Effect of resonant magnetic perturbations on low collisionality discharges in MAST and a comparison with ASDEX Upgrade

Sustained ELM mitigation has been achieved on MAST and AUG using RMPs with a range of toroidal mode numbers over a wide region of low to medium collisionality discharges. The ELM energy loss and peak heat loads at the divertor targets have been reduced. The ELM mitigation phase is typically associated with a drop in plasma density and overall stored energy. In one particular scenario on MAST, by carefully adjusting the fuelling it has been possible to counteract the drop in density and to produce plasmas with mitigated ELMs, reduced peak divertor heat flux and with minimal degradation in pedestal height and confined energy. While the applied resonant magnetic perturbation field can be a good indicator for the onset of ELM mitigation on MAST and AUG there are some cases where this is not the case and which clearly emphasise the need to take into account the plasma response to the applied perturbations. The plasma response calculations show that the increase in ELM frequency is correlated with the size of the edge peeling-tearing like response of the plasma and the distortions of the plasma boundary in the X-point region.Comment: 31 pages, 28 figures. This is an author-created, un-copyedited version of an article submitted for publication in Nuclear Fusion. IoP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from i

Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized

Entropic Splitter for Particle Separation

We present a particle separation mechanism which induces motion of particles of different sizes in opposite directions. The mechanism is based on the combined action of a driving force and an entropic rectification of the Brownian fluctuations caused by the asymmetric form of the channel along which particles proceed. The entropic splitting effect shown could be controlled upon variation of the geometrical parameters of the channel and could be implemented in narrow channels and microfluidic devices.Comment: 5 pages, 4 figures. Accepted for publication in Phys. Rev. Let

Multispecies virial expansions

We study the virial expansion of mixtures of countably many different types of particles. The main tool is the Lagrange–Good inversion formula, which has other applications such as counting coloured trees or studying probability generating functions in multi-type branching processes. We prove that the virial expansion converges absolutely in a domain of small densities. In addition, we establish that the virial coefficients can be expressed in terms of two-connected graphs

Pseudopotential study of binding properties of solids within generalized gradient approximations: The role of core-valence exchange-correlation

In ab initio pseudopotential calculations within density-functional theory the nonlinear exchange-correlation interaction between valence and core electrons is often treated linearly through the pseudopotential. We discuss the accuracy and limitations of this approximation regarding a comparison of the local density approximation (LDA) and generalized gradient approximations (GGA), which we find to describe core-valence exchange-correlation markedly different. (1) Evaluating the binding properties of a number of typical solids we demonstrate that the pseudopotential approach and namely the linearization of core-valence exchange-correlation are both accurate and limited in the same way in GGA as in LDA. (2) Examining the practice to carry out GGA calculations using pseudopotentials derived within LDA we show that the ensuing results differ significantly from those obtained using pseudopotentials derived within GGA. As principal source of these differences we identify the distinct behavior of core-valence exchange-correlation in LDA and GGA which, accordingly, contributes substantially to the GGA induced changes of calculated binding properties.Comment: 13 pages, 6 figures, submitted to Phys. Rev. B, other related publications can be found at http://www.rz-berlin.mpg.de/th/paper.htm

The global atmospheric electrical circuit and climate

Evidence is emerging for physical links among clouds, global temperatures, the global atmospheric electrical circuit and cosmic ray ionisation. The global circuit extends throughout the atmosphere from the planetary surface to the lower layers of the ionosphere. Cosmic rays are the principal source of atmospheric ions away from the continental boundary layer: the ions formed permit a vertical conduction current to flow in the fair weather part of the global circuit. Through the (inverse) solar modulation of cosmic rays, the resulting columnar ionisation changes may allow the global circuit to convey a solar influence to meteorological phenomena of the lower atmosphere. Electrical effects on non-thunderstorm clouds have been proposed to occur via the ion-assisted formation of ultra-fine aerosol, which can grow to sizes able to act as cloud condensation nuclei, or through the increased ice nucleation capability of charged aerosols. Even small atmospheric electrical modulations on the aerosol size distribution can affect cloud properties and modify the radiative balance of the atmosphere, through changes communicated globally by the atmospheric electrical circuit. Despite a long history of work in related areas of geophysics, the direct and inverse relationships between the global circuit and global climate remain largely quantitatively unexplored. From reviewing atmospheric electrical measurements made over two centuries and possible paleoclimate proxies, global atmospheric electrical circuit variability should be expected on many timescale

Truncated and Helix-Constrained Peptides with High Affinity and Specificity for the cFos Coiled-Coil of AP-1

Protein-based therapeutics feature large interacting surfaces. Protein folding endows structural stability to localised surface epitopes, imparting high affinity and target specificity upon interactions with binding partners. However, short synthetic peptides with sequences corresponding to such protein epitopes are unstructured in water and promiscuously bind to proteins with low affinity and specificity. Here we combine structural stability and target specificity of proteins, with low cost and rapid synthesis of small molecules, towards meeting the significant challenge of binding coiled coil proteins in transcriptional regulation. By iteratively truncating a Jun-based peptide from 37 to 22 residues, strategically incorporating i-->i+4 helix-inducing constraints, and positioning unnatural amino acids, we have produced short, water-stable, alpha-helical peptides that bind cFos. A three-dimensional NMR-derived structure for one peptide (24) confirmed a highly stable alpha-helix which was resistant to proteolytic degradation in serum. These short structured peptides are entropically pre-organized for binding with high affinity and specificity to cFos, a key component of the oncogenic transcriptional regulator Activator Protein-1 (AP-1). They competitively antagonized the cJun–cFos coiled-coil interaction. Truncating a Jun-based peptide from 37 to 22 residues decreased the binding enthalpy for cJun by ~9 kcal/mol, but this was compensated by increased conformational entropy (TDS ≤ 7.5 kcal/mol). This study demonstrates that rational design of short peptides constrained by alpha-helical cyclic pentapeptide modules is able to retain parental high helicity, as well as high affinity and specificity for cFos. These are important steps towards small antagonists of the cJun-cFos interaction that mediates gene transcription in cancer and inflammatory diseases

A search for point sources of EeV photons

Measurements of air showers made using the hybrid technique developed with the fluorescence and surface detectors of the Pierre Auger Observatory allow a sensitive search for point sources of EeV photons anywhere in the exposed sky. A multivariate analysis reduces the background of hadronic cosmic rays. The search is sensitive to a declination band from -85{\deg} to +20{\deg}, in an energy range from 10^17.3 eV to 10^18.5 eV. No photon point source has been detected. An upper limit on the photon flux has been derived for every direction. The mean value of the energy flux limit that results from this, assuming a photon spectral index of -2, is 0.06 eV cm^-2 s^-1, and no celestial direction exceeds 0.25 eV cm^-2 s^-1. These upper limits constrain scenarios in which EeV cosmic ray protons are emitted by non-transient sources in the Galaxy.Comment: 28 pages, 10 figures, accepted for publication in The Astrophysical Journa

Reconstruction of inclined air showers detected with the Pierre Auger Observatory

We describe the method devised to reconstruct inclined cosmic-ray air showers with zenith angles greater than $60^\circ$ detected with the surface array of the Pierre Auger Observatory. The measured signals at the ground level are fitted to muon density distributions predicted with atmospheric cascade models to obtain the relative shower size as an overall normalization parameter. The method is evaluated using simulated showers to test its performance. The energy of the cosmic rays is calibrated using a sub-sample of events reconstructed with both the fluorescence and surface array techniques. The reconstruction method described here provides the basis of complementary analyses including an independent measurement of the energy spectrum of ultra-high energy cosmic rays using very inclined events collected by the Pierre Auger Observatory.Comment: 27 pages, 19 figures, accepted for publication in Journal of Cosmology and Astroparticle Physics (JCAP

Highlights from the Pierre Auger Observatory

The Pierre Auger Observatory is the world's largest cosmic ray observatory. Our current exposure reaches nearly 40,000 km$^2$ str and provides us with an unprecedented quality data set. The performance and stability of the detectors and their enhancements are described. Data analyses have led to a number of major breakthroughs. Among these we discuss the energy spectrum and the searches for large-scale anisotropies. We present analyses of our X$_{max}$ data and show how it can be interpreted in terms of mass composition. We also describe some new analyses that extract mass sensitive parameters from the 100% duty cycle SD data. A coherent interpretation of all these recent results opens new directions. The consequences regarding the cosmic ray composition and the properties of UHECR sources are briefly discussed.Comment: 9 pages, 12 figures, talk given at the 33rd International Cosmic Ray Conference, Rio de Janeiro 201