Home About us Contact
|
Home About us Contact | ||
|
|
||
New Computer Program (new + computer_program)
Selected AbstractsNovel computer program for fast exact calculation of accessible and molecular surface areas and average surface curvatureJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2002Oleg V. Tsodikov Abstract New computer programs, SurfRace and FastSurf, perform fast calculations of the solvent accessible and molecular (solvent excluded) surface areas of macromolecules. Program SurfRace also calculates the areas of cavities inaccessible from the outside. We introduce the definition of average curvature of molecular surface and calculate average molecular surface curvatures for each atom in a structure. All surface area and curvature calculations are analytic and therefore yield exact values of these quantities. High calculation speed of this software is achieved primarily by avoiding computationally expensive mathematical procedures wherever possible and by efficient handling of surface data structures. The programs are written initially in the language C for PCs running Windows 2000/98/NT, but their code is portable to other platforms with only minor changes in input-output procedures. The algorithm is robust and does not ignore either multiplicity or degeneracy of atomic overlaps. Fast, memory-efficient and robust execution make this software attractive for applications both in computationally expensive energy minimization algorithms, such as docking or molecular dynamics simulations, and in stand-alone surface area and curvature calculations. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 600,609, 2002 [source] Successive expansion method of network planning applying symbolic analysis methodEUROPEAN TRANSACTIONS ON ELECTRICAL POWER, Issue 4 2002kokljev The conventional power system network successive expansion planning method is discussed in the context of the new paradigm of competitive electric power, energy and service market. In sequel, the paper presents an application of the conceptually new computer program, based on the symbolic analysis of load flows in power system networks. The network parameters and variables are defined as symbols. The symbolic analyzer which models analytically the power system DC load flows enables the sensitivity analysis of the power system to parameter and variable variations (costs, transfers, injections), a valuable tool for the expansion planning analysis. That virtue could not be found within the conventional approach, relying on compensation methods, precalculated distribution factors, and so on. This novel application sheds some light on the traditional power system network expansion planning method, as well as on its possible application within the system network expansion planning in the new environment assuming the competitive electric power market. [source] Three-dimensional elastoplastic analysis by triple-reciprocity boundary element methodINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN BIOMEDICAL ENGINEERING, Issue 8 2007Yoshihiro Ochiai Abstract In general, internal cells are required to solve elastoplastic problems using a conventional boundary element method (BEM). However, in this case, the merit of BEM, which is ease of data preparation, is lost. Triple-reciprocity BEM can be used to solve two-dimensional elastoplasticity problems with a small plastic deformation. In this study, it is shown that three-dimensional elastoplastic problems can be solved, without the use of internal cells, by the triple-reciprocity BEM. An initial strain formulation is adopted and the initial strain distribution is interpolated using boundary integral equations. A new computer program was developed and applied to solving several problems. Copyright © 2006 John Wiley & Sons, Ltd. [source] Meshless thermo-elastoplastic analysis by triple-reciprocity boundary element methodINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 13 2010Yoshihiro OchiaiArticle first published online: 18 SEP 200 Abstract In general, internal cells are required to solve thermo-elastoplasticity problems by a conventional boundary element method (BEM). However, in this case, the merit of BEM, which is the easy preparation of data, is lost. A conventional multiple-reciprocity boundary element method (MRBEM) cannot be used to solve elastoplasticity problems, because the distribution of initial strain or stress cannot be determined analytically. In this study, it is shown that without the use of internal cells, two-dimensional thermo-elastoplasticity problems can be solved by a triple-reciprocity BEM using a thin plate spline. Initial strain and stress formulations are adopted and the initial strain or stress distribution is interpolated using boundary integral equations. A new computer program was developed and applied to solve several problems. Copyright © 2009 John Wiley & Sons, Ltd. [source] Axial symmetric elasticity analysis in non-homogeneous bodies under gravitational load by triple-reciprocity boundary element methodINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 7 2009Yoshihiro Ochiai Abstract In general, internal cells are required to solve elasticity problems by involving a gravitational load in non-homogeneous bodies with variable mass density when using a conventional boundary element method (BEM). Then, the effect of mesh reduction is not achieved and one of the main merits of the BEM, which is the simplicity of data preparation, is lost. In this study, it is shown that the domain cells can be avoided by using the triple-reciprocity BEM formulation, where the density of domain integral is expressed in terms of other fields that are represented by boundary densities and/or source densities at isolated interior points. Utilizing the rotational symmetry, the triple-reciprocity BEM formulation is developed for axially symmetric elasticity problems in non-homogeneous bodies under gravitational force. A new computer program was developed and applied to solve several test problems. Copyright © 2008 John Wiley & Sons, Ltd. [source] A practical large-strain solid finite element for sheet formingINTERNATIONAL JOURNAL FOR NUMERICAL METHODS IN ENGINEERING, Issue 4 2005Jue Wang Abstract An alternative approach for developing practical large-strain finite elements has been introduced and used to create a three-dimensional solid element that exhibits no locking or hourglassing, but which is more easily and reliably derived and implemented than typical reduced-integration schemes with hourglassing control. Typical large-strain elements for forming applications rely on reduced integration to remove locking modes that occur with the coarse meshes that are necessary for practical use. This procedure introduces spurious zero-energy deformation modes that lead to hourglassing, which in turn is controlled by complex implementations that involve lengthy derivations, knowledge of the material model, and/or undetermined parameters. Thus, for a new material or new computer program, implementation of such elements is a daunting task. Wang,Wagoner-3-dimensions (WW3D), a mixed, hexahedral, three-dimensional solid element, was derived from the standard linear brick element by ignoring the strain components corresponding to locking modes while maintaining full integration (8 Gauss points). Thus, WW3D is easily implemented for any material law, with little chance of programming error, starting from programming for a readily available linear brick element. Surprisingly, this approach and resulting element perform similarly or better than standard solid elements in a series of numerical tests appearing in the literature. The element was also tested successfully for an applied sheet-forming analysis problem. Many variations on the scheme are also possible for deriving special-purpose elements. Copyright © 2005 John Wiley & Sons, Ltd. [source] QUALX: a computer program for qualitative analysis using powder diffraction dataJOURNAL OF APPLIED CRYSTALLOGRAPHY, Issue 4 2008Angela Altomare QUALX is a new computer program for phase identification using powder diffraction data. It uses the Powder Diffraction File database, where a search for the phase best matching the experimental powder diffraction pattern is carried out. The program is characterized by a high level of automation: the traditional steps aimed at interpreting the experimental pattern before the search (background estimation, peak search, peak intensity evaluation) are executed automatically. The search may be carried out via constraints on compound name and/or chemical elements. In addition, several graphical options requested interactively enable the user to perform zero point correction evaluation, K,2 stripping and smoothing. The program, written in Fortran95 and C++, runs on PCs under the Windows XP operating system. It is supported by a very effective graphical interface. [source] How to multiply a matrix of normal equations by an arbitrary vector using FFTACTA CRYSTALLOGRAPHICA SECTION A, Issue 6 2008Boris V. Strokopytov This paper describes a novel algorithm for multiplying a matrix of normal equations by an arbitrary real vector using the fast Fourier transform technique. The algorithm allows full-matrix least-squares refinement of macromolecular structures without explicit calculation of the normal matrix. The resulting equations have been implemented in a new computer program, FMLSQ. A preliminary version of the program has been tested on several protein structures. The consequences for crystallographic refinement of macromolecules are discussed in detail. [source] Time-series photometric spot modelling , VI.ASTRONOMISCHE NACHRICHTEN, Issue 3 2003A new computer code, its application to 23 years of photometry of the active giant IM Pegasi Abstract We present and apply a new computer program named SpotModeL to analyze single and multiple bandpass photometric data of spotted stars. It is based on the standard analytical formulae from Budding and Dorren. The program determines the position, size, and temperature of up to three spots by minimizing the fit residuals with the help of the Marquardt-Levenberg non-linear least-squares algorithm. We also expand this procedure to full time-series analysis of differential data, just as real observations would deliver. If multi-bandpass data are available, all bandpasses can be treated simultaneously and thus the spot temperature is solved for implicitly. The program may be downloaded and used by anyone. In this paper, we apply our code to an ,23 year long photometric dataset of the spotted RS CVn giant IM Peg. We extracted and modelled 33 individual light curves, additionally, we fitted the entire V dataset in one run. The resulting spot parameters reflect the long term light variability and reveal two active longitudes on the substellar point and on the antipode. The radius and longitude of the dominant spot show variations with 29.8 and 10.4 years period, respectively. Our multicolour data suggests that the spot temperature is increasing with the brightening of the star. The average spot temperature from V, IC is 3550 ± 150 K or approximately 900 K below the effective temperature of the star. [source] Angiosperm phylogeny inferred from 18S rDNA, vbcL, and atpB sequencesBOTANICAL JOURNAL OF THE LINNEAN SOCIETY, Issue 4 2000DOUGLAS E. SOLTIS A phylogenetic analysis of a combined data set for 560 angiosperms and seven outgroups based on three genes, 18S rDNA (1855 bp), rbcL (1428 bp), and atpB (1450 bp) representing a total of 4733 bp is presented. Parsimony analysis was expedited by use of a new computer program, the RATCHET. Parsimony jackknifing was performed to assess the support of clades. The combination of three data sets for numerous species has resulted in the most highly resolved and strongly supported topology yet obtained for angiosperms. In contrast to previous analyses based on single genes, much of the spine of the tree and most of the larger clades receive jackknife support 250%. Some of the noneudicots form a grade followed by a strongly supported eudicot clade. The early-branching angiosperms are Amborellaceae, Nymphaeaceae, and a clade of Austrobaileyaceae, Illiciaceae, and Schi-sandraceae. The remaining noneudicots, except Ceratophyllaceae, form a weakly supported core eumagnoliid clade comprising six well-supported subclades: Chloranthaceae, monocots, WinteraceaeICanellaceae, Piperales, Laurales, and Magnoliales. Ceratophyllaceae are sister to the eudicots. Within the well-supported eudicot clade, the early-diverging eudicots (e.g. Proteales, Ranunculales, Trochodendraceae, Sabiaceae) form a grade, followed by the core eudicots, the monophyly of which is also strongly supported. The core eudicots comprise six well-supported subclades: (1) Berberidopsidaceae/Aextoxicaceae; (2) Myrothamnaceae/ Gunneraceae; (3) Saxifragales, which are the sister to Vitaceae (including Leea) plus a strongly supported eurosid clade; (4) Santalales; (5) Caryophyllales, to which Dilleniaceae are sister; and (6) an asterid clade. The relationships among these six subclades of core eudicots do not receive strong support. This large data set has also helped place a number of enigmatic angiosperm families, including Podostemaceae, Aphloiaceae, and Ixerbaceae. This analysis further illustrates the tractability of large data sets and supports a recent, phylogenetically based, ordinal-level reclassification of the angiosperms based largely, but not exclusively, on molecular (DNA sequence) data. [source] Analyzing digital vector waveforms of 0,3000,Hz magnetic fields for health studies,BIOELECTROMAGNETICS, Issue 5 2010Joseph D. Bowman Abstract To improve the assessment of magnetic field exposures for occupational health studies, the Multiwave® System III (MW3) was developed to capture personal exposures to the three-dimensional magnetic field vector B(t) in the 0,3000,Hz band. To process hundreds of full-shift MW3 measurements from epidemiologic studies, new computer programs were developed to calculate the magnetic field's physical properties and its interaction with biological systems through various mechanisms (magnetic induction, radical pair interactions, ion resonance, etc.). For automated calculations in the frequency domain, the software uses new algorithms that remove artifacts in the magnetic field's Fourier transform due to electronic noise and the person's motion through perturbations in the geomagnetic field from steel objects. These algorithms correctly removed the Fourier transform artifacts in 92% of samples and have improved the accuracy of frequency-dependent metrics by as much as 3300%. The output of the MwBatch software is a matrix of 41 exposure metrics calculated for each 2/15,s sample combined with 8 summary metrics for the person's full-period exposure, giving 294 summary-exposure metrics for each person monitored. In addition, the MwVisualizer software graphically explores the magnetic field's vector trace, its component waveforms, and the metrics over time. The output was validated against spreadsheet calculations with pilot data. This software successfully analyzed full-shift MW3 monitoring with 507 electric utility workers, comprising over 1 million vector waveforms. The software's output can be used to test hypotheses about magnetic field biology and disease with biophysical models and also assess compliance with exposure limits. Bioelectromagnetics 31:391,405, 2010. © 2010 Wiley-Liss, Inc. [source] | ||||||||||||||||