Fluctuations of the Josephson current and electron-electron interactions in superconducting weak links

We derive a microscopic effective action for superconducting contacts with arbitrary transmission distribution of conducting channels. Provided fluctuations of the Josephson phase remain sufficiently small our formalism allows to fully describe fluctuation and interaction effects in such systems. As compared to the well studied tunneling limit our analysis yields a number of qualitatively new features which occur due to the presence of subgap Andreev bound states in the system. We investigate the equilibrium supercurrent noise and evaluate the electron-electron interaction correction to the Josephson current across superconducting contacts. At T=0 this correction is found to vanish for fully transparent contacts indicating the absence of Coulomb effects in this limit.Comment: 12 pages, 4 figure

Peptide size dependent active transport in the proteasome

We investigate the transport of proteins inside the proteasome and propose an active transport mechanism based on a spatially asymmetric interaction potential of peptide chains. The transport is driven by fluctuations which are always present in such systems. We compute the peptide-size dependent transport rate which is essential for the functioning of the proteasome. In agreement with recent experiments, varying temperature changes the transport mechanism qualitatively.Comment: 4 pages, 4 figure

Towards quantitative prediction of proteasomal digestion patterns of proteins

We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic model of the proteasomal degradation of proteins, which accounts for the protein translocation and the topology of the positioning of cleavage centers of a proteasome from first principles. For this model we develop the mathematical description based on a master-equation and techniques for reconstruction of the cleavage specificity inherent to proteins and the proteasomal translocation rates, which are a property of the proteasome specie, from mass spectroscopy data on digestion patterns. With these properties determined, one can quantitatively predict digestion patterns for new experimental set-ups. Additionally we design an experimental set-up for a synthetic polypeptide with a periodic sequence of amino acids, which enables especially reliable determination of translocation rates.Comment: 14 pages, 4 figures, submitted to J. Stat. Mech. (Special issue for proceedings of 5th Intl. Conf. on Unsolved Problems on Noise and Fluctuations in Physics, Biology & High Technology, Lyon (France), June 2-6, 2008

Detection of Epigenomic Network Community Oncomarkers

In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer. DNA methylation is a gene-regulatory pattern, and hence provides a means by which to assess genomic regulatory interactions. Network models are a natural way to represent and analyse groups of such interactions. The utility of network models also increases as the quantity of data and number of variables increase, making them increasingly relevant to large-scale genomic studies. We propose methodology to infer prognostic genomic networks from a DNA methylation-based measure of genomic interaction and association. We then show how to identify prognostic biomarkers from such networks, which we term `network community oncomarkers'. We illustrate the power of our proposed methodology in the context of a large publicly available breast cancer dataset