Conformational heterogeneity of tripeptides containing Boc-Leu-Aib as corner residues in the solid state

A critical analysis of single crystal X-ray diffraction studies on a series of terminally protected tripeptides containing a centrally positioned Aib (alpha-aminoisobutyric acid) residue has been reported. For the tripeptide series containing Boc-Ala-Aib as corner residues, all the reported peptides formed distorted type II beta-turn structures. Moreover, a series of Phe substituted analogues ( tripeptides with Boc-Phe-Aib) have also shown different beta-turn conformations. However, the Leu-modified analogues (tripeptides with Boc-Leu-Aib) disrupt the concept of beta-turn formation and adopt various conformations in the solid state. X-ray crystallography sheds some light on the conformational heterogeneity at atomic resolution. (c) 2007 Elsevier Ltd. All rights reserved.

A combined BIE-FE method for the Stokes equations

A numerical algorithm for the biharmonic equation in domains with piecewise smooth boundaries is presented. It is intended for problems describing the Stokes flow in the situations where one has corners or cusps formed by parts of the domain boundary and, due to the nature of the boundary conditions on these parts of the boundary, these regions have a global effect on the shape of the whole domain and hence have to be resolved with sufficient accuracy. The algorithm combines the boundary integral equation method for the main part of the flow domain and the finite-element method which is used to resolve the corner/cusp regions. Two parts of the solution are matched along a numerical ‘internal interface’ or, as a variant, two interfaces, and they are determined simultaneously by inverting a combined matrix in the course of iterations. The algorithm is illustrated by considering the flow configuration of ‘curtain coating’, a flow where a sheet of liquid impinges onto a moving solid substrate, which is particularly sensitive to what happens in the corner region formed, physically, by the free surface and the solid boundary. The ‘moving contact line problem’ is addressed in the framework of an earlier developed interface formation model which treats the dynamic contact angle as part of the solution, as opposed to it being a prescribed function of the contact line speed, as in the so-called ‘slip models’. Keywords: Dynamic contact angle; finite elements; free surface flows; hybrid numerical technique; Stokes equations.

In-street wind direction variability in the vicinity of a busy intersection in central London

We present results from fast-response wind measurements within and above a busy intersection between two street canyons (Marylebone Road and Gloucester Place) in Westminster, London taken as part of the DAPPLE (Dispersion of Air Pollution and Penetration into the Local Environment; www.dapple.org.uk) 2007 field campaign. The data reported here were collected using ultrasonic anemometers on the roof-top of a building adjacent to the intersection and at two heights on a pair of lamp-posts on opposite sides of the intersection. Site characteristics, data analysis and the variation of intersection flow with the above-roof wind direction (θref) are discussed. Evidence of both flow channelling and recirculation was identified within the canyon, only a few metres from the intersection for along-street and across-street roof-top winds respectively. Results also indicate that for oblique rooftop flows, the intersection flow is a complex combination of bifurcated channelled flows, recirculation and corner vortices. Asymmetries in local building geometry around the intersection and small changes in the background wind direction (changes in 15-min mean θref of 5–10 degrees) were also observed to have profound influences on the behaviour of intersection flow patterns. Consequently, short time-scale variability in the background flow direction can lead to highly scattered in-street mean flow angles masking the true multi-modal features of the flow and thus further complicating modelling challenges.

Puckering structure in the infrared spectrum of cyclobutane

The theory of rotational-pucker-vibrational transitions in the vibrational spectrum of cyclobutane is reviewed. Puckering sideband structure on the 1453 cm-1v14 infra-red fundamental of C4H8 has been observed and analysed, in terms of two slightly different puckering potential functions for the ground and the excited vibrational states. The results have been fitted to quartic-quadratic potential functions in the puckering coordinate, with a barrier to inversion of 503 cm-1 (1•44 kcal mole-1 = 6•02 kJ mole-1) in the ground state and 491 cm-1 in the excited state ν14 = 1. For reasonable assumptions about the reduced mass, the equilibrium dihedral angle of the C4 ring is determined to be about 35°, in agreement with previous estimates. Ueda and Shimanouchi's observations on the 2878 cm-1 C4H8 band have been re-analysed, and puckering sidebands have also been observed and analysed for the 1083 cm-1v14 infra-red fundamental of C4D8. Pure puckering transitions have been observed in the Raman spectrum of C4H8 vapour. All of these observations are shown to be consistent with the same ground state puckering potential function.

Use of a novel Hill-climbing genetic algorithm in protein folding simulations

We have developed a novel Hill-climbing genetic algorithm (GA) for simulation of protein folding. The program (written in C) builds a set of Cartesian points to represent an unfolded polypeptide's backbone. The dihedral angles determining the chain's configuration are stored in an array of chromosome structures that is copied and then mutated. The fitness of the mutated chain's configuration is determined by its radius of gyration. A four-helix bundle was used to optimise simulation conditions, and the program was compared with other, larger, genetic algorithms on a variety of structures. The program ran 50% faster than other GA programs. Overall, tests on 100 non-redundant structures gave comparable results to other genetic algorithms, with the Hill-climbing program running from between 20 and 50% faster. Examples including crambin, cytochrome c, cytochrome B and hemerythrin gave good secondary structure fits with overall alpha carbon atom rms deviations of between 5 and 5.6 Angstrom with an optimised hydrophobic term in the fitness function. (C) 2003 Elsevier Ltd. All rights reserved.

Catena-Poly[bis(ethane-1,2-diammonium) [manganese(II)-di-mu-phosphato-kappa O-4 : O ']]: a one-dimensional manganese phosphate

The title compound,{(C2H10N2)(2)[Mn(PO4)(2)]}(n), contains anionic square-twisted chains of formula [Mn(PO4)(2)](4-) constructed from corner-sharing four-membered rings of alternating MnO4 and PO4 units. The Mn and P atoms have distorted tetrahedral coordination and the Mn atom lies on a twofold axis. The linear manganese-phosphate chains are held together by hydrogen-bonding interactions involving the framework O atoms and the H atoms of the ethane-1,2-diammonium cations, which lie in the interchain spaces.

The synthesis and characterisation of two new iron thioantimonates: [Fe(en)(3)](2)Sb2S5 center dot 0.55H(2)O and [Fe(en)(3)](2)Sb4S8

Two new iron thioantimonates, [Fe(en)(3)](2)Sb2S5 (.) 0.55H(2)O (1) and [Fe(en)(3)](2)Sb4S8 (2). were synthesised under solvothermal conditions from the reactions of Sb2S3, FeCl2 and S in the presence of ethylenediamine at 413 and 438 K, respectively. The products were characterised by single-crystal X-ray diffraction, elemental analysis and SQUID magnetometry. Compound 1 is unusual in containing isolated Sb2S54- anions formed from two corner-sharing SbS33- trigonal pyramids. These units are arranged in rippled layers, 4 A apart, parallel to the bc-plane. Octahedrally coordinated [Fe(en)(3)](2+) cations lie in depressions within these anionic layers. In compound (2), repeated corner linking of SbS33- trigonal pyramids generates SbS2- chains, which may be considered as a polymerised form of the Sb2S54- anions in 1. The SbS2- chains are separated by [Fe(en)(3)](2+) cations. In both compounds, there is an extensive network of hydrogen bonds between the nitrogen atoms of the ethylenediamine ligands and the sulfur atoms of the anions and, in the case of 1, the uncoordinated water molecule. (c) 2005 Elsevier Ltd. All rights reserved.

Cytenamide acetic acid solvate

In the crystal structure of the title compound (systematic name: 5H-dibenzo[a,d]cycloheptatriene-5-carboxamide ethanoic acid solvate), C16H13NO center dot C2H4O2, the cytenamide and solvent molecules form a hydrogen-bonded R-2(2)(8) dimer motif, which is further connected to form a centrosymmetric double ring motif arrangement. The cycloheptene ring adopts a boat conformation and the dihedral angle between the least-squares planes through the two aromatic rings is 54.7 (2)degrees.

Robust classification of SAR imagery

In this work the G(A)(0) distribution is assumed as the universal model for amplitude Synthetic Aperture (SAR) imagery data under the Multiplicative Model. The observed data, therefore, is assumed to obey a G(A)(0) (alpha; gamma, n) law, where the parameter n is related to the speckle noise, and (alpha, gamma) are related to the ground truth, giving information about the background. Therefore, maps generated by the estimation of (alpha, gamma) in each coordinate can be used as the input for classification methods. Maximum likelihood estimators are derived and used to form estimated parameter maps. This estimation can be hampered by the presence of corner reflectors, man-made objects used to calibrate SAR images that produce large return values. In order to alleviate this contamination, robust (M) estimators are also derived for the universal model. Gaussian Maximum Likelihood classification is used to obtain maps using hard-to-deal-with simulated data, and the superiority of robust estimation is quantitatively assessed.

Wiener-System subspace identification for mobile wireless mm-wave networks

We discuss the feasibility of wireless terahertz communications links deployed in a metropolitan area and model the large-scale fading of such channels. The model takes into account reception through direct line of sight, ground and wall reflection, as well as diffraction around a corner. The movement of the receiver is modeled by an autonomous dynamic linear system in state space, whereas the geometric relations involved in the attenuation and multipath propagation of the electric field are described by a static nonlinear mapping. A subspace algorithm in conjunction with polynomial regression is used to identify a single-output Wiener model from time-domain measurements of the field intensity when the receiver motion is simulated using a constant angular speed and an exponentially decaying radius. The identification procedure is validated by using the model to perform q-step ahead predictions. The sensitivity of the algorithm to small-scale fading, detector noise, and atmospheric changes are discussed. The performance of the algorithm is tested in the diffraction zone assuming a range of emitter frequencies (2, 38, 60, 100, 140, and 400 GHz). Extensions of the simulation results to situations where a more complicated trajectory describes the motion of the receiver are also implemented, providing information on the performance of the algorithm under a worst case scenario. Finally, a sensitivity analysis to model parameters for the identified Wiener system is proposed.

An Exponentially Convergent Nonpolynomial Finite Element Method for Time-Harmonic Scattering from Polygons

In recent years nonpolynomial finite element methods have received increasing attention for the efficient solution of wave problems. As with their close cousin the method of particular solutions, high efficiency comes from using solutions to the Helmholtz equation as basis functions. We present and analyze such a method for the scattering of two-dimensional scalar waves from a polygonal domain that achieves exponential convergence purely by increasing the number of basis functions in each element. Key ingredients are the use of basis functions that capture the singularities at corners and the representation of the scattered field towards infinity by a combination of fundamental solutions. The solution is obtained by minimizing a least-squares functional, which we discretize in such a way that a matrix least-squares problem is obtained. We give computable exponential bounds on the rate of convergence of the least-squares functional that are in very good agreement with the observed numerical convergence. Challenging numerical examples, including a nonconvex polygon with several corner singularities, and a cavity domain, are solved to around 10 digits of accuracy with a few seconds of CPU time. The examples are implemented concisely with MPSpack, a MATLAB toolbox for wave computations with nonpolynomial basis functions, developed by the authors. A code example is included.

On the existence of extreme waves and the Stokes conjecture with vorticity

This is a study of singular solutions of the problem of traveling gravity water waves on flows with vorticity. We show that, for a certain class of vorticity functions, a sequence of regular waves converges to an extreme wave with stagnation points at its crests. We also show that, for any vorticity function, the profile of an extreme wave must have either a corner of 120° or a horizontal tangent at any stagnation point about which it is supposed symmetric. Moreover, the profile necessarily has a corner of 120° if the vorticity is nonnegative near the free surface.