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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. Stability of Surface Nanobubbles: A Molecular Dynamics Study

    NARCIS (Netherlands)

    Maheshwari, Shantanu; Hoef, van der Martin; Zhang, Xuehua; Lohse, Detlef

    2016-01-01

    The stability and growth or dissolution of a single surface nanobubble on a chemically patterned surface are studied by molecular dynamics simulations of binary mixtures consisting of Lennard-Jones (LJ) particles. Our simulations reveal how pinning of the three-phase contact line on the surface can

  3. 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...

  4. Phosphorylation modifies the molecular stability of β-amyloid deposits

    Science.gov (United States)

    Rezaei-Ghaleh, Nasrollah; Amininasab, Mehriar; Kumar, Sathish; Walter, Jochen; Zweckstetter, Markus

    2016-04-01

    Protein aggregation plays a crucial role in neurodegenerative diseases. A key feature of protein aggregates is their ubiquitous modification by phosphorylation. Little is known, however, about the molecular consequences of phosphorylation of protein aggregates. Here we show that phosphorylation of β-amyloid at serine 8 increases the stability of its pathogenic aggregates against high-pressure and SDS-induced dissociation. We further demonstrate that phosphorylation results in an elevated number of hydrogen bonds at the N terminus of β-amyloid, the region that is critically regulated by a variety of post-translational modifications. Because of the increased lifetime of phosphorylated β-amyloid aggregates, phosphorylation can promote the spreading of β-amyloid in Alzheimer pathogenesis. Our study suggests that regulation of the molecular stability of protein aggregates by post-translational modifications is a crucial factor for disease progression in the brain.

  5. A double molecular disc in NGC 6946: structure and stability

    CERN Document Server

    Romeo, Alessandro B

    2015-01-01

    The late-type spiral galaxy NGC 6946 is a prime example of molecular gas dynamics driven by `bars within bars'. Here we use data from the BIMA SONG and HERACLES surveys to analyse the structure and stability of its molecular disc. Our radial profiles exhibit a clear transition at distance R ~ 1 kpc from the galaxy centre. In particular, the surface density profile breaks at R ~ 0.8 kpc and is well fitted by a double exponential distribution with scale lengths R_1 ~ 200 pc and R_2 ~ 3 kpc, while the 1D velocity dispersion sigma decreases steeply in the central kpc and is approximately constant at larger radii. The fact that we derive and use the full radial profile of sigma rather than a constant value is perhaps the most novel feature of our stability analysis. We show that the profile of the Q stability parameter traced by CO emission is remarkably flat and well above unity, while the characteristic instability wavelength exhibits clear signatures of the nuclear starburst and inner bar within bar. We also sh...

  6. 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.

  7. Molecular dynamics simulation of thermal stability of nanocrystalline vanadium

    Institute of Scientific and Technical Information of China (English)

    WEI; Mingzhi; XIAO; Shifang; YUAN; Xiaojian; HU; Wangyu

    2006-01-01

    The microstructure and thermal stability of nanocrystalline vanadium with an average grain size ranging from 2.86 to 7.50 nm are calculated by means of the analytic embedded-atom method and molecular dynamics. The grain boundary and nanocrystalline grain atoms are differentiated by the common neighbor analysis method. The results indicate that the fraction of grain boundary increases with the grain size decreasing, and the mean energy of atoms is higher than that of coarse crystals. The thermal-stable temperatures of nanocrystalline vanadium are determined from the evolution of atomic energy, fraction of grain boundary and radial distribution function. It is shown that the stable temperature decreases obviously with the grain size decreasing. In addition the reasons which cause the grain growth of nanocrystalline vanadium are discussed.

  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. Ion channel stability and hydrogen bonding. Molecular modelling of channels formed by synthetic alamethicin analogues.

    Science.gov (United States)

    Breed, J; Kerr, I D; Molle, G; Duclohier, H; Sansom, M S

    1997-12-04

    Several analogues of the channel-forming peptaibol alamethicin have been demonstrated to exhibit faster switching between channel substates than does unmodified alamethicin. Molecular modelling studies are used to explore the possible molecular basis of these differences. Models of channels formed by alamethicin analogues were generated by restrained molecular dynamics in vacuo and refined by short molecular dynamics simulations with water molecules within and at either mouth of the channel. A decrease in backbone solvation was found to correlate with a decrease in open channel stability between alamethicin and an analogue in which all alpha-amino-isobutyric acid residues of alamethicin were replaced by leucine. A decrease in the extent of hydrogen-bonding at residue 7 correlates with lower open channel stabilities of analogues in which the glutamine at position 7 was replaced by smaller polar sidechains. These two observations indicate the importance of alamethicin/water H-bonds in stabilizing the open channel.

  11. Evaluating the stability of pharmacophore features using molecular dynamics simulations.

    Science.gov (United States)

    Wieder, Marcus; Perricone, Ugo; Boresch, Stefan; Seidel, Thomas; Langer, Thierry

    2016-02-12

    Molecular dynamics simulations of twelve protein-ligand systems were used to derive a single, structure based pharmacophore model for each system. These merged models combine the information from the initial experimental structure and from all snapshots saved during the simulation. We compared the merged pharmacophore models with the corresponding PDB pharmacophore models, i.e., the static models generated from an experimental structure in the usual manner. The frequency of individual features, of feature types and the occurrence of features not present in the static model derived from the experimental structure were analyzed. We observed both pharmacophore features not visible in the traditional approach, as well as features which disappeared rapidly during the molecular dynamics simulations and which may well be artifacts of the initial PDB structure-derived pharmacophore model. Our approach helps mitigate the sensitivity of structure based pharmacophore models to the single set of coordinates present in the experimental structure. Further, the frequency with which specific features occur during the MD simulation may aid in ranking the importance of individual features.

  12. Lifetimes and stabilities of familiar explosive molecular adduct complexes during ion mobility measurements.

    Science.gov (United States)

    McKenzie-Coe, Alan; DeBord, John Daniel; Ridgeway, Mark; Park, Melvin; Eiceman, Gary; Fernandez-Lima, Francisco

    2015-08-21

    Trapped ion mobility spectrometry coupled to mass spectrometry (TIMS-MS) was utilized for the separation and identification of familiar explosives in complex mixtures. For the first time, molecular adduct complex lifetimes, relative stability, binding energies and candidate structures are reported for familiar explosives. Experimental and theoretical results showed that the adduct size and reactivity, complex binding energy and the explosive structure tailor the stability of the molecular adduct complex. The flexibility of TIMS to adapt the mobility separation as a function of the molecular adduct complex stability (i.e., short or long IMS experiments/low or high IMS resolution) permits targeted measurements of explosives in complex mixtures with high confidence levels.

  13. 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.

  14. 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.

  15. A Molecular-Level View of the Physical Stability of Amorphous Solid Dispersions

    Science.gov (United States)

    Yuan, Xiaoda

    Many pharmaceutical compounds being developed in recent years are poorly soluble in water. This has led to insufficient oral bioavailability of many compounds in vitro. The amorphous formulation is one of the promising techniques to increase the oral bioavailability of these poorly water-soluble compounds. However, an amorphous drug substance is inherently unstable because it is a high energy form. In order to increase the physical stability, the amorphous drug is often formulated with a suitable polymer to form an amorphous solid dispersion. Previous research has suggested that the formation of an intimately mixed drug-polymer mixture contributes to the stabilization of the amorphous drug compound. The goal of this research is to better understand the role of miscibility, molecular interactions and mobility on the physical stability of amorphous solid dispersions. Methods were developed to detect different degrees of miscibility on nanometer scale and to quantify the extent of hydrogen-bonding interactions between the drug and the polymer. Miscibility, hydrogen-bonding interactions and molecular mobility were correlated with physical stability during a six-month period using three model systems. Overall, this research provides molecular-level insights into many factors that govern the physical stability of amorphous solid dispersions which can lead to a more effective design of stable amorphous formulations.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. Improved insights into protein thermal stability: from the molecular to the structurome scale.

    Science.gov (United States)

    Pucci, Fabrizio; Rooman, Marianne

    2016-11-13

    Despite the intense efforts of the last decades to understand the thermal stability of proteins, the mechanisms responsible for its modulation still remain debated. In this investigation, we tackle this issue by showing how a multiscale perspective can yield new insights. With the help of temperature-dependent statistical potentials, we analysed some amino acid interactions at the molecular level, which are suggested to be relevant for the enhancement of thermal resistance. We then investigated the thermal stability at the protein level by quantifying its modification upon amino acid substitutions. Finally, a large scale analysis of protein stability-at the structurome level-contributed to the clarification of the relation between stability and natural evolution, thereby showing that the mutational profile of proteins differs according to their thermal properties. Some considerations on how the multiscale approach could help in unravelling the protein stability mechanisms are briefly discussed.This article is part of the themed issue 'Multiscale modelling at the physics-chemistry-biology interface'.

  3. Emulating structural stability of Pseudomonas mendocina lipase: in silico mutagenesis and molecular dynamics studies.

    Science.gov (United States)

    Saravanan, Parameswaran; Dubey, Vikash Kumar; Patra, Sanjukta

    2014-11-01

    The need of alkaline detergent-stable lipases has been growing rapidly as they are highly attractive for the production of detergents, biodiesel, pharmaceuticals agents, and various other applications. Lipase from Pseudomonas mendocina (PML) is one such candidate with triglyceride activity and non-homologous with other reported Pseudomonas lipases. The present work provides insights on the role of amino acids toward structural stability of PML. PML was subjected to mutagenesis through in silico point mutations for emulating its structural stability, the foremost property to enhance biophysiochemical properties for industrial process. The structural effects of identified mutants on PML have been analyzed through comparative atomistic molecular dynamics simulations on wild type and mutants. The in silico mutants P187A and P219A were found to stabilize their respective local dynamics and improved the structural stability of PML. The current study sheds light on the rational engineering of PML through in silico methodologies to improvise its structural stability as well as prototype for rational engineering of the lipases.

  4. 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.

  5. Study of the Molecular Geometry, Electronic Structure, and Thermal Stability of Phosphazene and Heterophosphazene Rings with ab Initio Molecular Orbital Calculations

    NARCIS (Netherlands)

    Jaeger, C.R.; Debowski, M.A.; Manners, I.; Vancso, G.J.

    1999-01-01

    Ab initio molecular orbital calculations at the MP2/6-31G* level of theory have been used to study the molecular geometry, electronic structure, and the thermal stability of six-membered phosphazene and heterophosphazene rings. The studies included the phosphazene ring [NPCl2]3, the carbophosphazene

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. 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

  12. Thermal Stability of Annealed Germanium-Tin Alloys Grown by Molecular Beam Epitaxy

    Science.gov (United States)

    Bhargava, Nupur; Gupta, Jay Prakash; Faleev, Nikolai; Wielunski, Leszek; Kolodzey, James

    2017-01-01

    The thermal stability of undoped and boron-doped germanium tin (Ge1-x Sn x ) alloys grown by molecular beam epitaxy with varying composition and layer thickness was investigated. The alloys were annealed in forming gas at various temperatures up to 800°C for 1 min using rapid thermal processing, and were characterized using high-resolution x-ray diffraction and Rutherford backscattering spectrometry. It was found that the Ge1-x Sn x alloys were stable to well above the growth temperature, but the stability decreased with increasing thickness, Sn content, and doping. Ge1-x Sn x alloys with low Sn composition (x ˜ 0.025) were stable up to 700°C, and for a given Sn composition, the undoped alloys were more thermally stable than the doped alloys. As the thickness of the Ge0.975Sn0.025 alloys increased to about 950 nm, the temperature of thermal stability dropped to 500°C. As the Sn composition of the 90 nm-Ge1-x Sn x alloys increased up to x = 0.08, the temperature of thermal stability dropped to 300°C. At higher annealing temperatures, the Ge1-x Sn x alloy degraded with lower crystal quality, and a gradient in the Sn composition appeared, which may be due to Sn diffusion or segregation.

  13. 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.

  14. Fully stabilized mid-infrared frequency comb for high-precision molecular spectroscopy.

    Science.gov (United States)

    Vainio, Markku; Karhu, Juho

    2017-02-20

    A fully stabilized mid-infrared optical frequency comb spanning from 2.9 to 3.4 µm is described in this article. The comb is based on half-harmonic generation in a femtosecond optical parametric oscillator, which transfers the high phase coherence of a fully stabilized near-infrared Er-doped fiber laser comb to the mid-infrared region. The method is simple, as no phase-locked loops or reference lasers are needed. Precise locking of optical frequencies of the mid-infrared comb to the pump comb is experimentally verified at sub-20 mHz level, which corresponds to a fractional statistical uncertainty of 2 × 10-16 at the center frequency of the mid-infrared comb. The fully stabilized mid-infrared comb is an ideal tool for high-precision molecular spectroscopy, as well as for optical frequency metrology in the mid-infrared region, which is difficult to access with other stabilized frequency comb techniques.

  15. 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.

  16. 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.

  17. Stability and structure of quark matter in a molecular dynamics framework

    CERN Document Server

    Akimura, Y; Yoshinaga, N; Chiba, S; Akimura, Yuka; Maruyama, Toshiki; Yoshinaga, Naotaka; Chiba, Satoshi

    2005-01-01

    We study stability and structure of quark matters as a function of density in a framework of molecular dynamics (MD). Using appropriate effective interactions and the frictional cooling method, we search for the minimum energy of the system. Transition from confined to deconfined phase is observed at densities of 2 -- 3$\\rho_0$, where $\\rho_0$ is the nuclear matter saturation density. The $uds$ matter becomes more stable than the charge-neutral $ud$ matter at 3$\\rho_0$, but the $udd$ matter is the most stable even at high density.

  18. Stability and structure of quark matter in a molecular dynamics framework

    Energy Technology Data Exchange (ETDEWEB)

    Akimura, Yuka [Department of physics, Saitama University, Sakura-Ku, Saitama-Shi, 338-8570 (Japan); Advanced Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319-1195 (Japan); Maruyama, Toshiki [Advanced Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319-1195 (Japan); Yoshinaga, Naotaka [Department of physics, Saitama University, Sakura-Ku, Saitama-Shi, 338-8570 (Japan); Chiba, Satoshi [Advanced Science Research Center, Japan Atomic Energy Research Institute, Tokai, Ibaraki 319-1195 (Japan)

    2005-03-07

    We study stability and structure of quark matters as a function of density in a framework of molecular dynamics (MD). Using appropriate effective interactions and the frictional cooling method, we search for the minimum energy of the system. Transition from confined to deconfined phase is observed at densities of 2-3{rho}0, where {rho}0 is the nuclear matter saturation density. The uds matter becomes more stable than the electrically neutral ud matter at 3{rho}0, but the udd matter is the most stable even at high density.

  19. Molecular adaptation to an extreme environment: origin of the thermal stability of the pompeii worm collagen.

    Science.gov (United States)

    Sicot, F X; Mesnage, M; Masselot, M; Exposito, J Y; Garrone, R; Deutsch, J; Gaill, F

    2000-09-29

    The annelid Alvinella pompejana is probably the most heat-tolerant metazoan organism known. Previous results have shown that the level of thermal stability of its interstitial collagen is significantly greater than that of coastal annelids and of vent organisms, such as the vestimentiferan Riftia pachyptila, living in colder parts of the deep-sea hydrothermal environment. In order to investigate the molecular basis of this thermal behavior, we cloned and sequenced a large cDNA molecule coding the fibrillar collagen of Alvinella, including one half of the helical domain and the entire C-propeptide domain. For comparison, we also cloned the 3' part of the homologous cDNA from Riftia. Comparison of the corresponding helical domains of these two species, together with that of the previously sequenced domain of the coastal lugworm Arenicola marina, showed that the increase in proline content and in the number of stabilizing triplets correlate with the outstanding thermostability of the interstitial collagen of A. pompejana. Phylogenetic analysis showed that triple helical and the C-propeptide parts of the same collagen molecule evolve at different rates, in favor of an adaptive mechanism at the molecular level.

  20. Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

    Science.gov (United States)

    Zhang, Dawei; Lazim, Raudah

    2017-01-01

    In this study, we had exploited the advancement in computer technology to determine the stability of four apomyoglobin variants namely wild type, E109A, E109G and G65A/G73A by conducting conventional molecular dynamics simulations in explicit urea solution. Variations in RMSD, native contacts and solvent accessible surface area of the apomyoglobin variants during the simulation were calculated to probe the effect of mutation on the overall conformation of the protein. Subsequently, the mechanism leading to the destabilization of the apoMb variants was studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and RMSF. The results obtained here correlate well with the study conducted by Baldwin and Luo which showed improved stability of apomyoglobin with E109A mutation and contrariwise for E109G and G65A/G73A mutation. These positive observations showcase the feasibility of exploiting MD simulation in determining protein stability prior to protein expression. PMID:28300210

  1. The effect of ligands on the thermal stability of sulfotransferases: a molecular dynamics simulation study.

    Science.gov (United States)

    Zhang, Pu-pu; Zhao, Li; Long, Shi-yang; Tian, Pu

    2015-04-01

    Human cytosolic sulfotransferases (hSULTs) are important phase II metabolic enzymes. They catalyze transfer of the sulfuryl-group (-SO3) from 3'-phosphoadenosine 5'-phosphosulfate (PAPS) to the hydroxyl or primary amine moieties of a large number of endogenous and xenobiotic substrates. Broad selectivity and specificity of binding and activity within the sulfortransferases family could be detected by thermal denaturation assays, which have been made more and more suitable for high throughput screening based on recent technical advances. Here molecular dynamics simulations were used to explore the effect of the cofactor (PAPS) and substrate (LCA) on the thermal stability of the enzyme. It was found that the apo-enzyme unfolded fastest upon heating. The holo-enzyme with bound substrate LCA unfolded slowest. This thermo-denaturation order is consistent with that observed in experiments. Further it was found that the cofactor and substrate will pronouncedly increase the thermal stability of the active pocket regions that interact directly with the ligands. In addition, cofactor and substrate show noticeable synergy effect on the thermal stability of the enzyme.

  2. Knee simulator wear of vitamin E stabilized irradiated ultrahigh molecular weight polyethylene.

    Science.gov (United States)

    Micheli, Brad R; Wannomae, Keith K; Lozynsky, Andrew J; Christensen, Steven D; Muratoglu, Orhun K

    2012-01-01

    Wear and damage of ultrahigh molecular weight polyethylene (UHMWPE) tibial inserts used in total knee arthroplasty are accelerated by oxidation. Radiation crosslinking reduces wear but produces residual free radicals adversely affecting stability. One alternative to stabilize radiation-crosslinked UHMWPE is to infuse the material with vitamin E (vit E). We investigated the properties of 100-kGy e-beam-irradiated UHMWPE that was subsequently doped with vitamin E in comparison with conventional UHMWPE. Both polymers were sterilized with gamma irradiation in vacuum packaging. Vitamin E-doped UHMWPE showed lower wear before and after aging (2.4 ± 0.5 and 2.5 ± 0.8 mg/million cycle, respectively, vs 26.9 ± 3.5 and 40.8 ± 3.0 mg/million cycle for conventional UHMWPE). Conventional UHMWPE showed oxidation after accelerated aging, and its mechanical properties were adversely affected, whereas vit E-doped UHMWPE showed no oxidation or changes in its mechanical properties. Vitamin E stabilization of radiation-crosslinked UHMWPE resulted in low wear and high oxidation resistance; it is an alternative load-bearing material for total knee applications.

  3. Application of conventional molecular dynamics simulation in evaluating the stability of apomyoglobin in urea solution

    Science.gov (United States)

    Zhang, Dawei; Lazim, Raudah

    2017-03-01

    In this study, we had exploited the advancement in computer technology to determine the stability of four apomyoglobin variants namely wild type, E109A, E109G and G65A/G73A by conducting conventional molecular dynamics simulations in explicit urea solution. Variations in RMSD, native contacts and solvent accessible surface area of the apomyoglobin variants during the simulation were calculated to probe the effect of mutation on the overall conformation of the protein. Subsequently, the mechanism leading to the destabilization of the apoMb variants was studied through the calculation of correlation matrix, principal component analyses, hydrogen bond analyses and RMSF. The results obtained here correlate well with the study conducted by Baldwin and Luo which showed improved stability of apomyoglobin with E109A mutation and contrariwise for E109G and G65A/G73A mutation. These positive observations showcase the feasibility of exploiting MD simulation in determining protein stability prior to protein expression.

  4. Insight to the thermodynamic stability of molecular crystals through crystallographic studies of a multipolymorph system.

    Science.gov (United States)

    Ng, Alicia T; Lai, Chiajen; Dabros, Marta; Gao, Qi

    2014-11-01

    Five solvent-free polymorphs of a pharmaceutical compound were discovered during polymorph screening. Out of the five polymorphs, only one has strong intermolecular N-H···N hydrogen bonding, whereas the others exhibit only weak C-H···N and π-π stacking interactions in addition to all the other weak C-H···X and van der Waals interactions. The relative thermodynamic stability relationships among the polymorphs are not intuitive and quite complex due to enantiotropic phase behavior. For instance, the polymorph with the most efficient packing (i.e., highest density) is not always the most thermodynamically stable form, and the polymorph with strong intermolecular interactions is not thermodynamically more stable than the polymorph with weak intermolecular interactions at all temperatures. Nevertheless, systematic examination and comparison of the molecular packing and intermolecular interactions of these polymorphs provide insight into the importance of H-bonding and packing efficiency to the thermodynamic stability of a crystalline form, and how these effects are dependent on temperature. This study seeks to correlate single-crystal structure features with experimentally established thermodynamic stability, and provides an example where a polymorph with only van der Waals forces and weak intermolecular interactions can be more stable than a polymorph that displays strong H-bonding in its structural make-up.

  5. 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.

  6. 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.

  7. Effect of axial ligands on the molecular configurations, stability, reactivity, and photodynamic activities of silicon phthalocyanines.

    Science.gov (United States)

    Luan, Liqiang; Ding, Lanlan; Shi, Jiawei; Fang, Wenjuan; Ni, Yuxing; Liu, Wei

    2014-12-01

    To demonstrate the effect of axial ligands on the structure-activity relationship, a series of axially substituted silicon phthalocyanines (SiPcs) have been synthesized with changes to the axial ligands. The reactivity of the axial ligand upon shielding by the phthalocyanine ring current, along with their stability, photophysical, and photodynamic therapy (PDT) activities were compared and evaluated for the first time. As revealed by single-crystal XRD analysis, rotation of the axial -OMe ligands was observed in SiPc 3, which resulted in two molecular configurations coexisting synchronously in both the solid and solution states and causing a split of the phthalocyanine α protons in the (1)H NMR spectra that is significantly different from all SiPcs reported so far. The remarkable photostability, good singlet oxygen quantum yield, and efficient in vitro photodynamic activity synergistically show that compound 3 is one of the most promising photosensitizers for PDT.

  8. 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.

  9. 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...

  10. Multipressure Polytropes as Models for the Structure and Stability of Molecular Clouds. I. Theory

    Science.gov (United States)

    McKee, Christopher F.; Holliman, John H., II

    1999-09-01

    We present a theoretical formalism for determining the structure of molecular clouds and the precollapse conditions in star-forming regions. The model consists of a pressure-bounded, self-gravitating sphere of an ideal gas that is supported by several distinct pressures. Since each pressure component is assumed to obey a polytropic law Pi(r)~ργpi, we refer to these models as ``multipressure polytropes.'' We treat the case without rotation. The time evolution of one of these polytropes depends additionally on the adiabatic index γi of each component, which is modified to account for the effects of any thermal coupling to the environment of the cloud. We derive structure equations as well as perturbation equations for performing a linear stability analysis. Special attention is given to representing properly the significant pressure components in molecular clouds: thermal motions, static magnetic fields, and turbulence. The fundamental approximation in our treatment is that the effects of turbulent motions in supporting a cloud against gravity can be approximated by a polytropic pressure component. In particular, we approximate the turbulent motions as a superposition of Alfvén waves. We generalize the standard treatment of the stability of polytropes to allow for the flow of entropy in response to a perturbation, as expected for the entropy associated with wave pressure. In contrast to the pressure components within stars, the pressure components within interstellar clouds are ``soft,'' with polytropic indices γpiγpi. We find that the motions associated with Alfvén waves are somewhat less effective in supporting clouds than are the kinetic motions in an isothermal gas.

  11. 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.

  12. Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations

    Science.gov (United States)

    Liu, Kai; Watanabe, Etsurou; Kokubo, Hironori

    2017-02-01

    The binding mode prediction is of great importance to structure-based drug design. The discrimination of various binding poses of ligand generated by docking is a great challenge not only to docking score functions but also to the relatively expensive free energy calculation methods. Here we systematically analyzed the stability of various ligand poses under molecular dynamics (MD) simulation. First, a data set of 120 complexes was built based on the typical physicochemical properties of drug-like ligands. Three potential binding poses (one correct pose and two decoys) were selected for each ligand from self-docking in addition to the experimental pose. Then, five independent MD simulations for each pose were performed with different initial velocities for the statistical analysis. Finally, the stabilities of ligand poses under MD were evaluated and compared with the native one from crystal structure. We found that about 94% of the native poses were maintained stable during the simulations, which suggests that MD simulations are accurate enough to judge most experimental binding poses as stable properly. Interestingly, incorrect decoy poses were maintained much less and 38-44% of decoys could be excluded just by performing equilibrium MD simulations, though 56-62% of decoys were stable. The computationally-heavy binding free energy calculation can be performed only for these survived poses.

  13. 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...

  14. Stabilization of fenofibrate in low molecular weight hydroxypropylcellulose matrices produced by hot-melt extrusion.

    Science.gov (United States)

    Deng, Weibin; Majumdar, Soumyajit; Singh, Abhilasha; Shah, Sejal; Mohammed, Noorullah Naqvi; Jo, Seongbong; Pinto, Elanor; Tewari, Divya; Durig, Thomas; Repka, Michael A

    2013-02-01

    The objective of this study was to improve the dissolution rate and to enhance the stability of a poorly water-soluble and low glass-trasition temperature (T(g)) model drug, fenofibrate, in low molecular weight grades of hydroxypropylcellulose matrices produced by hot-melt extrusion (HME). Percent drug loading had a significant effect on the extrudability of the formulations. Dissolution rate of fenofibrate from melt extruded pellets was faster than that of the pure drug (p polymers were evaluated as stabilizing agents among which polyvinylpyrrolidone 17PF and amino methacrylate copolymer exhibited a significant inhibitory effect on fenofibrate recrystallization in the hot-melt extrudates. Subsequently immediate-release fenofibrate tablets were successfully developed and complete drug release was achieved within 5 min. The dissolution profile was comparable to that of a currently marketed formulation. The hot-melt extruded fenofibrate tablets were stable, and exhibited an unchanged drug release profile after 3-month storage at 40°C/75% RH.

  15. Differential scanning calorimetry in life science: thermodynamics, stability, molecular recognition and application in drug design.

    Science.gov (United States)

    Bruylants, G; Wouters, J; Michaux, C

    2005-01-01

    All biological phenomena depend on molecular recognition, which is either intermolecular like in ligand binding to a macromolecule or intramolecular like in protein folding. As a result, understanding the relationship between the structure of proteins and the energetics of their stability and binding with others (bio)molecules is a very interesting point in biochemistry and biotechnology. It is essential to the engineering of stable proteins and to the structure-based design of pharmaceutical ligands. The parameter generally used to characterize the stability of a system (the folded and unfolded state of the protein for example) is the equilibrium constant (K) or the free energy (deltaG(o)), which is the sum of enthalpic (deltaH(o)) and entropic (deltaS(o)) terms. These parameters are temperature dependent through the heat capacity change (deltaCp). The thermodynamic parameters deltaH(o) and deltaCp can be derived from spectroscopic experiments, using the van't Hoff method, or measured directly using calorimetry. Along with isothermal titration calorimetry (ITC), differential scanning calorimetry (DSC) is a powerful method, less described than ITC, for measuring directly the thermodynamic parameters which characterize biomolecules. In this article, we summarize the principal thermodynamics parameters, describe the DSC approach and review some systems to which it has been applied. DSC is much used for the study of the stability and the folding of biomolecules, but it can also be applied in order to understand biomolecular interactions and can thus be an interesting technique in the process of drug design.

  16. 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.

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

    Directory of Open Access Journals (Sweden)

    Jónsdóttir Svava

    2009-07-01

    Full Text Available Abstract Background 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 based on molecular dynamics (MD simulations of B-RAFWT and the B-RAFV600E, B-RAFK601E and B-RAFD594V mutants. A strong hydrogen bond network was identified in B-RAFWT in which the interactions between Lys601 and the well known catalytic residues Lys483, Glu501 and Asp594 play an important role. It was found that several mutations, which directly or indirectly destabilized the interactions between these residues within this network, contributed to the changes in B-RAF activity. Conclusion Our results showed that the above mechanisms lead to the disruption of the electrostatic interactions between the A-loop and the αC-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 form.

  18. Molecular Dynamics Study of the Foam Stability of a Mixed Surfactant System with and without Calcium Ions

    Science.gov (United States)

    Yang, Xiaozhen; Yang, Wenhong; Institute of Chemistry, CAS Team

    2011-03-01

    Foam stability performance of a mixture surfactant system with and without calcium ions, including linear alkylbenzene sulfonate (LAS) and sodium dodecyl sulfate (SDS), has been studied by molecular dynamics. Microscopic interaction analysis reveals that the fraction of free calcium ions, Xf , in film system indicates the extent of the foam stabilities when Xf is in different calcium ion zones. In the system without ions, we found the variable of the surfactant tail mass out of water film, W , is indicator of foam stability. Performance of the mixture system predicted here was supported by experiments.

  19. Structural investigations into the binding mode of novel neolignans Cmp10 and Cmp19 microtubule stabilizers by in silico molecular docking, molecular dynamics, and binding free energy calculations.

    Science.gov (United States)

    Tripathi, Shubhandra; Kumar, Akhil; Kumar, B Sathish; Negi, Arvind S; Sharma, Ashok

    2016-06-01

    Microtubule stabilizers provide an important mode of treatment via mitotic cell arrest of cancer cells. Recently, we reported two novel neolignans derivatives Cmp10 and Cmp19 showing anticancer activity and working as microtubule stabilizers at micromolar concentrations. In this study, we have explored the binding site, mode of binding, and stabilization by two novel microtubule stabilizers Cmp10 and Cmp19 using in silico molecular docking, molecular dynamics (MD) simulation, and binding free energy calculations. Molecular docking studies were performed to explore the β-tubulin binding site of Cmp10 and Cmp19. Further, MD simulations were used to probe the β-tubulin stabilization mechanism by Cmp10 and Cmp19. Binding affinity was also compared for Cmp10 and Cmp19 using binding free energy calculations. Our docking results revealed that both the compounds bind at Ptxl binding site in β-tubulin. MD simulation studies showed that Cmp10 and Cmp19 binding stabilizes M-loop (Phe272-Val288) residues of β-tubulin and prevent its dynamics, leading to a better packing between α and β subunits from adjacent tubulin dimers. In addition, His229, Ser280 and Gln281, and Arg278, Thr276, and Ser232 were found to be the key amino acid residues forming H-bonds with Cmp10 and Cmp19, respectively. Consequently, binding free energy calculations indicated that Cmp10 (-113.655 kJ/mol) had better binding compared to Cmp19 (-95.216 kJ/mol). This study provides useful insight for better understanding of the binding mechanism of Cmp10 and Cmp19 and will be helpful in designing novel microtubule stabilizers.

  20. All-atom and coarse-grained molecular dynamics simulations of a membrane protein stabilizing polymer.

    Science.gov (United States)

    Perlmutter, Jason D; Drasler, William J; Xie, Wangshen; Gao, Jiali; Popot, Jean-Luc; Sachs, Jonathan N

    2011-09-06

    Amphipathic polymers called amphipols (APols) have been developed as an alternative to detergents for stabilizing membrane proteins (MPs) in aqueous solutions. APols provide MPs with a particularly mild environment and, as a rule, keep them in a native functional state for longer periods than do detergents. Amphipol A8-35, a derivative of polyacrylate, is widely used and has been particularly well studied experimentally. In aqueous solutions, A8-35 molecules self-assemble into well-defined globular particles with a mass of ∼40 kDa and a R(g) of ∼2.4 nm. As a first step towards describing MP/A8-35 complexes by molecular dynamics (MD), we present three sets of simulations of the pure APol particle. First, we performed a series of all-atom MD (AAMD) simulations of the particle in solution, starting from an arbitrary initial configuration. Although AAMD simulations result in stable cohesive particles over a 45 ns simulation, the equilibration of the particle organization is limited. This motivated the use of coarse-grained MD (CGMD), allowing us to investigate processes on the microsecond time scale, including de novo particle assembly. We present a detailed description of the parametrization of the CGMD model from the AAMD simulations and a characterization of the resulting CGMD particles. Our third set of simulations utilizes reverse coarse-graining (rCG), through which we obtain all-atom coordinates from a CGMD simulation. This allows a higher-resolution characterization of a configuration determined by a long-timescale simulation. Excellent agreement is observed between MD models and experimental, small-angle neutron scattering data. The MD data provides new insight into the structure and dynamics of A8-35 particles, which is possibly relevant to the stabilizing effects of APols on MPs, as well as a starting point for modeling MP/A8-35 complexes.

  1. 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.

  2. Interference stabilization of autoionizing states in molecular $N_2$ studied by time- and angular-resolved photoelectron spectroscopy

    CERN Document Server

    Eckstein, Martin; Yang, Chung-Hsin; Sansone, Giuseppe; Vrakking, Marc J J; Ivanov, Misha; Kornilov, Oleg

    2016-01-01

    An autoionizing resonance in molecular N$_2$ is excited by an ultrashort XUV pulse and probed by a subsequent weak IR pulse, which ionizes the contributing Rydberg states. Time- and angular-resolved photoelectron spectra recorded with a velocity map imaging spectrometer reveal two electronic contributions with different angular distributions. One of them has an exponential decay rate of $20\\pm5$ fs, while the other one is shorter than 10 fs. This observation is interpreted as a manifestation of interference stabilization involving the two overlapping discrete Rydberg states. A formalism of interference stabilization for molecular ionization is developed and applied to describe the autoionizing resonance. The results of calculations reveal, that the effect of the interference stabilization is facilitated by rotationally-induced couplings of electronic states with different symmetry.

  3. A 3-fold "butterfly valve" in command of the encapsulation's kinetic stability. Molecular baskets at work.

    Science.gov (United States)

    Wang, Bao-Yu; Bao, Xiaoguang; Yan, Zhiqing; Maslak, Veselin; Hadad, Christopher M; Badjić, Jovica D

    2008-11-12

    Molecular basket 1, composed of a semirigid tris-norbornadiene framework and three revolving pyridine-based gates at the rim, has been built to "dynamically" enclose space and as such regulate molecular encapsulation. The gates were shown to fold via intramolecular hydrogen bonding and thereby form a C3nu symmetrical receptor: the 1H NMR resonance for the amide N-H protons of the pyridine gates appeared downfield (delta= 10.98 ppm), and the N-H vibrational stretch (IR) was observed at 3176 cm(-1). Accordingly, density functional theory (DFT, B3LYP) investigations revealed for the closed conformers of 1 to be energetically the most stable and dominant. The gearing of the pyridine "gates", about their axis, led to the interconversion of two dynamic enantiomers 1A and 1B comprising the clockwise and counterclockwise seam of intramolecular hydrogen bonds. Dynamic 1H NMR spectroscopic measurements and line-shape simulations suggested that the energy barrier of 10.0 kcal/mol (DeltaG++(A/B), 298 K) is required for the 1A/B interconversion, when CCl4 occupies the cavity of 1. Likewise, the activation free energy for CCl4 departing the basket was found to be 13.1 kcal/mol (DeltaG++, 298 K), whereas the thermodynamic stability of 1:CCl4 complex was -2.7 kcal/mol (DeltaGdegrees, 298 K). In view of that, CCl4 (but also (CH3)3CBr) was proposed to escape from, and a molecule of solvent to enter, the basket when the gates rotate about their axis: the exit of CCl4 requires the activation energy of 12.7 kcal/mol (DeltaG++(A/B) + DeltaGdegrees), similar to the experimentally found 13.1 kcal/mol (DeltaG++).

  4. Temperature stabilized effusion cell evaporation source for thin film deposition and molecular-beam epitaxy

    Science.gov (United States)

    Tiedje, H. F.; Brodie, D. E.

    2000-05-01

    A simple effusion cell evaporation source for thin film deposition and molecular-beam epitaxy is described. The source consists of a crucible with a thermocouple temperature sensor heated by a resistive crucible heater. Radiation heat transfer from the crucible to the thermocouple produces a consistent and reproducible thermocouple temperature for a given crucible temperature, without direct contact between the thermocouple and the crucible. The thermocouple temperature is somewhat less than the actual crucible temperature because of heat flow from the thermocouple junction along the thermocouple lead wires. In a typical case, the thermocouple temperature is 1007 °C while the crucible is at 1083 °C. The crucible temperature stability is estimated from the measured sensitivity of the evaporation rate of indium to temperature, and the observed variations in the evaporation rate for a fixed thermocouple temperature. The crucible temperature peak-to-peak variation over a one hour period is 1.2 °C. Machined molybdenum crucibles were used in the indium and copper sources for depositing CuInSe2 thin films for solar cells.

  5. Thermal Stability of Modified Insulation Paper Cellulose Based on Molecular Dynamics Simulation

    Directory of Open Access Journals (Sweden)

    Chao Tang

    2017-03-01

    Full Text Available In this paper, polysiloxane is used to modify insulation paper cellulose, and molecular dynamics methods are used to evaluate the glass transition temperature and mechanical properties of the paper before and after the modification. Analysis of the static mechanical performance of the model shows that, with increasing temperature, the elastic modulus of both the modified and unmodified cellulose models decreases gradually. However, the elastic modulus of the modified model is greater than that of the unmodified model. Using the specific volume method and calculation of the mean square displacement of the models, the glass transition temperature of the modified cellulose model is found to be 48 K higher than that of the unmodified model. Finally, the changes in the mechanical properties and glass transition temperature of the model are analyzed by energy and free volume theory. The glass transition temperatures of the unmodified and modified cellulose models are approximately 400 K and 450 K, respectively. These results are consistent with the conclusions obtained from the specific volume method and the calculation of the mean square displacement. It can be concluded that the modification of insulation paper cellulose with polysiloxane will effectively improve its thermal stability.

  6. 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...

  7. 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.

  8. Application of the stabilization method to the molecular states of LiHeT : Energies and radial couplings

    Energy Technology Data Exchange (ETDEWEB)

    Macias, A.; Mendizabal, R.; Pelayo, F.; Riera, A.; Yaez, M.

    1986-01-01

    We have used the stabilization method to perform calculations on autoionizing states of the LiHeT system which are involved in LiT +He collisions. The molecular energies and radial couplings are calculated with use of programs developed at our laboratory. For both short and large internuclear distances, the stabilization treatment is complemented by block-diagonalization techniques. Our calculations allow us to draw conclusions on the conditions under which these methods can be used to calculate energy positions and radial couplings for states that lie in an ionization continuum.

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. On the influence of hydrated imidazolium-based ionic liquid on protein structure stability: A molecular dynamics simulation study

    Science.gov (United States)

    Shao, Qiang

    2013-09-01

    The structure stability of three α-helix bundle (the B domain of protein A) in an imidazolium-based ionic liquid (1-butyl-3-methylimidazolium chloride (BMIM-Cl)) is studied by molecular dynamics simulations. Consistent with previous experiments, the present simulation results show that the native structure of the protein is consistently stabilized in BMIM-Cl solutions with different concentrations. It is observed that BMIM+ cations have a strong tendency to accumulate on protein surface whereas Cl- anions are expelled from protein. BMIM+ cations cannot only have electrostatic interactions with the carbonyl groups on backbone and the carboxylate groups on negatively charged side chains, but also have hydrophobic interactions with the side chains of non-polar residues. In the meanwhile, the accumulation of large-size BMIM+ cations on protein surface could remove the surrounding water molecules, reduce the hydrogen bonding from water to protein, and thus stabilize the backbone hydrogen bonds. In summary, the present study could improve our understanding of the molecular mechanism of the impact of water-miscible ionic liquid on protein structure.

  15. Molecular Control of Vascular Tube Morphogenesis and Stabilization: Regulation by Extracellular Matrix, Matrix Metalloproteinases, and Endothelial Cell-Pericyte Interactions

    Science.gov (United States)

    Davis, George E.; Stratman, Amber N.; Sacharidou, Anastasia

    Recent studies have revealed a critical role for both extracellular matrices and matrix metalloproteinases in the molecular control of vascular morphogenesis and stabilization in three-dimensional (3D) tissue environments. Key interactions involve endothelial cells (ECs) and pericytes, which coassemble to affect vessel formation, remodeling, and stabilization events during development and postnatal life. EC-pericyte interactions control extracellular matrix remodeling events including vascular basement membrane matrix assembly, a necessary step for endothelial tube maturation and stabilization. ECs form tube networks in 3D extracellular matrices in a manner dependent on integrins, membrane-type metalloproteinases, and the Rho GTPases, Cdc42 and Rac1. Recent work has defined an EC lumen signaling complex of proteins composed of these proteins that controls 3D matrix-specific signaling events required for these processes. The EC tube formation process results in the creation of a network of proteolytically generated vascular guidance tunnels. These tunnels are physical matrix spaces that regulate vascular tube remodeling and represent matrix conduits into which pericytes are recruited to allow dynamic cell-cell interactions with ECs. These dynamic EC-pericyte interactions induce vascular basement membrane matrix deposition, leading to vessel maturation and stabilization.

  16. 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...

  17. Molecular structure stability of short-chain chlorinated paraffins (SCCPs): Evidence from lattice compatibility and Simha-Somcynsky theories

    Science.gov (United States)

    Yumak, A.; Boubaker, K.; Petkova, P.; Yahsi, U.

    2015-10-01

    In is known that short-chain chlorinated paraffins (SCCPs) are highly complex technical mixtures of polychlorinated n-alkanes with single chlorine content. Due to their physical properties (viscosity, flame resistance) they are used in many different applications, such as lubricant additives, metal processing, leather fat-liquoring, plastics softening, PVC plasticizing and flame retardants in paints, adhesives and sealants. SCCPs are studied here in terms of processing-linked molecular structure stability, under Simha and Somcynsky-EOS theory calculations and elements from Simha-Somcynsky-related Lattice Compatibility Theory. Analyses were carried out on 1-chloropropane, 2-chloropropane, 1-chlorobutane, 2-chlorobutane, 1-chloro 2-methylane, and 2-chloro 2-methylane as (SCCPs) universal representatives. This paper gives evidence to this stability and reviews the current state of knowledge and highlights the need for further research in order to improve future (SCCPs) monitoring efforts.

  18. Radioactive nuclear waste stabilization - Aspects of solid-state molecular engineering and applied geochemistry

    Science.gov (United States)

    Haggerty, S. E.

    1983-01-01

    Stabilization techniques for the storage of radioactive wastes are surveyed, with emphasis on immobilization in a primary barrier of synthetic rock. The composition, half-life, and thermal-emission characteristics of the wastes are shown to require thermally stable immobilization enduring at least 100,000 years. Glass materials are determined to be incapable of withstanding the expected conditions, average temperatures of 100-500 C for the first 100 years. The geological-time stability of crystalline materials, ceramics or synthetic rocks, is examined in detail by comparing their components with similar naturally occurring minerals, especially those containing the same radioactive elements. The high-temperature environment over the first 100 years is seen as stabilizing, since it can recrystallize radiation-induced metamicts. The synthetic-rock stabilization technique is found to be essentially feasible, and improvements are suggested, including the substitution of nepheline with freudenbergite and priderite for alkaline-waste stabilization, the maintenance of low oxygen fugacity, and the dilution of the synthetic-rock pellets into an inert medium.

  19. 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)

    QIU Ling; GONG XueDong; JU XueHai; XIAO HeMing

    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 distance 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.

  20. 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

  1. Effects of molecular weight of PVA on formation, stability and deformation of compound droplets for ICF polymer shells

    Science.gov (United States)

    Liu, Meifang; Zheng, Yueqing; Li, Jie; Chen, Sufen; Liu, Yiyang; Li, Jing; Li, Bo; Zhang, Zhanwen

    2017-01-01

    Sphericity and wall thickness uniformity are some of the hardest specifications to fulfill, as required by inertial confined fusion (ICF) research for polymer shells prepared by the microencapsulation technique. Driven by the need to control the deformation of compound droplets, the effects of the molecular weight of poly(vinyl alcohol) (PVA) on the formation and stability of the droplets, as well as the sphericity and wall thickness uniformity of the resulting shells, were investigated. On increasing the molecular weight of the PVA, the densities of the external water phases (W2) are almost the same, but the viscosity of the W2 phase increases more quickly than the interfacial tension. This makes the detaching force increase more quickly than the upward one, causing the formation of compound droplets and detachment from the oil tube. On the other hand, the increase in interfacial tension makes the maximum pressures ( P max) in the O phase (O) of the compound droplets increase, causing them to rupture easily and decreasing their stability. However, for PVA with the same molecular weight, the viscous shear force in the flowing field reduces the role of gravity and makes the inner water droplet move towards the center of the compound droplet, decreasing its P max in the flowing field and improving its stability. Moreover, during the solidifying process, the viscous shear force increases more quickly than the interfacial tension force due to the quicker increase in viscosity with an increase in the molecular weight of the PVA. The increase in the viscous shear force can make the droplets deform, resulting in a decrease in their sphericity. However, the appropriate viscous shear force can also center the compound droplet—although they become decentered when the viscous shear force is too large, leading to the wall thickness uniformity increasing at first before decreasing quickly. The results presented in this work provide a more in-depth understanding of the

  2. 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

  3. 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.

  4. Foam stability related to polymer permeability. 1: Low molecular weight additives

    NARCIS (Netherlands)

    Bouma, R.H.B.; Nauta, W.J.; Arnauts, J.E.F.; Boomgaard, T. van den; Steuten, J.M.; Strathmann, H.

    1997-01-01

    In the production of polyethylene foams by extrusion with alkanes as a blowing agent, significant changes in the dimensions of extruded products are encountered. The dimensional stability of a foam with a structure of closed cells is improved by blending the polymer with small amounts of a low molec

  5. How ion properties determine the stability of a lipase enzyme in ionic liquids: a molecular dynamics study.

    Science.gov (United States)

    Klähn, Marco; Lim, Geraldine S; Wu, Ping

    2011-11-07

    The influence of eight different ionic liquid (IL) solvents on the stability of the lipase Candida antarctica lipase B (CAL-B) is investigated with molecular dynamics (MD) simulations. Considered ILs contain cations that are based either on imidazolium or guanidinium as well as nitrate, tetrafluoroborate or hexafluorophosphate anions. Partial unfolding of CAL-B is observed during high-temperature MD simulations and related changes of CAL-B regarding its radius of gyration, surface area, secondary structure, amount of solvent close to the backbone and interaction strength with the ILs are evaluated. CAL-B stability is influenced primarily by anions in the order NO(3)(-)≪ BF(4)(-) helices and an increase of surface area, radius of gyration and protein-IL total interaction strength of CAL-B, all of which describe a destabilization of the folded protein state. On the other hand, a destabilization of the protein core is facilitated when direct core-IL interactions are feasible. This is the case when long alkyl chains are involved or when particularly hydrophobic ILs induce major conformational changes that enable ILs direct access to the protein core. This core instability is characterized by a disintegration of β-sheets, diffusion of ions into CAL-B and increasing protein-IL van der Waals interactions. This process describes a stabilization of the unfolded protein state. Both of these processes reduce the folding free energy and thus destabilize CAL-B. The results of this work clarify the impact of ions on CAL-B stabilization. An extrapolation of the observed trends enables proposing novel ILs in which protein stability could be enhanced further.

  6. 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.

  7. Surface diffusion of molecular glasses: Material dependence and impact on physical stability

    Science.gov (United States)

    Ruan, Shigang; Zhang, Wei; Yu, Lian

    Surface diffusion coefficients have been measured for molecular glasses tris-naphthylbenzene (TNB) and PMMA oligomers by surface grating decay. Surface diffusion on TNB is vastly faster than bulk diffusion, by a factor of 107 at Tg, while the process is very slow on PMMA. Along with the previous results on o - terphenyl, nifedipine, indomethacin, and polystyrene oligomers, we find that surface diffusion slows down with increasing molecular size and intermolecular forces, whereas bulk diffusion has a weaker material dependence. The molecular glasses studied show fast crystal growth on the free surface. A general correlation is observed between the coefficient of surface diffusion and the velocity of surface crystal growth, indicating surface crystallization is supported by surface mobility. (Zhu, L., et al. Phys. Rev. Lett. 106 (2011): 256103; Zhang, W., et al. J. Phys. Chem. B 119 (2015): 5071-5078) Nsf.

  8. The effect of C-terminal helix on the stability of FF domain studied by molecular dynamics simulation.

    Science.gov (United States)

    Zhao, Liling; Cao, Zanxia; Wang, Jihua

    2012-01-01

    To investigate the effect of C-terminal helix on the stability of the FF domain, we studied the native domain FF3-71 from human HYPA/FBP11 and the truncated version FF3-60 with C-terminal helix being deleted by molecular dynamics simulations with GROMACS package and GROMOS 43A1 force field. The results indicated that the structures of truncated version FF3-60 were evident different from those of native partner FF3-71. Compared with FF3-71, the FF3-60 lost some native contacts and exhibited some similar structural characters to those of intermediate state. The C-terminal helix played a major role in stabilizing the FF3-71 domain. To a certain degree, the FF domain had a tendency to form an intermediate state without the C-terminal helix. In our knowledge, this was the first study to examine the role of C-terminal helix of FF domain in detail by molecular dynamics simulations, which was useful to understand the three-state folding mechanism of the small FF domain.

  9. 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.

  10. Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization.

    Science.gov (United States)

    George, Janine; Dronskowski, Richard

    2017-02-16

    Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

  11. Synthesis of Non-Toxic Silica Particles Stabilized by Molecular Complex Oleic-Acid/Sodium Oleate

    Directory of Open Access Journals (Sweden)

    Catalin Ilie Spataru

    2016-11-01

    Full Text Available The present work is focused on the preparation of biocompatible silica particles from sodium silicate, stabilized by a vesicular system containing oleic acid (OLA and its alkaline salt (OLANa. Silica nanoparticles were generated by the partial neutralization of oleic acid (OLA, with the sodium cation present in the aqueous solutions of sodium silicate. At the molar ratio OLA/Na+ = 2:1, the molar ratio (OLA/OLANa = 1:1 required to form vesicles, in which the carboxyl and carboxylate groups have equal concentrations, was achieved. In order to obtain hydrophobically modified silica particles, octadecyltriethoxysilane (ODTES was added in a sodium silicate sol–gel mixture at different molar ratios. The interactions between the octadecyl groups from the modified silica and the oleyl chains from the OLA/OLANa stabilizing system were investigated via simultaneous thermogravimetry (TG and differential scanning calorimetry (DSC (TG-DSC analyses.A significant decrease in vaporization enthalpy and an increase in amount of ODTES were observed. Additionally, that the hydrophobic interaction between OLA and ODTES has a strong impact on the hybrids’ final morphology and on their textural characteristics was revealed. The highest hydrodynamic average diameter and the most negative ζ potential were recorded for the hybrid in which the ODTES/sodium silicate molar ratio was 1:5. The obtained mesoporous silica particles, stabilized by the OLA/OLANa vesicular system, may find application as carriers for hydrophobic bioactive molecules.

  12. 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

    2015-12-02

    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.

  13. 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...

  14. 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.

  15. 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.

  16. 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.

  17. Studies on the molecular correlates of genomic stability in rat brain cells following Amalakirasayana therapy.

    Science.gov (United States)

    Swain, Umakanta; Sindhu, Kiran Kumar; Boda, Ushasri; Pothani, Suresh; Giridharan, Nappan V; Raghunath, Manchala; Rao, Kalluri Subba

    2012-04-01

    Adult Wistar NIN (WNIN) rats (6 months old) of both sexes were orally fed Amalakirasayana at a dose of 4.5 g per kg body weight, five days in a week. The Amalakirasayana was prepared by Arya Vaidya Sala, Kottakkal, Kerala, India, which is considered as gold standard. After 3, 9 and 15 months of such therapeutic regime, rats were sacrificed and various tissues including brain were removed. Isolated cell suspensions of neurons and astroglia were prepared from the cerebral cortex. DNA damage, as a prime indicator of the status of genomic stability was measured in terms of single (SSBs) and double strand breaks (DSBs) through (a). The "comet" assay and (b). The biochemical methods utilizing the unique properties of Escherichia coli DNA polymerase I (pol I) and calf thymus terminal transferase. The results convincingly indicate that while in control animals, there was a distinct increase in DNA damage with age in neurons and astrocytes, rasayana fed animals showed significantly less DNA damage in brain cells demonstrating beneficial effects of Rasayana therapy towards maintenance of genomic stability. DNA-damage may be the proximal cause of aging and strategies to reduce the rate of aging could be based on this fact.

  18. Combining comparative proteomics and molecular genetics uncovers regulators of synaptic and axonal stability and degeneration in vivo.

    Directory of Open Access Journals (Sweden)

    Thomas M Wishart

    Full Text Available Degeneration of synaptic and axonal compartments of neurons is an early event contributing to the pathogenesis of many neurodegenerative diseases, but the underlying molecular mechanisms remain unclear. Here, we demonstrate the effectiveness of a novel "top-down" approach for identifying proteins and functional pathways regulating neurodegeneration in distal compartments of neurons. A series of comparative quantitative proteomic screens on synapse-enriched fractions isolated from the mouse brain following injury identified dynamic perturbations occurring within the proteome during both initiation and onset phases of degeneration. In silico analyses highlighted significant clustering of proteins contributing to functional pathways regulating synaptic transmission and neurite development. Molecular markers of degeneration were conserved in injury and disease, with comparable responses observed in synapse-enriched fractions isolated from mouse models of Huntington's disease (HD and spinocerebellar ataxia type 5. An initial screen targeting thirteen degeneration-associated proteins using mutant Drosophila lines revealed six potential regulators of synaptic and axonal degeneration in vivo. Mutations in CALB2, ROCK2, DNAJC5/CSP, and HIBCH partially delayed injury-induced neurodegeneration. Conversely, mutations in DNAJC6 and ALDHA1 led to spontaneous degeneration of distal axons and synapses. A more detailed genetic analysis of DNAJC5/CSP mutants confirmed that loss of DNAJC5/CSP was neuroprotective, robustly delaying degeneration in axonal and synaptic compartments. Our study has identified conserved molecular responses occurring within synapse-enriched fractions of the mouse brain during the early stages of neurodegeneration, focused on functional networks modulating synaptic transmission and incorporating molecular chaperones, cytoskeletal modifiers, and calcium-binding proteins. We propose that the proteins and functional pathways identified in

  19. Molecular simulations of lipid systems: Edge stability and structure in pure and mixed bilayers

    Science.gov (United States)

    Jiang, Yong

    2007-12-01

    Understanding the structural, mechanical and dynamical properties of lipid self-assembled systems is fundamental to understand the behavior of the cell membrane. This thesis has investigated the equilibrium properties of lipid systems with edge defects through various molecular simulation techniques. The overall goal of this study is to understand the free energy terms of the edges and to develop efficient methods to sample equilibrium distributions of mixed-lipid systems. In the first main part of my thesis, an atomistic molecular model is used to study lipid ribbon which has two edges on both sides. Details of the edge structures, such as area per lipid and tail torsional statistics are presented. Line tension, calculated from pressure tensor in MD simulation has good agreement with result from other sources. To further investigate edge properties on a longer timescale and larger length scale, we have applied a coarse-grained forcefield on mixed lipid systems and try to interpret the edge fluctuations in terms of free energy parameters such as line tension and bending modulus. We have identified two regimes with quite different edge behavior: a high line tension regime and a low line tension regime. The last part of this thesis focuses on a hybrid Molecular dynamics and Configurational-bias Monte Carlo (MCMD) simulation method in which molecules can change their type by growing and shrinking the terminal acyl united carbon atoms. A two-step extension of the MCMD method has been developed to allow for a larger difference in the components' tail lengths. Results agreed well with previous one-step mutation results for a mixture with a length difference of four carbons. The current method can efficiently sample mixtures with a length difference of eight carbons, with a small portion of lipids of intermediate tail length. Preliminary results are obtained for "bicelle"-type (DMPC/DHPC) ribbons.

  20. 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....... It was found that several mutations, which directly or indirectly destabilized the interactions between these residues within this network, contributed to the changes in B-RAF activity. CONCLUSION: Our results showed that the above mechanisms lead to the disruption of the electrostatic interactions between...

  1. 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

  2. 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.

  3. 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.

  4. The kinetic and thermodynamic sorption and stabilization of multiwalled carbon nanotubes in natural organic matter surrogate solutions: the effect of surrogate molecular weight.

    Science.gov (United States)

    Li, Tingting; Lin, Daohui; Li, Lu; Wang, Zhengyu; Wu, Fengchang

    2014-03-01

    Styrene sulfonate (SS) and polystyrene sulfonates (PSSs) were used as surrogates of natural organic matter to study the effect of molecular weight (from 206.2 to 70,000 Da) on their sorption by a multiwalled carbon nanotube (MWCNT) and an activated carbon (AC) and on their stabilization of MWCNT suspension. Results indicate that surface-diffusion through the liquid-sorbent boundary was the rate-controlling step of the kinetic sorption of both MWCNTs and AC, and surface-occupying and pore-filling mechanisms respectively dominated the thermodynamic sorption of MWCNTs and AC. Sorption rates and capacities of MWCNTs and AC in molecular concentration of SS and PSS decreased with increasing molecular weight. The PSSs but not SS facilitated the stabilization of MWCNT suspension because of the increased electrosteric repulsion. The PSSs with more monomers had greater capabilities to stabilize the MWCNT suspension, but the capabilities were comparable after being normalized by the total monomer number.

  5. The Effect of Membrane Environment on Surfactant Protein C Stability Studied by Constant-pH Molecular Dynamics.

    Science.gov (United States)

    Carvalheda, Catarina A; Campos, Sara R R; Baptista, António M

    2015-10-26

    Pulmonary surfactant protein C (SP-C) is a small peptide with two covalently linked fatty acyl chains that plays a crucial role in the formation and stabilization of the pulmonary surfactant reservoirs during the compression and expansion steps of the respiratory cycle. Although its function is known to be tightly related to its highly hydrophobic character and key interactions maintained with specific lipid components, much is left to understand about its molecular mechanism of action. Also, although it adopts a mainly helical structure while associated with the membrane, factors as pH variation and deacylation have been shown to affect its stability and function. In this work, the conformational behavior of both the acylated and deacylated SP-C isoforms was studied in a DPPC bilayer under different pH conditions using constant-pH molecular dynamics simulations. Our findings show that both protein isoforms are remarkably stable over the studied pH range, even though the acylated isoform exhibits a labile helix-turn-helix motif rarely observed in the other isoform. We estimate similar tilt angles for the two isoforms over the studied pH range, with a generally higher degree of internalization of the basic N-terminal residues in the deacylated case, and observe and discuss some protonation-conformation coupling effects. Both isoforms establish contacts with the surrounding lipid molecules (preferentially with the sn-2 ester bonds) and have a local effect on the conformational behavior of the surrounding lipid molecules, the latter being more pronounced for acylated SP-C.

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

    Science.gov (United States)

    Liang, Yuchen; Huang, Jie; Zang, Pengyuan; Kim, Jiyoung; Hu, Walter

    2014-12-01

    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.

  7. 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.

  8. On the influence of the mixture of denaturants on protein structure stability: A molecular dynamics study

    Science.gov (United States)

    Shao, Qiang; Wang, Jinan; Zhu, Weiliang

    2014-09-01

    Mixtures of osmolytes and/or inorganic salts are present in the cell. Therefore, the understanding of the interplay of mixed osmolyte molecules and inorganic salts and their combined effects on protein structure is of fundamental importance. A novel test is presented to investigate the combined effects of urea and a chaotropic inorganic salt, potassium iodide (KI), on protein structure by using molecular dynamics simulation. It is found that the coexistence of KI and urea does not affect their respective distribution in solution. The solvation of KI salt in urea solution makes the electrostatic interactions of urea more favorable, promoting the hydrogen bonding between urea (and water) to protein backbone. The interactions from K+ and hydrogen bonding from urea and water to protein backbone work as the driving force for protein denaturation. The collaborative behavior of urea and KI salt thus enhances the denaturing ability of urea and KI mixed solution.

  9. Visualizing the Stability of Char: Molecular- to Micron-scale Observations of Char Incubated in a Tropical Soil

    Science.gov (United States)

    Heckman, K. A.; Ramon, C.; Weber, P. K.; Torn, M. S.; Pett-Ridge, J.; Nico, P. S.

    2014-12-01

    The persistence of pyrogenic materials (hereafter referred to as char) in terrestrial ecosystems is of interest both from a carbon cycle modelling perspective and a climate change mitigation standpoint. However, the fate of newly introduced char in soils remains unclear. Recent reviews attempting to summarize trends in char decomposition have come to differing conclusions, further stressing the complexity of factors dictating char stability in soils. The current dataset specifically addresses the stability of char additions to a tropical clay-rich soil, possible priming effects, and interactions among char, microbial communities and the mineral matrix. 13C- and 15N-labeled Acer rubrum(red maple) wood was combusted at 400°C and added to surface (0-10 cm) and subsurface (20-30 cm) soils from the Luquillo Experimental Forest, Puerto Rico. Soils were incubated for 13 and 345 days at 26°C. Following incubation, intact microaggregates were frozen and cryosectioned into thin sections of approximately 5 μm thickness and mounted on gold-coated quartz slides. Thin sections were examined by synchrotron-based Fourier transform infrared spectroscopy (SR-FTIR), scanning electron microscopy/energy dispersive X-ray spectroscopy (SEM/EDS), and high resolution secondary ion mass spectrometry (nanoSIMS). The combination of these μm to nm scale techniques allowed us to create corresponding spatial maps of native organic matter, char, and mineral phase distribution, track spatial variability in organic matter molecular structure, and dispersion of 13C and 15N isotopic labels. We present preliminary results indicating a high degree of stability of char in these wet tropical soils throughout the incubation period, suggesting that applied char may persist for long periods of time in similar soils.

  10. Thermal stability and unfolding pathways of hyperthermophilic and mesophilic periplasmic binding proteins studied by molecular dynamics simulation.

    Science.gov (United States)

    Chen, Lin; Li, Xue; Wang, Ruige; Fang, Fengqin; Yang, Wanli; Kan, Wei

    2016-07-01

    The ribose binding protein (RBP), a sugar-binding periplasmic protein, is involved in the transport and signaling processes in both prokaryotes and eukaryotes. Although several cellular and structural studies have been reported, a description of the thermostability of RBP at the molecular level remains elusive. Focused on the hyperthermophilic Thermoytoga maritima RBP (tmRBP) and mesophilic Escherichia coli homolog (ecRBP), we applied molecular dynamics simulations at four different temperatures (300, 380, 450, and 500 K) to obtain a deeper insight into the structural features responsible for the reduced thermostability of the ecRBP. The simulations results indicate that there are distinct structural differences in the unfolding pathway between the two homologs and the ecRBP unfolds faster than the hyperthermophilic homologs at certain temperatures in accordance with the lower thermal stability found experimentally. Essential dynamics analysis uncovers that the essential subspaces of ecRBP and tmRBP are non-overlapping and these two proteins show different directions of motion within the simulations trajectories. Such an understanding is required for designing efficient proteins with characteristics for a particular application.

  11. 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.

  12. Interfacial stability of CoSi2/Si structures grown by molecular beam epitaxy

    Science.gov (United States)

    George, T.; Fathauer, R. W.

    1992-01-01

    The stability of CoSi2/Si interfaces was examined in this study using columnar silicide structures grown on (111) Si substrates. In the first set of experiments, Co and Si were codeposited using MBE at 800 C and the resulting columnar silicide layer was capped by epitaxial Si. Deposition of Co on the surface of the Si capping layer at 800 C results in the growth of the buried silicide columns. The buried columns grow by subsurface diffusion of the deposited Co, suppressing the formation of surface islands of CoSi2. The column sidewalls appear to be less stable than the top and bottom interfaces, resulting in preferential lateral growth and ultimately in the coalescence of the columns to form a continuous buried CoSi2 layer. In the second set of experiments, annealing of a 250 nm-thick buried columnar layer at 1000 C under a 100 nm-thick Si capping layer results in the formation of a surface layer of CoSi2 with a reduction in the sizes of the CoSi2 columns. For a sample having a thicker Si capping layer the annealing leads to Ostwald ripening producing buried equiaxed columns. The high CoSi2/Si interfacial strain could provide the driving force for the observed behavior of the buried columns under high-temperature annealing.

  13. 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.

  14. 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.

  15. 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.

  16. 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

  17. 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...

  18. Stabilization by hydrophobic protection as a molecular mechanism for organic carbon sequestration in maize-amended rice paddy soils.

    Science.gov (United States)

    Song, X Y; Spaccini, R; Pan, G; Piccolo, A

    2013-08-01

    The hydrophobic components of soil organic matter (SOM) are reckoned to play an important role in the stabilization of soil organic carbon (SOC). The contribution of hydrophobic substances to SOC sequestration was evaluated in four different paddy soils in the South of China, following a 6-month incubation experiment with maize straw amendments. Soil samples included: a well developed paddy soil (TP) derived from clayey lacustrine deposits in the Tai Lake plain of Jiangsu; an acid clayey paddy soil (RP) derived from red earth in the rolling red soil area of Jiangxi; a weakly developed neutral paddy soil (PP) formed on Jurassic purple shale from Chongq; and a calcic Fluvisol (MS) derived from riverine sediments from a wetland along the Yangtze valley of Anhui, China. The SOC molecular composition after 30 and 180 days of incubation, was determined by off-line thermochemolysis followed by gas chromatography-mass spectrometry analysis. Lignin, lipids and carbohydrates were the predominant thermochemolysis products released from the treated soils. A selective preservation of hydrophobic OM, including lignin and lipids, was shown in maize amended soils with prolonged incubation. The decomposition of lignin and lipids was significantly slower in the TP and RP soils characterized by a larger content of extractable iron oxyhydrates (Fed) and lower pH. The overall increase in hydrophobic substances in maize incubated samples was correlated, positively, with total content of clay and Fed, and, negatively, with soil pH. Moreover, yields of both lignin and lipid components showed a significant relationship with SOC increase after incubation. These findings showed that the larger the lipid and lignin content of SOM, the greater was the stability of SOC, thereby suggesting that OM hydrophobic components may have an essential role in controlling the processes of OC sequestration in paddy soils of South China.

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

    Science.gov (United States)

    Radibratovic, Milica; Minic, Simeon; Stanic-Vucinic, Dragana; Nikolic, Milan; Milcic, Milos; Cirkovic Velickovic, Tanja

    2016-01-01

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

  20. 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.

  1. 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.

  2. 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.

  3. 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).

  4. High operational and environmental stability of high-mobility conjugated polymer field-effect transistors through the use of molecular additives

    Science.gov (United States)

    Nikolka, Mark; Nasrallah, Iyad; Rose, Bradley; Ravva, Mahesh Kumar; Broch, Katharina; Sadhanala, Aditya; Harkin, David; Charmet, Jerome; Hurhangee, Michael; Brown, Adam; Illig, Steffen; Too, Patrick; Jongman, Jan; McCulloch, Iain; Bredas, Jean-Luc; Sirringhaus, Henning

    2016-12-01

    Due to their low-temperature processing properties and inherent mechanical flexibility, conjugated polymer field-effect transistors (FETs) are promising candidates for enabling flexible electronic circuits and displays. Much progress has been made on materials performance; however, there remain significant concerns about operational and environmental stability, particularly in the context of applications that require a very high level of threshold voltage stability, such as active-matrix addressing of organic light-emitting diode displays. Here, we investigate the physical mechanisms behind operational and environmental degradation of high-mobility, p-type polymer FETs and demonstrate an effective route to improve device stability. We show that water incorporated in nanometre-sized voids within the polymer microstructure is the key factor in charge trapping and device degradation. By inserting molecular additives that displace water from these voids, it is possible to increase the stability as well as uniformity to a high level sufficient for demanding industrial applications.

  5. High operational and environmental stability of high-mobility conjugated polymer field-effect transistors through the use of molecular additives

    KAUST Repository

    Nikolka, Mark

    2016-12-12

    Due to their low-temperature processing properties and inherent mechanical flexibility, conjugated polymer field-effect transistors (FETs) are promising candidates for enabling flexible electronic circuits and displays. Much progress has been made on materials performance; however, there remain significant concerns about operational and environmental stability, particularly in the context of applications that require a very high level of threshold voltage stability, such as active-matrix addressing of organic light-emitting diode displays. Here, we investigate the physical mechanisms behind operational and environmental degradation of high-mobility, p-type polymer FETs and demonstrate an effective route to improve device stability. We show that water incorporated in nanometre-sized voids within the polymer microstructure is the key factor in charge trapping and device degradation. By inserting molecular additives that displace water from these voids, it is possible to increase the stability as well as uniformity to a high level sufficient for demanding industrial applications.

  6. Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation.

    Directory of Open Access Journals (Sweden)

    Matteo eLambrughi

    2012-11-01

    Full Text Available Cyclin-dependent kinase inhibitors (CKIs are key regulatory proteins of the eukaryotic cell cycle, which modulate cyclin-dependent kinase (Cdk activity. CKIs perform their inhibitory effect by the formation of ternary complexes with a target kinase and its cognate cyclin. These regulators generally belong to the class of intrinsically disordered proteins (IDPs, which lack a well-defined and organized three-dimensional structure in their free state, undergoing folding upon binding to specific partners. Unbound IDPs are not merely random-coil structures, but can present intrinsically folded structural units (IFSUs and collapsed conformations. These structural features can be relevant to protein function in vivo.The yeast CKI Sic1 is a 284-amino acid IDP that binds to Cdk1 in complex with the Clb5,6 cyclins, preventing phosphorylation of G1 substrates and, therefore, entrance to the S phase. Sic1 degradation, triggered by multiple phosphorylation events, promotes cell-cycle progression. Previous experimental studies pointed out a propensity of Sic1 and its isolated domains to populate both extended and compact conformations. The present contribution provides models of the compact conformations of the Sic1 kinase-inhibitory domain (KID by all-atom molecular-dynamics simulations in explicit solvent and in the absence of interactors. The results are integrated by spectroscopic and spectrometric data. Helical IFSUs are identified, along with networks of intramolecular interactions. The results identify a group of hub residues and electrostatic interactions which are likely to be involved in the stabilization of globular states.

  7. The molecular chaperone HSP70 binds to and stabilizes NOD2, an important protein involved in Crohn disease.

    Science.gov (United States)

    Mohanan, Vishnu; Grimes, Catherine Leimkuhler

    2014-07-04

    Microbes are detected by the pathogen-associated molecular patterns through specific host pattern recognition receptors. Nucleotide-binding oligomerization domain-containing protein 2 (NOD2) is an intracellular pattern recognition receptor that recognizes fragments of the bacterial cell wall. NOD2 is important to human biology; when it is mutated it loses the ability to respond properly to bacterial cell wall fragments. To determine the mechanisms of misactivation in the NOD2 Crohn mutants, we developed a cell-based system to screen for protein-protein interactors of NOD2. We identified heat shock protein 70 (HSP70) as a protein interactor of both wild type and Crohn mutant NOD2. HSP70 has previously been linked to inflammation, especially in the regulation of anti-inflammatory molecules. Induced HSP70 expression in cells increased the response of NOD2 to bacterial cell wall fragments. In addition, an HSP70 inhibitor, KNK437, was capable of decreasing NOD2-mediated NF-κB activation in response to bacterial cell wall stimulation. We found HSP70 to regulate the half-life of NOD2, as increasing the HSP70 level in cells increased the half-life of NOD2, and down-regulating HSP70 decreased the half-life of NOD2. The expression levels of the Crohn-associated NOD2 variants were less compared with wild type. The overexpression of HSP70 significantly increased NOD2 levels as well as the signaling capacity of the mutants. Thus, our study shows that restoring the stability of the NOD2 Crohn mutants is sufficient for rescuing the ability of these mutations to signal the presence of a bacterial cell wall ligand.

  8. Comparison between stability constants of cadmium and lead complexes with humic substances of different molecular weight isolated from Baltic Sea water

    Directory of Open Access Journals (Sweden)

    Waldemar Grzybowski

    2000-12-01

    Full Text Available The complexation of cadmium and lead with humic substances was studied using differential pulse anodic stripping voltammetry and a standard addition technique. The titration was done for humic substances of different molecular weight that had been isolated from seawater and subsequently redissolved in organic-free seawater. The different molecular weight fractions were obtained by ultrafiltration using 1000 D (Dalton, 5000 D and 10 000 D pore size filters. Comparison of the calculated stability constants suggests that the strengths of lead complexes in the analysed fractions are similar and that cadmium is complexed by the fraction smaller than 1000 D.

  9. Molecular Basis of Inactive B-RAF(WT) and B-RAF(V600E) Ligand Inhibition, Selectivity and Conformational Stability: An in Silico Study

    DEFF Research Database (Denmark)

    Fratev, Filip Filipov; Jonsdottir, Svava Osk; Mihaylova, E.

    2009-01-01

    The B-RAF kinase plays an important role both in tumor induction and maintenance in several cancers. The molecular basis of the inactive B-RAF(WT) and B-RAF(V600E) inhibition and selectivity of a series of inhibitors was examined with a combination of molecular dynamics (MD), free energy MM......-PBSA and local-binding energy (LBE) approaches. The conformational stability of the unbounded kinases and in particular the processes of the B-RAF(V600E) mutant activation were analyzed. A unique salt bridge network formed mainly by the catalytic residues was identified in the unbounded B-RAFs...

  10. 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)

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

    Science.gov (United States)

    Rajput, Nav Nidhi; Qu, Xiaohui; 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 (Mg(2+) → 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.

  12. 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

    2015-05-07

    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.

  13. Molecular statics calculations of proton binding to goethite surfaces: A new approach to estimation of stability constants for multisite surface complexation models

    Science.gov (United States)

    Rustad, James R.; Felmy, Andrew R.; Hay, Benjamin P.

    1996-05-01

    A new approach to estimating stability constants for proton binding in multisite surface complexation models is presented. The method is based on molecular statics computation of energies for the formation of proton vacancies and interstitials in ideal periodic slabs representing the (100), (110), (010), (001), and (021) surfaces of goethite. Gas-phase energies of clusters representing the hydrolysis products of ferric iron are calculated using the same potential energy functions used for the surface. These energies are linearly related to the hydrolysis constants for ferric iron in aqueous solution. Stability constants for proton binding at goethite surfaces are estimated by assuming the same log K- Δ E relationship for goethite surface protonation reactions. These stability constants predict a pH of zero charge of 8.9, in adequate agreement with measurements on CO 2-free goethite. The estimated stability constants differ significantly from previous estimations based on Pauling bond strength. We find that nearly all the surface oxide ions are reactive; nineteen of the twenty-six surface sites investigated have log Kint between 7.7 and 9.4. This implies a site density between fifteen and sixteen reactive sites/nm for crystals dominated by (110) and (021) crystal faces.

  14. Theoretical Insights into Three Types of Oxidized Starch-Based Adhesives: Chemical Stability, Water Resistance, and Shearing Viscosity from a Molecular Viewpoint

    Directory of Open Access Journals (Sweden)

    Liang Junxi

    2016-01-01

    Full Text Available To better understand the origin and difference associated with chemical stability, water resistance, and shearing viscosity of three types of different oxidized modified starch-based adhesives, a detailed theoretical investigation from a molecular viewpoint has been performed using the AM1 semiempirical level and the DFT-B3LYP level, respectively. As a result, our findings suggest that, by Mulliken population analysis (MPA, frontier orbital analysis, and electrostatic potential (EP analysis based on B3LYP/6-31G calculations, the chemical stability, water resistance, and shearing viscosity of the oxidized modified starch-based adhesives are uniformly improved and corresponding difference for each property presents an identical order: the oxidized grafted cross-linked starch-based adhesive > the oxidized grafted starch-based adhesive > the oxidized starch-based adhesive, which is well consistent with experimental results.

  15. 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.

  16. 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.

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis.

    Science.gov (United States)

    Chen, Lin; Zhang, Ji-Long; Yu, Li-Ying; Zheng, Qing-Chuan; Chu, Wen-Ting; Xue, Qiao; Zhang, Hong-Xing; Sun, Chia-Chung

    2012-10-18

    Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA. The simulation results indicate that Cren7 stabilizes DNA duplex in a certain temperature range in the binary complex compared with the unbound DNA molecules. At the same time, DNA molecules were found to undergo B-like to A-like form transitions with increased temperature. The results of statistical analyses of the H-bond and hydrophobic contacts show that some residues have significant influence on the structure of DNA molecules. Our work can give important information to understand the interactions of proteins with nucleic acids and other ligands.

  2. A Hamiltonian Replica Exchange Molecular Dynamics (MD Method for the Study of Folding, Based on the Analysis of the Stabilization Determinants of Proteins

    Directory of Open Access Journals (Sweden)

    Massimiliano Meli

    2013-06-01

    Full Text Available Herein, we present a novel Hamiltonian replica exchange protocol for classical molecular dynamics simulations of protein folding/unfolding. The scheme starts from the analysis of the energy-networks responsible for the stabilization of the folded conformation, by means of the energy-decomposition approach. In this framework, the compact energetic map of the native state is generated by a preliminary short molecular dynamics (MD simulation of the protein in explicit solvent. This map is simplified by means of an eigenvalue decomposition. The highest components of the eigenvector associated with the lowest eigenvalue indicate which sites, named “hot spots”, are likely to be responsible for the stability and correct folding of the protein. In the Hamiltonian replica exchange protocol, we use modified force-field parameters to treat the interparticle non-bonded potentials of the hot spots within the protein and between protein and solvent atoms, leaving unperturbed those relative to all other residues, as well as solvent-solvent interactions. We show that it is possible to reversibly simulate the folding/unfolding behavior of two test proteins, namely Villin HeadPiece HP35 (35 residues and Protein A (62 residues, using a limited number of replicas. We next discuss possible implications for the study of folding mechanisms via all atom simulations.

  3. Effects of hesperidin, a flavanone glycoside interaction on the conformation, stability, and aggregation of lysozyme: multispectroscopic and molecular dynamic simulation studies?

    Science.gov (United States)

    Ratnaparkhi, Aditi; Muthu, Shivani A; Shiriskar, Sonali M; Pissurlenkar, Raghuvir R S; Choudhary, Sinjan; Ahmad, Basir

    2015-09-01

    Hesperidin (HESP), a flavanone glycoside, shows high antioxidant properties and possess ability to go through the blood-brain barrier. Therefore, it could be a potential drug molecule against aggregation based diseases such as Alzheimer's, Parkinson's, and systemic amyloidoses. In this work, we investigated the potential of HESP to interact with hen egg-white lysozyme (HEWL) monomer and prevent its aggregation. The HESP-HEWL binding studies were performed using a fluorescence quenching technique, molecular docking and molecular dynamics simulations. We found a strong interaction of HESP with the lysozyme monomer (Ka, ~ 5 × 10(4) M(-1)) mainly through hydrogen bonding, water bridges, and hydrophobic interactions. We showed that HESP molecule spanned the highly aggregation prone region (amino acid residues 48-101) of HEWL and prevented its fibrillar aggregation. Further, we found that HESP binding completely inhibited amorphous aggregation of the protein induced by disulfide-reducing agent tries-(2-carboxyethyl) phosphine. Conformational and stability studies as followed by various tertiary and secondary structure probes revealed that HESP binding only marginally affected the lysozyme monomer conformation and increased both stability and reversibility of the protein against thermal denaturation. Future studies should investigate detail effects of HESP on solvent dynamics, structure, and toxicity of various aggregates. The answers to these questions will not only target the basic sciences, but also have application in biomedical and biotechnological sciences.

  4. Impact of molecular weight and degree of conjugation on the thermodynamics of DNA complexation and stability of polyethylenimine-graft-poly(ethylene glycol) copolymers.

    Science.gov (United States)

    Smith, Ryan J; Beck, Rachel W; Prevette, Lisa E

    2015-01-01

    Poly(ethylene glycol) (PEG) is often conjugated to polyethylenimine (PEI) to provide colloidal stability to PEI-DNA polyplexes and shield charge leading to toxicity. Here, a library of nine cationic copolymers was synthesized by grafting three molecular weights (750, 2000, 5000Da) of PEG to linear PEI at three conjugation ratios. Using isothermal titration calorimetry, we have quantified the thermodynamics of the associations between the copolymers and DNA and determined the extent to which binding is hindered as a function of PEG molecular weight and conjugation ratio. Low conjugation ratios of 750Da PEG to PEI resulted in little decrease in DNA affinity, but a significant decrease-up to two orders of magnitude-was found for the other copolymers. We identified limitations in determination of affinity using indirect assays (electrophoretic mobility shift and ethidium bromide exclusion) commonly used in the field. Dynamic light scattering of the DNA complexes at physiological ionic strength showed that PEI modifications that did not reduce DNA affinity also did not confer significant colloidal stability, a finding that was supported by calorimetric data on the aggregation process. These results quantify the DNA interaction thermodynamics of PEGylated polycations for the first time and indicate that there is an optimum PEG chain length and degree of substitution in the design of agents that have desirable properties for effective in vivo gene delivery.

  5. A Hamiltonian replica exchange molecular dynamics (MD) method for the study of folding, based on the analysis of the stabilization determinants of proteins.

    Science.gov (United States)

    Meli, Massimiliano; Colombo, Giorgio

    2013-06-06

    Herein, we present a novel Hamiltonian replica exchange protocol for classical molecular dynamics simulations of protein folding/unfolding. The scheme starts from the analysis of the energy-networks responsible for the stabilization of the folded conformation, by means of the energy-decomposition approach. In this framework, the compact energetic map of the native state is generated by a preliminary short molecular dynamics (MD) simulation of the protein in explicit solvent. This map is simplified by means of an eigenvalue decomposition. The highest components of the eigenvector associated with the lowest eigenvalue indicate which sites, named "hot spots", are likely to be responsible for the stability and correct folding of the protein. In the Hamiltonian replica exchange protocol, we use modified force-field parameters to treat the interparticle non-bonded potentials of the hot spots within the protein and between protein and solvent atoms, leaving unperturbed those relative to all other residues, as well as solvent-solvent interactions. We show that it is possible to reversibly simulate the folding/unfolding behavior of two test proteins, namely Villin HeadPiece HP35 (35 residues) and Protein A (62 residues), using a limited number of replicas. We next discuss possible implications for the study of folding mechanisms via all atom simulations.

  6. Room-Temperature Single-Electron Tunneling in Dendrimer-Stabilized Gold Nanoparticles Anchored at a Molecular Printboard

    NARCIS (Netherlands)

    Nijhuis, Christian A.; Oncel, Nuri; Huskens, Jurriaan; Zandvliet, Harold J.W.; Ravoo, Bart Jan; Poelsema, Bene; Reinhoudt, David N.

    2006-01-01

    Particle in a box: A gold nanoparticle is encapsulated in a fifth-generation guest dendrimer, which binds to a host self-assembled monolayer surface (see figure). The nanoparticle encapsulated in the “molecular box” is a supramolecular junction that exhibits single-electron tunneling at room tempera

  7. Theoretical insights into the effects of molar ratios on stabilities, mechanical properties, and detonation performance of CL-20/HMX cocrystal explosives by molecular dynamics simulation.

    Science.gov (United States)

    Hang, Gui-Yun; Yu, Wen-Li; Wang, Tao; Wang, Jin-Tao; Li, Zhen

    2017-01-01

    To research and estimate the effects of molar ratios on structures, stabilities, mechanical properties, and detonation properties of CL-20/HMX cocrystal explosive, the CL-20/HMX cocrystal explosive models with different molar ratios were established in Materials Studio (MS). The crystal parameters, structures, stabilities, mechanical properties, and some detonation parameters of different cocrystal explosives were obtained and compared. The molecular dynamics (MD) simulation results illustrate that the molar ratios of CL-20/HMX have a direct influence on the comprehensive performance of cocrystal explosive. The hardness and rigidity of the 1:1 cocrystal explosive was the poorest, while the plastic property and ductibility were the best, thus implying that the explosive has the best mechanical properties. Besides, it has the highest binding energy, so the stability and compatibility is the best. The cocrystal explosive has better detonation performance than HMX. In a word, the 1:1 cocrystal explosive is worth more attention and further research. This paper could offer some theoretical instructions and technological support, which could help in the design of the CL-20 cocrystal explosive.

  8. Molecular structure, tautomeric stability, protonation and deprotonation effects, vibrational, NMR and NBO analyses of 2,4-Dioxoimidazolidine-5-acetic acid (DOIAA) by quantum chemical calculations.

    Science.gov (United States)

    Sridevi, C; Velraj, G

    2014-01-01

    This study represents the conformation, tautomeric stability, protonation and deprotonation effects, vibrational, electronic, NBO and NMR aspects of 2,4-Dioxoimidazolidine-5-acetic acid (DOIAA). Theoretical calculations were performed by ab initio HF and density functional theory (DFT)/B3LYP method using 6-311++G(d,p) basis sets. Tautomerism and the effect of solvent on the tautomeric equilibria in the gas phase and in different solvents were studied. The protonation and deprotonation effects on the reactivity and conformations of DOIAA were investigated. Electronic transitions were also studied and the most prominent transition corresponds to π→π*. Natural bond orbital (NBO) analysis was also carried out to find the intramolecular interactions and their stabilization energy. In DOIAA, the interaction between the lone pair donor orbital (n(LP1N5)) and the acceptor antibonding orbital π*(C6O7) reveals the strong stabilization energy of 224.9 kJ mol(-1). Molecular electrostatic potential (MEP) was calculated to predict the reactive sites of the title compound. The NMR results indicated that the observed chemical shifts for NH, COOH protons of DOIAA not only depend on the structure of the molecule being studied but also on the nature of the solvent, concentration of the sample and the presence of the other exchangeable protons.

  9. Molecular dynamics investigations on the effect of D amino acid substitution in a triple-helix structure and the stability of collagen.

    Science.gov (United States)

    Punitha, V; Raman, S Sundar; Parthasarathi, R; Subramanian, V; Rao, J Raghava; Nair, Balachandran Unni; Ramasami, T

    2009-07-02

    Studies on the structure and stability of peptides and proteins during l-->d configurational change are certainly important for the designing of peptides with new biological activity and protein engineering. The l-->d amino acid (d AA) changes have been observed in aged proteins such as collagen. Hence, in this study, an attempt has been made to explore the effect of the replacement of l amino acid (l AA) in the model collagen-like peptides with d AA and the origin of structural stability (destability) has been traced using the molecular dynamics (MD) method employing the AMBER force field. Our results reveal that the substitution of d AA produces a large local disruption to the triple-helical structure. Formation of a kink (bulge) at the site of substitution is observed from the detailed analysis of MD trajectory. However, this local perturbation of kinked helix changes the direction of the helices and affects the relative orientation of the respective AA residues for helix-helix interaction, enough to affect the overall stability of the model collagen-like peptide. The destabilization energy per d Ala substitution is 7.87 kcal/mol, which is similar to the value for the Gly-->Ala mutation in collagen. Since the Gly-->Ala mutation is involved in genetic disorders such as osteogenesis imperfecta (OI), the l-->d configurational change may produce a similar effect on collagen.

  10. Influence of Molecular Weight of Carriers and Processing Parameters on the Extrudability, Drug Release, and Stability of Fenofibrate Formulations Processed by Hot-Melt Extrusion.

    Science.gov (United States)

    Alsulays, Bader B; Park, Jun-Bom; Alshehri, Sultan M; Morott, Joseph T; Alshahrani, Saad M; Tiwari, Roshan V; Alshetaili, Abdullah S; Majumdar, Soumyajit; Langley, Nigel; Kolter, Karl; Gryczke, Andreas; Repka, Michael A

    2015-10-01

    The objective of this study was to investigate the extrudability, drug release, and stability of fenofibrate (FF) formulations utilizing various hot-melt extrusion processing parameters and polyvinylpyrrolidone (PVP) polymers of various molecular weights. The different PVP grades selected for this study were Kollidon(®) 12 PF (K12), Kollidon(®) 30 (K30), and Kollidon(®) 90 F (K90). FF was extruded with these polymers at three drug loadings (15%, 25%, and 35% w/w). Additionally, for FF combined with each of the successfully extruded PVP grades (K12 and K30), the effects of two levels of processing parameters for screw design, screw speed, and barrel temperature were assessed. It was found that the FF with (K90) was not extrudable up to 35% drug loading. With low drug loading, the polymer viscosity significantly influenced the release of FF. The crystallinity remaining was vital in the highest drug-loaded formulation dissolution profile, and the glass transition temperature of the polymer significantly affected its stability. Modifying the screw configuration resulted in more than 95% post-extrusion drug content of the FF-K30 formulations. In contrast to FF-K30 formulations, FF release and stability with K12 were significantly influenced by the extrusion temperature and screw speed.

  11. 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 dUMP is substituted by a halogen atom. The MM/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).

  12. Molecular dynamics study on core-shell structure stability of aluminum encapsulated by nano-carbon materials

    Science.gov (United States)

    Yi, Qingwen; Xu, Jingcheng; Liu, Yi; Zhai, Dong; Zhou, Kai; Pan, Deng

    2017-02-01

    A ReaxFF reactive forcefield for aluminum-carbon composite system has been developed to investigate structural stability and thermal decomposition mechanism of nano-carbon materials coating aluminum particles. Research results indicated the Al@C particles were structurally stable in a broad temperature range from room temperature up to 2735 K. In particular, the broken carbon cage self-healed to reconstruct a more stable Al@C core-shell structure after Al atoms sequentially departing from carbon cage during thermal decomposition, proffering an effective protection for aluminum surface-activeness.

  13. Molecular cloning, expression profile, odorant affinity, and stability of two odorant-binding proteins in Macrocentrus cingulum Brischke (Hymenoptera: Braconidae).

    Science.gov (United States)

    Ahmed, Tofael; Zhang, Tiantao; Wang, Zhenying; He, Kanglai; Bai, Shuxiong

    2017-02-01

    The polyembryonic endoparasitoid wasp Macrocentrus cingulum Brischke (Hymenoptera: Braconidae) is deployed successfully as a biocontrol agent for corn pest insects from the Lepidopteran genus Ostrinia in Europe and throughout Asia, including Japan, Korea, and China. The odorants are recognized, bound, and solubilized by odorant-binding protein (OBP) in the initial biochemical recognition steps in olfaction that transport them across the sensillum lymph to initiate behavioral response. In the present study, we examine the odorant-binding effects on thermal stability of McinOBP2, McinOBP3, and their mutant form that lacks the third disulfide bonds. Real-time PCR experiments indicate that these two are expressed mainly in adult antennae, with expression levels differing by sex. Odorant-binding affinities of aldehydes, terpenoids, and aliphatic alcohols were measured with circular dichroism spectroscopy based on changes in the thermal stability of the proteins upon their affinities to odorants. The obtained results reveal higher affinity of trans-caryophelle, farnesene, and cis-3-Hexen-1-ol exhibits to both wild and mutant McinOBP2 and McinOBP3. Although conformational flexibility of the mutants and shape of binding cavity make differences in odorant affinity between the wild-type and mutant, it suggested that lacking the third disulfide bond in mutant proteins may have chance to incorrect folded structures that reduced the affinity to these odorants. In addition, CD spectra clearly indicate proteins enriched with α-helical content.

  14. 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).

  15. 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.

  16. 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. [Oregon Health & Science Univ., Portland, OR (United States)

    2014-08-01

    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).

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

    Science.gov (United States)

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

    2008-01-01

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

  18. 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.

  19. Stability and comparative analysis of AOT/water/isooctane reverse micelle system using dynamic light scattering and molecular dynamics.

    Science.gov (United States)

    Vasquez, V R; Williams, B C; Graeve, O A

    2011-03-31

    We use molecular dynamics (MD) and dynamic light scattering (DLS) measurements to analyze the size of reverse micellar structures in the AOT-water-isooctane system at different water-to-surfactant ratios at ambient temperature and pressure. We find good qualitative agreement for the size and morphology behavior of the reverse micelle structures between molecular dynamics calculations and DLS measurements; however, the average values for the reverse micelle size distributions are systematically larger for the DLS measurements. The latter tends to capture the average hydrodynamic size of the structures based on self-diffusion rather than the average physical size as measured in MD simulations, explaining the systematic deviations observed. The combination of MD with DLS allows a better interpretation of the experimental results, in particular for conditions where the structures are nonspherical, commonly observed at lower water-to-surfactant ratios. We also present and analyze the effect of zirconyl chloride on the micellar size distributions in this system. These type of salts are common for reverse micellar synthesis processes. We find that zirconyl chloride affects significantly the size distributions.

  20. A fundamental investigation of the surfactant-stabilized single-walled carbon nanotube/epoxy resin suspensions by molecular dynamics simulation

    Science.gov (United States)

    Rahmani, Farzin; Nouranian, Sasan; Mahdavi, Mina; O’Haver, John H.

    2017-01-01

    The surfactant-assisted stabilization of single-walled carbon nanotubes (SWCNTs) in SWCNT/epoxy resin suspensions were investigated for different surfactant types, concentrations, and temperatures using molecular dynamics simulation. One cationic surfactant, i.e. cetyltrimethylammonium bromide (CTAB), and three anionic surfactants, i.e. sodium dodecyl sulfate (SDS), sodium dodecylbenzenesulfonate (NaDDBS), and sodium cholate (SC), as well as a 1:1 mixture of CTAB and SDS were used. Potentials of mean force (PMFs) were generated between two fixed-size (6,6) SWCNTs for all neat (no surfactant) and surfactant-loaded SWCNT/epoxy resin systems at three different surfactant concentrations (0.25, 0.50, and 1.00 wt%) at room (298 K) and elevated temperature (398 K, only for low-surfactant-concentration systems). Overall, two distinct mechanisms of SWCNT stabilization by the surfactants were identified: (1) an increase in the SWCNT aggregation energy barrier due to the wrapping of the SWCNTs by the surfactant molecules, and (2) a constantly positive free energy (repulsion) for all SWCNT separation distances due to the encapsulation of the two approaching SWCNTs. With the second mechanism, there is a delay for the epoxy molecules to be pushed out from the space between the two SWCNTs. With an increase in the surfactant concentration, the first mechanism becomes more prevalent. With an increase in temperature to 398 K, all surfactants migrate to the suspending medium, thereby the second mechanism of SWCNT stabilization dominates. A drop in the SWCNT-surfactant binding energy is observed around 360–370 K, signifying the surfactant migration to the suspending medium. More or less, all surfactants stabilize the SWCNTs in an epoxy resin at one or more surfactant concentrations. However, NaDDBS exhibits a higher SWCNT aggregation barrier at high concentrations and both temperatures (298 K and 398 K), thereby providing a better SWCNT stabilization in the epoxy resin

  1. 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.

  2. 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.

  3. A novel molecular sieve supporting material for enhancing activity and stability of Ag3PO4 photocatalyst

    Science.gov (United States)

    Wu, Qiang; Wang, Peifu; Niu, Futao; Huang, Cunping; Li, Yang; Yao, Weifeng

    2016-08-01

    A small-pore silicon-substituted silicon aluminum phosphate (SAPO-34) molecular sieve, for the first time, is reported to significantly increase both the activity and life span of Ag3PO4 photocatalyst for visible-light degradation of methylene blue (MB) and rhodamine B (RhB). Results show that 60 wt.% Ag3PO4/SAPO-34 exhibits the highest photocatalytic degradation efficiencies for both MB (91.0% degradation within 2.0 min) and RhB (91.0% degradation within 7.0 min). In comparison, pure Ag3PO4 powder photocatalyst requires 8.0 min and 12.0 min for decomposing 91.0% of MB and RhB, respectively. During MB degradation the rate constant for 60 wt.% Ag3PO4/SAPO-34 increases 317.2% in comparison with the rate constant of pure Ag3PO4. This activity is also much higher than literature reported composite or supported Ag3PO4 photocatalysts. In three photocatalytic runs for the degradation of RhB, the rate constant for 60 wt.% Ag3PO4/SAPO-34 reduces from 0.33 to 0.18 min-1 (45.5% efficiency loss). In contrast, the rate constant of pure Ag3PO4 catalyst decreases from 0.2 to 0.07 min-1 (80.0% efficiency loss). All experimental results have shown that small pores and zero light absorption loss of SAPO-34 molecular sieves minimize Ag3PO4 loading, enhance photocatalytic activity and prolong the lifespan of Ag3PO4 photocatalyst.

  4. Conformational stability, molecular orbital studies (chemical hardness and potential), vibrational investigation and theoretical NBO analysis of 4-tert-butyl-3-methoxy-2,6-dinitrotoluene.

    Science.gov (United States)

    Saravanan, S; Balachandran, V; Vishwanathan, K

    2014-04-24

    The FT-IR and FT-Raman spectra of 4-tert-butyl-3-methoxy-2,6-dinitrotoluene (musk ambrette) have been recorded in the regions 4000-400 cm(-1) and 3500-100 cm(-1), respectively. The total energy calculations of musk ambrette were tried for the possible conformers. The molecular structure, geometry optimization, vibrational frequencies were obtained by the density functional theory (DFT) using B3LYP and LSDA method with 6-311G(d,p) basis set for the most stable conformer "C1". The complete assignments were performed on the basis of the potential energy distribution (PED) of the vibrational modes, calculated and the scaled values were compared with experimental FT-IR and FT-Raman spectra. The observed and the calculated frequencies are found to be in good agreement. The stability of the molecule arising from hyper conjugate interactions and the charge delocalization has been analyzed using bond orbital (NBO) analysis. The HOMO and LUMO energy gap reveals that the energy gap reflects the chemical activity of the molecule. The dipole moment (μ), polarizability (α), anisotropy polarizability (Δα) and first hyperpolarizability (βtot) of the molecule have been reported. The thermodynamic functions (heat capacity, entropy and enthalpy) were obtained for the range of temperature 100-1000 K. Information about the size, shape, charge density distribution and site of chemical reactivity of the molecule has been obtained by mapping electron density isosurface with molecular electrostatic potential (MEP).

  5. 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.

  6. High molecular weight PEGylation of human pancreatic polypeptide at position 22 improves stability and reduces food intake in mice

    DEFF Research Database (Denmark)

    Thieme, V; Jolly, N; Madsen, A N

    2016-01-01

    BACKGROUND AND PURPOSE: Human pancreatic polypeptide (hPP) is known to suppress appetite and food intake, thereby representing a potential therapeutic approach against obesity and associated metabolic disorders. The aim of this study was to improve hPP stability by covalent PEGylation with diverse...... fasting-induced food intake and bioavailability. KEY RESULTS: In human epithelia and colonic mucosal preparations, activity of the modified hPP peptides depended on the core sequence and latency of the peptides was related to PEG size. Peptides modified with a 22 kDa PEG (PEG22) remained intact in blood...... plasma and on incubation with liver homogenates for more than 96 h. Finally, hPP2-36 , [K(22) (PEG22)]hPP2-36 and [K(22) (PEG22),Q(34) ]hPP significantly reduced cumulative food intake in mice over 16 h after s.c. administration. CONCLUSIONS AND IMPLICATIONS: Modification with PEG22 at position 22...

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

    Science.gov (United States)

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

    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 enthalpically favored, but entropically hindered. Simulated adsorption isotherms show that a water monolayer will form even at the low water concentrations of water-saturated scCO2. Carbonation reactions readily occur at electron-rich terminal Oxygen sites adjacent to cation vacancies that readily form in the presence of a water monolayer. These results point to a carbonation mechanism that does not require prior carbonic acid formation in the bulk liquid. This work also highlights the modern capabilities of theoretical methods to address structure and reactivity at interfaces of high chemical complexity. PMID:26456362

  8. Molecular processes induced in primed seeds-increasing the potential to stabilize crop yields under drought conditions.

    Science.gov (United States)

    Wojtyla, Łukasz; Lechowska, Katarzyna; Kubala, Szymon; Garnczarska, Małgorzata

    2016-09-20

    Environmental stress factors such as drought, salinity, temperature extremes and rising CO2 negatively affect crop growth and productivity. Faced with the scarcity of water resources, drought is the most critical threat to world food security. This is particularly important in the context of climate change and an increasing world population. Seed priming is a very promising strategy in modern crop production management. Although it has been known for several years that seed priming can enhance seed quality and the effectiveness of stress responses of germinating seeds and seedlings, the molecular mechanisms involved in the acquisition of stress tolerance by primed seeds in the germination process and subsequent plant growth remain poorly understood. This review provides an overview of the metabolic changes modulated by priming, such as the activation of DNA repair and the antioxidant system, accumulation of aquaporins and late embryogenesis abundant proteins that contribute to enhanced drought stress tolerance. Moreover, the phenomenon of "priming memory," which is established during priming and can be recruited later when seeds or plants are exposed to stress, is highlighted.

  9. Modification of composition of a nanoemulsion with different cholesteryl ester molecular species: Effects on stability, peroxidation, and cell uptake

    Directory of Open Access Journals (Sweden)

    Cristina P Almeida

    2010-09-01

    Full Text Available Cristina P Almeida1, Carolina G Vital1, Thais C Contente1, Durvanei A Maria2, Raul C Maranhão1,31Lipid Metabolism Laboratory, Heart Institute (InCor, Medical School Hospital, 2Biochemistry and Biophysics Laboratories, Butantan Institute, 3Faculty of Pharmaceutical Sciences, University of São Paulo, São Paulo, BrazilPurpose: Use of lipid nanoemulsions as carriers of drugs for therapeutic or diagnostic purposes has been increasingly studied. Here, it was tested whether modifications of core particle constitution could affect the characteristics and biologic properties of lipid nanoemulsions. Methods: Three nanoemulsions were prepared using cholesteryl oleate, cholesteryl stearate, or cholesteryl linoleate as main core constituents. Particle size, stability, pH, peroxidation of the nanoemulsions, and cell survival and uptake by different cell lines were evaluated.Results: It was shown that cholesteryl stearate nanoemulsions had the greatest particle size and all three nanoemulsions were stable during the 237-day observation period. The pH of the three nanoemulsion preparations tended to decrease over time, but the decrease in pH of cholesteryl stearate was smaller than that of cholesteryl oleate and cholesteryl linoleate. Lipoperoxidation was greater in cholesteryl linoleate than in cholesteryl oleate and cholesteryl stearate. After four hours’ incubation of human umbilical vein endothelial cells (HUVEC with nanoemulsions, peroxidation was minimal in the presence of cholesteryl oleate and more pronounced with cholesteryl linoleate and cholesteryl stearate. In contrast, macrophage incubates showed the highest peroxidation rates with cholesteryl oleate. Cholesteryl linoleate induced the highest cell peroxidation rates, except in macrophages. Uptake of cholesteryl oleate nanoemulsion by HUVEC and fibroblasts was greater than that of cholesteryl linoleate and cholesteryl stearate. Uptake of the three nanoemulsions by monocytes was equal. Uptake of

  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. 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.

  14. Improvement in enzyme activity and stability by addition of low molecular weight polyethylene glycol to sodium bis(2-ethyl-L-hexyl)sulfosuccinate/isooctane reverse micellar system.

    Science.gov (United States)

    Talukder, M M R; Takeyama, T; Hayashi, Y; Wu, J C; Kawanishi, T; Shimizu, N; Ogino, C

    2003-08-01

    The activity and stability of Chromobacterium viscosum lipase (glycerolester hydrolase, EC 3.1.1.3)-catalyzed olive oil hydrolysis in sodium bis (2-ethyl-l-hexyl)sulfosuccinate (AOT)/isooctane reverse micelles is increased appreciably when low molecular weight polyethylene glycol (PEG 400) is added to the reverse micelles. To understand the effect of PEG 400 on the phase behavior of the reverse micellar system, the phase diagram of AOT/ PEG 400/water/isooctane system was studied. The influences of relevant parameters on the catalytic activity in AOT/PEG 400 reverse micelles were investigated and compared with the results in the simple AOT reverse micelles. In the presence of PEG 400, the linear decreasing trend of the lipase activity with AOT concentration, which is observed in the simple AOT reverse micelles, disappeared. Enzyme entrapped in AOT/PEG reverse micelles was very stable, retaining >75% of its initial activity after 60 d, whereas the half-life in simple AOT reverse micelles was 38 d. The kinetics parameter maximum velocity (Vmax) exhibiting the temperature dependence and the activation energy obtained by Arrhenius plot was suppressed significantly by the addition of PEG 400.

  15. 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.

  16. 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

  17. Preparation and Hydrothermal Stability of Hydrophobic HMS Molecular Sieve%疏水性 HMS 分子筛的制备及水热稳定性

    Institute of Scientific and Technical Information of China (English)

    王广建; 韩亚飞; 褚衍佩; 冯庆吉; 王芳

    2015-01-01

    以三甲基氯硅烷和六甲基二硅氮烷为硅烷化试剂,分别采用气相和液相硅烷化法对 HMS 分子筛进行表面改性制备疏水性 HMS 分子筛。考察了改性方法、硅烷试剂与分子筛摩尔比、反应温度和时间对硅烷化效果的影响,研究了改性前后HMS 的骨架特征、微观结构和疏水性、水热稳定性。结果表明:气相硅烷化法较液相法优势明显,硅烷化程度和效率均较高;在双硅烷化试剂、反应温度90℃、硅烷试剂与分子筛摩尔之比0.8、反应时间8 h 等条件下,改性前后 HMS 的静态水吸附量分别为45.46%和1.38%,疏水性得到明显提高。HMS 经硅烷化改性后保持介孔骨架结构和蠕虫状孔道,同时水热稳定性得到有效改善,800℃水蒸气处理6 h 后介孔结构仍然存在。%The hydrophobic HMS molecular sieve was prepared with trimethylchlorosilane and hexamethyldisilazane as silane agents by a vapor silylation method and a liquid silylation method. The effects of modification modes, reaction temperature and time, molar ratio of silane agents to HMS on the silylation were investigated. The framework character, microstructures and hydrophobic property, hydrothermal stability of HMS before and after modification were also analyzed. The results indicate that the gas phase method has some advantages such as its high efficiency and degree of silanization. The static water adsorption capacity of HMS before and after silanization are 45.38% and 1.38%, respectively, and the hydrophobic of HMS is enhanced under the optimal conditions (i.e., use of mixed silane agents, reaction temperature of 90 , reaction time of 8 h, and molar ratio of silane agents to HMS of 0.8). The℃hydrophobic HMS maintains the mesoporous structure and typical vermicular channel of HMS molecular sieve. Also, the hydrothermal stability of HMS is improved efficiently after modification, and the mesoporous structure is retained even after

  18. Molecular epidemiology of Coxiella burnetii in French livestock reveals the existence of three main genotype clusters and suggests species-specific associations as well as regional stability.

    Science.gov (United States)

    Joulié, Aurelien; Sidi-Boumedine, Karim; Bailly, Xavier; Gasqui, Patrick; Barry, Séverine; Jaffrelo, Lydia; Poncet, Charles; Abrial, David; Yang, Elise; Leblond, Agnès; Rousset, Elodie; Jourdain, Elsa

    2017-03-01

    Q fever is a worldwide zoonosis caused by the bacterium Coxiella burnetii. In domestic ruminants, Q fever main clinical manifestations are abortions. Although the clinical signs may differ between ruminant species, C. burnetii's genetic diversity remains understudied in enzootic areas. Here, we focused on France, where Q fever is enzootic, with the aims to (a) identify potential associations between C. burnetii genotypes and ruminant host species; (b) assess the distribution of C. burnetii genotypes both within French farms and across France's major livestock-farming regions; and (c) suggest a subset of markers for future genotypic studies. We used DNA samples collected between 2006 and 2015 from 301 females (160 cows, 76 ewes, 65 goats) aborted of Q fever within 7 different farming regions. C. burnetii diversity was determined using a multiple-locus variable-number of tandem repeat analysis (MLVA) considering 17 markers. Using a phylogenetic approach, we identified 3 main genotypic clusters divided into 12 sub-clusters. These clusters were significantly associated with ruminant species: almost all the cattle genotypes were found in a "cattle-specific" cluster whereas small ruminants genotypes essentially grouped into the two other clusters. The clusters also proved stable over space and time, some genotypes being more specifically observed in certain farming regions. We also observed some within-farm diversity but this diversity was restricted to a same genotypic cluster. Finally, we identified 6 MLVA markers that maximized the representativeness of the diversity described. Overall, we highlighted that molecular epidemiology is a relevant approach to assess C. burnetii's genetic diversity and to reveal the existence of species-specific associations and regional stability. These results will be valuable in the field to trace genotype circulation among ruminants and from ruminants to humans. Ultimately, the potential links between genotypes and virulence traits need

  19. 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.

  20. A crossed molecular beams study on the formation and energetics of the resonantly stabilized free i-C4H3(X2A‧) radical and its isotopomers

    Science.gov (United States)

    Gu, Xibin; Guo, Ying; Zhang, Fangtong; Mebel, Alexander M.; Kaiser, Ralf I.

    2007-06-01

    The chemical dynamics of the formation of the i-C 4H 3(X 2A') radical together with its partially deuterated isotopomers were investigated in eight crossed molecular beams experiments of dicarbon molecules in their XΣg+ electronic ground and in first excited a 3Π u state with (partially deuterated) ethylene at collision energies between 12.1 and 40.9 kJ mol -1. The center-of-mass angular distributions suggest that the reaction dynamics on the singlet and triplet surfaces are indirect and involve butatriene reaction intermediates. In case of the C 2/C 2H 4 reaction, the 'symmetric' singlet butatriene intermediate would lead solely to a symmetric center-of-mass angular distribution; however, in combination with isotopically labeled reactants, we deduced that triplet butatriene intermediates excited to B/C like rotations likely account for the observed asymmetries in the center-of-mass angular distributions at higher collision energies. The translational energy distributions are also indicative of the involvement of both the triplet and singlet surfaces which lead both to the i-C 4H 3(X 2A') radicals through lose (singlet) and tight (triplet) exit transitions states. Also, our experiments helped to determine the enthalpy of formation of the i-C 4H 3(X 2A') radical to be about 504 ± 10 kJ mol -1 in good agreement with previous computational studies suggesting 498-499 kJ mol -1. The explicit identification of the resonance-stabilized i-C 4H 3(X 2A') radical proposes that the reaction of dicarbon with ethylene can lead to formation of i-C 4H 3(X 2A') in combustion flames; the n-C 4H 3(X 2A') isomer is not formed in this reaction. This conclusion correlates nicely with Hansen's et al. flame experiments at the advanced light source observing only the i-C 4H 3(X 2A') radical in hydrocarbon flames.

  1. Molecular insights into the stabilization of protein-protein interactions with small molecule: The FKBP12-rapamycin-FRB case study

    Science.gov (United States)

    Chaurasia, Shilpi; Pieraccini, Stefano; De Gonda, Riccardo; Conti, Simone; Sironi, Maurizio

    2013-11-01

    Targetting protein-protein interactions is a challenging task in drug discovery process. Despite the challenges, several studies provided evidences for the development of small molecules modulating protein-protein interactions. Here we consider a typical case of protein-protein interaction stabilization: the complex between FKBP12 and FRB with rapamycin. We have analyzed the stability of the complex and characterized its interactions at the atomic level by performing free energy calculations and computational alanine scanning. It is shown that rapamycin stabilizes the complex by acting as a bridge between the two proteins; and the complex is stable only in the presence of rapamycin.

  2. 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.

  3. 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

    2014-10-03

    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.

  4. Modulating weak interactions for molecular recognition: a dynamic combinatorial analysis for assessing the contribution of electrostatics to the stability of CH-π bonds in water.

    Science.gov (United States)

    Jiménez-Moreno, Ester; Gómez, Ana M; Bastida, Agatha; Corzana, Francisco; Jiménez-Oses, Gonzalo; Jiménez-Barbero, Jesús; Asensio, Juan Luis

    2015-03-27

    Electrostatic and charge-transfer contributions to CH-π complexes can be modulated by attaching electron-withdrawing substituents to the carbon atom. While clearly stabilizing in the gas phase, the outcome of this chemical modification in water is more difficult to predict. Herein we provide a definitive and quantitative answer to this question employing a simple strategy based on dynamic combinatorial chemistry.

  5. 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

  6. 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

  7. Ideal Stabilization

    CERN Document Server

    Nesterenko, Mikhail

    2009-01-01

    We define and explore the concept of ideal stabilization. The program is ideally stabilizing if its every state is legitimate. Ideal stabilization allows the specification designer to prescribe with arbitrary degree of precision not only the fault-free program behavior but also its recovery operation. Specifications may or may not mention all possible states. We identify approaches to designing ideal stabilization to both kinds of specifications. For the first kind, we state the necessary condition for an ideally stabilizing solution. On the basis of this condition we prove that there is no ideally stabilizing solution to the leader election problem. We illustrate the utility of the concept by providing examples of well-known programs and proving them ideally stabilizing. Specifically, we prove ideal stabilization of the conflict manager, the alternator, the propagation of information with feedback and the alternating bit protocol.

  8. Is dynamic heterogeneity of water in presence of a protein denaturing agent different from that in presence of a protein stabilizer? A molecular dynamics simulation study

    Indian Academy of Sciences (India)

    SANDIPA INDRA; RANJIT BISWAS BISWAS

    2016-12-01

    Rotational and translational dynamic heterogeneities (DHs) of ambient aqueous solutions of trimethylamine-N-oxide (TMAO) and tetramethylurea (TMU) at several solute concentrations have been investigated and compared. Motional characteristics of water molecules at solute interfaces and in bulk solutionshave been thoroughly examined for the search of slow dynamics. Note, TMAO possesses zwitterionic structure and is a protein stabilizer whereas TMU is a neutral dipolar molecule and a strong denaturant. Results suggest that water-TMAO solutions possess stronger DH than water-TMU solutions with the solute concentration dependence being stronger for TMAO than for TMU. Diffusive dynamics slows down near the solute surface for both the solutes. Solvation structure shows TMAO-water interaction is stronger than TMU-waterinteraction, producing longer H-bond fluctuation timescale in TMAO solutions. In short, this paper presents, for the first time, a systematic and comparative study of motional features and inter-species interactions between aqueous solutions containing solutes that differ in their individual impacts on protein stability.

  9. 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

  10. A phenomenological study of yttria-stabilized zirconia at 1300 K with the Green-Kubo formulation and equilibrium molecular dynamics

    Science.gov (United States)

    Valadez Huerta, G.; Kelle, A.; Kabelac, S.

    2017-03-01

    In this study, we analyze the transport mechanisms in different yttria-stabilized zirconia compositions as an example for an ionic solid at 1300 K and zero pressure with EMD and the Green-Kubo formulation. As it can be interpreted from the partial and the total correlation functions of the micro fluxes, a certain amount of anions should be given to activate the diffusion of other anions. An incomplete vacancy diffusion favors the coupled effect of heat and diffusion. The heat conduction decreases for higher concentration of vacancies and the optimum of the diffusion is reproducible with this method. We predict a minimum of the thermo-diffusion conductivity at 10 mol% Y2O3. The understanding of the heat and electrical conduction of ionic solids and of the couple effect is essential in systems, where the gradients of different kind of forces are present.

  11. Stability characteristics and structural properties of single- and double-walled boron-nitride nanotubes under physical adsorption of Flavin mononucleotide (FMN) in aqueous environment using molecular dynamics simulations

    Energy Technology Data Exchange (ETDEWEB)

    Ansari, R., E-mail: r_ansari@guilan.ac.ir; Ajori, S., E-mail: Shahram_ajori1366@yahoo.com; Ameri, A.

    2016-03-15

    Graphical abstract: Structural properties and stability characteristics of single- and double-walled boron-nitride nanotubes functionalized with Flavin mononucleotide (FMN) in aqueous environment are investigated employing molecular dynamics simulations. - Highlights: • Structural and buckling analysis of boron-nitride nanotubes under physical adsorption of Flavin mononucleotide (FMN). • Gyration radius increases linearly as the weight percentage of FMN increases. • Presence of water molecules results in more expansion of FMN around BNNTs. • Critical buckling force of functionalized BNNTs is higher than that of pure BNNTs. • The critical strain of functionalized BNNTs is found to be lower than that of pure ones. - Abstract: The non-cytotoxic properties of Boron-nitride nanotubes (BNNTs) and the ability of stable interaction with biomolecules make them so promising for biological applications. In this research, molecular dynamics (MD) simulations are performed to investigate the structural properties and stability characteristics of single- and double-walled BNNTs under physical adsorption of Flavin mononucleotide (FMN) in vacuum and aqueous environments. According to the simulation results, gyration radius increases by rising the weight percentage of FMN. Also, the results demonstrate that critical buckling force of functionalized BNNTs increases in vacuum. Moreover, it is observed that by increasing the weight percentage of FMN, critical force of functionalized BNNTs rises. By contrast, critical strain reduces by functionalization of BNNTs in vacuum. Considering the aqueous environment, it is observed that gyration radius and critical buckling force of functionalized BNNTs increase more considerably than those of functionalized BNNTs in vacuum, whereas the critical strains approximately remain unchanged.

  12. 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)].

  13. 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.

  14. Role of the low-molecular-weight subunits PetL, PetG, and PetN in assembly, stability, and dimerization of the cytochrome b6f complex in tobacco.

    Science.gov (United States)

    Schwenkert, Serena; Legen, Julia; Takami, Tsuneaki; Shikanai, Toshiharu; Herrmann, Reinhold G; Meurer, Jörg

    2007-08-01

    The cytochrome b(6)f (Cyt b(6)f) complex in flowering plants contains nine conserved subunits, of which three, PetG, PetL, and PetN, are bitopic plastid-encoded low-molecular-weight proteins of largely unknown function. Homoplastomic knockout lines of the three genes have been generated in tobacco (Nicotiana tabacum 'Petit Havana') to analyze and compare their roles in assembly and stability of the complex. Deletion of petG or petN caused a bleached phenotype and loss of photosynthetic electron transport and photoautotrophy. Levels of all subunits that constitute the Cyt b(6)f complex were faintly detectable, indicating that both proteins are essential for the stability of the membrane complex. In contrast, DeltapetL plants accumulate about 50% of other Cyt b(6)f subunits, appear green, and grow photoautotrophically. However, DeltapetL plants show increased light sensitivity as compared to wild type. Assembly studies revealed that PetL is primarily required for proper conformation of the Rieske protein, leading to stability and formation of dimeric Cyt b(6)f complexes. Unlike wild type, phosphorylation levels of the outer antenna of photosystem II (PSII) are significantly decreased under state II conditions, although the plastoquinone pool is largely reduced in DeltapetL, as revealed by measurements of PSI and PSII redox states. This confirms the sensory role of the Cyt b(6)f complex in activation of the corresponding kinase. The reduced light-harvesting complex II phosphorylation did not affect state transition and association of light-harvesting complex II to PSI under state II conditions. Ferredoxin-dependent plastoquinone reduction, which functions in cyclic electron transport around PSI in vivo, was not impaired in DeltapetL.

  15. Synthesis of Mixed Tail Triphenylene Discotic Liquid Crystals:Molecular Symmetry and Oxygen-Atom Effect on the Stabilization of Columnar Mesophases

    Institute of Scientific and Technical Information of China (English)

    ZHAO Ke-Qing; HU Ping; WANG Bi-Qin; YU Wen-Hao; CHEN Hong-Mei; WANG Xin-Ling; SHIMIZU Yo

    2007-01-01

    Small change in chemical structure of discotic liquid crystals can cause big difference in their mesomorphism.Replacing of the alkoxy peripheral chains of triphenylene by oxygen-atom containing ester chains would result in novel mesomorphism. A series of mixed tail triphenylenes containing propoxyacetyloxy and alkoxy, abbreviated as C18H6(OCnH2n+1)3(OCOCH2OC3H7)3, n=4-8, and hexa(propyloxyacetyloxy)triphenylene, C18H6(OCOCH2OC3H7)6 were synthesized. Thermal gravimetry analysis (TGA) of three discogens showed that they had good thermal stability till 350℃. The mesomorphism was investigated through differential scanning calorimetry (DSC)and polarized optical microscopy (POM). The preliminary X-ray diffraction (XRD) results of one compound showed that it exhibited ordered hexagonal columnar (Colho) mesophase. These mixed tail triphenylene derivatives possessed much stable Colho mesophase and wider mesophase ranges than their hexaalkoxytriphenylene C18H6(OR)6 and hexaalkanoyloxytriphenylene C18H6(OCOR')6 analogues. The asymmetrical compounds 2,6,11-trialkoxy-3,7,10-tri(2-propyloxyacetyloxy)triphenylenes with n=5-8 displayed higher clearing points and wider temperature ranges than their symmetrical isomers 2,6,10-trialkoxy-3,7,11-tri(2-propyloxyacetyloxy)triphenylenes, while C18H6(OCOCH2OC3H7)6 had the highest clearing point due to the β-oxygen-atom effect.

  16. 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...

  17. 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.

  18. 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.

  19. 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

    2014-09-03

    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.

  20. Effects of Low-Molecular-Weight Fucoidan and High Stability Fucoxanthin on Glucose Homeostasis, Lipid Metabolism, and Liver Function in a Mouse Model of Type II Diabetes

    Directory of Open Access Journals (Sweden)

    Hong-Ting Victor Lin

    2017-04-01

    Full Text Available The combined effects of low-molecular-weight fucoidan (LMF and fucoxanthin (Fx in terms of antihyperglycemic, antihyperlipidemic, and hepatoprotective activities were investigated in a mouse model of type II diabetes. The intake of LMF, Fx, and LMF + Fx lowered the blood sugar and fasting blood sugar levels, and increased serum adiponectin levels. The significant decrease in urinary sugar was only observed in LMF + Fx supplementation. LMF and Fx had ameliorating effects on the hepatic tissue of db/db mice by increasing hepatic glycogen and antioxidative enzymes, and LMF was more effective than Fx at improving hepatic glucose metabolism. As for glucose and lipid metabolism in the adipose tissue, the expression of insulin receptor substrate (IRS-1, glucose transporter (GLUT, peroxisome proliferator-activated receptor gamma (PPARγ, and uncoupling protein (UCP-1 mRNAs in the adipose tissue of diabetic mice was significantly upregulated by Fx and LMF + Fx, and levels of inflammatory adipocytokines, such as adiponectin, tumor necrosis factor-α (TNF-α, and interleukin-6 (IL-6, were significantly modulated only by LMF + Fx supplementation. The efficacy of LMF + Fx supplementation on the decrease in urinary sugar and on glucose and lipid metabolism in the white adipose tissue of db/db mice was better than that of Fx or LMF alone, indicating the occurrence of a synergistic effect of LMF and Fx.

  1. Stability Functions

    CERN Document Server

    Burns, Daniel; Wang, Zuoqin

    2008-01-01

    In this article we discuss the role of stability functions in geometric invariant theory and apply stability function techniques to problems in toric geometry. In particular we show how one can use these techniques to recover results of Burns-Guillemin-Uribe and Shiffman-Tate-Zelditch on asymptotic properties of sections of holomorphic line bundles over toric varieties.

  2. Backstepping design for incremental stability

    CERN Document Server

    Zamani, Majid

    2010-01-01

    Stability is arguably one of the core concepts upon which our understanding of dynamical and control systems has been built. The related notion of incremental stability, however, has received much less attention until recently, when it was successfully used as a tool for the analysis and design of intrinsic observers, output regulation of nonlinear systems, frequency estimators, synchronization of coupled identical dynamical systems, symbolic models for nonlinear control systems, and bio-molecular systems. However, most of the existing controller design techniques provide controllers enforcing stability rather than incremental stability. Hence, there is a growing need to extend existing methods or develop new ones for the purpose of designing incrementally stabilizing controllers. In this paper, we develop a backstepping design approach for incremental stability. The effectiveness of the proposed method is illustrated by synthesizing a controller rendering a synchronous generator incrementally stable.

  3. 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.

  4. Stabilizing Niger

    DEFF Research Database (Denmark)

    Hahonou, Eric Komlavi

    international intervention in Niger. Their main objective is to secure their own strategic, economic and political interests by strengthening the Nigerien authorities through direct intervention and capacity building activities. For western states reinforcing state security institutions and stabilizing elite...

  5. Size-dependent shape and tilt transitions in In2O3 nanoislands grown on cubic Y-stabilized ZrO2(001) by molecular beam epitaxy.

    Science.gov (United States)

    Zhang, Kelvin H L; Bourlange, Anne; Egdell, Russell G; Collins, Stephen P; Bean, Richard J; Robinson, Ian K; Cowley, Roger A

    2012-08-28

    The growth of In(2)O(3) on cubic Y-stabilized ZrO(2)(001) by molecular beam epitaxy leads to formation of nanoscale islands which may tilt relative to the substrate in order to help accommodate the 1.7% tensile mismatch between the epilayer and the substrate. High-resolution synchrotron-based X-ray diffraction has been used in combination with atomic force microscopy to probe the evolution in island morphology, orientation, and tilt with island size. Very small islands formed at low substrate coverage are highly strained but exhibit no tilt, while intermediate islands are tilted randomly in all directions, giving rise to distinctive doughnut-shaped structure in three-dimensional reciprocal space isosurfaces. The largest islands with lateral sizes on the order of 1 μm tilt away from the four equivalent in-plane directions, giving three-dimensional scattering isosurfaces dominated by structure at the four corners of a square. Spatially resolved reciprocal space mapping using an X-ray beam with dimensions on the order of 1 μm suggests that the four-fold symmetry observed using a larger beam arises from averaging over an ensemble of islands, each with an individual tilt down one direction, rather than from the coexistence of differently tilted domains within a given island.

  6. Growth and stability of rocksalt Zn1-xMgxO epilayers and ZnO/MgO superlattice on MgO (100) substrate by molecular beam epitaxy.

    Science.gov (United States)

    Lu, C-Y James; Tu, Y-T; Yan, T; Trampert, A; Chang, L; Ploog, K H

    2016-06-07

    Zn1-xMgxO films with x = 0.04-0.50 grown on MgO (100) substrates by molecular beam epitaxy retain the rocksalt (rs) crystal structure and grow epitaxially for x ≥ 0.17. In addition, the rs-ZnO epilayer is observed to be stable up to a thickness of 5 nm and also in a ZnO/MgO superlattice sample. However, a portion of the superlattice has transformed to wurtzite (wz)-structure islands in a self-accommodated manner during growth. The transformation is a combination of a Bain distortion, an in-plane rotation of 14.5°, and a Peierls distortion, resulting in an orientation relationship of (100)rs//(101̄0)wz and 〈011〉rs ∼//〈1̄21̄3〉wz. In such a manner, the volume expansion is only necessary along the growth direction and the in-plane strains can be minimized. A negative pressure generated during the transformation of ZnO stabilizes the MgO into a wurtzite structure.

  7. 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.

  8. 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...

  9. 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....

  10. Stability of surface nanobubbles

    Science.gov (United States)

    Maheshwari, Shantanu; van der Hoef, Martin; Zhang, Xuehua; Lohse, Detlef

    2015-11-01

    We have studied the stability and dissolution of surface nanobubbles on the chemical heterogenous surface by performing Molecular Dynamics (MD) simulations of binary mixture consists of Lennard-Jones (LJ) particles. Recently our group has derived the exact expression for equilibrium contact angle of surface nanobubbles as a function of oversaturation of the gas concentration in bulk liquid and the lateral length of bubble. It has been showed that the contact line pinning and the oversaturation of gas concentration in bulk liquid is crucial in the stability of surface nanobubbles. Our simulations showed that how pinning of the three-phase contact line on the chemical heterogenous surface lead to the stability of the nanobubble. We have calculated the equilibrium contact angle by varying the gas concentration in bulk liquid and the lateral length of the bubble. Our results showed that the equilibrium contact angle follows the expression derived analytically by our group. We have also studied the bubble dissolution dynamics and showed the ''stick-jump'' mechanism which was also observed experimentally in case of dissolution of nanodrops.

  11. Statins in therapy: understanding their hydrophilicity, lipophilicity, binding to 3-hydroxy-3-methylglutaryl-CoA reductase, ability to cross the blood brain barrier and metabolic stability based on electrostatic molecular orbital studies.

    Science.gov (United States)

    Fong, Clifford W

    2014-10-06

    The atomic electrostatic potentials calculated by the CHELPG method have been shown to be sensitive indicators of the gas phase and solution properties of the statins. Solvation free energies in water, n-octanol and n-octane have been determined using the SMD solvent model. The percentage hydrophilicity and hydrophobicity (or lipophilicity) of the statins in solution have been determined using (a) the differences in solvation free energies between n-octanol and n-octane as a measure of hydrophilicity, and the solvation energy in octane as a measure of hydrophobicity (b) the sum of the atomic electrostatic charges on the hydrogen bonding and polar bonding nuclei of the common pharmacophore combined with a solvent measure of hydrophobicity, and (c) using the buried surface areas after statin binding to HMGCR to calculate the hydrophobicity of the bound statins. The data suggests that clinical definitions of statins as either "hydrophilic" or "lipophilic" based on experimental partition coefficients are misleading. An estimate of the binding energy between rosuvastatin and HMGCR has been made using: (a) a coulombic electrostatic interaction model, (b) the calculated desolvation and resolvation of the statin in water, and (c) the first shell transfer solvation energy as a proxy for the restructuring of the water molecules immediately adjacent to the active binding site of HMGCR prior to binding. Desolvation and resolvation of the statins before and after binding to HMGCR are major determinants of the energetics of the binding process. An analysis of the amphiphilic nature of lovastatin anion, acid and lactone and fluvastatin anion and their abilities to cross the blood brain barrier has indicated that this process may be dominated by desolvation and resolvation effects, rather than the statin molecular size or statin-lipid interactions within the bilayer. The ionization energy and electron affinity of the statins are sensitive physical indicators of the ease that the

  12. 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

  13. 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.

  14. Protein stability, flexibility and function

    DEFF Research Database (Denmark)

    Teilum, Kaare; Olsen, Johan G; Kragelund, Birthe B

    2011-01-01

    Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests for a de......Proteins rely on flexibility to respond to environmental changes, ligand binding and chemical modifications. Potentially, a perturbation that changes the flexibility of a protein may interfere with its function. Millions of mutations have been performed on thousands of proteins in quests...... for a delineation of the molecular details of their function. Several of these mutations interfered with the binding of a specific ligand with a concomitant effect on the stability of the protein scaffold. It has been ambiguous and not straightforward to recognize if any relationships exist between the stability...... of a protein and the affinity for its ligand. In this review, we present examples of proteins where changes in stability results in changes in affinity and of proteins where stability and affinity are uncorrelated. We discuss the possibility for a relationship between stability and binding. From the data...

  15. Erwin Schroedinger, Francis Crick and epigenetic stability.

    Science.gov (United States)

    Ogryzko, Vasily V

    2008-04-17

    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 led Schroedinger to promote the idea of a molecular code-script for explaining the stability of biological order.

  16. Erwin Schroedinger, Francis Crick and epigenetic stability

    Directory of Open Access Journals (Sweden)

    Ogryzko Vasily V

    2008-04-01

    Full Text Available Abstract 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 led Schroedinger to promote the idea of a molecular code-script for explaining the stability of biological order.

  17. 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.

  18. 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.

  19. 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.

  20. Functionalizable oligoprolines as molecular scaffolds.

    Science.gov (United States)

    Nagel, Yvonne A; Kuemin, Michael; Wennemers, Helma

    2011-01-01

    Azidoproline (Azp) containing oligoprolines are conformationally well-defined, helical molecular scaffolds that allow for facile functionalization. Within this article we describe the synthesis of Azp-containing oligoprolines and different strategies to introduce functional moieties. In addition, the influence of factors such as substituents at the y-position of proline as well as functional groups at the termini on the conformational stability of the molecular scaffolds are briefly presented.

  1. 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...

  2. Novel Antimicrobial Organic Thermal Stabilizer and Co-Stabilizer for Rigid PVC

    Directory of Open Access Journals (Sweden)

    Nadia A. Mohamed

    2012-07-01

    Full Text Available Biologically active N-benzoyl-4-(N-maleimido-phenylhydrazide (BMPH was synthesized and its structure was confirmed by elemental analysis and various spectral tools. It was examined as a thermal stabilizer and co-stabilizer for rigid poly (vinyl chloride at 180 °C in air. Blending BMPH with reference samples in different ratios greatly lengthens the thermal stability value and improves the extent of discoloration of PVC. TGA confirmed the improved stability of PVC in presence of the investigated organic stabilizer. GPC measurements were done to investigate the changes occurred in the molecular masses of the degraded samples of blank PVC and PVC in presence of the novel stabilizer. BMPH showed good antimicrobial activity towards two kinds of bacteria and two kinds of fungi.

  3. Virus engineering: functionalization and stabilization.

    Science.gov (United States)

    Mateu, Mauricio G

    2011-01-01

    Chemically and/or genetically engineered viruses, viral capsids and viral-like particles carry the promise of important and diverse applications in biomedicine, biotechnology and nanotechnology. Potential uses include new vaccines, vectors for gene therapy and targeted drug delivery, contrast agents for molecular imaging and building blocks for the construction of nanostructured materials and electronic nanodevices. For many of the contemplated applications, the improvement of the physical stability of viral particles may be critical to adequately meet the demanding physicochemical conditions they may encounter during production, storage and/or medical or industrial use. The first part of this review attempts to provide an updated general overview of the fast-moving, interdisciplinary virus engineering field; the second part focuses specifically on the modification of the physical stability of viral particles by protein engineering, an emerging subject that has not been reviewed before.

  4. 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.

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

    Directory of Open Access Journals (Sweden)

    Beata Żołnowska

    2016-06-01

    Full Text Available 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-ylbenzenesulfonamides 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.

  6. 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.

  7. 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...

  8. 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)....

  9. 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)

  10. 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....

  11. 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.

  12. 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

  13. Molecular dynamics

    NARCIS (Netherlands)

    Bergstra, J.A.; Bethke, I.

    2002-01-01

    Molecular dynamics is a model for the structure and meaning of object based programming systems. In molecular dynamics the memory state of a system is modeled as a fluid consisting of a collection of molecules. Each molecule is a collection of atoms with bindings between them. A computation is model

  14. Influence of water on anharmonicity, stability, and vibrational energy distribution of hydrogen-bonded adducts in atmospheric reactions: case study of the OH + isoprene reaction intermediate using ab initio molecular dynamics.

    Science.gov (United States)

    Dietrick, Scott M; Pacheco, Alexander B; Phatak, Prasad; Stevens, Philip S; Iyengar, Srinivasan S

    2012-01-12

    The effect of water on the stability and vibrational states of a hydroxy-isoprene adduct is probed through the introduction of 1-15 water molecules. It is found that when a static nuclear harmonic approximation is invoked there is a substantial red-shift of the alcohol O-H stretch (of the order of 800 cm(-1)) as a result of introduction of water. When potential energy surface sampling and associated anharmonicities are introduced through finite temperature ab initio dynamics, this hydroxy-isoprene OH stretch strongly couples with all the water vibrational modes as well as the hydroxy-isoprene OH bend modes. A new computational technique is introduced to probe the coupling between these modes. The method involves a two-dimensional, time-frequency analysis of the finite temperature vibrational properties. Such an analysis not only provides information about the modes that are coupled as a result of finite-temperature analysis, but also the temporal evolution of such coupling.

  15. 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.

  16. Stability and instability of the isoelectronic UO2(2+) and PaO2+ actinyl oxo-cations in aqueous solution from density functional theory based molecular dynamics.

    Science.gov (United States)

    Spezia, Riccardo; Siboulet, Bertrand; Abadie, Sacha; Vuilleumier, Rodolphe; Vitorge, Pierre

    2011-04-07

    In this work, Pa(V) monocations 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: [PaO(2)(H(2)O)(5)](+)(aq), [Pa(OH)(4)(H(2)O)(2)](+)(aq), [PaO(OH)(2)(H(2)O)(4)](+)(aq), and [Pa(OH)(4)(H(2)O)(3)](+)(aq). On the other hand, in the case of U(VI) only the uranyl, [UO(2)(H(2)O)(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 oxocations 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, protactinyl is found to have between 2 and 3 hydrogen bonds per oxygen atom while uranyl has between zero and one.

  17. Molecular geometry

    CERN Document Server

    Rodger, Alison

    1995-01-01

    Molecular Geometry discusses topics relevant to the arrangement of atoms. The book is comprised of seven chapters that tackle several areas of molecular geometry. Chapter 1 reviews the definition and determination of molecular geometry, while Chapter 2 discusses the unified view of stereochemistry and stereochemical changes. Chapter 3 covers the geometry of molecules of second row atoms, and Chapter 4 deals with the main group elements beyond the second row. The book also talks about the complexes of transition metals and f-block elements, and then covers the organometallic compounds and trans

  18. Polyhedral (in-)stability of protein crystals

    Science.gov (United States)

    Nanev, Christo N.; Penkova, Anita N.

    2002-04-01

    The polyhedral (in-)stability of monoclinic hen-egg white lysozyme (HEWL) crystals, grown by means of PEG-6000, and that of orthorhombic trypsin crystals has been investigated experimentally. On the basis of a quantitative theoretical analysis, it is compared with the polyhedral (in-)stability of tetragonal HEWL and cubic ferritin crystals. The unambiguous conclusion is that the phenomenon is due to the diffusive supply of matter. This conclusion is also supported by the fact that the phenomenon has common features for both proteins and small molecular crystals.

  19. 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...

  20. 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…

  1. Triphenylphosphine Stabilized Silver Carboxylates

    Institute of Scientific and Technical Information of China (English)

    Jian Lin HAN; Ying Zhong SHEN; Yi PAN

    2005-01-01

    A series of novel triphenylphosphine stabilized silver carboxylates, potential precursors for CVD growth of ultrafast interconnection link in microelectronic devices, have been prepared and characterized.

  2. Theoretic Prediction of Heat Decomposition Stability for General Organic Molecular or Drug%普通有机分子或药物热分解稳定性的理论预测

    Institute of Scientific and Technical Information of China (English)

    丁晓琴; 丁俊杰; 李大禹; 孙杨; 陈冀胜

    2012-01-01

    Density functional theory(DFT) calculations at the B3LYP/6-31G+(d,p) level were carried out for 32 random selected compounds in training set and 43 ones in testing set after determining the experimental half decomposition temperature Td( 1/2) or partial ones from literature. The calculated quantum chemical descriptors were used to construct quantitative structure-property relationship (QSPR) models of quadrupole moments (Q(u)) parameters with the molar thermal decomposition function Yd(1/2). The equation of QSPR is Yd( 1/2)= -8. 65747-3. 8954Q(u) for training set possessing a correlation coefficient of r2 = -0.99297, cross validation XV-r2=0. 99188 and F-test=4237. 343321. Further, the proposed model is validated by examining 43 compounds in testing set with a correlation coefficient of 0. 92304 between prediction and experiment Td( 1/2) values and a correlation coefficient of 0. 99345 between prediction and experiment Yd values. The selected compounds rank well with a certain space distribution of structure descriptors. The developed equation can be used to predict the heat decomposition stability for new designed or synthesized compounds or drugs in virtual screening.%采用密度泛函理论方法,在B3 LYP/6-31 +G(d,p)水平上,对任意选定的32个有机化合物或药物进行最低能量构象优化和结构参数理论计算.建立了四极矩参数Qü与半数摩尔热分解函数Yd(1/2)的相关方程,其定量构性关系(QSPR)方程为Yd(1/2)=-8.65747-3.8954Qü,相关系数为r2=-0.99297,交叉验证相关系数为XV-r2 =0.99188,F检验结果为4237.343321.训练集化合物的半数分解温度Td(1/2)的平均绝对预测误差(AVEDEV)为14.70 K.进一步利用该方程对测试集中43个分子进行预测验证,Td(1/2)的预测值与实验值的相关系数为0.92304,Yd的预测值与实验值的相关系数为0.99345,证实了所建立方法的可靠性.结构差异性分析表明,训练集和测试集中的化合物均较均

  3. 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.

  4. Ornithopter flight stabilization

    Science.gov (United States)

    Dietl, John M.; Garcia, Ephrahim

    2007-04-01

    The quasi-steady aerodynamics model and the vehicle dynamics model of ornithopter flight are explained, and numerical methods are described to capture limit cycle behavior in ornithopter flight. The Floquet method is used to determine stability in forward flight, and a linear discrete-time state-space model is developed. This is used to calculate stabilizing and disturbance-rejecting controllers.

  5. 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....

  6. 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....

  7. Visual attention and stability

    NARCIS (Netherlands)

    Mathot, Sebastiaan; Theeuwes, Jan

    2011-01-01

    In the present review, we address the relationship between attention and visual stability. Even though with each eye, head and body movement the retinal image changes dramatically, we perceive the world as stable and are able to perform visually guided actions. However, visual stability is not as co

  8. Basic principles of stability.

    Science.gov (United States)

    Egan, William; Schofield, Timothy

    2009-11-01

    An understanding of the principles of degradation, as well as the statistical tools for measuring product stability, is essential to management of product quality. Key to this is management of vaccine potency. Vaccine shelf life is best managed through determination of a minimum potency release requirement, which helps assure adequate potency throughout expiry. Use of statistical tools such a least squares regression analysis should be employed to model potency decay. The use of such tools provides incentive to properly design vaccine stability studies, while holding stability measurements to specification presents a disincentive for collecting valuable data. The laws of kinetics such as Arrhenius behavior help practitioners design effective accelerated stability programs, which can be utilized to manage stability after a process change. Design of stability studies should be carefully considered, with an eye to minimizing the variability of the stability parameter. In the case of measuring the degradation rate, testing at the beginning and the end of the study improves the precision of this estimate. Additional design considerations such as bracketing and matrixing improve the efficiency of stability evaluation of vaccines.

  9. The statistical stability phenomenon

    CERN Document Server

    Gorban, Igor I

    2017-01-01

    This monograph investigates violations of statistical stability of physical events, variables, and processes and develops a new physical-mathematical theory taking into consideration such violations – the theory of hyper-random phenomena. There are five parts. The first describes the phenomenon of statistical stability and its features, and develops methods for detecting violations of statistical stability, in particular when data is limited. The second part presents several examples of real processes of different physical nature and demonstrates the violation of statistical stability over broad observation intervals. The third part outlines the mathematical foundations of the theory of hyper-random phenomena, while the fourth develops the foundations of the mathematical analysis of divergent and many-valued functions. The fifth part contains theoretical and experimental studies of statistical laws where there is violation of statistical stability. The monograph should be of particular interest to engineers...

  10. Stabilizing Randomly Switched Systems

    CERN Document Server

    Chatterjee, Debasish

    2008-01-01

    This article is concerned with stability analysis and stabilization of randomly switched systems under a class of switching signals. The switching signal is modeled as a jump stochastic (not necessarily Markovian) process independent of the system state; it selects, at each instant of time, the active subsystem from a family of systems. Sufficient conditions for stochastic stability (almost sure, in the mean, and in probability) of the switched system are established when the subsystems do not possess control inputs, and not every subsystem is required to be stable. These conditions are employed to design stabilizing feedback controllers when the subsystems are affine in control. The analysis is carried out with the aid of multiple Lyapunov-like functions, and the analysis results together with universal formulae for feedback stabilization of nonlinear systems constitute our primary tools for control design

  11. 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.

  12. 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

  13. Molecular pathways

    DEFF Research Database (Denmark)

    Cox, Thomas R; Erler, Janine Terra

    2014-01-01

    that 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....

  14. Control of Collagen Triple Helix Stability by Phosphorylation.

    Science.gov (United States)

    Acevedo-Jake, Amanda M; Ngo, Daniel H; Hartgerink, Jeffrey D

    2017-03-10

    The phosphorylation of the collagen triple helix plays an important role in collagen synthesis, assembly, signaling, and immune response, although no reports detailing the effect this modification has on the structure and stability of the triple helix exist. Here we investigate the changes in stability and structure resulting from the phosphorylation of collagen. Additionally, the formation of pairwise interactions between phosphorylated residues and lysine is examined. In all tested cases, phosphorylation increases helix stability. When charged-pair interactions are possible, stabilization via phosphorylation can play a very large role, resulting inasmuch as a 13.0 °C increase in triple helix stability. Two-dimensional NMR and molecular modeling are used to study the local structure of the triple helix. Our results suggest a mechanism of action for phosphorylation in the regulation of collagen and also expand upon our understanding of pairwise amino acid stabilization of the collagen triple helix.

  15. 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

  16. 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.

  17. Stability analysis of ferrofluids

    Directory of Open Access Journals (Sweden)

    Katharina Duda

    2015-09-01

    Full Text Available Superparamagnetic iron oxides (SPIOs are used as tracer for the new imaging technique Magnetic Particle Imaging. The stability of ferrofluids for medical application has a great importance, in addition to the particle size. The shell material, which protects the iron core prior from agglomeration and sedimentation, can be degraded by various processes. Another important aspect of stability is the constant performance of magnetisation. Therefore, the measurement of the magnetisation of the particles must be controlled in order to ensure the stability of the samples.

  18. Life raft stabilizer

    Science.gov (United States)

    Radnofsky, M. I.; Barnett, J. H., Jr.; Harrison, F. L.; Marak, R. J. (Inventor)

    1973-01-01

    An improved life raft stabilizer for reducing rocking and substantially precluding capsizing is discussed. The stabilizer may be removably attached to the raft and is defined by flexible side walls which extend a considerable depth downwardly to one another in the water. The side walls, in conjunction with the floor of the raft, form a ballast enclosure. A weight is placed in the bottom of the enclosure and water port means are provided in the walls. Placement of the stabilizer in the water allows the weighted bottom to sink, producing submerged deployment thereof and permitting water to enter the enclosure through the port means, thus forming a ballast for the raft.

  19. Metallic alloy stability studies

    Science.gov (United States)

    Firth, G. C.

    1983-01-01

    The dimensional stability of candidate cryogenic wind tunnel model materials was investigated. Flat specimens of candidate materials were fabricated and cryo-cycled to assess relative dimensional stability. Existing 2-dimensional airfoil models as well as models in various stages of manufacture were also cryo-cycled. The tests indicate that 18 Ni maraging steel offers the greatest dimensional stability and that PH 13-8 Mo stainless steel is the most stable of the stainless steels. Dimensional stability is influenced primarily by metallurgical transformations (austenitic to martensitic) and manufacturing-induced stresses. These factors can be minimized by utilization of stable alloys, refinement of existing manufacturing techniques, and incorporation of new manufacturing technologies.

  20. 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.

  1. 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.

  2. Molecular cytogenetics.

    Science.gov (United States)

    Carpenter, N J

    2001-09-01

    In the past decade, clinical cytogenetics has undergone remarkable advancement as molecular biology techniques have been applied to conventional chromosome analysis. The limitations of conventional banding analysis in the accurate diagnosis and interpretation of certain chromosome abnormalities have largely been overcome by these new technologies, which include fluorescence in situ hybridization (FISH), comparative genomic hybridization (CGH), and multicolor FISH (M-FISH, SKY, and Rx-FISH). Clinical applications include diagnosis of microdeletion and microduplication syndromes, detection of subtelomeric rearrangements in idiopathic mental retardation, identification of marker and derivative chromosomes, prenatal diagnosis of trisomy syndromes, and gene rearrangements and gene amplification in tumors. Molecular cytogenetic methods have expanded the possibilities for precise genetic diagnoses, which are extremely important for clinical management of patients and appropriate counseling of their families.

  3. Molecular Fountain

    Science.gov (United States)

    Cheng, Cunfeng; van der Poel, Aernout P. P.; Jansen, Paul; Quintero-Pérez, Marina; Wall, Thomas E.; Ubachs, Wim; Bethlem, Hendrick L.

    2016-12-01

    The resolution of any spectroscopic or interferometric experiment is ultimately limited by the total time a particle is interrogated. Here we demonstrate the first molecular fountain, a development which permits hitherto unattainably long interrogation times with molecules. In our experiments, ammonia molecules are decelerated and cooled using electric fields, launched upwards with a velocity between 1.4 and 1.9 m/s and observed as they fall back under gravity. A combination of quadrupole lenses and bunching elements is used to shape the beam such that it has a large position spread and a small velocity spread (corresponding to a transverse temperature of free fall, while being strongly focused at the detection region. The molecules are in free fall for up to 266 ms, making it possible, in principle, to perform sub-Hz measurements in molecular systems and paving the way for stringent tests of fundamental physics theories.

  4. Stability and stabilization of industrial biocatalysts

    OpenAIRE

    Fattor, Diana

    2012-01-01

    Catalytic potential of enzymes is not fully exploited at industrial level and in chemistry due to technical difficulties and long time required for development of new processes. The main issues are: 1) The choice of the biocatalyst and the planning of reaction conditions still relies largely on empirical approaches, leading to long experimental studies; 2) There is still a short knowledge about molecular phenomena occurring in the microenvironment surrounding the enzyme and affecting...

  5. PFP solution stabilization

    Energy Technology Data Exchange (ETDEWEB)

    Aftanas, B.L.

    1996-04-30

    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.

  6. METHOD FOR STABILIZING KLYSTRONS

    Science.gov (United States)

    Magnuson, D.W.; Smith, D.F.

    1959-04-14

    High-frequency oscillators for the generation of microwaves, particularly a system for stabilizing frequency-modulated klystron oscillators of the reflex type, are described. The system takos advantage of the fact that a change in oscillator frequency will alter the normal phase displacement between the cavity and its modulator, creating an error voltage which is utilized to regulate the frequency of the oscillator and stabilize it.

  7. 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.

  8. Shearing stability of lubricants

    Science.gov (United States)

    Shiba, Y.; Gijyutsu, G.

    1984-01-01

    Shearing stabilities of lubricating oils containing a high mol. wt. polymer as a viscosity index improver were studied by use of ultrasound. The oils were degraded by cavitation and the degradation generally followed first order kinetics with the rate of degradation increasing with the intensity of the ultrasonic irradiation and the cumulative energy applied. The shear stability was mainly affected by the mol. wt. of the polymer additive and could be determined in a short time by mechanical shearing with ultrasound.

  9. Shearing stability of lubricants

    Energy Technology Data Exchange (ETDEWEB)

    Shiba, Y.; Gijyutsu, G.

    1984-03-01

    Shearing stabilities of lubricating oils containing a high mol. wt. polymer as a viscosity index improver were studied by use of ultrasound. The oils were degraded by cavitation and the degradation generally followed first order kinetics with the rate of degradation increasing with the intensity of the ultrasonic irradiation and the cumulative energy applied. The shear stability was mainly affected by the mol. wt. of the polymer additive and could be determined in a short time by mechanical shearing with ultrasound.

  10. Tetraphenylborate Solids Stability Tests

    Energy Technology Data Exchange (ETDEWEB)

    Walker, D.D. [Westinghouse Savannah River Company, AIKEN, SC (United States)

    1997-06-25

    Tetraphenylborate solids are a potentially large source of benzene in the slurries produced in the In-Tank Precipitation (ITP) 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. This report discusses current testing of the stability of tetraphenylborate solids.

  11. Food Fortification Stability Study

    Science.gov (United States)

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

    2017-01-01

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

  12. 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.

  13. 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.

  14. Molecular scale

    Directory of Open Access Journals (Sweden)

    Christopher H. Childers

    2016-03-01

    Full Text Available This manuscript demonstrates the molecular scale cure rate dependence of di-functional epoxide based thermoset polymers cured with amines. A series of cure heating ramp rates were used to determine the influence of ramp rate on the glass transition temperature (Tg and sub-Tg transitions and the average free volume hole size in these systems. The networks were comprised of 3,3′-diaminodiphenyl sulfone (33DDS and diglycidyl ether of bisphenol F (DGEBF and were cured at ramp rates ranging from 0.5 to 20 °C/min. Differential scanning calorimetry (DSC and NIR spectroscopy were used to explore the cure ramp rate dependence of the polymer network growth, whereas broadband dielectric spectroscopy (BDS and free volume hole size measurements were used to interrogate networks’ molecular level structural variations upon curing at variable heating ramp rates. It was found that although the Tg of the polymer matrices was similar, the NIR and DSC measurements revealed a strong correlation for how these networks grow in relation to the cure heating ramp rate. The free volume analysis and BDS results for the cured samples suggest differences in the molecular architecture of the matrix polymers due to cure heating rate dependence.

  15. Prediction of Factors Determining Changes in Stability in Protein Mutants

    OpenAIRE

    Parthiban, Vijayarangakannan

    2006-01-01

    Analysing the factors behind protein stability is a key research topic in molecular biology and has direct implications on protein structure prediction and protein-protein docking solutions. Protein stability upon point mutations were analysed using a distance dependant pair potential representing mainly through-space interactions and torsion angle potential representing neighbouring effects as a basic statistical mechanical setup for the analysis. The synergetic effect of accessible surface ...

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

    DEFF Research Database (Denmark)

    Christensen, Niels Johan; Kepp, Kasper Planeta

    2013-01-01

    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...

  17. Stabilization of molecular lanthanide polysulfides by bulky scorpionate ligands.

    Science.gov (United States)

    Kühling, Marcel; McDonald, Robert; Liebing, Phil; Hilfert, Liane; Ferguson, Michael J; Takats, Josef; Edelmann, Frank T

    2016-07-07

    Well-defined lanthanide polysulfide complexes containing S4(2-) and S5(2-) ligands, the samarium(iii) pentasulfide complex Sm(Tp(iPr2))(κ(1)-3,5-(i)Pr2Hpz)(S5) and the tetrasulfide-bridged binuclear ytterbium(iii) complex (μ-S4)[Yb(Tp(iPr2))(κ(1)-3,5-(i)Pr2Hpz)(κ(2)-3,5-(i)Pr2pz)]2 (Tp(iPr2) = hydro-tris(3,5-diisopropylpyrazolyl)borate), have been synthesized and structurally characterized by single-crystal X-ray diffraction.

  18. Development of Capsular Adhesive Systems and Evaluation of Their Stability.

    Science.gov (United States)

    1985-07-26

    AD-A159 913 DEVELOPMENT OF CAPSULAR ADHESIVE SYSTEMS AND EVALUATION ii OF THEIR STABILIT..(I) INSTITUTO NACIONAL OE TECNICA AEROESPACIRL MADRID...by polymerization of some low molecular monomeric consti- tuents, partially solubilized in the aqueous phase. The hazy liquid was discarded by...incomplete solubility of Loctite 270, it is assumed that the insoluble portion of this adhesive 5 concerns the high molecular polymeric constituent, inclu

  19. Molecular plasmonics

    CERN Document Server

    Fritzsche, Wolfgang

    2014-01-01

    Adopting a novel approach, this book provides a unique ""molecular perspective"" on plasmonics, concisely presenting the fundamentals and applications in a way suitable for beginners entering this hot field as well as for experienced researchers and practitioners. It begins by introducing readers to the optical effects that occur at the nanoscale and particularly their modification in the presence of biomolecules, followed by a concise yet thorough overview of the different methods for the actual fabrication of nanooptical materials. Further chapters address the relevant nanooptics, as well as

  20. Molecular nanomagnets

    CERN Document Server

    Gatteschi, Dante; Villain, Jacques

    2006-01-01

    Nanomagnetism is a rapidly expanding area of research which appears to be able to provide novel applications. Magnetic molecules are at the very bottom of the possible size of nanomagnets and they provide a unique opportunity to observe the coexistence of classical and quantum properties. The discovery in the early 90's that a cluster comprising twelve manganese ions shows hysteresis of molecular origin, and later proved evidence of quantum effects, opened a new research area whichis still flourishing through the collaboration of chemists and physicists. This book is the first attempt to cover

  1. Thermal stability of collagen triple helix.

    Science.gov (United States)

    Xu, Yujia

    2009-01-01

    Chief among the challenges of characterizing the thermal stability of the collagen triple helix are the lack of the reversibility of the thermal transition and the presence of multiple folding-unfolding steps during the thermal transition which rarely follows the simple two-state, all-or-none mechanism. Despite of the difficulties inherited in the quantitative depiction of the thermal transition of collagen, biophysical studies combined with proteolysis and mutagenesis approaches using full-chain collagens, short synthetic peptides, and recombinant collagen fragments have revealed molecular features of the thermal unfolding of the subdomains of collagen and led to a better understanding of the diverse biological functions of this versatile protein. The subdomain of collagen generally refers to a segment of the long, rope-like triple helical molecule that can unfold cooperatively as an independent unit whose properties (their size, location, and thermal stability) are considered essential for the molecular recognition during the self-assembly of collagen and during the interactions of collagen with other macromolecules. While the unfolding of segments of the triple helix at temperatures below the apparent melting temperature of the molecule has been used to interpret much of the features of the thermal unfolding of full-chain collagens, the thermal studies of short, synthetic peptides have firmly established the molecular basis of the subdomains by clearly demonstrating the close dependence of the thermal stability of a triple helix on the constituent amino acid residues at the X and the Y positions of the characteristic Gly-X-Y repeating sequence patterns of the triple helix. Studies using recombinant collagen fragments further revealed that in the context of the long, linear molecule, the stability of a segment of the triple helix is also modulated by long-range impact of the local interactions such as the interchain salt bridges. Together, the combined approaches

  2. Stability and rupture of archaebacterial cell membrane: a model study.

    Science.gov (United States)

    Li, Shuangyang; Zheng, Fengxian; Zhang, Xianren; Wang, Wenchuan

    2009-01-29

    It is known that the thermoacidophilic archaebacterium Sulfolobus acidocaldarius can grow in hot springs at 65-80 degrees C and live in acidic environments (pH 2-3); however, the origin of its unusual thermal stability remains unclear. In this work, using a vesicle as a model, we study the thermal stability and rupture of archaebacterial cell membrane. We perform a simulation investigation of the structure-property relationship of monolayer membrane formed by bolaform lipids and compare it with that of bilayer membrane formed by monopolar lipids. The origin of the unusually thermal stability of archaebacterial cell and the mechanism for its rupture are presented in molecular details.

  3. 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.

  4. Evolutionary stability of sex chromosomes in snakes

    Science.gov (United States)

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

    2015-01-01

    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. PMID:26702042

  5. 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.

  6. Marital stability and repartnering

    DEFF Research Database (Denmark)

    Martins, Mariana V; Costa, Patrício; Peterson, Brennan D

    2014-01-01

    starting a new cycle of fertility treatment and observed for a 5-year period of unsuccessful treatments. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): Marital stability and infertility-related stress. RESULT(S): The majority of patients (86%) remained with their initial partner, but 14% of participants...... separated and repartnered while pursuing fertility treatments. Marital stability significantly predicted the initial status of infertility stress and infertility stress growth levels. Specifically, patients who repartnered had higher infertility stress levels at all time points compared with those who...... a second union have higher initial levels of stress in their original relationship and higher changes in stress levels over the course of treatments. These findings suggest that high infertility-related stress levels before entering fertility treatment can negatively affect the stability of marital...

  7. D-Moduli Stabilization

    CERN Document Server

    Giedt, J

    2002-01-01

    The matter sector of four-dimensional effective supergravity models obtained from the weakly coupled heterotic string contains many moduli. In particular, flat directions of the D-term part of the scalar potential in the presence of an anomalous U(1) give rise to massless chiral multiplets which have been referred to elsewhere as D-moduli. The stabilization of these moduli is necessary for the determination of the large vacuum expectation values of complex scalar fields induced by the corresponding Fayet-Illiopoulos term. This stabilization is of phenomenological importance since these background values determine the effective theory below the scale of the anomalous U(1) symmetry breaking. In some simple models we illustrate the stabilization of these moduli due to the nonperturbative dynamics associated with gaugino condensation in a hidden sector. We find that background field configurations which are stable above the condensation scale no longer represent global minima once dynamical supersymmetry breaking...

  8. Molecular spintronics.

    Science.gov (United States)

    Sanvito, Stefano

    2011-06-01

    The electron spin made its debut in the device world only two decades ago but today our ability of detecting the spin state of a moving electron underpins the entire magnetic data storage industry. This technological revolution has been driven by a constant improvement in our understanding on how spins can be injected, manipulated and detected in the solid state, a field which is collectively named Spintronics. Recently a number of pioneering experiments and theoretical works suggest that organic materials can offer similar and perhaps superior performances in making spin-devices than the more conventional inorganic metals and semiconductors. Furthermore they can pave the way for radically new device concepts. This is Molecular Spintronics, a blossoming research area aimed at exploring how the unique properties of the organic world can marry the requirements of spin-devices. Importantly, after a first phase, where most of the research was focussed on exporting the concepts of inorganic spintronics to organic materials, the field has moved to a more mature age, where the exploitation of the unique properties of molecules has begun to emerge. Molecular spintronics now collects a diverse and interdisciplinary community ranging from device physicists to synthetic chemists to surface scientists. In this critical review, I will survey this fascinating, rapidly evolving, field with a particular eye on new directions and opportunities. The main differences and challenges with respect to standard spintronics will be discussed and so will be the potential cross-fertilization with other fields (177 references).

  9. Stabilization of reactive species by supramolecular encapsulation.

    Science.gov (United States)

    Galan, Albano; Ballester, Pablo

    2016-03-21

    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.

  10. Stability of boundary measures

    CERN Document Server

    Chazal, Frédéric; Mérigot, Quentin

    2007-01-01

    We introduce the boundary measure at scale r of a compact subset of the n-dimensional Euclidean space. We show how it can be computed for point clouds and suggest these measures can be used for feature detection. The main contribution of this work is the proof a quantitative stability theorem for boundary measures using tools of convex analysis and geometric measure theory. As a corollary we obtain a stability result for Federer's curvature measures of a compact, allowing to compute them from point-cloud approximations of the compact.

  11. 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

  12. 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

  13. 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.

  14. A stabilized pairing functional

    CERN Document Server

    Erler, J; Reinhard, P --G

    2008-01-01

    We propose a modified pairing functional for nuclear structure calculations which avoids the abrupt phase transition between pairing and non-pairing states. The intended application is the description of nuclear collective motion where the smoothing of the transition is compulsory to remove singularities. The stabilized pairing functional allows a thoroughly variational formulation, unlike the Lipkin-Nogami (LN) scheme which is often used for the purpose of smoothing. First applications to nuclear ground states and collective excitations prove the reliability and efficiency of the proposed stabilized pairing.

  15. 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.

  16. 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

  17. Increasing entropy for colloidal stabilization

    Science.gov (United States)

    Mo, Songping; Shao, Xuefeng; Chen, Ying; Cheng, Zhengdong

    2016-11-01

    Stability is of paramount importance in colloidal applications. Attraction between colloidal particles is believed to lead to particle aggregation and phase separation; hence, stability improvement can be achieved through either increasing repulsion or reducing attraction by modifying the fluid medium or by using additives. Two traditional mechanisms for colloidal stability are electrostatic stabilization and steric stabilization. However, stability improvement by mixing attractive and unstable particles has rarely been considered. Here, we emphasize the function of mixing entropy in colloidal stabilization. Dispersion stability improvement is demonstrated by mixing suspensions of attractive nanosized titania spheres and platelets. A three-dimensional phase diagram is proposed to illustrate the collaborative effects of particle mixing and particle attraction on colloidal stability. This discovery provides a novel method for enhancing colloidal stability and opens a novel opportunity for engineering applications.

  18. 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…

  19. Orbit Stabilization of Nanosat

    Energy Technology Data Exchange (ETDEWEB)

    JOHNSON,DAVID J.

    1999-12-01

    An algorithm is developed to control a pulsed {Delta}V thruster on a small satellite to allow it to fly in formation with a host satellite undergoing time dependent atmospheric drag deceleration. The algorithm uses four short thrusts per orbit to correct for differences in the average radii of the satellites due to differences in drag and one thrust to symmetrize the orbits. The radial difference between the orbits is the only input to the algorithm. The algorithm automatically stabilizes the orbits after ejection and includes provisions to allow azimuthal positional changes by modifying the drag compensation pulses. The algorithm gives radial and azimuthal deadbands of 50 cm and 3 m for a radial measurement accuracy of {+-} 5 cm and {+-} 60% period variation in the drag coefficient of the host. Approaches to further reduce the deadbands are described. The methodology of establishing a stable orbit after ejection is illustrated in an appendix. The results show the optimum ejection angle to minimize stabilization thrust is upward at 86{sup o} from the orbital velocity. At this angle the stabilization velocity that must be supplied by the thruster is half the ejection velocity. An ejection velocity of 0.02 m/sat 86{sup o} gives an azimuthal separation after ejection and orbit stabilization of 187 m. A description of liquid based gas thrusters suitable for the satellite control is included in an appendix.

  20. Electronic Stability Control

    Science.gov (United States)

    2013-12-05

    relationship between the steering wheel angle and lateral acceleration varies among vehicles because of differences in steering gear ratios, suspension...on-road, untripped truck rollovers by automatically decelerating the vehicle by applying the foundation brakes and reducing engine torque output...attributes: (1) Augments vehicle directional stability by applying and adjusting vehicle brake torques individually at each wheel position on at least

  1. Moral Hazard and Stability

    DEFF Research Database (Denmark)

    Tumennasan, Norovsambuu

    2014-01-01

    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...

  2. Stability through cycles

    NARCIS (Netherlands)

    E.A. de Groot (Bert); Ph.H.B.F. Franses (Philip Hans)

    2006-01-01

    textabstractEconomic variables like GDP growth, employment, interest rates and consumption show signs of cyclical behavior. Many variables display multiple cycles, with lengths ranging in between 5 to even up to 100 years. We argue that multiple cycles can be associated with long-run stability of th

  3. Stability through cycles

    NARCIS (Netherlands)

    Groot, de E.A. (Bert); Franses, P.H.P.H.

    2008-01-01

    Economic variables like GDP growth, employment, interest rates and consumption show signs of cyclical behavior. Many variables display multiple cycles, with periods ranging in between 5 to even up to 100 years. We argue that multiple cycles can be associated with long-run stability of the economic s

  4. Stability through cycles

    NARCIS (Netherlands)

    Groot, de E.A. (Bert); Franses, P.H.P.H.

    2006-01-01

    Economic variables like GDP growth, employment, interest rates and consumption show signs of cyclical behavior. Many variables display multiple cycles, with lengths ranging in between 5 to even up to 100 years. We argue that multiple cycles can be associated with long-run stability of the economic s

  5. 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.

  6. APPROACHES TO ENGINEER STABILITY OF BEETLE LUCIFERASES

    Directory of Open Access Journals (Sweden)

    Mikhail I. 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.

  7. All-carbon molecular tunnel junctions.

    Science.gov (United States)

    Yan, Haijun; Bergren, Adam Johan; McCreery, Richard L

    2011-11-30

    This Article explores the idea of using nonmetallic contacts for molecular electronics. Metal-free, all-carbon molecular electronic junctions were fabricated by orienting a layer of organic molecules between two carbon conductors with high yield (>90%) and good reproducibility (rsd of current density at 0.5 V carbon devices exhibit current density-voltage (J-V) behavior similar to those with metallic Cu top contacts. However, the all-carbon devices display enhanced stability to bias extremes and greatly improved thermal stability. Completed carbon/nitroazobenzene(NAB)/carbon junctions can sustain temperatures up to 300 °C in vacuum for 30 min and can be scanned at ±1 V for at least 1.2 × 10(9) cycles in air at 100 °C without a significant change in J-V characteristics. Furthermore, these all-carbon devices can withstand much higher voltages and current densities than can Cu-containing junctions, which fail upon oxidation and/or electromigration of the copper. The advantages of carbon contacts stem mainly from the strong covalent bonding in the disordered carbon materials, which resists electromigration or penetration into the molecular layer, and provides enhanced stability. These results highlight the significance of nonmetallic contacts for molecular electronics and the potential for integration of all-carbon molecular junctions with conventional microelectronics.

  8. 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

  9. 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.

  10. Stay Wet, Stay Stable? How Internal Water Helps Stability of Thermophilic Proteins

    OpenAIRE

    Chakraborty, Debashree; Taly, Antoine; Sterpone, Fabio

    2015-01-01

    We present a systematic computational investigation of the internal hydration of a set of homologous proteins of different stability content and molecular complexities. The goal of the study is to verify whether structural water can be part of the molecular mechanisms ensuring enhanced stability in thermophilic enzymes. Our free energy calculations show that internal hydration in the thermophilic variants is generally more favourable and that the cumulated effect of wetting multiple sites res...

  11. Molecular recognition by gold, silver and copper nanoparticles

    OpenAIRE

    2013-01-01

    The intrinsic physical properties of the noble metal nanoparticles, which are highly sensitive to the nature of their local molecular environment, make such systems ideal for the detection of molecular recognition events. The current review describes the state of the art concerning molecular recognition of Noble metal nanoparticles. In the first part the preparation of such nanoparticles is discussed along with methods of capping and stabilization. A brief discussion of the three common metho...

  12. Modification and investigation of silica particles as a foam stabilizer

    Science.gov (United States)

    Zhu, Qian; Zhou, Hua-lei; Song, Ying-xiao; Chang, Zhi-dong; Li, Wen-jun

    2017-02-01

    As a solid foam stabilizer, spherical silica particles with diameters ranging from 150 to 190 nm were prepared via an improved Stöber method and were subsequently modified using three different silane coupling agents to attain the optimum surface hydrophobicity of the particles. Fourier transform infrared (FTIR) spectra and the measured contact angles were used to characterize the surface properties of the prepared particles. The foam stability was investigated by the foam drainage half-life and the expansion viscoelastic modulus of the liquid film. The results demonstrate that all of the modified silica nanoparticles effectively improve the foam stability. The surface hydrophobicity of the modified particles is found to be a key factor influencing the foam stability. The optimum contact angle of the particles lies in the approximate range from 50° to 55°. The modifier molecular structure used can also influence the stabilizing foam property of the solid particles. The foam system stabilized by (CH3)2SiCl2-modified silica particles exhibits the highest stability; its drainage half-life at maximum increases by 27% compared to that of the blank foam system and is substantially greater than those of the foam systems stabilized by KH570- and KH550-modified particles.

  13. 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).

  14. 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.

  15. Stability of Ignition Transients

    Directory of Open Access Journals (Sweden)

    V.E. Zarko

    1991-07-01

    Full Text Available The problem of ignition stability arises in the case of the action of intense external heat stimuli when, resulting from the cut-off of solid substance heating, momentary ignition is followed by extinction. Physical pattern of solid propellant ignition is considered and ignition criteria available in the literature are discussed. It is shown that the above mentioned problem amounts to transient burning at a given arbitrary temperature distribution in the condensed phase. A brief survey of published data on experimental and theoretical studies on ignition stability is offered. The comparison between theory and experiment is shown to prove qualitatively the efficiency of the phenomenological approach in the theory. However, the methods of mathematical simulation as well as those of experimental studying of ignition phenomenon, especially at high fluxes, need to be improved.

  16. STABILIZED TRANSISTOR AMPLIFIER

    Science.gov (United States)

    Noe, J.B.

    1963-05-01

    A temperature stabilized transistor amplifier having a pair of transistors coupled in cascade relation that are capable of providing amplification through a temperature range of - 100 un. Concent 85% F to 400 un. Concent 85% F described. The stabilization of the amplifier is attained by coupling a feedback signal taken from the emitter of second transistor at a junction between two serially arranged biasing resistances in the circuit of the emitter of the second transistor to the base of the first transistor. Thus, a change in the emitter current of the second transistor is automatically corrected by the feedback adjustment of the base-emitter potential of the first transistor and by a corresponding change in the base-emitter potential of the second transistor. (AEC)

  17. 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.

  18. Determining postural stability

    Science.gov (United States)

    Lieberman, Erez (Inventor); Forth, Katharine E. (Inventor); Paloski, William H. (Inventor)

    2011-01-01

    A method for determining postural stability of a person can include acquiring a plurality of pressure data points over a period of time from at least one pressure sensor. The method can also include the step of identifying a postural state for each pressure data point to generate a plurality of postural states. The method can include the step of determining a postural state of the person at a point in time based on at least the plurality of postural states.

  19. 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.

  20. MULTIPLE OSCILLATION STABILIZING CONTROL.

    Energy Technology Data Exchange (ETDEWEB)

    YUE,M.; SCHLUETER,R.; AZARM,M.; BARI,R.

    2004-07-23

    This paper presents a strategy that may be used to guide stabilizing control design for multiple oscillations, which are difficult to control using conventional control design procedures. A multiple oscillation phenomena is observed in an example power system. A local bifurcation and an interarea bifurcation develop in an example power system due to multiple bifurcation parameter variations. The dynamic behaviors of the bifurcating system are complex due to the overlapping of the two different bifurcation subsystems and are shown to be difficult to control. The double bifurcations are studied in this paper and in order to stabilize them, three kind of {mu}-synthesis robust controls are designed, (a) {mu}-synthesis power system stabilizer (MPSS); (b) {mu}-synthesis SVC control (MSVC); and (c) a mixed MPSS/MSVC control. Based on the bifurcation subsystem analysis, the measurement signals and locations of the controls are selected. The control performances of three kind of controls are evaluated and compared. The conclusions are given according to the analysis and time simulation results.

  1. 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.

  2. 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 ...

  3. 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

  4. Better, Cheaper, Faster Molecular Dynamics

    Science.gov (United States)

    Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    Recent, revolutionary progress in genomics and structural, molecular and cellular biology has created new opportunities for molecular-level computer simulations of biological systems by providing vast amounts of data that require interpretation. These opportunities are further enhanced by the increasing availability of massively parallel computers. For many problems, the method of choice is classical molecular dynamics (iterative solving of Newton's equations of motion). It focuses on two main objectives. One is to calculate the relative stability of different states of the system. A typical problem that has' such an objective is computer-aided drug design. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), "native" state. Perhaps the best example of such a problem is protein folding. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to "quasi non-ergodicity", whereby a part of phase space is inaccessible on time scales of the simulation. To overcome this difficulty and to extend molecular dynamics to "biological" time scales (millisecond or longer) new physical formulations and new algorithmic developments are required. To be efficient they should account for natural limitations of multi-processor computer architecture. I will present work along these lines done in my group. In particular, I will focus on a new approach to calculating the free energies (stability) of different states and to overcoming "the curse of rare events". I will also discuss algorithmic improvements to multiple time step methods and to the treatment of slowly decaying, log-ranged, electrostatic effects.

  5. 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...

  6. 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.``

  7. 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.

  8. A nonlinear variable structure stabilizer for power system stability

    Energy Technology Data Exchange (ETDEWEB)

    Cao, Y.; Jiang, L.; Cheng, S.; Chen, D. (Huazhong Univ. of Science and Technology, Wuhan (China). Dept. of Electrical Power Engineering); Malik, O.P.; Hope, G.S. (Univ. of Calgary, Alberta (Canada). Dept. of Electrical and Computer Engineering)

    1994-09-01

    A nonlinear variable structure stabilizer is proposed in this paper. Design of this stabilizer involves the nonlinear transformation technique, the variable structure control technique and the linear system theory. Performance of the proposed nonlinear variable structure controller in a single machine connected to an infinite bus power and a multi-machine system with multi-mode oscillations is simulated. The responses of the system with the proposed stabilizer are compared with those obtained with some other kinds of stabilizers when the system is subjected to a variety of disturbances. Simulation results show that the nonlinear variable structure stabilizer gives satisfactory dynamic performance and good robustness.

  9. Thermal Behaviour of AP Based CMDB Propellants with Stabilizers

    Directory of Open Access Journals (Sweden)

    S. N. Asthana

    1992-07-01

    Full Text Available Stability test results and DTA studies indicate the superiority of molecular sieve (MS over zirconium silicate (ZrSiO/sub 4/ as the stabilizer for a composite modified double base (CMDB system. Shelf life as computed from autoignition test results was 30 years for MS-based composition which is almost double the life of ZrSiO/sub 4/, but approximately half the life of resorcinol-based composition which was used as a reference. Higher stabilizing effect of MS as compared to ZrSiO/sub 4/ has been explained on the basis of the presence of channels and cavities in its structure, which makes it an effective adsorbent for decomposition catalysing species. Poor stabilization capability of m-dinitrobenzene as compared to resorcinol suggests the catalytic involvement of acidic decomposition products of nitrate esters in autodecomposition process of CMDB propellants.

  10. End-group Influence on the Frontier Molecular Orbital Reorganization in Molecular Junctions -- Effect on Thermopower

    Science.gov (United States)

    Balachandran, Janakiraman; Reddy, Pramod; Dunietz, Barry; Gavini, Vikram

    2014-03-01

    The frontier molecular orbital (FMO) reorganization and in turn on the thermopower of the aromatic molecules trapped between metal electrodes (aka molecular junctions) depends on two effects namely (1) the stabilization effect - due to the physical presence of the metal electrode atoms and (2) change in e-e interactions - due to end-group mediated charge transfer. The stabilization effect always reduces the FMO energies. The charge transfer effect increases the FMO energies in charge-gaining molecules, which in turn opposes the stabilization effect resulting in a small overall shift. However, the charge transfer effect decreases the FMO energies in charge-losing molecules, which in turn complements the stabilization effect resulting in a large overall downward shift. This hypothesis is validated by delineating the shifts due to stabilization and charge-transfer effects independently. Further we also demonstrate the generality of the hypothesis by applying it on a wide range of aromatic molecules with different length and end-groups. Finally, we also present computationally efficient strategies, based on the proposed mechanism, to quantitatively compute the FMO reorganization which in turn has potential for high throughput analysis of molecular junctions.

  11. 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.)

  12. Cosmic baldness and stability

    Energy Technology Data Exchange (ETDEWEB)

    Panchapakesan, N.; Lohiya, D.

    1985-04-01

    The stability of the de Sitter metric and the relevance of the initial state of a domain which approaches a de Sitter universe asymptotically are investigated analytically, adapting the one-dimensional wave equation with effective potential derived by Khanal and Panchapakesan (1981), for the perturbations of the de Sitter-Schwarzschild metric, to the de Sitter case. It is demonstrated that initial nonspherical perturbations do not increase exponentially with time but rather decay, the frozen modes exponentially and the backscattered perturbations of finite angular momentum l as t to the -(2l - l). It is concluded that the cosmic horizon is stable and has no hair. 14 references.

  13. 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.

  14. Preparation of Astaxanthin Nanodispersions Using Gelatin-Based Stabilizer Systems

    Directory of Open Access Journals (Sweden)

    Navideh Anarjan

    2014-09-01

    Full Text Available The incorporation of lipophilic nutrients, such as astaxanthin (a fat soluble carotenoid in nanodispersion systems can either increase the water solubility, stability and bioavailability or widen their applications in aqueous food and pharmaceutical formulations. In this research, gelatin and its combinations with sucrose oleate as a small molecular emulsifier, sodium caseinate (SC as a protein and gum Arabic as a polysaccharide were used as stabilizer systems in the formation of astaxanthin nanodispersions via an emulsification-evaporation process. The results indicated that the addition of SC to gelatin in the stabilizer system could increase the chemical stability of astaxanthin nanodispersions significantly, while using a mixture of gelatin and sucrose oleate as a stabilizer led to production of nanodispersions with the smallest particle size (121.4 ± 8.6 nm. It was also shown that a combination of gelatin and gum Arabic could produce optimal astaxanthin nanodispersions in terms of physical stability (minimum polydispersity index (PDI and maximum zeta-potential. This study demonstrated that the mixture of surface active compounds showed higher emulsifying and stabilizing functionality compared to using them individually in the preparation of astaxanthin nanodispersions.

  15. Stability of the Levitron

    Science.gov (United States)

    Heflinger, Lee O.; Ridgway, S. L.; Simon, Martin D.

    1996-05-01

    The Levitron, manufactured by Fascinations in Seattle WA, successfully demonstrates magnetic suspension. A 22 gram spinning magnetic dipole top is supported by magnetic forces that balance its weight about 3.2 cm above a magnetized base, and it will float about two minutes until its spin rate has declined to about 1000 rpm. However, since in general it is not possible (The Feynman Lectures on Physics Volume II, 5-4) to have a potential energy minimum or maximum for any rigidly connected system of poles in a magnetic field, the stability of the Levitron is not obvious. Gyroscopic forces that prevent the top from flipping over and being attracted to the base have been suggested as the source of the stability (US Patent 5,404,062, Hones et al.). We find that fixing the direction of the top axis in space is not sufficient. An analysis and numerical integration of the five degree of freedom equations of motion of the top that includes gyroscopic precession around the local magnetic field lines do predict that the top will be supported stably up to spin speeds of 2100 rpm.

  16. Experimental and theoretical studies of the colloidal stability of nanoparticles-a general interpretation based on stability maps.

    Science.gov (United States)

    Segets, Doris; Marczak, Renata; Schäfer, Stefan; Paula, Carolin; Gnichwitz, Jan-Frederik; Hirsch, Andreas; Peukert, Wolfgang

    2011-06-28

    The current work addresses the understanding of the stabilization of nanoparticles in suspension. Specifically, we study ZnO in ethanol for which the influence of particle size and reactant ratio as well as surface coverage on colloidal stability in dependence of the purification progress was investigated. The results revealed that the well-known ζ-potential determines not only the colloidal stability but also the surface coverage of acetate groups bound to the particle surface. The acetate groups act as molecular spacers between the nanoparticles and prevent agglomeration. Next to DLVO calculations based on the theory of Derjaguin, Landau, Verwey and Overbeek using a core-shell model we find that the stability is better understood in terms of dimensionless numbers which represent attractive forces as well as electrostatic repulsion, steric effects, transport properties, and particle concentration. Evaluating the colloidal stability in dependence of time by means of UV-vis absorption measurements a stability map for ZnO is derived. From this map it becomes clear that the dimensionless steric contribution to colloidal stability scales with a stability parameter including dimensionless repulsion and attraction as well as particle concentration and diffusivity of the particles according to a power law with an exponent of -0.5. Finally, we show that our approach is valid for other stabilizing molecules like cationic dendrons and is generally applicable for a wide range of other material systems within the limitations of vanishing van der Waals forces in refractive index matched situations, vanishing ζ-potential and systems without a stabilizing shell around the particle surface.

  17. Stay Wet, Stay Stable? How Internal Water Helps the Stability of Thermophilic Proteins.

    Science.gov (United States)

    Chakraborty, Debashree; Taly, Antoine; Sterpone, Fabio

    2015-10-08

    We present a systematic computational investigation of the internal hydration of a set of homologous proteins of different stability content and molecular complexities. The goal of the study is to verify whether structural water can be part of the molecular mechanisms ensuring enhanced stability in thermophilic enzymes. Our free-energy calculations show that internal hydration in the thermophilic variants is generally more favorable, and that the cumulated effect of wetting multiple sites results in a meaningful contribution to stability. Moreover, thanks to a more effective capability to retain internal water, some thermophilic proteins benefit by a systematic gain from internal wetting up to their optimal working temperature. Our work supports the idea that internal wetting can be viewed as an alternative molecular variable to be tuned for increasing protein stability.

  18. Stay Wet, Stay Stable? How Internal Water Helps Stability of Thermophilic Proteins

    Science.gov (United States)

    Chakraborty, Debashree; Taly, Antoine; Sterpone, Fabio

    2017-01-01

    We present a systematic computational investigation of the internal hydration of a set of homologous proteins of different stability content and molecular complexities. The goal of the study is to verify whether structural water can be part of the molecular mechanisms ensuring enhanced stability in thermophilic enzymes. Our free energy calculations show that internal hydration in the thermophilic variants is generally more favourable and that the cumulated effect of wetting multiple sites results in a meaningful contribution to stability. Moreover, thanks to a more effective capability to retain internal water some thermophilic proteins benefit of a systematic gain from internal wetting up to their optimal working temperature. Our work supports the idea that internal wetting can be viewed as an alternative molecular variable to be tuned for increasing protein stability. PMID:26335353

  19. 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.

  20. 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.

  1. 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

  2. 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

  3. 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.

  4. Amino acids as co-amorphous stabilizers for poorly water-soluble drugs - Part 2

    DEFF Research Database (Denmark)

    Löbmann, K.; Laitinen, R.; Strachan, C.;

    2013-01-01

    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...... 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. © 2013 Elsevier B.V. All rights reserved....... 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...

  5. Stability of Curvature Measures

    CERN Document Server

    Chazal, Frédéric; Lieutier, André; Thibert, Boris

    2008-01-01

    We address the problem of curvature estimation from sampled compact sets. The main contribution is a stability result: we show that the gaussian, mean or anisotropic curvature measures of the offset of a compact set K with positive $\\mu$-reach can be estimated by the same curvature measures of the offset of a compact set K' close to K in the Hausdorff sense. We show how these curvature measures can be computed for finite unions of balls. The curvature measures of the offset of a compact set with positive $\\mu$-reach can thus be approximated by the curvature measures of the offset of a point-cloud sample. These results can also be interpreted as a framework for an effective and robust notion of curvature.

  6. Regional Stability & Peacebuilding

    DEFF Research Database (Denmark)

    It seems that regional decision makers during the last two decades has been unable to produce a sustainable peacebuilding plan for the region and it is questionable whether any remarkable change will occur in the near future. Some would argue that the political differences are simply too far apart...... continue to face, internal challenges even if agreements with a conflicting state are settled. This only underlines the necessity of initiating sustainable initiatives that are capable of affecting politicians from within, or even to some extent have the capability to bypass the political level....... With contributions from leading international scholars within the field of security studies this book sets out to explain the main security knots preventing stability to emerge and on that basis to test whether a different approach in addressing these knots. By pursuing an innovative and different approach...

  7. Stabilizing posture through imagery.

    Science.gov (United States)

    Papalia, Eleonora; Manzoni, Diego; Santarcangelo, Enrica L

    2014-01-01

    Abstract In the general population, suppression of vision modulates body sway by increasing the center of pressure (CoP) velocity, while a light fingertip touch reduces the area of the CoP displacement in blindfolded subjects. This study assessed whether imagined fixation and fingertip touch differentially stabilize posture in subjects with high (highs) and low (lows) hypnotizability. Visual and tactile imageries were ineffective in lows. In highs, the effects of visual imagery could not be evaluated because the real information was ineffective; real tactile stimulation was effective only on velocity, but the imagery effects could not be definitely assessed owing to low effect size. The highs' larger variability could account for this and represents the most important finding.

  8. The Dynamics of Stability

    DEFF Research Database (Denmark)

    Hedegaard, Troels Fage

    politiske aktører der greb disse muligheder. Disse historiske faktorer, der hjalp med at skabe opbakning til velfærdsstaten, er dog blevet svækket med tiden, mens støtten til modellen forbliver stabil. Denne umiddelbare modsætning er denne afhandlings omdrejningspunkt. Derfor vender jeg I denne afhandling...... trække på policy feedback teori, som den primære teoretiske ramme, og ud fra dette beskrive og teste sociale mekanismer der kan forklare den vedvarende opbakning til velfærdsmodellen. Disse social mekanismer eksisterer ikke kun i de nordiske lande, men skulle være mere udbredt her, og kan dermed hjælpe...

  9. Entrepreneurship and Employment Stability

    DEFF Research Database (Denmark)

    Failla, Virgilio; Melillo, Francesca; Reichstein, Toke

    2017-01-01

    are identified and empirically explored: (i) job matching, (ii) labour market value, and (iii) personal commitment. Entrepreneurs appear to be more productive and thus better matched compared to wageworkers. However, they also appear to be locked in entrepreneurship because of their anticipated lower value......This paper challenges the conventional belief that entrepreneurship is an unstable career path. Using longitudinal matched employer–employee data from Denmark, the analysis reveals that a transition to entrepreneurship decreases individual's employment turnover tendency. Three explanations...... in the labour market and because of their personal attachment to the venture. The counter-intuitive finding – entrepreneurship yields greater employment stability – only holds with respect to subsequent transitions to wagework and not for new venture founding. The results have implications for our understanding...

  10. 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.

  11. 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.

  12. 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.

  13. On molecular graph comparison.

    Science.gov (United States)

    Melo, Jenny A; Daza, Edgar

    2011-06-01

    Since the last half of the nineteenth century, molecular graphs have been present in several branches of chemistry. When used for molecular structure representation, they have been compared after mapping the corresponding graphs into mathematical objects. However, direct molecular comparison of molecular graphs is a research field less explored. The goal of this mini-review is to show some distance and similarity coefficients which were proposed to directly compare molecular graphs or which could be useful to do so.

  14. Understanding molecular structure from molecular mechanics.

    Science.gov (United States)

    Allinger, Norman L

    2011-04-01

    Molecular mechanics gives us a well known model of molecular structure. It is less widely recognized that valence bond theory gives us structures which offer a direct interpretation of molecular mechanics formulations and parameters. The electronic effects well-known in physical organic chemistry can be directly interpreted in terms of valence bond structures, and hence quantitatively calculated and understood. The basic theory is outlined in this paper, and examples of the effects, and their interpretation in illustrative examples is presented.

  15. 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...

  16. Molecular dynamics simulation on the struatural stability of [0 1 ¯1] tilt incoherent Σ3 gain boundaries in pure copper*%纯铜[01¯1]倾侧型非共格Σ3晶界结构稳定性分子动力学模拟研究*

    Institute of Scientific and Technical Information of China (English)

    董垒; 王卫国

    2013-01-01

      有研究表明,非共格Σ3晶界的行为在中低层错能面心立方金属晶界特征分布演化中发挥着重要作用.为了掌握不同界面匹配的非共格Σ3晶界的特性,本文利用分子动力学(MD)模拟方法首先研究了纯铜的[01¯1]倾侧型非共格Σ3晶界在700-1100 K 温度范围内和常压下的结构稳定性. MD 模拟采用原子间相互作用长程经验多体势,步长为5×10−15 s.模拟结果表明:所研究的五个非共格Σ3晶界,其结构稳定性存在很大差异,其一般规律是,与(111)/(¯111)共格孪晶界之间的夹角(Φ角)越小,晶界匹配值越大,则非共格Σ3晶界越稳定;反之亦然.Φ角最小的(255)/(¯211)非共格Σ3晶界较稳定,在退火过程中几乎不发生变化.随着Φ角的增大,非共格Σ3晶界不再稳定,这类晶界会通过 Miller 指数较高一侧晶体每三层原子面合并为一层原子面(或 Miller 指数较低一侧晶体每一层原子面分解为三层原子面)的机理转变为亚稳的“台阶”状晶界,台阶面部分地处于精确的能量极低的{111}/{111}共格孪晶界上;当提高温度退火时,这种“台阶”状晶界最终会全部转变成稳定平直的{111}/{111}共格孪晶界.%It has been reported that incoherent Σ3 boundaries play an important role in the evolution of grain boundary characteristic distri-bution in the low to medium stacking fault energy in face-centered cubic metals. In order to ascertain the characteristics of incoherentΣ3 boundaries with varied (h1k1l1)/(h2k2l2) interface matching, the structural stability of [0 1 ¯1] tilt incoherent Σ3 grain boundaries in pure copper, at temperatures ranging from 700 to 1100 K and under the normal pressure, was studied by molecular dynamics (MD) simulations. Long-range empirical potential (LREP) was used in the simulation in which the time-step was chosen to be 5 × 10−15 s (5 fs). Simulation results show that the structural

  17. 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....

  18. 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.

  19. Emulsion stability: determination from turbidity

    Energy Technology Data Exchange (ETDEWEB)

    Reddy, S.R.; Fogler, H.S.

    1981-01-01

    The relationship between particle size and concentration and turbidity has been developed for a polydispersed system. The stability of acoustically prepared emulsions of C36H74 in water were determined from turbidimetry and found to be in agreement with the stability determined by the freezing method. The turbidimetry method can be used for determining the stability of various emulsions easily and inexpensively. 11 references.

  20. 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.

  1. 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.

  2. 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)

  3. 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.

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

    Science.gov (United States)

    Zhu, ZhengXi

    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 ripening and recrystallization. The lower solubility the drug is of, the greater stability the nanoparticles have. Chemically bonding drug compounds with cleavable hydrophobic moieties to form prodrugs were used to enhance their hydrophobicity and thus the nanoparticle stability. It opened a generic strategy to enhance the stability of nanoparticles formed via FNP. beta-carotene, paclitaxel, paclitaxel prodrug, betulin, hydrocortisone, and hydrocortisone prodrug as the drugs were studied. Solubility parameter (delta), and octanol/water partition coefficients (LogP), provide hydrophobicity indicators for the compounds. LogP showed a good correlation with the nanoparticle stability. An empirical rule was built to conveniently predict particle stability for randomly selected drugs. To optimize the process conditions, two-stream confined impinging jet mixer (CIJ) and four-stream confined vortex jet mixer were used. The particle size was studied by varying drug and polymer concentrations, and flow rate (corresponding to Reynolds number (Re)). To extend the FNP technique, this dissertation demonstrated successful creation of stabilized nanoparticles by integrating an in-situ reactive coupling of a hydrophilic polymer block with a hydrophobic one with FNP. The kinetics of the fast coupling reaction was studied. This dissertation also introduced polyelectrolytes (i.e., epsilon-polylysine, poly(ethylene imine), and chitosan) into FNP to electrosterically stabilize nanoparticles.

  5. Stability in skipping gaits

    Science.gov (United States)

    Andrada, Emanuel; Müller, Roy; Blickhan, Reinhard

    2016-11-01

    As an alternative to walking and running, humans are able to skip. However, adult humans avoid it. This fact seems to be related to the higher energetic costs associated with skipping. Still, children, some birds, lemurs and lizards use skipping gaits during daily locomotion. We combined experimental data on humans with numerical simulations to test whether stability and robustness motivate this choice. Parameters for modelling were obtained from 10 male subjects. They locomoted using unilateral skipping along a 12 m runway. We used a bipedal spring loaded inverted pendulum to model and to describe the dynamics of skipping. The subjects displayed higher peak ground reaction forces and leg stiffness in the first landing leg (trailing leg) compared to the second landing leg (leading leg). In numerical simulations, we found that skipping is stable across an amazing speed range from skipping on the spot to fast running speeds. Higher leg stiffness in the trailing leg permits longer strides at same system energy. However, this strategy is at the same time less robust to sudden drop perturbations than skipping with a stiffer leading leg. A slightly higher stiffness in the leading leg is most robust, but might be costlier.

  6. Stability of Polytropes

    CERN Document Server

    Fronsdal, Christian

    2007-01-01

    This paper is an investigation of the stability of some ideal stars. It is in- tended as a study in General Relativity, with emphasis on the coupling to matter, eventually aimed at a better understanding of very strong gravitational fields and Black Holes. The work is based on an action principle for the complete system of metric and matter fields. We propose a complete revision of the treatment of boundary conditions. An ideal star in our terminology has spherical symmetry and an isentropic equation of state. In our first work on this subject it was assumed that the density vanishes beyond a finite distance from the origin. But it is difficult to decide what the proper boundary conditions should be and we are consequently skeptical of the concept of a fixed boundary. In this paper we investigate the double polytrope, characterized by a polytropic index n less than 5 in the bulk of the star and a value larger than 5 in an outer atmosphere that extends to infinity. It has no fixed boundary but a region of crit...

  7. Stabilizing multicellularity through ratcheting

    Science.gov (United States)

    Libby, Eric; Conlin, Peter L.; Kerr, Ben; Ratcliff, William C.

    2016-01-01

    The evolutionary transition to multicellularity probably began with the formation of simple undifferentiated cellular groups. Such groups evolve readily in diverse lineages of extant unicellular taxa, suggesting that there are few genetic barriers to this first key step. This may act as a double-edged sword: labile transitions between unicellular and multicellular states may facilitate the evolution of simple multicellularity, but reversion to a unicellular state may inhibit the evolution of increased complexity. In this paper, we examine how multicellular adaptations can act as evolutionary ‘ratchets’, limiting the potential for reversion to unicellularity. We consider a nascent multicellular lineage growing in an environment that varies between favouring multicellularity and favouring unicellularity. The first type of ratcheting mutations increase cell-level fitness in a multicellular context but are costly in a single-celled context, reducing the fitness of revertants. The second type of ratcheting mutations directly decrease the probability that a mutation will result in reversion (either as a pleiotropic consequence or via direct modification of switch rates). We show that both types of ratcheting mutations act to stabilize the multicellular state. We also identify synergistic effects between the two types of ratcheting mutations in which the presence of one creates the selective conditions favouring the other. Ratcheting mutations may play a key role in diverse evolutionary transitions in individuality, sustaining selection on the new higher-level organism by constraining evolutionary reversion. This article is part of the themed issue ‘The major synthetic evolutionary transitions’. PMID:27431522

  8. 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.

  9. PROFITABILITY AND FINANCIAL STABILITY

    Directory of Open Access Journals (Sweden)

    CĂRUNTU CONSTANTIN

    2011-09-01

    Full Text Available The business activity allows identifying two categories of flows: flows of results and cash flows. Flows affect the income and expenses, participating in training result, the company's profitability. Financial flows involved in their formation both monetary items (which drive the monetary input or output and thus implies a cash flow, and non-cash items (affecting the result, without leading to a cash flow. Are equally identifiable cash flows that do not involve an immediate effect on the outcome or effect on the result equivalent to that spread on the treasury. Financial equilibrium in a general manner evokes the idea of harmony between different elements of a system, which in finance is harmonization of resources with the needs. Financial equilibrium can be defined by the company's ability to secure payment of its proceeds without interruption to current liabilities incurred in implementing its object of activity or tax laws, so it can avoid the risk of bankruptcy. Maintaining financial stability is the essential condition of survival of the enterprise, financial and balanced assessment must take into account the concrete conditions of the occurrence of default.

  10. 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.

  11. 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...

  12. 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

  13. 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....

  14. 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.

  15. 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.

  16. 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)

  17. 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).

  18. Stability of compressible boundary layers

    Science.gov (United States)

    Nayfeh, Ali H.

    1989-01-01

    The stability of compressible 2-D and 3-D boundary layers is reviewed. The stability of 2-D compressible flows differs from that of incompressible flows in two important features: There is more than one mode of instability contributing to the growth of disturbances in supersonic laminar boundary layers and the most unstable first mode wave is 3-D. Whereas viscosity has a destabilizing effect on incompressible flows, it is stabilizing for high supersonic Mach numbers. Whereas cooling stabilizes first mode waves, it destabilizes second mode waves. However, second order waves can be stabilized by suction and favorable pressure gradients. The influence of the nonparallelism on the spatial growth rate of disturbances is evaluated. The growth rate depends on the flow variable as well as the distance from the body. Floquet theory is used to investigate the subharmonic secondary instability.

  19. Project Management Plan Solution Stabilization

    Energy Technology Data Exchange (ETDEWEB)

    SATO, P.K.

    1999-08-31

    This plan presents the overall objectives, description, justification and planning for the Plutonium Finishing Plant (PFP) Solutions Stabilization subproject. The intent of this plan is to describe how this project will be managed and integrated with other facility stabilization and deactivation activities. This plan supplements the overall integrated plan presented in the Integrated Project Management Plan (IPMP) for the Plutonium Finishing Plant Stabilization and Deactivation Project, HNF-3617. This project plan is the top-level definitive project management document for the PFP Solution Stabilization subproject. It specifies the technical, schedule, requirements and the cost baselines to manage the execution of the Solution Stabilization subproject. Any deviations to the document must be authorized through the appropriate change control process.

  20. Transient stability and emergency control

    Institute of Scientific and Technical Information of China (English)

    2009-01-01

    Comparability of emergency control strategies with different instability modes is the key issue to decide 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 principle, an emergency control algorithm framework was established to handle transient stability assessment, 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 comparability of various control locations. The simulations on the New-England System verified the proposed emergency control method for stabilizing transient stability.

  1. 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.

  2. 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.

  3. 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.

  4. A method to study in vivo stability of DNA nanostructures.

    Science.gov (United States)

    Surana, Sunaina; Bhatia, Dhiraj; Krishnan, Yamuna

    2013-11-01

    DNA nanostructures are rationally designed, synthetic, nanoscale assemblies obtained from one or more DNA sequences by their self-assembly. Due to the molecularly programmable as well as modular nature of DNA, such designer DNA architectures have great potential for in cellulo and in vivo applications. However, demonstrations of functionality in living systems necessitates a method to assess the in vivo stability of the relevant nanostructures. Here, we outline a method to quantitatively assay the stability and lifetime of various DNA nanostructures in vivo. This exploits the property of intact DNA nanostructures being uptaken by the coelomocytes of the multicellular model organism Caenorhabditis elegans. These studies reveal that the present fluorescence based assay in coelomocytes of C. elegans is an useful in vivo test bed for measuring DNA nanostructure stability.

  5. Thermal and mechanical stability of zeolitic imidazolate frameworks polymorphs

    Energy Technology Data Exchange (ETDEWEB)

    Bouëssel du Bourg, Lila; Ortiz, Aurélie U.; Coudert, François-Xavier, E-mail: fx.coudert@chimie-paristech.fr [PSL Research University, Chimie ParisTech – CNRS, Institut de Recherche de Chimie Paris, 75005 Paris (France); Boutin, Anne [École Normale Supérieure, PSL Research University, Département de Chimie, Sorbonne Universités – UPMC Univ Paris 06, CNRS UMR 8640 PASTEUR, 24 rue Lhomond, 75005 Paris (France)

    2014-12-01

    Theoretical studies on the experimental feasibility of hypothetical Zeolitic Imidazolate Frameworks (ZIFs) have focused so far on relative energy of various polymorphs by energy minimization at the quantum chemical level. We present here a systematic study of stability of 18 ZIFs as a function of temperature and pressure by molecular dynamics simulations. This approach allows us to better understand the limited stability of some experimental structures upon solvent or guest removal. We also find that many of the hypothetical ZIFs proposed in the literature are not stable at room temperature. Mechanical and thermal stability criteria thus need to be considered for the prediction of new MOF structures. Finally, we predict a variety of thermal expansion behavior for ZIFs as a function of framework topology, with some materials showing large negative volume thermal expansion.

  6. 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.

  7. 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.

  8. Quantitative Evaluation of the Stability of Engineered Water Soluble Nanoparticles

    Science.gov (United States)

    Mulvihill, M. J.; Habas, S.; Mokari, T.; Wan, J.

    2009-12-01

    Stability of nanoparticle solutions is a key factor dictating the bioavailability and transport characteristics of nanoparticles (NPs) in the environment. The synthesis of materials with dimensions less than 100 nm relies on the ability to stabilize surfaces. If the stabilization of the material is disrupted by aggregation, precipitation, or dissolution, the chemical and physical properties often revert to the properties of the bulk material or molecular constituents. We synthesized CdSe and gold NPs, and studied their aggregation rate and the critical coagulation concentration (CCC) using Dynamic Light Scattering (DLS). The chemical and physical properties of our NPs have been characterized by Transmission Electron Microscopy (TEM), UV-VIS spectroscopy, IR spectroscopy, Zeta potential measurements, and Nuclear Magnetic Resonance (NMR) measurements. This comprehensive approach to synthesis and characterization enables the isolation of design parameters with greater precision that can be obtained using commercially available NPs. This research evaluates NP design parameters including composition, size, and surface coating, as a function of concentration, pH, and ionic strength, to determine which factors most affect NP stability. The aggregation characteristics of both gold NPs and cadmium selinide NPs, which are between 2-12 nm in diameter, and have been capped with various ligands, have been studied. While previous work demonstrates that these variables influence stability, it does not systematically compare their relative significance. Our results indicate that changing the ligand shell radically affects the stability of NP as a function of both pH and ionic strength, while changing the material from CdSe to gold has only a moderate influence on the stability and aggregation characteristics of our particles. Additionally, the ligand charge, length, and binding affinity all significantly effect NP stability. Funding was provided by the U.S. Department of Energy

  9. Molecular-sized fluorescent nanodiamonds

    Science.gov (United States)

    Vlasov, Igor I.; Shiryaev, Andrey A.; Rendler, Torsten; Steinert, Steffen; Lee, Sang-Yun; Antonov, Denis; Vörös, Márton; Jelezko, Fedor; Fisenko, Anatolii V.; Semjonova, Lubov F.; Biskupek, Johannes; Kaiser, Ute; Lebedev, Oleg I.; Sildos, Ilmo; Hemmer, Philip. R.; Konov, Vitaly I.; Gali, Adam; Wrachtrup, Jörg

    2014-01-01

    Doping of carbon nanoparticles with impurity atoms is central to their application. However, doping has proven elusive for very small carbon nanoparticles because of their limited availability and a lack of fundamental understanding of impurity stability in such nanostructures. Here, we show that isolated diamond nanoparticles as small as 1.6 nm, comprising only ~400 carbon atoms, are capable of housing stable photoluminescent colour centres, namely the silicon vacancy (SiV). Surprisingly, fluorescence from SiVs is stable over time, and few or only single colour centres are found per nanocrystal. We also observe size-dependent SiV emission supported by quantum-chemical simulation of SiV energy levels in small nanodiamonds. Our work opens the way to investigating the physics and chemistry of molecular-sized cubic carbon clusters and promises the application of ultrasmall non-perturbative fluorescent nanoparticles as markers in microscopy and sensing.

  10. Novel active stabilization technology in highly crosslinked UHMWPEs for superior stability

    Science.gov (United States)

    Oral, Ebru; Neils, Andrew L.; Wannomae, Keith K.; Muratoglu, Orhun K.

    2014-12-01

    Radiation cross-linked ultrahigh molecular weight polyethylene (UHMWPE) is the bearing of choice in joint arthroplasty. The demands on the longevity of this polymer are likely to increase with the recently advancing deterioration of the performance of alternative metal-on-metal implants. Vitamin E-stabilized, cross-linked UHMWPEs are considered the next generation of improved UHMWPE bearing surfaces for improving the oxidation resistance of the polymer. It was recently discovered that in the absence of radiation-induced free radicals, lipids absorbed into UHMWPE from the synovial fluid can initiate oxidation and result in new free radical-mediated oxidation mechanisms. In the presence of radiation-induced free radicals, it is possible for the polymer to oxidize through both existing free radicals at the time of implantation and through newly formed free radicals in vivo. Thus, we showed that reducing the radiation-induced free radicals in vitamin E-stabilized UHMWPE would increase its oxidative stability and presumably lead to improved longevity. We describe mechanical annealing and warm irradiation of irradiated vitamin E blends as novel methods to eliminate 99% of radiation-induced free radicals without sacrificing crystallinity. These are significant improvements in the processing of highly cross-linked UHMWPE for joint implants with improved longevity.

  11. Characterization of gamma-stabilized PP with blends of hindered amine/phenolic stabilizers

    Energy Technology Data Exchange (ETDEWEB)

    Albano, C. [Centro de Quimica, Laboratorio de Polimeros, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas (Venezuela); Universidad Central de Venezuela, Facultad de Ingenieria, Escuela de Ingenieria Quimica, Caracas (Venezuela)], E-mail: calbano@ivic.ve; Perera, R. [Departamento de Mecanica, Universidad Simon Bolivar, Caracas (Venezuela)], E-mail: rperera@usb.ve; Karam, A.; Sanchez, Y. [Centro de Quimica, Laboratorio de Polimeros, Instituto Venezolano de Investigaciones Cientificas (IVIC), Caracas (Venezuela); Silva, P. [Centro de Fisica, Laboratorio de la Materia Condensada, Instituto Venezolano de Investigaciones Cientificas, Caracas (Venezuela)

    2007-12-15

    In this work, the effect of {gamma} radiation at doses of 25 and 50 kGy on polypropylene (PP) stabilized with a binary system of antioxidants of the phenol-hindered amine type (BHT-Chimassorb 994) at different compositions (0.1/0.2, 0.1/0.5, 0.1/0.8) was studied. The results showed that the carbonyl index (I{sub c}) of the stabilized samples drastically decreases when compared to that of the pure PP sample. Nonetheless, the I{sub c} values of the different stabilized samples were very similar after irradiation. On the other hand, the average molecular weights (M{sub w} and M{sub n}) and melt flow index (MFI) values decrease in all the samples after irradiation. This effect is less pronounced in PP with 0.1/0.8 of the binary blend of antioxidants. The melting and crystallization peak temperatures and the crystallinity degree remained almost unchanged and the tensile properties such as Young's modulus and tensile strength did not vary either, except for the elongation at break, which decreases in less proportion in those blends of PP with the antioxidants, independently of the absorbed dose.

  12. 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.

  13. 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.

  14. 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

  15. Improving the stability of peptidic radiotracers by the introduction of artificial scaffolds: which structure element is most useful?

    Science.gov (United States)

    Bacher, Lisa; Fischer, Gabriel; Litau, Shanna; Schirrmacher, Ralf; Wängler, Björn; Baller, Marko; Wängler, Carmen

    2015-08-01

    Peptidic radiotracers are highly potent substances for the specific in vivo imaging of various biological targets with Single Photon Emission Computed Tomography and Positron Emission Tomography. However, some radiolabeled peptides such as bombesin analogs were shown to exhibit only a limited stability, hampering a successful target visualization. One option to positively influence the stability of radiolabeled peptides is the introduction of certain artificial molecular scaffolds. In order to comparatively assess the influence of different structure elements on the stability of radiolabeled peptides and to identify those structure elements being most useful for peptide radiotracer stabilization, several monomeric and dimeric bombesin derivatives were synthesized, exhibiting differing molecular designs and the chelator NODAGA for (68) Ga-labeling. The radiolabeled peptides were evaluated regarding their in vitro stability in human serum to determine the influence of the introduced molecular scaffolds on the peptides' serum stabilities. The results of the evaluations showed that the introduction of scaffold structures and the overall molecular design have a substantial impact on the stabilities of the resulting peptidic radiotracers. But besides some general trends found using certain scaffold structures, the obtained results point to the necessity to empirically assess their influence on stability for each susceptible peptidic radiotracer individually.

  16. 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

  17. Passive stabilization in a linear MHD stability code

    Energy Technology Data Exchange (ETDEWEB)

    Todd, A.M.M.

    1980-03-01

    Utilizing a Galerkin procedure to calculate the vacuum contribution to the ideal MHD Lagrangian, the implementation of realistic boundary conditions are described in a linear stability code. The procedure permits calculation of the effect of arbitrary conducting structure on ideal MHD instabilities, as opposed to the prior use of an encircling shell. The passive stabilization of conducting coils on the tokamak vertical instability is calculated within the PEST code and gives excellent agreement with 2-D time dependent simulations of PDX.

  18. Nonparallel stability of boundary layers

    Science.gov (United States)

    Nayfeh, Ali H.

    1987-01-01

    The asymptotic formulations of the nonparallel linear stability of incompressible growing boundary layers are critically reviewed. These formulations can be divided into two approaches. The first approach combines a numerical method with either the method of multiple scales, or the method of averaging, of the Wentzel-Kramers-Brillouin (WKB) approximation; all these methods yield the same result. The second approach combined a multi-structure theory with the method of multiple scales. The first approach yields results that are in excellent agreement with all available experimental data, including the growth rates as well as the neutral stability curve. The derivation of the linear stability of the incompressible growing boundary layers is explained.

  19. Plutonium stabilization and packaging system

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-05-01

    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.

  20. 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.

  1. 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.

  2. 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.

  3. Correlations between biochemical characteristics and foam-forming and -stabilizing ability of whey and casein hydrolysates.

    Science.gov (United States)

    van der Ven, Cornelly; Gruppen, Harry; de Bont, Dries B A; Voragen, Alphons G J

    2002-05-08

    Whey protein and casein were hydrolyzed with 11 commercially available enzymes. Foam properties of 44 samples were measured and were related to biochemical properties of the hydrolysates using statistical data analysis. All casein hydrolysates formed high initial foam levels, whereas whey hydrolysates differed in their foam-forming abilities. Regression analysis using the molecular weight distribution of whey hydrolysates as predictors showed that the hydrolysate fraction containing peptides of 3-5 kDa was most strongly related to foam formation. Foam stability of whey hydrolysates and of most casein hydrolysates was inferior to that of the intact proteins. The foam stability of casein hydrolysate foams was correlated to the molecular weight distribution of the hydrolysates; a high proportion of peptides >7 kDa, composed of both intact casein and high molecular weight peptides, was positively related to foam stability.

  4. 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.

  5. 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.

  6. 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.

  7. Molecular mobility in glassy dispersions

    Energy Technology Data Exchange (ETDEWEB)

    Mehta, Mehak [Univ. of Minnesota, Minneapolis, MN (United States). Dept. of Pharmaceutics; McKenna, Gregory B. [Texas Tech Univ., Lubbock, TX (United States). Dept. of Chemical Engineering; Suryanarayanan, Raj [Univ. of Minnesota, Minneapolis, MN (United States). Dept. of Pharmaceutics

    2016-05-27

    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.

  8. Carbon Nanotube Based Molecular Electronics

    Science.gov (United States)

    Srivastava, Deepak; Saini, Subhash; Menon, Madhu

    1998-01-01

    Carbon nanotubes and the nanotube heterojunctions have recently emerged as excellent candidates for nanoscale molecular electronic device components. Experimental measurements on the conductivity, rectifying behavior and conductivity-chirality correlation have also been made. While quasi-one dimensional simple heterojunctions between nanotubes with different electronic behavior can be generated by introduction of a pair of heptagon-pentagon defects in an otherwise all hexagon graphene sheet. Other complex 3- and 4-point junctions may require other mechanisms. Structural stability as well as local electronic density of states of various nanotube junctions are investigated using a generalized tight-binding molecular dynamics (GDBMD) scheme that incorporates non-orthogonality of the orbitals. The junctions investigated include straight and small angle heterojunctions of various chiralities and diameters; as well as more complex 'T' and 'Y' junctions which do not always obey the usual pentagon-heptagon pair rule. The study of local density of states (LDOS) reveal many interesting features, most prominent among them being the defect-induced states in the gap. The proposed three and four pointjunctions are one of the smallest possible tunnel junctions made entirely of carbon atoms. Furthermore the electronic behavior of the nanotube based device components can be taylored by doping with group III-V elements such as B and N, and BN nanotubes as a wide band gap semiconductor has also been realized in experiments. Structural properties of heteroatomic nanotubes comprising C, B and N will be discussed.

  9. Design of phage-displayed cystine-stabilized mini-protein libraries for proteinaceous binder engineering.

    Science.gov (United States)

    Chang, Hung-Ju; Yang, An-Suei

    2014-01-01

    Cystine-stabilized mini-proteins are important scaffolds in the combinatorial search of binders for molecular recognition. The structural determinants of a cystine-stabilized scaffold are the critical residues determining the formation of the native disulfide-bonding configuration, and thus should remain unchanged in the combinatorial libraries so as to allow a large portion of the library sequences to be compatible with the scaffold structure. A high-throughput molecular evolution procedure has been developed to select and screen for the polypeptide sequences folding into a specific cystine-stabilized structure. Patterns of sequence preference that emerge from the resultant sequence profiles provide structural determinant information, which facilitates the designs of combinatorial libraries for combinatorial approaches as in phage display. This methodology enables artificial cystine-stabilized proteins to be engineered with enhanced folding and binding properties.

  10. 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.

  11. Stabilizing Moduli with String Cosmology

    CERN Document Server

    Watson, S

    2005-01-01

    In this talk I will discuss the role of finite temperature quantum corrections in string cosmology and show that they can lead to a stabilization mechanism for the volume moduli. I will show that from the higher dimensional perspective this results from the effect of states of enhanced symmetry on the one-loop free energy. These states lead not only to stabilization, but also suggest an alternative model for cold dark matter. At late times, when the low energy effective field theory gives the appropriate description of the dynamics, the moduli will begin to slow-roll and stabilization will generically fail. However, stabilization can be recovered by considering cosmological particle production near the points of enhanced symmetry leading to the process known as moduli trapping.

  12. 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.

  13. Financial Stability and Financial Inclusion

    OpenAIRE

    Morgan, Peter J; Pontines, Victor

    2014-01-01

    Developing economies are seeking to promote financial inclusion, i.e., greater access to financial services for low-income households and firms, as part of their overall strategies for economic and financial development. This raises the question of whether financial stability and financial inclusion are, broadly speaking, substitutes or complements. In other words, does the move toward greater financial inclusion tend to increase or decrease financial stability? A number of studies have sugge...

  14. 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.

  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. Stability of Pharmaceuticals in Space

    Science.gov (United States)

    Nguyen, Y-Uyen

    2009-01-01

    Stability testing is a tool used to access shelf life and effects of storage conditions for pharmaceutical formulations. Early research from the International Space Station (ISS) revealed that some medications may have degraded while in space. This potential loss of medication efficacy would be very dangerous to Crew health. The aim of this research project, Stability of Pharmacotherapeutic Compounds, is to study how the stability of pharmaceutical compounds is affected by environmental conditions in space. Four identical pharmaceutical payload kits containing medications in different dosage forms (liquid for injection, tablet, capsule, ointment and suppository) were transported to the ISS aboard a Space Shuttle. One of the four kits was stored on that Shuttle and the other three were stored on the ISS for return to Earth at various time intervals aboard a pre-designated Shuttle flight. The Pharmacotherapeutics laboratory used stability test as defined by the United States Pharmacopeia (USP), to access the degree of degradation to the Payload kit medications that may have occurred during space flight. Once these medications returned, the results of stability test performed on them were compared to those from the matching ground controls stored on Earth. Analyses of the results obtained from physical and chemical stability assessments on these payload medications will provide researchers additional tools to promote safe and efficacious medications for space exploration.

  17. 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.

  18. Quantum Phase Analysis of Field-Free Molecular Alignment

    CERN Document Server

    Yun, Sang Jae; Lee, Jongmin; Nam, Chang Hee

    2015-01-01

    We present quantum mechanical explanations for unresolved phenomena observed in field-free molecular alignment by a femtosecond laser pulse. Quantum phase analysis of molecular rotational states reveals the physical origin of the following phenomena: strong alignment peaks appear periodically, and the temporal shape of each alignment peak changes in an orderly fashion depending on molecular species; the strongest alignment is not achieved at the first peak; the transition between aligned and anti-aligned states is very fast compared to the time scale of rotational dynamics. These features are understood in a unified way analogous to that describing a carrier-envelope-phase-stabilized mode-locked laser.

  19. 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.

  20. 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.

  1. Electron beam assisted synthesis of silver nanoparticle in chitosan stabilizer: Preparation, stability and inhibition of building fungi studies

    Science.gov (United States)

    Jannoo, Kanokwan; Teerapatsakul, Churapa; Punyanut, Adisak; Pasanphan, Wanvimol

    2015-07-01

    Silver nanoparticles (AgNPs) in chitosan (CS) stabilizer were successfully synthesized using electron beam irradiation. The effects of irradiation dose, molecular weight (MW) of CS stabilizer, concentration of AgNO3 precursor and addition of tert-butanol on AgNPs production were studied. The stability of the AgNPs under different temperatures and storage times were also investigated. The AgNPs formation in CS was observed using UV-vis, FT-IR and XRD. The characteristic surface plasmon resonance (SPR) of the obtained AgNPs was around 418 nm. The CS stabilizer and its MW, AgNO3 precursor and irradiation doses are important parameters for the synthesis of AgNPs. The optimum addition of 20% v/v tert-butanol could assist the formation of AgNPs. The AgNPs in CS stabilizer were stable over a period of one year when the samples were kept at 5 °C. The AgNPs observed from TEM images were spherical with an average particle size in the range of 5-20 nm depending on the irradiation doses. The AgNPs in CS solution effectively inhibited the growth of several fungi, i.e., Curvularia lunata, Trichoderma sp., Penicillium sp. and Aspergillus niger, which commonly found on the building surface.

  2. Functional characterization of protein stabilized emulsions: creaming stability

    Energy Technology Data Exchange (ETDEWEB)

    Tornberg, E.

    1978-01-01

    Protein stabilized emulsions have been prepared in a recirculating emulsification system, where flow velocity, power and energy input have been controlled and measured. Three different types of emulsifying equipment have been used, namely a turbo-mixer, an ultrasonic device and a valve homogenizer. The protein systems studied were a soybean protein isolate, a whey protein concentrate (WPC) and a sodium caseinate, and the emulsions obtained were characterized in terms of creaming stability. It was found that although the power and energy consumption during emulsification were the same, the creaming stabilities differed as a function of the emulsifying apparatus used, increased power and energy input contributed in general to an improved creaming stability up to a certain limit, whereupon it leveled off. The emulsifying efficiency of the turbo-mixer is poorest in terms of creaming stability of the emulsions formed, whereas the ultrasonic device most generally is the best choice of equipment at lower power input. At an increase of power consumption the valve homogenizer is an equally good alternative, or even better.

  3. 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...

  4. 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.

  5. 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.

  6. 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.

  7. Molecular dynamics simulations

    OpenAIRE

    Tarmyshov, Konstantin B.

    2007-01-01

    Molecular simulations can provide a detailed picture of a desired chemical, physical, or biological process. It has been developed over last 50 years and is being used now to solve a large variety of problems in many different fields. In particular, quantum calculations are very helpful to study small systems at a high resolution where electronic structure of compounds is accounted for. Molecular dynamics simulations, in turn, are employed to study development of a certain molecular ensemble ...

  8. 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.

  9. Atomic and molecular supernovae

    Energy Technology Data Exchange (ETDEWEB)

    Liu, W.

    1997-12-01

    Atomic and molecular physics of supernovae is discussed with an emphasis on the importance of detailed treatments of the critical atomic and molecular processes with the best available atomic and molecular data. The observations of molecules in SN 1987A are interpreted through a combination of spectral and chemical modelings, leading to strong constraints on the mixing and nucleosynthesis of the supernova. The non-equilibrium chemistry is used to argue that carbon dust can form in the oxygen-rich clumps where the efficient molecular cooling makes the nucleation of dust grains possible. For Type Ia supernovae, the analyses of their nebular spectra lead to strong constraints on the supernova explosion models.

  10. 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....

  11. 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

  12. 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…

  13. 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.

  14. Material Stabilization Project Management Plan

    Energy Technology Data Exchange (ETDEWEB)

    SPEER, D.R.

    1999-09-01

    This plan presents the overall objectives, description, justification and planning for the plutonium Finishing Plant (PFP) Materials Stabilization project. The intent of this plan is to describe how this project will be managed and integrated with other facility stabilization and deactivation activities. This plan supplements the overall integrated plan presented in the Plutonium Finishing Plant Integrated Project Management Plan (IPMP), HNF-3617, Rev. 0. This is the top-level definitive project management document that specifies the technical (work scope), schedule, and cost baselines to manager the execution of this project. It describes the organizational approach and roles/responsibilities to be implemented to execute the project. This plan is under configuration management and any deviations must be authorized by appropriate change control action. Materials stabilization is designated the responsibility to open and stabilize containers of plutonium metal, oxides, alloys, compounds, and sources. Each of these items is at least 30 weight percent plutonium/uranium. The output of this project will be containers of materials in a safe and stable form suitable for storage pending final packaging and/or transportation offsite. The corrosion products along with oxides and compounds will be stabilized via muffle furnaces to reduce the materials to high fired oxides.

  15. 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.

  16. Development of emotional stability scale

    Directory of Open Access Journals (Sweden)

    M Chaturvedi

    2010-01-01

    Full Text Available Background: Emotional stability remains the central theme in personality studies. The concept of stable emotional behavior at any level is that which reflects the fruits of normal emotional development. The study aims at development of an emotional stability scale. Materials and Methods: Based on available literature the components of emotional stability were identified and 250 items were developed, covering each component. Two-stage elimination of items was carried out, i.e. through judges′ opinions and item analysis. Results: Fifty items with highest ′t′ values covering 5 dimensions of emotional stability viz pessimism vs. optimism, anxiety vs. calm, aggression vs. tolerance., dependence vs. autonomy., apathy vs. empathy were retained in the final scale. Reliability as checked by Cronbach′s alpha was .81 and by split half method it was .79. Content validity and construct validity were checked. Norms are given in the form of cumulative percentages. Conclusion: Based on the psychometric principles a 50 item, self-administered 5 point Lickert type rating scale was developed for measurement of emotional stability.

  17. 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.

  18. Nuclear structure far from stability

    CERN Document Server

    Vretenar, D

    2005-01-01

    Modern nuclear structure theory is rapidly evolving towards regions of exotic short-lived nuclei far from stability, nuclear astrophysics applications, and bridging the gap between low-energy QCD and the phenomenology of finite nuclei. The principal objective is to build a consistent microscopic theoretical framework that will provide a unified description of bulk properties, nuclear excitations and reactions. Stringent constraints on the microscopic approach to nuclear dynamics, effective nuclear interactions, and nuclear energy density functionals, are obtained from studies of the structure and stability of exotic nuclei with extreme isospin values, as well as extended asymmetric nucleonic matter. Recent theoretical advances in the description of structure phenomena in exotic nuclei far from stability are reviewed.

  19. Nuclear structure far from stability

    Science.gov (United States)

    Vretenar, D.

    2005-04-01

    Modern nuclear structure theory is rapidly evolving towards regions of exotic shortlived nuclei far from stability, nuclear astrophysics applications, and bridging the gap between low-energy QCD and the phenomenology of finite nuclei. The principal objective is to build a consistent microscopic theoretical framework that will provide a unified description of bulk properties, nuclear excitations and reactions. Stringent constraints on the microscopic approach to nuclear dynamics, effective nuclear interactions, and nuclear energy density functionals, are obtained from studies of the structure and stability of exotic nuclei with extreme isospin values, as well as extended asymmetric nucleonic matter. Recent theoretical advances in the description of structure phenomena in exotic nuclei far from stability are reviewed.

  20. Hydraulic Stability of Accropode Armour

    DEFF Research Database (Denmark)

    Jensen, T.; Burcharth, H. F.; Frigaard, Peter

    , 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......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...

  1. Stabilization of Branching Queueing Networks

    CERN Document Server

    Brázdil, Tomáš

    2011-01-01

    Queueing networks are gaining attraction for the performance analysis of parallel computer systems. A Jackson network is a set of interconnected servers, where the completion of a job at server i may result in the creation of a new job for server j. We propose to extend Jackson networks by "branching" and by "control" features. Both extensions are new and substantially expand the modelling power of Jackson networks. On the other hand, the extensions raise computational questions, particularly concerning the stability of the networks, i.e, the ergodicity of the underlying Markov chain. We show for our extended model that it is decidable in polynomial time if there exists a controller that achieves stability. Moreover, if such a controller exists, one can efficiently compute a static randomized controller which stabilizes the network in a very strong sense; in particular, all moments of the queue sizes are finite.

  2. Flotation control -- A multivariable stabilizer

    Energy Technology Data Exchange (ETDEWEB)

    Schubert, J.H.; Henning, R.G.D.; Hulbert, D.G.; Craig, I.K. [Mintek, Randburg (South Africa)

    1995-12-31

    This paper presents a stabilizing controller for flotation plants which uses a quasi-multivariable technique. The controller monitors all the levels in the plant, and by anticipating interactions between various parts of the plant, is able to stabilize the plant far more successfully than the normal plant control. Once stabilizing control has been achieved, optimization of the process becomes easier and more sustainable. An estimate of the improvement in metallurgical performance is made and a singular value analysis was conducted to verify that the multivariable algorithm will theoretically control better than a collection of individual PID loops. Metallurgical results are presented to show that the improvements are attainable in practice. Control by the Mintek algorithm was alternated with normal plant control, to show that the improvements are statistically significant.

  3. Stability of Boolean Multiplex Networks

    CERN Document Server

    Cozzo, Emanuele; Moreno, Yamir

    2012-01-01

    We extend the formalism of Random Boolean Networks with canalizing rules to multilevel complex networks. The formalism allows to model genetic networks in which each gene might take part in more than one signaling pathway. We use a semi-annealed approach to study the stability of this class of models when coupled in a multiplex network and show that the analytical results are in good agreement with numerical simulations. Our main finding is that the multiplex structure provides a mechanism for the stabilization of the system and of chaotic regimes of individual layers. Our results help understanding why some genetic networks that are theoretically expected to operate in the chaotic regime can actually display dynamical stability.

  4. A systematic molecular circuit design method for gene networks under biochemical time delays and molecular noises

    Directory of Open Access Journals (Sweden)

    Chang Yu-Te

    2008-11-01

    Full Text Available Abstract Background Gene networks in nanoscale are of nonlinear stochastic process. Time delays are common and substantial in these biochemical processes due to gene transcription, translation, posttranslation protein modification and diffusion. Molecular noises in gene networks come from intrinsic fluctuations, transmitted noise from upstream genes, and the global noise affecting all genes. Knowledge of molecular noise filtering and biochemical process delay compensation in gene networks is crucial to understand the signal processing in gene networks and the design of noise-tolerant and delay-robust gene circuits for synthetic biology. Results A nonlinear stochastic dynamic model with multiple time delays is proposed for describing a gene network under process delays, intrinsic molecular fluctuations, and extrinsic molecular noises. Then, the stochastic biochemical processing scheme of gene regulatory networks for attenuating these molecular noises and compensating process delays is investigated from the nonlinear signal processing perspective. In order to improve the robust stability for delay toleration and noise filtering, a robust gene circuit for nonlinear stochastic time-delay gene networks is engineered based on the nonlinear robust H∞ stochastic filtering scheme. Further, in order to avoid solving these complicated noise-tolerant and delay-robust design problems, based on Takagi-Sugeno (T-S fuzzy time-delay model and linear matrix inequalities (LMIs technique, a systematic gene circuit design method is proposed to simplify the design procedure. Conclusion The proposed gene circuit design method has much potential for application to systems biology, synthetic biology and drug design when a gene regulatory network has to be designed for improving its robust stability and filtering ability of disease-perturbed gene network or when a synthetic gene network needs to perform robustly under process delays and molecular noises.

  5. Xanthan gum stabilized gold nanoparticles: characterization, biocompatibility, stability and cytotoxicity.

    Science.gov (United States)

    Pooja, Deep; Panyaram, Sravani; Kulhari, Hitesh; Rachamalla, Shyam S; Sistla, Ramakrishna

    2014-09-22

    Xanthan gum (XG) has been widely used in food, pharmaceutical and cosmetic industries. In the present study, we explored the potential of XG in the synthesis of gold nanoparticle. XG was used as both reducing and stabilizing agent. The effect of various formulation and process variables such as temperature, reaction time, gum concentration, gum volume and gold concentration, in GNP preparation was determined. The XG stabilized, rubey-red XGNP were obtained with 5 ml of XG aqueous solution (1.5 mg/ml). The optimum temperature was 80°C whereas the reaction time was 3 h. The optimized nanoparticles were also investigated as drug delivery carrier for doxorubicin hydrochloride. DOX loaded gold nanoparticles (DXGP) were characterized by dynamic light scattering, TEM, FTIR, and DSC analysis. The synthesized nanoparticle showed mean particle size of 15-20 nm and zeta potential -29.1 mV. The colloidal stability of DXGP was studied under different conditions of pH, electrolytes and serum. Nanoparticles were found to be stable at pH range between pH 5-9 and NaCl concentration up to 0.5 M. In serum, nanoparticles showed significant stability up to 24h. During toxicity studies, nanoparticles were found biocompatible and non-toxic. Compared with free DOX, DXGP displayed 3 times more cytotoxicity in A549 cells. In conclusion, this study provided an insight to synthesize GNP without using harsh chemicals.

  6. 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.

  7. Structures and Stabilization Mechanisms in Chemically Stabilized Ceramics

    Science.gov (United States)

    Gai-Boyes, Pratibha L.; Saltzberg, Michael A.; Vega, Alexander

    1993-09-01

    Structural complexities and disorder in chemically stabilized cristobalites (CSC), which are room temperature silica-based ceramics, prepared by a wet chemical route, are described. CSC displays many of the structural characteristics of the high temperature cristobalite, elucidated by HREM and X-ray diffraction. In-situ electron diffraction and NMR results suggest that the disorder is structural and is static.

  8. Translational Influence on Messenger Stability

    DEFF Research Database (Denmark)

    Eriksen, Mette

    , on messenger stability was examined. Depending on the translation initiation frequency, the chance of an initial ribosome trailing the RNA polymerase get better for better initiation sites, thus protecting transcription from termination by Rho. A polarity assay in which the activity of the downstream lac......-termination to be a global phenomena in gene regulation. The influence of codon usage in the early coding region on messenger stability was examined, in order to establish how fast or slow the ribosome has to decode the sequence for it to protect the messenger from degradation. The experiments demonstrated that very fast...

  9. Foaming volume and foam stability

    Science.gov (United States)

    Ross, Sydney

    1947-01-01

    A method of measuring foaming volume is described and investigated to establish the critical factors in its operation. Data on foaming volumes and foam stabilities are given for a series of hydrocarbons and for a range of concentrations of aqueous ethylene-glycol solutions. It is shown that the amount of foam formed depends on the machinery of its production as well as on properties of the liquid, whereas the stability of the foam produced, within specified mechanical limitations, is primarily a function of the liquid.

  10. Stability of facetted translation shells

    DEFF Research Database (Denmark)

    Almegaard, Henrik; Vanggaard, Ole

    2004-01-01

    This article is discussing the spatial stability i.e. rigidity of double curved shell surfaces under different support conditions. It is based upon a method developed by Henrik Almegaard, as part of the theory concerning the stringer system (ALM04a).......This article is discussing the spatial stability i.e. rigidity of double curved shell surfaces under different support conditions. It is based upon a method developed by Henrik Almegaard, as part of the theory concerning the stringer system (ALM04a)....

  11. 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,

  12. Molecular Stirrers in Action

    NARCIS (Netherlands)

    Chen, Jiawen; Kistemaker, Jos C. M.; Robertus, Jort; Feringa, Ben L.

    2014-01-01

    A series of first-generation light-driven molecular motors with rigid substituents of varying length was synthesized to act as "molecular stirrers". Their rotary motion was studied by H-1 NMR and UV-vis absorption spectroscopy in a variety of solvents with different polarity and viscosity. Quantitat

  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. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. On the Dynamic Stability of a Missile

    Directory of Open Access Journals (Sweden)

    K.C. Sharma

    1977-01-01

    Full Text Available The P-method given by Parks and Pritchard has been used to discuss the stability behaviour of a missile in free flight. General stability criteria for aerodynamic stabilisation have been obtained for slowly varying coefficients. The effect of pressure gradient on the stability of a coasting rocket has been explicitly examined. It is observed that the positive Magnus moment parameter ensures stability whereas a negative moment parameter would enhance the requirements of a larger stability margin.

  20. Stability of Rocket Flight during Burning

    Directory of Open Access Journals (Sweden)

    T. N. Srivastava

    1967-10-01

    Full Text Available Stability of the rocket motion during burning is discussed taking into consideration gravity, aerodynamic forces and torques. Conditions for stabilizing the rocket motion are investigated. Analysis for initial and final phases of burning is given separately. Stability regions of the projected motions on two dimensional co-ordinate planes are obtained and thereby stability region of the actual motion is derived. Stability diagrams illustrate statically and dynamically stable and unstable regions.

  1. Stability of personality traits in adulthood

    OpenAIRE

    Allemand, Mathias; Gruenenfelder-Steiger, Andrea E; Hill, Patrick L.

    2013-01-01

    Stability represents a fundamental concept in developmental theory and research. In this article we give an overview of recent work on personality traits and their stability in adulthood. First, we define personality traits and stability. Second, we present empirical evidence supporting change and stability of personality traits across the adult years with respect to conceptually and statistically different forms of stability. Third, we describe mechanisms and processes that enable trait stab...

  2. Management of bipolar depression with Lamotrigine: an antiepileptic mood stabilizer

    Directory of Open Access Journals (Sweden)

    Kedar S Prabhavalkar

    2015-10-01

    Full Text Available The efficacy of lamotrigine in the treatment of focal epilepsies have already been reported in several case reports and open studies, which is thought to act by inhibiting glutamate release through voltage-sensitive sodium channels blockade and neuronal membrane stabilization. However, recent findings have also illustrated the importance of lamotrigine in alleviating the depressive symptoms of bipolar disorder, without causing mood destabilization or precipitating mania. Currently, no mood stabilizers are available having equal efficacy in the treatment of both mania and depression, two of which forms the extreme sides of the bipolar disorder. Lamotrigine, a well established anticonvulsant has received regulatory approval for the treatment and prevention of bipolar depression in more than 30 countries worldwide. Lamotrigine, acts through several molecular targets and overcomes the major limitation of other conventional antidepressants by stabilizing mood from ‘below baseline’ thereby preventing switches to mania or episode acceleration, thus being effective for bipolar I disorder. Recent studies have also suggested that these observations could also be extended to patients with bipolar II disorder. Thus, lamotrigine may supposedly fulfill the unmet requirement for an effective depression mood stabilizer.

  3. Stathmin is required for stability of the Drosophila neuromuscular junction.

    Science.gov (United States)

    Graf, Ethan R; Heerssen, Heather M; Wright, Christina M; Davis, Graeme W; DiAntonio, Aaron

    2011-10-19

    Synaptic connections can be stably maintained for prolonged periods, yet can be rapidly disassembled during the developmental refinement of neural circuitry and following cytological insults that lead to neurodegeneration. To date, the molecular mechanisms that determine whether a synapse will persist versus being remodeled or eliminated remain poorly understood. Mutations in Drosophila stathmin were isolated in two independent genetic screens that sought mutations leading to impaired synapse stability at the Drosophila neuromuscular junction (NMJ). Here we demonstrate that Stathmin, a protein that associates with microtubules and can function as a point of signaling integration, is necessary to maintain the stability of the Drosophila NMJ. We show that Stathmin protein is widely distributed within motoneurons and that loss of Stathmin causes impaired NMJ growth and stability. In addition, we show that stathmin mutants display evidence of defective axonal transport, a common feature associated with neuronal degeneration and altered synapse stability. The disassembly of the NMJ in stathmin includes a predictable sequence of cytological events, suggesting that a common program of synapse disassembly is induced following the loss of Stathmin protein. These data define a required function for Stathmin during synapse maintenance in a model system in which there is only a single stathmin gene, enabling future genetic investigation of Stathmin function with potential relevance to the cause and progression of neuromuscular degenerative disease.

  4. Enzyme stabilization by linear chain polymers in ultrafiltration membrane reactors

    Energy Technology Data Exchange (ETDEWEB)

    Greco, G.; Gianfreda, L.

    1981-10-01

    The experimental results discussed in this article concern pi-nitrophenylphosphate hydrolysis by acid phosphatase in an ultrafiltration membrane reactor. The basic conclusions drawn are : 1) Linking the enzyme to a soluble support does not give rise to an increase in its stability while the chemical manipulations involved result in marked reductions in enzymic activity. 2) Enzyme entrapment within a proteic gel produces a considerable increase in its thermal stability as compared to the diluted native enzyme; this presumably stems from drastic reductions in enzyme mobility. 3) Correspondingly, considerable reductions occur in enzyme activity that depend on substrate mass transfer resistances within the gel layer. 4) Small amounts of linear chain water-soluble synthetic polymers (polyacrylamides) give rise to high macromolecular concentration levels in the reactor region where the enzyme is dynamically immobilized and produce the same enzyme stabilization as gel entrapment. 5) Only minor substrate mass transfer limitations take place in this region and hence enzyme activity is virtually unaffected. 6) Both effects (stabilization and slight activity reduction) seem not to depend strongly on the characteristics of the soluble polymer (molecular weight and ionic character). (Refs. 16).

  5. Experimental and theoretical investigations into the stability of cyclic aminals

    Directory of Open Access Journals (Sweden)

    Edgar Sawatzky

    2016-10-01

    Full Text Available Background: Cyclic aminals are core features of natural products, drug molecules and important synthetic intermediates. Despite their relevance, systematic investigations into their stability towards hydrolysis depending on the pH value are lacking.Results: A set of cyclic aminals was synthesized and their stability quantified by kinetic measurements. Steric and electronic effects were investigated by choosing appropriate groups. Both molecular mechanics (MM and density functional theory (DFT based studies were applied to support and explain the results obtained. Rapid decomposition is observed in acidic aqueous media for all cyclic aminals which occurs as a reversible reaction. Electronic effects do not seem relevant with regard to stability, but the magnitude of the conformational energy of the ring system and pKa values of the N-3 nitrogen atom.Conclusion: Cyclic aminals are stable compounds when not exposed to acidic media and their stability is mainly dependent on the conformational energy of the ring system. Therefore, for the preparation and work-up of these valuable synthetic intermediates and natural products, appropriate conditions have to be chosen and for application as drug molecules their sensitivity towards hydrolysis has to be taken into account.

  6. Cluster stability scores for microarray data in cancer studies

    Directory of Open Access Journals (Sweden)

    Ghosh Debashis

    2003-09-01

    Full Text Available Abstract Background A potential benefit of profiling of tissue samples using microarrays is the generation of molecular fingerprints that will define subtypes of disease. Hierarchical clustering has been the primary analytical tool used to define disease subtypes from microarray experiments in cancer settings. Assessing cluster reliability poses a major complication in analyzing output from clustering procedures. While most work has focused on estimating the number of clusters in a dataset, the question of stability of individual-level clusters has not been addressed. Results We address this problem by developing cluster stability scores using subsampling techniques. These scores exploit the redundancy in biologically discriminatory information on the chip. Our approach is generic and can be used with any clustering method. We propose procedures for calculating cluster stability scores for situations involving both known and unknown numbers of clusters. We also develop cluster-size adjusted stability scores. The method is illustrated by application to data three cancer studies; one involving childhood cancers, the second involving B-cell lymphoma, and the final is from a malignant melanoma study. Availability Code implementing the proposed analytic method can be obtained at the second author's website.

  7. On core stability and extendability

    OpenAIRE

    Shellshear, Evan

    2007-01-01

    This paper investigates conditions under which the core of a TU cooperative game is stable. In particular the author extends the idea of extendability to find new conditions under which the core is stable. It is also shown that these new conditions are not necessary for core stability.

  8. Stability of Molten Core Materials

    Energy Technology Data Exchange (ETDEWEB)

    Layne Pincock; Wendell Hintze

    2013-01-01

    The purpose of this report is to document a literature and data search for data and information pertaining to the stability of nuclear reactor molten core materials. This includes data and analysis from TMI-2 fuel and INL’s LOFT (Loss of Fluid Test) reactor project and other sources.

  9. Transverse stability of Kawahara solitons

    DEFF Research Database (Denmark)

    Karpman, V.I.

    1993-01-01

    The transverse stability of the planar solitons described by the fifth-order Korteweg-de Vries equation (Kawahara solitons) is studied. It is shown that the planar solitons are unstable with respect to bending if the coefficient at the fifth-derivative term is positive and stable if it is negative...

  10. The condition for dynamic stability

    NARCIS (Netherlands)

    Hof, AL; Gazendam, MGJ; Sinke, WE

    2005-01-01

    The well-known condition for standing stability in static situations is that the vertical projection of the centre of mass (CoM) should be within the base of support (BoS). On the basis of a simple inverted pendulum model, an extension of this rule is proposed for dynamical situations: the position

  11. Homological stability of diffeomorphism groups

    DEFF Research Database (Denmark)

    Berglund, Alexander; Madsen, Ib Henning

    2013-01-01

    In this paper we prove a stability theorem for block diffeomorphisms of 2d -dimensional manifolds that are connected sums of S d ×S d . Combining this with a recent theorem of S. Galatius and O. Randal-Williams and Morlet’s lemma of disjunction, we determine the homology of the classifying space ...

  12. The stability of lifestyle behaviour

    NARCIS (Netherlands)

    Mulder, M; Ranchor, AV; Sanderman, R; Bouma, J; van den Heuvel, WJA

    1998-01-01

    Background The stability of Lifestyle behaviour has been studied over a 4-year period in a sample of 1400 men in The Netherlands. The influence of both socioeconomic status and age was studied in relation to lifestyle behaviour change. Methods Lifestyle behaviour was analysed by means of index score

  13. Quantum Contextuality with Stabilizer States

    Directory of Open Access Journals (Sweden)

    Jiri Vala

    2013-06-01

    Full Text Available The Pauli groups are ubiquitous in quantum information theory because of their usefulness in describing quantum states and operations and their readily understood symmetry properties. In addition, the most well-understood quantum error correcting codes—stabilizer codes—are built using Pauli operators. The eigenstates of these operators—stabilizer states—display a structure (e.g., mutual orthogonality relationships that has made them useful in examples of multi-qubit non-locality and contextuality. Here, we apply the graph-theoretical contextuality formalism of Cabello, Severini and Winter to sets of stabilizer states, with particular attention to the effect of generalizing two-level qubit systems to odd prime d-level qudit systems. While state-independent contextuality using two-qubit states does not generalize to qudits, we show explicitly how state-dependent contextuality associated with a Bell inequality does generalize. Along the way we note various structural properties of stabilizer states, with respect to their orthogonality relationships, which may be of independent interest.

  14. Stochastic Shadowing and Stochastic Stability

    OpenAIRE

    Todorov, Dmitry

    2014-01-01

    The notion of stochastic shadowing property is introduced. Relations to stochastic stability and standard shadowing are studied. Using tent map as an example it is proved that, in contrast to what happens for standard shadowing, there are significantly non-uniformly hyperbolic systems that satisfy stochastic shadowing property.

  15. Simultaneous stabilization using genetic algorithms

    Energy Technology Data Exchange (ETDEWEB)

    Benson, R.W.; Schmitendorf, W.E. (California Univ., Irvine, CA (USA). Dept. of Mechanical Engineering)

    1991-01-01

    This paper considers the problem of simultaneously stabilizing a set of plants using full state feedback. The problem is converted to a simple optimization problem which is solved by a genetic algorithm. Several examples demonstrate the utility of this method. 14 refs., 8 figs.

  16. Genome stability in Caenorhabditis elegans

    NARCIS (Netherlands)

    Haaften, G.W. van

    2006-01-01

    Genome stability is closely linked to cancer. Most, if not all tumor cells show some form of genome instability, mutations can range from single point mutations to gross chromosomal rearrangements and aneuploidy. Genome instability is believed to be the driving force behind tumorigenesis. In order t

  17. Postmortem stability of Ebola virus.

    Science.gov (United States)

    Prescott, Joseph; Bushmaker, Trenton; Fischer, Robert; Miazgowicz, Kerri; Judson, Seth; Munster, Vincent J

    2015-05-01

    The ongoing Ebola virus outbreak in West Africa has highlighted questions regarding stability of the virus and detection of RNA from corpses. We used Ebola virus-infected macaques to model humans who died of Ebola virus disease. Viable virus was isolated <7 days posteuthanasia; viral RNA was detectable for 10 weeks.

  18. Gravitational Stability of Boson Stars

    CERN Document Server

    Kusmartsev, Fjodor V; Schunck, Franz E

    1991-01-01

    We investigate the stability of general-relativistic boson stars by classifying singularities of differential mappings and compare it with the results of perturbation theory. Depending on the particle number, the star has the following regimes of behavior: stable, metastable, pulsation, and collapse.

  19. Dynamical stability of Hamiltonian systems

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    Dynamical stability has become the center of study on Hamiltonian system. In this article we intro-duce the recent development in some areas closely related to this topic, such as the KAM theory, Mather theory, Arnolddiffusion and non-singular collision of n-body problem.

  20. Rudder roll stabilization for ships

    NARCIS (Netherlands)

    Amerongen, van J.; Klugt, van der P.G.M.; Nauta Lemke, van H.R.

    1990-01-01

    This paper describes the design of an autopilot for rudder roll stabilization for ships. This autopilot uses the rudder not only for course keeping but also for reduction of the roll. The system has a series of properties which make the controller design far from straightforward: the process has onl

  1. BOUNDARY STABILIZATION OF TIMOSHENKO BEAM

    Institute of Scientific and Technical Information of China (English)

    YAN Qingxu

    2000-01-01

    In this paper, the stabilization problem of Timoshenko beam by some nonlinear boundary feedback controls is considered. By virtue of nonlinear semigroup theory and energy-perturbed method, it is shown that the vibration of the beam under the proposed control action decays exponentially or in negative power of time t as t → ∞.

  2. Tren-based analogues of bacillibactin: structure and stability.

    Science.gov (United States)

    Dertz, Emily A; Xu, Jide; Raymond, Kenneth N

    2006-07-10

    Synthetic analogues were designed to highlight the effect of the glycine moiety of bacillibactin on the overall stability of the ferric complex as compared to synthetic analogues of enterobactin. Insertion of a variety of amino acids to catecholamide analogues based on a Tren (tris(2-aminoethyl)amine) backbone increased the overall acidity of the ligands, causing an enhancement of the stability of the resulting ferric complex as compared to TRENCAM. Solution thermodynamic behavior of these siderophores and their synthetic analogues was investigated through potentiometric and spectrophotometric titrations. X-ray crystallography, circular dichroism, and molecular modeling were used to determine the chirality and geometry of the ferric complexes of bacillibactin and its analogues. In contrast to the Tren scaffold, addition of a glycine to the catechol chelating arms causes an inversion of the trilactone backbone, resulting in opposite chiralities of the two siderophores and a destabilization of the ferric complex of bacillibactin compared to ferric enterobactin.

  3. Increased polyamines alter chromatin and stabilize autoantigens in autoimmune diseases

    Directory of Open Access Journals (Sweden)

    Wesley H. Brooks

    2013-04-01

    Full Text Available Polyamines are small cations with unique combinations of charge and length that give them many putative interactions in cells. Polyamines are essential since they are involved in replication, transcription, translation, and stabilization of macro-molecular complexes. However, polyamine synthesis competes with cellular methylation for S-adenosylmethionine, the methyl donor. Also, polyamine degradation can generate reactive molecules like acrolein. Therefore, polyamine levels are tightly controlled. This control may be compromised in autoimmune diseases since elevated polyamine levels are seen in autoimmune diseases. Here a hypothesis is presented explaining how polyamines can stabilize autoantigens. In addition, the hypothesis explains how polyamines can inappropriately activate enzymes involved in NETosis, a process in which chromatin is modified and extruded from cells as extracellular traps that bind pathogens during an immune response. This polyamine-induced enzymatic activity can lead to an increase in NETosis resulting in release of autoantigenic material and tissue damage.

  4. Oxidative enzymatic gelation of sugar beet pectin for emulsion stabilization

    DEFF Research Database (Denmark)

    Abang Zaidel, Dayang Norulfairuz; Meyer, Anne S.

    2013-01-01

    Pectin from sugar beet is derived from the sugar beet pulp residue which results when sugar beets are processed for sucrose extraction. The sugar beet pectin has poor gelationability by the classic divalentcation molecular mechanism because of a relatively high acetylation degree and short...... polygalacturonate backbone chain length. However, due to the feruloyl-substitutions on the side chains, the sugar beet pectic polysaccharides can be cross-linked via enzyme catalyzed oxidation. The enzyme kinetics and functionality of such oxidativelycross-linked sugar beet pectin, in relation to stabilizing...... emulsions has recently been investigated in model food emulsions. This paper reviews the pectin chemistry, enzymatic oxidative gelation mechanisms, interaction mechanisms of the sugar beet pectin with the emulsion droplets and explores how the gelation affects the rheology and stability of emulsion systems...

  5. 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.

  6. Muscle giants: molecular scaffolds in sarcomerogenesis.

    Science.gov (United States)

    Kontrogianni-Konstantopoulos, Aikaterini; Ackermann, Maegen A; Bowman, Amber L; Yap, Solomon V; Bloch, Robert J

    2009-10-01

    Myofibrillogenesis in striated muscles is a highly complex process that depends on the coordinated assembly and integration of a large number of contractile, cytoskeletal, and signaling proteins into regular arrays, the sarcomeres. It is also associated with the stereotypical assembly of the sarcoplasmic reticulum and the transverse tubules around each sarcomere. Three giant, muscle-specific proteins, titin (3-4 MDa), nebulin (600-800 kDa), and obscurin (approximately 720-900 kDa), have been proposed to play important roles in the assembly and stabilization of sarcomeres. There is a large amount of data showing that each of these molecules interacts with several to many different protein ligands, regulating their activity and localizing them to particular sites within or surrounding sarcomeres. Consistent with this, mutations in each of these proteins have been linked to skeletal and cardiac myopathies or to muscular dystrophies. The evidence that any of them plays a role as a "molecular template," "molecular blueprint," or "molecular ruler" is less definitive, however. Here we review the structure and function of titin, nebulin, and obscurin, with the literature supporting a role for them as scaffolding molecules and the contradictory evidence regarding their roles as molecular guides in sarcomerogenesis.

  7. Molecular Population Genetics

    Science.gov (United States)

    Casillas, Sònia; Barbadilla, Antonio

    2017-01-01

    Molecular population genetics aims to explain genetic variation and molecular evolution from population genetics principles. The field was born 50 years ago with the first measures of genetic variation in allozyme loci, continued with the nucleotide sequencing era, and is currently in the era of population genomics. During this period, molecular population genetics has been revolutionized by progress in data acquisition and theoretical developments. The conceptual elegance of the neutral theory of molecular evolution or the footprint carved by natural selection on the patterns of genetic variation are two examples of the vast number of inspiring findings of population genetics research. Since the inception of the field, Drosophila has been the prominent model species: molecular variation in populations was first described in Drosophila and most of the population genetics hypotheses were tested in Drosophila species. In this review, we describe the main concepts, methods, and landmarks of molecular population genetics, using the Drosophila model as a reference. We describe the different genetic data sets made available by advances in molecular technologies, and the theoretical developments fostered by these data. Finally, we review the results and new insights provided by the population genomics approach, and conclude by enumerating challenges and new lines of inquiry posed by increasingly large population scale sequence data. PMID:28270526

  8. Stability of the perforated layer (PL) phase in diblock copolymer melts

    DEFF Research Database (Denmark)

    Hajduk, Damian A; Takenouchi, Hiroshi; Hillmyer, Marc A;

    1997-01-01

    We reexamine the stability of hexagonally modulated layer (HML) and hexagonally perforated layer (HPL) morphologies in a number of block copolymer systems of low to moderate molecular weight. Using small-angle X-ray scattering and dynamic mechanical spectroscopy, we show that these structures are...

  9. Induction in vitro and stability of Mycobacterium tuberculosis resistance to ofloxacin

    Institute of Scientific and Technical Information of China (English)

    杨华

    2014-01-01

    Objective To induct Mycobacterium tuberculosis(MTB)resistance with ofloxacin(Ofx)of stepwise increasing concentration in vitro,investigate stability to fluoroquinolone(FQs)antibiotic of MTB,and analyze the molecular mechanism and mutation specialty of drug resistance preliminarily.Methods MTB Standard strain

  10. Stability of polymersomes prepared by size exclusion chromatography and extrusion

    OpenAIRE

    Bartenstein, Julia E.; Robertson, James; Battaglia, Giuseppe; Wuge H. Briscoe

    2016-01-01

    In this work, stability of poly(butadiene)-poly(ethylene oxide) (PBD-PEO) polymersomes, self-assembled from two polymers with different molecular weights (PBD32-PEO21 and PBD125-PEO80) in either pure H2O or phosphate buffered saline (PBS), is studied. Polymersome dispersions usually show large polydispersity, and it is thus desirable to separate different-sized vesicles if a narrow size distribution is required, e.g. for model systems in certain applications. This is typically achieved by ext...

  11. Exploring the stability of dimers through protein structure topology.

    Science.gov (United States)

    Di Paola, Luisa; Mei, Giampiero; Di Venere, Almerinda; Giuliani, Alessandro

    2016-01-01

    Protein homodimers pose some intriguing questions about the relation between structure and stability. We approached the problem by means of a topological methodology based on protein contact networks. We correlated local interface descriptors with structure and energy global properties of the systems under analysis. We demonstrated that the graph energy, formerly applied to the analysis of unconjugated hydrocarbons structures, is the bridge between the topological and energetic description of protein complexes. This is a first step for the generation of a "protein structural formula", analogous to the molecular graphs in organic chemistry.

  12. USING BIOPOLYMERS TO STABILIZE THE PROTEIN OXYGEN FOAM

    Directory of Open Access Journals (Sweden)

    N. V. Nepovinnyh

    2013-01-01

    Full Text Available The cottage cheese whey as an oxygen cocktail foaming base and natural juices as a flavoring ingredient are analyzed. The lifetime of foam generated by the serum proteins is not long: foam falls off rapidly; because from the foam liquid is released (syneresis. The effects of plant polysaccharides on the stabilization of the protein foam oxygen cocktail is studied. It was shown that the use of plant polysaccharides (guar gum, high methoxyl citrus pectin, locust been gum prolong the life of the foam up to 20 times, compared with conventional blowing agents. It was found that oxygen foam properties depend on the molecular weight of guar gum.

  13. 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

  14. Molecular heat pump.

    Science.gov (United States)

    Segal, Dvira; Nitzan, Abraham

    2006-02-01

    We propose a molecular device that pumps heat against a thermal gradient. The system consists of a molecular element connecting two thermal reservoirs that are characterized by different spectral properties. The pumping action is achieved by applying an external force that periodically modulates molecular levels. This modulation affects periodic oscillations of the internal temperature of the molecule and the strength of its coupling to each reservoir resulting in a net heat flow in the desired direction. The heat flow is examined in the slow and fast modulation limits and for different modulation wave forms, thus making it possible to optimize the device performance.

  15. Molecularly Imprinted Membranes

    Directory of Open Access Journals (Sweden)

    Fabrizio Caldera

    2012-07-01

    Full Text Available Although the roots of molecularly imprinted polymers lie in the beginning of 1930s in the past century, they have had an exponential growth only 40–50 years later by the works of Wulff and especially by Mosbach. More recently, it was also proved that molecular imprinted membranes (i.e., polymer thin films that show recognition properties at molecular level of the template molecule are used in their formation. Different procedures and potential application in separation processes and catalysis are reported. The influences of different parameters on the discrimination abilities are also discussed.

  16. Nitrogen oxides under pressure: stability, ionization, polymerization, and superconductivity.

    Science.gov (United States)

    Li, Dongxu; Oganov, Artem R; Dong, Xiao; Zhou, Xiang-Feng; Zhu, Qiang; Qian, Guangrui; Dong, Huafeng

    2015-11-17

    Nitrogen oxides are textbook class of molecular compounds, with extensive industrial applications. Nitrogen and oxygen are also among the most abundant elements in the universe. We explore the N-O system at 0 K and up to 500 GPa though ab initio evolutionary simulations. Results show that two phase transformations of stable molecular NO2 occur at 7 and 64 GPa, and followed by decomposition of NO2 at 91 GPa. All of the NO(+)NO3(-) structures are found to be metastable at T = 0 K, so experimentally reported ionic NO(+)NO3(-) is either metastable or stabilized by temperature. N2O5 becomes stable at 9 GPa, and transforms from P-1 to C2/c structure at 51 GPa. NO becomes thermodynamically stable at 198 GPa. This polymeric phase is superconducting (Tc = 2.0 K) and contains a -N-N- backbone.

  17. Protein stability: a crystallographer’s perspective

    Energy Technology Data Exchange (ETDEWEB)

    Deller, Marc C., E-mail: mdeller@stanford.edu [Stanford University, Shriram Center, 443 Via Ortega, Room 097, MC5082, Stanford, CA 94305-4125 (United States); Kong, Leopold [National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institutes of Health (NIH), Building 8, Room 1A03, 8 Center Drive, Bethesda, MD 20814 (United States); Rupp, Bernhard [k.-k. Hofkristallamt, 91 Audrey Place, Vista, CA 92084 (United States); Medical University of Innsbruck, Schöpfstrasse 41, A-6020 Innsbruck (Austria)

    2016-01-26

    An understanding of protein stability is essential for optimizing the expression, purification and crystallization of proteins. In this review, discussion will focus on factors affecting protein stability on a somewhat practical level, particularly from the view of a protein crystallographer. Protein stability is a topic of major interest for the biotechnology, pharmaceutical and food industries, in addition to being a daily consideration for academic researchers studying proteins. An understanding of protein stability is essential for optimizing the expression, purification, formulation, storage and structural studies of proteins. In this review, discussion will focus on factors affecting protein stability, on a somewhat practical level, particularly from the view of a protein crystallographer. The differences between protein conformational stability and protein compositional stability will be discussed, along with a brief introduction to key methods useful for analyzing protein stability. Finally, tactics for addressing protein-stability issues during protein expression, purification and crystallization will be discussed.

  18. Soy protein isolate molecular level contributions to bulk adhesive properties

    Science.gov (United States)

    Shera, Jeanne Norton

    Increasing environmental awareness and the recognized health hazards of formaldehyde-based resins has prompted a strong demand for environmentally-responsible adhesives for wood composites. Soy protein-based adhesives have been shown to be commercially viable with 90-day shelf stability and composite physical properties comparable to those of commercial formaldehyde-based particleboards. The main research focus is to isolate and characterize the molecular level features in soy protein isolate responsible for providing mechanical properties, storage stability, and water resistance during adhesive formulation, processing, and wood composite fabrication. Commercial composite board will be reviewed to enhance our understanding of the individual components and processes required for particleboard production. The levels of protein structure will be defined and an overview of current bio-based technology will be presented. In the process, the logic for utilizing soy protein as a sole binder in the adhesive will be reinforced. Variables such as adhesive components, pH, divalent ions, blend aging, protein molecular weight, formulation solids content, and soy protein functionalization will relate the bulk properties of soy protein adhesives to the molecular configuration of the soybean protein. This work has demonstrated that when intermolecular beta-sheet interactions and protein long-range order is disrupted, viscosity and mechanical properties decrease. Storage stability can be maintained through the stabilization of intermolecular beta-sheet interactions. When molecular weight is reduced through enzymatic digestion, long-range order is disrupted and viscosity and mechanical properties decrease accordingly. Processibility and physical properties must be balanced to increase solids while maintaining low viscosity, desirable mechanical properties, and adequate storage stability. The structure of the soybean protein must be related to the particleboard bulk mechanical

  19. Theoretical study of structure and stability of small gadolinium carboxylate complexes in liquid scintillator solvents.

    Science.gov (United States)

    Huang, Pin-Wen

    2014-09-01

    The structural properties of three small gadolinium carboxylate complexes in three liquid scintillator solvents (pseudocumene, linear alkylbenzene, and phenyl xylylethane) were theoretically investigated using density functional theory (B3LYP/LC-RECP) and polarizable continuum model (PCM). The average interaction energy between gadolinium atom and carboxylate ligand (E(int)) and the energy difference of the highest singly occupied molecular orbital and lowest unoccupied molecular orbital (Δ(SL)) were calculated to evaluate and compare the relative stability of these complexes in solvents. The calculation results show that the larger (with a longer alkyl chain) gadolinium carboxylate complex has greater stability than the smaller one, while these gadolinium carboxylates in linear alkylbenzene were found to have greater stability than those in the other two solvents.

  20. The Molecular Foundry (TMF)

    Data.gov (United States)

    Federal Laboratory Consortium — Founded in 2006 by the Department of Energy (DOE), the Molecular Foundry is a critical part of the DOE's National Nanotechnology Initiative, a multi-agency framework...