Robust Charge-based Qubit Encoding

We propose a simple encoding of charge-based quantum dot qubits which protects against fluctuating electric fields by charge symmetry. We analyse the reduction of coupling to noise due to nearby charge traps and present single qubit gates. The relative advantage of the encoding increases with lower charge trap density.Comment: 6 Pages, 7 Figures. Published Versio

Nonequilibrium transport in quantum impurity models: Exact path integral simulations

We simulate the nonequilibrium dynamics of two generic many-body quantum impurity models by employing the recently developed iterative influence-functional path integral method [Phys. Rev. B {\bf 82}, 205323 (2010)]. This general approach is presented here in the context of quantum transport in molecular electronic junctions. Models of particular interest include the single impurity Anderson model and the related spinless two-state Anderson dot. In both cases we study the time evolution of the dot occupation and the current characteristics at finite temperature. A comparison to mean-field results is presented, when applicable

Cassini observations reveal a regime of zonostrophic macroturbulence on Jupiter

In December 2000, the Cassini fly-by near Jupiter delivered high-resolution images of Jupiter’s clouds over the entire planet in a band between 50°N and 50°S. Three daily-averaged two-dimensional velocity snapshots extracted from these images are used to perform spectral analysis of jovian atmospheric macroturbulence. A similar analysis is also performed on alternative data documented by Choi and Showman (Choi, D., Showman, A. [2011]. Icarus 216, 597–609), based on a different method of image processing. The inter-comparison of the products of both analyses ensures a better constraint of the spectral estimates. Both analyses reveal strong anisotropy of the kinetic energy spectrum. The zonal spectrum is very steep and most of the kinetic energy resides in slowly evolving, alternating zonal (west–east) jets, while the non-zonal, or residual spectrum obeys the Kolmogorov–Kraichnan law specific to two-dimensional turbulence in the range of the inverse energy cascade. The spectral data is used to estimate the inverse cascade rate ∊ and the zonostrophy index Rβ for the first time. Although both datasets yield somewhat different values of ∊, it is estimated to be in the range 0.5–1.0 × 10−5 m2 s−3. The ensuing values of Rβ ≳ 5 belong well in the range of zonostrophic turbulence whose threshold corresponds to Rβ ≃ 2.5. We infer that the large-scale circulation is maintained by an anisotropic inverse energy cascade. The removal of the Great Red Spot from both datasets has no significant effect upon either the spectra or the inverse cascade rate. The spectral data are used to compute the rate of the energy exchange, W, between the non-zonal structures and the large-scale zonal flow. It is found that instantaneous values of W may exceed ∊ by an order of magnitude. Previous numerical simulations with a barotropic model suggest that W and ∊ attain comparable values only after averaging of W over a sufficiently long time. Near-instantaneous values of W that have been routinely used to infer the rate of the kinetic energy supply to Jupiter’s zonal flow may therefore significantly overestimate ∊. This disparity between W and ∊ may resolve the long-standing conundrum of an unrealistically high rate of energy transfer to the zonal flow. The meridional diffusivity Kϕ in the regime of zonostrophic turbulence is given by an expression that depends on ∊. The value of Kϕ estimated from the spectra is compared against data from the dispersion of stratospheric gases and debris resulting from the Shoemaker-Levy 9 comet and Wesley asteroid impacts in 1994 and 2009 respectively. Not only is Kϕ found to be consistent with estimates for both impacts, but the eddy diffusivity found from observations appears to be scale-independent. This behaviour could be a consequence of the interaction between anisotropic turbulence and Rossby waves specific to the regime of zonostrophic macroturbulence

Adaptive rationality: An evolutionary perspective on cognitive bias

A casual look at the literature in social cognition reveals a vast collection of biases, errors, violations of rational choice, and failures to maximize utility. One is tempted to draw the conclusion that the human mind is woefully muddled. We present a three-category evolutionary taxonomy of evidence of biases: biases are (a) heuristics, (b) error management effects, or (c) experimental artifacts. We conclude that much of the research on cognitive biases can be profitably reframed and understood in evolutionary terms. An adaptationist perspective suggests that the mind is remarkably well designed for important problems of survival and reproduction, and not fundamentally irrational. Our analysis is not an apologia intended to place the rational mind on a pedestal for admiration. Rather, it promises practical outcomes including a clearer view of the architecture of systems for judgment and decision making, and exposure of clashes between adaptations designed for the ancestral past and the demands of the present

Automatically extracting functionally equivalent proteins from SwissProt

In summary, FOSTA provides an automated analysis of annotations in UniProtKB/Swiss-Prot to enable groups of proteins already annotated as functionally equivalent, to be extracted. Our results demonstrate that the vast majority of UniProtKB/Swiss-Prot functional annotations are of high quality, and that FOSTA can interpret annotations successfully. Where FOSTA is not successful, we are able to highlight inconsistencies in UniProtKB/Swiss-Prot annotation. Most of these would have presented equal difficulties for manual interpretation of annotations. We discuss limitations and possible future extensions to FOSTA, and recommend changes to the UniProtKB/Swiss-Prot format, which would facilitate text-mining of UniProtKB/Swiss-Prot

Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes

BACKGROUND: Lineage-specific, or taxonomically restricted genes (TRGs), especially those that are species and strain-specific, are of special interest because they are expected to play a role in defining exclusive ecological adaptations to particular niches. Despite this, they are relatively poorly studied and little understood, in large part because many are still orphans or only have homologues in very closely related isolates. This lack of homology confounds attempts to establish the likelihood that a hypothetical gene is expressed and, if so, to determine the putative function of the protein. METHODOLOGY/PRINCIPAL FINDINGS: We have developed "QIPP" ("Quality Index for Predicted Proteins"), an index that scores the "quality" of a protein based on non-homology-based criteria. QIPP can be used to assign a value between zero and one to any protein based on comparing its features to other proteins in a given genome. We have used QIPP to rank the predicted proteins in the proteomes of Bacteria and Archaea. This ranking reveals that there is a large amount of variation in QIPP scores, and identifies many high-scoring orphans as potentially "authentic" (expressed) orphans. There are significant differences in the distributions of QIPP scores between orphan and non-orphan genes for many genomes and a trend for less well-conserved genes to have lower QIPP scores. CONCLUSIONS: The implication of this work is that QIPP scores can be used to further annotate predicted proteins with information that is independent of homology. Such information can be used to prioritize candidates for further analysis. Data generated for this study can be found in the OrphanMine at http://www.genomics.ceh.ac.uk/orphan_mine

BioGPS: an extensible and customizable portal for querying and organizing gene annotation resources

BioGPS is a community based customisable gene annotation portal bringing together gene annotation resources on to a single platform

Toward community standards in the quest for orthologs

The identification of orthologs—genes pairs descended from a common ancestor through speciation, rather than duplication—has emerged as an essential component of many bioinformatics applications, ranging from the annotation of new genomes to experimental target prioritization. Yet, the development and application of orthology inference methods is hampered by the lack of consensus on source proteomes, file formats and benchmarks. The second ‘Quest for Orthologs' meeting brought together stakeholders from various communities to address these challenges. We report on achievements and outcomes of this meeting, focusing on topics of particular relevance to the research community at large. The Quest for Orthologs consortium is an open community that welcomes contributions from all researchers interested in orthology research and applications. Contact: [email protected]

MACSIMS : multiple alignment of complete sequences information management system

BACKGROUND: In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. New information management systems are now needed for the collection, validation and analysis of the vast amount of heterogeneous data available. Multiple alignments of complete sequences provide an ideal environment for the integration of this information in the context of the protein family. RESULTS: MACSIMS is a multiple alignment-based information management program that combines the advantages of both knowledge-based and ab initio sequence analysis methods. Structural and functional information is retrieved automatically from the public databases. In the multiple alignment, homologous regions are identified and the retrieved data is evaluated and propagated from known to unknown sequences with these reliable regions. In a large-scale evaluation, the specificity of the propagated sequence features is estimated to be >99%, i.e. very few false positive predictions are made. MACSIMS is then used to characterise mutations in a test set of 100 proteins that are known to be involved in human genetic diseases. The number of sequence features associated with these proteins was increased by 60%, compared to the features available in the public databases. An XML format output file allows automatic parsing of the MACSIM results, while a graphical display using the JalView program allows manual analysis. CONCLUSION: MACSIMS is a new information management system that incorporates detailed analyses of protein families at the structural, functional and evolutionary levels. MACSIMS thus provides a unique environment that facilitates knowledge extraction and the presentation of the most pertinent information to the biologist. A web server and the source code are available at