Information Technology/Large-Scale Data Handling

The experience of light source users has been transformed in recent years by large increases in flux and brightness, revolutionary new optics and detectors, and automation and advanced sample environments. Beamlines are producing data at rates and volumes that challenge the capabilities of even the most experienced user groups. Meanwhile, the community of synchrotron users continues to grow in size and diversity: researchers come from physics, material science, energy and battery research, geology, biology, chemistry, art history, and more. Almost every natural science domain is being advanced through the techniques employed at these facilities, but a significant fraction of these researchers are first-time or infrequent users of a particular beamline. The combination of an expanding base of new users and increased beamline capabilities is leading to an increase in the amount of “dark data” that is not analyzed fully (or, in some cases, at all).     

ALS User Meeting Highlights Accomplishments and Challenges

The 2014 ALS User Meeting, held in Berkeley, California, from October 6-8, 2014, launched with a welcome from UEC Chair Peter Nico and remarks from Associate Lab Director for Energy and Environmental Sciences, Don DePaolo. ALS Director Roger Falcone then addressed the gathering, noting that while the past year has been tough in terms of funding for the ALS, there were also many scientific achievements to highlight and a record number of users with an impressive number of publications.     

Absolute absorption cross section measurements of CO2 in the wavelength region 163–200 nm and the temperature dependence

Laboratory measurements of the absorption cross section of CO₂ at the temperatures 195 and 295 K have been made throughout the wavelength region 163–200 nm by using a high resolution grating spectrometer. Cross sections at 195 K are smaller than those at 295 K, and the band structures are more emphasized as expected. In combining with our previous measurements [J. Quant. Spectrosc. Radiat. Transfer, 55 (1996) 53], the absorption cross sections of CO₂ are available in the wavelength region 117.8–200.0 nm at 295 K and 117.8–192.5 nm at 195 K.     

Dynamic aspects of small bubble and hydrophilic solid encounters

The capture of solid particles suspended in aqueous solution by rising gas bubbles involves hydrodynamic and physicochemical processes that are central to colloid science. Of the collision, attachment and aggregate stability aspects to the bubble-particle interaction, the crucial attachment process is least understood. This is especially true of hydrophilic solids. We review the current literature regarding each component of the bubble-particle attachment process, from the free-rise of a small, clean single bubble, to the collision, film drainage and interactions which dominate the attachment rate. There is a particular focus on recent studies which employ single, very small bubbles as analysis probes, enabling the dynamic bubble-hydrophilic particle interaction to be investigated, avoiding complications which arise from fluid inertia, deformation of the liquid-vapour interface and the possibility of surfactant contamination.     

Structural basis of telomeric RNA quadruplex--acridine ligand recognition

Human telomeric DNA is now known to be transcribed into noncoding RNA sequences, termed TERRA. These sequences, which are believed to play roles in the regulation of telomere function, can form higher-order quadruplex structures and may themselves be the target of therapeutic intervention. The crystal structure of a TERRA quadruplex-acridine small-molecule complex at a resolution of 2.60 ?, is reported here and contrasts remarkably with the structure of the analogous DNA quadruplex complex. The bimolecular RNA complex has a parallel-stranded topology with propeller-like UUA loops. These loops are held in particular conformations by multiple hydrogen bonds involving the O2' hydroxyl groups of the ribonucleotide sugars and play an active role in binding the acridine molecules to the RNA quadruplex. By contrast, the analogous DNA quadruplex complex has simpler 1:1 acridine binding, with no loop involvement. There are significant loop conformational changes in the RNA quadruplex compared to the native TERRA quadruplex (Collie, G. W.; Haider, S. M.; Neidle, S.; Parkinson, G. N. Nucleic Acids Res. 2010, 38, 5569 - 5580), which have implications for the future design of small molecules targeting TERRA quadruplexes, and RNA quadruplexes more generally.     

Gravity Probe B: final results of a space experiment to test general relativity

Gravity Probe B, launched 20 April 2004, is a space experiment testing two fundamental predictions of Einstein's theory of general relativity (GR), the geodetic and frame-dragging effects, by means of cryogenic gyroscopes in Earth orbit. Data collection started 28 August 2004 and ended 14 August 2005. Analysis of the data from all four gyroscopes results in a geodetic drift rate of -6601.8±18.3 mas/yr and a frame-dragging drift rate of -37.2±7.2 mas/yr, to be compared with the GR predictions of -6606.1 mas/yr and -39.2 mas/yr, respectively ("mas" is milliarcsecond; 1 mas=4.848×10(-9) rad).     

A metastable Fe(A) termination at the Fe3O4(001) surface

A metastable Fe(A) terminated Fe₃O₄(001) surface was prepared by tailoring the surface preparation conditions. STM, LEIS and LEED are utilized to demonstrate that annealing the Ar⁺ sputtered surface to 350 °C produces an Fe(A) terminated surface with a (√2 × √2)R45° superstructure. Within the superstructure both single Fe atoms and Fe dimer species are observed. The surface is reoxidized upon annealing to higher temperatures, eventually leading to the recovery of the energetically favorable Jahn–Teller distorted surface at 700 °C. The ability to reproducibly prepare the Fe(A) termination in this simple manner will allow investigations into the structure–function relationship for this important technological material.     

Medium energy ion scattering investigation of methylthiolate-induced modification of the Au(111) surface

100 keV H⁺ scattering has been used to investigate the structure of the methylthiolate/Au(111) interface in the Au(111)(√3 × √3)R30° phase. Adsorption of the thiolate onto the clean Au(111) surface leads to a large drop in the scattered ion yield due to the lifting of the clean surface ‘herring-bone’ reconstruction, but the thiolate-covered surface shows an ion yield higher than that of an unreconstructed Au(111) surface, providing direct evidence of a significant number of Au atoms that are displaced from their bulk-terminated positions at the buried interface. Simulations for two different Au adatoms models at the interface, namely, the Au-adatom-monothiolate (AAM) and Au-adatom-dithiolate (AAD) models, show significant sensitivity to the exact values of interlayer spacings and atomic vibrational amplitudes, but the comparison with experimental results appears to favour the AAD model with 0.17 ML Au adatoms in bridging sites at the interface.     

Why is RCM Favoured Over Dimerisation? Predicting and Estimating Thermodynamic Effective Molarities by Solution Experiments and Electronic Structure Calculations

The thermodynamic effective molarities of a series of simple cycloalkenes, synthesised from α,ω-dienes by reaction with Grubbs' second generation precatalyst, have been evaluated. Effective molarities were measured from a series of small scale metathesis reactions and agreed well with empirical predictions derived from the number of rotors and the product ring strain. The use of electronic structure calculations (at the M06-L/6-311G** level of theory) was explored for predicting thermodynamic effective molarities in ring-closing metathesis. However, it was found that it was necessary to apply a correction to DFT-derived free energies to account for the entropic effects of solvation.     

A dual-responsive ferrocene-functionalised PDA liposome

In this Letter we report a ferrocene-functionalised polydiacetylene liposome that has the propensity to respond colorimetrically and electrochemically upon binding to a cyclodextrin oligomer.