Structure-based identification and clustering of protein families and superfamilies

Summary We describe an approach to protein structure comparison designed to detect distantly related proteins of similar fold, where the procedure must be sufficiently flexible to take into account the elasticity of protein folds without losing specificity. Protein structures are represented as a series of secondary structure elements, where for each element a local environment describes its relations with the elements that surround it. Secondary structures are then aligned by comparing their features and local environments. The procedure is illustrated with searches of a database of 468 protein structures in order to identify proteins of similar topology to porcine pepsin, porphobilinogen deaminase and serum amyloid P-component. In all cases the searches correctly identify protein structures of similar fold as the search proteins. Multiple cross-comparisons of protein structures allow the clustering of proteins of similar fold. This is exemplified with a clustering of /- and -class protein structures. We discuss applications of the comparison and clustering of three-dimensional protein structures to comparative modelling and structure-based protein design.     

Generalized solutions of a stochastic partial differential equation

We discuss the Cauchy problem of a certain stochastic parabolic partial differential equation arising in the nonlinear filtering theory, where the initial data and the nonhomogeneous noise term of the equation are given by Schwartz distributions. The generalized (distributional) solution is represented by a partial (conditional) generalized expectation ofT(t)° _0,t ^–1 , whereT(t) is a stochastic process with values in distributions and _s,t is a stochastic flow generated by a certain stochastic differential equation. The representation is used for getting estimates of the solution with respect to Sobolev norms.Further, by applying the partial Malliavin calculus of Kusuoka-Stroock, we show that any generalized solution is aC -function under a condition similar to Hörmander's hypoellipticity condition.     

On the two-dimensional stochastic Ising model in the phase coexistence region near the critical point

We consider the two-dimensional stochastic Ising model in finite square with free boundary conditions, at inverse temperature >₀ and zero external field. Using duality and recent results of Ioffe on the Wulff construction close to the critical temperature, we extend some of the results obtained by Martinelli in the low-temperature regime to any temperature below the critical one. In particular we show that the gap in the spectrum of the generator of the dynamics goes to zero in the thermodynamic limit as an exponential of the side length of , with a rate constant determined by the surface tension along one of the coordinate axes. We also extend to the same range of temperatures the result due to Shlosman on the equilibrium large deviations of the magnetization with free boundary conditions.     

Fubini theorem for anticipating stochastic integrals in Hilbert space

Let (X,l,) be a measure space, letW be a cylindrical Hilbert-Wiener process, and let be an anticipating integrable process-valued function onX. We prove, under natural assumptions on, that there exists a measurable version Y_x,x X, of the anticipating integral of(x) such that the integral _x Y_x(dx) is a version of the anticipating integral of _X (x)(dx). We apply this anticipating Fubini theorem to study solutions of a class of stochastic evolution equations in Hilbert space.     

Droplet dynamics for asymmetric Ising model

Nucleation from a metastable state is studied for an anisotropic Ising model at very low temperatures. It turns out that the critical nucleus as well as configurations on a typical path to it differ from the Wulff shape of an equilibrium droplet.     

Detector comparison for sulfur and chlorine detection with laser induced breakdown spectroscopy in the near-infrared-region

Laser-induced breakdown spectroscopy has been employed for the investigation of the sulfur and chlorine content of building materials. Both, chloride and sulfate ions are major damaging species affecting the stability and lifetime of a structure. Chlorine and sulfur are mostly detected in the VUV and the NIR. In case of building materials the main elements like calcium or iron have many strong spectral lines over the whole spectral range, so that trace elements can only be detected in spectral windows unaffected from these lines. With regard to a preferably simply, robust against dust and vibrations and portable setup only the NIR spectral features are used for civil engineering applications.

Most detectors, mainly CCD cameras have rapidly decreasing quantum efficiency in the NIR. Also the quantum efficiency of the photocathode of CCD-Detectors with image intensifier is decreasing in the NIR. Different CCD-detectors were tested with respect to high quantum efficiency and high dynamic range, which is necessary for simultaneous detection of weak spectral lines from trace elements and intense spectral lines from main elements.

The measurements are made on reference samples consisting of cement, hydrated cement, cement mortar and concrete with well-defined amounts of the trace elements. Experimental conditions are chosen for an optimum intensity of the trace element spectral lines. The detector systems are compared by limit of detections and the signal to noise ratio.     

Charge calculations in molecular mechanics. Part 8 Partial atomic charges from classical calculations

Summary The CHARGE2 programme, which involves the classical calculation of both the inductive and resonance contributions to the partial atomic charges in molecules is described, and the charges and electrostatic potentials obtained presented for some illustrative examples.In substituted methanes (CH₃X, CF₃X, CCl₃X) the effects of varying the electronegativity of the substituents and the - and -substituent contributions are clearly illustrated for a variety of substituent groups X.The problems involved in the inclusion of silicon into this scheme are detailed, together with the methods of overcoming them. The partial atomic charges ( and contributions) and electrostatic potentials for some silicon oxygen compounds are presented and discussed.The partial atomic charges from CHARGE2 for all the natural amino acids as their N-acetyl, N-methyl-amides are given and compared with those obtained from the AMBER and ECEPP/2 force fields. Considerable differences in these figures are observed, with the AMBER charges consistently much larger than those from the other two methods.The CHARGE2 partial atomic charges and electrostatic potentials for the four common nucleic acids, adenine, cytosine, guanine and thymine, are given and compared with those derived from other calculations. Again there is general similarity but also there are considerable differences, with those from the AMBER force field somewhat larger than the other methods.For previous parts in this series, see Refs. 1-7.     

内噪声作用下的随机共振算法对弱信号的检测

基于随机共振理论提出了一种简便、有效地检测弱信号的方法。在内噪声协同作用下，通过调节输入噪声信号的大小能较好地提高系统输出信号的信噪比，从而实现检测背景噪声很强的弱信号的目的。应用于模拟信号和实验信号的结果证明了方法是可行的。     

Visualisation of interlaboratory comparison results in PomPlots

In this work a novel graphical method is applied to the presentation of intercomparison results. This is demonstrated with the results of a recent intercomparison in measuring the ¹³⁷Cs, ⁴⁰K, and ⁹⁰Sr activity concentration in milk powder. The “PomPlot”, an intuitive graphical method, is used for producing a summary overview of the participants’ results of a common measurand. The “PomPlot” displays (relative) deviations of individual results from the reference value on the horizontal axis and (relative) uncertainties on the vertical axis.     

The stochastic Boltzmann equation and hydrodynamic fluctuations

Based on the assumption of a kinetic equation in space, a stochastic differential equation of the one-particle distribution is derived without the use of the linear approximation. It is just the Boltzmann equation with a Langevin-fluctuating force term. The result is the general form of the linearized Boltzmann equation with fluctuations found by Bixon and Zwanzig and by Fox and Uhlenbeck. It reduces to the general Landau-Lifshitz equations of fluid dynamics in the presence of fluctuations in a similar hydrodynamic approximation to that used by Chapman and Enskog with respect to the Boltzmann equation.This work received financial support from the Alexander von Humboldt Foundation.