A saxpy formulation for plane rotations

An algorithm for pre- or post-multiplication of a matrix by a plane rotation, using only three vector saxpy operations instead of the four vector operations usually considered necessary, is described. No auxiliary storage for overwriting is required. The method is shown to be numerically stable.     

Vibrational Spectroscopy and Conformational Structure of Protonated Polyalanine Peptides Isolated in the Gas Phase

The conformational structures of protonated polyalanine peptides, Ala(n)H(+), have been investigated in the gas phase for n = 3, 4, 5, and 7 using a combination of resonant-infrared multiphoton dissociation (R-IRMPD) spectroscopy in the NH and OH stretch regions and quantum chemical calculations. Agreement between theoretical IR and experimental R-IRMPD spectral features has enabled the assignment of specific hydrogen-bonded conformational motifs in the short protonated peptides and revealed their conformational evolution under elevated-temperature conditions, as a function of increasing chain length. The shortest peptide, Ala(3)H(+), adopts a mixture of extended and cyclic chain conformations, protonated, respectively, at a backbone carbonyl or the N-terminus. The longer peptides adopt folded, cyclic, and globular charge-solvated conformations protonated at the N-terminus, consistent with previous ion-mobility studies. The longest peptide, Ala(7)H(+), adopts a globular conformation with the N-terminus completely charge-solvated, demonstrating the emergence of "physiologically relevant" intramolecular interactions in the peptide backbone. The computed conformational relative free energies highlight the importance of entropic contributions in these peptides.     

Fabrication process parameters significantly affect the perovskite oxygen carriers materials (OCM) performance in chemical looping with oxygen uncoupling (CLOU)

Journal of Thermal Analysis and Calorimetry - The CLOU performance of the CaTixMn0.9?xMg0.1O3 (CMTM) perovskite-type system was investigated, comparing materials produced at laboratory scale...     

Intramolecular interactions in protonated peptides: H+ PheGlyGly and H+ GlyGlyPhe

The conformations of protonated PheGlyGly and GlyGlyPhe tripeptides, generated at temperatures approximately 300-350 K through a photochemical mechanism, were investigated in the gas phase using R-IRMPD spectroscopy in the OH and NH stretch region in combination with quantum chemistry calculations. The results aid characterisation of their conformational landscapes and specifically, help identify the intramolecular interactions that control the peptide conformations. The dominant intramolecular interaction in protonated PheGlyGly operates between the N-and C-termini but in protonated GlyGlyPhe there is a strong cation-pi interaction. The observation of a cation-pi interaction in the warm ions highlights its strong, stable nature.     

Additively decomposed quasiconvex functions

Letf be a real-valued function defined on the product ofm finite-dimensional open convex setsX ₁, ,X _m .Assume thatf is quasiconvex and is the sum of nonconstant functionsf ₁, ,f _m defined on the respective factor sets. Then everyf _i is continuous; with at most one exception every functionf _i is convex; if the exception arises, all the other functions have a strict convexity property and the nonconvex function has several of the differentiability properties of a convex function.We define the convexity index of a functionf _i appearing as a term in an additive decomposition of a quasiconvex function, and we study the properties of that index. In particular, in the case of two one-dimensional factor sets, we characterize the quasiconvexity of an additively decomposed functionf either in terms of the nonnegativity of the sum of the convexity indices off ₁ andf ₂, or, equivalently, in terms of the separation of the graphs off ₁ andf ₂ by means of a logarithmic function. We investigate the extension of these results to the case ofm factor sets of arbitrary finite dimensions. The introduction discusses applications to economic theory.     

The effect of the mixing process on reaction kinetics

If the chemical rate constants of the initial reaction steps are large, any observed value of these constants may be affected by the mixing process. To investigate the effect of mixing efficiency on reaction kinetics we use two previously analyzed reaction systems, namely the glutamic aspartic aminotransferase system and the hemoglobin/O₂ system. A time constant k_a for the mixing process is introduced and four values for this parameter are considered, with the fastest essentially corresponding to complete mixing before any reaction can take place. The remaining three values are associated with mixing instruments, since they may be attainable in the real world. To evaluate the mixing efficiency (and conversely determine underlying k_a values) from observed kinetics, mixing was combined with chemical relaxation by temperature jumps initiated at different points in time during the mixing process. Computer simulations permit the development of specific criteria to determine (in reverse) appropriate values of k_a. In this respect, the aminotransferase system proved to be more revealing than the hemoglobin system. © 2003 Wiley Periodicals, Inc. Int J Chem Kinet 35: 484–496, 2003     

Mechanistic insights into the C55-P targeting lipopeptide antibiotics revealed by structure–activity studies and high-resolution crystal structures

The continued rise of antibiotic resistance is a global concern that threatens to undermine many aspects of modern medical practice. Key to addressing this threat is the discovery and development of new antibiotics that operate by unexploited modes of action. The so-called calcium-dependent lipopeptide antibiotics (CDAs) are an important emerging class of natural products that provides a source of new antibiotic agents rich in structural and mechanistic diversity. Notable in this regard is the subset of CDAs comprising the laspartomycins and amphomycins/friulimicins that specifically target the bacterial cell wall precursor undecaprenyl phosphate (C₅₅-P). In this study we describe the design and synthesis of new C₅₅-P-targeting CDAs with structural features drawn from both the laspartomycin and amphomycin/friulimicin classes. Assessment of these lipopeptides revealed previously unknown and surprisingly subtle structural features that are required for antibacterial activity. High-resolution crystal structures further indicate that the amphomycin/friulimicin-like lipopeptides adopt a unique crystal packing that governs their interaction with C₅₅-P and provides an explanation for their antibacterial effect. In addition, live-cell microscopy studies provide further insights into the biological activity of the C₅₅-P targeting CDAs highlighting their unique mechanism of action relative to the clinically used CDA daptomycin.

Structural and mechanistic studies give new insights into calcium-dependent lipopeptide antibiotics that target C₅₅-P.     

Numerical solution of separable nonlinear equations with a singular matrix at the solution

Numerical Algorithms - We present a numerical method for solving the separable nonlinear equation A(y)z + b(y) =?0, where A(y) is an m × N matrix and b(y) is a vector, with y ∈Rn...     

Infrared spectroscopy and structure of photochemically protonated biomolecules in the gas phase: a noradrenaline analogue, lysine and alanyl alanine

A novel photochemical technique combined with mass spectrometry and resonant infrared multiphoton dissociation spectroscopy (R-IRMPD) has been used to record infrared vibrational spectra of the free protonated noradrenaline analogue, 2-amino-1-phenylethanol (APE-H(+)), the amino acid, lysine (Lys-H(+)), and the dipeptide, alanyl alanine (Ala-Ala-H(+)) in the gas phase. Coupling their spectra, obtained in the OH, NH and CH stretch regions, with ab initio calculations has allowed assignment of their preferred protonation sites and conformations. This simple technique will have wide applicability in future investigations of protonated biomolecular structure and conformation.