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Stabilization Mechanisms (stabilization + mechanism)
Selected AbstractsStabilization mechanisms of organic matter in four temperate soils: Development and application of a conceptual model,JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE, Issue 1 2008Margit von Lützow Abstract Based on recent findings in the literature, we developed a process-oriented conceptual model that integrates all three process groups of organic matter (OM) stabilization in soils namely (1) selective preservation of recalcitrant compounds, (2) spatial inaccessibility to decomposer organisms, and (3) interactions of OM with minerals and metal ions. The model concept relates the diverse stabilization mechanisms to active, intermediate, and passive pools. The formation of the passive pool is regarded as hierarchical structured co-action of various processes that are active under specific pedogenetic conditions. To evaluate the model, we used data of pool sizes and turnover times of soil OM fractions from horizons of two acid forest and two agricultural soils. Selective preservation of recalcitrant compounds is relevant in the active pool and particularly in soil horizons with high C contents. Biogenic aggregation preserves OM in the intermediate pool and is limited to topsoil horizons. Spatial inaccessibility due to the occlusion of OM in clay microstructures and due to the formation of hydrophobic surfaces stabilizes OM in the passive pool. If present, charcoal contributes to the passive pool mainly in topsoil horizons. The importance of organo-mineral interactions for OM stabilization in the passive pool is well-known and increases with soil depth. Hydrophobicity is particularly relevant in acid soils and in soils with considerable inputs of charcoal. We conclude that the stabilization potentials of soils are site- and horizon-specific. Furthermore, management affects key stabilization mechanisms. Tillage increases the importance of organo-mineral interactions for OM stabilization, and in Ap horizons with high microbial activity and C turnover, organo-mineral interactions can contribute to OM stabilization in the intermediate pool. The application of our model showed that we need a better understanding of processes causing spatial inaccessibility of OM to decomposers in the passive pool. [source] The ,I/,III-tubulin isoforms and their complexes with antimitotic agentsFEBS JOURNAL, Issue 14 2006Docking, molecular dynamics studies Both microtubule destabilizer and stabilizer agents are important molecules in anticancer therapy. In particular, paclitaxel has been demonstrated to be effective for the treatment of ovarian, breast, and nonsmall cell lung carcinomas. It has been shown that emergence of resistance against this agent correlates with an increase in the relative abundance of tubulin isoform ,III and that the more recently discovered IDN5390 can be effectively used once resistance has emerged. In this paper, we analyze the binding modes of these antimitotic agents to type I and III isoforms of ,-tubulin by computational methods. Our results are able to provide a molecular explanation of the experimental data. Using the same protocol, we could also show that no preference for any of the two isoforms can be detected for epothilone A, a potentially very interesting drug for which no data about the emergence of resistance is currently available. Our analysis provides structural insights about the recognition mode and the stabilization mechanism of these antimitotic agents and provides useful suggestions for the design of more potent and selective antimitotic agents. [source] Non-linear version of stabilized conforming nodal integration for Galerkin mesh-free methodsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 12 2002Jiun-Shyan Chen Abstract A stabilized conforming (SC) nodal integration, which meets the integration constraint in the Galerkin mesh-free approximation, is generalized for non-linear problems. Using a Lagrangian discretization, the integration constraints for SC nodal integration are imposed in the undeformed configuration. This is accomplished by introducing a Lagrangian strain smoothing to the deformation gradient, and by performing a nodal integration in the undeformed configuration. The proposed method is independent to the path dependency of the materials. An assumed strain method is employed to formulate the discrete equilibrium equations, and the smoothed deformation gradient serves as the stabilization mechanism in the nodally integrated variational equation. Eigenvalue analysis demonstrated that the proposed strain smoothing provides a stabilization to the nodally integrated discrete equations. By employing Lagrangian shape functions, the computation of smoothed gradient matrix for deformation gradient is only necessary in the initial stage, and it can be stored and reused in the subsequent load steps. A significant gain in computational efficiency is achieved, as well as enhanced accuracy, in comparison with the mesh-free solution using Gauss integration. The performance of the proposed method is shown to be quite robust in dealing with non-uniform discretization. Copyright © 2002 John Wiley & Sons, Ltd. [source] Atomic-resolution crystal structure of Borrelia burgdorferi outer surface protein A via surface engineeringPROTEIN SCIENCE, Issue 8 2006Koki Makabe Abstract Outer surface protein A (OspA) from Borrelia burgdorferi has an unusual dumbbell-shaped structure in which two globular domains are connected with a "single-layer" ,-sheet (SLB). The protein is highly soluble, and it has been recalcitrant to crystallization. Only OspA complexes with Fab fragments have been successfully crystallized. OspA contains a large number of Lys and Glu residues, and these "high entropy" residues may disfavor crystal packing because some of them would need to be immobilized in forming a crystal lattice. We rationally designed a total of 13 surface mutations in which Lys and Glu residues were replaced with Ala or Ser. We successfully crystallized the mutant OspA without a bound Fab fragment and extended structure analysis to a 1.15 Å resolution. The new high-resolution structure revealed a unique backbone hydration pattern of the SLB segment in which water molecules fill the "weak spots" on both faces of the antiparallel ,-sheet. These well-defined water molecules provide additional structural links between adjacent ,-strands, and thus they may be important for maintaining the rigidity of the SLB that inherently lacks tight packing afforded by a hydrophobic core. The structure also revealed new information on the side-chain dynamics and on a solvent-accessible cavity in the core of the C-terminal globular domain. This work demonstrates the utility of extensive surface mutation in crystallizing recalcitrant proteins and dramatically improving the resolution of crystal structures, and provides new insights into the stabilization mechanism of OspA. [source] Liquid-Phase Exfoliation of Nanotubes and GrapheneADVANCED FUNCTIONAL MATERIALS, Issue 23 2009Jonathan N. Coleman Abstract Many applications of carbon nanotubes require the exfoliation of the nanotubes to give individual tubes in the liquid phase. This requires the dispersion, exfoliation, and stabilization of nanotubes in a variety of liquids. In this paper recent work in this area is reviewed, focusing on results from the author's group. It begins by reviewing stabilization mechanisms before exploring research into the exfoliation of nanotubes in solvents, by using surfactants or biomolecules and by covalent attachment of molecules. The concentration dependence of the degree of exfoliation in each case will be highlighted. In addition research into the dispersion mechanism for each dispersant type is discussed. Most importantly, dispersion quality metrics for all dispersants are compared. From this analysis, it is concluded that functionalized nanotubes can be exfoliated to the greatest degree. Finally, the extension of this work to the liquid phase exfoliation of graphite to give graphene is reviewed. [source] On the Stability of Amorphous Minerals in Lobster CuticleADVANCED MATERIALS, Issue 40 2009Ali Al-Sawalmih In situ X-ray diffraction during heating of lobster cuticle reveals three regions of thermally induced transformations: 1)Chitin decomposition, 2) amorphous calcium carbonate (ACC) , calcite transformation, and 3) amorphous calcium phosphate (ACP) , hydroxyapatite transformation. These results provide new insights into the stabilization mechanisms of amorphous biominerals based on ACC and ACP. [source] CBS versus GLS stabilization of the incompressible Navier,Stokes equations and the role of the time step as stabilization parameterINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 2 2002R. Codina Abstract In this work we compare two apparently different stabilization procedures for the finite element approximation of the incompressible Navier,Stokes equations. The first is the characteristic-based split (CBS). It combines the characteristic Galerkin method to deal with convection dominated flows with a classical splitting technique, which in some cases allows us to use equal velocity,pressure interpolations. The second approach is the Galerkin-least-squares (GLS) method, in which a least-squares form of the element residual is added to the basic Galerkin equations. It is shown that both formulations display similar stabilization mechanisms, provided the stabilization parameter of the GLS method is identified with the time step of the CBS approach. This identification can be understood from a formal Fourier analysis of the linearized problem. Copyright © 2001 John Wiley & Sons, Ltd. [source] Stabilization mechanisms of organic matter in four temperate soils: Development and application of a conceptual model,JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE, Issue 1 2008Margit von Lützow Abstract Based on recent findings in the literature, we developed a process-oriented conceptual model that integrates all three process groups of organic matter (OM) stabilization in soils namely (1) selective preservation of recalcitrant compounds, (2) spatial inaccessibility to decomposer organisms, and (3) interactions of OM with minerals and metal ions. The model concept relates the diverse stabilization mechanisms to active, intermediate, and passive pools. The formation of the passive pool is regarded as hierarchical structured co-action of various processes that are active under specific pedogenetic conditions. To evaluate the model, we used data of pool sizes and turnover times of soil OM fractions from horizons of two acid forest and two agricultural soils. Selective preservation of recalcitrant compounds is relevant in the active pool and particularly in soil horizons with high C contents. Biogenic aggregation preserves OM in the intermediate pool and is limited to topsoil horizons. Spatial inaccessibility due to the occlusion of OM in clay microstructures and due to the formation of hydrophobic surfaces stabilizes OM in the passive pool. If present, charcoal contributes to the passive pool mainly in topsoil horizons. The importance of organo-mineral interactions for OM stabilization in the passive pool is well-known and increases with soil depth. Hydrophobicity is particularly relevant in acid soils and in soils with considerable inputs of charcoal. We conclude that the stabilization potentials of soils are site- and horizon-specific. Furthermore, management affects key stabilization mechanisms. Tillage increases the importance of organo-mineral interactions for OM stabilization, and in Ap horizons with high microbial activity and C turnover, organo-mineral interactions can contribute to OM stabilization in the intermediate pool. The application of our model showed that we need a better understanding of processes causing spatial inaccessibility of OM to decomposers in the passive pool. [source] Effect of hindered piperidine light stabilizer molecular structure and UV absorber addition on the oxidation of HDPE.JOURNAL OF VINYL & ADDITIVE TECHNOLOGY, Issue 4 2004Part 2: Mechanistic aspects, electron spin resonance spectroscopy study, molecular modeling The first in this series of papers explored the effect of the structural characteristics of 2,2,6,6-tetramethylpiperidine-based hindered amine light stabilizers (HALS) on the thermal and photostabilization of high-density polyethylene. In the second part, the energies (stabilities) of the nitroxyl radicals and various intermediate species have been predicted using AccuModel® and related to stabilization performance and electron spin resonance (ESR) spectral data. Nitroxyl radicals with low predicted stability generally afforded improved thermal and photostabilization. ESR spectra were used to obtain values of nitroxyl radical concentration ([>NO·]) and g -factor as a function of pre-aging time for combinations of pre-aged HDPE and >NH HALS. Demethylation reactions of > N-methyl HALS resulted in uselessly weak ESR spectra. The HALS that afforded poor thermal oxidative stabilization gave rise to pronounced minima in [>NO·] that coincided with a maximum in hydroperoxide concentration. The g -factor values indicated that a predominant nitroxyl canonical form generally promoted superior thermal oxidative stabilization, whereas a predominance of the dipolar N·+O, form promoted superior photo-oxidative stabilization. These trends may be related to greater radical-scavenging and peroxide-trapping effects, respectively. Molecular modeling and ESR spectra can therefore provide valuable insight into the effectiveness of HALS and stabilization mechanisms. J. Vinyl Addit. Technol. 10:159,167, 2004. © 2004 Society of Plastics Engineers. [source] | ||||||||||||||||