title: Effective Riemannian Diffusion Model for Conformational Dynamics of Biomolecular Systems.
abstract: We present a Riemannian formalism for effective diffusion of biomolecules in collective variable spaces that provides a robust framework for conformational free energy calculation methods. Unlike their Euclidean counterparts, the Riemannian potential of mean force (PMF) and minimum free energy path (MFEP) are invariant under coordinate transformations. The presented formalism can be readily employed to modify the collective variable based enhanced sampling techniques, such as umbrella sampling (US) commonly used in biomolecular simulations, to take into account the role of intrinsic geometry of collective variable space. Although our model is mathematically equivalent to a Euclidean diffusion with a position-dependent diffusion tensor, the Riemannian formulation provides a more convenient framework for free energy calculation methods and path-finding algorithms aimed at characterizing the effective conformational dynamics of biomolecules. A simple three-dimensional toy model and a pentapeptide (met-enkephalin) simulated in an explicit solvent environment are used to illustrate the workings of the formalism and its implementation.
authors.affiliation: Department of Physics, North Carolina State University , Raleigh, North Carolina 27695, United States.
authors.forename: Ashkan
authors.initials: A
authors.lastname: Fakharzadeh
authors.affiliation: Department of Chemistry and Biochemistry, University of Arkansas , Fayetteville, Arkansas 72701, United States.
authors.forename: Mahmoud
authors.identifier: http://orcid.org/0000-0002-0601-402X
authors.initials: M
authors.lastname: Moradi
mesh_terms: D000465:Algorithms; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation