W asymmetries at CDF and D0

We present recent W and charged lepton asymmetry measurements from the CDF and D0 experiments. Theoretical predictions agree with the CDF W asymmetry, measured using a new matrix element technique. These theoretical predictions are less consistent with the latest lepton asymmetry measurements from D0 and CDF, especially for high charged lepton transverse momentum.Comment: 6 pages, 6 figure

A Model for the Thermodynamics of Globular Proteins

Comments: 6 pages RevTeX, 6 Postscript figures. We review a statistical mechanics treatment of the stability of globular proteins based on a simple model Hamiltonian taking into account protein self interactions and protein-water interactions. The model contains both hot and cold folding transitions. In addition it predicts a critical point at a given temperature and chemical potential of the surrounding water. The universality class of this critical point is new

Pathways in Two-State Protein Folding

The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that folding is guided. We reconcile these two seemingly contradictory observations quantitatively in a schematic model of protein folding. We propose a new dynamical transition temperature which is lower than the thermodynamic one, in qualitative agreement with in vivo measurement of protein stability using E.coli. Finally we demonstrate that our framework is easily generalized to encompass cold unfolding, and make predictions that relate the sharpness of the cold and hot unfolding transitions.Comment: 4 pages RevTeX, 5 Postscript figur

The D0 Run IIb Luminosity Measurement

An assessment of the recorded integrated luminosity is presented for data collected with the D0 detector at the Fermilab Tevatron Collider from June 2006 to September 2011 (Run IIb). In addition, a measurement of the effective cross section for inelastic interactions, also referred to as the luminosity constant, is reported. This measurement incorporates new features that lead to a substantial improvement in the precision of the result. A luminosity constant of \sigma_{LM} = 48.3\pm1.9\pm0.6 mb is obtained, where the first uncertainty is due to the accuracy of the inelastic cross section used by both CDF and D0, and the second uncertainty is due to D0 sources. The recorded luminosity for the highest E_T jet trigger is L_rec = 9.2 \pm 0.4 fb^{-1}, with a relative uncertainty of 4.3%.Comment: 20 pages, 23 figure

Metabolic Futile Cycles and Their Functions: A Systems Analysis of Energy and Control

It has long been hypothesized that futile cycles in cellular metabolism are involved in the regulation of biochemical pathways. Following the work of Newsholme and Crabtree, we develop a quantitative theory for this idea based on open-system thermodynamics and metabolic control analysis. It is shown that the {\it stoichiometric sensitivity} of an intermediary metabolite concentration with respect to changes in steady-state flux is governed by the effective equilibrium constant of the intermediate formation, and the equilibrium can be regulated by a futile cycle. The direction of the shift in the effective equilibrium constant depends on the direction of operation of the futile cycle. High stoichiometric sensitivity corresponds to ultrasensitivity of an intermediate concentration to net flow through a pathway; low stoichiometric sensitivity corresponds to super-robustness of concentration with respect to changes in flux. Both cases potentially play important roles in metabolic regulation. Futile cycles actively shift the effective equilibrium by expending energy; the magnitude of changes in effective equilibria and sensitivities is a function of the amount of energy used by a futile cycle. This proposed mechanism for control by futile cycles works remarkably similarly to kinetic proofreading in biosynthesis. The sensitivity of the system is also intimately related to the rate of concentration fluctuations of intermediate metabolites. The possibly different roles of the two major mechanisms for cellular biochemical regulation, namely reversible chemical modifications via futile cycles and shifting equilibrium by macromolecular binding, are discussed.Comment: 11 pages, 5 figure

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