Nuclear structure studies with the 7Li(e,e'p) reaction

Experimental momentum distributions for the transitions to the ground state and first excited state of 6He have been measured via the reaction 7Li(e,e'p)6He, in the missing momentum range from -70 to 260 MeV/c. They are compared to theoretical distributions calculated with mean-field wave functions and with variational Monte Carlo (VMC) wave functions which include strong state-dependent correlations in both 7Li and 6He. These VMC calculations provide a parameter-free prediction of the momentum distribution that reproduces the measured data, including its normalization. The deduced summed spectroscopic factor for the two transitions is 0.58 +/- 0.05, in perfect agreement with the VMC value of 0.60. This is the first successful comparison of experiment and ab initio theory for spectroscopic factors in p-shell nuclei.Comment: 4 pages, 3 figure

Primary osteoblast-like cells from patients with end-stage kidney disease reflect gene expression, proliferation, and mineralization characteristics ex vivo.

Osteocytes regulate bone turnover and mineralization in chronic kidney disease. As osteocytes are derived from osteoblasts, alterations in osteoblast function may regulate osteoblast maturation, osteocytic transition, bone turnover, and skeletal mineralization. Thus, primary osteoblast-like cells were cultured from bone chips obtained from 24 pediatric ESKD patients. RNA expression in cultured cells was compared with RNA expression in cells from healthy individuals, to RNA expression in the bone core itself, and to parameters of bone histomorphometry. Proliferation and mineralization rates of patient cells were compared with rates in healthy control cells. Associations were observed between bone osteoid accumulation, as assessed by bone histomorphometry, and bone core RNA expression of osterix, matrix gla protein, parathyroid hormone receptor 1, and RANKL. Gene expression of osteoblast markers was increased in cells from ESKD patients and signaling genes including Cyp24A1, Cyp27B1, VDR, and NHERF1 correlated between cells and bone cores. Cells from patients with high turnover renal osteodystrophy proliferated more rapidly and mineralized more slowly than did cells from healthy controls. Thus, primary osteoblasts obtained from patients with ESKD retain changes in gene expression ex vivo that are also observed in bone core specimens. Evaluation of these cells in vitro may provide further insights into the abnormal bone biology that persists, despite current therapies, in patients with ESKD

Progress of the National Air Quality Cooperation Programme (NSL)

Om de luchtkwaliteit in Nederland te verbeteren is het Nationaal Samenwerkingsprogramma Luchtkwaliteit (NSL) opgezet. In dit programma werken de Rijksoverheid en decentrale overheden samen om te zorgen dat Nederland overal tijdig aan de grenswaarden voor fijnstof (2011) en stikstofdioxide (2015) zal voldoen. Om de voortgang te volgen is bij het NSL een monitoringsprogramma opgezet. Centraal onderdeel daarvan is een rekeninstrument waarvoor de overheden de brongegevens aanleveren. De daaruitvolgende rekenresultaten zijn vervolgens door het Bureau Monitoring (samenwerkingsverband RIVM en InfoMil) samengevoegd in voorliggende voortgangsrapportage. De prognoses voor 2011 en 2015 laten zien dat voor een groot deel van Nederland de resultaten onder de Europese grenswaarden voor PM10 (fijnstof) en NO2 liggen. Op een aantal plekken zijn er wel nieuwe of grotere overschrijdingen van de PM10- en NO2-grenswaarden zichtbaar. Bij de fijnstof (PM10) overschrijdingen gaat het hoofdzakelijk om locaties bij veehouderijen en een aantal industriele gebieden. Vooral nabij veehouderijen is op een aantal plekken nog sprake van grote overschrijdingen die lastig voor medio 2011 op te lossen zijn. De huidige prognose voor de concentraties stikstofdioxide in 2015 laat een minder gunstige ontwikkeling zien ten opzichte van wat is berekend in de vaststelling van het NSL. Dit komt voor een belangrijk deel door tegenvallende verkeersemissies wat heeft geleid tot een aantal nieuwe overschrijdingen. De nu in de prognoses berekende concentraties liggen op veel locaties net onder de grenswaarde. Met veel concentraties net onder de grenswaarde neemt het aantal overschrijdingen snel toe bij een tegenvaller in een van de gemaakte aannamen. In combinatie met een grote en deels onbekende onzekerheid in de rekenresultaten vormt dit een risico voor het behalen van de doelstelling van het NSL.The NSL has been put in place to improve air quality in the Netherlands and to ensure that the Netherlands meets the date of compliance with the EU limit values for particulate matter and nitrogen dioxide. Local, regional and national authorities work together within the framework of this programme to ensure that these goals are met. A monitoring programme, centred around a specially designed assessment tool, has been set up to monitor the progress. This tool uses data that the participating authorities are required to provide as part of the annual monitoring cycle. The results of the tool have been bundled by the Bureau Monitoring into this progress report. The prognosis for 2011 and 2015, based on the results obtained using the assessment tool, are that the concentrations of PM10 and NO2 fall below the EU limit values in most parts of the Netherlands. However, exceedances of the limit values do occur at specific locations. For PM10, these exceedances mostly occur close to a number of industrial sites and stock farms. Particularly high exceedances in the vicinity of these stock farms will make it difficult to meet the limit values by mid 2011 at these locations. The prognostications for NO2 show a less favourable decline in NO2 concentrations than was modelled at the establishment of the NSL. This is mostly due to the decline in traffic emissions falling short of expectations, resulting in new exceedances. At many locations, the calculated concentrations in the prognostications fall just under the limit value and, consequently, there will be a large increase in the number of exceedances when one or more of the premises become less favourable. This possibility, together with the large and partially unknown uncertainty in the calculation results, add up to a risk for not meeting the limit values by the date of compliance.VRO

Geodynamo and mantle convection simulations on the Earth Simulator using the Yin-Yang grid

We have developed finite difference codes based on the Yin-Yang grid for the geodynamo simulation and the mantle convection simulation. The Yin-Yang grid is a kind of spherical overset grid that is composed of two identical component grids. The intrinsic simplicity of the mesh configuration of the Yin-Yang grid enables us to develop highly optimized simulation codes on massively parallel supercomputers. The Yin-Yang geodynamo code has achieved 15.2 Tflops with 4096 processors on the Earth Simulator. This represents 46% of the theoretical peak performance. The Yin-Yang mantle code has enabled us to carry out mantle convection simulations in realistic regimes with a Rayleigh number of $10^7$ including strongly temperature-dependent viscosity with spatial contrast up to $10^6$.Comment: Plenary talk at SciDAC 200

Inferring the time-dependent complex Ginzburg-Landau equation from modulus data

We present a formalism for inferring the equation of evolution of a complex wave field that is known to obey an otherwise unspecified (2+1)-dimensional time-dependent complex Ginzburg-Landau equation, given field moduli over three closely-spaced planes. The phase of the complex wave field is retrieved via a non-interferometric method, and all terms in the equation of evolution are determined using only the magnitude of the complex wave field. The formalism is tested using simulated data for a generalized nonlinear system with a single-component complex wave field. The method can be generalized to multi-component complex fields.Comment: 9 pages, 9 figure

System-based proteomic and metabonomic analysis of the Df(16)A+/- mouse identifies potential miR-185 targets and molecular pathway alterations

Deletions on chromosome 22q11.2 are a strong genetic risk factor for development of schizophrenia and cognitive dysfunction. We employed shotgun liquid chromatography-mass spectrometry (LC-MS) proteomic and metabonomic profiling approaches on prefrontal cortex (PFC) and hippocampal (HPC) tissue from Df(16)A +/- mice, a model of the 22q11.2 deletion syndrome. Proteomic results were compared with previous transcriptomic profiling studies of the same brain regions. The aim was to investigate how the combined effect of the 22q11.2 deletion and the corresponding miRNA dysregulation affects the cell biology at the systems level. The proteomic brain profiling analysis revealed PFC and HPC changes in various molecular pathways associated with chromatin remodelling and RNA transcription, indicative of an epigenetic component of the 22q11.2DS. Further, alterations in glycolysis/gluconeogenesis, mitochondrial function and lipid biosynthesis were identified. Metabonomic profiling substantiated the proteomic findings by identifying changes in 22q11.2 deletion syndrome (22q11.2DS)-related pathways, such as changes in ceramide phosphoethanolamines, sphingomyelin, carnitines, tyrosine derivates and panthothenic acid. The proteomic findings were confirmed using selected reaction monitoring mass spectrometry, validating decreased levels of several proteins encoded on 22q11.2, increased levels of the computationally predicted putative miR-185 targets UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase 110 kDa subunit (OGT1) and kinesin heavy chain isoform 5A and alterations in the non-miR-185 targets serine/threonine-protein phosphatase 2B catalytic subunit gamma isoform, neurofilament light chain and vesicular glutamate transporter 1. Furthermore, alterations in the proteins associated with mammalian target of rapamycin signalling were detected in the PFC and with glutamatergic signalling in the hippocampus. Based on the proteomic and metabonomic findings, we were able to develop a schematic model summarizing the most prominent molecular network findings in the Df(16)A +/- mouse. Interestingly, the implicated pathways can be linked to one of the most consistent and strongest proteomic candidates, (OGT1), which is a predicted miR-185 target. Our results provide novel insights into system-biological mechanisms associated with the 22q11DS, which may be linked to cognitive dysfunction and an increased risk to develop schizophrenia. Further investigation of these pathways could help to identify novel drug targets for the treatment of schizophrenia

Fourier Acceleration of Langevin Molecular Dynamics

Fourier acceleration has been successfully applied to the simulation of lattice field theories for more than a decade. In this paper, we extend the method to the dynamics of discrete particles moving in continuum. Although our method is based on a mapping of the particles' dynamics to a regular grid so that discrete Fourier transforms may be taken, it should be emphasized that the introduction of the grid is a purely algorithmic device and that no smoothing, coarse-graining or mean-field approximations are made. The method thus can be applied to the equations of motion of molecular dynamics (MD), or its Langevin or Brownian variants. For example, in Langevin MD simulations our acceleration technique permits a straightforward spectral decomposition of forces so that the long-wavelength modes are integrated with a longer time step, thereby reducing the time required to reach equilibrium or to decorrelate the system in equilibrium. Speedup factors of up to 30 are observed relative to pure (unaccelerated) Langevin MD. As with acceleration of critical lattice models, even further gains relative to the unaccelerated method are expected for larger systems. Preliminary results for Fourier-accelerated molecular dynamics are presented in order to illustrate the basic concepts. Possible extensions of the method and further lines of research are discussed.Comment: 11 pages, two illustrations included using graphic

Tips for implementing multigrid methods on domains containing holes

As part of our development of a computer code to perform 3D `constrained evolution' of Einstein's equations in 3+1 form, we discuss issues regarding the efficient solution of elliptic equations on domains containing holes (i.e., excised regions), via the multigrid method. We consider as a test case the Poisson equation with a nonlinear term added, as a means of illustrating the principles involved, and move to a "real world" 3-dimensional problem which is the solution of the conformally flat Hamiltonian constraint with Dirichlet and Robin boundary conditions. Using our vertex-centered multigrid code, we demonstrate globally second-order-accurate solutions of elliptic equations over domains containing holes, in two and three spatial dimensions. Keys to the success of this method are the choice of the restriction operator near the holes and definition of the location of the inner boundary. In some cases (e.g. two holes in two dimensions), more and more smoothing may be required as the mesh spacing decreases to zero; however for the resolutions currently of interest to many numerical relativists, it is feasible to maintain second order convergence by concentrating smoothing (spatially) where it is needed most. This paper, and our publicly available source code, are intended to serve as semi-pedagogical guides for those who may wish to implement similar schemes.Comment: 18 pages, 11 figures, LaTeX. Added clarifications and references re. scope of paper, mathematical foundations, relevance of work. Accepted for publication in Classical & Quantum Gravit

Two-dimensional turbulence in magnetised plasmas

In an inhomogeneous magnetised plasma the transport of energy and particles perpendicular to the magnetic field is in general mainly caused by quasi two-dimensional turbulent fluid mixing. The physics of turbulence and structure formation is of ubiquitous importance to every magnetically confined laboratory plasma for experimental or industrial application. Specifically, high temperature plasmas for fusion energy research are also dominated by the properties of this turbulent transport. Self-organisation of turbulent vortices to mesoscopic structures like zonal flows is related to the formation of transport barriers that can significantly enhance the confinement of a fusion plasma. This subject of great importance in research is rarely touched on in introductory plasma physics or continuum dynamics courses. Here a brief tutorial on 2D fluid and plasma turbulence is presented as an introduction to the field, appropriate for inclusion in undergraduate and graduate courses.Comment: This is an author-created, un-copyedited version of an article published in European Journal of Physics. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at doi: 10.1088/0143-0807/29/5/00