Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling

Yi, Zheng; Lindner, Benjamin; Prinz, Jan -Hendrik; Noe, Frank; Smith, Jeremy C.

doi:10.1063/1.4824071

Title: Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling

Journal Article · Fri Nov 01 00:00:00 EDT 2013 · Journal of Chemical Physics

DOI:https://doi.org/10.1063/1.4824071· OSTI ID:1265947

Yi, Zheng ^[1]; Lindner, Benjamin ^[1]; Prinz, Jan -Hendrik ^[2]; Noe, Frank ^[2]; Smith, Jeremy C. ^[1]

Univ. of Tennessee, Knoxville, TN (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
FU Berlin, Berlin (Germany)

Here, neutron scattering experiments directly probe the dynamics of complex molecules on the sub pico- to microsecond time scales. However, the assignment of the relaxations seen experimentally to specific structural rearrangements is difficult, since many of the underlying dynamical processes may exist on similar timescales. In an accompanying article, we present a theoretical approach to the analysis of molecular dynamics simulations with a Markov State Model (MSM) that permits the direct identification of structural transitions leading to each contributing relaxation process. Here, we demonstrate the use of the method by applying it to the configurational dynamics of the well-characterized alanine dipeptide. A practical procedure for deriving the MSM from an MD is introduced. The result is a 9-state MSM in the space of the backbone dihedral angles and the side-chain methyl group. The agreement between the quasielastic spectrum calculated directly from the atomic trajectories and that derived from the Markov state model is excellent. The dependence on the wavevector of the individual Markov processes is described. The procedure means that it is now practicable to interpret quasielastic scattering spectra in terms of well-defined intramolecular transitions with minimal a priori assumptions as to the nature of the dynamics taking place.

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Research Organization:: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)

Sponsoring Organization:: USDOE Laboratory Directed Research and Development (LDRD) Program

DOE Contract Number:: AC05-00OR22725

OSTI ID:: 1265947

Journal Information:: Journal of Chemical Physics, Vol. 139, Issue 17; ISSN 0021-9606

Publisher:: American Institute of Physics (AIP)

Country of Publication:: United States

Language:: English

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