Vacancy ordered phases and one-dimensional quasiperiodicity

The metastable vacancy ordered phases observed in aluminium transition metal alloys on rapid solidification or vapour deposition can be considered as a periodic arrangement of a truncated quasiperiodic string based on the Fibonacci sequence along the left angle bracket111right-pointing angle bracket stacking direction of the original CsCl cell. Using the projection formalism developed in the context of quasicrystals, the diffraction patterns of the vacancy ordered phases are calculated for both commensurate and incommensurate projection from a periodic cubic cell in four dimensions. These are compared with experimentally observed patterns. It is shown that at increasingly longer periodicity the patterns from commensurate crystals become indistinguishable from the truly quasiperiodic one. It is suggested that there is a strong link between vacancy ordered phases and quasicrystals.

Some mechanisms of excitation of a railway wheel

Railway wheel vibrations are caused by a number of mechanisms. Two of these are considered: (a) gravitational load reaction acting on different points of the wheel rim, as the wheel rolls on, and (b) random fluctuating forces generated at the contact patch by roughness on the mating surfaces of the wheel and rail. The wheel is idealized as a thin ring, and the analysis is limited to a single wheel rolling on a rail. It is shown that the first mechanism results in a stationary pattern of vibration, which would not radiate any sound. The acceleration caused by roughness-excited forces is much higher at higher frequencies, but is of the same order as that caused by load reaction at lower frequencies. The computed acceleration level (and hence the radiated SPL) caused by roughness is comparable with the observed values, and is seen to increase by about 10 dB for a doubling of the wagon speed. The driving point impedance of the periodic rail-sleeper system at the contact patch, which is used in the analysis, is derived in a companion paper.

Flow over a cylinder with a hinged-splitter plate

Previous work on rigid splitter plates in the wake of a bluff body has shown that the primary vortex shedding can be suppressed for sufficiently long splitter plates. In the present work, we study the problem of a hinged-splitter plate in the wake of a circular cylinder. The splitter plate can rotate about the hinge at the base of the cylinder due to the unsteady fluid forces acting on it, and hence the communication between the two sides of the wake is not totally disrupted as in the rigid splitter plate case. In our study, we investigate this problem in the limit where the stiffness and internal damping associated with the hinge are negligible, and the mass ratio of the splitter plate is small. The experiments show that the splitter plate oscillations increase with Reynolds numbers at low values of Re, and are found to reach a saturation amplitude level at higher Re, Re>4000. This type of saturation amplitude level that appears to continue indefinitely with Re, appears to be related to the fact that there is no structural restoring force, and has been observed previously for transversely oscillating cylinders with no restorin force. In the present case, the saturation tip amplitude level can be tip to 0.45D, where D is the cylinder diameter. For this hinged-rigid splitter plate case, it is found that the splitter plate length to cylinder diameter ratio (L/D) is crucial in determining the character and magnitude of the oscillations. For small splitter plate length (L/D <= 3.0), the oscillations appear to be nearly periodic with tip amplitudes of about 0.45D nearly independent of L/D. The nondiinensional oscillation frequencies (fD/U) on the other hand are found to continuously vary with L/D from fD/U approximate to 0.2 at L/D = 1 to fD/U approximate to 0.1 at L/D = 3. As the splitter plate length is further increased beyond L/D >= 4.0, the character of the splitter plate oscillations suddenly changes. The oscillations become aperiodic with much smaller amplitudes. In this long splitter plate regime, the spectra of the oscillations become broadband, and are reminiscent of the change in character of the wake oscillations seen in the earlier fixed-rigid splitter plate case for L/D >= 5.0. In the present case of the hinged-splitter plate, the sudden transition seen as the splitter plate length (L/D) is increased from 3 to 4 may be attributed to the fact that the wake vortices are no longer able to synchronize with the plate motions for larger splitter plate lengths. Hence, as observed in other vortex-induced vibration problems, the oscillations becomeaperiodic and the amplitude reduces dramatically.

Wall Shear Fluctuations in a Turbulent Boundary Layer

IN the last two decades, the instantaneous structure of a turbulent boundary layer has been examined by many in an effort to understand the dynamics of the flow. Distinct and well-defined flow patterns that seem to have great relevance to the turbulence production mechanism have been observed in the wall region.1'2 The flow near the wall is intermittent with periodic eruptions of the fluid, a phenomenon generally termed "bursting process." Earlier investigations in this field were limited to liquid flows at low speeds and the entire flowpattern was observed using flow visualization techniques.Study was later extended to boundary-layer flows in windtunnels at higher speeds and Reynolds numbers using hot-wiresignals for the analysis of the bursting phenomenon.

CSSI-PRO: a method for secondary structure type editing, assignment and estimation in proteins using linear combination of backbone chemical shifts

Estimation of secondary structure in polypeptides is important for studying their structure, folding and dynamics. In NMR spectroscopy, such information is generally obtained after sequence specific resonance assignments are completed. We present here a new methodology for assignment of secondary structure type to spin systems in proteins directly from NMR spectra, without prior knowledge of resonance assignments. The methodology, named Combination of Shifts for Secondary Structure Identification in Proteins (CSSI-PRO), involves detection of specific linear combination of backbone H-1(alpha) and C-13' chemical shifts in a two-dimensional (2D) NMR experiment based on G-matrix Fourier transform (GFT) NMR spectroscopy. Such linear combinations of shifts facilitate editing of residues belonging to alpha-helical/beta-strand regions into distinct spectral regions nearly independent of the amino acid type, thereby allowing the estimation of overall secondary structure content of the protein. Comparison of the predicted secondary structure content with those estimated based on their respective 3D structures and/or the method of Chemical Shift Index for 237 proteins gives a correlation of more than 90% and an overall rmsd of 7.0%, which is comparable to other biophysical techniques used for structural characterization of proteins. Taken together, this methodology has a wide range of applications in NMR spectroscopy such as rapid protein structure determination, monitoring conformational changes in protein-folding/ligand-binding studies and automated resonance assignment.

Probing into the role of conserved N-glycosylation sites in the Tyrosinase glycoprotein family

N-linked glycosylation has a profound effect on the proper folding, oligomerization and stability of glycoproteins. These glycans impart many properties to proteins that may be important for their proper functioning, besides having a tendency to exert a chaperone-like effect on them. Certain glycosylation sites in a protein however, are more important than other sites for their function and stability. It has been observed that some N-glycosylation sites are conserved over families of glycoproteins over evolution, one such being the tyrosinase related protein family. The role of these conserved N-glycosylation sites in their trafficking, sorting, stability and activity has been examined here. By scrutinizing the different glycosylation sites on this family of glycoproteins it was inferred that different sites in the same family of polypeptides can perform distinct functions and conserved sites across the paralogues may perform diverse functions.

Charged-soliton excitations in statistical mechanics

A method is developed for demonstrating how solitons with some internal periodic motion may emerge as elementary excitations in the statistical mechanics of field systems. The procedure is demonstrated in the context of complex scalar fields which can, for appropriate choices of the Lagrangian, yield charge-carrying solitons with such internal motion. The derivation uses the techniques of the steepest-descent method for functional integrals. It is shown that, despite the constraint of some fixed total charge, a gaslike excitation of such charged solitons does emerge.

Is 3'-nucleotide rigid?

Conformational analysis of nucleic acids and polynucleotides is far more complex than that of proteins and polypeptides, due to five single bond rotations in addition to the sugar puckerings in the monomer. Sundaralingam1 proposed the concept of the 'rigid' nucleotides from analysis of crystal structure data, with the flexibility allowed only about the phosphodiester bonds. However, the crystal structure of deoxyguanosine-5'−phosphate2,3 indicates at gt conformation about the C-4'−C-5' bond against gg in a conformationally rigid nudeotide1. Jack et al. 4 considered the flexibility of nucleotides in tRNA about the C-4'−C-5' bond, thereby introducing the concept of 'non-rigid' ribonucleotides. Conformational flexibility of the f uranose ring in DNA and RNA and their energetics using classical and quantum chemical methods have been reported5−8. We have examined the flexibility of 3'-nucleotides. alpha, the most important of the conformational parameters defining the 3'-end of a nucleotide unit9, has a value in the range 195°−270° in all the 3'-nucleotides, dinucleoside monophosphates and higher oligomers which have been surveyed. A survey of the proposed structures of polyribonudeotides10,11 also shows the values of a to be greater than 200°. However, the structures proposed for B-DNA by Arnott and Hukins12,13 and D-DNA by Arnott et al. 14 have values of alpha of 155° and 141° respectively, much lower than the lowest observed value. The structure for B-DNA has two strong, short contacts (C-2'...OP-1 = 2.64 Å and HC-2"...OP-1 = 1.79 Å) which lead to an energetically unfavourable conformation. Hence, it is of interest to investigate whether, by allowing flexibility to the sugar moiety in the nucleotide unit, it is possible to make the structure energetically favourable. Here, conformational energy calculations were carried out to determine the range of alpha which would give rise to energetically favoured conformations with different sugar puckerings. Our analysis has shown that the theoretically obtained range is nearly the same as the preferred range in crystals, indicating the flexibility of the 3'-nucleotides.

The nonequilibrium region of a mixing layer

Experiments were conducted in the nonequilibrium region of a free mixing layer with unequal freestream velocities. Four velocity ratios U(1)/U(2) of 0.32, 0.46, 0.74, and 0.96 were used in this investigation. The growth of the shear layer as well as the velocity adjustment in the near wake were examined. There was reasonable agreement between the measured mean velocity profiles and those computed using the K-epsilon turbulence model. Some periodic turbulence velocity fluctuations were observed in the mixing layer, but their frequency remained the same along the flow.

A Need for FSH in Maintaining Fertility of Adult Male Subhuman Primates

Adult fertile male bonnet monkeys (Macaca radiata) were continuously deprived of endogenous follicle stimulating hormone (FSH) support for 240 days by injecting them with 1 ml of characterized monkey antiserum to oFSH every 48 hr; control monkeys received during the same period normal monkey serum instead. Testicular function was assessed at periodic intervals by (a) carrying out differential counting of sperm in the ejaculate obtained and (b) determining the hyaluronidase activity as well as in vitro 3H thymidine incorporation into DNA of testicular tissue removed at biopsy. Both the quality (viability and motility) of the sperms voided and the total sperm counts showed marked decreases as a function of time of immunization, the first significant reduction being noted by 100 days. FSH deprivation affected both the biochemical parameters used to test testicular functionality they being reduced at ∼200 days by 50%-60%. The fertility of these monkeys was evaluated at periodic times after 90 days of treatment by means of mating studies. FSH deprivation had rendered the monkeys incapable of impregnating any of the females used. Testosterone and luteinizing hormone (LH) levels remained unchanged following FSH antiserum injection. With cessation of antiserum treatment testicular function and fertility were completely restored to normalcy, indicating that the observed effect was specifically due to FSH deprivation. This study thus provides conclusive evidence for the involvement of FSH in maintenance of testicular function and fertility in the adult male primate.

L2-stability of nonstationary feedback systems: Frequency-domain criteria

A frequency-domain positivity condition is derived for linear time-varying operators in2and is used to develop2stability criteria for linear and nonlinear feedback systems. These criteria permit the use of a very general class of operators in2with nonstationary kernels, as multipliers. More specific results are obtained by using a first-order differential operator with a time-varying coefficient as multiplier. Finally, by employing periodic multipliers, improved stability criteria are derived for the nonlinear damped Mathieu equation with a forcing function.

Crystal structure of the amino acid-vitamin complex lysine pantothenatestar, open

L-Lysine d-pantothenate, a 1:1 amino acid-vitamin complex, crystallizes in the monoclinic space group P21 with Image Full-size image (1K) .The structure has been solved by direct methods and refined to an R value of 0.053 for 1868 observed reflections. The zwitterionic positively charged lysine molecules in the structure assume the sterically most favourable conformation with an all-trans side chain trans to the α-carboxylate group. The pantothenate anion has a somewhat folded conformation stabilised by an intramolecular bifurcated hydrogen bond. The unlike molecules aggregate into separate alternating layers. The molecules in the lysine layers form a head-to-tail sequence parallel to the a-axis. The interactions which hold the adjacent layers together include those between the side chain amino group of lysine and the carboxylate group in the pantothenate anion. The geometry of these interactions is such that each carboxylate group is sandwiched between two amino groups in a periodic arrangement of alternating carboxylate and amino groups.

Neutron-diffraction study of structure and conformation of nucleotide uridine-5 phosphate (disodium salt)

Acta Crystallographica Section A: Foundations of Crystallography covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination by diffraction methods using X-rays, neutrons and electrons. The structures include periodic and aperiodic crystals, and non-periodic disordered materials, and the corresponding Bragg, satellite and diffuse scattering, thermal motion and symmetry aspects. Spatial resolutions range from the subatomic domain in charge-density studies to nanodimensional imperfections such as dislocations and twin walls. The chemistry encompasses metals, alloys, and inorganic, organic and biological materials. Structure prediction and properties such as the theory of phase transformations are also covered.

Analytical method for solving a set of infinite simultaneous equations

It is shown that a method based on the principle of analytic continuation can be used to solve a set of infinite simultaneous equations encountered in solving for the electric field of a periodic electrode structure.

Application of Laplace transform technique to the solution of certain third-order non-linear systems

A number of papers have appeared on the application of operational methods and in particular the Laplace transform to problems concerning non-linear systems of one kind or other. This, however, has met with only partial success in solving a class of non-linear problems as each approach has some limitations and drawbacks. In this study the approach of Baycura has been extended to certain third-order non-linear systems subjected to non-periodic excitations, as this approximate method combines the advantages of engineering accuracy with ease of application to such problems. Under non-periodic excitations the method provides a procedure for estimating quickly the maximum response amplitude, which is important from the point of view of a designer. Limitations of such a procedure are brought out and the method is illustrated by an example taken from a physical situation.