title: Dynamic neutron scattering from conformational dynamics. I. Theory and Markov models.
abstract: The dynamics of complex molecules can be directly probed by inelastic neutron scattering experiments. However, many of the underlying dynamical processes may exist on similar timescales, which makes it difficult to assign processes seen experimentally to specific structural rearrangements. Here, we show how Markov models can be used to connect structural changes observed in molecular dynamics simulation directly to the relaxation processes probed by scattering experiments. For this, a conformational dynamics theory of dynamical neutron and X-ray scattering is developed, following our previous approach for computing dynamical fingerprints of time-correlation functions [F. Noé, S. Doose, I. Daidone, M. Löllmann, J. Chodera, M. Sauer, and J. Smith, Proc. Natl. Acad. Sci. U.S.A. 108, 4822 (2011)]. Markov modeling is used to approximate the relaxation processes and timescales of the molecule via the eigenvectors and eigenvalues of a transition matrix between conformational substates. This procedure allows the establishment of a complete set of exponential decay functions and a full decomposition into the individual contributions, i.e., the contribution of every atom and dynamical process to each experimental relaxation process.
authors.affiliation: University of Tennessee/Oak Ridge National Laboratory Center for Molecular Biophysics, P.O. Box 2008, 1 Bethel Valley Rd., 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: Benjamin
authors.initials: B
authors.lastname: Lindner
authors.forename: Zheng
authors.initials: Z
authors.lastname: Yi
authors.forename: Jan-Hendrik
authors.initials: JH
authors.lastname: Prinz
authors.forename: Jeremy C
authors.initials: JC
authors.lastname: Smith
authors.forename: Frank
authors.initials: F
authors.lastname: Noé
mesh_terms: D000409:Alanine / Q000737:chemistry*; D004151:Dipeptides / Q000737:chemistry*; D008390:Markov Chains; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D033363:Neutron Diffraction; D013997:Time Factors; D014961:X-Ray Diffraction
chemical_list: D004151:Dipeptides; D000409:Alanine