Temperature compensation of NdFeB permanent magnets

Permanent magnet blocks of NdFeB have a relatively high maximum energy product. Because of its relatively low Curie temperature, however, NdFeB has a large temperature coefficient for its residual induction. The temperature coefficients of the relative magnetic fields ({Delta}B/B)/{Delta}T in the air gap of NdFeB dipole magnets were reduced from {minus}1.1 {times} 10{sup {minus}3}/c to less than 2 {times} 10{sup {minus}5}/{degree}C under operating temperatures of {+-} 6 C. This was achieved passively by using 1.25-mm-thick strips of 30%-Ni-Fe alloy as flux shunts for the NdFeB blocks. The magnets with soft-steel poles and flux-return yokes were assembled and measured in a temperature-controlled environment

Dynamical fingerprints for probing individual relaxation processes in biomolecular dynamics with simulations and kinetic experiments

There is a gap between kinetic experiment and simulation in their views of the dynamics of complex biomolecular systems. Whereas experiments typically reveal only a few readily discernible exponential relaxations, simulations often indicate complex multistate behavior. Here, a theoretical framework is presented that reconciles these two approaches. The central concept is “dynamical fingerprints” which contain peaks at the time scales of the dynamical processes involved with amplitudes determined by the experimental observable. Fingerprints can be generated from both experimental and simulation data, and their comparison by matching peaks permits assignment of structural changes present in the simulation to experimentally observed relaxation processes. The approach is applied here to a test case interpreting single molecule fluorescence correlation spectroscopy experiments on a set of fluorescent peptides with molecular dynamics simulations. The peptides exhibit complex kinetics shown to be consistent with the apparent simplicity of the experimental data. Moreover, the fingerprint approach can be used to design new experiments with site-specific labels that optimally probe specific dynamical processes in the molecule under investigation

Investigation of open-loop beam motion at low frequencies at the APS

Sources of transverse beam motion in the APS storage ring have been investigated for ground-motion- and water-system-induced vibrations of the magnet and vacuum systems, and for power supply ripple. The displacement of magnets in a bandwidth of 4-30 Hz have been reduced significantly by inserting viscoelastic damping pads between the girder supports and pedestals, and by welding the magnet cooling headers to the ceiling of the storage ring tunnel. Current ripple on magnet power supplies was identified as a source of horizontal beam motion. Beam motion was measured without the closed-orbit feedback system activated. At {beta}{sub x} = 15.4 m and {beta}{sub y} = 10.4 m the rms beam motion in the 0.02-30 Hz band was 22.7 {mu}m and 6.3 {mu}m in the horizontal and verticle planes, respectively. A few narrow-band structures of the horizontal beam motion spectrum in the 1-4 Hz band have to be investigated further to identify the sources

The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy

Conformational fluctuations of single-stranded DNA (ssDNA) oligonucleotides were studied in aqueous solution by monitoring contact-induced fluorescence quenching of the oxazine fluorophore MR121 by intrinsic guanosine residues (dG). We applied fluorescence correlation spectroscopy as well as steady-state and time-resolved fluorescence spectroscopy to analyze kinetics of DNA hairpin folding. We first characterized the reporter system by investigating bimolecular quenching interactions between MR121 and guanosine monophosphate in aqueous solution estimating rate constants, efficiency and stability for formation of quenched complexes. We then studied the kinetics of complex formation between MR121 and dG residues site-specifically incorporated in DNA hairpins. To uncover the initial steps of DNA hairpin folding we investigated complex formation in ssDNA carrying one or two complementary base pairs (dC–dG pairs) that could hybridize to form a short stem. Our data show that incorporation of a single dC–dG pair leads to non-exponential decays for opening and closing kinetics and reduces rate constants by one to two orders of magnitude. We found positive activation enthalpies independent of the number of dC–dG pairs. These results imply that the rate limiting step of DNA hairpin folding is not determined by loop dynamics, or by mismatches in the stem, but rather by interactions between stem and loop nucleotides

Detection of Atherosclerosis by Small RNA-Sequencing Analysis of Extracellular Vesicle Enriched Serum Samples

Atherosclerosis can occur throughout the arterial vascular system and lead to various diseases. Early diagnosis of atherosclerotic processes and of individual disease patterns would be more likely to be successful if targeted therapies were available. For this, it is important to find reliable biomarkers that are easily accessible and with little inconvenience for patients. There are many cell culture, animal model or tissue studies that found biomarkers at the microRNA (miRNA) and mRNA level describing atherosclerotic processes. However, little is known about their potential as circulating and liquid biopsy markers in patients. In this study, we examined serum-derived miRNA – profiles from 129 patients and 28 volunteers to identify potential biomarkers. The patients had four different atherosclerotic manifestations: abdominal aneurysm (n = 35), coronary heart disease (n = 34), carotid artery stenosis (n = 24) and peripheral arterial disease (n = 36). The samples were processed with an extracellular vesicle enrichment protocol, total-RNA extraction and small RNA-sequencing were performed. A differential expression analysis was performed bioinformatically to find potentially regulated miRNA biomarkers. Resulting miRNA candidates served as a starting point for an overrepresentation analysis in which relevant target mRNAs were identified. The Gene Ontology database revealed relevant biological functions in relation to atherosclerotic processes. In patients, expression of specific miRNAs changed significantly compared to healthy volunteers; 27 differentially expressed miRNAs were identified. We were able to detect a group-specific miRNA fingerprint: miR-122-5p, miR-2110 and miR-483-5p for abdominal aortic aneurysm, miR-370-3p and miR-409-3p for coronary heart disease, miR-335-3p, miR-381-3p, miR493-5p and miR654-3p for carotid artery stenosis, miR-199a-5p, miR-215-5p, miR-3168, miR-582-3p and miR-769-5p for peripheral arterial disease. The results of the study show that some of the identified miRNAs have already been associated with atherosclerosis in previous studies. Overrepresentation analysis on this data detected biological processes that are clearly relevant for atherosclerosis, its development and progression showing the potential of these miRNAs as biomarker candidates. In a next step, the relevance of these findings on the mRNA level is to be investigated and substantiated

A plan for the development of superconducting Undulator prototypes for LCLS-II and future FELs

Undulators serve as the primary source of radiation for modern storage rings, and more recently for the advent of Free-Electron Lasers (FELs). The performance of future FELs can be greatly enhanced using the much higher magnetic fields of superconducting undulators (SCU) [1]. For example, the LCLS-II hard x-ray undulator can be shortened by up to 70 m using an SCU in place of a PMU (permanent magnet undulator), or its spectral performance can be critically improved when using a similar length. In addition, SCUs are expected to be orders of magnitude less sensitive to radiation dose; a major issue at LCLS-II with its 1-MHz electron bunch rate. We present a funded R&D collaboration between SLAC, ANL, and LBNL, which aims to demonstrate the viability of superconducting undulators for FELs by building, testing, measuring, and tuning two 1.5-m long planar SCU prototypes using two different technologies: NbTi at ANL and Nb Sn at LBNL. Our goal is to review and reassess the LCLS-II HXR baseline plans (PMU) in July of 2015, after the development and evaluation of both prototypes, possibly in favor of an SCU for LCLS-II.

Anomalous Dispersion with Edges in the Soft X-ray Region: First Results of Diffraction from Single Crystals of Trypsin Near the K-Absorption Edge of Sulfur

Anomalous dispersion of X-ray diffraction at wavelengths near the X-ray K-absorption edge of sulfur at wavelengths around 5 Å has been applied to single crystals of trypsin obtained from an ammonium sulfate solution. The multiwavelength anomalous-dispersion method based on 775 unique reflections (+183 Bijvoet mates) measured at three wavelengths near the K-absorption edge of sulfur in trypsin (two methionines and disulfide bridges of six cystines) reproduces the known features of the trypsin structure of a resolution of 4 Å. It appears that there is anisotropic anomalous scattering from the disulfide bridges of cystine. The multiwavelength anomalous solvent contrast shows up at wavelengths near the K-absorption edge of the sulfate ions, which is shifted by 10 eV to higher energies with respect to that of sulfur in trypsin. The influence of the complex contrast of trypsin in 2.5 M ammonium sulfate on the dispersion of a low-order reflection is analyzed. The measurement of anomalous dispersion of X-ray diffraction at long wavelengths beyond 5 Å requires a special diffractometer, the features of which are presented. An outstanding one is a detector system consisting of four multiwire proportional counters. Its efficiency is compared with that of imaging plates. The influence of radiation damage with soft X-ray diffraction from single crystals of trypsin is presented and possible remedies are discussed

Hydrogen-Bond Driven Loop-Closure Kinetics in Unfolded Polypeptide Chains

Characterization of the length dependence of end-to-end loop-closure kinetics in unfolded polypeptide chains provides an understanding of early steps in protein folding. Here, loop-closure in poly-glycine-serine peptides is investigated by combining single-molecule fluorescence spectroscopy with molecular dynamics simulation. For chains containing more than 10 peptide bonds loop-closing rate constants on the 20–100 nanosecond time range exhibit a power-law length dependence. However, this scaling breaks down for shorter peptides, which exhibit slower kinetics arising from a perturbation induced by the dye reporter system used in the experimental setup. The loop-closure kinetics in the longer peptides is found to be determined by the formation of intra-peptide hydrogen bonds and transient β-sheet structure, that accelerate the search for contacts among residues distant in sequence relative to the case of a polypeptide chain in which hydrogen bonds cannot form. Hydrogen-bond-driven polypeptide-chain collapse in unfolded peptides under physiological conditions found here is not only consistent with hierarchical models of protein folding, that highlights the importance of secondary structure formation early in the folding process, but is also shown to speed up the search for productive folding events

Bayesian inference of accurate population sizes and FRET efficiencies from single diffusing biomolecules.

It is of significant biophysical interest to obtain accurate intramolecular distance information and population sizes from single-molecule Förster resonance energy transfer (smFRET) data obtained from biomolecules in solution. Experimental methods of increasing cost and complexity are being developed to improve the accuracy and precision of data collection. However, the analysis of smFRET data sets currently relies on simplistic, and often arbitrary methods, for the selection and denoising of fluorescent bursts. Although these methods are satisfactory for the analysis of simple, low-noise systems with intermediate FRET efficiencies, they display systematic inaccuracies when applied to more complex systems. We have developed an inference method for the analysis of smFRET data from solution studies based on rigorous model-based Bayesian techniques. We implement a Monte Carlo Markov chain (MCMC) based algorithm that simultaneously estimates population sizes and intramolecular distance information directly from a raw smFRET data set, with no intermediate event selection and denoising steps. Here, we present both our parametric model of the smFRET process and the algorithm developed for data analysis. We test the algorithm using a combination of simulated data sets and data from dual-labeled DNA molecules. We demonstrate that our model-based method systematically outperforms threshold-based techniques in accurately inferring both population sizes and intramolecular distances.This is the final published version. It's also available from ACS in Analytical Chemistry: http://pubs.acs.org/doi/pdf/10.1021/ac501188r