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Detailed Structure (detailed + structure)
Selected AbstractsInnovation of visualized interactive tools for learning molecular simulation curriculumCOMPUTER APPLICATIONS IN ENGINEERING EDUCATION, Issue 1 2010Wen-Tsai Sung Abstract The goal of molecular simulation stability is to predict the detailed structure and physical properties of molecules in bioengineer's experiment curriculum. This work succeeds in citing minimum energy and some computer graphics technologies to support this theme. Molecular structure is that given the uncountable number of possible conformations for a protein, how we can determine the lowest energy structure. In this article the authors employed the previous researches-WebDeGrator and some existing molecular graphics tools to simulate various protein folding, ligand acceptor interaction, and molecular visualization. For this reason, bioengineer experimental curriculum will be visualization and interactive among learning members. Finally, Simpson's Taxonomy and pre- and post-test examinations are applied to System Evaluation, and molecular simulation and minimum energy will be discussed. © 2009 Wiley Periodicals, Inc. Comput Appl Eng Educ 18: 28,40, 2010; Published online in Wiley InterScience (www.interscience.wiley.com); DOI 10.1002/cae.20226 [source] Sequential integrated inversion of refraction and wide-angle reflection traveltimes and gravity data for two-dimensional velocity structuresGEOPHYSICAL JOURNAL INTERNATIONAL, Issue 3 2000Rosaria Tondi A new algorithm is presented for the integrated 2-D inversion of seismic traveltime and gravity data. The algorithm adopts the ,maximum likelihood' regularization scheme. We construct a ,probability density function' which includes three kinds of information: information derived from gravity measurements; information derived from the seismic traveltime inversion procedure applied to the model; and information on the physical correlation among the density and the velocity parameters. We assume a linear relation between density and velocity, which can be node-dependent; that is, we can choose different relationships for different parts of the velocity,density grid. In addition, our procedure allows us to consider a covariance matrix related to the error propagation in linking density to velocity. We use seismic data to estimate starting velocity values and the position of boundary nodes. Subsequently, the sequential integrated inversion (SII) optimizes the layer velocities and densities for our models. The procedure is applicable, as an additional step, to any type of seismic tomographic inversion. We illustrate the method by comparing the velocity models recovered from a standard seismic traveltime inversion with those retrieved using our algorithm. The inversion of synthetic data calculated for a 2-D isotropic, laterally inhomogeneous model shows the stability and accuracy of this procedure, demonstrates the improvements to the recovery of true velocity anomalies, and proves that this technique can efficiently overcome some of the limitations of both gravity and seismic traveltime inversions, when they are used independently. An interpretation of field data from the 1994 Vesuvius test experiment is also presented. At depths down to 4.5 km, the model retrieved after a SII shows a more detailed structure than the model obtained from an interpretation of seismic traveltime only, and yields additional information for a further study of the area. [source] Time-Resolved Small-Angle Neutron Scattering as a Tool for Studying Controlled Release from Liposomes using Polymer-Enzyme ConjugatesMACROMOLECULAR RAPID COMMUNICATIONS, Issue 19 2010Elaine L. Ferguson Abstract The action of phospholipase A2 (PLA2) on 1,2-dipalmitoyl- sn -glycero-3-phosphocholine (DPPC) liposomes (vesicles) , an integral component in the polymer enzyme liposome therapy (PELT) mechanism (R. Duncan et al., J. Controlled Release2001, 74, 135) for the controlled delivery of poorly soluble therapeutic molecules within liposomes , may be "masked" by conjugation to the biodegradable polymer dextrin and subsequently regenerated by the endogenous enzyme , -amylase that degrades the dextrin; that is, incorporating the so-called polymer-unmasked-masked protein therapy (PUMPT) approach (R. Duncan, et al. Biomacromolecules2008, 9, 1146). Small-angle neutron scattering (SANS) has been used to quantify the detailed structure of DPPC liposomes and any perturbation in that structure induced by the presence of PLA2 in native, "masked" (dextrin,PLA2 conjugate) and an in situ , -amylase-unmasked form. A time-dependent degradation of the vesicular structure was observed for the two active PLA2 cases, but not for the masked case. This study demonstrates that the PLA2 -induced hydrolysis of the DPPC , and the associated rupture of the liposome and the release of the enclosed material , may be controlled through masking with dextrin. Accordingly, the viability of using such a combinatorial nanomedicine approach as a general route for the controlled delivery of poorly soluble therapeutic molecules is shown. [source] 3C 254: MERLIN observations of a highly asymmetric quasarMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2006P. Thomasson ABSTRACT Multifrequency, high-resolution radio observations of the quasar 3C 254 using the Multi-Element Radio-linked Interferometer Network (MERLIN) are presented. The quasar has a highly asymmetric radio structure, with the eastern component of the double-lobed structure being much closer to the nucleus and significantly less polarized than the western one. However, the two lobes are more symmetric in their total flux densities. The observations show the detailed structure of the hotspots which are very different on opposite sides of the radio core, reveal no radio jet and suggest that the oppositely directed jets may be intrinsically asymmetric. [source] Variability in active galactic nuclei: confrontation of models with observationsMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 1 2002M.R.S. Hawkins The variability of active galactic nuclei (AGN) has long held the promise of shedding light on their detailed structure, and possibly other astrophysical phenomena. Different emission mechanisms lead to different patterns of variability in flux, which are in principle easily distinguishable. Recent predictions for the expected spectrum of variations for various models are now in such a form that they can be compared with the observed statistical properties of AGN light curves from large-scale monitoring programmes. In this paper, we use the results of a long-term monitoring programme of a large sample of quasars and Seyfert galaxies, as well as individual light curves from the literature, to distinguish between the various model predictions. The results favour a model based on accretion disc instability over the starburst model, where the variation comes from a succession of supernova bursts, but it also appears that much of the observed variation in quasars is due to gravitational microlensing. [source] The structure of the solar convective overshooting zoneMONTHLY NOTICES OF THE ROYAL ASTRONOMICAL SOCIETY, Issue 4 2001D.R. Xiong Using a non-local theory of convection, we calculated the structure of the solar convection zone, paying special attention to the detailed structure of the lower overshooting zone. Our results show that an extended transition zone exists near the bottom of the convection zone, where the temperature gradient turns smoothly from adiabatic in the convection zone to radiative in solar interior. A super-radiative temperature region is found in the overshooting zone under the solar convection zone, where , , and . The extension of the super-radiative region (defined by l is about 0.63 HP (0.053 R,). A careful comparison of the distribution of adiabatic sound speed and density with the local one is carried out. It is found, strikingly, that the distribution of adiabatic sound speed and density of our model is roughly consistent with the results of reversion from solar oscillation observations. [source] Mesoscale simulations of organized convection: Importance of convective equilibriumTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 616 2006J. M. Done Abstract The validity of convective parametrization breaks down at the resolution of mesoscale models, and the success of parametrized versus explicit treatments of convection is likely to depend on the large-scale environment. In this paper we examine the hypothesis that a key feature determining the sensitivity to the environment is whether the forcing of convection is sufficiently homogeneous and slowly varying that the convection can be considered to be in equilibrium. Two case studies of mesoscale convective systems over the UK, one where equilibrium conditions are expected and one where equilibrium is unlikely, are simulated using a mesoscale forecasting model. The time evolution of area-average convective available potential energy and the time evolution and magnitude of the timescale of convective adjustment are consistent with the hypothesis of equilibrium for case 1 and non-equilibrium for case 2. For each case, three experiments are performed with different partitionings between parametrized and explicit convection: fully parametrized convection, fully explicit convection and a simulation with significant amounts of both. In the equilibrium case, bulk properties of the convection such as area-integrated rain rates are insensitive to the treatment of convection. However, the detailed structure of the precipitation field changes; the simulation with parametrized convection behaves well and produces a smooth field that follows the forcing region, and the simulation with explicit convection has a small number of localized intense regions of precipitation that track with the mid-levelflow. For the non-equilibrium case, bulk properties of the convection such as area-integrated rain rates are sensitive to the treatment of convection. The simulation with explicit convection behaves similarly to the equilibrium case with a few localized precipitation regions. In contrast, the cumulus parametrization fails dramatically and develops intense propagating bows of precipitation that were not observed. The simulations with both parametrized and explicit convection follow the pattern seen in the other experiments, with a transition over the duration of the run from parametrized to explicit precipitation. The impact of convection on the large-scaleflow, as measured by upper-level wind and potential-vorticity perturbations, is very sensitive to the partitioning of convection for both cases. © Royal Meteorological Society, 2006. Contributions by P. A. Clark and M. E. B. Gray are Crown Copyright. [source] Preliminary crystallographic characterization of the Grb2 SH2 domain in complex with a FAK-derived phosphotyrosyl peptideACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 2 2010Hsiao-Hsin Chen Growth factor receptor-bound protein 2 (Grb2) is an adaptor protein with a single SH2 domain that specifically binds to focal adhesion kinase (FAK) when residue Tyr925 of FAK is phosphorylated. The Grb2,FAK interaction is associated with cellular integrin-activated signal transduction events leading to the activation of the Ras-MAPK pathway. Crystals of the Grb2 SH2 domain in complex with a phosphopeptide corresponding to residues 921,930 of FAK have been obtained using the sitting-drop vapour-diffusion technique. The crystals belonged to space group P3121, with unit-cell parameters a = b = 102.7, c = 127.6,Å, , = , = 90.0, , = 120.0°. A diffraction data set was collected from a flash-cooled crystal at 100,K to 2.49,Å resolution using synchrotron radiation. Structure determination by molecular replacement and analysis of the detailed structure of the complex are currently in progress. [source] Structure of an elastin-mimetic polypeptide by solid-state NMR chemical shift analysisBIOPOLYMERS, Issue 2 2003M. Hong Abstract The conformation of an elastin-mimetic recombinant protein, [(VPGVG)4(VPGKG)]39, is investigated using solid-state NMR spectroscopy. The protein is extensively labeled with 13C and 15N, and two-dimensional 13C- 13C and 15N- 13C correlation experiments were carried out to resolve and assign the isotropic chemical shifts of the various sites. The Pro 15N, 13C,, and 13C, isotropic shifts, and the Gly-3 C, isotropic and anisotropic chemical shifts support the predominance of type-II ,-turn structure at the Pro-Gly pair but reject a type-I ,-turn. The Val-1 preceding Pro adopts mostly ,-sheet torsion angles, while the Val-4 chemical shifts are intermediate between those of helix and sheet. The protein exhibits a significant conformational distribution, shown by the broad line widths of the 15N and 13C spectra. The average chemical shifts of the solid protein are similar to the values in solution, suggesting that the low-hydration polypeptide maintains the same conformation as in solution. The ability to measure these conformational restraints by solid-state NMR opens the possibility of determining the detailed structure of this class of fibrous proteins through torsion angles and distances. © 2003 Wiley Periodicals, Inc. Biopolymers 70: 158,168, 2003 [source] The Enantiomer of Octreotate Binds to All Five Somatostatin Receptors with Almost Equal Micromolar Affinity , A Comparison with SANDOSTATIN®CHEMISTRY & BIODIVERSITY, Issue 7 2008James Gardiner Abstract Octreotate (1b) is the octreotide (SANDOSTATIN®; 1a) analogue, carrying a C-terminal CO2H (Thr) instead of the CH2OH (threoninol) group. In pursuit of our interest in unnatural peptides, we have now synthesized (by the solid-phase Fmoc method) the enantiomeric form 2 of octreotate and determined its affinity for the five human somatostatin (SRIF) receptors (hsst1,5). The binding was found to be 9.1, 4.1, 1.0, 1.4, and 4.2,,M, respectively. This almost equal one-digit micromolar affinity of ent -octreotate (2) to all five receptors contrasts with the behavior of most other somatostatin mimics including SANDOSTATIN® (octreotide; 1a) and [Tyr3]-octreotate (1c), which have affinities for the various receptors differing up to and above 104 -fold. Thus, the structure of the new compound does not prevent binding, albeit more weakly than its pseudo -enantiomer octreotide, and there is hardly any selectivity of the peptide,protein interaction (PPI) for any one of the five SRIF G-protein coupled receptors (GPCRs). Since the detailed structure(s) of these membrane-embedded receptors is unknown (no X-ray structure!), the result described here may be useful for modeling structures by comparing the affinities of the numerous known somatostatin mimics. [source] A comparative study of transformation of micellar structures in CTAB and TTAB binary systems using Positron Lifetime SpectroscopyPHYSICA STATUS SOLIDI (C) - CURRENT TOPICS IN SOLID STATE PHYSICS, Issue 11 2009R. Yadav Abstract The micellar structures of cetyl-tri-methyl ammonium bromide (CTAB) and its homologues have been investigated employing several conventional techniques. However, due to lack of sensitivity inherent in these techniques and the perturbation introduced by the probe, the detailed structures of the aggregates in the so-called single phase regions of these systems are far from being fully understood. Positron has been found to be a useful non-destructive probe for investigating micellar structures in surfactant systems [1-3] The present study is an effort to get a better insight into the micellar structures and their transformations in CTAB and TTAB aqueous binary systems Positron lifetime spectroscopy has been employed to study these systems covering a wide range of surfactant concentrations. A comparative study of the results obtained for the two surfactant systems have been discussed in this paper. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] The wonders of magnetism,BIOELECTROMAGNETICS, Issue 1 2003Thomas S. Tenforde Abstract In this acceptance address for the Bioelectromagnetics Society's 2001 d'Arsonval Award, Dr. Tenforde reviews the highlights of the nonionizing field aspects of his research and scientific service career. These are focused in four areas: (a) development and application of microelectrophoretic methods to probe the surface chemistry of normal and cancerous cells; (b) research on the biophysical mechanisms of interaction and the dosimetry of static and extremely low frequency magnetic fields; (c) application of extremely high intensity magnetic fields in several spectroscopic methods for probing the detailed structures of large biological macromolecules; and (d) development of national and international guidelines for the exposure of workers and members of the general public to electromagnetic fields with frequencies spanning the entire nonionizing electromagnetic spectrum. Bioelectromagnetics 24:3,11, 2003. © 2002 Wiley-Liss, Inc. [source] | ||||||||||||||||