Identifying aspirin polymorphs from combined DFT-based crystal structure prediction and solid-state NMR

A combined experimental and computational approach was used to distinguish between different polymorphs of the pharmaceutical drug aspirin. This method involves the use of ab initio random structure searching (AIRSS), a density functional theory (DFT)-based crystal structure prediction method for the high-accuracy prediction of polymorphic structures, with DFT calculations of nuclear magnetic resonance (NMR) parameters and solid-state NMR experiments at natural abundance. AIRSS was used to predict the crystal structures of form-I and form-II of aspirin. The root-mean-square deviation between experimental and calculated ¹H chemical shifts was used to identify form-I as the polymorph present in the experimental sample, the selection being successful despite the large similarities between the molecular environments in the crystals of the two polymorphs.     

3-D vertical ray shooting and 2-D point enclosure, range searching, and arc shooting amidst convex fat objects

We present a new data structure for a set of n convex simply-shaped fat objects in the plane, and use it to obtain efficient and rather simple solutions to several problems including (i) vertical ray shooting—preprocess a set of n non-intersecting convex simply-shaped flat objects in 3-space, whose xy-projections are fat, for efficient vertical ray shooting queries, (ii) point enclosure—preprocess a set C of n convex simply-shaped fat objects in the plane, so that the k objects containing a query point p can be reported efficiently, (iii) bounded-size range searching— preprocess a set C of n convex fat polygons, so that the k objects intersecting a “not-too-large” query polygon can be reported efficiently, and (iv) bounded-size segment shooting—preprocess a set C as in (iii), so that the first object (if exists) hit by a “not-too-long” oriented query segment can be found efficiently. For the first three problems we construct data structures of size O(λ_s(n)log³n), where s is the maximum number of intersections between the boundaries of the (xy-projections) of any pair of objects, and λ_s(n) is the maximum length of (n, s) Davenport-Schinzel sequences. The data structure for the fourth problem is of size O(λ_s(n)log²n). The query time in the first problem is O(log⁴n), the query time in the second and third problems is O(log³n + klog²n), and the query time in the fourth problem is O(log³n).

We also present a simple algorithm for computing a depth order for a set as in (i), that is based on the solution to the vertical ray shooting problem. (A depth order for , if exists, is a linear order of , such that, if K₁, K₂ and K₁ lies vertically above K₂, then K₁ precedes K₂.) Unlike the algorithm of Agarwal et al. (1995) that might output a false order when a depth order does not exist, the new algorithm is able to determine whether such an order exists, and it is often more efficient in practical situations than the former algorithm.     

A note on the unsteady boundary layers over a flat plate

The unsteady boundary layer over a semi-infinite flat plate was investigated in this paper. The flow involves the unsteady flow over a flat plate with leading edge accretion or ablation. The momentum boundary layer was further analyzed and it was shown that the leading edge ablation had a similar effect to the wall mass injection or upstream wall movement making the fluid blown away from the wall. The thermal boundary layer of the same flow was also studied. Results show that the leading edge accretion or ablation can greatly change the fluid motion and the heat transfer characteristics.     

Manufacturing cell formation using similarity coefficients and a parallel genetic TSP algorithm: Formulation and comparison

Many algorithms have been proposed to form manufacturing cells from component routings. However, many of these do not have the capability of solving large problems. We propose a procedure using similarity coefficients and a parallel genetic implementation of a TSP algorithm that is capable of solving large problems of up to 1000 parts and 1000 machines. In addition, we also compare our procedure with many existing procedures using nine well-known problems from the literature.

The results show that the proposed procedure compares well with the existing procedures and should be useful to practitioners and researchers.     

A competitive algorithm in searching for many edges in a hypergraph

We give a competitive algorithm to identify all d defective edges in a hypergraph with d unknown. Damaschke did the d=1 case for 2-graphs, Triesch extended the d=1 case to r-graphs, and Johann did the general d case for 2-graphs. So ours is the first attempt to solve the searching for defective edges problem in its full generality. Further, all the above three papers assumed d known. We give a competitive algorithm where d is unknown.     

Scaling impacted structures

Summary The problem of non-scalability of structures under impact loads caused by strain-rate effects is solved in this article by properly correcting the impact velocity. The technique relies on the use of an alternative dimensionless basis, together with a mathematical model which allows the calculation of a correction factor for the impact velocity. This new velocity, when applied to the model, makes it to assure the satisfaction of the scaling laws. The indirect similitude method detailed here is applied to two strain-rate sensitive structures, a double plate under in-plane impact and a beam subjected to a blast load. The results show a very good agreement so that the model and a prototype made from strain rate sensitive materials behave the same.accepted for publication 3 March 2004     

On similarity and scaling of the radiative transfer equation

The present paper shows how the well-known similarity and scaling concepts are properties of the radiative transfer equation and not specifically of the degree of anisotropy of the phase function. It is shown that the key assumption regarding the angular dependence of the radiative field is essential in determining both the value for the parameter used to scale the radiative transfer, as well as the number of streams used in calculating the radiances for various atmospheric problems. Simulations performed on realistic type of cirrus clouds, characterized by strongly anisotropic functions, demonstrates the superior computational advantage for accurately simulating radiances. A new approach for determining the scaling parameter is introduced.     

MENTHOR,a database system for the storage and retrieval of three-dimensional molecular structures and associated data searchable by substructural,biologic, physical,or geometric properties

Summary MENTHOR is a database system for the storage and retrieval of three-dimensional coordinate and charge information on molecules as well as of traditional biological and physical properties. Our molecular graphics system retrieves from MENTHOR structural information in individual molecules and receptor map/macromolecular binding site hypotheses. Substructural searches of MENTHOR are used to find starting coordinates for molecular modeling and traditional database searches of MENTHOR identify compounds for which modeling is needed. It also forms the data to be searched with ALLADDIN, our substructure/geometric search program. MENTHOR expedites molecular modeling by organizing previous work and facilitating transmission of information between individuals. Examples from modeling of D-2 receptor agonists are shown.     

Application of similarity aggregation techniques to a population of paraplegic patients

We studied a population of paraplegic patients in order to give prominence to a possible relationship between the topography of their spinal lesion and the occurrence of special articular diseases (P.O.A.). According to the motor and sensory state of their spinal cord, we first tried to obtain a classification of these lesions (the usual one schematically separates ‘flaccid’ and ‘rigid’ paraplegics). We mainly put the emphasis on this clustering step of the study:

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Study of spectral analytical data using fingerprints and scaled similarity measurements

A new chemoinformatic model has been developed for enlarging the differences between spectra and applied to differentiation of wines according to the criteria grape origin and variety and ageing process. The model is based on generation of fingerprints from normalised spectra, using empirical parameters and a set of 120 samples. After generation of the fingerprints, similarity matrixes were built on the basis of the Tanimoto similarity index between the fingerprints of the samples. Calculation of the Tanimoto index was modified to adapt the index to the characteristics of the analytical measurements. Thus, scaling factors taking into account pattern fingerprints generated from a group of samples with common characteristics were used. In addition, a modified expression for calculating the Tanimoto index was employed. Principal-components analysis (PCA) and soft independent modelling of class analogy (SIMCA) were applied to the similarity matrixes. The results obtained are discussed as a function of the normalisation method employed, the empirical factor used in generation of the fingerprints, and selection of samples for building the pattern fingerprint, etc. Finally, results from differentiation of wines are compared with those obtained by applying PCA to the unprocessed spectra as stated by the proposed model.