An algorithm for packing regular multistrand polypeptide structures by energy minimization

An algorithm has been developed for packing polypeptide chains by energy minimization subject to regularity conditions, in which regularity is maintained without the addition of pseudoenergy terms by defining the energy as a function of appropriately chosen independent variables. The gradient of the energy with respect to the independent variables is calculated analytically. The speed and efficiency of convergence of the algorithm to a local energy minimum are comparable to those of existing algorithms for minimizing the energy of a single polypeptide chain. The algorithm has been used to reinvestigate the minimum-energy regular structures of three-stranded (L -Ala)₈, three-stranded (L -Val)₆, five-stranded (L -Ile)₆, and the regular and truncated three-stranded (Gly-L -Pro-L -Pro)₄ triple helices. Local minima with improved packing energies, but with essentially unchanged geometrical properties, were obtained in all cases. The algorithm was also used to reinvestigate the structures proposed previously for the I and II forms of crystalline silk fibroin. The silk II structure was reproduced with slightly improved packing and little other change. The orthorhombic silk I structure showed more change and considerably improved packing energy, but the new regular monoclinic silk I structure had considerably higher energy. The results support the structure proposed previously for silk II and the orthorhombic structure, but not the monoclinic structure proposed for silk I. © 1994 by John Wiley & Sons, Inc.     

Origins and structures of background ions produced by fast-atom bombardment of glycerol

Accurate mass measurements were used to assign elemental compositions and tandem mass spectrometry was used to characterize the peak-at-every-mass background ions produced by kiloelectron-volt-particle bombardment of neat fast-atom bombardment matrices. The majority of the background ions observed in the mass spectrum of neat glycerol was identified. On the basis of the experiments with glycerol, a theory for the formation of background ions is presented. Results are discussed according to the chemical and physical changes that ygoe;on-volt-particle bombardment produces in the matrix.     

Effects of target gas in collision-induced dissociation using a double quadrupole mass spectrometer and radiofrequency

Collision-induced dissociation (CID) of polyatomic ions sampled from an rf-powered glow discharge is examined by using three target gases including atomic (Ar and Xe) and molecular species (N2). Collisions with these targets in the first quadrupole of the double quadrupole system result in the loss of discharge species by dissociation, symmetric and asymmetric charge exchange, and scattering, each to varying degrees. These processes are seen to be a function of the relative mass, size... and ionization potentials of the target species, as well as the collision center-of-mass energies. In light of the comparisons, xenon appears to be the best collision target for both CID and charge exchange because of its relatively low ionization potential and high dissociation efficiency of polyatornic species. Evidence for both symmetric and asymmetric charge exchange is presented for Ar and Xe target gases.     

The influence of the liquid crystalline core geometry on the mesogenicity of novel chiral 2-(4-substituted-phenoxy)propanonitriles

The synthesis and characterization of seven novel (R)-2-(4-substituted-phenoxy)propanonitriles are described. The propanonitriles were prepared to evaluate their potential use as thermochromics and ferroelectric dopants, as well as to determine their twist sense properties. The materials exhibit smectic and chiral nematic phases of high thermal stability; the mesogenic behaviour of the nitriles is directly related to the type of two-ring core unit employed. The effects of the different molecular geometries and polarizabilities of the liquid crystalline cores on mesophase stability are discussed, particularly in relation to other members of this series. The chiral nematic phase of the propanonitriles is assigned as having a left-handed twist sense from contact preparation studies, and this is in agreement with rules relating absolute configuration and molecular structure to helical twist sense.     

Immobilized polysiloxanes as stationary phases for high-performance liquid chromatography and solid phase extraction

Polysiloxanes immobilized onto the surfaces of porous silica particles have proven to be good stationary phases for the separation of multiresidues of pesticides and their metabolic/degradation products by reversed-phase high-performance liquid chromatography (RP-HPLC). Similar materials have proven effective for pre-concentration and clean-up procedures using solid phase extraction. The present paper describes the preparation and some applications of several of these packing materials.     

Correlation between Al2O3 particles and interface of Al-Al2O3 coatings by cold spray

Al-Al₂O₃ composite coatings with different Al₂O₃ particle shapes were prepared on Si and Al substrate by cold spray. The powder compositions of metal (Al) and ceramic (Al₂O₃) having different sizes and agglomerations were varied into ratios of 10:1 wt% and 1:1 wt%. Al₂O₃ particles were successfully incorporated into the soft metal matrix of Al. It was found that crater formation between the coatings and substrate, which is typical characteristic signature of cold spray could be affected by initial starting Al₂O₃ particles. In addition, when the large hard particles of fused Al₂O₃ were employed, the deep and big craters were generated at the interface between coatings and hard substrates. In the case of pure soft metal coating such as Al on hard substrate, it is very hard to get proper adhesion due to lack of crater formation. Therefore, the composite coating would have certain advantages.     

Finding Robust Solutions Using Local Search

This paper investigates how a local search metaheuristic for continuous optimisation can be adapted so that it finds broad peaks, corresponding to robust solutions. This is relevant in problems in which uncertain or noisy data is present. When using a genetic or evolutionary algorithm, it is standard practice to perturb solutions once before evaluating them, using noise from a given distribution. This approach however, is not valid when using population-less techniques like local search and other heuristics that use local search. For those algorithms to find robust solutions, each solution needs to be perturbed and evaluated several times, and these evaluations need to be combined into a measure of robustness. In this paper, we examine how many of these evaluations are needed to reliably find a robust solution. We also examine the effect of the parameters of the noise distribution. Using a simple tabu search procedure, the proposed approach is tested on several functions found in the literature. This revised version was published online in August 2006 with corrections to the Cover Date.     

Nonlinear dynamics of charged particles interacting with combined ac-dc electromagnetic fields

A nonlinear Lorenz model describing interactions between charged particles and combined ac-dc electromagnetic fields is studied for various combinations of frequencies, field strengths and relative angle (θ) between the ac and dc magnetic fields. Strong directional effects on the magnitude and location of resonant particle motion are observed when θ is varied and the regular resonance windows in the aligned field (θ = 0) and linear version of the model studied previously by Durney etaal., break up to form irregular and less well pronounced regions of large and small particle displacements when nonlinearities are taken into account. The length of time takne to achieve resonant behaviour also becomes larger and more variable when nonlinearities are present. The possible relevance of these effects to interactions between electromagnetic fields and biological media is briefly discussed.