Akademik Çıktılar

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Citation - WoS: 4
Citation - Scopus: 4
Convergence analysis and numerical solution of the benjamin-bona-mahony equation by lie-trotter splitting
(Tubitak Scientific & Technological Research Council Turkey, 2018) Zurnaci, Fatma; Gucuyenen Kaymak, Nurcan; Seydaoglu, Muaz; Tanoglu, Gamze
In this paper, an operator splitting method is used to analyze nonlinear Benjamin-Bona-Mahony-type equations. We split the equation into an unbounded linear part and a bounded nonlinear part and then Lie-Trotter splitting is applied to the equation. The local error bounds are obtained by using the approach based on the differential theory of operators in a Banach space and the quadrature error estimates via Lie commutator bounds. The global error estimate is obtained via Lady Windermere's fan argument. Finally, to confirm the expected convergence order, numerical examples are studied.
Citation - WoS: 73
Evidence for water-tuned structural differences in proteins: an approach emphasizing variations inlocal hydrophilicity
(Public Library Science, 2012) Akdogan, Yasar; Reichenwallner, Joerg; Hinderberger, Dariush
We present experimental evidence for the significant effect that water can have on the functional structure of proteins in solution. Human (HSA) and Bovine Serum Albumin (BSA) have an amino acid sequence identity of 75.52% and are chosen as model proteins. We employ EPR-based nanoscale distance measurements using double electron-electron resonance (DEER) spectroscopy and both albumins loaded with long chain fatty acids (FAs) in solution to globally (yet indirectly) characterize the tertiary protein structures from the bound ligands' points of view. The complete primary structures and crystal structures of HSA and as of recently also BSA are available. We complement the picture as we have recently determined the DEER-derived solution structure of HSA and here present the corresponding BSA solution structure. The characteristic asymmetric FA distribution in the crystal structure of HSA can surprisingly be observed by DEER in BSA in solution. This indicates that the BSA conformational ensemble in solution seems to be narrow and close to the crystal structure of HSA. In contrast, for HSA in solution a much more symmetric FA distribution was found. Thus, conformational adaptability and flexibility dominate in the HSA solution structure while BSA seems to lack these properties. We further show that differences in amino acid hydropathies of specific structural regions in both proteins can be used to correlate the observed difference in the global (tertiary) solution structures with the differences on the primary structure level.

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