929 research outputs found
Sheath ionization model of beam emissions from large spacecraft
An analytical model of the charging of a spacecraft emitting electron and ion beams has been applied to the case of large spacecraft. In this model, ionization occurs in the sheath due to the return current. Charge neutralization of spherical space charge flow is examined by solving analytical equations numerically. Parametric studies of potential large spacecraft are performed. As in the case of small spacecraft, the ions created in the sheath by the returning current play a large role in determining spacecraft potential
The amylase gene cluster in house mice (Mus musculus) was subject to repeated introgression including the rescue of a pseudogene
Amylase gene clusters have been implicated in adaptive copy number changes in response to the amount of starch in the diet of humans and mammals. However, this interpretation has been questioned for humans and for mammals there is a paucity of information from natural populations
Site-selective adsorption of naphthalene-tetracarboxylic-dianhydride on Ag(110): First-principles calculations
The mechanism of adsorption of the
1,4,5,8-naphthalene-tetracarboxylic-dianhydride (NTCDA) molecule on the Ag(110)
surface is elucidated on the basis of extensive density functional theory
calculations. This molecule, together with its perylene counterpart, PTCDA, are
archetype organic semiconductors investigated experimentally over the past 20
years. We find that the bonding of the molecule to the substrate is highly
site-selective, being determined by electron transfer to the LUMO of the
molecule and local electrostatic attraction between negatively charged carboxyl
oxygens and positively charged silver atoms in [1-10] atomic rows. The
adsorption energy in the most stable site is 0.9eV. A similar mechanism is
expected to govern the adsorption of PTCDA on Ag(110) as well.Comment: 8 pages, 4 figures, high-quality figures available upon reques
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
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
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
Analysis of Microsatellite Polymorphism in Inbred Knockout Mice
Previously, we found that the genotype of 42 out of 198 mouse microsatellite loci, which are distributed among all chromosomes except the Y chromosome, changed from monomorphism to polymorphism (CMP) in a genetically modified inbred mouse strain. In this study, we further examined whether CMP also relates to the homologous recombination in gene knockout (KO) mouse strains. The same 42 microsatellite loci were analyzed by polymerase chain reaction (PCR) in 29 KO inbred mouse strains via short tandem sequence repeat (STR) scanning and direct sequence cloning to justify microsatellite polymorphisms. The C57BL/6J and 129 mouse strains, from which these 29 KO mice were derived, were chosen as the background controls. The results indicated that 10 out of 42 (23.8%) loci showed CMP in some of these mouse strains. Except for the trinucleotide repeat locus of D3Mit22, which had microsatellite CMP in strain number 9, the core sequences of the remaining 41 loci were dinucleotide repeats, and 9 out of 41 (21.95%) showed CMPs among detected mouse strains. However, 11 out of 29 (37.9%) KO mice strains were recognized as having CMPs. The popular dinucleotide motifs in CMP were (TG)n (50%, 2/4), followed by (GT)n (27.27%, 3/11) and (CA)n (23.08%, 3/13). The microsatellite CMP in (CT)n and (AG)n repeats were 20% (1/5). According to cloning sequencing results, 6 KO mouse strains showed insertions of nucleotides whereas 1 showed a deletion. Furthermore, 2 loci (D13Mit3 and D14Mit102) revealed CMP in 2 strains, and mouse strain number 9 showed CMPs in two loci (D3Mit22 and D13Mit3) simultaneously. Collectively, these results indicated that microsatellite polymorphisms were present in the examined inbred KO mice
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
The Kondo Resonance in Electron Spectroscopy
The Kondo resonance is the spectral manifestation of the Kondo properties of
the impurity Anderson model, and also plays a central role in the dynamical
mean-field theory (DMFT) for correlated electron lattice systems. This article
presents an overview of electron spectroscopy studies of the resonance for the
4f electrons of cerium compounds, and for the 3d electrons of V_2O_3, including
beginning efforts at using angle resolved photoemission to determine the
k-dependence of the resonance. The overview includes the comparison and
analysis of spectroscopy data with theoretical spectra as calculated for the
impurity model and as obtained by DMFT, and the Kondo volume collapse
calculation of the cerium alpha-gamma phase transition boundary, with its
spectroscopic underpinnings.Comment: 32 pages, 11 figures, 151 references; paper for special issue of J.
Phys. Soc. Jpn. on "Kondo Effect--40 Years after the Discovery
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