Non-protein amino acids in peptide design

An overview of the use of non-protein amino acids in the design of conformationally well-defined peptides, based on work from the author’s laboratory, is discussed. The crystal structures of several designed oligopeptides illustrate the useα-aminoisobutyric acid (Aib) in the construction of helices, D-amino acids in the design of helix termination segments and^DPro-Xxx segments for nucleating ofβ-hairpin structures.β- andγ-amino acid residues have been used to expand the range of designed polypeptide structures. Dedicated to Professor C N R Rao on his 70th birthday     

Two-Frequency Autowave Processes in the Complex Ginzburg–Landau Equation

We study the complex Ginzburg–Landau equation with zero Neumann boundary conditions on a finite interval and establish that this boundary problem (with suitably chosen parameters) has countably many stable two-dimensional self-similar tori. The case of periodic boundary conditions is also investigated.     

Retardation characteristics and birefringence of a multiple-order crystalline quartz plate

A crystalline quartz plate of thickness 1.070 mm is calibrated between 370 and 794 nm. Throughout this spectral interval, the retardance varied by 32π and the plate introduced quarterwave retardance 16 times at different wavelengths. The birefringence (n_e−n_o) of crystalline quartz was calculated as a single quantity and varied from 0.00971 at 370 nm to 0.00891 at 794 nm. All measurements were carried out at 23°C.     

Refraction holodiagrams and Snell's law

The refraction holodiagram RHD is analyzed here with respect to the law of refraction. Particularly, we study the surface that exactly conjugates by refraction a virtual point source with a real image or conversely. By using the total optical path as a parameter we build a diagram that consists in a family of Descartes ovals of the apple type that contains the Pascal's limaçon as a particular extreme case and the spherical surface with the Weierstrass points as another. These representations permit the straightforward application of Fermat's principle in the case of arbitrary refracting surfaces and show the shape of generalized Fresnel's zones in the intersections with any surface. Snell's law is applied to rays incident on the apple type surfaces to find out the conditions for exact conjugation. Sensitivity to optical path variations is also discussed. The RHD curves family can be represented in a Cartesian way where the ovals appear as equally spaced straight lines.     

Calculation of the vibrational spectra of copper crystals with vacancies

The local vibrational spectra of copper crystals containing vacancies are calculated using the pair atomic potential derived in the framework of the resonance pseudopotential theory. The calculations are performed by a recursive method with due regard for the symmetry of the defect region. The frequencies of the vacancy-induced resonance vibrations of different symmetries are determined.     

The action of an electron beam on dust structures in a plasma

The action of an electron beam on ordered dust structures in glow and low-pressure RF discharges was studied experimentally. The electron beam produces destruction and dynamic displacement of the dust structure. In the center of a dust structure, an electron beam with a low electron energy (tens of eV) at currents up to 1 mA caused structural disordering and “melting” in the region of its action but did not excite external crystal regions. Local action of an electron beam with a high electron energy (25 keV) and a beam current above 10 mA caused deformation of the whole dust structure and shifted it in the horizontal direction so that it was carried away from the RF discharge zone. The effect of dust structure displacements can be used to locally remove particles from a plasma.     

Dynamic interaction of plasma flow with the hot boundary layer of a geomagnetic trap

The study of the interaction between collisionless plasma flow and stagnant plasma revealed the presence of an outer boundary layer at the border of a geomagnetic trap, where the super-Alfvén subsonic laminar flow changes over to the dynamic regime characterized by the formation of accelerated magnetosonic jets and decelerated Alfvén flows with characteristic relaxation times of 10–20 min. The nonlinear interaction of fluctuations in the initial flow with the waves reflected from an obstacle explains the observed flow chaotization. The Cherenkov resonance of the magnetosonic jet with the fluctuation beats between the boundary layer and the incoming flow is the possible mechanism of its formation. In the flow reference system, the incoming particles are accelerated by the electric fields at the border of boundary layer that arise self-consistently as a result of the preceding wave-particle interactions; the inertial drift of the incoming ions in a transverse electric field increasing toward the border explains quantitatively the observed ion acceleration. The magnetosonic jets may carry away downstream up to a half of the unperturbed flow momentum, and their dynamic pressure is an order of magnitude higher than the magnetic pressure at the obstacle border. The appearance of nonequilibrium jets and the boundary-layer fluctuations are synchronized by the magnetosonic oscillations of the incoming flow at frequencies of 1–2 mHz.     

Features of the Quenching of the Triplet States of Water-Soluble Porphyrins by Molecular Oxygen

Using the methods of time-resolved absorption spectroscopy, we have investigated the features of quenching, by molecular oxygen, of the excited triplet states of water-soluble 5,10,15,20-tetrakis-(4-N-methylpyridyl)-porphyrin (H₂TMPyP) and 5,10,15,20-tetrakis-(4-sulfonatophenyl)-porphyrin (H₂TSPP) in water–ethanol solutions. It has been revealed that for both compounds the rate constant of quenching of the triplet states increases with increasing viscosity of the medium. Quenching of the excited triplet states of the dissociated (in water) and undissociated (in ethanol) forms of water-soluble porphyrins occurs with a different efficiency, and the rate constant of quenching the triplet states by molecular oxygen k _T thereby is higher for the dissociated form. It has been shown by means of mathematical modeling that the experimental results obtained can be described in terms of the change in the rate constants of intracomplex transitions in the porphyrin–oxygen collisional complex at varied solution viscosity and their difference for the dissociated and undissociated forms of water-soluble porphyrin.     

Homology of Lagrangian submanifolds in cotangent bundles

In this paper we find homological restrictions on Lagrangians in cotangent bundles of spheres and Lens spaces. This research was supported by the Israel Science Foundation (grand No. 205/02).     

Karhunen–Loeve representations of turbulent channel flows using the method of snapshots

For three‐dimensional flows with one inhomogeneous spatial coordinate and two periodic directions, the Karhunen–Loeve procedure is typically formulated as a spatial eigenvalue problem. This is normally referred to as the direct method (DM). Here we derive an equivalent formulation in which the eigenvalue problem is formulated in the temporal coordinate. It is shown that this so‐called method of snapshots (MOS) has some numerical advantages when compared to the DM. In particular, the MOS can be formulated purely as a matrix composed of scalars, thus avoiding the need to construct a matrix of matrices as in the DM. In addition, the MOS avoids the need for so‐called weight functions, which emerge in the DM as a result of the non‐uniform grid typically employed in the inhomogeneous direction. The avoidance of such weight functions, which may exhibit singular behaviour, guarantees satisfaction of the boundary conditions. The MOS is applied to data sets recently obtained from the direct simulation of turbulence in a channel in which viscoelasticity is imparted to the fluid using a Giesekus model. The analysis reveals a steep drop in the dimensionality of the turbulence as viscoelasticity is increased. This is consistent with the results that have been obtained with other viscoelastic models, thus revealing an essential generic feature of polymer‐induced drag reduced turbulent flows. Published in 2006 by John Wiley & Sons, Ltd.