title: Dynamic neutron scattering from conformational dynamics. II. Application using molecular dynamics simulation and Markov modeling.
abstract: 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.
authors.affiliation: University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, P.O. Box 2008, 1 Bethel Valley Road, Oak Ridge, Tennessee 37831, USA and Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, M407 Walters Life Sciences, 1414 Cumberland Avenue, Knoxville, Tennessee 37996, USA.
authors.forename: Zheng
authors.initials: Z
authors.lastname: Yi
authors.forename: Benjamin
authors.initials: B
authors.lastname: Lindner
authors.forename: Jan-Hendrik
authors.initials: JH
authors.lastname: Prinz
authors.forename: Frank
authors.initials: F
authors.lastname: Noé
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
mesh_terms: D000409:Alanine / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D008390:Markov Chains; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D033363:Neutron Diffraction
chemical_list: D004151:Dipeptides; D000409:Alanine