Two-particle interference in standard and Bohmian quantum mechanics

The compatibility of standard and Bohmian quantum mechanics has recently been challenged in the context of two-particle interference, both from a theoretical and an experimental point of view. We analyze different setups proposed and derive corresponding exact forms for Bohmian equations of motion. The equations are then solved numerically, and shown to reproduce standard quantum-mechanical results.Comment: Minor corrections, 2 references added, version to appear in J. Phys.

Impact of loss on the wave dynamics in photonic waveguide lattices

We analyze the impact of loss in lattices of coupled optical waveguides and find that in such case, the hopping between adjacent waveguides is necessarily complex. This results not only in a transition of the light spreading from ballistic to diffusive, but also in a new kind of diffraction that is caused by loss dispersion. We prove our theoretical results with experimental observations.Comment: Accepted for publication in PRL, 5+8 pages (Paper + Supplemental material), 4 figure

Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics

Background
High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures. 
Results
We developed Yeast Features, an intuitive online tool to help establish the significance of finding a diverse set of shared features among a collection of yeast proteins. A total of 18,786 features from the Saccharomyces Genome Database are considered, including annotation based on the Gene Ontology’s molecular function, biological process and cellular compartment, as well as conserved domains, protein-protein and genetic interactions, complexes, metabolic pathways, phenotypes and publications. The significance of shared features is estimated using a hypergeometric probability, but novel options exist to improve the significance by adding background knowledge of the experimental system. For instance, increased statistical significance is achieved in gene deletion experiments because interactions with essential genes will never be observed. We further demonstrate the utility by suggesting the functional roles of the indirect targets of an aminoglycoside with a known mechanism of action, and also the targets of an herbal extract with a previously unknown mode of action. The identification of shared functional features may also be used to propose novel roles for proteins of unknown function, including a role in protein synthesis for YKL075C.
Conclusions
Yeast Features (YF) is an easy to use web-based application (http://software.dumontierlab.com/yeastfeatures/) which can identify and prioritize features that are shared among a set of yeast proteins. This approach is shown to be valuable in the analysis of complex data sets, in which the extracted associations revealed significant functional relationships among the gene products.
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