1,435 research outputs found
Noise at a Fermi-edge singularity
We present noise measurements of self-assembled InAs quantum dots at high
magnetic fields. In comparison to I-V characteristics at zero magnetic field we
notice a strong current overshoot which is due to a Fermi-edge singularity. We
observe an enhanced suppression in the shot noise power simultaneous to the
current overshoot which is attributed to the electron-electron interaction in
the Fermi-edge singularity
Capillary Electrochromatography – Challenges and Opportunities for Coupling with Mass Spectrometry
Capillary electrochromatography (CEC) has attracted considerable interest within recent years because of its potential to generate very high efficiencies within relatively short analysis time. Since CEC combines the attributes of both capillary electrophoresis (CE) and high-performance
liquid chromatography (HPLC), neutral as well as charged analytes can be separated. Usually, CEC is performed with UV detection, but mass spectrometry (MS) is becoming a more common detection method because additional information about the molecular weight and the structure of an analyte can
be obtained. Due to the low flow rates in the packed capillary and the small sample amounts that are required, CEC is ideally suited for the implementation into miniaturized systems and for coupling with MS. While numerous advantages have been made in CEC/MS, the coupling technique is still
in a development and growth stage. So far, the development of the technique seems to be limited by the lack of robust and automated specially designed CEC instruments and CEC interfaces. As soon as these practical constraints have been solved, CEC/MS will be a powerful separation/detection
technique with unrivaled sensitivity and specifity. This article aims at highlighting the potential of CEC as coupling technique with mass spectrometry
Nonmonotonic dependence of the absolute entropy on temperature in supercooled Stillinger-Weber silicon
Using a recently developed thermodynamic integration method, we compute the
precise values of the excess Gibbs free energy (G^e) of the high density liquid
(HDL) phase with respect to the crystalline phase at different temperatures (T)
in the supercooled region of the Stillinger-Weber (SW) silicon [F. H.
Stillinger and T. A. Weber, Phys. Rev. B. 32, 5262 (1985)]. Based on the slope
of G^e with respect to T, we find that the absolute entropy of the HDL phase
increases as its enthalpy changes from the equilibrium value at T \ge 1065 K to
the value corresponding to a non-equilibrium state at 1060 K. We find that the
volume distribution in the equilibrium HDL phases become progressively broader
as the temperature is reduced to 1060 K, exhibiting van-der-Waals (VDW) loop in
the pressure-volume curves. Our results provides insight into the thermodynamic
cause of the transition from the HDL phase to the low density phases in SW
silicon, observed in earlier studies near 1060 K at zero pressure.Comment: This version is accepted for publication in Journal of Statistical
Physics (11 figures, 1 table
Properties of a continuous-random-network model for amorphous systems
We use a Monte Carlo bond-switching method to study systematically the
thermodynamic properties of a "continuous random network" model, the canonical
model for such amorphous systems as a-Si and a-SiO. Simulations show
first-order "melting" into an amorphous state, and clear evidence for a glass
transition in the supercooled liquid. The random-network model is also extended
to study heterogeneous structures, such as the interface between amorphous and
crystalline Si.Comment: Revtex file with 4 figure
Rabl's model of the interphase chromosome arrangement tested in Chinise hamster cells by premature chromosome condensation and laser-UV-microbeam experiments
In 1885 Carl Rabl published his theory on the internal structure of the interphase nucleus. We have tested two predictions of this theory in fibroblasts grown in vitro from a female Chinese hamster, namely (1) the Rabl-orientation of interphase chromosomes and (2) the stability of the chromosome arrangement established in telophase throughout the subsequent interphase. Tests were carried out by premature chromosome condensation (PCC) and laser-UV-microirradiation of the interphase nucleus. Rabl-orientation of chromosomes was observed in G1 PCCs and G2 PCCs. The cell nucleus was microirradiated in G1 at one or two sites and pulse-labelled with 3H-thymidine for 2h. Cells were processed for autoradiography either immediately thereafter or after an additional growth period of 10 to 60h. Autoradiographs show unscheduled DNA synthesis (UDS) in the microirradiated nuclear part(s). The distribution of labelled chromatin was evaluated in autoradiographs from 1035 cells after microirradiation of a single nuclear site and from 253 cells after microirradiation of two sites. After 30 to 60h postincubation the labelled regions still appeared coherent although the average size of the labelled nuclear area fr increased from 14.2% (0h) to 26.5% (60h). The relative distance dr, i.e. the distance between two microirradiated sites divided by the diameter of the whole nucleus, showed a slight decrease with increasing incubation time. Nine metaphase figures were evaluated for UDS-label after microirradiation of the nuclear edge in G1. An average of 4.3 chromosomes per cell were labelled. Several chromosomes showed joint labelling of both distal chromosome arms including the telomeres, while the centromeric region was free from label. This label pattern is interpreted as the result of a V-shaped orientation of these particular chromosomes in the interphase nucleus with their telomeric regions close to each other at the nuclear edge. Our data support the tested predictions of the Rabl-model. Small time-dependent changes of the nuclear space occupied by single chromosomes and of their relative positions in the interphase nucleus seem possible, while the territorial organization of interphase chromosomes and their arrangement in general is maintained during interphase. The present limitations of the methods used for this study are discussed
Stratify or adjust? Dealing with multiple populations when evaluating rare variants
The unrelated individuals sample from Genetic Analysis Workshop 17 consists of a small number of subjects from eight population samples and genetic data composed mostly of rare variants. We compare two simple approaches to collapsing rare variants within genes for their utility in identifying genes that affect phenotype. We also compare results from stratified analyses to those from a pooled analysis that uses ethnicity as a covariate. We found that the two collapsing approaches were similarly effective in identifying genes that contain causative variants in these data. However, including population as a covariate was not an effective substitute for analyzing the subpopulations separately when only one subpopulation contained a rare variant linked to the phenotype
Application of collapsing methods for continuous traits to the Genetic Analysis Workshop 17 exome sequence data
Genetic Analysis Workshop 17 used real sequence data from the 1000 Genomes Project and simulated phenotypes influenced by a large number of rare variants. Our aim is to evaluate the performance of various collapsing methods that were developed for analysis of multiple rare variants. We apply collapsing methods to continuous phenotypes Q1 and Q2 for all 200 replicates of the unrelated individuals data. Within each gene, we collapse (1) all SNPs, (2) all SNPs with minor allele frequency (MAF) < 0.05, and (3) nonsynonymous SNPs with MAF < 0.05. We consider two tests when collapsing variants: using the proportion of variants and using the presence/absence of any variant. We also compare our results to a single-marker analysis using PLINK. For phenotype Q1, the proportion test for collapsing rare nonsynonymous SNPs often performed the best. Two genes (FLT1 and KDR) had statistically significant results. A single-marker analysis using PLINK also provided statistically significant results for some SNPs within these two genes. For phenotype Q2, collapsing rare nonsynonymous SNPs performed the best, with almost no difference between proportion and presence tests. However, neither collapsing methods nor a single-marker analysis provided statistically significant results at the true genes for Q2. We also found that a large number of noncausal genes had high correlations with causal genes for Q1 and Q2, which may account for inflated false positives
Evaluating methods for combining rare variant data in pathway-based tests of genetic association
Analyzing sets of genes in genome-wide association studies is a relatively new approach that aims to capitalize on biological knowledge about the interactions of genes in biological pathways. This approach, called pathway analysis or gene set analysis, has not yet been applied to the analysis of rare variants. Applying pathway analysis to rare variants offers two competing approaches. In the first approach rare variant statistics are used to generate p-values for each gene (e.g., combined multivariate collapsing [CMC] or weighted-sum [WS]) and the gene-level p-values are combined using standard pathway analysis methods (e.g., gene set enrichment analysis or Fisher’s combined probability method). In the second approach, rare variant methods (e.g., CMC and WS) are applied directly to sets of single-nucleotide polymorphisms (SNPs) representing all SNPs within genes in a pathway. In this paper we use simulated phenotype and real next-generation sequencing data from Genetic Analysis Workshop 17 to analyze sets of rare variants using these two competing approaches. The initial results suggest substantial differences in the methods, with Fisher’s combined probability method and the direct application of the WS method yielding the best power. Evidence suggests that the WS method works well in most situations, although Fisher’s method was more likely to be optimal when the number of causal SNPs in the set was low but the risk of the causal SNPs was high
Enrichment analysis of genetic association in genes and pathways by aggregating signals from both rare and common variants
New high-throughput sequencing technologies have brought forth opportunities for unbiased analysis of thousands of rare genomic variants in genome-wide association studies of complex diseases. Because it is hard to detect single rare variants with appreciable effect sizes at the population level, existing methods mostly aggregate effects of multiple markers by collapsing the rare variants in genes (or genomic regions). We hypothesize that a higher level of aggregation can further improve association signal strength. Using the Genetic Analysis Workshop 17 simulated data, we test a two-step strategy that first applies a collapsing method in a gene-level analysis and then aggregates the gene-level test results by performing an enrichment analysis in gene sets. We find that the gene set approach which combines signals across multiple genes outperforms testing individual genes separately and that the power of the gene set enrichment test is further improved by proper adjustment of statistics to account for gene-wise differences
An Effective-Medium Tight-Binding Model for Silicon
A new method for calculating the total energy of Si systems is presented. The
method is based on the effective-medium theory concept of a reference system.
Instead of calculating the energy of an atom in the system of interest a
reference system is introduced where the local surroundings are similar. The
energy of the reference system can be calculated selfconsistently once and for
all while the energy difference to the reference system can be obtained
approximately. We propose to calculate it using the tight-binding LMTO scheme
with the Atomic-Sphere Approximation(ASA) for the potential, and by using the
ASA with charge-conserving spheres we are able to treat open system without
introducing empty spheres. All steps in the calculational method is {\em ab
initio} in the sense that all quantities entering are calculated from first
principles without any fitting to experiment. A complete and detailed
description of the method is given together with test calculations of the
energies of phonons, elastic constants, different structures, surfaces and
surface reconstructions. We compare the results to calculations using an
empirical tight-binding scheme.Comment: 26 pages (11 uuencoded Postscript figures appended), LaTeX,
CAMP-090594-
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