Browsing by Subject "Structural dynamics"

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    Cryogenic X-ray crystallographic studies of biomacromolecules at Turkish light source "Turkish DeLight"
    (TÜBİTAK, 2023-01-01) Atalay, N.; Akcan, E. K.; Gül, M.; Ayan, E.; Destan, E.; Ertem, F. B.; Tokay, N.; Çakılkaya, B.; Nergiz, Z.; Karakadıoğlu, G.; Kepçeoğlu, A.; Yapıcı, İ.; Tosun, B.; Baldır, N.; Yıldırım, G.; Johnson, J. A.; Güven, Ö.; Shafiei, A.; Arslan, N. E.; Yılmaz, M.; Kulakman, C.; Paydos, S. S.; Çinal, Zeynep Sena; Şabanoğlu, K.; Pazarçeviren, A.; Yılmaz, A.; Canbay, B.; Aşcı, B.; Kartal, E.; Tavlı, S.; Çalıseki, M.; Göç, G.; Mermer, A.; Yeşilay, G.; Altuntaş, S.; Tateishi, H.; Otsuka, M.; Fujita, M.; Tekin, Ş.; Çiftçi, H.; Durdağı, S.; Dinler Doğanay, G.; Karaca, E.; Kaplan Türköz, B.; Kabasakal, B. V.; Katı, A.; Demirci, H.
    X-ray crystallography is a robust and powerful structural biology technique that provides high-resolution atomic structures of biomacromolecules. Scientists use this technique to unravel mechanistic and structural details of biological macromolecules (e.g., proteins, nucleic acids, protein complexes, protein-nucleic acid complexes, or large biological compartments). Since its inception, single-crystal cryocrystallography has never been performed in Türkiye due to the lack of a single-crystal X-ray diffractometer. The X-ray diffraction facility recently established at the University of Health Sciences, İstanbul, Türkiye will enable Turkish and international researchers to easily perform high-resolution structural analysis of biomacromolecules from single crystals. Here, we describe the technical and practical outlook of a state-of-the-art home-source X-ray, using lysozyme as a model protein. The methods and practice described in this article can be applied to any biological sample for structural studies. Therefore, this article will be a valuable practical guide from sample preparation to data analysis.
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    Uncertainty and dissipation
    (Katholieke Universiteit Leuven, 2012-09) Carcaterra, A.; Akay, Adnan
    This paper discusses the question of the energy confinement in mechanical structures in the light of the uncertainties affecting the natural frequencies of the system. More precisely, recent studies have shown that energy can be introduced to a linear system with near irreversibility, or energy within a system can migrate to a subsystem nearly irreversibly, even in the absence of dissipation, provided that the system has a particular natural frequency distribution. In this paper, the case of uncertainties in the system's natural frequencies is discussed and a remarkable statistical property of the natural frequency is derived for permanent energy confinement within a part of the system. The results demonstrate the existence of a special class of linear non-dissipative dynamic systems that exhibit nearly-irreversible energy confinement (IEC) if they satisfy a minimum-variance-response (MIVAR) property. In this case, if the probability density function of the natural frequencies has a special distribution, the conservative system shows an unexpected decaying impulse response. © (2012) by the Katholieke Universiteit Leuven Department of Mechanical Engineering All rights reserved.