Dynamic Complexity of Chaotic Transitions in High-Dimensional Classical Dynamics: Leu-Enkephalin Folding

@incollection{citeulike:2573813, abstract = {Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A β-turn transition is investigated by calculating the topological complexity (in the “computational mechanics” framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the β-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a “quasi-regular” dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. Keywords: folding, enkephalin, dynamic complexity, computational mechanics.}, author = {Nerukh, Dmitry and Karvounis, George and Glen, Robert }, citeulike-article-id = {2573813}, doi = {http://dx.doi.org/10.1007/11875741\_13}, journal = {Computational Life Sciences II}, keywords = {complexity-measure-applications, computational-mechanics}, pages = {129--140}, posted-at = {2008-03-23 06:59:31}, priority = {2}, title = {Dynamic Complexity of Chaotic Transitions in High-Dimensional Classical Dynamics: Leu-Enkephalin Folding}, url = {http://dx.doi.org/10.1007/11875741\_13}, year = {2006} }

TY - CHAP ID - citeulike:2573813 L3 - citeulike-article-id:2573813 TI - Dynamic Complexity of Chaotic Transitions in High-Dimensional Classical Dynamics: Leu-Enkephalin Folding JF - Computational Life Sciences II SP - 129 EP - 140 N2 - Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A β-turn transition is investigated by calculating the topological complexity (in the “computational mechanics” framework [J. P. Crutchfield and K. Young, Phys. Rev. Lett., 63, 105 (1989)]) of the dynamics of both the peptide and the neighbouring water molecules. The complexity of the atomic trajectories of the (relatively short) simulations used in this study reflect the degree of phase space mixing in the system. It is demonstrated that the dynamic complexity of the hydrogen atoms of the peptide and almost all of the hydrogens of the neighbouring waters exhibit a minimum precisely at the moment of the β-turn transition. This indicates the appearance of simplified periodic patterns in the atomic motion, which could correspond to high-dimensional tori in the phase space. It is hypothesized that this behaviour is the manifestation of the effect described in the approach to molecular transitions by Komatsuzaki and Berry [T. Komatsuzaki and R.S. Berry, Adv. Chem. Phys., 123, 79 (2002)], where a “quasi-regular” dynamics at the transition is suggested. Therefore, for the first time, the less chaotic character of the folding transition in a realistic molecular system is demonstrated. Keywords: folding, enkephalin, dynamic complexity, computational mechanics. KW - complexity-measure-applications KW - computational-mechanics AU - Nerukh, Dmitry AU - Karvounis, George AU - Glen, Robert PY - 2006/// UR - http://dx.doi.org/10.1007/11875741_13 ER -