Cavity search: An algorithm for the isolation and display of cavity-like binding regions

Summary A set of algorithms designed to enhance the display of protein binding cavities is presented. These algorithms, collectively entitled CAVITY SEARCH, allow the user to isolate and fully define the extent of a particular cavity. Solid modeling techniques are employed to produce a detailed cast of the active site region, which can then be color-coded to show electrostatic and steric interactions between the protein cavity and a bound ligand.     

Differentiation identities for hypergeometric functions

It is well-known that differentiation of hypergeometric function multiplied by a certain power function yields another hypergeometric function with a different set of parameters. Such differentiation identities for hypergeometric functions have been used widely in various fields of applied mathematics and natural sciences. In this expository note, we provide a simple proof of the differentiation identities, which is based only on the definition of the coefficients for the power series expansion of the hypergeometric functions.     

Isolation, Mapping, DNA Sequence and RFLPs Studies of Random Single-Copy DNA Segments on Human X Chromosome

Using the total human/mouse DNA as the probe, screening has been carried out three times with in situ plaque hybridization to obtain the single-copy DNA sequence from the human X chromosome genomic library. The effective rate of screening is 1. 45%. DNAs from clones containing single-copy inserts have been analyzed by a panel of hybrid cells with or without human X chromosome. Three segments, designated by DXFD52,73,75, are mapped to the X chromosome. DXFD52 has been precisely localized on Xq12-q13 with in situ chromosomal hybridization. DXFD52 has been partially sequenced. The results indicate that DXFD52 is a new isolated single-copy segment on the X chromosome. Great progress in the RFLPs study with DXFD52 has been achieved in the population of Chongqing, Sichuan Province. The results show that the DXFD52 can be used to detect the RFLP with Hind Ⅲ, Bgl Ⅱ, and Hinf Ⅰ. DXFD52 will be a potential "landmark" for the construction of the complete linkage map of human genome and the analysis of genomic s     

Some nonlinear problems in servomechanisms

Summary A mathematical model for a hydraulic servomechanism is constructed. It is shown that the model, in general, reduces to a nonlinear third-order equation of the formxx+(₁+xx+–₂ x=p(t). Under certain conditions imposed on the constants involved, it is proved that above equation possesses a periodic solution.     

Some remarks on the modulus of continuity of a conformal mapping of the disk onto a Jordan domain

Letd(;z, t) be the smallest diameter of the arcs of a Jordan curve with endsz andt. Consider the rapidity of decreasing ofd(;)=sup{d(;z, t):z, t , ¦z–t¦} (as 0,0) as a measure of nicety of . Letg(x) (x0) be a continuous and nondecreasing function such thatg(x)x,g(0)=0. Put¯g(x)=g(x)+x, h(x)=(¯g(x))². LetH(x) be an arbitrary primitive of 1/h ^–1(x). Note that the functionH ^–1 x is positive and increasing on (–, +),H ^–1 0 asx– andH ^–1+ asx +. The following statement is proved in the paper.Translated fromMatematicheskie Zametki, Vol. 60, No. 2, pp. 176–184, August, 1996.This research was supported by the Russian Foundation for Basic Research under grant No. 93-01-00236 and by the International Science Foundation under grant No. NCF000.     

Crumpled laminations and manifolds of nonfinite type

Using a group-theoretic construction due to Bestvina and Brady, we build -manifolds which admit partitions into closed, connected -manifolds but which do not have finite homotopy type.

     

Derivative of the exponential mapping for infinite dimensional lie groups

It is proved that for infinite dimensional Lie groups in the sense of the differential calculus of Frölicher and Kriegl the derivative of the exponential mappings is given by the formula d(exp)(X)Y=d_exp(X)(e) ₀ ¹ Ad_exp(–tX) Y dt, where stands for the left translation ande is the neutral element.This work was supported by the Alexander von Humboldt-Stiftung.     

RECENT PROGRESS OF NANO-MECHANICAL MAPPING

 Nano-mechanical mapping by atomic force microscopy has been developed as an useful application to measure mechanical properties of soft materials at nanometer scale. To date, the Hertzian theory was used for analyzing force-distance curves as the simplest model among several contact mechanics between elastic bodies. However, the preexisting methods based on this theory do not consider the adhesive interaction in principle, which cannot be neglected in the ambient condition. A new analytical method was introduced to estimate the elasticity and the adhesive energy simultaneously by means of the JKR theory, describing adhesive contact between elastic materials. Poly(dimethylsiloxane) (PDMS) and isobutylene-co-isoprene rubber (IIR) were analyzed to verify the applicable limit of the JKR analysis. For elastic samples such as PDMS, the force-deformation plots obtained experimentally were consistent with JKR theoretical curves. Meanwhile, for viscoelastic samples, especially for IIR, the experimental plots revealed large deviations from JKR curves depending on scanning velocity and maximum loading force. Some nano-rheological arguments were employed based on the difference between these specimens.     

Characterization of individual atmospheric particles by element mapping in electron probe microanalysis

In this paper procedures for the characterization of individual aerosol particles by element mapping in the electron microprobe are presented. The number, size and qualitative chemical composition of particles is derived from a combination of secondary or backscattered electron images and element distribution maps. Accuracy of the size distribution and reliability of the qualitative analysis procedure were checked with silicate samples. In order to obtain a semi-quantitative estimate of the chemical composition of individual particles the count rates taken from element distribution maps are corrected for matrix and geometric effects using particle ZAF procedures.Dedicated to Professor Dr. rer. nat. Dr. h.c. Hubertus Nickel on the occasion of his 65th birthday     

PHOTOEMISSION WITHIN AND BEYOND THE ONE-STEP MODEL

Photoemission in the vacuum ultraviolet photon regime has proved to be an effective tool for the investigation of valence band surface electronic structure. The interpretation cannot be exclusively confined to the valence bands but has to consider cross sections with realistic final states consistently designed within the one-step model. Therefore especially in the surface sensitive photoemission, several effects hide the final goal of deducing the energetic and wavefunction structure together with microscopic potential parameters through a convincing agreement of calculated with measured spectra. The final states band structure is much less well understood than the valence band structure under consideration. The optical potential, which controls the surface sensitivity through the underlying damping mechanisms, widely relies on empirical assumptions. Furthermore, the photon field is not only strongly influenced but in the vicinity of the plasma frequency also deteriorated by the electronic response. In view of high resolution spectroscopy the accuracy of the data interpretation is affected, and in fact, band-mapping methods are no longer valid. Examples of recent calculations to account for these effects are reviewed.