Pitch-angle scattering in magnetostatic turbulence. I. Test-particle simulations and the validity of analytical results

Context. Spacecraft observations have motivated the need for a refined description of the phase-space distribution function. Of particular importance is the pitch-angle diffusion coefficient that occurs in the Fokker-Planck transport equation. Aims. Simulations and analytical test-particle theories are compared to verify the diffusion description of particle transport, which does not allow for non-Markovian behavior. Methods. A Monte-Carlo simulation code was used to trace the trajectories of test particles moving in turbulent magnetic fields. From the ensemble average, the pitch-angle Fokker-Planck coefficient is obtained via the mean square displacement. Results. It is shown that, while excellent agreement with analytical theories can be obtained for slab turbulence, considerable deviations are found for isotropic turbulence. In addition, all Fokker-Planck coefficients tend to zero for high time values.Comment: 8 pages, 10 figures, accepted for publication in Astron. Astrophy

Electron energy loss spectroscopy with parallel readout of energy and momentum

We introduce a high energy resolution electron source that matches the requirements for parallel readout of energy and momentum of modern hemispherical electron energy analyzers. The system is designed as an add-on device to typical photoemission chambers. Due to the multiplex gain, a complete phonon dispersion of a Cu(111) surface was measured in seven minutes with 4 meV energy resolution

A novel high-current, high-resolution, low-kinetic-energy electron source for inverse photoemission spectroscopy

A high-current electron source for inverse photoemission spectroscopy (IPES) is described. The source comprises a thermal cathode electron emission system, an electrostatic deflector-monochromator, and a lens system for variable kinetic energy (1.6 - 20 eV) at the target. When scaled to the energy resolution, the electron current is an order of magnitude higher than that of previously described electron sources developed in the context of electron energy loss spectroscopy. Surprisingly, the experimentally measured energy resolution turned out to be significantly better than calculated by standard programs, which include the electron-electron repulsion in the continuum approximation. The achieved currents are also significantly higher than predicted. We attribute this "inverse Boersch-effect" to a mechanism of velocity selection in the forward direction by binary electron-electron collisions

Numerical solution of the linear dispersion relation in a relativistic pair plasma

We describe an algorithm that computes the linear dispersion relation of waves and instabilities in relativistic plasmas within a Vlasov-Maxwell description. The method used is fully relativistic and involves explicit integration of particle orbits along the unperturbed equilibrium trajectories. We check the algorithm against the dispersion curves for a single component magnetised plasma and for an unmagnetised plasma with counter-streaming components in the non-relativistic case. New results on the growth rate of the Weibel or two-stream instability in a hot unmagnetised pair plasma consisting of two counter-streaming relativistic Maxwellians are presented. These are relevant to the physics of the relativistic plasmas found in gamma-ray bursts, relativistic jets and pulsar winds.Comment: Accepted by Plasma Physics and Controlled Fusio

The role of the segmentation gene hairy in Tribolium

Hairy stripes in Tribolium are generated during blastoderm and germ band extension, but a direct role for Tc-h in trunk segmentation was not found. We have studied here several aspects of hairy function and expression in Tribolium, to further elucidate its role. First, we show that there is no functional redundancy with other hairy paralogues in Tribolium. Second, we cloned the hairy orthologue from Tribolium confusum and show that its expression mimics that of Tribolium castaneum, implying that stripe expression should be functional in some way. Third, we show that the dynamics of stripe formation in the growth zone is not compatible with an oscillatory mechanism comparable to the one driving the expression of hairy homologues in vertebrates. Fourth, we use parental RNAi experiments to study Tc-h function and we find that mandible and labium are particularly sensitive to loss of Tc-h, reminiscent of a pair-rule function in the head region. In addition, lack of Tc-h leads to cell death in the gnathal region at later embryonic stages, resulting in a detachment of the head. Cell death patterns are also altered in the midline. Finally, we have analysed the effect of Tc-h knockdown on two of the target genes of hairy in Drosophila, namely fushi tarazu and paired. We find that the trunk expression of Tc-h is required to regulate Tc-ftz, although Tc-ftz is itself also not required for trunk segmentation in Tribolium. Our results imply that there is considerable divergence in hairy function between Tribolium and Drosophila

A Revised Design for Microarray Experiments to Account for Experimental Noise and Uncertainty of Probe Response

Background Although microarrays are analysis tools in biomedical research, they are known to yield noisy output that usually requires experimental confirmation. To tackle this problem, many studies have developed rules for optimizing probe design and devised complex statistical tools to analyze the output. However, less emphasis has been placed on systematically identifying the noise component as part of the experimental procedure. One source of noise is the variance in probe binding, which can be assessed by replicating array probes. The second source is poor probe performance, which can be assessed by calibrating the array based on a dilution series of target molecules. Using model experiments for copy number variation and gene expression measurements, we investigate here a revised design for microarray experiments that addresses both of these sources of variance. Results Two custom arrays were used to evaluate the revised design: one based on 25 mer probes from an Affymetrix design and the other based on 60 mer probes from an Agilent design. To assess experimental variance in probe binding, all probes were replicated ten times. To assess probe performance, the probes were calibrated using a dilution series of target molecules and the signal response was fitted to an adsorption model. We found that significant variance of the signal could be controlled by averaging across probes and removing probes that are nonresponsive or poorly responsive in the calibration experiment. Taking this into account, one can obtain a more reliable signal with the added option of obtaining absolute rather than relative measurements. Conclusion The assessment of technical variance within the experiments, combined with the calibration of probes allows to remove poorly responding probes and yields more reliable signals for the remaining ones. Once an array is properly calibrated, absolute quantification of signals becomes straight forward, alleviating the need for normalization and reference hybridizations

Quantum transport through STM-lifted single PTCDA molecules

Using a scanning tunneling microscope we have measured the quantum conductance through a PTCDA molecule for different configurations of the tip-molecule-surface junction. A peculiar conductance resonance arises at the Fermi level for certain tip to surface distances. We have relaxed the molecular junction coordinates and calculated transport by means of the Landauer/Keldysh approach. The zero bias transmission calculated for fixed tip positions in lateral dimensions but different tip substrate distances show a clear shift and sharpening of the molecular chemisorption level on increasing the STM-surface distance, in agreement with experiment.Comment: accepted for publication in Applied Physics

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

Optimization of sequence alignment for simple sequence repeat regions

Abstract Background Microsatellites, or simple sequence repeats (SSRs), are tandemly repeated DNA sequences, including tandem copies of specific sequences no longer than six bases, that are distributed in the genome. SSR has been used as a molecular marker because it is easy to detect and is used in a range of applications, including genetic diversity, genome mapping, and marker assisted selection. It is also very mutable because of slipping in the DNA polymerase during DNA replication. This unique mutation increases the insertion/deletion (INDELs) mutation frequency to a high ratio - more than other types of molecular markers such as single nucleotide polymorphism (SNPs). SNPs are more frequent than INDELs. Therefore, all designed algorithms for sequence alignment fit the vast majority of the genomic sequence without considering microsatellite regions, as unique sequences that require special consideration. The old algorithm is limited in its application because there are many overlaps between different repeat units which result in false evolutionary relationships. Findings To overcome the limitation of the aligning algorithm when dealing with SSR loci, a new algorithm was developed using PERL script with a Tk graphical interface. This program is based on aligning sequences after determining the repeated units first, and the last SSR nucleotides positions. This results in a shifting process according to the inserted repeated unit type. When studying the phylogenic relations before and after applying the new algorithm, many differences in the trees were obtained by increasing the SSR length and complexity. However, less distance between different linage had been observed after applying the new algorithm. Conclusions The new algorithm produces better estimates for aligning SSR loci because it reflects more reliable evolutionary relations between different linages. It reduces overlapping during SSR alignment, which results in a more realistic phylogenic relationship.</p

Fermi-liquid instabilities at magnetic quantum phase transitions

This review discusses instabilities of the Fermi-liquid state of conduction electrons in metals with particular emphasis on magnetic quantum critical points. Both the existing theoretical concepts and experimental data on selected materials are presented; with the aim of assessing the validity of presently available theory. After briefly recalling the fundamentals of Fermi-liquid theory, the local Fermi-liquid state in quantum impurity models and their lattice versions is described. Next, the scaling concepts applicable to quantum phase transitions are presented. The Hertz-Millis-Moriya theory of quantum phase transitions is described in detail. The breakdown of the latter is analyzed in several examples. In the final part experimental data on heavy-fermion materials and transition-metal alloys are reviewed and confronted with existing theory.Comment: 62 pages, 29 figs, review article for Rev. Mod. Phys; (v2) discussion extended, refs added; (v3) shortened; final version as publishe