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Physical Significance (physical + significance)
Selected AbstractsDiffusion induced segregation in the case of the ternary system sphalerite, chalcopyrite and cubaniteCRYSTAL RESEARCH AND TECHNOLOGY, Issue 11 2004T. Blesgen Abstract A mathematical model for describing natural and experimental diffusion induced segregation (DIS) in the case of a (Zn,Fe)S single crystal with three coexisting phases is derived. As main result, a new and quite general segregation principle for ternary systems is discovered where one phase has a flat free energy density and serves as catalyst for the segregation of the other two phases. The model includes also a stochastic noise term to represent fluctuations of the copper concentration. Numerical simulations in 2-d underline the physical significance of the model and allow to make quantitative predictions. (© 2004 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Flammability ranking of foliage species by factor analysis of physical and chemical pyric propertiesFIRE AND MATERIALS, Issue 6 2008Yanlong Shan Abstract In this paper, factor analysis is introduced to evaluate the flammability of 55 foliage species that may be used in China for construction of the fuel break network of forest strips with lower flammability. Six pyric parameters, i.e. air dry moisture content, absolute dry moisture content, ignition point, ash content, caloric value and extractive content, are measured and used as variables for factor analysis. The covariance analysis shows that four principal factors can be extracted to reflect the flammability in different physical and chemical senses. In terms of the contributions of the four factors to the variances and the physical significance of the relevant parameters, the four factors are, respectively, termed as ,flaming factor,' ,air dry factor,' ,ash factor' and ,absolute dry factor.' The stability of the factor analysis method is examined by a different number of samples considered, and the variation degrees of the orderings indicate that the method has high reliability to measure the total flammability of foliage species. The results of the flammability evaluation are verified by comparison with the recommended tree species in the Chinese technology standard. Copyright © 2008 John Wiley & Sons, Ltd. [source] Second-order analysis and design of steel structures allowing for member and frame imperfectionsINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 5 2005J. X. Gu Abstract Conventional linear analysis is deficient in handling the design of slender frames since the effective length and other non-linear effects are difficult to assess accurately. Some proposed non-linear analyses cannot be directly employed for practical design since they are unable to re-produce the buckling curves of the basic structural element, a simple column under axial force, by a single element per member. This paper describes an advanced element, using the same physical significance as the advanced and second-order analysis proposed by a number of researchers and the BS5950(2000) and AS4100 (1995), for practical design of slender steel frames. The proposed element captures the physical behaviour of a structural member that the buckling strength of the member can be predicted using a single element per member and without assuming any effective length. Copyright © 2004 John Wiley & Sons, Ltd. [source] Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2002Abstract QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169,176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (,16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 Å) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product,reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute ,40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1314,1322, 2002 [source] A molecular viewer for the analysis of TLS rigid-body motion in macromoleculesACTA CRYSTALLOGRAPHICA SECTION D, Issue 4 2005Jay Painter TLS (translation/libration/screw) models describe rigid-body vibrational motions of arbitrary objects. A single-group TLS model can be used to approximate the vibration of an entire protein molecule within a crystal lattice. More complex TLS models are broadly applicable to describing inter-domain and other internal vibrational modes of proteins. Such models can be derived and refined from crystallographic data, but they can also be used to describe the vibrational modes observed through other physical techniques or derived from molecular dynamics. The use of TLS models for protein motion has been relatively limited, partly because the physical meaning of the refined TLS parameters is not intuitive. Here, a molecular viewer, TLSView, is introduced using OpenGL and based on the mmLib library for describing and manipulating macromolecular structural models. This visualization tool allows an intuitive understanding of the physical significance of TLS models derived from crystallographic or other data and may be used as an interactive tool to display and interpret inter-domain or other motions in protein structural models. TLSView may also be used to prepare, analyze and validate TLS models for crystallographic refinement. [source] | |||||||||||||