MIPS: analysis and annotation of proteins from whole genomes in 2005

The Munich Information Center for Protein Sequences (MIPS at the GSF), Neuherberg, Germany, provides resources related to genome information. Manually curated databases for several reference organisms are maintained. Several of these databases are described elsewhere in this and other recent NAR database issues. In a complementary effort, a comprehensive set of >400 genomes automatically annotated with the PEDANT system are maintained. The main goal of our current work on creating and maintaining genome databases is to extend gene centered information to information on interactions within a generic comprehensive framework. We have concentrated our efforts along three lines (i) the development of suitable comprehensive data structures and database technology, communication and query tools to include a wide range of different types of information enabling the representation of complex information such as functional modules or networks Genome Research Environment System, (ii) the development of databases covering computable information such as the basic evolutionary relations among all genes, namely SIMAP, the sequence similarity matrix and the CABiNet network analysis framework and (iii) the compilation and manual annotation of information related to interactions such as protein–protein interactions or other types of relations (e.g. MPCDB, MPPI, CYGD). All databases described and the detailed descriptions of our projects can be accessed through the MIPS WWW server ()

On the origin of the Boson peak in globular proteins

We study the Boson Peak phenomenology experimentally observed in globular proteins by means of elastic network models. These models are suitable for an analytic treatment in the framework of Euclidean Random Matrix theory, whose predictions can be numerically tested on real proteins structures. We find that the emergence of the Boson Peak is strictly related to an intrinsic mechanical instability of the protein, in close similarity to what is thought to happen in glasses. The biological implications of this conclusion are also discussed by focusing on a representative case study.Comment: Proceedings of the X International Workshop on Disordered Systems, Molveno (2006

MIPS: analysis and annotation of genome information in 2007

The Munich Information Center for Protein Sequences (MIPS-GSF, Neuherberg, Germany) combines automatic processing of large amounts of sequences with manual annotation of selected model genomes. Due to the massive growth of the available data, the depth of annotation varies widely between independent databases. Also, the criteria for the transfer of information from known to orthologous sequences are diverse. To cope with the task of global in-depth genome annotation has become unfeasible. Therefore, our efforts are dedicated to three levels of annotation: (i) the curation of selected genomes, in particular from fungal and plant taxa (e.g. CYGD, MNCDB, MatDB), (ii) the comprehensive, consistent, automatic annotation employing exhaustive methods for the computation of sequence similarities and sequence-related attributes as well as the classification of individual sequences (SIMAP, PEDANT and FunCat) and (iii) the compilation of manually curated databases for protein interactions based on scrutinized information from the literature to serve as an accepted set of reliable annotated interaction data (MPACT, MPPI, CORUM). All databases and tools described as well as the detailed descriptions of our projects can be accessed through the MIPS web server (http://mips.gsf.de)

Effective Lagrangians in 2+ϵ2 + \epsilon Dimensions

The failure of the the loop expansion and effective lagrangians in two dimensions, which traditionally hinges on a power counting argument is considered. We establish that the book keeping device for the loop expansion, a role played by (the reciprocal of) the pion-decay constant itself vanishes for $d=2$, thereby going beyond the power counting argument. We point the connection of our results to the distinct phases of the candidate for the effective lagrangians, the non-linear sigma model, in $d=2+\epsilon$, and eventually for $d=2$. In light of our results, we recall some of the relavant features of the multi-flavor Schwinger and large $N_f$ $QCD_2$ as candidates for the underlying theory in $d=2$.Comment: 13 pages plain LaTeX, to be run twice. Replaced with expanded and corrected version. One footnote adde

GiViP: A Visual Profiler for Distributed Graph Processing Systems

Analyzing large-scale graphs provides valuable insights in different application scenarios. While many graph processing systems working on top of distributed infrastructures have been proposed to deal with big graphs, the tasks of profiling and debugging their massive computations remain time consuming and error-prone. This paper presents GiViP, a visual profiler for distributed graph processing systems based on a Pregel-like computation model. GiViP captures the huge amount of messages exchanged throughout a computation and provides an interactive user interface for the visual analysis of the collected data. We show how to take advantage of GiViP to detect anomalies related to the computation and to the infrastructure, such as slow computing units and anomalous message patterns.Comment: Appears in the Proceedings of the 25th International Symposium on Graph Drawing and Network Visualization (GD 2017

Degenerate Rotating Black Holes, Chiral CFTs and Fermi Surfaces I - Analytic Results for Quasinormal Modes

In this work we discuss charged rotating black holes in $AdS_5 \times S^5$ that degenerate to extremal black holes with zero entropy. These black holes have scaling properties between charge and angular momentum similar to those of Fermi surface operators in a subsector of $\mathcal{N}=4$ SYM. We add a massless uncharged scalar to the five dimensional supergravity theory, such that it still forms a consistent truncation of the type IIB ten dimensional supergravity and analyze its quasinormal modes. Separating the equation of motion to a radial and angular part, we proceed to solve the radial equation using the asymptotic matching expansion method applied to a Heun equation with two nearby singularities. We use the continued fraction method for the angular Heun equation and obtain numerical results for the quasinormal modes. In the case of the supersymmetric black hole we present some analytic results for the decay rates of the scalar perturbations. The spectrum of quasinormal modes obtained is similar to that of a chiral 1+1 CFT, which is consistent with the conjectured field-theoretic dual. In addition, some of the modes can be found analytically.Comment: 41 pages, 1 figure, LaTeX; v2: typos corrected, references adde

Thermal Fluctuations of Induced Fermion Number

We analyze the phemomenon of induced fermion number at finite temperature. At finite temperature, the induced fermion number $$ is a thermal expectation value, and we compute the finite temperature fluctuations, $(\Delta N)^2=-^2$. While the zero temperature induced fermion number is topological and is a sharp observable, the finite temperature induced fermion number is generically nontopological, and is not a sharp observable. The fluctuations are due to the mixing of states inherent in any finite temperature expectation value. We analyze in detail two different cases in 1+1 dimensional field theory: fermions in a kink background, and fermions in a chiral sigma model background. At zero temperature the induced fermion numbers for these two cases are very similar, but at finite temperature they are very different. The sigma model case is generic and the induced fermion number is nontopological, but the kink case is special and the fermion number is topological, even at finite temperature. There is a simple physical interpretation of all these results in terms of the spectrum of the fermions in the relevant background, and many of the results generalize to higher dimensional models.Comment: 17 pgs, 9 figs, RevTex

CORUM: the comprehensive resource of mammalian protein complexes

Protein complexes are key molecular entities that integrate multiple gene products to perform cellular functions. The CORUM (http://mips.gsf.de/genre/proj/corum/index.html) database is a collection of experimentally verified mammalian protein complexes. Information is manually derived by critical reading of the scientific literature from expert annotators. Information about protein complexes includes protein complex names, subunits, literature references as well as the function of the complexes. For functional annotation, we use the FunCat catalogue that enables to organize the protein complex space into biologically meaningful subsets. The database contains more than 1750 protein complexes that are built from 2400 different genes, thus representing 12% of the protein-coding genes in human. A web-based system is available to query, view and download the data. CORUM provides a comprehensive dataset of protein complexes for discoveries in systems biology, analyses of protein networks and protein complex-associated diseases. Comparable to the MIPS reference dataset of protein complexes from yeast, CORUM intends to serve as a reference for mammalian protein complexes

Renormalization of QCD_2

The low energy infrared scaling of the multi-color 2-dimensional quantum chromodynamics is determined in the framework of its bosonized model by using the functional renormalization group method with gliding sharp cut-off k in momentum space in the local potential approximation. The model exhibits a single phase with a superuniversal effective potential.Comment: 15 pages, 3 figures, final versio

Charmed Baryon Strong Coupling Constants in a Light-Front Quark Model

Light-Front quark model spin wave functions are employed to calculate the three independent couplings g_{\Sigma_c \Lambda_c \pi}, f_{\Lambda_{c1} \Sigma_c \pi} and f_{\Lambda^{*}_{c1} \Sigma_c \pi} of S-wave to S-wave and P-wave to S-wave one-pion transitions. It is found that g_{\Sigma_c \Lambda_c \pi}=6.81 MeV^{-1}, f_{\Lambda_{c1} \Sigma_c \pi}=1.16 and f_{\Lambda^{*}_{c1} \Sigma_c \pi}=0.96 . 10^{-4} MeV^{-2}. We also predict decay rates for specific strong transitions of charmed baryons.Comment: 21 Pages, No figures, LaTeX, some typos correcte