Modeling two-state cooperativity in protein folding

A protein model with the pairwise interaction energies varying as local environment changes, i.e., including some kinds of collective effect between the contacts, is proposed. Lattice Monte Carlo simulations on the thermodynamical characteristics and free energy profile show a well-defined two-state behavior and cooperativity of folding for such a model. As a comparison, related simulations for the usual G\={o} model, where the interaction energies are independent of the local conformations, are also made. Our results indicate that the evolution of interactions during the folding process plays an important role in the two-state cooperativity in protein folding.Comment: 5 figure

Filling the Gap: a Tool to Automate Parameter Estimation for Software Performance Models

© 2015 ACM.Software performance engineering heavily relies on application and resource models that enable the prediction of Quality-of-Service metrics. Critical to these models is the accuracy of their parameters, the value of which can change with the application and the resources where it is deployed. In this paper we introduce the Filling-the-gap (FG) tool, which automates the parameter estimation of application performance models. This tool implements a set of statistical routines to estimate the parameters of performance models, which are automatically executed using monitoring information kept in a local database

Symbolic Computation of Polynomial Conserved Densities, Generalized Symmetries, and Recursion Operators for Nonlinear Differential-Difference Equations

Algorithms for the symbolic computation of polynomial conserved densities, fluxes, generalized symmetries, and recursion operators for systems of nonlinear differential-difference equations are presented. In the algorithms we use discrete versions of the Fréchet and variational derivatives, as well as discrete Euler and homotopy operators. The algorithms are illustrated for prototypical nonlinear polynomial lattices, including the Kac-van Moerbeke (Volterra) and Toda lattices. Results are shown for the modified Volterra and Ablowitz-Ladik lattices

How Saturated are Absorption Lines in the Broad Absorption Line Quasar PG 1411+442 ?

Recently, convincing evidence was found for extremely large X-ray absorption by column densities $> 10^{23} cm^{-2}$ in broad absorption line quasars. One consequence of this is that any soft X-ray emission from these QSOs would be the scattered light or leaked light from partially covering absorbing material. A detection of the unabsorbed soft X-ray and absorbed hard X-ray compo nent will allow to determine the total column density as well as the effective covering factor of the absorbing material, which can be hardly obtained from the UV absorption lines. Brinkmann et al. (1999) showed that both the unabsorbed and absorbed components are detected in the nearby very bright broad absorption line quasar PG 1411+442. In this letter, we make a further analysis of the broad band X-ray spectrum and the UV spectrum from HST, and demonstrate that broad absorption lines are completely saturated at the bottom of absorption troughs.Comment: 6 pages, 3 postscript figures. to appear in Astrophy. J. Letter

Recent Trends in Hospitalization for Acute Myocardial Infarction in Beijing: Increasing Overall Burden and a Transition From ST-Segment Elevation to Non-ST-Segment Elevation Myocardial Infarction in a Population-Based Study

Comparable data on trends of hospitalization rates for ST-segment elevation myocardial infarction (STEMI) and non-STEMI (NSTEMI) remain unavailable in representative Asian populations.To examine the temporal trends of hospitalization for acute myocardial infarction (AMI) and its subtypes in Beijing.Patients hospitalized for AMI in Beijing from January 1, 2007 to December 31, 2012 were identified from the validated Hospital Discharge Information System. Trends in hospitalization rates, in-hospital mortality, length of stay (LOS), and hospitalization costs were analyzed by regression models for total AMI and for STEMI and NSTEMI separately. In total, 77,943 patients were admitted for AMI in Beijing during the 6 years, among whom 67.5% were males and 62.4% had STEMI. During the period, the rate of AMI hospitalization per 100,000 population increased by 31.2% (from 55.8 to 73.3 per 100,000 population) after age standardization, with a slight decrease in STEMI but a 3-fold increase in NSTEMI. The ratio of STEMI to NSTEMI decreased dramatically from 6.5:1.0 to 1.3:1.0. The age-standardized in-hospital mortality decreased from 11.2% to 8.6%, with a significant decreasing trend evident for STEMI in males and females (P < 0.001) and for NSTEMI in males (P = 0.02). The rate of percutaneous coronary intervention increased from 28.7% to 55.6% among STEMI patients. The total cost for AMI hospitalization increased by 56.8% after adjusting for inflation, although the LOS decreased by 1 day.The hospitalization burden for AMI has been increasing in Beijing with a transition from STEMI to NSTEMI. Diverse temporal trends in AMI subtypes from the unselected "real-world" data in Beijing may help to guide the management of AMI in China and other developing countries