title: Dimensional reduction of Markov state models from renormalization group theory.
abstract: Renormalization Group (RG) theory provides the theoretical framework to define rigorous effective theories, i.e., systematic low-resolution approximations of arbitrary microscopic models. Markov state models are shown to be rigorous effective theories for Molecular Dynamics (MD). Based on this fact, we use real space RG to vary the resolution of the stochastic model and define an algorithm for clustering microstates into macrostates. The result is a lower dimensional stochastic model which, by construction, provides the optimal coarse-grained Markovian representation of the system's relaxation kinetics. To illustrate and validate our theory, we analyze a number of test systems of increasing complexity, ranging from synthetic toy models to two realistic applications, built form all-atom MD simulations. The computational cost of computing the low-dimensional model remains affordable on a desktop computer even for thousands of microstates.
authors: Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14 Povo, Trento 38123 , Italy.
authors: S
authors: S
authors: Orioli
authors: Dipartimento di Fisica, Università degli Studi di Trento, Via Sommarive 14 Povo, Trento 38123 , Italy.
authors: P
authors: P
authors: Faccioli
mesh_terms: D007700:Kinetics; D008390:Markov Chains; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D011506:Proteins / Q000737:chemistry / Q000378:metabolism; D013269:Stochastic Processes
chemical_list: D011506:Proteins