissue and organs with silicic acid such that these materials may be used as biocomposites. In many instances, these materials retain their original biological activity and may be used in harsh conditions which would otherwise destroy the integrity of the biological material. In certain instances, these biomaterials may be storage stable for long periods of time and reconstituted after storage to return the biological material back to its original form. In addition, by exposing an entire cell to form CSCs, the CSCs may function to provide a unique system to study enzymes or a cascade of enzymes which are otherwise unavailable.

Cell-based composite materials with programmed structures and functions

DOEpatents

Kaehr, Bryan J.; Brinker, C. Jeffrey; Townson, Jason L.

2018-05-15

The present invention is directed to the use of silicic acid to transform biological materials, including cellular architecture into inorganic materials to provide biocomposites (nanomaterials) with stabilized structure and function. In the present invention, there has been discovered a means to stabilize the structure and function of biological materials, including cells, biomolecules, peptides, proteins (especially including enzymes), lipids, lipid vesicles, polysaccharides, cytoskeletal filaments, tissue and organs with silicic acid such that these materials may be used as biocomposites. In many instances, these materials retain their original biological activity and may be used in harsh conditions which would otherwise destroy the integrity of the biological material. In certain instances, these biomaterials may be storage stable for long periods of time and reconstituted after storage to return the biological material back to its original form. In addition, by exposing an entire cell to form CSCs, the CSCs may function to provide a unique system to study enzymes or a cascade of enzymes which are otherwise unavailable.

Space structures concepts and materials

NASA Technical Reports Server (NTRS)

Nowitzky, A. M.; Supan, E. C.

1988-01-01

An extension is preseted of the evaluation of graphite/aluminum metal matrix composites (MMC) for space structures application. A tubular DWG graphite/aluminum truss assembly was fabricated having the structural integrity and thermal stability needed for space application. DWG is a proprietary thin ply continuous graphite reinforced aluminum composite. The truss end fittings were constructed using the discontinuous ceramic particulate reinforced MMC DWAl 20 (trademark). Thermal stability was incorporated in the truss by utilizing high stiffness, negative coefficient of thermal expansion (CTE) P100 graphite fibers in a 6061 aluminum matrix, crossplied to provide minimized CTE in the assembled truss. Tube CTE was designed to be slightly negative to offset the effects of the end fitting and sleeve, CTE values of which are approx. 1/2 that of aluminum. In the design of the truss configuration, the CTE contribution of each component was evaluated to establish the component dimension and layup configuration required to provide a net zero CTE in the subassemblies which would then translate to a zero CTE for the entire truss bay produced.

Full depth reclamation : workshop materials.

DOT National Transportation Integrated Search

2011-01-01

Rehabilitating an old pavement by pulverizing and stabilizing the existing pavement is a process referred to as Full Depth Reclamation (FDR). This process shows great potential as an economical rehabilitation alternative that provides deep structural...

(Hyper)thermophilic enzymes: production and purification.

PubMed

Falcicchio, Pierpaolo; Levisson, Mark; Kengen, Servé W M; Koutsopoulos, Sotirios

2014-01-01

The discovery of thermophilic and hyperthermophilic microorganisms, thriving at environmental temperatures near or above 100 °C, has revolutionized our ideas about the upper temperature limit at which life can exist. The characterization of (hyper)thermostable proteins has broadened our understanding and presented new opportunities for solving one of the most challenging problems in biophysics: how is structural stability and biological function maintained at high temperatures where "normal" proteins undergo dramatic structural changes? In our laboratory we have purified and studied many thermostable and hyperthermostable proteins in an attempt to determine the molecular basis of heat stability. Here, we present methods to express such proteins and enzymes in E. coli and provide a general protocol for overproduction and purification. The ability to produce enzymes that retain their stability and activity at elevated temperatures creates exciting opportunities for a wide range of biocatalytic applications.

On the buckling of hexagonal boron nitride nanoribbons via structural mechanics

NASA Astrophysics Data System (ADS)

Giannopoulos, Georgios I.

2018-03-01

Monolayer hexagonal boron nitride nanoribbons have similar crystal structure as graphene nanoribbons, have excellent mechanical, thermal insulating and dielectric properties and additionally present chemical stability. These allotropes of boron nitride can be used in novel applications, in which graphene is not compatible, to achieve remarkable performance. The purpose of the present work is to provide theoretical estimations regarding the buckling response of hexagonal boron nitride monolayer under compressive axial loadings. For this reason, a structural mechanics method is formulated which employs the exact equilibrium atomistic structure of the specific two-dimensional nanomaterial. In order to represent the interatomic interactions appearing between boron and nitrogen atoms, the Dreiding potential model is adopted which is realized by the use of three-dimensional, two-noded, spring-like finite elements of appropriate stiffness matrices. The critical compressive loads that cause the buckling of hexagonal boron nitride nanoribbons are computed with respect to their size and chirality while some indicative buckled shapes of them are illustrated. Important conclusions arise regarding the effect of the size and chirality on the structural stability of the hexagonal boron nitride monolayers. An analytical buckling formula, which provides good fitting of the numerical outcome, is proposed.

The fuzzy oil drop model, based on hydrophobicity density distribution, generalizes the influence of water environment on protein structure and function.

PubMed

Banach, Mateusz; Konieczny, Leszek; Roterman, Irena

2014-10-21

In this paper we show that the fuzzy oil drop model represents a general framework for describing the generation of hydrophobic cores in proteins and thus provides insight into the influence of the water environment upon protein structure and stability. The model has been successfully applied in the study of a wide range of proteins, however this paper focuses specifically on domains representing immunoglobulin-like folds. Here we provide evidence that immunoglobulin-like domains, despite being structurally similar, differ with respect to their participation in the generation of hydrophobic core. It is shown that β-structural fragments in β-barrels participate in hydrophobic core formation in a highly differentiated manner. Quantitatively measured participation in core formation helps explain the variable stability of proteins and is shown to be related to their biological properties. This also includes the known tendency of immunoglobulin domains to form amyloids, as shown using transthyretin to reveal the clear relation between amyloidogenic properties and structural characteristics based on the fuzzy oil drop model. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

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

PubMed Central

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

2012-01-01

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

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

PubMed

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

2012-04-01

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

Experimental and Theoretical Evaluation of the Stability of True MOF Polymorphs Explains Their Mechanochemical Interconversions.

PubMed

Akimbekov, Zamirbek; Katsenis, Athanassios D; Nagabhushana, G P; Ayoub, Ghada; Arhangelskis, Mihails; Morris, Andrew J; Friščić, Tomislav; Navrotsky, Alexandra

2017-06-14

We provide the first combined experimental and theoretical evaluation of how differences in ligand structure and framework topology affect the relative stabilities of isocompositional (i.e., true polymorph) metal-organic frameworks (MOFs). We used solution calorimetry and periodic DFT calculations to analyze the thermodynamics of two families of topologically distinct polymorphs of zinc zeolitic imidazolate frameworks (ZIFs) based on 2-methyl- and 2-ethylimidazolate linkers, demonstrating a correlation between measured thermodynamic stability and density, and a pronounced effect of the ligand substituent on their stability. The results show that mechanochemical syntheses and transformations of ZIFs are consistent with Ostwald's rule of stages and proceed toward thermodynamically increasingly stable, more dense phases.

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

PubMed

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

2013-01-01

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

Stabilization of Functional Recombinant Cannabinoid Receptor CB2 in Detergent Micelles and Lipid Bilayers

PubMed Central

Vukoti, Krishna; Kimura, Tomohiro; Macke, Laura; Gawrisch, Klaus; Yeliseev, Alexei

2012-01-01

Elucidation of the molecular mechanisms of activation of G protein-coupled receptors (GPCRs) is among the most challenging tasks for modern membrane biology. For studies by high resolution analytical methods, these integral membrane receptors have to be expressed in large quantities, solubilized from cell membranes and purified in detergent micelles, which may result in a severe destabilization and a loss of function. Here, we report insights into differential effects of detergents, lipids and cannabinoid ligands on stability of the recombinant cannabinoid receptor CB2, and provide guidelines for preparation and handling of the fully functional receptor suitable for a wide array of downstream applications. While we previously described the expression in Escherichia coli, purification and liposome-reconstitution of multi-milligram quantities of CB2, here we report an efficient stabilization of the recombinant receptor in micelles - crucial for functional and structural characterization. The effects of detergents, lipids and specific ligands on structural stability of CB2 were assessed by studying activation of G proteins by the purified receptor reconstituted into liposomes. Functional structure of the ligand binding pocket of the receptor was confirmed by binding of 2H-labeled ligand measured by solid-state NMR. We demonstrate that a concerted action of an anionic cholesterol derivative, cholesteryl hemisuccinate (CHS) and high affinity cannabinoid ligands CP-55,940 or SR-144,528 are required for efficient stabilization of the functional fold of CB2 in dodecyl maltoside (DDM)/CHAPS detergent solutions. Similar to CHS, the negatively charged phospholipids with the serine headgroup (PS) exerted significant stabilizing effects in micelles while uncharged phospholipids were not effective. The purified CB2 reconstituted into lipid bilayers retained functionality for up to several weeks enabling high resolution structural studies of this GPCR at physiologically relevant conditions. PMID:23056277

Structural and ferromagnetic properties of an orthorhombic phase of MnBi stabilized with Rh additions

DOE PAGES

Taufour, Valentin; Thimmaiah, Srinivasa; March, Stephen; ...

2015-07-28

The article addresses the possibility of alloy elements in MnBi which may modify the thermodynamic stability of the NiAs-type structure without significantly degrading the magnetic properties. The addition of small amounts of Rh and Mn provides an improvement in the thermal stability with some degradation of the magnetic properties. The small amounts of Rh and Mn additions in MnBi stabilize an orthorhombic phase whose structural and magnetic properties are closely related to the ones of the previously reported high-temperature phase of MnBi (HT MnBi). The properties of the HT MnBi, which is stable between 613 and 719 K, have notmore » been studied in detail because of its transformation to the stable low-temperature MnBi (LT MnBi), making measurements near and below its Curie temperature difficult. The Rh-stabilized MnBi with chemical formula Mn 1.0625–xRh xBi [x=0.02(1)] adopts a new superstructure of the NiAs/Ni 2In structure family. It is ferromagnetic below a Curie temperature of 416 K. The critical exponents of the ferromagnetic transition are not of the mean-field type but are closer to those associated with the Ising model in three dimensions. The magnetic anisotropy is uniaxial; the anisotropy energy is rather large, and it does not increase when raising the temperature, contrary to what happens in LT MnBi. The saturation magnetization is approximately 3μB/f.u. at low temperatures. Thus, while this exact composition may not be application ready, it does show that alloying is a viable route to modifying the stability of this class of rare-earth-free magnet alloys.« less

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

DOEpatents

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

2007-04-24

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

Stability Mechanisms of a Thermophilic Laccase Probed by Molecular Dynamics

PubMed Central

Christensen, Niels J.; Kepp, Kasper P.

2013-01-01

Laccases are highly stable, industrially important enzymes capable of oxidizing a large range of substrates. Causes for their stability are, as for other proteins, poorly understood. In this work, multiple-seed molecular dynamics (MD) was applied to a Trametes versicolor laccase in response to variable ionic strengths, temperatures, and glycosylation status. Near-physiological conditions provided excellent agreement with the crystal structure (average RMSD ∼0.92 Å) and residual agreement with experimental B-factors. The persistence of backbone hydrogen bonds was identified as a key descriptor of structural response to environment, whereas solvent-accessibility, radius of gyration, and fluctuations were only locally relevant. Backbone hydrogen bonds decreased systematically with temperature in all simulations (∼9 per 50 K), probing structural changes associated with enthalpy-entropy compensation. Approaching T opt (∼350 K) from 300 K, this change correlated with a beginning “unzipping” of critical β-sheets. 0 M ionic strength triggered partial denucleation of the C-terminal (known experimentally to be sensitive) at 400 K, suggesting a general salt stabilization effect. In contrast, F− (but not Cl−) specifically impaired secondary structure by formation of strong hydrogen bonds with backbone NH, providing a mechanism for experimentally observed small anion destabilization, potentially remedied by site-directed mutagenesis at critical intrusion sites. N-glycosylation was found to support structural integrity by increasing persistent backbone hydrogen bonds by ∼4 across simulations, mainly via prevention of F− intrusion. Hydrogen-bond loss in distinct loop regions and ends of critical β-sheets suggest potential strategies for laboratory optimization of these industrially important enzymes. PMID:23658618

An MHD variational principle that admits reconnection

NASA Technical Reports Server (NTRS)

Rilee, M. L.; Sudan, R. N.; Pfirsch, D.

1997-01-01

The variational approach of Pfirsch and Sudan's averaged magnetohydrodynamics (MHD) to the stability of a line-tied current layer is summarized. The effect of line-tying on current sheets that might arise in line-tied magnetic flux tubes by estimating the growth rates of a resistive instability using a variational method. The results show that this method provides a potentially new technique to gauge the stability of nearly ideal magnetohydrodynamic systems. The primary implication for the stability of solar coronal structures is that tearing modes are probably constant at work removing magnetic shear from the solar corona.

Structural rearrangement of β-lactoglobulin at different oil-water interfaces and its effect on emulsion stability.

PubMed

Zhai, Jiali; Wooster, Tim J; Hoffmann, Søren V; Lee, Tzong-Hsien; Augustin, Mary Ann; Aguilar, Marie-Isabel

2011-08-02

Understanding the factors that control protein structure and stability at the oil-water interface continues to be a major focus to optimize the formulation of protein-stabilized emulsions. In this study, a combination of synchrotron radiation circular dichroism spectroscopy, front-face fluorescence spectroscopy, and dual polarization interferometry (DPI) was used to characterize the conformation and geometric structure of β-lactoglobulin (β-Lg) upon adsorption to two oil-water interfaces: a hexadecane-water interface and a tricaprylin-water interface. The results show that, upon adsorption to both oil-water interfaces, β-Lg went through a β-sheet to α-helix transition with a corresponding loss of its globular tertiary structure. The degree of conformational change was also a function of the oil phase polarity. The hexadecane oil induced a much higher degree of non-native α-helix compared to the tricaprylin oil. In contrast to the β-Lg conformation in solution, the non-native α-helical-rich conformation of β-Lg at the interface was resistant to further conformational change upon heating. DPI measurements suggest that β-Lg formed a thin dense layer at emulsion droplet surfaces. The effects of high temperature and the presence of salt on these β-Lg emulsions were then investigated by monitoring changes in the ζ-potential and particle size. In the absence of salt, high electrostatic repulsion meant β-Lg-stabilized emulsions were resistant to heating to 90 °C. Adding salt (120 mM NaCl) before or after heating led to emulsion flocculation due to the screening of the electrostatic repulsion between colloidal particles. This study has provided insight into the structural properties of proteins adsorbed at the oil-water interface and has implications in the formulation and production of emulsions stabilized by globular proteins.

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...

Highly sensitive rotation sensing based on orthogonal fiber-optic structures

NASA Astrophysics Data System (ADS)

Yang, Yi; Wang, Zi-nan; Xu, Lian-yu; Wang, Cui-yun; Jia, Lei; Yu, Xiao-qi; Shao, Shan; Li, Zheng-bin

2011-08-01

In traditional fiber-optic gyroscopes (FOG), the polarization state of counter propagating waves is critically controlled, and only the mode polarized along one particular direction survives. This is important for a traditional single mode fiber gyroscope as the requirement of reciprocity. However, there are some fatal defects such as low accuracy and poor bias stability in traditional structures. In this paper, based on the idea of polarization multiplexing, a double-polarization structure is put forward and experimentally studied. In highly birefringent fibers or standard single mode fibers with induced anisotropy, two orthogonal polarization modes can be used at the same time. Therefore, in polarization maintaining fibers (PMF), each pair of counter propagating beams preserve reciprocity within their own polarization state. Two series of sensing results are gotten in the fast and slow axes in PMF. The two sensing results have their own systematic drifts and the correlation of random noise in them is approximately zero. So, beams in fast and slow axes work as two independent and orthogonal gyroscopes. In this way, amount of information is doubled, providing opportunity to eliminate noise and improve sensitivity. Theoretically, this double-polarization structure can achieve a sensitivity of 10-18 deg/h. Computer simulation demonstrates that random noise and systematic drifts are largely reduced in this novel structure. In experiment, a forty-hour stability test targeting the earth's rotation velocity is carried out. Experiment result shows that the orthogonal fiber-optic structure has two big advantages compared with traditional ones. Firstly, the structure gets true value without any bias correction in any axis and even time-varying bias does not affect the acquisition of true value. The unbiasedness makes the structure very attractive when sudden disturbances or temperature drifts existing in working environment. Secondly, the structure lowers bias for more than two orders and enhances bias stability for an order higher (compared with single axis result), achieving a bias stability of 0.01 deg/h. The evidences from all aspects convincingly show that the orthogonal fiber-optic structure is robust against environmental disturbance and material defects, achieving high stability and sensitivity.

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

PubMed

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

2012-05-01

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

Metal Hydride Nanoparticles with Ultrahigh Structural Stability and Hydrogen Storage Activity Derived from Microencapsulated Nanoconfinement.

PubMed

Zhang, Jiguang; Zhu, Yunfeng; Lin, Huaijun; Liu, Yana; Zhang, Yao; Li, Shenyang; Ma, Zhongliang; Li, Liquan

2017-06-01

Metal hydrides (MHs) have recently been designed for hydrogen sensors, switchable mirrors, rechargeable batteries, and other energy-storage and conversion-related applications. The demands of MHs, particular fast hydrogen absorption/desorption kinetics, have brought their sizes to nanoscale. However, the nanostructured MHs generally suffer from surface passivation and low aggregation-resisting structural stability upon absorption/desorption. This study reports a novel strategy named microencapsulated nanoconfinement to realize local synthesis of nano-MHs, which possess ultrahigh structural stability and superior desorption kinetics. Monodispersed Mg 2 NiH 4 single crystal nanoparticles (NPs) are in situ encapsulated on the surface of graphene sheets (GS) through facile gas-solid reactions. This well-defined MgO coating layer with a thickness of ≈3 nm efficiently separates the NPs from each other to prevent aggregation during hydrogen absorption/desorption cycles, leading to excellent thermal and mechanical stability. More interestingly, the MgO layer shows superior gas-selective permeability to prevent further oxidation of Mg 2 NiH 4 meanwhile accessible for hydrogen absorption/desorption. As a result, an extremely low activation energy (31.2 kJ mol -1 ) for the dehydrogenation reaction is achieved. This study provides alternative insights into designing nanosized MHs with both excellent hydrogen storage activity and thermal/mechanical stability exempting surface modification by agents. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advances in methods to characterize ligand-induced ionic lock and rotamer toggle molecular switch in G protein-coupled receptors.

PubMed

Xie, Xiang-Qun; Chowdhury, Ananda

2013-01-01

Structural biology of GPCRs has made significant progress upon recently developed technologies for GPCRs expression/purification and elucidation of GPCRs crystal structures. The crystal structures provide a snapshot of the receptor structural disposition of GPCRs itself or with cocrystallized ligands, and the results are congruent with biophysical and computer modeling studies reported about GPCRs conformational and dynamics flexibility, regulated activation, and the various stabilizing interactions, such as "molecular switches." The molecular switches generally constitute the most conserved domains within a particular GPCR superfamily. Often agonist-induced receptor activation proceeds by the disruption of majority of these interactions, while antagonist and inverse agonist act as blockers and structural stabilizers, respectively. Several elegant studies, particularly for the β2AR, have demonstrated the relationship between ligand structure, receptor conformational changes, and corresponding pharmacological outcomes. Thus, it is of great importance to understand GPCRs activation related to cell signaling pathways. Herein, we summarize the steps to produce functional GPCRs, generate suitably fluorescent labeled GPCRs and the procedure to use that to understand if ligand-induced activation can proceed by activation of the GPCRs via ionic lock switch and/or rotamer toggle switch mechanisms. Such understanding of ligand structure and mechanism of receptor activation will provide great insight toward uncovering newer pathways of GPCR activation and aid in structure-based drug design. Copyright © 2013 Elsevier Inc. All rights reserved.

Structure and stability insights into tumour suppressor p53 evolutionary related proteins.

PubMed

Pagano, Bruno; Jama, Abdullah; Martinez, Pierre; Akanho, Ester; Bui, Tam T T; Drake, Alex F; Fraternali, Franca; Nikolova, Penka V

2013-01-01

The p53 family of genes and their protein products, namely, p53, p63 and p73, have over one billion years of evolutionary history. Advances in computational biology and genomics are enabling studies of the complexities of the molecular evolution of p53 protein family to decipher the underpinnings of key biological conditions spanning from cancer through to various metabolic and developmental disorders and facilitate the design of personalised medicines. However, a complete understanding of the inherent nature of the thermodynamic and structural stability of the p53 protein family is still lacking. This is due, to a degree, to the lack of comprehensive structural information for a large number of homologous proteins and to an incomplete knowledge of the intrinsic factors responsible for their stability and how these might influence function. Here we investigate the thermal stability, secondary structure and folding properties of the DNA-binding domains (DBDs) of a range of proteins from the p53 family using biophysical methods. While the N- and the C-terminal domains of the p53 family show sequence diversity and are normally targets for post-translational modifications and alternative splicing, the central DBD is highly conserved. Together with data obtained from Molecular Dynamics simulations in solution and with structure based homology modelling, our results provide further insights into the molecular properties of evolutionary related p53 proteins. We identify some marked structural differences within the p53 family, which could account for the divergence in biological functions as well as the subtleties manifested in the oligomerization properties of this family.

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.

Thermodynamic insights into 2-thiouridine-enhanced RNA hybridization

PubMed Central

Larsen, Aaron T.; Fahrenbach, Albert C.; Sheng, Jia; Pian, Julia; Szostak, Jack W.

2015-01-01

Nucleobase modifications dramatically alter nucleic acid structure and thermodynamics. 2-thiouridine (s2U) is a modified nucleobase found in tRNAs and known to stabilize U:A base pairs and destabilize U:G wobble pairs. The recently reported crystal structures of s2U-containing RNA duplexes do not entirely explain the mechanisms responsible for the stabilizing effect of s2U or whether this effect is entropic or enthalpic in origin. We present here thermodynamic evaluations of duplex formation using ITC and UV thermal denaturation with RNA duplexes containing internal s2U:A and s2U:U pairs and their native counterparts. These results indicate that s2U stabilizes both duplexes. The stabilizing effect is entropic in origin and likely results from the s2U-induced preorganization of the single-stranded RNA prior to hybridization. The same preorganizing effect is likely responsible for structurally resolving the s2U:U pair-containing duplex into a single conformation with a well-defined H-bond geometry. We also evaluate the effect of s2U on single strand conformation using UV- and CD-monitored thermal denaturation and on nucleoside conformation using 1H NMR spectroscopy, MD and umbrella sampling. These results provide insights into the effects that nucleobase modification has on RNA structure and thermodynamics and inform efforts toward improving both ribozyme-catalyzed and nonenzymatic RNA copying. PMID:26240387

Clusters of isoleucine, leucine, and valine side chains define cores of stability in high-energy states of globular proteins: Sequence determinants of structure and stability.

PubMed

Kathuria, Sagar V; Chan, Yvonne H; Nobrega, R Paul; Özen, Ayşegül; Matthews, C Robert

2016-03-01

Measurements of protection against exchange of main chain amide hydrogens (NH) with solvent hydrogens in globular proteins have provided remarkable insights into the structures of rare high-energy states that populate their folding free-energy surfaces. Lacking, however, has been a unifying theory that rationalizes these high-energy states in terms of the structures and sequences of their resident proteins. The Branched Aliphatic Side Chain (BASiC) hypothesis has been developed to explain the observed patterns of protection in a pair of TIM barrel proteins. This hypothesis supposes that the side chains of isoleucine, leucine, and valine (ILV) residues often form large hydrophobic clusters that very effectively impede the penetration of water to their underlying hydrogen bond networks and, thereby, enhance the protection against solvent exchange. The linkage between the secondary and tertiary structures enables these ILV clusters to serve as cores of stability in high-energy partially folded states. Statistically significant correlations between the locations of large ILV clusters in native conformations and strong protection against exchange for a variety of motifs reported in the literature support the generality of the BASiC hypothesis. The results also illustrate the necessity to elaborate this simple hypothesis to account for the roles of adjacent hydrocarbon moieties in defining stability cores of partially folded states along folding reaction coordinates. © 2015 The Protein Society.

Transport, fate, and long-term impacts of metal oxide nanoparticles on the stability of an anaerobic methanogenic system with anaerobic granular sludge.

PubMed

Li, Huiting; Cui, Fuyi; Liu, Zhiquan; Li, Dapeng

2017-06-01

The fate and long-term effect of different metal oxide (TiO 2 , CuO and ZnO) nanoparticles (NPs) on anaerobic granular sludge (AGS) was evaluated in an anaerobic methanogenic system. Operation stability and structural characteristics of the granules were compared, the metabolism changes in the microbial community were quantified, and NPs fate were investigated. CuO NPs had greatest toxic effect on AGS after extended exposure, whereas ZnO NPs benefited methanogenesis temporarily (no more than 5d). The inhibition on AGS caused by NPs varied due to the unique structure of AGS and different toxic mechanism. Structural changes of AGS provided new evidence that tested NPs have different toxicity. Copyright © 2017 Elsevier Ltd. All rights reserved.

First principles studies of structure stability and lithium intercalation of ZnCo2 O4

NASA Astrophysics Data System (ADS)

Zhang, Yanning; Liu, Weiwei; Beijing Computational Science Research Center Team

Among the metal oxides, which are the most widely investigated alternative anodes for use in lithium ion batteries (LIBs), binary and ternary transition metal oxides have received special attention due to their high capacity values. ZnCo2O4 is a promising candidate as anode for LIB, and one can expect a total capacity corresponding to 7.0 - 8.33 mol of recyclable Li per mole of ZnCo2O4. Here we studied the structural stability, electronic properties, lithium intercalation and diffusion barrier of ZnCo2O4 through density functional calculations. The calculated structural and energetic parameters are comparable with experiments. Our theoretical studies provide insights in understanding the mechanism of lithium ion displacement reactions in this ternary metal oxide.

Nighttime atmospheric stability changes and their effects on the temporal intensity of a mesoscale convective complex

NASA Technical Reports Server (NTRS)

Hovis, Jeffrey S.; Brundidge, Kenneth C.

1987-01-01

A method of interpolating atmospheric soundings while reducing the errors associated with simple time interpolation was developed. The purpose of this was to provide a means to determine atmospheric stability at times between standard soundings and to relate changes in stability to intensity changes in an MCC. Four MCC cases were chosen for study with this method with four stability indices being included. The discussion centers on three aspects for each stability parameter examined: the stability field in the vicinity of the storm and its changes in structure and magnitude during the lifetime of the storm, the average stability within the storm boundary as a function of time and its relation to storm intensity, and the apparent flux of stability parameter into the storm as a consequence of low-level storm relative flow. It was found that the results differed among the four stability parameters, sometimes in a conflicting fashion. Thus, an interpolation of how the storm intensity is related to the changing environmental stability depends upon the particular index utilized. Some explanation for this problem is offered.

Torsional Restraint Problem of Steel Cold-Formed Beams Restrained By Planar Members

NASA Astrophysics Data System (ADS)

Balázs, Ivan; Melcher, Jindřich; Pešek, Ondřej

2017-10-01

The effect of continuous or discrete lateral and torsional restraints of metal thinwalled members along their spans can positively influence their buckling resistance and thus contribute to more economical structural design. The prevention of displacement and rotation of the cross-section results in stabilization of the member. The restraints can practically be provided e.g. by planar members of cladding supported by metal members (purlins, girts). The rate of stabilization of a member can be quantified using values of shear and rotational stiffness provided by the adjacent planar members. While the lateral restraint effected by certain shear stiffness can be often considered as sufficient, the complete torsional restraint can be safely considered in some practical cases only. Otherwise the values of the appropriate rotational stiffness provided by adjacent planar members may not be satisfactory to ensure full torsional restraint and only incomplete restraint is available. Its verification should be performed using theoretical and experimental analyses. The paper focuses on problem of steel thin-walled coldformed beams stabilized by planar members and investigates the effect of the magnitude of the rotational stiffness provided by the planar members on the resistance of the steel members. Cold-formed steel beams supporting planar members of cladding are considered. Full lateral restraint and incomplete torsional restraint are assumed. Numerical analyses performed using a finite element method software indicate considerable influence of the torsional restraint on the buckling resistance of a steel thin-walled member. Utilization of the torsional restraint in the frame of sizing of a stabilized beam can result in more efficient structural design. The paper quantifies this effect for some selected cases and summarizes results of numerical analysis.

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

NASA Astrophysics Data System (ADS)

Herbrik, Marlene; Kokkotas, Kostas D.

2017-04-01

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

Stabilization of Human Serum Albumin by the Binding of Phycocyanobilin, a Bioactive Chromophore of Blue-Green Alga Spirulina: Molecular Dynamics and Experimental Study

PubMed Central

Stanic-Vucinic, Dragana; Nikolic, Milan; Milcic, Milos; Cirkovic Velickovic, Tanja

2016-01-01

Phycocyanobilin (PCB) binds with high affinity (2.2 x 106 M-1 at 25°C) to human serum albumin (HSA) at sites located in IB and IIA subdomains. The aim of this study was to examine effects of PCB binding on protein conformation and stability. Using 300 ns molecular dynamics (MD) simulations, UV-VIS spectrophotometry, CD, FT-IR, spectrofluorimetry, thermal denaturation and susceptibility to trypsin digestion, we studied the effects of PCB binding on the stability and rigidity of HSA, as well as the conformational changes in PCB itself upon binding to the protein. MD simulation results demonstrated that HSA with PCB bound at any of the two sites showed greater rigidity and lower overall and individual domain flexibility compared to free HSA. Experimental data demonstrated an increase in the α-helical content of the protein and thermal and proteolytic stability upon ligand binding. PCB bound to HSA undergoes a conformational change to a more elongated conformation in the binding pockets of HSA. PCB binding to HSA stabilizes the structure of this flexible transport protein, making it more thermostable and resistant to proteolysis. The results from this work explain at molecular level, conformational changes and stabilization of HSA structure upon ligand binding. The resultant increased thermal and proteolytic stability of HSA may provide greater longevity to HSA in plasma. PMID:27959940

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

PubMed Central

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

2016-01-01

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

Domain swapping dissection in Thermotoga maritima arginine binding protein: How structural flexibility may compensate destabilization.

PubMed

Smaldone, Giovanni; Berisio, Rita; Balasco, Nicole; D'Auria, Sabato; Vitagliano, Luigi; Ruggiero, Alessia

2018-05-31

Thermotoga maritima Arginine Binding Protein (TmArgBP) is a valuable candidate for arginine biosensing in diagnostics. This protein is endowed with unusual structural properties that include an extraordinary thermal/chemical stability, a domain swapped structure that undergoes large tertiary and quaternary structural transition, and the ability to form non-canonical oligomeric species. As the intrinsic stability of TmArgBP allows for extensive protein manipulations, we here dissected its structure in two parts: its main body deprived of the swapping fragment (TmArgBP 20-233 ) and the C-terminal peptide corresponding to the helical swapping element. Both elements have been characterized independently or in combination using a repertoire of biophysical/structural techniques. Present investigations clearly indicate that TmArgBP 20-233 represents a better scaffold for arginine sensing compared to the wild-type protein. Moreover, our data demonstrate that the ligand-free and the ligand-bound forms respond very differently to this helix deletion. This drastic perturbation has an important impact on the ligand-bound form of TmArgBP 20-233 stability whereas it barely affects its ligand-free state. The crystallographic structures of these forms provide a rationale to this puzzling observation. Indeed, the arginine-bound state is very rigid and virtually unchanged upon protein truncation. On the other hand, the flexible ligand-free TmArgBP 20-233 is able to adopt a novel state as a consequence of the helix deletion. Therefore, the flexibility of the ligand-free form endows this state with a remarkable robustness upon severe perturbations. In this scenario, TmArgBP dissection highlights an intriguing connection between destabilizing/stabilizing effects and the overall flexibility that could operate also in other proteins. Copyright © 2018 Elsevier B.V. All rights reserved.

Stabilization of the predominant disease-causing aldolase variant (A149P) with zwitterionic osmolytes.

PubMed

Stopa, Jack D; Chandani, Sushil; Tolan, Dean R

2011-02-08

Hereditary fructose intolerance (HFI) is a disease of carbohydrate metabolism that can result in hyperuricemia, hypoglycemia, liver and kidney failure, coma, and death. Currently, the only treatment for HFI is a strict fructose-free diet. HFI arises from aldolase B deficiency, and the most predominant HFI mutation is an alanine to proline substitution at position 149 (A149P). The resulting aldolase B with the A149P substitution (AP-aldolase) has activity that is <100-fold that of the wild type. The X-ray crystal structure of AP-aldolase at both 4 and 18 °C reveals disordered adjacent loops of the (α/β)(8) fold centered around the substitution, which leads to a dimeric structure as opposed to the wild-type tetramer. The effects of osmolytes were tested for restoration of structure and function. An initial screen of osmolytes (glycerol, sucrose, polyethylene glycol, 2,4-methylpentanediol, glutamic acid, arginine, glycine, proline, betaine, sarcosine, and trimethylamine N-oxide) reveals that glycine, along with similarly structured compounds, betaine and sarcosine, protects AP-aldolase structure and activity from thermal inactivation. The concentration and functional moieties required for thermal protection show a zwitterion requirement. The effects of osmolytes in restoring structure and function of AP-aldolase are described. Testing of zwitterionic osmolytes of increasing size and decreasing fractional polar surface area suggests that osmolyte-mediated AP-aldolase stabilization occurs neither primarily through excluded volume effects nor through transfer free energy effects. These data suggest that AP-aldolase is stabilized by binding to the native structure, and they provide a foundation for developing stabilizing compounds for potential therapeutics for HFI.

Soft interactions and volume exclusion by polymeric crowders can stabilize or destabilize transient structure in disordered proteins depending on polymer concentration.

PubMed

Rusinga, Farai I; Weis, David D

2017-08-01

The effects of macromolecular crowding on the transient structure of intrinsically disordered proteins is not well-understood. Crowding by biological molecules inside cells could modulate transient structure and alter IDP function. Volume exclusion theory and observations of structured proteins suggest that IDP transient structure would be stabilized by macromolecular crowding. Amide hydrogen exchange (HX) of IDPs in highly concentrated polymer solutions would provide valuable insights into IDP transient structure under crowded conditions. Here, we have used mass spectrometry to measure HX by a transiently helical random coil domain of the activator of thyroid and retinoid receptor (ACTR) in solutions containing 300 g L -1 and 400 g L -1 of Ficoll, a synthetic polysaccharide, using a recently-developed strong cation exchange-based cleanup method [Rusinga, et al., Anal Chem 2017;89:1275-1282]. Transiently helical regions of ACTR exchanged faster in 300 g L -1 Ficoll than in dilute buffer. In contrast, one transient helix exchanged more slowly in 400 g L -1 Ficoll. Nonspecific interactions destabilize ACTR helicity in 300 g L -1 Ficoll because ACTR engages with the Ficoll polymer mesh. In contrast, 400 g L -1 Ficoll is a semi-dilute solution where ACTR cannot engage the Ficoll mesh. At this higher concentration, volume exclusion stabilizes ACTR helicity because ACTR is compacted in interstitial spaces between Ficoll molecules. Our results suggest that the interplay between nonspecific interactions and volume exclusion in different cellular compartments could modulate IDP function by altering the stability of IDP transient structures. Proteins 2017; 85:1468-1479. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Nonequilibrium stabilization of an RNA/protein droplet emulsion by nuclear actin

NASA Astrophysics Data System (ADS)

Brangwynne, Clifford

2013-03-01

Actin plays a structural role in the cytoplasm. However, actin takes on new functions and structures in the nucleus that are poorly understood. The nuclei of the large oocytes of the frog X. laevisspecifically accumulate actin to reach high concentrations; however, it remains unclear if this actin polymerizes into a network, and what, if any, structural role such an actin network might play. Here, we use microrheological and confocal imaging techniques to probe the local architecture and mechanics of the nucleus. Our data show that actin forms a weak network that spatially organizes the nucleus by kinetically stabilizing embedded liquid-like RNA/protein bodies which are important for cell growth. In actin-disrupted nuclei this RNA/protein droplet emulsion is destabilized leading to homotypic coalescence into single large droplets. Our data provide intriguing new insights into why large cell nuclei require an actin-based structural scaffold.

Enhanced stabilization of collagen by furfural.

PubMed

Lakra, Rachita; Kiran, Manikantan Syamala; Usha, Ramamoorthy; Mohan, Ranganathan; Sundaresan, Raja; Korrapati, Purna Sai

2014-04-01

Furfural (2-furancarboxaldehyde), a product derived from plant pentosans, has been investigated for its interaction with collagen. Introduction of furfural during fibril formation enhanced the thermal and mechanical stability of collagen. Collagen films treated with furfural exhibited higher denaturation temperature (Td) (p<0.04) and showed a 3-fold increase in Young's modulus (p<0.04) at higher concentration. Furfural and furfural treated collagen films did not have any cytotoxic effect. Rheological characterization showed an increase in shear stress and shear viscosity with increasing shear rate for treated collagen. Circular dichroism (CD) studies indicated that the furfural did not have any impact on triple helical structure of collagen. Scanning electron microscopy (SEM) of furfural treated collagen exhibited small sized porous structure in comparison with untreated collagen. Thus this study provides an alternate ecologically safe crosslinking agent for improving the stability of collagen for biomedical and industrial applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Laccase-based biocathodes: Comparison of chitosan and Nafion.

PubMed

El Ichi-Ribault, S; Zebda, A; Laaroussi, A; Reverdy-Bruas, N; Chaussy, D; Belgacem, M N; Suherman, A L; Cinquin, P; Martin, D K

2016-09-21

Chitosan and Nafion(®) are both reported as interesting polymers to be integrated into the structure of 3D electrodes for biofuel cells. Their advantage is mainly related to their chemical properties, which have a positive impact on the stability of electrodes such as the laccase-based biocathode. For optimal function in implantable applications the biocathode requires coating with a biocompatible semi-permeable membrane that is designed to prevent the loss of enzyme activity and to protect the structure of the biocathode. Since such membranes are integrated into the electrodes ultimately implanted, they must be fully characterized to demonstrate that there is no interference with the performance of the electrode. In the present study, we demonstrate that chitosan provides superior stability compared with Nafion(®) and should be considered as an optimum solution to enhance the biocompatibility and the stability of 3D bioelectrodes. Copyright © 2016 Elsevier B.V. All rights reserved.

Does 1-Allyl-3-methylimidazolium chloride Act as a Biocompatible Solvent for Stem Bromelain?

PubMed

Jha, Indrani; Bisht, Meena; Venkatesu, Pannuru

2016-06-30

The broader scope of ILs in chemical sciences particularly in pharmaceutical, bioanalytical and many more applications is increasing day by day. Hitherto, a very less amount of research is available in the depiction of conformational stability, activity, and thermal stability of enzymes in the presence of ILs. In the present study, the perturbation in the structure, stability, and activity of stem bromelain (BM) has been observed in the presence of 1-allyl-3-methylimidazolium chloride ([Amim][Cl]) using various techniques. This is the first report in which the influence of [Amim][Cl] has been studied on the enzyme BM. Fluorescence spectroscopy has been utilized to map out the changes in the environment around tryptophan (Trp) residues of BM and also to discuss the variations in the thermal stability of BM as an outcome of its interaction with the IL at different concentrations. Further, the work delineates the denaturing effect of high concentration of IL on enzyme structure and activity. It dictates the fact that low concentrations (0.01-0.10 M) of [Amim][Cl] are only changing the structural arrangement of the protein without having harsh consequences on its activity and stability. However, high concentrations of IL proved to be totally devastating for both activity and stability of BM. The observed decrease in the stability of BM at high concentration may be due to the combined effect of cation and anion interactions with the protein residues. The present work is successful in dictating the probable mechanism of interaction between BM and [Amim][Cl]. These results can prove to be fruitful in the studies of enzymes in aqueous IL systems since the used IL is thermally stable and nonvolatile in nature thereby providing a pathway of alteration in the activity of enzymes in potentially green systems.

Synthesis, reactivity and application studies for different biolubricants

PubMed Central

2014-01-01

Vegetable oils have different unique properties owing to their unique chemical structure. Vegetable oils have a greater ability to lubricate and have higher viscosity indices. Therefore, they are being more closely examined as base oil for biolubricants and functional fluids. In spite of their many advantages, vegetable oils suffer from two major drawbacks of inadequate oxidative stability and poor low-temperature properties, which hinder their utilization as biolubricant base oils. Transforming alkene groups in fatty acids to other stable functional groups could improve the oxidative stability, whereas reducing structural uniformity of the oil by attaching alkyl side chains could improve the low-temperature performance. In that light, the epoxidation of unsaturated fatty acids is very interesting as it can provide diverse side chains arising from the mono- or di-epoxidation of the unsaturated fatty acid. Oxirane ring opening by an acid-catalyzed reaction with a suitable reagent provides interesting polyfunctional compounds. PMID:24612780

Space Shuttle Earth Observation sensors pointing and stabilization requirements study

NASA Technical Reports Server (NTRS)

1976-01-01

The shuttle orbiter inertial measurement unit (IMU), located in the orbiter cabin, is used to supply inertial attitude reference signals; and, in conjunction with the onboard navigation system, can provide a pointing capability of the navigation base accurate to within plus or minus 0.5 deg for earth viewing missions. This pointing accuracy can degrade to approximately plus or minus 2.0 deg for payloads located in the aft bay due to structural flexure of the shuttle vehicle, payload structural and mounting misalignments, and calibration errors with respect to the navigation base. Drawbacks to obtaining pointing accuracy by using the orbiter RCS jets are discussed. Supplemental electromechanical pointing systems are developed to provide independent pointing for individual sensors, or sensor groupings. The missions considered and the sensors required for these missions and the parameters of each sensor are described. Assumptions made to derive pointing and stabilization requirements are delineated.

High-resolution of particle contacts via fluorophore exclusion in deep-imaging of jammed colloidal packings

NASA Astrophysics Data System (ADS)

Kyeyune-Nyombi, Eru; Morone, Flaviano; Liu, Wenwei; Li, Shuiqing; Gilchrist, M. Lane; Makse, Hernán A.

2018-01-01

Understanding the structural properties of random packings of jammed colloids requires an unprecedented high-resolution determination of the contact network providing mechanical stability to the packing. Here, we address the determination of the contact network by a novel strategy based on fluorophore signal exclusion of quantum dot nanoparticles from the contact points. We use fluorescence labeling schemes on particles inspired by biology and biointerface science in conjunction with fluorophore exclusion at the contact region. The method provides high-resolution contact network data that allows us to measure structural properties of the colloidal packing near marginal stability. We determine scaling laws of force distributions, soft modes, correlation functions, coordination number and free volume that define the universality class of jammed colloidal packings and can be compared with theoretical predictions. The contact detection method opens up further experimental testing at the interface of jamming and glass physics.

Tertiary and Quaternary Ammonium-Phosphate Ionic Liquids as Lubricant Additives

DOE PAGES

Barnhill, William C.; Luo, Huimin; Meyer, III, Harry M; ...

2016-06-23

In this work we investigated the feasibility of five quaternary (aprotic) and four tertiary (protic) ammonium ionic liquids (ILs) with an identical organophosphate anion as lubricant antiwear additives. Viscosity, oil solubility, thermal stability, and corrosivity of the candidate ILs were characterized and correlated to the molecular structure. The protic group exhibits higher oil solubility than the aprotic group, and longer alkyl chains seem to provide better oil solubility and higher thermal stability. Selected ILs were applied as oil additives in steel-cast iron tribological tests and demonstrated promising anti-scuffing and anti-wear functionality. The thickness, nanostructure, coverage and composition of the tribofilmmore » formed by the besting performing IL were revealed by surface characterization for mechanistic understanding of the tribochemical interactions between the IL and metal surface. Results provide fundamental insights of the correlations among the molecular structure, physiochemical properties and lubricating performance for ammonium-phosphate ILs.« less

Tertiary and Quaternary Ammonium-Phosphate Ionic Liquids as Lubricant Additives

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

Barnhill, William C.; Luo, Huimin; Meyer, III, Harry M

In this work we investigated the feasibility of five quaternary (aprotic) and four tertiary (protic) ammonium ionic liquids (ILs) with an identical organophosphate anion as lubricant antiwear additives. Viscosity, oil solubility, thermal stability, and corrosivity of the candidate ILs were characterized and correlated to the molecular structure. The protic group exhibits higher oil solubility than the aprotic group, and longer alkyl chains seem to provide better oil solubility and higher thermal stability. Selected ILs were applied as oil additives in steel-cast iron tribological tests and demonstrated promising anti-scuffing and anti-wear functionality. The thickness, nanostructure, coverage and composition of the tribofilmmore » formed by the besting performing IL were revealed by surface characterization for mechanistic understanding of the tribochemical interactions between the IL and metal surface. Results provide fundamental insights of the correlations among the molecular structure, physiochemical properties and lubricating performance for ammonium-phosphate ILs.« less

Structural insights into biased G protein-coupled receptor signaling revealed by fluorescence spectroscopy.

PubMed

Rahmeh, Rita; Damian, Marjorie; Cottet, Martin; Orcel, Hélène; Mendre, Christiane; Durroux, Thierry; Sharma, K Shivaji; Durand, Grégory; Pucci, Bernard; Trinquet, Eric; Zwier, Jurriaan M; Deupi, Xavier; Bron, Patrick; Banères, Jean-Louis; Mouillac, Bernard; Granier, Sébastien

2012-04-24

G protein-coupled receptors (GPCRs) are seven-transmembrane proteins that mediate most cellular responses to hormones and neurotransmitters, representing the largest group of therapeutic targets. Recent studies show that some GPCRs signal through both G protein and arrestin pathways in a ligand-specific manner. Ligands that direct signaling through a specific pathway are known as biased ligands. The arginine-vasopressin type 2 receptor (V2R), a prototypical peptide-activated GPCR, is an ideal model system to investigate the structural basis of biased signaling. Although the native hormone arginine-vasopressin leads to activation of both the stimulatory G protein (Gs) for the adenylyl cyclase and arrestin pathways, synthetic ligands exhibit highly biased signaling through either Gs alone or arrestin alone. We used purified V2R stabilized in neutral amphipols and developed fluorescence-based assays to investigate the structural basis of biased signaling for the V2R. Our studies demonstrate that the Gs-biased agonist stabilizes a conformation that is distinct from that stabilized by the arrestin-biased agonists. This study provides unique insights into the structural mechanisms of GPCR activation by biased ligands that may be relevant to the design of pathway-biased drugs.

Load Sharing Among Collateral Ligaments, Articular Surfaces, and the Tibial Post in Constrained Condylar Knee Arthroplasty.

PubMed

Wang, Xiaonan; Malik, Aamer; Bartel, Donald L; Wright, Timothy M; Padgett, Douglas E

2016-08-01

The normal knee joint maintains stable motion during activities of daily living. After total knee arthroplasty (TKA), stability is achieved by the conformity of the bearing surfaces of the implant components, ligaments, and constraint structures incorporated in the implant design. The large, rectangular tibial post in constrained condylar knee (CCK) arthroplasty, often used in revision surgery, provides added stability, but increases susceptibility to polyethylene wear as it contacts the intercondylar box on the femoral component. We examined coronal plane stability to understand the relative contributions of the mechanisms that act to stabilize the CCK knee under varus-valgus loading, namely, load distribution between the medial and lateral condyles, contact of the tibial post with the femoral intercondylar box, and elongation of the collateral ligaments. A robot testing system was used to determine the joint stability in human cadaveric knees as described by the moment versus angular rotation behavior under varus-valgus moments at 0 deg, 30 deg, and 90 deg of flexion. The angular rotation of the CCK knee in response to the physiological moments was limited to ≤1.5 deg. The primary stabilizing mechanism was the redistribution of the contact force on the bearing surfaces. Contact between the tibial post and the femoral box provided a secondary stabilizing mechanism after lift-off of a condyle had occurred. Collateral ligaments provide limited stability because little ligament elongation occurred under such small angular rotations. Compressive loads applied across the knee joint, such as would occur with the application of muscle forces, enhanced the ability of the bearing surfaces to provide resisting internal varus-valgus moment and, thus, reduced the exposure of the tibial post to the external varus-valgus loads. Our results suggest that the CCK stability can be refined by considering both the geometry of the bearing surfaces and the contacting geometry between the tibial post and femoral box.

Newly-recognized roles of factor XIII in thrombosis

PubMed Central

Byrnes, James R.; Wolberg, Alisa S.

2017-01-01

Arterial and venous thrombosis are major contributors to coagulation-associated morbidity and mortality. Greater understanding of mechanisms leading to thrombus formation and stability is expected to lead to improved treatment strategies. Factor XIII (FXIII) is a transglutaminase found in plasma and platelets. During thrombosis, activated FXIII crosslinks fibrin and promotes thrombus stability. Recent studies have provided new information about FXIII activity during coagulation and its effects on clot composition and function. These findings reveal newly-recognized roles for FXIII in thrombosis. Herein, we review published literature on FXIII biology and effects on fibrin structure and stability, epidemiologic data associating FXIII with thrombosis, and evidence from animal models indicating FXIII has an essential role in determining thrombus stability, composition, and size. PMID:27056150

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

PubMed

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

2017-08-13

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

Entropic formulation for the protein folding process: Hydrophobic stability correlates with folding rates

NASA Astrophysics Data System (ADS)

Dal Molin, J. P.; Caliri, A.

2018-01-01

Here we focus on the conformational search for the native structure when it is ruled by the hydrophobic effect and steric specificities coming from amino acids. Our main tool of investigation is a 3D lattice model provided by a ten-letter alphabet, the stereochemical model. This minimalist model was conceived for Monte Carlo (MC) simulations when one keeps in mind the kinetic behavior of protein-like chains in solution. We have three central goals here. The first one is to characterize the folding time (τ) by two distinct sampling methods, so we present two sets of 103 MC simulations for a fast protein-like sequence. The resulting sets of characteristic folding times, τ and τq were obtained by the application of the standard Metropolis algorithm (MA), as well as by an enhanced algorithm (Mq A). The finding for τq shows two things: (i) the chain-solvent hydrophobic interactions {hk } plus a set of inter-residues steric constraints {ci,j } are able to emulate the conformational search for the native structure. For each one of the 103MC performed simulations, the target is always found within a finite time window; (ii) the ratio τq / τ ≅ 1 / 10 suggests that the effect of local thermal fluctuations, encompassed by the Tsallis weight, provides to the chain an innate efficiency to escape from energetic and steric traps. We performed additional MC simulations with variations of our design rule to attest this first result, both algorithms the MA and the Mq A were applied to a restricted set of targets, a physical insight is provided. Our second finding was obtained by a set of 600 independent MC simulations, only performed with the Mq A applied to an extended set of 200 representative targets, our native structures. The results show how structural patterns should modulate τq, which cover four orders of magnitude; this finding is our second goal. The third, and last result, was obtained with a special kind of simulation performed with the purpose to explore a possible connection between the hydrophobic component of protein stability and the native structural topology. We simulated those same 200 targets again with the Mq A, only. However, this time we evaluated the relative frequency {ϕq } in which each target visits its corresponding native structure along an appropriate simulation time. Due to the presence of the hydrophobic effect in our approach we obtained a strong correlation between the stability and the folding rate (R = 0 . 85). So, as faster a sequence found its target, as larger is the hydrophobic component of its stability. The strong correlation fulfills our last goal. This final finding suggests that the hydrophobic effect could not be a general stabilizing factor for proteins.

Multimetallic nanoparticle catalysts with enhanced electrooxidation

DOEpatents

Sun, Shouheng; Zhang, Sen; Zhu, Huiyuan; Guo, Shaojun

2015-07-28

A new structure-control strategy to optimize nanoparticle catalysis is provided. The presence of Au in FePtAu facilitates FePt structure transformation from chemically disordered face centered cubic (fcc) structure to chemically ordered face centered tetragonal (fct) structure, and further promotes formic acid oxidation reaction (FAOR). The fct-FePtAu nanoparticles show high CO poisoning resistance, achieve mass activity as high as about 2810 mA/mg Pt, and retain greater than 90% activity after a 13 hour stability test.

Low-carbon martensitic steels. Alloying and properties

NASA Astrophysics Data System (ADS)

Kleiner, L. M.; Shatsov, A. A.; Larinin, D. M.

2011-03-01

Requirements on the structure of a steel with structural strength and a set of characteristics higher than those of medium-carbon steels with a structure of tempered sorbite are formulated. Principles for choosing compositions for process-adaptable low-carbon martensitic steels are presented. The combination of carbon and alloying elements providing high stability of austenite in the ranges of normal and intermediate transformations is determined, which makes it possible to obtain lath martensite in slow cooling.

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.

Nanocarbon networks for advanced rechargeable lithium batteries.

PubMed

Xin, Sen; Guo, Yu-Guo; Wan, Li-Jun

2012-10-16

Carbon is one of the essential elements in energy storage. In rechargeable lithium batteries, researchers have considered many types of nanostructured carbons, such as carbon nanoparticles, carbon nanotubes, graphene, and nanoporous carbon, as anode materials and, especially, as key components for building advanced composite electrode materials. Nanocarbons can form efficient three-dimensional conducting networks that improve the performance of electrode materials suffering from the limited kinetics of lithium storage. Although the porous structure guarantees a fast migration of Li ions, the nanocarbon network can serve as an effective matrix for dispersing the active materials to prevent them from agglomerating. The nanocarbon network also affords an efficient electron pathway to provide better electrical contacts. Because of their structural stability and flexibility, nanocarbon networks can alleviate the stress and volume changes that occur in active materials during the Li insertion/extraction process. Through the elegant design of hierarchical electrode materials with nanocarbon networks, researchers can improve both the kinetic performance and the structural stability of the electrode material, which leads to optimal battery capacity, cycling stability, and rate capability. This Account summarizes recent progress in the structural design, chemical synthesis, and characterization of the electrochemical properties of nanocarbon networks for Li-ion batteries. In such systems, storage occurs primarily in the non-carbon components, while carbon acts as the conductor and as the structural buffer. We emphasize representative nanocarbon networks including those that use carbon nanotubes and graphene. We discuss the role of carbon in enhancing the performance of various electrode materials in areas such as Li storage, Li ion and electron transport, and structural stability during cycling. We especially highlight the use of graphene to construct the carbon conducting network for alloy anodes, such as Si and Ge, to accelerate electron transport, alleviate volume change, and prevent the agglomeration of active nanoparticles. Finally, we describe the power of nanocarbon networks for the next generation rechargeable lithium batteries, including Li-S, Li-O(2), and Li-organic batteries, and provide insights into the design of ideal nanocarbon networks for these devices. In addition, we address the ways in which nanocarbon networks can expand the applications of rechargeable lithium batteries into the emerging fields of stationary energy storage and transportation.

Picometer resolution interferometric characterization of the dimensional stability of zero CTE CFRP

NASA Astrophysics Data System (ADS)

Cordero Machado, Jorge; Heinrich, Thomas; Schuldt, Thilo; Gohlke, Martin; Lucarelli, Stefano; Weise, Dennis; Johann, Ulrich; Peters, Achim; Braxmaier, Claus

2008-07-01

Highly stable but lightweight structural materials are essential for the realization of spaceborne optical instruments, for example telescopes. In terms of optical performance, usually tight tolerances on the absolute spacing between telescope mirrors have to be maintained from integration on ground to operation in final orbit. Furthermore, a certain stability of the telescope structure must typically be ensured in the measurement band. Particular challenging requirements have to be met for the LISA Mission (Laser Interferometer Space Antenna), where the spacing between primary and secondary mirror must be stable to a few picometers. Only few materials offer sufficient thermal stability to provide such performance. Candidates are for example Zerodur and Carbon-Fiber Reinforced Plastic (CFRP), where the latter is preferred in terms of mechanical stiffness and robustness. We are currently investigating the suitability of CFRP with respect to the LISA requirements by characterization of its dimensional stability with heterodyne laser interferometry. The special, highly symmetric interferometer setup offers a noise level of 2 pm/√Hz at 0.1Hz and above, and therefore represents a unique tool for this purpose. Various procedures for the determination of the coefficient of thermal expansion (CTE) have been investigated, both on a test sample with negative CTE, as well as on a CFRP tube specifically tuned to provide a theoretical zero expansion in the axial dimension.

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.

Some observations of a sheared Rayleigh-Taylor/Benard instability

NASA Technical Reports Server (NTRS)

Humphrey, J. A. C.; Marcus, D. L.

1987-01-01

An account is provided of preliminary flow visualization observations made in an unstably stratified flow with shear superimposed. The structures observed appear to be the superposition of a Rayleigh-Taylor/Benard instability and a Kelvin-Helmholtz instability. Aside from its intrinsic fundamental value, the study of these structures is of special interest to theoreticians developing nonlinear stability calculation methodologies.

Geostrophic Vortex Dynamics

DTIC Science & Technology

1988-10-01

Generalized Kirchhoff Vortices 176 B. The 2-Level Rankine Vortex: Critical Points & Stability 181 C. Tripolar Coherent Euler Vortices 186 7...spontaneously in spectral simulations. One such example is provided by the tripolar vortex structureE which will be examined in detail in Chapter 6. It...of the tripolar coherent vortex structures that have recently been observed in very high resolution numerical simulations of two- dimensional

Stability of mixed time integration schemes for transient thermal analysis

NASA Technical Reports Server (NTRS)

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

1982-01-01

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

Fetal bovine serum influences the stability and bioactivity of resveratrol analogues: A polyphenol-protein interaction approach.

PubMed

Tang, Fen; Xie, Yixi; Cao, Hui; Yang, Hua; Chen, Xiaoqing; Xiao, Jianbo

2017-03-15

Fetal bovine serum (FBS) is a universal growth supplement of cell and tissue culture media. Herein, the influences of FBS on the stability and antioxidant activity of 21 resveratrol analogues were investigated using a polyphenol-protein interaction approach. The structure-stability relationships of resveratrol analogues in FBS showed a clear decrease in the stability of hydroxylated resveratrol analogues in the order: resorcinol-type>pyrogallol-type>catechol-type. The glycosylation and methoxylation of resveratrol analogues enhanced their stability. A linear relationship between the stability of resveratrol analogues in FBS and the affinity of resveratrol analogues-FBS interaction was found. The oxidation process is not the only factor governing the stability of resveratrol analogues in FBS. These results facilitated the insightful investigation of the role of polyphenol-protein interactions in serum, thereby providing some fundamental clues for future clinical research and pharmacological studies on natural small molecules. Copyright © 2016 Elsevier Ltd. All rights reserved.

Robust controller design for flexible structures using normalized coprime factor plant descriptions

NASA Technical Reports Server (NTRS)

Armstrong, Ernest S.

1993-01-01

Stabilization is a fundamental requirement in the design of feedback compensators for flexible structures. The search for the largest neighborhood around a given design plant for which a single controller produces closed-loop stability can be formulated as an H(sub infinity) control problem. The use of normalized coprime factor plant descriptions, in which the plant perturbations are defined as additive modifications to the coprime factors, leads to a closed-form expression for the maximum neighborhood boundary allowing optimal and suboptimal H(sub infinity) compensators to be computed directly without the usual gamma iteration. A summary of the theory on robust stabilization using normalized coprime factor plant descriptions is presented, and the application of the theory to the computation of robustly stable compensators for the phase version of the Control-Structures Interaction (CSI) Evolutionary Model is described. Results from the application indicate that the suboptimal version of the theory has the potential of providing the bases for the computation of low-authority compensators that are robustly stable to expected variations in design model parameters and additive unmodeled dynamics.

An existence criterion for low-dimensional materials

NASA Astrophysics Data System (ADS)

Chen, Jiapeng; Wang, Biao; Hu, Yangfan

2017-10-01

The discovery of graphene and other two-dimensional (2-D) materials has stimulated a general interest in low-dimensional (low-D) materials. Whereas long time ago, Peierls (1935) and Landau's (1937) theoretical work demonstrated that any one- and two-dimensional materials could not exist in any finite temperature environment. Then, two basic issues became a central concern for many researchers: How can stable low-D materials exist? What kind of low-D materials are stable? Here, we establish an energy stability criterion for low-D materials, which seeks to provide a clear answer to these questions. For a certain kind of element, the stability of its specific low-D structure is determined by several derivatives of its interatomic potential. This atomistic-based approach is then applied to study any straight/planar, low-D, equal-bond-length elemental materials. We found that 1-D monatomic chains, 2-D honeycomb lattices, square lattices, and triangular lattices are the only four permissible structures, and the stability of these structures can only be understood by assuming multi-body interatomic potentials. Using this approach, the stable existence of graphene, silicene and germanene can be explained.

Development of an Efficient G‐Quadruplex‐Stabilised Thrombin‐Binding Aptamer Containing a Three‐Carbon Spacer Molecule

PubMed Central

Aaldering, Lukas J.; Poongavanam, Vasanthanathan; Langkjær, Niels; Murugan, N. Arul; Jørgensen, Per Trolle; Wengel, Jesper

2017-01-01

Abstract The thrombin‐binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G‐quadruplex‐forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three‐carbon spacer (spacer‐C3), unlocked nucleic acid (UNA) and 3′‐amino‐modified UNA (amino‐UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G‐quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer‐C3 introduction at the T7 loop position (TBA‐SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA‐SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties. PMID:28150905

Development of an Efficient G-Quadruplex-Stabilised Thrombin-Binding Aptamer Containing a Three-Carbon Spacer Molecule.

PubMed

Aaldering, Lukas J; Poongavanam, Vasanthanathan; Langkjaer, Niels; Murugan, N Arul; Jørgensen, Per Trolle; Wengel, Jesper; Veedu, Rakesh N

2017-04-18

The thrombin-binding aptamer (TBA), which shows anticoagulant properties, is one of the most studied G-quadruplex-forming aptamers. In this study, we investigated the impact of different chemical modifications such as a three-carbon spacer (spacer-C 3 ), unlocked nucleic acid (UNA) and 3'-amino-modified UNA (amino-UNA) on the structural dynamics and stability of TBA. All three modifications were incorporated at three different loop positions (T3, T7, T12) of the TBA G-quadruplex structure to result in a series of TBA variants and their stability was studied by thermal denaturation; folding was studied by circular dichroism spectroscopy and thrombin clotting time. The results showed that spacer-C 3 introduction at the T7 loop position (TBA-SP7) significantly improved stability and thrombin clotting time while maintaining a similar binding affinity as TBA to thrombin. Detailed molecular modelling experiments provided novel insights into the experimental observations, further supporting the efficacy of TBA-SP7. The results of this study could provide valuable information for future designs of TBA analogues with superior thrombin inhibition properties. © 2017 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

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

NASA Astrophysics Data System (ADS)

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

2016-11-01

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

Recent Developments of Graphene Oxide-Based Membranes: A Review

PubMed Central

Ma, Jinxia; Ping, Dan; Dong, Xinfa

2017-01-01

Membrane-based separation technology has attracted great interest in many separation fields due to its advantages of easy-operation, energy-efficiency, easy scale-up, and environmental friendliness. The development of novel membrane materials and membrane structures is an urgent demand to promote membrane-based separation technology. Graphene oxide (GO), as an emerging star nano-building material, has showed great potential in the membrane-based separation field. In this review paper, the latest research progress in GO-based membranes focused on adjusting membrane structure and enhancing their mechanical strength as well as structural stability in aqueous environment is highlighted and discussed in detail. First, we briefly reviewed the preparation and characterization of GO. Then, the preparation method, characterization, and type of GO-based membrane are summarized. Finally, the advancements of GO-based membrane in adjusting membrane structure and enhancing their mechanical strength, as well as structural stability in aqueous environment, are particularly discussed. This review hopefully provides a new avenue for the innovative developments of GO-based membrane in various membrane applications. PMID:28895877

Hydration Changes upon DNA Folding Studied by Osmotic Stress Experiments

PubMed Central

Nakano, Shu-ichi; Yamaguchi, Daisuke; Tateishi-Karimata, Hisae; Miyoshi, Daisuke; Sugimoto, Naoki

2012-01-01

The thermal stability of nucleic acid structures is perturbed under the conditions that mimic the intracellular environment, typically rich in inert components and under osmotic stress. We now describe the thermodynamic stability of DNA oligonucleotide structures in the presence of high background concentrations of neutral cosolutes. Small cosolutes destabilize the basepair structures, and the DNA structures consisting of the same nearest-neighbor composition show similar thermodynamic parameters in the presence of various types of cosolutes. The osmotic stress experiments reveal that water binding to flexible loops, unstable mismatches, and an abasic site upon DNA folding are almost negligible, whereas the binding to stable mismatch pairs is significant. The studies using the basepair-mimic nucleosides and the peptide nucleic acid suggest that the sugar-phosphate backbone and the integrity of the basepair conformation make important contributions to the binding of water molecules to the DNA bases and helical grooves. The study of the DNA hydration provides the basis for understanding and predicting nucleic acid structures in nonaqueous solvent systems. PMID:22735531

Recent Developments of Graphene Oxide-Based Membranes: A Review.

PubMed

Ma, Jinxia; Ping, Dan; Dong, Xinfa

2017-09-12

Membrane-based separation technology has attracted great interest in many separation fields due to its advantages of easy-operation, energy-efficiency, easy scale-up, and environmental friendliness. The development of novel membrane materials and membrane structures is an urgent demand to promote membrane-based separation technology. Graphene oxide (GO), as an emerging star nano-building material, has showed great potential in the membrane-based separation field. In this review paper, the latest research progress in GO-based membranes focused on adjusting membrane structure and enhancing their mechanical strength as well as structural stability in aqueous environment is highlighted and discussed in detail. First, we briefly reviewed the preparation and characterization of GO. Then, the preparation method, characterization, and type of GO-based membrane are summarized. Finally, the advancements of GO-based membrane in adjusting membrane structure and enhancing their mechanical strength, as well as structural stability in aqueous environment, are particularly discussed. This review hopefully provides a new avenue for the innovative developments of GO-based membrane in various membrane applications.

Triosephosphate isomerase I170V alters catalytic site, enhances stability and induces pathology in a Drosophila model of TPI deficiency

DOE PAGES

Roland, Bartholomew P.; Amrich, Christopher G.; Kammerer, Charles J.; ...

2014-10-16

Triosephosphate isomerase (TPI) is a glycolytic enzyme which homodimerizes for full catalytic activity. Mutations of the TPI gene elicit a disease known as TPI Deficiency, a glycolytic enzymopathy noted for its unique severity of neurological symptoms. Evidence suggests that TPI Deficiency pathogenesis may be due to conformational changes of the protein, likely affecting dimerization and protein stability. In this report, we genetically and physically characterize a human disease-associated TPI mutation caused by an I170V substitution. Human TPI I170V elicits behavioral abnormalities in Drosophila. An examination of hTPI I170V enzyme kinetics revealed this substitution reduced catalytic turnover, while assessments of thermalmore » stability demonstrated an increase in enzyme stability. Furthermore, the crystal structure of the homodimeric I170V mutant reveals changes in the geometry of critical residues within the catalytic pocket. In the end, collectively these data reveal new observations of the structural and kinetic determinants of TPI deficiency pathology, providing new insights into disease pathogenesis.« less

CIP (cleaning-in-place) stability of AlGaN/GaN pH sensors.

PubMed

Linkohr, St; Pletschen, W; Schwarz, S U; Anzt, J; Cimalla, V; Ambacher, O

2013-02-20

The CIP stability of pH sensitive ion-sensitive field-effect transistors based on AlGaN/GaN heterostructures was investigated. For epitaxial AlGaN/GaN films with high structural quality, CIP tests did not degrade the sensor surface and pH sensitivities of 55-58 mV/pH were achieved. Several different passivation schemes based on SiO(x), SiN(x), AlN, and nanocrystalline diamond were compared with special attention given to compatibility to standard microelectronic device technologies as well as biocompatibility of the passivation films. The CIP stability was evaluated with a main focus on the morphological stability. All stacks containing a SiO₂ or an AlN layer were etched by the NaOH solution in the CIP process. Reliable passivations withstanding the NaOH solution were provided by stacks of ICP-CVD grown and sputtered SiN(x) as well as diamond reinforced passivations. Drift levels about 0.001 pH/h and stable sensitivity over several CIP cycles were achieved for optimized sensor structures. Copyright © 2012 Elsevier B.V. All rights reserved.

Folding a Protein with Equal Probability of Being Helix or Hairpin

PubMed Central

Lin, Chun-Yu; Chen, Nan-Yow; Mou, Chung Yu

2012-01-01

We explore the possibility for the native structure of a protein being inherently multiconformational in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence 2DX4: INYWLAHAKAGYIVHWTA is constructed. It is shown that 2DX4 possesses two nearly degenerate native structures: one is a helix structure with the other a hairpinlike structure, and their free energy difference is <2% of that of local minima. Two degenerate native structures are stabilized by an energy barrier of ∼10 kcal/mol. Furthermore, the hydrogen-bond and dipole-dipole interactions are found to be two major competing interactions in transforming one conformation into the other. Our results indicate that two degenerate native structures are stabilized by subtle balance between different interactions in proteins. In particular, for small proteins, balance between the hydrogen-bond and dipole-dipole interactions happens for proteins of sizes being ∼18 amino acids and is shown to the main driving mechanism for the occurrence of degeneracy. These results provide important clues to the study of native structures of proteins. PMID:22828336

Method of growing films by flame synthesis using a stagnation-flow reactor

DOEpatents

Hahn, David W.; Edwards, Christopher F.

1998-01-01

A method of stabilizing a strained flame in a stagnation flow reactor. By causing a highly strained flame to be divided into a large number of equal size segments it is possible to stablize a highly strained flame that is on the verge of extinction, thereby providing for higher film growth rates. The flame stabilizer is an annular ring mounted coaxially and coplanar with the substrate upon which the film is growing and having a number of vertical pillars mounted on the top surface, thereby increasing the number of azimuthal nodes into which the flame is divided and preserving an axisymmetric structure necessary for stability.

Habilitation of auditory and vestibular dysfunction.

PubMed

Snapp, Hillary A; Schubert, Michael C

2012-04-01

Although unilateral hearing loss is often the initial sign of vestibular schwannoma (VS), the pathogenesis of the associated structures within the cerebellopontine angle can result in vestibular, facial, or vascular symptoms. Removal of a VS causes deficits in hearing, balance, and gaze stability. The resulting hearing loss eliminates the benefits of binaural listening that provide localization, loudness summation, and listening-in-noise ability. Reduced balance and gaze stability increase fall risk. This review discusses modern treatment options for auditory and vestibular rehabilitation including contralateral routing of signals (CROS), bilateral CROS, bone-anchored implants, tinnitus management, gaze and gait stability exercises. Copyright © 2012 Elsevier Inc. All rights reserved.

Predicting the tolerated sequences for proteins and protein interfaces using RosettaBackrub flexible backbone design.

PubMed

Smith, Colin A; Kortemme, Tanja

2011-01-01

Predicting the set of sequences that are tolerated by a protein or protein interface, while maintaining a desired function, is useful for characterizing protein interaction specificity and for computationally designing sequence libraries to engineer proteins with new functions. Here we provide a general method, a detailed set of protocols, and several benchmarks and analyses for estimating tolerated sequences using flexible backbone protein design implemented in the Rosetta molecular modeling software suite. The input to the method is at least one experimentally determined three-dimensional protein structure or high-quality model. The starting structure(s) are expanded or refined into a conformational ensemble using Monte Carlo simulations consisting of backrub backbone and side chain moves in Rosetta. The method then uses a combination of simulated annealing and genetic algorithm optimization methods to enrich for low-energy sequences for the individual members of the ensemble. To emphasize certain functional requirements (e.g. forming a binding interface), interactions between and within parts of the structure (e.g. domains) can be reweighted in the scoring function. Results from each backbone structure are merged together to create a single estimate for the tolerated sequence space. We provide an extensive description of the protocol and its parameters, all source code, example analysis scripts and three tests applying this method to finding sequences predicted to stabilize proteins or protein interfaces. The generality of this method makes many other applications possible, for example stabilizing interactions with small molecules, DNA, or RNA. Through the use of within-domain reweighting and/or multistate design, it may also be possible to use this method to find sequences that stabilize particular protein conformations or binding interactions over others.

Molecular Dynamics Simulation Study on the Binding and Stabilization Mechanism of Antiprion Compounds to the "Hot Spot" Region of PrPC.

PubMed

Zhou, Shuangyan; Liu, Xuewei; An, Xiaoli; Yao, Xiaojun; Liu, Huanxiang

2017-11-15

Structural transitions in the prion protein from the cellular form, PrP C , into the pathological isoform, PrP Sc , are regarded as the main cause of the transmissible spongiform encephalopathies, also known as prion diseases. Hence, discovering and designing effective antiprion drugs that can inhibit PrP C to PrP Sc conversion is regarded as a promising way to cure prion disease. Among several strategies to inhibit PrP C to PrP Sc conversion, stabilizing the native PrP C via specific binding is believed to be one of the valuable approaches and many antiprion compounds have been reported based on this strategy. However, the detailed mechanism to stabilize the native PrP C is still unknown. As such, to unravel the stabilizing mechanism of these compounds to PrP C is valuable for the further design and discovery of antiprion compounds. In this study, by molecular dynamics simulation method, we investigated the stabilizing mechanism of several antiprion compounds on PrP C that were previously reported to have specific binding to the "hot spot" region of PrP C . Our simulation results reveal that the stabilization mechanism of specific binding compounds can be summarized as (I) to stabilize both the flexible C-terminal of α2 and the hydrophobic core, such as BMD42-29 and GN8; (II) to stabilize the hydrophobic core, such as J1 and GJP49; (III) to stabilize the overall structure of PrP C by high binding affinity, as NPR-056. In addition, as indicated by the H-bond analysis and decomposition analysis of binding free energy, the residues N159 and Q160 play an important role in the specific binding of the studied compounds and all these compounds interact with PrP C in a similar way with the key interacting residues L130 in the β1 strand, P158, N159, Q160, etc. in the α1-β2 loop, and H187, T190, T191, etc. in the α2 C-terminus although the compounds have large structural difference. As a whole, our obtained results can provide some insights into the specific binding mechanism of main antiprion compounds to the "hot spot" region of PrP C at the molecular level and also provide guidance for effective antiprion drug design in the future.

Discovery of Critical Residues for Viral Entry and Inhibition through Structural Insight of HIV-1 Fusion Inhibitor CP621–652*

PubMed Central

Chong, Huihui; Yao, Xue; Qiu, Zonglin; Qin, Bo; Han, Ruiyun; Waltersperger, Sandro; Wang, Meitian; Cui, Sheng; He, Yuxian

2012-01-01

The core structure of HIV-1 gp41 is a stable six-helix bundle (6-HB) folded by its trimeric N- and C-terminal heptad repeats (NHR and CHR). We previously identified that the 621QIWNNMT627 motif located at the upstream region of gp41 CHR plays critical roles for the stabilization of the 6-HB core and peptide CP621–652 containing this motif is a potent HIV-1 fusion inhibitor, however, the molecular determinants underlying the stability and anti-HIV activity remained elusive. In this study, we determined the high-resolution crystal structure of CP621–652 complexed by T21. We find that the 621QIWNNMT627 motif does not maintain the α-helical conformation. Instead, residues Met626 and Thr627 form a unique hook-like structure (denoted as M-T hook), in which Thr627 redirects the peptide chain to position Met626 above the left side of the hydrophobic pocket on the NHR trimer. The side chain of Met626 caps the hydrophobic pocket, stabilizing the interaction between the pocket and the pocket-binding domain. Our mutagenesis studies demonstrate that mutations of the M-T hook residues could completely abolish HIV-1 Env-mediated cell fusion and virus entry, and significantly destabilize the interaction of NHR and CHR peptides and reduce the anti-HIV activity of CP621–652. Our results identify an unusual structural feature that stabilizes the six-helix bundle, providing novel insights into the mechanisms of HIV-1 fusion and inhibition. PMID:22511760

A Subset of Autism-Associated Genes Regulate the Structural Stability of Neurons

PubMed Central

Lin, Yu-Chih; Frei, Jeannine A.; Kilander, Michaela B. C.; Shen, Wenjuan; Blatt, Gene J.

2016-01-01

Autism spectrum disorder (ASD) comprises a range of neurological conditions that affect individuals’ ability to communicate and interact with others. People with ASD often exhibit marked qualitative difficulties in social interaction, communication, and behavior. Alterations in neurite arborization and dendritic spine morphology, including size, shape, and number, are hallmarks of almost all neurological conditions, including ASD. As experimental evidence emerges in recent years, it becomes clear that although there is broad heterogeneity of identified autism risk genes, many of them converge into similar cellular pathways, including those regulating neurite outgrowth, synapse formation and spine stability, and synaptic plasticity. These mechanisms together regulate the structural stability of neurons and are vulnerable targets in ASD. In this review, we discuss the current understanding of those autism risk genes that affect the structural connectivity of neurons. We sub-categorize them into (1) cytoskeletal regulators, e.g., motors and small RhoGTPase regulators; (2) adhesion molecules, e.g., cadherins, NCAM, and neurexin superfamily; (3) cell surface receptors, e.g., glutamatergic receptors and receptor tyrosine kinases; (4) signaling molecules, e.g., protein kinases and phosphatases; and (5) synaptic proteins, e.g., vesicle and scaffolding proteins. Although the roles of some of these genes in maintaining neuronal structural stability are well studied, how mutations contribute to the autism phenotype is still largely unknown. Investigating whether and how the neuronal structure and function are affected when these genes are mutated will provide insights toward developing effective interventions aimed at improving the lives of people with autism and their families. PMID:27909399

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.

Two-dimensional infrared spectroscopic study on the thermally induced structural changes of glutaraldehyde-crosslinked collagen

NASA Astrophysics Data System (ADS)

Tian, Zhenhua; Wu, Kun; Liu, Wentao; Shen, Lirui; Li, Guoying

2015-04-01

The thermal stability of collagen solution (5 mg/mL) crosslinked by glutaraldehyde (GTA) [GTA/collagen (w/w) = 0.5] was measured by differential scanning calorimetry and Fourier transform infrared spectroscopy (FTIR), and the thermally induced structural changes were analyzed using two-dimensional (2D) correlation spectra. The denaturation temperature (Td) and enthalpy change (ΔH) of crosslinked collagen were respectively about 27 °C and 88 J/g higher than those of native collagen, illuminating the thermal stability increased. With the increase of temperature, the red-shift of absorption bands and the decreased AIII/A1455 value obtained from FTIR spectra indicated that hydrogen bonds were weakened and the unwinding of triple helix occurred for both native and crosslinked collagens; whereas the less changes in red-shifting and AIII/A1455 values for crosslinked collagen also confirmed the increase in thermal stability. Additionally, the 2D correlation analysis provided information about the thermally induced structural changes. In the 2D synchronous spectra, the intensities of auto-peaks at 1655 and 1555 cm-1, respectively assigned to amide I band (Cdbnd O stretching vibration) and amide II band (combination of Nsbnd H bending and Csbnd N stretching vibrations) in helical conformation were weaker for crosslinked collagen than those for native collagen, indicating that the helical structure of crosslinked collagen was less sensitive to temperature. Moreover, the sequence of the band intensity variations showed that the band at 1555 cm-1 moved backwards owing to the addition of GTA, demonstrating that the response of helical structure of crosslinked collagen to the increased temperature lagged. It was speculated that the stabilization of collagen by GTA was due to the reinforcement of triple helical structure.

Two-dimensional infrared spectroscopic study on the thermally induced structural changes of glutaraldehyde-crosslinked collagen.

PubMed

Tian, Zhenhua; Wu, Kun; Liu, Wentao; Shen, Lirui; Li, Guoying

2015-04-05

The thermal stability of collagen solution (5 mg/mL) crosslinked by glutaraldehyde (GTA) [GTA/collagen (w/w)=0.5] was measured by differential scanning calorimetry and Fourier transform infrared spectroscopy (FTIR), and the thermally induced structural changes were analyzed using two-dimensional (2D) correlation spectra. The denaturation temperature (Td) and enthalpy change (ΔH) of crosslinked collagen were respectively about 27°C and 88 J/g higher than those of native collagen, illuminating the thermal stability increased. With the increase of temperature, the red-shift of absorption bands and the decreased AIII/A1455 value obtained from FTIR spectra indicated that hydrogen bonds were weakened and the unwinding of triple helix occurred for both native and crosslinked collagens; whereas the less changes in red-shifting and AIII/A1455 values for crosslinked collagen also confirmed the increase in thermal stability. Additionally, the 2D correlation analysis provided information about the thermally induced structural changes. In the 2D synchronous spectra, the intensities of auto-peaks at 1655 and 1555 cm(-1), respectively assigned to amide I band (CO stretching vibration) and amide II band (combination of NH bending and CN stretching vibrations) in helical conformation were weaker for crosslinked collagen than those for native collagen, indicating that the helical structure of crosslinked collagen was less sensitive to temperature. Moreover, the sequence of the band intensity variations showed that the band at 1555 cm(-1) moved backwards owing to the addition of GTA, demonstrating that the response of helical structure of crosslinked collagen to the increased temperature lagged. It was speculated that the stabilization of collagen by GTA was due to the reinforcement of triple helical structure. Copyright © 2015 Elsevier B.V. All rights reserved.

Aminooxylated Carbohydrates: Synthesis and Applications.

PubMed

Pifferi, Carlo; Daskhan, Gour Chand; Fiore, Michele; Shiao, Tze Chieh; Roy, René; Renaudet, Olivier

2017-08-09

Among other classes of biomolecules, carbohydrates and glycoconjugates are widely involved in numerous biological functions. In addition to addressing the related synthetic challenges, glycochemists have invested intense efforts in providing access to structures that can be used to study, activate, or inhibit these biological processes. Over the past few decades, aminooxylated carbohydrates have been found to be key building blocks for achieving these goals. This review provides the first in-depth overview covering several aspects related to the syntheses and applications of aminooxylated carbohydrates. After a brief introduction to oxime bonds and their relative stabilities compared to related C═N functions, synthetic aspects of oxime ligation and methodologies for introducing the aminooxy functionality onto both glycofuranosyls and glycopyranosyls are described. The subsequent section focuses on biological applications involving aminooxylated carbohydrates as components for the construcion of diverse architectures. Mimetics of natural structures represent useful tools for better understanding the features that drive carbohydrate-receptor interaction, their biological output and they also represent interesting structures with improved stability and tunable properties. In the next section, multivalent structures such as glycoclusters and glycodendrimers obtained through oxime ligation are described in terms of synthetic design and their biological applications such as immunomodulators. The second-to-last section discusses miscellaneous applications of oxime-based glycoconjugates, such as enantioselective catalysis and glycosylated oligonucleotides, and conclusions and perspectives are provided in the last section.

Hard alpha-keratin degradation inside a tissue under high flux X-ray synchrotron micro-beam: a multi-scale time-resolved study.

PubMed

Leccia, Emilie; Gourrier, Aurélien; Doucet, Jean; Briki, Fatma

2010-04-01

X-rays interact strongly with biological organisms. Synchrotron radiation sources deliver very intense X-ray photon fluxes within micro- or submicro cross-section beams, resulting in doses larger than the MGy. The relevance of synchrotron radiation analyses of biological materials is therefore questionable since such doses, million times higher than the ones used in radiotherapy, can cause huge damages in tissues, with regard to not only DNA, but also proteic and lipid organizations. Very few data concerning the effect of very high X-ray doses in tissues are available in the literature. We present here an analysis of the structural phenomena which occur when the model tissue of human hair is irradiated by a synchrotron X-ray micro-beam. The choice of hair is supported by its hierarchical and partially ordered keratin structure which can be analysed inside the tissue by X-ray diffraction. To assess the damages caused by hard X-ray micro-beams (1 microm(2) cross-section), short exposure time scattering SAXS/WAXS patterns have been recorded at beamline ID13 (ESRF) after various irradiation times. Various modifications of the scattering patterns are observed, they provide fine insight of the radiation damages at various hierarchical levels and also unexpectedly provide information about the stability of the various hierarchical structural levels. It appears that the molecular level, i.e. the alpha helices which are stabilized by hydrogen bonds and the alpha-helical coiled coils which are stabilized by hydrophobic interactions, is more sensitive to radiation than the supramolecular architecture of the keratin filament and the filament packing within the keratin associated proteins matrix, which is stabilized by disulphide bonds. (c) 2009 Elsevier Inc. All rights reserved.

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

Final Scientific/Technical Report

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

Reeder, Richard; Phillips, Brian

A variety of calcifying organisms produce a transient or metastable amorphous calcium carbonate (ACC) precursor phase that is assembled and subsequently transformed into a crystalline biomineral, typically calcite or aragonite. The complex shapes, hierarchical structures, and unique physical properties of the biominerals that result from this calcification pathway have stimulated interest in adapting these concepts for the design and creation of bio-inspired functional materials in the laboratory. ACC also forms as a reactive precursor in diverse inorganic systems and is likely to play a much broader role in calcium carbonate formation. Knowledge of the structure, composition, and behavior of thismore » metastable phase is critical for establishing a structural and mechanistic framework for calcium carbonate formation and its role in biogeochemical processes, including carbon cycling. Minor additives, such as magnesium, phosphorus, and organic macromolecules, are known to play important roles in controlling ACC stability, transformation kinetics, and selection of final crystalline polymorph. Molecular water also occurs in many types of ACC and is thought to play a structural role in its stability and transformation behavior. One of the major challenges that remain unresolved is identification of the structural basis for the role of these minor additives and molecular water. The absence of long-range order in ACC, and other amorphous phases, has posed a challenge for study by techniques commonly used for crystalline solids. Preliminary studies in our group show that the combination of two techniques, synchrotron X-ray-based pair distribution function (PDF) analysis and nuclear magnetic resonance (NMR) spectroscopy can provide entirely new insight to structural properties of synthetic ACC over length scales that are most relevant for understanding its transformation properties. Building on preliminary experiments, we propose a systematic study of synthesis, structure, and transformation behavior in abiotic systems. The work will specifically address the influence of phosphate as a minor additive. PDF analysis will utilize total X-ray scattering data collected at synchrotron facilities optimized for this method and will provide direct characterization of the short- and intermediate-range structure of ACC synthesized under controlled conditions. Parallel computational work using reverse Monte Carlo methods will allow structural models to be constructed for a more complete analysis of PDF results. NMR spectroscopy, using a variety of single- and double-resonance techniques, will provide information on H and CO3 components, including dynamical properties, and their relationship to stabilizing additives. PDF and NMR results will be complemented by parallel studies using X-ray absorption and FT-IR spectroscopy to allow direct comparison to previous studies. These techniques will be used to follow the transformation of different ACC samples, with specific additives, to crystalline phases under controlled condition (e.g., relative humidity). This work will provide the structural and mechanistic basis for understanding ACC stability, its transformation behavior, and the factors that govern polymorph selection. This new insight will directly benefit researchers in diverse fields, as well as adding to the framework of knowledge for understanding and controlling calcium carbonate formation in natural and engineered systems.« less

The transition of ground-based space environmental effects testing to the space environment

NASA Technical Reports Server (NTRS)

Zaat, Stephen V.; Schaefer, Glen A.; Wallace, John F.

1991-01-01

The goal of the space flight program at the Center for Commercial Development of Space (CCDS)--Materials for Space Structures is to provide environmentally stable structural materials to support the continued humanization and commercialization of the space frontier. Information on environmental stability will be obtained through space exposure, evaluation, documentation, and subsequent return to the supplier of the candidate material for internal investigation. This program provides engineering and scientific service to space systems development firms and also exposes CCDS development candidate materials to space environments representative of in-flight conditions. The maintenance of a technological edge in space for NASA suggests the immediate search for space materials that maintain their structural integrity and remain environmentally stable. The materials being considered for long-lived space structures are complex, high strength/weight ratio composites. In order for these new candidate materials to qualify for use in space structures, they must undergo strenuous testing to determine their reliability and stability when subjected to the space environment. Ultraviolet radiation, atomic oxygen, debris/micrometeoroids, charged particles radiation, and thermal fatigue all influence the design of space structural materials. The investigation of these environmental interactions is the key purpose of this center. Some of the topics discussed with respect to the above information include: the Space Transportation System, mission planning, spaceborne experiments, and space flight payloads.

Free energy landscapes for initiation and branching of protein aggregation.

PubMed

Zheng, Weihua; Schafer, Nicholas P; Wolynes, Peter G

2013-12-17

Experiments on artificial multidomain protein constructs have probed the early stages of aggregation processes, but structural details of the species that initiate aggregation remain elusive. Using the associative-memory, water-mediated, structure and energy model known as AWSEM, a transferable coarse-grained protein model, we performed simulations of fused constructs composed of up to four copies of the Titin I27 domain or its mutant I27* (I59E). Free energy calculations enable us to quantify the conditions under which such multidomain constructs will spontaneously misfold. Consistent with experimental results, the dimer of I27 is found to be the smallest spontaneously misfolding construct. Our results show how structurally distinct misfolded states can be stabilized under different thermodynamic conditions, and this result provides a plausible link between the single-molecule misfolding experiments under native conditions and aggregation experiments under denaturing conditions. The conditions for spontaneous misfolding are determined by the interplay among temperature, effective local protein concentration, and the strength of the interdomain interactions. Above the folding temperature, fusing additional domains to the monomer destabilizes the native state, and the entropically stabilized amyloid-like state is favored. Because it is primarily energetically stabilized, the domain-swapped state is more likely to be important under native conditions. Both protofibril-like and branching structures are found in annealing simulations starting from extended structures, and these structures suggest a possible connection between the existence of multiple amyloidogenic segments in each domain and the formation of branched, amorphous aggregates as opposed to linear fibrillar structures.

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.

Discriminating between stabilizing and destabilizing protein design mutations via recombination and simulation.

PubMed

Johnson, Lucas B; Gintner, Lucas P; Park, Sehoo; Snow, Christopher D

2015-08-01

Accuracy of current computational protein design (CPD) methods is limited by inherent approximations in energy potentials and sampling. These limitations are often used to qualitatively explain design failures; however, relatively few studies provide specific examples or quantitative details that can be used to improve future CPD methods. Expanding the design method to include a library of sequences provides data that is well suited for discriminating between stabilizing and destabilizing design elements. Using thermophilic endoglucanase E1 from Acidothermus cellulolyticus as a model enzyme, we computationally designed a sequence with 60 mutations. The design sequence was rationally divided into structural blocks and recombined with the wild-type sequence. Resulting chimeras were assessed for activity and thermostability. Surprisingly, unlike previous chimera libraries, regression analysis based on one- and two-body effects was not sufficient for predicting chimera stability. Analysis of molecular dynamics simulations proved helpful in distinguishing stabilizing and destabilizing mutations. Reverting to the wild-type amino acid at destabilized sites partially regained design stability, and introducing predicted stabilizing mutations in wild-type E1 significantly enhanced thermostability. The ability to isolate stabilizing and destabilizing elements in computational design offers an opportunity to interpret previous design failures and improve future CPD methods. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Nanostructured Mineral Coatings Stabilize Proteins for Therapeutic Delivery.

PubMed

Yu, Xiaohua; Biedrzycki, Adam H; Khalil, Andrew S; Hess, Dalton; Umhoefer, Jennifer M; Markel, Mark D; Murphy, William L

2017-09-01

Proteins tend to lose their biological activity due to their fragile structural conformation during formulation, storage, and delivery. Thus, the inability to stabilize proteins in controlled-release systems represents a major obstacle in drug delivery. Here, a bone mineral inspired protein stabilization strategy is presented, which uses nanostructured mineral coatings on medical devices. Proteins bound within the nanostructured coatings demonstrate enhanced stability against extreme external stressors, including organic solvents, proteases, and ethylene oxide gas sterilization. The protein stabilization effect is attributed to the maintenance of protein conformational structure, which is closely related to the nanoscale feature sizes of the mineral coatings. Basic fibroblast growth factor (bFGF) released from a nanostructured mineral coating maintains its biological activity for weeks during release, while it maintains activity for less than 7 d during release from commonly used polymeric microspheres. Delivery of the growth factors bFGF and vascular endothelial growth factor using a mineral coated surgical suture significantly improves functional Achilles tendon healing in a rabbit model, resulting in increased vascularization, more mature collagen fiber organization, and a two fold improvement in mechanical properties. The findings of this study demonstrate that biomimetic interactions between proteins and nanostructured minerals provide a new, broadly applicable mechanism to stabilize proteins in the context of drug delivery and regenerative medicine. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Temporal Stability of DSM-5 Posttraumatic Stress Disorder Criteria in a Problem Drinking Sample

PubMed Central

Keane, Terence M.; Rubin, Amy; Lachowicz, Mark; Brief, Deborah; Enggasser, Justin L.; Roy, Monica; Hermos, John; Helmuth, Eric; Rosenbloom, David

2014-01-01

The Diagnostic and Statistical Manual-5 (DSM-5) reformulated Posttraumatic Stress Disorder (PTSD) based partially on research showing there were four main factors that underlie the symptoms of the disorder. The primary aim of this study was to examine the temporal stability of the DSM-5 factors as measured by the Posttraumatic Stress Disorder Checklist for DSM-5 (PCL-5; Weathers et al., 2010). Confirmatory factor analyses were conducted to examine the structure of DSM-5 PTSD, and temporal stability over three time points was examined to determine if the measure reflects a consistent construct over time. Our sample was 507 combat-exposed veterans of Iraq and Afghanistan who enrolled in an online intervention for problem drinking and combat-related stress (masked for review). We administered the PCL-5 at baseline, 8-week post intervention, and 3-month follow-up assessments. The DSM-5 model provided an adequate fit to the data at baseline. Tests of equality of form and equality of factor loadings demonstrated stability of the factor structure over time, indicating temporal stability. This study confirms the results of previous research supporting the DSM-5 model of PTSD symptoms (Elhai et al., 2012; Miller et al., 2012). This is the first study to demonstrate the temporal stability of the PCL-5, indicating its use in longitudinal studies will measure the same construct over time. PMID:24932642

Design and Control of Flapping Wing Micro Air Vehicles

DTIC Science & Technology

2011-09-01

unsteady, low Re aerodynamics, micro-fabrication, and fluid - structure interaction. However, research into flapping wing control of such MAVs...and flown in confined spaces such as urban canyons, caves and indoors. MAVs will provide an organic ISR capability to small combat teams in the...Designing for highly coupled fluid -structure interactions  Micro-fabrication  Stability characterization and control Of these challenges, the most

Computational evidence for stable inorganic fullerene-like structures of ceramic and semiconductor materials

NASA Astrophysics Data System (ADS)

Chang, Ch; Patzer, A. B. C.; Sedlmayr, E.; Steinke, T.; Sülzle, D.

2001-12-01

Theoretical electronic structure techniques have become an indispensible and powerful means for predicting molecular properties and designing new materials. Based on a density functional approach and guided by geometric considerations we provide evidence for some specific inorganic fullerene-like cage molecules of ceramic and semiconductor materials which exhibit high energetic stability and point group symmetry as well as nearly perfect spherical shape.

Optimal stabilization of Boolean networks through collective influence

NASA Astrophysics Data System (ADS)

Wang, Jiannan; Pei, Sen; Wei, Wei; Feng, Xiangnan; Zheng, Zhiming

2018-03-01

Boolean networks have attracted much attention due to their wide applications in describing dynamics of biological systems. During past decades, much effort has been invested in unveiling how network structure and update rules affect the stability of Boolean networks. In this paper, we aim to identify and control a minimal set of influential nodes that is capable of stabilizing an unstable Boolean network. For locally treelike Boolean networks with biased truth tables, we propose a greedy algorithm to identify influential nodes in Boolean networks by minimizing the largest eigenvalue of a modified nonbacktracking matrix. We test the performance of the proposed collective influence algorithm on four different networks. Results show that the collective influence algorithm can stabilize each network with a smaller set of nodes compared with other heuristic algorithms. Our work provides a new insight into the mechanism that determines the stability of Boolean networks, which may find applications in identifying virulence genes that lead to serious diseases.

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

NASA Astrophysics Data System (ADS)

Lin, Z. D.; Shi, H.

2018-02-01

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

The conformational flexibility of the carboxy terminal residues 105–114 is a key modulator of the catalytic activity and stability of Macrophage Migration Inhibitory Factor (MIF)†

PubMed Central

El-Turk, Farah; Cascella, Michele; Ouertatani-Sakouhi, Hajer; Narayanan, Raghavendran Lakshmi; Leng, Lin; Bucala, Richard; Hweckstetter, Markus; Rothlisberger, Ursula; Lashuel, Hilal A.

2013-01-01

Macrophage migration inhibitory factor (MIF) is a multifunctional protein and a major mediator of innate immunity. Although X-ray crystallography revealed that MIF exists as a homotrimer, its oligomerization state in vivo as well as the factors governing its oligomerization and stability remain poorly understood. The C-terminal region of MIF is highly conserved and participates in several intramolecular interactions that suggest a role in modulating the stability and biochemical activity of MIF. To determine the importance of these interactions, point mutations (A48P, L46A), insertions (P107) at the monomer-monomer interfaces, and C-terminal deletion (Δ110-114NSTFA and Δ105–114NVGWNNSTFA) variants were designed and their structural properties, thermodynamic stability, oligomerization state, catalytic activity and receptor binding were characterized using a battery of biophysical methods. The C-terminal deletion mutants ΔC5 huMIF1-109 and ΔC10 huMIF1-104 were enzymatically inactive and thermodynamically less stable than wild type MIF. Analytical ultracentrifugation studies demonstrate that both C-terminal mutants sediment as trimers and exhibit similar binding to CD74 as the wild type protein. Disrupting the conformation of the C-terminal region 105–114 and increasing its conformational flexibility through the insertion of a proline residue at position 107 was sufficient to reproduce the structural, biochemical and thermodynamic properties of the deletion mutants. P107 MIF forms an enzymatically inactive trimer and exhibits reduced thermodynamic stability relative to the wild type protein. To provide a rationale for the changes induced by these mutations at the molecular level, we also performed molecular dynamics simulations on these mutants in comparison to the wild type MIF. Together, our studies demonstrate that inter-subunit interactions involving the C-terminal region 105–114, including a salt-bridge interaction between Arg73 of one monomer and the carboxy terminus of a neighbouring monomer, play critical roles in modulating tertiary structure stabilization, enzymatic activity, and thermodynamic stability of MIF, but not its oligomerization state and receptor binding properties. Our results suggest that targeting the C-terminal region could provide new strategies for allosteric modulation of MIF enzymatic activity and the development of novel inhibitors of MIF tautomerase activity. PMID:18795803

X-ray structures define human P2X3 receptor gating cycle and antagonist action

PubMed Central

Mansoor, Steven E.; Lü, Wei; Oosterheert, Wout; Shekhar, Mrinal; Tajkhorshid, Emad; Gouaux, Eric

2016-01-01

Summary P2X receptors are trimeric, non-selective cation channels activated by ATP that play important roles in cardiovascular, neuronal and immune systems. Despite their central function in human physiology and as potential targets of therapeutic agents, there are no structures of human P2X receptors. Mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structure of the pore-forming transmembrane domains remain unclear. We report x-ray crystal structures of human P2X3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/desensitized and antagonist-bound closed states. The open state structure harbors an intracellular motif we term the “cytoplasmic cap”, that stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. Competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements underpinning P2X receptor gating and provide a foundation for development of new pharmacologic agents. PMID:27626375

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

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

PubMed

Davis, Jeffrey M

2014-12-01

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

Understanding the Physical and Molecular Basis of Stability of Arabidopsis DNA Pol λ under UV-B and High NaCl Stress.

PubMed

Roy, Sujit; Banerjee, Victor; Das, Kali Pada

2015-01-01

Here, we have investigated the physical and molecular basis of stability of Arabidopsis DNA Pol λ, the sole X family DNA polymerase member in plant genome, under UV-B and salinity stress in connection with the function of the N-terminal BRCT (breast cancer-associated C terminus) domain and Ser-Pro rich region in the regulation of the overall structure of this protein. Tryptophan fluorescence studies, fluorescence quenching and Bis-ANS binding experiments using purified recombinant full length Pol λ and its N-terminal deletion forms have revealed UV-B induced conformational change in BRCT domain deficient Pol λ. On the other hand, the highly conserved C-terminal catalytic core PolX domain maintained its tertiary folds under similar condition. Circular dichroism (CD) and fourier transform infrared (FT-IR) spectral studies have indicated appreciable change in the secondary structural elements in UV-B exposed BRCT domain deficient Pol λ. Increased thermodynamic stability of the C-terminal catalytic core domain suggested destabilizing effect of the N-terminal Ser-Pro rich region on the protein structure. Urea-induced equilibrium unfolding studies have revealed increased stability of Pol λ and its N-terminal deletion mutants at high NaCl concentration. In vivo aggregation studies using transient expression systems in Arabidopsis and tobacco indicated possible aggregation of Pol λ lacking the BRCT domain. Immunoprecipitation assays revealed interaction of Pol λ with the eukaryotic molecular chaperone HSP90, suggesting the possibility of regulation of Pol λ stability by HSP90 in plant cell. Overall, our results have provided one of the first comprehensive information on the biophysical characteristics of Pol λ and indicated the importance of both BRCT and Ser-Pro rich modules in regulating the stability of this protein under genotoxic stress in plants.

Ultrastable α phase nickel hydroxide as energy storage materials for alkaline secondary batteries

NASA Astrophysics Data System (ADS)

Huang, Haili; Guo, Yinjian; Cheng, Yuanhui

2018-03-01

α Phase nickel hydroxide (α-Ni(OH)2) has higher theoretical capacity than that of commercial β phase Ni(OH)2. But the low stability inhibits its wide application in alkaline rechargeable batteries. Here, we propose a totally new idea to stabilize α phase Ni(OH)2 by introducing large organic molecule into the interlayer spacing together with doping multivalent cobalt into the layered Ni(OH)2 host. Ethylene glycol is served as neutral stabilizer in the interlayer spacing. Nickel is substituted by cobalt to increase the electrostatic attraction between layered Ni(OH)2 host and anion ions in the interlayer spacing. Polyethylene glycol (PEG-200) is utilized to design a three-dimensional network structure. This prepared α-Ni(OH)2-20 exhibits specific capacity as high as 334 mAh g-1and good structural stability even after immersing into strong alkaline zincate solution for 20 days. Ni(OH)2 electrode with a specific capacity of 35 mAh cm-2 is fabricated and used as positive electrode in zinc-nickel single flow batteries, which also shows good cycling stability. This result can provide an important guideline for the rational design and preparation of highly active and stable α phase Ni(OH)2 for alkaline secondary battery.

Effects of the central potassium ions on the G-quadruplex and stabilizer binding.

PubMed

Wang, Zhiguo; Liu, Jun-Ping

2017-03-01

Human telomeres undertake the structure of intra-molecular parallel G-quadruplex in the presence of K + in eukaryotic cell. Stabilization of the telomere G-quadruplex represents a potential strategy to prevent telomere lengthening by telomerase in cancer therapy. Current work demonstrates that the binding of central K + with the parallel G-quadruplex is a coordinated water directed step-wise process. The K + above the top G-tetrad is prone to leak into environment and the 5'-adenine quickly flips over the top G-tetrad, leading to the bottom gate of G-tetrads as the only viable pathway of K + binding. Present molecular dynamics studies on the two most potent stabilizers RHPS4 and BRACO-19 reveal that the central K + has little influence on the binding conformations of the bound stabilizers. But without the central K + , either RHPS4 or BRACO-19 cannot stabilize the structure of G-quadruplex. The binding strength of stabilizers evaluated by the MM-PBSA method follows the order of BRACO-19> RHPS4, which agrees with the experimental results. The difference in binding affinities between RHPS4 and BRACO-19 is probably related to the ability to form intramolecular hydrogen bonds and favorable van del Waals interactions with G-quadruplex. In the models that have one central K + located at the upper/lower binding site, the corresponding top/bottom stacked stabilizers show more favorable binding affinities, indicating the apparent promoting effect of central K + on the stabilizer binding. Our findings provide further insights into the regulatory effect of K + on the G-quadruplex targeted binding, which is meaningful to the development of G-quadruplex stabilizers. Copyright © 2017 Elsevier Inc. All rights reserved.

Stability Mechanisms of Laccase Isoforms using a Modified FoldX Protocol Applicable to Widely Different Proteins.

PubMed

Christensen, Niels J; Kepp, Kasper P

2013-07-09

A recent computational protocol that accurately predicts and rationalizes protein multisite mutant stabilities has been extended to handle widely different isoforms of laccases. We apply the protocol to four isoenzymes of Trametes versicolor laccase (TvL) with variable lengths (498-503 residues) and thermostability (Topt ∼ 45-80 °C) and with 67-77% sequence identity. The extended protocol uses (i) statistical averaging, (ii) a molecular-dynamics-validated "compromise" homology model to minimize bias that causes proteins close in sequence to a structural template to be too stable due to having the benefits of the better sampled template (typically from a crystal structure), (iii) correction for hysteresis that favors the input template to overdestabilize, and (iv) a preparative protocol to provide robust input sequences of equal length. The computed ΔΔG values are in good agreement with the major trends in experimental stabilities; that is, the approach may be applicable for fast estimates of the relative stabilities of proteins with as little as 70% identity, something that is currently extremely challenging. The computed stability changes associated with variations are Gaussian-distributed, in good agreement with experimental distributions of stability effects from mutation. The residues causing the differential stability of the four isoforms are consistent with a range of compiled laccase wild type data, suggesting that we may have identified general drivers of laccase stability. Several sites near Cu, notably 79, 241, and 245, or near substrate, mainly 265, are identified that contribute to stability-function trade-offs, of relevance to the search for new proficient and stable variants of these important industrial enzymes.

Stepwise Adaptations to Low Temperature as Revealed by Multiple Mutants of Psychrophilic α-Amylase from Antarctic Bacterium*

PubMed Central

Cipolla, Alexandre; D'Amico, Salvino; Barumandzadeh, Roya; Matagne, André; Feller, Georges

2011-01-01

The mutants Mut5 and Mut5CC from a psychrophilic α-amylase bear representative stabilizing interactions found in the heat-stable porcine pancreatic α-amylase but lacking in the cold-active enzyme from an Antarctic bacterium. From an evolutionary perspective, these mutants can be regarded as structural intermediates between the psychrophilic and the mesophilic enzymes. We found that these engineered interactions improve all the investigated parameters related to protein stability as follows: compactness; kinetically driven stability; thermodynamic stability; resistance toward chemical denaturation, and the kinetics of unfolding/refolding. Concomitantly to this improved stability, both mutants have lost the kinetic optimization to low temperature activity displayed by the parent psychrophilic enzyme. These results provide strong experimental support to the hypothesis assuming that the disappearance of stabilizing interactions in psychrophilic enzymes increases the amplitude of concerted motions required by catalysis and the dynamics of active site residues at low temperature, leading to a higher activity. PMID:21900238

Control of Flexible Structures (COFS) Flight Experiment Background and Description

NASA Technical Reports Server (NTRS)

Hanks, B. R.

1985-01-01

A fundamental problem in designing and delivering large space structures to orbit is to provide sufficient structural stiffness and static configuration precision to meet performance requirements. These requirements are directly related to control requirements and the degree of control system sophistication available to supplement the as-built structure. Background and rationale are presented for a research study in structures, structural dynamics, and controls using a relatively large, flexible beam as a focus. This experiment would address fundamental problems applicable to large, flexible space structures in general and would involve a combination of ground tests, flight behavior prediction, and instrumented orbital tests. Intended to be multidisciplinary but basic within each discipline, the experiment should provide improved understanding and confidence in making design trades between structural conservatism and control system sophistication for meeting static shape and dynamic response/stability requirements. Quantitative results should be obtained for use in improving the validity of ground tests for verifying flight performance analyses.

Theory of buckling and post-buckling behavior of elastic structures

NASA Technical Reports Server (NTRS)

Budiansky, B.

1974-01-01

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

Decentralized control of large-scale systems: Fixed modes, sensitivity and parametric robustness. Ph.D. Thesis - Universite Paul Sabatier, 1985

NASA Technical Reports Server (NTRS)

Tarras, A.

1987-01-01

The problem of stabilization/pole placement under structural constraints of large scale linear systems is discussed. The existence of a solution to this problem is expressed in terms of fixed modes. The aim is to provide a bibliographic survey of the available results concerning the fixed modes (characterization, elimination, control structure selection to avoid them, control design in their absence) and to present the author's contribution to this problem which can be summarized by the use of the mode sensitivity concept to detect or to avoid them, the use of vibrational control to stabilize them, and the addition of parametric robustness considerations to design an optimal decentralized robust control.

Micromachined silicon acoustic delay line with 3D-printed micro linkers and tapered input for improved structural stability and acoustic directivity

NASA Astrophysics Data System (ADS)

Cho, Y.; Kumar, A.; Xu, S.; Zou, J.

2016-10-01

Recent studies have shown that micromachined silicon acoustic delay lines can provide a promising solution to achieve real-time photoacoustic tomography without the need for complex transducer arrays and data acquisition electronics. To achieve deeper imaging depth and wider field of view, a longer delay time and therefore delay length are required. However, as the length of the delay line increases, it becomes more vulnerable to structural instability due to reduced mechanical stiffness. In this paper, we report the design, fabrication, and testing of a new silicon acoustic delay line enhanced with 3D printed polymer micro linker structures. First, mechanical deformation of the silicon acoustic delay line (with and without linker structures) under gravity was simulated by using finite element method. Second, the acoustic crosstalk and acoustic attenuation caused by the polymer micro linker structures were evaluated with both numerical simulation and ultrasound transmission testing. The result shows that the use of the polymer micro linker structures significantly improves the structural stability of the silicon acoustic delay lines without creating additional acoustic attenuation and crosstalk. In addition, the improvement of the acoustic acceptance angle of the silicon acoustic delay lines was also investigated to better suppress the reception of unwanted ultrasound signals outside of the imaging plane. These two improvements are expected to provide an effective solution to eliminate current limitations on the achievable acoustic delay time and out-of-plane imaging resolution of micromachined silicon acoustic delay line arrays.

Rare-earth metals in nickel aluminide-based alloys: III. Structure and properties of multicomponent Ni3Al-based alloys

NASA Astrophysics Data System (ADS)

Bazyleva, O. A.; Povarova, K. B.; Kazanskaya, N. K.; Drozdov, A. A.

2009-04-01

The possibility of increasing the life of heterophase cast light Ni3Al-based superalloys at temperatures higher than 0.8 T m of Ni3Al is studied when their directional structure is additionally stabilized by nanoprecipitates, which form upon additional alloying of these alloys by refractory and active metals, and using special methods for preparing and melting of an alloy charge. The effect of the method of introducing the main components and refractory reaction-active and surface-active alloying elements into Ni3Al-based cast superalloys, which are thermally stable natural composite materials of the eutectic type, on the structure-phase state and the life of these alloys is studied. When these alloys are melted, it is necessary to perform a set of measures to form particles of refractory oxide cores covered with the β-NiAl phase and, then, γ'prim-Ni3Al phase precipitates during solidification. The latter phase forms the outer shell of grain nuclei, which provides high thermal stability and hot strength of an intermetallic compound-based alloy. As a result, a modified structure that is stabilized by the nanoprecipitates of nickel and aluminum lanthanides and the nanoprecipitates of phases containing refractory metals is formed. This structure enhances the life of the alloy at 1000 °C by a factor of 1.8-2.5.

Structure Dependence of Lysosomal Transit of Chitosan-Based Polyplexes for Gene Delivery.

PubMed

Thibault, Marc; Lavertu, Marc; Astolfi, Mélina; Buschmann, Michael D

2016-10-01

Chitosan-based polyplexes are known to traffic through lysosomes for a relatively long time, independent of the degree of deacetylation (DDA) and the number average molecular weight (Mn) of the polymer, even though both of these parameters have profound effects on polyplex stability and transfection efficiency. A better understanding of the lysosomal barrier is paramount to the rational design of vectors capable of overcoming obstacles to transgene expression. The aim of the present study was to investigate if lysosomal transit affects chitosan-based polyplex transfection efficiency in a structure-dependent (DDA, Mn) manner. Toward this end, we analyzed the effects of intracellular trafficking modifying agents on transfection efficiency and intracellular vesicular trafficking of polyplexes with different structural properties and stabilities or nucleic acid binding affinity. The use of agents that modify endosome/lysosome acidification and transit processes by distinct mechanisms and their effect on cell viability, polyplex uptake, vesicular trafficking, and transfection efficiency revealed novel and strong chitosan structure-dependent consequences of lysosomal transit. Inhibiting lysosomal transit using chloroquine significantly increased the efficiency of unstable polyplexes, while having minimal effects for polyplexes with intermediate or high stability. In parallel, specifically inhibiting the acidification of vesicles abrogated transfection for all formulations, suggesting that vesicular acidification is essential to promote transfection, most probably by facilitating lysosomal escape. These results provide novel insights into the structure-performance relationship of chitosan-based gene delivery systems.

Amorphous Mixed-Valence Vanadium Oxide/Exfoliated Carbon Cloth Structure Shows a Record High Cycling Stability.

PubMed

Song, Yu; Liu, Tian-Yu; Yao, Bin; Kou, Tian-Yi; Feng, Dong-Yang; Liu, Xiao-Xia; Li, Yat

2017-04-01

Previous studies show that vanadium oxides suffer from severe capacity loss during cycling in the liquid electrolyte, which has hindered their applications in electrochemical energy storage. The electrochemical instability is mainly due to chemical dissolution and structural pulverization of vanadium oxides during charge/discharge cyclings. In this study the authors demonstrate that amorphous mixed-valence vanadium oxide deposited on exfoliated carbon cloth (CC) can address these two limitations simultaneously. The results suggest that tuning the V 4+ /V 5+ ratio of vanadium oxide can efficiently suppress the dissolution of the active materials. The oxygen-functionalized carbon shell on exfoliated CC can bind strongly with VO x via the formation of COV bonding, which retains the electrode integrity and suppresses the structural degradation of the oxide during charging/discharging. The uptake of structural water during charging and discharging processes also plays an important role in activating the electrode material. The amorphous mixed-valence vanadium oxide without any protective coating exhibits record-high cycling stability in the aqueous electrolyte with no capacitive decay in 100 000 cycles. This work provides new insights on stabilizing vanadium oxide, which is critical for the development of vanadium oxide based energy storage devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Trends in Thermostability Provide Information on the Nature of Substrate, Inhibitor, and Lipid Interactions with Mitochondrial Carriers*

PubMed Central

Crichton, Paul G.; Lee, Yang; Ruprecht, Jonathan J.; Cerson, Elizabeth; Thangaratnarajah, Chancievan; King, Martin S.; Kunji, Edmund R. S.

2015-01-01

Mitochondrial carriers, including uncoupling proteins, are unstable in detergents, which hampers structural and mechanistic studies. To investigate carrier stability, we have purified ligand-free carriers and assessed their stability with a fluorescence-based thermostability assay that monitors protein unfolding with a thiol-reactive dye. We find that mitochondrial carriers from both mesophilic and thermophilic organisms exhibit poor stability in mild detergents, indicating that instability is inherent to the protein family. Trends in the thermostability of yeast ADP/ATP carrier AAC2 and ovine uncoupling protein UCP1 allow optimal conditions for stability in detergents to be established but also provide mechanistic insights into the interactions of lipids, substrates, and inhibitors with these proteins. Both proteins exhibit similar stability profiles across various detergents, where stability increases with the size of the associated detergent micelle. Detailed analysis shows that lipids stabilize carriers indirectly by increasing the associated detergent micelle size, but cardiolipin stabilizes by direct interactions as well. Cardiolipin reverses destabilizing effects of ADP and bongkrekic acid on AAC2 and enhances large stabilizing effects of carboxyatractyloside, revealing that this lipid interacts in the m-state and possibly other states of the transport cycle, despite being in a dynamic interface. Fatty acid activators destabilize UCP1 in a similar way, which can also be prevented by cardiolipin, indicating that they interact like transport substrates. Our controls show that carriers can be soluble but unfolded in some commonly used detergents, such as the zwitterionic Fos-choline-12, which emphasizes the need for simple validation assays like the one used here. PMID:25653283

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.

Method of growing films by flame synthesis using a stagnation-flow reactor

DOEpatents

Hahn, D.W.; Edwards, C.F.

1998-11-24

A method is described for stabilizing a strained flame in a stagnation flow reactor. By causing a highly strained flame to be divided into a large number of equal size segments it is possible to stablize a highly strained flame that is on the verge of extinction, thereby providing for higher film growth rates. The flame stabilizer is an annular ring mounted coaxially and coplanar with the substrate upon which the film is growing and having a number of vertical pillars mounted on the top surface, thereby increasing the number of azimuthal nodes into which the flame is divided and preserving an axisymmetric structure necessary for stability. 5 figs.

Stabilizing and destabilizing effects of phenylalanine --> F5-phenylalanine mutations on the folding of a small protein.

PubMed

Woll, Matthew G; Hadley, Erik B; Mecozzi, Sandro; Gellman, Samuel H

2006-12-20

We report a systematic evaluation of phenylalanine-to-pentafluorophenylalanine (Phe --> F5-Phe) mutants for the 35-residue chicken villin headpiece subdomain (c-VHP), the hydrophobic core of which features a cluster of three Phe side chains (residues 6, 10, and 17). Phe --> F5-Phe mutations are interesting because aryl-perfluoroaryl interactions of optimal geometry are intrinsically more favorable than aryl-aryl interactions and because perfluoroaryl units are more hydrophobic than are analogous aryl units. One mutant, Phe-10 --> F5-Phe, provides enhanced tertiary structural stability relative to the native sequence. The other six mutants analyzed caused a decrease in stability.

A Molecular Simulation Study of Antibody-Antigen Interactions on Surfaces for the Rational Design of Next-Generation Antibody Microarrays

NASA Astrophysics Data System (ADS)

Bush, Derek B.

Antibody microarrays constitute a next-generation sensing platform that has the potential to revolutionize the way that molecular detection is conducted in many scientific fields. Unfortunately, current technologies have not found mainstream use because of reliability problems that undermine trust in their results. Although several factors are involved, it is believed that undesirable protein interactions with the array surface are a fundamental source of problems where little detail about the molecular-level biophysics are known. A better understanding of antibody stability and antibody-antigen binding on the array surface is needed to improve microarray technology. Despite the availability of many laboratory methods for studying protein stability and binding, these methods either do not work when the protein is attached to a surface or they do not provide the atomistic structural information that is needed to better understand protein behavior on the surface. As a result, molecular simulation has emerged as the primary method for studying proteins on surfaces because it can provide metrics and views of atomistic structures and molecular motion. Using an advanced, coarse-grain, protein-surface model this study investigated how antibodies react to and function on different types of surfaces. Three topics were addressed: (1) the stability of individual antibodies on surfaces, (2) antibody binding to small antigens while on a surface, and (3) antibody binding to large antigens while on a surface. The results indicate that immobilizing antibodies or antibody fragments in an upright orientation on a hydrophilic surface can provide the molecules with thermal stability similar to their native aqueous stability, enhance antigen binding strength, and minimize the entropic cost of binding. Furthermore, the results indicate that it is more difficult for large antigens to approach the surface than small antigens, that multiple binding sites can aid antigen binding, and that antigen flexiblity simultaneously helps and hinders the binding process as it approaches the surface. The results provide hope that next-generation microarrays and other devices decorated with proteins can be improved through rational design.

Disruption of the Putative Vascular Leak Peptide Sequence in the Stabilized Ricin Vaccine Candidate RTA1-33/44-198

PubMed Central

Janosi, Laszlo; Compton, Jaimee R.; Legler, Patricia M.; Steele, Keith E.; Davis, Jon M.; Matyas, Gary R.; Millard, Charles B.

2013-01-01

Vitetta and colleagues identified and characterized a putative vascular leak peptide (VLP) consensus sequence in recombinant ricin toxin A-chain (RTA) that contributed to dose-limiting human toxicity when RTA was administered intravenously in large quantities during chemotherapy. We disrupted this potentially toxic site within the more stable RTA1-33/44-198 vaccine immunogen and determined the impact of these mutations on protein stability, structure and protective immunogenicity using an experimental intranasal ricin challenge model in BALB/c mice to determine if the mutations were compatible. Single amino acid substitutions at the positions corresponding with RTA D75 (to A, or N) and V76 (to I, or M) had minor effects on the apparent protein melting temperature of RTA1-33/44-198 but all four variants retained greater apparent stability than the parent RTA. Moreover, each VLP(−) variant tested provided protection comparable with that of RTA1-33/44-198 against supralethal intranasal ricin challenge as judged by animal survival and several biomarkers. To understand better how VLP substitutions and mutations near the VLP site impact epitope structure, we introduced a previously described thermal stabilizing disulfide bond (R48C/T77C) along with the D75N or V76I substitutions in RTA1-33/44-198. The D75N mutation was compatible with the adjacent stabilizing R48C/T77C disulfide bond and the Tm was unaffected, whereas the V76I mutation was less compatible with the adjacent disulfide bond involving C77. A crystal structure of the RTA1-33/44-198 R48C/T77C/D75N variant showed that the structural integrity of the immunogen was largely conserved and that a stable immunogen could be produced from E. coli. We conclude that it is feasible to disrupt the VLP site in RTA1-33/44-198 with little or no impact on apparent protein stability or protective efficacy in mice and such variants can be stabilized further by introduction of a disulfide bond. PMID:23364220

The orientation construction of S and N dual-doped discoid-like graphene with high-rate electrode property

NASA Astrophysics Data System (ADS)

Song, Xinyu; Ma, Xinlong; Ning, Guoqing; Gao, Daowei; Yu, Zhiqing; Xiao, Zhihua

2018-06-01

The orientation construction of S and N dual-doped discoid-like graphene (labeled as SNDG) is achieved by regular arrangement of the polycyclic aromatics in pitch molecules using natural diatomites as templates. The superior electrochemical energy storage ability of SNDG is demonstrated by cathode and anode tests, respectively. The synergistic effects of the robust scaffold coupled with the hollow structure, unique porous structure, the excellent structural stability and the dual-doping of S and N lead to the electrode property enhancement in terms of rate capability and durability. The Li ion hybrid capacitor using SNDG as both anode and cathode, presents excellent long-term cycling stability and markedly energy and power densities (up to 143 Wh kg-1 and 13,548 W kg-1). This work provides a novel pathway to realize the mass production of high-rate electrode materials via the high value-added utilization of pitch.

Dipole-allowed direct band gap silicon superlattices

PubMed Central

Oh, Young Jun; Lee, In-Ho; Kim, Sunghyun; Lee, Jooyoung; Chang, Kee Joo

2015-01-01

Silicon is the most popular material used in electronic devices. However, its poor optical properties owing to its indirect band gap nature limit its usage in optoelectronic devices. Here we present the discovery of super-stable pure-silicon superlattice structures that can serve as promising materials for solar cell applications and can lead to the realization of pure Si-based optoelectronic devices. The structures are almost identical to that of bulk Si except that defective layers are intercalated in the diamond lattice. The superlattices exhibit dipole-allowed direct band gaps as well as indirect band gaps, providing ideal conditions for the investigation of a direct-to-indirect band gap transition. The fact that almost all structural portions of the superlattices originate from bulk Si warrants their stability and good lattice matching with bulk Si. Through first-principles molecular dynamics simulations, we confirmed their thermal stability and propose a possible method to synthesize the defective layer through wafer bonding. PMID:26656482

Water entrapment and structure ordering as protection mechanisms for protein structural preservation

NASA Astrophysics Data System (ADS)

Arsiccio, A.; Pisano, R.

2018-02-01

In this paper, molecular dynamics is used to further gain insight into the mechanisms by which typical pharmaceutical excipients preserve the protein structure. More specifically, the water entrapment scenario will be analyzed, which states that excipients form a cage around the protein, entrapping and slowing water molecules. Human growth hormone will be used as a model protein, but the results obtained are generally applicable. We will show that water entrapment, as well as the other mechanisms of protein stabilization in the dried state proposed so far, may be related to the formation of a dense hydrogen bonding network between excipient molecules. We will also present a simple phenomenological model capable of explaining the behavior and stabilizing effect provided by typical cryo- and lyo-protectants. This model uses, as input data, molecular properties which can be easily evaluated. We will finally show that the model predictions compare fairly well with experimental data.

In Situ Synthesis of Vertical Standing Nanosized NiO Encapsulated in Graphene as Electrodes for High-Performance Supercapacitors.

PubMed

Lin, Jinghuang; Jia, Henan; Liang, Haoyan; Chen, Shulin; Cai, Yifei; Qi, Junlei; Qu, Chaoqun; Cao, Jian; Fei, Weidong; Feng, Jicai

2018-03-01

NiO is a promising electrode material for supercapacitors. Herein, the novel vertically standing nanosized NiO encapsulated in graphene layers (G@NiO) are rationally designed and synthesized as nanosheet arrays. This unique vertical standing structure of G@NiO nanosheet arrays can enlarge the accessible surface area with electrolytes, and has the benefits of short ion diffusion path and good charge transport. Further, an interconnected graphene conductive network acts as binder to encapsulate the nanosized NiO particles as core-shell structure, which can promote the charge transport and maintain the structural stability. Consequently, the optimized G@NiO hybrid electrodes exhibit a remarkably enhanced specific capacity up to 1073 C g -1 and excellent cycling stability. This study provides a facial strategy to design and construct high-performance metal oxides for energy storage.

AuRu/AC as an effective catalyst for hydrogenation reactions

DOE PAGES

Villa, Alberto; Chan-Thaw, Carine E.; Campisi, Sebastiano; ...

2015-03-23

AuRu bimetallic catalysts have been prepared by sequential deposition of Au on Ru or vice versa obtaining different nanostructures: when Ru has been deposited on Au, a Au core–Ru shell has been observed, whereas the deposition of Au on Ru leads to a bimetallic phase with Ru enrichment on the surface. In the latter case, the unexpected Ru enrichment could be attributed to the weak adhesion of Ru on the carbon support, thus allowing Ru particles to diffuse on Au particles. Both structures result very active in catalysing the liquid phase hydrogenolysis of glycerol and levulinic acid but the activity,more » the selectivity and the stability depend on the structure of the bimetallic nanoparticles. Ru@Au/AC core–shell structure mostly behaved as the monometallic Ru, whereas the presence of bimetallic AuRu phase in Au@Ru/AC provides a great beneficial effect on both activity and stability.« less

Cubic martensite in high carbon steel

NASA Astrophysics Data System (ADS)

Chen, Yulin; Xiao, Wenlong; Jiao, Kun; Ping, Dehai; Xu, Huibin; Zhao, Xinqing; Wang, Yunzhi

2018-05-01

A distinguished structural characteristic of martensite in Fe-C steels is its tetragonality originating from carbon atoms occupying only one set of the three available octahedral interstitial sites in the body-centered-cubic (bcc) Fe lattice. Such a body-centered-tetragonal (bct) structure is believed to be thermodynamically stable because of elastic interactions between the interstitial carbon atoms. For such phase stability, however, there has been a lack of direct experimental evidence despite extensive studies of phase transformations in steels over one century. In this Rapid Communication, we report that the martensite formed in a high carbon Fe-8Ni-1.26C (wt%) steel at room temperature induced by applied stress/strain has actually a bcc rather than a bct crystal structure. This finding not only challenges the existing theories on the stability of bcc vs bct martensite in high carbon steels, but also provides insights into the mechanism for martensitic transformation in ferrous alloys.

Proceedings of the Workshop on Identification and Control of Flexible Space Structures, Volume 2

NASA Technical Reports Server (NTRS)

Rodriguez, G. (Editor)

1985-01-01

The results of a workshop on identification and control of flexible space structures held in San Diego, CA, July 4 to 6, 1984 are discussed. The main objectives of the workshop were to provide a forum to exchange ideas in exploring the most advanced modeling, estimation, identification and control methodologies to flexible space structures. The workshop responded to the rapidly growing interest within NASA in large space systems (space station, platforms, antennas, flight experiments) currently under design. Dynamic structural analysis, control theory, structural vibration and stability, and distributed parameter systems are discussed.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

A structural equation model relating impaired sensorimotor function, fear of falling and gait patterns in older people.

PubMed

Menz, Hylton B; Lord, Stephen R; Fitzpatrick, Richard C

2007-02-01

Many falls in older people occur while walking, however the mechanisms responsible for gait instability are poorly understood. Therefore, the aim of this study was to develop a plausible model describing the relationships between impaired sensorimotor function, fear of falling and gait patterns in older people. Temporo-spatial gait parameters and acceleration patterns of the head and pelvis were obtained from 100 community-dwelling older people aged between 75 and 93 years while walking on an irregular walkway. A theoretical model was developed to explain the relationships between these variables, assuming that head stability is a primary output of the postural control system when walking. This model was then tested using structural equation modeling, a statistical technique which enables the testing of a set of regression equations simultaneously. The structural equation model indicated that: (i) reduced step length has a significant direct and indirect association with reduced head stability; (ii) impaired sensorimotor function is significantly associated with reduced head stability, but this effect is largely indirect, mediated by reduced step length, and; (iii) fear of falling is significantly associated with reduced step length, but has little direct influence on head stability. These findings provide useful insights into the possible mechanisms underlying gait characteristics and risk of falling in older people. Particularly important is the indication that fear-related step length shortening may be maladaptive.

How ligands improve the hydrothermal stability and affect the adsorption in the IRMOF family.

PubMed

Bellarosa, Luca; Gutiérrez-Sevillano, Juan J; Calero, Sofía; López, Núria

2013-10-28

Metal-Organic Frameworks are considered to be the next generation of sorbents both because of their synthetic versatility and high selectivity potential. In the first generation (IRMOF), the main drawback for commercial implementation is the lack of hydrothermal stability. Even if several studies have been conducted to elucidate the reasons behind their structural weakness in humid environments, how apparently small changes in the stoichiometry of the building units affect the stability of the lattice is still poorly understood. Using density functional theory and ab initio molecular dynamics we investigated the reason behind the different behaviour of several substituted IRMOF-1 structures. We show that hydrophilic variations in the organic linkers work as new basins of attraction for the incoming water molecules, thus depleting the water content at the metal center. To confirm this, we performed Monte Carlo simulations to provide insights into the adsorption energies and check the effectiveness of the adsorption sites in the substituted structures for a variety of polar and non-polar molecules. The results show that linker modification affects molecular adsorption and can improve the overall stability of the lattice redirecting water to the new sites in the case of hydrophilic units. Three key parameters have been singled out to rationalize this behaviour, and used to predict the favoured adsorption sites in the case of gas mixtures.

Control-structure interaction in precision pointing servo loops

NASA Technical Reports Server (NTRS)

Spanos, John T.

1989-01-01

The control-structure interaction problem is addressed via stability analysis of a generic linear servo loop model. With the plant described by the rigid body mode and a single elastic mode, structural flexibility is categorized into one of three types: (1) appendage, (2) in-the-loop minimum phase, and (3) in-the-loop nonminimum phase. Closing the loop with proportional-derivative (PD) control action and introducing sensor roll-off dynamics in the feedback path, stability conditions are obtained. Trade studies are conducted with modal frequency, modal participation, modal damping, loop bandwidth, and sensor bandwidth treated as free parameters. Results indicate that appendage modes are most likely to produce instability if they are near the sensor rolloff, whereas in-the-loop modes are most dangerous near the loop bandwidth. The main goal of this paper is to provide a fundamental understanding of the control-structure interaction problem so that it may benefit the design of complex spacecraft and pointing system servo loops. In this framework, the JPL Pathfinder gimbal pointer is considered as an example.

High performance EUV multilayer structures insensitive to capping layer optical parameters.

PubMed

Pelizzo, Maria Guglielmina; Suman, Michele; Monaco, Gianni; Nicolosi, Piergiorgio; Windt, David L

2008-09-15

We have designed and tested a-periodic multilayer structures containing protective capping layers in order to obtain improved stability with respect to any possible changes of the capping layer optical properties (due to oxidation and contamination, for example)-while simultaneously maximizing the EUV reflection efficiency for specific applications, and in particular for EUV lithography. Such coatings may be particularly useful in EUV lithographic apparatus, because they provide both high integrated photon flux and higher stability to the harsh operating environment, which can affect seriously the performance of the multilayer-coated projector system optics. In this work, an evolutive algorithm has been developed in order to design these a-periodic structures, which have been proven to have also the property of stable performance with respect to random layer thickness errors that might occur during coating deposition. Prototypes have been fabricated, and tested with EUV and X-ray reflectometry, and secondary electron spectroscopy. The experimental results clearly show improved performance of our new a-periodic coatings design compared with standard periodic multilayer structures.

Flexible all-carbon photovoltaics with improved thermal stability

NASA Astrophysics Data System (ADS)

Tang, Chun; Ishihara, Hidetaka; Sodhi, Jaskiranjeet; Chen, Yen-Chang; Siordia, Andrew; Martini, Ashlie; Tung, Vincent C.

2015-04-01

The structurally robust nature of nanocarbon allotropes, e.g., semiconducting single-walled carbon nanotubes (SWCNTs) and C60s, makes them tantalizing candidates for thermally stable and mechanically flexible photovoltaic applications. However, C60s rapidly dissociate away from the basal of SWCNTs under thermal stimuli as a result of weak intermolecular forces that "lock up" the binary assemblies. Here, we explore use of graphene nanoribbons (GNRs) as geometrically tailored protecting layers to suppress the unwanted dissociation of C60s. The underlying mechanisms are explained using a combination of molecular dynamics simulations and transition state theory, revealing the temperature dependent disassociation of C60s from the SWCNT basal plane. Our strategy provides fundamental guidelines for integrating all-carbon based nano-p/n junctions with optimized structural and thermal stability. External quantum efficiency and output current-voltage characteristics are used to experimentally quantify the effectiveness of GNR membranes under high temperature annealing. Further, the resulting C60:SWCNT:GNR ternary composites display excellent mechanical stability, even after iterative bending tests.

Conformational Changes in Orotidine 5-Monophosphate Decarboxylase: "Remote" Residues That Stabilize the Active Conformation

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

Wood, B.; Amyes, T; Fedorov, A

2010-01-01

The structural factors responsible for the extraordinary rate enhancement ({approx}10{sup 17}) of the reaction catalyzed by orotidine 5{prime}-monophosphate decarboxylase (OMPDC) have not been defined. Catalysis requires a conformational change that closes an active site loop and 'clamps' the orotate base proximal to hydrogen-bonded networks that destabilize the substrate and stabilize the intermediate. In the OMPDC from Methanobacter thermoautotrophicus, a 'remote' structurally conserved cluster of hydrophobic residues that includes Val 182 in the active site loop is assembled in the closed, catalytically active conformation. Substitution of these residues with Ala decreases k{sub cat}/K{sub m} with a minimal effect on k{sub cat},more » providing evidence that the cluster stabilizes the closed conformation. The intrinsic binding energies of the 5{prime}-phosphate group of orotidine 5{prime}-monophosphate for the mutant enzymes are similar to that for the wild type, supporting this conclusion.« less

Osmolyte effects on helix formation in peptides and the stability of coiled-coils

PubMed Central

Celinski, Scott A.; Scholtz, J. Martin

2002-01-01

The ability of several naturally occurring substances known as osmolytes to induce helix formation in an alanine-based peptide have been investigated. As predicted by the osmophobic effect hypothesis, the osmolytes studies here do induce helix formation. Trimethylamine-N-oxide (TMAO) is the best structure-inducing osmolytes investigated here, but it is not as effective in promoting helix formation as the common cosolvent trifluoroethanol (TFE). We also provide a semiquantitative study of the ability of TMAO to induce helix formation and urea, which acts as a helix (and protein) denaturant. We find that on a molar basis, these agents are exactly counteractive as structure inducing and unfolding agents. Finally, we extend the investigations to the effects of urea and TMAO on the stability of a dimeric coiled-coil peptide and find identical results. Together these results support the tenets of the osmophobic hypothesis and highlight the importance of the polypeptide backbone in protein folding and stability. PMID:12142459

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

Roland, Bartholomew P.; Amrich, Christopher G.; Kammerer, Charles J.

Triosephosphate isomerase (TPI) is a glycolytic enzyme which homodimerizes for full catalytic activity. Mutations of the TPI gene elicit a disease known as TPI Deficiency, a glycolytic enzymopathy noted for its unique severity of neurological symptoms. Evidence suggests that TPI Deficiency pathogenesis may be due to conformational changes of the protein, likely affecting dimerization and protein stability. In this report, we genetically and physically characterize a human disease-associated TPI mutation caused by an I170V substitution. Human TPI I170V elicits behavioral abnormalities in Drosophila. An examination of hTPI I170V enzyme kinetics revealed this substitution reduced catalytic turnover, while assessments of thermalmore » stability demonstrated an increase in enzyme stability. Furthermore, the crystal structure of the homodimeric I170V mutant reveals changes in the geometry of critical residues within the catalytic pocket. In the end, collectively these data reveal new observations of the structural and kinetic determinants of TPI deficiency pathology, providing new insights into disease pathogenesis.« less

Molecular mechanism for USP7-mediated DNMT1 stabilization by acetylation

NASA Astrophysics Data System (ADS)

Cheng, Jingdong; Yang, Huirong; Fang, Jian; Ma, Lixiang; Gong, Rui; Wang, Ping; Li, Ze; Xu, Yanhui

2015-05-01

DNMT1 is an important epigenetic regulator that plays a key role in the maintenance of DNA methylation. Here we determined the crystal structure of DNMT1 in complex with USP7 at 2.9 Å resolution. The interaction between the two proteins is primarily mediated by an acidic pocket in USP7 and Lysine residues within DNMT1's KG linker. This intermolecular interaction is required for USP7-mediated stabilization of DNMT1. Acetylation of the KG linker Lysine residues impair DNMT1-USP7 interaction and promote the degradation of DNMT1. Treatment with HDAC inhibitors results in an increase in acetylated DNMT1 and decreased total DNMT1 protein. This negative correlation is observed in differentiated neuronal cells and pancreatic cancer cells. Our studies reveal that USP7-mediated stabilization of DNMT1 is regulated by acetylation and provide a structural basis for the design of inhibitors, targeting the DNMT1-USP7 interaction surface for therapeutic applications.

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

NASA Astrophysics Data System (ADS)

Sun, Yuming; Wu, Christine Qiong

2012-12-01

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

Structural insights into methanol-stable variants of lipase T6 from Geobacillus stearothermophilus.

PubMed

Dror, Adi; Kanteev, Margarita; Kagan, Irit; Gihaz, Shalev; Shahar, Anat; Fishman, Ayelet

2015-11-01

Enzymatic production of biodiesel by transesterification of triglycerides and alcohol, catalyzed by lipases, offers an environmentally friendly and efficient alternative to the chemically catalyzed process while using low-grade feedstocks. Methanol is utilized frequently as the alcohol in the reaction due to its reactivity and low cost. However, one of the major drawbacks of the enzymatic system is the presence of high methanol concentrations which leads to methanol-induced unfolding and inactivation of the biocatalyst. Therefore, a methanol-stable lipase is of great interest for the biodiesel industry. In this study, protein engineering was applied to substitute charged surface residues with hydrophobic ones to enhance the stability in methanol of a lipase from Geobacillus stearothermophilus T6. We identified a methanol-stable variant, R374W, and combined it with a variant found previously, H86Y/A269T. The triple mutant, H86Y/A269T/R374W, had a half-life value at 70 % methanol of 324 min which reflects an 87-fold enhanced stability compared to the wild type together with elevated thermostability in buffer and in 50 % methanol. This variant also exhibited an improved biodiesel yield from waste chicken oil compared to commercial Lipolase 100L® and Novozyme® CALB. Crystal structures of the wild type and the methanol-stable variants provided insights regarding structure-stability correlations. The most prominent features were the extensive formation of new hydrogen bonds between surface residues directly or mediated by structural water molecules and the stabilization of Zn and Ca binding sites. Mutation sites were also characterized by lower B-factor values calculated from the X-ray structures indicating improved rigidity.

Solvent dielectric effect and side chain mutation on the structural stability of Burkholderia cepacia lipase active site: a quantum mechanical/molecular mechanics study.

PubMed

Tahan, A; Monajjemi, M

2011-12-01

Quantum mechanical and molecular dynamics methods were used to analyze the structure and stability of neutral and zwitterionic configurations of the extracted active site sequence from a Burkholderia cepacia lipase, histidyl-seryl-glutamin (His86-Ser87-Gln88) and its mutated form, histidyl-cysteyl-glutamin (His86-Cys87-Gln88) in vacuum and different solvents. The effects of solvent dielectric constant, explicit and implicit water molecules and side chain mutation on the structure and stability of this sequence in both neutral and zwitterionic forms are represented. The quantum mechanics computations represent that the relative stability of zwitterionic and neutral configurations depends on the solvent structure and its dielectric constant. Therefore, in vacuum and the considered non-polar solvents, the neutral form of the interested sequences is more stable than the zwitterionic form, while their zwitterionic form is more stable than the neutral form in the aqueous solution and the investigated polar solvents in most cases. However, on the potential energy surfaces calculated, there is a barrier to proton transfer from the positively charged ammonium group to the negatively charged carboxylat group or from the ammonium group to the adjacent carbonyl oxygen and or from side chain oxygen and sulfur to negatively charged carboxylat group. Molecular dynamics simulations (MD) were also performed by using periodic boundary conditions for the zwitterionic configuration of the hydrated molecules in a box of water molecules. The obtained results demonstrated that the presence of explicit water molecules provides the more compact structures of the studied molecules. These simulations also indicated that side chain mutation and replacement of sulfur with oxygen leads to reduction of molecular flexibility and packing.

Performance and quality-control standards for composite floor, wall, and truss framing

Treesearch

Gerald A. Koenigshof

1985-01-01

Users must be assured that composite structural members are satisfactory for their intended purposes. Standards are provided for strength, stiffness, durability, and dimensional stability of composite floor, wall, and truss-framing members. Methods for enforcing compliance with the standards are suggested.

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

PubMed

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

2017-06-01

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

Structure evolution and thermal stability of high-energy density Li-ion battery cathode Li 2VO 2F

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

Wang, Xiaoya; Huang, Yiqing; Ji, Dongsheng

Lithium-ion batteries (LIBs) provide high-energy-density electrochemical energy storage, which plays a central role in advancing technologies ranging from portable electronics to electric vehicles (EVs). However, a demand for lighter, more compact devices and for extended range EVs continues to fuel the need for higher energy density storage systems. Li 2VO 2F, which is synthesized in its lithiated state, allows two-electron transfer per formula during the electrochemical reaction providing a high theoretical capacity of 462 mAh/g. Herein, the synthesis and electrochemical performance of Li 2VO 2F are optimized. The thermal stability of Li 2VO 2F, which is related to the safetymore » of a battery is studied by thermal gravimetric analysis. The structure and vanadium oxidation state evolution along Li cycling are studied by ex-situ X-ray diffraction and absorption techniques. It is shown that the rock-salt structure of pristine Li 2VO 2F is stable up to at least 250°C, and is preserved upon Li cycling, which proceeds by the solid-solution mechanism. However, not all Li can be removed from the structure upon charge to 4.5 V, limiting the experimentally obtained capacity.« less

Structure evolution and thermal stability of high-energy density Li-ion battery cathode Li 2VO 2F

DOE PAGES

Wang, Xiaoya; Huang, Yiqing; Ji, Dongsheng; ...

2017-05-24

Lithium-ion batteries (LIBs) provide high-energy-density electrochemical energy storage, which plays a central role in advancing technologies ranging from portable electronics to electric vehicles (EVs). However, a demand for lighter, more compact devices and for extended range EVs continues to fuel the need for higher energy density storage systems. Li 2VO 2F, which is synthesized in its lithiated state, allows two-electron transfer per formula during the electrochemical reaction providing a high theoretical capacity of 462 mAh/g. Herein, the synthesis and electrochemical performance of Li 2VO 2F are optimized. The thermal stability of Li 2VO 2F, which is related to the safetymore » of a battery is studied by thermal gravimetric analysis. The structure and vanadium oxidation state evolution along Li cycling are studied by ex-situ X-ray diffraction and absorption techniques. It is shown that the rock-salt structure of pristine Li 2VO 2F is stable up to at least 250°C, and is preserved upon Li cycling, which proceeds by the solid-solution mechanism. However, not all Li can be removed from the structure upon charge to 4.5 V, limiting the experimentally obtained capacity.« less

Evolutionary Dynamics on Protein Bi-stability Landscapes can Potentially Resolve Adaptive Conflicts

PubMed Central

Sikosek, Tobias; Bornberg-Bauer, Erich; Chan, Hue Sun

2012-01-01

Experimental studies have shown that some proteins exist in two alternative native-state conformations. It has been proposed that such bi-stable proteins can potentially function as evolutionary bridges at the interface between two neutral networks of protein sequences that fold uniquely into the two different native conformations. Under adaptive conflict scenarios, bi-stable proteins may be of particular advantage if they simultaneously provide two beneficial biological functions. However, computational models that simulate protein structure evolution do not yet recognize the importance of bi-stability. Here we use a biophysical model to analyze sequence space to identify bi-stable or multi-stable proteins with two or more equally stable native-state structures. The inclusion of such proteins enhances phenotype connectivity between neutral networks in sequence space. Consideration of the sequence space neighborhood of bridge proteins revealed that bi-stability decreases gradually with each mutation that takes the sequence further away from an exactly bi-stable protein. With relaxed selection pressures, we found that bi-stable proteins in our model are highly successful under simulated adaptive conflict. Inspired by these model predictions, we developed a method to identify real proteins in the PDB with bridge-like properties, and have verified a clear bi-stability gradient for a series of mutants studied by Alexander et al. (Proc Nat Acad Sci USA 2009, 106:21149–21154) that connect two sequences that fold uniquely into two different native structures via a bridge-like intermediate mutant sequence. Based on these findings, new testable predictions for future studies on protein bi-stability and evolution are discussed. PMID:23028272

Improving the accuracy of protein stability predictions with multistate design using a variety of backbone ensembles.

PubMed

Davey, James A; Chica, Roberto A

2014-05-01

Multistate computational protein design (MSD) with backbone ensembles approximating conformational flexibility can predict higher quality sequences than single-state design with a single fixed backbone. However, it is currently unclear what characteristics of backbone ensembles are required for the accurate prediction of protein sequence stability. In this study, we aimed to improve the accuracy of protein stability predictions made with MSD by using a variety of backbone ensembles to recapitulate the experimentally measured stability of 85 Streptococcal protein G domain β1 sequences. Ensembles tested here include an NMR ensemble as well as those generated by molecular dynamics (MD) simulations, by Backrub motions, and by PertMin, a new method that we developed involving the perturbation of atomic coordinates followed by energy minimization. MSD with the PertMin ensembles resulted in the most accurate predictions by providing the highest number of stable sequences in the top 25, and by correctly binning sequences as stable or unstable with the highest success rate (≈90%) and the lowest number of false positives. The performance of PertMin ensembles is due to the fact that their members closely resemble the input crystal structure and have low potential energy. Conversely, the NMR ensemble as well as those generated by MD simulations at 500 or 1000 K reduced prediction accuracy due to their low structural similarity to the crystal structure. The ensembles tested herein thus represent on- or off-target models of the native protein fold and could be used in future studies to design for desired properties other than stability. Copyright © 2013 Wiley Periodicals, Inc.

Developing a Novel, Interdisciplinary Approach to Study Protein Unfolding

NASA Astrophysics Data System (ADS)

Bentley, Ian; Link, Justin

2013-03-01

The ability of a protein to function is a direct result of its ability to properly obtain its native, folded structure. In order to determine the structural stability of proteins and to gain knowledge of their folding mechanism, we must develop protocols that allow us to monitor the controlled unfolding of proteins. Here, we investigate the stability of cytochrome c, a well-studied, model protein, under denaturing conditions using circular dichroism (CD) and fluorescence. Using either a chemical denaturant (Guanidine HCl) or heat, we can cause a protein to gradually unfold. The changes in the fluorescence and CD spectra can provide insight into the stability of proteins by providing us with thermodynamic parameters such as the Gibbs free energy, melting temperature and enthalpy. Research in this lab has been explored with mutant proteins and change in CD signal, however further work must still be done to observe their unfolding monitored by fluorescence. This technique will allow us to determine which regions of native cytochrome c have the greatest impact on the protein folding process. The objective of this session is to present recent work in developing a protocol to observe the unfolding of wild type and mutant proteins with fluorescence. The Borcer Fund, The John A. Hauck Foundation, and Xavier University

Design, Synthesis, and Evaluation of Novel p-(methylthio)styryl Substituted Quindoline Derivatives as Neuroblastoma RAS (NRAS) Repressors via Specific Stabilizing the RNA G-Quadruplex.

PubMed

Peng, Wang; Sun, Zhi-Yin; Zhang, Qi; Cheng, Sui-Qi; Wang, Shi-Ke; Wang, Xiao-Na; Kuang, Guo-Tao; Su, Xiao-Xuan; Tan, Jia-Heng; Huang, Zhi-Shu; Ou, Tian-Miao

2018-05-25

The human proto-oncogene neuroblastoma RAS (NRAS) contains a guanine-rich sequence in the 5'-untranslated regions (5'-UTR) of the mRNA that could form an RNA G-quadruplex structure. This structure acts as a repressor for NRAS translation and could be a potential target for anti-cancer drugs. Our previous studies found an effective scaffold, the quindoline scaffold, for binding and stabilizing the DNA G-quadruplex structures. Here, basing on the previous studies and reported RNA-specific probes, a series of novel p-(methylthio)styryl substituted quindoline (MSQ) derivatives were designed, synthesized and evaluated as NRAS RNA G-quadruplex ligands. Panels of experiments turned out that the introduction of p-(methylthio)styryl side chain could enhance the specific binding to the NRAS RNA G-quadruplex. One of the hits, 4a-10, showed strong stabilizing activity on the G-quadruplex, and subsequently repressed NRAS's translation and inhibited tumor cells proliferation. Our finding provided a novel strategy to discover novel NRAS repressors by specifically binding to the RNA G-quadruplex in the 5'-UTR of mRNA.

Electrochemical performance and durability of carbon supported Pt catalyst in contact with aqueous and polymeric proton conductors.

PubMed

Andersen, Shuang Ma; Skou, Eivind

2014-10-08

Significant differences in catalyst performance and durability are often observed between the use of a liquid electrolyte (e.g., sulfuric acid), and a solid polymer electrolyte (e.g., Nafion). To understand this phenomenon, we studied the electrochemical behavior of a commercially available carbon supported platinum catalyst in four different electrode structures: catalyst powder (CP), catalyst ionomer electrode (CIE), half membrane electrode assembly (HMEA), and full membrane electrode assembly (FMEA) in both ex situ and in situ experiments under a simulated start/stop cycle. We found that the catalyst performance and stability are very much influenced by the presence of the Nafion ionomers. The proton conducting phase provided by the ionomer and the self-assembled electrode structure render the catalysts a higher utilization and better stability. This is probably due to an enhanced dispersion, an improved proton-catalyst interface, the restriction of catalyst particle aggregation, and the improved stability of the ionomer phase especially after the lamination. Therefore, an innovative electrode HMEA design for ex-situ catalyst characterization is proposed. The electrode structure is identical to the one used in a real fuel cell, where the protons transport takes place solely through solid state proton conducting phase.

Impact of IgG Fc-Oligosaccharides on Recombinant Monoclonal Antibody Structure, Stability, Safety, and Efficacy.

PubMed

Liu, Hongcheng; Nowak, Christine; Andrien, Bruce; Shao, Mei; Ponniah, Gomathinayagam; Neill, Alyssa

2017-09-01

Glycosylation of the conserved asparagine residue in the CH2 domain is the most common posttranslational modification of recombinant monoclonal antibodies. Ideally, a consistent oligosaccharide profile should be maintained from early clinical material to commercial material for the development of recombinant monoclonal therapeutics, though variation in the profile is a typical result of process changes. The risk of oligosaccharide variation posed to further development is required to be thoroughly evaluated based on its impact on antibody structure, stability, efficacy and safety. The variation should be controlled within a range so that there is no detrimental impact on safety and efficacy and thus allowing the use of early phase safety and efficacy data to support project advancement to later phase. This review article focuses on the current scientific understanding of the commonly observed oligosaccharides found in recombinant monoclonal antibodies and their impact on structure, stability and biological functions, which are the basis to evaluate safety and efficacy. It also provides a brief discussion on critical quality attribute (CQA) assessment with regard to oligosaccharides based on the mechanism of action (MOA). © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 33:1173-1181, 2017. © 2017 American Institute of Chemical Engineers.

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

NASA Technical Reports Server (NTRS)

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

1987-01-01

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

Sorbitol counteracts temperature- and chemical-induced denaturation of a recombinant α-amylase from alkaliphilic Bacillus sp. TS-23.

PubMed

Chi, Meng-Chun; Wu, Tai-Jung; Chen, Hsing-Ling; Lo, Huei-Fen; Lin, Long-Liu

2012-12-01

Enzymes are highly complex systems with a substantial degree of structural variability in their folded state. In the presence of cosolvents, fluctuations among vast numbers of folded and unfolded conformations occur via many different pathways; alternatively, certain conformations can be stabilized or destabilized. To understand the contribution of osmolytes to the stabilization of structural changes and enzymatic activity of a truncated Bacillus sp. TS-23 α-amylase (BACΔNC), we monitored amylolytic activity, circular dichroism, and fluorescence as a function of osmolytes. In the presence of trimethylamine N-oxide (TMAO) and sorbitol, BACΔNC activity was retained significantly at elevated temperatures. As compared to the control, the secondary structures of this enzyme were essentially conserved upon the addition of these two kinds of osmolytes. Fluorescence results revealed that the temperature-induced conformational change of BACΔNC was prevented by TMAO and sorbitol. However, glycerol did not provide profound protection against thermal denaturation of the enzyme. Sorbitol was further found to counteract guanidine hydrochloride- and SDS-induced denaturation of BACΔNC. Thus, some well-known naturally occurring osmolytes make a dominant contribution to the stabilization of BACΔNC.

Crystal Structures of RMI1 and RMI2, Two OB-Fold Regulatory Subunits of the BLM Complex

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

Wang, Feng; Yang, Yuting; Singh, Thiyam Ramsing

Mutations in BLM, a RecQ-like helicase, are linked to the autosomal recessive cancer-prone disorder Bloom's syndrome. BLM associates with topoisomerase (Topo) III{alpha}, RMI1, and RMI2 to form the BLM complex that is essential for genome stability. The RMI1-RMI2 heterodimer stimulates the dissolution of double Holliday junction into non-crossover recombinants mediated by BLM-Topo III{alpha} and is essential for stabilizing the BLM complex. However, the molecular basis of these functions of RMI1 and RMI2 remains unclear. Here we report the crystal structures of multiple domains of RMI1-RMI2, providing direct confirmation of the existence of three oligonucleotide/oligosaccharide binding (OB)-folds in RMI1-RMI2. Our structuralmore » and biochemical analyses revealed an unexpected insertion motif in RMI1N-OB, which is important for stimulating the dHJ dissolution. We also revealed the structural basis of the interaction between RMI1C-OB and RMI2-OB and demonstrated the functional importance of the RMI1-RMI2 interaction in genome stability maintenance.« less

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.

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

Vener, M. V., E-mail: mikhail.vener@gmail.com; Odinokov, A. V.; Wehmeyer, C.

Salt bridges and ionic interactions play an important role in protein stability, protein-protein interactions, and protein folding. Here, we provide the classical MD simulations of the structure and IR signatures of the arginine (Arg)–glutamate (Glu) salt bridge. The Arg-Glu model is based on the infinite polyalanine antiparallel two-stranded β-sheet structure. The 1 μs NPT simulations show that it preferably exists as a salt bridge (a contact ion pair). Bidentate (the end-on and side-on structures) and monodentate (the backside structure) configurations are localized [Donald et al., Proteins 79, 898–915 (2011)]. These structures are stabilized by the short {sup +}N–H⋯O{sup −} bonds.more » Their relative stability depends on a force field used in the MD simulations. The side-on structure is the most stable in terms of the OPLS-AA force field. If AMBER ff99SB-ILDN is used, the backside structure is the most stable. Compared with experimental data, simulations using the OPLS all-atom (OPLS-AA) force field describe the stability of the salt bridge structures quite realistically. It decreases in the following order: side-on > end-on > backside. The most stable side-on structure lives several nanoseconds. The less stable backside structure exists a few tenth of a nanosecond. Several short-living species (solvent shared, completely separately solvated ionic groups ion pairs, etc.) are also localized. Their lifetime is a few tens of picoseconds or less. Conformational flexibility of amino acids forming the salt bridge is investigated. The spectral signature of the Arg-Glu salt bridge is the IR-intensive band around 2200 cm{sup −1}. It is caused by the asymmetric stretching vibrations of the {sup +}N–H⋯O{sup −} fragment. Result of the present paper suggests that infrared spectroscopy in the 2000–2800 frequency region may be a rapid and quantitative method for the study of salt bridges in peptides and ionic interactions between proteins. This region is usually not considered in spectroscopic studies of peptides and proteins.« less

De novo design of the hydrophobic core of ubiquitin.

PubMed Central

Lazar, G. A.; Desjarlais, J. R.; Handel, T. M.

1997-01-01

We have previously reported the development and evaluation of a computational program to assist in the design of hydrophobic cores of proteins. In an effort to investigate the role of core packing in protein structure, we have used this program, referred to as Repacking of Cores (ROC), to design several variants of the protein ubiquitin. Nine ubiquitin variants containing from three to eight hydrophobic core mutations were constructed, purified, and characterized in terms of their stability and their ability to adopt a uniquely folded native-like conformation. In general, designed ubiquitin variants are more stable than control variants in which the hydrophobic core was chosen randomly. However, in contrast to previous results with 434 cro, all designs are destabilized relative to the wild-type (WT) protein. This raises the possibility that beta-sheet structures have more stringent packing requirements than alpha-helical proteins. A more striking observation is that all variants, including random controls, adopt fairly well-defined conformations, regardless of their stability. This result supports conclusions from the cro studies that non-core residues contribute significantly to the conformational uniqueness of these proteins while core packing largely affects protein stability and has less impact on the nature or uniqueness of the fold. Concurrent with the above work, we used stability data on the nine ubiquitin variants to evaluate and improve the predictive ability of our core packing algorithm. Additional versions of the program were generated that differ in potential function parameters and sampling of side chain conformers. Reasonable correlations between experimental and predicted stabilities suggest the program will be useful in future studies to design variants with stabilities closer to that of the native protein. Taken together, the present study provides further clarification of the role of specific packing interactions in protein structure and stability, and demonstrates the benefit of using systematic computational methods to predict core packing arrangements for the design of proteins. PMID:9194177

Aeroelastic Stability Investigations for Large-scale Vertical Axis Wind Turbines

NASA Astrophysics Data System (ADS)

Owens, B. C.; Griffith, D. T.

2014-06-01

The availability of offshore wind resources in coastal regions, along with a high concentration of load centers in these areas, makes offshore wind energy an attractive opportunity for clean renewable electricity production. High infrastructure costs such as the offshore support structure and operation and maintenance costs for offshore wind technology, however, are significant obstacles that need to be overcome to make offshore wind a more cost-effective option. A vertical-axis wind turbine (VAWT) rotor configuration offers a potential transformative technology solution that significantly lowers cost of energy for offshore wind due to its inherent advantages for the offshore market. However, several potential challenges exist for VAWTs and this paper addresses one of them with an initial investigation of dynamic aeroelastic stability for large-scale, multi-megawatt VAWTs. The aeroelastic formulation and solution method from the BLade Aeroelastic STability Tool (BLAST) for HAWT blades was employed to extend the analysis capability of a newly developed structural dynamics design tool for VAWTs. This investigation considers the effect of configuration geometry, material system choice, and number of blades on the aeroelastic stability of a VAWT, and provides an initial scoping for potential aeroelastic instabilities in large-scale VAWT designs.

Influence of Endo- and Exocyclic Heteroatoms on Stabilities and 1,3-Dipolar Cycloaddition Reactivities of Mesoionic Azomethine Ylides and Imines.

PubMed

Champagne, Pier Alexandre; Houk, K N

2017-10-20

The geometries, stabilities, and 1,3-dipolar cycloaddition reactivities of 24 mesoionic azomethine ylides and imines were investigated using density functional theory calculations at the M06-2X/6-311+G-(d,p)/M06-2X/6-31G-(d) level. The computed structures highlight how the commonly used "aromatic" resonance form should be replaced by two more accurate resonance structures. Stabilities of the dipoles were assessed by various homodesmotic schemes and are consistent with these compounds being nonaromatic. The activation free energies with ethylene or acetylene range from 11.8 to 36.6 kcal/mol. Within each dipole type, the predicted cycloaddition reactivities correlate with the reaction energies and the resonance stabilization energies provided by the various substituents. Endocyclic (X) heteroatoms increase the reactivity of the 1,3-dipoles in the order of O > NH ≅ S, whereas exocyclic (Y) substituents increase it in the order of CH 2 > NH > O > S. Distortion/interaction analysis indicated that the difference in reactivity between differently substituted 1,3-dipoles is driven by distortion, whereas the difference between azomethine ylides and imines is related to lower interaction energies of imines with the dipolarophiles.

De novo self-assembling collagen heterotrimers using explicit positive and negative design.

PubMed

Xu, Fei; Zhang, Lei; Koder, Ronald L; Nanda, Vikas

2010-03-23

We sought to computationally design model collagen peptides that specifically associate as heterotrimers. Computational design has been successfully applied to the creation of new protein folds and functions. Despite the high abundance of collagen and its key role in numerous biological processes, fibrous proteins have received little attention as computational design targets. Collagens are composed of three polypeptide chains that wind into triple helices. We developed a discrete computational model to design heterotrimer-forming collagen-like peptides. Stability and specificity of oligomerization were concurrently targeted using a combined positive and negative design approach. The sequences of three 30-residue peptides, A, B, and C, were optimized to favor charge-pair interactions in an ABC heterotrimer, while disfavoring the 26 competing oligomers (i.e., AAA, ABB, BCA). Peptides were synthesized and characterized for thermal stability and triple-helical structure by circular dichroism and NMR. A unique A:B:C-type species was not achieved. Negative design was partially successful, with only A + B and B + C competing mixtures formed. Analysis of computed versus experimental stabilities helps to clarify the role of electrostatics and secondary-structure propensities determining collagen stability and to provide important insight into how subsequent designs can be improved.

Crystal structure of chiral gammaPNA with complementary DNA strand: insights into the stability and specificity of recognition and conformational preorganization.

PubMed

Yeh, Joanne I; Shivachev, Boris; Rapireddy, Srinivas; Crawford, Matthew J; Gil, Roberto R; Du, Shoucheng; Madrid, Marcela; Ly, Danith H

2010-08-11

We have determined the structure of a PNA-DNA duplex to 1.7 A resolution by multiple-wavelength anomalous diffraction phasing method on a zinc derivative. This structure represents the first high-resolution 3D view of a hybrid duplex containing a contiguous chiral PNA strand with complete gamma-backbone modification ("gammaPNA"). Unlike the achiral counterpart, which adopts a random-fold, this particular gammaPNA is already preorganized into a right-handed helix as a single strand. The new structure illustrates the unique characteristics of this modified PNA, possessing conformational flexibility while maintaining sufficient structural integrity to ultimately adopt the preferred P-helical conformation upon hybridization with DNA. The unusual structural adaptability found in the gammaPNA strand is crucial for enabling the accommodation of backbone modifications while constraining conformational states. In conjunction with NMR analysis characterizing the structures and substructures of the individual building blocks, these results provide unprecedented insights into how this new class of chiral gammaPNA is preorganized and stabilized, before and after hybridization with a cDNA strand. Such knowledge is crucial for the future design and development of PNA for applications in biology, biotechnology, and medicine.

Insights from molecular dynamics simulations for computational protein design.

PubMed

Childers, Matthew Carter; Daggett, Valerie

2017-02-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures.

Insights from molecular dynamics simulations for computational protein design

PubMed Central

Childers, Matthew Carter; Daggett, Valerie

2017-01-01

A grand challenge in the field of structural biology is to design and engineer proteins that exhibit targeted functions. Although much success on this front has been achieved, design success rates remain low, an ever-present reminder of our limited understanding of the relationship between amino acid sequences and the structures they adopt. In addition to experimental techniques and rational design strategies, computational methods have been employed to aid in the design and engineering of proteins. Molecular dynamics (MD) is one such method that simulates the motions of proteins according to classical dynamics. Here, we review how insights into protein dynamics derived from MD simulations have influenced the design of proteins. One of the greatest strengths of MD is its capacity to reveal information beyond what is available in the static structures deposited in the Protein Data Bank. In this regard simulations can be used to directly guide protein design by providing atomistic details of the dynamic molecular interactions contributing to protein stability and function. MD simulations can also be used as a virtual screening tool to rank, select, identify, and assess potential designs. MD is uniquely poised to inform protein design efforts where the application requires realistic models of protein dynamics and atomic level descriptions of the relationship between dynamics and function. Here, we review cases where MD simulations was used to modulate protein stability and protein function by providing information regarding the conformation(s), conformational transitions, interactions, and dynamics that govern stability and function. In addition, we discuss cases where conformations from protein folding/unfolding simulations have been exploited for protein design, yielding novel outcomes that could not be obtained from static structures. PMID:28239489

Buffet induced structural/flight-control system interaction of the X-29A aircraft

NASA Technical Reports Server (NTRS)

Voracek, David F.; Clarke, Robert

1991-01-01

High angle-of-attack flight regime research is currently being conducted for modern fighter aircraft at the NASA Ames Research Center's Dryden Flight Research Facility. This flight regime provides enhanced maneuverability to fighter pilots in combat situations. Flight research data are being acquired to compare and validate advanced computational fluid dynamic solutions and wind-tunnel models. High angle-of-attack flight creates unique aerodynamic phenomena including wing rock and buffet on the airframe. These phenomena increase the level of excitation of the structural modes, especially on the vertical and horizontal stabilizers. With high gain digital flight-control systems, this structural response may result in an aeroservoelastic interaction. A structural interaction on the X-29A aircraft was observed during high angle-of-attack flight testing. The roll and yaw rate gyros sensed the aircraft's structural modes at 11, 13, and 16 Hz. The rate gyro output signals were then amplified through the flight-control laws and sent as commands to the flaperons and rudder. The flight data indicated that as the angle of attack increased, the amplitude of the buffet on the vertical stabilizer increased, which resulted in more excitation to the structural modes. The flight-control system sensors and command signals showed this increase in modal power at the structural frequencies up to a 30 degree angle-of-attack. Beyond a 30 degree angle-of-attack, the vertical stabilizer response, the feedback sensor amplitude, and control surface command signal amplitude remained relatively constant. Data are presented that show the increased modal power in the aircraft structural accelerometers, the feedback sensors, and the command signals as a function of angle of attack. This structural interaction is traced from the aerodynamic buffet to the flight-control surfaces.

Static stability of a three-dimensional space truss. M.S. Thesis - Case Western Reserve Univ., 1994

NASA Technical Reports Server (NTRS)

Shaker, John F.

1995-01-01

In order to deploy large flexible space structures it is necessary to develop support systems that are strong and lightweight. The most recent example of this aerospace design need is vividly evident in the space station solar array assembly. In order to accommodate both weight limitations and strength performance criteria, ABLE Engineering has developed the Folding Articulating Square Truss (FASTMast) support structure. The FASTMast is a space truss/mechanism hybrid that can provide system support while adhering to stringent packaging demands. However, due to its slender nature and anticipated loading, stability characterization is a critical part of the design process. Furthermore, the dire consequences surely to result from a catastrophic instability quickly provide the motivation for careful examination of this problem. The fundamental components of the space station solar array system are the (1) solar array blanket system, (2) FASTMast support structure, and (3) mast canister assembly. The FASTMast once fully deployed from the canister will provide support to the solar array blankets. A unique feature of this structure is that the system responds linearly within a certain range of operating loads and nonlinearly when that range is exceeded. The source of nonlinear behavior in this case is due to a changing stiffness state resulting from an inability of diagonal members to resist applied loads. The principal objective of this study was to establish the failure modes involving instability of the FASTMast structure. Also of great interest during this effort was to establish a reliable analytical approach capable of effectively predicting critical values at which the mast becomes unstable. Due to the dual nature of structural response inherent to this problem, both linear and nonlinear analyses are required to characterize the mast in terms of stability. The approach employed herein is one that can be considered systematic in nature. The analysis begins with one and two-dimensional failure models of the system and its important components. From knowledge gained through preliminary analyses a foundation is developed for three-dimensional analyses of the FASTMast structure. The three-dimensional finite element (FE) analysis presented here involves a FASTMast system one-tenth the size of the actual flight unit. Although this study does not yield failure analysis results that apply directly to the flight article, it does establish a method by which the full-scale mast can be evaluated.

Static stability of a three-dimensional space truss

NASA Astrophysics Data System (ADS)

Shaker, John F.

1995-05-01

In order to deploy large flexible space structures it is necessary to develop support systems that are strong and lightweight. The most recent example of this aerospace design need is vividly evident in the space station solar array assembly. In order to accommodate both weight limitations and strength performance criteria, ABLE Engineering has developed the Folding Articulating Square Truss (FASTMast) support structure. The FASTMast is a space truss/mechanism hybrid that can provide system support while adhering to stringent packaging demands. However, due to its slender nature and anticipated loading, stability characterization is a critical part of the design process. Furthermore, the dire consequences surely to result from a catastrophic instability quickly provide the motivation for careful examination of this problem. The fundamental components of the space station solar array system are the (1) solar array blanket system, (2) FASTMast support structure, and (3) mast canister assembly. The FASTMast once fully deployed from the canister will provide support to the solar array blankets. A unique feature of this structure is that the system responds linearly within a certain range of operating loads and nonlinearly when that range is exceeded. The source of nonlinear behavior in this case is due to a changing stiffness state resulting from an inability of diagonal members to resist applied loads. The principal objective of this study was to establish the failure modes involving instability of the FASTMast structure. Also of great interest during this effort was to establish a reliable analytical approach capable of effectively predicting critical values at which the mast becomes unstable. Due to the dual nature of structural response inherent to this problem, both linear and nonlinear analyses are required to characterize the mast in terms of stability. The approach employed herein is one that can be considered systematic in nature. The analysis begins with one and two-dimensional failure models of the system and its important components. From knowledge gained through preliminary analyses a foundation is developed for three-dimensional analyses of the FASTMast structure. The three-dimensional finite element (FE) analysis presented here involves a FASTMast system one-tenth the size of the actual flight unit. Although this study does not yield failure analysis results that apply directly to the flight article, it does establish a method by which the full-scale mast can be evaluated.

High-Accuracy Ring Laser Gyroscopes: Earth Rotation Rate and Relativistic Effects

NASA Astrophysics Data System (ADS)

Beverini, N.; Di Virgilio, A.; Belfi, J.; Ortolan, A.; Schreiber, K. U.; Gebauer, A.; Klügel, T.

2016-06-01

The Gross Ring G is a square ring laser gyroscope, built as a monolithic Zerodur structure with 4 m length on all sides. It has demonstrated that a large ring laser provides a sensitivity high enough to measure the rotational rate of the Earth with a high precision of ΔΩE < 10-8. It is possible to show that further improvement in accuracy could allow the observation of the metric frame dragging, produced by the Earth rotating mass (Lense-Thirring effect), as predicted by General Relativity. Furthermore, it can provide a local measurement of the Earth rotational rate with a sensitivity near to that provided by the international system IERS. The GINGER project is intending to take this level of sensitivity further and to improve the accuracy and the long-term stability. A monolithic structure similar to the G ring laser is not available for GINGER. Therefore the preliminary goal is the demonstration of the feasibility of a larger gyroscope structure, where the mechanical stability is obtained through an active control of the geometry. A prototype moderate size gyroscope (GP-2) has been set up in Pisa in order to test this active control of the ring geometry, while a second structure (GINGERino) has been installed inside the Gran Sasso underground laboratory in order to investigate the properties of a deep underground laboratory in view of an installation of a future GINGER apparatus. The preliminary data on these two latter instruments are presented.

Crystal Structure of Human Dual-Specificity Tyrosine-Regulated Kinase 3 Reveals New Structural Features and Insights into its Auto-phosphorylation.

PubMed

Kim, Kuglae; Cha, Jeong Seok; Cho, Yong-Soon; Kim, Hoyoung; Chang, Nienping; Kim, Hye-Jung; Cho, Hyun-Soo

2018-05-11

Dual-specificity tyrosine-regulated kinases (DYRKs) auto-phosphorylate a critical tyrosine residue in their activation loop and phosphorylate their substrate on serine and threonine residues. The auto-phosphorylation occurs intramolecularly and is a one-off event. DYRK3 is selectively expressed at a high level in hematopoietic cells and attenuates erythroblast development, leading to anemia. In the present study, we determined the crystal structure of the mature form of human DYRK3 in complex with harmine, an ATP competitive inhibitor. The crystal structure revealed a phosphorylation site, residue S350, whose phosphorylation increases the stability of DYRK3 and enhances its kinase activity. In addition, our structural and biochemical assays suggest that the N-terminal auto-phosphorylation accessory domain stabilizes the DYRK3 protein, followed by auto-phosphorylation of the tyrosine of the activation loop, which is important for kinase activity. Finally, our docking analysis provides information for the design of novel and potent therapeutics to treat anemia. Copyright © 2018 Elsevier Ltd. All rights reserved.

Observations on the structural degradation of silver during simultaneous exposure to oxidizing and reducing environments

NASA Astrophysics Data System (ADS)

Singh, Prabhakar; Yang, Zhenguo; Viswanathan, Vish; Stevenson, Jeff W.

2004-06-01

The structural stability of silver (Ag) in dual atmosphere exposure conditions, which are representative of solid oxide fuel cell (SOFC) current collector and gas seals, has been examined in the 600 800 °C temperature range. Experiments conducted on Ag tubular sections exposed to flowing H2-3% H2O (inside the tube) and air (outside the tube) showed extensive porosity formation along the grain boundaries in the bulk metal. Similar tubular sections, when exposed to air only (both inside and outside the tube), showed no bulk porosity or structural changes. It is postulated that the porosity formation in the bulk metal is related to the formation of gaseous H2O bubbles due to simultaneous diffusion of hydrogen and oxygen followed by subsequent interaction resulting in the formation of steam. Thermochemical processes that are responsible for structural degradation are presented and discussed. Based on experimental observations, it is concluded that Ag metal may not provide adequate long-term structural stability under a dual-environment condition that is typical of interconnects or gas seals in intermediate temperature SOFCs.

Structures and physical properties of gaseous metal cationized biological ions.

PubMed

Burt, Michael B; Fridgen, Travis D

2012-01-01

Metal chelation can alter the activity of free biomolecules by modifying their structures or stabilizing higher energy tautomers. In recent years, mass spectrometric techniques have been used to investigate the effects of metal complexation with proteins, nucleobases and nucleotides, where small conformational changes can have significant physiological consequences. In particular, infrared multiple photon dissociation spectroscopy has emerged as an important tool for determining the structure and reactivity of gas-phase ions. Unlike other mass spectrometric approaches, this method is able to directly resolve structural isomers using characteristic vibrational signatures. Other activation and dissociation methods, such as blackbody infrared radiative dissociation or collision-induced dissociation can also reveal information about the thermochemistry and dissociative pathways of these biological ions. This information can then be used to provide information about the structures of the ionic complexes under study. In this article, we review the use of gas-phase techniques in characterizing metal-bound biomolecules. Particular attention will be given to our own contributions, which detail the ability of metal cations to disrupt nucleobase pairs, direct the self-assembly of nucleobase clusters and stabilize non-canonical isomers of amino acids.

Challenges and Perspectives for NASICON-Type Electrode Materials for Advanced Sodium-Ion Batteries.

PubMed

Chen, Shuangqiang; Wu, Chao; Shen, Laifa; Zhu, Changbao; Huang, Yuanye; Xi, Kai; Maier, Joachim; Yu, Yan

2017-12-01

Sodium-ion batteries (SIBs) have attracted increasing attention in the past decades, because of high overall abundance of precursors, their even geographical distribution, and low cost. Apart from inherent thermodynamic disadvantages, SIBs have to overcome multiple kinetic problems, such as fast capacity decay, low rate capacities and low Coulombic efficiencies. A special case is sodium super ion conductor (NASICON)-based electrode materials as they exhibit - besides pronounced structural stability - exceptionally high ion conductivity, rendering them most promising for sodium storage. Owing to the limiting, comparatively low electronic conductivity, nano-structuring is a prerequisite for achieving satisfactory rate-capability. In this review, we analyze advantages and disadvantages of NASICON-type electrode materials and highlight electrode structure design principles for obtaining the desired electrochemical performance. Moreover, we give an overview of recent approaches to enhance electrical conductivity and structural stability of cathode and anode materials based on NASICON structure. We believe that this review provides a pertinent insight into relevant design principles and inspires further research in this respect. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploring for the optimal structural design for the 3D-printing technology for cranial reconstruction: a biomechanical and histological study comparison of solid vs. porous structure.

PubMed

Lim, Jun Young; Kim, Namhyun; Park, Jong-Chul; Yoo, Sun K; Shin, Dong Ah; Shim, Kyu-Won

2017-09-01

Cranioplasty for recovering skull defects carries the risk for a number of complications. Various materials are used, including autologous bone graft, metallic materials, and non-metallic materials, each of which has advantages and disadvantages. If the use of autologous bone is not feasible, those artificial materials also have constraints in the case of complex anatomy and/or irregular defects. This study used metal 3D-printing technology to overcome these existing drawbacks and analyze the clinical and mechanical performance requirements. To find an optimal structure that satisfied the structural and mechanical stability requirements, we evaluated biomechanical stability using finite element analysis (FEA) and mechanical testing. To ensure clinical applicability, the model was subjected to histological evaluation. Each specimen was implanted in the femur of a rabbit and was evaluated using histological measurements and push-out test. We believe that our data will provide the basis for future applications of a variety of unit structures and further clinical trials and research, as well as the direction for the study of other patient-specific implants.

Cold-Adapted Enzymes

NASA Astrophysics Data System (ADS)

Georlette, D.; Bentahir, M.; Claverie, P.; Collins, T.; D'amico, S.; Delille, D.; Feller, G.; Gratia, E.; Hoyoux, A.; Lonhienne, T.; Meuwis, M.-a.; Zecchinon, L.; Gerday, Ch.

In the last few years, increased attention has been focused on enzymes produced by cold-adapted micro-organisms. It has emerged that psychrophilic enzymes represent an extremely powerful tool in both protein folding investigations and for biotechnological purposes. Such enzymes are characterised by an increased thermosensitivity and, most of them, by a higher catalytic efficiency at low and moderate temperatures, when compared to their mesophilic counterparts. The high thermosensitivity probably originates from an increased flexibility of either a selected area of the molecular edifice or the overall protein structure, providing enhanced abilities to undergo conformational changes during catalysis at low temperatures. Structure modelling and recent crystallographic data have allowed to elucidate the structural parameters that could be involved in this higher resilience. It was demonstrated that each psychrophilic enzyme adopts its own adaptive strategy. It appears, moreover, that there is a continuum in the strategy of protein adaptation to temperature, as the previously mentioned structural parameters are implicated in the stability of thermophilic proteins. Additional 3D crystal structures, site-directed and random mutagenesis experiments should now be undertaken to further investigate the stability-flexibility-activity relationship.

Device for calorimetric measurement

DOEpatents

King, William P; Lee, Jungchul

2015-01-13

In one aspect, provided herein is a single crystal silicon microcalorimeter, for example useful for high temperature operation and long-term stability of calorimetric measurements. Microcalorimeters described herein include microcalorimeter embodiments having a suspended structure and comprising single crystal silicon. Also provided herein are methods for making calorimetric measurements, for example, on small quantities of materials or for determining the energy content of combustible material having an unknown composition.

Removal of a C-terminal serine residue proximal to the inter-chain disulfide bond of a human IgG1 lambda light chain mediates enhanced antibody stability and antibody dependent cell-mediated cytotoxicity

PubMed Central

Shen, Yang; Zeng, Lin; Zhu, Aiping; Blanc, Tim; Patel, Dipa; Pennello, Anthony; Bari, Amtul; Ng, Stanley; Persaud, Kris; Kang, Yun (Kenneth); Balderes, Paul; Surguladze, David; Hindi, Sagit; Zhou, Qinwei; Ludwig, Dale L.; Snavely, Marshall

2013-01-01

Optimization of biophysical properties is a critical success factor for the developability of monoclonal antibodies with potential therapeutic applications. The inter-domain disulfide bond between light chain (Lc) and heavy chain (Hc) in human IgG1 lends structural support for antibody scaffold stability, optimal antigen binding, and normal Fc function. Recently, human IgG1λ has been suggested to exhibit significantly greater susceptibility to reduction of the inter Lc-Hc disulfide bond relative to the same disulfide bond in human IgG1κ. To understand the molecular basis for this observed difference in stability, the sequence and structure of human IgG1λ and human IgG1κ were compared. Based on this Lc comparison, three single mutations were made in the λ Lc proximal to the cysteine residue, which forms a disulfide bond with the Hc. We determined that deletion of S214 (dS) improved resistance of the association between Lc and Hc to thermal stress. In addition, deletion of this terminal serine from the Lc of IgG1λ provided further benefit, including an increase in stability at elevated pH, increased yield from transient transfection, and improved in vitro antibody dependent cell-mediated cytotoxicity (ADCC). These observations support the conclusion that the presence of the terminal serine of the λ Lc creates a weaker inter-chain disulfide bond between the Lc and Hc, leading to slightly reduced stability and a potential compromise in IgG1λ function. Our data from a human IgG1λ provide a basis for further investigation of the effects of deleting terminal serine from λLc on the stability and function of other human IgG1λ antibodies. PMID:23567210

Flow-induced conformational changes in gelatin structure and colloidal stabilization.

PubMed

Akbulut, Mustafa; Reddy, Naveen K; Bechtloff, Bernd; Koltzenburg, Sebastian; Vermant, Jan; Prud'homme, Robert K

2008-09-02

Flow can change the rate at which solutes adsorb on surfaces by changing mass transfer to the surface, but moreover, flow can induce changes in the conformation of macromolecules in solution by providing sufficient stresses to perturb the segmental distribution function. However, there are few studies where the effect of flow on macromolecules has been shown to alter the structure of macromolecules adsorbed on surfaces. We have studied how the local energy dissipation alters the adsorption of gelatin onto polystyrene nanoparticles ( r = 85 nm). The change in the nature of the adsorbed layer is manifest in the change in the ability of the nanoparticles to resist aggregation. Circular dichroism spectroscopy was used to assess conformational changes in gelatin, and dynamic light scattering was used to assess the colloid stability. Experiments were conducted in a vortex jet mixer where energy density and mixing times have been quantified; mixing of the gelatin and unstable nanoparticles occurs on the order of milliseconds. The adsorption of the gelatin provides steric stabilization to the nanoparticles. We found that the stability of the gelatin-adsorbed nanoparticles increased with increasing mixing velocities: when the mixing velocities were changed from 0.9 to 550 m/s, the radius of the nanoclusters (aggregates) formed 12 h after the mixing decreased from 2620 to 600 nm. Increasing temperature also gave rise to similar trends in the stability behavior with increasing temperature, leading to increasing colloid stability. Linear flow birefringence studies also suggested that the velocity fields in the mixer are sufficiently strong to produce conformational changes in the gelatin. These results suggest that the energy dissipation produced by mixing can activate conformational changes in gelatin to alter its adsorption on the surfaces of nanoparticles. Understanding how such conformational changes in gelatin can be driven by local fluid mechanics and how these changes are related to the adsorption behavior of gelatin is very important both industrially and scientifically.

B-52 stability augmentation system reliability

NASA Technical Reports Server (NTRS)

Bowling, T. C.; Key, L. W.

1976-01-01

The B-52 SAS (Stability Augmentation System) was developed and retrofitted to nearly 300 aircraft. It actively controls B-52 structural bending, provides improved yaw and pitch damping through sensors and electronic control channels, and puts complete reliance on hydraulic control power for rudder and elevators. The system has experienced over 300,000 flight hours and has exhibited service reliability comparable to the results of the reliability test program. Development experience points out numerous lessons with potential application in the mechanization and development of advanced technology control systems of high reliability.

Gi- and Gs-coupled GPCRs show different modes of G-protein binding.

PubMed

Van Eps, Ned; Altenbach, Christian; Caro, Lydia N; Latorraca, Naomi R; Hollingsworth, Scott A; Dror, Ron O; Ernst, Oliver P; Hubbell, Wayne L

2018-03-06

More than two decades ago, the activation mechanism for the membrane-bound photoreceptor and prototypical G protein-coupled receptor (GPCR) rhodopsin was uncovered. Upon light-induced changes in ligand-receptor interaction, movement of specific transmembrane helices within the receptor opens a crevice at the cytoplasmic surface, allowing for coupling of heterotrimeric guanine nucleotide-binding proteins (G proteins). The general features of this activation mechanism are conserved across the GPCR superfamily. Nevertheless, GPCRs have selectivity for distinct G-protein family members, but the mechanism of selectivity remains elusive. Structures of GPCRs in complex with the stimulatory G protein, G s , and an accessory nanobody to stabilize the complex have been reported, providing information on the intermolecular interactions. However, to reveal the structural selectivity filters, it will be necessary to determine GPCR-G protein structures involving other G-protein subtypes. In addition, it is important to obtain structures in the absence of a nanobody that may influence the structure. Here, we present a model for a rhodopsin-G protein complex derived from intermolecular distance constraints between the activated receptor and the inhibitory G protein, G i , using electron paramagnetic resonance spectroscopy and spin-labeling methodologies. Molecular dynamics simulations demonstrated the overall stability of the modeled complex. In the rhodopsin-G i complex, G i engages rhodopsin in a manner distinct from previous GPCR-G s structures, providing insight into specificity determinants. Copyright © 2018 the Author(s). Published by PNAS.

Structural characterization of human heme oxygenase-1 in complex with azole-based inhibitors.

PubMed

Rahman, Mona N; Vlahakis, Jason Z; Roman, Gheorghe; Vukomanovic, Dragic; Szarek, Walter A; Nakatsu, Kanji; Jia, Zongchao

2010-03-01

The development of inhibitors specific for heme oxygenases (HO) aims to provide powerful tools in understanding the HO system. Based on the lead structure (2S, 4S)-2-[2-(4-chlorophenyl)ethyl]-2-[(1H-imidazol-1-yl)methyl]-4-[((4-aminophenyl)thio)methyl]-1,3-dioxolane (azalanstat, QC-1) we have synthesized structural modifications to develop novel and selective HO inhibitors. The structural study of human HO-1 (hHO-1) in complex with a select group of the inhibitors was initiated using X-ray crystallographic techniques. Comparison of the structures of four such compounds each in complex with hHO-1 revealed a common binding mode, despite having different structural fragments. The compounds bind to the distal side of heme through an azole "anchor" which coordinates with the heme iron. An expansion of the distal pocket, mainly due to distal helix flexibility, allows accommodation of the compounds without displacing heme or the critical Asp140 residue. Rather, binding displaces a catalytically critical water molecule and disrupts an ordered hydrogen-bond network involving Asp140. The presence of a triazole "anchor" may provide further stability via a hydrogen bond with the protein. A hydrophobic pocket acts to stabilize the region occupied by the phenyl or adamantanyl moieties of these compounds. Further, a secondary hydrophobic pocket is formed via "induced fit" to accommodate bulky substituents at the 4-position of the dioxolane ring. Copyright 2009 Elsevier Inc. All rights reserved.

Flash Nanoprecipitation: Prediction and Enhancement of Particle Stability via Drug Structure

PubMed Central

2015-01-01

Flash nanoprecipitation (FNP) can generate hydrophobic drug nanoparticles in ∼100 nm with a much higher drug loading (e.g., > 40 wt %) than traditional nanocarriers (e.g., < 20 wt %). This paper studies the effects of drug molecules on nanoparticle stability made via FNP and demonstrates that chemically bonding a drug compound (e.g., paclitaxel) with a cleavable hydrophobic moiety of organosilicate (e.g., triethoxysilicate) is able to enhance the particle size stability. A nonionic amphiphilic diblock copolymer, poly(lactic-co-glycolic acid)-block-poly(ethylene glycol) (PLGA-b-PEG), is used as a model surfactant to provide steric stabilization. The experiments here show that the lower the drug solubility in the aqueous medium, the more stable the particles in terms of Ostwald ripening, which are consistent with the prediction by the LSW theory. The initial particle size distribution is sufficiently narrow and of insignificance to Ostwald ripening. To correlate the particle stability with hydrophobicity, this study introduces the n-octanol/water partition coefficient (LogP), a hydrophobicity indication, into the FNP technique. A comparison of various drugs and their analogues shows that LogP of a drug is a better hydrophobicity indication than the solubility parameter (δ) and correlates well with the particle stability. Empirically, with ACDLogP > ∼12, nanoparticles have good stability; with ∼2 < ACDLogP < ∼9, nanoparticles show fast Ostwald ripening and interparticle recrystallization; with ACDLogP < ∼2, the drug is very likely difficult to form nanoparticles. This rule creates a quick way to predict particle stability for a randomly selected drug structure and helps to enable a fast preclinical drug screen. PMID:24484077

Chemical modification of Saccharomycopsis fibuligera R64 α-amylase to improve its stability against thermal, chelator, and proteolytic inactivation.

PubMed

Ismaya, Wangsa Tirta; Hasan, Khomaini; Kardi, Idar; Zainuri, Amalia; Rahmawaty, Rinrin Irma; Permanahadi, Satyawisnu; El Viera, Baiq Vera; Harinanto, Gunawan; Gaffar, Shabarni; Natalia, Dessy; Subroto, Toto; Soemitro, Soetijoso

2013-05-01

α-Amylase catalyzes hydrolysis of starch to oligosaccharides, which are further degraded to simple sugars. The enzyme has been widely used in food and textile industries and recently, in generation of renewable energy. An α-amylase from yeast Saccharomycopsis fibuligera R64 (Sfamy) is active at 50 °C and capable of degrading raw starch, making it attractive for the aforementioned applications. To improve its characteristics as well as to provide information for structural study ab initio, the enzyme was chemically modified by acid anhydrides (nonpolar groups), glyoxylic acid (GA) (polar group), dimethyl adipimidate (DMA) (cross-linking), and polyethylene glycol (PEG) (hydrophilization). Introduction of nonpolar groups increased enzyme stability up to 18 times, while modification by a cross-linking agent resulted in protection of the calcium ion, which is essential for enzyme activity and integrity. The hydrophilization with PEG resulted in protection against tryptic digestion. The chemical modification of Sfamy by various modifiers has thereby resulted in improvement of its characteristics and provided systematic information beneficial for structural study of the enzyme. An in silico structural study of the enzyme improved the interpretation of the results.

Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection.

PubMed

Ding, Hong; Dwaraknath, Shyam S; Garten, Lauren; Ndione, Paul; Ginley, David; Persson, Kristin A

2016-05-25

With the ultimate goal of finding new polymorphs through targeted synthesis conditions and techniques, we outline a computational framework to select optimal substrates for epitaxial growth using first principle calculations of formation energies, elastic strain energy, and topological information. To demonstrate the approach, we study the stabilization of metastable VO2 compounds which provides a rich chemical and structural polymorph space. We find that common polymorph statistics, lattice matching, and energy above hull considerations recommends homostructural growth on TiO2 substrates, where the VO2 brookite phase would be preferentially grown on the a-c TiO2 brookite plane while the columbite and anatase structures favor the a-b plane on the respective TiO2 phases. Overall, we find that a model which incorporates a geometric unit cell area matching between the substrate and the target film as well as the resulting strain energy density of the film provide qualitative agreement with experimental observations for the heterostructural growth of known VO2 polymorphs: rutile, A and B phases. The minimal interfacial geometry matching and estimated strain energy criteria provide several suggestions for substrates and substrate-film orientations for the heterostructural growth of the hitherto hypothetical anatase, brookite, and columbite polymorphs. These criteria serve as a preliminary guidance for the experimental efforts stabilizing new materials and/or polymorphs through epitaxy. The current screening algorithm is being integrated within the Materials Project online framework and data and hence publicly available.

Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection

DOE PAGES

Ding, Hong; Dwaraknath, Shyam S.; Garten, Lauren; ...

2016-05-04

With the ultimate goal of finding new polymorphs through targeted synthesis conditions and techniques, we outline a computational framework to select optimal substrates for epitaxial growth using first principle calculations of formation energies, elastic strain energy, and topological information. To demonstrate the approach, we study the stabilization of metastable VO 2 compounds which provides a rich chemical and structural polymorph space. Here, we find that common polymorph statistics, lattice matching, and energy above hull considerations recommends homostructural growth on TiO 2 substrates, where the VO 2 brookite phase would be preferentially grown on the a-c TiO 2 brookite plane whilemore » the columbite and anatase structures favor the a-b plane on the respective TiO 2 phases. Overall, we find that a model which incorporates a geometric unit cell area matching between the substrate and the target film as well as the resulting strain energy density of the film provide qualitative agreement with experimental observations for the heterostructural growth of known VO 2 polymorphs: rutile, A and B phases. The minimal interfacial geometry matching and estimated strain energy criteria provide several suggestions for substrates and substrate-film orientations for the heterostructural growth of the hitherto hypothetical anatase, brookite, and columbite polymorphs. Our criteria serve as a preliminary guidance for the experimental efforts stabilizing new materials and/or polymorphs through epitaxy. The current screening algorithm is being integrated within the Materials Project online framework and data and hence publicly available.« less

Computational Approach for Epitaxial Polymorph Stabilization through Substrate Selection

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

Ding, Hong; Dwaraknath, Shyam S.; Garten, Lauren

With the ultimate goal of finding new polymorphs through targeted synthesis conditions and techniques, we outline a computational framework to select optimal substrates for epitaxial growth using first principle calculations of formation energies, elastic strain energy, and topological information. To demonstrate the approach, we study the stabilization of metastable VO 2 compounds which provides a rich chemical and structural polymorph space. Here, we find that common polymorph statistics, lattice matching, and energy above hull considerations recommends homostructural growth on TiO 2 substrates, where the VO 2 brookite phase would be preferentially grown on the a-c TiO 2 brookite plane whilemore » the columbite and anatase structures favor the a-b plane on the respective TiO 2 phases. Overall, we find that a model which incorporates a geometric unit cell area matching between the substrate and the target film as well as the resulting strain energy density of the film provide qualitative agreement with experimental observations for the heterostructural growth of known VO 2 polymorphs: rutile, A and B phases. The minimal interfacial geometry matching and estimated strain energy criteria provide several suggestions for substrates and substrate-film orientations for the heterostructural growth of the hitherto hypothetical anatase, brookite, and columbite polymorphs. Our criteria serve as a preliminary guidance for the experimental efforts stabilizing new materials and/or polymorphs through epitaxy. The current screening algorithm is being integrated within the Materials Project online framework and data and hence publicly available.« less

Rich in life but poor in data: the known knowns and known unknowns of modelling how soil biology drives soil structure

NASA Astrophysics Data System (ADS)

Hallett, Paul; Ogden, Mike

2015-04-01

Soil biology has a fascinating capacity to manipulate pore structure by altering or overcoming hydrological and mechanical properties of soil. Many have postulated, quite rightly, that this capacity of soil biology to 'engineer' its habitat drives its diversity, improves competitiveness and increases resilience to external stresses. A large body of observational research has quantified pore structure evolution accompanied by the growth of organisms in soil. Specific compounds that are exuded by organisms or the biological structures they create have been isolated and found to correlate well with observed changes to pore structure or soil stability. This presentation will provide an overview of basic mechanical and hydrological properties of soil that are affected by biology, and consider missing data that are essential to model how they impact soil structure evolution. Major knowledge gaps that prevent progress will be identified and suggestions will be made of how research in this area should progress. We call for more research to gain a process based understanding of structure formation by biology, to complement observational studies of soil structure before and after imposed biological activity. Significant advancement has already been made in modelling soil stabilisation by plant roots, by combining data on root biomechanics, root-soil interactions and soil mechanical properties. Approaches for this work were developed from earlier materials science and geotechnical engineering research, and the same ethos should be adopted to model the impacts of other biological compounds. Fungal hyphae likely reinforce soils in a similar way to plant roots, with successful biomechanical measurements of these micron diameter structures achieved with micromechanical test frames. Extending root reinforcement models to fungi would not be a straightforward exercise, however, as interparticle bonding and changes to pore water caused by fungal exudates could have a major impact on structure formation and stability. Biological exudates from fungi, bacteria or roots have been found to decrease surface tension and increase viscosity of pore water, with observed impacts to soil strength and water retention. Modelling approaches developed in granular mechanics and geotechnical engineering could be built upon to incorporate biological transformations of hydrological and mechanical properties of soil. With new testing approaches, adapted from materials science, pore scale hydromechanical impacts from biological exudates can be quantified. The research can be complemented with model organisms with differences in biological structures (e.g. root hair mutants), exudation or other properties. Coupled with technological advances that provide 4D imaging of soil structure at relatively rapid capture rates, the potential opportunities to disentangle and model how biology drives soil structure evolution and stability are vast. By quantifying basic soil hydrological and mechanical processes that are driven by soil biology, unknown unknowns may also emerge, providing new insight into how soils function.

Evaluation of biochars by temperature programmed oxidation/mass spectrometry

Treesearch

Michael Jackson; Thomas Eberhardt; Akwasi Boateng; Charles Mullen; Les Groom

2013-01-01

Biochars produced from thermochemical conversions of biomass were evaluated by temperature programmed oxidation (TPO). This technique, used to characterize carbon deposits on petroleum cracking catalysts, provides information on the oxidative stability of carbonaceous solids, where higher temperature reactivity indicates greater structural order, an important property...

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

PubMed Central

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

2017-01-01

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

Effect of sugar additives on stability of human serum albumin during vacuum foam drying and storage.

PubMed

Hajare, A A; More, H N; Pisal, S S

2011-11-01

No literature on the protein stabilization of human serum albumin (HSA) by vacuum foam drying (VFD) has been reported. The purpose of this study was to investigate the effect of sugar-additive systems on the stability of HSA by VFD. For the assessment, HSA was formulated with sucrose and mannitol, respectively, alone or in combination with stabilizers, which were vacuum foam dried and stored at 25C. Protein content of the resulting dried formulations was analyzed by Lowry method. Fourier-transform infrared spectroscopy (FT-IR) analysis of the HSA secondary structure showed apparent protein structure-stabilizing effects of the amorphous sugar and phosphate combination during the VFD. In particular, sucrose-sodium phosphate monobasic mixture provide an interesting alternative to pure saccharide formulations due to their high glass transition temperatures and their increased ability to maintain a low melting transition temperature in the presence of small amounts of water. Inhibition of the sucrose crystallization in solutions under vacuum resulted in highly amorphous sucrose. Changes in the endothermic melting transition suggested reduced sucrose molecular mobility with increase in the sodium phosphate ratio. The addition of phosphate salts to sugar systems has several interesting features that merit its consideration in formulations to protect dehydrated labile biomaterials. In conclusion, our data suggest that sucrose and phosphate as additives seem to protect HSA during VFD better than lyophilized products and also maintain its stability in the VFD state during storage.

Fuel electrode containing pre-sintered nickel/zirconia for a solid oxide fuel cell

DOEpatents

Ruka, Roswell J.; Vora, Shailesh D.

2001-01-01

A fuel cell structure (2) is provided, having a pre-sintered nickel-zirconia fuel electrode (6) and an air electrode (4), with a ceramic electrolyte (5) disposed between the electrodes, where the pre-sintered fuel electrode (6) contains particles selected from the group consisting of nickel oxide, cobalt and cerium dioxide particles and mixtures thereof, and titanium dioxide particles, within a matrix of yttria-stabilized zirconia and spaced-apart filamentary nickel strings having a chain structure, and where the fuel electrode can be sintered to provide an active solid oxide fuel cell.

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.

The crystallization and structural analysis of cellulases (and other glycoside hydrolases): strategies and tactics.

PubMed

Roberts, Shirley M; Davies, Gideon J

2012-01-01

The three-dimensional (3-D) structures of cellulases, and other glycoside hydrolases, are a central feature of research in carbohydrate chemistry and biochemistry. 3-D structure is used to inform protein engineering campaigns, both academic and industrial, which are typically used to improve the stability or activity of an enzyme. Examples of classical protein engineering goals include higher thermal stability, reduced metal-ion dependency, detergent and protease resistance, decreased product inhibition, and altered specificity. 3-D structure may also be used to interpret the behavior of enzyme variants that are derived from screening or random mutagenesis approaches, with a view to establishing an iterative design process. In other areas, 3-D structure is used as one of the many tools to probe enzymatic catalysis, typically dovetailing with physical organic chemistry approaches to provide complete reaction mechanisms for enzymes by visualizing catalytic site interactions at different stages of the reaction. Such mechanistic insight is not only fundamentally important, impacting on inhibitor and drug design approaches with ramifications way beyond cellulose hydrolysis, but also provides the framework for the design of enzyme variants to use as biocatalysts for the synthesis of bespoke oligosaccharides. Here we review some of the strategies and tactics that may be applied to the X-ray structure solution of cellulases (and other carbohydrate-active enzymes). The general approach is first to decide why you are doing the work, then to establish correct domain boundaries for truncated constructs (typically the catalytic domain only), and finally to pursue crystallization of pure, homogeneous, and monodisperse protein with appropriate ligand and additive combinations. Cellulase-specific strategies are important for the delineation of domain boundaries, while glycoside hydrolases generally also present challenges and opportunities for the selection and optimization of ligands to both aid crystallization, and also provide structural and mechanistic insight. As the many roles for plant cell wall degrading enzymes increase, so does the need for rapid high-quality structure determination to provide a sound structural foundation for understanding mechanism and specificity, and for future protein engineering strategies. Copyright © 2012 Elsevier Inc. All rights reserved.

Stability of some Cactaceae proteins based on fluorescence, circular dichroism, and differential scanning calorimetry measurements.

PubMed

Gorinstein, S; Zemser, M; Vargas-Albores, F; Ochoa, J L; Paredes-Lopez, O; Scheler, C; Aksu, S; Salnikow, J

1999-02-01

Characterization of three cactus proteins (native and denatured) from Machaerocereus gummosus (Pitahaya agria), Lophocereu schottii (Garambullo), and Cholla opuntia (Cholla), was based on electrophoretic, fluorescence, CD (circular dichroism), DSC (differential scanning calorimetry), and FT-IR (Fourier transform infrared) measurements. The obtained results of intrinsic fluorescence, DSC, and CD were dissimilar for the three species of cactus, providing evidence of differences in secondary and tertiary structures. Cactus proteins may be situated in the following order corresponding to their relative stability: Machaerocereus gummosus (Pitahaya agria) > Cholla opuntia (Cholla) > Lophocereu schottii (Garambullo). Thermodynamic properties of proteins and their changes upon denaturation (temperature of denaturation, enthalphy, and the number of ruptured hydrogen bonds) were correlated with the secondary structure of proteins and disappearance of alpha-helix.

Laser-assisted formation of micropores and nanobubbles in sclera promote stable normalization of intraocular pressure

NASA Astrophysics Data System (ADS)

Baum, Olga; Wachsmann-Hogiu, Sebastian; Milner, Thomas; Sobol, Emil

2017-06-01

Pores in sclera enhance uveoscleral water outflow and can normalize intraocular pressure in glaucomatous eyes. The aims of this study are to demonstrate laser-induced formation of pores with a dendritic structure and to answer the questions: How is a pore system stable and can laser treatment provide a long-lasting pressure stabilization effect? Effect of 1.56 µm laser radiation on porcine eye sclera was studied using atomic force microscopy and super resolution structured irradiation microscopy with fluorescent markers. Results suggest that the pores with a complex spatial configuration can arise as a result of laser irradiation and that laser-generated stable gas nanobubbles coated with calcium ions allow pore stabilization in the sclera. Our results support a laser based approach for treatment of glaucoma.

First principles calculations of stability and lithium intercalation potentials of ZnCo2O4

NASA Astrophysics Data System (ADS)

Yu, L. C.; Wu, J.; Liu, H.; Zhang, Y. N.

2015-03-01

Among the metal oxides, which are the most widely investigated alternative anodes for use in lithium ion batteries (LIBs), binary and ternary tin oxides have received special attention due to their high capacity values. ZnCo2O4 is a promising candidate as the anode material for LIB, and one can expect a total capacity corresponding to 7.0 - 8.33 mol of recyclable Li per mole of ZnCo2O4. Here we studied the structural stability, electronic properties, diffusion barrier and lithium intercalation potentials of ZnCo2O4 through density functional calculations. The calculated structural and energetic parameters are comparable with experiments. Our DFT studies provide insights in understanding the mechanism of lithium ion displacement reactions in this ternary metal oxide.

Structural patterns in Swedish health policy: a 30-year perspective.

PubMed

Saltman, Richard B

2015-04-01

This perspective reviews key institutional and organizational patterns in Swedish health care over the last 30 years, probing the roots of several complicated policy questions that concern present-day Swedish decision-makers. It explores in particular the ongoing structural tension between stability, on the one hand, and the necessary levels of innovation and dynamism demanded by the current period of major clinical, technological, economic, social and supranational (EU) change. Where useful, the article compares Swedish developments with those in the other three European Nordic countries as well as other northern European health systems. Sweden's health sector evolution can provide valuable insight for other countries into the complexity involved in re-thinking tradeoffs between policies that emphasize stability as against those that encourage innovation in health sector governance and provision.

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

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.

Mathematics, Thermodynamics, and Modeling to Address Ten Common Misconceptions about Protein Structure, Folding, and Stability

ERIC Educational Resources Information Center

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…

Unveiling the Structural Evolution of Ag 1.2Mn 8O 16 under Coulombically Controlled (De)Lithiation

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

Huang, Jianping; Hu, Xiaobing; Brady, Alexander B.

MnO 2 materials are considered promising cathode materials for rechargeable lithium, sodium, and magnesium batteries due to their earth abundance and environmental friendliness. One polymorph of MnO 2, α-MnO 2, has 2 × 2 tunnels (4.6 Å × 4.6 Å) in its structural framework, which provide facile diffusion pathways for guest ions. In this work, a silver-ion-containing α-MnO 2 (Ag 1.2Mn 8O 16) is examined as a candidate cathode material for Li based batteries. Electrochemical stability of Ag 1.2Mn 8O 16 is investigated through Coulombically controlled reduction under 2 or 4 molar electron equivalents (e.e.). Terminal discharge voltage remains almostmore » constant under 2 e.e. of cycling, whereas it continuously decreases under repetitive reduction by 4 e.e. Thus, detailed structural analyses were utilized to investigate the structural evolution upon lithiation. Significant increases in lattice a (17.7%) and atomic distances (~4.8%) are observed when x in Li xAg 1.2Mn 8O 16 is >4. Ag metal forms at this level of lithiation concomitant with a large structural distortion to the Mn–O framework. In contrast, lattice a only expands by 2.2% and Mn–O/Mn-Mn distances show minor changes (~1.4%) at x < 2. The structural deformation (tunnel breakage) at x > 4 inhibits the recovery of the original structure, leading to poor cycle stability at high lithiation levels. This report establishes the correlation among local structure changes, amorphization processes, formation of Ag 0, and long-term cycle stability for this silver-containing α-MnO 2 type material at both low and high lithiation levels.« less

Unveiling the Structural Evolution of Ag 1.2Mn 8O 16 under Coulombically Controlled (De)Lithiation

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

Huang, Jianping; Hu, Xiaobing; Brady, Alexander B.

MnO 2 materials are considered promising cathode materials for rechargeable lithium, sodium, and magnesi-um batteries due to their earth abundance and environmental friendliness. One polymorph of MnO 2, α-MnO 2, has 2×2 tunnels (4.6 Å × 4.6 Å) in its structural framework, which provide facile diffusion pathways for guest ions. In this work, a silver ion containing α-MnO 2 (Ag 1.2Mn 8O 16) is examined as a candidate cathode material for Li based batteries. Electro-chemical stability of Ag 1.2Mn 8O 16 is investigated through Coulombically controlled reduction under 2 or 4 molar electron equivalents (e.e.). Terminal discharge voltage remains almostmore » constant under 2 e.e. of cycling, whereas it continuously decreases under repetitive reduction by 4 e.e. Thus, detailed structural analyses were utilized to investigate the structural evolution upon lithiation. Significant increases in lattice a (17.7 %) and atomic distances (~4.8 %) are observed when x in Li xAg 1.2Mn 8O 16 is >4. Ag metal forms at this level of lithiation concomitant with a large structural distortion to the Mn-O framework. In contrast, lattice a only expands by 2.2 % and Mn-O/Mn-Mn distances show minor changes (~1.4 %) at x <2. The structural deformation (tunnel breakage) at x >4 inhibits the recovery of the original structure, leading to poor cycle stability at high lithiation levels. This report establishes the correlation among local structure changes, amorphization processes, formation of Ag 0 and long term cycle stability for this silver containing α-MnO 2 type material at both low and high lithiation levels.« less

Molecular Evolutionary Constraints that Determine the Avirulence State of Clostridium botulinum C2 Toxin.

PubMed

Prisilla, A; Prathiviraj, R; Chellapandi, P

2017-04-01

Clostridium botulinum (group-III) is an anaerobic bacterium producing C2 toxin along with botulinum neurotoxins. C2 toxin is belonged to binary toxin A family in bacterial ADP-ribosylation superfamily. A structural and functional diversity of binary toxin A family was inferred from different evolutionary constraints to determine the avirulence state of C2 toxin. Evolutionary genetic analyses revealed evidence of C2 toxin cluster evolution through horizontal gene transfer from the phage or plasmid origins, site-specific insertion by gene divergence, and homologous recombination event. It has also described that residue in conserved NAD-binding core, family-specific domain structure, and functional motifs found to predetermine its virulence state. Any mutational changes in these residues destabilized its structure-function relationship. Avirulent mutants of C2 toxin were screened and selected from a crucial site required for catalytic function of C2I and pore-forming function of C2II. We found coevolved amino acid pairs contributing an essential role in stabilization of its local structural environment. Avirulent toxins selected in this study were evaluated by detecting evolutionary constraints in stability of protein backbone structure, folding and conformational dynamic space, and antigenic peptides. We found 4 avirulent mutants of C2I and 5 mutants of C2II showing more stability in their local structural environment and backbone structure with rapid fold rate, and low conformational flexibility at mutated sites. Since, evolutionary constraints-free mutants with lack of catalytic and pore-forming function suggested as potential immunogenic candidates for treating C. botulinum infected poultry and veterinary animals. Single amino acid substitution in C2 toxin thus provides a major importance to understand its structure-function link, not only of a molecule but also of the pathogenesis.

Unveiling the Structural Evolution of Ag 1.2Mn 8O 16 under Coulombically Controlled (De)Lithiation

DOE PAGES

Huang, Jianping; Hu, Xiaobing; Brady, Alexander B.; ...

2017-12-17

MnO 2 materials are considered promising cathode materials for rechargeable lithium, sodium, and magnesi-um batteries due to their earth abundance and environmental friendliness. One polymorph of MnO 2, α-MnO 2, has 2×2 tunnels (4.6 Å × 4.6 Å) in its structural framework, which provide facile diffusion pathways for guest ions. In this work, a silver ion containing α-MnO 2 (Ag 1.2Mn 8O 16) is examined as a candidate cathode material for Li based batteries. Electro-chemical stability of Ag 1.2Mn 8O 16 is investigated through Coulombically controlled reduction under 2 or 4 molar electron equivalents (e.e.). Terminal discharge voltage remains almostmore » constant under 2 e.e. of cycling, whereas it continuously decreases under repetitive reduction by 4 e.e. Thus, detailed structural analyses were utilized to investigate the structural evolution upon lithiation. Significant increases in lattice a (17.7 %) and atomic distances (~4.8 %) are observed when x in Li xAg 1.2Mn 8O 16 is >4. Ag metal forms at this level of lithiation concomitant with a large structural distortion to the Mn-O framework. In contrast, lattice a only expands by 2.2 % and Mn-O/Mn-Mn distances show minor changes (~1.4 %) at x <2. The structural deformation (tunnel breakage) at x >4 inhibits the recovery of the original structure, leading to poor cycle stability at high lithiation levels. This report establishes the correlation among local structure changes, amorphization processes, formation of Ag 0 and long term cycle stability for this silver containing α-MnO 2 type material at both low and high lithiation levels.« less

Structural stability of DNA origami nanostructures in the presence of chaotropic agents

NASA Astrophysics Data System (ADS)

Ramakrishnan, Saminathan; Krainer, Georg; Grundmeier, Guido; Schlierf, Michael; Keller, Adrian

2016-05-01

DNA origami represent powerful platforms for single-molecule investigations of biomolecular processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concentration and temperature. At room temperature, the DNA origami triangles are stable up to at least 24 h in both denaturants at concentrations as high as 6 M. At elevated temperatures, however, structural stability is governed by variations in the melting temperature of the individual staple strands. Therefore, the global melting temperature of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temperature, its attack results in less structural damage than observed for urea under equivalent conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual experimental requirements. Overall, their high stability renders DNA origami promising platforms for biomolecular studies in the presence of chaotropic agents, including single-molecule protein folding or structural switching.DNA origami represent powerful platforms for single-molecule investigations of biomolecular processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concentration and temperature. At room temperature, the DNA origami triangles are stable up to at least 24 h in both denaturants at concentrations as high as 6 M. At elevated temperatures, however, structural stability is governed by variations in the melting temperature of the individual staple strands. Therefore, the global melting temperature of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temperature, its attack results in less structural damage than observed for urea under equivalent conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual experimental requirements. Overall, their high stability renders DNA origami promising platforms for biomolecular studies in the presence of chaotropic agents, including single-molecule protein folding or structural switching. Electronic supplementary information (ESI) available: Melting curves without baseline subtraction, AFM images of DNA origami after 24 h incubation, calculated melting temperatures of all staple strands. See DOI: 10.1039/c6nr00835f

Structural Responses and Finite Element Modeling of Hakka Tulou Rammed Earth Structures

NASA Astrophysics Data System (ADS)

Sranislawski, Daniel

Hakka Tulous are rammed earth structures that have survived the effects of aging and natural elements upwards of even over a thousand years. These structures have housed the Hakka people of the Fujian Province, China in natural yet modern housing that has provided benefits over newer building materials. The key building material, rammed earth, which is used for the walls of the Hakka Tulou structures, has provided structural stability along with thermal comfort to the respective inhabitants of the Hakka Tulous. Through material testing and analysis this study has examined how the Tulou structures have maintained their structural stability while also providing thermal comfort. Reports of self healing cracks in the rammed earth walls were also analyzed for their validity in this study. The study has found that although the story of the self healing crack cannot be validated, there is reason to believe that with the existence of lime, some type of autogenous healing could occur on a small scale. The study has also found, through the use of nondestructive testing, that both the internal wooden systems (flooring, roof, and column support) and the rammed earth walls, are still structurally sound. Also, rammed earth's high thermal mass along with the use of sufficient shading has allowed for a delay release of heat energy from the walls of the Tulous, thus providing thermal comfort that can be felt during both night and day temperatures. The Hakka Tulou structures have been found to resist destruction from natural disasters such as strong earthquakes even when more modern construction has not. Through finite element modeling, this study has shown that the high volume of rammed earth used in the construction of the Hakka Tulous helps dissipate lateral force energy into much lower stresses for the rammed earth wall. This absorption of lateral force energy allows the rammed earth structures to survive even the strongest of earthquakes experienced in the region. The Hakka Tulou, if rated by the LEED green building certification program, would earn the highest certification as this rammed earth construction has offered efficient living for hundreds of years. As historic as these rammed earth structures are, they present an environmentally friendly option to structures of the future.

Wetting and Dewetting Transitions on Submerged Superhydrophobic Surfaces with Hierarchical Structures.

PubMed

Wu, Huaping; Yang, Zhe; Cao, Binbin; Zhang, Zheng; Zhu, Kai; Wu, Bingbing; Jiang, Shaofei; Chai, Guozhong

2017-01-10

The wetting transition on submersed superhydrophobic surfaces with hierarchical structures and the influence of trapped air on superhydrophobic stability are predicted based on the thermodynamics and mechanical analyses. The dewetting transition on the hierarchically structured surfaces is investigated, and two necessary thermodynamic conditions and a mechanical balance condition for dewetting transition are proposed. The corresponding thermodynamic phase diagram of reversible transition and the critical reversed pressure well explain the experimental results reported previously. Our theory provides a useful guideline for precise controlling of breaking down and recovering of superhydrophobicity by designing superhydrophobic surfaces with hierarchical structures under water.

NUCLEAR REACTORS

DOEpatents

Long, E.; Ashley, J.W.

1958-12-16

A graphite moderator structure is described for a gas-cooled nuclear reactor having a vertical orlentation wherein the structure is physically stable with regard to dlmensional changes due to Wigner growth properties of the graphite, and leakage of coolant gas along spaces in the structure is reduced. The structure is comprised of stacks of unlform right prismatic graphite blocks positioned in layers extending in the direction of the lengths of the blocks, the adjacent end faces of the blocks being separated by pairs of tiles. The blocks and tiles have central bores which are in alignment when assembled and are provided with cooperatlng keys and keyways for physical stability.

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

PubMed

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

2017-11-29

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

Effect of gamma radiation on the stability of UV replicated composite mirrors

NASA Astrophysics Data System (ADS)

Zaldivar, Rafael J.; Kim, Hyun I.; Ferrelli, Geena L.

2018-04-01

Composite replicated mirrors are gaining increasing attention for space-based applications due to their lower density, tailorable mechanical properties, and rapid manufacturing times over state-of-the-art glass mirrors. Ultraviolet (UV)-cured mirrors provide a route by which high-quality mirrors can be manufactured at relatively low processing temperatures that minimize residual stresses. The successful utilization of these mirrors requires nanometer scale dimensional stability after both thermal cycling and hygrothermal exposure. We investigate the effect of gamma irradiation as a process to improve the stability of UV replicated mirrors. Gamma radiation exposure was shown to increase the cure state of these mirrors as evidenced by an increase in modulus, glass transition temperature, and the thermal degradation behavior with dosage. Gas chromatography-mass spectroscopy also showed evidence of consumption of the primary monomers and initiation of the photosensitive agent with gamma exposure. The gamma-exposed mirrors exhibited significant improvement in stability even after multiple thermal cycling in comparison with nonirradiated composite mirrors. Though improvements in the cure state contribute to the overall stability, the radiation dosage was also shown to reduce the film stress of the mirror by over 80% as evidenced using Stoney replicated specimens. This reduction in residual stress is encouraging considering the utilization of these structures for space applications. This paper shows that replicated composite mirrors are a viable alternative to conventional optical structures.

Structure and energetic basis of overrepresented λ light chain in systemic light chain amyloidosis patients.

PubMed

Zhao, Jun; Zhang, Baohong; Zhu, Jianwei; Nussinov, Ruth; Ma, Buyong

2018-06-01

Amyloid formation and deposition of immunoglobulin light-chain proteins in systemic amyloidosis (AL) cause major organ failures. While the κ light-chain is dominant (λ/κ=1:2) in healthy individuals, λ is highly overrepresented (λ/κ=3:1) in AL patients. The structural basis of the amyloid formation and the sequence preference are unknown. We examined the correlation between sequence and structural stability of dimeric variable domains of immunoglobulin light chains using molecular dynamics simulations of 24 representative dimer interfaces, followed by energy evaluation of conformational ensembles for 20 AL patients' light chain sequences. We identified a stable interface with displaced N-terminal residues, provides the structural basis for AL protein fibrils formation. Proline isomerization may cause the N-terminus to adopt amyloid-prone conformations. We found that λ light-chains prefer misfolded dimer conformation, while κ chain structures are stabilized by a natively folded dimer. Our study may facilitate structure-based small molecule and antibody design to inhibit AL. This article is part of a Special Issue entitled: Accelerating Precision Medicine through Genetic and Genomic Big Data Analysis edited by Yudong Cai & Tao Huang. Copyright © 2017 Elsevier B.V. All rights reserved.

Bacterial collagen-like proteins that form triple-helical structures

PubMed Central

Yu, Zhuoxin; An, Bo; Ramshaw, John A.M.; Brodsky, Barbara

2014-01-01

A large number of collagen-like proteins have been identified in bacteria during the past ten years, principally from analysis of genome databases. These bacterial collagens share the distinctive Gly-Xaa-Yaa repeating amino acid sequence of animal collagens which underlies their unique triple-helical structure. A number of the bacterial collagens have been expressed in E. coli, and they all adopt a triple-helix conformation. Unlike animal collagens, these bacterial proteins do not contain the post-translationally modified amino acid, hydroxyproline, which is known to stabilize the triple-helix structure and may promote self-assembly. Despite the absence of collagen hydroxylation, the triple-helix structures of the bacterial collagens studied exhibit a high thermal stability of 35–39 °C, close to that seen for mammalian collagens. These bacterial collagens are readily produced in large quantities by recombinant methods, either in the original amino acid sequence or in genetically manipulated sequences. This new family of recombinant, easy to modify collagens could provide a novel system for investigating structural and functional motifs in animal collagens and could also form the basis of new biomedical materials with designed structural properties and functions. PMID:24434612

X-ray structures define human P2X(3) receptor gating cycle and antagonist action.

PubMed

Mansoor, Steven E; Lü, Wei; Oosterheert, Wout; Shekhar, Mrinal; Tajkhorshid, Emad; Gouaux, Eric

2016-10-06

P2X receptors are trimeric, non-selective cation channels activated by ATP that have important roles in the cardiovascular, neuronal and immune systems. Despite their central function in human physiology and although they are potential targets of therapeutic agents, there are no structures of human P2X receptors. The mechanisms of receptor desensitization and ion permeation, principles of antagonism, and complete structures of the pore-forming transmembrane domains of these receptors remain unclear. Here we report X-ray crystal structures of the human P2X 3 receptor in apo/resting, agonist-bound/open-pore, agonist-bound/closed-pore/desensitized and antagonist-bound/closed states. The open state structure harbours an intracellular motif we term the 'cytoplasmic cap', which stabilizes the open state of the ion channel pore and creates lateral, phospholipid-lined cytoplasmic fenestrations for water and ion egress. The competitive antagonists TNP-ATP and A-317491 stabilize the apo/resting state and reveal the interactions responsible for competitive inhibition. These structures illuminate the conformational rearrangements that underlie P2X receptor gating and provide a foundation for the development of new pharmacological agents.

Asp133 Residue in NhaA Na+/H+ Antiporter Is Required for Stability Cation Binding and Transport.

PubMed

Rimon, Abraham; Dwivedi, Manish; Friedler, Assaf; Padan, Etana

2018-03-16

Na + /H + antiporters have a crucial role in pH and Na + homeostasis in cells. The crystal structure of NhaA, the main antiporter of Escherichia coli, has provided general insights into antiporter mechanisms and revealed a previously unknown structural fold, which has since been identified in several secondary active transporters. This unique structural fold is very delicately electrostatically balanced. Asp133 and Lys 300 have been ascribed essential roles in this balance and, more generally, in the structure and function of the antiporter. In this work, we show the multiple roles of Asp133 in NhaA: (i) The residue's negative charge is critical for the stability of the NhaA structure. (ii) Its main chain is part of the active site. (iii) Its side chain functions as an alkaline-pH-dependent gate, changing the protein's conformation from an inward-facing conformation at acidic pH to an outward-open conformation at alkaline pH, opening the periplasm funnel. On the basis of the experimental data, we propose a tentative mechanism integrating the structural and functional roles of Asp133. Copyright © 2018 Elsevier Ltd. All rights reserved.

Finite element simulation of structural performance on flexible pavements with stabilized base/treated sub-base materials under accelerated loading : research project capsule.

DOT National Transportation Integrated Search

2008-12-01

PROBLEM: The full-scale accelerated pavement testing (APT) provides a unique tool for pavement : engineers to directly collect pavement performance and failure data under heavy : wheel loading. However, running a full-scale APT experiment is very exp...

Protein Chemistry: A Graduate Course in Pharmaceutical Biotechnology at the University of Kansas.

ERIC Educational Resources Information Center

Manning, Mark C.; Mitchell, James W.

1991-01-01

The University of Kansas course in pharmaceutical biotechnology aims at providing students with an understanding of the basic chemical and structural characteristics making protein pharmaceuticals unique and distinct. In addition, stability and analysis of proteins are emphasized. Attention given to molecular biology, drug delivery, and…

Helping Young Children in Frightening Times.

ERIC Educational Resources Information Center

Young Children, 2001

2001-01-01

Presents ways parents and other adults can help young children deal with tragedy and violence in the wake of terrorist attacks on the United States. Suggests giving reassurance and physical comfort, providing structure and stability, expecting a range of reactions, helping children to talk if they are ready, turning off the television, and…

Vocal Fold Epithelial Barrier in Health and Injury: A Research Review

ERIC Educational Resources Information Center

Levendoski, Elizabeth Erickson; Leydon, Ciara; Thibeault, Susan L.

2014-01-01

Purpose: Vocal fold epithelium is composed of layers of individual epithelial cells joined by junctional complexes constituting a unique interface with the external environment. This barrier provides structural stability to the vocal folds and protects underlying connective tissue from injury while being nearly continuously exposed to potentially…

Change or Durability? The Contribution of Metaconceptual Awareness in Preservice Early Childhood Teachers' Learning of Science Concepts

NASA Astrophysics Data System (ADS)

Saçkes, Mesut; Trundle, Kathy Cabe

2017-06-01

This longitudinal study examined the role of metaconceptual awareness in the change and the durability of preservice teachers' conceptual understandings over the course of several months. Sixteen preservice early childhood teachers participated in the study. Semi-structured interviews were conducted to reveal the participants' conceptual understandings of lunar phases (pre, post, and delayed-post) and level of metaconceptual awareness (delayed-post only). Based on the change and stability in participants' conceptual understandings from pre to post and from post to delayed-post interviews, participants' conceptual understandings were assigned into three groups that described the profile of their long-term conceptual understandings: " decay or stability", " continuous growth", and " growth and stability". The results indicated that participants in the " continuous growth" and " growth and stability" groups had significantly higher metaconceptual awareness scores than participants in the " decay or stability" group. The results provided evidence that metaconceptual awareness plays a more decisive role in the restructuring of conceptual understandings than the durability of conceptual understandings.

Self-Management and Transition Readiness Assessment: Development, Reliability, and Factor Structure of the STARx Questionnaire.

PubMed

Ferris, M; Cohen, S; Haberman, C; Javalkar, K; Massengill, S; Mahan, J D; Kim, S; Bickford, K; Cantu, G; Medeiros, M; Phillips, A; Ferris, M T; Hooper, S R

2015-01-01

The Self-Management and Transition to Adulthood with Rx=Treatment (STARx) Questionnaire was developed to collect information on self-management and health care transition (HCT) skills, via self-report, in a broad population of adolescents and young adults (AYAs) with chronic conditions. Over several iterations, the STARx questionnaire was created with AYA, family, and health provider input. The development and pilot testing of the STARx Questionnaire took place with the assistance of 1219 AYAs with different chronic health conditions, in multiple institutions and settings over three phases: item development, pilot testing, reliability and factor structuring. The three development phases resulted in a final version of the STARx Questionnaire. The exploratory factor analysis of the third version of the 18-item STARx identified six factors that accounted for about 65% of the variance: Medication management, Provider communication, Engagement during appointments, Disease knowledge, Adult health responsibilities, and Resource utilization. Reliability estimates revealed good internal consistency and temporal stability, with the alpha coefficient for the overall scale being .80. The STARx was developmentally sensitive, with older patients scoring significantly higher on nearly every factor than younger patients. The STARx Questionnaire is a reliable, self-report tool with adequate internal consistency, temporal stability, and a strong, multidimensional factor structure. It provides another assessment strategy to measure self-management and transition skills in AYAs with chronic conditions. Copyright © 2015 Elsevier Inc. 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

Advanced materials for multilayer mirrors for extreme ultraviolet solar astronomy.

PubMed

Bogachev, S A; Chkhalo, N I; Kuzin, S V; Pariev, D E; Polkovnikov, V N; Salashchenko, N N; Shestov, S V; Zuev, S Y

2016-03-20

We provide an analysis of contemporary multilayer optics for extreme ultraviolet (EUV) solar astronomy in the wavelength ranges: λ=12.9-13.3  nm, λ=17-21  nm, λ=28-33  nm, and λ=58.4  nm. We found new material pairs, which will make new spaceborne experiments possible due to the high reflection efficiencies, spectral resolution, and long-term stabilities of the proposed multilayer coatings. In the spectral range λ=13  nm, Mo/Be multilayer mirrors were shown to demonstrate a better ratio of reflection efficiency and spectral resolution compared with the commonly used Mo/Si. In the spectral range λ=17-21  nm, a new multilayer structure Al/Si was proposed, which had higher spectral resolution along with comparable reflection efficiency compared with the commonly used Al/Zr multilayer structures. In the spectral range λ=30  nm, the Si/B₄C/Mg/Cr multilayer structure turned out to best obey reflection efficiency and long-term stability. The B₄C and Cr layers prevented mutual diffusion of the Si and Mg layers. For the spectral range λ=58  nm, a new multilayer Mo/Mg-based structure was developed; its reflection efficiency and long-term stability have been analyzed. We also investigated intrinsic stresses inherent for most of the multilayer structures and proposed possibilities for stress elimination.

Structure Stabilization by Mixed Anions in Oxyfluoride Cathodes for High-Energy Lithium Batteries

DOE PAGES

Kim, Sung-Wook; Pereira, Nathalie; Chernova, Natasha A.; ...

2015-08-24

Mixed-anion oxyfluorides (i.e., FeO xF 2-x) are an appealing alternative to pure fluorides as high-capacity cathodes in lithium batteries, with enhanced cyclability via oxygen substitution. Yet, it is still unclear how the mixed anions impact the local phase transformation and structural stability of oxyfluorides during cycling due to the complexity of electrochemical reactions, involving both lithium intercalation and conversion. Herein, we investigated the local chemical and structural ordering in FeO 0.7F 1.3 at length scales spanning from single particles to the bulk electrode, via a combination of electron spectrum-imaging, magnetization, electrochemistry, and synchrotron X-ray measurements. The FeO 0.7F 1.3more » nanoparticles retain a FeF 2-like rutile structure but chemically heterogeneous, with an F-rich core covered by thin O-rich shell. Upon lithiation the O-rich rutile phase is transformed into Li—Fe—O(—F) rocksalt that has high lattice coherency with converted metallic Fe, a feature that may facilitate the local electron and ion transport. The O-rich rocksalt is highly stable over lithiation/delithiation and thus advantageous to maintain the integrity of the particle, and due to its predominant distribution on the surface, it is expected to prevent the catalytic interaction of Fe with electrolyte. Our findings of the structural origin of cycling stability in oxyfluorides may provide insights into developing viable high-energy electrodes for lithium batteries.« less

A generative, probabilistic model of local protein structure.

PubMed

Boomsma, Wouter; Mardia, Kanti V; Taylor, Charles C; Ferkinghoff-Borg, Jesper; Krogh, Anders; Hamelryck, Thomas

2008-07-01

Despite significant progress in recent years, protein structure prediction maintains its status as one of the prime unsolved problems in computational biology. One of the key remaining challenges is an efficient probabilistic exploration of the structural space that correctly reflects the relative conformational stabilities. Here, we present a fully probabilistic, continuous model of local protein structure in atomic detail. The generative model makes efficient conformational sampling possible and provides a framework for the rigorous analysis of local sequence-structure correlations in the native state. Our method represents a significant theoretical and practical improvement over the widely used fragment assembly technique by avoiding the drawbacks associated with a discrete and nonprobabilistic approach.

Clar's sextet rule is a consequence of the sigma-electron framework.

PubMed

Maksić, Zvonimir B; Barić, Danijela; Müller, Thomas

2006-08-24

A number of condensed PAHs are examined to identify the underlying reasons governing empirical Clar's rule taking benzene as a limiting case. It is found that the so-called Clar's structures are the only minima on the MP2(fc) potential energy hypersurfaces, meaning that other conceivable valence isomers are nonexistent. The influence of the electron correlation energies to the stability of Clar's structures is substantial with predominating influence of the sigma-electrons. However, the contributions arising from the sigma- and pi-electron correlation energies are approximately the same, if Clar's structures are compared with some artificial pi-electron localized or graphite-like delocalized planar systems. Analysis of the Hartree-Fock (HF) energies provides a compelling evidence that the origin of stability of Clar's structures lies in a decrease of the positive T, V(ee) and V(nn) energy terms relative to some characteristic virtual "delocalized" or "localized" model geometries. Partitioning of the mixed and terms in the sigma- and pi-type contributions, by using the stockholder (SHR), equipartitioning (EQP) and standard pi (SPI) schemes, unequivocally shows that the driving force leading to Clar's structures are more favorable sigma-type interactions. All these conclusions hold for the archetypal benzene too, which could be considered as a limiting Clar system. Finally, the boundaries of Clar's hypothesis and some common misconceptions are briefly discussed. Perusal of the geometric parameters and pi-bond orders reveals that there are no benzene rings completely "vacant" or "fully occupied" by the pi-electrons, envisaged by Clar in his picture of condensed benzenoid compounds. Instead, there are six-membered rings with higher and lower total pi-electron density. The bond length anisotropy of the former rings is smaller. It is concluded that Clar's proposition is a useful rule of thumb providing qualitative information on the stability of the PAH systems, which in turn should not be overinterpreted.

Formation of two-dimensional CuSe on Cu(111) at very low selenium coverage

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

Walen, Holly; Liu, Da -Jiang; Oh, Junepyo

2016-05-09

Here, using scanning tunneling microscopy (STM), we observe that adsorption of Se on Cu(111) produces islands with (√3 x √3)R30° structure, at Se coverages far below the structure's ideal coverage of 1/3 ML. Based on density functional theory (DFT), these islands cannot form due to attractive interactions between chemisorbed Se atoms. DFT shows that incorporating Cu atoms into the √3-Se lattice stabilizes the structure, which provides a plausible explanation for the experimental observations.

Structure of a Highly Active Cephalopod S-crystallin Mutant: New Molecular Evidence for Evolution from an Active Enzyme into Lens-Refractive Protein

PubMed Central

Tan, Wei-Hung; Cheng, Shu-Chun; Liu, Yu-Tung; Wu, Cheng-Guo; Lin, Min-Han; Chen, Chiao-Che; Lin, Chao-Hsiung; Chou, Chi-Yuan

2016-01-01

Crystallins are found widely in animal lenses and have important functions due to their refractive properties. In the coleoid cephalopods, a lens with a graded refractive index provides good vision and is required for survival. Cephalopod S-crystallin is thought to have evolved from glutathione S-transferase (GST) with various homologs differentially expressed in the lens. However, there is no direct structural information that helps to delineate the mechanisms by which S-crystallin could have evolved. Here we report the structural and biochemical characterization of novel S-crystallin-glutathione complex. The 2.35-Å crystal structure of a S-crystallin mutant from Octopus vulgaris reveals an active-site architecture that is different from that of GST. S-crystallin has a preference for glutathione binding, although almost lost its GST enzymatic activity. We’ve also identified four historical mutations that are able to produce a “GST-like” S-crystallin that has regained activity. This protein recapitulates the evolution of S-crystallin from GST. Protein stability studies suggest that S-crystallin is stabilized by glutathione binding to prevent its aggregation; this contrasts with GST-σ, which do not possess this protection. We suggest that a tradeoff between enzyme activity and the stability of the lens protein might have been one of the major driving force behind lens evolution. PMID:27499004

Structural stability of E. coli transketolase to temperature and pH denaturation.

PubMed

Jahromi, Raha R F; Morris, Phattaraporn; Martinez-Torres, Ruben J; Dalby, Paul A

2011-09-10

We have previously shown that the denaturation of TK with urea follows a non-aggregating though irreversible denaturation pathway in which the cofactor binding appears to become altered but without dissociating, then followed at higher urea by partial denaturation of the homodimer prior to any further unfolding or dissociation of the two monomers. Urea is not typically present during biocatalysis, whereas access to TK enzymes that retain activity at increased temperature and extreme pH would be useful for operation under conditions that increase substrate and product stability or solubility. To provide further insight into the underlying causes of its deactivation in process conditions, we have characterised the effects of temperature and pH on the structure, stability, aggregation and activity of Escherichia coli transketolase. The activity of TK was initially found to progressively improve after pre-incubation at increasing temperatures. Loss of activity at higher temperature and low pH resulted primarily from protein denaturation and subsequent irreversible aggregation. By contrast, high pH resulted in the formation of a native-like state that was only partially inactive. The apo-TK enzyme structure content also increased at pH 9 to converge on that of the holo-TK. While cofactor dissociation was previously proposed for high pH deactivation, the observed structural changes in apo-TK but not holo-TK indicate a more complex mechanism. Copyright © 2011 Elsevier B.V. All rights reserved.

Quantification of the Influence of Protein-Protein Interactions on Adsorbed Protein Structure and Bioactivity

PubMed Central

Wei, Yang; Thyparambil, Aby A.; Latour, Robert A.

2013-01-01

While protein-surface interactions have been widely studied, relatively little is understood at this time regarding how protein-surface interaction effects are influenced by protein-protein interactions and how these effects combine with the internal stability of a protein to influence its adsorbed-state structure and bioactivity. The objectives of this study were to develop a method to study these combined effects under widely varying protein-protein interaction conditions using hen egg-white lysozyme (HEWL) adsorbed on silica glass, poly(methyl methacrylate), and polyethylene as our model systems. In order to vary protein-protein interaction effects over a wide range, HEWL was first adsorbed to each surface type under widely varying protein solution concentrations for 2 h to saturate the surface, followed by immersion in pure buffer solution for 15 h to equilibrate the adsorbed protein layers in the absence of additionally adsorbing protein. Periodic measurements were made at selected time points of the areal density of the adsorbed protein layer as an indicator of the level of protein-protein interaction effects within the layer, and these values were then correlated with measurements of the adsorbed protein’s secondary structure and bioactivity. The results from these studies indicate that protein-protein interaction effects help stabilize the structure of HEWL adsorbed on silica glass, have little influence on the structural behavior of HEWL on HDPE, and actually serve to destabilize HEWL’s structure on PMMA. The bioactivity of HEWL on silica glass and HDPE was found to decrease in direct proportion to the degree of adsorption-induce protein unfolding. A direct correlation between bioactivity and the conformational state of adsorbed HEWL was less apparent on PMMA, thus suggesting that other factors influenced HEWL’s bioactivity on this surface, such as the accessibility of HEWL’s bioactive site being blocked by neighboring proteins or the surface itself. The developed methods provide an effective means to characterize the influence of protein-protein interaction effects and provide new molecular-level insights into how protein-protein interaction effects combine with protein-surface interaction and internal protein stability effects to influence the structure and bioactivity of adsorbed protein. PMID:23751416

Interfaces in Heterogeneous Catalysts: Advancing Mechanistic Understanding through Atomic-Scale Measurements.

PubMed

Gao, Wenpei; Hood, Zachary D; Chi, Miaofang

2017-04-18

Developing novel catalysts with high efficiency and selectivity is critical for enabling future clean energy conversion technologies. Interfaces in catalyst systems have long been considered the most critical factor in controlling catalytic reaction mechanisms. Interfaces include not only the catalyst surface but also interfaces within catalyst particles and those formed by constructing heterogeneous catalysts. The atomic and electronic structures of catalytic surfaces govern the kinetics of binding and release of reactant molecules from surface atoms. Interfaces within catalysts are introduced to enhance the intrinsic activity and stability of the catalyst by tuning the surface atomic and chemical structures. Examples include interfaces between the core and shell, twin or domain boundaries, or phase boundaries within single catalyst particles. In supported catalyst nanoparticles (NPs), the interface between the metallic NP and support serves as a critical tuning factor for enhancing catalytic activity. Surface electronic structure can be indirectly tuned and catalytically active sites can be increased through the use of supporting oxides. Tuning interfaces in catalyst systems has been identified as an important strategy in the design of novel catalysts. However, the governing principle of how interfaces contribute to catalyst behavior, especially in terms of interactions with intermediates and their stability during electrochemical operation, are largely unknown. This is mainly due to the evolving nature of such interfaces. Small changes in the structural and chemical configuration of these interfaces may result in altering the catalytic performance. These interfacial arrangements evolve continuously during synthesis, processing, use, and even static operation. A technique that can probe the local atomic and electronic interfacial structures with high precision while monitoring the dynamic interfacial behavior in situ is essential for elucidating the role of interfaces and providing deeper insight for fine-tuning and optimizing catalyst properties. Scanning transmission electron microscopy (STEM) has long been a primary characterization technique used for studying nanomaterials because of its exceptional imaging resolution and simultaneous chemical analysis. Over the past decade, advances in STEM, that is, the commercialization of both aberration correctors and monochromators, have significantly improved the spatial and energy resolution. Imaging atomic structures with subangstrom resolution and identifying chemical species with single-atom sensitivity are now routine for STEM. These advancements have greatly benefitted catalytic research. For example, the roles of lattice strain and surface elemental distribution and their effect on catalytic stability and reactivity have been well documented in bimetallic catalysts. In addition, three-dimensional atomic structures revealed by STEM tomography have been integrated in theoretical modeling for predictive catalyst NP design. Recent developments in stable electronic and mechanical devices have opened opportunities to monitor the evolution of catalysts in operando under synthesis and reaction conditions; high-speed direct electron detectors have achieved sub-millisecond time resolutions and allow for rapid structural and chemical changes to be captured. Investigations of catalysts using these latest microscopy techniques have provided new insights into atomic-level catalytic mechanisms. Further integration of new microscopy methods is expected to provide multidimensional descriptions of interfaces under relevant synthesis and reaction conditions. In this Account, we discuss recent insights on understanding catalyst activity, selectivity, and stability using advanced STEM techniques, with an emphasis on how critical interfaces dictate the performance of precious metal-based heterogeneous catalysts. The role of extended interfacial structures, including those between core and shell, between separate phases and twinned grains, between the catalyst surface and gas, and between metal and support are discussed. We also provide an outlook on how emerging electron microscopy techniques, such as vibrational spectroscopy and electron ptychography, will impact future catalysis research.

Structural stability of DNA origami nanostructures in the presence of chaotropic agents.

PubMed

Ramakrishnan, Saminathan; Krainer, Georg; Grundmeier, Guido; Schlierf, Michael; Keller, Adrian

2016-05-21

DNA origami represent powerful platforms for single-molecule investigations of biomolecular processes. The required structural integrity of the DNA origami may, however, pose significant limitations regarding their applicability, for instance in protein folding studies that require strongly denaturing conditions. Here, we therefore report a detailed study on the stability of 2D DNA origami triangles in the presence of the strong chaotropic denaturing agents urea and guanidinium chloride (GdmCl) and its dependence on concentration and temperature. At room temperature, the DNA origami triangles are stable up to at least 24 h in both denaturants at concentrations as high as 6 M. At elevated temperatures, however, structural stability is governed by variations in the melting temperature of the individual staple strands. Therefore, the global melting temperature of the DNA origami does not represent an accurate measure of their structural stability. Although GdmCl has a stronger effect on the global melting temperature, its attack results in less structural damage than observed for urea under equivalent conditions. This enhanced structural stability most likely originates from the ionic nature of GdmCl. By rational design of the arrangement and lengths of the individual staple strands used for the folding of a particular shape, however, the structural stability of DNA origami may be enhanced even further to meet individual experimental requirements. Overall, their high stability renders DNA origami promising platforms for biomolecular studies in the presence of chaotropic agents, including single-molecule protein folding or structural switching.

Stability of Magnetically-Suppressed Solutal Convection In Protein Crystal Growth

NASA Technical Reports Server (NTRS)

Leslie, F. W.; Ramachandran, N.

2005-01-01

The effect of convection during the crystallization of proteins is not very well understood. In a gravitational field, convection is caused by crystal sedimentation and by solutal buoyancy induced flow and these can lead to crystal imperfections. While crystallization in microgravity can approach diffusion limited growth conditions (no convection), terrestrially strong magnetic fields can be used to control fluid flow and sedimentation effects. In this work, a theory is presented on the stability of solutal convection of a magnetized fluid in the presence of a magnetic field. The requirements for stability are developed and compared to experiments performed within the bore of a superconducting magnet. The theoretical predictions are in good agreement with the experiments and show solutal convection can be stabilized if the surrounding fluid has larger magnetic susceptibility and the magnetic field has a specific structure. Discussion on the application of the technique to protein crystallization is also provided.

Calculated performance, stability and maneuverability of high-speed tilting-prop-rotor aircraft

NASA Technical Reports Server (NTRS)

Johnson, Wayne; Lau, Benton H.; Bowles, Jeffrey V.

1986-01-01

The feasibility of operating tilting-prop-rotor aircraft at high speeds is examined by calculating the performance, stability, and maneuverability of representative configurations. The rotor performance is examined in high-speed cruise and in hover. The whirl-flutter stability of the coupled-wing and rotor motion is calculated in the cruise mode. Maneuverability is examined in terms of the rotor-thrust limit during turns in helicopter configuration. Rotor airfoils, rotor-hub configuration, wing airfoil, and airframe structural weights representing demonstrated advance technology are discussed. Key rotor and airframe parameters are optimized for high-speed performance and stability. The basic aircraft-design parameters are optimized for minimum gross weight. To provide a focus for the calculations, two high-speed tilt-rotor aircraft are considered: a 46-passenger, civil transport and an air-combat/escort fighter, both with design speeds of about 400 knots. It is concluded that such high-speed tilt-rotor aircraft are quite practical.

Translational and rotational knee joint stability in anterior and posterior cruciate-retaining knee arthroplasty.

PubMed

Lo, JiaHsuan; Müller, Otto; Dilger, Torsten; Wülker, Nikolaus; Wünschel, Markus

2011-12-01

This study investigated passive translational and rotational stability properties of the intact knee joint, after bicruciate-retaining bi-compartmental knee arthroplasty (BKA) and after posterior cruciate retaining total knee arthroplasty (TKA). Fourteen human cadaveric knee specimens were used in this study, and a robotic manipulator with six-axis force/torque sensor was used to test the joint laxity in anterior-posterior translation, valgus-varus, and internal-external rotation. The results show the knee joint stability after bicruciate-retaining BKA is similar to that of the native knee. On the other hand, the PCL-retaining TKA results in inferior joint stability in valgus, varus, external rotation, anterior and, surprisingly, posterior directions. Our findings suggest that, provided functional ligamentous structures, bicruciate-retaining BKA is a biomechanically attractive treatment for joint degenerative disease. Copyright © 2010 Elsevier B.V. All rights reserved.

Recent advances in the applications of ionic liquids in protein stability and activity: a review.

PubMed

Patel, Rajan; Kumari, Meena; Khan, Abbul Bashar

2014-04-01

Room temperatures ionic liquids are considered as miraculous solvents for biological system. Due to their inimitable properties and large variety of applications, they have been widely used in enzyme catalysis and protein stability and separation. The related information present in the current review is helpful to the researchers working in the field of biotechnology and biochemistry to design or choose an ionic liquid that can serve as a noble and selective solvent for any particular enzymatic reaction, protein preservation and other protein based applications. We have extensively analyzed the methods used for studying the protein-IL interaction which is useful in providing information about structural and conformational dynamics of protein. This can be helpful to develop and understanding about the effect of ionic liquids on stability and activity of proteins. In addition, the affect of physico-chemical properties of ionic liquids, viz. hydrogen bond capacity and hydrophobicity on protein stability are discussed.

High-Thermal- and Air-Stability Cathode Material with Concentration-Gradient Buffer for Li-Ion Batteries.

PubMed

Shi, Ji-Lei; Qi, Ran; Zhang, Xu-Dong; Wang, Peng-Fei; Fu, Wei-Gui; Yin, Ya-Xia; Xu, Jian; Wan, Li-Jun; Guo, Yu-Guo

2017-12-13

Delivery of high capacity with high thermal and air stability is a great challenge in the development of Ni-rich layered cathodes for commercialized Li-ion batteries (LIBs). Herein we present a surface concentration-gradient spherical particle with varying elemental composition from the outer end LiNi 1/3 Co 1/3 Mn 1/3 O 2 (NCM) to the inner end LiNi 0.8 Co 0.15 Al 0.05 O 2 (NCA). This cathode material with the merit of NCM concentration-gradient protective buffer and the inner NCA core shows high capacity retention of 99.8% after 200 cycles at 0.5 C. Furthermore, this cathode material exhibits much improved thermal and air stability compared with bare NCA. These results provide new insights into the structural design of high-performance cathodes with high energy density, long life span, and storage stability materials for LIBs in the future.

Intelligence by mechanics.

PubMed

Blickhan, Reinhard; Seyfarth, Andre; Geyer, Hartmut; Grimmer, Sten; Wagner, Heiko; Günther, Michael

2007-01-15

Research on the biomechanics of animal and human locomotion provides insight into basic principles of locomotion and respective implications for construction and control. Nearly elastic operation of the leg is necessary to reproduce the basic dynamics in walking and running. Elastic leg operation can be modelled with a spring-mass model. This model can be used as a template with respect to both gaits in the construction and control of legged machines. With respect to the segmented leg, the humanoid arrangement saves energy and ensures structural stability. With the quasi-elastic operation the leg inherits the property of self-stability, i.e. the ability to stabilize a system in the presence of disturbances without sensing the disturbance or its direct effects. Self-stability can be conserved in the presence of musculature with its crucial damping property. To ensure secure foothold visco-elastic suspended muscles serve as shock absorbers. Experiments with technically implemented leg models, which explore some of these principles, are promising.

High-internal-phase emulsions stabilized by metal-organic frameworks and derivation of ultralight metal-organic aerogels

PubMed Central

Zhang, Bingxing; Zhang, Jianling; Liu, Chengcheng; Peng, Li; Sang, Xinxin; Han, Buxing; Ma, Xue; Luo, Tian; Tan, Xiuniang; Yang, Guanying

2016-01-01

To design high-internal-phase emulsion (HIPE) systems is of great interest from the viewpoints of both fundamental researches and practical applications. Here we demonstrate for the first time the utilization of metal-organic framework (MOF) for HIPE formation. By stirring the mixture of water, oil and MOF at room temperature, the HIPE stabilized by the assembly of MOF nanocrystals at oil-water interface could be formed. The MOF-stabilized HIPE provides a novel route to produce highly porous metal-organic aerogel (MOA) monolith. After removing the liquids from the MOF-stabilized HIPE, the ultralight MOA with density as low as 0.01 g·cm−3 was obtained. The HIPE approach for MOA formation has unique advantages and is versatile in producing different kinds of ultralight MOAs with tunable porosities and structures. PMID:26892258

Generating functions and stability study of multivariate self-excited epidemic processes

NASA Astrophysics Data System (ADS)

Saichev, A. I.; Sornette, D.

2011-09-01

We present a stability study of the class of multivariate self-excited Hawkes point processes, that can model natural and social systems, including earthquakes, epileptic seizures and the dynamics of neuron assemblies, bursts of exchanges in social communities, interactions between Internet bloggers, bank network fragility and cascading of failures, national sovereign default contagion, and so on. We present the general theory of multivariate generating functions to derive the number of events over all generations of various types that are triggered by a mother event of a given type. We obtain the stability domains of various systems, as a function of the topological structure of the mutual excitations across different event types. We find that mutual triggering tends to provide a significant extension of the stability (or subcritical) domain compared with the case where event types are decoupled, that is, when an event of a given type can only trigger events of the same type.

The stability of AID and its function in class-switching are critically sensitive to the identity of its nuclear-export sequence

PubMed Central

Geisberger, Roland; Rada, Cristina; Neuberger, Michael S.

2009-01-01

The carboxyterminal region of activation-induced deaminase (AID) is required for its function in Ig class switch recombination (CSR) and also contains a nuclear-export sequence (NES). Here, based on an extensive fine-structure mutation analysis of the AID NES, as well as from AID chimeras bearing heterologous NESs, we show that while a functional NES is indeed essential for CSR, it is not sufficient. The precise nature of the NES is critical both for AID stabilization and CSR function: minor changes in the NES can perturb stabilization and CSR without jeopardizing nuclear export. The results indicate that the AID NES fulfills a function beyond simply providing a signal for nuclear export and suggest the possibility that the quality of exportin-binding may be critical to the stabilization of AID and its activity in CSR. PMID:19351893

Analogues as a check of predicted drift stability at Yucca Mountain, Nevada

USGS Publications Warehouse

Stuckless, J.S.

2006-01-01

Calculations made by the U.S. Department of Energy's Yucca Mountain Project as part of the licensing of a proposed geologic repository in southwestern Nevada for the disposal of high-level radioactive waste, predict that emplacement tunnels will remain open with little collapse long after ground support has disintegrated. This conclusion includes the effects of anticipated seismic events. Natural analogues cannot provide a quantitative test of this conclusion, but they can provide a reasonableness test by examining the naturally occuring and anthropogenic examples of stability of subterranean openings. Available data from a variety of sources, combined with limited observations by the author, show that natural underground openings tend to resist collapse for millions of years and that anthropogenic subterranean openings have remained open from before recorded history through today. This stability is true even in seismically active areas. In fact, the archaeological record is heavily skewed toward preservation of underground structures relative to those found at the surface.

New class of de Sitter vacua in string theory compactifications

NASA Astrophysics Data System (ADS)

Achúcarro, Ana; Ortiz, Pablo; Sousa, Kepa

2016-10-01

String theory contains few known working examples of de Sitter vacua, four-dimensional universes with a positive cosmological constant. A notorious obstacle is the stabilization of a large number—sometimes hundreds—of moduli fields that characterize the compact dimensions. We study the stability of a class of supersymmetric moduli (the complex structure moduli and dilaton in type-IIB flux compactifications) in the regime where the volume of the compact space is large but not exponentially large. We show that, if the number of moduli is very large, random matrix theory provides a new stability condition, a lower bound on the volume. We find a new class of stable vacua where the mass spectrum of these supersymmetric moduli is gapped, without requiring a large mass hierarchy between moduli sectors or any fine-tuning of the superpotential. We provide the first explicit example of this class of vacua in the P[1,1 ,1 ,6 ,9 ] 4 model. A distinguishing feature is that all fermions in the supersymmetric sector are lighter than the gravitino.

Atomistic and coarse-grained computer simulations of raft-like lipid mixtures.

PubMed

Pandit, Sagar A; Scott, H Larry

2007-01-01

Computer modeling can provide insights into the existence, structure, size, and thermodynamic stability of localized raft-like regions in membranes. However, the challenges in the construction and simulation of accurate models of heterogeneous membranes are great. The primary obstacle in modeling the lateral organization within a membrane is the relatively slow lateral diffusion rate for lipid molecules. Microsecond or longer time-scales are needed to fully model the formation and stability of a raft in a membra ne. Atomistic simulations currently are not able to reach this scale, but they do provide quantitative information on the intermolecular forces and correlations that are involved in lateral organization. In this chapter, the steps needed to carry out and analyze atomistic simulations of hydrated lipid bilayers having heterogeneous composition are outlined. It is then shown how the data from a molecular dynamics simulation can be used to construct a coarse-grained model for the heterogeneous bilayer that can predict the lateral organization and stability of rafts at up to millisecond time-scales.

Advanced aeroservoelastic stabilization techniques for hypersonic flight vehicles

NASA Technical Reports Server (NTRS)

Chan, Samuel Y.; Cheng, Peter Y.; Myers, Thomas T.; Klyde, David H.; Magdaleno, Raymond E.; Mcruer, Duane T.

1992-01-01

Advanced high performance vehicles, including Single-Stage-To-Orbit (SSTO) hypersonic flight vehicles, that are statically unstable, require higher bandwidth flight control systems to compensate for the instability resulting in interactions between the flight control system, the engine/propulsion dynamics, and the low frequency structural modes. Military specifications, such as MIL-F-9490D and MIL-F-87242, tend to limit treatment of structural modes to conventional gain stabilization techniques. The conventional gain stabilization techniques, however, introduce low frequency effective time delays which can be troublesome from a flying qualities standpoint. These time delays can be alleviated by appropriate blending of gain and phase stabilization techniques (referred to as Hybrid Phase Stabilization or HPS) for the low frequency structural modes. The potential of using HPS for compensating structural mode interaction was previously explored. It was shown that effective time delay was significantly reduced with the use of HPS; however, the HPS design was seen to have greater residual response than a conventional gain stablized design. Additional work performed to advance and refine the HPS design procedure, to further develop residual response metrics as a basis for alternative structural stability specifications, and to develop strategies for validating HPS design and specification concepts in manned simulation is presented. Stabilization design sensitivity to structural uncertainties and aircraft-centered requirements are also assessed.

Large scale analysis of the mutational landscape in β-glucuronidase: A major player of mucopolysaccharidosis type VII.

PubMed

Khan, Faez Iqbal; Shahbaaz, Mohd; Bisetty, Krishna; Waheed, Abdul; Sly, William S; Ahmad, Faizan; Hassan, Md Imtaiyaz

2016-01-15

The lysosomal storage disorders are a group of 50 unique inherited diseases characterized by unseemly lipid storage in lysosomes. These malfunctions arise due to genetic mutations that result in deficiency or reduced activities of the lysosomal enzymes, which are responsible for catabolism of biological macromolecules. Sly syndrome or mucopolysaccharidosis type VII is a lysosomal storage disorder associated with the deficiency of β-glucuronidase (EC 3.2.1.31) that catalyzes the hydrolysis of β-D-glucuronic acid residues from the non-reducing terminal of glycosaminoglycan. The effects of the disease causing mutations on the framework of the sequences and structure of β-glucuronidase (GUSBp) were analyzed utilizing a variety of bioinformatic tools. These analyses showed that 211 mutations may result in alteration of the biological activity of GUSBp, including previously experimentally validated mutations. Finally, we refined 90 disease causing mutations, which presumably cause a significant impact on the structure, function, and stability of GUSBp. Stability analyses showed that mutations p.Phe208Pro, p.Phe539Gly, p.Leu622Gly, p.Ile499Gly and p.Ile586Gly caused the highest impact on GUSBp stability and function because of destabilization of the protein structure. Furthermore, structures of wild type and mutant GUSBp were subjected to molecular dynamics simulation to examine the relative structural behaviors in the explicit conditions of water. In a broader view, the use of in silico approaches provided a useful understanding of the effect of single point mutations on the structure-function relationship of GUSBp. Copyright © 2015 Elsevier B.V. All rights reserved.

Monolithic solid-state lasers for spaceflight

NASA Astrophysics Data System (ADS)

Krainak, Michael A.; Yu, Anthony W.; Stephen, Mark A.; Merritt, Scott; Glebov, Leonid; Glebova, Larissa; Ryasnyanskiy, Aleksandr; Smirnov, Vadim; Mu, Xiaodong; Meissner, Stephanie; Meissner, Helmuth

2015-02-01

A new solution for building high power, solid state lasers for space flight is to fabricate the whole laser resonator in a single (monolithic) structure or alternatively to build a contiguous diffusion bonded or welded structure. Monolithic lasers provide numerous advantages for space flight solid-state lasers by minimizing misalignment concerns. The closed cavity is immune to contamination. The number of components is minimized thus increasing reliability. Bragg mirrors serve as the high reflector and output coupler thus minimizing optical coatings and coating damage. The Bragg mirrors also provide spectral and spatial mode selection for high fidelity. The monolithic structure allows short cavities resulting in short pulses. Passive saturable absorber Q-switches provide a soft aperture for spatial mode filtering and improved pointing stability. We will review our recent commercial and in-house developments toward fully monolithic solid-state lasers.

Stabilities of ant nests and their adjacent soils

NASA Astrophysics Data System (ADS)

Echezona, B. C.; Igwe, C. A.

2012-10-01

Nests habour ants and termites and protect them from harsh environmental conditions. The structural stabilities of nests were studied to ascertain their relative vulnerability to environmental stresses. Arboreal-ant nests were pried from different trees, while epigeous-termite nests were excavated from soil surface within the sample area. Soils without any visible sign of ant or termite activity were also sampled 6 m away from the nests as control. Laboratory analysis result showed that irrespective of the tree hosts, the aggregate stabilities of the ant nests were lower than those of the ground termite, with nests formed on Cola nitida significantly showing lower aggregate stability (19.7%) than other antnest structures. Clay dispersion ratio, moisture content, water stable aggregate class <0.25mm and sand mass were each negatively correlated with aggregate stability, while water stable aggregate class1.00-0.50 mm gave a positive correlation. Nest structures were dominated more by water stable aggregate class >2.00 mm but path analysis demonstrated that water stable aggregate class <0.25 mm contributed most to the higher aggregate stability of the termite nest than the other nest. Nest aggregates had greater structural stability compared to the control soil. The higher structural stability of termite nests over other nest and soil was considered a better adaptive mechanism against body desiccation.

Role of N-terminal residues on folding and stability of C-phycoerythrin: simulation and urea-induced denaturation studies.

PubMed

Anwer, Khalid; Sonani, Ravi; Madamwar, Datta; Singh, Parvesh; Khan, Faez; Bisetty, Krishna; Ahmad, Faizan; Hassan, Md Imtaiyaz

2015-01-01

The conformational state of biliproteins can be determined by optical properties of the covalently linked chromophores. Recently determined crystal structure of truncated form of α-subunit of cyanobacterial phycoerythrin (αC-PE) from Phormidium tenue provides a new insight into the structure-function relationship of αC-PE. To compare their stabilities, we have measured urea-induced denaturation transitions of the full length αC-PE (FL-αC-PE) and truncated αC-PE (Tr-αC-PE) followed by observing changes in absorbance at 565 nm, fluorescence at 350 and 573 nm, and circular dichroism at 222 nm as a function of [urea], the molar concentration of urea. The transition curve of each protein was analyzed for ΔG(D)(0), the value of Gibbs free energy change on denaturation (ΔG(D)) in the absence of urea; m, the slope (=∂∆G(D)/∂[urea]), and C(m), the midpoint of the denaturation curve, i.e. [urea] at which ΔG(D) = 0. A difference of about 10% in ΔG(D)(0) observed between FL-αC-PE and Tr-αC-PE, suggests that the two proteins are almost equally stable, and the natural deletion of 31 residues from the N-terminal side of the full length protein does not alter its stability. Furthermore, normalization of probes shows that the urea-induced denaturation of both the proteins is a two-state process. Folding of both structural variants (Tr-αC-PE and FL-αC-PE) of P. tenue were also studied using molecular dynamics simulations at 300 K. The results show clearly that the stability of the proteins is evenly distributed over the whole structure indicating no significant role of N-terminal residues in the stability of both proteins.

The development of real-time stability supports visual working memory performance: Young children's feature binding can be improved through perceptual structure.

PubMed

Simmering, Vanessa R; Wood, Chelsey M

2017-08-01

Working memory is a basic cognitive process that predicts higher-level skills. A central question in theories of working memory development is the generality of the mechanisms proposed to explain improvements in performance. Prior theories have been closely tied to particular tasks and/or age groups, limiting their generalizability. The cognitive dynamics theory of visual working memory development has been proposed to overcome this limitation. From this perspective, developmental improvements arise through the coordination of cognitive processes to meet demands of different behavioral tasks. This notion is described as real-time stability, and can be probed through experiments that assess how changing task demands impact children's performance. The current studies test this account by probing visual working memory for colors and shapes in a change detection task that compares detection of changes to new features versus swaps in color-shape binding. In Experiment 1, 3- to 4-year-old children showed impairments specific to binding swaps, as predicted by decreased real-time stability early in development; 5- to 6-year-old children showed a slight advantage on binding swaps, but 7- to 8-year-old children and adults showed no difference across trial types. Experiment 2 tested the proposed explanation of young children's binding impairment through added perceptual structure, which supported the stability and precision of feature localization in memory-a process key to detecting binding swaps. This additional structure improved young children's binding swap detection, but not new-feature detection or adults' performance. These results provide further evidence for the cognitive dynamics and real-time stability explanation of visual working memory development. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Molecular adaptability of nucleoside diphosphate kinase b from trypanosomatid parasites: stability, oligomerization and structural determinants of nucleotide binding.

PubMed

Souza, Tatiana A C B; Trindade, Daniel M; Tonoli, Celisa C C; Santos, Camila R; Ward, Richard J; Arni, Raghuvir K; Oliveira, Arthur H C; Murakami, Mário T

2011-07-01

Nucleoside diphosphate kinases play a crucial role in the purine-salvage pathway of trypanosomatid protozoa and have been found in the secretome of Leishmania sp., suggesting a function related to host-cell integrity for the benefit of the parasite. Due to their importance for housekeeping functions in the parasite and by prolonging the life of host cells in infection, they become an attractive target for drug discovery and design. In this work, we describe the first structural characterization of nucleoside diphosphate kinases b from trypanosomatid parasites (tNDKbs) providing insights into their oligomerization, stability and structural determinants for nucleotide binding. Crystallographic studies of LmNDKb when complexed with phosphate, AMP and ADP showed that the crucial hydrogen-bonding residues involved in the nucleotide interaction are fully conserved in tNDKbs. Depending on the nature of the ligand, the nucleotide-binding pocket undergoes conformational changes, which leads to different cavity volumes. SAXS experiments showed that tNDKbs, like other eukaryotic NDKs, form a hexamer in solution and their oligomeric state does not rely on the presence of nucleotides or mimetics. Fluorescence-based thermal-shift assays demonstrated slightly higher stability of tNDKbs compared to human NDKb (HsNDKb), which is in agreement with the fact that tNDKbs are secreted and subjected to variations of temperature in the host cells during infection and disease development. Moreover, tNDKbs were stabilized upon nucleotide binding, whereas HsNDKb was not influenced. Contrasts on the surface electrostatic potential around the nucleotide-binding pocket might be a determinant for nucleotide affinity and protein stability differentiation. All these together demonstrated the molecular adaptation of parasite NDKbs in order to exert their biological functions intra-parasite and when secreted by regulating ATP levels of host cells.

Contribution of cutinase serine 42 side chain to the stabilization of the oxyanion transition state.

PubMed

Nicolas, A; Egmond, M; Verrips, C T; de Vlieg, J; Longhi, S; Cambillau, C; Martinez, C

1996-01-16

Cutinase from the fungus Fusarium solani pisi is a lipolytic enzyme able to hydrolyze both aggregated and soluble substrates. It therefore provides a powerful tool for probing the mechanisms underlying lipid hydrolysis. Lipolytic enzymes have a catalytic machinery similar to those present in serine proteinases. It is characterized by the triad Ser, His, and Asp (Glu) residues, by an oxyanion binding site that stabilizes the transition state via hydrogen bonds with two main chain amide groups, and possibly by other determinants. It has been suggested on the basis of a covalently bond inhibitor that the cutinase oxyanion hole may consist not only of two main chain amide groups but also of the Ser42 O gamma side chain. Among the esterases and the serine and the cysteine proteases, only Streptomyces scabies esterase, subtilisin, and papain, respectively, have a side chain residue which is involved in the oxyanion hole formation. The position of the cutinase Ser42 side chain is structurally conserved in Rhizomucor miehei lipase with Ser82 O gamma, in Rhizopus delemar lipase with Thr83 O gamma 1, and in Candida antartica B lipase with Thr40 O gamma 1. To evaluate the increase in the tetrahedral intermediate stability provided by Ser42 O gamma, we mutated Ser42 into Ala. Furthermore, since the proper orientation of Ser42 O gamma is directed by Asn84, we mutated Asn84 into Ala, Leu, Asp, and Trp, respectively, to investigate the contribution of this indirect interaction to the stabilization of the oxyanion hole. The S42A mutation resulted in a drastic decrease in the activity (450-fold) without significantly perturbing the three-dimensional structure. The N84A and N84L mutations had milder kinetic effects and did not disrupt the structure of the active site, whereas the N84W and N84D mutations abolished the enzymatic activity due to drastic steric and electrostatic effects, respectively.

B38: an all-boron fullerene analogue

NASA Astrophysics Data System (ADS)

Lv, Jian; Wang, Yanchao; Zhu, Li; Ma, Yanming

2014-09-01

Fullerene-like structures formed by elements other than carbon have long been sought. Finding all-boron (B) fullerene-like structures is challenging due to the geometrical frustration arising from competitions among various structural motifs. We report here the prediction of a B38 fullerene analogue found through first-principles swarm structure searching calculations. The structure is highly symmetric and consists of 56 triangles and four hexagons, which provide an optimal void in the center of the cage. Energetically, it is more favorable than the planar and tubular structures, and possesses an unusually high chemical stability: a large energy gap (~2.25 eV) and a high double aromaticity, superior to those of most aromatic quasi-planar B12 and double-ring B20 clusters. Our findings represent a key step forward towards to the understanding of structures of medium-sized B clusters and map out the experimental direction of the synthesis of an all-B fullerene analogue.Fullerene-like structures formed by elements other than carbon have long been sought. Finding all-boron (B) fullerene-like structures is challenging due to the geometrical frustration arising from competitions among various structural motifs. We report here the prediction of a B38 fullerene analogue found through first-principles swarm structure searching calculations. The structure is highly symmetric and consists of 56 triangles and four hexagons, which provide an optimal void in the center of the cage. Energetically, it is more favorable than the planar and tubular structures, and possesses an unusually high chemical stability: a large energy gap (~2.25 eV) and a high double aromaticity, superior to those of most aromatic quasi-planar B12 and double-ring B20 clusters. Our findings represent a key step forward towards to the understanding of structures of medium-sized B clusters and map out the experimental direction of the synthesis of an all-B fullerene analogue. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01846j

Structural changes and thermal stability of charged LiNixMnyCozO₂ cathode materials studied by combined in situ time-resolved XRD and mass spectroscopy.

PubMed

Bak, Seong-Min; Hu, Enyuan; Zhou, Yongning; Yu, Xiqian; Senanayake, Sanjaya D; Cho, Sung-Jin; Kim, Kwang-Bum; Chung, Kyung Yoon; Yang, Xiao-Qing; Nam, Kyung-Wan

2014-12-24

Thermal stability of charged LiNixMnyCozO2 (NMC, with x + y + z = 1, x:y:z = 4:3:3 (NMC433), 5:3:2 (NMC532), 6:2:2 (NMC622), and 8:1:1 (NMC811)) cathode materials is systematically studied using combined in situ time-resolved X-ray diffraction and mass spectroscopy (TR-XRD/MS) techniques upon heating up to 600 °C. The TR-XRD/MS results indicate that the content of Ni, Co, and Mn significantly affects both the structural changes and the oxygen release features during heating: the more Ni and less Co and Mn, the lower the onset temperature of the phase transition (i.e., thermal decomposition) and the larger amount of oxygen release. Interestingly, the NMC532 seems to be the optimized composition to maintain a reasonably good thermal stability, comparable to the low-nickel-content materials (e.g., NMC333 and NMC433), while having a high capacity close to the high-nickel-content materials (e.g., NMC811 and NMC622). The origin of the thermal decomposition of NMC cathode materials was elucidated by the changes in the oxidation states of each transition metal (TM) cations (i.e., Ni, Co, and Mn) and their site preferences during thermal decomposition. It is revealed that Mn ions mainly occupy the 3a octahedral sites of a layered structure (R3̅m) but Co ions prefer to migrate to the 8a tetrahedral sites of a spinel structure (Fd3̅m) during the thermal decomposition. Such element-dependent cation migration plays a very important role in the thermal stability of NMC cathode materials. The reasonably good thermal stability and high capacity characteristics of the NMC532 composition is originated from the well-balanced ratio of nickel content to manganese and cobalt contents. This systematic study provides insight into the rational design of NMC-based cathode materials with a desired balance between thermal stability and high energy density.

Structural changes and thermal stability of charged LiNi xMn yCo zO 2 cathode materials studied by combined in situ time-resolved XRD and mass spectroscopy

DOE PAGES

Bak, Seong -Min; Hu, Enyuan; Zhou, Yongning; ...

2014-11-24

Thermal stability of charged LiNi xMn yCo zO 2 (NMC, with x + y + z = 1, x:y:z = 4:3:3 (NMC433), 5:3:2 (NMC532), 6:2:2 (NMC622), and 8:1:1 (NMC811)) cathode materials is systematically studied using combined in situ time- resolved X-ray diffraction and mass spectroscopy (TR-XRD/MS) techniques upon heating up to 600 °C. The TR-XRD/MS results indicate that the content of Ni, Co, and Mn significantly affects both the structural changes and the oxygen release features during heating: the more Ni and less Co and Mn, the lower the onset temperature of the phase transition (i.e., thermal decomposition) and themore » larger amount of oxygen release. Interestingly, the NMC532 seems to be the optimized composition to maintain a reasonably good thermal stability, comparable to the low-nickel-content materials (e.g., NMC333 and NMC433), while having a high capacity close to the high-nickel-content materials (e.g., NMC811 and NMC622). The origin of the thermal decomposition of NMC cathode materials was elucidated by the changes in the oxidation states of each transition metal (TM) cations (i.e., Ni, Co, and Mn) and their site preferences during thermal decomposition. It is revealed that Mn ions mainly occupy the 3a octahedral sites of a layered structure (R3¯m) but Co ions prefer to migrate to the 8a tetrahedral sites of a spinel structure (Fd3¯m) during the thermal decomposition. Such element-dependent cation migration plays a very important role in the thermal stability of NMC cathode materials. The reasonably good thermal stability and high capacity characteristics of the NMC532 composition is originated from the well-balanced ratio of nickel content to manganese and cobalt contents. As a result, this systematic study provides insight into the rational design of NMC-based cathode materials with a desired balance between thermal stability and high energy density.« less

Quantum Mechanical Approach to Understanding Structural, Electronic and Mechanical Properties of Intermetallics

DTIC Science & Technology

1989-01-26

Understanding Structural , Electronic and Mechanical Properties of Tntermetallics by A.J. Freeman, Principal Investigator ABSTRACT The primary goal of...like LI or Mg would lower EF into the minimum in the DOS and hence stabilize the L1 2 . A. Structural Phase Stability of Titanium Aluminides Most...34 Structural Stability Calculations in the Titanium -Aluminium System", Conf. on Titanium Aluminides , Wright-Patterson Air Force Base, Nov. 1986

Double-Layer Structured CO2 Adsorbent Functionalized with Modified Polyethyleneimine for High Physical and Chemical Stability.

PubMed

Jeon, Sunbin; Jung, Hyunchul; Kim, Sung Hyun; Lee, Ki Bong

2018-06-18

CO 2 capture using polyethyleneimine (PEI)-impregnated silica adsorbents has been receiving a lot of attention. However, the absence of physical stability (evaporation and leaching of amine) and chemical stability (urea formation) of the PEI-impregnated silica adsorbent has been generally established. Therefore, in this study, a double-layer impregnated structure, developed using modified PEI, is newly proposed to enhance the physical and chemical stabilities of the adsorbent. Epoxy-modified PEI and diepoxide-cross-linked PEI were impregnated via a dry impregnation method in the first and second layers, respectively. The physical stability of the double-layer structured adsorbent was noticeably enhanced when compared to the conventional adsorbents with a single layer. In addition to the enhanced physical stability, the result of simulated temperature swing adsorption cycles revealed that the double-layer structured adsorbent presented a high potential working capacity (3.5 mmol/g) and less urea formation under CO 2 -rich regeneration conditions. The enhanced physical and chemical stabilities as well as the high CO 2 working capacity of the double-layer structured adsorbent were mainly attributed to the second layer consisting of diepoxide-cross-linked PEI.

The Effects of Molecular Crowding on the Structure and Stability of G-Quadruplexes with an Abasic Site

PubMed Central

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

2011-01-01

Both cellular environmental factors and chemical modifications critically affect the properties of nucleic acids. However, the structure and stability of DNA containing abasic sites under cell-mimicking molecular crowding conditions remain unclear. Here, we investigated the molecular crowding effects on the structure and stability of the G-quadruplexes including a single abasic site. Structural analysis by circular dichroism showed that molecular crowding by PEG200 did not affect the topology of the G-quadruplex structure with or without an abasic site. Thermodynamic analysis further demonstrated that the degree of stabilization of the G-quadruplex by molecular crowding decreased with substitution of an abasic site for a single guanine. Notably, we found that the molecular crowding effects on the enthalpy change for G-quadruplex formation had a linear relationship with the abasic site effects depending on its position. These results are useful for predicting the structure and stability of G-quadruplexes with abasic sites in the cell-mimicking conditions. PMID:21949901

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

NASA Technical Reports Server (NTRS)

Venkatesan, C.; Friedmann, P. P.

1987-01-01

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

CsPbBr3 perovskites: Theoretical and experimental investigation on water-assisted transition from nanowire formation to degradation

NASA Astrophysics Data System (ADS)

Akbali, B.; Topcu, G.; Guner, T.; Ozcan, M.; Demir, M. M.; Sahin, H.

2018-03-01

Recent advances in colloidal synthesis methods have led to an increased research focus on halide perovskites. Due to the highly ionic crystal structure of perovskite materials, a stability issue pops up, especially against polar solvents such as water. In this study, we investigate water-driven structural evolution of CsPbBr3 by performing experiments and state-of-the-art first-principles calculations. It is seen that while an optical image shows the gradual degradation of the yellowish CsPbBr3 structure under daylight, UV illumination reveals that the degradation of crystals takes place in two steps: transition from a blue-emitting to green-emitting structure and and then a transition from a green-emitting phase to complete degradation. We found that as-synthesized CsPbBr3 nanowires (NWs) emit blue light under a 254 nm UV source. Before the degradation, first, CsPbBr3 NWs undergo a water-driven structural transition to form large bundles. It is also seen that formation of such bundles provides longer-term environmental stability. In addition theoretical calculations revealed the strength of the interaction of water molecules with ligands and surfaces of CsPbBr3 and provide an atomistic-level explanation to a transition from ligand-covered NWs to bundle formation. Further interaction of green-light-emitting bundles with water causes complete degradation of CsPbBr3 and the photoluminescence signal is entirely quenched. Moreover, Raman and x-ray-diffraction measurements revealed that completely degraded regions are decomposed to PbBr2 and CsBr precursors. We believe that the findings of this study may provide further insight into the degradation mechanism of CsPbBr3 perovskite by water.

Stabilizing Effects of Bacterial Biofilms: EPS Penetration and Redistribution of Bed Stability Down the Sediment Profile

NASA Astrophysics Data System (ADS)

Chen, X. D.; Zhang, C. K.; Zhou, Z.; Gong, Z.; Zhou, J. J.; Tao, J. F.; Paterson, D. M.; Feng, Q.

2017-12-01

Biofilms, consisting of microorganisms and their secreted extracellular polymeric substances (EPSs), serve as "ecosystem engineers" stabilizing sedimentary environments. Natural sediment bed provides an excellent substratum for biofilm growth. The porous structure and rich nutrients allow the EPS matrix to spread deeper into the bed. A series of laboratory-controlled experiments were conducted to investigate sediment colonization of Bacillus subtilis and the penetration of EPS into the sediment bed with incubation time. In addition to EPS accumulation on the bed surface, EPS also penetrated downward. However, EPS distribution developed strong vertical heterogeneity with a much higher content in the surface layer than in the bottom layer. Scanning electron microscope images of vertical layers also displayed different micromorphological properties of sediment-EPS matrix. In addition, colloidal and bound EPSs exhibited distinctive distribution patterns. After the full incubation, the biosedimentary beds were eroded to test the variation of bed stability induced by biological effects. This research provides an important reference for the prediction of sediment transport and hence deepens the understanding of the biologically mediated sediment system and broadens the scope of the burgeoning research field of "biomorphodynamics."

Stability and Change of Social Goals in Adolescence

PubMed Central

Trucco, Elisa M.; Wright, Aidan G. C.; Colder, Craig R.

2013-01-01

Objective This study provides a comprehensive analysis of continuity and change in social goals using the interpersonal circumplex (IPC) model across adolescence (ages 11 – 16). Five complementary definitions of stability were examined: structural, rank-order, absolute, individual, and ipsative. Method Data were taken from a longitudinal study of early adolescent problem behavior. Social goals were assessed during each wave with data collection occurring at three annual intervals (Wave 1, ages 10-12). A community sample of adolescents (n = 387) was recruited. Adolescents were evenly split on gender and a majority (82.7%) was White. Results Results suggest a modest increase in stability across social goals; yet, significant interindividual heterogeneity. Although levels of Agentic and Communal factors increase over time, these patterns were driven by decreases in the Submissive and Separate octants. Conclusions This offers evidence for the utility of examining lower-order facets of interpersonal dispositions as it provides a nuanced picture of adolescent personality development. Furthermore, findings suggest that change and continuity in social goals may both be relevant in this developmental period. The difficulty is accounting for trait stability as well as change, and the IPC model may be particularly useful for meeting this challenge. PMID:23998889

Predicting RNA 3D structure using a coarse-grain helix-centered model

PubMed Central

Kerpedjiev, Peter; Höner zu Siederdissen, Christian; Hofacker, Ivo L.

2015-01-01

A 3D model of RNA structure can provide information about its function and regulation that is not possible with just the sequence or secondary structure. Current models suffer from low accuracy and long running times and either neglect or presume knowledge of the long-range interactions which stabilize the tertiary structure. Our coarse-grained, helix-based, tertiary structure model operates with only a few degrees of freedom compared with all-atom models while preserving the ability to sample tertiary structures given a secondary structure. It strikes a balance between the precision of an all-atom tertiary structure model and the simplicity and effectiveness of a secondary structure representation. It provides a simplified tool for exploring global arrangements of helices and loops within RNA structures. We provide an example of a novel energy function relying only on the positions of stems and loops. We show that coupling our model to this energy function produces predictions as good as or better than the current state of the art tools. We propose that given the wide range of conformational space that needs to be explored, a coarse-grain approach can explore more conformations in less iterations than an all-atom model coupled to a fine-grain energy function. Finally, we emphasize the overarching theme of providing an ensemble of predicted structures, something which our tool excels at, rather than providing a handful of the lowest energy structures. PMID:25904133

Human glucose-6-phosphate dehydrogenase: the crystal structure reveals a structural NADP(+) molecule and provides insights into enzyme deficiency.

PubMed

Au, S W; Gover, S; Lam, V M; Adams, M J

2000-03-15

Glucose-6-phosphate dehydrogenase (G6PD) catalyses the first committed step in the pentose phosphate pathway; the generation of NADPH by this enzyme is essential for protection against oxidative stress. The human enzyme is in a dimer<-->tetramer equilibrium and its stability is dependent on NADP(+) concentration. G6PD deficiency results from many different point mutations in the X-linked gene encoding G6PD and is the most common human enzymopathy. Severe deficiency causes chronic non-spherocytic haemolytic anaemia; the usual symptoms are neonatal jaundice, favism and haemolytic anaemia. We have determined the first crystal structure of a human G6PD (the mutant Canton, Arg459-->Leu) at 3 A resolution. The tetramer is a dimer of dimers. Despite very similar dimer topology, there are two major differences from G6PD of Leuconostoc mesenteroides: a structural NADP(+) molecule, close to the dimer interface but integral to the subunit, is visible in all subunits of the human enzyme; and an intrasubunit disulphide bond tethers the otherwise disordered N-terminal segment. The few dimer-dimer contacts making the tetramer are charge-charge interactions. The importance of NADP(+) for stability is explained by the structural NADP(+) site, which is not conserved in prokaryotes. The structure shows that point mutations causing severe deficiency predominate close to the structural NADP(+) and the dimer interface, primarily affecting the stability of the molecule. They also indicate that a stable dimer is essential to retain activity in vivo. As there is an absolute requirement for some G6PD activity, residues essential for coenzyme or substrate binding are rarely modified.

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

Active Control of Generalized Complex Modal Structures in a Stochastic Environment

DTIC Science & Technology

1992-05-15

began with the design of a baseline controller. The system of interest was a MIMO, heavily damped structure with complex modes, and the control objective...feed-through term in our system that was due to the use of accelerometers as sensors. This provided an acceptable baseline solution to our I problem...to which we could compare our ideas for improvement. One area in which the baseline design was deficient was robust stability to unstructured

Structure and Mechanical Properties of Al-Cu-Fe-X Alloys with Excellent Thermal Stability.

PubMed

Školáková, Andrea; Novák, Pavel; Mejzlíková, Lucie; Průša, Filip; Salvetr, Pavel; Vojtěch, Dalibor

2017-11-05

In this work, the structure and mechanical properties of innovative Al-Cu-Fe based alloys were studied. We focused on preparation and characterization of rapidly solidified and hot extruded Al-Cu-Fe, Al-Cu-Fe-Ni and Al-Cu-Fe-Cr alloys. The content of transition metals affects mechanical properties and structure. For this reason, microstructure, phase composition, hardness and thermal stability have been investigated in this study. The results showed exceptional thermal stability of these alloys and very good values of mechanical properties. Alloying by chromium ensured the highest thermal stability, while nickel addition refined the structure of the consolidated alloy. High thermal stability of all tested alloys was described in context with the transformation of the quasicrystalline phases to other types of intermetallics.

Structure and Mechanical Properties of Al-Cu-Fe-X Alloys with Excellent Thermal Stability

PubMed Central

Školáková, Andrea; Novák, Pavel; Mejzlíková, Lucie; Průša, Filip; Salvetr, Pavel; Vojtěch, Dalibor

2017-01-01

In this work, the structure and mechanical properties of innovative Al-Cu-Fe based alloys were studied. We focused on preparation and characterization of rapidly solidified and hot extruded Al-Cu-Fe, Al-Cu-Fe-Ni and Al-Cu-Fe-Cr alloys. The content of transition metals affects mechanical properties and structure. For this reason, microstructure, phase composition, hardness and thermal stability have been investigated in this study. The results showed exceptional thermal stability of these alloys and very good values of mechanical properties. Alloying by chromium ensured the highest thermal stability, while nickel addition refined the structure of the consolidated alloy. High thermal stability of all tested alloys was described in context with the transformation of the quasicrystalline phases to other types of intermetallics. PMID:29113096

Elucidating the Solvation Structure and Dynamics of Lithium Polysulfides Resulting from Competitive Salt and Solvent Interactions

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

Rajput, Nav Nidhi; Murugesan, Vijayakumar; Shin, Yongwoo

2017-04-10

Fundamental molecular level understanding of functional properties of liquid solutions provides an important basis for designing optimized electrolytes for numerous applica-tions. In particular, exhaustive knowledge of solvation structure, stability and transport properties is critical for developing stable electrolytes for fast charging and high energy density next-generation energy storage systems. Here we report the correlation between solubility, solvation structure and translational dynamics of a lithium salt (Li-TFSI) and polysulfides species using well-benchmarked classical molecular dynamics simulations combined with nuclear magnetic resonance (NMR). It is observed that the polysulfide chain length has a significant effect on the ion-ion and ion-solvent interaction asmore » well as on the diffusion coefficient of the ionic species in solution. In particular, extensive cluster formation is observed in lower order poly-sulfides (Sx2-; x≤4), whereas the longer polysulfides (Sx2-; x>4) show high solubility and slow dynamics in the solu-tion. It is observed that optimal solvent/salt ratio is essen-tial to control the solubility and conductivity as the addi-tion of Li salt increases the solubility but decreases the mo-bility of the ionic species. This work provides a coupled theoretical and experimental study of bulk solvation struc-ture and transport properties of multi-component electro-lyte systems, yielding design metrics for developing optimal electrolytes with improved stability and solubility.« less

Strategy Diversity Stabilizes Mutualism through Investment Cycles, Phase Polymorphism, and Spatial Bubbles

PubMed Central

Boza, Gergely; Kun, Ádám; Scheuring, István; Dieckmann, Ulf

2012-01-01

There is continuing interest in understanding factors that facilitate the evolution and stability of cooperation within and between species. Such interactions will often involve plasticity in investment behavior, in response to the interacting partner's investments. Our aim here is to investigate the evolution and stability of reciprocal investment behavior in interspecific interactions, a key phenomenon strongly supported by experimental observations. In particular, we present a comprehensive analysis of a continuous reciprocal investment game between mutualists, both in well-mixed and spatially structured populations, and we demonstrate a series of novel mechanisms for maintaining interspecific mutualism. We demonstrate that mutualistic partners invariably follow investment cycles, during which mutualism first increases, before both partners eventually reduce their investments to zero, so that these cycles always conclude with full defection. We show that the key mechanism for stabilizing mutualism is phase polymorphism along the investment cycle. Although mutualistic partners perpetually change their strategies, the community-level distribution of investment levels becomes stationary. In spatially structured populations, the maintenance of polymorphism is further facilitated by dynamic mosaic structures, in which mutualistic partners form expanding and collapsing spatial bubbles or clusters. Additionally, we reveal strategy-diversity thresholds, both for well-mixed and spatially structured mutualistic communities, and discuss factors for meeting these thresholds, and thus maintaining mutualism. Our results demonstrate that interspecific mutualism, when considered as plastic investment behavior, can be unstable, and, in agreement with empirical observations, may involve a polymorphism of investment levels, varying both in space and in time. Identifying the mechanisms maintaining such polymorphism, and hence mutualism in natural communities, provides a significant step towards understanding the coevolution and population dynamics of mutualistic interactions. PMID:23166478

Role of different β-turns in β-hairpin conformation and stability studied by optical spectroscopy.

PubMed

Wu, Ling; McElheny, Dan; Setnicka, Vladimír; Hilario, Jovencio; Keiderling, Timothy A

2012-01-01

Model β-hairpin peptides based on variations in the turn sequence of Cochran's tryptophan zipper peptide, SWTWENGKWTWK, were studied using electronic circular dichroism (ECD), fluorescence, and infrared (IR) spectroscopies. The trpzip2 Asn-Gly turn sequence was substituted with Thr-Gly, Aib-Gly, (D)Pro-Gly, and Gly-Asn (trpzip1) to study the impact of turn stability on β-hairpin formation. Stability and conformational changes of these hairpins were monitored by thermodynamic analyses of the temperature variation of both FTIR (amide I') and ECD spectral intensities. These changes were fit to a two-state model which yielded different T(m) values, representing the folding/unfolding process, for hairpins with different β-turns. Different β-turns show systematic contributions to hairpin structure formation, and their inclusion in hairpin design can modify the folding pathways. Aib-Gly or (D)Pro-Gly sequences stabilize the turn resulting in residual Trp-Trp interaction at high temperatures, but at the same time the β-structure (cross strand H-bonds) can become less stable due to constraints of the turn, as seen for (D)Pro-Gly. The structure of the Aib-Gly turn containing hairpin was determined by NMR and was shown to be like trpzip2 (Asn-Gly turn) as regards turn and strand geometries, but to differ from trpzip1 (Gly-Asn turn). The Munoz and Eaton statistical mechanically derived multistate model, tested as an alternate point of view, represented contributions from H-bonds and hydrophobic interactions as well as conformational change as interdependent. Use of different spectral methods that vary in dependence on these physical interactions along with the structural variations provided insight to the complex folding pathways of these small, well-folded peptides. Copyright © 2011 Wiley Periodicals, Inc.

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.

Molecular dynamics study of structure H clathrate hydrates of methane and large guest molecules.

PubMed

Susilo, Robin; Alavi, Saman; Ripmeester, John A; Englezos, Peter

2008-05-21

Methane storage in structure H (sH) clathrate hydrates is attractive due to the relatively higher stability of sH as compared to structure I methane hydrate. The additional stability is gained without losing a significant amount of gas storage density as happens in the case of structure II (sII) methane clathrate. Our previous work has showed that the selection of a specific large molecule guest substance (LMGS) as the sH hydrate former is critical in obtaining the optimum conditions for crystallization kinetics, hydrate stability, and methane content. In this work, molecular dynamics simulations are employed to provide further insight regarding the dependence of methane occupancy on the type of the LMGS and pressure. Moreover, the preference of methane molecules to occupy the small (5(12)) or medium (4(3)5(6)6(3)) cages and the minimum cage occupancy required to maintain sH clathrate mechanical stability are examined. We found that thermodynamically, methane occupancy depends on pressure but not on the nature of the LMGS. The experimentally observed differences in methane occupancy for different LMGS may be attributed to the differences in crystallization kinetics and/or the nonequilibrium conditions during the formation. It is also predicted that full methane occupancies in both small and medium clathrate cages are preferred at higher pressures but these cages are not fully occupied at lower pressures. It was found that both small and medium cages are equally favored for occupancy by methane guests and at the same methane content, the system suffers a free energy penalty if only one type of cage is occupied. The simulations confirm the instability of the hydrate when the small and medium cages are empty. Hydrate decomposition was observed when less than 40% of the small and medium cages are occupied.

Strategy diversity stabilizes mutualism through investment cycles, phase polymorphism, and spatial bubbles.

PubMed

Boza, Gergely; Kun, Adám; Scheuring, István; Dieckmann, Ulf

2012-01-01

There is continuing interest in understanding factors that facilitate the evolution and stability of cooperation within and between species. Such interactions will often involve plasticity in investment behavior, in response to the interacting partner's investments. Our aim here is to investigate the evolution and stability of reciprocal investment behavior in interspecific interactions, a key phenomenon strongly supported by experimental observations. In particular, we present a comprehensive analysis of a continuous reciprocal investment game between mutualists, both in well-mixed and spatially structured populations, and we demonstrate a series of novel mechanisms for maintaining interspecific mutualism. We demonstrate that mutualistic partners invariably follow investment cycles, during which mutualism first increases, before both partners eventually reduce their investments to zero, so that these cycles always conclude with full defection. We show that the key mechanism for stabilizing mutualism is phase polymorphism along the investment cycle. Although mutualistic partners perpetually change their strategies, the community-level distribution of investment levels becomes stationary. In spatially structured populations, the maintenance of polymorphism is further facilitated by dynamic mosaic structures, in which mutualistic partners form expanding and collapsing spatial bubbles or clusters. Additionally, we reveal strategy-diversity thresholds, both for well-mixed and spatially structured mutualistic communities, and discuss factors for meeting these thresholds, and thus maintaining mutualism. Our results demonstrate that interspecific mutualism, when considered as plastic investment behavior, can be unstable, and, in agreement with empirical observations, may involve a polymorphism of investment levels, varying both in space and in time. Identifying the mechanisms maintaining such polymorphism, and hence mutualism in natural communities, provides a significant step towards understanding the coevolution and population dynamics of mutualistic interactions.

Characterization and Higher-Order Structure Assessment of an Interchain Cysteine-Based ADC: Impact of Drug Loading and Distribution on the Mechanism of Aggregation.

PubMed

Guo, Jianxin; Kumar, Sandeep; Chipley, Mark; Marcq, Olivier; Gupta, Devansh; Jin, Zhaowei; Tomar, Dheeraj S; Swabowski, Cecily; Smith, Jacquelynn; Starkey, Jason A; Singh, Satish K

2016-03-16

The impact of drug loading and distribution on higher order structure and physical stability of an interchain cysteine-based antibody drug conjugate (ADC) has been studied. An IgG1 mAb was conjugated with a cytotoxic auristatin payload following the reduction of interchain disulfides. The 2-D LC-MS analysis shows that there is a preference for certain isomers within the various drug to antibody ratios (DARs). The physical stability of the unconjugated monoclonal antibody, the ADC, and isolated conjugated species with specific DAR, were compared using calorimetric, thermal, chemical denaturation and molecular modeling techniques, as well as techniques to assess hydrophobicity. The DAR was determined to have a significant impact on the biophysical properties and stability of the ADC. The CH2 domain was significantly perturbed in the DAR6 species, which was attributable to quaternary structural changes as assessed by molecular modeling. At accelerated storage temperatures, the DAR6 rapidly forms higher molecular mass species, whereas the DAR2 and the unconjugated mAb were largely stable. Chemical denaturation study indicates that DAR6 may form multimers while DAR2 and DAR4 primarily exist in monomeric forms in solution at ambient conditions. The physical state differences were correlated with a dramatic increase in the hydrophobicity and a reduction in the surface tension of the DAR6 compared to lower DAR species. Molecular modeling of the various DAR species and their conformers demonstrates that the auristatin-based linker payload directly contributes to the hydrophobicity of the ADC molecule. Higher order structural characterization provides insight into the impact of conjugation on the conformational and colloidal factors that determine the physical stability of cysteine-based ADCs, with implications for process and formulation development.

Effect of polarization on the stability of a helix dimer

NASA Astrophysics Data System (ADS)

Wang, Xing Y.; Zhang, John Z. H.

2011-01-01

Molecular dynamics (MD) simulations have been carried out to study helix-helix interaction using both standard AMBER and polarized force fields. Comparison of the two simulations shows that electrostatic polarization of intra-protein hydrogen bonds plays a significant role in stabilizing the structure of helix dimer. This stabilizing effect is clearly demonstrated by examining the monomer structure, helix crossing angle and stability of backbone hydrogen bonds under AMBER and PPC. Since reliable prediction of protein-protein structure is a significant challenge, the current study should help shed light on the importance of electrostatic polarization of protein in helix-helix interaction and helix bundle structures.

Predicting 3D structure and stability of RNA pseudoknots in monovalent and divalent ion solutions.

PubMed

Shi, Ya-Zhou; Jin, Lei; Feng, Chen-Jie; Tan, Ya-Lan; Tan, Zhi-Jie

2018-06-01

RNA pseudoknots are a kind of minimal RNA tertiary structural motifs, and their three-dimensional (3D) structures and stability play essential roles in a variety of biological functions. Therefore, to predict 3D structures and stability of RNA pseudoknots is essential for understanding their functions. In the work, we employed our previously developed coarse-grained model with implicit salt to make extensive predictions and comprehensive analyses on the 3D structures and stability for RNA pseudoknots in monovalent/divalent ion solutions. The comparisons with available experimental data show that our model can successfully predict the 3D structures of RNA pseudoknots from their sequences, and can also make reliable predictions for the stability of RNA pseudoknots with different lengths and sequences over a wide range of monovalent/divalent ion concentrations. Furthermore, we made comprehensive analyses on the unfolding pathway for various RNA pseudoknots in ion solutions. Our analyses for extensive pseudokonts and the wide range of monovalent/divalent ion concentrations verify that the unfolding pathway of RNA pseudoknots is mainly dependent on the relative stability of unfolded intermediate states, and show that the unfolding pathway of RNA pseudoknots can be significantly modulated by their sequences and solution ion conditions.

6-Thioguanine alters the structure and stability of duplex DNA and inhibits quadruplex DNA formation.

PubMed

Marathias, V M; Sawicki, M J; Bolton, P H

1999-07-15

The ability to chemically synthesize biomolecules has opened up the opportunity to observe changes in structure and activity that occur upon single atom substitution. In favorable cases this can provide information about the roles of individual atoms. The substitution of 6-thioguanine (6SG) for guanine is a potentially very useful single atom substitution as 6SG has optical, photocrosslinking, metal ion binding and other properties of potential utility. In addition, 6-mercaptopurine is a clinically important pro-drug that is activated by conversion into 6SG by cells. The results presented here indicate that the presence of 6SG blocks the formation of quadruplex DNA. The presence of 6SG alters the structure and lowers the thermal stability of duplex DNA, but duplex DNA can be formed in the presence of 6SG. These results indicate that some of the cytotoxic activity of 6SG may be due to disruption of the quadruplex structures formed by telomere and other DNAs. This additional mode of action is consistent with the delayed onset of cytotoxicity.

Application of PolyHIPE Membrane with Tricaprylmethylammonium Chloride for Cr(VI) Ion Separation: Parameters and Mechanism of Transport Relating to the Pore Structure

PubMed Central

Chen, Jyh-Herng; Le, Thi Tuyet Mai; Hsu, Kai-Chung

2018-01-01

The structural characteristics of membrane support directly affect the performance of carrier facilitated transport membrane. A highly porous PolyHIPE impregnated with Aliquat 336 is proposed for Cr(VI) separation. PolyHIPE consisting of poly(styrene-co-2-ethylhexyl acrylate) copolymer crosslinked with divinylbenzene has the pore structure characteristic of large pore spaces interconnected with small window throats. The unique pore structure provides the membrane with high flux and stability. The experimental results indicate that the effective diffusion coefficient D* of Cr(VI) through Aliquat 336/PolyHIPE membrane is as high as 1.75 × 10−11 m2 s−1. Transport study shows that the diffusion of Cr(VI) through Aliquat 336/PolyHIPE membrane can be attributed to the jumping transport mechanism. The hydraulic stability experiment shows that the membrane is quite stable, with recovery rates remaining at 95%, even after 10 consecutive cycles of operation. The separation study demonstrates the potential application of this new type of membrane for Cr(VI) recovery. PMID:29498709

Effect of TiO2 photocatalytic activity in a HDPE-based food packaging on the structural and microbiological stability of a short-ripened cheese.

PubMed

Gumiero, Matteo; Peressini, Donatella; Pizzariello, Andrea; Sensidoni, Alessandro; Iacumin, Lucilla; Comi, Giuseppe; Toniolo, Rosanna

2013-06-01

A high density polyethylene (HDPE)/calcium carbonate (CaCO(3)) film containing TiO(2) was prepared via blown film extrusion process. The photocatalytic properties of this film were evaluated by voltammetric, UV-Vis spectrophotometric and gas chromatographic measurements following the decomposition rate of suitably selected molecular probes, such as 4-hydroxybenzoic acid and methylene blue. The film containing 1% w/w of TiO(2) displayed a profitable and reproducible photoinduced degradation activity towards target organic compounds. The effect of packaging photocatalytic activity on the structural and microbiological stability of a short-ripened cheese was studied. Cheese structure was assessed by dynamic, small deformation rheological tests. A container consisting of a multilayer material, where the layer brought in contact with the food, made from the HDPE+CaCO(3)+TiO(2) composite matrix, was able to provide a greater maintenance of the original cheese structure than a rigid container currently used, mainly due to the inhibition of lactic acid bacteria and coliforms. Copyright © 2012 Elsevier Ltd. All rights reserved.

The generalized scattering coefficient method for plane wave scattering in layered structures

NASA Astrophysics Data System (ADS)

Liu, Yu; Li, Chao; Wang, Huai-Yu; Zhou, Yun-Song

2017-02-01

The generalized scattering coefficient (GSC) method is pedagogically derived and employed to study the scattering of plane waves in homogeneous and inhomogeneous layered structures. The numerical stabilities and accuracies of this method and other commonly used numerical methods are discussed and compared. For homogeneous layered structures, concise scattering formulas with clear physical interpretations and strong numerical stability are obtained by introducing the GSCs. For inhomogeneous layered structures, three numerical methods are employed: the staircase approximation method, the power series expansion method, and the differential equation based on the GSCs. We investigate the accuracies and convergence behaviors of these methods by comparing their predictions to the exact results. The conclusions are as follows. The staircase approximation method has a slow convergence in spite of its simple and intuitive implementation, and a fine stratification within the inhomogeneous layer is required for obtaining accurate results. The expansion method results are sensitive to the expansion order, and the treatment becomes very complicated for relatively complex configurations, which restricts its applicability. By contrast, the GSC-based differential equation possesses a simple implementation while providing fast and accurate results.

Application of PolyHIPE Membrane with Tricaprylmethylammonium Chloride for Cr(VI) Ion Separation: Parameters and Mechanism of Transport Relating to the Pore Structure.

PubMed

Chen, Jyh-Herng; Le, Thi Tuyet Mai; Hsu, Kai-Chung

2018-03-02

The structural characteristics of membrane support directly affect the performance of carrier facilitated transport membrane. A highly porous PolyHIPE impregnated with Aliquat 336 is proposed for Cr(VI) separation. PolyHIPE consisting of poly(styrene- co -2-ethylhexyl acrylate) copolymer crosslinked with divinylbenzene has the pore structure characteristic of large pore spaces interconnected with small window throats. The unique pore structure provides the membrane with high flux and stability. The experimental results indicate that the effective diffusion coefficient D* of Cr(VI) through Aliquat 336/PolyHIPE membrane is as high as 1.75 × 10 -11 m² s -1 . Transport study shows that the diffusion of Cr(VI) through Aliquat 336/PolyHIPE membrane can be attributed to the jumping transport mechanism. The hydraulic stability experiment shows that the membrane is quite stable, with recovery rates remaining at 95%, even after 10 consecutive cycles of operation. The separation study demonstrates the potential application of this new type of membrane for Cr(VI) recovery.

Structural coloration of chitosan coated cellulose fabrics by electrostatic self-assembled poly (styrene-methyl methacrylate-acrylic acid) photonic crystals.

PubMed

Yavuz, Gönül; Zille, Andrea; Seventekin, Necdet; Souto, Antonio P

2018-08-01

The structural coloration of a chitosan-coated woven cotton fabric obtained by glutaraldehyde-stabilized deposition of electrostatic self-assembled monodisperse and spherically uniform (250 nm) poly (styrene-methyl methacrylate-acrylic acid) photonic crystal nanospheres (P(St-MMA-AA)) was investigated. Bright iridescent coatings displaying different colors in function of the viewing angle were obtained. The SEM, diffuse reflectance spectroscopy, TGA, DSC and FTIR analyses confirm the presence of structural color and the glutaraldehyde and chitosan ability to provide durable chemical bonding between cotton fabric and photonic crystal (PCs) coating with the highest degradation temperature and the lowest enthalpy. The coatings are characterized by a mixture of face-centered cubic and hexagonal close-packed arrays alternating random packing regions. For the first time a cost-efficient structural coloration with high washing and light fastness using self-assembled P(St-MMA-AA) photonic crystals was successfully developed onto woven cotton fabric using chitosan and/or glutaraldehyde as stabilizing agent opening new strategies for the development of dye-free coloration of textiles. Copyright © 2018 Elsevier Ltd. All rights reserved.

The role of stabilization centers in protein thermal stability

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

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

2016-02-26

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

Structure-activity relationships on the study of β-galactosidase folding/unfolding due to interactions with immobilization additives: Triton X-100 and ethanol.

PubMed

Soto, Dayana; Escobar, Sindy; Guzmán, Fanny; Cárdenas, Constanza; Bernal, Claudia; Mesa, Monica

2017-03-01

Improving the enzyme stability is a challenge for allowing their practical application. The surfactants are stabilizing agents, however, there are still questions about their influence on enzyme properties. The structure-activity/stability relationship for β-galactosidase from Bacillus circulans is studied here by Circular Dichroism and activity measurements, as a function of temperature and pH. The tendency of preserving the β-sheet and α-helix structures at temperatures below 65°C and different pH is the result of the balance between the large- and short-range effects, respecting to the active site. This information is fundamental for explaining the structural changes of this enzyme in the presence of Triton X-100 surfactant and ethanol. The enzyme thermal stabilization in the presence of this surfactant responds to the rearrangement of the secondary structure for having optimal activity/stability. The effect of ethanol is more related with changes in the dielectric properties of the aqueous solution than with protein structural transformations. These results contribute to understand the effects of surfactant-enzyme interactions on the enzyme behavior, from the structural point of view and to rationalize the surfactant-based stabilizing strategies for β-galactosidades. Copyright © 2016 Elsevier B.V. All rights reserved.

Recent Advances in the Inverted Planar Structure of Perovskite Solar Cells.

PubMed

Meng, Lei; You, Jingbi; Guo, Tzung-Fang; Yang, Yang

2016-01-19

Inorganic-organic hybrid perovskite solar cells research could be traced back to 2009, and initially showed 3.8% efficiency. After 6 years of efforts, the efficiency has been pushed to 20.1%. The pace of development was much faster than that of any type of solar cell technology. In addition to high efficiency, the device fabrication is a low-cost solution process. Due to these advantages, a large number of scientists have been immersed into this promising area. In the past 6 years, much of the research on perovskite solar cells has been focused on planar and mesoporous device structures employing an n-type TiO2 layer as the bottom electron transport layer. These architectures have achieved champion device efficiencies. However, they still possess unwanted features. Mesoporous structures require a high temperature (>450 °C) sintering process for the TiO2 scaffold, which will increase the cost and also not be compatible with flexible substrates. While the planar structures based on TiO2 (regular structure) usually suffer from a large degree of J-V hysteresis. Recently, another emerging structure, referred to as an "inverted" planar device structure (i.e., p-i-n), uses p-type and n-type materials as bottom and top charge transport layers, respectively. This structure derived from organic solar cells, and the charge transport layers used in organic photovoltaics were successfully transferred into perovskite solar cells. The p-i-n structure of perovskite solar cells has shown efficiencies as high as 18%, lower temperature processing, flexibility, and, furthermore, negligible J-V hysteresis effects. In this Account, we will provide a comprehensive comparison of the mesoporous and planar structures, and also the regular and inverted of planar structures. Later, we will focus the discussion on the development of the inverted planar structure of perovskite solar cells, including film growth, band alignment, stability, and hysteresis. In the film growth part, several methods for obtaining high quality perovskite films are reviewed. In the interface engineering parts, the effect of hole transport layer on subsequent perovskite film growth and their interface band alignment, and also the effect of electron transport layers on charge transport and interface contact will be discussed. As concerns stability, the role of charge transport layers especially the top electron transport layer in the devices stability will be concluded. In the hysteresis part, possible reasons for hysteresis free in inverted planar structure are provided. At the end of this Account, future development and possible solutions to the remaining challenges facing the commercialization of perovskite solar cells are discussed.

Understanding the Physical and Molecular Basis of Stability of Arabidopsis DNA Pol λ under UV-B and High NaCl Stress

PubMed Central

Das, Kali Pada

2015-01-01

Here, we have investigated the physical and molecular basis of stability of Arabidopsis DNA Pol λ, the sole X family DNA polymerase member in plant genome, under UV-B and salinity stress in connection with the function of the N-terminal BRCT (breast cancer-associated C terminus) domain and Ser-Pro rich region in the regulation of the overall structure of this protein. Tryptophan fluorescence studies, fluorescence quenching and Bis-ANS binding experiments using purified recombinant full length Pol λ and its N-terminal deletion forms have revealed UV-B induced conformational change in BRCT domain deficient Pol λ. On the other hand, the highly conserved C-terminal catalytic core PolX domain maintained its tertiary folds under similar condition. Circular dichroism (CD) and fourier transform infrared (FT-IR) spectral studies have indicated appreciable change in the secondary structural elements in UV-B exposed BRCT domain deficient Pol λ. Increased thermodynamic stability of the C-terminal catalytic core domain suggested destabilizing effect of the N-terminal Ser-Pro rich region on the protein structure. Urea-induced equilibrium unfolding studies have revealed increased stability of Pol λ and its N-terminal deletion mutants at high NaCl concentration. In vivo aggregation studies using transient expression systems in Arabidopsis and tobacco indicated possible aggregation of Pol λ lacking the BRCT domain. Immunoprecipitation assays revealed interaction of Pol λ with the eukaryotic molecular chaperone HSP90, suggesting the possibility of regulation of Pol λ stability by HSP90 in plant cell. Overall, our results have provided one of the first comprehensive information on the biophysical characteristics of Pol λ and indicated the importance of both BRCT and Ser-Pro rich modules in regulating the stability of this protein under genotoxic stress in plants. PMID:26230318

Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization.

PubMed

Wulff, Günter; Liu, Junqiu

2012-02-21

The impressive efficiency and selectivity of biological catalysts has engendered a long-standing effort to understand the details of enzyme action. It is widely accepted that enzymes accelerate reactions through their steric and electronic complementarity to the reactants in the rate-determining transition states. Thus, tight binding to the transition state of a reactant (rather than to the corresponding substrate) lowers the activation energy of the reaction, providing strong catalytic activity. Debates concerning the fundamentals of enzyme catalysis continue, however, and non-natural enzyme mimics offer important additional insight in this area. Molecular structures that mimic enzymes through the design of a predetermined binding site that stabilizes the transition state of a desired reaction are invaluable in this regard. Catalytic antibodies, which can be quite active when raised against stable transition state analogues of the corresponding reaction, represent particularly successful examples. Recently, synthetic chemistry has begun to match nature's ability to produce antibody-like binding sites with high affinities for the transition state. Thus, synthetic, molecularly imprinted polymers have been engineered to provide enzyme-like specificity and activity, and they now represent a powerful tool for creating highly efficient catalysts. In this Account, we review recent efforts to develop enzyme models through the concept of transition state stabilization. In particular, models for carboxypeptidase A were prepared through the molecular imprinting of synthetic polymers. On the basis of successful experiments with phosphonic esters as templates to arrange amidinium groups in the active site, the method was further improved by combining the concept of transition state stabilization with the introduction of special catalytic moieties, such as metal ions in a defined orientation in the active site. In this way, the imprinted polymers were able to provide both an electrostatic stabilization for the transition state through the amidinium group as well as a synergism of transition state recognition and metal ion catalysis. The result was an excellent catalyst for carbonate hydrolysis. These enzyme mimics represent the most active catalysts ever prepared through the molecular imprinting strategy. Their catalytic activity, catalytic efficiency, and catalytic proficiency clearly surpass those of the corresponding catalytic antibodies. The active structures in natural enzymes evolve within soluble proteins, typically by the refining of the folding of one polypeptide chain. To incorporate these characteristics into synthetic polymers, we used the concept of transition state stabilization to develop soluble, nanosized carboxypeptidase A models using a new polymerization method we term the "post-dilution polymerization method". With this methodology, we were able to prepare soluble, highly cross-linked, single-molecule nanoparticles. These particles have controlled molecular weights (39 kDa, for example) and, on average, one catalytically active site per particle. Our strategies have made it possible to obtain efficient new enzyme models and further advance the structural and functional analogy with natural enzymes. Moreover, this bioinspired design based on molecular imprinting in synthetic polymers offers further support for the concept of transition state stabilization in catalysis.

A network analysis of the Chinese stock market

NASA Astrophysics Data System (ADS)

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

2009-07-01

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

Evidence of covalent synergy in silicon–sulfur–graphene yielding highly efficient and long-life lithium-ion batteries

DOE PAGES

Hassan, Fathy M.; Batmaz, Rasim; Li, Jingde; ...

2015-10-26

Silicon has the potential to revolutionize the energy storage capacities of lithium-ion batteries to meet the ever increasing power demands of next generation technologies. To avoid the operational stability problems of silicon-based anodes, we propose synergistic physicochemical alteration of electrode structures during their design. This capitalizes on covalent interaction of Si nanoparticles with sulfur-doped graphene and with cyclized polyacrylonitrile to provide a robust nanoarchitecture. This hierarchical structure stabilized the solid electrolyte interphase leading to superior reversible capacity of over 1,000 mAh g -1 for 2,275 cycles at 2 A g -1. Furthermore, the nanoarchitectured design lowered the contact of themore » electrolyte to the electrode leading to not only high coulombic efficiency of 99.9% but also maintaining high stability even with high electrode loading associated with 3.4 mAh cm -2. As a result, the excellent performance combined with the simplistic, scalable and non-hazardous approach render the process as a very promising candidate for Li-ion battery technology.« less

First-principles study on structural, thermal, mechanical and dynamic stability of T'-MoS2.

PubMed

Liu, Y C; Wang, V; Xia, M G; Zhang, S L

2017-03-08

Using first-principles density functional theory calculations, we investigate the structure, stability, optical modes and electronic band gap of a distorted tetragonal MoS 2 monolayer (T'-MoS 2 ). Our simulated scanning tunnel microscopy (STM) images of T'-MoS 2 are dramatically similar to those STM images which were identified as K x (H 2 O) y MoS 2 from a previous experimental study. This similarity suggests that T'-MoS 2 might have already been experimentally observed, but due to being unexpected was misidentified. Furthermore, we verify the stability of T'-MoS 2 from the thermal, mechanical and dynamic aspects, by ab initio molecular dynamics simulation, elastic constants evaluation and phonon band structure calculation based on density functional perturbation theory, respectively. In addition, we calculate the eigenfrequencies and eigenvectors of the optical modes of T'-MoS 2 at [Formula: see text] point and distinguish their Raman and infrared activity by pointing out their irreducible representations using group theory. At the same time, we compare the Raman modes of T'-MoS 2 with those of H-MoS 2 and T-MoS 2 . Our results provide useful guidance for further experimental identification and characterization of T'-MoS 2 .

Spectroscopic and thermodynamic insights into the interaction between proflavine and human telomeric G-quadruplex DNA.

PubMed

Kumar, Vivek; Sengupta, Abhigyan; Gavvala, Krishna; Koninti, Raj Kumar; Hazra, Partha

2014-09-25

The G-quadruplex (GQ-DNA), an alternative structure motif of DNA, has emerged as a novel and exciting target for anticancer drug discovery. GQ-DNA formed in the presence of monovalent cations (Na(+)/K(+)) by human telomeric DNA is a point of interest due to their direct relevance for cellular aging and abnormal cell growths. Small molecules that selectively target and stabilize G-quadruplex structures are considered to be potential therapeutic anticancer agents. Herein, we probe G-quadruplex and proflavine (a well-known DNA intercalator, hence acting as an anticarcinogen) association through steady state and time-resolved fluorescence spectroscopy to explore the effect of stabilization of GQ-DNA by this well-known DNA intercalator. The structural modifications of G-quadruplex upon binding are highlighted through circular dichroism (CD) spectra. Moreover, a detailed insight into the thermodynamics of this interaction has been provided though isothermal titration calorimetry (ITC) studies. The thermodynamic parameters obtained from ITC help to gain knowledge about the nature as well as the driving forces of binding. This present study shows that proflavine (PF) can act as a stabilizer of telomeric GQ-DNA through an entropically as well as enthalpically feasible process with high binding affinity and thereby can be considered as a potential telomerase inhibitor.

Fast-pulverization enabled simultaneous enhancement on cycling stability and rate capability of C@NiFe2O4 hierarchical fibrous bundle

NASA Astrophysics Data System (ADS)

Chen, Zerui; Zhang, Yu; Wang, Xiaoling; Sun, Wenping; Dou, Shixue; Huang, Xin; Shi, Bi

2017-09-01

Electrochemical-grinding induced pulverization is the origin of capacity fading in NiFe2O4. Increasing current density normally accelerates the pulverization that deteriorates lithium storage properties of NiFe2O4. Here we show that the high current induced fast-pulverization can serve as an efficient activation strategy for quick and simultaneous enhancement on cycling stability and rate capability of NiFe2O4 nanoparticles (NPs) that are densely packed on the hierarchically structured carbon nanofiber strand. At a high current density, the pulverization of NiFe2O4 NPs can be accomplished in a few cycles exposing more active surface. During the fast-pulverization, the hierarchically structured carbon nanofiber strand maintains conductive contact for the densely packed NiFe2O4 NPs regardless of charge or discharge, which also effectively suppresses the repetitive breaks and growths of solid-electrolyte-interphase (SEI) via multiple-level structural adaption that favourites the quick formation of a thin and dense SEI, thus providing strong interparticle connectivity with enhancement on cycling stability and rate capability (e.g. doubled capacity). Our findings demonstrate the potential importance of high current induced fast-pulverization as an efficient activation strategy for achieving durable electrode materials suffering from electrochemical-grinding effects.

The Venus SAGE Atmospheric Structure Investigation

NASA Technical Reports Server (NTRS)

Colaprete, Anthony; Crisp, Dave; LaBaw, Clayton; Morse, Stephanie

2005-01-01

Experiment goals and objectives are: a) To accurately define the state properties as a function of altitude from below the 10(exp -4) mb level (approx.150 km) to 92 bars (surface); b) To measure the stability of the atmosphere, and identify convective layers and stable layers, where they exist; c) To detect cloud levels from changes in the lapse rate at their boundaries; d) To provide state properties within the cloud levels, and thus provide supplementary information on cloud composition; e) To search for and characterize wave structure within the atmosphere; f) To search for and measure the intensity and scale of turbulence; g) To measure descent and surface wind speed and direction; h) To provide Lander altitude and attitude during decent for descent imaging analysis; and i) To provide a back-up landing sensor.

Central Band Interosseous Membrane Reconstruction For Forearm Longitudinal Instability.

PubMed

Adams, Julie E; Culp, Randall W; Osterman, A Lee

2016-08-01

The Essex-Lopresti injury results from injuries to the stabilizing structures of the forearm, the radial head, the interosseous membrane, and the triangular fibrocartilage complex. We describe principles in approaching the patient with an acute or chronic Essex-Lopresti injury and describe surgical techniques to address these challenging cases both in the acute and chronic setting and describe outcomes of these techniques. Further research into the role of the interosseous ligament in providing longitudinal and transverse stability to the forearm is likely to change our understanding of the Essex-Lopresti injury and alter management strategies.

Hierarchical polymerized high internal phase emulsions synthesized from surfactant-stabilized emulsion templates.

PubMed

Wong, Ling L C; Villafranca, Pedro M Baiz; Menner, Angelika; Bismarck, Alexander

2013-05-21

In building construction, structural elements, such as lattice girders, are positioned specifically to support the mainframe of a building. This arrangement provides additional structural hierarchy, facilitating the transfer of load to its foundation while keeping the building weight down. We applied the same concept when synthesizing hierarchical open-celled macroporous polymers from high internal phase emulsion (HIPE) templates stabilized by varying concentrations of a polymeric non-ionic surfactant from 0.75 to 20 w/vol %. These hierarchical poly(merized)HIPEs have multimodally distributed pores, which are efficiently arranged to enhance the load transfer mechanism in the polymer foam. As a result, hierarchical polyHIPEs produced from HIPEs stabilized by 5 vol % surfactant showed a 93% improvement in Young's moduli compared to conventional polyHIPEs produced from HIPEs stabilized by 20 vol % of surfactant with the same porosity of 84%. The finite element method (FEM) was used to determine the effect of pore hierarchy on the mechanical performance of porous polymers under small periodic compressions. Results from the FEM showed a clear improvement in Young's moduli for simulated hierarchical porous geometries. This methodology could be further adapted as a predictive tool to determine the influence of hierarchy on the mechanical properties of a range of porous materials.

Stability and structural properties of gene regulation networks with coregulation rules.

PubMed

Warrell, Jonathan; Mhlanga, Musa

2017-05-07

Coregulation of the expression of groups of genes has been extensively demonstrated empirically in bacterial and eukaryotic systems. Such coregulation can arise through the use of shared regulatory motifs, which allow the coordinated expression of modules (and module groups) of functionally related genes across the genome. Coregulation can also arise through the physical association of multi-gene complexes through chromosomal looping, which are then transcribed together. We present a general formalism for modeling coregulation rules in the framework of Random Boolean Networks (RBN), and develop specific models for transcription factor networks with modular structure (including module groups, and multi-input modules (MIM) with autoregulation) and multi-gene complexes (including hierarchical differentiation between multi-gene complex members). We develop a mean-field approach to analyse the dynamical stability of large networks incorporating coregulation, and show that autoregulated MIM and hierarchical gene-complex models can achieve greater stability than networks without coregulation whose rules have matching activation frequency. We provide further analysis of the stability of small networks of both kinds through simulations. We also characterize several general properties of the transients and attractors in the hierarchical coregulation model, and show using simulations that the steady-state distribution factorizes hierarchically as a Bayesian network in a Markov Jump Process analogue of the RBN model. Copyright © 2017. Published by Elsevier Ltd.

Probing Immobilization Mechanism of alpha-chymotrypsin onto Carbon Nanotube in Organic Media by Molecular Dynamics Simulation

PubMed Central

Zhang, Liyun; Xiao, Xiuchan; Yuan, Yuan; Guo, Yanzhi; Li, Menglong; Pu, Xuemei

2015-01-01

The enzyme immobilization has been adopted to enhance the activity and stability of enzymes in non-aqueous enzymatic catalysis. However, the activation and stabilization mechanism has been poorly understood on experiments. Thus, we used molecular dynamics simulation to study the adsorption of α-chymotrypsin (α-ChT) on carbon nanotube (CNT) in aqueous solution and heptane media. The results indicate that α-ChT has stronger affinity with CNT in aqueous solution than in heptane media, as confirmed by more adsorption atoms, larger contact area and higher binding free energies. Although the immobilization causes significant structure deviations from the crystal one, no significant changes in secondary structure of the enzyme upon adsorption are observed in the two media. Different from aqueous solution, the stabilization effects on some local regions far from the surface of CNT were observed in heptane media, in particular for S1 pocket, which should contribute to the preservation of specificity reported by experiments. Also, CNT displays to some extent stabilization role in retaining the catalytic H-bond network of the active site in heptane media, which should be associated with the enhanced activity of enzymes. The observations from the work can provide valuable information for improving the catalytic properties of enzymes in non-aqueous media. PMID:25787884

Properties of nanocellulose isolated from corncob residue using sulfuric acid, formic acid, oxidative and mechanical methods.

PubMed

Liu, Chao; Li, Bin; Du, Haishun; Lv, Dong; Zhang, Yuedong; Yu, Guang; Mu, Xindong; Peng, Hui

2016-10-20

In this work, nanocellulose was extracted from bleached corncob residue (CCR), an underutilized lignocellulose waste from furfural industry, using four different methods (i.e. sulfuric acid hydrolysis, formic acid (FA) hydrolysis, 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO)-mediated oxidation, and pulp refining, respectively). The self-assembled structure, morphology, dimension, crystallinity, chemical structure and thermal stability of prepared nanocellulose were investigated. FA hydrolysis produced longer cellulose nanocrystals (CNCs) than the one obtained by sulfuric acid hydrolysis, and resulted in high crystallinity and thermal stability due to its preferential degradation of amorphous cellulose and lignin. The cellulose nanofibrils (CNFs) with fine and individualized structure could be isolated by TEMPO-mediated oxidation. In comparison with other nanocellulose products, the intensive pulp refining led to the CNFs with the longest length and the thickest diameter. This comparative study can help to provide an insight into the utilization of CCR as a potential source for nanocellulose production. Copyright © 2016 Elsevier Ltd. All rights reserved.

Active vibration absorber for CSI evolutionary model: Design and experimental results

NASA Technical Reports Server (NTRS)

Bruner, Anne M.; Belvin, W. Keith; Horta, Lucas G.; Juang, Jer-Nan

1991-01-01

The development of control of large flexible structures technology must include practical demonstration to aid in the understanding and characterization of controlled structures in space. To support this effort, a testbed facility was developed to study practical implementation of new control technologies under realistic conditions. The design is discussed of a second order, acceleration feedback controller which acts as an active vibration absorber. This controller provides guaranteed stability margins for collocated sensor/actuator pairs in the absence of sensor/actuator dynamics and computational time delay. The primary performance objective considered is damping augmentation of the first nine structural modes. Comparison of experimental and predicted closed loop damping is presented, including test and simulation time histories for open and closed loop cases. Although the simulation and test results are not in full agreement, robustness of this design under model uncertainty is demonstrated. The basic advantage of this second order controller design is that the stability of the controller is model independent.

A cautionary note concerning the use of stabilized weights in marginal structural models.

PubMed

Talbot, Denis; Atherton, Juli; Rossi, Amanda M; Bacon, Simon L; Lefebvre, Geneviève

2015-02-28

Marginal structural models are commonly used to estimate the causal effect of a time-varying treatment in presence of time-dependent confounding. When fitting an MSM to data, the analyst must specify both the structural model for the outcome and the treatment models for the inverse-probability-of-treatment weights. The use of stabilized weights is recommended because they are generally less variable than the standard weights. In this paper, we are concerned with the use of the common stabilized weights when the structural model is specified to only consider partial treatment history, such as the current or most recent treatments. We present various examples of settings where these stabilized weights yield biased inferences while the standard weights do not. These issues are first investigated on the basis of simulated data and subsequently exemplified using data from the Honolulu Heart Program. Unlike common stabilized weights, we find that basic stabilized weights offer some protection against bias in structural models designed to estimate current or most recent treatment effects. Copyright © 2014 John Wiley & Sons, Ltd.

Factorial structure of the German version of the dimensional assessment of personality pathology-basic questionnaire in clinical and nonclinical samples.

PubMed

Pukrop, R; Gentil, I; Steinbring, I; Steinmeyer, E

2001-10-01

The Dimensional Assessment of Personality Pathology-Basic Questionnaire (DAPP-BQ) assesses 18 traits to provide a systematic representation of the overall domain of personality disorders. We tested the cross-cultural stability of the prediction that four higher-order factors (Emotional Dysregulation, Dissocial Behavior, Inhibitedness, and Compulsivity) underlie the 18 basic traits. A total of 81 patients who were primarily treated for an Axis II personality disorder and N = 166 healthy control patients completed the German version of the DAPP-BQ. Results clearly confirmed cross-cultural stability of the postulated four-factor structure in both samples, accounting for 74.7% (clinical sample), and 65.7% (nonclinical sample) of the total variance. All four higher-order factors showed specific correlational relationships with dimensional assessments of DSM-IV personality disorders.

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

NASA Technical Reports Server (NTRS)

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

2004-01-01

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

Orbital Maneuvering Engine Feed System Coupled Stability Investigation, Computer User's Manual

NASA Technical Reports Server (NTRS)

Schuman, M. D.; Fertig, K. W.; Hunting, J. K.; Kahn, D. R.

1975-01-01

An operating manual for the feed system coupled stability model was given, in partial fulfillment of a program designed to develop, verify, and document a digital computer model that can be used to analyze and predict engine/feed system coupled instabilities in pressure-fed storable propellant propulsion systems over a frequency range of 10 to 1,000 Hz. The first section describes the analytical approach to modelling the feed system hydrodynamics, combustion dynamics, chamber dynamics, and overall engineering model structure, and presents the governing equations in each of the technical areas. This is followed by the program user's guide, which is a complete description of the structure and operation of the computerized model. Last, appendices provide an alphabetized FORTRAN symbol table, detailed program logic diagrams, computer code listings, and sample case input and output data listings.

Stack sampling apparatus

DOEpatents

Lind, Randall F; Lloyd, Peter D; Love, Lonnie J; Noakes, Mark W; Pin, Francois G; Richardson, Bradley S; Rowe, John C

2014-09-16

An apparatus for obtaining samples from a structure includes a support member, at least one stabilizing member, and at least one moveable member. The stabilizing member has a first portion coupled to the support member and a second portion configured to engage with the structure to restrict relative movement between the support member and the structure. The stabilizing member is radially expandable from a first configuration where the second portion does not engage with a surface of the structure to a second configuration where the second portion engages with the surface of the structure.

Minimization and Optimization of Designed β-Hairpin Folds

PubMed Central

Andersen, Niels H.; Olsen, Katherine A.; Fesinmeyer, R. Matthew; Tan, Xu; Hudson, F. Michael; Eidenschink, Lisa A.; Farazi, Shabnam R.

2011-01-01

Mimimized β hairpins have provided additional data on the geometric preferences of Trp interactions in TW-loop-WT motifs. This motif imparts significant fold stability to peptides as short as 8 residues. High-resolution NMR structures of a 16- (KKWTWNPATGKWTWQE, ΔGU298 ≥ +7 kJ/mol) and 12-residue (KTWNPATGKWTE, ΔGU298 = +5.05 kJ/mol) hairpin reveal a common turn geometry and edge-to-face (EtF) packing motif and a cation-π interaction between Lys1 and the Trp residue nearest the C-terminus. The magnitude of a CD exciton couplet (due to the two Trp residues) and the chemical shifts of a Trp Hε3 site (shifted upfield by 2.4 ppm due to the EtF stacking geometry) provided near-identical measures of folding. CD melts of representative peptides with the –TW-loop-WT- motif provided the thermodynamic parameters for folding, which reflect enthalpically driven folding at laboratory temperatures with a small ΔCp for unfolding (+420 JK−1/mol). In the case of Asx-Pro-Xaa-Thr-Gly-Xaa loops, mutations established that the two most important residues in this class of direction-reversing loops are Asx and Gly: mutation to alanine is destabilizing by about 6 and 2 kJ/mol, respectively. All indicators of structuring are retained in a minimized 8-residue construct (Ac-WNPATGKW-NH2) with the fold stability reduced to ΔGU278 = −0.7 kJ/mol. NMR and CD comparisons indicate that -TWXNGKWT- (X = S, I) sequences also forms the same hairpin-stabilizing W/W interaction. PMID:16669679

Bismaleimides and related maleimido polymers as matrix resins

NASA Technical Reports Server (NTRS)

Parker, J. A.; Kourtides, D. A.; Fohlen, G. M.

1985-01-01

Significant processing and property improvements can be achieved by copolymerization of state-of-the-art bisimides with various vinyl stilbazole derivatives to give both fire resistance and high-temperature properties from hot-melt compositions. Significant improvement in mechanical properties is achieved through these modifications, which may make these new matrix resins ideal candidates for fireworthy secondary graphite composite structures. Phosphorous modifications of maleimido polymers through phosphonate structure and tricyclophosphazene derivatives provide families of new matrix resins for short-time applications in severe thermo-oxidative environments. With further research these may provide matrix resins for long-term thermo-oxidative stability of advanced composites at temperatures up to 400 to 500 C.

Ship-in-a-bottle catalysts

DOEpatents

Haw, James F.; Song, Weiguo

2006-07-18

In accordance with the present invention there is provided a novel catalyst system in which the catalytic structure is tailormade at the nanometer scale using the invention's novel ship-in-a-bottle synthesis techniques. The invention describes modified forms of solid catalysts for use in heterogeneous catalysis that have a microporous structure defined by nanocages. Examples include zeolites, SAPOs, and analogous materials that have the controlled pore dimensions and hydrothermal stability required for many industrial processes. The invention provides for modification of these catalysts using reagents that are small enough to pass through the windows used to access the cages. The small reagents are then reacted to form larger molecules in the cages.

Evaluation of three electronic noses for detecting incipient wood decay

Treesearch

Manuela Baietto; Alphus D. Wilson; Daniele Bassi; Francesco Ferrini

2010-01-01

Tree assessment methodologies, currently used to evaluate the structural stability of individual urban trees, usually involve a visual analysis followed by measurements of the internal soundness of wood using various instruments that are often invasive, expensive, or inadequate for use within the urban environment. Moreover, most conventional instruments do not provide...

Chapter 7: Nondestructive Testing in the Urban Forest

Treesearch

R. Bruce Allison; Xiping Wang

2015-01-01

Trees within an urban community provide measurable aesthetic, social, ecological and economic benefits. When growing normally and stably, they contribute to making a city more livable and comfortable for its inhabitants. However, as large physical structures in close proximity to people and property, their failure can cause harm. The science of tree stability analysis...

On Group Stability in Hierarchies and Networks.

ERIC Educational Resources Information Center

Demange, Gabrielle

2004-01-01

A hierarchical structure is a widespread organizational form in many areas. My aim in this paper is to provide a rationale for this fact based on two premises. First, a group organizes itself so as to achieve efficient coordination. Second, efficient coordination is achieved only if subgroups as well as individuals agree to cooperate. Even in…

A Framework for Building and Reasoning with Adaptive and Interoperable PMESII Models

DTIC Science & Technology

2007-11-01

Description Logic SOA Service Oriented Architecture SPARQL Simple Protocol And RDF Query Language SQL Standard Query Language SROM Stability and...another by providing a more expressive ontological structure for one of the models, e.g., semantic networks can be mapped to first- order logical...Pellet is an open-source reasoner that works with OWL-DL. It accepts the SPARQL protocol and RDF query language ( SPARQL ) and provides a Java API to

2 H-1,2,3-Triazole-Based Dipeptidyl Nitriles: Potent, Selective, and Trypanocidal Rhodesain Inhibitors by Structure-Based Design.

PubMed

Giroud, Maude; Kuhn, Bernd; Saint-Auret, Sarah; Kuratli, Christoph; Martin, Rainer E; Schuler, Franz; Diederich, François; Kaiser, Marcel; Brun, Reto; Schirmeister, Tanja; Haap, Wolfgang

2018-04-26

Macrocyclic inhibitors of rhodesain (RD), a parasitic cysteine protease and drug target for the treatment of human African trypanosomiasis, have shown low metabolic stability at the macrocyclic ether bridge. A series of acyclic dipeptidyl nitriles was developed using structure-based design (PDB ID: 6EX8 ). The selectivity against the closely related cysteine protease human cathepsin L (hCatL) was substantially improved, up to 507-fold. In the S2 pocket, 3,4-dichlorophenylalanine residues provided high trypanocidal activities. In the S3 pocket, aromatic residues provided enhanced selectivity against hCatL. RD inhibition ( K i values) and in vitro cell-growth of Trypanosoma brucei rhodesiense (IC 50 values) were measured in the nanomolar range. Triazole-based ligands, obtained by a safe, gram-scale flow production of ethyl 1 H-1,2,3-triazole-4-carboxylate, showed excellent metabolic stability in human liver microsomes and in vivo half-lives of up to 1.53 h in mice. When orally administered to infected mice, parasitaemia was reduced but without complete removal of the parasites.

Atlantic salmon Salmo salar in the chalk streams of England are genetically unique.

PubMed

Ikediashi, C; Paris, J R; King, R A; Beaumont, W R C; Ibbotson, A; Stevens, J R

2018-03-01

Recent research has identified genetic groups of Atlantic salmon Salmo salar that show association with geological and environmental boundaries. This study focuses on one particular subgroup of the species inhabiting the chalk streams of southern England, U.K. These fish are genetically distinct from other British and European S. salar populations and have previously demonstrated markedly low admixture with populations in neighbouring regions. The genetic population structure of S. salar occupying five chalk streams was explored using 16 microsatellite loci. The analysis provides evidence of the genetic distinctiveness of chalk-stream S. salar in southern England, in comparison with populations from non-chalk regions elsewhere in western Europe. Little genetic differentiation exists between the chalk-stream populations and a pattern of isolation by distance was evident. Furthermore, evidence of temporal stability of S. salar populations across the five chalk streams was found. This work provides new insights into the temporal stability and lack of genetic population sub-structuring within a unique component of the species' range of S. salar. © 2018 The Fisheries Society of the British Isles.

Role of Hydrophobic Clusters and Long-Range Contact Networks in the Folding of (α/β)8 Barrel Proteins

PubMed Central

Selvaraj, S.; Gromiha, M. Michael

2003-01-01

Analysis on the three dimensional structures of (α/β)8 barrel proteins provides ample light to understand the factors that are responsible for directing and maintaining their common fold. In this work, the hydrophobically enriched clusters are identified in 92% of the considered (α/β)8 barrel proteins. The residue segments with hydrophobic clusters have high thermal stability. Further, these clusters are formed and stabilized through long-range interactions. Specifically, a network of long-range contacts connects adjacent β-strands of the (α/β)8 barrel domain and the hydrophobic clusters. The implications of hydrophobic clusters and long-range networks in providing a feasible common mechanism for the folding of (α/β)8 barrel proteins are proposed. PMID:12609894

Composite S-layer lipid structures

PubMed Central

Schuster, Bernhard; Sleytr, Uwe B.

2010-01-01

Designing and utilization of biomimetic membrane systems generated by bottom-up processes is a rapidly growing scientific and engineering field. Elucidation of the supramolecular construction principle of archaeal cell envelopes composed of S-layer stabilized lipid membranes led to new strategies for generating highly stable functional lipid membranes at meso- and macroscopic scale. In this review, we provide a state of the art survey how S-layer proteins, lipids, and polysaccharides may be used as basic building blocks for the assembly of S-layer supported lipid membranes. These biomimetic membrane systems are distinguished by a nanopatterned fluidity, enhanced stability and longevity and thus, provide a dedicated reconstitution matrix for membrane-active peptides and transmembrane proteins. Exciting areas for application of composite S-layer membrane systems concern sensor systems involving specific membrane functions. PMID:19303933

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

PubMed

Takahashi, Shuntaro; Sugimoto, Naoki

2017-09-18

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

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.

Structural and Functional Properties of Soy Protein Isolates Modified by Soy Soluble Polysaccharides.

PubMed

Xu, Yan-Teng; Liu, Ling-Ling

2016-09-28

Aiming to achieve the modification to soy protein isolate (SPI) by soy soluble polysaccharides (SSPS), electrically driven complex systems were first established in the environment of pH 3.0, and then reconstituted SPI particles with different SPI-SSPS ratios were obtained under freeze-drying process. Through this treatment, the structures of SPI particles were partly unfolded and adsorbed SSPS mainly via hydrophobic interactions and hydrogen bonding with larger particle sizes. The adherence of SSPS decreased the surface hydrophobicity of reconstituted SPI particles, but exerted not much influence on the emulsifying and foaming activities and increased the corresponding stabilities due to enhancing the unfolded extent of structure and improving the conformation flexibility. Reconstituted SPI-SSPS particles might rearrange and link each other due to the presence of SSPS on the air-water interface to better stabilize these systems. At SPI-SSPS ratio of 10:1, lower temperature was required to form gels with lower gel intensity and porous structure. The findings provide a further comprehension to the relationship between structures and functional properties of SPI modified by SSPS and the feasibility of applying these reconstituted particles to needed areas.

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

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

Tjong, Harianto; Li, Wenyuan; Kalhor, Reza

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

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

DOE PAGES

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

2016-03-07

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

On the stability of equilibrium for a reformulated foreign trade model of three countries

NASA Astrophysics Data System (ADS)

Dassios, Ioannis K.; Kalogeropoulos, Grigoris

2014-06-01

In this paper, we study the stability of equilibrium for a foreign trade model consisting of three countries. As the gravity equation has been proven an excellent tool of analysis and adequately stable over time and space all over the world, we further enhance the problem to three masses. We use the basic Structure of Heckscher-Ohlin-Samuelson model. The national income equals consumption outlays plus investment plus exports minus imports. The proposed reformulation of the problem focus on two basic concepts: (1) the delay inherited in our economic variables and (2) the interaction effect along the three economies involved. Stability and stabilizability conditions are investigated while numerical examples provide further insight and better understanding. Finally, a generalization of the gravity equation is somehow obtained for the model.

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

NASA Astrophysics Data System (ADS)

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

2011-10-01

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

Controller Synthesis for Periodically Forced Chaotic Systems

NASA Astrophysics Data System (ADS)

Basso, Michele; Genesio, Roberto; Giovanardi, Lorenzo

Delayed feedback controllers are an appealing tool for stabilization of periodic orbits in chaotic systems. Despite their conceptual simplicity, specific and reliable design procedures are difficult to obtain, partly also because of their inherent infinite-dimensional structure. This chapter considers the use of finite dimensional linear time invariant controllers for stabilization of periodic solutions in a general class of sinusoidally forced nonlinear systems. For such controllers — which can be interpreted as rational approximations of the delayed ones — we provide a computationally attractive synthesis technique based on Linear Matrix Inequalities (LMIs), by mixing results concerning absolute stability of nonlinear systems and robustness of uncertain linear systems. The resulting controllers prove to be effective for chaos suppression in electronic circuits and systems, as shown by two different application examples.

Bipartite entangled stabilizer mutually unbiased bases as maximum cliques of Cayley graphs

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

Dam, Wim van; Howard, Mark; Department of Physics, University of California, Santa Barbara, California 93106

2011-07-15

We examine the existence and structure of particular sets of mutually unbiased bases (MUBs) in bipartite qudit systems. In contrast to well-known power-of-prime MUB constructions, we restrict ourselves to using maximally entangled stabilizer states as MUB vectors. Consequently, these bipartite entangled stabilizer MUBs (BES MUBs) provide no local information, but are sufficient and minimal for decomposing a wide variety of interesting operators including (mixtures of) Jamiolkowski states, entanglement witnesses, and more. The problem of finding such BES MUBs can be mapped, in a natural way, to that of finding maximum cliques in a family of Cayley graphs. Some relationships withmore » known power-of-prime MUB constructions are discussed, and observables for BES MUBs are given explicitly in terms of Pauli operators.« less

Bipartite entangled stabilizer mutually unbiased bases as maximum cliques of Cayley graphs

NASA Astrophysics Data System (ADS)

van Dam, Wim; Howard, Mark

2011-07-01

We examine the existence and structure of particular sets of mutually unbiased bases (MUBs) in bipartite qudit systems. In contrast to well-known power-of-prime MUB constructions, we restrict ourselves to using maximally entangled stabilizer states as MUB vectors. Consequently, these bipartite entangled stabilizer MUBs (BES MUBs) provide no local information, but are sufficient and minimal for decomposing a wide variety of interesting operators including (mixtures of) Jamiołkowski states, entanglement witnesses, and more. The problem of finding such BES MUBs can be mapped, in a natural way, to that of finding maximum cliques in a family of Cayley graphs. Some relationships with known power-of-prime MUB constructions are discussed, and observables for BES MUBs are given explicitly in terms of Pauli operators.

Merits and limitations of the mode switching rate stabilization pacing algorithms in the implantable cardioverter defibrillator.

PubMed

Dijkman, B; Wellens, H J

2001-09-01

The 7250 Jewel AF Medtronic model of ICD is the first implantable device in which both therapies for atrial arrhythmias and pacing algorithms for atrial arrhythmia prevention are available. Feasibility of that extensive atrial arrhythmia management requires correct and synergic functioning of different algorithms to control arrhythmias. The ability of the new pacing algorithms to stabilize the atrial rate following termination of treated atrial arrhythmias was evaluated in the marker channel registration of 600 spontaneously occurring episodes in 15 patients with the Jewel AF. All patients (55+/-15 years) had structural heart disease and documented atrial and ventricular arrhythmias. Dual chamber rate stabilization pacing was present in 245 (41 %) of episodes following arrhythmia termination and was a part of the mode switching operation during which pacing was provided in the dynamic DDI mode. This algorithm could function as the atrial rate stabilization pacing only when there was a slow spontaneous atrial rhythm or in presence of atrial premature beats conducted to the ventricles with a normal AV time. In case of atrial premature beats with delayed or absent conduction to the ventricles and in case of ventricular premature beats, the algorithm stabilized the ventricular rate. The rate stabilization pacing in DDI mode during sinus rhythm following atrial arrhythmia termination was often extended in time due to the device-based definition of arrhythmia termination. This was also the case in patients, in whom the DDD mode with true atrial rate stabilization algorithm was programmed. The rate stabilization algorithms in the Jewel AF applied after atrial arrhythmia termination provide pacing that is not based on the timing of atrial events. Only under certain circumstances the algorithm can function as atrial rate stabilization pacing. Adjustments in availability and functioning of the rate stabilization algorithms might be of benefit for the clinical performance of pacing as part of device therapy for atrial arrhythmias.