Toolkit for simulated commissioning of storage-ring light sources and application to the advanced light source upgrade accumulator

We present a new accelerator toolbox (AT)-based toolkit for simulating the commissioning of light-source storage rings. The toolkit provides a framework for supporting high-level scripts to represent with realism the various procedures (e.g., orbit and optics correction, beam-based alignment, etc.) encountered during commissioning and is designed to mirror as closely as possible the reality as seen from the control room. Emphasis is placed on the inclusion of a comprehensive set of error sources and faithful modeling of beam diagnostics. The toolkit capabilities are demonstrated in an application to the recent design and commissioning studies of the Advanced Light Source Upgrade (ALS-U) Accumulator Ring, a short-time successful commissioning of which will be critical to the overall ALS-U project success

Effects of micelle nature and concentration on the acid dissociation constants of the metal extractor PADA

The pyridine-2-azo-p-dimethylaniline (PADA) ligand presents two acid dissociation constants, being pKa1 related to the pyridinium and pKa2 related to the anilinium residue. These have been measured by spectrophotometric titrations in aqueous solutions containing either the anionic (SDS), or the non–ionic (Triton X-100) or the cationic (DTAC) surfactants. The pKai shifts of the charged systems from that of the PADA/Triton X-100 reference (∆pKai0) are compared. For PADA/DTAC ∆pKa10 = 0.05 and ∆pKa20 = 0.6. For PADA/SDS ∆pKa10 = 2.1 and ∆pKa20 = 2.1 both yielding the value of -126 mV for the surface potential (ψ) of SDS. The ψ value, lying between the calculated Stern potential and the zeta potential, indicates that the dye is located on the SDS micelles between the fixed and the shear layer. In contrast, the behaviour of PADA/DTAC is explained assuming that the positively charged deprotonation sites of PADA are forced to protrude towards the bulk solvent by the positive charges of DTAC micelles. The shifts of the apparent pKai from the aqueous values (∆pKaiw) have also been analysed. Concerning PADA/Triton X-100, the shifts ∆pKa1w = -0.1 and ∆pKa2w = -0.9 are rationalized in terms of dielectric constant reduction at the reaction sites. Concerning PADA/DTAC, ∆pKa1w= -0.05 and ∆pKa2w= -0.3 whereas, for PADA/SDS, ∆pKa1w = 2.0 and ∆pKa2w = 1.2. The pKa2w values decrease on raising the surfactant concentrations for all the investigated systems. This behaviour is explained assuming that the increase of the overall micellar surface and, by consequence, of the reaction sites number, results in a site dilution effect which disfavours proton association. The addition of NaCl induces changes of pKa1 and pKa2 which are explained in terms of (large) reduction of ψ for PADA/SDS and of (small) reduction of the dielectric constant for the other systems

Mechanistic aspects of thioflavin-T self-aggregation and DNA binding: evidence for dimer attack on DNA grooves

Thioflavin-T (TFT) is a fluorescent marker widely employed in biomedical research but the mechanism of its binding to polynucleotides has been poorly understood. This paper presents a study of the mechanisms of TFT self-aggregation and binding to DNA. Relaxation kinetics of TFT solutions show that the cyanine undergoes dimerization followed by dimer isomerisation. The interaction of TFT with DNA has been investigated using static methods, such as spectrophotometric and spectrofluorometric titrations under different conditions (salt content, temperature), fluorescence quenching, viscometric experiments and the T-jump relaxation method. The combined use of these techniques enabled us to show that the TFT monomer undergoes intercalation between the DNA base pairs and external binding according to a branched mechanism. Moreover, it has also been observed that, under dye excess conditions, the TFT dimer binds to the DNA grooves. The molecular structures of intercalated TFT and the groove-bound TFT dimer are obtained by performing QM/MM MD simulations

Origin of ferroelectricity in the multiferroic barium fluorides BaMF4

We present a first principles study of the series of multiferroic barium fluorides with the composition BaMF4, where M is Mn, Fe, Co, or Ni. We discuss trends in the structural, electronic, and magnetic properties, and we show that the ferroelectricity in these systems results from the "freezing in" of a single unstable polar phonon mode. In contrast to the case of the standard perovskite ferroelectrics, this structural distortion is not accompanied by charge transfer between cations and anions. Thus, the ferroelectric instability in the multiferroic barium fluorides arises solely due to size effects and the special geometrical constraints of the underlying crystal structure.Comment: 8 pages, 6 figures, 3 table

Complex Systems Science: Dreams of Universality, Reality of Interdisciplinarity

Using a large database (~ 215 000 records) of relevant articles, we empirically study the "complex systems" field and its claims to find universal principles applying to systems in general. The study of references shared by the papers allows us to obtain a global point of view on the structure of this highly interdisciplinary field. We show that its overall coherence does not arise from a universal theory but instead from computational techniques and fruitful adaptations of the idea of self-organization to specific systems. We also find that communication between different disciplines goes through specific "trading zones", ie sub-communities that create an interface around specific tools (a DNA microchip) or concepts (a network).Comment: Journal of the American Society for Information Science and Technology (2012) 10.1002/asi.2264

The experience of dysgeusia in allogenic hematopoietic cell transplantation survivors: A qualitative study

Background: Taste disorders are one of the most common side effects of treatment in oncology patients and often occur after allogeneic hematopoietic cell transplantation (allo-HCT). Dysgeusia is rarely a life-threatening complication, therefore, in many cases it does not receive close medical attention. Furthermore, information about this disorder is largely based on the clinician’s own experience. However, taste disorders, can impact on the quality of life in survivors of allo-HCT, and compromise their enjoyment of eating, food intake, weight and nutritional status. The number of performed annual transplantations continues to grow annually and the number of older long-term survivors increases. There is little literature that is focused on studies of survivors of allo-HCT with taste disorders. We conducted a qualitative descriptive study to explore experiences of dysgeusia in patients that have undergone of allo-HCT and examined what strategies they used to mitigate it. Methods: Using purposive sampling, survivors of allo-HCT were recruited. Audiotape interviews were conducted until data saturation was achieved. Each interview was transcribed verbatim, and content analyses were performed to extract significant themes and subthemes. Results: Three major themes embracing various aspects of allo-HCT survivors’ experiences were identified: 1) the shape of taste; 2) everything is irritating and it is arduous to eat; 3) finding new strategies to overcome the problems. Together, they highlight the experiences of survivors showing how taste disorders can affect the physical, psychological and social dimensions of a person for the rest of their life. Conclusions: A cumulative burden is the result of dysgeusia and its clinical course reinforced also by related symptoms. Healthcare professionals must focus their attention on the management of these symptoms and offer interventions to safeguard the patient’s social, physical and psychological well-being. Finally, further research is needed to explore the experiences of allo-HTC patients who have taste disorders throughout their cancer journey that introduces a more holistic approach which involves health professionals, caregivers and family members

Deflections in Magnet Fringe Fields

A transverse multipole expansion is derived, including the longitudinal components necessarily present in regions of varying magnetic field profile. It can be used for exact numerical orbit following through the fringe field regions of magnets whose end designs introduce no extraneous components, {\it i.e.} fields not required to be present by Maxwell's equations. Analytic evaluations of the deflections are obtained in various approximations. Mainly emphasized is a ``straight-line approximation'', in which particle orbits are treated as straight lines through the fringe field regions. This approximation leads to a readily-evaluated figure of merit, the ratio of r.m.s. end deflection to nominal body deflection, that can be used to determine whether or not a fringe field can be neglected. Deflections in ``critical'' cases (e.g. near intersection regions) are analysed in the same approximation.Comment: To be published in Physical Review

The Three-Dipole Kicker Injection Scheme for the ALS-U Accumulator Ring

The ALS-U light source will implement on-axis single-train swap-out injection employing an accumulator between the booster and storage rings. The accumulator ring design is a twelve period triple-bend achromat that will be installed along the inner circumference of the storage-ring tunnel. A non-conventional injection scheme will be utilized for top-off off-axis injection from the booster into the accumulator ring meant to accommodate a large $\sim 300$~nm emittance beam into a vacuum-chamber with a limiting horizontal aperture radius as small as $8$ mm. The scheme incorporates three dipole kickers distributed over three sectors, with two kickers perturbing the stored beam and the third affecting both the stored and the injected beam trajectories. This paper describes this ``3DK'' injection scheme and how it fits the accumulator ring's particular requirements. We describe the design and optimization process, and how we evaluated its fitness as a solution for booster-to-accumulator ring injection.Comment: 13 pages, 20 figure

Correlação entre deterioração fisiológica pós-colheita e características agronômicas em mandioca.

O conhecimento das associações entre as características produtivas da mandioca (Manihot esculenta Crantz) pode auxiliar os programas de melhoramento genético a praticarem a seleção indireta. Isto é especialmente válido para características de difícil mensuração, como é o caso da deterioração fisiológica pós-colheita (DFPC). De modo geral, as correlações possuem causas genéticas pelo fato de alguns genes afetarem simultaneamente duas características, positiva ou negativamente. Neste sentido, o objetivo desse trabalho foi estimar as correlações fenotípicas entre DFPC e atributos agronômicos