Computer generation of distance polynomials of graphs

A computer program is developed to compute distance polynomials of graphs containing up to 200 vertices. The code also computes the eigenvalues and the eigenvectors of the distance matrix. It requires as input only the neighborhood information from which the program constructs the distance matrix. The eigenvalues and eigenvectors are computed using the Givens-Householder method while the characteristic polynomials of the distance matrix are constructed using the codes developed by the author before. The newly developed codes are tested out on many graphs containing large numbers of vertices. It is shown that some cyclic isospectral graphs are differentiated by their distance polynomials although distance polynomials themselves are in general not unique structural invariants.     

Compare-Conformer: a program for the rapid comparison of molecular conformers based on interatomic distances and torsion angles.

A computer program for comparison of the conformations of a number of related molecular structures is described. The comparisons are performed on either interatomic distances or torsion angles. The comparisons are accomplished on ordered pairs of distances or torsion angles, and the distance comparisons can be performed in a manner that allows permutation of the distance pairs being compared. The algorithm utilizes bit-string Boolean operations that allow the comparisons to be performed rapidly. The program should be useful for computer-assisted molecular modeling studies in which the viable conformers of bioactive analogues are compared in order to locate those conformers that place key substituents in the same spatial orientation.     

Improvements to the distance geometry algorithm for conformational sampling of cyclic structures

Modifications to the distance geometry algorithm as embodied in the program DGEOM have been made to improve sampling capabilities. Specifically, torsion angle sampling replaces distance sampling for 1,4 atomic relationships and correlated distance sampling is disabled. The effects of these modifications are illustrated by comparing the different sets of conformations produced for butane. In addition, these changes are shown to increase the conformational sampling of two medium-sized rings, cycloheptadecane and caprylolactam. The current results for these molecules are compared to those of other conformational searching methods.     

AGGREGATES: Finding structures in simulation results of solutions

Molecular Dynamic and Monte‐Carlo simulations are widely used to investigate the structure and physical properties of solids and liquids at a molecular level. Tools to extract the most relevant information from the obtained results are, however, in considerable demand. One such tool, the program AGGREGATES, is described in this work. Based on distance criteria, the program searches trajectory files for the presence of molecular clusters and computes several statistical and shape properties for these structures. Tools designed to investigate the local organization and the molecular conformations in the clusters are also available. Among these, it is introduced a new approach to perform a First Shell Analysis, by looking for the presence of atomic contacts between molecules. These elements are particularly useful to obtain information on molecular assembly processes (such as the nucleation of crystals or colloidal particles) or to investigate polymorphism in organic compounds. The program features are illustrated here through the investigation of the 4′‐hydroxyacetophenone + ethanol system. © 2017 Wiley Periodicals, Inc.     

任意多阶梯度场强毛细管凝胶电泳中谱带的迁移和展宽

在自行制备的毛细管凝胶电泳柱上，通过实验考察毛细管凝胶电泳（ＣＧＥ）中场强（Ｅ）和组分迁移率（μ）的关系，发现在一般ＣＧＥ使用的场强范围内，μ随Ｅ增大而成近似线性的增加。并讨论了产生这种现象的原因。以此为基础提供了任意多阶梯度场强毛细管凝胶电泳中组分的迁移时间和距离的计算公式，用于编制计算机程序。     

Vectorizing a general purpose molecular dynamics simulation program

A molecular dynamics program for arbitrary molecular mixtures is presented. All intramolecular degrees of freedom are treated explicitly, which means that the program is based on central forces only. A double time step technique has been devised in order to separate rapidly varying, covalent forces from slowly varying ones. Typically, the ratio between the different time steps is about 10, with only a minor computational effort spent in the evaluation of the covalent forces. The program source code is arranged so as to obtain maximal efficiency on a vector processor, while still being portable. On a Cray 1A, a typical simulation of an ion-chelate in aqueous solution with 984 atoms requires a total of 29 μs/interaction with a spherical cutoff distance of 10Å.     

Cluster analysis of molecular conformations

We describe a method for locating clusters of geometrically similar conformers in ensembles of chemical conformations. We first calculate the pairwise interconformational distance matrix in either torsional or Cartesian space and then use an agglomerative, single-link clustering method to define a hierarchy of clusterings in the same space. Especially good clusterings are distinguished by high values of the separation ratio: the ratio of the shortest intercluster distance to the characteristic threshold distance defining the clustering. We also discuss other statistics. The method has been embodied in a program called XCluster, which can display the distance matrix, the hierarchy of clusterings, and the clustering statistics in a variety of formats. XCluster can also write out the clustered conformations for subsequent or simultaneous viewing with a molecular visualization program. We demonstrate the sorts of insight that this approach affords with examples obtained from conformational search and molecular dynamics procedures. © 1994 by John Wiley & Sons, Inc.     

Systematic drug receptor mapping: A new approach to the analysis of conformational energy calculations of flexible molecules with application to dopaminergic and adrenergic agonists

The computer program PRODIS is used to find low energy conformations of flexible molecules by searching the potential energy surface(s) of one or more torsion angles via rigid rotation. The n-dimensional grid of energy versus torsion angles is then converted to a Boltzman probability distribution, with the probability being represented not as a function of torsion angle, but rather a distance between two atoms. These atoms are chosen by comparison with a known, active analogue in which certain atoms have previously been determined as requirements for drug activity. PRODIS produces a list of low energy conformations, their corresponding interatomic distances and the Boltzman probability for each distance ±0.125, as well as the total probability for each conformation. The user also specifies a target interatomic distance and range (usually derived from a more rigid analogue) for which PRODIS lists all conformations and their Boltzman probability that meet this distance.     

Software news and updates. Carma: a molecular dynamics analysis program

A computer program has been developed to aid the analysis of molecular dynamics trajectories. The program is tuned for macromolecular large-scale problems and supports features such as removal of global translations-rotations of the solute, calculation of average distance maps and their corresponding standard deviations, calculation of the variance-covariance and cross-correlation matrices, and principal component analysis of trajectories with the added ability to create artificial trajectories based on selected eigenvectors. Limited graphics (trajectory viewing) capabilities are also available.     

高效毛细管电泳紫外检测器光路的特殊性及其优化

紫外检测器用于高效毛细管电泳（ＨＰＣＥ）的主要难题在光路中,ＨＰＣＥ中熔融石英毛细管（内径通常在５０μｍ左右）直接放在光路中,一方面光程短,另一方面,光在透镜及毛细管界面上的折射与反射使光程常比毛细管内径短,甚至可能绕过毛细管内腔［１,２］．本文编制...     

3D hydrogen bond thermodynamics (HYBOT) potentials in molecular modelling

A new approach is proposed to more accurately estimate the energies of H-bond interactions in three-dimensional (3D) molecular modelling. The approach is based on the use of H-bond acceptor and donor enthalpy factor values calculated by means of program HYBOT, the use of a sigmoid relationship to determine the optimum H-bond distances and established force-field methods to determine distance and angle dependencies. The base-pair interactions in a short A-form RNA double-helix are presented as an example of enthalpy calculations of hydrogen bonding for a model system.     

Stereospecific assignments of protein NMR resonances based on the tertiary structure and 2D/3D NOE data

In many cases of protein structure determination by NMR a high-quality structure is required. An important contribution to structural precision is stereospecific assignment of magnetically nonequivalent prochiral methylene and methyl groups, eliminating the need for introducing pseudoatoms and pseudoatom corrections in distance restraint lists. Here, we introduce the stereospecific assignment program that uses the resonance assignment, a preliminary 3D structure and 2D and/or 3D nuclear Overhauser effect spectroscopy peak lists for stereospecific assignment. For each prochiral group the algorithm automatically calculates a score for the two different stereospecific assignment possibilities, taking into account the presence and intensity of the nuclear Overhauser effect (NOE) peaks that are expected from the local environment of each prochiral group (i.e., the close neighbors). The performance of the algorithm has been tested and used on NMR data of alpha-helical and beta-sheet proteins using homology models and/or X-ray structures. The program produced no erroneous stereospecific assignments provided the NOEs were carefully picked and the 3D model was sufficiently accurate. The set of NOE distance restraints produced by nmr2st using the results of the SSA module was superior in generating good-quality ensembles of NMR structures (low deviations from upper limits in conjunction with low root-mean-square-deviation values) in the first round of structure calculations. The program uses a novel approach that employs the entire 3D structure of the protein to obtain stereospecific assignment; it can be used to speed up the NMR structure refinement and to increase the quality of the final NMR ensemble even when no scalar or residual dipolar coupling information is available.     

Structural characterization of proteins with an attached ATCUN motif by paramagnetic relaxation enhancement NMR spectroscopy

The use of a short, three-residue Cu(2+)-binding sequence, the ATCUN motif, is presented as an approach for extracting long-range distance restraints from relaxation enhancement NMR spectroscopy. The ATCUN motif is prepended to the N-termini of proteins and binds Cu(2+) with a very high affinity. Relaxation rates of amide protons in ATCUN-tagged protein in the presence and absence of Cu(2+) can be converted into distance restraints and used for structure refinement by using a new routine, PMAG, that has been written for the structure calculation program CNS. The utility of the approach is demonstrated with an application to ATCUN-tagged ubiquitin. Excellent agreement between measured relaxation rates and those calculated on the basis of the X-ray structure of the protein have been obtained.     

稀土在土壤中运移数值模拟研究

９种不同性质土壤Ｃｅ和Ｎｄ吸附和度达５０％时，用同位素示踪法和数值模拟法对ＲＥ运移进行比较，发现两者对极大多数土壤有较好的拟合性。说明该数值模拟程序对预测稀土长期在土壤中运移具有一定的可靠性。预测结果表明，在自然降雨量情况下，ＲＥ吸附饱和度１０％时，在吸附容量小的酸性土壤中，ＲＥ下移约每年１ｃｍ，吸附容量中等的中性、策酸性土壤，每两年约下移１ｃｍ而吸附容量较大的碱性土壤，ＲＥ很难被雨水运移。     

Quality management education over the Internet

We describe a program for continuing education in Quality management and metrology. It may be followed by class lectures, by videoconference or by individual distance learning over the Internet. An important feature for students who attend classes is visits to selected institutions for demonstrations of quality management in practice. For students using distance learning, multimedia presentations containing a total of 2 h of video and supporting documentation is the alternative to the visits. The program is aimed at personnel from all fields, and its emphasis is on the generality of quality principles, attitudes and motivation for quality thinking, measurements in quality work, as well as the use of system audits and other elements of quality management in related fields.     

Continuous-time random walk models of DNA electrophoresis in a post array: part I. Evaluation of existing models

Several continuous-time random walk (CTRW) models exist to predict the dynamics of DNA in micropost arrays, but none of them quantitatively describes the separation seen in experiments or simulations. In Part I of this series, we examine the assumptions underlying these models by observing single molecules of λ DNA during electrophoresis in a regular, hexagonal array of oxidized silicon posts. Our analysis takes advantage of a combination of single-molecule videomicroscopy and previous Brownian dynamics simulations. Using a custom-tracking program, we automatically identify DNA-post collisions and thus study a large ensemble of events. Our results show that the hold-up time and the distance between collisions for consecutive collisions are uncorrelated. The distance between collisions is a random variable, but it can be smaller than the minimum value predicted by existing models of DNA transport in post arrays. The current CTRW models correctly predict the exponential decay in the probability density of the collision hold-up times, but they fail to account for the influence of finite-sized posts on short hold-up times. The shortcomings of the existing models identified here motivate the development of a new CTRW approach, which is presented in Part II of this series.     

Valeur moyenne du rayon solaire obtenue à l'observatoire de la Côte d'Azur (Astrolabe solaire du site de Calern: 1975–1998)

We propose a mean value for the solar radius based on by a program of visual observations and CCD measurements carried out at the Côte d'Azur Observatory between 1975 and 1998. The working assumption is that there are no variations in the semi-diameter. Over a set of more than 8 000 observations, the mean value amounts to 959.51 ± 0.01″ for a solar radius seen from a distance of 1 astronomical unit. As visual and CCD series are closely linked, the coherence of the results calls for some qualification of visual observations. Apparent variations of the solar radius recorded over more than 20 years will be addressed in a future note.