Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: Leu-Enkephalin folding

Dmitry Nerukh, George Karvounis, Robert C. Glen

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-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 ß-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.
Original languageEnglish
Title of host publicationComputational life sciences II
Subtitle of host publicationsecond international symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006. Proceedings
EditorsMichael R. Berthold, Robert C. Glen, Ingrid Fischer
Place of PublicationBerlin (DE)
PublisherSpringer
Pages129-140
Number of pages12
ISBN (Electronic)978-3-540-45768-8
ISBN (Print)978-3-540-45767-1
DOIs
Publication statusPublished - 2006
Event2nd International Symposium on Computational Life sciences - Cambridge, United Kingdom
Duration: 27 Sep 200629 Sep 2006

Publication series

NameLecture notes in computer science
PublisherSpringer
Volume4216
ISSN (Print)0302-9743
ISSN (Electronic)1611-3349

Symposium

Symposium2nd International Symposium on Computational Life sciences
Abbreviated titleCompLife 2006
CountryUnited Kingdom
CityCambridge
Period27/09/0629/09/06

Fingerprint

folding
peptides
computational mechanics
water
hydrogen atoms
trajectories
molecular dynamics
moments
hydrogen
molecules
simulation

Keywords

  • folding
  • enkephalin
  • dynamic complexity
  • computational mechanics

Cite this

Nerukh, D., Karvounis, G., & Glen, R. C. (2006). Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: Leu-Enkephalin folding. In M. R. Berthold, R. C. Glen, & I. Fischer (Eds.), Computational life sciences II: second international symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006. Proceedings (pp. 129-140). (Lecture notes in computer science; Vol. 4216). Berlin (DE): Springer. https://doi.org/10.1007/11875741_13
Nerukh, Dmitry ; Karvounis, George ; Glen, Robert C. / Dynamic complexity of chaotic transitions in high-dimensional classical dynamics : Leu-Enkephalin folding. Computational life sciences II: second international symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006. Proceedings. editor / Michael R. Berthold ; Robert C. Glen ; Ingrid Fischer. Berlin (DE) : Springer, 2006. pp. 129-140 (Lecture notes in computer science).
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abstract = "Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A {\ss}-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 {\ss}-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.",
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Nerukh, D, Karvounis, G & Glen, RC 2006, Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: Leu-Enkephalin folding. in MR Berthold, RC Glen & I Fischer (eds), Computational life sciences II: second international symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006. Proceedings. Lecture notes in computer science, vol. 4216, Springer, Berlin (DE), pp. 129-140, 2nd International Symposium on Computational Life sciences, Cambridge, United Kingdom, 27/09/06. https://doi.org/10.1007/11875741_13

Dynamic complexity of chaotic transitions in high-dimensional classical dynamics : Leu-Enkephalin folding. / Nerukh, Dmitry; Karvounis, George; Glen, Robert C.

Computational life sciences II: second international symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006. Proceedings. ed. / Michael R. Berthold; Robert C. Glen; Ingrid Fischer. Berlin (DE) : Springer, 2006. p. 129-140 (Lecture notes in computer science; Vol. 4216).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

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AB - Leu-Enkephalin in explicit water is simulated using classical molecular dynamics. A ß-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 ß-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.

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Nerukh D, Karvounis G, Glen RC. Dynamic complexity of chaotic transitions in high-dimensional classical dynamics: Leu-Enkephalin folding. In Berthold MR, Glen RC, Fischer I, editors, Computational life sciences II: second international symposium, CompLife 2006, Cambridge, UK, September 27-29, 2006. Proceedings. Berlin (DE): Springer. 2006. p. 129-140. (Lecture notes in computer science). https://doi.org/10.1007/11875741_13