Physics of Particles and Nuclei Letters

, Volume 5, Issue 3, pp 189-195

First online:

Scaling laws and memory effects in the dynamics of liquids and proteins

  • G. R. KnellerAffiliated withCentre de Biophysique Moléculaire, CNRSSynchrotron Soleil, L’Orme de Merisiers Email author 
  • , K. HinsenAffiliated withCentre de Biophysique Moléculaire, CNRSSynchrotron Soleil, L’Orme de Merisiers
  • , G. SutmannAffiliated withCentral Institute for Applied Mathematics (ZAM) and John von Neumann Institute for Computing (NIC), Research Centre Jülich
  • , V. CalandriniAffiliated withInstitut Laue-Langevin

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Recent progress in the numerical calculation of memory functions from molecular dynamics simulations allowed the gaining of deeper insight into the relaxation dynamics of liquids and proteins. The concept of memory functions goes back to the work of R. Zwanzig on the generalized Langevin equation, and it was the basis for the development of various dynamical models for liquids. In this article we present briefly a method for the numerical calculation of memory functions, which is then applied to study their scaling behavior in normal and fractional Brownian dynamics. It has been shown recently that the model of fractional Brownian dynamics constitutes effectively a link between protein dynamics on the nanosecond time scale, which is accessible to molecular dynamics simulations and thermal neutron scattering, and the much longer time scale of functional protein dynamics, which can be studied by fluorescence correlation spectroscopy.

PACS numbers

02.60.Cb 32.20.-r 85.35.Lr