One-dimensional classical adjoint SU(2) Coulomb Gas

The equation of state of a one-dimensional classical nonrelativistic Coulomb gas of particles in the adjoint representation of SU(2) is given. The problem is solved both with and without sources in the fundamental representation at either end of the system. The gas exhibits confining properties at low densities and temperatures and deconfinement in the limit of high densities and temperatures. However, there is no phase transition to a regime where the string tension vanishes identically; true deconfinement only happens for infinite densities and temperatures. In the low density, low temperature limit, a new type of collective behavior is observed.Comment: 6 pages, 1 postscript figur

The local structure of topological charge fluctuations in QCD

We introduce the Dirac eigenmode filtering of topological charge density associated with Ginsparg-Wilson fermions as a tool to investigate the local structure of topological charge fluctuations in QCD. The resulting framework is used to demonstrate that the bulk of topological charge in QCD does not appear in the form of unit quantized lumps. This means that the mixing of "would-be" zeromodes associated with such lumps is probably not the prevalent microscopic mechanism for spontaneous chiral symmetry breaking in QCD. To characterize the coherent local behavior in topological charge density at low energy, we compute the charges contained in maximal coherent spheres enclosing non-overlapping peaks. We find a continuous distribution essentially ending at ~0.5. Finally, we study, for the first time, the overlap-operator topological-charge-density correlators and find consistency with non-positivity at nonzero physical distance. This represents a non-trivial check on the locality (in gauge paths) of the overlap Dirac operator for realistic gauge backgrounds.Comment: 3 pages, 4 figures, talk, Lattice2002(topology

Protein Molecular Function Prediction by Bayesian Phylogenomics

We present a statistical graphical model to infer specific molecular function for unannotated protein sequences using homology. Based on phylogenomic principles, SIFTER (Statistical Inference of Function Through Evolutionary Relationships) accurately predicts molecular function for members of a protein family given a reconciled phylogeny and available function annotations, even when the data are sparse or noisy. Our method produced specific and consistent molecular function predictions across 100 Pfam families in comparison to the Gene Ontology annotation database, BLAST, GOtcha, and Orthostrapper. We performed a more detailed exploration of functional predictions on the adenosine-5′-monophosphate/adenosine deaminase family and the lactate/malate dehydrogenase family, in the former case comparing the predictions against a gold standard set of published functional characterizations. Given function annotations for 3% of the proteins in the deaminase family, SIFTER achieves 96% accuracy in predicting molecular function for experimentally characterized proteins as reported in the literature. The accuracy of SIFTER on this dataset is a significant improvement over other currently available methods such as BLAST (75%), GeneQuiz (64%), GOtcha (89%), and Orthostrapper (11%). We also experimentally characterized the adenosine deaminase from Plasmodium falciparum, confirming SIFTER's prediction. The results illustrate the predictive power of exploiting a statistical model of function evolution in phylogenomic problems. A software implementation of SIFTER is available from the authors

Evidence for fine tuning of fermionic modes in lattice gluodynamics

We consider properties of zero and near-zero fermionic modes in lattice gluodynamics. The modes are known to be sensitive to the topology of the underlying gluonic fields in the quantum vacuum state of the gluodynamics. We find evidence that these modes are fine tuned, that is exhibit sensitivity to both physical (one can say, hadronic) scale and to the ultraviolet cutoff. Namely, the density of the states is in physical units while the localization volume of the modes tends to zero in physical units with the lattice spacing tending to zero. We discuss briefly possible theoretical implications and also include some general, review-type remarks.Comment: 7 pages, 7 eps figures, uses JETP Letters style (included); substantial stylistic changes, discussions added, conclusions unchanged. Supplementary materials and computer animations are available at http://lattice.itep.ru/overla