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