Prediction of chromatographic retention and protein identification in liquid chromatography/mass spectrometry

Liquid chromatography coupled on- or off-line with mass spectrometry is rapidly advancing as a tool in proteomics capable of dealing with the inherent complexity in biology and complementing conventional approaches based on two-dimensional gel electrophoresis. Proteins can be identified by proteolytic digestion and peptide mass fingerprinting or by searching databases using short-sequence tags generated by tandem mass spectrometry. This paper shows that information on the chromatographic behavior of peptides can assist protein identification by peptide mass fingerprinting in liquid chromatography/mass spectrometry. This additional information is significant and already available at no extra experimental cost.     

Synthesis of branched 'nanotrees' by controlled seeding of multiple branching events

The formation of nanostructures with controlled size and morphology has been the focus of intensive research in recent years. Such nanostructures are important in the development of nanoscale devices and in the exploitation of the properties of nanomaterials. Here we show how tree-like nanostructures ('nanotrees') can be formed in a highly controlled way. The process involves the self-assembled growth of semiconductor nanowires via the vapour-liquid-solid growth mode. This bottom-up method uses initial seeding by catalytic nanoparticles to form the trunk, followed by the sequential seeding of branching structures. Each level of branching is controlled in terms of branch length, diameter and number, as well as chemical composition. We show, by high-resolution transmission electron microscopy, that the branching mechanism gives continuous crystalline (monolithic) structures throughout the extended and complex tree-like structures. The controlled seeding method that we report here has potential as a generic means of forming complex branching structures, and may also offer opportunities for applications, such as the mimicking of photosynthesis in nanotrees.     

Detection of phosphorylated peptides in proteomic analyses using microfluidic compact disk technology

A compact disk (CD)-based microfluidic method for selective detection of phosphopeptides by mass spectrometry is described. It combines immobilized metal affinity chromatography (IMAC) and enzymatic dephosphorylation. Phosphoproteins are digested with trypsin and processed on the CD using nanoliter scale IMAC with and without subsequent in situ alkaline phosphatase treatment. This is followed by on-CD matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. Dephosphorylation of the IMAC-enriched peptides allows selective phosphopeptide detection based on the differential mass maps generated (mass shifts of 80 Da or multiples of 80 Da). The CD contains 96 microstructures, each with a 16 nL IMAC microfluidic column. Movement of liquid is controlled by differential spinning of the disk. Up to 48 samples are distributed onto the CD in two equal sets. One set is for phosphopeptide enrichment only, the other for identical phosphopeptide enrichment but combined with in situ dephosphorylation. Peptides are eluted from the columns directly into MALDI target areas, still on the CD, using a solvent containing the MALDI matrix. After crystallization, the CD is inserted into a MALDI mass spectrometer for analysis down to the femtomole level. The average success rate in phosphopeptide detection is over 90%. Applied to noncharacterized samples, the method identified two novel phosphorylation sites, Thr 735 and Ser 737, in the ligand-binding domain of the human mineralocorticoid receptor.     

Water and Solute Movement in Air Pollution Control Residues Measured by Time-Domain Reflectometry

The mobility of pollutants from air pollution control (APC) residues is strongly influenced by its contact with water. This study aims to verify the applicability of time-domain reflectometry (TDR) to infer water and solute movement in situ in an APC residue–compost mixture in a laboratory column. The calibrated dielectric permittivity–volumetric water content relationship (K?θv) for the material shows a distinct plateau at midrange volumetric water contents, which are underestimated by Topp’s K?θv model throughout the studied range. The coating of probes enables a clear TDR signal collection and analysis up to electrical conductivity values of 280?mS?cm?1. Heterogeneities in packing and channel flow in the column are revealed by TDR measurements. Water contents inferred by TDR signal analysis require careful interpretation when used in materials such as APC residues, due to the high amount of water bound in the hydration shells of ions released into the pore water.     

Simple and accurate four-node axisymmetric element

Based on the assumed strain method, a simple four-node axisymmetric solid element is introduced. The assumed strain field is carefully selected to preserve the correct rank of the element stiffness matrix and to achieve high accuracy. The strain field is developed in conjunction with orthogonal projections and no matrix inversions are needed. The coarse mesh accuracy in bending and in typical axisymmetric load cases is excellent even for nearly incompressible materials. The strain-driven format obtained is well suited for materials with non-linear stress–strain relations. Several numerical examples are presented where the excellent performance of the proposed simple element is verified. Copyright © 2006 John Wiley & Sons, Ltd.     

Strategies to obtain pattern fidelity in nanowire growth from large-area surfaces patterned using nanoimprint lithography

Position controlled nanowire growth is important for nanowire-based optoelectronic components which rely on light emission or light absorption. For solar energy harvesting applications, dense arrays of nanowires are needed; however, a major obstacle to obtaining dense nanowire arrays is seed particle displacement and coalescing during the annealing stage prior to nanowire growth. Here, we explore three different strategies to improve pattern preservation of large-area catalyst particle arrays defined by nanoimprint lithography for nanowire growth. First, we see that heat treating the growth substrate prior to nanoimprint lithography improves pattern preservation. Second, we explore the possibility of improving pattern preservation by fixing the seed particles in place prior to annealing by modifying the growth procedure. And third, we show that a SiN _x growth mask can fully prevent seed particle displacement. We show how these strategies allow us to greatly improve the pattern fidelity of grown InP nanowire arrays with dimensions suitable for solar cell applications, ultimately achieving 100% pattern preservation over the sampled area. The generic nature of these strategies is supported through the synthesis of GaAs and GaP nanowires.

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The robust vehicle routing problem with time windows

This paper addresses the robust vehicle routing problem with time windows. We are motivated by a problem that arises in maritime transportation where delays are frequent and should be taken into account. Our model only allows routes that are feasible for all values of the travel times in a predetermined uncertainty polytope, which yields a robust optimization problem. We propose two new formulations for the robust problem, each based on a different robust approach. The first formulation extends the well-known resource inequalities formulation by employing adjustable robust optimization. We propose two techniques, which, using the structure of the problem, allow to reduce significantly the number of extreme points of the uncertainty polytope. The second formulation generalizes a path inequalities formulation to the uncertain context. The uncertainty appears implicitly in this formulation, so that we develop a new cutting plane technique for robust combinatorial optimization problems with complicated constraints. In particular, efficient separation procedures are discussed. We compare the two formulations on a test bed composed of maritime transportation instances. These results show that the solution times are similar for both formulations while being significantly faster than the solutions times of a layered formulation recently proposed for the problem.