title: Conformational modes in biomolecules: dynamics and approximate invariance.
abstract: Understanding the physical mechanisms behind the folding and conformational dynamics of biomolecules is one of the major unsolved challenges of soft matter theory. In this contribution, a theoretical framework for biomolecular dynamics is introduced, employing selected aspects of statistical mechanics, dimensionality reduction, the perturbation theory, and the theory of matrices. Biomolecular dynamics is represented by time-dependent orthogonal conformational modes, the dynamics of the modes is investigated, and invariant properties that persist are identified. As an example, the dynamics of a human prion protein is considered. The theory provides a rigorous background for assessing the stable dynamical properties of biomolecules, such as their coarse-grained structure, through a multiscale approach using short subnanosecond segments of molecular dynamics trajectories. Furthermore, the paper offers a theoretical platform for models of conformational changes in macromolecules, which may allow complementing molecular dynamics simulations.
authors.affiliation: Centre for Mathematical Biology, University of Alberta, Edmonton, Alberta, Canada.
authors.forename: Alex
authors.initials: A
authors.lastname: Potapov
authors.forename: Maria
authors.initials: M
authors.lastname: Stepanova
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D008958:Models, Molecular; D008968:Molecular Conformation
chemical_list: D001704:Biopolymers