A two-sided Arnoldi algorithm with stopping criterion and MIMO selection procedure

In this paper we introduce a two-sided Arnoldi method for the reduction of high order linear systems and we propose useful extensions, first of all a stopping criterion to find a suitable order for the reduced model and secondly, a selection procedure to significantly improve the performance in the multi-input multi-output (MIMO) case. One application is in micro-electro-mechanical systems (MEMS). We consider a thermo-electric micro thruster model, and a comparison between the commonly used Arnoldi algorithm and the two-sided Arnoldi is performed.     

Working group report: Heavy-ion physics and quark-gluon plasma

This is the report of Heavy Ion Physics and Quark-Gluon Plasma at WHEPP-09 which was part of Working Group-4. Discussion and work on some aspects of quark-gluon plasma believed to have created in heavy-ion collisions and in early Universe are reported.     

The Beamline X28C of the Center for Synchrotron Biosciences: a National Resource for Biomolecular Structure and Dynamics Experiments Using Synchrotron Footprinting

Structural mapping of proteins and nucleic acids with high resolution in solution is of critical importance for understanding their biological function. A wide range of footprinting technologies have been developed over the last ten years to address this need. Beamline X28C, a white‐beam X‐ray source at the National Synchrotron Light Source of Brookhaven National Laboratory, functions as a platform for synchrotron footprinting research and further technology development in this growing field. An expanding set of user groups utilize this national resource funded by the National Institute of Biomedical Imaging and Bioengineering of the National Institutes of Health. The facility is operated by the Center for Synchrotron Biosciences and the Center for Proteomics of Case Western Reserve University. The facility includes instrumentation suitable for conducting both steady‐state and millisecond time‐resolved footprinting experiments based on the production of hydroxyl radicals by X‐rays. Footprinting studies of nucleic acids are routinely conducted with X‐ray exposures of tens of milliseconds, which include studies of nucleic acid folding and their interactions with proteins. This technology can also be used to study protein structure and dynamics in solution as well as protein–protein interactions in large macromolecular complexes. This article provides an overview of the X28C beamline technology and defines protocols for its adoption at other synchrotron facilities. Lastly, several examples of published results provide illustrations of the kinds of experiments likely to be successful using these approaches.     

Subcellular localization of the antidepressant-sensitive norepinephrine transporter

Background  

Reuptake of synaptic norepinephrine (NE) via the antidepressant-sensitive NE transporter (NET) supports efficient noradrenergic signaling and presynaptic NE homeostasis. Limited, and somewhat contradictory, information currently describes the axonal transport and localization of NET in neurons.     

结构非线性分析中求解预定荷载水平的改进弧长法

本文对目前广泛应用于结构非线性分析之中的弧长法进行改进。改进后的弧长法除保持原有优点外，能够在自动跟踪结构非线性平衡路径的同时，进一步求得位于结构平衡睡径任一区段的任意预先指定的荷载水平及相应的变形。本文的方法可以推广应用于求解预先指定的应力或位移。数值算例表明了本文方法的计算精度、效率及可靠性。     

Hydroxyl radical probe of the surface of lysozyme by synchrotron radiolysis and mass spectrometry.

A new approach is reported that combines synchrotron radiolysis and mass spectrometry to probe the surface of proteins. Hydroxyl radicals produced upon the radiolysis of protein solutions with synchrotron light for several milliseconds result in the reaction of amino acid side chains. This results in the formation of stable oxidation products where the level of oxidation at the reactive residues is influenced by the accessibility of their side chains to the bulk solvent. The aromatic and sulfur-containing residues have been found to react preferentially in accord with previous peptide studies. The sites of oxidation have been determined by tandem mass spectrometry. The rate of oxidation at these reactive markers has been measured for each of the proteolytic peptides as a function of exposure time based on the relative proportion of modified and unmodified peptide ions detected by mass spectrometry. Oxidation rates have been found to correlate closely with a theoretical measure of the accessibility of residue side chains to the bulk solvent in the native protein structure. The synchrotron-based approach is able to distinguish the relative accessibility of the tryptophan residue side chains of lysozyme at positions 62 and 123 from each other and all other tryptophan residues based on their rates of oxidation.