Is the rigid-body assumption reasonable?: Insights into the effects of dynamics on the electrostatic analysis of barnase-barstar

Electrostatically-driven association of proteins is important to many biological functions, and understanding which amino acid residues contribute to these interactions is crucial to protein design. Theoretical calculations that are used to elucidate the role of electrostatics in association are typically based on a single experimentally determined protein structure, while an underlying rigid-body assumption is adopted. The goal of this study was to investigate the role of conformational fluctuations on electrostatic interaction energies, as applied to the electrostatic analysis of barnase-barstar. For our calculations, we apply theoretical alanine-scan mutagenesis to introduce charge perturbations by replacing every ionizable residue with alanine, one at a time. Electrostatic clustering and free energy calculations based on the Poisson-Boltzmann method are used to evaluate the effects of each perturbation. Molecular dynamics simulations are performed for the barnase-barstar parent complex and seven experimental alanine mutations from the literature, in order to introduce relaxation before and after mutation. We discuss the effects of dynamics, in the form of pre- and post-mutation relaxation, on electrostatic clustering and free energies of association in light of experimental data. We also examine the utility of nine electrostatic similarity methods for clustering of barnase alanine-scan mutants. Our calculations suggest that the rigid-body assumption is reasonable for electrostatic calculations of barnase-barstar.     

Energy average formula of photon gas rederived by using the generalised Hermann-Feynman theorem

By virtue of the generalised Hermann-Feynmam theorem we re-derive the energy average formula of photon gas. This is another useful application of the theorem.     

Improper choosability of graphs and maximum average degree

Improper choosability of planar graphs has been widely studied. In particular, ?krekovski investigated the smallest integer g_k such that every planar graph of girth at least g_k is k‐improper 2‐choosable. He proved [9] that 6 ≤ g₁ ≤ 9; 5 ≤ g₂ ≤ 7; 5 ≤ g₃ ≤ 6; and ? k ≥ 4, g_k = 5. In this article, we study the greatest real M(k, l) such that every graph of maximum average degree less than M(k, l) is k‐improper l‐choosable. We prove that if l ≥ 2 then . As a corollary, we deduce that g₁ ≤ 8 and g₂ ≤ 6, and we obtain new results for graphs of higher genus. We also provide an upper bound for M(k, l). This implies that for any fixed l, . © 2006 Wiley Periodicals, Inc. J Graph Theory 52: 181–199, 2006     

Constraints on models with a break in the primordial power spectrum

One of the characteristics of the “Matter Bounce” scenario, an alternative to cosmological inflation for producing a scale-invariant spectrum of primordial adiabatic fluctuations on large scales, is a break in the power spectrum at a characteristic scale, below which the spectral index changes from ns=1$n_s=1$ to ns=3$n_s=3$. We study the constraints which current cosmological data place on the location of such a break, and more generally on the position of the break and the slope at length scales smaller than the break. The observational data we use include the WMAP five-year data set (WMAP5), other CMB data from BOOMERanG, CBI, VSA, and ACBAR, large-scale structure data from the Sloan Digital Sky Survey (SDSS, their luminous red galaxies sample), Type Ia Supernovae data (the “Union” compilation), and the Sloan Digital Sky Survey Lyman-α forest power spectrum (Lyα) data. We employ the Markov Chain Monte Carlo method to constrain the features in the primordial power spectrum which are motivated by the matter bounce model. We give an upper limit on the length scale where the break in the spectrum occurs.     

Cosmology with torsion: An alternative to cosmic inflation

We propose a simple scenario which explains why our Universe appears spatially flat, homogeneous and isotropic. We use the Einstein–Cartan–Kibble–Sciama (ECKS) theory of gravity which naturally extends general relativity to include the spin of matter. The torsion of spacetime generates gravitational repulsion in the early Universe filled with quarks and leptons, preventing the cosmological singularity: the Universe expands from a state of minimum but finite radius. We show that the dynamics of the closed Universe immediately after this state naturally solves the flatness and horizon problems in cosmology because of an extremely small and negative torsion density parameter, ΩS≈−¹⁰⁻⁶⁹${\Omega }_S\approx -{10}^{-69}$. Thus the ECKS gravity provides a compelling alternative to speculative mechanisms of standard cosmic inflation. This scenario also suggests that the contraction of our Universe preceding the bounce at the minimum radius may correspond to the dynamics of matter inside a collapsing black hole existing in another universe, which could explain the origin of the Big Bang.     

基于支持向量回归的豆油期货数据分析

随着期货市场在经济中的影响逐渐增强,对期货市场的研究具有实际意义.选取豆油期货指数进行研究,首先将数据进行归一化处理,然后选用支持向量回归方法建模分析.分析结果表明该方法对短期内的数据预测具有较好的效果,对了解期货市场的近期走势提供一些借鉴.     

二重非齐次马氏链的遍历性及其应用

给出二重非齐次马氏链的强遍历性,绝对平均强遍历性,Cesaro平均收敛的概念．利用二维马氏链的遍历性和C-K方程,建立了二维马氏链与二重非齐次马氏链遍历性的关系．并讨论了齐次二重马氏链绝对平均强遍历与强遍历的等价性．最后给出Cesaro平均收敛在马氏决策过程和信息论中应用．     

AVERAGE ONESIDED WIDTHS OF SOBOLEV AND BESOV CLASSES

The article concerns the average onesided widths of the Sobolev and Besov classes and the classes of functions with bounded moduli of smoothness. The weak asymptotic results are obtained for the corresponding quantities.     

Fast Computation of Auxiliary Quantities in Local Polynomial Regression

Abstract

We investigate the extension of binning methodology to fast computation of several auxiliary quantities that arise in local polynomial smoothing. Examples include degrees of freedom measures, cross-validation functions, variance estimates, and exact measures of error. It is shown that the computational effort required for such approximations is of the same order of magnitude as that required for a binned local polynomial smooth.     

Some generalized limit theorems concerning delayed sums of random sequence

For a sequence of arbitrarily dependent m-valued random variables (Xn) n∈N , the generalized strong limit theorem of the delayed average is investigated. In our proof, we improved the method proposed by Liu [6] . As an application, we also studied some limit properties of delayed average for inhomogeneous Markov chains.