Charmonium Suppression - Interplay of Hadronic and Partonic Degrees of Freedom

Last year the E866-group of the Fermilab measured the $x_F$ dependence of $J/\Psi$ and $\Psi'$ suppression in $pA$ collisions. We discuss two of the effects found in that experiment with regard to color coherence effects: the different suppression of the $J/\Psi$ and the $\Psi'$ at $x_F<0$ and the significant suppression of both at large $x_F$. The small $x_F$ regions is dominated by fully formed charmonium states and thus enables us to discuss the formation time and the cross section of the different charmonium states. In the large $x_F$ region the interaction of the charmonium states with nuclear matter has to be described by partonic degrees of freedom, because in that kinematic domain the formation time is much larger than the nuclear radii. The understanding of this region will be crucial for the interpretation of the data of the future heavy ion colliders RHIC and LHC.Comment: 4 pages, 1 table, 1 figure, Contribution to the Proceedings of the 15th Particles and Nuclei International Conference (PANIC 99), Uppsala, Sweden, June 10-16, 199

Dynamics of Competitive Evolution on a Smooth Landscape

We study competitive DNA sequence evolution directed by {\it in vitro} protein binding. The steady-state dynamics of this process is well described by a shape-preserving pulse which decelerates and eventually reaches equilibrium. We explain this dynamical behavior within a continuum mean-field framework. Analytical results obtained on the motion of the pulse agree with simulations. Furthermore, finite population correction to the mean-field results are found to be insignificant.Comment: 4 pages, 2 figures, revised, to appear in Phys. Rev. Let

Critical Review Of Quark Gluon Plasma Signals

Compelling evidence for a new form of matter has been claimed to be formed in Pb+Pb collisions at SPS. We critically review two suggested signatures for this new state of matter: First the suppression of the J/$\Psi$, which should be strongly suppressed in the QGP by two different mechanisms, the color-screening and the QCD-photoeffect. Secondly the measured particle, in particular strange hadronic, ratios might signal the freeze-out from a quark-gluon phase.Comment: 7 pages 6 figures, Contribution to the Proceedings of CRIS 2000, 3rd Catania Relativistic Ion Studies, Acicastello, Italy, May 22-26, 200

Kinetic Accessibility of Buried DNA Sites in Nucleosomes

Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and reburial on the site position, which is measurable experimentally and pertinent to gene regulation. We find the dependence to be roughly described by a random walker model. Close inspection reveals a surprising physical effect of flexibility-assisted barrier crossing, which we characterize within a toy model, the "semiflexible Brownian rotor."Comment: final version as published in Phys. Rev. Let

Optimal flexibility for conformational transitions in macromolecules

Conformational transitions in macromolecular complexes often involve the reorientation of lever-like structures. Using a simple theoretical model, we show that the rate of such transitions is drastically enhanced if the lever is bendable, e.g. at a localized "hinge''. Surprisingly, the transition is fastest with an intermediate flexibility of the hinge. In this intermediate regime, the transition rate is also least sensitive to the amount of "cargo'' attached to the lever arm, which could be exploited by molecular motors. To explain this effect, we generalize the Kramers-Langer theory for multi-dimensional barrier crossing to configuration dependent mobility matrices.Comment: 4 pages, 4 figure

Can Momentum Correlations Proof Kinetic Equilibration in Heavy Ion Collisions at 160 AGeV?

We perform an event-by-event analysis of the transverse momentum distribution of final state particles in central Pb(160AGeV)+Pb collisions within a microscopic non-equilibrium transport model (UrQMD). Strong influence of rescattering is found. The extracted momentum distributions show less fluctuations in A+A collisions than in p+p reactions. This is in contrast to simplified p+p extrapolations and random walk models.Comment: 9 pages, 3 eps figures, submitted to Phys. Lett.

Translocation of structured polynucleotides through nanopores

We investigate theoretically the translocation of structured RNA/DNA molecules through narrow pores which allow single but not double strands to pass. The unzipping of basepaired regions within the molecules presents significant kinetic barriers for the translocation process. We show that this circumstance may be exploited to determine the full basepairing pattern of polynucleotides, including RNA pseudoknots. The crucial requirement is that the translocation dynamics (i.e., the length of the translocated molecular segment) needs to be recorded as a function of time with a spatial resolution of a few nucleotides. This could be achieved, for instance, by applying a mechanical driving force for translocation and recording force-extension curves (FEC's) with a device such as an atomic force microscope or optical tweezers. Our analysis suggests that with this added spatial resolution, nanopores could be transformed into a powerful experimental tool to study the folding of nucleic acids.Comment: 9 pages, 5 figure