2,033 research outputs found
Sequence Effects on DNA Entropic Elasticity
DNA stretching experiments are usually interpreted using the worm-like chain
model; the persistence length A appearing in the model is then interpreted as
the elastic stiffness of the double helix. In fact the persistence length
obtained by this method is a combination of bend stiffness and intrinsic bend
effects reflecting sequence information, just as at zero stretching force. This
observation resolves the discrepancy between the value of A measured in these
experiments and the larger ``dynamic persistence length'' measured by other
means. On the other hand, the twist persistence length deduced from
torsionally-constrained stretching experiments suffers no such correction. Our
calculation is very simple and analytic; it applies to DNA and other polymers
with weak intrinsic disorder.Comment: LaTeX; postscript available at
http://dept.physics.upenn.edu/~nelson/index.shtm
Renaissance of the ~1 TeV Fixed-Target Program
This document describes the physics potential of a new fixed-target program
based on a ~1 TeV proton source. Two proton sources are potentially available
in the future: the existing Tevatron at Fermilab, which can provide 800 GeV
protons for fixed-target physics, and a possible upgrade to the SPS at CERN,
called SPS+, which would produce 1 TeV protons on target. In this paper we use
an example Tevatron fixed-target program to illustrate the high discovery
potential possible in the charm and neutrino sectors. We highlight examples
which are either unique to the program or difficult to accomplish at other
venues.Comment: 31 pages, 11 figure
Statistical-mechanical lattice models for protein-DNA binding in chromatin
Statistical-mechanical lattice models for protein-DNA binding are well
established as a method to describe complex ligand binding equilibriums
measured in vitro with purified DNA and protein components. Recently, a new
field of applications has opened up for this approach since it has become
possible to experimentally quantify genome-wide protein occupancies in relation
to the DNA sequence. In particular, the organization of the eukaryotic genome
by histone proteins into a nucleoprotein complex termed chromatin has been
recognized as a key parameter that controls the access of transcription factors
to the DNA sequence. New approaches have to be developed to derive statistical
mechanical lattice descriptions of chromatin-associated protein-DNA
interactions. Here, we present the theoretical framework for lattice models of
histone-DNA interactions in chromatin and investigate the (competitive) DNA
binding of other chromosomal proteins and transcription factors. The results
have a number of applications for quantitative models for the regulation of
gene expression.Comment: 19 pages, 7 figures, accepted author manuscript, to appear in J.
Phys.: Cond. Mat
Parton Distributions Working Group
The main focus of this working group was to investigate the different issues
associated with the development of quantitative tools to estimate parton
distribution functions uncertainties. In the conclusion, we introduce a
"Manifesto" that describes an optimal method for reporting data.Comment: Report of the Parton Distributions Working Group of the 'QCD and Weak
Boson Physics workshop in preparation for Run II at the Fermilab Tevatron'.
Co-Conveners: L. de Barbaro, S.A. Keller, S. Kuhlmann, H. Schellman, and
W.-K. Tun
A Precise Determination of Electroweak Parameters in Neutrino-Nucleon Scattering
The NuTeV collaboration has extracted sin^2theta_W from the ratios of neutral
current to charged current neutrino and anti-neutrino cross-sections. Our
value, sin^2theta_W(on-shell)=0.2277+/-0.0013(stat)+/-0.0009(syst), is three
standard deviations above the standard model prediction. We also present a
model independent analysis of the same data.Comment: ReVTeX, 5 pp, 1fig; v2. revised SM prediction; v3. more sig. digits
in Eqns 6-7, fix error in Eqn
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