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The spatial disposition and relative orientation of sequential base pair steps are also expressed in terms of standard rigid body parameters. Conventional torsional parameters and assorted virtual distances and angles are used to characterize molecular conformation, with automatic conformational classifications based on derived parameters known to distinguish different helical forms.
The popular Calladine—Drew block schematic representation of DNA structure 42 can be produced, either in isolation or in combination with other graphic images. A total of 55 regular DNA and RNA helical structures, based on the fiber diffraction of extended polymers 43 — 52can also be constructed for arbitrary sequences. The interchangeable description of base pair structure at a local dimeric or helical level facilitates the analysis and modeling of nucleic acid conformational transitions.
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This method uniquely defines the position and orientation, i. The base pairing information needed for the analysis routine is generated automatically with a utility program which identifies all residues in close contact. Other base pairs with hydrogen bonds to backbone atoms are also identified, along with base triplets, tetrads and pentads see examples below. Once a base pair is located on the basis of geometric criteria, the hydrogen bonding patterns are checked, allowing for the identification of unexpected pairings.
Each base pair is uniquely characterized by a set of six rigid body parameters Fig. Publication quality best view images of the base pairs, in various styles, with hydrogen bonds and base rings optionally color coded by residue type, can be automatically generated see below. Modified bases are mapped to standard counterparts, e.ic! berlin locking hinge
Base pair parameters Each base has two unique faces, arising from molecular asymmetry 5354which can be distinguished with the standard nucleic acid base reference frame. For Watson—Crick base pairs, such as the A—U pair in Figure 2 a, the faces of the two bases are of the opposite sense, corresponding to two antiparallel strands. This convention is simpler but in essence the same as the normal versus flipped concept of base pairing introduced by Burkard et al.
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Since the six base pair parameters uniquely define the relative position and orientation of two bases, they can be used to reconstruct the base pair. Moreover, the parameters provide a simple mechanism for classification of structures 55 and database searching X.
Among the six base pair parameters, only Shear, Stretch and Opening are critical in characterizing key hydrogen bonding features, i.
Buckle, Propeller and Stagger, in contrast, are secondary parameters, which simply describe the imperfections, i. The parameters so defined have simple geometrical meanings. Geometrically, its key feature is a —2.
As noted previously 20differences in Shear between neighboring base pairs lead to the discrepancies in dinucleotide Twist reported by others 5758 The new standard base reference frame 20which is implemented in 3DNA, leads to twist angles in close agreement with those obtained from Curves. All base pair parameters are thus calculated with respect to a common standard. The finely dotted lines in the representation in Figure 3 of base pairs from the 0.
The base pair parameters and hydrogen bond characteristics of a representative example of each of the 28 classic base pair types with two or more hydrogen bonds between bases 2 are listed in Supplementary Material Table S1. As noted above, all but five of the base pairs are found in the high resolution 2. Transgenic replacement of the endogenous fast muscle isovariant hinge A exon 15a in Drosophila melanogaster indirect flight muscle with the slow muscle hinge B exon 15b allows examination of the structural and functional changes when only this region of the myosin molecule is different.
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Hinge B was previously shown to increase myosin rod length, increase A-band and sarcomere length, and decrease flight performance compared to hinge A. Structurally, the longer A-band and sarcomere lengths found in the hinge B myofibrils appear to be due to the longitudinal addition of myosin heads.
Functionally, hinge B, although a significant distance from the myosin catalytic domain, alters myosin kinetics in a manner consistent with this region increasing myosin rod length. These structural and functional changes combine to decrease whole fly wing-beat frequency and flight performance.
Our results indicate that this hinge region plays an important role in determining myosin kinetics and in regulating thick and thin filament lengths as well as sarcomere length. For over a century, wave-energy conversion devices have been proposed, but none has emerged as a clearly practical and economical solution.
One promising system is the McCabe Wave Pump MWPan articulated-barge system consisting of three barges hinged together with a large horizontal plate attached below the central barge.
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Water pumps are driven by the relative pitching motions of the barges excited by ocean waves. This high-pressure water can be used to produce potable water or electricity.
A simulation of the motions of a generic hinged-barge system is developed.