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At least 415 records · Page 23Linked to original sources
PubMed1987

An optimized computational method for determining the beta dose distribution using a multiple-element thermoluminescent dosimeter system.

This paper describes an optimization method for determining the beta dose distribution in tissue, and it describes the associated testing and verification. The method uses electron transport theory and optimization techniques to analyze the responses of a three-element thermoluminescent dosimeter (TLD) system. Specifically, the method determines the effective beta energy distribution incident on the dosimeter system, and thus the system performs as a beta spectrometer. Electron transport theory provides the mathematical model for performing the optimization calculation. In this calculation, parameters are determined that produce calculated doses for each of the chip/absorber components in the three-element TLD system. The resulting optimized parameters describe an effective incident beta distribution. This method can be used to determine the beta dose specifically at 7 mg X cm-2 or at any depth of interest. The doses at 7 mg X cm-2 in tissue determined by this method are compared to those experimentally determined using an extrapolation chamber. For a great variety of pure beta sources having different incident beta energy distributions, good agreement is found. The results are also compared to those produced by a commonly used empirical algorithm. Although the optimization method produces somewhat better results, the advantage of the optimization method is that its performance is not sensitive to the specific method of calibration.

Algorithms↗
PubMed1985

Long bone torsion: II. A combined experimental and computational method for determining an effective shear modulus.

A technique is established which allows an effective torsional shear modulus to be determined for long bones, while remaining nondestructive to whole bone specimens. Strain gages are bonded to the diaphysis of the bone. Strains are then recorded under pure torsional loads. Theoretical stress predictions are combined with experimental strain recordings to arrive at a modulus value. Shear modulus calculations for four canine radii are reported using theoretical stress predictions from circular, elliptical and finite element models of the transverse bone geometry. The effective shear modulus, obtained from an average of the shear moduli determined at strain gage locations, serves to average the heterogeneous shear modulus distribution over the cross section. The shear modulus obtained is that associated with the "circumferential" direction in transverse planes.

Animals↗
PubMed2002

Computational aeroacoustics of phonation, part I: Computational methods and sound generation mechanisms.

The aerodynamic generation of sound during phonation was studied using direct numerical simulations of the airflow and the sound field in a rigid pipe with a modulated orifice. Forced oscillations with an imposed wall motion were considered, neglecting fluid-structure interactions. The compressible, two-dimensional, axisymmetric form of the Navier-Stokes equations were numerically integrated using highly accurate finite difference methods. A moving grid was used to model the effects of the moving walls. The geometry and flow conditions were selected to approximate the flow within an idealized human glottis and vocal tract during phonation. Direct simulations of the flow and farfield sound were performed for several wall motion programs, and flow conditions. An acoustic analogy based on the Ffowcs Williams-Hawkings equation was then used to decompose the acoustic source into its monopole, dipole, and quadrupole contributions for analysis. The predictions of the farfield acoustic pressure using the acoustic analogy were in excellent agreement with results from the direct numerical simulations. It was found that the dominant sound production mechanism was a dipole induced by the net force exerted by the surfaces of the glottis walls on the fluid along the direction of sound wave propagation. A monopole mechanism, specifically sound from the volume of fluid displaced by the wall motion, was found to be comparatively weak at the frequency considered (125 Hz). The orifice geometry was found to have only a weak influence on the amplitude of the radiated sound.

Acoustics↗
PubMed2003

X-ray-induced DNA double-strand breaks in mouse l1210 cells: a new computational method for analyzing neutral filter elution data.

The aim of this article is to present a method for studying the shape of the dose and repair responses for X-ray-induced double-strand breaks (DSBs) as measured by neutral filter elution (NFE). The approach is closely related to a method we developed for the use of specific molecular size markers and used for determination of the absolute number of randomly distributed radiation-induced DSBs by pulsed-field gel electrophoresis (PFGE). Mouse leukemia L1210 cells were X-irradiated with 0-50 Gy. Samples were then evaluated both with PFGE and with NFE. Assuming that with both migration (PFGE) and elution (NFE), a heterogeneous population of double-stranded DNA fragments will start with the smallest fragments and proceed with increasingly larger fragments, it is possible to match the migration behavior of fractions of fragments smaller than a certain size to the fraction eluted at a specific time. This assumption does not exclude the possibility of DNA being sheared in the NFE filter. The yield, as determined by the size markers in PFGE, was used to find the corresponding elution times in the NFE experiment. These experimentally used elution times could then reversely be interpreted as size markers which finally were used to calculate DSBs/Mbp as a function of X-ray dose. The resulting lines were almost straight. The data were also plotted as relative elution and showed that, as expected, the dose response then appears with a more pronounced sigmoid shape.

Animals↗
PubMed2000

A novel computational method for predicting the transmembrane structure of G-protein coupled receptors: application to human C5aR and C3aR.

A novel algorithm was applied to the sequences of bacteriorhodopsin (BRh), of rhodopsin (Rh), and of the two human anaphylatoxin receptors, C5a-receptor (hC5aR) and C3a-receptor (hC3aR), that predicts their transmembrane domains (TMD) according to energy criteria alone, on the basis of their sequences and a template structure for each. Two consecutive criteria were applied for the predictions: the first is hydrophobicity of a sequence of residues, which determines the candidate stretches of residues that form one of the transmembrane helices. The second criterion is an energy function composed of inter residue contact energies, of hydrophobic contributions due to membrane exposure and of the interactions of a few residues with the phospholipid head groups. The sequence of candidate residues for each helix is longer than that of the template, and is finally determined by threading each of the candidate stretches on each of the template helices and evaluating the energy for all possible configurations. Contact energies between residues were taken from a database (Miyazawa S and Jernigan RL (1996) J Mol Biol 256 623-44). The algorithm predicts well the TMD structure of BRh based on its own template, and the TMD structure of Rh conforms well with the model of Baldwin et al (Baldwin JM Schertler GFX and Unger VM (1997) J Biol Chem 272 144-64). Results for the construction of the TMD of hC5aR and hC3aR were compared, employing the template structure of Rh. Most of the results for these receptors are in accord with alignments and with mutation experiments on hC5aR and hC3aR. The predictions may serve as a basis for future mutagenesis experiments of these receptors.

Algorithms↗
PubMed2001

Rational procedure for 3D-QSAR analysis using TRNOE experiments and computational methods: application to thermolysin inhibitors.

The success or failure of 3D QSAR, particularly CoMFA, is most strongly dependent, especially for flexible compounds, on the conformation of the molecule used in the analysis, and on the orientation of the molecule relative to the other molecules in 3D space (i.e., alignment). The present study suggests a rational procedure for the estimation of binding conformation that uses the transferred nuclear Overhauser effect (TRNOE) experiment in combination with conformational analysis using CAMDAS (Conformational Analyzer with Molecular Dynamics And Sampling) program that is developed in our laboratory. In the next step the TRNOE-obtained conformation can be used as a reference template in order to obtain alignment of other ligands, that have a common binding site. In this step we used the SUPERPOSE program created in our laboratory, in order to estimate the binding conformation of other compounds, and to simultaneously obtain the alignment of compounds for CoMFA. The resulting CoMFA models could be expected to closely reproduce the interaction mode with protein represented by the reported X-ray results. In order to confirm the validity of our procedure described above, we show its application in obtaining CoMFA models of thermolysin inhibitors. We obtained twenty CoMFA models, and that with the highest q2 value (q2 = 0.701) was found to provide an interaction mode very similar to that represented by the X-ray results.

Molecular Conformation↗