464 research outputs found
Charmonium Suppression - Interplay of Hadronic and Partonic Degrees of Freedom
Last year the E866-group of the Fermilab measured the dependence of
and suppression in collisions. We discuss two of the
effects found in that experiment with regard to color coherence effects: the
different suppression of the and the at and the
significant suppression of both at large . The small 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 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/, 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
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