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Florian Göltl, Jürgen Hafner
The importance of dispersion forces for the correct description of the adsorption of short alkanes in Na-exchanged and purely siliceous chabazite has been investigated at different levels of theory: (i) standard density-functional (DFT) calculations using the Perdew, Burke, and Ernzerhof (PBE) exchange-correlation functional in the generalized gradient approximation, (ii) dispersion corrections based on empirical force fields according to Grimme [J. Computat. Chem. 134, 1463 (2004)- PBE-d], (iii) calculations based on the van der Waals density functional (vdW-DF) proposed by Dion et al...
February 14, 2011: Journal of Chemical Physics
B Das, H Meirovitch, I M Navon
Energy minimization plays an important role in structure determination and analysis of proteins, peptides, and other organic molecules; therefore, development of efficient minimization algorithms is important. Recently, Morales and Nocedal developed hybrid methods for large-scale unconstrained optimization that interlace iterations of the limited-memory BFGS method (L-BFGS) and the Hessian-free Newton method (Computat Opt Appl 2002, 21, 143-154). We test the performance of this approach as compared to those of the L-BFGS algorithm of Liu and Nocedal and the truncated Newton (TN) with automatic preconditioner of Nash, as applied to the protein bovine pancreatic trypsin inhibitor (BPTI) and a loop of the protein ribonuclease A...
July 30, 2003: Journal of Computational Chemistry
S Matis, Y Xu, M Shah, X Guan, J R Einstein, R Mural, E Uberbacher
Detection of RNA polymerase II promoters and polyadenylation sites helps to locate gene boundaries and can enhance accurate gene recognition and modeling in genomic DNA sequence. We describe a system which can be used to detect polyadenylation sites and thus delineate the 3' boundary of a gene, and discuss improvements to a system first described in Matis et al. (1995) [Matis S., Shah M., Mural R. J. & Uberbacher E.C. (1995) Proc. First Wrld Conf. Computat. Med., Public Hlth, Biotechnol. (Wrld Sci.) (in press)...
March 1996: Computers & Chemistry
M Lech, M Sanecki
No abstract text is available yet for this article.
July 1972: Ginekologia Polska
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