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Sample records for ag-thiocrownethers molecular stability

  1. Evolution of molecular phenotypes under stabilizing selection

    Science.gov (United States)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes.

  2. SYNTHESIS AND CHARACTERIZATION OF NEW STABILIZERS WITH OPTIMAL MOLECULAR WEIGHT

    Institute of Scientific and Technical Information of China (English)

    Jiang-qing Pan

    2001-01-01

    Over 2 × l08 tons of polymers are produced every year, and a large portion of polymers faces the degradation problem. There are many effective methods to protect polymers against degradation and the addition of stabilizers to polymer remains the most convenient and effective way of enhancing polymer life and performance. In this article, a series of effective stabilizers with optimal molecular weight (MW), including common, monomeric and polymeric stabilizers (antioxidant and light stabilizer) were synthesized using isocyanation, controlled isocyanation, hydrosilylation, epoxide addition, macroreaction of stabilizing functional compounds and polymerization of monomeric stabilizers. The sructure and performance of these new stabilizers were characterized by using IR, NMR, MS, UV-spectra, XPS and elemental analysis. The current development of stabilizer synthesis was also reviewed.``

  3. On Hadamard stability and dissipative stability of the molecular stress function model of nonlinear viscoelasticity

    OpenAIRE

    Voyiatzis, Evangelos; Tsenoglou, Christos J.; Boudouvis, Andreas G.

    2009-01-01

    Abstract We study the stability characteristics of the Molecular Stress Function (MSF) model, i.e. a constitutive theory based on molecular arguments that extends the original Doi-Edwards theory to the case of branched polymers and without assuming that the tension in the deformed polymer chain is equal to its equilibrium value. We derive analytical, closed-form conditions for Hadamard stability under general 3-D high-frequency, short-amplitude wave disturbances in bi-quadratic for...

  4. Stability of molecular dynamics simulations of classical systems

    DEFF Research Database (Denmark)

    Toxværd, Søren

    2012-01-01

    The existence of a shadow Hamiltonian for discrete classical dynamics, obtained by an asymptotic expansion for a discrete symplectic algorithm, is employed to determine the limit of stability for molecular dynamics (MD) simulations with respect to the time-increment h of the discrete dynamics....... The method is also used to investigate higher-order central difference algorithms, which are symplectic and also have shadow Hamiltonians, and for which one can also determine the exact criteria for the limit of stability of a single harmonic mode. A fourth-order central difference algorithm gives...

  5. Molecular crowding effects on stability of DNA double helix

    Science.gov (United States)

    Singh, Amar; Singh, Navin

    2016-05-01

    Cellular environmental conditions critically affect the structure and stability of double stranded DNA (dsDNA) molecule. It is known that 20-30% of the total volume of the cell is occupied by the molecular crowders. The presence of these crowders, reduces the free space available to the base pairs of a DNA molecule, hence the movement of base pair is restricted. Here, we study the thermal opening of dsDNA molecule using Peyrard Bishop Dauxois (PBD) model. The presence of crowders in the model, that mimic those found in the cell nucleus, is realized through the potential term. Using the equilibrium statistical calculations, we find melting profile and melting probabilities of the chain. The opening of DNA molecule in the presence of these crowders is shown through the density plots. This study reveals that the stability of dsDNA molecule is influenced by entropic as well as enthalpic effects and is more stable in the crowded environment.

  6. A molecular anchor for stabilizing triple-helical DNA.

    OpenAIRE

    Fox, K. R.; Polucci, P; Jenkins, T. C.; Neidle, S

    1995-01-01

    Molecular modeling has been used to predict that 2,6-disubstituted amidoanthraquinones, and not the 1,4 series, should preferentially interact with and stabilize triple-stranded DNA structures over duplex DNA. This is due to marked differences in the nature of chromophore-base stacking and groove accessibility for the two series. A DNA foot-printing method that monitors the extent of protection from DNase I cleavage on triplex formation has been used to examine the effects of a number of synt...

  7. Stability mechanisms of a thermophilic laccase probed by molecular dynamics

    DEFF Research Database (Denmark)

    Christensen, Niels Johan; Kepp, Kasper Planeta

    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...... 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...... 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....

  8. Thermodynamic Stability of Structure H Hydrates Based on the Molecular Properties of Large Guest Molecules

    Directory of Open Access Journals (Sweden)

    Ryo Ohmura

    2012-02-01

    Full Text Available This paper report analyses of thermodynamic stability of structure-H clathrate hydrates formed with methane and large guest molecules in terms of their gas phase molecular sizes and molar masses for the selection of a large guest molecule providing better hydrate stability. We investigated the correlation among the gas phase molecular sizes, the molar masses of large molecule guest substances, and the equilibrium pressures. The results suggest that there exists a molecular-size value for the best stability. Also, at a given molecule size, better stability may be available when the large molecule guest substance has a larger molar mass.

  9. Molecular hydrogelators of peptoid-peptide conjugates with superior stability against enzyme digestion

    Science.gov (United States)

    Wu, Zhidan; Tan, Ming; Chen, Xuemei; Yang, Zhimou; Wang, Ling

    2012-05-01

    We report on molecular hydrogelators based on peptoid-peptide conjugates with good biocompatibility to different cells and superior stability against proteinase K digestion.We report on molecular hydrogelators based on peptoid-peptide conjugates with good biocompatibility to different cells and superior stability against proteinase K digestion. Electronic supplementary information (ESI) available: Synthesis and characterization of gelators, dynamic strain sweep, cell viability, and procedure to determine the stability of compounds against proteinase K digestion. See DOI: 10.1039/c2nr30408b

  10. MOLECULAR DYNAMICS SIMULATION OF STRUCTURE STABILITY OF SILVER NANOCLUSTERS

    Institute of Scientific and Technical Information of China (English)

    W.H. Qi

    2006-01-01

    The structures of Ag clusters with sizes n=13 to 1157 are studied by tight binding molecular dynamics simulation. It is found that the stable structures of Ag clusters follow the sequence amorphous-crystalline-amorphous-crystalline with the cluster size increasing from 13 to 1157.Furthermore, all the shells of Ag clusters are different from the structure of the corresponding bulk Ag.

  11. Low Molecular Weight Chitosan–Insulin Polyelectrolyte Complex: Characterization and Stability Studies

    Directory of Open Access Journals (Sweden)

    Zakieh I. Al-Kurdi

    2015-03-01

    Full Text Available The aim of the work reported herein was to investigate the effect of various low molecular weight chitosans (LMWCs on the stability of insulin using USP HPLC methods. Insulin was found to be stable in a polyelectrolyte complex (PEC consisting of insulin and LMWC in the presence of a Tris-buffer at pH 6.5. In the presence of LMWC, the stability of insulin increased with decreasing molecular weight of LMWC; 13 kDa LMWC was the most efficient molecular weight for enhancing the physical and chemical stability of insulin. Solubilization of insulin-LMWC polyelectrolyte complex (I-LMWC PEC in a reverse micelle (RM system, administered to diabetic rats, results in an oral delivery system for insulin with acceptable bioactivity.

  12. Substrate and head group modifications for enhanced stability in molecular electronic devices

    Science.gov (United States)

    Ferrato, Michael-Anthony

    Poor Self-Assembled Monolayer (SAM) stability is a barrier which impedes the incorporation of molecular layers as functional components in electronic device architectures. Here we investigate the molecular electronic characteristics of two well established approaches to enhancing SAM stability. In Chapter 2 we investigate the electrochemical modification of Au substrates by the underpotential deposition of silver monolayers (AgUPD). In Chapter 3 we study chelating dithiophosphinic acid (DTPA) head groups to anchor SAM molecules to substrates. Based on molecular electronic characterization using EGaIn Tip testbeds, we observed that AgUPD substrates maintained the inherent electronic character of n-alkanethiolate SAMs, but reduced charge transport by almost 1 order of magnitude as compared with the same SAMs on bulk Au substrates. Similar molecular electronic characterization of (diphenyl)dithiophosphinic acid SAMs on Au substrates revealed that the DTPA head group induced a ~3 order of magnitude drop in charge transport as compared with analogous thiophenol SAMs.

  13. Stabilization of Ab Initio Molecular Dynamics Simulations at Large Time Steps

    CERN Document Server

    Tsuchida, Eiji

    2014-01-01

    The Verlet method is still widely used to integrate the equations of motion in ab initio molecular dynamics simulations. We show that the stability limit of the Verlet method may be significantly increased by setting an upper limit on the kinetic energy of each atom with only a small loss in accuracy. The validity of this approach is demonstrated for molten lithium fluoride.

  14. Stability of Y/MCM-48 composite molecular sieve with mesoporous and microporous structures

    Directory of Open Access Journals (Sweden)

    Qian Zhao

    2014-12-01

    Full Text Available Y/MCM-48 composite molecular sieve was hydrothermally synthesized at different crystallization temperatures and crystallization times using ethyl orthosilicate as Si source and cetyltrimethyl ammonium bromide as template with the aid of fluoride ions and was characterized by X-ray diffraction, N2 physical adsorption technique, scanning electron microscopy and transmission electron microscopy. The thermal, hydrothermal, acidic, and basic stabilities of the Y/MCM-48 composite were investigated. The results show that Y/MCM-48 composite molecular sieve with meso- and microporous structures was synthesized successfully at 120 °C for 36 h. The Y/MCM-48 composite has the surface area of 864 m2/g and the average pore size is ca. 2.48 nm. The bi-porous structure in composite molecular sieve still maintains its stability even after thermal treatment at 800 °C for 4 h or hydrothermal treatment at 100 °C for 48 h. After treatment in 1 mol/L hydrochloric acid solution or 1 mol/L sodium hydroxide solution for 48 h, the Y/MCM-48 composite exhibits good acidic stability. The acidic stability is superior to the basic stability at the same treatment time.

  15. Tidal stability of giant molecular clouds in the Large Magellanic Cloud

    CERN Document Server

    Thilliez, E; Hughes, A; Wong, T

    2013-01-01

    Star formation does not occur until the onset of gravitational collapse inside giant molecular clouds. However, the conditions that initiate cloud collapse and regulate the star formation process remain poorly understood. Local processes such as turbulence and magnetic fields can act to promote or prevent collapse. On larger scales, the galactic potential can also influence cloud stability and is traditionally assessed by the tidal and shear effects. In this paper, we examine the stability of giant molecular clouds (GMCs) in the Large Magellanic Cloud (LMC) against shear and the galactic tide using CO data from the Magellanic Mopra Assessment (MAGMA) and rotation curve data from the literature. We calculate the tidal acceleration experienced by individual GMCs and determine the minimum cloud mass required for tidal stability. We also calculate the shear parameter, which is a measure of a clouds susceptibility to disruption via shearing forces in the galactic disk. We examine whether there are correlations bet...

  16. Effect of Molecular Structure on Stability of Organic Nanoparticles Formed by Bodipy Dimers.

    Science.gov (United States)

    Lin, Wenhai; Zhang, Wei; Sun, Tingting; Gu, Jingkai; Xie, Zhigang; Jing, Xiabin

    2016-09-20

    The objective was to evaluate the stability of organic nanoparticles made from Bodipy dimers. Bodipy dimers with different length of linkers were synthesized via multicomponent Passerini reaction, and could form the fluorescent nanoparticles (FNPs) through nanoprecipitation. Bodipy-dimers FNPs with long chain linker indicated better stability in biological condition than those with short one as revealed by changes of diameter and size distribution. The FNPs possessed high physical homogeneity and low cytotoxicity. The molecular structure dependent stability was also validated by confocal laser scanning microscope based on the dissociation-induced fluorescence recovering. Importantly, stable FNPs also could be used to load hydrophobic cargoes and deliver them into cytoplasm. We believe this systematic study between structure and stability might open new opportunities for designing stable nanoparticles for various applications. PMID:27571251

  17. Cellular Viscosity in Prokaryotes and Thermal Stability of Low Molecular Weight Biomolecules.

    Science.gov (United States)

    Cuecas, Alba; Cruces, Jorge; Galisteo-López, Juan F; Peng, Xiaojun; Gonzalez, Juan M

    2016-08-23

    Some low molecular weight biomolecules, i.e., NAD(P)H, are unstable at high temperatures. The use of these biomolecules by thermophilic microorganisms has been scarcely analyzed. Herein, NADH stability has been studied at different temperatures and viscosities. NADH decay increased at increasing temperatures. At increasing viscosities, NADH decay rates decreased. Thus, maintaining relatively high cellular viscosity in cells could result in increased stability of low molecular weight biomolecules (i.e., NADH) at high temperatures, unlike what was previously deduced from studies in diluted water solutions. Cellular viscosity was determined using a fluorescent molecular rotor in various prokaryotes covering the range from 10 to 100°C. Some mesophiles showed the capability of changing cellular viscosity depending on growth temperature. Thermophiles and extreme thermophiles presented a relatively high cellular viscosity, suggesting this strategy as a reasonable mechanism to thrive under these high temperatures. Results substantiate the capability of thermophiles and extreme thermophiles (growth range 50-80°C) to stabilize and use generally considered unstable, universal low molecular weight biomolecules. In addition, this study represents a first report, to our knowledge, on cellular viscosity measurements in prokaryotes and it shows the dependency of prokaryotic cellular viscosity on species and growth temperature. PMID:27558730

  18. A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

    Science.gov (United States)

    Hu, Xiaohua; Chen, Nana; Li, Weichen

    2016-07-01

    Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide. PMID:27365051

  19. Kinetic stabilization against the oxidation reaction induced by a silaalkane cage in a thiophene-bridged molecular gyroscope.

    Science.gov (United States)

    Setaka, Wataru; Ohmizu, Soichiro; Kira, Mitsuo

    2014-02-01

    Macrocage molecules with a bridged rotor have been synthesized as molecular gyroscopes. The kinetics of the oxidation reaction of the thiophene-bridged molecular gyroscope, whose thiophene ring was bridged inside a silaalkane cage, was investigated. A remarkable kinetic stabilization against the oxidation of the thiophene moiety induced by the molecular cage framework was observed.

  20. Efficient electronic coupling and improved stability with dithiocarbamate-based molecular junctions

    Science.gov (United States)

    von Wrochem, Florian; Gao, Deqing; Scholz, Frank; Nothofer, Heinz-Georg; Nelles, Gabriele; Wessels, Jurina M.

    2010-08-01

    Molecular electronic devices require stable and highly conductive contacts between the metal electrodes and molecules. Thiols and amines are widely used to attach molecules to metals, but they form poor electrical contacts and lack the robustness required for device applications. Here, we demonstrate that dithiocarbamates provide superior electrical contact and thermal stability when compared to thiols on metals. Ultraviolet photoelectron spectroscopy and density functional theory show the presence of electronic states at 0.6 eV below the Fermi level of Au, which effectively reduce the charge injection barrier across the metal-molecule interface. Charge transport measurements across oligophenylene monolayers reveal that the conductance of terphenyl-dithiocarbamate junctions is two orders of magnitude higher than that of terphenyl-thiolate junctions. The stability and low contact resistance of dithiocarbamate-based molecular junctions represent a significant step towards the development of robust, organic-based electronic circuits.

  1. Stability of a melittin pore in a lipid bilayer a molecular dynamics study

    OpenAIRE

    Lin, J -H; Baumgärtner, A

    2000-01-01

    We have investigated the configuration and the stability of a single membrane pore bound by four melittin molecules and embedded in a fully hydrated bilayer lipid membrane. We used molecular dynamics simulations up to 5.8 ns. It is found that the initial tetrameric configuration decays with increasing time into a stable trimer and one monomer. This continuous transformation is accompanied by a lateral expansion of the aqueous pore exhibiting a final size comparable to experimental findings. T...

  2. Remote Stabilization of Copper Paddlewheel Based Molecular Building Blocks in Metal-Organic Frameworks

    Energy Technology Data Exchange (ETDEWEB)

    Gao, Wen-Yang; Cai, Rong; Pham, Tony; Forrest, Katherine A.; Hogan, Adam; Nugent, Patrick; Williams, Kia; Wojtas, Lukasz; Luebke, Ryan; Weseli; #324; ski, Lukasz J.; Zaworotko, Michael J.; Space, Brian; Chen, Yu-Sheng; Eddaoudi, Mohamed; Shi, Xiaodong; Ma, Shengqian (KAUST); (UC); (USF); (WVU)

    2015-08-21

    Copper paddlewheel based molecular building blocks (MBBs) are ubiquitous and have been widely employed for the construction of highly porous metal–organic frameworks (MOFs). However, most copper paddlewheel based MOFs fail to retain their structural integrity in the presence of water. This instability is directly correlated to the plausible displacement of coordinating carboxylates in the copper paddlewheel MBB, [Cu₂(O₂C-)₄], by the strongly coordinating water molecules. In this comprehensive study, we illustrate the chemical stability control in the rht-MOF platform via strengthening the coordinating bonds within the triangular inorganic MBB, [Cu₃O(N4–x(CH)xC-)₃] (x = 0, 1, or 2). Remotely, the chemical stabilization propagated into the paddlewheel MBB to afford isoreticular rht-MOFs with remarkably enhanced water/chemical stabilities compared to the prototypal rht-MOF-1.

  3. Fluid-bicontinuous gels stabilized by interfacial colloids: low and high molecular weight fluids

    International Nuclear Information System (INIS)

    Carefully tuned composite materials can have properties wholly unlike those of their separate constituents. We review the development of one example: colloid-stabilized emulsions with bicontinuous liquid domains. These non-equilibrium structures resemble the sponge mesophase of surfactants; however, in the colloid-stabilized case the interface separating the liquid domains is itself semi-solid. The arrangement of domains is created by arresting liquid-liquid phase separation via spinodal decomposition. Dispersed colloids exhibiting partial wettability become trapped on the newly created interface and jam together as the domains coarsen. Similar structures have been created in polymer blends stabilized using either interfacial nanoparticles or clay platelets. Here it has been possible to create the domain arrangement either by phase separation or by direct mixing of the melt. The low molecular weight liquid and polymer based structures have been developed independently and much can be learnt by comparing the two. (topical review)

  4. Remote stabilization of copper paddlewheel based molecular building blocks in metal-organic frameworks

    KAUST Repository

    Gao, Wenyang

    2015-03-24

    Copper paddlewheel based molecular building blocks (MBBs) are ubiquitous and have been widely employed for the construction of highly porous metal-organic frameworks (MOFs). However, most copper paddlewheel based MOFs fail to retain their structural integrity in the presence of water. This instability is directly correlated to the plausible displacement of coordinating carboxylates in the copper paddlewheel MBB, [Cu2(O2C-)4], by the strongly coordinating water molecules. In this comprehensive study, we illustrate the chemical stability control in the rht-MOF platform via strengthening the coordinating bonds within the triangular inorganic MBB, [Cu3O(N4-x(CH)xC-)3] (x = 0, 1, or 2). Remotely, the chemical stabilization propagated into the paddlewheel MBB to afford isoreticular rht-MOFs with remarkably enhanced water/chemical stabilities compared to the prototypal rht-MOF-1. © 2015 American Chemical Society.

  5. Highly Transient Molecular Interactions Underlie the Stability of Kinetochore–Microtubule Attachment During Cell Division

    Science.gov (United States)

    Zaytsev, Anatoly V.; Ataullakhanov, Fazly I.; Grishchuk, Ekaterina L.

    2013-01-01

    Chromosome segregation during mitosis is mediated by spindle microtubules that attach to chromosomal kinetochores with strong yet labile links. The exact molecular composition of the kinetochore–microtubule interface is not known but microtubules are thought to bind to kinetochores via the specialized microtubule-binding sites, which contain multiple microtubule-binding proteins. During prometaphase the lifetime of microtubule attachments is short but in metaphase it increases 3-fold, presumably owing to dephosphorylation of the microtubule-binding proteins that increases their affinity. Here, we use mathematical modeling to examine in quantitative and systematic manner the general relationships between the molecular properties of microtubule-binding proteins and the resulting stability of microtubule attachment to the protein-containing kinetochore site. We show that when the protein connections are stochastic, the physiological rate of microtubule turnover is achieved only if these molecular interactions are very transient, each lasting fraction of a second. This “microscopic” time is almost four orders of magnitude shorter than the characteristic time of kinetochore–microtubule attachment. Cooperativity of the microtubule-binding events further increases the disparity of these time scales. Furthermore, for all values of kinetic parameters the microtubule stability is very sensitive to the minor changes in the molecular constants. Such sensitivity of the lifetime of microtubule attachment to the kinetics and cooperativity of molecular interactions at the microtubule-binding site may hinder the accurate regulation of kinetochore–microtubule stability during mitotic progression, and it necessitates detailed experimental examination of the microtubule-binding properties of kinetochore-localized proteins. PMID:24376473

  6. Highly Transient Molecular Interactions Underlie the Stability of Kinetochore-Microtubule Attachment During Cell Division.

    Science.gov (United States)

    Zaytsev, Anatoly V; Ataullakhanov, Fazly I; Grishchuk, Ekaterina L

    2013-12-13

    Chromosome segregation during mitosis is mediated by spindle microtubules that attach to chromosomal kinetochores with strong yet labile links. The exact molecular composition of the kinetochore-microtubule interface is not known but microtubules are thought to bind to kinetochores via the specialized microtubule-binding sites, which contain multiple microtubule-binding proteins. During prometaphase the lifetime of microtubule attachments is short but in metaphase it increases 3-fold, presumably owing to dephosphorylation of the microtubule-binding proteins that increases their affinity. Here, we use mathematical modeling to examine in quantitative and systematic manner the general relationships between the molecular properties of microtubule-binding proteins and the resulting stability of microtubule attachment to the protein-containing kinetochore site. We show that when the protein connections are stochastic, the physiological rate of microtubule turnover is achieved only if these molecular interactions are very transient, each lasting fraction of a second. This "microscopic" time is almost four orders of magnitude shorter than the characteristic time of kinetochore-microtubule attachment. Cooperativity of the microtubule-binding events further increases the disparity of these time scales. Furthermore, for all values of kinetic parameters the microtubule stability is very sensitive to the minor changes in the molecular constants. Such sensitivity of the lifetime of microtubule attachment to the kinetics and cooperativity of molecular interactions at the microtubule-binding site may hinder the accurate regulation of kinetochore-microtubule stability during mitotic progression, and it necessitates detailed experimental examination of the microtubule-binding properties of kinetochore-localized proteins. PMID:24376473

  7. Molecular Dynamics Driven Design of pH-Stabilized Mutants of MNEI, a Sweet Protein.

    Directory of Open Access Journals (Sweden)

    Serena Leone

    Full Text Available MNEI is a single chain derivative of monellin, a plant protein that can interact with the human sweet taste receptor, being therefore perceived as sweet. This unusual physiological activity makes MNEI a potential template for the design of new sugar replacers for the food and beverage industry. Unfortunately, applications of MNEI have been so far limited by its intrinsic sensitivity to some pH and temperature conditions, which could occur in industrial processes. Changes in physical parameters can, in fact, lead to irreversible protein denaturation, as well as aggregation and precipitation. It has been previously shown that the correlation between pH and stability in MNEI derives from the presence of a single glutamic residue in a hydrophobic pocket of the protein. We have used molecular dynamics to study the consequences, at the atomic level, of the protonation state of such residue and have identified the network of intramolecular interactions responsible for MNEI stability at acidic pH. Based on this information, we have designed a pH-independent, stabilized mutant of MNEI and confirmed its increased stability by both molecular modeling and experimental techniques.

  8. Passivation of Molecular n-Doping: Exploring the Limits of Air Stability

    KAUST Repository

    Tietze, Max Lutz

    2016-03-03

    © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. Molecular doping is a key technique for flexible and low-cost organic complementary semiconductor technologies that requires both efficient and stable p- and n-type doping. However, in contrast to molecular p-dopants, highly efficient n-type dopants are commonly sensitive to rapid degradation in air due to their low ionization energies (IEs) required for electron donation, e.g., IE = 2.4 eV for tetrakis(1,3,4,6,7,8-hexahydro-2H-pyrimido[1,2-a]pyrimidinato)ditungsten(II) (W2(hpp)4). Here, the air stability of various host:W2(hpp)4 combinations is compared by conductivity measurements and photoemission spectroscopy. A partial passivation of the n-doping against degradation is found, with this effect identified to depend on the specific energy levels of the host material. Since host-W2(hpp)4 electronic wavefunction hybridization is unlikely due to confinement of the dopant highest occupied molecular orbital (HOMO) to its molecular center, this finding is explained via stabilization of the dopant by single-electron transfer to a host material whose energy levels are sufficiently low for avoiding further charge transfer to oxygen-water complexes. Our results show the feasibility of temporarily handling n-doped organic thin films in air, e.g., during structuring of organic field effect transistors (OFETs) by lithography.

  9. Learning Probabilistic Models of Hydrogen Bond Stability from Molecular Dynamics Simulation Trajectories

    KAUST Repository

    Chikalov, Igor

    2011-04-02

    Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. H-bonds involving atoms from residues that are close to each other in the main-chain sequence stabilize secondary structure elements. H-bonds between atoms from distant residues stabilize a protein’s tertiary structure. However, H-bonds greatly vary in stability. They form and break while a protein deforms. For instance, the transition of a protein from a nonfunctional to a functional state may require some H-bonds to break and others to form. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor. Other local interactions may reinforce (or weaken) an H-bond. This paper describes inductive learning methods to train a protein-independent probabilistic model of H-bond stability from molecular dynamics (MD) simulation trajectories. The training data describes H-bond occurrences at successive times along these trajectories by the values of attributes called predictors. A trained model is constructed in the form of a regression tree in which each non-leaf node is a Boolean test (split) on a predictor. Each occurrence of an H-bond maps to a path in this tree from the root to a leaf node. Its predicted stability is associated with the leaf node. Experimental results demonstrate that such models can predict H-bond stability quite well. In particular, their performance is roughly 20% better than that of models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a given conformation. The paper discusses several extensions that may yield further improvements.

  10. A molecular thermodynamic model for the stability of hepatitis B capsids

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Jehoon; Wu, Jianzhong, E-mail: jwu@engr.ucr.edu [Department of Chemical and Environmental Engineering, University of California, Riverside, California 92521 (United States)

    2014-06-21

    Self-assembly of capsid proteins and genome encapsidation are two critical steps in the life cycle of most plant and animal viruses. A theoretical description of such processes from a physiochemical perspective may help better understand viral replication and morphogenesis thus provide fresh insights into the experimental studies of antiviral strategies. In this work, we propose a molecular thermodynamic model for predicting the stability of Hepatitis B virus (HBV) capsids either with or without loading nucleic materials. With the key components represented by coarse-grained thermodynamic models, the theoretical predictions are in excellent agreement with experimental data for the formation free energies of empty T4 capsids over a broad range of temperature and ion concentrations. The theoretical model predicts T3/T4 dimorphism also in good agreement with the capsid formation at in vivo and in vitro conditions. In addition, we have studied the stability of the viral particles in response to physiological cellular conditions with the explicit consideration of the hydrophobic association of capsid subunits, electrostatic interactions, molecular excluded volume effects, entropy of mixing, and conformational changes of the biomolecular species. The course-grained model captures the essential features of the HBV nucleocapsid stability revealed by recent experiments.

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

    Science.gov (United States)

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

    2011-01-01

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

  12. A molecular thermodynamic model for the stability of hepatitis B capsids

    Science.gov (United States)

    Kim, Jehoon; Wu, Jianzhong

    2014-06-01

    Self-assembly of capsid proteins and genome encapsidation are two critical steps in the life cycle of most plant and animal viruses. A theoretical description of such processes from a physiochemical perspective may help better understand viral replication and morphogenesis thus provide fresh insights into the experimental studies of antiviral strategies. In this work, we propose a molecular thermodynamic model for predicting the stability of Hepatitis B virus (HBV) capsids either with or without loading nucleic materials. With the key components represented by coarse-grained thermodynamic models, the theoretical predictions are in excellent agreement with experimental data for the formation free energies of empty T4 capsids over a broad range of temperature and ion concentrations. The theoretical model predicts T3/T4 dimorphism also in good agreement with the capsid formation at in vivo and in vitro conditions. In addition, we have studied the stability of the viral particles in response to physiological cellular conditions with the explicit consideration of the hydrophobic association of capsid subunits, electrostatic interactions, molecular excluded volume effects, entropy of mixing, and conformational changes of the biomolecular species. The course-grained model captures the essential features of the HBV nucleocapsid stability revealed by recent experiments.

  13. Thermal stability and molecular ordering of organic semiconductor monolayers: effect of an anchor group.

    Science.gov (United States)

    Jones, Andrew O F; Knauer, Philipp; Resel, Roland; Ringk, Andreas; Strohriegl, Peter; Werzer, Oliver; Sferrazza, Michele

    2015-06-01

    The thermal stability and molecular order in monolayers of two organic semiconductors, PBI-PA and PBI-alkyl, based on perylene derivatives with an identical molecular structure except for an anchor group for attachment to the substrate in PBI-PA, are reported. In situ X-ray reflectivity measurements are used to follow the stability of these monolayers in terms of order and thickness as temperature is increased. Films have thicknesses corresponding approximately to the length of one molecule; molecules stand upright on the substrate with a defined structure. PBI-PA monolayers have a high degree of order at room temperature and a stable film exists up to 250 °C, but decomposes rapidly above 300 °C. In contrast, stable physisorbed PBI-alkyl monolayers only exist up to 100 °C. Above the bulk melting point at 200 °C no more order exists. The results encourage using anchor groups in monolayers for various applications as it allows enhanced stability at the interface with the substrate.

  14. Molecular basis of differential B-pentamer stability of Shiga toxins 1 and 2.

    Directory of Open Access Journals (Sweden)

    Deborah G Conrady

    Full Text Available Escherichia coli strain O157:H7 is a major cause of food poisoning that can result in severe diarrhea and, in some cases, renal failure. The pathogenesis of E. coli O157:H7 is in large part due to the production of Shiga toxin (Stx, an AB(5 toxin that consists of a ribosomal RNA-cleaving A-subunit surrounded by a pentamer of receptor-binding B subunits. There are two major isoforms, Stx1 and Stx2, which differ dramatically in potency despite having 57% sequence identity. Animal studies and epidemiological studies show Stx2 is associated with more severe disease. Although the molecular basis of this difference is unknown, data suggest it is associated with the B-subunit. Mass spectrometry studies have suggested differential B-pentamer stability between Stx1 and Stx2. We have examined the relative stability of the B-pentamers in solution. Analytical ultracentrifugation using purified B-subunits demonstrates that Stx2B, the more deadly isoform, shows decreased pentamer stability compared to Stx1B (EC(50 = 2.3 µM vs. EC(50 = 0.043 µM for Stx1B. X-ray crystal structures of Stx1B and Stx2B identified a glutamine in Stx2 (versus leucine in Stx1 within the otherwise strongly hydrophobic interface between B-subunits. Interchanging these residues switches the stability phenotype of the B-pentamers of Stx1 and Stx2, as demonstrated by analytical ultracentrifugation and circular dichroism. These studies demonstrate a profound difference in stability of the B-pentamers in Stx1 and Stx2, illustrate the mechanistic basis for this differential stability, and provide novel reagents to test the basis for differential pathogenicity of these toxins.

  15. Molecular Basis of Differential B-Pentamer Stability of Shiga Toxins 1 and 2

    Energy Technology Data Exchange (ETDEWEB)

    Conrady, Deborah G.; Flagler, Michael J.; Friedmann, David R.; Vander Wielen, Bradley D.; Kovall, Rhett A.; Weiss, Alison A.; Herr, Andrew B. (UCIN-MED)

    2012-06-27

    Escherichia coli strain O157:H7 is a major cause of food poisoning that can result in severe diarrhea and, in some cases, renal failure. The pathogenesis of E. coli O157:H7 is in large part due to the production of Shiga toxin (Stx), an AB{sub 5} toxin that consists of a ribosomal RNA-cleaving A-subunit surrounded by a pentamer of receptor-binding B subunits. There are two major isoforms, Stx1 and Stx2, which differ dramatically in potency despite having 57% sequence identity. Animal studies and epidemiological studies show Stx2 is associated with more severe disease. Although the molecular basis of this difference is unknown, data suggest it is associated with the B-subunit. Mass spectrometry studies have suggested differential B-pentamer stability between Stx1 and Stx2. We have examined the relative stability of the B-pentamers in solution. Analytical ultracentrifugation using purified B-subunits demonstrates that Stx2B, the more deadly isoform, shows decreased pentamer stability compared to Stx1B (EC{sub 50} = 2.3 {micro}M vs. EC{sub 50} = 0.043 {micro}M for Stx1B). X-ray crystal structures of Stx1B and Stx2B identified a glutamine in Stx2 (versus leucine in Stx1) within the otherwise strongly hydrophobic interface between B-subunits. Interchanging these residues switches the stability phenotype of the B-pentamers of Stx1 and Stx2, as demonstrated by analytical ultracentrifugation and circular dichroism. These studies demonstrate a profound difference in stability of the B-pentamers in Stx1 and Stx2, illustrate the mechanistic basis for this differential stability, and provide novel reagents to test the basis for differential pathogenicity of these toxins.

  16. Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization.

    Science.gov (United States)

    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

  17. Insight into the stability of cross-beta amyloid fibril from molecular dynamics simulation.

    Science.gov (United States)

    Chen, Yue; He, Yong-Jie; Wu, Maoying; Yan, Guanwen; Li, Yixue; Zhang, Jian; Chen, Hai-Feng

    2010-06-01

    Amyloid fibrils are considered to play causal roles in the pathogenesis of amyloid-related degenerative diseases such as Alzheimer's disease, type II diabetes mellitus, the transmissible spongiform encephalopathies, and prion disease. The mechanism of fibril formation is still hotly debated and remains an important open question. In this study, we utilized molecular dynamics (MD) simulation to analyze the stability of hexamer for eight class peptides. The MD results suggest that VEALYL and MVGGVV-1 are the most stable ones, then SNQNNY, followed by LYQLEN, MVGGVV-2, VQIVYK, SSTSAA, and GGVVIA. The statistics result indicates that hydrophobic residues play a key role in stabilizing the zipper interface. Single point and two linkage mutants of MVGGVV-1 confirmed that both Met1 and Val2 are key hydrophobic residues. This is consistent with the statistics analysis. The stability results of oligomer for MVGGVV-1 suggest that the intermediate state should be trimer (3-0) and tetramer (2-2). These methods can be used in stabilization study of other amyloid fibril.

  18. Molecular markers for genetic stability of intergeneric hybrids Fragaria x Potentilla derived from tissue culture

    Directory of Open Access Journals (Sweden)

    Anca Nicoleta SUTAN

    2009-11-01

    Full Text Available The effect of growth regulators, explant source and culture age on genetic stability of plants obtained from tissue culture propagation of ornamental strawberry “Serenata” were examined. Genomic DNAs of in vitro-derived shoots and control plant were extracted and compared by RAPD-PCR analyses. Ten primers (from 48 previously tested were selected and used in RAPD analysis to prove the clonal fidelity (i.e. genetic stability of the tissue culture-derived ornamental strawberry plants. The lack of polymorphisms in micropropagated plants screened through molecular markers was used to suggest genetic fidelity. Identicaly banding patterns of the RAPD profiles obtaining from vitroplants, regenerated via organogenesis or meristems culture, suggested that in the ornamental strawberry, variety “Serenata”, neither explant source, nor callus age or limited number of subcultures, in basal media supplemented with low concentration of growth regulators, were associated with occurence of somaclonal variation.

  19. Molecular Simulation of Solubility and Diffusion of Hindered-Amine Light Stabilizers (HALS) in Polyethylene

    Science.gov (United States)

    Nath, Shyamal K.; de Pablo, Juan J.; Debellis, Anthony

    1997-03-01

    Hindered-amine light stabilizers (HALS) are some of the most common additives employed for prevention of photooxidation in polymers. One of the major problems encountered in polymer stabilization is that of physical loss of the additives. Such loss limits the life of the polymer and, more importantly, it can have serious consequences when the polymer is to be used for food packaging and other toxicity-sensitive applications. The loss of additives is related to their solubility and diffusion coefficient in polymers. In this work, a novel Monte Carlo formalism is proposed to determine the solubility of commercially available HALS (Tinuvin 770) in polyethylene. Diffusion coefficients is also determined by conventional molecular dynamics simulations. We report results for the solubility and diffusion of HALS in polyethylene as a function of temperature, pressure and density. We also examine the effects of branching on these quantities, and we use our findings to propose HALS structures with attractive compatibility and diffusive characteristics.

  20. Molecularly Rigid Microporous Polyamine Captures and Stabilizes Conducting Platinum Nanoparticle Networks.

    Science.gov (United States)

    He, Daping; He, Dong Sheng; Yang, Jinlong; Low, Ze-Xian; Malpass-Evans, Richard; Carta, Mariolino; McKeown, Neil B; Marken, Frank

    2016-08-31

    A molecularly rigid polyamine based on a polymer of intrinsic microporosity (PIM-EA-TB) is shown to capture and stabilize platinum nanoparticles during colloid synthesis in the rigid framework. Stabilization here refers to avoiding aggregation without loss of surface reactivity. In the resulting rigid framework with embedded platinum nanoparticles, the volume ratio of platinum to PIM-EA-TB in starting materials is varied systematically from approximately 1.0 to 0.1 with the resulting platinum nanoparticle diameter varying from approximately 4.2 to 3.1 nm, respectively. Elemental analysis suggests that only a fraction of the polymer is "captured" to give nanocomposites rich in platinum. A transition occurs from electrically conducting and electrochemically active (with shorter average interparticle distance) to nonconducting and only partially electrochemically active (with longer average interparticle distance) polymer-platinum composites. The conducting nanoparticle network in the porous rigid macromolecular framework could be beneficial in electrocatalysis and in sensing applications. PMID:27509837

  1. Electrodynamics—molecular dynamics simulations of the stability of Cu nanotips under high electric field

    Science.gov (United States)

    Veske, Mihkel; Parviainen, Stefan; Zadin, Vahur; Aabloo, Alvo; Djurabekova, Flyura

    2016-06-01

    The shape memory effect and pseudoelasticity in Cu nanowires represent a possible pair of mechanisms that prevents high aspect ratio nanosized field electron emitters from being stable at room temperature and permits their growth under high electric field. By utilizing hybrid electrodynamics–molecular dynamics simulations, we show that a global electric field of 1 GV m‑1 or more significantly increases the stability and critical temperature of spontaneous reorientation of nanosized    Cu field emitters. We also show that in the studied tips the stabilizing effect of an external applied electric field is an order of magnitude greater than the destabilization caused by the field emission current. We detect the critical temperature of spontaneous reorientation using a tool that spots changes in crystal structure. The method is compatible with techniques that consider the change in potential energy, has a wider range of applicability and allows different stages in the reorientation processes to be pinpointed.

  2. An in silico study of the molecular basis of B-RAF activation and conformational stability

    DEFF Research Database (Denmark)

    Fratev, Filip Filipov; Jonsdottir, Svava Osk

    2009-01-01

    B-RAF kinase plays an important role both in tumour induction and maintenance in several cancers and it is an attractive new drug target. However, the structural basis of the B-RAF activation is still not well understood. RESULTS: In this study we suggest a novel molecular basis of B-RAF activation...... the A-loop and the alphaC-helix in the activating mutants, which presumably contribute to the flipping of the activation segment to an active form. Conversely, in the B-RAFD594V mutant that has impaired kinase activity, and in B-RAFWT these interactions were strong and stabilized the kinase inactive...

  3. Molecular dynamics studies on the structural stability of wild-type dog prion protein.

    Science.gov (United States)

    Zhang, Jiapu; Liu, David D W

    2011-06-01

    Prion diseases such as Creutzfeldt-Jakob disease, variant Creutzfeldt-Jakob diseases, Gerstmann-Sträussler-Scheinker syndrome, Fatal Familial Insomnia, Kuru in humans, scrapie in sheep, bovine spongiform encephalopathy (or 'mad-cow' disease) and chronic wasting disease in cattle are invariably fatal and highly infectious neurodegenerative diseases affecting humans and animals. However, by now there have not been some effective therapeutic approaches to treat all these prion diseases. In 2008, canine mammals including dogs (canis familials) were the first time academically reported to be resistant to prion diseases (Vaccine 26: 2601-2614 (2008)). Thus, it is very worth studying the molecular structures of dog prion protein to obtain insights into the immunity of dogs to prion diseases. This paper studies the molecular structural dynamics of wild-type dog prion protein. The comparison analyses with rabbit prion protein show that the dog prion protein has stable molecular structures whether under neutral or low pH environments. We also find that the salt bridges such as D177-R163 contribute to the structural stability of wild-type rabbit prion protein under neutral pH environment. PMID:21469747

  4. Bis(triisopropylsilylethynyl)pentacene/Au(111) interface: Coupling, molecular orientation, and thermal stability

    KAUST Repository

    Gnoli, Andrea

    2014-10-02

    The assembly and the orientation of functionalized pentacene at the interface with inorganics strongly influence both the electric contact and the charge transport in organic electronic devices. In this study electronic spectroscopies and theoretical modeling are combined to investigate the properties of the bis(triisopropylsilylethynyl)pentacene (TIPS-Pc)/Au(111) interface as a function of the molecular coverage to compare the molecular state in the gas phase and in the adsorbed phase and to determine the thermal stability of TIPS-Pc in contact with gold. Our results show that in the free molecule only the acene atoms directly bonded to the ligands are affected by the functionalization. Adsorption on Au(111) leads to a weak coupling which causes only modest binding energy shifts in the TIPS-Pc and substrate core level spectra. In the first monolayer the acene plane form an angle of 33 ± 2° with the Au(111) surface at variance with the vertical geometry reported for thicker solution-processed or evaporated films, whereas the presence of configurational disorder was observed in the multilayer. The thermal annealing of the TIPS-Pc/Au(111) interface reveals the ligand desorption at ∼470 K, which leaves the backbone of the decomposed molecule flat-lying on the metal surface as in the case of the unmodified pentacene. The weak interaction with the metal substrate causes the molecular dissociation to occur 60 K below the thermal decomposition taking place in thick drop-cast films.

  5. Learning probabilistic models of hydrogen bond stability from molecular dynamics simulation trajectories

    KAUST Repository

    Chikalov, Igor

    2011-02-15

    Background: Hydrogen bonds (H-bonds) play a key role in both the formation and stabilization of protein structures. They form and break while a protein deforms, for instance during the transition from a non-functional to a functional state. The intrinsic strength of an individual H-bond has been studied from an energetic viewpoint, but energy alone may not be a very good predictor.Methods: This paper describes inductive learning methods to train protein-independent probabilistic models of H-bond stability from molecular dynamics (MD) simulation trajectories of various proteins. The training data contains 32 input attributes (predictors) that describe an H-bond and its local environment in a conformation c and the output attribute is the probability that the H-bond will be present in an arbitrary conformation of this protein achievable from c within a time duration ?. We model dependence of the output variable on the predictors by a regression tree.Results: Several models are built using 6 MD simulation trajectories containing over 4000 distinct H-bonds (millions of occurrences). Experimental results demonstrate that such models can predict H-bond stability quite well. They perform roughly 20% better than models based on H-bond energy alone. In addition, they can accurately identify a large fraction of the least stable H-bonds in a conformation. In most tests, about 80% of the 10% H-bonds predicted as the least stable are actually among the 10% truly least stable. The important attributes identified during the tree construction are consistent with previous findings.Conclusions: We use inductive learning methods to build protein-independent probabilistic models to study H-bond stability, and demonstrate that the models perform better than H-bond energy alone. 2011 Chikalov et al; licensee BioMed Central Ltd.

  6. Stability of helium bubbles in alpha-iron: A molecular dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Lucas, G. [Ecole Polytechnique Federale de Lausanne (EPFL), Centre de Recherche en Physique des Plasmas, Association Euratom-Confederation Suisse, CH 5332 Villigen PSI (Switzerland)], E-mail: guillaume.lucas@psi.ch; Schaeublin, R. [Ecole Polytechnique Federale de Lausanne (EPFL), Centre de Recherche en Physique des Plasmas, Association Euratom-Confederation Suisse, CH 5332 Villigen PSI (Switzerland)

    2009-04-30

    Molecular dynamics simulations were performed to estimate the dissociation energies of helium interstitials, vacancies and self-interstitial atoms from small helium-vacancy clusters. Several sets of empirical potentials have been tested and compared with available ab initio calculations in order to provide the best combination of potentials to study the stability of small helium bubbles. The behavior of the cluster seems to be better described using Ackland potential for the Fe-Fe interactions and Juslin potential for the Fe-He interactions. From the calculations, it appears that the dissociation energies mainly depend on the helium-to-vacancy ratio rather than the cluster size. The helium/vacancy crossover slightly varies with increasing number of vacancies, but the crossover defining the loop-punching regime decreases strongly with increasing cluster sizes.

  7. Stability of helium bubbles in alpha-iron: A molecular dynamics study

    Science.gov (United States)

    Lucas, G.; Schäublin, R.

    2009-04-01

    Molecular dynamics simulations were performed to estimate the dissociation energies of helium interstitials, vacancies and self-interstitial atoms from small helium-vacancy clusters. Several sets of empirical potentials have been tested and compared with available ab initio calculations in order to provide the best combination of potentials to study the stability of small helium bubbles. The behavior of the cluster seems to be better described using Ackland potential for the Fe-Fe interactions and Juslin potential for the Fe-He interactions. From the calculations, it appears that the dissociation energies mainly depend on the helium-to-vacancy ratio rather than the cluster size. The helium/vacancy crossover slightly varies with increasing number of vacancies, but the crossover defining the loop-punching regime decreases strongly with increasing cluster sizes.

  8. Polymer Nanofibers with Outstanding Thermal Conductivity and Thermal Stability: Fundamental Linkage between Molecular Characteristics and Macroscopic Thermal Properties

    CERN Document Server

    Zhang, Teng; Luo, Tengfei

    2014-01-01

    Polymer nanofibers with high thermal conductivities and outstanding thermal stabilities are highly desirable in heat transfer-critical applications such as thermal management, heat exchangers and energy storage. In this work, we unlock the fundamental relations between the thermal conductivity and thermal stability of polymer nanofibers and their molecular characteristics by studying the temperature-induced phase transitions and thermal transport of a series of polymer nanofibers. Ten different polymer nanofibers with systematically chosen molecular structures are studied using large scale molecular dynamics simulations. We found that high thermal conductivity and good thermal stability can be achieved in polymers with rigid backbones, exemplified by {\\pi}-conjugated polymers, due to suppressed segmental rotations and large phonon group velocities. The low probability of segmental rotation does not only prevent temperature-induced phase transition but also enables long phonon mean free paths due to reduced di...

  9. Molecular Mechanism of AHSP-Mediated Stabilization of Alpha-Hemoglobin

    Energy Technology Data Exchange (ETDEWEB)

    Feng,L.; Gell, D.; Zhou, S.; Gu, L.; Kong, Y.; Li, J.; Hu, M.; Yan, N.; Lee, C.; et al.

    2005-01-01

    Hemoglobin A (HbA), the oxygen delivery system in humans, comprises two alpha and two beta subunits. Free alpha-hemoglobin (alphaHb) is unstable, and its precipitation contributes to the pathophysiology of beta thalassemia. In erythrocytes, the alpha-hemoglobin stabilizing protein (AHSP) binds alphaHb and inhibits its precipitation. The crystal structure of AHSP bound to Fe(II)-alphaHb reveals that AHSP specifically recognizes the G and H helices of alphaHb through a hydrophobic interface that largely recapitulates the alpha1-beta1 interface of hemoglobin. The AHSP-alphaHb interactions are extensive but suboptimal, explaining why beta-hemoglobin can competitively displace AHSP to form HbA. Remarkably, the Fe(II)-heme group in AHSP bound alphaHb is coordinated by the distal but not the proximal histidine. Importantly, binding to AHSP facilitates the conversion of oxy-alphaHb to a deoxygenated, oxidized [Fe(III)], nonreactive form in which all six coordinate positions are occupied. These observations reveal the molecular mechanisms by which AHSP stabilizes free alphaHb.

  10. Molecular Dynamics Study of Stability and Diffusion of Graphene-Based Drug Delivery Systems

    Directory of Open Access Journals (Sweden)

    Xiunan Wang

    2015-01-01

    Full Text Available Graphene, a two-dimensional nanomaterial with unique biomedical properties, has attracted great attention due to its potential applications in graphene-based drug delivery systems (DDS. In this work graphene sheets with various sizes and graphene oxide functionalized with polyethylene glycol (GO-PEG are utilized as nanocarriers to load anticancer drug molecules including CE6, DOX, MTX, and SN38. We carried out molecular dynamics calculations to explore the energetic stabilities and diffusion behaviors of the complex systems with focuses on the effects of the sizes and functionalization of graphene sheets as well as the number and types of drug molecules. Our study shows that the binding of graphene-drug complex is favorable when the drug molecules and finite graphene sheets become comparable in sizes. The boundaries of finite sized graphene sheets restrict the movement of drug molecules. The double-side loading often slows down the diffusion of drug molecules compared with the single-side loading. The drug molecules bind more strongly with GO-PEG than with pristine graphene sheets, demonstrating the advantages of functionalization in improving the stability and biocompatibility of graphene-based DDS.

  11. Molecular dynamics study of the stability of a carbon nanotube atop a catalytic nanoparticle

    CERN Document Server

    Verkhovtsev, Alexey V; Solov'yov, Andrey V

    2014-01-01

    The stability of a single-walled carbon nanotube placed on top of a catalytic nickel nanoparticle is investigated by means of molecular dynamics simulations. As a case study, we consider the $(12,0)$ nanotube consisting of 720 carbon atoms and the icosahedral Ni$_{309}$ cluster. An explicit set of constant-temperature simulations is performed in order to cover a broad temperature range from 400 to 1200 K, at which a successful growth of carbon nanotubes has been achieved experimentally by means of chemical vapor deposition. The stability of the system depending on parameters of the involved interatomic interactions is analyzed. It is demonstrated that different scenarios of the nanotube dynamics atop the nanoparticle are possible depending on the parameters of the Ni-C potential. When the interaction is weak the nanotube is stable and resembles its highly symmetric structure, while an increase of the interaction energy leads to the abrupt collapse of the nanotube in the initial stage of simulation. In order t...

  12. Thermal stability of hepatitis E virus assessed by a molecular biological approach

    Directory of Open Access Journals (Sweden)

    Appel Bernd

    2011-10-01

    Full Text Available Abstract Background Hepatitis E virus (HEV is a pathogen of emerging concern in industrialized countries. The consumption of wild boar meat has been identified as one risk factor for autochthonous HEV infections. Only limited information is available about thermal stability of HEV, mainly due to the lack of rapid and efficient cell culture systems for measurement of HEV infectivity. Methods A molecular biological method was implemented in order to distinguish disassembled from intact viral particles using RNase treatment followed by quantitative real-time RT-PCR. The method was applied to a wild boar liver suspension containing HEV genotype 3. Results Time-course analyses indicated that the decline of protected RNA could be described by a biphasic model with an initial decrease followed by a stationary phase. The stationary phase was reached after 1 hour at 4°C, 3 days at 22°C and 7 days at 37°C with log reductions of 0.34, 0.45 and 1.24, respectively. Protected RNA was detectable until the end of the experiments at day 50 or 70. Heat exposure for 1 minute resulted in a log reduction of 0.48 at 70°C and increased with higher temperatures to 3.67 at 95°C. Although HEV infectivity titration by inoculation of the liver suspension onto three cell lines did not succeed, the results of the RNase-based method are in accordance with published cell culture-based data. Conclusions Measurement of intact viral particles using the RNase-based method may provide data on the stability of RNA viruses when cell culture-based infectivity titrations are not efficient or not available. The method enables processing of large sample numbers and may be suitable to estimate stability of HEV in different types of food.

  13. Thermal stability of interface voids in Cu grain boundaries with molecular dynamic simulations

    Science.gov (United States)

    Xydou, A.; Parviainen, S.; Aicheler, M.; Djurabekova, F.

    2016-09-01

    By means of molecular dynamic simulations, the stability of cylindrical voids is examined with respect to the diffusion bonding procedure. To do this, the effect of grain boundaries between the grains of different crystallographic orientations on the void closing time was studied at high temperatures from 0.7 up to 0.94 of the bulk melting temperature ({{T}\\text{m}} ). The diameter of the voids varied from 3.5 to 6.5 nm. A thermal instability occurring at high temperatures at the surface of the void placed in a grain boundary triggered the eventual closure of the void at all examined temperatures. The closing time has an exponential dependence on the examined temperature values. A model based on the defect diffusion theory is developed to predict the closing time for voids of macroscopic size. The diffusion coefficient within the grain boundaries is found to be overall higher than the diffusion coefficient in the region around the void surface. The activation energy for the diffusion in the grain boundary is calculated based on molecular dynamic simulations. This value agrees well with the experimental given in the Ashby maps for the creep in copper via Coble GB diffusion.

  14. MOLECULAR-DYNAMICS SIMULATION OF THE STABILITY OF A 22-RESIDUE ALPHA-HELIX IN WATER AND 30-PERCENT TRIFLUOROETHANOL

    NARCIS (Netherlands)

    VANBUUREN, AR; BERENDSEN, HJC

    1993-01-01

    A molecular dynamics (MD) simulation was performed on the alpha-helix H8-HC5, the C-terminal part of myoglobin (residue 132-153), under periodic boundary conditions in two different solutions, water and water with 30% (v/v) 2,2,2-trifluoroethanol (TFE), at 300 K to investigate the stability of the h

  15. Stability of Culex quinquefasciatus resistance to Bacillus sphaericus evaluated by molecular tools.

    Science.gov (United States)

    Amorim, Liliane Barbosa; de Barros, Rosineide Arruda; Chalegre, Karlos Diogo de Melo; de Oliveira, Cláudia Maria Fontes; Regis, Lêda Narcisa; Silva-Filha, Maria Helena Neves Lobo

    2010-04-01

    Bacillus sphaericus binary toxin action on Culex quinquefasciatus larvae relies on the binding to Cqm1alpha-glucosidases, which act as midgut receptors. Resistance of two laboratory-selected colonies is associated with the allele cqm1(REC) that prevents Cqm1 expression as membrane-bound molecules. This study evaluated stability of resistance after the interruption of selection pressure and introduction of susceptible individuals in these colonies. Bioassays showed that frequency of resistant larvae did not decrease throughout 11 generations, under these conditions, and it was associated to a similar frequency of larvae lacking the Cqm1alpha-glucosidase receptor, detected by in gel enzymatic assays. Direct screening of the cqm1(REC) allele, by specific PCR, showed that its frequency remained stable throughout 11 generations. Parental resistant colony did not display biological costs regarding fecundity, fertility and pupal weight and data from susceptibility assays, enzymatic assays and PCR screening showed that cqm1(REC) was not disfavored in competition with the susceptible allele and persisted in the progenies, in the lack of selection pressure. Characterization of molecular basis of resistance is essential for developing diagnostic tools and data have relevant implication for the establishment of strategies for resistance management. PMID:20211258

  16. Stabilization

    Directory of Open Access Journals (Sweden)

    Muhammad H. Al-Malack

    2016-07-01

    Full Text Available Fuel oil flyash (FFA produced in power and water desalination plants firing crude oils in the Kingdom of Saudi Arabia is being disposed in landfills, which increases the burden on the environment, therefore, FFA utilization must be encouraged. In the current research, the effect of adding FFA on the engineering properties of two indigenous soils, namely sand and marl, was investigated. FFA was added at concentrations of 5%, 10% and 15% to both soils with and without the addition of Portland cement. Mixtures of the stabilized soils were thoroughly evaluated using compaction, California Bearing Ratio (CBR, unconfined compressive strength (USC and durability tests. Results of these tests indicated that stabilized sand mixtures could not attain the ACI strength requirements. However, marl was found to satisfy the ACI strength requirement when only 5% of FFA was added together with 5% of cement. When the FFA was increased to 10% and 15%, the mixture’s strength was found to decrease to values below the ACI requirements. Results of the Toxicity Characteristics Leaching Procedure (TCLP, which was performed on samples that passed the ACI requirements, indicated that FFA must be cautiously used in soil stabilization.

  17. Cavity-induced phase stability to decelerate a fast molecular beam via feedback-controlled time-varying optical pumps

    CERN Document Server

    Lan, Zhihao

    2014-01-01

    We have identified a novel phase stability mechanism from the intracavity field-induced self-organization of a fast-moving molecular beam into travelling molecular packets in the bad cavity regime, which is then used to decelerate the molecular packets by feedback-controlled time-varying laser pumps to the cavity. We first applied the linear stability analysis to derive an expression for this self-organization in the adiabatic limit and show that the self-organization of the beam leads to the formation of travelling molecular packets, which in turn function as a dynamic Bragg grating, thus modulating periodically the intracavity field by superradiant scattering of the pump photons. The modulation encodes the position information of the molecular packets into the output of the intracavity field instantaneously. We then applied time-varying laser pumps that are automatically switched by the output of the intracavity field to slow down the molecular packets via a feedback mechanism and found that most of the mol...

  18. Amino acids as co-amorphous stabilizers for poorly water-soluble drugs--Part 2: molecular interactions.

    Science.gov (United States)

    Löbmann, Korbinian; Laitinen, Riikka; Strachan, Clare; Rades, Thomas; Grohganz, Holger

    2013-11-01

    The formation of co-amorphous drug-drug mixtures has proved to be a powerful approach to stabilize the amorphous form and at the same time increase the dissolution of poorly water-soluble drugs. Molecular interactions in these co-amorphous formulations can play a crucial role in stabilization and dissolution enhancement. In this regard, Fourier-transform infrared spectroscopy (FTIR) is a valuable tool to analyze the molecular near range order of the compounds in the co-amorphous mixtures. In this study, several co-amorphous drugs--low molecular weight excipient blends--have been analyzed with FTIR spectroscopy. Molecular interactions of the drugs carbamazepine and indomethacin with the amino acids arginine, phenylalanine, and tryptophan were investigated. The amino acids were chosen from the biological target site of both drugs and prepared as co-amorphous formulations together with the drugs by vibrational ball milling. A detailed analysis of the FTIR spectra of these formulations revealed specific peak shifts in the vibrational modes of functional groups of drug and amino acid, as long as one amino acid from the biological target site was present in the blends. These peak shifts indicate that the drugs formed specific molecular interactions (hydrogen bonding and π-π interactions) with the amino acids. In the drug-amino acid mixtures that contained amino acids which were not present at the biological target site, no such interactions were identified. This study shows the potential of amino acids as small molecular weight excipients in co-amorphous formulations to stabilize the amorphous form of a poorly water-soluble drug through strong and specific molecular interactions with the drug.

  19. Molecular mechanism of mutant p53 stabilization: the role of HSP70 and MDM2.

    Directory of Open Access Journals (Sweden)

    Milena Wiech

    Full Text Available Numerous p53 missense mutations possess gain-of-function activities. Studies in mouse models have demonstrated that the stabilization of p53 R172H (R175H in human mutant protein, by currently unknown factors, is a prerequisite for its oncogenic gain-of-function phenotype such as tumour progression and metastasis. Here we show that MDM2-dependent ubiquitination and degradation of p53 R175H mutant protein in mouse embryonic fibroblasts is partially inhibited by increasing concentration of heat shock protein 70 (HSP70/HSPA1-A. These phenomena correlate well with the appearance of HSP70-dependent folding intermediates in the form of dynamic cytoplasmic spots containing aggregate-prone p53 R175H and several molecular chaperones. We propose that a transient but recurrent interaction with HSP70 may lead to an increase in mutant p53 protein half-life. In the presence of MDM2 these pseudoaggregates can form stable amyloid-like structures, which occasionally merge into an aggresome. Interestingly, formation of folding intermediates is not observed in the presence of HSC70/HSPA8, the dominant-negative K71S variant of HSP70 or HSP70 inhibitor. In cancer cells, where endogenous HSP70 levels are already elevated, mutant p53 protein forms nuclear aggregates without the addition of exogenous HSP70. Aggregates containing p53 are also visible under conditions where p53 is partially unfolded: 37°C for temperature-sensitive variant p53 V143A and 42°C for wild-type p53. Refolding kinetics of p53 indicate that HSP70 causes transient exposure of p53 aggregate-prone domain(s. We propose that formation of HSP70- and MDM2-dependent protein coaggregates in tumours with high levels of these two proteins could be one of the mechanisms by which mutant p53 is stabilized. Moreover, sequestration of p73 tumour suppressor protein by these nuclear aggregates may lead to gain-of-function phenotypes.

  20. Biochemical stability and molecular dynamic characterization of Aspergillus fumigatus cystathionine γ-lyase in response to various reaction effectors.

    Science.gov (United States)

    El-Sayed, Ashraf S A; Abdel-Azeim, Safwat; Ibrahim, Hend M; Yassin, Marwa A; Abdel-Ghany, Salah E; Esener, Sadik; Ali, Gul Shad

    2015-12-01

    Cystathionine γ-lyase (CGL) is a key enzyme in the methionine-cysteine cycle in all living organisms forming cysteine, α-ketobutyrate and ammonia via homocysteine and cystathionine intermediates. Although, human and plant CGLs have been extensively studied at the molecular and mechanistic levels, there has been little work on the molecular and catalytic properties of fungal CGL. Herein, we studied in detail for the first time the molecular and catalytic stability of Aspergillus fumigatus CGL, since conformational instability, inactivation and structural antigenicity are the main limitations of the PLP-dependent enzymes on various therapeutic uses. We examined these properties in response to buffer compositions, stabilizing and destabilizing agents using Differential Scanning Fluorometery (DSF), steady state and gel-based fluorescence of the intrinsic hydrophobic core, stability of internal aldimine linkage and catalytic properties. The activity of the recombinant A. fumigatus CGL was 13.8U/mg. The melting temperature (Tm) of CGL in potassium phosphate buffer (pH 7.0-8.0) was 73.3°C, with ∼3°C upshifting in MES and sodium phosphate buffers (pH 7.0). The conformational thermal stability was increased in potassium phosphate, sodium phosphate and MES buffers, in contrast to Tris-HCl, HEPES (pH 7.0) and CAPS (pH 9.0-10.0). The thermal stability and activity of CGL was slightly increased in the presence of trehalose and glycerol that might be due to hydration of the enzyme backbone, unlike the denaturing effect of GdmCl and urea. Modification of surface CGL glutamic and aspartic acids had no significant effect on the enzyme conformational and catalytic stability. Molecular modeling and dynamics simulations unveil the high conformational stability of the overall scaffold of CGL with high flexibility at the non-structural regions. CGL structure has eight buried Trp residues, which are reoriented to the enzyme surface and get exposed to the solvent under perturbation

  1. Biochemical Stability and Molecular Dynamic Characterization of Aspergillus fumigatus Cystathionine γ-Lyase in Response to Various Reaction Effectors

    KAUST Repository

    El-Sayed, Ashraf S.A.

    2015-08-11

    Cystathionine γ-lyase (CGL) is a key enzyme in the methionine-cysteine cycle in all living organisms forming cysteine, α-ketobutyrate and ammonia via homocysteine and cystathionine intermediates. Although, human and plant CGLs have been extensively studied at the molecular and mechanistic levels, there has been little work on the molecular and catalytic properties of fungal CGL. Herein, we studied in detail for the first time the molecular and catalytic stability of Aspergillus fumigatus CGL, since conformational instability, inactivation and structural antigenicity are the main limitations of the PLP-dependent enzymes on various therapeutic uses. We examined these properties in response to buffer compositions, stabilizing and destabilizing agents using Differential Scanning Fluorometery (DSF), steady state and gel-based fluorescence of the intrinsic hydrophobic core, stability of internal aldimine linkage and catalytic properties. The activity of the recombinant A. fumigatus CGL was 13.8 U/mg. The melting temperature (Tm) of CGL in potassium phosphate buffer (pH 7.0-8.0) was 73.3 °C, with ∼3 °C upshifting in MES and sodium phosphate buffers (pH 7.0). The conformational thermal stability was increased in potassium phosphate, sodium phosphate and MES buffers, in contrast to Tris-HCl, HEPES (pH 7.0) and CAPS (pH 9.0-10.0). The thermal stability and activity of CGL was slightly increased in the presence of trehalose and glycerol that might be due to hydration of the enzyme backbone, unlike the denaturing effect of GdmCl and urea. Modification of surface CGL glutamic and aspartic acids had no significant effect on the enzyme conformational and catalytic stability. Molecular modeling and dynamics simulations unveil the high conformational stability of the overall scaffold of CGL with high flexibility at the non-structural regions. CGL structure has eight buried Trp residues, which are reoriented to the enzyme surface and get exposed to the solvent under

  2. Stability optimisation of molecular electronic devices based on  nanoelectrode–nanoparticle bridge platform in air and different storage liquids

    Energy Technology Data Exchange (ETDEWEB)

    Jafri, S. H. M. [Mirpur University of Science and Technology, Department of Electrical Engineering (Pakistan); Blom, T. [Uppsala University, The Ångström Laboratory, Department of Engineering Sciences (Sweden); Wallner, A.; Ottosson, H., E-mail: Henrik.Ottosson@kemi.uu.se [Uppsala University, The Biomedical Centre, Department of Chemistry (Sweden); Leifer, K., E-mail: Klaus.Leifer@angstrom.uu.se [Uppsala University, The Ångström Laboratory, Department of Engineering Sciences (Sweden)

    2014-12-15

    The long-term stability of metal nanoparticle–molecule junctions in molecular electronic devices based on nanoelectrodes (NEL) is a major challenge in the effort to bring related molecular electronic devices to application. To optimize the reproducibility of molecular electronic nanodevices, the time-dependent modification of such junctions as exposed to different media needs to be known. Here, we have studied (1) the stability of Au-NEL and (2) the electrical stability of molecule–Au nanoparticle (AuNP) junctions themselves with the molecule being  1,8-octanedithiol (ODT). Both the NELs only and the junctions were exposed to air and liquids such as deionized water, tetrahydrofuran, toluene and tetramethylethylenediamine (TMEDA) over a period of 1 month. The nanogaps remained stable in width when stored in either deionized water or toluene, whereas the current through 1,8-octanedithiol–NP junctions remained most stable when stored in TMEDA as compared to other solvents. Although it is difficult to follow the chemical processes in such devices in the 10-nm range with analytical methods, the behavior can be interpreted from known interactions of solvent molecules with electrodes and ODT.

  3. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA

    Directory of Open Access Journals (Sweden)

    Anna Aviñó

    2016-02-01

    Full Text Available Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide by ultraviolet (UV, circular dichroism (CD and nuclear magnetic resonance (NMR spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO is RNA. In addition, DNA triplexes (D:D·D are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions.

  4. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA.

    Science.gov (United States)

    Aviñó, Anna; Mazzini, Stefania; Gargallo, Raimundo; Eritja, Ramon

    2016-01-01

    Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide) by ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO) is RNA. In addition, DNA triplexes (D:D·D) are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D) is only slightly decreased. The kinetic of triplex formation with RNA-TFO is slower than with DNA-TFO and the thermal stability of the triplex is increased with the salt concentration in EtOH-water solutions. Accordingly, RNA could be considered a potential molecule to form a stable triplex for regulatory purposes in molecular crowding conditions. PMID:26861295

  5. On-chip multi spectral frequency standard replication by stabilizing a microring resonator to a molecular line

    Science.gov (United States)

    Zektzer, Roy; Stern, Liron; Mazurski, Noa; Levy, Uriel

    2016-07-01

    Stabilized laser lines are highly desired for myriad of applications ranging from precise measurements to optical communications. While stabilization can be obtained by using molecular or atomic absorption references, these are limited to specific frequencies. On the other hand, resonators can be used as wide band frequency references. Unfortunately, such resonators are unstable and inaccurate. Here, we propose and experimentally demonstrate a chip-scale multispectral frequency standard replication operating in the spectral range of the near IR. This is obtained by frequency locking a microring resonator (MRR) to an acetylene absorption line. The MRR consists of a Si3N4 waveguides with microheater on top of it. The thermo-optic effect is utilized to lock one of the MRR resonances to an acetylene line. This locked MRR is then used to stabilize other laser sources at 980 nm and 1550 nm wavelength. By beating the stabilized laser to another stabilized laser, we obtained frequency instability floor of 4 ×10-9 at around 100 s in terms of Allan deviation. Such stable and accurate chip scale sources are expected to serve as important building block in diverse fields such as communication and metrology.

  6. How hydrophobicity and the glycosylation site of glycans affect protein folding and stability: a molecular dynamics simulation.

    Science.gov (United States)

    Lu, Diannan; Yang, Cheng; Liu, Zheng

    2012-01-12

    Glycosylation is one of the most common post-translational modifications in the biosynthesis of protein, but its effect on the protein conformational transitions underpinning folding and stabilization is poorly understood. In this study, we present a coarse-grained off-lattice 46-β barrel model protein glycosylated by glycans with different hydrophobicity and glycosylation sites to examine the effect of glycans on protein folding and stabilization using a Langevin dynamics simulation, in which an H term was proposed as the index of the hydrophobicity of glycan. Compared with its native counterpart, introducing glycans of suitable hydrophobicity (0.1 enthalpy effect. The simulations have shown both the stabilization and the destabilization effects of glycosylation, as experimentally reported in the literature, and provided molecular insight into glycosylated proteins. The understanding of the effects of glycans with different hydrophobicities on the folding and stability of protein, as attempted by the present work, is helpful not only to explain the stabilization and destabilization effect of real glycoproteins but also to design protein-polymer conjugates for biotechnological purposes.

  7. Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

    CERN Document Server

    Rossi, Mariana; Ceriotti, Michele

    2016-01-01

    Molecular crystals often exist in multiple competing polymorphs, showing significantly different physico-chemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form: A real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenge...

  8. Thermodynamic stability and crystallization behavior of molecular complexes with TEP host

    Science.gov (United States)

    Fijiwara, Atsushi; Kitamura, Mitsutaka

    2013-06-01

    In the crystallization of molecular complex (co-crystal, clathrate complex), polymorphism in regard to the host structure frequently appears. Previously, we studied the release process of the biocide, CMI (5-chloro-2-methyl-4-isothiazolin-3-one) from the molecular complex with TEP (1,1,2,2-tetrakis(4-hydroxyphenyl)ethane) (TEP·2CMI) in methanol-water mixed solvents. It was clear that the release process of the biocide (CMI) is composed of the transformation from the TEP·2CMI crystal to a more stable molecular complex crystal with solvent. In this work, the crystallization was performed in the methanol solutions including TEP and CMI at constant temperature (298 K and 308 K). It appeared that two kinds of TEP molecular complexes (TEP·2CMI and TEP·2MeOH) crystallize competitively. The crystallization zone of each molecular complex was shown in the map using the coordinates of initial concentrations of TEP and CMI. In the boundary zone both molecular complexes appeared and the transformation from TEP·2CMI to TEP·2MeOH was observed, indicating that the stable form is TEP·2MeOH. Without the boundary zone the corresponding stable form crystallized in each zone. The value of the initial concentration ratio of CMI/TEP for the selective crystallization of TEP·2CMI was higher at 298 K (1.54) than that (1.36) at 308 K. The equilibrium concentrations of TEP and CMI in the presence of two molecular complexes were expressed using the dissociation constants of the molecular complexes and it was indicated that the dissociation of TEP·2CMI highly increases with temperature

  9. Molecular Determinants of Virulence and Stability of a Reporter-Expressing H5N1 Influenza A Virus

    OpenAIRE

    Zhao, Dongming; Fukuyama, Satoshi; Yamada, Shinya; Lopes, Tiago J. S.; Maemura, Tadashi; Katsura, Hiroaki; Ozawa, Makoto; Watanabe, Shinji; Neumann, Gabriele; Kawaoka, Yoshihiro

    2015-01-01

    We previously reported that an H5N1 virus carrying the Venus reporter gene, which was inserted into the NS gene segment from the A/Puerto Rico/8/1934(H1N1) virus (Venus-H5N1 virus), became more lethal to mice, and the reporter gene was stably maintained after mouse adaptation compared with the wild-type Venus-H5N1 (WT-Venus-H5N1) virus. However, the basis for this difference in virulence and Venus stability was unclear. Here, we investigated the molecular determinants behind this virulence an...

  10. Molecular Packing and Arrangement Govern the Photo-Oxidative Stability of Organic Photovoltaic Materials

    KAUST Repository

    Mateker, William R.

    2015-08-19

    For long-term performance chemically robust materials are desired for organic solar cells (OSCs). Illuminating neat films of OSC materials in air and tracking the rate of absorption loss, or photobleaching, can quickly screen a material’s photo-chemical stability. In this report, we photobleach neat films of OSC materials including polymers, solution-processed oligomers, solution-processed small molecules, and vacuum-deposited small molecules. Across the materials we test, we observe photobleaching rates that span seven orders of magnitude. Furthermore, we find that the film morphology of any particular material impacts the observed photobleaching rate, and that amorphous films photobleach faster than crystalline ones. In an extreme case, films of amorphous rubrene photobleach at a rate 2500 times faster than polycrystalline films. When we compare density to photobleaching rate, we find that stability increases with density. We also investigate the relationship between backbone planarity and chemical reactivity. The polymer PBDTTPD is more photostable than it’s more twisted and less ordered furan derivitative, PBDFTPD. Finally, we relate our work to what is known about the chemical stability of structural polymers, organic pigments, and organic light emitting diode materials. For the highest chemical stability, planar materials that form dense, crystalline film morphologies should be designed for OSCs.

  11. Size and molecular flexibility of sugars determine the storage stability of freeze-dried proteins

    NARCIS (Netherlands)

    Tonnis, W. F.; Mensink, M. A.; de Jager, A.; Maarschalk, K. van der Voort; Frijlink, H. W.; Hinrichs, W. L. J.

    2015-01-01

    Protein-based biopharmaceuticals are generally produced as aqueous solutions and stored refrigerated to obtain sufficient shelf life. Alternatively, proteins may be freeze-dried in the presence of sugars to allow storage stability at ambient conditions for prolonged periods. However, to act as a sta

  12. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

    Science.gov (United States)

    Su, Ji-Guo; Zhao, Shu-Xin; Wang, Xiao-Feng; Li, Chun-Hua; Li, Jing-Yuan

    2016-08-01

    Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties. PMID:27444879

  13. Effects of ligand binding on the mechanical stability of protein GB1 studied by steered molecular dynamics simulation.

    Science.gov (United States)

    Su, Ji-Guo; Zhao, Shu-Xin; Wang, Xiao-Feng; Li, Chun-Hua; Li, Jing-Yuan

    2016-08-01

    Regulation of the mechanical properties of proteins plays an important role in many biological processes, and sheds light on the design of biomaterials comprised of protein. At present, strategies to regulate protein mechanical stability focus mainly on direct modulation of the force-bearing region of the protein. Interestingly, the mechanical stability of GB1 can be significantly enhanced by the binding of Fc fragments of human IgG antibody, where the binding site is distant from the force-bearing region of the protein. The mechanism of this long-range allosteric control of protein mechanics is still elusive. In this work, the impact of ligand binding on the mechanical stability of GB1 was investigated using steered molecular dynamics simulation, and a mechanism underlying the enhanced protein mechanical stability is proposed. We found that the external force causes deformation of both force-bearing region and ligand binding site. In other words, there is a long-range coupling between these two regions. The binding of ligand restricts the distortion of the binding site and reduces the deformation of the force-bearing region through a long-range allosteric communication, which thus improves the overall mechanical stability of the protein. The simulation results are very consistent with previous experimental observations. Our studies thus provide atomic-level insights into the mechanical unfolding process of GB1, and explain the impact of ligand binding on the mechanical properties of the protein through long-range allosteric regulation, which should facilitate effective modulation of protein mechanical properties.

  14. Structural features and thermal stability of molecular complexes of 25,26,27,28-Tetrahydroxycalix[4]arene with solvents

    Science.gov (United States)

    Surov, O. V.; Voronova, M. I.; Plevina, E. V.; Barannikov, V. P.; Smirnov, P. R.; Mamardashvili, N. Zh.

    2014-08-01

    A single crystal of the complex 25,26,27,28-tetrahydroxycalix[4]arene with hexane is grown via slow evaporation of a solution, and its full structure is determined. A molecular complex of 25,26,27,28-tetrahydroxycalix[4]arene with toluene is prepared for the first time, and its thermal stability is studied. The kinetic curves of the sorption of saturated vapors of acetone, acetonitrile, n-hexane, and toluene on 25,26,27,28-tetrahydroxycalix[4]arene are experimentally obtained. It is shown that the sorption of acetonitrile vapors on 25,26,27,28-tetrahydroxycalix[4]arene is characterized by a pronounced maximum corresponding to a stoichiometry of 1: 1. It is assumed that the structural reorganization of 25,26,27,28-tetrahydroxycalix[4]arene results in the transport of acetonitrile molecules within the molecular crystal, followed by complexation to form a thermodynamically stable hexagonal structure. The high thermal stability of solvates of 25,26,27,28-tetrahydroxycalix[4]arene is found to be due to the strict proportionality of the form and size of a guest molecule to those of the cavity of a host molecule.

  15. Anharmonic and Quantum Fluctuations in Molecular Crystals: A First-Principles Study of the Stability of Paracetamol

    Science.gov (United States)

    Rossi, Mariana; Gasparotto, Piero; Ceriotti, Michele

    2016-09-01

    Molecular crystals often exist in multiple competing polymorphs, showing significantly different physicochemical properties. Computational crystal structure prediction is key to interpret and guide the search for the most stable or useful form, a real challenge due to the combinatorial search space, and the complex interplay of subtle effects that work together to determine the relative stability of different structures. Here we take a comprehensive approach based on different flavors of thermodynamic integration in order to estimate all contributions to the free energies of these systems with density-functional theory, including the oft-neglected anharmonic contributions and nuclear quantum effects. We take the two main stable forms of paracetamol as a paradigmatic example. We find that anharmonic contributions, different descriptions of van der Waals interactions, and nuclear quantum effects all matter to quantitatively determine the stability of different phases. Our analysis highlights the many challenges inherent in the development of a quantitative and predictive framework to model molecular crystals. However, it also indicates which of the components of the free energy can benefit from a cancellation of errors that can redeem the predictive power of approximate models, and suggests simple steps that could be taken to improve the reliability of ab initio crystal structure prediction.

  16. C{sub 60}-derived nanobaskets: stability, vibrational signatures, and molecular trapping

    Energy Technology Data Exchange (ETDEWEB)

    Dos Santos, S G; Pires, M S; Lemos, V; Freire, V N [Departamento de Fisica, Universidade Federal do Ceara, Caixa Postal 6030, 60455-900 Fortaleza, Ceara (Brazil); Caetano, E W S [Instituto Federal de Educacao, Ciencia e Tecnologia do Ceara, Av. 13 de Maio, 2081, Benfica, 60040-531 Fortaleza, Ceara (Brazil); Galvao, D S [Instituto de Fisica Gleb Wataghin, Universidade Estadual de Campinas, 13083-970, Campinas, Sao Paulo (Brazil); Sato, F [Departamento de Fisica, ICE, Universidade Federal de Juiz de Fora, 36036-330, Juiz de Fora, Minas Gerais (Brazil); Albuquerque, E L [Departamento de Fisica Teorica e Experimental, Universidade Federal do Rio Grande do Norte, 59072-970 Natal, Rio Grande do Norte (Brazil)

    2009-09-30

    C{sub 60}-derived nanobaskets, with chemical formulae (symmetry point group) C{sub 40}H{sub 10} (C{sub 5v}), C{sub 39}H{sub 12} (C{sub 3v}), C{sub 46}H{sub 12} (C{sub 2v}), were investigated. Molecular dynamic simulations (MDSs) indicate that the molecules preserve their bonding frame for temperatures up to 300 K (simulation time 100 ps), and maintain atomic cohesion for at least 4 ps at temperatures up to 3500 K. The infrared spectra of the C{sub 60}-derived nanobaskets were simulated through density functional theory (DFT) calculations, allowing for the attribution of infrared signatures specific to each carbon nanobasket. The possibility of using C{sub 60}-derived nanobaskets as molecular containers is demonstrated by performing a DFT study of their bonding to hydrogen, water, and L-alanine. The carbon nanostructures presented here show a higher bonding energy ({approx}1.0 eV), suggesting that a family of nanostructures, C{sub n}-derived (n = 60,70,76,80, etc) nanobaskets, could work as molecular containers, paving the way for future developments such as tunable traps for complex molecular systems.

  17. Stability of Chloropyromorphite in Ryegrass Rhizosphere as Affected by Root-Secreted Low Molecular Weight Organic Acids

    Science.gov (United States)

    Wei, Wei; Wang, Yu; Wang, Zheng; Han, Ruiming; Li, Shiyin; Wei, Zhenggui; Zhang, Yong

    2016-01-01

    Understanding the stability of chloropyromorphite (CPY) is of considerable benefit for improving risk assessment and remediation strategies in contaminated water and soil. The stability of CPY in the rhizosphere of phosphorus-deficient ryegrass was evaluated to elucidate the role of root-secreted low molecular weight organic acids (LMWOAs) on the dissolution of CPY. Results showed that CPY treatments significantly reduced the ryegrass biomass and rhizosphere pH. The presence of calcium nitrate extractable lead (Pb) and phosphorus (P) suggested that CPY in the rhizosphere could be bioavailable, because P and Pb uptake by ryegrass potentially provided a significant concentration gradient that would promote CPY dissolution. Pb accumulation and translocation in ryegrass was found to be significantly higher in P-sufficient conditions than in P-deficient conditions. CPY treatments significantly enhanced root exudation of LMWOAs irrigated with P-nutrient solution or P-free nutrient solution. Oxalic acid was the dominant species in root-secreted LMWOAs of ryegrass under P-free nutrient solution treatments, suggesting that root-secreted oxalic acid may be the driving force of root-induced dissolution of CPY. Hence, our work, provides clarifying hints on the role of LMWOAs in controlling the stability of CPY in the rhizosphere. PMID:27494023

  18. Stability of Chloropyromorphite in Ryegrass Rhizosphere as Affected by Root-Secreted Low Molecular Weight Organic Acids.

    Science.gov (United States)

    Wei, Wei; Wang, Yu; Wang, Zheng; Han, Ruiming; Li, Shiyin; Wei, Zhenggui; Zhang, Yong

    2016-01-01

    Understanding the stability of chloropyromorphite (CPY) is of considerable benefit for improving risk assessment and remediation strategies in contaminated water and soil. The stability of CPY in the rhizosphere of phosphorus-deficient ryegrass was evaluated to elucidate the role of root-secreted low molecular weight organic acids (LMWOAs) on the dissolution of CPY. Results showed that CPY treatments significantly reduced the ryegrass biomass and rhizosphere pH. The presence of calcium nitrate extractable lead (Pb) and phosphorus (P) suggested that CPY in the rhizosphere could be bioavailable, because P and Pb uptake by ryegrass potentially provided a significant concentration gradient that would promote CPY dissolution. Pb accumulation and translocation in ryegrass was found to be significantly higher in P-sufficient conditions than in P-deficient conditions. CPY treatments significantly enhanced root exudation of LMWOAs irrigated with P-nutrient solution or P-free nutrient solution. Oxalic acid was the dominant species in root-secreted LMWOAs of ryegrass under P-free nutrient solution treatments, suggesting that root-secreted oxalic acid may be the driving force of root-induced dissolution of CPY. Hence, our work, provides clarifying hints on the role of LMWOAs in controlling the stability of CPY in the rhizosphere. PMID:27494023

  19. Bcl-2 regulates HIF-1alpha protein stabilization in hypoxic melanoma cells via the molecular chaperone HSP90.

    Directory of Open Access Journals (Sweden)

    Daniela Trisciuoglio

    Full Text Available BACKGROUND: Hypoxia-Inducible Factor 1 (HIF-1 is a transcription factor that is a critical mediator of the cellular response to hypoxia. Enhanced levels of HIF-1alpha, the oxygen-regulated subunit of HIF-1, is often associated with increased tumour angiogenesis, metastasis, therapeutic resistance and poor prognosis. It is in this context that we previously demonstrated that under hypoxia, bcl-2 protein promotes HIF-1/Vascular Endothelial Growth Factor (VEGF-mediated tumour angiogenesis. METHODOLOGY/PRINCIPAL FINDINGS: By using human melanoma cell lines and their stable or transient derivative bcl-2 overexpressing cells, the current study identified HIF-1alpha protein stabilization as a key regulator for the induction of HIF-1 by bcl-2 under hypoxia. We also demonstrated that bcl-2-induced accumulation of HIF-1alpha protein during hypoxia was not due to an increased gene transcription or protein synthesis. In fact, it was related to a modulation of HIF-1alpha protein expression at a post-translational level, indeed its degradation rate was faster in the control lines than in bcl-2 transfectants. The bcl-2-induced HIF-1alpha stabilization in response to low oxygen tension conditions was achieved through the impairment of ubiquitin-dependent HIF-1alpha degradation involving the molecular chaperone HSP90, but it was not dependent on the prolyl hydroxylation of HIF-1alpha protein. We also showed that bcl-2, HIF-1alpha and HSP90 proteins form a tri-complex that may contribute to enhancing the stability of the HIF-1alpha protein in bcl-2 overexpressing clones under hypoxic conditions. Finally, by using genetic and pharmacological approaches we proved that HSP90 is involved in bcl-2-dependent stabilization of HIF-1alpha protein during hypoxia, and in particular the isoform HSP90beta is the main player in this phenomenon. CONCLUSIONS/SIGNIFICANCE: We identified the stabilization of HIF-1alpha protein as a mechanism through which bcl-2 induces the

  20. Bcl-2 Regulates HIF-1α Protein Stabilization in Hypoxic Melanoma Cells via the Molecular Chaperone HSP90

    Science.gov (United States)

    Trisciuoglio, Daniela; Gabellini, Chiara; Desideri, Marianna; Ziparo, Elio; Zupi, Gabriella; Del Bufalo, Donatella

    2010-01-01

    Background Hypoxia-Inducible Factor 1 (HIF-1) is a transcription factor that is a critical mediator of the cellular response to hypoxia. Enhanced levels of HIF-1α, the oxygen-regulated subunit of HIF-1, is often associated with increased tumour angiogenesis, metastasis, therapeutic resistance and poor prognosis. It is in this context that we previously demonstrated that under hypoxia, bcl-2 protein promotes HIF-1/Vascular Endothelial Growth Factor (VEGF)-mediated tumour angiogenesis. Methodology/Principal Findings By using human melanoma cell lines and their stable or transient derivative bcl-2 overexpressing cells, the current study identified HIF-1α protein stabilization as a key regulator for the induction of HIF-1 by bcl-2 under hypoxia. We also demonstrated that bcl-2-induced accumulation of HIF-1α protein during hypoxia was not due to an increased gene transcription or protein synthesis. In fact, it was related to a modulation of HIF-1α protein expression at a post-translational level, indeed its degradation rate was faster in the control lines than in bcl-2 transfectants. The bcl-2-induced HIF-1α stabilization in response to low oxygen tension conditions was achieved through the impairment of ubiquitin-dependent HIF-1α degradation involving the molecular chaperone HSP90, but it was not dependent on the prolyl hydroxylation of HIF-1α protein. We also showed that bcl-2, HIF-1α and HSP90 proteins form a tri-complex that may contribute to enhancing the stability of the HIF-1α protein in bcl-2 overexpressing clones under hypoxic conditions. Finally, by using genetic and pharmacological approaches we proved that HSP90 is involved in bcl-2-dependent stabilization of HIF-1α protein during hypoxia, and in particular the isoform HSP90β is the main player in this phenomenon. Conclusions/Significance We identified the stabilization of HIF-1α protein as a mechanism through which bcl-2 induces the activation of HIF-1 in hypoxic tumour cells involving the

  1. Polyethylenimine Interfacial Layers in Inverted Organic Photovoltaic Devices: Effects of Ethoxylation and Molecular Weight on Efficiency and Temporal Stability.

    Science.gov (United States)

    Courtright, Brett A E; Jenekhe, Samson A

    2015-12-01

    We report a comparative study of polyethylenimine (PEI) and ethoxylated-polyethylenimine (PEIE) cathode buffer layers in high performance inverted organic photovoltaic devices. The work function of the indium-tin oxide (ITO)/zinc oxide (ZnO) cathode was reduced substantially (Δφ = 0.73-1.09 eV) as the molecular weight of PEI was varied from 800 g mol(-1) to 750 000 g mol(-1) compared with the observed much smaller reduction when using a PEIE thin film (Δφ = 0.56 eV). The reference inverted polymer solar cells based on the small band gap polymer PBDTT-FTTE (ITO/ZnO/PBDTT-FTTE:PC70BM/MoO3/Ag), without a cathode buffer layer, had an average power conversion efficiency (PCE) of 6.06 ± 0.22%. Incorporation of a PEIE cathode buffer layer in the same PBDTT-FTTE:PC70BM blend devices gave an enhanced performance with a PCE of 7.37 ± 0.53%. In contrast, an even greater photovoltaic efficiency with a PCE of 8.22 ± 0.10% was obtained in similar PBDTT-FTTE:PC70BM blend solar cells containing a PEI cathode buffer layer. The temporal stability of the inverted polymer solar cells was found to increase with increasing molecular weight of the cathode buffer layer. The results show that PEI is superior to PEIE as a cathode buffer layer in high performance organic photovoltaic devices and that the highest molecular weight PEI interlayer provides the highest temporal stability.

  2. Polyethylenimine Interfacial Layers in Inverted Organic Photovoltaic Devices: Effects of Ethoxylation and Molecular Weight on Efficiency and Temporal Stability.

    Science.gov (United States)

    Courtright, Brett A E; Jenekhe, Samson A

    2015-12-01

    We report a comparative study of polyethylenimine (PEI) and ethoxylated-polyethylenimine (PEIE) cathode buffer layers in high performance inverted organic photovoltaic devices. The work function of the indium-tin oxide (ITO)/zinc oxide (ZnO) cathode was reduced substantially (Δφ = 0.73-1.09 eV) as the molecular weight of PEI was varied from 800 g mol(-1) to 750 000 g mol(-1) compared with the observed much smaller reduction when using a PEIE thin film (Δφ = 0.56 eV). The reference inverted polymer solar cells based on the small band gap polymer PBDTT-FTTE (ITO/ZnO/PBDTT-FTTE:PC70BM/MoO3/Ag), without a cathode buffer layer, had an average power conversion efficiency (PCE) of 6.06 ± 0.22%. Incorporation of a PEIE cathode buffer layer in the same PBDTT-FTTE:PC70BM blend devices gave an enhanced performance with a PCE of 7.37 ± 0.53%. In contrast, an even greater photovoltaic efficiency with a PCE of 8.22 ± 0.10% was obtained in similar PBDTT-FTTE:PC70BM blend solar cells containing a PEI cathode buffer layer. The temporal stability of the inverted polymer solar cells was found to increase with increasing molecular weight of the cathode buffer layer. The results show that PEI is superior to PEIE as a cathode buffer layer in high performance organic photovoltaic devices and that the highest molecular weight PEI interlayer provides the highest temporal stability. PMID:26550983

  3. Interfacial properties of asymmetrically functionalized citrate-stabilized gold and silver nanoparticles related to molecular adsorption

    Science.gov (United States)

    Park, Jong-Won

    A detailed understanding of the conformation of adsorbed molecules and regional surface functionalization of metal nanoparticles (MNPs) is challenging for nanometer-size (10 -- 100 m) materials and necessary for fundamental studies and applications. The studies are motivated by open questions related to surface chemistry of noble MNPs. Although citrate-stabilized gold NPs (AuNPs) have been widely used, the citrate layer is not well-understood. Thiols have been suggested to displace citrate anions adsorbed on metal surfaces due to strong gold-sulfur interaction, but quantitative experimental evidence of the extent of ligand-exchange has not been reported. Whereas asymmetrically-functionalized AuNPs are utilized for nanoparticle assembly due to the interparticle coupling of localized surface plasmons, the interface between asymmetric nanoparticles in single assemblies has not been studied. Noble MNPs with sizes smaller than citrate-stabilized AuNPs also need to be surface-modified for stability in water for biological applications. The dissertation presents investigations of the chemical and physical properties of gold and silver NPs (AgNPs) related to ligand adsorption at the metal surface. Firstly, self-assembled layers of citrate adsorbed on AuNP (111), (110), and (100) surfaces were proposed, based on geometric considerations and spectroscopic investigations by infrared (IR) and X-ray photoelectron spectroscopy (XPS). Adsorption characteristics of citrate are the unique structure of adsorbed species, intermolecular interactions through hydrogen bonds and van der Waals attractions, bilayer formation, surface coverage, nanoparticle-stabilization role, and chirality. Secondly, IR and XPS studies showed coadsorption of thiolate on the surface of citrate-stabilized AuNPs. Steric, chelating effects and intermolecular interactions are the origins of the strong adsorption of citrate on AuNP surfaces. Surface coverage was determined from XPS analyses. Thirdly, an

  4. Molecular basis of the structural stability of hemochromatosis factor E: A combined molecular dynamic simulation and GdmCl-induced denaturation study.

    Science.gov (United States)

    Khan, Parvez; Parkash, Amresh; Islam, Asimul; Ahmad, Faizan; Hassan, Md Imtaiyaz

    2016-03-01

    Hemochromatosis factor E (HFE) is a member of class I MHC family and plays a significant role in the iron homeostasis. Denaturation of HFE induced by guanidinium chloride (GdmCl) was measured by monitoring changes in [θ]222 (mean residue ellipticity at 222 nm), intrinsic fluorescence emission intensity at 346 nm (F346 ) and the difference absorption coefficient at 287 nm (Δε287) at pH 8.0 and 25°C. Coincidence of denaturation curves of these optical properties suggests that GdmCl-induced denaturation (native (N) state ↔ denatured (D) state) is a two-state process. The GdmCl-induced denaturation was found reversible in the entire concentration range of the denaturant. All denaturation curves were analyzed for ΔGD0, Gibbs free energy change associated with the denaturation equilibrium (N state ↔ D state) in the absence of GdmCl, which is a measure of HFE stability. We further performed molecular dynamics simulation for 40 ns to see the effect of GdmCl on the structural stability of HFE. A well defined correlation was established between in vitro and in silico studies. PMID:26537310

  5. Molecular Dynamics Studies on the Structural Stability of Wild-Type Rabbit Prion Protein: Surface Electrostatic Charge Distributions

    CERN Document Server

    Zhang, Jiapu

    2011-01-01

    Prion diseases cover a large range of neurodegenerative diseases in humans and animals, which are invariably fatal and highly infectious. By now there have not been some effective therapeutic approaches or medications to treat all prion diseases. Fortunately, numerous experimental experiences have showed that rabbits are resistant to infection from prion diseases isolated from other species, and recently the molecular structures of rabbit prion protein and its mutants were released into protein data bank. Prion diseases are "protein structural conformational" diseases. Thus, in order to reveal some secrets of prion diseases, it is amenable to study rabbits by techniques of the molecular structure and its dynamics. Wen et al. (PLoS One 5(10) e13273 (2010), Journal of Biological Chemistry 285(41) 31682-31693 (2010)) reported the surface of NMR RaPrPC(124-228) molecular snapshot has a large land of continuous positive charge distribution, which contributes to the structural stability of rabbit prion protein. Thi...

  6. Stability of the proton-to-electron mass ratio tested with molecular spectroscopy using an optical link to frequency reference

    Energy Technology Data Exchange (ETDEWEB)

    Amy-Klein, Anne; Lopez, Olivier; Daussy, Christophe; Kefelian, Fabien; Chardonnet, Christian [LPL, CNRS, Universite Paris-13, Villetaneuse (France); Shelkovnikov, Alexander [LPL, CNRS, Universite Paris-13, Villetaneuse (France); Lebedev Physical Institute, Moscow (Russian Federation); Butcher, Robert J. [LPL, CNRS, Universite Paris-13, Villetaneuse (France); Cavendish Laboratory, Cambridge (United Kingdom); Jiang, Haifeng; Santarelli, Giorgio [LNE-SYRTE, Observatoire de Paris, CNRS, UPMC (France)

    2010-07-01

    Time and frequency metrology has experienced a lot of developments since ten years leading to the possibility of many fundamental tests of physics, as, for example, the search for a temporal variation of fundamental constants. However these tests are limited to macroscopic resonators or atomic systems while molecular systems are still difficult to probe with a high sensitivity, since experiments on molecules lacks of absolute frequency measurements set-ups. In that context, we have developed an optical link between our lab and the LNE-SYRTE, which allows us to benefit from their frequency references. Using this link, we performed the first experimental comparison of a molecular clock to an atomic clock, which gives a direct line to the proton-to-electron mass ratio stability. Recently, we extended the frequency dissemination technique to non-dedicated fibers of the telecommunication network simultaneously carrying digital data from the Internet traffic. This is very challenging for the development of transcontinental atomic and molecular clocks comparisons.

  7. In vitro propagation of Puya berteroniana and assessment of genetic stability in regenerants using molecular markers

    OpenAIRE

    Štréblová, Petra

    2014-01-01

    Puya berteroniana (Bromeliaceae) is a plant with very attractive turquoise flowers that have a great potential to be used for ornamental purposes in a large scale. The aim of this thesis was optimization of in vitro propagation and assessment of genetic fidelity using molecular markers and flow cytometry. An efficient protocol for in vitro propagation via direct morphogenesis was established. Benzylaminopurine (BAP) and zeatin alone or in combination with ? – naphthaleneacetic acid (NAA) ...

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

    Directory of Open Access Journals (Sweden)

    Farah El-Turk

    Full Text Available 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.

  9. Thermal and hydrothermal stability of ZrMCM-41 mesoporous molecular sieves obtained by microwave irradiation

    Indian Academy of Sciences (India)

    T S Jiang; Y H Li; X P Zhou; Q Zhao; H B Yin

    2010-05-01

    ZrMCM-41 mesoporous molecular sieves were synthesized by using the zirconium sulfate as zirconium source and using cetyltrimethyl ammonium bromide as a template under microwave irradiation condition. The samples were characterized by X-ray diffraction (XRD), transmission electron microscopy (TEM), X-ray photoelectron spectroscopy (XPS), inductive coupled plasma (ICP) technique, Fourier transform infrared spectroscopy (FT-IR) and N2 physical adsorption, respectively. The effect of the different initial ZrO2 : SiO2 molar ratio, the different thermal treatment temperature and hydrothermal treatment time on textural property was investigated. The results show that the obtained products possess a typical mesoporous structure of MCM-41 and have specific surface areas in the range of 598.1 ∼ 971.4 m2/g and average pore sizes in the range of ca. 2.46 ∼ 3.43 nm. On the other hand, the BET specific surface area and pore volume of the synthesized ZrMCM-41 mesoporous molecular sieve decrease with the increased amount of zirconium incorporated in the starting material, the rise of thermal treatment temperature and the prolonging of hydrothermal treatment time, the mesoporous ordering deteriorates. The mesoporous structure of the ZrMCM-41 mesoporous molecular sieve still retains after calcination at 750°C for 3 h or hydrothermal treatment at 100°C for 6 days, however, the mesoporous ordering is poor.

  10. Molecular Orbital Studies for Na Chemisorption on the Ga-stabilized GaAs(100) Surface

    International Nuclear Information System (INIS)

    Using the ASED-MO total energy calculations of the model clusters, we have investigated the adsorption site and the corresponding adsorption bond length of Na on the Ga-stabilized GaAs(100) surface. The bridge site (III) is the most stable site for the adsorption, and the distance between Na and the surface is 1.47 A. Our calculations suggest that this bridge site (III), the furthest one from the As atoms, is the most effective adsorption site of Na. It suggests that Na may interact more effectively with Ga than with As in the low Na coverage

  11. Stabilization of ferroelectricity in KNO3 embedded into MCM-41 molecular sieves

    International Nuclear Information System (INIS)

    Measurements of the linear permittivity and third-order harmonic generation were carried out for KNO3 loaded molecular sieves MCM-41 with pores of 37 and 26 A in comparison with bulk potassium nitrate. The samples were warmed up to 423 and 463 K from room temperature. The ferroelectric phase III was shown to occur upon cooling in both nanocomposites after warming till 463 K when it emerges also in bulk KNO3. Nanoconfinement led to the pronounced broadening of the temperature range of ferroelectricity. While under the thermal conditions when phase III does not arise in bulk KNO3, ferroelectricity was found only within pores of 26 A.

  12. Thermal stability of epitaxial Fe films grown on Si substrates by molecular beam epitaxy

    International Nuclear Information System (INIS)

    Epitaxial Fe films are grown on Si(0 0 1) and Si(1 1 1) substrates by molecular beam epitaxy at room temperature. Several samples of one Fe/Si structure are subjected to rapid thermal annealing from 100 to 500 °C. The annealing impact on the morphological, magnetic properties and interfacial heterostructures of these samples is examined by atomic force microscopy, vibrating sample magnetometer and transmission electron microscopy, respectively. The results demonstrate that the material system Fe/Si grown at room temperature exhibits an abrupt interface and is thermally stable up to a temperature of 150 °C.

  13. Combined single cell AFM manipulation and TIRFM for probing the molecular stability of multilayer fibrinogen matrices

    Energy Technology Data Exchange (ETDEWEB)

    Christenson, W. [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); Center for Biological Physics, Arizona State University, Tempe, AZ 85287 (United States); Yermolenko, I. [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); School of Life Sciences, Arizona State University, Tempe, AZ 85287 (United States); Plochberger, B. [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); Camacho-Alanis, F.; Ros, A. [Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 85287 (United States); Ugarova, T.P. [School of Life Sciences, Arizona State University, Tempe, AZ 85287 (United States); Ros, R., E-mail: Robert.Ros@asu.edu [Department of Physics, Arizona State University, Tempe, AZ 85287 (United States); Center for Biological Physics, Arizona State University, Tempe, AZ 85287 (United States)

    2014-01-15

    Adsorption of fibrinogen on various surfaces produces a nanoscale multilayer matrix, which strongly reduces the adhesion of platelets and leukocytes with implications for hemostasis and blood compatibility of biomaterials. The nonadhesive properties of fibrinogen matrices are based on their extensibility, ensuing the inability to transduce strong mechanical forces via cellular integrins and resulting in weak intracellular signaling. In addition, reduced cell adhesion may arise from the weaker associations between fibrinogen molecules in the superficial layers of the matrix. Such reduced stability would allow integrins to pull fibrinogen molecules out of the matrix with comparable or smaller forces than required to break integrin–fibrinogen bonds. To examine this possibility, we developed a method based on the combination of total internal reflection fluorescence microscopy, single cell manipulation with an atomic force microscope and microcontact printing to study the transfer of fibrinogen molecules out of a matrix onto cells. We calculated the average fluorescence intensities per pixel for wild-type HEK 293 (HEK WT) and HEK 293 cells expressing leukocyte integrin Mac-1 (HEK Mac-1) before and after contact with multilayered matrices of fluorescently labeled fibrinogen. For contact times of 500 s, HEK Mac-1 cells show a median increase of 57% of the fluorescence intensity compared to 6% for HEK WT cells. The results suggest that the integrin Mac-1-fibrinogen interactions are stronger than the intermolecular fibrinogen interactions in the superficial layer of the matrix. The low mechanical stability of the multilayer fibrinogen surface may contribute to the reduced cell adhesive properties of fibrinogen-coated substrates. We anticipate that the described method can be applied to various cell types to examine their integrin-mediated adhesion to the extracellular matrices with a variable protein composition. - Highlights: • We present a method combining

  14. On the stability of the disordered molecular alloy phase of ammonia hemihydrate

    Energy Technology Data Exchange (ETDEWEB)

    Wilson, C. W. [Diamond Light Source, Ltd., Harwell, Didcot, Oxfordshire OX11 0DE (United Kingdom); SUPA, School of Physics and Astronomy, Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); Bull, C. L. [SUPA, School of Physics and Astronomy, Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom); ISIS Facility, STFC Rutherford Appleton Laboratory, Harwell, Didcot, Oxfordshire OX11 0QX (United Kingdom); Stinton, G. W.; Amos, D. M.; Donnelly, M.-E.; Loveday, J. S. [SUPA, School of Physics and Astronomy, Centre for Science at Extreme Conditions, University of Edinburgh, Edinburgh EH9 3JZ (United Kingdom)

    2015-03-07

    The disordered-molecular-alloy phase (DMA) of ammonia hydrates [J. S. Loveday and R. J. Nelmes, Phys. Rev. Lett. 83, 4329 (1999)] is unique in that it has substitutional disorder of ammonia and water over the molecular sites of a body centred cubic lattice. Whilst this structure has been observed in ammonia di- and mono-hydrate compositions, it has not been conclusively observed in the ammonia hemihydrate system. This work presents investigations of the structural behaviour of ammonia hemihydrate as a function of P and T. The indications of earlier studies [Ma et al. RSC Adv. 2, 4290 (2012)] that the DMA structure could be produced by compression of ammonia hemihydrate above 20 GPa at ambient temperature are confirmed. In addition, the DMA structure was found to form reversibly both from the melt, and on warming of ammonia hemihydrate phase-II, in the pressure range between 4 and 8 GPa. The route used to make the DMA structure from ammonia mono- and di-hydrates—compression at 170 K to 6 GPa followed by warming to ambient temperature—was found not to produce the DMA structure for ammonia hemihydrate. These results provide the first strong evidence that DMA is a thermodynamically stable form. A high-pressure phase diagram for ammonia hemihydrate is proposed which has importance for planetary modelling.

  15. Cation-pi interactions stabilize the structure of the antimicrobial peptide indolicidin near membranes: molecular dynamics simulations

    DEFF Research Database (Denmark)

    Khandelia, Himanshu; Kaznessis, Yiannis N

    2007-01-01

    We implemented molecular dynamics simulations of the 13-residue antimicrobial peptide indolicidin (ILPWKWPWWPWRR-NH2) in dodecylphosphocholine (DPC) and sodium dodecyl sulfate (SDS) micelles. In DPC, a persistent cation-pi interaction between TRP11 and ARG13 defined the structure of the peptide...... to the sulfate groups leads to an extended peptide structure. To the best of our knowledge, this is the first time that a cation-pi interaction between peptide side chains has been shown to stabilize the structure of a small antimicrobial peptide. The simulations are in excellent agreement with available...... experimental measurements: the backbone of the peptide is more ordered in DPC than in SDS; the tryptophan side chains pack against the backbone in DPC and point away from the backbone in SDS; the rms fluctuation of the peptide backbone and peptide side chains is greater in SDS than in DPC; and the peptide...

  16. Molecular and morphological aspects of annealing-induced stabilization of starch crystallites.

    Science.gov (United States)

    Gomand, Sara V; Lamberts, Lieve; Gommes, Cedric J; Visser, Richard G F; Delcour, Jan A; Goderis, Bart

    2012-05-14

    A unique series of potato (mutant) starches with highly different amylopectin/amylose (AP/AM) ratios was annealed in excess water at stepwise increasing temperatures to increase the starch melting (or gelatinization) temperatures in aqueous suspensions. Small-angle X-ray scattering (SAXS) experiments revealed that the lamellar starch crystals gain stability upon annealing via thickening for high-AM starch, whereas the crystal surface energy decreases for AM-free starch. In starches with intermediate AP/AM ratio, both mechanisms occur, but the surface energy reduction mechanism prevails. Crystal thickening seems to be associated with the cocrystallization of AM with AP, leading to very disordered nanomorphologies for which a new SAXS data interpretation scheme needed to be developed. Annealing affects neither the crystal internal structure nor the spherulitic morphology on a micrometer length scale.

  17. Quantum-chemical simulation of the stability of molecular complexes of iodine with cluster fragments of solvents

    International Nuclear Information System (INIS)

    The electronic structures and relative stabilities of clusters of compositions I2 · Bn (n = 1- 5) and Bn · I2 · Bm (m, n = 1, 2) (m, n = 1, 2), where B is H2O, CH3OH, (CH3)2SO, CH3CN, and CHCl3, were studied using ab initio calculations (RHF, MP2(full), and B3PW91 methods) in the HW+(3d) and 6-31G++(d,p) basis sets. It was found that the iodine molecule in the studied clusters is retained by two basically different types of interactions: -Y...I-I and -X-H...I-I; for both coordination types, the interaction energy of iodine with solvent clusters decreases in the series: ((CH3)2SO)n · I2 → (CH3OH)n · I2 → (H2O)n · I2 → (CH3CN)n · I2 → (CHCl3)n → I2. It was found that, to a first approximation, the data obtained correlate with the results of spectrophotometric studies of the stability of molecular complexes of iodine with solvents

  18. Resolving hot spots in the C-terminal dimerization domain that determine the stability of the molecular chaperone Hsp90.

    Directory of Open Access Journals (Sweden)

    Emanuele Ciglia

    Full Text Available Human heat shock protein of 90 kDa (hHsp90 is a homodimer that has an essential role in facilitating malignant transformation at the molecular level. Inhibiting hHsp90 function is a validated approach for treating different types of tumors. Inhibiting the dimerization of hHsp90 via its C-terminal domain (CTD should provide a novel way to therapeutically interfere with hHsp90 function. Here, we predicted hot spot residues that cluster in the CTD dimerization interface by a structural decomposition of the effective energy of binding computed by the MM-GBSA approach and confirmed these predictions using in silico alanine scanning with DrugScore(PPI. Mutation of these residues to alanine caused a significant decrease in the melting temperature according to differential scanning fluorimetry experiments, indicating a reduced stability of the mutant hHsp90 complexes. Size exclusion chromatography and multi-angle light scattering studies demonstrate that the reduced stability of the mutant hHsp90 correlates with a lower complex stoichiometry due to the disruption of the dimerization interface. These results suggest that the identified hot spot residues can be used as a pharmacophoric template for identifying and designing small-molecule inhibitors of hHsp90 dimerization.

  19. Molecular layer deposition of APTES on silicon nanowire biosensors: Surface characterization, stability and pH response

    Energy Technology Data Exchange (ETDEWEB)

    Liang, Yuchen [Department of Electrical Engineering, University of Texas at Dallas, Richardson, TX 75080 (United States); Huang, Jie [Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, TX 75080 (United States); Zang, Pengyuan [Department of Electrical Engineering, University of Texas at Dallas, Richardson, TX 75080 (United States); Kim, Jiyoung [Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, TX 75080 (United States); Hu, Walter, E-mail: walter.hu@utdallas.edu [Department of Electrical Engineering, University of Texas at Dallas, Richardson, TX 75080 (United States)

    2014-12-15

    Graphical abstract: - Abstract: We report the use of molecular layer deposition (MLD) for depositing 3-aminopropyltriethoxysilane (APTES) on a silicon dioxide surface. The APTES monolayer was characterized using spectroscopic ellipsometry, contact angle goniometry, and atomic force microscopy. Effects of reaction time of repeating pulses and simultaneous feeding of water vapor with APTES were tested. The results indicate that the synergistic effects of water vapor and reaction time are significant for the formation of a stable monolayer. Additionally, increasing the number of repeating pulses improved the APTES surface coverage but led to saturation after 10 pulses. In comparing MLD with solution-phase deposition, the APTES surface coverage and the surface quality were nearly equivalent. The hydrolytic stability of the resulting films was also studied. The results confirmed that the hydrolysis process was necessary for MLD to obtain stable surface chemistry. Furthermore, we compared the pH sensing results of Si nanowire field effect transistors (Si NWFETs) modified by both the MLD and solution methods. The highly repeatable pH sensing results reflected the stability of APTES monolayers. The results also showed an improved pH response of the sensor prepared by MLD compared to the one prepared by the solution treatment, which indicated higher surface coverage of APTES.

  20. Trimethylamine-N-oxide switches from stabilizing nature: A mechanistic outlook through experimental techniques and molecular dynamics simulation.

    Science.gov (United States)

    Rani, Anjeeta; Jayaraj, Abhilash; Jayaram, B; Pannuru, Venkatesu

    2016-01-01

    In adaptation biology of the discovery of the intracellular osmolytes, the osmolytes are found to play a central role in cellular homeostasis and stress response. A number of models using these molecules are now poised to address a wide range of problems in biology. Here, a combination of biophysical measurements and molecular dynamics (MD) simulation method is used to examine the effect of trimethylamine-N-oxide (TMAO) on stem bromelain (BM) structure, stability and function. From the analysis of our results, we found that TMAO destabilizes BM hydrophobic pockets and active site as a result of concerted polar and non-polar interactions which is strongly evidenced by MD simulation carried out for 250 ns. This destabilization is enthalpically favourable at higher concentrations of TMAO while entropically unfavourable. However, to the best of our knowledge, the results constitute first detailed unambiguous proof of destabilizing effect of most commonly addressed TMAO on the interactions governing stability of BM and present plausible mechanism of protein unfolding by TMAO. PMID:27025561

  1. Thermal stability of CdZnO thin films grown by molecular-beam epitaxy

    International Nuclear Information System (INIS)

    CdZnO thin films with near-band-edge (NBE) photoluminescence (PL) emission from 2.39 eV to 2.74 eV were grown by plasma-assisted molecular-beam epitaxy on c-plane sapphire substrates with 800 deg. C in situ annealing. CdZnO thin films evolve from pure wurtzite (wz) structure, to mixture of wz and rock-salt (rs) structures confirmed by X-ray diffraction studies. Rapid-thermo-annealing (RTA) was performed on in situ annealed CdZnO samples. Pure wz CdZnO shows insignificant NBE PL peak shift after RTA, while mixture structure CdZnO shows evident blue shifts due to phase change after annealing, indicating the rs phase CdZnO changes to wz phase CdZnO during RTA process.

  2. Sr flux stability against oxidation in oxide-molecular-beam-epitaxy environment: Flux, geometry, and pressure dependence

    International Nuclear Information System (INIS)

    Maintaining stable fluxes for multiple source elements is a challenging task when the source materials have significantly different oxygen affinities in a complex-oxide molecular-beam-epitaxy (MBE) environment. Considering that Sr is one of the most easily oxidized and widely used elements in various complex oxides, we took Sr as a probe to investigate the flux-stability problem in a number of different conditions. Source oxidation was less for higher flux, extended port geometry, and unmelted source shape. The extended port geometry also eliminated the flux transient after opening a source shutter as observed in the standard port. We also found that the source oxidation occurred more easily on the crucible wall than on the surface of the source material. Atomic oxygen, in spite of its stronger oxidation effectiveness, did not make any difference in source oxidation as compared to molecular oxygen in this geometry. Our results may provide a guide for solutions to the source oxidation problem in oxide-MBE system.

  3. Exploration of structural stability in deleterious nsSNPs of the XPA gene: A molecular dynamics approach

    Directory of Open Access Journals (Sweden)

    N NagaSundaram

    2011-01-01

    Full Text Available Background: Distinguishing the deleterious from the massive number of non-functional nsSNPs that occur within a single genome is a considerable challenge in mutation research. In this approach, we have used the existing in silico methods to explore the mutation-structure-function relationship in the XPA gene. Materials and Methods: We used the Sorting Intolerant From Tolerant (SIFT, Polymorphism Phenotyping (PolyPhen, I-Mutant 2.0, and the Protein Analysis THrough Evolutionary Relationships methods to predict the effects of deleterious nsSNPs on protein function and evaluated the impact of mutation on protein stability by Molecular Dynamics simulations. Results: By comparing the scores of all the four in silico methods, nsSNP with an ID rs104894131 at position C108F was predicted to be highly deleterious. We extended our Molecular dynamics approach to gain insight into the impact of this non-synonymous polymorphism on structural changes that may affect the activity of the XPA gene. Conclusion: Based on the in silico methods score, potential energy, root-mean-square deviation, and root-mean-square fluctuation, we predict that deleterious nsSNP at position C108F would play a significant role in causing disease by the XPA gene. Our approach would present the application of in silico tools in understanding the functional variation from the perspective of structure, evolution, and phenotype.

  4. New insight into the stability of CaCO3 surfaces and nanoparticles via molecular simulation.

    Science.gov (United States)

    Bano, A Matthew; Rodger, P Mark; Quigley, David

    2014-07-01

    Using updated and improved atomistic models for the polymorphs of calcium carbonate and their constituent ions in solution, we revisit the question of surface energetics and nanoparticle stability. Using a simple lattice-based Monte Carlo scheme, we generate nanoparticle configurations in vacuum for all three biologically relevant polymorphs of calcium carbonate and establish that the bulk energetic ordering of polymorphs persists to the nanoscale. In aqueous environments, results based on surface enthalpy alone indicate that formation of mineral-water interfaces is marginally favorable in many cases. Including an estimate of lost entropy due to formation of structured water layers is sufficient to reverse this observation, implying a delicate balance of enthalpy and entropy at crystalline CaCO3. In contradiction to some previous studies, we find that small calcite nanoparticles with diameters in the range of 1.8-4.1 nm do not retain an ordered structure on nanosecond time scales. The consequences of these results for simulation studies of biomineralization are discussed.

  5. The Hsp110 molecular chaperone stabilizes apolipoprotein B from endoplasmic reticulum-associated degradation (ERAD).

    Science.gov (United States)

    Hrizo, Stacy L; Gusarova, Viktoria; Habiel, David M; Goeckeler, Jennifer L; Fisher, Edward A; Brodsky, Jeffrey L

    2007-11-01

    Apolipoprotein B (apoB) is the most abundant protein in low density lipoproteins and plays key roles in cholesterol homeostasis. The co-translational degradation of apoB is controlled by fatty acid levels in the endoplasmic reticulum (ER) and is mediated by the proteasome. To define the mechanism of apoB degradation, we employed a cell-free system in which proteasome-dependent degradation is recapitulated with yeast cytosol, and we developed an apoB yeast expression system. We discovered that a yeast Hsp110, Sse1p, associates with and stabilizes apoB, which contrasts with data indicating that select Hsp70s and Hsp90s facilitate apoB degradation. However, the Ssb Hsp70 chaperones have no effect on apoB turnover. To determine whether our results are relevant in mammalian cells, Hsp110 was overexpressed in hepatocytes, and enhanced apoB secretion was observed. This study indicates that chaperones within distinct complexes can play unique roles during ER-associated degradation (ERAD), establishes a role for Sse1/Hsp110 in ERAD, and identifies Hsp110 as a target to lower cholesterol. PMID:17823116

  6. Solvent effect on molecular structure, IR spectra, thermodynamic properties and chemical stability of zoledronic acid: DFT study.

    Science.gov (United States)

    Liu, Qingzhu; Qiu, Ling; Wang, Yang; Lv, Gaochao; Liu, Guiqing; Wang, Shanshan; Lin, Jianguo

    2016-04-01

    Zoledronic acid (ZL) has been used widely for treating skeletal diseases because of its high potency in inhibiting bone resorption. A detailed understanding of its physicochemical characteristics may be of great significance in both medicinal chemistry and structural biology for the design of novel bisphosphonates with higher activity. In the present work, the monoclinic (IM) and triclinic (IT) polymorphs of ZL in the gas phase and the aqueous phase were studied by density functional theory (DFT) method at the B3LYP/6-311++G** level. The polarizable continuum model (PCM) was employed to study the solvent effect on structures and properties. The optimized IM and IT conformations in both phases are in reasonable agreement with the experimental structures with the overall mean absolute percent deviation (MAPD%) less than 3.1 %. The presence of intramolecular hydrogen bond within both conformations was identified in the solvent. The IR spectra were simulated and assigned in detail, which agreed well with the experimental data. The intramolecular hydrogen bonding interactions resulted in the shift of vibrational frequencies of hydroxyl to the low band by 12-22 cm(-1) and 24-26 cm(-1) for IM and IT conformations, respectively. Their thermodynamic properties were also calculated based on the harmonic vibrational analysis, including standard heat capacity (C(°)p,m), entropy (S(°)m), and enthalpy (H(°)m). The molecular stability, hydrogen bonding interaction and other electronic properties have been further analyzed by the natural bond orbital (NBO), atoms in molecules (AIM), molecular electrostatic potential (MEP) and frontier molecular orbital (FMO) analysis. PMID:26994018

  7. Enhanced mechanical stability of interlayer dielectrics with self-organized molecular pores

    Science.gov (United States)

    Pandey, Akanksha

    final product. It has been shown in this thesis that the pores introduced through structural arrangement of atoms can provide much better mechanical and chemical reliability during the fabrication process as compared to the pores introduced through removal of large segments of material from the sample. Electrical properties of the material are measured using ellipsometer and changes in properties with processes like annealing and plasma exposure are discussed in detail. Mechanical properties of the material are measured using nano-indentation and ball indentation tests. To study the molecular structure and changes in molecular structure with processes like annealing, FTIR and XPS techniques are used. An alternative curing method for traditional subtractive films has also been proposed to enhance the material's resistance to viscoplastic deformation.

  8. The molecular basis for stability of heterochromatin-mediated silencing in mammals

    Directory of Open Access Journals (Sweden)

    Hiragami-Hamada Kyoko

    2009-11-01

    Full Text Available Abstract The archetypal epigenetic phenomenon of position effect variegation (PEV in Drosophila occurs when a gene is brought abnormally close to heterochromatin, resulting in stochastic silencing of the affected gene in a proportion of cells that would normally express it. PEV has been instrumental in unraveling epigenetic mechanisms. Using an in vivo mammalian model for PEV we have extensively investigated the molecular basis for heterochromatin-mediated gene silencing. Here we distinguish 'epigenetic effects' from other cellular differences by studying ex vivo cells that are identical, apart from the expression of the variegating gene which is silenced in a proportion of the cells. By separating cells according to transgene expression we show here that silencing appears to be associated with histone H3 lysine 9 trimethylation (H3K9me3, DNA methylation and the localization of the silenced gene to a specific nuclear compartment enriched in these modifications. In contrast, histone H3 acetylation (H3Ac and lysine 4 di or tri methylation (H3K4me2/3 are the predominant modifications associated with expression where we see the gene in a euchromatic compartment. Interestingly, DNA methylation and inaccessibility, rather than H3K9me3, correlated most strongly with resistance to de-repression by cellular activation. These results have important implications for understanding the contribution of specific factors involved in the establishment and maintenance of gene silencing and activation in vivo.

  9. Molecular mechanism of the synergistic effects of vitrification solutions on the stability of phospholipid bilayers.

    Science.gov (United States)

    Hughes, Zak E; Mancera, Ricardo L

    2014-06-17

    The vitrification solutions used in the cryopreservation of biological samples aim to minimize the deleterious formation of ice by dehydrating cells and promoting the formation of the glassy state of water. They contain a mixture of different cryoprotective agents (CPAs) in water, typically polyhydroxylated alcohols and/or dimethyl sulfoxide (DMSO), which can damage cell membranes. Molecular dynamics simulations have been used to investigate the behavior of pure DPPC, pure DOPC, and mixed DOPC-β-sitosterol bilayers solvated in a vitrification solution containing glycerol, ethylene glycol, and DMSO at concentrations that approximate the widely used plant vitrification solution 2. As in the case of solutions containing a single CPA, the vitrification solution causes the bilayer to thin and become disordered, and pores form in the case of some bilayers. Importantly, the degree of thinning is, however, substantially reduced compared to solutions of DMSO containing the same total CPA concentration. The reduction in the damage done to the bilayers is a result of the ability of the polyhydroxylated species (especially glycerol) to form hydrogen bonds to the lipid and sterol molecules of the bilayer. A decrease in the amount of DMSO in the vitrification solution with a corresponding increase in the amount of glycerol or ethylene glycol diminishes further its damaging effect due to increased hydrogen bonding of the polyol species to the bilayer headgroups. These findings rationalize, to our knowledge for the first time, the synergistic effects of combining different CPAs, and form the basis for the optimization of vitrification solutions. PMID:24940779

  10. PHENANTHROLINE-STABILIZED PALLADIUM NANOPARTICLES IN POLYETHYLENE GLYCOL—AN ACTIVE AND RECYCLABLE CATALYST SYSTEM FOR THE SELECTIVE HYDROGENATION OF OLEFINS USING MOLECULAR HYDROGEN

    Science.gov (United States)

    1,10-Phenanthroline-stabilized palladium nanoparticles dispersed in a polyethylene glycol (PEG) matrix is synthesized which is found to be a stable and active catalyst for the selective hydrogenation of olefins using molecular hydrogen under mild reaction conditions. A variety of...

  11. The influence of the binding of low molecular weight surfactants on the thermal stability and secondary structure of IgG

    NARCIS (Netherlands)

    Vermeer, AWP; Norde, W

    2000-01-01

    The effect of low molecular weight surfactants on the thermal stability of immunoglobulin G is studied by differential scanning calorimetry. The corresponding change in the secondary structure is investigated using circular dichroism spectroscopy and the rate of aggregate formation, both in the pres

  12. Structure and stability in TMC-1: Analysis of NH3 molecular line and Herschel continuum data

    Science.gov (United States)

    Fehér, O.; Tóth, L. V.; Ward-Thompson, D.; Kirk, J.; Kraus, A.; Pelkonen, V.-M.; Pintér, S.; Zahorecz, S.

    2016-05-01

    Aims: We examined the velocity, density, and temperature structure of Taurus molecular cloud-1 (TMC-1), a filamentary cloud in a nearby quiescent star forming area, to understand its morphology and evolution. Methods: We observed high signal-to-noise (S/N), high velocity resolution NH3(1,1), and (2, 2) emission on an extended map. By fitting multiple hyperfine-split line profiles to the NH3(1, 1) spectra, we derived the velocity distribution of the line components and calculated gas parameters on several positions. Herschel SPIRE far-infrared continuum observations were reduced and used to calculate the physical parameters of the Planck Galactic Cold Clumps (PGCCs) in the region, including the two in TMC-1. The morphology of TMC-1 was investigated with several types of clustering methods in the parameter space consisting of position, velocity, and column density. Results: Our Herschel-based column density map shows a main ridge with two local maxima and a separated peak to the south-west. The H2 column densities and dust colour temperatures are in the range of 0.5-3.3 × 1022 cm-2 and 10.5-12 K, respectively. The NH3 column densities and H2 volume densities are in the range of 2.8-14.2 × 1014 cm-2 and 0.4-2.8 × 104 cm-3. Kinetic temperatures are typically very low with a minimum of 9 K at the maximum NH3 and H2 column density region. The kinetic temperature maximum was found at the protostar IRAS 04381+2540 with a value of 13.7 K. The kinetic temperatures vary similarly to the colour temperatures in spite of the fact that densities are lower than the critical density for coupling between the gas and dust phase. The k-means clustering method separated four sub-filaments in TMC-1 with masses of 32.5, 19.6, 28.9, and 45.9 M⊙ and low turbulent velocity dispersion in the range of 0.13-0.2 km s-1. Conclusions: The main ridge of TMC-1 is composed of four sub-filaments that are close to gravitational equilibrium. We label these TMC-1F1 through F4. The sub-filaments TMC

  13. The energy and stability of helium-related cluster in nickel: A study of molecular dynamics simulation

    Science.gov (United States)

    Gong, Hengfeng; Wang, Chengbin; Zhang, Wei; Xu, Jian; Huai, Ping; Deng, Huiqiu; Hu, Wangyu

    2016-02-01

    Using molecular dynamics simulation, we investigated the energy and stability of helium-related cluster in nickel. All the binding energies of the He-related clusters are demonstrated to be positive and increase with the cluster sizes. Due to the pre-existed self-interstitial nickel atom, the trapping capability of vacancy to defects becomes weak. Besides, the minimum energy configurations of He-related clusters exhibit the very high symmetry in the local atomistic environment. And for the HeN and HeNV1SIA1 clusters, the average length of He-He bonds shortens, but it elongates for the HeNV1 clusters with helium cluster sizes. The helium-to-vacancy ratio plays a decisive role on the binding energies of HeNVM cluster. These results can provide some excellent clues to insight the initial stage of helium bubbles nucleation and growth in the Ni-based alloys for the Generation-IV Molten Salt Reactor.

  14. Nonlinear stability of pulsational mode of gravitational collapse in self-gravitating hydrostatically bounded dust molecular cloud

    Indian Academy of Sciences (India)

    P K Karmakar

    2011-06-01

    The pulsational mode of gravitational collapse (PMGC) in a hydrostatically bounded dust molecular cloud is responsible for the evolution of tremendous amount of energy during star formation. The source of free energy for this gravito-electrostatic instability lies in the associated self-gravity of the dispersed phase of relatively huge dust grains of solid matter over the gaseous phase of background plasma. The nonlinear stability of the same PMGC in an infinite dusty plasma model (plane geometry approximation for large wavelength fluctuation in the absence of curvature effects) is studied in a hydrostatic kind of homogeneous equilibrium configuration. By the standard reductive perturbation technique, a Korteweg–de Vries (KdV) equation for investigating the nonlinear evolution of the lowest order perturbed self-gravitational potential is developed in a time-stationary (steady-state) form, which is studied analytically as well as numerically. Different nonlinear structures (soliton-like and soliton chain-like) are found to exist in different situations. Astrophysical situations, relevant to it, are briefly discussed.

  15. Molecular Dynamics Study of Stability of Solid Solutions and Amorphous Phase in the Cu-Al System

    Institute of Scientific and Technical Information of China (English)

    YANG Bin; LAI Wen-Sheng

    2009-01-01

    The relative stability of fcc and bcc solid solutions and amorphous phase with different compositions in the Cu-Al system is studied by molecular dynamics simulations with n-body potentials.For Cu1-xAlx alloys,the calculations show that the fcc solid solution has the lowest energies in the composition region with x<0.32 or x>0.72,while the bcc solid solution has the lowest energies in the central composition range,in agreement with the ball-milling experiments that a single bcc solid solution with 0.30<x< 0.70 is obtained.The evolution of structures in solid solutions and amorphous phase is studied by the coordination number (CN) and bond-length analysis so as to unveil the underlying physics.It is found that the energy sequence among three phases is determined by the competition in energy change originating from the bond length and CNs (or the number of bonds).

  16. Atomic structure and thermal stability of interfaces between metallic glass and embedding nano-crystallites revealed by molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Gao, X.Z.; Yang, G.Q.; Xu, B.; Qi, C.; Kong, L.T., E-mail: konglt@sjtu.edu.cn; Li, J.F.

    2015-10-25

    Molecular dynamics simulations were performed to investigate the atomic structure and thermal stability of interfaces formed between amorphous Cu{sub 50}Zr{sub 50} matrix and embedding B2 CuZr nano-crystallites. The interfaces are found to be rather abrupt, and their widths show negligible dependence on the nano-crystallite size. Local atomic configuration in the interfacial region is dominated by geometry characterized by Voronoi polyhedra <0,5,2,6> and <0,4,4,6>, and the contents of these polyhedra also exhibit apparent size dependence, which in turn results in an increasing trend in the interfacial energy against the nano-crystallite size. Annealing of the interface models at elevated temperatures will also enrich these characterizing polyhedra. While when the temperature is as high as the glass transition temperature of the matrix, growth of the nano-crystallites will be appreciable. The growth activation energy also shows size dependence, which is lower for larger nano-crystallites, suggesting that large nano-crystallites are prone to grow upon thermal disturbance. - Highlights: • Special clusters characterizing the local geometry are abundant in the interfaces. • Their content varies with the size of the embedding nano-crystallite. • In turn, size dependences in interfacial thermodynamics and kinetics are observed.

  17. Gas kinematics on giant molecular cloud scales in M51 with PAWS: Cloud stabilization through dynamical pressure

    Energy Technology Data Exchange (ETDEWEB)

    Meidt, Sharon E.; Schinnerer, Eva; Hughes, Annie; Colombo, Dario [Max-Planck-Institut für Astronomie/Königstuhl 17 D-69117 Heidelberg (Germany); García-Burillo, Santiago [Observatorio Astronómico Nacional - OAN, Observatorio de Madrid Alfonso XII, 3, E-28014 - Madrid (Spain); Pety, Jérôme; Schuster, Karl F.; Dumas, Galle [Institut de Radioastronomie Millimétrique, 300 Rue de la Piscine, F-38406 Saint Martin d' Hères (France); Dobbs, Clare L. [School of Physics and Astronomy, University of Exeter, Stocker Road, Exeter EX4 4QL (United Kingdom); Kramer, Carsten [Instituto Radioastronomía Milimétrica, Avenida Divina Pastora 7, Nucleo Central, E-18012 Granada (Spain); Leroy, Adam K. [National Radio Astronomy Observatory, 520 Edgemont Road, Charlottesville, VA 22903 (United States); Thompson, Todd A. [Department of Astronomy, The Ohio State University, 140 West 18th Avenue, Columbus, OH 43210 (United States)

    2013-12-10

    We use the high spatial and spectral resolution of the PAWS CO(1-0) survey of the inner 9 kpc of the iconic spiral galaxy M51 to examine the effects of gas streaming motions on the star-forming properties of individual giant molecular clouds (GMCs). We compare our view of gas flows in M51—which arise due to departures from axisymmetry in the gravitational potential (i.e., the nuclear bar and spiral arms)—with the global pattern of star formation as traced by Hα and 24 μm emission. We find that the dynamical environment of GMCs strongly affects their ability to form stars, in the sense that GMCs situated in regions with large streaming motions can be stabilized, while similarly massive GMCs in regions without streaming go on to efficiently form stars. We argue that this is the result of reduced surface pressure felt by clouds embedded in an ambient medium undergoing large streaming motions, which prevent collapse. Indeed, the variation in gas depletion time expected based on the observed streaming motions throughout the disk of M51 quantitatively agrees with the variation in the observed gas depletion time scale. The example of M51 shows that streaming motions, triggered by gravitational instabilities in the form of bars and spiral arms, can alter the star formation law; this can explain the variation in gas depletion time among galaxies with different masses and morphologies. In particular, we can explain the long gas depletion times in spiral galaxies compared with dwarf galaxies and starbursts. We suggest that adding a dynamical pressure term to the canonical free-fall time produces a single star formation law that can be applied to all star-forming regions and galaxies across cosmic time.

  18. Multistep Molecular Dynamics Simulations Identify the Highly Cooperative Activity of Melittin in Recognizing and Stabilizing Membrane Pores.

    Science.gov (United States)

    Sun, Delin; Forsman, Jan; Woodward, Clifford E

    2015-09-01

    The prototypical antimicrobial peptide, melittin, is well-known for its ability to induce pores in zwitterionic model lipid membranes. However, the mechanism by which melittin accomplishes this is not fully understood. We have conducted all-atom and coarse-grained molecular dynamics simulations which suggest that melittin employs a highly cooperative mechanism for the induction of both small and large membrane pores. The process by which this peptide induces membrane pores appears to be driven by its affinity to membrane defects via its N-terminus region. In our simulations, a membrane defect was deliberately created through either lipid flip-flop or the reorientation of one adsorbed melittin peptide. In a cooperative response, other melittin molecules also inserted their N-termini into the created defect, thus lowering the overall free energy. The insertion of these peptide molecules ultimately allowed the defect to develop into a small transmembrane pore, with an estimated diameter of ∼1.5 nm and a lifetime of the order of tens of milliseconds. In the presence of a finite membrane tension, we show that this small pore can act as a nucleation site for the stochastic rupture of the lipid bilayer, so as to create a much larger pore. We found that a threshold membrane tension of 25 mN/m was needed to create a ruptured pore. Furthermore, by actively accumulating at its edge, adsorbed peptides are able to cooperatively stabilize this larger pore. The defect-mediated pore formation mechanism revealed in this work may also apply to other amphipathic membrane-active peptides. PMID:26267389

  19. Probing Molecular Interactions of Asphaltenes in Heptol Using a Surface Forces Apparatus: Implications on Stability of Water-in-Oil Emulsions.

    Science.gov (United States)

    Zhang, Ling; Shi, Chen; Lu, Qingye; Liu, Qingxia; Zeng, Hongbo

    2016-05-17

    The behaviors and molecular interactions of asphaltenes are related to many challenging issues in oil production. In this study, the molecular interaction mechanism of asphaltenes in Heptol solvents of varying toluene/n-heptane ratio were directly measured using a surface forces apparatus (SFA). The results showed that the interactions between asphaltene surfaces gradually changed from pure repulsion to weak adhesion as the weight ratio of toluene (ω) in Heptol decreased from ω = 1 to 0. The measured repulsion was mainly due to the steric interactions between swelling asphaltene molecules and/aggregates. The micropipet technique was applied to test the stability of two water-in-oil emulsion droplets attached to glass pipettes. A computer-controlled 4-roll mill fluidic device was also built in-house to investigate the interaction of free-suspending water-in-oil emulsions under dynamic flow conditions. Both micropipet and 4-roll mill fluidic tests demonstrate that asphaltenes adsorbed at oil/water interfaces play a critical role in stabilizing the emulsion drops, in agreement with the repulsion measured between asphaltene surfaces in toluene using SFA, and that interfacial sliding or shearing is generally required to destabilize the protective interfacial apshaltene layers which facilitates the coalescence of emulsion drops. Our results provide insights into the fundamental understanding of molecular interaction mechanisms of asphaltenes in organic solvents and stabilization/destabilization behaviors of water-in-oil emulsions with asphaltenes. PMID:27128395

  20. Stabilization of coacervate systems by products of abiogenic oxidation of low-molecular-weight compounds using the energy of. gamma. radiation

    Energy Technology Data Exchange (ETDEWEB)

    Evreinova, T.N.; Kuzin, A.M.; Kryukova, L.M.; Kameneva, T.G.; Khrust, Yu.R.

    1976-01-01

    The purpose of the study was to determine the possibility of stabilization of protein-carbohydrate and protein-nucleic acid systems by products of the abiogenic oxidation of pyrocatechol, pyrogallol, and o-dianisidine using the energy of gamma radiation. The protein-nucleic acid system was produced by mixing the following reagents: histone, DNA, acetate buffer, and a solution of oxidized compounds. The protein-carbohydrate system was produced by mixing the following reagents: histone, gum arabic, acetate buffer, and a solution of oxidized compounds. Results indicated that the stabilization of coacervate systems occurs when stabilizing low-molecular-weight compounds of the type of quinones and the imino form of o-dianisidine are included in them. These compounds may be formed under the action of physical factors without the participation of enzymes. (HLW)

  1. New aspects on stability Analysis of a planar charge - varying collisional dust molecular cloud with finite thermal inertia

    International Nuclear Information System (INIS)

    A theoretical evolutionary model for the nonlinear stability analysis of a planar dust molecular cloud (DMC) in quasi-neutral hydrodynamic equilibrium on the Jeans scales of space and time is developed. It is based on a self-gravitating multi-fluid model consisting of the warm electrons and ions, and the inertial cold dust grains with partial ionization. The Jeans assumption of self-gravitating uniform medium is adopted for fiducially analytical simplification by neglecting the zero-order field. So, the equilibrium is justifiably treated initially as “homogeneous”, thereby validating nonlinear local analysis. The lowest-order finite inertial correction of the thermal species (thermal inertia, which is conventionally neglected), heavier grain-charge fluctuation and all the possible collisional dynamics are included simultaneously amid non-equilibrium plasma inhomogeneities. We apply a standard multiple scaling technique methodologically to show that the Eigenmodes are collectively governed by a new electrostatic driven Korteweg-de Vries (d-KdV) equation having a self-consistent nonlinear driving source, and self-gravitational Korteweg-de Vries (KdV) equation with neither a source, nor a sink. A detailed numerical shape - analysis with judicious multi-parameter variation parametrically portrays the excitation of electrostatic Eigenmodes evolving as damped oscillatory shocks (nonconservative) with the increasing global amplitude due to the source, and extended two-tail compressive solitons (conservative), when the source-strength becomes very weak. In contrast, the self-gravitational counterparts grow as bell-shaped rarefactive soliton-like structures (conservative). The correlative effect of diverse plasma parameters on the amplitudes and patterns is explicitly investigated. Interestingly, this is conjectured that the grain-mass plays a key role in the Eigenmode shaping (growth and decay) through the interplaying processes of pulsating gravito

  2. Impact of pH on molecular structure and surface properties of lentil legumin-like protein and its application as foam stabilizer.

    Science.gov (United States)

    Jarpa-Parra, M; Bamdad, F; Tian, Z; Zeng, Hongbo; Temelli, Feral; Chen, L

    2015-08-01

    The capacity of a protein to form and stabilize foams and emulsions depends on its structural characteristics and its physicochemical properties. The structural properties of lentil legumin-like protein including molecular weight, hydrodynamic size, surface charge and hydrophobicity, and conformation were studied in relation to its air-water interfacial behaviors. Kinetics study suggested that the foaming stability was closely related to the surface conformation of the protein that strongly affected adsorption and re-organization of the protein layer at the air-water interface. Foams prepared at neutral pH showed dense and strong networks at the interface, where combination of the α-helix secondary structure, medium hydrodynamic molecular size, and balance between solubility/hydrophobicity all contributed to the formation of such strong protein network at the interface. At pH 5.0, the protein formed a dense and thick network composed of randomly aggregated protein particles at the air-water interface. Whereas at pH 3.0, the unordered structure increased intra-protein flexibility producing a less compact and relaxed interface that reduces elasticity modulus with time and reduced foam resistance against collapse. This research revealed that lentil legumin-like protein could form long-life foams at mild acidic and neutral pH. The potential for use of lentil protein as a novel foaming plant-based stabilizer is demonstrated in food and non-food applications where stable, long-life foams are required. PMID:26005930

  3. The coupling between stability and ion pair formation in magnesium electrolytes from first-principles quantum mechanics and classical molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Rajput, Nav Nidhi; Qu, Xiaohuui; Sa, Niya; Burrell, Anthony K.; Persson, Kristin A.

    2015-03-11

    In this work we uncover a novel effect between concentration dependent ion pair formation and anion stability at reducing potentials, e.g., at the metal anode. Through comprehensive calculations using both first-principles as well as well-benchmarked classical molecular dynamics over a matrix of electrolytes, covering solvents and salt anions with a broad range in chemistry, we elucidate systematic correlations between molecular level interactions and composite electrolyte properties, such as electrochemical stability, solvation structure, and dynamics. We find that Mg electrolytes are highly prone to ion pair formation, even at modest concentrations, for a wide range of solvents with different dielectric constants, which have implications for dynamics as well as charge transfer. Specifically, we observe that, at Mg metal potentials, the ion pair undergoes partial reduction at the Mg cation center (Mg2+ -> Mg+), which competes with the charge transfer mechanism and can activate the anion to render it susceptible to decomposition. Specifically, TFSI exhibits a significant bond weakening while paired with the transient, partially reduced Mg+. In contrast, BH4 and BF4 are shown to be chemically stable in a reduced ion pair configuration. Furthermore, we observe that higher order glymes as well as DMSO improve the solubility of Mg salts, but only the longer glyme chains reduce the dynamics of the ions in solution. This information provides critical design metrics for future electrolytes as it elucidates a close connection between bulk solvation and cathodic stability as well as the dynamics of the salt.

  4. The Effect of Small Cosolutes that Mimic Molecular Crowding Conditions on the Stability of Triplexes Involving Duplex DNA

    OpenAIRE

    Aviñó, Anna; Mazzini, Stefania; Gargallo, Raimundo; Eritja, Ramon

    2016-01-01

    Triplex stability is studied in crowding conditions using small cosolutes (ethanol, acetonitrile and dimethylsulfoxide) by ultraviolet (UV), circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The results indicate that the triplex is formed preferentially when the triplex forming oligonucleotide (TFO) is RNA. In addition, DNA triplexes (D:D·D) are clearly less stable in cosolute solutions while the stability of the RNA triplexes (R:D·D) is only slightly decreased. The...

  5. A combined molecular dynamic and quantum mechanic study of the solvent and guest molecule effect on the stability and length of heterocyclic peptide nanotubes.

    Science.gov (United States)

    Izadyar, Mohammad; Khavani, Mohammad; Housaindokht, Mohammad Reza

    2015-05-01

    Molecular dynamic simulations were performed to investigate the stability of heterocyclic peptide nanotubes composed of 1,4-disubstituted-1,2,3-triazol ε-amino acid. 45 ns MD simulations were conducted on the cyclic peptide nanotube (CPNT) and cyclic peptide dimer in methanol, chloroform, and water and revealed that these structures are more stable in nonpolar solvents. MM-PBSA and MM-GBSA calculations were employed to analyze the solvent effect on the stability and length of the CPNT. These calculations showed that CPNT in chloroform was more stable and longer as compared to other solvents. In addition, the effect of the guest molecule (ethanol) inside the dimer and CPNT was investigated. The obtained results confirmed that guest molecule(s) stabilized the dimer and CPNT in all solvents. Quantum chemistry calculations on the cyclic peptide dimer were performed at the M06-2X/6-31G(d) level in the gas phase and three solvents. The obtained results from the quantum chemistry study were in good agreement with the MD simulation results. DFT calculations showed that the guest molecule stabilized the dimer structure and electrostatically interacted with the cyclic peptide dimer. Finally, for investigation of the solvent effects on the hydrogen bonds of the cyclic peptide dimer, NBO and AIM analysis were performed.

  6. Substituent effect on the molecular stability,group interaction,detonation performance,and thermolysis mechanism of nitroamino-substituted cyclopentanes and cyclohexanes

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Density functional theory (DFT) method has been employed to study the effect of nitroamino group as a substituent in cyclopentane and cyclohexane, which usually construct the polycyclic or caged nitra-mines. Molecular structures were investigated at the B3LYP/6-31G** level, and isodesmic reactions were designed for calculating the group interactions. The results show that the group interactions ac-cord with the group additivity, increasing with the increasing number of nitroamino groups. The dis-tance between substituents influences the interactions. Detonation performances were evaluated by the Kamlet-Jacobs equations based on the predicted densities and heats of formation, while thermal stability and pyrolysis mechanism were studied by the computations of bond dissociation energy (BDE). It is found that the contributions of nitroamino groups to the detonation heat, detonation velocity, detonation pressure, and stability all deviate from the group additivity. Only 3a, 3b, and 9a-9c may be novel potential candidates of high energy density materials (HEDMs) according to the quantitative cri-teria of HEDM (ρ≈ 1.9 g/cm3, D ≈ 9.0 km/s, P ≈ 40.0 GPa). Stability decreases with the increasing number of N-NO2 groups, and homolysis of N-NO2 bond is the initial step in the thermolysis of the title com-pounds. Coupled with the demand of thermal stability (BDE > 20 kcal/mol), only 1,2,4-trinitrotriazacy-clohexane and 1,2,4,5-tetranitrotetraazacyclohexane are suggested as feasible energetic materials. These results may provide basic information for the molecular design of HEDMs.

  7. 55th Annual Canadian Society for Molecular Biosciences Conference on Epigenetics and Genomic Stability. Whistler, British Columbia, Canada, 14–18 March 2012.

    Science.gov (United States)

    Nelson, Christopher J; Ausió, Juan

    2012-06-01

    The 55th Annual Canadian Society for Molecular Biosciences Conference on Epigenetics and Genomic Stability in Whistler, Canada, 14-18 March 2012, brought together 31 speakers from different nationalities. The organizing committee, led by Jim Davie (Chair) at the University of Manitoba (Manitoba, Canada), consisted of several established researchers in the fields of chromatin and epigenetics from across Canada. The meeting was centered on the contribution of epigenetics to gene expression, DNA damage and repair, and the role of environmental factors. A few interesting talks on replication added some insightful information on the controversial issue of histone post-translational modifications as genuine epigenetic marks that are inherited through cell division.

  8. Role of Hydrophobic Mutations on the Binding Affinity and Stability of Blood Coagulation Factor VIIIa: A Computational Molecular Dynamics and Free-Energy Analysis

    OpenAIRE

    Venkateswarlu, Divi

    2014-01-01

    Factor VIIIa is a non-covalently bound hetero-trimer among A1, A2 and A3-C1-C2 domains and an essential co-factor for factor IXa enzyme during proteolytic activation of factor X zymogen. The relatively weak interactions between A2 and the interface A1/A3 domains dampen the functional stability of FVIIIa in plasma and results in rapid degradation. We studied the mutational effect of three charged residues (Asp519, Glu665 and Asp666) to several hydrophobic residues by molecular dynamics simulat...

  9. Bisindeno-annulated pentacenes with exceptionally high photo-stability and ordered molecular packing: Simple synthesis by a regio-selective Scholl reaction

    KAUST Repository

    Naibi Lakshminarayana, Arun

    2015-01-01

    Bisindeno-annulated pentacenes 3a and 3b were synthesized by a simple regio-selective, FeCl3-mediated Scholl reaction from the corresponding 6,13-diaryl pentacene precursors. The fusion of two indeno-units dramatically changes the electronic properties and chemical reactivity of pentacene and the obtained compounds exhibited exceptionally high photo-stability in the solution, with a half-life time of 11.2 (3a) and 32.0 (3b) days under ambient light and air conditions. Ordered molecular packing with a small π-π stacking distance was observed in the single crystals of 3a and 3b. Our research provides a promising strategy to access stable higher order acenes with controlled molecular order. This journal is

  10. Processing stability of cross-linked starches in acid sauce applications and identification of some of the molecular factors involved

    NARCIS (Netherlands)

    Steeneken, P.A.M.; Woortman, A.J.J.; Oudhuis, A.A.C.M.

    2011-01-01

    The thickening functionality of four acetylated di-starch adipates with variations in starch source and amylose and adipate contents was evaluated in a simplified small-scale model sauce system at fourteen processing conditions with variations in temperature, shear, and pH. A processing stability fa

  11. Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase.

    Science.gov (United States)

    Sharma, Reetu; Sastry, G Narahari

    2015-01-01

    Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant's functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies.

  12. Deciphering the Dynamics of Non-Covalent Interactions Affecting Thermal Stability of a Protein: Molecular Dynamics Study on Point Mutant of Thermus thermophilus Isopropylmalate Dehydrogenase.

    Directory of Open Access Journals (Sweden)

    Reetu Sharma

    Full Text Available Thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. Substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. Exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. In this study dynamic changes in the non-covalent interactions are studied to decipher the deterministic features of thermal stability of a protein considering a case study of a point mutant in Thermus thermophilus isopropylmalate dehydrogenase. A total of four molecular dynamic simulations of 0.2 μs were carried out on wild type and mutant's functional dimers at 300 K and 337 K. Higher thermal stability of the mutant as compared to wild type is revealed by root mean square deviation, root mean square fluctuations and Cα-Cα distance with an increase in temperature from 300 K to 337 K. Most of the regions of wild type fluctuate higher than the corresponding regions of mutant with an increase in temperature. Cα-Cα distance analysis suggests that long distance networks are significantly affected in wild type as compared to the mutant. Short lived contacts are higher in wild type, while long lived contacts are lost at 337 K. The mutant forms less hydrogen bonds with water as compared to wild type at 337 K. In contrast to wild type, the mutant shows significant increase in unique saltbridges, hydrogen bonds and hydrophobic contacts at 337 K. The current study indicates that there is a strong inter-dependence of thermal stability on the way in which non-covalent interactions reorganize, and it is rewarding to explore this connection in single mutant studies.

  13. ALS as a distal axonopathy : molecular mechanisms affecting neuromuscular junction stability in the presymptomatic stages of the disease

    NARCIS (Netherlands)

    Moloney, Elizabeth B; de Winter, Fred; Verhaagen, J.

    2014-01-01

    Amyotrophic Lateral Sclerosis (ALS) is being redefined as a distal axonopathy, in that many molecular changes influencing motor neuron degeneration occur at the neuromuscular junction (NMJ) at very early stages of the disease prior to symptom onset. A huge variety of genetic and environmental causes

  14. Structure, dynamics and stability of water/scCO2/mineral interfaces from ab initio molecular dynamics simulations

    OpenAIRE

    Mal-Soon Lee; B. Peter McGrail; Roger Rousseau; Vassiliki-Alexandra Glezakou

    2015-01-01

    The boundary layer at solid-liquid interfaces is a unique reaction environment that poses significant scientific challenges to characterize and understand by experimentation alone. Using ab initio molecular dynamics (AIMD) methods, we report on the structure and dynamics of boundary layer formation, cation mobilization and carbonation under geologic carbon sequestration scenarios (T = 323 K and P = 90 bar) on a prototypical anorthite (001) surface. At low coverage, water film formation is ent...

  15. Effect of halogen substitutions on dUMP to stability of thymidylate synthase/dUMP/mTHF ternary complex using molecular dynamics simulation.

    Science.gov (United States)

    Kaiyawet, Nopporn; Rungrotmongkol, Thanyada; Hannongbua, Supot

    2013-06-24

    The stability of the thymidylate synthase (TS)/2-deoxyuridine-5-monophosphate (dUMP)/5,10-methylene-5,6,7,8-tetrahydrofolate (mTHF) ternary complex formation and Michael addition are considered as important steps that are involved in the inhibition mechanism of the anticancer prodrug 5-fluorouracil (5-FU). Here, the effect of three different halogen substitutions on the C-5 position of the dUMP (XdUMPs = FdUMP, CldUMP, and BrdUMP), the normal substrate, on the stability of the TS/dUMP and TS/dUMP/mTHF binary and ternary complexes, respectively, was investigated via molecular dynamics simulation. The simulated results revealed that the stability of all the systems was substantially increased by mTHF binding to the catalytic pocket. In the ternary complex, a much greater stabilization of the dUMP and XdUMPs through electrostatic interactions, including charge-charge and hydrogen bond interactions, was found compared to mTHF. An additional unique hydrogen bond between the substituted fluorine of FdUMP and the hydroxyl group of the TS Y94 residue was observed in both the binary and ternary complexes. The distance between the S(-) atom of the TS C146 residue and the C6 atom of dUMP, at PBSA binding free energy revealed the significant role of the bridging waters around the ligands in the increased binding affinity (∼10 kcal/mol) of dUMP/XdUMP, either alone or together with mTHF, toward TS. The order of the averaged binding affinity in the ternary systems was found to be CldUMP ≈ FdUMP > dUMP > BrdUMP, suggesting that CldUMP could be a potent candidate TS inhibitor, the same as FdUMP (the metabolite form of 5-FU). PMID:23705822

  16. Investigation of the impact of annealing on global molecular mobility in glasses: optimization for stabilization of amorphous pharmaceuticals.

    Science.gov (United States)

    Luthra, Suman A; Hodge, Ian M; Pikal, Michael J

    2008-09-01

    The purpose of this research was to investigate the effect of annealing on the molecular mobility in lyophilized glasses using differential scanning calorimetry (DSC) and isothermal microcalorimetry (IMC) techniques. A second objective that emerged was a systematic study of the unusual pre-T(g) thermal events that were observed during DSC warming scans after annealing. Aspartame lyophilized with three different excipients; sucrose, trehalose and poly vinyl pyrrolidone (PVP) was studied. The aim of this work was to quantify the decrease in mobility in amorphous lyophilized aspartame formulations upon systematic postlyophilization annealing. DSC scans of aspartame:sucrose formulation (T(g) = 73 degrees C) showed the presence of a pre-T(g) endotherm which disappeared upon annealing. Aspartame:trehalose (T(g) = 112 degrees C) and aspartame:PVP (T(g) = 100 degrees C) showed a broad exotherm before T(g) and annealing caused appearance of endothermic peaks before T(g). This work also employed IMC to measure the global molecular mobility represented by structural relaxation time (tau(beta)) in both un-annealed and annealed formulations. The effect of annealing on the enthalpy relaxation of lyophilized glasses, as measured by DSC and IMC, was consistent with the behavior predicted using the Tool-Narayanaswamy-Moynihan (TNM) phenomenology (Luthra et al., 2007, in press). The results show that the systems annealed at T(g) -15 degrees C to T(g) -20 degrees C have the lowest molecular mobility. PMID:18200533

  17. Sterility, mechanical properties, and molecular stability of polylactide internal-fixation devices treated with low-temperature plasmas.

    Science.gov (United States)

    Gogolewski, S; Mainil-Varlet, P; Dillon, J G

    1996-10-01

    The effect of low-temperature plasma on sterility, molecular, mechanical, and crystalline properties of poly (L-lactide), poly (L/D-lactide) and poly (L/DL-lactide) was investigated. Polymers were treated for 15 and 30 min at 100 W with nitrogen, argon, oxygen, and carbon dioxide plasma. All polymers treated with oxygen or carbon dioxide plasma were rendered sterile after 15 min of treatment. Only 70% of the samples treated under similar conditions with nitrogen or argon plasma were sterile. Extension of the exposure time to 30 min and increasing power to 200 W did not improve sterilization efficiency. Plasma sterilization, under the conditions used, caused no significant decrease or increase in overall molecular weight or polydispersity of the polylactides used. In most instances the effect of plasma sterilization was to slightly increase the overall molecular weight of the polymers studied. Treatment with argon plasma led to a more consistent increase in molecular weight than did treatment with nitrogen, oxygen, or carbon dioxide. Analysis of the surface (skin) of a poly(L-lactide) injection-molded rod following plasma sterilization indicated an increase in molecular weight as related to the interior (core) of the rod. Comparison of Mark-Houwink plots for the surface and interior of poly(L-lactide) injection-molded rods following plasma sterilization indicated an increase in chain branching for the surface relative to the interior of the rod. Generally the highly crystalline poly(L-lactide) was less susceptible to change upon plasma treatment than was the less crystalline poly(L/D-lactide) and poly(L/DL-lactide). The mechanical properties (shear strength, bending strength, and moduli) of the polylactides were not affected by plasma treatment. The overall melting temperature and the heat of melting of polylactides studied were not affected by plasma treatment. The melting temperature of the skin of the samples was about 1 degree C higher than the melting

  18. Final Report: Manganese Redox Mediation of UO2 Stability and Uranium Fate in the Subsurface: Molecular and Meter Scale Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Tebo, Bradley M. [OSHU; Tebo, Bradley M.

    2014-09-02

    One strategy to remediate U contamination in the subsurface is the immobilization of U via injection of an electron donor, e.g., acetate, which leads to stimulation of the bioreduction of U(VI), the more mobile form of U, to U(IV), the less mobile form. This process is inevitably accompanied by the sequential reductive dissolution of Mn and Fe oxides and often continuing into sulfate-reducing conditions. When these reducing zones, which accumulate U(IV), experience oxidizing conditions, reduced Fe and Mn can be reoxidized forming Fe and Mn oxides that, along with O2, can impact the stability of U(IV). The focus of our project has been to investigate (i) the effects of Mn(II) on the dissolution of UO2 under both reducing and oxidizing conditions, (ii) the oxidative dissolution of UO2 by soluble Mn(III), (iii) the fate of U once it is oxidized by MnO2 in both laboratory and field settings, and (iv) the effects of groundwater constituents on the coupled Mn(II)/U(IV) oxidation process. Additionally, studies of the interaction of Se, found at the DOE site at Rifle, CO, and Mn cycling were initiated to understand if observed seasonal fluctuations of Se and Mn are directly linked and whether any such linkages can affect the stability of U(IV).

  19. Molecular anions of polydeprotonated naphthalenes: An investigation on the metastability and deprotonation energies using nuclear-charge stabilization method

    Energy Technology Data Exchange (ETDEWEB)

    Sangwan, Poonam; Vikas, E-mail: qlabspu@pu.ac.in, E-mail: qlabspu@yahoo.com [Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigrah 160014 (India)

    2016-01-28

    The dianions and trianions of doubly- and triply-deprotonated naphthalenes are investigated using density functional theory (DFT) computations employing hybrid, long-range, and dispersion corrected exchange-correlation functionals. The investigated polyanionic species are found to be metastable with negative electron affinity and are further treated using a nuclear-charge stabilization method. The tunneling lifetimes of these anionic species were estimated to be a few femtoseconds. Notably, the deprotonated energies (DPEs) of naphthalene leading to the formation of triply deprotonated trianions are observed to be affected by the metastability of the dianions and trianions. For the deprotonation of doubly deprotonated dianions, the DPE calculated using the improved methodology based on the stabilization method is found to be nearly 100 kcal/mol more than that computed using the conventional procedure. Though the various DFT approximations employed are in a good agreement for predicting the lifetimes of the metastable species but in the prediction of electron-affinities and deprotonation energies, the dispersion-corrected DFT-D3 significantly disagrees with the long-range corrected DFT methods employing cam-B3LYP and ωB97XD exchange-correlation functionals.

  20. Study of iron structure stability in high temperature molten lead-bismuth eutectic with oxygen injection using molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Arkundato, Artoto [Physics Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Su' ud, Zaki [Physics Department, Faculty of Mathematical and Natural Sciences, Bandung Institute of Technology, Jl. Ganesha 10, Bandung (Indonesia); Sudarko [Chemistry Department, Faculty of Mathematical and Natural Sciences, Jember University, Jl. Kalimantan 37 Jember (Indonesia); Shafii, Mohammad Ali [Physics Department, Faculty of Mathematical and Natural Sciences, Andalas University, Padang (Indonesia); Celino, Massimo [ENEA, CR Casaccia, Via Anguillarese 301, Rome (Italy)

    2014-09-30

    Corrosion of structural materials in high temperature molten lead-bismuth eutectic is a major problem for design of PbBi cooled reactor. One technique to inhibit corrosion process is to inject oxygen into coolant. In this paper we study and focus on a way of inhibiting the corrosion of iron using molecular dynamics method. For the simulation results we concluded that effective corrosion inhibition of iron may be achieved by injection 0.0532 wt% to 0.1156 wt% oxygen into liquid lead-bismuth. At this oxygen concentration the structure of iron material will be maintained at about 70% in bcc crystal structure during interaction with liquid metal.

  1. Assessing protein stability of the dimeric DNA-binding domain of E2 human papillomavirus 18 with molecular dynamics

    OpenAIRE

    Raúl Isea; José Luis Ramírez; Johan Hoebeke

    2010-01-01

    The objective of this study is to understand the structural flexibility and curvature of the E2 protein of human papillomavirus type 18 using molecular dynamics (6 ns). E2 is required for viral DNA replication and its disruption could be an anti-viral strategy. E2 is a dimer, with each monomer folding into a stable open-faced β-sandwich. We calculated the mobility of the E2 dimer and found that it was asymmetric. These different mobilities of E2 monomers suggest that drugs or vaccines co...

  2. Assessing protein stability of the dimeric DNA-binding domain of E2 human papillomavirus 18 with molecular dynamics

    Directory of Open Access Journals (Sweden)

    Raúl Isea

    2010-03-01

    Full Text Available The objective of this study is to understand the structural flexibility and curvature of the E2 protein of human papillomavirus type 18 using molecular dynamics (6 ns. E2 is required for viral DNA replication and its disruption could be an anti-viral strategy. E2 is a dimer, with each monomer folding into a stable open-faced β-sandwich. We calculated the mobility of the E2 dimer and found that it was asymmetric. These different mobilities of E2 monomers suggest that drugs or vaccines could be targeted to the interface between the two monomers.

  3. Assessing protein stability of the dimeric DNA-binding domain of E2 human papillomavirus 18 with molecular dynamics.

    Science.gov (United States)

    Isea, Raúl; Ramírez, José Luis; Hoebeke, Johan

    2010-03-01

    The objective of this study is to understand the structural flexibility and curvature of the E2 protein of human papillomavirus type 18 using molecular dynamics (6 ns). E2 is required for viral DNA replication and its disruption could be an anti-viral strategy. E2 is a dimer, with each monomer folding into a stable open-faced beta-sandwich. We calculated the mobility of the E2 dimer and found that it was asymmetric. These different mobilities of E2 monomers suggest that drugs or vaccines could be targeted to the interface between the two monomers. PMID:20428668

  4. Role of hydrophobic mutations on the binding affinity and stability of blood coagulation factor VIIIa: a computational molecular dynamics and free-energy analysis.

    Science.gov (United States)

    Venkateswarlu, Divi

    2014-07-18

    Factor VIIIa is a non-covalently bound hetero-trimer among A1, A2 and A3-C1-C2 domains and an essential co-factor for factor IXa enzyme during proteolytic activation of factor X zymogen. The relatively weak interactions between A2 and the interface A1/A3 domains dampen the functional stability of FVIIIa in plasma and results in rapid degradation. We studied the mutational effect of three charged residues (Asp519, Glu665 and Asp666) to several hydrophobic residues by molecular dynamics simulations. Analysis of the binding free energy by MM-PBSA and MM-GBSA methods shows that the mutation of Asp519 and Glu665 residues to either Val or Ala enhance the A2 domain binding affinity in agreement with the experimental site-specific mutagenesis data. Mutation of Asp666 to Val, Tyr, Met and Phe showed largest improvement in the A2-domain binding among the eight hydrophobic mutants studied. Our studies suggest that the enrichment of hydrophobic interactions in the buried surface regions of A2 domain plays crucial role in improving the overall stability of FVIIIa. PMID:24952158

  5. Stability of the β-structure in prion protein: A molecular dynamics study based on polarized force field

    Science.gov (United States)

    Xu, Zhijun; Lazim, Raudah; Mei, Ye; Zhang, Dawei

    2012-06-01

    Conformational changes of the antiparallel β-sheet in normal cellular prion protein (PrPC) of rat, bovine, and human are investigated by molecular dynamics simulations in both neutral and acidic environment. Using a recently developed simulation method based on an on-the-fly polarized protein-specific charge (PPC) update scheme during the simulation process, we evaluate and compare the cross-species performances of the β-sheet during the early stage transition from the PrPC to its mutant configuration. Through this study, we observe the growth of the β-sheet structure in all species studied with the extent of elongation in β-sheet being different across the three species.

  6. Stability of transmembrane amyloid β-peptide and membrane integrity tested by molecular modeling of site-specific Aβ42 mutations.

    Directory of Open Access Journals (Sweden)

    Chetan Poojari

    Full Text Available Interactions of the amyloid β-protein (Aβ with neuronal cell membranes, leading to the disruption of membrane integrity, are considered to play a key role in the development of Alzheimer's disease. Natural mutations in Aβ42, such as the Arctic mutation (E22G have been shown to increase Aβ42 aggregation and neurotoxicity, leading to the early-onset of Alzheimer's disease. A correlation between the propensity of Aβ42 to form protofibrils and its effect on neuronal dysfunction and degeneration has been established. Using rational mutagenesis of the Aβ42 peptide it was further revealed that the aggregation of different Aβ42 mutants in lipid membranes results in a variety of polymorphic aggregates in a mutation dependent manner. The mutant peptides also have a variable ability to disrupt bilayer integrity. To further test the connection between Aβ42 mutation and peptide-membrane interactions, we perform molecular dynamics simulations of membrane-inserted Aβ42 variants (wild-type and E22G, D23G, E22G/D23G, K16M/K28M and K16M/E22G/D23G/K28M mutants as β-sheet monomers and tetramers. The effects of charged residues on transmembrane Aβ42 stability and membrane integrity are analyzed at atomistic level. We observe an increased stability for the E22G Aβ42 peptide and a decreased stability for D23G compared to wild-type Aβ42, while D23G has the largest membrane-disruptive effect. These results support the experimental observation that the altered toxicity arising from mutations in Aβ is not only a result of the altered aggregation propensity, but also originates from modified Aβ interactions with neuronal membranes.

  7. MOLECULAR BIOLOGICAL EVIDENCES FOR THE GENETIC STABILITY OF DOXORUBICIN RESISTANT CELL LINE S-180R IN VIVO

    Institute of Scientific and Technical Information of China (English)

    Zheng Guoqiang; Han Fusheng; Zhang Tingjun; Zhan Maocheng; Chen Xiangling; Xu Guangwei

    1998-01-01

    Objective: In order to assess the genetic stability of doxorubicin resistance sarcoma S-180R cell line in vivo.Methods: The drug resistant genes and molecules were examined by flow cytometry, Southern blot, Northern blot and RT-PCR. Results: The results showed that drugefflux in S-180R increased nearly 100-folds, as compared with its parent cells, the rate of half peak width resistant cell/peak high decreased from 0.56 to 0.23 measured by flow cytometry after two years. The mdr1 gene amplified and overexpressed significantly in S-180R and the expression of topoisomerase Ⅱα gene decreased remarkably in S-180R. There was no significant different of the MRP expression between S-180R and S-180.Conclusion: These results indicated that drug resistance of S-180R was maintained and also increased. The major mechanism of drug resistance is the amplification and overexpression of mdr1 gene, the decreased expression of topoisomerase Ⅱα also contributed to it. So, S-180R is an ideal experimental model for the study of doxorubicin resistance and its reversion in vivo.

  8. 高稳定性介孔分子筛的合成与表征%SYNTHESIS AND CHARACTERIZATION OF HIGHLY STABILIZED MESOPOROUS MOLECULAR SIEVES

    Institute of Scientific and Technical Information of China (English)

    姜廷顺; 赵谦; 陆路德; 殷恒波

    2006-01-01

    Highly stabilized mesoporous molecular sieves were synthesized by the hydrothermal method using natural clay and sodium silicate as raw materials and cetyltrimethyl ammonium bromide as a template. The samples were characterized by means of X-ray diffraction, transmission electron microscopy, specific Surface area analysis, Fourier transform infrared spectroscopy and N2 physical adsorption. The results show that the synthesized mesoporous molecular sieve has a specific surface area over 550 m2/g and an average pore size of 2.72 nm. The pore structure is not damaged after calcination at 850 ℃ for 3 h or hydrothermal treatment at 100 ℃ for 10 d. The mesoporous ordering is improved, but the pores contract and the specific surface area decreases after hydrothermal treatment. The stability of the synthesized mesoporous molecular sieves is enhanced because natural clay was used as a raw material.%以天然黏土和硅酸钠为原料、十六烷基三甲基溴化铵为模板剂,水热法合成了有序性好的高稳定性介孔分子筛.用粉末X射线衍射、透射电镜、Fourier变换红外光谱和比表面积孔径分析等方法对所合成的介孔分子筛进行了表征.结果表明:所合成的介孔分子筛的比表面积大于550m2/g,平均孔径为2.72nm.样品经850℃焙烧3 h,100℃水热处理10 d,介孔分子筛的介孔结构没有被破坏,并且热处理使孔发生收缩,比表面积减小,水热处理使介孔的有序性变得更好,天然黏土为原料提高了介孔分子筛的水热稳定性.

  9. Quantum molecular dynamics: Numerical methods and physical study of the structure, thermodynamics, stability and fragmentation of sodium metallic clusters

    International Nuclear Information System (INIS)

    The aim of this thesis is to study metallic sodium clusters by numerical simulation. We have developed two ab initio molecular dynamics programs within the formalism of density functional theory. The first is based on the semi-classical extended Thomas-Fermi approach. We use a real-space grid and a Car-Parrinello-like scheme. The computational cost is O(N), and we have built a pseudopotential that speeds up the calculations. By neglecting quantum shell effects, we are able to study a very large set of clusters. We show that sodium cluster energies fit well a liquid drop formula, by adjusting a few parameters. We have investigated breathing modes, surface oscillations and the net charge density. We have shown that the surface energy varies strongly with temperature, and that clusters have a lower melting point than bulk material. We have calculated fission barriers by a constraint method. The second program is based on the quantum Kohn-Sham approach. We use a real-space grid, and combine a generalized Broyden scheme for assuring self-consistency with an iterative Davidson-Lanczos algorithm for solving the Eigen-problem. The cost of the method is much higher. First of all, we have calculated some stable structures for small clusters and their energetics. We obtained very good agreement with previous works. Then, we have investigated highly charged cluster dynamics. We have identified a chaotic fission process. For high fissility systems, we observe a multi-fragmentation dynamics and we find preferential emission of monomers on a characteristic time scale less than a pico-second. This has been simulated for the first time, with the help of our adaptive grid method which follows each fragment as they move apart during the fragmentation. (author)

  10. Experimental and molecular dynamics studies showed that CBP KIX mutation affects the stability of CBP:c-Myb complex.

    Science.gov (United States)

    Odoux, Anne; Jindal, Darren; Tamas, Tamara C; Lim, Benjamin W H; Pollard, Drake; Xu, Wu

    2016-06-01

    The coactivators CBP (CREBBP) and its paralog p300 (EP300), two conserved multi-domain proteins in eukaryotic organisms, regulate gene expression in part by binding DNA-binding transcription factors. It was previously reported that the CBP/p300 KIX domain mutant (Y650A, A654Q, and Y658A) altered both c-Myb-dependent gene activation and repression, and that mice with these three point mutations had reduced numbers of platelets, B cells, T cells, and red blood cells. Here, our transient transfection assays demonstrated that mouse embryonic fibroblast cells containing the same mutations in the KIX domain and without a wild-type allele of either CBP or p300, showed decreased c-Myb-mediated transcription. Dr. Wright's group solved a 3-D structure of the mouse CBP:c-Myb complex using NMR. To take advantage of the experimental structure and function data and improved theoretical calculation methods, we performed MD simulations of CBP KIX, CBP KIX with the mutations, and c-Myb, as well as binding energy analysis for both the wild-type and mutant complexes. The binding between CBP and c-Myb is mainly mediated by a shallow hydrophobic groove in the center where the side-chain of Leu302 of c-Myb plays an essential role and two salt bridges at the two ends. We found that the KIX mutations slightly decreased stability of the CBP:c-Myb complex as demonstrated by higher binding energy calculated using either MM/PBSA or MM/GBSA methods. More specifically, the KIX mutations affected the two salt bridges between CBP and c-Myb (CBP-R646 and c-Myb-E306; CBP-E665 and c-Myb-R294). Our studies also revealed differing dynamics of the hydrogen bonds between CBP-R646 and c-Myb-E306 and between CBP-E665 and c-Myb-R294 caused by the CBP KIX mutations. In the wild-type CBP:c-Myb complex, both of the hydrogen bonds stayed relatively stable. In contrast, in the mutant CBP:c-Myb complex, hydrogen bonds between R646 and E306 showed an increasing trend followed by a decreasing trend, and hydrogen

  11. The effects of threonine phosphorylation on the stability and dynamics of the central molecular switch region of 18.5-kDa myelin basic protein.

    Directory of Open Access Journals (Sweden)

    Kenrick A Vassall

    Full Text Available The classic isoforms of myelin basic protein (MBP are essential for the formation and maintenance of myelin in the central nervous system of higher vertebrates. The protein is involved in all facets of the development, compaction, and stabilization of the multilamellar myelin sheath, and also interacts with cytoskeletal and signaling proteins. The predominant 18.5-kDa isoform of MBP is an intrinsically-disordered protein that is a candidate auto-antigen in the human demyelinating disease multiple sclerosis. A highly-conserved central segment within classic MBP consists of a proline-rich region (murine 18.5-kDa sequence -T92-P93-R94-T95-P96-P97-P98-S99- containing a putative SH3-ligand, adjacent to a region that forms an amphipathic α-helix (P82-I90 upon interaction with membranes, or under membrane-mimetic conditions. The T92 and T95 residues within the proline-rich region can be post-translationally modified through phosphorylation by mitogen-activated protein (MAP kinases. Here, we have investigated the structure of the α-helical and proline-rich regions in dilute aqueous buffer, and have evaluated the effects of phosphorylation at T92 and T95 on the stability and dynamics of the α-helical region, by utilizing four 36-residue peptides (S72-S107 with differing phosphorylation status. Nuclear magnetic resonance spectroscopy reveals that both the α-helical as well as the proline-rich regions are disordered in aqueous buffer, whereas they are both structured in a lipid environment (cf., Ahmed et al., Biochemistry 51, 7475-9487, 2012. Thermodynamic analysis of trifluoroethanol-titration curves monitored by circular dichroism spectroscopy reveals that phosphorylation, especially at residue T92, impedes formation of the amphipathic α-helix. This conclusion is supported by molecular dynamics simulations, which further illustrate that phosphorylation reduces the folding reversibility of the α-helix upon temperature perturbation and affect the

  12. The effects of threonine phosphorylation on the stability and dynamics of the central molecular switch region of 18.5-kDa myelin basic protein.

    Science.gov (United States)

    Vassall, Kenrick A; Bessonov, Kyrylo; De Avila, Miguel; Polverini, Eugenia; Harauz, George

    2013-01-01

    The classic isoforms of myelin basic protein (MBP) are essential for the formation and maintenance of myelin in the central nervous system of higher vertebrates. The protein is involved in all facets of the development, compaction, and stabilization of the multilamellar myelin sheath, and also interacts with cytoskeletal and signaling proteins. The predominant 18.5-kDa isoform of MBP is an intrinsically-disordered protein that is a candidate auto-antigen in the human demyelinating disease multiple sclerosis. A highly-conserved central segment within classic MBP consists of a proline-rich region (murine 18.5-kDa sequence -T92-P93-R94-T95-P96-P97-P98-S99-) containing a putative SH3-ligand, adjacent to a region that forms an amphipathic α-helix (P82-I90) upon interaction with membranes, or under membrane-mimetic conditions. The T92 and T95 residues within the proline-rich region can be post-translationally modified through phosphorylation by mitogen-activated protein (MAP) kinases. Here, we have investigated the structure of the α-helical and proline-rich regions in dilute aqueous buffer, and have evaluated the effects of phosphorylation at T92 and T95 on the stability and dynamics of the α-helical region, by utilizing four 36-residue peptides (S72-S107) with differing phosphorylation status. Nuclear magnetic resonance spectroscopy reveals that both the α-helical as well as the proline-rich regions are disordered in aqueous buffer, whereas they are both structured in a lipid environment (cf., Ahmed et al., Biochemistry 51, 7475-9487, 2012). Thermodynamic analysis of trifluoroethanol-titration curves monitored by circular dichroism spectroscopy reveals that phosphorylation, especially at residue T92, impedes formation of the amphipathic α-helix. This conclusion is supported by molecular dynamics simulations, which further illustrate that phosphorylation reduces the folding reversibility of the α-helix upon temperature perturbation and affect the global structure

  13. The molecular organization of the beta-sheet region in Corneous beta-proteins (beta-keratins) of sauropsids explains its stability and polymerization into filaments.

    Science.gov (United States)

    Calvaresi, Matteo; Eckhart, Leopold; Alibardi, Lorenzo

    2016-06-01

    The hard corneous material of avian and reptilian scales, claws, beak and feathers is mainly derived from the presence of proteins formerly known as beta-keratins but now termed Corneous beta-proteins of sauropsids to distinguish them from keratins, which are members of the intermediate filament protein family. The modeling of the conserved 34 amino acid residues long central beta-sheet region of Corneous beta-proteins using an ab initio protein folding and structure prediction algorithm indicates that this region is formed by four antiparallel beta-sheets. Molecular dynamic simulations and Molecular Mechanics/Poisson Boltzmann Surface Area (MM-PBSA) analysis showed that the disposition of polar and apolar amino acids within the beta-region gives rise to an amphipathic core whose stability is further increased, especially in an aqueous environment, by the association into a dimer due to apolar interactions and specific amino-acid interactions. The dimers in turn polymerize into a 3nm thick linear beta-filament due to van der Waals and hydrogen-bond interactions. It is suggested that once this nuclear core of anti-parallel sheets evolved in the genome of a reptilian ancestor of the extant reptiles and birds about 300 millions years ago, new properties emerged in the corneous material forming scales, claws, beaks and feathers in these amniotes based on the tendency of these unique corneous proteins to form stable filaments different from keratin intermediate filaments or sterical structures formed by other corneous proteins so far known. PMID:26965557

  14. In Vitro Mass Multiplication and Assessment of Genetic Stability of In Vitro Raised Artemisia absinthium L. Plants Using ISSR and SSAP Molecular Markers

    Directory of Open Access Journals (Sweden)

    B. Kour

    2014-01-01

    Full Text Available The present investigations were made attempting to develop a rapid, reliable, and reproducible in vitro regeneration protocol for Artemisia absinthium L., a medicinal plant of Kashmir Himalayas. Out of several auxin-cytokinin combinations tested, Murashige and Skoog’s (MS medium supplemented with 0.5 mgL−1 2,4-dichlorophenoxyacetic acid (2,4-D and 0.5 mgL−1 kinetin (Kn was found to be the best for the callus induction. On the other hand, 4.5 mgL−1 6-benzylaminopurine (BAP and 0.5 mgL−1 1-α-naphthaleneacetic acid (NAA in the medium resulted in maximum shoot induction from the callus. Similarly, BAP and NAA at a concentration of 1.5 mgL−1 and 0.5 mgL−1, respectively, proved to be the best for the multiple shoot induction from nodal explants. Numerous shoots were obtained from nodal explants after third subculture. In vitro rooting was maximum on medium containing indole-3-butyric acid (IBA at 0.5 mgL−1. The genetic stability of the in vitro raised plants of Artemisia absinthium was assessed using the intersimple sequence repeat (ISSR and sequence-specific amplification polymorphism (SSAP molecular markers. Both markers were able to detect the somaclonal variations in the callus regenerated plants, while no variation was detected in the plants regenerated from the nodal explants. SSAP has been found to be more useful in detection of variability as compared to ISSR molecular marker. The results of present study concluded that the direct regeneration protocol will be useful for the production of true to type plants of this medicinally important plant. This will go a long way in reducing the pressure on the natural populations for the secondary metabolite production, especially for extraction of essential oils.

  15. Post Hartree-Fock studies of the canonical Watson-Crick DNA base pairs: molecular structure and the nature of stability.

    Science.gov (United States)

    Danilov, Victor I; Anisimov, Victor M

    2005-02-01

    Gas-phase gradient optimization was carried out on the canonical Watson-Crick DNA base pairs using the second-order Møller-Plesset perturbation method at the 6-31G(d) and 6-31G(d,p) basis sets. It is detected that full geometry optimization at the MP2 level leads to an intrinsically nonplanar propeller-twisted and buckled geometry of G-C and A-T base pairs; while HF and DFT methods predict perfect planar or almost planar geometry of the base pairs. Supposedly the nonplanarity of the pairs is caused by pyramidalization of the amino nitrogen atoms, which is underestimated by the HF and DFT methods. This justifies the importance of geometry optimization at the MP2 level for obtaining reliable prediction of the charge distribution, molecular dipole moments and geometrical structure of the base pairs. The Morokuma-Kitaura and the Reduced Variational Space methods of the decomposition for molecular HF interaction energies were used for investigation of the hydrogen bonding in the Watson-Crick base pairs. It is shown that the HF stability of the hydrogen-bonded DNA base pairs originates mainly from electrostatic interactions. At the same time, the calculated magnitude of the second order intramolecular correlation correction to the Coulomb energy showed that electron correlation reduces the contribution of the electrostatic term to the attractive interaction for the A-T and G-C base pairs. Polarization, charge transfer and dispersion interactions also make considerable contribution to the attraction energy of bases. PMID:15588110

  16. Low-molecular-weight fucoidan and high-stability fucoxanthin from brown seaweed exert prebiotics and anti-inflammatory activities in Caco-2 cells

    Directory of Open Access Journals (Sweden)

    Pai-An Hwang

    2016-08-01

    Full Text Available Background: The aim of this study is to investigate the anti-inflammatory effects of low-molecular-weight fucoidan (LMF and high-stability fucoxanthin (HS-Fucox in a lipopolysaccharide-induced inflammatory Caco-2 cell line co-culture with B. lactis. Methods: We used various methods such as transepithelial resistance (TER assay, cytokine secretion assay, and tight junction protein mRNA expression assay to examine LMF and HS-Fucox anti-inflammatory properties. Results: LMF and HS-Fucox activated probiotic growth and reduced the inflammation of the intestinal epithelial cells. Moreover, the combination of LMFHS-Fucox dramatically enhanced the intestinal epithelial barrier and immune function against the lipopolysaccharide effect by inhibiting IL-1β and TNF-α and promoting IL-10 and IFN-γ. Conclusion: These findings suggested that LMF and HS-Fucox, alone or in combination, could be the potential natural compounds to enhance the immune system and have an anti-inflammatory effect on the intestinal cells.

  17. Transient stability of the helical pattern of region F19-L22 of the N-terminal domain of p53: a molecular dynamics simulation study.

    Science.gov (United States)

    Espinoza-Fonseca, L Michel; Trujillo-Ferrara, José G

    2006-04-28

    Two molecular dynamics simulations of the region E17-N29 of p53 (p53(17-29)) at different temperatures were performed for a total time of 0.2 micros, to study the conformational landscape of this region. Previous studies have suggested that this region displays different structural motifs, such as helix of a double beta-turn, and that its secondary structure might be transiently stable. Interestingly, in this study it was found that the region F19-L25, and particularly its fragment F19-L22, display a stable, transient helical pattern at sub-microsecond periods. The region F19-L22, which contains one of the most important residues needed for the interaction of p53 with MDM2, seems to be formed and stabilized by the existence of one hydrophobic and one aromatic cluster. The main function of these clusters is to help their surrounding area to desolvate, to allow the hydrogen bond network, therefore favoring the formation of a stable helix. This preliminary study would be useful for a better understanding of the structure and function of the N-terminal domain of p53 and its implications for the control of different types of cancer. PMID:16530164

  18. Enhanced stability of a naringenin/2,6-dimethyl β-cyclodextrin inclusion complex: molecular dynamics and free energy calculations based on MM- and QM-PBSA/GBSA.

    Science.gov (United States)

    Sangpheak, Waratchada; Khuntawee, Wasinee; Wolschann, Peter; Pongsawasdi, Piamsook; Rungrotmongkol, Thanyada

    2014-05-01

    The structure, dynamic behavior and binding affinity of the inclusion complexes between naringenin and the two cyclodextrins (CDs), β-CD and its 2,6-dimethyl derivative (DM-β-CD), were theoretically studied by multiple molecular dynamics simulations and free energy calculations. Naringenin most likely prefers to bind with CDs through the phenyl ring. Although a lower hydrogen bond formation of naringenin with the 3-hydroxyl group of DM-β-CD (relative to β-CD) was observed, the higher cavity could encapsulate almost the whole naringenin molecule. In contrast for the naringenin/β-CD complex, the phenyl ring feasibly passed through the primary rim resulting in the chromone ring binding inside instead. MM-PBSA/GBSA and QM-PBSA/GBSA binding free energies strongly suggested a greater stability of the naringenin/DM-β-CD inclusion complex. Van der Waals force played an important role as the key guest-host interaction for the complexation between naringenin and each cyclodextrin. PMID:24681901

  19. Gas source molecular beam epitaxy and thermal stability of Si{sub 1-x} Ge{sub x}/Si superlattice materials

    Energy Technology Data Exchange (ETDEWEB)

    Zou, L.F.; Acosta-Ortiz, S.E. [Centro de Investigaciones en Optica A.C. Unidad Aguascalientes. Juan de Montoro No. 207. Zona Centro, 20000 Aguascalientes (Mexico); Zou, L.X. [Computer Science Department, Zhongnan University for Nationalities Wuhan, Hubei 430074 (China); Regalado, L.E. [Centro de Investigaciones en Optica, Loma del Bosque No. 115, Loma del Campestre C.P. 37000, Leon, Guanajuato (Mexico); Sun, D.Z.; Wang, Z.G. [Institute of Semiconductors, Chinese Academy of Sciences, Beijing 100083 (China)

    1998-12-31

    Gas source molecular beam epitaxy has been used to grow Si{sub 1-x} Ge{sub x} alloys and Si{sub 1-x} Ge{sub x}/Si multi-quantum wells (MQWs) on (100) Si substrates with Si{sub 2}H{sub 6} and GeH{sub 4} as sources. Heterostructures and MQWs with mirror-like surface morphology, good crystalline quality, and abrupt interfaces have been studied by a variety of in situ and ex situ techniques. The structural stability and strain relaxation in Si{sub 1-x} Ge{sub x}/ Si heterostructures have been investigated, and compared to that in the As ion-implanted Si{sub 1-x} Ge{sub x} epilayers. The results show that the strain relaxation mechanism of the non-implanted Si{sub 1-x} Ge{sub x} epilayers is different form that of the As ion-implanted Si{sub 1-x} Ge{sub x} epilayers. (Author)

  20. Structural Stability, Transitions, and Interactions within SoxYZCD-Thiosulphate from Sulfurimonas denitrificans: An In Silico Molecular Outlook for Maintaining Environmental Sulphur Cycle

    Science.gov (United States)

    Banerjee, Arundhati

    2016-01-01

    Thiosulphate oxidation (an essential mechanism) serves to maintain the global sulphur cycle. Earlier experimental and computational studies dealt with environmental thiosulphate oxidation but none dealt with thiosulphate oxidation from deep ocean belts. Wet-laboratory experimental research shows that epsilon-proteobacteria Sulfurimonas denitrificans possess sox (sulphur-oxidizing) operon and perform thiosulphate oxidation efficiently underneath the oceans. From this specific sox operon, SoxCD complex recycles the thiosulphate-bound SoxY from SoxYZ complex to balance the environmental sulphur cycle. So, four chief proteins were variedly modeled and relevant simulated interactive structures were obtained. The final simulated tetraprotein complex (SoxYZCD) from docked SoxYZ and SoxCD complexes was disclosed to be a highly interactive one with predominant ionic residues. Free energy of folding, solvent accessibility, and conformational shifts (coil-like conformation to helices and sheets) were observed in SoxYZ complex after interacting with SoxCD. The stability of the complex (SoxYZCD) after simulation was also observed through the electrostatic surface potential values. These evaluations were rationalized via biostatistics. This aids SoxCD for recycling SoxY along with thiosulphate, which remains interconnected by four H-bonds with SoxY. Therefore, this novel exploration is endowed with the detailed molecular viewpoint for maintaining the sulphur cycle (globally) including the ocean belts. PMID:27777586

  1. Molecular dynamics simulations on pars intercerebralis major peptide-C (PMP-C) reveal the role of glycosylation and disulfide bonds in its enhanced structural stability and function.

    Science.gov (United States)

    Kaushik, Sandeep; Mohanty, Debasisa; Surolia, Avadhesha

    2012-01-01

    Fucosylation of Thr 9 in pars intercerebralis major peptide-C (PMP-C) enhances its structural stability and functional ability as a serine protease inhibitor. In order to understand the role of disulfide bonds and glycosylation on the structure and function of PMP-C, we have carried out multiple explicit solvent molecular dynamics (MD) simulations on fucosylated and non-fucosylated forms of PMP-C, both in the presence and absence of the disulfide bonds. Our simulations revealed that there were no significant structural changes in the native disulfide bonded forms of PMP-C due to fucosylation. On the other hand, the non-fucosylated form of PMP-C without disulfide bonds showed larger deviations from the starting structure than the fucosylated form. However, the structural deviations were restricted to the terminal regions while core β-sheet retained its hydrogen bonded structure even in absence of disulfide bonds as well as fucosylation. Interestingly, fucosylation of disulfide bonded native PMP-C led to a decreased thermal flexibility in the residue stretch 29-32 which is known to interact with the active site of the target proteases. Our analysis revealed that disulfide bonds covalently connect the residue stretch 29-32 to the central β-sheet of PMP-C and using a novel network of side chain interactions and disulfide bonds fucosylation at Thr 9 is altering the flexibility of the stretch 29-32 located at a distal site. Thus, our simulations explain for the first time, how presence of disulfide bonds between conserved cysteines and fucosylation enhance the function of PMP-C as a protease inhibitor.

  2. Molecular beam epitaxy of the van der Waals heterostructure MoTe2 on MoS2: phase, thermal, and chemical stability

    Science.gov (United States)

    Coy Diaz, Horacio; Chaghi, Redhouane; Ma, Yujing; Batzill, Matthias

    2015-12-01

    (Sub)monolayer MoTe2 is grown by molecular beam epitaxy on a bulk MoS2 substrate. The film morphology, the thermally induced transformation of structural and compositional phases, as well as the chemical stability upon exposure to atmosphere are investigated by scanning tunneling microscopy and photoemission spectroscopy. Predominantly, semiconducting α-MoTe2 islands are obtained under tellurium rich growth conditions and a substrate temperature of 200 °C. Under less tellurium-rich conditions, elongated and meandering MoTe2-x strands are formed rather than compact islands. Similarly, annealing of initial α-MoTe2 islands to above 500 °C causes the loss of tellurium and possibly transformation into the same MoTe2-x strands. Consequently, under vacuum conditions the the transformation of α-MoTe2 monolayers into the semimetallic β -MoTe2 high temperature phase is accompanied by a loss of Te and formation of MoTe2-x phase. The obtained tellurium deficient MoTe2-x phase is almost metallic but a small band gap of a few tens meV remains. The as-grown α-MoTe2 islands exhibit a moiré structure with ˜2.6 nm periodicity. This periodicity implies a rotation of ˜56° between the MoTe2 and MoS2. We assign the observation of a specific rotation angle for the grown MoTe2 islands with respect to the MoS2 substrate to the lowest energy adsorption configuration for MoTe2 monolayers on MoS2 substrates. Exposure of the as grown films to atmosphere results in oxidation of the MoTe2 film. The oxidized film maintains the two-dimensional island morphology of the initial film and thus is a candidate for a 2D (amorphous) oxide layer on MoS2.

  3. Order through disorder: hyper-mobile C-terminal residues stabilize the folded state of a helical peptide. a molecular dynamics study.

    Directory of Open Access Journals (Sweden)

    Kalliopi K Patapati

    Full Text Available Conventional wisdom has it that the presence of disordered regions in the three-dimensional structures of polypeptides not only does not contribute significantly to the thermodynamic stability of their folded state, but, on the contrary, that the presence of disorder leads to a decrease of the corresponding proteins' stability. We have performed extensive 3.4 µs long folding simulations (in explicit solvent and with full electrostatics of an undecamer peptide of experimentally known helical structure, both with and without its disordered (four residue long C-terminal tail. Our simulations clearly indicate that the presence of the apparently disordered (in structural terms C-terminal tail, increases the thermodynamic stability of the peptide's folded (helical state. These results show that at least for the case of relatively short peptides, the interplay between thermodynamic stability and the apparent structural stability can be rather subtle, with even disordered regions contributing significantly to the stability of the folded state. Our results have clear implications for the understanding of peptide energetics and the design of foldable peptides.

  4. The identification and quantification of a high molecular weight light stabilizer in polycarbonate by application of an online coupling of size exclusion chromatography in stopped flow mode with pyrolysis gas chromatography time of flight mass spectroscopy.

    Science.gov (United States)

    Brander, Eric; Wold, Christian

    2014-10-01

    The identification and quantification of a high molecular weight light stabilizer (Uvinul 3030™) in an unknown polycarbonate sample was achieved through the application of SEC-Py-TOF-GCMS. A size exclusion column optimized to achieve resolution in the lower mass range was applied to allow the fractionation of an individual additive peak. A commercially available sampling interface was operated in stop flow mode and fractions were pyrolyzed to allow chromatographic separation of the fragments of the otherwise non-volatile stabilizer. After identification on the basis of accurate mass and elemental composition of the additive the quantification was compared using the available SEC-UV and SEC-PY-GC-TOFMS data. The resulting method provided a high degree of certainty in identification and flexibility in quantification expected to be applicable to other additives of similar volatilities or functional class.

  5. A bracket approach to improve the stability and gas sorption performance of a metal-organic framework via in situ incorporating the size-matching molecular building blocks.

    Science.gov (United States)

    Chen, Di-Ming; Tian, Jia-Yue; Liu, Chun-Sen; Du, Miao

    2016-06-28

    Incorporating the in situ formed size-matching molecular building blocks (MBBs) into the open channels will remarkably improve the robustness and gas sorption performance of an evacuated metal-organic framework. As a result, such MBBs can transfer the open metal sites from the framework walls to the channel centers and separate the large channels into multiple smaller voids, leading to a molecular sieving effect and high-performance gas-separation of the modified material. PMID:27301546

  6. Molecular dynamics simulations of aqueous urea solutions: Study of dimer stability and solution structure, and calculation of the total nitrogen radial distribution function GN(r

    NARCIS (Netherlands)

    Boek, E.S.; Briels, W.J.

    1993-01-01

    Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary

  7. Cable Stability

    CERN Document Server

    Bottura, L

    2014-01-01

    Superconductor stability is at the core of the design of any successful cable and magnet application. This chapter reviews the initial understanding of the stability mechanism, and reviews matters of importance for stability such as the nature and magnitude of the perturbation spectrum and the cooling mechanisms. Various stability strategies are studied, providing criteria that depend on the desired design and operating conditions.

  8. Effects of High-molecular Protein and Proteinase A on the Foam Stability of Pure Draft Beer%高分子蛋白和蛋白酶A对纯生啤酒泡沫稳定性的影响

    Institute of Scientific and Technical Information of China (English)

    姜珊; 张彦青; 杜金华; 李惠萍; 董倩倩; 房慧婧; 李琳

    2014-01-01

    In this study, the key factors influencing the foam stability of pure draft beer were investigated. The content of high-molecular protein and the activity of proteinase A were detected by Coomassie brilliant blue method and fluorescence-based assay in both beer brewing and beer storage process, respectively. The results showed that, different fermenting parameters in each fermenting vessels resulted in significant difference in the change of high-molecular protein content and proteinase A activity. During the fermenting stage, high-molecular protein content decreased slowly from 350~407.6 mg/L in wort to 180.1~243.1 mg/L in product beer, and proteinase A activity strengthened slowly prior to yeast harvest-ing and reached the highest levels of 18.27~30.13 U/mL, after yeast harvesting, proteinase A activity reduced and finally its activity in product beer was only 19.06%~36.4%of the previous highest value. Through the tracing of high-molecular protein content and proteinase A activity in product pure draft beer and the analysis of their effects on beer foam stability, it was found that there was significant positive relations between high-molecular protein content and foam stability (r=0.794, P<0.01), however, there was no significant relations between proteinase A activity and foam stability/high-molecular protein content.%利用考马斯亮蓝法、荧光底物法分别跟踪检测啤酒酿造和贮存过程中高分子蛋白含量及蛋白酶A活力变化,研究影响纯生啤酒泡沫稳定性的关键因素。结果表明,各发酵罐因发酵阶段工艺参数的不同,导致高分子蛋白含量及蛋白酶A活力变化趋势存在明显差异。发酵阶段高分子蛋白含量缓慢降低,由入罐麦汁时的350~407.6 mg/L降到成品酒时的180.1~243.1 mg/L;蛋白酶A活力在回收酵母前增加,后达到最高值,其范围是18.27~30.13 U/mL,回收酵母后蛋白酶A活力下降,最终在成品酒中的蛋白酶A活力检测值

  9. The Effects of Threonine Phosphorylation on the Stability and Dynamics of the Central Molecular Switch Region of 18.5-kDa Myelin Basic Protein

    OpenAIRE

    Vassall, Kenrick A.; Kyrylo Bessonov; Miguel De Avila; Eugenia Polverini; George Harauz

    2013-01-01

    The classic isoforms of myelin basic protein (MBP) are essential for the formation and maintenance of myelin in the central nervous system of higher vertebrates. The protein is involved in all facets of the development, compaction, and stabilization of the multilamellar myelin sheath, and also interacts with cytoskeletal and signaling proteins. The predominant 18.5-kDa isoform of MBP is an intrinsically-disordered protein that is a candidate auto-antigen in the human demyelinating disease mul...

  10. Development of potato transgenic plants and molecular and genetic analyses of their integration stability and transgene expression efficiency using vegetative and sexual propagation

    International Nuclear Information System (INIS)

    Agrobacterium mediated transformation of potato (Solanum tuberosum L.) and the stability of integration, expression and inheritance of transgenes were investigated. Over 400 kanamycin resistant transgenic plants with the nptII, gus, tt (insect toxin of Bacillus thuringiensis, variety kurstaki) and tg (fusion of tt and gus under the 35S promoter) foreign genes were obtained from eight potato genotypes by co-cultivation of the leaf discs with A. tumefaciens LBA 4404 (pBI 121), A. tumefaciens 3850 (pGV 941tg) and A. rchizogenes A4 (pGV 941tt). Southern blot analysis showed that more than 80% of the regenerating plants had one or several copies of the foreign genes. Selection for kanamycin resistance and Southern blot analysis revealed the stability of inheritance of transgenes by vegetative propagation of the plants via cloning and through tubers. However, 0.3% of the plants lost the nptII gene during the cloning process. About 500 self-pollinated seeds of four independently obtained transgenic clones were harvested. Analysis of the phenotypic segregation of the transgenic progeny on selective medium with kanamycin (50 mg/L) was made and compared with the controls. Inheritance and expression of the nptII transgene in the progeny of all four transgenic clones were shown, although the character of segregation appeared to differ in the various clones

  11. Fluctuating asymmetry and genetic variability in the roe deer (Capreolus capreolus): a test of the developmental stability hypothesis in mammals using neutral molecular markers.

    Science.gov (United States)

    Zachos, F E; Hartl, G B; Suchentrunk, F

    2007-06-01

    Fluctuating asymmetry (FA), used as an indicator of developmental stability, has long been hypothesized to be negatively correlated with genetic variability as a consequence of more variable organisms being better suited to buffer developmental pathways against environmental stress. However, it is still a matter of debate if this is due to metabolic properties of enzymes encoded by certain key loci or rather to overall genomic heterozygosity. Previous analyses suggest that there might be a general difference between homeo- and poikilotherms in that only the latter tend to exhibit the negative correlation predicted by theory. In the present study, we addressed these questions by analysing roe deer (Capreolus capreolus) from five German populations with regard to FA in metric and non-metric skull and mandible traits as well as variability at eight microsatellite loci. Genetic variability was quantified by heterozygosity and mean d2 parameters, and although the latter did not show any relationship with FA, we found for the first time a statistically significant negative correlation of microsatellite heterozygosity and non-metric FA among populations. Because microsatellites are non-coding markers, this may be interpreted as evidence for the role of overall genomic heterozygosity in determining developmental stability. To test if the threshold character of non-metric traits is responsible for the metric vs non-metric difference we also carried out calculations where we treated our metric traits as threshold values. This, however, did not yield significant correlations between FA and genetic variability either. PMID:17375126

  12. Water reduction by a p-GaInP2 photoelectrode stabilized by an amorphous TiO2 coating and a molecular cobalt catalyst

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Jing; Yan, Yong; Young, James L.; Steirer, K. Xerxes; Neale, Nathan R.; Turner, John A.

    2015-12-21

    Producing hydrogen through solar water splitting requires the coverage of large land areas. Abundant metal-based molecular catalysts offer scalability, but only if they match noble metal activities. We report on a highly active p-GaInP2 photocathode protected through a 35-nm TiO2 layer functionalized by a cobaloxime molecular catalyst (GaInP2-TiO2-cobaloxime). This photoelectrode mediates H2 production with a current density of ~9"0mA"0cm-2 at a potential of 0"0V versus RHE under 1-sun illumination at pH"013. The calculated turnover number for the catalyst during a 20-h period is 139,000, with an average turnover frequency of 1.9"0s-1. Bare GaInP2 shows a rapid current decay, whereas the GaInP2-TiO2-cobaloxime electrode shows

  13. Stability and molecular dynamics of chloroxylenol (API of antiseptics and drugs) in solid state studied by 35Cl-NQR spectroscopy and DFT calculations

    Science.gov (United States)

    Latosińska, J. N.; Tomczak, M. A.; Kasprzak, J.

    2009-02-01

    Thermal stability of 4-chloro-3,5-dimethyl-phenol (chloroxylenol) in solid state has been studied by 35Cl-NQR spectroscopy. Two NQR resonance lines at the frequencies 34.348 and 34.415 MHz at 77 K have been assigned to chlorine atoms from two crystallographically inequivalent molecules on the basis of the B3LYP/6-311++G∗∗ results. The temperature dependence of the resonance frequency and full width at half maximum suggest the occurrence of small-angle torsional oscillations of the mean activation energy of 3.83 kJ/mol and rotation of both methyl groups around their symmetry axis C3 with the activation energies 12.49 and 11.27 kJ/mol for CH3 in molecule A and B, respectively. B3LYP/6-311++G∗∗ method reproduced very well the activation energies of both motions.

  14. Binding properties of ruthenium(II) complexes [Ru(bpy)2(ppn)](2+) and [Ru(phen)2(ppn)](2+) with triplex RNA: As molecular "light switches" and stabilizers for poly(U)·poly(A)*poly(U) triplex.

    Science.gov (United States)

    Li, Jia; Sun, Yanmei; Zhu, Zhiyuan; Zhao, Hong; Tan, Lifeng

    2016-08-01

    Stable RNA triplexes play key roles in many biological processes, while triplexes are thermodynamically less stable than the corresponding duplexes due to the Hoogsteen base pairing. To understand the factors affecting the stabilization of RNA triplexes by octahedral ruthenium(II) complexes, the binding of [Ru(bpy)2(ppn)](2+) (1, bpy=2,2'-bipyridine, ppn=2,4-diaminopyrimido[5,6-b]dipyrido[2,3-f:2',3'-h]quinoxaline) and [Ru(phen)2(ppn)](2+) (2, phen=1,10-phenanthroline) to poly(U)·poly(A)*poly(U) (· denotes the Watson-Crick base pairing and * denotes the Hoogsteen base pairing) has been investigated. The main results obtained here suggest that complexes 1 and 2 can serve as molecular "light switches" and stabilizers for poly(U)·poly(A)*poly(U), while the effectiveness of complex 2 are more marked, suggesting that the hydrophobicity of ancillary ligands has a significant effect on the two Ru(II) complexes binding to poly(U)·poly(A)*poly(U). This study further advances our knowledge on the binding of RNA triplexes with metal complexes, particularly with octahedral ruthenium polypyridyl complexes. PMID:27287059

  15. Thermal stability and relaxation mechanisms in compressively strained Ge0.94Sn0.06 thin films grown by molecular beam epitaxy

    Science.gov (United States)

    Fleischmann, C.; Lieten, R. R.; Hermann, P.; Hönicke, P.; Beckhoff, B.; Seidel, F.; Richard, O.; Bender, H.; Shimura, Y.; Zaima, S.; Uchida, N.; Temst, K.; Vandervorst, W.; Vantomme, A.

    2016-08-01

    Strained Ge1-xSnx thin films have recently attracted a lot of attention as promising high mobility or light emitting materials for future micro- and optoelectronic devices. While they can be grown nowadays with high crystal quality, the mechanism by which strain energy is relieved upon thermal treatments remains speculative. To this end, we investigated the evolution (and the interplay) of composition, strain, and morphology of strained Ge0.94Sn0.06 films with temperature. We observed a diffusion-driven formation of Sn-enriched islands (and their self-organization) as well as surface depressions (pits), resulting in phase separation and (local) reduction in strain energy, respectively. Remarkably, these compositional and morphological instabilities were found to be the dominating mechanisms to relieve energy, implying that the relaxation via misfit generation and propagation is not intrinsic to compressively strained Ge0.94Sn0.06 films grown by molecular beam epitaxy.

  16. Molecular dynamics simulations of aqueous urea solutions: Study of dimer stability and solution structure, and calculation of the total nitrogen radial distribution function GN(r)

    Science.gov (United States)

    Boek, E. S.; Briels, W. J.

    1993-01-01

    Molecular dynamics simulations have been performed in order to study the structure of two molal urea solutions in D2O. Several initial dimer configurations were considered for an adequate sampling of phase space. Eventually all of them appeared to be unstable, when system size and periodic boundary conditions are chosen properly, even after a very careful equilibration. The total nitrogen scattering function GN(r), calculated from these simulations, is in good agreement with neutron scattering experiments when both intra- and intermolecular correlations are considered and the experimental truncation ripples are introduced by a Fourier transform of GN(r) back and forth. The simple pair potential model that we used gives results in good agreement with experiments and with a much more involved potential model, recently described in the literature [J. Chem. Phys. 95, 8419 (1991)].

  17. Cross-linked low molecular weight glycopeptide-mediated gene delivery: relationship between DNA metabolic stability and the level of transient gene expression in vivo.

    Science.gov (United States)

    Yang, Y; Park, Y; Man, S; Liu, Y; Rice, K G

    2001-12-01

    DNA co-condensates were formed by reacting [125I]DNA with an admixture of a high-mannose glycopeptide (Man9-CWK(18)) and either of two poly(ethylene glycol) peptides (PEG-VS-CWK(18) or PEG-SS-CWK(18)) followed by cross-linking with 6-50 mol equiv of glutaraldehyde. [125I]DNA co-condensates were administered intravenously in mice to determine the influence of peptide DNA formulation parameters on specific targeting to Kupffer cells. Optimal targeting to Kupffer cells required the combined use of 50 mol % Man9-CWK(18) and PEG-CWK(18) to mediate specific recognition by the mannose receptor to Kupffer cells. The cellular uptake of cross-linked Man9-CWK(18)/PEG-CWK(18) DNA co-condensates was receptor mediated since Kupffer cell targeting was inhibited by pre-administration of Man-bovine serum albumin (BSA) but not BSA. An optimized formulation targeted 60% of the dose to the liver, with 80% of the liver-targeted DNA localized to Kupffer cells. Cross-linking with either 6, 15, or 50 mol equiv of glutaraldehyde led to a corresponding decrease in the metabolism rate of DNA in liver as measured by half-live- of 4, 6, and 39 h, respectively. Tail vein dosing of 50 microg of DNA co-condensates cross-linked with 6 mol equiv of glutaraldehyde produced detectable levels of human alpha1-antitrypsin in blood after 12 h, which peaked at day six and persisted for 10 days. The level of human alpha1-antitrypsin was elevated two-fold each day when dosing with DNA co-condensates cross-linked with 15 mol equiv of glutaraldehyde, revealing a correlation between the metabolic stability of the DNA in liver and level of gene expression. In addition to possessing greater metabolic stability, DNA co-condensates cross-linked with 50 mol equiv of glutaraldehyde, but lacking a targeting ligand, avoided rapid liver uptake and possessed a prolonged pharmacokinetic half-life, providing insight into a means to target DNA condensates to peripheral tissues. PMID:11745760

  18. Dissociative adsorption of molecular deuterium and thermal stability onto hydrogenated, bare and ion beam damaged poly- and single crystalline diamond surfaces

    Science.gov (United States)

    Michaelson, Sh.; Chandran, M.; Zalkind, S.; Shamir, N.; Akhvlediani, R.; Hoffman, A.

    2015-12-01

    In this work we report on dissociative adsorption of deuterium (D2) on bare, hydrogenated and ion beam bombarded polycrystalline and single crystalline diamond surfaces. Polycrystalline diamond films with an average grain size of ~ 300 nm were deposited on silicon substrates by hot filament chemical vapor deposition technique from methane/hydrogen gas mixture. Deposited films were characterized using Raman spectroscopy, atomic force microscopy and scanning electron microscopy to estimate the phase composition and microstructure. High resolution electron energy loss spectroscopy and direct recoil spectrometry were used to study hydrogen (deuterium) bonding configuration of the upper surface region. Near surface amorphization was achieved by 1 keV Ar+ implantation at ~ 1 × 1015 ions/cm2 at room temperature (RT). As deposited and Ar+ bombarded films are annealed to 500-1000 °C in ultra-high vacuum conditions and also under D2 partial pressure of 5 × 10- 6 Torr. For comparison, key experiments were repeated on the single crystal (100) diamond. Our results clearly show the preferential dissociative adsorption of D2 on low hybridized carbon (sp/sp2) states with activation temperature as low as RT, but with a lower thermal stability compared to pure diamond Csbnd D bonds.

  19. Theory for strength and stability of an unusual "ligand-receptor" bond: a microtubule attached to a wall by molecular motor tethers

    CERN Document Server

    Ghanti, Dipanwita

    2016-01-01

    A microtubule (MT) is a tubular stiff filament formed by a hierarchical organization of tubulin proteins. We develop a stochastic kinetic model for studying the strength and stability of a pre-formed attachment of a MT with a rigid wall where the MT is tethered to the wall by a group of motor proteins. Such an attachment, formed by the specific interactions between the MT and the motors, is an analog of ligand-receptor bonds, the MT and the motors anchored on the wall being the counterparts of the ligand and receptors, respectively. However, unlike other ligands, the length of a MT can change with time because of its polymerization-depolymerization kinetics. The simple model developed here is motivated by the MTs linked to the cell cortex by dynein motors. We present the theory for both force-ramp and force-clamp conditions. In the force-ramp protocol we investigate the strength of the attachment by assuming imposition of a time-dependent external load tension that increases linearly with time till the attach...

  20. Stability and molecular dynamics of solid lasamide (API of diuretic and antivirial drugs) studied by 1H NMR spectroscopy and DFT methods

    Science.gov (United States)

    Latosińska, J. N.; Latosińska, M.; Medycki, W.

    2009-08-01

    Temperature dependence of the relaxation time T1 (in the ranges: 10-200 K at 24.667 MHz; 105-460 K at 90 MHz) and the second moment of the NMR line for protons M2 (in the range: 130-400 K, 24.667 MHz) in a polycrystalline sample of 2,4-dichloro-5-sulfamoyl-benzoic acid (lasamide) an Active Pharmaceutical Ingredient of both diuretic and antiviral drugs have been measured. The results have revealed two activation processes: the concerted proton transfer in inter-molecular double hydrogen bonds (the low-temperature T1 minimum at about 92 K; the activation energy 5.02 kJ/mol) and the jumps of the -NH 2 group (the high-temperature, 2 Gs 2 reduction of the second moment; the activation energy 48 kJ/mol). The low-temperature flattening of the T1 dependence stretched up to the helium temperatures indicating the incoherent tunnelling in the proton transfer dynamics.

  1. Morphological and microstructural stability of N-polar InAlN thin films grown on free-standing GaN substrates by molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Hardy, Matthew T., E-mail: matthew.hardy.ctr@nrl.navy.mil; Storm, David F.; Downey, Brian P.; Katzer, D. Scott; Meyer, David J. [Electronics Science and Technology Division, Naval Research Laboratory, 4555 Overlook Avenue SW, Washington DC 20375 (United States); McConkie, Thomas O.; Smith, David J. [Department of Physics, Arizona State University, Tempe, Arizona 85287-1504 (United States); Nepal, Neeraj [Sotera Defense Solutions, 2200 Defense Hwy Suite 405, Crofton, Maryland 21114 (United States)

    2016-03-15

    The sensitivity of the surface morphology and microstructure of N-polar-oriented InAlN to variations in composition, temperature, and layer thickness for thin films grown by plasma-assisted molecular beam epitaxy (PAMBE) has been investigated. Lateral compositional inhomogeneity is present in N-rich InAlN films grown at low temperature, and phase segregation is exacerbated with increasing InN fraction. A smooth, step-flow surface morphology and elimination of compositional inhomogeneity can be achieved at a growth temperature 50 °C above the onset of In evaporation (650 °C). A GaN/AlN/GaN/200-nm InAlN heterostructure had a sheet charge density of 1.7 × 10{sup 13 }cm{sup −2} and no degradation in mobility (1760 cm{sup 2}/V s) relative to 15-nm-thick InAlN layers. Demonstration of thick-barrier high-electron-mobility transistors with good direct-current characteristics shows that device quality, thick InAlN layers can be successfully grown by PAMBE.

  2. Ca(2+) -complex stability of GAPAGPLIVPY peptide in gas and aqueous phase, investigated by affinity capillary electrophoresis and molecular dynamics simulations and compared to mass spectrometric results.

    Science.gov (United States)

    Nachbar, Markus; El Deeb, Sami; Mozafari, Mona; Alhazmi, Hassan A; Preu, Lutz; Redweik, Sabine; Lehmann, Wolf Dieter; Wätzig, Hermann

    2016-03-01

    Strong, sequence-specific gas-phase bindings between proline-rich peptides and alkaline earth metal ions in nanoESI-MS experiments were reported by Lehmann et al. (Rapid Commun. Mass Spectrom. 2006, 20, 2404-2410), however its relevance for physiological-like aqueous phase is uncertain. Therefore, the complexes should also be studied in aqueous solution and the relevance of the MS method for binding studies be evaluated. A mobility shift ACE method was used for determining the binding between the small peptide GAPAGPLIVPY and various metal ions in aqueous solution. The findings were compared to the MS results and further explained using computational methods. While the MS data showed a strong alkaline earth ion binding, the ACE results showed nonsignificant binding. The proposed vacuum state complex also decomposed during a molecular dynamic simulation in aqueous solution. This study shows that the formed stable peptide-metal ion adducts in the gas phase by ESI-MS does not imply the existence of analogous adducts in the aqueous phase. Comparing peptide-metal ion interaction under the gaseous MS and aqueous ACE conditions showed huge difference in binding behavior.

  3. Molecular dynamic simulation studies on the effect of one residue chain staggering on the structure and stability of heterotrimeric collagen-like peptides with interruption.

    Science.gov (United States)

    Singam, Ettayapuram Ramaprasad Azhagiya; Balamurugan, Kanagasabai; Gopalakrishnan, Ravimohan; Subramanian, Sundar Raman; Subramanian, Venkatesan; Ramasami, Thirumalachari

    2012-11-01

    A systematic molecular dynamics (MD) simulation has been carried out on collagen-like peptides with different combinations of interruptions in the Gly-X(AA) -Y(AA) repeats. Although experimental studies have been carried out to elucidate the structural consequences of homotrimeric collagen-like peptides, this is the first report on the structural effect on the heterotrimeric models with G4G and G1G breaks present simultaneously in the constituent chains with difference in one residue chain staggering. The results reveal that the axial registry of the interrupted region changes significantly from that of conventional triple helical peptide without interruption. Further, results from MD simulations show the formation of a kink in the interrupted region of the triple-helical peptides. The conformational analysis reveals that the interruption in the Gly-X(AA) -Y(AA) pattern in these peptides induces β-strand conformation in triple helical peptides. The conventional hydrogen bonds in the interrupted triad are affected and new nonconventional H-bonds are formed in the triple helical structure, and as a result interrupted region becomes locally fragile. MM-PBSA calculations on the different systems clearly suggest that the binding affinity varies marginally due to one residue staggering. However, it is found from the structural parameters that hydrogen-bonding pattern differs significantly due to the difference in the staggering of chains. PMID:22899360

  4. Cholera toxin B subunit-five-stranded α-helical coiled-coil fusion protein: "five-to-five" molecular chimera displays robust physicochemical stability.

    Science.gov (United States)

    Arakawa, Takeshi; Harakuni, Tetsuya

    2014-09-01

    To create a physicochemically stable cholera toxin (CT) B subunit (CTB), it was fused to the five-stranded α-helical coiled-coil domain of cartilage oligomeric matrix protein (COMP). The chimeric fusion protein (CTB-COMP) was expressed in Pichia pastoris, predominantly as a pentamer, and retained its affinity for the monosialoganglioside GM1, a natural receptor of CT. The fusion protein displayed thermostability, tolerating the boiling temperature of water for 10min, whereas unfused CTB readily dissociated to its monomers and lost its affinity for GM1. The fusion protein also displayed resistance to strong acid at pHs as low as 0.1, and to the protein denaturant sodium dodecyl sulfate at concentrations up to 10%. Intranasal administration of the fusion protein to mice induced anti-B subunit serum IgG, even after the protein was boiled, whereas unfused CTB showed no thermostable mucosal immunogenicity. This study demonstrates that CTB fused to a pentameric α-helical coiled coil has a novel physicochemical phenotype, which may provide important insight into the molecular design of enterotoxin-B-subunit-based vaccines and vaccine delivery molecules. PMID:25045819

  5. Stability and instability of the isoelectronic UO22+ and PaO2+ actinyl oxo-cations in aqueous solution from density functional theory based molecular dynamics

    International Nuclear Information System (INIS)

    In this work, Pa(V) mono-cations have been studied in liquid water by means of density functional theory (DFT) based molecular dynamic simulations (CPMD) and compared with their U(VI) isoelectronic counterparts to understand the peculiar chemical behavior of Pa(V) in aqueous solution. Four different Pa(V) monocationic isomers appear to be stable in liquid water from our simulations: [PaO2(H2O)5]+(aq), [Pa(OH)4(H2O)2]+(aq), [PaO(OH)2(H2O)4]+(aq), and [Pa(OH)4(H2O)3]+(aq). On the other hand, in the case of U(VI) only the uranyl, [UO2(H2O)5]2+(aq), is stable. The other species containing hydroxyl groups replacing one or two oxo bonds are readily converted to uranyl. The Pa-OH bond is stable, while it is suddenly broken in U-OH. This makes possible the formation of a broad variety of Pa(V) species in water and participates to its unique chemical behavior in aqueous solution. Further, the two actinyl oxo-cations in water are different in the ability of the oxygen atoms to form stable and extended H-bond networks for Pa(V) contrary to U(VI). In particular, prot-actinyl is found to have between 2 and 3 hydrogen bonds per oxygen atom while uranyl has between zero and one. (authors)

  6. 真空条件下肌酐的葫芦脲包合物的稳定性研究%Investigation on the inclusion stability of creatinine-cucurbits[n](n=5, 6, 7) by molecular simulation

    Institute of Scientific and Technical Information of China (English)

    张燕; 李代禧; 翟振; 刘宝林; 张冬兵; 刘立; 余华星

    2012-01-01

    葫芦脲因其特殊的结构特征,在主客体化学以及药物缓释等方面都具有潜在的价值.本文利用分子动力学模拟和Gaussian 量子化学计算研究了肌酐的葫芦脲[n](n=5,6,7)的包合物在常温下的动态结构稳定性和热力学稳定性.在真空条件下,通过分子动力学模拟包合物在常温时的动态结构和运动轨迹,揭示了包合物的相对稳定性,并根据包合物的氢键及质心运动分析结果可知,肌酐-葫芦脲[7]包合物是稳定包合物.肌酐-葫芦脲[7]经热力学分析的吉布斯自由能变为负值,说明肌酐-葫芦脲[7]包合物的热力学也较稳定,这与分子动力学分析的结果一致.该结果表明,葫芦脲[7]对肌酐具有特异性亲和作用,理论上,可以利用葫芦脲[7]的这种特异性亲和作用清除尿毒症病人血液中过量的肌酐.%Cucurbits have potential values on host-guest chemistry and the release of medicine because of their special structural properties. In current research, molecular dynamics simulation and Gaussian quantum chemical calculation were used to investigate the dynamic structure and thennodynamic stability of cucurbits [n](n=5, 6, 7) with creatinine at room temperature. The simulation results revealed the inclusion's relative stability by analyzing their dynamic structure and trajectories in vacuum. The analysis on H-bond and center of mass trajectories proved creatinine-cucurbit[7] was stable. Thermodynamics properties derived from quantum chemical calculation also explained that creatinme-cucurbit[7] inclusion was thermodynamic stable. These results were consistent with those of molecular dynamics simulation. The experiment suggested that cucurbits[7] could be used to remove excessive creatinine in the uremic patients' blood because of the specific affinity with creatinine.

  7. Ensuring Stability

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    "Stable"will be a key word for China’s economy in 2012.That’s the beat set at the annual Central Economic Work Conference held in Beijing on December 12-14,which reviewed this year’s development and mapped out plans for the next year.Policymakers at the conference decided to keep macroeconomic policies stable,seek a stable and relatively fast economic growth,stabilize consumer prices and maintain social stability in 2012.On the basis of stability,the government will transform the development model,deepen reform and improve people’s livelihood.

  8. Against Stabilization

    Directory of Open Access Journals (Sweden)

    Roger Mac Ginty

    2012-11-01

    Full Text Available This is a polemic against the concept and practice of stabilization as practiced by leading states from the global north in peace support interventions. It is not an argument against stability. Instead, it depicts stabilization as an essentially conservative doctrine that runs counter to its stated aims of enhancing local participation and legitimacy. It is an agenda of control that privileges notions of assimilation with international (western standards and mainstreams the military into peace-support operations. As a result, the value of peace is undercut.

  9. Structure of molecular aggregates and its effect on the stability of heavy oil%重质油中的分子聚集结构及其对重质油稳定性的影响

    Institute of Scientific and Technical Information of China (English)

    张胜飞; 徐俊波; 温浩

    2011-01-01

    The aggregation phenomenon of fraction molecules is one of the most evident features of heavy oil, which influences seriously the viscosity and stability of heavy oil. A dissipative particle dynamics (DPD) method modified by Zhang et al. Is applied in this work to study the structure of molecular aggregates in heavy oil and its effect on the stability of heavy oil. The heavy oil is represented as the mixture of the coarse-grained DPD model molecules of asphaltene, resin, aromatic, saturate and light fraction, in accordance with molecular structures of the fractions in heavy oil. The DPD simulations show that the coarse-grained DPD models and DPD parameters used in this work can predict well the structure of molecular aggregates in heavy oil. The heavy oil exhibits as a polydispersed colloid system. The ordered structure of aggregates depends greatly on the molecular structure of asphaltenes. Deflocculation of the resins is observed in the simulations, which can reduce the phase splits and coagulation of heavy oil. The fractions of aromatic, saturate and light fraction in heavy oil perform as the continuous phase in colloid system. The prediction of stability of heavy oil presented in this work is consisted with the Shell's SARA cross plot. For the certain value of asphaltene-aromatic mass ratio mAspb/Marom, the heavy oil will be stable as the asphaltene-resin mass ratio maspb/mResun is low. A critical value of asphaltene-resin mass ratio exists. The coagulation of heavy oil will occur when the higher asphaltene-resin mass ratio is approached. The extension of the stable region of heavy oil will be observed when the asphaltene-aromatic mass ratio mAspb/mArom reduced.%重质油组分分子的聚集是重质油最显著的特征之一,重质油的高粘特性和相态稳定性均与此聚集行为有紧密的联系.为克服实验研究获得重质油微观聚集结构的困难,本文采用Zhang等人针对重质油体系改进的耗散粒子动力学(DPD)方法,研

  10. MOLECULAR REPLICATOR DYNAMICS

    OpenAIRE

    BÄRBEL M. R. STADLER; Stadler, Peter F

    2003-01-01

    Template-dependent replication at the molecular level is the basis of reproduction in nature. A detailed understanding of the peculiarities of the chemical reaction kinetics associated with replication processes is therefore an indispensible prerequisite for any understanding of evolution at the molecular level. Networks of interacting self-replicating species can give rise to a wealth of different dynamical phenomena, from competitive exclusion to permanent coexistence, from global stability...

  11. PARALLEL STABILIZATION

    Institute of Scientific and Technical Information of China (English)

    J.L.LIONS

    1999-01-01

    A new algorithm for the stabilization of (possibly turbulent, chaotic) distributed systems, governed by linear or non linear systems of equations is presented. The SPA (Stabilization Parallel Algorithm) is based on a systematic parallel decomposition of the problem (related to arbitrarily overlapping decomposition of domains) and on a penalty argument. SPA is presented here for the case of linear parabolic equations: with distrjbuted or boundary control. It extends to practically all linear and non linear evolution equations, as it will be presented in several other publications.

  12. Stability of Organic Nanowires

    DEFF Research Database (Denmark)

    Balzer, F.; Schiek, M.; Wallmann, I.;

    2011-01-01

    The morphological stability of organic nanowires over time and under thermal load is of major importance for their use in any device. In this study the growth and stability of organic nanowires from a naphthyl end-capped thiophene grown by organic molecular beam deposition is investigated via...... atomic force microscopy (AFM). Aging experiments under ambient conditions already show substantial morphological changes. Nanoscopic organic clusters, which initially coexist with the nanowires, vanish within hours. Thermal annealing of nanowire samples leads to even more pronounced morphology changes......, such as a strong decrease in nanowire number density, a strong increase in nanowire height, and the formation of new types of crystallites. This happens even before sublimation of organic material starts. These experiments also shine new light on the formation process of the nanowires....

  13. Stabilizing Movements

    DEFF Research Database (Denmark)

    Norbäck, Maria; Helin, Jenny; Raviola, Elena

    2014-01-01

    of turbulent times. Departing from a process perspective to organizational change and insights from Bakhtin's notion of ‘double-voicing’, which means that people borrow other people's words in their own talk, two main contributions are offered. First, we show how stability cannot be taken for granted...

  14. Before Stabilization

    DEFF Research Database (Denmark)

    Plesner, Ursula; Horst, Maja

    2013-01-01

    to the literature on the relationship between ICTs and organizing, but with a distinct focus on innovation communication and distributed innovation processes taking place before ICTs are stabilized, issues which cannot be captured by studies of diffusion and adaptation of new ICTs within single organizations....

  15. Macroeconomic stability

    DEFF Research Database (Denmark)

    Jespersen, Jesper

    2004-01-01

    It is demonstrated that full employment and sustainable development not necessarily are conflicting goals. On the other hand macroeconomic stability cannot be obtained without a deliberate labour sharing policy and a shift in the composition of private consumption away from traditional material...

  16. Molecular physics

    CERN Document Server

    Williams, Dudley

    2013-01-01

    Methods of Experimental Physics, Volume 3: Molecular Physics focuses on molecular theory, spectroscopy, resonance, molecular beams, and electric and thermodynamic properties. The manuscript first considers the origins of molecular theory, molecular physics, and molecular spectroscopy, as well as microwave spectroscopy, electronic spectra, and Raman effect. The text then ponders on diffraction methods of molecular structure determination and resonance studies. Topics include techniques of electron, neutron, and x-ray diffraction and nuclear magnetic, nuclear quadropole, and electron spin reson

  17. Stabilizing brokerage.

    Science.gov (United States)

    Stovel, Katherine; Golub, Benjamin; Milgrom, Eva M Meyersson

    2011-12-27

    A variety of social and economic arrangements exist to facilitate the exchange of goods, services, and information over gaps in social structure. Each of these arrangements bears some relationship to the idea of brokerage, but this brokerage is rarely like the pure and formal economic intermediation seen in some modern markets. Indeed, for reasons illuminated by existing sociological and economic models, brokerage is a fragile relationship. In this paper, we review the causes of instability in brokerage and identify three social mechanisms that can stabilize fragile brokerage relationships: social isolation, broker capture, and organizational grafting. Each of these mechanisms rests on the emergence or existence of supporting institutions. We suggest that organizational grafting may be the most stable and effective resolution to the tensions inherent in brokerage, but it is also the most institutionally demanding.

  18. STABILIZED OSCILLATOR

    Science.gov (United States)

    Jessen, P.L.; Price, H.J.

    1958-03-18

    This patent relates to sine-wave generators and in particular describes a generator with a novel feedback circuit resulting in improved frequency stability. The generator comprises two triodes having a common cathode circuit connected to oscillate at a frequency and amplitude at which the loop galn of the circutt ls unity, and another pair of triodes having a common cathode circuit arranged as a conventional amplifier. A signal is conducted from the osciliator through a frequency selective network to the amplifier and fed back to the osciliator. The unique feature of the feedback circuit is the amplifier operates in the nonlinear portion of its tube characteristics thereby providing a relatively constant feedback voltage to the oscillator irrespective of the amplitude of its input signal.

  19. DNA-triplex stabilizing properties of 8-aminoguanine

    OpenAIRE

    Soliva, Robert; Güimil García, Ramón; Blas, J. Ramón; Eritja Casadellà, Ramón; Asensio, Juan Luis; González, Carlos; Luque, F. Javier; Orozco, Modesto

    2000-01-01

    A DNA-triplex stabilizing purine (8-aminoguanine) is designed based on molecular modeling and synthesized. The substitution of guanine by 8-aminoguanine largely stabilizes the triplex both at neutral and acidic pH, as suggested by molecular dynamics and thermodynamic integration calculations, and demonstrated by melting experiments. NMR experiments confirm the triplex-stabilizing properties of 8-aminoguanine and demonstrate that few changes are found in the structure of the triplex due to the...

  20. mutL Gene:a Spontaneous Molecular Switch to Regulate Bacterial Genetic Stability%mutL基因:自发调节细菌遗传稳定性的分子开关

    Institute of Scientific and Technical Information of China (English)

    陈芳; 刘树林

    2008-01-01

    MutL is one of the core proteins involved in mismatch repair(MMR).It is a weak AT-Pase and binds nonspecifically to DNA.It has been deemed a"matchmaker"as it interacts with.and in some cases stimulates,the activity of a large number of proteins,such as MutS,MutH,UwD and B clamp.Defects in mutL gene result in significantly increased rates of spontaneous mutation and horncologous recombi_nation in bacteria.Recently,we have identified a deletion of one of three tandem 6 bp repeats within mutL(6 bp AmutL)in Salmonella typhimurium LT7.This defect is associated with genome diversification of LT7 and contributed greatly to genetic instability.As the conversion between mutL and 6 bp △mutL could take place spontaneously,we propose that the mutL gene may play a role as a molecular switch to regulate the function of MMR and,especially,the genetic stability of bacteria in adaptation to changing environments.%MutL是错配修复(mismatch repair,MMR)系统的关键组分之一,它具有较弱的AT-Pase活性并能非特异性结合DNA.由于MutL与其他MMR蛋白如MutS、MutH、UvrD及B clamp等之间存在广泛的相互作用,并能在一定程度上刺激它们活性.因此,MutL被广泛认为是MMR过程中关键的分子媒娘.mutL基因缺陷的菌株具有显著增高的自发突变率和同源重组频率.最近,我们在鼠伤寒沙门菌m高变异株的mutL基因中发现一个6碱基串联重复序列的缺失,这种缺陷型mutL(6h·p△mutL)基因可大大促进细菌基因结构的多样化和遗传的不稳定性,并能与mutL自发相互转化.因此,我们认为,mutL可通过这种转化适时而精确地调控MMR系统功能,从而在细菌进化过程充当自发调控遗传稳定性的分子开关.

  1. Stability and demulsification of emulsions stabilized by asphaltenes or resins.

    Science.gov (United States)

    Xia, Lixin; Lu, Shiwei; Cao, Guoying

    2004-03-15

    Experimental data are presented to show the influence of asphaltenes and resins on the stability and demulsification of emulsions. It was found that emulsion stability was related to the concentrations of the asphaltene and resin in the crude oil, and the state of dispersion of the asphaltenes and resins (molecular vs colloidal) was critical to the strength or rigidity of interfacial films and hence to the stability of the emulsions. Based on this research, a possible emulsion minimization approach in refineries, which can be implemented utilizing microwave radiation, is also suggested. Comparing with conventional heating, microwave radiation can enhance the demulsification rate by an order of magnitude. The demulsification efficiency reaches 100% in a very short time under microwave radiation. PMID:14972628

  2. Magnetismo Molecular (Molecular Magentism)

    Energy Technology Data Exchange (ETDEWEB)

    Reis, Mario S [Universidade Federal Fluminense, Brasil; Moreira Dos Santos, Antonio F [ORNL

    2010-07-01

    The new synthesis processes in chemistry open a new world of research, new and surprising materials never before found in nature can now be synthesized and, as a wonderful result, observed a series of physical phenomena never before imagined. Among these are many new materials the molecular magnets, the subject of this book and magnetic properties that are often reflections of the quantum behavior of these materials. Aside from the wonderful experience of exploring something new, the theoretical models that describe the behavior these magnetic materials are, in most cases, soluble analytically, which allows us to know in detail the physical mechanisms governing these materials. Still, the academic interest in parallel this subject, these materials have a number of properties that are promising to be used in technological devices, such as in computers quantum magnetic recording, magnetocaloric effect, spintronics and many other devices. This volume will journey through the world of molecular magnets, from the structural description of these materials to state of the art research.

  3. Synthesis and stability test of radiogadolinium(III)-DOTA-PAMAM G3.0-trastuzumab as SPECT-MRI molecular imaging agent for diagnosis of HER-2 positive breast cancer

    OpenAIRE

    Hardiani Rahmania; Abdul Mutalib; Martalena Ramli; Jutti Levita

    2015-01-01

    Nonivasive diagnosis of cancer can be provided by molecular imaging using hybrid modality to obtain better sensitivity, specificity and depiction localization of the disease. In this study, we developed a new molecular imaging agent, radiogadolinium(III)-DOTA-PAMAM G3.0-trastuzumab in the form of 147Gd-DOTA-PAMAM G3.0-trastuzumab, that can be both target-specific radiopharmaceutical in SPECT as well as targeted contrast agent in MRI for the purpose of diagnosis of HER-2 positive breast cancer...

  4. Molecular Electronics

    OpenAIRE

    Heath, James R.

    2009-01-01

    Molecular electronics describes the field in which molecules are utilized as the active (switching, sensing, etc.) or passive (current rectifiers, surface passivants) elements in electronic devices. This review focuses on experimental aspects of molecular electronics that researchers have elucidated over the past decade or so and that relate to the fabrication of molecular electronic devices in which the molecular components are readily distinguished within the electronic properties of the de...

  5. Erwin Schroedinger, Francis Crick and epigenetic stability

    CERN Document Server

    Ogryzko, Vasily

    2007-01-01

    Schroedinger's book 'What is Life?' is widely credited for having played a crucial role in development of molecular and cellular biology. My essay revisits the issues raised by this book from the modern perspective of epigenetics and systems biology. I contrast two classes of potential mechanisms of epigenetic stability: 'epigenetic templating' and 'systems biology' approaches, and consider them from the point of view expressed by Schroedinger. I also discuss how quantum entanglement, a nonclassical feature of quantum mechanics, can help to address the 'problem of small numbers' that lead Schroedinger to promote the idea of molecular code-script for explanation of stability of biological order.

  6. Molecular Plasmonics

    Science.gov (United States)

    Wilson, Andrew J.; Willets, Katherine A.

    2016-06-01

    In this review, we survey recent advances in the field of molecular plasmonics beyond the traditional sensing modality. Molecular plasmonics is explored in the context of the complex interaction between plasmon resonances and molecules and the ability of molecules to support plasmons self-consistently. First, spectroscopic changes induced by the interaction between molecular and plasmonic resonances are discussed, followed by examples of how tuning molecular properties leads to active molecular plasmonic systems. Next, the role of the position and polarizability of a molecular adsorbate on surface-enhanced Raman scattering signals is examined experimentally and theoretically. Finally, we introduce recent research focused on using molecules as plasmonic materials. Each of these examples is intended to highlight the role of molecules as integral components in coupled molecule-plasmon systems, as well as to show the diversity of applications in molecular plasmonics.

  7. Plutonium inventories for stabilization and stabilized materials

    Energy Technology Data Exchange (ETDEWEB)

    Williams, A.K.

    1996-05-01

    The objective of the breakout session was to identify characteristics of materials containing plutonium, the need to stabilize these materials for storage, and plans to accomplish the stabilization activities. All current stabilization activities are driven by the Defense Nuclear Facilities Safety Board Recommendation 94-1 (May 26, 1994) and by the recently completed Plutonium ES&H Vulnerability Assessment (DOE-EH-0415). The Implementation Plan for accomplishing stabilization of plutonium-bearing residues in response to the Recommendation and the Assessment was published by DOE on February 28, 1995. This Implementation Plan (IP) commits to stabilizing problem materials within 3 years, and stabilizing all other materials within 8 years. The IP identifies approximately 20 metric tons of plutonium requiring stabilization and/or repackaging. A further breakdown shows this material to consist of 8.5 metric tons of plutonium metal and alloys, 5.5 metric tons of plutonium as oxide, and 6 metric tons of plutonium as residues. Stabilization of the metal and oxide categories containing greater than 50 weight percent plutonium is covered by DOE Standard {open_quotes}Criteria for Safe Storage of Plutonium Metals and Oxides{close_quotes} December, 1994 (DOE-STD-3013-94). This standard establishes criteria for safe storage of stabilized plutonium metals and oxides for up to 50 years. Each of the DOE sites and contractors with large plutonium inventories has either started or is preparing to start stabilization activities to meet these criteria.

  8. Trapped particle stability for the kinetic stabilizer

    Science.gov (United States)

    Berk, H. L.; Pratt, J.

    2011-08-01

    A kinetically stabilized axially symmetric tandem mirror (KSTM) uses the momentum flux of low-energy, unconfined particles that sample only the outer end-regions of the mirror plugs, where large favourable field-line curvature exists. The window of operation is determined for achieving magnetohydrodynamic (MHD) stability with tolerable energy drain from the kinetic stabilizer. Then MHD stable systems are analysed for stability of the trapped particle mode. This mode is characterized by the detachment of the central-cell plasma from the kinetic-stabilizer region without inducing field-line bending. Stability of the trapped particle mode is sensitive to the electron connection between the stabilizer and the end plug. It is found that the stability condition for the trapped particle mode is more constraining than the stability condition for the MHD mode, and it is challenging to satisfy the required power constraint. Furthermore, a severe power drain may arise from the necessary connection of low-energy electrons in the kinetic stabilizer to the central region.

  9. Novel 5-Substituted 2-(Aylmethylthio)-4-chloro-N-(5-aryl-1,2,4-triazin-3-yl)benzenesulfonamides: Synthesis, Molecular Structure, Anticancer Activity, Apoptosis-Inducing Activity and Metabolic Stability.

    Science.gov (United States)

    Żołnowska, Beata; Sławiński, Jarosław; Pogorzelska, Aneta; Szafrański, Krzysztof; Kawiak, Anna; Stasiłojć, Grzegorz; Belka, Mariusz; Ulenberg, Szymon; Bączek, Tomasz; Chojnacki, Jarosław

    2016-01-01

    A series of novel 5-substituted 2-(arylmethylthio)-4-chloro-N-(5-aryl-1,2,4-triazin-3-yl) benzenesulfonamide derivatives 27-60 have been synthesized by the reaction of aminoguanidines with an appropriate phenylglyoxal hydrate in glacial acetic acid. A majority of the compounds showed cytotoxic activity toward the human cancer cell lines HCT-116, HeLa and MCF-7, with IC50 values below 100 μM. It was found that for the analogues 36-38 the naphthyl moiety contributed significantly to the anticancer activity. Cytometric analysis of translocation of phosphatidylserine as well as mitochondrial membrane potential and cell cycle revealed that the most active compounds 37 (HCT-116 and HeLa) and 46 (MCF-7) inhibited the proliferation of cells by increasing the number of apoptotic cells. Apoptotic-like, dose dependent changes in morphology of cell lines were also noticed after treatment with 37 and 46. Moreover, triazines 37 and 46 induced caspase activity in the HCT-116, HeLa and MCF-7 cell lines. Selected compounds were tested for metabolic stability in the presence of pooled human liver microsomes and NADPH, both R² and Ar = 4-CF₃-C₆H₄ moiety in 2-(R²-methylthio)-N-(5-aryl-1,2,4-triazin-3-yl)benzenesulfonamides simultaneously increased metabolic stability. The results pointed to 37 as a hit compound with a good cytotoxicity against HCT-116 (IC50 = 36 μM), HeLa (IC50 = 34 μM) cell lines, apoptosis-inducing activity and moderate metabolic stability. PMID:27338337

  10. Polymeric stabilization of colloidal asphaltenes

    Science.gov (United States)

    Hashmi, Sara; Firoozabadi, Abbas

    2010-03-01

    Asphaltenes, the heaviest component of crude oil, cause many problems in petroleum extraction and recovery. Operationally defined as insoluble in long chain alkanes but soluble in toluene, asphaltenes have been described by bulk thermodynamic models such as the Flory-Huggins theory. However, bulk models work well only for asphaltenes in good solvents. Characterization of asphaltenes in poor solvents remains elusive: molecular scale asphaltenes readily aggregate to the colloidal scale and become highly unstable in solution. We investigate the ability of polymers to stabilize colloidal asphaltene suspensions in heptane. In the absence of added polymer, sedimentation measurements reveal dynamics reminiscent of collapsing gels. Adding polymers to colloidal asphaltene suspensions can delay the characteristic sedimentation time by orders of magnitude. Light scattering results suggest that the mechanism of stabilization may be related to a decrease in both particle size and polydispersity as a function of added polymer.

  11. Trapped Particle Stability for the Kinetic Stabilizer

    CERN Document Server

    Berk, H L

    2011-01-01

    A kinetically stabilized axially symmetric tandem mirror (KSTM) uses the momentum flux of low-energy, unconfined particles that sample only the outer end-regions of the mirror plugs, where large favorable field-line curvature exists. The window of operation is determined for achieving MHD stability with tolerable energy drain from the kinetic stabilizer. Then MHD stable systems are analyzed for stability of the trapped particle mode. This mode is characterized by the detachment of the central-cell plasma from the kinetic stabilizer region without inducing field-line bending. Stability of the trapped particle mode is sensitive to the electron connection between the stabilizer and the end plug. It is found that the stability condition for the trapped particle mode is more constraining than the stability condition for the MHD mode, and it is challenging to satisfy the required power constraint. Furthermore a severe power drain may arise from the necessary connection of low-energy electrons in the kinetic stabili...

  12. Molecular Gastronomy

    OpenAIRE

    Burke, Roisin; This, Herve; Kelly, Alan

    2016-01-01

    Molecular gastronomy may be defined as the scientific discipline that explores the phenomena occurring during culinary transformations. In contrast with traditional approaches of food science and technology, which considered mostly the chemistry, physics, or biology of food ingredients and industrial transformations, the focus is on phenomena occurring during the preparation of dishes. Applications building on the principles of molecular gastronomy, such as ‘Molecular Cooking’ and ‘Note-by-No...

  13. Molecular Magnetocapacitance

    OpenAIRE

    Wu, Yu-ning; Zhang, Xiao-Guang; Cheng, Hai-Ping

    2012-01-01

    Capacitance of a nanoscale system is usually thought of having two contributions, a classical electrostatic contribution and a quantum contribution dependent on the density of states and/or molecular orbitals close to the Fermi energy. In this letter we demonstrate that in molecular nano-magnets and other magnetic nanoscale systems, the quantum part of the capacitance becomes spin-dependent, and is tunable by an external magnetic field. This molecular magnetocapacitance can be realized using ...

  14. Molecular Spintronics

    OpenAIRE

    Shiraishi, Masashi; Ikoma, Tadaaki

    2011-01-01

    Molecular spintronics is recognized to as an attractive new research direction in a field of spintronics, following to metallic spintronics and inorganic semiconductor spintronics, and attracts many people in recent decades. The purpose of this manuscript is to describe the history of molecular spintronics by introducing important achievements and to show the current status of this field. In addition, the authors briefly introduce several theories for implementing studies in molecular spintro...

  15. Molecular pharmacognosy

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    This article analyzes the background and significance of molecular pharmacognosy,including the molecular identification of medicinal raw materials,phylogenetic evolution of medicinal plants and animals,evaluation and preservation of germplasm resources for medicinal plants and animals,etiology of endangerment and protection of endangered medicinal plants and animals,biosynthesis and bioregulation of active components in medicinal plants,and characteristics and the molecular bases of top-geoherbs.

  16. Hybrid ceramic nanosieves: Stabilizing nanopores with organic links

    NARCIS (Netherlands)

    H.L. Castricum; A. Sah; R. Kreiter; D.H.A. Blank; J.F. Vente; J.E. ten Elshof

    2008-01-01

    Unprecedented hydrothermal stability in functional membranes has been obtained with hybrid organic-inorganic nanoporous materials, enabling long-term application in energy-efficient molecular separation, including dehydration up to at least 150 °C.

  17. Stability and instability in quantum mechanics

    International Nuclear Information System (INIS)

    This work is an attempt to describe the problem of stability and instabilities of quantum systems and involving very delicate experiments in molecular physics and solid state physics. A kind of transition to chaos occurs and few theoretical models have been proposed to investigate such a transition but it is better to use the term instabilities waiting for calling such an effect quantum chaos

  18. Triazatriangulene as binding group for molecular electronics

    DEFF Research Database (Denmark)

    Wei, Zhongming; Wang, Xintai; Borges, Anders;

    2014-01-01

    The triazatriangulene (TATA) ring system was investigated as a binding group for tunnel junctions of molecular wires on gold surfaces. Self-assembled monolayers (SAMs) of TATA platforms with three different lengths of phenylene wires were fabricated, and their electrical conductance was recorded ...... with its high stability and directionality make this binding group very attractive for molecular electronic measurements and devices. (Figure Presented)....

  19. Workshop on Feedback Stabilization of MHD Stabilities

    Energy Technology Data Exchange (ETDEWEB)

    McGuire, K.; Kugel, H. [Princeton Univ., NJ (United States). Plasma Physics Lab.; La Haye, R. [General Atomics, San Diego, CA (United States); Mauel, M. [Columbia Univ., New York, NY (United States). Dept. of Applied Physics; Nevins, W. [Lawrence Livermore National Lab., CA (United States); Prager, S. [Wisconsin Univ., Madison, WI (United States). Dept. of Physics

    1996-12-31

    The feedback stabilization of MHD instabilities is an area of research that is critical for improving the performance and economic attractiveness of magnetic confinement devices. A Workshop dedicated to feedback stabilization of MHD instabilities was held from December 11-13, 1996 at the Princeton Plasma Physics Laboratory, Princeton NJ, USA. The resulting presentations, conclusions, and recommendations are summarized.

  20. Molecular Diagnostics

    OpenAIRE

    Choe, Hyonmin; Deirmengian, Carl A; Hickok, Noreen J.; Morrison, Tiffany N.; Tuan, Rocky S.

    2015-01-01

    Orthopaedic infections are complex conditions that require immediate diagnosis and accurate identification of the causative organisms to facilitate appropriate management. Conventional methodologies for diagnosis of these infections sometimes lack accuracy or sufficient rapidity. Current molecular diagnostics are an emerging area of bench-to-bedside research in orthopaedic infections. Examples of promising molecular diagnostics include measurement of a specific biomarker in the synovial fluid...

  1. Theoretical investigation of structure and stability of complexes with molecular hydrogen of Cu+·(H2)n (n=1-4) and L·Cu+·H2 (L=CO,N2,H2O,NH3,CN- and BH4-) type

    International Nuclear Information System (INIS)

    Nonempirical MO LCAO SCF method was used to calculate structures and stability of Cu+ ion complexes with molecular hydrogen of Cu+·(H2)n and L·Cu+·H2 (L+CO,N2,H2O,NH3,CN- and BH4-) type. It was found that energies of successive addition of H2 molecules decreased monotonously from ∼54 to ∼13 kJ with n growth from 1 to 4. Energy of Cu+-H2 bond decreases if additional ligands L enter the coordination sphere of Cu+. This weakening is more pronounced for L=CO,N2 and BH4- (by ∼6-8 kJ), as compared with H2O,NH3 and CN-. Qualitative model for explaining slight effects of mutual effect of L and H2 is suggested. It is shown that π-acceptor properties of L ligands are the most important ones

  2. Deactivation efficiency of stabilized bactericidal emulsions.

    Science.gov (United States)

    Vyhnalkova, Renata; Eisenberg, Adi; van de Ven, Theo G M

    2011-09-20

    Biocide emulsions stabilized with various stabilizing agents were prepared and characterized, and their efficiency in bacteria deactivation was evaluated. A number of stabilizing agents were tested for their stabilizing effect on emulsions of thiocyanomethylthiobenzothiazole (TCMTB) biocide. Two agents, the most successful in stabilizing the biocide, were chosen for further studies: high molecular weight polyethyleneimine (PEI) and an amphiphilic block copolymer of poly(caprolactone)-b-poly(acrylic acid) (PCL(33)-b-PAA(33)). The emulsion droplet sizes varied between 325 and 500 nm. Deactivation of bacteria was studied by exposing E. coli ATCC 11229 bacteria dispersions to emulsions stabilized by positively charged PEI or negatively charged PCL-b-PAA micelles and by measuring their absorbance; E. coli do not grow with time in the presence of biocide emulsions. PEI molecules alone act as biocide and deactivate the bacteria. PCL-b-PAA micelles as stabilizing agent do not affect the growth of the E. coli ; bacteria are deactivated by TCMTB released from the emulsion droplets. The kinetics of emulsion dissolution studies revealed for both stabilizing agents a decrease in droplet size with time while the emulsions were subjected to dialysis. The biocide was released from the emulsions within ∼250 min; the droplet shells consist mostly of PEI or PCL-b-PAA insoluble complexes with the biocide, which do not dissolve during dialysis. SEM images confirm the presence of residual crumbled shells with holes after 24 h of dialysis. PMID:21823610

  3. Estimation of Stability Constants of Complex Compounds

    Directory of Open Access Journals (Sweden)

    Raos, N.

    Full Text Available The stability constant of a complex generally depends on the electronic, stereochemical and steric factors, as well as on the chelate effect and interaction of the complex, metal and ligand with water. In the first part of the paper we discuss the Irving-Williams order of stability of bivalent transition metal ion complexes from Mn2+ to Zn2+, along with the HSAB model (hard and soft acids and bases of stability. The second part describes three kinds of models for the estimation of the stability constants of complex compounds. First are those based on molecular mechanics, which were used mainly for the estimation of the enantioselectivity effect, i. e. Gibbs energy differences between MLL and MDL isomers. The second kind of models are mechanistic, that rest on the presumption of linear dependence of measured stability constants of the complexes with the same ligand (stability constants of mono- and bis-complexes, protonation constants, etc.. The third kind of models are heuristic (QSPR, which encompass molecular descriptors calculated by the method of overlapping spheres (OS, as well as topological indices. Among the variety of topological indices, connectivity indices proved best. They were calculated for the ligand and various representations of the coordination compound structure.

  4. Thermal stability of the aromatic fraction of Safaniya crude oil (Middle East): experimental study, kinetic scheme by molecular classes and geochemical implications; Stabilite thermique de la fraction aromatique de l'huile brute safaniya (Moyen-Orient): etude experimentale, schema cinetique par classes moleculaires et implications geochimiques

    Energy Technology Data Exchange (ETDEWEB)

    Al Darouich, T.

    2005-07-15

    The thermal evolution of reservoir oils is controlled by the kinetics of cracking reactions. The present work is concerned with the study of the thermal stability of the light aromatic components (C{sub 6}-C{sub 14}) of crude oils under geological conditions. The aim is to predict this stability through a mode l derived from laboratory pyrolyses. The light cut < 250 deg. C of Safaniya crude oil, corresponding to the C{sub 15} components, was obtained by fractionated distillation; pure aromatic fraction was then separated by liquid chromatography. Detailed molecular characterisation of the aromatic fraction was acquired using HPLC, GC and GC/MS. Then, quantified individual aromatic compounds were lumped into six molecular classes: BTXN, methyl-aromatics, alkyl-aromatics, naphthenic-aromatics, indene and sulphur - containing aromatics. Pyrolyses of the aromatic fraction were performed in gold tubes at 100 bars and different temperature/time conditions in a wide range (1 to 93%) of global conversion. Pyrolysis effluents were analysed and lumped into classes. The pyrolysis data were used to elaborate a semi - empirical kinetic scheme of 13 stoichiometric reactions for the primary and secondary cracking of the unstable classes. The scheme kinetic parameters were first estimated, and then numerically optimised, with the constraints of mass balance and hydrogen conservation. A set of pyrolysis experiments was performed at 375 deg.C under high pressures: 400, 800 and 1200 bars. Increasing slowing down in conversion rate with increasing pressure was thus observed compared to experiments at 100 bars. A slight selective effect of pressure on the different aromatic classes of the charge and on the product distribution was evidenced. The extrapolation of the kinetic model to the conditions of Elgin Field (North Sea) showed that pressure effect should shift the thermal cracking of light aromatics to higher temperatures by almost 8 deg. C. (author)

  5. Nuclear molecular states

    International Nuclear Information System (INIS)

    The effects of polarization on the stability of α-cluster structures in 8Be and 12C nuclei are studied in the intrinsic states. The extent of the polarization of α-clusters is investigated by employing a molecular-orbital model. Two α-cluster structure of 8Be is shown to be extremely stable, and a triangular configuration of three α-clusters is also shown to be stable, but the polarizations of α-clusters are found rather large. Gruemmer--Faessler's method is discussed and their results are shown to be trivial

  6. Stability of Dolos Slopes

    DEFF Research Database (Denmark)

    Brorsen, Michael; Burcharth, Hans F.; Larsen, Torben

    The stability of dolos armour blocks against wave attack has been investigated in wave model studies.......The stability of dolos armour blocks against wave attack has been investigated in wave model studies....

  7. K stability and stability of chiral ring

    CERN Document Server

    Collins, Tristan C; Yau, Shing-Tung

    2016-01-01

    We define a notion of stability for chiral ring of four dimensional N=1 theory by introducing test chiral rings and generalized a maximization. We conjecture that a chiral ring is the chiral ring of a superconformal field theory if and only if it is stable. We then study N=1 field theory derived from D3 branes probing a three-fold singularity X, and show that the K stability which implies the existence of Ricci-flat conic metric on X is equivalent to the stability of chiral ring of the corresponding field theory.

  8. Stability of parallel flows

    CERN Document Server

    Betchov, R

    2012-01-01

    Stability of Parallel Flows provides information pertinent to hydrodynamical stability. This book explores the stability problems that occur in various fields, including electronics, mechanics, oceanography, administration, economics, as well as naval and aeronautical engineering. Organized into two parts encompassing 10 chapters, this book starts with an overview of the general equations of a two-dimensional incompressible flow. This text then explores the stability of a laminar boundary layer and presents the equation of the inviscid approximation. Other chapters present the general equation

  9. A transient α-helical molecular recognition element in the disordered N-terminus of the Sgs1 helicase is critical for chromosome stability and binding of Top3/Rmi1.

    Science.gov (United States)

    Kennedy, Jessica A; Daughdrill, Gary W; Schmidt, Kristina H

    2013-12-01

    The RecQ-like DNA helicase family is essential for the maintenance of genome stability in all organisms. Sgs1, a member of this family in Saccharomyces cerevisiae, regulates early and late steps of double-strand break repair by homologous recombination. Using nuclear magnetic resonance spectroscopy, we show that the N-terminal 125 residues of Sgs1 are disordered and contain a transient α-helix that extends from residue 25 to 38. Based on the residue-specific knowledge of transient secondary structure, we designed proline mutations to disrupt this α-helix and observed hypersensitivity to DNA damaging agents and increased frequency of genome rearrangements. In vitro binding assays show that the defects of the proline mutants are the result of impaired binding of Top3 and Rmi1 to Sgs1. Extending mutagenesis N-terminally revealed a second functionally critical region that spans residues 9-17. Depending on the position of the proline substitution in the helix functional impairment of Sgs1 function varied, gradually increasing from the C- to the N-terminus. The multiscale approach we used to interrogate structure/function relationships in the long disordered N-terminal segment of Sgs1 allowed us to precisely define a functionally critical region and should be generally applicable to other disordered proteins. PMID:24038467

  10. Molecular Electronics

    DEFF Research Database (Denmark)

    Jennum, Karsten Stein

    This thesis includes the synthesis and characterisation of organic compounds designed for molecular electronics. The synthesised organic molecules are mainly based on two motifs, the obigo(phenyleneethynylenes) (OPE)s and tetrathiafulvalene (TTF) as shown below. These two scaffolds (OPE and TTF......) are chemically merged together to form cruciform-like structures that are an essential part of the thesis. The cruciform molecules were subjected to molecular conductance measurements to explore their capability towards single-crystal field-effect transistors (Part 1), molecular wires, and single electron......, however, was obtained by a study of a single molecular transistor. The investigated OPE5-TTF compound was captured in a three-terminal experiment, whereby manipulation of the molecule’s electronic spin was possible in different charge states. Thus, we demonstrated how the cruciform molecules could...

  11. Molecular sciences

    International Nuclear Information System (INIS)

    The research in molecular sciences summarized includes photochemistry, radiation chemistry, geophysics, electromechanics, heavy-element oxidizers , heavy element chemistry collisions, atoms, organic solids. A list of publications is included

  12. Synthesis and stability test of radiogadolinium(III-DOTA-PAMAM G3.0-trastuzumab as SPECT-MRI molecular imaging agent for diagnosis of HER-2 positive breast cancer

    Directory of Open Access Journals (Sweden)

    Hardiani Rahmania

    2015-01-01

    Full Text Available Nonivasive diagnosis of cancer can be provided by molecular imaging using hybrid modality to obtain better sensitivity, specificity and depiction localization of the disease. In this study, we developed a new molecular imaging agent, radiogadolinium(III-DOTA-PAMAM G3.0-trastuzumab in the form of 147Gd-DOTA-PAMAM G3.0-trastuzumab, that can be both target-specific radiopharmaceutical in SPECT as well as targeted contrast agent in MRI for the purpose of diagnosis of HER-2 positive breast cancer. 147Gd radionuclide emits γ-rays that can be used in SPECT modality, but because of technical constraint, 147Gd radionuclide was simulated by its radioisotope, 153Gd. Gd-DOTA complex has also been known as good MRI contrast agent. PAMAM G3.0 is useful to concentrate Gd-DOTA compelexes in large quantities, thus minimizing the number of trastuzumab molecules used. Trastuzumab is human monoclonal antibody that can spesifically interact with HER-2. Synthesis of radiogadolinium(III-DOTA-PAMAM G3.0-trastuzumab was initiated by conjugating DOTA NHS ester ligand with PAMAM G3.0 dendrimer. The DOTA-PAMAM G3.0 produced was conjugated to trastuzumab molecule and labeled with 153Gd. Characterization DOTA-PAMAM G3.0-trastuzumab immunoconjugate was performed using HPLC system equipped with SEC. The formation of immunoconjugate was indicated by the shorter retention time (6.82 min compared to that of trastuzumab (7.06 min. Radiochemical purity of radiogadolinium(III-DOTA-PAMAM G3.0-trastuzumab was >99% after purification process by PD-10 desalting column. Radiogadolinium(III-DOTA-PAMAM G3.0-trastuzumab compound was stable at room temperature and at 2–8 0C as indicated by its radiochemical purity 97.6 ± 0.5%–99.1 ± 0.5% after 144 h storage.

  13. Molecular farming

    OpenAIRE

    Merck, K.B.; Vereijken, J M

    2006-01-01

    Molecular Farming is a new and emerging technology that promises relatively cheap and flexible production of large quantities of pharmaceuticals in genetically modified plants. Many stakeholders are involved in the production of pharmaceuticals in plants, which complicates the discussion on the possible benefits and disadvantages to a great extent. Discussions about Molecular Farming are often about technical and economic aspects, but other aspects like safety and ethical and societal aspects...

  14. Molecular printing

    OpenAIRE

    Braunschweig, Adam B.; Huo, Fengwei; Mirkin, Chad A.

    2009-01-01

    Molecular printing techniques, which involve the direct transfer of molecules to a substrate with submicrometre resolution, have been extensively developed over the past decade and have enabled many applications. Arrays of features on this scale have been used to direct materials assembly, in nanoelectronics, and as tools for genetic analysis and disease detection. The past decade has witnessed the maturation of molecular printing led by two synergistic technologies: dip-pen nanolithography a...

  15. Molecular Nanoelectronics

    OpenAIRE

    Vuillaume, Dominique

    2010-01-01

    Molecular electronics is envisioned as a promising candidate for the nanoelectronics of the future. More than a possible answer to ultimate miniaturization problem in nanoelectronics, molecular electronics is foreseen as a possible way to assemble a large numbers of nanoscale objects (molecules, nanoparticules, nanotubes and nanowires) to form new devices and circuit architectures. It is also an interesting approach to significantly reduce the fabrication costs, as well as the energetical cos...

  16. Feedback stabilization initiative

    International Nuclear Information System (INIS)

    Much progress has been made in attaining high confinement regimes in magnetic confinement devices. These operating modes tend to be transient, however, due to the onset of MHD instabilities, and their stabilization is critical for improved performance at steady state. This report describes the Feedback Stabilization Initiative (FSI), a broad-based, multi-institutional effort to develop and implement methods for raising the achievable plasma betas through active MHD feedback stabilization. A key element in this proposed effort is the Feedback Stabilization Experiment (FSX), a medium-sized, national facility that would be specifically dedicated to demonstrating beta improvement in reactor relevant plasmas by using a variety of MHD feedback stabilization schemes

  17. Moringa coagulant as a stabilizer for amorphous solids: Part I.

    Science.gov (United States)

    Bhende, Santosh; Jadhav, Namdeo

    2012-06-01

    Stabilization of amorphous state is a focal area for formulators to reap benefits related with solubility and consequently bioavailability of poorly soluble drugs. In the present work, an attempt has been made to explore the potential of moringa coagulant as an amorphous state stabilizer by investigating its role in stabilization of spray-dried (amorphous) ibuprofen, meloxicam and felodipine. Thermal studies like glass forming ability, glass transition temperature, hot stage microscopy and DSC were carried out for understanding thermodynamic stabilization of drugs. PXRD and dissolution studies were performed to support contribution of moringa coagulant. Studies showed that hydrogen bonding and electrostatic interactions between drug and moringa coagulant are responsible for amorphous state stabilization as explored by ATR-FTIR and molecular docking. Especially, H-bonding was found to be predominant mechanism for drug stabilization. Therein, arginine (basic amino acid in coagulant) exhibited various interactions and played important role in stabilization of aforesaid amorphous drugs. PMID:22359158

  18. Molecular physics

    CERN Document Server

    Demtröder, Wolfgang

    2008-01-01

    The richly illustrated book comprehensively explains the important principles of diatomic and polyatomic molecules and their spectra in two separate, distinct parts. The first part concentrates on the theoretical aspects of molecular physics, such as the vibration, rotation, electronic states, potential curves, and spectra of molecules. The different methods of approximation for the calculation of electronic wave functions and their energy are also covered. The introduction of basics terms used in group theory and their meaning in molecular physics enables an elegant description of polyatomic

  19. Molecular pathways

    DEFF Research Database (Denmark)

    Cox, Thomas R; Erler, Janine Terra

    2014-01-01

    45% of deaths in the developed world are linked to fibrotic disease. Fibrosis and cancer are known to be inextricably linked; however, we are only just beginning to understand the common and overlapping molecular pathways between the two. Here, we discuss what is known about the intersection of...... fibrosis and cancer, with a focus on cancer metastasis, and highlight some of the exciting new potential clinical targets that are emerging from analysis of the molecular pathways associated with these two devastating diseases. Clin Cancer Res; 20(14); 3637-43. ©2014 AACR....

  20. Molecular modeling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-01-01

    Full Text Available The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular modeling. Molecular modeling is a rapidly developing discipline, and has been supported by the dramatic improvements in computer hardware and software in recent years.

  1. Internet Addiction: Stability and Change

    Science.gov (United States)

    Huang, Chiungjung

    2010-01-01

    This longitudinal study examined five indices of stability and change in Internet addiction: structural stability, mean-level stability, differential stability, individual-level stability, and ipsative stability. The study sample was 351 undergraduate students from end of freshman year to end of junior year. Convergent findings revealed stability…

  2. Molecular gastronomy

    Science.gov (United States)

    This, Hervé

    2005-01-01

    For centuries, cooks have been applying recipes without looking for the mechanisms of the culinary transformations. A scientific discipline that explores these changes from raw ingredients to eating the final dish, is developing into its own field, termed molecular gastronomy. Here, one of the founders of the discipline discusses its aims and importance.

  3. Molecular photobiology.

    OpenAIRE

    Nikkels, Arjen; Pierard, Claudine; Pierard, Gérald

    2005-01-01

    Photochemical reactions are numerous in the skin. They generate reactive oxygen species and other biochemical alterations as well. According to their nature, the molecular components of the skin which have been altered by these mechanisms can be repaired with various degrees of efficacy. Peer reviewed

  4. Molecular photovoltaics

    OpenAIRE

    Moser, Jacques E.; Bonnôte, Pierre; Grätzel, Michael

    1998-01-01

    Photoinduced charge transfer processes involving molecules adsorbed at interfaces are a fascinating topic which is presently attracting wide attention. Our investigations have focused on the identification of the factors that control the dynamics of such processes. The goal is to design molecular electronic devices that achieve efficient light-induced charge separation. Applications of similar systems in photochromic and electrochromic devices also appear feasible.

  5. Molecular farming

    NARCIS (Netherlands)

    Merck, K.B.; Vereijken, J.M.

    2006-01-01

    Molecular Farming is a new and emerging technology that promises relatively cheap and flexible production of large quantities of pharmaceuticals in genetically modified plants. Many stakeholders are involved in the production of pharmaceuticals in plants, which complicates the discussion on the poss

  6. Adhesive–cohesive model for protein compressibility: An alternative perspective on stability

    OpenAIRE

    Dadarlat, Voichita M.; Post, Carol Beth

    2003-01-01

    As a dynamic property of folded proteins, protein compressibility provides important information about the forces that govern structural stability. We relate intrinsic compressibility to stability by using molecular dynamics to identify a molecular basis for the variation in compressibility among globular proteins. We find that excess surface charge accounts for this variation not only for the proteins simulated by molecular dynamics but also for a larger set of globular proteins. This depend...

  7. Stabilization of elusive silicon oxides.

    Science.gov (United States)

    Wang, Yuzhong; Chen, Mingwei; Xie, Yaoming; Wei, Pingrong; Schaefer, Henry F; Schleyer, Paul von R; Robinson, Gregory H

    2015-06-01

    Molecular SiO2 and other simple silicon oxides have remained elusive despite the indispensable use of silicon dioxide materials in advanced electronic devices. Owing to the great reactivity of silicon-oxygen double bonds, as well as the low oxidation state of silicon atoms, the chemistry of simple silicon oxides is essentially unknown. We now report that the soluble disilicon compound, L:Si=Si:L (where L: = :C{N(2,6-(i)Pr2C6H3)CH}2), can be directly oxidized by N2O and O2 to give the carbene-stabilized Si2O3 and Si2O4 moieties, respectively. The nature of the silicon oxide units in these compounds is probed by spectroscopic methods, complementary computations and single-crystal X-ray diffraction.

  8. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, Charlotte S; Trandum, Christa; Larsen, Nanna Brink;

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (Tm) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal alpha-helix was of major importance to the conformational stability of calreticulin....

  9. Temperature stabilized phase detector

    Science.gov (United States)

    Lo, Y.

    1981-01-01

    The construction, tests, and performance of a temperature stabilized phase detector are discussed. It has a frequency stability of 5 parts in 10 to the 16th power at 100 MHz, with a temperature step of 20 C (15 to 35 C).

  10. Conformational stability of calreticulin

    DEFF Research Database (Denmark)

    Jørgensen, C.S.; Trandum, C.; Larsen, N.;

    2005-01-01

    The conformational stability of calreticulin was investigated. Apparent unfolding temperatures (T-m) increased from 31 degrees C at pH 5 to 51 degrees C at pH 9, but electrophoretic analysis revealed that calreticulin oligomerized instead of unfolding. Structural analyses showed that the single C......-terminal a-helix was of major importance to the conformational stability of calreticulin....

  11. Radion Cosmology and Stabilization

    CERN Document Server

    Chakraborty, Sumanta

    2014-01-01

    We have solved the Einstein equation in 5D spacetime for Randall Sundrum Brane world model with time dependent radion field. We have shown how inflation could compactify the extra dimension such that it become unobservable today. We also propose a mechanism for stabilizing the time dependent radion field following Goldberger Wise mechanism and have obtained the stabilized value.

  12. Stability: general considerations

    International Nuclear Information System (INIS)

    This chapter is concerned with determining the stability properties of ideal MHD equilibria. The problem of stability can be stated qualitatively as follows. The existence of an MHD equilibrium state implies a situation where the sum of the forces acting on the plasma is zero. If the plasma is perturbed from this state, the resulting perturbed forces either restore the plasma to its original equilibrium (stability) or cause a further enhancement of the initial disturbance (instability). Chapter 8 begins with a discussion of a mathematical definition of stability particularly applicable to ideal MHD. Next, a short derivation is presented of the dispersion relation for waves in an infinite homogeneous MHD plasma. These waves play an important role in providing intuition into the dynamical behavior of an MHD plasma. Following this is a rather extensive discussion of the formulation of the general linearized stability problem, starting with the equations of motion and culminating with the development of the Energy Principle, a powerful method for testing stability. Having established the Energy Principle, it is then possible to address the role of plasma compressibility on ideal MHD stability in a general manner. This demonstrates the relationship between the ideal and collisionless MHD stability boundaries. Next, a rather subtle point is investigated concerning whether the region outside the main plasma core is more accurately described by a vacuum or by a relatively cold, but still perfectly conducting, force-free plasma. Finally, a brief discussion is presented of the general classification of ideal MHD instabilities

  13. Stability of charged membranes

    OpenAIRE

    Bensimon, D; David, F.; Leibler, S.; Pumir, A.

    1990-01-01

    The electrostatic contribution to the bending elastic modulus of charged phospholipid bilayers in an ionic solution is computed. It is found to be the same for conducting and non-conducting membranes and is always stabilizing. This stability for free membranes is shown to be a simple consequence of the vanishing of the physical surface tension.

  14. Molecular Modelling

    Directory of Open Access Journals (Sweden)

    Aarti Sharma

    2009-12-01

    Full Text Available

    The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important
    tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and
    the exponential growth of the knowledge of protein structures have made it possible for organic compounds to tailored to
    decrease harmful side effects and increase the potency. This article provides a detailed description of the techniques
    employed in molecular modeling. Molecular modelling is a rapidly developing discipline, and has been supported from
    the dramatic improvements in computer hardware and software in recent years.

  15. Molecular Mechanics

    OpenAIRE

    Vanommeslaeghe, Kenno; Guvench, Olgun; Alexander D MacKerell

    2014-01-01

    Molecular Mechanics (MM) force fields are the methods of choice for protein simulations, which are essential in the study of conformational flexibility. Given the importance of protein flexibility in drug binding, MM is involved in most if not all Computational Structure-Based Drug Discovery (CSBDD) projects. This section introduces the reader to the fundamentals of MM, with a special emphasis on how the target data used in the parametrization of force fields determine their strengths and wea...

  16. Molecular Quarkonium

    OpenAIRE

    Voloshin, M. B.

    2006-01-01

    I discuss topics related to four-quark states of the `molecular quarkonium' type, i.e. resonances that could be considered as (dominantly) made from a heavy meson and antimeson. Of the so far observed resonances such picture is very likely applicable to the state X(3872), and I also discuss its possible relevance to the peak near the $D^* {\\bar D}^*$ threshold in $e^+e^-$ annihilation.

  17. Molecular Morphology

    OpenAIRE

    Donath, Alexander

    2011-01-01

    A fundamental problem in biology is the reconstruction of the relatedness of all (extant) species. Traditionally, systematists employ visually recognizable characters of organisms for classification and evolutionary analysis. Recent developments in molecular and computational biology, however, lead to a whole different perspective on how to address the problem of inferring relatedness. The discovery of molecules, carrying genetic information, and the comparison of their primary structure h...

  18. Molecular Diagnosis

    OpenAIRE

    Hoar, David I.

    1987-01-01

    Recombinant DNA technology, one of the major controversial areas of biological research in the late 1970s, is now rapidly providing new avenues for diagnosis and treatment. With the early recognition that extensive DNA variation exists in human populations, molecular genetic diagnosis of a variety of common hereditary diseases has become a reality. Recent identification of the location of the gene (or genes) for cystic fibrosis and adult polycystic kidney disease, and characterization of the ...

  19. Molecular modeling

    OpenAIRE

    Aarti Sharma; Himanshu Gupta

    2009-01-01

    The use of computational chemistry in the development of novel pharmaceuticals is becoming an increasingly important tool. In the past, drugs were simply screened for effectiveness. The recent advances in computing power and the exponential growth of the knowledge of protein structures have made it possible for organic compounds to be tailored to decrease the harmful side effects and increase the potency. This article provides a detailed description of the techniques employed in molecular mod...

  20. Molecular Modeling

    Science.gov (United States)

    Holmes, Jon L.

    1999-06-01

    Molecular modeling has trickled down from the realm of pharmaceutical and research laboratories into the realm of undergraduate chemistry instruction. It has opened avenues for the visualization of chemical concepts that previously were difficult or impossible to convey. I am sure that many of you have developed exercises using the various molecular modeling tools. It is the desire of this Journal to become an avenue for you to share these exercises among your colleagues. It is to this end that Ron Starkey has agreed to edit such a column and to publish not only the description of such exercises, but also the software documents they use. The WWW is the obvious medium to distribute this combination and so accepted submissions will appear online as a feature of JCE Internet. Typical molecular modeling exercise: finding conformation energies. Molecular Modeling Exercises and Experiments is the latest feature column of JCE Internet, joining Conceptual Questions and Challenge Problems, Hal's Picks, and Mathcad in the Chemistry Curriculum. JCE Internet continues to seek submissions in these areas of interest and submissions of general interest. If you have developed materials and would like to submit them, please see our Guide to Submissions for more information. The Chemical Education Resource Shelf, Equipment Buyers Guide, and WWW Site Review would also like to hear about chemistry textbooks and software, equipment, and WWW sites, respectively. Please consult JCE Internet Features to learn more about these resources at JCE Online. Email Announcements Would you like to be informed by email when the latest issue of the Journal is available online? when a new JCE Software title is shipping? when a new JCE Internet article has been published or is available for Open Review? when your subscription is about to expire? A new feature of JCE Online makes this possible. Visit our Guestbook to learn how. When you submit the form on this page, which includes your email address

  1. Drilling string stabilizer

    Energy Technology Data Exchange (ETDEWEB)

    Reznik, L.A.; Gurevich, D.A.; Korsakov, N.T.; Savich, M.S.; Ulitskiy, Ye.N.; Zinchenko, V.K.

    1981-04-15

    A stabilizer of a drilling string is suggested which is installed in the turning of a rod and contains two half shells with graduated mutually joining surfaces and fixing connecting element made in the form of a pin. In order to improve the reliable operation and to simplify the assembly-disassembly, the mutually joining surfaces of the half shells are made with a Z-shape, while the connecting fixing element is made in the form of a clamp and is placed between the ends of the stabilizer and the broad turning. The connecting surfaces of the rod of the stabilizer have an unrounded shape.

  2. Designed metalloprotein stabilizes a semiquinone radical.

    Science.gov (United States)

    Ulas, Gözde; Lemmin, Thomas; Wu, Yibing; Gassner, George T; DeGrado, William F

    2016-04-01

    Enzymes use binding energy to stabilize their substrates in high-energy states that are otherwise inaccessible at ambient temperature. Here we show that a de novo designed Zn(II) metalloprotein stabilizes a chemically reactive organic radical that is otherwise unstable in aqueous media. The protein binds tightly to and stabilizes the radical semiquinone form of 3,5-di-tert-butylcatechol. Solution NMR spectroscopy in conjunction with molecular dynamics simulations show that the substrate binds in the active site pocket where it is stabilized by metal-ligand interactions as well as by burial of its hydrophobic groups. Spectrochemical redox titrations show that the protein stabilized the semiquinone by reducing the electrochemical midpoint potential for its formation via the one-electron oxidation of the catechol by approximately 400 mV (9 kcal mol(-1)). Therefore, the inherent chemical properties of the radical were changed drastically by harnessing its binding energy to the metalloprotein. This model sets the basis for designed enzymes with radical cofactors to tackle challenging chemistry. PMID:27001731

  3. Designed metalloprotein stabilizes a semiquinone radical

    Science.gov (United States)

    Ulas, Gözde; Lemmin, Thomas; Wu, Yibing; Gassner, George T.; Degrado, William F.

    2016-04-01

    Enzymes use binding energy to stabilize their substrates in high-energy states that are otherwise inaccessible at ambient temperature. Here we show that a de novo designed Zn(II) metalloprotein stabilizes a chemically reactive organic radical that is otherwise unstable in aqueous media. The protein binds tightly to and stabilizes the radical semiquinone form of 3,5-di-tert-butylcatechol. Solution NMR spectroscopy in conjunction with molecular dynamics simulations show that the substrate binds in the active site pocket where it is stabilized by metal-ligand interactions as well as by burial of its hydrophobic groups. Spectrochemical redox titrations show that the protein stabilized the semiquinone by reducing the electrochemical midpoint potential for its formation via the one-electron oxidation of the catechol by approximately 400 mV (9 kcal mol-1). Therefore, the inherent chemical properties of the radical were changed drastically by harnessing its binding energy to the metalloprotein. This model sets the basis for designed enzymes with radical cofactors to tackle challenging chemistry.

  4. Nonlinear hydrodynamic stability

    CERN Document Server

    Isichenko, M B

    1998-01-01

    The variational principle of V. I. Arnold [J. Appl. Math. Mech. Vol. 29, P. 1002 (1965)] is extended to the general conservative inhomogeneous, compressible, and conducting fluid. The concept of iso-vortical flows is generalized to an "invariant foliation" of the phase space. The foliation, which may or may not correspond to explicit conservation laws, is derived from the equations of motion and used for Lyapunov stability. A nonlinear three-dimensional (magneto-) hydrodynamic stability criterion is formulated.

  5. Thermodynamic Stability of Wormholes

    CERN Document Server

    Sajadi, S N

    2016-01-01

    In the context of GR, we study the thermodynamic stability of evolving Lorentzian wormholes at the apparent horizon. The average pressure of the anisotrropic components is considered as the pressure of the wormhole. According to the requirements of stable equilibrium in conventional thermodynamics, we calculate the heat capacity at constant pressure and Gibbs free energy and analyze the local and global thermodynamic stability of the wormhole.

  6. Automatic Fiscal Stabilizers

    Directory of Open Access Journals (Sweden)

    Narcis Eduard Mitu

    2013-11-01

    Full Text Available Policies or institutions (built into an economic system that automatically tend to dampen economic cycle fluctuations in income, employment, etc., without direct government intervention. For example, in boom times, progressive income tax automatically reduces money supply as incomes and spendings rise. Similarly, in recessionary times, payment of unemployment benefits injects more money in the system and stimulates demand. Also called automatic stabilizers or built-in stabilizers.

  7. PFP solution stabilization

    International Nuclear Information System (INIS)

    This Functional Design Criteria (FDC) addresses remediation of the plutonium-bearing solutions currently in inventory at the Plutonium Finishing Plant (PFP). The recommendation from the Environmental Impact Statement (EIS) is that the solutions be treated thermally and stabilized as a solid for long term storage. For solutions which are not discardable, the baseline plan is to utilize a denitration process to stabilize the solutions prior to packaging for storage

  8. Stability of settlement space

    OpenAIRE

    Fikfak, Alenka

    2015-01-01

    Characteristics of settlements patterns and forms are encompassed between stability and instability. We evaluate them according to their historical value, but their image, as perceived today after centuries of changing, adapting and transformation, cannot be recognised in its original form. Time is the "super-factor" that balances, determines and transforms internal forces of settlement structures, and is decisively conditioned by social links. Instability can change to stability and vice ver...

  9. COLLAGEN STRUCTURE AND STABILITY

    OpenAIRE

    Shoulders, Matthew D.; Raines, Ronald T.

    2009-01-01

    Collagen is the most abundant protein in animals. This fibrous, structural protein comprises a right-handed bundle of three parallel, left-handed polyproline II-type helices. Much progress has been made in elucidating the structure of collagen triple helices and the physicochemical basis for their stability. New evidence demonstrates that stereoelectronic effects and preorganization play a key role in that stability. The fibrillar structure of type I collagen–the prototypical collagen fibril–...

  10. Food Fortification Stability Study

    Science.gov (United States)

    Sirmons, T. A.; Cooper, M. R.; Douglas, G. L.

    2016-01-01

    This study aims to assess the stability of vitamin content, sensory acceptability and color variation in fortified spaceflight foods over a period of 2 years. Findings will identify optimal formulation, processing, and storage conditions to maintain stability and acceptability of commercially available fortification nutrients. Changes in food quality are being monitored to indicate whether fortification affects quality over time (compared to the unfortified control), thus indicating their potential for use on long-duration missions.

  11. Geometry, stability and thermal transport of hydrogenated graphene nanoquilts

    OpenAIRE

    Zhang, Zhongwei; Xie, Yuee; Peng, Qing; Chen, Yuanping

    2016-01-01

    Geometry, stability, and thermal transport of graphene nanoquilts folded by hydrogenation are studied using molecular dynamics simulations. The hydrogenated graphene nanoquilts show increased thermodynamic stability and better transport properties than folded graphene structures without hydrogenation. For the two-fold graphene nanoquilt, both geometry and thermal conductivity are very sensitive to the adsorbed hydrogen chains, which is interpreted by the red-shift of PDOS. For the multi-fold ...

  12. Molecular biological study on genetic stability of the genome

    International Nuclear Information System (INIS)

    A population cytogenetic study has been performed in 1022 healthy subjects and 547 cancer patients to determine baseline frequencies of autosomal rate fragile sites. Out of 17 rare autosomal fragile sites defined in HBM9 (1985), the following six were detected: fra(2)(q11), fra(10)(q25), fra(11)(q13), fra(11)(q23), fra(16)(q22) and fra(17)(q12). Other three new fragile sites were also detected: fra(8)(q24.1), fra(11)(q15.1) and fra(16)(p12.1). They were all distamycin A-inducible and located at the junctions of G/R-bands. The incidence of these autosomal fragile sites was 5% in both healthy subjects and cancer patients. Distamycin A-induced fragile sites may play a role in the etiology of leukemia, myeloproliferative disorders, and gynecological tumors. The present study also examined the mechanism of fragile X expression associated with fragile X syndrome in thymidine-prototrophic and auxotrophic human-mouse somatic cell hybrids. In these hybrid cells, both low and high thymidylate stresses were found to be effective in inducing fragile X expression, even in a hybrid clone that retained a fragile X chromosome as the only human chromosome. An addition of deoxycytidine completely abolished the effect of high thymidylate stress achieved by excess amounts of thymidine. It is concluded that the expression is an intrinsic property of the fragile X mutation resulting from chromosomal change in a special class of replicons with polypurine/polypyrimidine DNA sequence. (Namekawa, K)

  13. Aquifer stability investigations

    Energy Technology Data Exchange (ETDEWEB)

    Allen, R.D.; Doherty, T.J.

    1981-09-01

    The study of compressed air energy storage (CAES) in porous rock reservoirs is carried out within the Reservoir Stability Studies Program at Pacific Northwest Laboratory. The goal of the study is to establish criteria for long-term stability of aquifer CAES reservoirs. These criteria are intended to be guidelines and check lists that utilities and architect-engineering firms may use to evaluate reservoir stability at candidate CAES sites. These criteria will be quantitative where possible, qualitative where necessary, and will provide a focal point for CAES relevant geotechnical knowledge, whether developed within this study or available from petroleum, mining or other geotechnical practices using rock materials. The Reservoir Stability Studies Program had four major activities: a state-of-the-art survey to establish preliminary stability criteria and identify areas requiring research and development; numerical modeling; laboratory testing to provide data for use in numerical models and to investigate fundamental rock mechanics, thermal, fluid, and geochemical response of aquifer materials; and field studies to verify the feasibility of air injection and recovery under CAES conditions in an aquifer, to validate and refine the stability criteria, and to evaluate the accuracy and adequacy of the numerical and experimental methodologies developed in previous work. Three phases of study, including preliminary criteria formulation, numerical model development, and experimental assessment of CAES reservoir materials have been completed. Present activity consists of construction and operation of the aquifer field test, and associated numerical and experimental work in support of that activity. Work is presently planned to be complete by 1983 at the end of the field test. At that time the final stability criteria for aquifers will be issued. Attached here also are preliminary criteria for aquifers.

  14. MHz unidirectional rotation of molecular rotary motors

    NARCIS (Netherlands)

    Klok, Martin; Boyle, Nicola; Pryce, Mary T.; Meetsma, Auke; Browne, Wesley R.; Feringa, Ben L.

    2008-01-01

    A combination of cryogenic UV-vis and CD spectroscopy and transient absorption spectroscopy at ambient temperature is used to study a new class of unidirectional rotary molecular motors. Stabilization of unstable intermediates is achieved below 95 K in propane solution for the structure with the fas

  15. Evolutionary stability of sex chromosomes in snakes.

    Science.gov (United States)

    Rovatsos, Michail; Vukić, Jasna; Lymberakis, Petros; Kratochvíl, Lukáš

    2015-12-22

    Amniote vertebrates possess various mechanisms of sex determination, but their variability is not equally distributed. The large evolutionary stability of sex chromosomes in viviparous mammals and birds was believed to be connected with their endothermy. However, some ectotherm lineages seem to be comparably conserved in sex determination, but previously there was a lack of molecular evidence to confirm this. Here, we document a stability of sex chromosomes in advanced snakes based on the testing of Z-specificity of genes using quantitative PCR (qPCR) across 37 snake species (our qPCR technique is suitable for molecular sexing in potentially all advanced snakes). We discovered that at least part of sex chromosomes is homologous across all families of caenophidian snakes (Acrochordidae, Xenodermatidae, Pareatidae, Viperidae, Homalopsidae, Colubridae, Elapidae and Lamprophiidae). The emergence of differentiated sex chromosomes can be dated back to about 60 Ma and preceded the extensive diversification of advanced snakes, the group with more than 3000 species. The Z-specific genes of caenophidian snakes are (pseudo)autosomal in the members of the snake families Pythonidae, Xenopeltidae, Boidae, Erycidae and Sanziniidae, as well as in outgroups with differentiated sex chromosomes such as monitor lizards, iguanas and chameleons. Along with iguanas, advanced snakes are therefore another example of ectothermic amniotes with a long-term stability of sex chromosomes comparable with endotherms.

  16. Stabilization of reactive species by supramolecular encapsulation.

    Science.gov (United States)

    Galan, Albano; Ballester, Pablo

    2016-03-14

    Molecular containers have attracted the interest of supramolecular chemists since the early beginnings of the field. Cavitands' inner cavities were quickly exploited by Cram and Warmuth to construct covalent containers able to stabilize and assist the characterization of short-lived reactive species such as cyclobutadiene or o-benzyne. Since then, more complex molecular architectures have been prepared able to store and isolate a myriad of fleeting species (i.e. organometallic compounds, cationic species, radical initiators…). In this review we cover selected examples of the stabilization of reactive species by encapsulation in molecular containers from the first reports of covalent containers described by Cram et al. to the most recent examples of containers with self-assembled structure (metal coordination cages and hydrogen bonded capsules). Finally, we briefly review examples reported by Rebek et al. in which elusive reaction intermediates could be detected in the inner cavities of self-folding resorcin[4]arene cavitands by the formation of covalent host-guest complexes. The utilization of encapsulated reactive species in catalysis or synthesis is not covered. PMID:26797259

  17. Optically switchable molecular device using microsphere based junctions

    Science.gov (United States)

    Faramarzi, V.; Raimondo, C.; Reinders, F.; Mayor, M.; Samorı, P.; Doudin, B.

    2011-12-01

    Metallic planar electrodes are bridged using microspheres coated with chemisorbed azobenzene self-assembled monolayers. The circuit exhibits light-induced switching, with reproducibility over 90%, as statistically determined and compared to junctions incorporating photo-insensitive alkanethiol layers. Microsphere interconnects provide direct access to molecular transport properties, with reliability and stability, making multifunctional molecular electronics devices possible.

  18. Laser Frequency Stabilization

    Science.gov (United States)

    Donelan, Darsa; Mueller, Guido; Thorpe, James; Livas, Jeffrey

    2011-01-01

    Laser ranging and interferometry are essential technologies allowing for many astounding new spacebased missions such as the Laser Interferometer Space Antenna (LISA) to measure gravitational radiation emitted from distant super massive black hole mergers or distributed aperture telescopes with unprecedented angular resolution in the NIR or visible regime. The requirements on laser frequency noise depend on the residual motion and the distances between the spacecraft forming the interferometer. The intrinsic frequency stability of commercial lasers is several orders of magnitude above these requirements. Therefore, it is necessary for lasers to be stabilized to an ultrastable frequency reference so that they can be used to sense and control distances between spacecraft. Various optical frequency references and frequency stabilization schemes are considered and investigated for the applicability and usefulness for space-based interferometry missions.

  19. Generalized Lotka stability.

    Science.gov (United States)

    Smith, J D H; Zhang, C

    2015-08-01

    The recently developed macroscopic approach to demography describes the age distribution of mothers and the net maternity function for a given human population entirely in terms of five parameters. Tracking of these parameters provides a number of new tools for analyzing populations and predicting their future states. Within the macroscopic approach, the new concept of generalized Lotka stability is presented in this paper, as an extension of a strong version of classic Lotka stability. The two leading parameters of the macroscopic approach, the Malthusian parameter r and the perturbation s, are computed from population data and plotted in two-dimensional parameter space. Generalized Lotka stability is then defined in terms of the movement of the (r,s)-vector over time. It may be observed in a number of human populations at specific periods of their history.

  20. Continuous Finite Element Methods of Molecular Dynamics Simulations

    Directory of Open Access Journals (Sweden)

    Qiong Tang

    2015-01-01

    Full Text Available Molecular dynamics simulations are necessary to perform very long integration times. In this paper, we discuss continuous finite element methods for molecular dynamics simulation problems. Our numerical results about AB diatomic molecular system and A2B triatomic molecules show that linear finite element and quadratic finite element methods can better preserve the motion characteristics of molecular dynamics, that is, properties of energy conservation and long-term stability. So finite element method is also a reliable method to simulate long-time classical trajectory of molecular systems.

  1. Magnetohydrodynamic stability of tokamaks

    CERN Document Server

    Zohm, Hartmut

    2014-01-01

    This book bridges the gap between general plasma physics lectures and the real world problems in MHD stability. In order to support the understanding of concepts and their implication, it refers to real world problems such as toroidal mode coupling or nonlinear evolution in a conceptual and phenomenological approach. Detailed mathematical treatment will involve classical linear stability analysis and an outline of more recent concepts such as the ballooning formalism. The book is based on lectures that the author has given to Master and PhD students in Fusion Plasma Physics. Due its strong lin

  2. Progress on plutonium stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Hurt, D. [Defense Nuclear Facilities Safety Board, Washington, DC (United States)

    1996-05-01

    The Defense Nuclear Facilities Safety Board has safety oversight responsibility for most of the facilities where unstable forms of plutonium are being processed and packaged for interim storage. The Board has issued recommendations on plutonium stabilization and has has a considerable influence on DOE`s stabilization schedules and priorities. The Board has not made any recommendations on long-term plutonium disposition, although it may get more involved in the future if DOE develops plans to use defense nuclear facilities for disposition activities.

  3. Thermodynamic Stability of Nanobubbles

    CERN Document Server

    Attard, Phil

    2015-01-01

    The observed stability of nanobubbles contradicts the well-known result in classical nucleation theory, that the critical radius is both microscopic and thermodynamically unstable. Here nanoscopic stability is shown to be the combined result of two non-classical mechanisms. It is shown that the surface tension decreases with increasing supersaturation, and that this gives a nanoscopic critical radius. Whilst neither a free spherical bubble nor a hemispherical bubble mobile on an hydrophobic surface are stable, it is shown that an immobilized hemispherical bubble with a pinned contact rim is stable and that the total entropy is a maximum at the critical radius.

  4. Stability of dynamical systems

    CERN Document Server

    Liao, Xiaoxin; Yu, P 0

    2007-01-01

    The main purpose of developing stability theory is to examine dynamic responses of a system to disturbances as the time approaches infinity. It has been and still is the object of intense investigations due to its intrinsic interest and its relevance to all practical systems in engineering, finance, natural science and social science. This monograph provides some state-of-the-art expositions of major advances in fundamental stability theories and methods for dynamic systems of ODE and DDE types and in limit cycle, normal form and Hopf bifurcation control of nonlinear dynamic systems.ʺ Presents

  5. Anisotropic Stars II Stability

    CERN Document Server

    Dev, K; Dev, Krsna; Gleiser, Marcelo

    2003-01-01

    We investigate the stability of self-gravitating spherically symmetric anisotropic spheres under radial perturbations. We consider both the Newtonian and the full general-relativistic perturbation treatment. In the general-relativistic case, we extend the variational formalism for spheres with isotropic pressure developed by Chandrasekhar. We find that, in general, when the tangential pressure is greater than the radial pressure, the stability of the anisotropic sphere is enhanced when compared to isotropic configurations. In particular, anisotropic spheres are found to be stable for smaller values of the adiabatic index $\\gamma$.

  6. Stellarator theory and stability

    International Nuclear Information System (INIS)

    This report summarizes our work in the past year on stellarator transport theory and stability. We have developed two methods of calculating diffusion rates due to ripple transport: a ''hybrid'' bounce-averaged/guiding-center Monte Carlo code, and a numerical method of solving the bounce-averaged Fokker-Planck equation. We have modified a one-dimensional transport code to describe the Wisconsin stellarator experiments and applied it to interpret experimental results, and we have studied stability in stellarators by writing a computer code which solves the linearized ''double-adiabatic'' equations as an initial value problem. 20 refs., 7 figs

  7. Stability of heterodyne terahertz receivers

    NARCIS (Netherlands)

    Kooi, J.W.; Baselmans, J.J.A.; Baryshev, A.; Schieder, R.; Hajenius, M.; Gao, J.R.; Klapwijk, T.M.; Voronov, B.; Gol'tsman, G.

    2006-01-01

    In this paper we discuss the stability of heterodyne terahertz receivers based on small volume NbN phonon cooled hot electron bolometers (HEBs). The stability of these receivers can be broken down in two parts: the intrinsic stability of the HEB mixer and the stability of the local oscillator (LO) s

  8. Approaches to engineer stability of beetle luciferases

    Directory of Open Access Journals (Sweden)

    Mikhail Koksharov

    2012-09-01

    Full Text Available Luciferase enzymes from fireflies and other beetles have many important applications in molecular biology, biotechnology, analytical chemistry and several other areas. Many novel beetle luciferases with promising properties have been reported in the recent years. However, actual and potential applications of wild-type beetle luciferases are often limited by insufficient stability or decrease in activity of the enzyme at the conditions of a particular assay. Various examples of genetic engineering of the enhanced beetle luciferases have been reported that successfully solve or alleviate many of these limitations. This mini-review summarizes the recent advances in development of mutant luciferases with improved stability and activity characteristics. It discusses the common limitations of wild-type luciferases in different applications and presents the efficient approaches that can be used to address these problems.

  9. Sprinkler Bifurcations and Stability

    Science.gov (United States)

    Sorensen, Jody; Rykken, Elyn

    2010-01-01

    After discussing common bifurcations of a one-parameter family of single variable functions, we introduce sprinkler bifurcations, in which any number of new fixed points emanate from a single point. Based on observations of these and other bifurcations, we then prove a number of general results about the stabilities of fixed points near a…

  10. Tetraphenylborate Solids Stability Tests

    International Nuclear Information System (INIS)

    Tetraphenylborate solids provide a potentially large source of benzene in the slurries produced in the In-Tank Precipitation process. The stability of the solids is an important consideration in the safety analysis of the process and we desire an understanding of the factors that influence the rate of conversion of the solids to benzene

  11. STABILIZED PINCH MACHINE

    Science.gov (United States)

    Anderson, O.A.

    1962-04-24

    A device for heating and confining a high temperature gas or plasma utilizing the linear pinch effect is described. The pinch discharge produced is the form of an elongated cylinder. The electrical discharge current is returned in parallel along an axial and a concentric conductor whereby the magnetic field of the conductors compresses and stabilizes the pinch discharge against lateral instability. (AEC)

  12. Recombination technologies for enhanced transgene stability in bioengineered insects

    Science.gov (United States)

    Transposon-based vectors currently provide the most suitable gene transfer systems for insect germ-line transformation and are used for molecular improvement of the Sterile Insect Technique. However, the long time stability of genome-integrated transposon constructs depends on the absence of transpo...

  13. Stability of excited nuclei in a dynamical simulation

    International Nuclear Information System (INIS)

    We investigate the stability of excited 197Au nuclei with respect to multifragmentation using a dynamical simulation based on molecular dynamics and restructured aggregation. We focus attention on 3 kinds of excitations: heat, compression and rotation. We also study the influence of a geometrical perturbation created when a projectile drills a hole in a 197Au nucleus

  14. The role of macromolecular stability in desiccation tolerance.

    NARCIS (Netherlands)

    Wolkers, W.

    1998-01-01

    The work presented in this thesis concerns a study on the molecular interactions that play a role in the macromolecular stability of desiccation-tolerant higher plant organs. Fourier transform infrared microspectroscopy was used as the main experimental technique to assess macromolecular structures

  15. Structure Stability of Ⅰ-Type Carbon Nanotube Junctions

    Institute of Scientific and Technical Information of China (English)

    夏丹; 袁喆; 李家明

    2002-01-01

    Carbon nanotubes with junctions may play an important role in future ‘nanoelectronics' and future ‘nano devices'.In particular, junctions constructed with metal and semiconducting nanotubes have potential applications. Basedon the orthogonal tight-binding molecular dynamics method, we present our study of the structure stability ofI-type carbon nanotube junctions.

  16. Proteolytically stabilizing fibronectin without compromising cell and gelatin binding activity.

    Science.gov (United States)

    Zhang, Chen; Ramanathan, Anand; Karuri, Nancy Wangechi

    2015-01-01

    Excessive proteolytic degradation of fibronectin (FN) has been implicated in impaired tissue repair in chronic wounds. We previously reported two strategies for stabilizing FN against proteolytic degradation; the first conjugated polyethylene glycol (PEG) through cysteine residues and the second conjugated PEG chains of varying molecular weight on lysine residues. PEGylation of FN via lysine residues resulted in increased resistance to proteolysis with increasing PEG size, but an overall decrease in biological activity, as characterized by cell and gelatin binding. Our latest method to stabilize FN against proteolysis masks functional regions in the protein during lysine PEGylation. FN is PEGylated while it is bound to gelatin Sepharose beads with 2, 5, and 10 kDa PEG precursors. This results in partially PEGylated FN that is more stable than native FN and whose proteolytic stability increases with PEG molecular weight. Unlike completely PEGylated FN, partially PEGylated FN has cell adhesion, gelatin binding, and matrix assembly responses that are comparable to native FN. This is new evidence of how PEGylation variables can be used to stabilize FN while retaining its activity. The conjugates developed herein can be used to dissect molecular mechanisms mediated by FN stability and functionality, and address the problem of FN degradation in chronic wounds.

  17. Axisymmetric annular curtain stability

    International Nuclear Information System (INIS)

    A temporal stability analysis was carried out to investigate the stability of an axially moving viscous annular liquid jet subject to axisymmetric disturbances in surrounding co-flowing viscous gas media. We investigated in this study the effects of inertia, surface tension, the gas-to-liquid density ratio, the inner-to-outer radius ratio and the gas-to-liquid viscosity ratio on the stability of the jet. With an increase in inertia, the growth rate of the unstable disturbances is found to increase. The dominant (or most unstable) wavenumber decreases with increasing Reynolds number for larger values of the gas-to-liquid viscosity ratio. However, an opposite tendency for the most unstable wavenumber is predicted for small viscosity ratio in the same inertia range. The surrounding gas density, in the presence of viscosity, always reduces the growth rate, hence stabilizing the flow. There exists a critical value of the density ratio above which the flow becomes stable for very small viscosity ratio, whereas for large viscosity ratio, no stable flow appears in the same range of the density ratio. The curvature has a significant destabilizing effect on the thin annular jet, whereas for a relatively thick jet, the maximum growth rate decreases as the inner radius increases, irrespective of the surrounding gas viscosity. The degree of instability increases with Weber number for a relatively large viscosity ratio. In contrast, for small viscosity ratio, the growth rate exhibits a dramatic dependence on the surface tension. There is a small Weber number range, which depends on the viscosity ratio, where the flow is stable. The viscosity ratio always stabilizes the flow. However, the dominant wavenumber increases with increasing viscosity ratio. The range of unstable wavenumbers is affected only by the curvature effect. (paper)

  18. Structure and stability in TMC-1

    Science.gov (United States)

    Toth, L. Viktor; Fehér, Orsolya; Ward-Thompson, Derek; Zahorecz, Sarolta; Pelkonen, Veli-Matti

    2015-08-01

    We examine the velocity and density structure of Taurus Molecular Cloud-1 (TMC-1) in order to understand the morphology, the evolution and the fragmentation of a filamentary cloud in a nearby quiescent star forming region. High signal-to-noise ammonia rotational inversion line spectral mapping and Herschel FIR measurements were used to derive the physical parameters of the gas and the dust inside the filament. We present temperature and density calculations from both the continuum maps and the molecular line spectra with high spatial resolution (40"). We use various methods to identify objects (clumps) along the ridge and we describe their structure, physical state and stability taking into account the turbulent and thermal support of the clumps, and prove to be unstable for contraction.

  19. Influence of particle size and preparation methods on the physical and chemical stability of amorphous simvastatin

    DEFF Research Database (Denmark)

    Zhang, Fang; Aaltonen, Jaakko; Tian, Fang;

    2009-01-01

    This study investigated the factors influencing the stability of amorphous simvastatin. Quench-cooled amorphous simvastatin in two particle size ranges, 150-180 microm (QC-big) and ... stability were investigated. Physical stability (crystallization) of amorphous simvastatin stored at two conditions was monitored by X-ray powder diffractometry (XRPD) and diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS). Assessment of enthalpy relaxation of amorphous forms was conducted...... using DSC in order to link the physical and chemical stability with molecular mobility. Chemical stability was studied with high-performance liquid chromatography (HPLC). Results obtained from the current study revealed that the solubility of amorphous forms prepared by both methods was enhanced...

  20. Stabilization and anomalous hydration of collagen fibril under heating.

    Directory of Open Access Journals (Sweden)

    Sasun G Gevorkian

    Full Text Available BACKGROUND: Type I collagen is the most common protein among higher vertebrates. It forms the basis of fibrous connective tissues (tendon, chord, skin, bones and ensures mechanical stability and strength of these tissues. It is known, however, that separate triple-helical collagen macromolecules are unstable at physiological temperatures. We want to understand the mechanism of collagen stability at the intermolecular level. To this end, we study the collagen fibril, an intermediate level in the collagen hierarchy between triple-helical macromolecule and tendon. METHODOLOGY/PRINCIPAL FINDING: When heating a native fibril sample, its Young's modulus decreases in temperature range 20-58°C due to partial denaturation of triple-helices, but it is approximately constant at 58-75°C, because of stabilization by inter-molecular interactions. The stabilization temperature range 58-75°C has two further important features: here the fibril absorbs water under heating and the internal friction displays a peak. We relate these experimental findings to restructuring of collagen triple-helices in fibril. A theoretical description of the experimental results is provided via a generalization of the standard Zimm-Bragg model for the helix-coil transition. It takes into account intermolecular interactions of collagen triple-helices in fibril and describes water adsorption via the Langmuir mechanism. CONCLUSION/SIGNIFICANCE: We uncovered an inter-molecular mechanism that stabilizes the fibril made of unstable collagen macromolecules. This mechanism can be relevant for explaining stability of collagen.

  1. Stability Criterion for Humanoid Running

    Institute of Scientific and Technical Information of China (English)

    LIZhao-Hui; HUANGQiang; LIKe-Jie

    2005-01-01

    A humanoid robot has high mobility but possibly risks of tipping over. Until now, one main topic on humanoid robots is to study the walking stability; the issue of the running stability has rarely been investigated. The running is different from the walking, and is more difficult to maintain its dynamic stability. The objective of this paper is to study the stability criterion for humanoid running based on the whole dynamics. First, the cycle and the dynamics of running are analyzed. Then, the stability criterion of humanoid running is presented. Finally, the effectiveness of the proposed stability criterion is illustrated by a dynamic simulation example using a dynamic analysis and design system (DADS).

  2. Hillslope hydrology and stability

    Science.gov (United States)

    Lu, Ning; Godt, Jonathan

    2012-01-01

    Landslides are caused by a failure of the mechanical balance within hillslopes. This balance is governed by two coupled physical processes: hydrological or subsurface flow and stress. The stabilizing strength of hillslope materials depends on effective stress, which is diminished by rainfall. This book presents a cutting-edge quantitative approach to understanding hydro-mechanical processes across variably saturated hillslope environments and to the study and prediction of rainfall-induced landslides. Topics covered include historic synthesis of hillslope geomorphology and hydrology, total and effective stress distributions, critical reviews of shear strength of hillslope materials and different bases for stability analysis. Exercises and homework problems are provided for students to engage with the theory in practice. This is an invaluable resource for graduate students and researchers in hydrology, geomorphology, engineering geology, geotechnical engineering and geomechanics and for professionals in the fields of civil and environmental engineering and natural hazard analysis.

  3. Colloidal Stability and Thermal Stability of Magnetic Fluids

    OpenAIRE

    I.M. Arefyev; T.A. Arefyeva; Yu.B. Kazakov

    2013-01-01

    Colloidal and thermal stabilities of magnetic fluids define the service life of magneto-liquid equipment. The results of the research into colloidal and thermal stabilities of original synthesized magnetic fluids based on kerosene, siloxane fluid and synthetic hydrocarbon oil are presented. The method of carrying agent substitution was used in the research into colloidal stability. The thermal tests were conducted in the research into thermal stability. The conclusions about the prospects of ...

  4. Rigid Pipelay Curve Stability

    OpenAIRE

    Andersson, Christian

    2014-01-01

    Pipeline installation would generally involve curved sections in the horizontal plane, due to existing subsea infrastructure or natural seabed characteristics. At a small curve radius, the lateral seabed friction could be insufficient providing on-bottom stability of the pipeline. Hence, additional measures like lateral supports, so called turnpoints, may be required. The effect of installing such turnpoints have been studied in this thesis, using a computer software called SIMLA. Both static...

  5. Einstein universes stabilized

    OpenAIRE

    Scholz, Erhard

    2007-01-01

    The hypothesis that gravitational self-binding energy may be the source for the vacuum energy term of cosmology is studied in a Newtonian Ansatz. For spherical spaces the attractive force of gravitation and the negative pressure of the vacuum energy term form a self stabilizing system under very reasonable restrictions for the parameters, among them a characteristic coefficient \\beta of self energy. In the Weyl geometric approach to cosmological redshift, Einstein-Weyl universes with observat...

  6. Diffusion Flame Stabilization

    Science.gov (United States)

    Takahashi, Fumiaki; Katta, Viswanath R.

    2007-01-01

    Diffusion flames are commonly used for industrial burners in furnaces and flares. Oxygen/fuel burners are usually diffusion burners, primarily for safety reasons, to prevent flashback and explosion in a potentially dangerous system. Furthermore, in most fires, condensed materials pyrolyze, vaporize, and burn in air as diffusion flames. As a result of the interaction of a diffusion flame with burner or condensed-fuel surfaces, a quenched space is formed, thus leaving a diffusion flame edge, which plays an important role in flame holding in combustion systems and fire spread through condensed fuels. Despite a long history of jet diffusion flame studies, lifting/blowoff mechanisms have not yet been fully understood, compared to those of premixed flames. In this study, the structure and stability of diffusion flames of gaseous hydrocarbon fuels in coflowing air at normal earth gravity have been investigated experimentally and computationally. Measurements of the critical mean jet velocity (U(sub jc)) of methane, ethane, or propane at lifting or blowoff were made as a function of the coflowing air velocity (U(sub a)) using a tube burner (i.d.: 2.87 mm) (Fig. 1, left). By using a computational fluid dynamics code with 33 species and 112 elementary reaction steps, the internal chemical-kinetic structures of the stabilizing region of methane and propane flames were investigated (Fig. 1, right). A peak reactivity spot, i.e., reaction kernel, is formed in the flame stabilizing region due to back-diffusion of heat and radical species against an oxygen-rich incoming flow, thus holding the trailing diffusion flame. The simulated flame base moved downstream under flow conditions close to the measured stability limit.

  7. Chromium and Genomic Stability

    OpenAIRE

    Wise, Sandra S.; Wise, John Pierce

    2011-01-01

    Many metals serve as micronutrients which protect against genomic instability. Chromium is most abundant in its trivalent and hexavalent forms. Trivalent chromium has historically been considered an essential element, though recent data indicate that while it can have pharmacological effects and value, it is not essential. There are no data indicating that trivalent chromium promotes genomic stability and, instead may promote genomic instability. Hexavalent chromium is widely accepted as high...

  8. Heterotic moduli stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Cicoli, M. [Bologna Univ. (Italy). Dipt. Fisica ed Astronomia; INFN, Bologna (Italy); Adbus Salam ICTP, Trieste (Italy); De Alwis, S. [Adbus Salam ICTP, Trieste (Italy); Colorado Univ., Boulder, CO (United States). UCB 390 Physics Dept.; Westphal, A. [DESY Hamburg (Germany). Theory Group

    2013-04-15

    We perform a systematic analysis of moduli stabilization for weakly coupled heterotic string theory compactified on smooth Calabi-Yau three-folds. We focus on both supersymmetric and supersymmetry breaking vacua of generic (0,2) compactifications obtained by minimising the total (F+D)-term scalar potential. After reviewing how to stabilise all the geometric moduli in a supersymmetric way by including fractional fluxes, non-perturbative and threshold effects, we show that the inclusion of {alpha}' corrections leads to new de Sitter or nearly Minkowski vacua which break supersymmetry spontaneously. The minimum lies at moderately large volumes of all the geometric moduli, at perturbative values of the string coupling and at the right phenomenological value of the GUT gauge coupling. However the structure of the heterotic 3-form flux used for complex structure moduli stabilization does not contain enough freedom to tune the superpotential. This results in the generic prediction of high-scale supersymmetry breaking around the GUT scale. We finally provide a dynamical derivation of anisotropic compactifications with stabilized moduli which allow for perturbative gauge coupling unification around 10{sup 16} GeV.

  9. Improved roof stabilization technologies

    International Nuclear Information System (INIS)

    Decontamination and decommissioning (D and D) activities require that personnel have access to all areas of structures, some of which are more than 40 years old. In many cases, these structures have remained in a standby condition for up to 10 years; few preventative maintenance activities have been performed on them because of lack of funding or a defined future plan of action. This situation has led to deteriorated building conditions, resulting in potential personnel safety hazards. In addition, leaky roofs allow water to enter the buildings, which can cause the spread of contamination and increase building deterioration, worsening the already unsafe working conditions. To ensure worker safety and facilitate building dismantlement, the assessment of roof stabilization techniques applicable to US Department of Energy (DOE) structures has become an important issue. During Fiscal year 1997 (FY97), a comprehensive reliability-based model for the structural stabilization analysis of roof system in complex structures was developed. The model consists of three major components: a material testing method, a deterministic structural computer model, and a reliability-based optimization, and probabilistic analyses of roof structures can be implemented. Given site-specific needs, this model recommends the most appropriate roof stabilization system. This model will give not only an accurate evaluation of the existing roof system in complex structures, but it will also be a reliable method to aid the decision-making process. This final report includes in its appendix a Users' Manual for the Program of Deterministic and Reliability Analysis of Roof Structures

  10. Stability of large systems

    Science.gov (United States)

    Hastings, Harold

    2007-03-01

    We address a long-standing dilemma concerning stability of large systems. MacArthur (1955) and Hutchinson (1959) argued that more ``complex'' natural systems tended to be more stable than less complex systems based upon energy flow. May (1972) argued the opposite, using random matrix models; see Cohen and Newman (1984, 1985), Bai and Yin (1986). We show that in some sense both are right: under reasonable scaling assumptions on interaction strength, Lyapunov stability increases but structural stability decreases as complexity is increased (c.f. Harrison, 1979; Hastings, 1984). We apply this result to a variety of network systems. References: Bai, Z.D. & Yin, Y.Q. 1986. Probab. Th. Rel. Fields 73, 555. Cohen, J.E., & Newman, C.M. 1984. Annals Probab. 12, 283; 1985. Theoret. Biol. 113, 153. Harrison, G.W. 1979. Amer. Natur. 113, 659. Hastings, H.M. 1984. BioSystems 17, 171. Hastings, H.M., Juhasz, F., & Schreiber, M. 1992. .Proc. Royal Soc., Ser. B. 249, 223. Hutchinson, G.E. 1959. Amer. Natur. 93, 145, MacArthur, R. H. 1955. Ecology 35, 533, May, R.M. 1972. Nature 238, 413.

  11. Properties of Stabilizing Computations

    Directory of Open Access Journals (Sweden)

    Mark Burgin

    2015-04-01

    Full Text Available Models play an important role in the development of computerscience and information technology applications. Turing machine isone of the most popular model of computing devices andcomputations. This model, or more exactly, a family of models,provides means for exploration of capabilities of informationtechnology. However, a Turing machine stops after giving a result.In contrast to this, computers, networks and their software, suchas an operating system, very often work without stopping but givevarious results. There are different modes of such functioning andTuring machines do not provide adequate models for theseprocesses. One of the closest to halting computation isstabilizing computation when the output has to stabilize in orderto become the result of a computational process. Such stabilizingcomputations are modeled by inductive Turing machines. Incomparison with Turing machines, inductive Turing machinesrepresent the next step in the development of computer scienceproviding better models for contemporary computers and computernetworks. At the same time, inductive Turing machines reflectpivotal traits of stabilizing computational processes. In thispaper, we study relations between different modes of inductiveTuring machines functioning. In particular, it is demonstratedthat acceptation by output stabilizing and acceptation by statestabilizing are linguistically equivalent.

  12. Electoral Stability and Rigidity

    CERN Document Server

    Levy, Michael Y

    2016-01-01

    Some argue that political stability is best served through a two-party system. This study refutes this. The author mathematically defines the stability and rigidity of electoral systems comprised of any quantity of electors and parties. In fact, stability is a function of the quantity of electors - i.e., the number of occupied seats at the table. As the number of electors increases, the properties of an electorate are increasingly well resolved, and well described by those of an electorate that is least excessive -- that is to say an electorate that is closest to equilibrium. Further, electoral rigidity is a function of the quantity of parties and their probabilities of representation. An absolutely rigid system admits no fluctuations -- whatever happens to one elector will happen to all electors. As the quantity of parties increases so does the number of party lines, and with it the quantity of alternatives with which to respond to an external stimulus. Rigidity is significant in a social system that places ...

  13. Vibrational stability of graphene

    Directory of Open Access Journals (Sweden)

    Yangfan Hu

    2013-05-01

    Full Text Available The mechanical stability of graphene as temperature rises is analyzed based on three different self-consistent phonon (SCP models. Compared with three-dimensional (3-D materials, the critical temperature Ti at which instability occurs for graphene is much closer to its melting temperature Tm obtained from Monte Carlo simulation (Ti ≃ 2Tm, K. V. Zakharchenko, A. Fasolino, J. H. Los, and M. I. Katsnelson, J. Phys. Condens. Matter 23, 202202. This suggests that thermal vibration plays a significant role in melting of graphene while melting for 3-D materials is often dominated by topologic defects. This peculiar property of graphene derives from its high structural anisotropy, which is characterized by the vibrational anisotropic coefficient (VAC, defined upon its Lindermann ratios in different directions. For any carbon based material with a graphene-like structure, the VAC value must be smaller than 5.4 to maintain its stability. It is also found that the high VAC value of graphene is responsible for its negative thermal expansion coefficient at low temperature range. We believe that the VAC can be regarded as a new criterion concerning the vibrational stability of any low-dimensional (low-D materials.

  14. Extracellular gadolinium contrast agents: Differences in stability

    International Nuclear Information System (INIS)

    Extracellular gadolinium contrast agents (Gd-CA) are either linear or macrocyclic chelates available as ionic or non-ionic preparations. The molecular structure whether cyclic or linear and ionicity determines the stability of Gd-CA. Linear chelates are flexible open chains which do not offer a strong binding to Gd3+. In contrast, the macrocyclic chelates offer a strong binding to Gd3+ by the virtue of being preorganized rigid rings of almost optimal size to cage the gadolinium atom. Non-ionic preparations are also less stable in comparison to the ionic ones as the binding between Gd3+ with the negatively charged carboxyl groups is stronger in comparison to that with amides or alcohol in the non-ionic preparations. According to stability constants and kinetic measurements, the most stable Gd-CM is the ionic-macrocyclic chelate Gd-DOTA and the least stable agents are the non-ionic linear chelates gadodiamide and gadoversetamide. In vivo data confirmed the low stability of non-ionic linear chelates but no significant difference was observed amongst the macrocyclic agents whether ionic (Gd-DOTA) or non-ionic such as Gd-HP-DO3A and Gd-BT-DO3A. The stability of Gd-CA seems to be an important factor in the pathogenesis of the serious complication of nephrogenic systemic fibrosis. Gd-CA of low stability are likely to undergo transmetallation and release free Gd ions that deposit in tissue and attract circulating fibrocytes to initiate the process of fibrosis. No cases of NSF have been observed so far after the exclusive use of the stable macrocyclic Gd-CA

  15. Extracellular gadolinium contrast agents: Differences in stability

    Energy Technology Data Exchange (ETDEWEB)

    Morcos, S.K. [Department of Diagnostic Imaging, Sheffield Teaching Hospitals NHS Foundation Trust, Northern General Hospital, Sheffield S5 7AU (United Kingdom)], E-mail: sameh.morcos@sth.nhs.uk

    2008-05-15

    Extracellular gadolinium contrast agents (Gd-CA) are either linear or macrocyclic chelates available as ionic or non-ionic preparations. The molecular structure whether cyclic or linear and ionicity determines the stability of Gd-CA. Linear chelates are flexible open chains which do not offer a strong binding to Gd{sup 3+}. In contrast, the macrocyclic chelates offer a strong binding to Gd{sup 3+} by the virtue of being preorganized rigid rings of almost optimal size to cage the gadolinium atom. Non-ionic preparations are also less stable in comparison to the ionic ones as the binding between Gd{sup 3+} with the negatively charged carboxyl groups is stronger in comparison to that with amides or alcohol in the non-ionic preparations. According to stability constants and kinetic measurements, the most stable Gd-CM is the ionic-macrocyclic chelate Gd-DOTA and the least stable agents are the non-ionic linear chelates gadodiamide and gadoversetamide. In vivo data confirmed the low stability of non-ionic linear chelates but no significant difference was observed amongst the macrocyclic agents whether ionic (Gd-DOTA) or non-ionic such as Gd-HP-DO3A and Gd-BT-DO3A. The stability of Gd-CA seems to be an important factor in the pathogenesis of the serious complication of nephrogenic systemic fibrosis. Gd-CA of low stability are likely to undergo transmetallation and release free Gd ions that deposit in tissue and attract circulating fibrocytes to initiate the process of fibrosis. No cases of NSF have been observed so far after the exclusive use of the stable macrocyclic Gd-CA.

  16. Physical stability of caseinate stabilized emulsions during heating.

    NARCIS (Netherlands)

    Cruijsen, J.M.M.

    1996-01-01

    The physical stability of caseinate stabilized emulsions was studied during heating (80- 120°C). Coagulation, coalescence and phase separation of the caseinate emulsions was studied using objective heat stability tests. The physical changes were characterized by light microscopy, particle size measu

  17. Glycosylation and thermodynamic versus kinetic stability of horseradish peroxidase

    DEFF Research Database (Denmark)

    Tams, J.W.; Welinder, Karen G.

    1998-01-01

    Glycoprotein stability, glycoprotein unfolding, horseradish peroxidase, thermodynamic stability, kinetik stability......Glycoprotein stability, glycoprotein unfolding, horseradish peroxidase, thermodynamic stability, kinetik stability...

  18. Compact, CO2-stabilized tuneable laser at 2.05 microns

    CERN Document Server

    Westergaard, Philip G; Henriksen, Martin R; Michieletto, Mattia; Triches, Marco; Lyngsø, Jens K; Hald, Jan

    2016-01-01

    We demonstrate a compact fibre-based laser system at 2.05 microns stabilized to a CO2 transition using frequency modulation spectroscopy of a gas-filled hollow-core fibre. The laser exhibits an absolute frequency accuracy of 5 MHz, a frequency stability noise floor of better than 7 kHz or 5e-11 and is tunable within +/-200 MHz from the molecular resonance frequency while retaining roughly this stability and accuracy.

  19. The Stability of Icosahedral Cluster and the Range of Interaction Potential

    Institute of Scientific and Technical Information of China (English)

    DING Feng; WANG Jin-Lan; SHEN Wei-Feng; WANG Bao-Lin; LI Hui; WANG Guang-Hou

    2001-01-01

    The relation between the stability of icosahedral clusters and the range of interaction potential is discussed.We found that the stability of icosahedral clusters nay decrease with decreasing range of interaction potential. A simple formula about the critical number of icosahedral clusters and the range of interaction potential (M1/3c = A1 + A2r2eff)was proposed. The calculation of the stability of icosahedral fullerence molecular clusters shows that our idea is right.``

  20. Complementary analysis techniques applied on optimizing suspensions of yttria stabilized zirconia

    DEFF Research Database (Denmark)

    Della Negra, Michela; Foghmoes, Søren Preben Vagn; Klemensø, Trine

    2016-01-01

    Three different polymers with different functional groups and similar molecular weight were tested as dispersing agents for suspensions of yttria stabilized zirconia in ethanol: polyvinyl pyrrolidone, polyethylene imine, polyvinyl butyral/acetal. The stability of the system was assessed considering...... excellent performance of polyvinyl pyrrolidone and polyethylene imine as dispersing agents. The stability and dispersing power were finally utilized for preparing concentrated suspensions for tape casting and subsequently to sinter the tapes into dense ceramic pieces....

  1. Respective importance of protein folding and glycosylation in the thermal stability of recombinant feruloyl esterase A

    NARCIS (Netherlands)

    Benoit, Isabelle; Asther, Michèle; Sulzenbacher, Gerlind; Record, Eric; Marmuse, Laurence; Parsiegla, Goetz; Gimbert, Isabelle; Asther, Marcel; Bignon, Christophe

    2006-01-01

    The thermal stability of four molecular forms (native, refolded, glycosylated, non-glycosylated) of feruloyl esterase A (FAEA) was studied. From the most to the least thermo-resistant, the four molecular species ranked as follows: (i) glycosylated form produced native, (ii) non-glycosylated form pro

  2. Temperature-Stabilized Phase Detector

    Science.gov (United States)

    Yeeman, L.

    1985-01-01

    Precise temperature stabilized phase detector for clock signal distribution maintains 100-MHz signal with stability of 5 parts in 10 to the 16th power even for step changes of 20 degrees C in ambient temperature. Stabilization achieved by heating unit to 45 degrees C and maintaining temperature through bridge circuit.

  3. Arctic Submarine Slope Stability

    Science.gov (United States)

    Winkelmann, D.; Geissler, W.

    2010-12-01

    Submarine landsliding represents aside submarine earthquakes major natural hazard to coastal and sea-floor infrastructure as well as to coastal communities due to their ability to generate large-scale tsunamis with their socio-economic consequences. The investigation of submarine landslides, their conditions and trigger mechanisms, recurrence rates and potential impact remains an important task for the evaluation of risks in coastal management and offshore industrial activities. In the light of a changing globe with warming oceans and rising sea-level accompanied by increasing human population along coasts and enhanced near- and offshore activities, slope stability issues gain more importance than ever before. The Arctic exhibits the most rapid and drastic changes and is predicted to change even faster. Aside rising air temperatures, enhanced inflow of less cooled Atlantic water into the Arctic Ocean reduces sea-ice cover and warms the surroundings. Slope stability is challenged considering large areas of permafrost and hydrates. The Hinlopen/Yermak Megaslide (HYM) north of Svalbard is the first and so far only reported large-scale submarine landslide in the Arctic Ocean. The HYM exhibits the highest headwalls that have been found on siliciclastic margins. With more than 10.000 square kilometer areal extent and app. 2.400 cubic kilometer of involved sedimentary material, it is one of the largest exposed submarine slides worldwide. Geometry and age put this slide in a special position in discussing submarine slope stability on glaciated continental margins. The HYM occurred 30 ka ago, when the global sea-level dropped by app. 50 m within less than one millennium due to rapid onset of global glaciation. It probably caused a tsunami with circum-Arctic impact and wave heights exceeding 130 meters. The HYM affected the slope stability field in its neighbourhood by removal of support. Post-megaslide slope instability as expressed in creeping and smaller-scaled slides are

  4. Molecular complexes of phenols with DDQ

    Indian Academy of Sciences (India)

    T Vinod Kumar; T Veeraiah; G Venkateshwarlu

    2000-04-01

    Molecular complexes of phenols with DDQ have been studied spectrophotometrically in the temperature range of 10-30°C in a solvent (CHCl3) of low polarity under low donor concentrations. All the complexes exhibit one CT band each in the wavelength region where acceptor and donor do not have any absorption. The complexes are inferred to be of the - type and have y configuration in which the donor molecular orbital encompasses the substituent. The ionization potentials of the donors, the stability constants and thermodynamic parameters of the complexes have been evaluated.

  5. Moral Hazard and Stability

    DEFF Research Database (Denmark)

    Tumennasan, Norovsambuu

    2014-01-01

    Economists perceive moral hazard as an undesirable problem because it undermines efficiency. Carefully designed contracts can mitigate the moral hazard problem, but this assumes that a team is already formed. This paper demonstrates that these contracts are sometimes the reason why teams do...... not form. Formally, we study the team formation problem in which the agents’ efforts are not verifiable and the size of teams does not exceed quota r . We show that if the team members cannot make transfers, then moral hazard affects stability positively in a large class of games. For example, a stable...

  6. Measuring autocratic regime stability

    Directory of Open Access Journals (Sweden)

    Joseph Wright

    2016-01-01

    Full Text Available Researchers measure regime stability in autocratic contexts using a variety of data sources that capture distinct concepts. Often this research uses concepts developed for the study of democratic politics, such as leadership change or institutionalized authority, to construct measures of regime breakdown in non-democratic contexts. This article assesses whether the measure a researcher chooses influences the results they obtain by examining data on executive leadership, political authority, and autocratic regimes. We illustrate the conceptual differences between these variables by extending recent studies in the literature on the political consequences of non-tax revenue and unearned foreign income.

  7. Einstein universes stabilized

    CERN Document Server

    Scholz, Erhard

    2007-01-01

    The hypothesis that gravitational self-binding energy may be the source for the vacuum energy term of cosmology is studied in a Newtonian Ansatz. For spherical spaces the attractive force of gravitation and the negative pressure of the vacuum energy term form a self stabilizing system under very reasonable restrictions for the parameters, among them a characteristic coefficient \\beta of self energy. In the Weyl geometric approach to cosmological redshift, Einstein-Weyl universes with observational restrictions of the curvature parameters are dynamically stable, if \\beta is about 40 % smaller than in the exact Newton Ansatz or if the space geometry is elliptical.

  8. STABILITY PARAMETERS IN LENTIL

    Directory of Open Access Journals (Sweden)

    B TUBA BİÇER

    2007-04-01

    Full Text Available Fourteen lentil genotypes were tested for grain yield in Southeastern Anatolia ecological conditions, over our consecutive years to classify these cultivars for yield stability. Seed yield ranged from 1.903 t/ha to 1.367 t/ha. RM76, RM601 and RM152 showed regression coeffi cient above 1.00, but RM76 among these lines was consistently produced the highest yields. The unstable cultivars, RM601 and RM152 had the highest S2 values and high C.V. for grain yield.

  9. Radion cosmology and stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Chakraborty, Sumanta [IUCAA, Ganeshkhind, Pune University Campus, Post Bag 4, Pune (India); SenGupta, Soumitra [Indian Association for the Cultivation of Science, Department of Theoretical Physics, Kolkata (India)

    2014-09-15

    We solve the Einstein equation in five-dimensional space-time for Randall-Sundrum Brane world model with time dependent radion field to study the variation of brane scale factor with time. We have shown that as the radion field decreases with time compactifying the extra dimension, the scale factor increases exponentially with time leading to an inflationary scenario. We have also proposed a time dependent generalization of the Goldberger-Wise moduli stabilization mechanism to explain the time evolution of the radion field to reach a stable value, after which the scale factor on the brane exits from inflationary expansion. (orig.)

  10. Complementarity and Stability Conditions

    CERN Document Server

    Georgi, Howard

    2016-01-01

    We discuss the issue of complementarity between the confining phase and the Higgs phase for gauge theories in which there are no light particles below the scale of confinement or spontaneous symmetry breaking. We show with a number of examples that even though the low energy effective theories are the same (and trivial), we can sometimes argue that the two phases have different heavy stable particles and thus cannot be complementary. We suggest that such "stability conditions" can be a useful physical check for complementarity.

  11. Sustainability, Stability, and Resilience

    Directory of Open Access Journals (Sweden)

    Brian Walker

    1997-06-01

    Full Text Available The purpose of this essay is to define and refine the concepts of stability and resilience and to demonstrate their value in understanding the behavior of exploited systems. Some ecological systems display several possible stable states. They may also show a hysteresis effect in which, even after a long time, the state of the system may be partly determined by its history. The concept of resilience depends upon our objectives, the types of disturbances that we anticipate, control measures that are available, and the time scale of interest.

  12. Computer aided Warship Stability Assessment

    Directory of Open Access Journals (Sweden)

    R. P. Arora

    1987-10-01

    Full Text Available Computer aided warship stability assessment, software program effectively puts a ship stability expert onboard and provides ship board personnel with a rapid and accurate means to assess changes in vessel's stability. These changes may be :Routine - as the ship is loaded/unloaded in harbour or due to consumables enroute.Emergency - when the ship suffers collision/battle damage underway and begins to take on water.After assessing the stability status, the program helps the crew to determine the actions needed to restore optimum stability.

  13. Correlated Flexible Molecular Coding and Molecular Evolvability

    OpenAIRE

    Husimi, Y; Aita, T.; Tabuchi, I.

    2002-01-01

    Evolvability of biopolymers is based on molecular coding. The molecular coding is represented by biopolymer function vs monomeric sequence relationship, that is, a proper fitness landscape on the sequence space. On the other hand, molecular coding is mostly realized by monomeric sequence vs biopolymer structure relationship. We suggest the evolution of evolvability based on flexible or multiplex coding originating from flexible or polymorphic conformation of evolving biopolymers. We report a ...

  14. Stability of phantom wormholes

    International Nuclear Information System (INIS)

    It has recently been shown that traversable wormholes may be supported by phantom energy. In this work phantom wormhole geometries are modeled by matching an interior traversable wormhole solution, governed by the equation of state p=ωρ with ω<-1, to an exterior vacuum spacetime at a finite junction interface. The stability analysis of these phantom wormholes to linearized spherically symmetric perturbations about static equilibrium solutions is carried out. A master equation dictating the stability regions is deduced, and by separating the cases of a positive and a negative surface energy density, it is found that the respective stable equilibrium configurations may be increased by strategically varying the wormhole throat radius. The first model considered, in the absence of a thin shell, is that of an asymptotically flat phantom wormhole spacetime. The second model constructed is that of an isotropic pressure phantom wormhole, which is of particular interest, as the notion of phantom energy is that of a spatially homogeneous cosmic fluid, although it may be extended to inhomogeneous spherically symmetric spacetimes

  15. Gender and family stability

    Directory of Open Access Journals (Sweden)

    2001-02-01

    Full Text Available The increasing trend of partnership disruption among families with children in recent decades has been accompanied by substantial changes in traditional gender roles in industrialized countries. Yet, relatively little is known about the effects of changing gender relations on family stability in the European context. In this paper, we study such gender influences at the familial and societal level in Sweden and Hungary between the mid-1960s and the early 1990s. We focus on the disruption of the first parental union (i.e. the union in which a couple's first child was born. Our analysis is based on data extracted from the Swedish and Hungarian Fertility and Family Surveys of 1992/93. We use the method of hazard regression. The results suggest (i that the establishment of the dual-earner family model influences family stability only if it is accompanied by some changes in traditional gender relations within the family, and (ii that women's and men's labor-market behavior have different effects in spite of the relatively long history of women's (also mothers' labor-force participation in both Sweden and Hungary.

  16. Foam stability in microgravity

    Science.gov (United States)

    Vandewalle, N.; Caps, H.; Delon, G.; Saint-Jalmes, A.; Rio, E.; Saulnier, L.; Adler, M.; Biance, A. L.; Pitois, O.; Cohen Addad, S.; Hohler, R.; Weaire, D.; Hutzler, S.; Langevin, D.

    2011-12-01

    Within the context of the ESA FOAM project, we have studied the stability of aqueous and non-aqueous foams both on Earth and in microgravity. Foams are dispersions of gas into liquid or solid. On Earth, the lifetime of a foam is limited by the free drainage. By drainage, we are referring to the irreversible flow of liquid through the foam (leading to the accumulation of liquid at the foam bottom, and to a global liquid content decreases within the foam). When the liquid films become thinner, they eventually break, and the foam collapses. In microgravity, this process is no more present and foams containing large amounts of liquid can be studied for longer time. While the difference between foaming and not-foaming solutions is clear, the case of slightly-foaming solutions is more complicated. On Earth, such mixtures are observed to produce unstable froth for a couple of seconds. However, these latter solutions may produce foam in microgravity. We have studied both configurations for different solutions composed of common surfactant, proteins, anti-foaming agents or silicon oil. Surprising results have been obtained, emphasizing the role played by gravity on the foam stabilization process.

  17. Foam stability in microgravity

    International Nuclear Information System (INIS)

    Within the context of the ESA FOAM project, we have studied the stability of aqueous and non-aqueous foams both on Earth and in microgravity. Foams are dispersions of gas into liquid or solid. On Earth, the lifetime of a foam is limited by the free drainage. By drainage, we are referring to the irreversible flow of liquid through the foam (leading to the accumulation of liquid at the foam bottom, and to a global liquid content decreases within the foam). When the liquid films become thinner, they eventually break, and the foam collapses. In microgravity, this process is no more present and foams containing large amounts of liquid can be studied for longer time. While the difference between foaming and not-foaming solutions is clear, the case of slightly-foaming solutions is more complicated. On Earth, such mixtures are observed to produce unstable froth for a couple of seconds. However, these latter solutions may produce foam in microgravity. We have studied both configurations for different solutions composed of common surfactant, proteins, anti-foaming agents or silicon oil. Surprising results have been obtained, emphasizing the role played by gravity on the foam stabilization process.

  18. Radiolytic stabilization of industrial poly(methyl methacrylate)

    International Nuclear Information System (INIS)

    Poly(methyl methacrylate), PMMA, Acrigel, a Brazilian polymer, is used in the manufacture of medical supplies sterilisable by ionizing radiation. However, when PMMA is gamma-irradiated it undergoes main chain scissions, which promote molecular degradation causing reduction in its physical properties. Therefore, radiolytic stabilization of PMMA is important for to become it commercially radio sterilisable. In this work we investigated the radiolytic stabilization of PMMA by using HALS (Hindered Amine Light Stabilizer) additive, commercially used for photo and thermo oxidative stabilization of polymers. The investigation of the radiation-induced main chain scissions was carried out by viscometric method. The additive added to the polymer system at 0.3 % w/w promotes a molecular radioprotection of 61%. That means a reduction of G value (scissions/100 eV) from 2.6 to 1.0. In addition, the glassy transition temperature (Tg) of PMMA (no additive), significantly changed by radiation, does not change when PMMA (with additive) is irradiated. TGA analysis showed that the additive promotes thermal stability to the system, increasing decomposition temperature of PMMA. Spectroscopy analysis, FT-IR and RMN (1H), showed that the radioprotector additive added to the system does not change the PMMA structure. Analysis on mechanical (tensile strength and elongation at break) and optical (yellowness index and refractive index) properties showed a good influence of the additive on polymer system. (author)

  19. Progress on RNAi-based molecular medicines

    OpenAIRE

    Chen J; Xie JP

    2012-01-01

    Jing Chen, Jianping XieInstitute of Modern Biopharmaceuticals, State Key Laboratory Breeding Base of Ministry of Education Eco-Environment of the Three Gorges Reservoir Region, School of Life Sciences, Southwest University, Chongqing, ChinaAbstract: RNA interference (RNAi) is a promising strategy to suppress the expression of disease-relevant genes and induce post-transcriptional gene silencing. Their simplicity and stability endow RNAi with great advantages in molecular medicine. Several RNA...

  20. Improved Inhibition of Telomerase by Short Twisted Intercalating Nucleic Acids under Molecular Crowding Conditions

    DEFF Research Database (Denmark)

    Agarwal, Tani; Pradhan, Devranjan; Géci, Imrich;

    2012-01-01

    crowding conditions mimicking physiological milieu, stabilization of the telomeric G-quadruplex is often lost. We attempted to demonstrate the enhanced G-quadruplex stabilizing ability under molecular conditions by using twisted intercalating nucleic acids (TINA)-modified oligonucleotides. We have shown......-based telomerase repeat amplification assay (TRAP) assay as well as nondenaturing polyacrylamide gel electrophoresis-based TRAP, we demonstrate remarkable enhancement in their anti-telomerase activity even under molecular crowding conditions. This is the first time in which a G-quadruplex stabilizing agent has...... demonstrated enhanced activity even under molecular crowding conditions....

  1. Theoretical and experimental studies of the stability of drug-drug interact.

    Science.gov (United States)

    Soares, Monica F R; Alves, Lariza D S; Nadvorny, Daniela; Soares-Sobrinho, José L; Rolim-Neto, Pedro J

    2016-11-01

    Several factors can intervene in the molecular properties and consequently in the stability of drugs. The molecular complexes formation often occur due to favor the formation of hydrogen bonds, leading the system to configuration more energy stable. This work we aim to investigate through theoretical and experimental methods the relation between stability and properties of molecular complexes the molecular complex formed between the drugs, efavirenz (EFV), lamivudine (3TC) and zidovudine (AZT). With this study was possible determining the most stable complex formed between the compounds evaluated. In addition the energy and structural properties of the complex formed in relation to its individual components allowed us to evaluate the stability of the same. PMID:27267283

  2. Stability and metastability of bromine clathrate polymorphs.

    Science.gov (United States)

    Nguyen, Andrew H; Molinero, Valeria

    2013-05-23

    Clathrate hydrates are crystals in which water forms a network of fully hydrogen-bonded polyhedral cages that contain small guests. Clathrate hydrates occur mostly in two cubic crystal polymorphs, sI and sII. Bromine is one of two guests that yield a hydrate with the tetragonal structure (TS), the topological dual of the Frank-Kasper σ phase. There has been a long-standing disagreement on whether bromine hydrate also forms metastable sI and sII crystals. To date there are no data on the thermodynamic range of stability (e.g., the melting temperatures) of the metastable polymorphs. Here we use molecular dynamics simulations with the coarse-grained model of water mW to (i) investigate the thermodynamic stability of the empty and guest-filled the sI, sII, TS, and HS-I hydrate polymorphs, (ii) develop a coarse-grained model of bromine compatible with mW water, and (iii) evaluate the stability of the bromine hydrate polymorphs. The mW model predicts the same relative energy of the empty clathrate polymorphs and the same phase diagram as a function of water-guest interaction than the fully atomistic TIP4P water model. There is a narrow region in water-guest parameter space for which TS is marginally more stable than sI or sII. We parametrize a coarse-grained model of bromine compatible with mW water and use it to determine the order of stability of the bromine hydrate polymorphs. The melting temperatures of the bromine hydrate polymorphs predicted by the coarse-grained model are 281 ± 1 K for TS, 279 ± 1 K for sII, and 276 ± 1 K for sI. The closeness of the melting temperatures supports the plausibility of formation of metastable sII and sI bromine hydrates.

  3. MONETARY STABILITY VERSUS FINANCIAL STABILITY IN ADJUSTING THE REAL ECONOMY

    Directory of Open Access Journals (Sweden)

    Strezariu Iulia Ana-Maria

    2010-12-01

    Full Text Available Nowadays, in the economic theory and practice, theres commonly held idea that the primary objective of monetary policy should be price stability. However, the possibility of achieving this goal depends on the development and stability of the financial system. Even though financial stability represents a prerequisite for reaching the objective of price stability, the relationship manifests itself in reverse also. In the long term, the two objectives support and reinforce each other, but in the short term, there may occur certain incompatibilities, thus resulting in the central banks dilemma of abandoning one in favor of the other. This paper aims to investigate precisely the circumstances in which the policies pursued to ensure price stability can cause or worsen financial stability.

  4. Stability versus Optimality

    Science.gov (United States)

    Inanloo, B.

    2011-12-01

    The Caspian Sea is considered to be the largest inland body of water in the world, which located between the Caucasus Mountains and Central Asia. The Caspian Sea has been a source of the most contentious international conflicts between five littoral states now borders the sea: Azerbaijan, Iran, Kazakhstan, Russia, and Turkmenistan. The conflict over the legal status of this international body of water as an aftermath of the breakup of the Soviet Union in 1991. Since then the parties have been negotiating without coming up with any agreement neither on the ownerships of waters, nor the oil and natural gas beneath them. The number of involved stakeholders, the unusual characteristics of the Caspian Sea in considering it as a lake or a sea, and a large number of external parties are interested in the valuable resources of the Sea has made this conflict complex and unique. This paper intends to apply methods to find the best allocation schemes considering acceptability and stability of selected solution to share the Caspian Sea and its resources fairly and efficiently. Although, there are several allocation methods in solving such allocation problems, however, most of those seek a socially optimal solution that can satisfy majority of criteria or decision makers, while, in practice, especially in multi-nation problems, such solution may not be necessarily a stable solution and to be acceptable to all parties. Hence, there is need to apply a method that considers stability and acceptability of solutions to find a solution with high chance to be agreed upon that. Application of some distance-based methods in studying the Caspian Sea conflict provides some policy insights useful for finding solutions that can resolve the dispute. In this study, we use methods such as Goal Programming, Compromise Programming, and considering stability of solution the logic of Power Index is used to find a division rule that is stable negotiators. The results of this study shows that the

  5. Food Fortification Stability Study

    Science.gov (United States)

    Sirmons, T.; Cooper, M.; Douglas, G.

    2017-01-01

    NASA has established the goal of traveling beyond low-Earth orbit and extending manned exploration to Mars. The length of proposed Mars missions and the lack of resupply missions increases the importance of nutritional content in the food system, which will need a five-year shelf life. The purpose of this research is to assess the stability of vitamin supplementation in traditionally processed spaceflight foods. It is expected that commercially available fortification nutrients will remain stable through a long duration exploration mission at sufficient levels if compatible formulation, processing, and storage temperatures are achieved. Five vitamins (vitamin E, vitamin K, pantothenic acid, folic acid, and thiamin) were blended into a vitamin premix (DSM, Freeport, TX) such that the vitamin concentration per serving equaled 25% of the recommended daily intake after two years of ambient storage. Four freeze-dried foods (Scrambled Eggs, Italian Vegetables, Potatoes Au Gratin, Noodles and Chicken) and four thermo-stabilized foods (Curry Sauce with Vegetables, Chicken Noodle Soup, Grilled Pork Chop, Rice with Butter) were produced, with and without the vitamin premix, to assess the impact of the added fortification on color and taste and to determine the stability of supplemental vitamins in spaceflight foods. The addition of fortification to spaceflight foods did not greatly alter the organoleptic properties of most products. In most cases, overall acceptability scores remained above 6.0 (minimum acceptable score) following six months and one year of low-temperature storage. Likewise, the color of fortified products appears to be preserved over one year of storage. The only exceptions were Grilled pork Chop and Chicken Noodle Soup whose individual components appeareddegrade rapidly over one year of storage. Finally, most vitamins appeared to be stable during long-term storage. The only exception was thiamin, which degraded rapidly during the first year of storage at

  6. Molecular Imprinting Fibrous Membranes of Poly(acrylonitrile-co-acrylic acid) Prepared by Electrospinning

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    @@ Introduction Over the past few decades, molecular imprinting has been described as a technology for preparing "molecular doors" which can be matched to "template keys". It has been found to be a simple and effective approach to introduce specific recognition sites into synthetic polymers, namely, to create molecular imprinting polymers[1-4]. Remarkable features such as stability,ease of preparation and low cost, have made molecular imprinting polymers particularly attractive in chemical sensors, catalysis, drug delivery, and dedicated separations.

  7. Intra-membrane molecular interactions of K+ channel proteins :

    Energy Technology Data Exchange (ETDEWEB)

    Moczydlowski, Edward G.

    2013-07-01

    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 was 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.

  8. Colloidal Stability and Thermal Stability of Magnetic Fluids

    Directory of Open Access Journals (Sweden)

    I.M. Arefyev

    2013-12-01

    Full Text Available Colloidal and thermal stabilities of magnetic fluids define the service life of magneto-liquid equipment. The results of the research into colloidal and thermal stabilities of original synthesized magnetic fluids based on kerosene, siloxane fluid and synthetic hydrocarbon oil are presented. The method of carrying agent substitution was used in the research into colloidal stability. The thermal tests were conducted in the research into thermal stability. The conclusions about the prospects of synthesized magnetic fluids using in technical equipment are made on the basis of received experimental data.

  9. Stability and Stabilization of Block-cascading Switched Linear Systems

    Institute of Scientific and Technical Information of China (English)

    Ya-Hong Zhu; Dai-Zhan Cheng

    2006-01-01

    The main purpose of this paper is to investigate the problem of quadratic stability and stabilization in switched linear systems using reducible Lie algebra. First, we investigate the structure of all real invariant subspaces for a given linear system. The result is then used to provide a comparable cascading form for switching models. Using the commoncascading form, a common quadratic Lyapunov function is (QLFs) is explored by finding common QLFs of diagonal blocks.In addition, a cascading Quaker Lemma is proved. Combining it with stability results, the problem of feedback stabilization for a class of switched linear systems is solved.

  10. IMPROVED ROOF STABILIZATION TECHNOLOGIES

    International Nuclear Information System (INIS)

    Many U.S. Department of Energy (DOE) remediation sites have performed roof repair and roof replacement to stabilize facilities prior to performing deactivation and decommissioning (D and D) activities. This project will review the decision criteria used by these DOE sites, along with the type of repair system used for each different roof type. Based on this information, along with that compiled from roofing experts, a decision-making tool will be generated to aid in selecting the proper roof repair systems. Where appropriate, innovative technologies will be reviewed and applied to the decision-making tool to determine their applicability. Based on the results, applied research and development will be conducted to develop a method to repair these existing roofing systems, while providing protection for the D and D worker in a cost-efficient manner

  11. Stability in designer gravity

    Science.gov (United States)

    Hertog, Thomas; Hollands, Stefan

    2005-12-01

    We study the stability of designer gravity theories, in which one considers gravity coupled to a tachyonic scalar with anti-de Sitter (AdS) boundary conditions defined by a smooth function W. We construct Hamiltonian generators of the asymptotic symmetries using the covariant phase space method of Wald et al and find that they differ from the spinor charges except when W = 0. The positivity of the spinor charge is used to establish a lower bound on the conserved energy of any solution that satisfies boundary conditions for which W has a global minimum. A large class of designer gravity theories therefore have a stable ground state, which the AdS/CFT correspondence indicates should be the lowest energy soliton. We make progress towards proving this by showing that minimum energy solutions are static. The generalization of our results to designer gravity theories in higher dimensions involving several tachyonic scalars is discussed.

  12. Vibrations and Stability

    DEFF Research Database (Denmark)

    Thomsen, Jon Juel

    and physics. This edition includes a new chapter on the useful effects of fast vibrations and many new exercise problems. Written for: Students in mechanical or structural engineering. Keywords: Nonlinear Vibrations, Bifurcations, Chaotic Vibrations, Vibrations and Stability.......About this textbook An ideal text for students that ties together classical and modern topics of advanced vibration analysis in an interesting and lucid manner. It provides students with a background in elementary vibrations with the tools necessary for understanding and analyzing more complex...... dynamical phenomena that can be encountered in engineering and scientific practice. It progresses steadily from linear vibration theory over various levels of nonlinearity to bifurcation analysis, global dynamics and chaotic vibrations. It trains the student to analyze simple models, recognize nonlinear...

  13. Linearity stabilizes discrete breathers

    Indian Academy of Sciences (India)

    T R Krishna Mohan; Surajit Sen

    2011-11-01

    The study of the dynamics of 1D chains with both harmonic and nonlinear interactions, as in the Fermi–Pasta–Ulam (FPU) and related problems, has played a central role in efforts to identify the broad consequences of nonlinearity in these systems. Here we study the dynamics of highly localized excitations, or discrete breathers, which are known to be initiated by the quasistatic stretching of bonds between adjacent particles. We show via dynamical simulations that acoustic waves introduced by the harmonic term stabilize the discrete breather by suppressing the breather’s tendency to delocalize and disperse. We conclude that the harmonic term, and hence acoustic waves, are essential for the existence of localized breathers in these systems.

  14. IMPROVED ROOF STABILIZATION TECHNOLOGIES

    Energy Technology Data Exchange (ETDEWEB)

    M.A. Ebadian, Ph.D.

    1999-01-01

    Many U.S. Department of Energy (DOE) remediation sites have performed roof repair and roof replacement to stabilize facilities prior to performing deactivation and decommissioning (D&D) activities. This project will review the decision criteria used by these DOE sites, along with the type of repair system used for each different roof type. Based on this information, along with that compiled from roofing experts, a decision-making tool will be generated to aid in selecting the proper roof repair systems. Where appropriate, innovative technologies will be reviewed and applied to the decision-making tool to determine their applicability. Based on the results, applied research and development will be conducted to develop a method to repair these existing roofing systems, while providing protection for the D and D worker in a cost-efficient manner.

  15. Adaptive molecular convergence: Molecular evolution versus molecular phylogenetics

    OpenAIRE

    Castoe, Todd A.; de Koning, A. P. Jason; Pollock, David D.

    2010-01-01

    Definitive identification of convergent evolution, the acquisition of the same biological trait in unrelated lineages, provides one of the most compelling sources of evidence for natural selection. Although numerous examples of convergent morphological evolution are well known (such as the independent development of wings in birds and mammals), cases of convergent evolution at the molecular-genetic level appear to be quite rare. We recently discovered a remarkable case of convergent molecular...

  16. Stability Conditions for Online Learnability

    CERN Document Server

    Ross, Stephane

    2011-01-01

    Stability is a general notion that quantifies the sensitivity of a learning algorithm's output to small change in the training dataset (e.g. deletion or replacement of a single training sample). Such conditions have recently been shown to be more powerful to characterize learnability in the general learning setting under i.i.d. samples where uniform convergence is not necessary for learnability, but where stability is both sufficient and necessary for learnability. We here show that similar stability conditions are also sufficient for online learnability, i.e. whether there exists a learning algorithm such that under any sequence of examples (potentially chosen adversarially) produces a sequence of hypotheses that has no regret in the limit with respect to the best hypothesis in hindsight. We introduce online stability, a stability condition related to uniform-leave-one-out stability in the batch setting, that is sufficient for online learnability. In particular we show that popular classes of online learners...

  17. Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation

    International Nuclear Information System (INIS)

    We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus

  18. Stability of Polymer Solar Cells

    OpenAIRE

    Jørgensen, Mikkel; Norrman, Kion; Gevorgyan, Suren A.; Tromholt, Thomas; Andreasen, Birgitta; Krebs, Frederik C.

    2011-01-01

    Organic photovoltaics (OPVs) evolve in an exponential manner in the two key areas of efficiency and stability. The power conversion efficiency (PCE) has in the last decade been increased by almost a factor of ten approaching 10%. A main concern has been the stability that was previously measured in minutes, but can now, in favorable circumstances, exceed many thousands of hours. This astonishing achievement is the subject of this article, which reviews the developments in stability/degradatio...

  19. Stability problems in hyperinflation models

    OpenAIRE

    Zink, Helmut

    1993-01-01

    Traditional monetary models of hyperinflation suffer from severe stability problems: equilibria with realistic comparative-static properties are unstable while those with unrealistic comparative statics are stable. In the present paper I develop a model of hyperinflation which is based on an analysis of firms' payment behavior and which uses a weaker concept of stability. The stability properties of this model are consistent with the empirical evidence.

  20. Stability of oblique shock front

    Institute of Scientific and Technical Information of China (English)

    CHEN; Shuxing(陈恕行)

    2002-01-01

    The stability of the weak planar oblique shock front with respect to the perturbation of the wall is discussed. By the analysis of the formation and the global construction of shock and its asymptotic behaviour for stationary supersonic flow along a smooth rigid wall we obtain the stability of the solution containing a weak planar shock front. The stability can be used to single out a physically reasonable solution together with the entropy condition.

  1. Advancement of Molecular Morphology

    Institute of Scientific and Technical Information of China (English)

    顾江

    2004-01-01

    @@ Molecular morphology is a new discipline of medical science that studies morphology at the molecular level. This includes the investigation of occurrence and distribution of proteins, peptides, DNA and RNA sequences at the tissue, cellular, and ultrastructural levels.

  2. Stability performance of the SBWR

    International Nuclear Information System (INIS)

    The stability of boiling water reactors (BWRs) has been a consideration of designers, operators, and regulators since the start-up of early BWRs. Recently, instability phenomena of two different modes (corewide oscillations and regional oscillations) were observed in several BWR plants. These raised additional concerns related to BWR stability. For the simplified BWR (SBWR) design, the approach is to eliminate instability as a concern by assuring a large margin to the stability limits. A conservative set of stability criteria (core decay ratio ≤ 0.4 and channel decay ratio ≤ 0.3 for all expected steady-state operating conditions and moderate frequency transients) is imposed on the SBWR design. During the initial SBWR design, engineering judgment based on operating experience was relied on to select plant parameters that have significant effects on reactor stability. A comparison between the SBWR design and an operating BWR, which had stability test data available, to show that the SBWR design is thermal-hydraulically stable was performed to illustrate this process. After the design was selected, stability analysis was performed to confirm whether the stability criteria had been met. Several iterations were required to obtain the optimal SBWR design. This paper presents a qualitative comparison between the SBWR design and an operating BWR, and the SBWR stability performance as analyzed by a frequency domain code and a three-dimensional thermal-hydraulic code, TRACG

  3. Black Molecular Adsorber Coatings for Spaceflight Applications

    Science.gov (United States)

    Abraham, Nithin Susan; Hasegawa, Mark Makoto; Straka, Sharon A.

    2014-01-01

    The molecular adsorber coating is a new technology that was developed to mitigate the risk of on-orbit molecular contamination on spaceflight missions. The application of this coating would be ideal near highly sensitive, interior surfaces and instruments that are negatively impacted by outgassed molecules from materials, such as plastics, adhesives, lubricants, epoxies, and other similar compounds. This current, sprayable paint technology is comprised of inorganic white materials made from highly porous zeolite. In addition to good adhesion performance, thermal stability, and adsorptive capability, the molecular adsorber coating offers favorable thermal control characteristics. However, low reflectivity properties, which are typically offered by black thermal control coatings, are desired for some spaceflight applications. For example, black coatings are used on interior surfaces, in particular, on instrument baffles for optical stray light control. Similarly, they are also used within light paths between optical systems, such as telescopes, to absorb light. Recent efforts have been made to transform the white molecular adsorber coating into a black coating with similar adsorptive properties. This result is achieved by optimizing the current formulation with black pigments, while still maintaining its adsorption capability for outgassing control. Different binder to pigment ratios, coating thicknesses, and spray application techniques were explored to develop a black version of the molecular adsorber coating. During the development process, coating performance and adsorption characteristics were studied. The preliminary work performed on black molecular adsorber coatings thus far is very promising. Continued development and testing is necessary for its use on future contamination sensitive spaceflight missions.

  4. Basic molecular spectroscopy

    CERN Document Server

    Gorry, PA

    1985-01-01

    BASIC Molecular Spectroscopy discusses the utilization of the Beginner's All-purpose Symbolic Instruction Code (BASIC) programming language in molecular spectroscopy. The book is comprised of five chapters that provide an introduction to molecular spectroscopy through programs written in BASIC. The coverage of the text includes rotational spectra, vibrational spectra, and Raman and electronic spectra. The book will be of great use to students who are currently taking a course in molecular spectroscopy.

  5. Polymer friction Molecular Dynamics

    OpenAIRE

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    2010-01-01

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to ...

  6. Cardiovascular molecular MR imaging

    OpenAIRE

    Lamb, H J; van der Meer, R. W.; Roos, A. (Anna); Bax, J J

    2007-01-01

    Introduction Cardiovascular molecular imaging is a rapidly evolving field of research, aiming to image and quantify molecular and cellular targets in vivo. MR imaging has some inherent properties that make it very suitable for cardiovascular molecular imaging. Until now, only a limited number of studies have been published on cardiovascular molecular imaging using MR imaging. Review In the current review, MR techniques that have already shown potential are discussed. Metabolic MR imaging can ...

  7. Protein stability and enzyme activity at extreme biological temperatures

    Energy Technology Data Exchange (ETDEWEB)

    Feller, Georges, E-mail: gfeller@ulg.ac.b [Laboratory of Biochemistry, Centre for Protein Engineering, Institute of Chemistry B6a, University of Liege, B-4000 Liege (Belgium)

    2010-08-18

    Psychrophilic microorganisms thrive in permanently cold environments, even at subzero temperatures. To maintain metabolic rates compatible with sustained life, they have improved the dynamics of their protein structures, thereby enabling appropriate molecular motions required for biological activity at low temperatures. As a consequence of this structural flexibility, psychrophilic proteins are unstable and heat-labile. In the upper range of biological temperatures, thermophiles and hyperthermophiles grow at temperatures > 100 {sup 0}C and synthesize ultra-stable proteins. However, thermophilic enzymes are nearly inactive at room temperature as a result of their compactness and rigidity. At the molecular level, both types of extremophilic proteins have adapted the same structural factors, but in opposite directions, to address either activity at low temperatures or stability in hot environments. A model based on folding funnels is proposed accounting for the stability-activity relationships in extremophilic proteins. (topical review)

  8. Stabilization of G protein-coupled receptors by point mutations

    Directory of Open Access Journals (Sweden)

    Franziska eHeydenreich

    2015-04-01

    Full Text Available G protein-coupled receptors (GPCRs are flexible integral membrane proteins involved in transmembrane signaling. Their involvement in many physiological processes makes them interesting targets for drug development. Determination of the structure of these receptors will help to design more specific drugs, however, their structural characterization has so far been hampered by the low expression and their inherent instability in detergents which made protein engineering indispensable for structural and biophysical characterization.Several approaches to stabilize the receptors in a particular conformation have led to breakthroughs in GPCR structure determination. These include truncations of the flexible regions, stabilization by antibodies and nanobodies, fusion partners, high affinity and covalently bound ligands as well as conformational stabilization by mutagenesis. In this review we focus on stabilization of GPCRs by insertion of point mutations, which lead to increased conformational and thermal stability as well as improved expression levels. We summarize existing mutagenesis strategies with different coverage of GPCR sequence space and depth of information, design and transferability of mutations and the molecular basis for stabilization. We also discuss whether mutations alter the structure and pharmacological properties of GPCRs.

  9. Stabilization Mechanisms of Water-in-Crude Oil Emulsions

    Science.gov (United States)

    Nour, Abdurahman H.; Suliman, A.; Hadow, Mahmmoud M.

    During the lifting and production of crude oil, water/oil emulsions are created. They are stabilized by asphaltenes and resins which are colloidally dispersed in the crude oil. Asphaltenes consist mainly of polar heterocompounds. It is known that they decrease the interfacial tension between oil and water and form stable interfacial films. Both effects favour the formation and stabilization of emulsions. Resins are complex high-molecular-weight compounds that are not soluble in ethylacetate, but are soluble in n-heptane. Their interfacial activity is less than that of asphaltenes. The role of resins in stabilizing emulsions has also been debated in literature. This study reports the results of experimental investigation of various factors affecting the stability of emulsions which are considered to be undesirable for a number of reasons, including both up-stream and down-stream operation in the petroleum industry. It was found that, the (R/A) ratio affects the emulsion and dispersion stabilities. High resin/asphaltene ratios decrease the emulsion stability.

  10. Food Fortification Stability Study

    Science.gov (United States)

    Sirmons, T.; Cooper, M.; Douglas, G.

    2016-01-01

    NASA has established the goal of traveling beyond low-Earth orbit and extending manned exploration to Mars. The length of proposed Mars missions and the lack of resupply missions increases the importance of nutritional content in the food system, which will need a five year shelf life. The purpose of this research is to assess the stability of vitamin supplementation in traditionally processed spaceflight foods. It is expected that commercially available fortification nutrients will remain stable through a long duration exploration mission at sufficient levels if compatible formulation, processing, and storage temperatures are achieved. Five vitamins (vitamin E, vitamin K, pantothenic acid, folic acid, and thiamin) were blended into a vitamin premix (DSM, Freeport, TX) such that the vitamin concentration per serving equaled 25% of the recommended daily intake after two years of ambient storage. Four freeze-dried foods (Scrambled Eggs, Italian Vegetables, Potatoes Au Gratin, Noodles and Chicken) and four thermostabilized foods (Curry Sauce with Vegetables, Chicken Noodle Soup, Grilled Pork Chop, Rice with Butter) were produced, with and without the vitamin premix, to assess the impact of the added fortification on color and taste and to determine the stability of supplemental vitamins in spaceflight foods. The addition of fortification to spaceflight foods did not greatly alter the organoleptic properties of most products. In most cases, overall acceptability scores remained above 6.0 (minimum acceptable score) following six months and one year of low-temperature storage. Likewise, the color of fortified products appears to be preserved over one year of storage. The only exception was Grilled pork Chop and Chicken Noodle Soup whose individual components appear to degrade rapidly over one year of storage. Finally, most vitamins appear to be stable during long-term storage. The only exception was thiamin, which degraded rapidly during the first year of storage at 35

  11. Physical Chemistry of Molecular

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    @@ Established in 2009, the group consists of six researchers and more than 70 research assistants and graduate students from the CAS Key Laboratory of Molecular Nanostructures and Nanotechnologies at the CAS Institute of Chemistry.Its research focuses on the physical chemistry involved in molecular assembly, molecular nanostructures, functional nanomaterials and conceptual nano-devices.

  12. A graph theoretical approach for assessing bio-macromolecular complex structural stability.

    Science.gov (United States)

    Del Carpio, Carlos Adriel; Iulian Florea, Mihai; Suzuki, Ai; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Ichiishi, Eiichiro; Miyamoto, Akira

    2009-11-01

    Fast and proper assessment of bio macro-molecular complex structural rigidity as a measure of structural stability can be useful in systematic studies to predict molecular function, and can also enable the design of rapid scoring functions to rank automatically generated bio-molecular complexes. Based on the graph theoretical approach of Jacobs et al. [Jacobs DJ, Rader AJ, Kuhn LA, Thorpe MF (2001) Protein flexibility predictions using graph theory. Proteins: Struct Funct Genet 44:150-165] for expressing molecular flexibility, we propose a new scheme to analyze the structural stability of bio-molecular complexes. This analysis is performed in terms of the identification in interacting subunits of clusters of flappy amino acids (those constituting regions of potential internal motion) that undergo an increase in rigidity at complex formation. Gains in structural rigidity of the interacting subunits upon bio-molecular complex formation can be evaluated by expansion of the network of intra-molecular inter-atomic interactions to include inter-molecular inter-atomic interaction terms. We propose two indices for quantifying this change: one local, which can express localized (at the amino acid level) structural rigidity, the other global to express overall structural stability for the complex. The new system is validated with a series of protein complex structures reported in the protein data bank. Finally, the indices are used as scoring coefficients to rank automatically generated protein complex decoys.

  13. Polymer Stabilized Nanosuspensions Formed via Flash Nanoprecipitation: Nanoparticle Formation, Formulation, and Stability

    Science.gov (United States)

    Zhu, ZhengXi

    Nanoparticles loaded with hydrophobic components (e.g., active pharmaceutical ingredients, medical diagnostic agents, nutritional or personal care chemicals, catalysts, dyes/pigments, and substances with exceptional magnetic/optical/electronic/thermal properties) have tremendous industrial applications. The common desire is to efficiently generate nanoparticles with a desired size, size distribution, and size stability. Recently, Flash NanoPrecipition (FNP) technique with a fast, continuous, and easily scalable process has been developed to efficiently generate hydrophobe-loaded nanoparticles. This dissertation extended this technique, optimized process conditions and material formulations, and gave new insights into the mechanism and kinetics of nanoparticle formation. This dissertation demonstrated successful generation of spherical beta-carotene nanoparticles with an average diameter of 50--100 nm (90 wt% nanoparticles below 200 nm), good size stability (maintained an average diameter below 200 nm for at least one week in saline), and much higher loading (80--90 wt%) than traditional carriers, such as micelles and polymersomes (typically FNP were proposed. To optimize the material formulations, either polyelectrolytes (i.e., epsilon-polylysine, branched and linear poly(ethylene imine), and chitosan) or amphiphilic diblock copolymers (i.e., polystyrene-b-poly(ethylene glycol) (PS-b-PEG), polycarprolactone-b-poly(ethylene glycol) (PCL-b-PEG), poly(lactic acid)-b-poly(ethylene glycol) (PLA-b-PEG), and poly(lactic-co-glycolic acid)-b-poly(ethylene glycol) (PLGA-b-PEG)) were selectively screened to study the nanoparticle size, distribution, and stability. The effect of the molecular weight of the polymers and pH were also studied. Chitosan and PLGA-b-PEG best stabilized the beta-carotene nanoparticles. Solubility of the hydrophobic drug solute in the aqueous mixture was considered to dominate the nanoparticle stability (i.e., size and morphology) in terms of Ostwald

  14. Stability Analysis and Stability Chart for Unsaturated Residual Soil Slope

    Directory of Open Access Journals (Sweden)

    Bugang B.K. Haut

    2006-01-01

    Full Text Available In tropical residual soils most hill slope failures are caused by rainfall. It is therefore important to consider dynamic hydrological conditions when attempting to analyze the stability of residual soil slopes. This paper describes a coupled hydrology/stability model that has been developed to overcome the limitations of the standard method of analysis used to investigate stability of tropical soil slopes. A computational hydrology – limit equilibrium stability analysis model is outlined and examples are provided of the model output capabilities in terms of design charts. Although nowadays most realistic problem should be analyzed by computer and stability charts are mainly used to analyze simple slopes, they can be useful for preliminary analysis and enable the designer to quickly assess the sensitivity of a problem to changes in different input parameters.

  15. Neurons of the Dentate Molecular Layer in the Rabbit Hippocampus

    OpenAIRE

    Sancho-Bielsa, Francisco J.; Navarro-López, Juan D.; Gregori Alonso-Llosa; Asunción Molowny; Xavier Ponsoda; Javier Yajeya; Carlos López-García

    2012-01-01

    The molecular layer of the dentate gyrus appears as the main entrance gate for information into the hippocampus, i.e., where the perforant path axons from the entorhinal cortex synapse onto the spines and dendrites of granule cells. A few dispersed neuronal somata appear intermingled in between and probably control the flow of information in this area. In rabbits, the number of neurons in the molecular layer increases in the first week of postnatal life and then stabilizes to appear permanent...

  16. First-principles modelling of molecular single-electron transistors

    OpenAIRE

    Stokbro, Kurt

    2010-01-01

    We present a first-principles method for calculating the charging energy of a molecular single-electron transistor operating in the Coulomb blockade regime. The properties of the molecule are modeled using density-functional theory, the environment is described by a continuum model, and the interaction between the molecule and the environment are included through the Poisson equation. The model is used to calculate the charge stability diagrams of a benzene and C$_{60}$ molecular single-elect...

  17. Cooee bitumen II: Stability of linear asphaltene nanoaggregates

    OpenAIRE

    Lemarchand, Claire,; Schrøder, Thomas; Dyre, J.C.; Hansen, Jesper Schmidt

    2014-01-01

    Asphaltene and smaller aromatic molecules tend to form linear nanoaggregates in bitumen. Over the years bitumen undergoes chemical aging and during this process, the size of the nanoaggregate increases. This increase is associated with an increase in viscosity and brittleness of the bitumen, eventually leading to road deterioration. This paper focuses on understanding the mechanisms behind nanoaggregate size and stability. We used molecular dynamics simulations to quantify the probability of ...

  18. Stability of hydrocarbons at deep Earth pressures and temperatures

    OpenAIRE

    Spanu, Leonardo; Donadio, Davide; Hohl, Detlef; Schwegler, Eric; Galli, Giulia

    2011-01-01

    Determining the thermochemical properties of hydrocarbons (HCs) at high pressure and temperature is a key step toward understanding carbon reservoirs and fluxes in the deep Earth. The stability of carbon-hydrogen systems at depths greater than a few thousand meters is poorly understood and the extent of abiogenic HCs in the Earth mantle remains controversial. We report ab initio molecular dynamics simulations and free energy calculations aimed at investigating the formation of higher HCs from...

  19. Capsule-train stability

    Science.gov (United States)

    Bryngelson, Spencer H.; Freund, Jonathan B.

    2016-07-01

    Elastic capsules flowing in small enough tubes, such as red blood cells in capillaries, are well known to line up into regular single-file trains. The stability of such trains in somewhat wider channels, where this organization is not observed, is studied in a two-dimensional model system that includes full coupling between the viscous flow and suspended capsules. A diverse set of linearly amplifying disturbances, both long-time asymptotic (modal) and transient (nonmodal) perturbations, is identified and analyzed. These have a range of amplification rates and their corresponding forms are wavelike, typically dominated by one of five principal perturbation classes: longitudinal and transverse translations, tilts, and symmetric and asymmetric shape distortions. Finite-amplitude transiently amplifying perturbations are shown to provide a mechanism that can bypass slower asymptotic modal linear growth and precipitate the onset of nonlinear effects. Direct numerical simulations are used to verify the linear analysis and track the subsequent transition of the regular capsule trains into an apparently chaotic flow.

  20. Hydrocode subcycling stability

    International Nuclear Information System (INIS)

    The method of artificial viscosity was originally designed by von Neumann and Richtmyer for calculating the propagation of waves in materials that were hydrodynamic and rate-independent (e.g., ideal gas law). However, hydrocodes (such as WONDY) based on this method continue to expand their repertoire of material laws even unto material laws that are rate-dependent (e.g., Maxwell's material law). Restrictions on the timestep required for stability with material laws that are rate-dependent can be considerably more severe than restrictions of the Courant-Friedrichs-Lewy (CFL) type that are imposed in these hydrocodes. These very small timesteps can make computations very expensive. An alternative is to go ahead and integrate the conservation laws with the usual CFL timestep while subcycling (integrating with a smaller timestep) the integration of the stress-rate equation. If the subcycling is done with a large enough number of subcycles (i.e., with a small enough subcycle timestep), then the calculation is stable. Specifically, the number of subcycles must be one greater than the ratio of the CFL timestep to the relaxation time of the material

  1. Predicting the chemical stability of monatomic chains

    Science.gov (United States)

    Lin, Zheng-Zhe; Chen, Xi

    2013-02-01

    A simple model for evaluating the thermal atomic transfer rates in nanosystems (Lin Z.-Z. et al., EPL, 94 (2011) 40002) was developed to predict the chemical reaction rates of nanosystems with small gas molecules. The accuracy of the model was verified by MD simulations for molecular adsorption and desorption on a monatomic chain. By the prediction, a monatomic carbon chain should survive for 1.2 × 102 years in the ambient of 1 atm O2 at room temperature, and it is very invulnerable to N2, H2O, NO2, CO and CO2, while a monatomic gold chain quickly ruptures in vacuum. It is worth noting that since the model can be easily applied via common ab initio calculations, it could be widely used in the prediction of chemical stability of nanosystems.

  2. Effect of sorbitol and glycerol on the stability of trypsin and difference between their stabilization effects in the various solvents.

    Science.gov (United States)

    Pazhang, Mohammad; Mehrnejad, Faramarz; Pazhang, Yaghub; Falahati, Hanieh; Chaparzadeh, Nader

    2016-01-01

    The effect of glycerol and sorbitol on the stability of porcine pancreas trypsin was investigated in this work. Molecular dynamics simulation and thermostability results showed that trypsin has two flexible regions, and polyols (sorbitol and glycerol) stabilize the enzyme by decreasing the flexibility of these regions. Radial distribution function results exhibited that sorbitol and glycerol were excluded from the first water layer of the enzyme, therefore decrease the flexibility of the regions by preferential exclusion. Also, results showed that the stabilization effect of sorbitol is more than glycerol. This observation could be because of the larger decrease in the fluctuations of trypsin in the presence of sorbitol. We also examined the role of solvent's hydrophobicity in enzyme stabilization by sorbitol and glycerol. To do so, the thermostability of trypsin was evaluated in the presence of solvents with different hydrophobicity (methanol, ethanol, isopropanol and n-propanol) in addition to the polyols. Our results depicted that glycerol is a better stabilizer than sorbitol in the presence of hydrophobic solvents (n-propanol), whereas sorbitol is a better stabilizer than glycerol in the presence of hydrophilic solvents (methanol).

  3. Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments

    NARCIS (Netherlands)

    Bennett, W. F. Drew; MacCallum, Justin L.; Hinner, Marlon J.; Marrink, Siewert J.; Tieleman, D. Peter

    2009-01-01

    The relative stability of cholesterol in cellular membranes and the thermodynamics of fluctuations from equilibrium have important consequences for sterol trafficking and lateral domain formation. We used molecular dynamics computer simulations to investigate the partitioning of cholesterol in a sys

  4. Stability of Polymer Solar Cells

    DEFF Research Database (Denmark)

    Jørgensen, Mikkel; Norrman, Kion; Gevorgyan, Suren;

    2012-01-01

    Organic photovoltaics (OPVs) evolve in an exponential manner in the two key areas of efficiency and stability. The power conversion efficiency (PCE) has in the last decade been increased by almost a factor of ten approaching 10%. A main concern has been the stability that was previously measured...

  5. Dynamic stability of compact stars

    OpenAIRE

    Bisnovatyi-Kogan, G. S.

    2004-01-01

    After some historical remarks we discuss different criteria of dynamical stability of stars, and properties of the critical states where dynamical stability is lost, leading to collapse with formation of the neutron star or a black hole. At the end some observational and theoretical problems related to quark stars are discussed.

  6. Exponential Stabilization of Underactuated Vehicles

    Energy Technology Data Exchange (ETDEWEB)

    Pettersen, K.Y.

    1996-12-31

    Underactuated vehicles are vehicles with fewer independent control actuators than degrees of freedom to be controlled. Such vehicles may be used in inspection of sub-sea cables, inspection and maintenance of offshore oil drilling platforms, and similar. This doctoral thesis discusses feedback stabilization of underactuated vehicles. The main objective has been to further develop methods from stabilization of nonholonomic systems to arrive at methods that are applicable to underactuated vehicles. A nonlinear model including both dynamics and kinematics is used to describe the vehicles, which may be surface vessels, spacecraft or autonomous underwater vehicles (AUVs). It is shown that for a certain class of underactuated vehicles the stabilization problem is not solvable by linear control theory. A new stability result for a class of homogeneous time-varying systems is derived and shown to be an important tool for developing continuous periodic time-varying feedback laws that stabilize underactuated vehicles without involving cancellation of dynamics. For position and orientation control of a surface vessel without side thruster a new continuous periodic feedback law is proposed that does not cancel any dynamics, and that exponentially stabilizes the origin of the underactuated surface vessel. A further issue considered is the stabilization of the attitude of an AUV. Finally, the thesis discusses stabilization of both position and attitude of an underactuated AUV. 55 refs., 28 figs.

  7. Vibrations and Stability: Solved Problems

    DEFF Research Database (Denmark)

    Thomsen, Jon Juel

    Worked out solutions for exercise problems in J. J. Thomsen 'Vibrations and Stability: Advanced Theory, Analysis, and Tools', Springer, Berlin - Heidelberg, 2003.......Worked out solutions for exercise problems in J. J. Thomsen 'Vibrations and Stability: Advanced Theory, Analysis, and Tools', Springer, Berlin - Heidelberg, 2003....

  8. Marital Satisfaction and Marital Stability

    Science.gov (United States)

    Lenthall, Gerald

    1977-01-01

    Marital satisfaction is viewed as a function of the comparison between one's marital expectations and one's marital outcome. Marital stability is viewed as a function of the comparison between one's best available marital alternative and one's marital outcome. Hence, marital satisfaction and marital stability can differ. (Author)

  9. Proteolytic stability in colloidal systems.

    NARCIS (Netherlands)

    Maste, M.C.L.

    1996-01-01

    Proteolytic enzymes in liquid detergents suffer from lack of stability in the sense that activity diminishes with time. Although the phenomenon could be attributed to several factors, the influence of colloidal surfaces on the enzymatic stability was investigated. Besides the types of surfaces that

  10. Practical stability of nonlinear systems

    CERN Document Server

    Lakshmikantham, Vangipuram; Martynyuk, Anatolii Andreevich

    1990-01-01

    This is the first book that deals with practical stability and its development. It presents a systematic study of the theory of practical stability in terms of two different measures and arbitrary sets and demonstrates the manifestations of general Lyapunov's method by showing how this effective technique can be adapted to investigate various apparently diverse nonlinear problems including control systems and multivalued differential equations.

  11. Macromolecular Brushes as Stabilizers of Hydrophobic Solute Nanoparticles.

    Science.gov (United States)

    Luo, Hanying; Raciti, David; Wang, Chao; Herrera-Alonso, Margarita

    2016-06-01

    Macromolecular brushes bearing poly(ethylene glycol) and poly(d,l-lactide) side chains were used to stabilize hydrophobic solute nanoparticles formed by a rapid change in solvent quality. Unlike linear diblock copolymers with the same hydrophilic and hydrophobic block chemistries, the brush copolymer enabled the formation of ellipsoidal β-carotene nanoparticles, which in cosolvent mixtures developed into rod-like structures, resulting from a combination of Ostwald ripening and particle aggregation. The stabilizing ability of the copolymer was highly dependent on the mobility of the hydrophobic component, influenced by its molecular weight. As shown here, asymmetric amphiphilic macromolecular brushes of this type may be used as hydrophobic drug stabilizers and potentially assist the shape control of nonspherical aggregate morphologies. PMID:27035279

  12. Thermal stability of silicon nanowires:atomistic simulation study

    Institute of Scientific and Technical Information of China (English)

    Liu Wen-Liang; Zhang Kai-Wang; Zhong Jian-Xin

    2009-01-01

    Using the Stillinger-Weber (SW) potential model, we investigate the thermal stability of pristine silicon nanowires based on classical molecular dynamics (MD) simulations. We explore the structural evolutions and the Lindemann indices of silicon nanowires at different temperatures in order to unveil atomic-level melting behaviour of silicon nanowires.The simulation results show that silicon nanowires with surface reconstructions have higher thermal stability than those without surface reconstructions, and that silicon nanowires with perpendicular dimmer rows on the two (100) surfaces have somewhat higher thermal stability than nanowires with parallel dimmer rows on the two (100) surfaces. Furthermore, the melting temperature of silicon nanowires increases as their diameter increases and reaches a saturation value close to the melting temperature of bulk silicon. The value of the Lindemann index for melting silicon nanowires is 0.037.

  13. Loop and water effect on stability of intertriplex DNA

    Science.gov (United States)

    Yang, Linjing; Lee, Imshik; Wang, Chen; Li, Qing; Bai, Chunli

    1998-02-01

    Stability of four intratriplexes and one intertriplex influenced by loops and water have been investigated by molecular mechanics calculation. The four intratriplexes are 5'-d(TC) 6-d(T) m-d(CT) 6-d(C) n-d(AG) 6-3' ( m, n = 3 or 4), the corresponding intertriplex is d(TC) 6∗d(AG) 6·d(CT) 6 (·, Watson-Crick hydrogen bond; ∗, Hoogsteen hydrogen bond). We studied in detail how loops and water would effect intra- and interstrand interactions of the five triplexes, respectively. The results showed that the existence of loops may have limited impact on the stability of the concerned triplex structures, regardless of water environment. In contrast, water molecules do have appreciable effects on triplex stability. Sugar conformations of the five triplexes were also discussed in this paper. The theoretical results are in good agreement with the FT-IR experiments.

  14. Enhanced Mechanical Stability of Gold Nanotips through Carbon Nanocone Encapsulation

    Science.gov (United States)

    Cano-Marquez, Abraham G.; Schmidt, Wesller G.; Ribeiro-Soares, Jenaina; Gustavo Cançado, Luiz; Rodrigues, Wagner N.; Santos, Adelina P.; Furtado, Clascidia A.; Autreto, Pedro A. S.; Paupitz, Ricardo; Galvão, Douglas S.; Jorio, Ado

    2015-06-01

    Gold is a noble metal that, in comparison with silver and copper, has the advantage of corrosion resistance. Despite its high conductivity, chemical stability and biocompatibility, gold exhibits high plasticity, which limits its applications in some nanodevices. Here, we report an experimental and theoretical study on how to attain enhanced mechanical stability of gold nanotips. The gold tips were fabricated by chemical etching and further encapsulated with carbon nanocones via nanomanipulation. Atomic force microscopy experiments were carried out to test their mechanical stability. Molecular dynamics simulations show that the encapsulated nanocone changes the strain release mechanisms at the nanoscale by blocking gold atomic sliding, redistributing the strain along the whole nanostructure. The carbon nanocones are conducting and can induce magnetism, thus opening new avenues on the exploitation of transport, mechanical and magnetic properties of gold covered by sp2 carbon at the nanoscale.

  15. Atomistic mechanisms governing structural stability change of zinc antimony thermoelectrics

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Xiaolong [Frontier Institute of Science and Technology, Xi' an Jiaotong University, Xi' an 710054 (China); Lin, Jianping, E-mail: jaredlin@163.com [School of Materials Science and Engineering, Xiamen University of Technology, Xiamen 361024 (China); Qiao, Guanjun [State Key Laboratory for Mechanical Behavior of Materials, Xi' an Jiaotong University, Xi' an 710049 (China); Wang, Zhao, E-mail: zwangzhao@gmail.com [Frontier Institute of Science and Technology, Xi' an Jiaotong University, Xi' an 710054 (China); State Key Laboratory for Mechanical Behavior of Materials, Xi' an Jiaotong University, Xi' an 710049 (China)

    2015-01-05

    The structural stability of thermoelectric materials is a subject of growing importance for their energy harvesting applications. Here, we study the microscopic mechanisms governing the structural stability change of zinc antimony at its working temperature, using molecular dynamics combined with experimental measurements of the electrical and thermal conductivity. Our results show that the temperature-dependence of the thermal and electrical transport coefficients is strongly correlated with a structural transition. This is found to be associated with a relaxation process, in which a group of Zn atoms migrates between interstitial sites. This atom migration gradually leads to a stabilizing structural transition of the entire crystal framework, and then results in a more stable crystal structure of β–Zn{sub 4}Sb{sub 3} at high temperature.

  16. Engineering molecular machines

    Science.gov (United States)

    Erman, Burak

    2016-04-01

    Biological molecular motors use chemical energy, mostly in the form of ATP hydrolysis, and convert it to mechanical energy. Correlated thermal fluctuations are essential for the function of a molecular machine and it is the hydrolysis of ATP that modifies the correlated fluctuations of the system. Correlations are consequences of the molecular architecture of the protein. The idea that synthetic molecular machines may be constructed by designing the proper molecular architecture is challenging. In their paper, Sarkar et al (2016 New J. Phys. 18 043006) propose a synthetic molecular motor based on the coarse grained elastic network model of proteins and show by numerical simulations that motor function is realized, ranging from deterministic to thermal, depending on temperature. This work opens up a new range of possibilities of molecular architecture based engine design.

  17. Workshop on molecular animation.

    Science.gov (United States)

    Bromberg, Sarina; Chiu, Wah; Ferrin, Thomas E

    2010-10-13

    From February 25 to 26, 2010, in San Francisco, the Resource for Biocomputing, Visualization, and Informatics (RBVI) and the National Center for Macromolecular Imaging (NCMI) hosted a molecular animation workshop for 21 structural biologists, molecular animators, and creators of molecular visualization software. Molecular animation aims to visualize scientific understanding of biomolecular processes and structures. The primary goal of the workshop was to identify the necessary tools for producing high-quality molecular animations, understanding complex molecular and cellular structures, creating publication supplementary materials and conference presentations, and teaching science to students and the public. Another use of molecular animation emerged in the workshop: helping to focus scientific inquiry about the motions of molecules and enhancing informal communication within and between laboratories.

  18. Stability of Evolving Agent Populations

    CERN Document Server

    Briscoe, G

    2007-01-01

    Stability is perhaps the most desired feature in the systems that we design. It is important for us to be able to predict the response of a Multi-Agent System (MAS) to various environmental conditions prior to its actual deployment. The Chli-DeWilde agent stability measure views a MAS as a discrete time Markov chain with a potentially unknown transition probabilities. A MAS is considered to be stable when its state, a stochastic process, has converged to an equilibrium distribution. We investigate an extension of their agent stability definition to include MASs with evolutionary dynamics, focusing on evolving agent populations. Additionally, using our extended agent stability measure, we construct an entropy-based definition for the degree of instability. An example system, the Digital Ecosystem, is considered in detail to investigate the stability of an evolving agent population through simulations. The results are consistent with the original Chli-DeWilde measure.

  19. NONLINEAR STABILITY FOR EADY'S MODEL

    Institute of Scientific and Technical Information of China (English)

    LIU Yong-ming; QIU Ling-cun

    2005-01-01

    Poincaré type integral inequality plays an important role in the study of nonlinear stability ( in the sense of Arnold's second theorem) for three-dimensional quasigeostophic flow. The nonlinear stability of Eady's model is one of the most important cases in the application of the method. But the best nonlinear stability criterion obtained so far and the linear stability criterion are not coincident. The two criteria coincide only when the period of the channel is infinite.additional conservation law of momentum and by rigorous estimate of integral inequality. So the new nonlinear stability criterion was obtained, which shows that for Eady 's model in the periodic channel, the linear stable implies the nonlinear stable.

  20. Market dispatch incorporating stability constraints

    International Nuclear Information System (INIS)

    Stability aspects have often been incorporated in the electricity market dispatch/pricing procedure using trial-and-error methods, or approximated in the dispatch optimisation directly as a set of linear constraints on generation/transmission. This paper presents the preliminary experiences with the development of a market optimal power flow (OPF) model that incorporates both transient and voltage stability constraints. The resultant dispatch and prices are expected to exhibit the impact of accurately modelled stability limits that are hitherto largely unknown. This model allows integrated representation of both voltage and transient stability. It, however, entails very significant computational complexities. A complete resolution of all these issues is beyond the scope of this paper, although some initial thoughts to simplify computation are discussed. The importance of stability constraints on market dispatch and prices is discussed around a simple 9-bus system example. (author)

  1. Representation theory and homological stability

    CERN Document Server

    Church, Thomas

    2010-01-01

    We introduce the idea of *representation stability* (and several variations) for a sequence of representations V_n of groups G_n. One main goal is to expand the important and well-studied concept of homological stability so that it applies to a much broader variety of examples. Representation stability also provides a framework in which to find and to predict patterns, from classical representation theory (Littlewood--Richardson and Murnaghan rules, stability of Schur functors), to cohomology of groups (pure braid, Torelli and congruence groups), to Lie algebras and their homology, to the (equivariant) cohomology of flag and Schubert varieties, to combinatorics (the (n+1)^(n-1) conjecture). The majority of this paper is devoted to exposing this phenomenon through examples. In doing this we obtain applications, theorems, and conjectures. Beyond the discovery of new phenomena, the viewpoint of representation stability can be useful in solving problems outside the theory. In addition to the applications given in...

  2. Jet dynamics and stability

    Directory of Open Access Journals (Sweden)

    Perucho M.

    2013-12-01

    Full Text Available The dynamics and stability of extragalactic jets may be strongly influenced by small (and probable di_erences in pressure between the jet and the ambient and within the jet itself. The former give rise to expansion and recollimation of the jet. This occurs in the form of conical shocks, or Mach disks, if the pressure di_erence is large enough. Pressure asymmetries within the jet may trigger the development of helical patterns via coupling to kink current-driven instability, or to helical Kelvin-Helmholtz instability, depending on the physical conditions in the jet. I summarize here the evidence collected during the last years on the presence of recollimation shocks and waves in jets. In the jet of CTA 102 evidence has been found for (travelingshock-(standingshock interaction in the core-region (0.1 mas from the core, using information from the light-curve of the source combined with VLBI data. The conclusions derived have been confirmed by numerical simulations combined with emission calculations that have allowed to study the spectral evolution of the perturbed jet. Helical structures can also be identified in radio-jets. The ridge-line of emission of the jet of S5 0836+710 has been identified as a physical structure corresponding to a wave developing in the jet flow. I review here the evidence that has allowed to reach this conclusion, along with an associated caveat. Current data do not allow to distinguish between magnetic or hydrodynamical instabilities. I finally discuss the importance of these linear and non-linear waves for jet evolution.

  3. Chronotypes and rhythm stability in mice.

    Science.gov (United States)

    Wicht, Helmut; Korf, Horst-Werner; Ackermann, Hanns; Ekhart, Daniel; Fischer, Claudia; Pfeffer, Martina

    2014-02-01

    Humans come in different chronotypes: The phase of their sleep-wake cycle with respect to the phase of the external, sidereal cycle of night and day differs. Colloquially, the early chronotypes are addressed as "larks," the late ones as "owls." The human chronotype can be quantified in hours and minutes of local time by determining the median of the sleep phase. Demographically, early and late human chronotypes differ with respect to the stability of their rhythms and the prevalence of several widespread diseases and risk factors, such as depression, nicotine abuse, and others. Inbred mice are widely used in chronobiological research as model organisms, but up to now there was no way to chronotype them. We have developed a method to chronotype mice in hours and fractions of hours by measuring the median of activity (MoA) and have shown that different mouse strains have significantly different MoAs and, thus, chronotypes. We have further developed methods to estimate the stability of the behavioral rhythms and found that "late" mice have relatively instable rhythms. Our methods permit the use of inbred mice for investigations into the molecular and genetic background of the chronotype and the prevalence of risks and diseases that are associated with it. PMID:24079808

  4. Molecular mobility in glassy dispersions

    Science.gov (United States)

    Mehta, Mehak; McKenna, Gregory B.; Suryanarayanan, Raj

    2016-05-01

    Dielectric spectroscopy was used to characterize the structural relaxation in pharmaceutical dispersions containing nifedipine (NIF) and either poly(vinyl) pyrrolidone (PVP) or hydroxypropyl methylcellulose acetate succinate (HPMCAS). The shape of the dielectric response (permittivity versus log time) curve was observed to be independent of temperature. Thus, for the pure NIF as well as the dispersions, the validity of the time-temperature superposition principle was established. Furthermore, though the shape of the full dielectric response varied with polymer concentration, the regime related to the α- or structural relaxation was found to superimpose for the dispersions, though not with the response of the NIF itself. Hence, there is a limited time-temperature-concentration superposition for these systems as well. Therefore, in this polymer concentration range, calculation of long relaxation times in these glass-forming systems becomes possible. We found that strong drug-polymer hydrogen bonding interactions improved the physical stability (i.e., delayed crystallization) by reducing the molecular mobility. The strength of hydrogen bonding, structural relaxation time, and crystallization followed the order: NIF-PV P>NIF-HPMCAS>NIF. With an increase in polymer concentration, the relaxation times were longer indicating a decrease in molecular mobility. The temperature dependence of relaxation time, in other words fragility, was independent of polymer concentration. This is the first application of the superposition principle to characterize structural relaxation in glassy pharmaceutical dispersions.

  5. Quantifying Stability in Complex Networks: From Linear to Basin Stability

    Science.gov (United States)

    Kurths, Jürgen

    The human brain, power grids, arrays of coupled lasers and the Amazon rainforest are all characterized by multistability. The likelihood that these systems will remain in the most desirable of their many stable states depends on their stability against significant perturbations, particularly in a state space populated by undesirable states. Here we claim that the traditional linearization-based approach to stability is in several cases too local to adequately assess how stable a state is. Instead, we quantify it in terms of basin stability, a new measure related to the volume of the basin of attraction. Basin stability is non-local, nonlinear and easily applicable, even to high-dimensional systems. It provides a long-sought-after explanation for the surprisingly regular topologies of neural networks and power grids, which have eluded theoretical description based solely on linear stability. Specifically, we employ a component-wise version of basin stability, a nonlinear inspection scheme, to investigate how a grid's degree of stability is influenced by certain patterns in the wiring topology. Various statistics from our ensemble simulations all support one main finding: The widespread and cheapest of all connection schemes, namely dead ends and dead trees, strongly diminish stability. For the Northern European power system we demonstrate that the inverse is also true: `Healing' dead ends by addition of transmission lines substantially enhances stability. This indicates a crucial smart-design principle for tomorrow's sustainable power grids: add just a few more lines to avoid dead ends. Further, we analyse the particular function of certain network motifs to promote the stability of the system. Here we uncover the impact of so-called detour motifs on the appearance of nodes with a poor stability score and discuss the implications for power grid design. Moreover, it will be shown that basin stability enables uncovering the mechanism for explosive synchronization and

  6. Coupling of molecular vibrons with contact phonon reservoirs

    International Nuclear Information System (INIS)

    In this paper we describe a computational method for coupling localized molecular vibrations with contact phonons using a Green's function formalism. The phonon Green's function is constructed from the dynamical matrix of the contact-molecule-contact coupled system. Within this formalism we identify the imaginary part of the self-energy as the vibron lifetime for decay into contact phonons. This first-principles calculation allows us to compute the microscopic energy dissipation and the heat transport from the molecule to the contacts. This is a fundamental step for the evaluation of the power dissipated in molecular devices and for studying the thermal stability of molecular devices

  7. Carbon stabilization mechanisms in Ecuadorian Andosols

    Science.gov (United States)

    Jansen, Boris; Tonneijck, Femke; Nierop, Klaas; Verstraten, Koos

    2010-05-01

    Volcanic ash soils contain very large stocks of soil organic matter (SOM) per unit area. Consequently, they constitute potential sources or sinks of the greenhouse gas CO2. Whether soils become a net carbon source or sink upon climate and/or land-use change depends on the stability of SOM against decomposition, which is influenced by stabilisation mechanisms in the soil. To clarify the role of chemical and physical carbon stabilisation mechanisms in volcanic ash soils, we applied selective extraction techniques, performed X-ray diffraction analyses of the clay fraction and estimated pore size distributions at various depths in the top- and subsoil along an altitudinal transect in the Ecuadorian Andes. The transect encompassed a sequence of paleosols under natural upper montane forest as well as grassland (páramo). From several soils SOM was further characterized at a molecular level using GC/MS analyses of extractable lipids and Pyrolysis-GC/MS analyses of bulk organic matter. Our results show that organic carbon stocks under forest as well as páramo vegetation roughly doubled global averages for volcanic ash soils. The carbon stabilization mechanisms involved are: i) direct stabilization of SOM in organo-metallic (Al-OM) complexes; ii) indirect protection of SOM through low soil pH and toxic levels of Al; and iii) physical protection of SOM due to a very high microporosity. When examining the organic carbon at a molecular level, interestingly we found extensive degradation of lignin while extractable lipids were preferentially preserved, hinting at fungal degradation in the face of inhibited bacterial decomposition. Both vegetation types contributed to soil acidification, thus increasing SOM accumulation and inducing positive feedbacks. Most types of land-use change will result in immediate and substantial carbon loss to the atmosphere. Our results stress the urgent need to protect the Tropical Andes 'hotspot' from destructive land-use change, not only for the

  8. Stability of dispersions in polar organic media. I. Electrostatic stabilization

    NARCIS (Netherlands)

    Rooy, N. de; Bruyn, P.L. de; Overbeek, J.Th.G.

    1980-01-01

    Electrostatically stabilized sols of silver, silver iodide, α-goethite, and copper phthalocyanine in methanol, ethanol, isopropanol, and acetone have been prepared and characterized. Coagulation concentrations with electrolytes of various charge numbers have been determined in water, in organic solv

  9. Field investigation of keyblock stability

    Energy Technology Data Exchange (ETDEWEB)

    Yow, J.L. Jr.

    1985-04-01

    Discontinuities in a rock mass can intersect an excavation surface to form discrete blocks (keyblocks) which can be unstable. This engineering problem is divided into two parts: block identification, and evaluation of block stability. One stable keyblock and thirteen fallen keyblocks were observed in field investigations at the Nevada Test Site. Nine blocks were measured in detail sufficient to allow back-analysis of their stability. Measurements included block geometry, and discontinuity roughness and compressive strength. Back-analysis correctly predicted stability or failure in all but two cases. These two exceptions involved situations that violated the stress assumptions of the stability calculations. Keyblock faces correlated well with known joint set orientations. The effect of tunnel orientation on keyblock frequency was apparent. Back-analysis of physical models successfully predicted block pullout force for two-dimensional models of unit thickness. Two-dimensional (2D) and three-dimensional (3D) analytic models for the stability of simple pyramidal keyblocks were examined. Calculated stability is greater for 3D analyses than for 2D analyses. Calculated keyblock stability increases with larger in situ stress magnitudes, larger lateral stress ratios, and larger shear strengths. Discontinuity stiffness controls block displacement more strongly than it does stability itself. Large keyblocks are less stable than small ones, and stability increases as blocks become more slender. Rock mass temperature decreases reduce the confining stress magnitudes and can lead to failure. The pattern of stresses affecting each block face explains conceptually the occurrence of pyramidal keyblocks that are truncated near their apex.

  10. Field investigation of keyblock stability

    International Nuclear Information System (INIS)

    Discontinuities in a rock mass can intersect an excavation surface to form discrete blocks (keyblocks) which can be unstable. This engineering problem is divided into two parts: block identification, and evaluation of block stability. One stable keyblock and thirteen fallen keyblocks were observed in field investigations at the Nevada Test Site. Nine blocks were measured in detail sufficient to allow back-analysis of their stability. Measurements included block geometry, and discontinuity roughness and compressive strength. Back-analysis correctly predicted stability or failure in all but two cases. These two exceptions involved situations that violated the stress assumptions of the stability calculations. Keyblock faces correlated well with known joint set orientations. The effect of tunnel orientation on keyblock frequency was apparent. Back-analysis of physical models successfully predicted block pullout force for two-dimensional models of unit thickness. Two-dimensional (2D) and three-dimensional (3D) analytic models for the stability of simple pyramidal keyblocks were examined. Calculated stability is greater for 3D analyses than for 2D analyses. Calculated keyblock stability increases with larger in situ stress magnitudes, larger lateral stress ratios, and larger shear strengths. Discontinuity stiffness controls block displacement more strongly than it does stability itself. Large keyblocks are less stable than small ones, and stability increases as blocks become more slender. Rock mass temperature decreases reduce the confining stress magnitudes and can lead to failure. The pattern of stresses affecting each block face explains conceptually the occurrence of pyramidal keyblocks that are truncated near their apex

  11. Stability indicators in network reconstruction.

    Science.gov (United States)

    Filosi, Michele; Visintainer, Roberto; Riccadonna, Samantha; Jurman, Giuseppe; Furlanello, Cesare

    2014-01-01

    The number of available algorithms to infer a biological network from a dataset of high-throughput measurements is overwhelming and keeps growing. However, evaluating their performance is unfeasible unless a 'gold standard' is available to measure how close the reconstructed network is to the ground truth. One measure of this is the stability of these predictions to data resampling approaches. We introduce NetSI, a family of Network Stability Indicators, to assess quantitatively the stability of a reconstructed network in terms of inference variability due to data subsampling. In order to evaluate network stability, the main NetSI methods use a global/local network metric in combination with a resampling (bootstrap or cross-validation) procedure. In addition, we provide two normalized variability scores over data resampling to measure edge weight stability and node degree stability, and then introduce a stability ranking for edges and nodes. A complete implementation of the NetSI indicators, including the Hamming-Ipsen-Mikhailov (HIM) network distance adopted in this paper is available with the R package nettools. We demonstrate the use of the NetSI family by measuring network stability on four datasets against alternative network reconstruction methods. First, the effect of sample size on stability of inferred networks is studied in a gold standard framework on yeast-like data from the Gene Net Weaver simulator. We also consider the impact of varying modularity on a set of structurally different networks (50 nodes, from 2 to 10 modules), and then of complex feature covariance structure, showing the different behaviours of standard reconstruction methods based on Pearson correlation, Maximum Information Coefficient (MIC) and False Discovery Rate (FDR) strategy. Finally, we demonstrate a strong combined effect of different reconstruction methods and phenotype subgroups on a hepatocellular carcinoma miRNA microarray dataset (240 subjects), and we validate the

  12. Stability indicators in network reconstruction.

    Directory of Open Access Journals (Sweden)

    Michele Filosi

    Full Text Available The number of available algorithms to infer a biological network from a dataset of high-throughput measurements is overwhelming and keeps growing. However, evaluating their performance is unfeasible unless a 'gold standard' is available to measure how close the reconstructed network is to the ground truth. One measure of this is the stability of these predictions to data resampling approaches. We introduce NetSI, a family of Network Stability Indicators, to assess quantitatively the stability of a reconstructed network in terms of inference variability due to data subsampling. In order to evaluate network stability, the main NetSI methods use a global/local network metric in combination with a resampling (bootstrap or cross-validation procedure. In addition, we provide two normalized variability scores over data resampling to measure edge weight stability and node degree stability, and then introduce a stability ranking for edges and nodes. A complete implementation of the NetSI indicators, including the Hamming-Ipsen-Mikhailov (HIM network distance adopted in this paper is available with the R package nettools. We demonstrate the use of the NetSI family by measuring network stability on four datasets against alternative network reconstruction methods. First, the effect of sample size on stability of inferred networks is studied in a gold standard framework on yeast-like data from the Gene Net Weaver simulator. We also consider the impact of varying modularity on a set of structurally different networks (50 nodes, from 2 to 10 modules, and then of complex feature covariance structure, showing the different behaviours of standard reconstruction methods based on Pearson correlation, Maximum Information Coefficient (MIC and False Discovery Rate (FDR strategy. Finally, we demonstrate a strong combined effect of different reconstruction methods and phenotype subgroups on a hepatocellular carcinoma miRNA microarray dataset (240 subjects, and we

  13. Sludge Stabilization Campaign blend plan

    Energy Technology Data Exchange (ETDEWEB)

    De Vries, M.L.

    1994-10-04

    This sludge stabilization blend plan documents the material to be processed and the order of processing for the FY95 Sludge Stabilization Campaign. The primary mission of this process is to reduce the inventory of unstable plutonium bearing sludge. The source of the sludge is residual and glovebox floor sweepings from the production of material at the Plutonium Finishing Plant (PFP). The reactive sludge is currently being stored in various gloveboxes at PFP. There are two types of the plutonium bearing material that will be thermally stabilized in the muffle furnace: Plutonium Reclamation Facility (PRF) sludge and Remote Mechanical C (RMC) Line material.

  14. STABILITY OF SWITCHED POLYNOMIAL SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    Zhiqiang LI; Yupeng QIAO; Hongsheng QI; Daizhan CHENG

    2008-01-01

    This paper investigates the stability of (switched) polynomial systems. Using semi-tensor product of matrices, the paper develops two tools for testing the stability of a (switched) polynomial system. One is to convert a product of multi-variable polynomials into a canonical form, and the other is an easily verifiable sufficient condition to justify whether a multi-variable polynomial is positive definite. Using these two tools, the authors construct a polynomial function as a candidate Lyapunov function and via testing its derivative the authors provide some sufficient conditions for the global stability of polynomial systems.

  15. Plutonium stabilization and packaging system

    International Nuclear Information System (INIS)

    This document describes the functional design of the Plutonium Stabilization and Packaging System (Pu SPS). The objective of this system is to stabilize and package plutonium metals and oxides of greater than 50% wt, as well as other selected isotopes, in accordance with the requirements of the DOE standard for safe storage of these materials for 50 years. This system will support completion of stabilization and packaging campaigns of the inventory at a number of affected sites before the year 2002. The package will be standard for all sites and will provide a minimum of two uncontaminated, organics free confinement barriers for the packaged material

  16. 46 CFR 178.210 - Stability information.

    Science.gov (United States)

    2010-10-01

    ... 46 Shipping 7 2010-10-01 2010-10-01 false Stability information. 178.210 Section 178.210 Shipping... information. (a) Stability information (stability details indicated on the Certificate of Inspection, a... section. Enough stability information, including stability calculations and assumptions made to use...

  17. The Variation and Stability Analysis of Wheat Dough Stability Time

    Institute of Scientific and Technical Information of China (English)

    TIAN Ji-chun; HU Rui-bo; DENG Zhi-ying; WANG Yan-xun

    2007-01-01

    Farinograph dough stability time is an important index for classifying wheat, and it often indicates the most appropriate end use for the wheat cultivars. This study aimed at the problem of large fluctuations in dough stability time that occurs during the commercial wheat production. The variations in the dough stability time and its consistency across locations and years were analyzed using 12 principal high-quality wheat cultivars (varieties) obtained from Shandong Province,China, which were grown at nine different locations for three successive years. The results showed that the coefficient of variation for the dough stability time ranged from 24.29 to 49.60% across different varieties, locations, and years. Additive main effects and multiplicative interaction (AMMI) analysis indicated that there were significant interactions for the dough stability time between the varieties, the growth locations, and the years. The genotype effect was the most noticeable, followed by the interaction of the genotype and the environment. The environmental effect was the least significant. The interactions between the varieties and the locations differ considerably, however, each cultivar (variety) apparently has a specific adaptability to the growth location. Therefore, for the successful commercial scale production of the high-quality wheat varieties, both the selection of proper cultivars and its most suitable growth locations to meet the desired requirements for the dough mixing stability time are important.

  18. MATLAB Stability and Control Toolbox Trim and Static Stability Module

    Science.gov (United States)

    Kenny, Sean P.; Crespo, Luis

    2012-01-01

    MATLAB Stability and Control Toolbox (MASCOT) utilizes geometric, aerodynamic, and inertial inputs to calculate air vehicle stability in a variety of critical flight conditions. The code is based on fundamental, non-linear equations of motion and is able to translate results into a qualitative, graphical scale useful to the non-expert. MASCOT was created to provide the conceptual aircraft designer accurate predictions of air vehicle stability and control characteristics. The code takes as input mass property data in the form of an inertia tensor, aerodynamic loading data, and propulsion (i.e. thrust) loading data. Using fundamental nonlinear equations of motion, MASCOT then calculates vehicle trim and static stability data for the desired flight condition(s). Available flight conditions include six horizontal and six landing rotation conditions with varying options for engine out, crosswind, and sideslip, plus three take-off rotation conditions. Results are displayed through a unique graphical interface developed to provide the non-stability and control expert conceptual design engineer a qualitative scale indicating whether the vehicle has acceptable, marginal, or unacceptable static stability characteristics. If desired, the user can also examine the detailed, quantitative results.

  19. Standardized molecular typing.

    Science.gov (United States)

    Müller, F M; Lischewski, A; Harmsen, D; Hacker, J

    1999-01-01

    Molecular typing methods are useful tools in molecular mycology. The results of these biotyping procedures may help to identify pathogenic strains in order to detect sources of nosocomial infection and for the investigation of epidemiological relationships. With respect to the facultative pathogen, Candida albicans, various methods such as pulse-field gel electrophoresis (PFGE), restriction fragment length polymorphism (RFLP), DNA fingerprinting methods and hybridization with repetitive DNA elements have been described as useful tools in molecular epidemiology. The previously described hybridization method with the Candida albicans specific CARE-2 probe and subsequent rehybridization with a molecular size marker is a standardized reproducible typing method for comparison of results obtained in different laboratories. In a larger epidemiological study conducted at the University Hospital of Würzburg analysing clinical C. albicans isolates, we were able to describe relationships between sequential patient isolates. These findings demonstrate that standardized molecular typing methods are a powerful tool in molecular mycology studies. PMID:10865907

  20. Fullerene-based Anchoring Groups for Molecular Electronics

    DEFF Research Database (Denmark)

    Martin, Christian A.; Ding, Dapeng; Sørensen, Jakob Kryger;

    2008-01-01

    We present results on a new fullerene-based anchoring group for molecular electronics. Using lithographic mechanically controllable break junctions in vacuum we have determined the conductance and stability of single-molecule junctions of 1,4-bis(fullero[c]pyrrolidin-1-yl)benzene. The compound can...

  1. The morpholino molecular beacon for specific RNA visualization in vivo.

    Science.gov (United States)

    Chen, Jianbin; Wu, Jikui; Hong, Yunhan

    2016-02-21

    A non-invasive fluorescent probe, morpholino molecular beacon (MO-MB), was designed for RNA visualization in vivo. Featuring negligible toxicity, stability, and high target specificity in living embryos, MO-MB is superior to conventional probes and has the potential for specific RNA visualization in basic biological and clinical research. PMID:26810703

  2. The morpholino molecular beacon for specific RNA visualization in vivo.

    Science.gov (United States)

    Chen, Jianbin; Wu, Jikui; Hong, Yunhan

    2016-02-21

    A non-invasive fluorescent probe, morpholino molecular beacon (MO-MB), was designed for RNA visualization in vivo. Featuring negligible toxicity, stability, and high target specificity in living embryos, MO-MB is superior to conventional probes and has the potential for specific RNA visualization in basic biological and clinical research.

  3. Sober Topological Molecular Lattices

    Institute of Scientific and Technical Information of China (English)

    张德学; 李永明

    2003-01-01

    A topological molecular lattice (TML) is a pair (L, T), where L is a completely distributive lattice and r is a subframe of L. There is an obvious forgetful functor from the category TML of TML's to the category Loc of locales. In this note,it is showed that this forgetful functor has a right adjoint. Then, by this adjunction,a special kind of topological molecular lattices called sober topological molecular lattices is introduced and investigated.

  4. Molecular imaging in oncology

    OpenAIRE

    Dzik-Jurasz, A S K

    2004-01-01

    Cancer is a genetic disease that manifests in loss of normal cellular homeostatic mechanisms. The biology and therapeutic modulation of neoplasia occurs at the molecular level. An understanding of these molecular processes is therefore required to develop novel prognostic and early biomarkers of response. In addition to clinical applications, increased impetus for the development of such technologies has been catalysed by pharmaceutical companies investing in the development of molecular ther...

  5. Molecular Epidemiology of Rotaviruses

    OpenAIRE

    Nakagomi, Osamu

    2004-01-01

    Molecular epidemiology of rotaviruses emerged a little over 25 years ago as a fascinating branch of science that utilized then cutting-edge technology of RNA polyacrylamide gel electrophoresis. Molecular epidemiology, as I have observed it closely almost since its dawn, is an ever-evolving discipline which has incorporated the advances of the related sciences including molecular evolutionary biology and ecology, while it is firmly and deeply rooted in the edifice of epidemiology of infectious...

  6. Dense molecular thermodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, J.D.; Shaw, M.S.; Holian, B.L.

    1983-01-01

    We are examining the thermodynamics of dense molecular fluids from the theoretical view. Our interests range from modeling single-species, spherically symmetric, atomic systems, through adding the complication of nonspherical molecular potentials, to mixing various molecular species with the inclusion of chemistry. We discuss what has been accomplished and evaluate the directions to be taken in attacking the unsolved problems. The various theoretical approaches, both analytic and numerical, are presented. We finish with a discussion of the recent advance in treating nonspherical molecular potentials with effective spherical potentials in the calculation of thermodynamics.

  7. Polymer friction Molecular Dynamics

    DEFF Research Database (Denmark)

    Sivebæk, Ion Marius; Samoilov, Vladimir N.; Persson, Bo N. J.

    We present molecular dynamics friction calculations for confined hydrocarbon solids with molecular lengths from 20 to 1400 carbon atoms. Two cases are considered: a) polymer sliding against a hard substrate, and b) polymer sliding on polymer. In the first setup the shear stresses are relatively...... independent of molecular length. For polymer sliding on polymer the friction is significantly larger, and dependent on the molecular chain length. In both cases, the shear stresses are proportional to the squeezing pressure and finite at zero load, indicating an adhesional contribution to the friction force....

  8. Noise Stability of SIS Receivers

    Science.gov (United States)

    Kooi, J. W.; Chattopadhyay, G.; Thielman, M.; Phillips, T. G.; Schieder, R.

    2000-05-01

    There is a strong interest in the submillimeter astronomy community to increase the IF bandwidth of SIS receivers in order to better facilitate broad spectral linewidth and continuum observations of extragalactic sources. However, with an increase in receiver IF bandwidth there is a decrease in the mixer stability. This in turn effects the integration efficiency and quality of the measurement. In order to better understand the noise mechanisms responsible for reducing the receiver stability, we employed a technique first described by D.W. Allan and later elaborated upon by Schieder et al. In this paper we address a variety of factors that degrade the noise stability of SIS receivers. The goal of this exercise is to make recommendations aimed at maximizing SIS receiver stability.

  9. Hydrodynamic stability and stellar oscillations

    Indian Academy of Sciences (India)

    H M Antia

    2011-07-01

    Chandrasekhar’s monograph on Hydrodynamic and hydromagnetic stability, published in 1961, is a standard reference on linear stability theory. It gives a detailed account of stability of fluid flow in a variety of circumstances, including convection, stability of Couette flow, Rayleigh–Taylor instability, Kelvin–Helmholtz instability as well as the Jean’s instability for star formation. In most cases he has extended these studies to include effects of rotation and magnetic field. In a later paper he has given a variational formulation for equations of non-radial stellar oscillations. This forms the basis for helioseismic inversion techniques as well as extension to include the effect of rotation, magnetic field and other large-scale flows using a perturbation treatment.

  10. Slope stability in surface mining

    Energy Technology Data Exchange (ETDEWEB)

    Hustrulid, W.A.; McCarter, M.K.; Van Zyl, D.J.A. (eds.)

    2000-07-01

    The volume contains a total of 49 invited papers in four sections entitled: rock slope design considerations; case studies in rock slope stability; stability of waste rock embankments; and tailings and heap leaching. Three papers are directly relevant to coal mining: coal mine highwall stability by Ben Seegmiller; construction and operation of a major mined-rock disposal facility at Elkview Coal Corporation, British Colombia by Brent Zeitz; and steepened spoil slopes at Bridger Coal Company, by William Gerhard. The papers were invited in the long time lapse between the 3rd and 4th international conference on stability in open pit mining to supplement earlier proceedings. Immediately following the publication of this volume, a symposium was held in conjunction with the 2001 SME annual meeting in Denver, Colorado, USA.

  11. Borate Minerals and RNA Stability

    Directory of Open Access Journals (Sweden)

    Ernesto Di Mauro

    2010-08-01

    Full Text Available The abiotic origin of genetic polymers faces two major problems: a prebiotically plausible polymerization mechanism and the maintenance of their polymerized state outside a cellular environment. The stabilizing action of borate on ribose having been reported, we have explored the possibility that borate minerals stabilize RNA. We observe that borate itself does not stabilize RNA. The analysis of a large panel of minerals tested in various physical-chemical conditions shows that in general no protection on RNA backbone is exerted, with the interesting exception of ludwigite (Mg2Fe3+BO5. Stability is a fundamental property of nucleic polymers and borate is an abundant component of the planet, hence the prebiotic interest of this analysis.

  12. Stability ordering of cycle expansions

    CERN Document Server

    Dettmann, C P

    1997-01-01

    We propose that cycle expansions be ordered with respect to stability rather than orbit length for many chaotic systems, particularly those exhibiting crises. This is illustrated with the strong field Lorentz gas, where we obtain significant improvements over traditional approaches.

  13. Stability of Axisymmetric Liquid Bridges

    CERN Document Server

    Rubinstein, Boris

    2016-01-01

    We study stability of axisymmetric liquid bridges between two axisymmetric solid bodies in the absence of gravity under arbitrary asymmetric perturbations which are expanded into a set of angular Fourier modes. We determine the stability region boundary for every angular mode in case of both fixed and free contact lines. Application of this approach allows us to demonstrate existence of stable convex nodoid menisci between two spheres.

  14. Computer Aided Transient Stability Analysis

    OpenAIRE

    Nihad M. Al-Rawi; Afaneen Anwar; Ahmed M. Abdul-Majeed

    2007-01-01

    A program for handling and improving the transient stability of the Iraqi Super Grid electrical network was developed. The idea was demonstrated by applying it to the outages of the main generating units. The methodology was built upon a state of increasing power transfer through the healthy portion of network during disturbances. There were three parts concerned; the first part was the developing of the load flow program using fast decoupled method and the transient stability program using M...

  15. Statistical models for stability studies

    OpenAIRE

    Uwimpuhwe, Germaine

    2015-01-01

    Stability studies are conducted at all phases of the drug development cycle, with the main objective of having a stable product on market. In this project we aimed at evaluating if the shelf life could be extended from 24 (current shelf life) to 36 months, quantifying pharmaceutical stability such as shelf life, release limit, degradation rate ( annually and at the end of both shelf lives) and consumer/producer risk. The assay data are longitudinal from 50 different batches, whi...

  16. Anthocyanin stability: a chemometrical approach

    OpenAIRE

    Cabrita, Luís; Fossen, Torgils; Flåten, Geir R.; Andersen, Øyvind M

    2002-01-01

    The stability of cyanidin 3-glucoside towards five different factors (pH, anthocyanin concentration, sodium chloride concentration, ascorbic acid concentration, Oxygen) was studied during 60 days storage at room temperature using a 2^4-1 reduced factorial design. The influence of each individual parameter on anthocyanin stability was found to vary as a function of time. Sodium chloride and ascorbic acid were, respectively, the variables most contributing to and against antho...

  17. Citrate-Stabilized Gold Nanorods

    OpenAIRE

    Mehtala, Jonathan G; Zemlyanov, Dmitry Y.; Max, Joann P.; Kadasala, Naveen; Zhao, Shou; Wei, Alexander

    2014-01-01

    Stable aqueous dispersions of citrate-stabilized gold nanorods (cit-GNRs) have been prepared in scalable fashion by surfactant exchange from cetyltrimethylammonium bromide (CTAB)-stabilized GNRs, using polystyrenesulfonate (PSS) as a detergent. The surfactant exchange process was monitored by infrared spectroscopy, surface-enhanced Raman scattering (SERS), and X-ray photoelectron spectroscopy (XPS). The latter established the quantitative displacement of CTAB (by PSS) and of PSS (by citrate)....

  18. Market liquidity and financial stability.

    OpenAIRE

    CROCKETT, A.

    2008-01-01

    Stability in financial institutions and in financial markets are closely intertwined. Banks and other financial institutions need liquid markets through which to conduct risk management. And markets need the back-up liquidity lines provided by financial institutions. Market liquidity depends not only on objective, exogenous factors, but also on endogenous market dynamics. Central banks responsible for systemic stability need to consider how far their traditional responsibility for the health ...

  19. Reliability criteria for voltage stability

    Energy Technology Data Exchange (ETDEWEB)

    Taylor, Carson W.; Silverstein, Brian L. [Bonneville Power Administration, Portland, OR (United States)

    1994-12-31

    In face of costs pressures, there is need to allocate scare resources more effectively in order to achieve voltage stability. This naturally leads to development of probabilistic criteria and notions of rick management. In this paper it is presented a discussion about criteria for long term voltage stability limited to the case in which the time frames are topically several minutes. (author) 14 refs., 1 fig.

  20. The Role of Cross-Chain Ionic Interactions for the Stability of Collagen Model Peptides

    OpenAIRE

    Keshwani, Neelam; Banerjee, Shounak; Brodsky, Barbara; Makhatadze, George I.

    2013-01-01

    The contribution of ionic interactions to the stability of the collagen triple helix was studied using molecular dynamics (MD) simulations and biophysical methods. To this end, we examined the stability of a host-guest collagen model peptide, Ac-GPOGPOGPYGXOGPOGPO-NH2, substituting KGE, KGD, EGK, and DGK for the YGX sequence. All-atom, implicit solvent MD simulations show that the fraction of cross-chain ionic interactions formed is different, with the most pronounced in the KGE and KGD seque...

  1. Molecular interaction of PCB153 to human serum albumin: Insights from spectroscopic and molecular modeling studies

    International Nuclear Information System (INIS)

    Highlights: ► We identify the binding mode of PCB153 to human serum albumin (HSA). ► Spectroscopic and molecular modeling results reveal that PCB153 binds at the site II. ► The interaction is mainly governed by hydrophobic and hydrogen bond forces. ► The work helps to probe transporting, distribution and toxicity effect of PCBs. -- Abstract: Polychlorinated biphenyls (PCBs) possessed much potential hazard to environment because of its chemical stability and biological toxicity. Here, we identified the binding mode of a representative compound, PCB153, to human serum albumin (HSA) using fluorescence and molecular dynamics simulation methods. The fluorescence study showed that the intrinsic fluorescence of HSA was quenched by addition of PCB153 through a static quenching mechanism. The thermodynamic analysis proved the binding behavior was mainly governed by hydrophobic force. Furthermore, as evidenced by site marker displacement experiments using two probe compounds, it revealed that PCB153 acted exactly on subdomain IIIA (site II) of HSA. On the other hand, the molecular dynamics studies as well as free energy calculations made another important contribution to understand the conformational changes of HSA and the stability of HSA-PCB153 system. Molecular docking revealed PCB153 can bind in a large hydrophobic activity of subdomain IIIA by the hydrophobic interaction and hydrogen bond interactions between chlorine atoms and residue ASN391. The present work provided reasonable models helping us further understand the transporting, distribution and toxicity effect of PCBs when it spread into human blood serum

  2. Molecular interaction of PCB153 to human serum albumin: Insights from spectroscopic and molecular modeling studies

    Energy Technology Data Exchange (ETDEWEB)

    Han, Chao; Fang, Senbiao; Cao, Huiming; Lu, Yan; Ma, Yaqiong [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Wei, Dongfeng [Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700 (China); Xie, Xiaoyun [College of Earth and Environmental Science, Lanzhou University, Lanzhou 730000 (China); Liu, Xiaohua [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Li, Xin [College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471003 (China); Fei, Dongqing [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Zhao, Chunyan, E-mail: zhaochy07@lzu.edu.cn [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China)

    2013-03-15

    Highlights: ► We identify the binding mode of PCB153 to human serum albumin (HSA). ► Spectroscopic and molecular modeling results reveal that PCB153 binds at the site II. ► The interaction is mainly governed by hydrophobic and hydrogen bond forces. ► The work helps to probe transporting, distribution and toxicity effect of PCBs. -- Abstract: Polychlorinated biphenyls (PCBs) possessed much potential hazard to environment because of its chemical stability and biological toxicity. Here, we identified the binding mode of a representative compound, PCB153, to human serum albumin (HSA) using fluorescence and molecular dynamics simulation methods. The fluorescence study showed that the intrinsic fluorescence of HSA was quenched by addition of PCB153 through a static quenching mechanism. The thermodynamic analysis proved the binding behavior was mainly governed by hydrophobic force. Furthermore, as evidenced by site marker displacement experiments using two probe compounds, it revealed that PCB153 acted exactly on subdomain IIIA (site II) of HSA. On the other hand, the molecular dynamics studies as well as free energy calculations made another important contribution to understand the conformational changes of HSA and the stability of HSA-PCB153 system. Molecular docking revealed PCB153 can bind in a large hydrophobic activity of subdomain IIIA by the hydrophobic interaction and hydrogen bond interactions between chlorine atoms and residue ASN391. The present work provided reasonable models helping us further understand the transporting, distribution and toxicity effect of PCBs when it spread into human blood serum.

  3. Stability measures in arid ecosystems

    Science.gov (United States)

    Nosshi, M. I.; Brunsell, N. A.; Koerner, S.

    2015-12-01

    Stability, the capacity of ecosystems to persist in the face of change, has proven its relevance as a fundamental component of ecological theory. Here, we would like to explore meaningful and quantifiable metrics to define stability, with a focus on highly variable arid and semi-arid savanna ecosystems. Recognizing the importance of a characteristic timescale to any definition of stability, our metrics will be focused scales from annual to multi-annual, capturing different aspects of stability. Our three measures of stability, in increasing order of temporal scale, are: (1) Ecosystem resistance, quantified as the degree to which the system maintains its mean state in response to a perturbation (drought), based on inter-annual variability in Normalized Difference Vegetation Index (NDVI). (2) An optimization approach, relevant to arid systems with pulse dynamics, that models vegetation structure and function based on a trade off between the ability to respond to resource availability and avoid stress. (3) Community resilience, measured as species turnover rate (β diversity). Understanding the nature of stability in structurally-diverse arid ecosystems, which are highly variable, yields theoretical insight which has practical implications.

  4. Stability of p53 homologs.

    Directory of Open Access Journals (Sweden)

    Tobias Brandt

    Full Text Available Most proteins have not evolved for maximal thermal stability. Some are only marginally stable, as for example, the DNA-binding domains of p53 and its homologs, whose kinetic and thermodynamic stabilities are strongly correlated. Here, we applied high-throughput methods using a real-time PCR thermocycler to study the stability of several full-length orthologs and paralogs of the p53 family of transcription factors, which have diverse functions, ranging from tumour suppression to control of developmental processes. From isothermal denaturation fluorimetry and differential scanning fluorimetry, we found that full-length proteins showed the same correlation between kinetic and thermodynamic stability as their isolated DNA-binding domains. The stabilities of the full-length p53 orthologs were marginal and correlated with the temperature of their organism, paralleling the stability of the isolated DNA-binding domains. Additionally, the paralogs p63 and p73 were significantly more stable and long-lived than p53. The short half-life of p53 orthologs and the greater persistence of the paralogs may be biologically relevant.

  5. Rheological properties of poly(vinylpiyrrolidone) as a function of molecular weight

    DEFF Research Database (Denmark)

    Marani, Debora; Sudireddy, Bhaskar Reddy; Kiebach, Wolff-Ragnar;

    2014-01-01

    to evaluate the viscosity molecular weight (Mv) via an empirically modified Mark-Houwink-Sakurada (MHS) equation. The MHS equation parameters (a and K), and the polydispersity correction factor (qMHS) were also evaluated. Molecular weight was found to affect only the amount of PVP required for achieving full...... stabilized dispersions Indeed, no influence on the packing properties was observed....

  6. Visualizing Protein Interactions and Dynamics: Evolving a Visual Language for Molecular Animation

    Science.gov (United States)

    Jenkinson, Jodie; McGill, Gael

    2012-01-01

    Undergraduate biology education provides students with a number of learning challenges. Subject areas that are particularly difficult to understand include protein conformational change and stability, diffusion and random molecular motion, and molecular crowding. In this study, we examined the relative effectiveness of three-dimensional…

  7. Theoretical aspects of enterprise financial stability management

    Directory of Open Access Journals (Sweden)

    Kovalova Tatiana Volodymyrivna

    2015-10-01

    Full Text Available In the article questions related to the aspects of financial stability management, in particular were analyzed, opinions of scientists in relation to a concept «financial stability management» were analyzed; external and internal pre-conditions of loss of financial stability are considered; the offered measures are in relation to stabilizing of financial stability of enterprises in the conditions of financial instability; determination of concept «financial stability management» was improved.

  8. Long term stability of power systems

    Energy Technology Data Exchange (ETDEWEB)

    Kundur, P.; Gao, B. [Powertech Labs. Inc., Surrey, BC (Canada)

    1994-12-31

    Power system long term stability is still a developing subject. In this paper we provide our perspectives and experiences related to long term stability. The paper begins with the description of the nature of the long term stability problem, followed by the discussion of issues related to the modeling and solution techniques of tools for long term stability analysis. Cases studies are presented to illustrate the voltage stability aspect and plant dynamics aspect of long term stability. (author) 20 refs., 11 figs.

  9. Stabilization of magnetorheological suspensions by polyacrylic acid polymers.

    Science.gov (United States)

    Viota, J L; de Vicente, J; Durán, J D G; Delgado, A V

    2005-04-15

    This work is devoted to the synthesis and stabilization of magnetorheological suspensions constituted by monodisperse micrometer-sized magnetite spheres in aqueous media. The electrical double-layer characteristics of the solid/liquid interface were studied in the absence and presence of adsorbed layers of high molecular weight polyacrylic acids (PAA; Carbopol). Since the Carbopol-covered particles can be thought of as "soft" colloids, Ohshima's theory was used to gain information of the surface potential and the charge density of the polymer layer. The effect of the pH of the solution on the double-layer characteristics is related to the different conformations of the adsorbed molecules provoked by the dissociation of the acrylic groups present in polymer molecules. The stability of the suspensions was experimentally studied for different pH and polymer concentrations, and in the absence or presence of a weak magnetic field applied. The stability of the suspensions was explained using the classical DLVO theory of colloidal stability extended to account for hydration, steric, and magnetic interactions between particles. Diagrams of potential energy vs interparticle distance show the predominant effect of steric, hydrophilic/hydrophobic, and magnetic interactions on the whole stability of the system. The best conditions to obtain stable suspensions were found when strong steric and hydrophilic repulsions hinder the coagulation between polymer-covered particles, simultaneously avoiding sedimentation by the thickening effect of the polymer solution. When a not too high molecular weight PAA was employed in a low concentration, the task of a long-time antisettling effect compatible with the desired magnetic response of the fluid was achieved. PMID:15780292

  10. Mesoporous molecular sieve catalysts

    DEFF Research Database (Denmark)

    Højholt, Karen Thrane

    This thesis deals with a very specific class of molecular sieves known as zeolites. Zeolites are a class of crystalline aluminosilicates characterised by pores or cavities of molecular dimensions as part of their crystal structure. In this work zeolites were modified for the use and understanding...

  11. Making molecular machines work

    NARCIS (Netherlands)

    Browne, Wesley R.; Feringa, Ben L.

    2006-01-01

    In this review we chart recent advances in what is at once an old and very new field of endeavour the achievement of control of motion at the molecular level including solid-state and surface-mounted rotors, and its natural progression to the development of synthetic molecular machines. Besides a di

  12. Advancement of Molecular Morphology

    Institute of Scientific and Technical Information of China (English)

    顾江

    2004-01-01

    Molecular morphology is a new discipline of medical science that studies morphology at the molecular level. This includes the investigation of occurrence and distribution of proteins, peptides, DNA and RNA sequences at the tissue, cellular, and uhrastructural levels. Morphology is defined as a field of science investigating the shape,

  13. Multifunctionality in molecular magnetism.

    Science.gov (United States)

    Pinkowicz, Dawid; Czarnecki, Bernard; Reczyński, Mateusz; Arczyński, Mirosław

    2015-01-01

    Molecular magnetism draws from the fundamental ideas of structural chemistry and combines them with experimental physics resulting in one of the highest profile current topics, namely molecular materials that exhibit multifunctionality. Recent advances in the design of new generations of multifunctional molecular magnets that retain the functions of the building blocks and exhibit non-trivial magnetic properties at higher temperatures provide promising evidence that they may be useful for the future construction of nanoscale devices. This article is not a complete review but is rather an introduction into thefascinating world of multifunctional solids with magnetism as the leitmotif. We provide a subjective selection and discussion of the most inspiring examples of multifunctional molecular magnets: magnetic sponges, guest-responsive magnets, molecular magnets with ionic conductivity, photomagnets and non-centrosymmetric and chiral magnets.

  14. Molecular diodes and applications.

    Science.gov (United States)

    Kumar, M Jagadesh

    2007-01-01

    Due to the huge power consumption and expensive fabrication methods required, down scaling silicon devices to sub-100 nm dimensions is becoming very unattractive. On the other hand, it is easier to build electronic circuits using molecules since they are small and their properties can be tuned. In this review, we first discuss the building blocks of molecular electronics. We then describe how these building blocks can be used to build single molecule based digital logic such as AND, OR and XOR gates. The distinction of these molecular electronic building blocks is that for first time, (i) the Tour wires are used as the conductive backbone for the rectifying junctions, (ii) donor/acceptor principles are implemented in the molecular wire itself and (iii) the logic gates are realized using molecular rectifying diodes embedded in the molecular conducting wire itself. PMID:19076020

  15. Stability Analysis and Stabilization of Miduk Heap Leaching Structure, Iran

    Directory of Open Access Journals (Sweden)

    Mehdi Amini

    2013-06-01

    Full Text Available To construct copper heap leaching structures, a stepped heap of ore is placed over an isolated sloping surface and then washed with sulphuric acid. The isolated bed of such a heap consists of some natural and geosynthetic layers. Shear strength parameters between these layers are low, so they form the possible sliding surfaces of the heaps. Economic and environmental considerations call for studying such slides. In this study, firstly, results of the laboratory tests carried on the materials of the heap leaching structures bed are presented. Then, the instability mechanisms of such structures are investigated and proper approaches are summarized for their stabilization. Finally, stability of the Miduk copper heap is evaluated as a case history, and appropriate approaches and their effects are discussed for its stabilization.

  16. High beta and second stability region transport and stability analysis

    International Nuclear Information System (INIS)

    This document summarizes progress made on the research of high beta and second region transport and stability. In the area second stability region studies we report on an investigation of the possibility of second region access in the center of TFTR ''supershots.'' The instabilities found may coincide with experimental observation. Significant progress has been made on the resistive stability properties of high beta poloidal ''supershot'' discharges. For these studies profiles were taken from the TRANSP transport analysis code which analyzes experimental data. Invoking flattening of the pressure profile on mode rational surfaces causes tearing modes to persist into the experimental range of interest. Further, the experimental observation of the modes seems to be consistent with the predictions of the MHD model. In addition, code development in several areas has proceeded

  17. Matlab Stability and Control Toolbox: Trim and Static Stability Module

    Science.gov (United States)

    Crespo, Luis G.; Kenny, Sean P.

    2006-01-01

    This paper presents the technical background of the Trim and Static module of the Matlab Stability and Control Toolbox. This module performs a low-fidelity stability and control assessment of an aircraft model for a set of flight critical conditions. This is attained by determining if the control authority available for trim is sufficient and if the static stability characteristics are adequate. These conditions can be selected from a prescribed set or can be specified to meet particular requirements. The prescribed set of conditions includes horizontal flight, take-off rotation, landing flare, steady roll, steady turn and pull-up/ push-over flight, for which several operating conditions can be specified. A mathematical model was developed allowing for six-dimensional trim, adjustable inertial properties, asymmetric vehicle layouts, arbitrary number of engines, multi-axial thrust vectoring, engine(s)-out conditions, crosswind and gyroscopic effects.

  18. U31: Vehicle Stability and Dynamics: Electronic Stability Control

    Energy Technology Data Exchange (ETDEWEB)

    Petrolino, Joseph [National Transportation Research Center (NTRC); Spezia, Tony [National Transportation Research Center (NTRC); Arant, Michael [Clemson University; Delorenzis, Damon [Clemson University; LaClair, Tim J [ORNL; Lim, Alvin [Auburn University, Auburn, Alabama; Pape, Doug [Battelle

    2011-01-01

    A team led by NTRCI is working to improve the roll and yaw stability of heavy duty combination trucks through developing stability algorithms, assembling demonstration hardware, and investigating robust wireless communication. Modern electronic stability control (ESC) products automatically slow a vehicle rounding a corner too quickly or apply individual brakes when necessary to improve the steering characteristics of a vehicle. Air brake systems in North America provide no electronic communication between a tractor and semitrailer, limiting the degree to which control systems can be optimized. Prior research has demonstrated stability improvements where dynamic measurements and control commands are communicated between units of a vehicle. Three related activities were undertaken: (1) Develop an algorithm for the optimum yaw and roll control of a combination vehicle. Vehicle state parameters needed to control the vehicle and the proper brake response were determined. An integrated stability control for the tractor and semitrailer requires communication between the two units. Dynamic models were used to assess the algorithm. (2) Implement the ESC algorithm in the laboratory. Hardware components suitable for the harsh environment for measurement, sensor-to-controller communication, and semitrailer-to-tractor communication and brake actuation were specified and assembled as a working system. The goal was to collect the needed vehicle state information, transmit the information to the ESC system, and then actuate the brakes in response to controller commands. (3) Develop a wireless network with the data rate and reliability necessary to communicate dynamic signals for a vehicle stability control system. Adaptive connectivity-aware, multi-hop routing was selected because it can perform in the harsh environment where packet collisions and fading often will exist. The protocol is to give high priority to urgent messages.

  19. Molecular and trophic mechanisms of tumorigenesis.

    Science.gov (United States)

    Levy, Andy

    2008-03-01

    A significant proportion of pituitary macroadenomas, and by definition all microadenomas, regain trophic stability after an initial period of deregulated growth. Classical proto-oncogene activation and tumor suppressor mutation are rarely responsible, and no histologic or molecular markers reliably predict behavior. GNAS1 activation and the mutations associated with multiple endocrine neoplasia type 1 and Carney complex, aryl hydrocarbon receptor interacting protein gene mutations, and a narrowing region of chromosome 11q13 in familial isolated acromegaly together account for such a small proportion of pituitary adenomas that the pituitary adenoma pathogenic epiphany is surely yet to come. PMID:18226729

  20. Molecular Recognition Studies on Modified Cyclodextrins

    Institute of Scientific and Technical Information of China (English)

    LIU,Yu; YOU,Chang-Cheng

    2001-01-01

    This account deacribes our research progress in recent years in the areas of the molecular recognition studies on modified cy clodextrins, including positively charged cyclodextrins, cy clodextrin derivatives with hydrophobic substituent, and dimeric cyclodextrins. Calorimetric titration and various spec trometric techniques were employed to determine the complex stability constants, as well as the thermodynamic parameters, for their inclusion complexation with diverse guest molecules. The results obtained have heen discussed from the viewpoint of size/shape-matching, induced-fit, geometric compensation, and multiple recognition. Thermodynamically, the compen satory relationship between △H and T△S was found to be ex hibited in the inclusion complexation of modified cyclodextrin.

  1. Molecular mechanism for the umami taste synergism.

    Science.gov (United States)

    Zhang, Feng; Klebansky, Boris; Fine, Richard M; Xu, Hong; Pronin, Alexey; Liu, Haitian; Tachdjian, Catherine; Li, Xiaodong

    2008-12-30

    Umami is one of the 5 basic taste qualities. The umami taste of L-glutamate can be drastically enhanced by 5' ribonucleotides and the synergy is a hallmark of this taste quality. The umami taste receptor is a heteromeric complex of 2 class C G-protein-coupled receptors, T1R1 and T1R3. Here we elucidate the molecular mechanism of the synergy using chimeric T1R receptors, site-directed mutagenesis, and molecular modeling. We propose a cooperative ligand-binding model involving the Venus flytrap domain of T1R1, where L-glutamate binds close to the hinge region, and 5' ribonucleotides bind to an adjacent site close to the opening of the flytrap to further stabilize the closed conformation. This unique mechanism may apply to other class C G-protein-coupled receptors.

  2. Molecular mechanism of the sweet taste enhancers.

    Science.gov (United States)

    Zhang, Feng; Klebansky, Boris; Fine, Richard M; Liu, Haitian; Xu, Hong; Servant, Guy; Zoller, Mark; Tachdjian, Catherine; Li, Xiaodong

    2010-03-01

    Positive allosteric modulators of the human sweet taste receptor have been developed as a new way of reducing dietary sugar intake. Besides their potential health benefit, the sweet taste enhancers are also valuable tool molecules to study the general mechanism of positive allosteric modulations of T1R taste receptors. Using chimeric receptors, mutagenesis, and molecular modeling, we reveal how these sweet enhancers work at the molecular level. Our data argue that the sweet enhancers follow a similar mechanism as the natural umami taste enhancer molecules. Whereas the sweeteners bind to the hinge region and induce the closure of the Venus flytrap domain of T1R2, the enhancers bind close to the opening and further stabilize the closed and active conformation of the receptor.

  3. Molecular phospholipid films on solid supports

    DEFF Research Database (Denmark)

    Czolkos, Ilja; Jesorka, Aldo; Orwar, Owe

    2011-01-01

    Phospholipid membranes are versatile structures for mimicking biological surfaces. Bilayer and monolayer membranes can be formed on solid supports, leading to enhanced stability and accessibility of the biomimetic molecular film. This has facilitated functional studies of membrane proteins...... and aided the development of membrane-based applications in, for example, biosensing, self-assembled reaction kinetics and catalysis. Assembly and preparation of lipid films on supporting surfaces is a challenging engineering task with the goal of fabricating mechanically, chemically and thermodynamically...... stable lipid membranes. In this review, the current state of the art of molecularly thin lipid layer fabrication is presented with an emphasis on support materials, film formation mechanisms, characterisation methods, and applications....

  4. Can the UN Stabilize Mali? Towards a UN Stabilization Doctrine?

    Directory of Open Access Journals (Sweden)

    Arthur Boutellis

    2015-06-01

    Full Text Available Almost two years after the deployment of the United Nations Multidimensional Integrated Stabilization Mission in Mali (MINUSMA in July 2013, the increasing number of asymmetric terrorist attacks targeting UN peacekeepers – in the context of a drawn-out peace process – has raised a number of questions in Mali, the sub-region, and in New York, over the relevance and adequacies of MINUSMA’s mandate and capabilities. It also raises a broader issue, of whether the consent-based UN peacekeeping tool is appropriate and can be effective in carrying out stabilization mandates in such a context and what doctrine such operations should be based on. The UN is indeed under increasing pressure from host countries and some African troop-contributing countries to go on the offensive. Member States have also increasingly recognized terrorism and organized crime as a strategic threat, and while opposed to the UN directly engaging in counterterrorism (CT operations, some may wish to see the UN playing a greater stabilization role following the January 2013 French military intervention in Mali. However, little guidance and means have been given so far to UN missions for dealing with such threats and implementing effective stabilization mandates. The High-Level Panel on Peace Operations, which recently released its report, noted that the usage of the term “stabilization” by the UN requires clarification. This article analyses the complex and evolving nature of threats in northern Mali and implications for MINUSMA and describes the military and political tools – including mediation – so far available within and outside the UN. The article concludes that the UN is bound to move towards stabilization when and if deployed in contexts such as Mali’s if it wants to remain relevant. However, such a move should be based on an overarching UN stabilization doctrine and context-specific UN-wide stabilization strategies which are first and foremost political

  5. Improved Simulation of Stabilizer Circuits

    CERN Document Server

    Aaronson, S; Aaronson, Scott; Gottesman, Daniel

    2004-01-01

    The Gottesman-Knill theorem says that a stabilizer circuit -- that is, a quantum circuit consisting solely of CNOT, Hadamard, and phase gates -- can be simulated efficiently on a classical computer. This paper improves that theorem in several directions. * By removing the need for Gaussian elimination, we make the simulation algorithm much faster at the cost of a factor-2 increase in the number of bits needed to represent a state. We have implemented the improved algorithm in a freely-available program called CHP (CNOT-Hadamard-Phase), which can handle thousands of qubits easily. * We show that the problem of simulating stabilizer circuits is complete for the classical complexity class ParityL, which means that stabilizer circuits are probably not even universal for classical computation. * We give efficient algorithms for computing the inner product between two stabilizer states, putting any n-qubit stabilizer circuit into a "canonical form" that requires at most O(n^2/log n) gates, and other useful tasks. *...

  6. On hovercraft overwater heave stability

    Science.gov (United States)

    Hinchey, M. J.; Sullivan, P. A.

    1993-05-01

    The dynamic heave stability of an air cushion vehicle or hovercraft hovering over deep water without forward motion is investigated analytically. The principal feature of the analysis is the modeling of the motion of the water surface beneath the cushion caused by fluctuations in the pressure of the cushion or cavity air. This surface motion interacts with the vehicle dynamics by modulating both the volume and exit flow area of the cushion. For analytical simplicity, the geometry chosen for study is a 2D section of a rigid wall plenum chamber; this enables exploitation of classical linear wave formulas developed by Lamb for the surface motion generated by a spatially uniform surface pressure oscillating sinusoidally in time. To assess stability characteristics, the Nyquist criterion is applied to the linearized equations. Results are presented for two cases: one is representative of a small test vehicle, and the other of a large ice-breaking platform. They show that the water surface motion significantly affects stability through both of the proposed mechanisms, with cushion exit flow area modulation usually being more important. A feature of the results is that as the weight of a vehicle decreases many stability transitions occur. This suggests that simple guidelines for avoiding instability may not exist, so that stability augmentation devices may be required for vehicles designed to hover for extended periods over water.

  7. Transient stability and emergency control

    Institute of Scientific and Technical Information of China (English)

    ZHANG XueMin; MEI ShengWei; WU ShengYu

    2009-01-01

    Comparability of emergency control strategies with different instability modes is the key issue to de-cide which control strategy to be implemented. This paper considers that the essential factor causing instability should be used to form a unified standard to assess the effectiveness of control strategies with different instability modes. Thus a switching control stabilization principle was proposed based on elimination of the unbalanced energy between mechanical and electrical energies of generator sets. Along this way, the difficulty of seeking a Lyapunov function was circumvented. According to the prin-ciple, an emergency control algorithm framework was established to handle transient stability as-sessment, control location selection and control amount evaluation. Within the framework, this paper studied instability mode transition, then proposed an algorithm based on prediction function and a new approach to normalized stability margin stemmed from static EEAC method, which can increase com-parability of various control locations. The simulations on the New-England System verified the pro-posed emergency control method for stabilizing transient stability.

  8. Evolution of an Antibiotic Resistance Enzyme Constrained by Stability and Activity Trade-offs

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Xiaojun; Minasov, George; Shoichet, Brian K. (NWU)

    2010-03-08

    Pressured by antibiotic use, resistance enzymes have been evolving new activities. Does such evolution have a cost? To investigate this question at the molecular level, clinically isolated mutants of the {beta}-lactamase TEM-1 were studied. When purified, mutant enzymes had increased activity against cephalosporin antibiotics but lost both thermodynamic stability and kinetic activity against their ancestral targets, penicillins. The X-ray crystallographic structures of three mutant enzymes were determined. These structures suggest that activity gain and stability loss is related to an enlarged active site cavity in the mutant enzymes. In several clinically isolated mutant enzymes, a secondary substitution is observed far from the active site (Met182 {yields} Thr). This substitution had little effect on enzyme activity but restored stability lost by substitutions near the active site. This regained stability conferred an advantage in vivo. This pattern of stability loss and restoration may be common in the evolution of new enzyme activity.

  9. Fragment oriented molecular shapes.

    Science.gov (United States)

    Hain, Ethan; Camacho, Carlos J; Koes, David Ryan

    2016-05-01

    Molecular shape is an important concept in drug design and virtual screening. Shape similarity typically uses either alignment methods, which dynamically optimize molecular poses with respect to the query molecular shape, or feature vector methods, which are computationally less demanding but less accurate. The computational cost of alignment can be reduced by pre-aligning shapes, as is done with the Volumetric-Aligned Molecular Shapes (VAMS) method. Here, we introduce and evaluate fragment oriented molecular shapes (FOMS), where shapes are aligned based on molecular fragments. FOMS enables the use of shape constraints, a novel method for precisely specifying molecular shape queries that provides the ability to perform partial shape matching and supports search algorithms that function on an interactive time scale. When evaluated using the challenging Maximum Unbiased Validation dataset, shape constraints were able to extract significantly enriched subsets of compounds for the majority of targets, and FOMS matched or exceeded the performance of both VAMS and an optimizing alignment method of shape similarity search. PMID:27085751

  10. Circadian molecular clock in lung pathophysiology.

    Science.gov (United States)

    Sundar, Isaac K; Yao, Hongwei; Sellix, Michael T; Rahman, Irfan

    2015-11-15

    Disrupted daily or circadian rhythms of lung function and inflammatory responses are common features of chronic airway diseases. At the molecular level these circadian rhythms depend on the activity of an autoregulatory feedback loop oscillator of clock gene transcription factors, including the BMAL1:CLOCK activator complex and the repressors PERIOD and CRYPTOCHROME. The key nuclear receptors and transcription factors REV-ERBα and RORα regulate Bmal1 expression and provide stability to the oscillator. Circadian clock dysfunction is implicated in both immune and inflammatory responses to environmental, inflammatory, and infectious agents. Molecular clock function is altered by exposomes, tobacco smoke, lipopolysaccharide, hyperoxia, allergens, bleomycin, as well as bacterial and viral infections. The deacetylase Sirtuin 1 (SIRT1) regulates the timing of the clock through acetylation of BMAL1 and PER2 and controls the clock-dependent functions, which can also be affected by environmental stressors. Environmental agents and redox modulation may alter the levels of REV-ERBα and RORα in lung tissue in association with a heightened DNA damage response, cellular senescence, and inflammation. A reciprocal relationship exists between the molecular clock and immune/inflammatory responses in the lungs. Molecular clock function in lung cells may be used as a biomarker of disease severity and exacerbations or for assessing the efficacy of chronotherapy for disease management. Here, we provide a comprehensive overview of clock-controlled cellular and molecular functions in the lungs and highlight the repercussions of clock disruption on the pathophysiology of chronic airway diseases and their exacerbations. Furthermore, we highlight the potential for the molecular clock as a novel chronopharmacological target for the management of lung pathophysiology.

  11. Stabilizing effect of epoxidized sunflower oil as a secondary stabilizer for Ca/Hg stabilized PVC

    Directory of Open Access Journals (Sweden)

    2008-01-01

    Full Text Available Unsaturated triglyceride oil sunflower was epoxidized and characterized by chemical and spectroscopic methods. Epoxidized sunflower oil (ESO was used as an organic thermal co-stabilizer for rigid poly(vinyl chloride (PVC in the presence of tricalcium dicitrate (Ca3(C6H5O72 and mercury (II acetate (Hg(CH3COO2. The thermo-oxidative degradation of PVC was studied in the presence of these ternary stabilizer systems at 170, 180, 190 and 200°C in N2 atmosphere. The effects of metal carboxylate combination Ca/Hg in the absence and in the presence of epoxidized sunflower oil on static heat treatment of PVC have been studied. The formation of polyene sequences was investigated by UV-visible and FT-IR spectroscopy and by comparing viscosity data obtained in the presence and in the absence of the additives. It was found that the additives retard the rate of degradation and reduce the extent of polymer chain scission associated with the thermal degradation of poly(vinyl chloride. Synergistic effects were found when stabilizer was blended in 50:50 weight ratios with either. It was found that ESO exerted a stabilizing effect on the degradation of PVC. The activation energy for degraded PVC in absence of stabilizers was 38.6 kJ•mol–1 and in the presence of Ca/Hg and Ca/Hg/ESO were 53.3 and 64.7 kJ•mol–1 respectively. In order of compare the efficiency of the epoxidized sunflower oil with these metal soap stabilizers, thermal stabilities were evaluated on the basis of evolved hydrogen chloride determined by conductometry technique and degree of discoloration are discussed.

  12. Fingerprinting Electronic Molecular Complexes in Liquid

    Science.gov (United States)

    Nirmalraj, Peter; La Rosa, Andrea; Thompson, Damien; Sousa, Marilyne; Martin, Nazario; Gotsmann, Bernd; Riel, Heike

    2016-01-01

    Predicting the electronic framework of an organic molecule under practical conditions is essential if the molecules are to be wired in a realistic circuit. This demands a clear description of the molecular energy levels and dynamics as it adapts to the feedback from its evolving chemical environment and the surface topology. Here, we address this issue by monitoring in real-time the structural stability and intrinsic molecular resonance states of fullerene (C60)-based hybrid molecules in the presence of the solvent. Energetic levels of C60 hybrids are resolved by in situ scanning tunnelling spectroscopy with an energy resolution in the order of 0.1 eV at room-temperature. An ultra-thin organic spacer layer serves to limit contact metal-molecule energy overlap. The measured molecular conductance gap spread is statistically benchmarked against first principles electronic structure calculations and used to quantify the diversity in electronic species within a standard population of molecules. These findings provide important progress towards understanding conduction mechanisms at a single-molecular level and in serving as useful guidelines for rational design of robust nanoscale devices based on functional organic molecules.

  13. Molecular Engineering of DNA: Molecular Beacons

    OpenAIRE

    Wang, Kemin; Tang, Zhiwen; Yang, Chaoyong James; Kim, Youngmi; Fang, Xiaohong; Li, Wei; Wu, Yanrong; Medley, Colin D.; Cao, Zehui; Jun LI; Colon, Patrick; Lin, Hui; Tan, Weihong

    2009-01-01

    Molecular beacons (MBs) are specifically designed DNA hairpin structures that are widely used as fluorescent probes. Applications of MBs range from genetic screening, biosensor development, biochip construction, and the detection of single-nucleotide polymorphisms to mRNA monitoring in living cells. The inherent signal-transduction mechanism of MBs enables the analysis of target oligonucleotides without the separation of unbound probes. The MB stem–loop structure holds the fluorescence-donor ...

  14. The Stability of Standing Waves

    CERN Document Server

    Riecke, H; Riecke, Hermann; Kramer, Lorenz

    1998-01-01

    We determine the modulational stability of standing waves in quasi-onedimensional systems slightly above the threshold of a supercritical Hopf bifurcation. The stability limits are given by two different long-wavelength destabilisation mechanisms and generically also a short-wavelength destabilisation. The Eckhaus parabola is shifted off-center and can be convex from below or above. For nonzero group velocity the Newell criterion, which near the crossover from standing to traveling waves becomes a rather weak condition, does not determine the destabilisation of all standing waves in one dimension. The cross-over to the non-local equations that are asymptotically valid near threshold is discussed in detail. Our results yield necessary conditions for the stability of traveling rectangles in quasi-twodimensional systems with axial anisotropy and form a starting point for understanding the spatio-temporal chaos of traveling oblique rolls observed in electroconvection of nematic liquid crystals.

  15. Hydraulic Stability of Accropode Armour

    DEFF Research Database (Denmark)

    Jensen, T.; Burcharth, H. F.; Frigaard, Peter

    The present report describes the hydraulic model tests of Accropode armour layers carried out at the Hydraulics Laboratory at Aalborg University from November 1995 through March 1996. The objective of the model tests was to investigate the hydraulic stability of Accropode armour layers......, and to assess the influence of core permeability on the hydraulic stability of Accropodes. Two structures were examined, one with a relatively permeable core and one with a relatively impermeable core. In November/December 1995, Ph.D.-student Marten Christensen carried out the model tests on the structure...... with permeable core (crushed granite with a gradation of 5-8 mm). The outcome of this study is described in "Hydraulic Stability of Single-Layer Dolos and Accropode Armour Layers" by Christensen & Burcharth (1995). In January/February 1996, Research Assistant Thomas Jensen carried out a similar study...

  16. Nanocapsules templated on liquid cores stabilized by graft amphiphilic polyelectrolytes

    Science.gov (United States)

    Szafraniec, Joanna; Janik, Małgorzata; Odrobińska, Joanna; Zapotoczny, Szczepan

    2015-03-01

    A surfactant-free method of preparation of nanocapsules templated on liquid cores using amphiphilic graft polyelectrolytes was developed. A model photoactive copolymer, poly(sodium 2-acrylamido-2-methyl-1-propanesulfonate) with grafted poly(vinylnaphthalene) chains (PAMPS-graft-PVN) was used to stabilize toluene droplets in an aqueous emulsion. The macromolecules, due to their amphiphilic character and the presence of strong ionic groups, tend to undergo intramolecular aggregation in water but at the water-oil interface less compact conformation is preferred with PVN grafts anchoring in the oil phase and the charged PAMPS main chains residing in the aqueous phase, thus stabilizing the nanoemulsion droplets. Formation of such nanocapsules was confirmed by dynamic light scattering measurements as well as SEM and cryo-TEM imaging. Grafting density and content of the chromophores in the graft copolymers were varied in order to achieve high stability of the coated nanodroplets. It was shown that the capsules are better stabilized by the copolymers with many short hydrophobic grafts than with fewer but longer ones. Use of photoactive polyelectrolytes enabled spectroscopic investigation of the relationship between conformation of the macromolecules and stabilization of the oil-core nanocapsules. Long-term stability of the nanocapsules was achieved and further increased by multilayer shell formation using polyelectrolytes deposited via the layer-by-layer approach. The obtained capsules served as efficient nanocontainers for a hydrophobic fluorescent probe. The proposed strategy of nanocapsule preparation may be easily extended to biologically relevant polymers and applied to fabricate liquid core nanodelivery systems without the need of using low molecular weight additives which may have adverse effects in numerous biomedical applications.A surfactant-free method of preparation of nanocapsules templated on liquid cores using amphiphilic graft polyelectrolytes was developed

  17. Modeling of molecular properties

    CERN Document Server

    Comba, Peter

    2011-01-01

    Molecular modeling encompasses applied theoretical approaches and computational techniques to model structures and properties of molecular compounds and materials in order to predict and / or interpret their properties. The modeling covered in this book ranges from methods for small chemical to large biological molecules and materials. With its comprehensive coverage of important research fields in molecular and materials science, this is a must-have for all organic, inorganic and biochemists as well as materials scientists interested in applied theoretical and computational chemistry. The 28

  18. Stability and stabilization of linear systems with saturating actuators

    CERN Document Server

    Tarbouriech, Sophie; Gomes da Silva Jr, João Manoel; Queinnec, Isabelle

    2011-01-01

    Gives the reader an in-depth understanding of the phenomena caused by the more-or-less ubiquitous problem of actuator saturation. Proposes methods and algorithms designed to avoid, manage or overcome the effects of actuator saturation. Uses a state-space approach to ensure local and global stability of the systems considered. Compilation of fifteen years' worth of research results.

  19. Concepts of stability and control

    International Nuclear Information System (INIS)

    The first part of the paper deals with the role transfer functions play in control problems (closed loop, Nyquist stability criterion, sampled data systems and z-transforms; the ''hog cycle''; spring oscillations; Lyapunov functions; the Zubov method; positive-real functions and the Popov criterion; the circle criterion; linear time-delay systems; equations with periodic coefficients; stability of repeated processes). In the second part the author considers the control of systems which are described by partial differential equations (heat-conduction equation; wave equation; control of the heat and the wave equations; parasitic oscillations; noise in linear systems; discrete noise processes). Many examples are given and briefly discussed. (author)

  20. An introduction to stability theory

    CERN Document Server

    Pillay, Anand

    2008-01-01

    This introductory treatment covers the basic concepts and machinery of stability theory. Lemmas, corollaries, proofs, and notes assist readers in working through and understanding the material and applications. Full of examples, theorems, propositions, and problems, it is suitable for graduate students in logic and mathematics, professional mathematicians, and computer scientists. Chapter 1 introduces the notions of definable type, heir, and coheir. A discussion of stability and order follows, along with definitions of forking that follow the approach of Lascar and Poizat, plus a consideration

  1. Strapdown stabilization for imaging seekers

    Science.gov (United States)

    Rudin, Russell T.

    1993-06-01

    A feasibility study of strapdown stabilization for high-resolution imaging systems was performed for the missile body motion inputs. A tactical high-resolution platform system was used to develop a linear state space model and a detailed nonlinear planar simulation. The latter took into account gimbal inertia, inertial sensors, position sensors, friction, mechanical alignment, compliances, and control loop compensation. Platform stabilization performance was predicted by analyzing a low-cost inertial quartz rate sensor and a higher-cost higher performance fiber optic gyro.

  2. Stability Analysis of Bow Shocks

    Science.gov (United States)

    Buren, David Van

    1995-01-01

    We present a linear stability analysis of bow shocks created by the interaction of a spherical wind moving with respect to its surrounding medium. The bounding shocks are assumed isothermal and with Mach number M = infinity. Following Soker (1990) we study the evolution of short wavelength perturbations. We find that the motion is unstable in this limit. Moreover, the ratio of the wind velocity v(sub w) to the star velocity v(sub *) characterizes the stability properties. Bow shocks with fast winds for which v(sub *)/v(sub w)>1.

  3. Stability analysis of nonlinear systems

    CERN Document Server

    Lakshmikantham, Vangipuram; Martynyuk, Anatoly A

    2015-01-01

    The book investigates stability theory in terms of two different measure, exhibiting the advantage of employing families of Lyapunov functions and treats the theory of a variety of inequalities, clearly bringing out the underlying theme. It also demonstrates manifestations of the general Lyapunov method, showing how this technique can be adapted to various apparently diverse nonlinear problems. Furthermore it discusses the application of theoretical results to several different models chosen from real world phenomena, furnishing data that is particularly relevant for practitioners. Stability Analysis of Nonlinear Systems is an invaluable single-sourse reference for industrial and applied mathematicians, statisticians, engineers, researchers in the applied sciences, and graduate students studying differential equations.

  4. Stability of inner planetary systems

    Science.gov (United States)

    Szebehely, V.

    1979-01-01

    The stability of inner planetary systems with arbitrary mass ratios is studied on the basis of the model of the plane restricted three-body problem. A quantitative stability criterion is obtained in terms of the difference between the critical value of the Jacobi constants (at which bifurcation can occur) and the critical value corresponding to a planetary orbit. An orbit is stable if it cannot leave a region that contains only the larger central body (Hill). For small values of the mass parameter, the maximum dimensionless radius of a Hill-stable orbit is 1 minus 2.4 times the cube root of the mass parameter.

  5. Torsatron equilibrium and stability studies

    International Nuclear Information System (INIS)

    Equilibrium and stability results are presented for the Advanced Toroidal Facility (ATF) device. The results of three-dimensional equilibrium calculations and free boundary average method calculations are shown to be in good agreement with previous fixed boundary average method results. These favorable comparisons serve as a valuable validation of the simple and computationally efficient fixed boundary average method. Stability calculations for the free boundary average method equilibria are also in good agreement with fixed boundary calculations, showing instability only when the plasma is shifted inward with an applied vertical field

  6. BIBO Stability of Continuous Time Systems

    Institute of Scientific and Technical Information of China (English)

    HUANG Yuan-qing; ZENG Wei; ZHONG Shou-ming

    2005-01-01

    In this paper, the problems of the stability analysis and BIBO stabilization for the switched systems are considered. Applying a stabilizing local state feedback to each subsystem, the sufficient conditions of the asymptotically stable and BIBO stabilization for the switched systems are obtained by means of the method of Lyapunov function and the method of inequality analysis.

  7. Fuel traps: mapping stability via water association.

    Energy Technology Data Exchange (ETDEWEB)

    Rempe, Susan L.; Clawson, Jacalyn S.; Greathouse, Jeffery A.; Alam, Todd M; Leung, Kevin; Varma, Sameer; Sabo, Dubravko; Martin, Marcus Gary; Cygan, Randall Timothy

    2007-03-01

    Hydrogen storage is a key enabling technology required for attaining a hydrogen-based economy. Fundamental research can reveal the underlying principles controlling hydrogen uptake and release by storage materials, and also aid in characterizing and designing novel storage materials. New ideas for hydrogen storage materials come from exploiting the properties of hydrophobic hydration, which refers to water s ability to stabilize, by its mode of association, specific structures under specific conditions. Although hydrogen was always considered too small to support the formation of solid clathrate hydrate structures, exciting new experiments show that water traps hydrogen molecules at conditions of low temperatures and moderate pressures. Hydrogen release is accomplished by simple warming. While these experiments lend credibility to the idea that water could form an environmentally attractive alternative storage compound for hydrogen fuel, which would advance our nation s goals of attaining a hydrogen-based economy, much work is yet required to understand and realize the full potential of clathrate hydrates for hydrogen storage. Here we undertake theoretical studies of hydrogen in water to establish a firm foundation for predictive work on clathrate hydrate H{sub 2} storage capabilities. Using molecular simulation and statistical mechanical theories based in part on quantum mechanical descriptions of molecular interactions, we characterize the interactions between hydrogen and liquid water in terms of structural and thermodynamic properties. In the process we validate classical force field models of hydrogen in water and discover new features of hydrophobic hydration that impact problems in both energy technology and biology. Finally, we predict hydrogen occupancy in the small and large cages of hydrogen clathrate hydrates, a property unresolved by previous experimental and theoretical work.

  8. ROBUST STABILITY ANALYSIS FOR RAILWAY VEHICLE SYSTEMS

    Institute of Scientific and Technical Information of China (English)

    Wang Yong; Zeng Jing; Cao Dengqing

    2003-01-01

    The lateral stability for railway vehicle dynamic system with uncertain parameters and nonlinear uncertain force vector is studied by using the Lyapunov stability theory. A robust stability condition for the considered system is derived, and the obtained stability bounds are not necessarily symmetric with respect to the origin in the parameter space. The lateral stability analysis for a railway bogie model is analyzed by using the proposed approach. The symmetric and asymmetric results are both given and the influence of the adjustable parameter ( on the stability bounds is also discussed. With the help of the proposed method, the robust stability analysis can provide a reference for the design of the railway vehicle systems.

  9. Are there molecular signatures?

    Energy Technology Data Exchange (ETDEWEB)

    Bennett, W.P.

    1995-10-01

    This report describes molecular signatures and mutational spectrum analysis. The mutation spectrum is defined as the type and location of DNA base change. There are currently about five well documented cases. Mutations and radon-associated tumors are discussed.

  10. Molecular Mechanisms of Preeclampsia

    OpenAIRE

    Vitoratos, N.; Hassiakos, D.; C. Iavazzo

    2012-01-01

    Preeclampsia is one of the leading causes of maternal morbidity/mortality. The pathogenesis of preeclampsia is still under investigation. The aim of this paper is to present the molecular mechanisms implicating in the pathway leading to preeclampsia.

  11. Molecular Gastronomy: An Introduction

    OpenAIRE

    Burke, Roisin; Kelly, Alan L.; This, Hervé

    2016-01-01

    Abstract In the world of food science, Molecular Gastronomy is a term which is relatively new, but describes the convergence of the two long-established core food disciplines, i.e., food science and the art of the chef.

  12. Molecular ion photofragment spectroscopy

    International Nuclear Information System (INIS)

    A new molecular ion photofragment spectrometer is described which features a supersonic molecular beam ion source and a radio frequency octapole ion trap interaction region. This unique combination allows several techniques to be applied to the problem of detecting a photon absorption event of a molecular ion. In particular, it may be possible to obtain low resolution survey spectra of exotic molecular ions by using a direct vibrational predissociation process, or by using other more indirect detection methods. The use of the spectrometer is demonstrated by measuring the lifetime of the O2+(4π/sub u/) metastable state which is found to consist of two main components: the 4π/sub 5/2/ and 4π/sub -1/2/ spin components having a long lifetime (approx. 129 ms) and the 4π/sub 3/2/ and 4π/sub 1/2/ spin components having a short lifetime (approx. 6 ms)

  13. Atomic and Molecular Interactions

    International Nuclear Information System (INIS)

    The Gordon Research Conference (GRC) on Atomic and Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field

  14. Molecular electronic junction transport

    DEFF Research Database (Denmark)

    Solomon, Gemma C.; Herrmann, Carmen; Ratner, Mark

    2012-01-01

    Whenasinglemolecule,oracollectionofmolecules,isplacedbetween two electrodes and voltage is applied, one has a molecular transport junction. We discuss such junctions, their properties, their description, and some of their applications. The discussion is qualitative rather than quantitative, and f...

  15. Molecular imaging in oncology

    Energy Technology Data Exchange (ETDEWEB)

    Schober, Otmar; Riemann, Burkhard (eds.) [Universitaetsklinikum Muenster (Germany). Klinik fuer Nuklearmedizin

    2013-02-01

    Considers in detail all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. Examines technological issues and probe design. Discusses preclinical studies in detail, with particular attention to multimodality imaging. Presents current clinical use of PET/CT, SPECT/CT, and optical imagingWritten by acknowledged experts. The impact of molecular imaging on diagnostics, therapy, and follow-up in oncology is increasing significantly. The process of molecular imaging includes key biotarget identification, design of specific molecular imaging probes, and their preclinical evaluation, e.g., in vivo using small animal studies. A multitude of such innovative molecular imaging probes have already entered clinical diagnostics in oncology. There is no doubt that in future the emphasis will be on multimodality imaging in which morphological, functional, and molecular imaging techniques are combined in a single clinical investigation that will optimize diagnostic processes. This handbook addresses all aspects of molecular imaging in oncology, ranging from basic research to clinical applications in the era of evidence-based medicine. The first section is devoted to technology and probe design, and examines a variety of PET and SPECT tracers as well as multimodality probes. Preclinical studies are then discussed in detail, with particular attention to multimodality imaging. In the third section, diverse clinical applications are presented, and the book closes by looking at future challenges. This handbook will be of value to all who are interested in the revolution in diagnostic oncology that is being brought about by molecular imaging.

  16. Phylogenetic molecular function annotation

    OpenAIRE

    Barbara E Engelhardt; Jordan, Michael I.; Repo, Susanna T; Brenner, Steven E

    2009-01-01

    It is now easier to discover thousands of protein sequences in a new microbial genome than it is to biochemically characterize the specific activity of a single protein of unknown function. The molecular functions of protein sequences have typically been predicted using homology-based computational methods, which rely on the principle that homologous proteins share a similar function. However, some protein families include groups of proteins with different molecular functions. A phylogenetic ...

  17. Cardiovascular Molecular Imaging

    OpenAIRE

    Khanicheh, Elham

    2009-01-01

    Although there have been significant improvements in the treatment of cardiovascular diseases they still remain the main cause of morbidity and mortality globally. Currently available diagnostic approaches may not be adequate to detect pathologic changes during the early disease stages, which may be valuable for risk stratification and also to assess a response to a therapy. Therefore molecular imaging techniques such as Contrast Enhanced Ultrasound (CEU) molecular imaging to noninvasively i...

  18. Molecular mechanisms in gliomagenesis

    DEFF Research Database (Denmark)

    Hulleman, Esther; Helin, Kristian

    2005-01-01

    , in order to design novel therapies and treatments for GBM, research has recently intensified to identify the cellular and molecular mechanisms leading to GBM formation. Modeling of astrocytomas by genetic manipulation of mice suggests that deregulation of the pathways that control gliogenesis during normal......-scale genomics and proteomics in combination with relevant mouse models will most likely provide novel insights into the molecular mechanisms underlying glioma formation and will hopefully lead to development of treatment modalities for GBM....

  19. Open source molecular modeling.

    Science.gov (United States)

    Pirhadi, Somayeh; Sunseri, Jocelyn; Koes, David Ryan

    2016-09-01

    The success of molecular modeling and computational chemistry efforts are, by definition, dependent on quality software applications. Open source software development provides many advantages to users of modeling applications, not the least of which is that the software is free and completely extendable. In this review we categorize, enumerate, and describe available open source software packages for molecular modeling and computational chemistry. An updated online version of this catalog can be found at https://opensourcemolecularmodeling.github.io.

  20. Towards molecular photochemionics

    OpenAIRE

    Margherita Venturi; Vincenzo Balzani; Roberto Ballardini; Alberto Credi; M. Teresa Gandolfi

    2004-01-01

    In the last few years there has been a great interest in developing electronics at a molecular level (molecular electronics), e.g. to construct miniaturized electric circuits that would be much smaller than the corresponding micron-scale digital logic circuits fabricated on conventional solid-state semiconductor chips. An alternative possibility to the use of electron fluxes as a means for information processing (electronics) is that of using optical beams (photonics), but up until now scarce...