scholarly journals Probing turbulence in OMC1 at the star forming scale: observations and simulations

2006 ◽  
Vol 2 (S237) ◽  
pp. 183-187
Author(s):  
Maiken Gustafsson ◽  
Axel Brandenburg ◽  
Jean-Louis Lemaire ◽  
David Field
Keyword(s):  
Selection Effect ◽  
Power Laws ◽  
Structure Functions ◽  
Higher Order ◽  
Radial Velocities ◽  
Order Structure ◽  
Vibrationally Excited ◽  
Hydrodynamic Turbulence ◽  
Star Forming

AbstractUsing radial velocities of vibrationally excited H2 emission in OMC1 we present the structure functions and the scaling of the structure functions with their order at scales ranging from 70 AU to 30000 AU extending earlier related studies to scales lower by two orders of magnitude. The structure functions for OMC1 show clear deviations from power laws at 1500 AU. The scaling of the higher order structure functions with order deviates from predicted theoretical scalings. Observational results are compared with simulations of supersonic hydrodynamic turbulence. The unusual scaling is explained as a selection effect of preferentially observing the shocked part of the gas. The simulations are unable to reproduce the deviations from power laws of the structure functions.

Scaling of second- and higher-order structure functions in turbulent boundary layers

2015 ◽  
Vol 769 ◽  
pp. 654-686 ◽  
Author(s):  
C. M. de Silva ◽  
I. Marusic ◽  
J. D. Woodcock ◽  
C. Meneveau
Keyword(s):  
Large Scale ◽  
Scaling Laws ◽  
Strong Support ◽  
Structure Functions ◽  
Higher Order ◽  
Wall Turbulence ◽  
Inertial Subrange ◽  
Order Structure ◽  
Logarithmic Scaling ◽  
Logarithmic Region

The statistical properties of wall turbulence in the logarithmic region are investigated using structure functions of the streamwise velocity. To this end, datasets that span several orders of magnitude of Reynolds numbers are used, up to$Re_{{\it\tau}}=O(10^{6})$, providing uniquely large scale separations for scrutinising previously proposed scaling laws. For the second-order structure functions strong support is found simultaneously for power-law scalings in the Kolmogorov inertial subrange and for logarithmic scaling at larger scales within the inertial range ($z<r\ll {\it\delta}$, where$z$is the distance from the wall,$r$the scale, and${\it\delta}$the boundary layer thickness). The observed scalings are shown to agree between the datasets, which include both temporal and spatial velocity signals and span from laboratory to atmospheric flows, showing a degree of universality in the results presented. An examination of higher even-order structure functions also shows support for logarithmic scaling behaviour for$z<r\ll {\it\delta}$, provided that the Reynolds number is sufficiently high. These findings are interpreted by generalising the work of Meneveau & Marusic (J. Fluid Mech., vol. 719, 2013) and introducing bridging relations between higher-order moments of velocity fluctuations and structure functions. Further, a physical model based on the attached-eddy hypothesis is utilised to derive various properties of the structure functions for the energy-containing scales of the logarithmic region. The descriptions derived from the model are shown to be supported by the experimental data.

Macrocycles of Higher Ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Macrocycles of Higher ortho-Phenylenes: Assembly and Folding

2019 ◽  
Author(s):  
Zacharias Kinney ◽  
Viraj Kirinda ◽  
Scott Hartley
Keyword(s):  
Chemical Shift ◽  
Higher Order ◽  
Order Structure ◽  
Complex Geometries ◽  
Spatial Relationships ◽  
Predominant Species ◽  
Bite Angle ◽  
Direct Assembly

<p>Higher-order structure in abiotic foldamer systems represents an important but largely unrealized goal. As one approach to this challenge, covalent assembly can be used to assemble macrocycles with foldamer subunits in well-defined spatial relationships. Such systems have previously been shown to exhibit self-sorting, new folding motifs, and dynamic stereoisomerism, yet there remain important questions about the interplay between folding and macrocyclization and the effect of structural confinement on folding behavior. Here, we explore the dynamic covalent assembly of extended <i>ortho</i>-phenylenes (hexamer and decamer) with rod-shaped linkers. Characteristic <sup>1</sup>H chemical shift differences between cyclic and acyclic systems can be compared with computational conformer libraries to determine the folding states of the macrocycles. We show that the bite angle provides a measure of the fit of an <i>o</i>-phenylene conformer within a shape-persistent macrocycle, affecting both assembly and ultimate folding behavior. For the <i>o</i>-phenylene hexamer, the bite angle and conformer stability work synergistically to direct assembly toward triangular [3+3] macrocycles of well-folded oligomers. For the decamer, the energetic accessibility of conformers with small bite angles allows [2+2] macrocycles to be formed as the predominant species. In these systems, the <i>o</i>-phenylenes are forced into unusual folding states, preferentially adopting a backbone geometry with distinct helical blocks of opposite handedness. The results show that simple geometric restrictions can be used to direct foldamers toward increasingly complex geometries.</p>

Current Trends in Biotherapeutic Higher Order Structure Characterization by Irreversible Covalent Footprinting Mass Spectrometry

2019 ◽  
Vol 26 (1) ◽  
pp. 35-43 ◽  
Author(s):  
Natalie K. Garcia ◽  
Galahad Deperalta ◽  
Aaron T. Wecksler
Keyword(s):  
Mass Spectrometry ◽  
Protein Structure ◽  
Protein Interactions ◽  
Quaternary Structure ◽  
Solvent Accessibility ◽  
Higher Order ◽  
Structure Characterization ◽  
Order Structure ◽  
Protein Footprinting ◽  
Wide Range

Background: Biotherapeutics, particularly monoclonal antibodies (mAbs), are a maturing class of drugs capable of treating a wide range of diseases. Therapeutic function and solutionstability are linked to the proper three-dimensional organization of the primary sequence into Higher Order Structure (HOS) as well as the timescales of protein motions (dynamics). Methods that directly monitor protein HOS and dynamics are important for mapping therapeutically relevant protein-protein interactions and assessing properly folded structures. Irreversible covalent protein footprinting Mass Spectrometry (MS) tools, such as site-specific amino acid labeling and hydroxyl radical footprinting are analytical techniques capable of monitoring the side chain solvent accessibility influenced by tertiary and quaternary structure. Here we discuss the methodology, examples of biotherapeutic applications, and the future directions of irreversible covalent protein footprinting MS in biotherapeutic research and development. Conclusion: Bottom-up mass spectrometry using irreversible labeling techniques provide valuable information for characterizing solution-phase protein structure. Examples range from epitope mapping and protein-ligand interactions, to probing challenging structures of membrane proteins. By paring these techniques with hydrogen-deuterium exchange, spectroscopic analysis, or static-phase structural data such as crystallography or electron microscopy, a comprehensive understanding of protein structure can be obtained.

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