Exotic Baryons in Two-Dimensional QCD

Two-dimensional QCD has often been used as a laboratory for studying the full four-dimensional theory, providing, for example, an explicit realization of baryons as solitons. We review aspects of conventional baryons in two-dimensional QCD, including the classical and quantum contributions to their masses. We then discuss the spectrum of exotic baryons in two-dimensional QCD, commenting on the solitonic radius inferred from the excitation spectrum as well as the two-dimensional version of the Goldberger-Treiman relation relating meson couplings to current matrix elements. Two-dimensional QCD provides strong overall support to the chiral-soliton picture for the structure of normal and exotic baryons in four dimensions.Comment: 15 pages latex, no figure

On the stability of quark solitons in QCD

We critically re-examine our earlier derivation of the effective low energy action for QCD in 4 dimensions with chiral fields transforming non-trivially under both color and flavor, using the method of anomaly integration. We find several changes with respect to our previous results, leading to much more compact expressions, and making it easier to compare with results of other approaches to the same problem. With the amended effective action, we find that there are no stable soliton solutions. In the context of the quark soliton program, we interpret this as an indication that the full low-energy effective action must include additional terms, reflecting possible modifications at short distances and/or the non-trivial structure of the gauge fields in the vacuum, such as \neq 0. Such terms are absent in the formalism based on anomaly integration

Metastable tight knots in a worm-like polymer

Based on an estimate of the knot entropy of a worm-like chain we predict that the interplay of bending energy and confinement entropy will result in a compact metastable configuration of the knot that will diffuse, without spreading, along the contour of the semi-flexible polymer until it reaches one of the chain ends. Our estimate of the size of the knot as a function of its topological invariant (ideal aspect ratio) agrees with recent experimental results of knotted dsDNA. Further experimental tests of our ideas are proposed.Comment: 4 pages, 3 figure

DNA in nanopore-counterion condensation and coion depletion

Molecular dynamics simulations are used to study the equilibrium distribution of monovalent ions in a nanopore connecting two water reservoirs separated by a membrane, both for the empty pore and that with a single stranded DNA molecule inside. In the presence of DNA, the counterions condense on the stretched macromolecule effectively neutralizing it, and nearly complete depletion of coions from the pore is observed. The implications of our results for experiments on DNA translocation through alpha-hemolysin nanopores are discussed.Comment: 8 pages, 2 figure

The promoters of human cell cycle genes integrate signals from two tumor suppressive pathways during cellular transformation

Deciphering regulatory events that drive malignant transformation represents a major challenge for systems biology. Here we analyzed genome-wide transcription profiling of an in-vitro transformation process. We focused on a cluster of genes whose expression levels increased as a function of p53 and p16INK4A tumor suppressors inactivation. This cluster predominantly consists of cell cycle genes and constitutes a signature of a diversity of cancers. By linking expression profiles of the genes in the cluster with the dynamic behavior of p53 and p16INK4A, we identified a promoter architecture that integrates signals from the two tumor suppressive channels and that maps their activity onto distinct levels of expression of the cell cycle genes, which in turn, correspond to different cellular proliferation rates. Taking components of the mitotic spindle as an example, we experimentally verified our predictions that p53-mediated transcriptional repression of several of these novel targets is dependent on the activities of p21, NFY and E2F. Our study demonstrates how a well-controlled transformation process allows linking between gene expression, promoter architecture and activity of upstream signaling molecules.Comment: To appear in Molecular Systems Biolog