Markov state models (MSMs) are a powerful framework for analyzing dynamical systems,
such as molecular dynamics (MD) simulations, that have gained widespread use over the …

Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

A goal in the kinetic characterization of a macromolecular system is the description of its
slow relaxation processes via (i) identification of the structural changes involved in these …

Markov state models of molecular kinetics (MSMs), in which the long-time statistical
dynamics of a molecule is approximated by a Markov chain on a discrete partition of …

A fundamental appreciation for how biological macromolecules work requires knowledge of
structure and dynamics. Molecular dynamics simulations provide powerful tools for the …

Quantitatively accurate all-atom molecular dynamics (MD) simulations of protein folding
have long been considered a holy grail of computational biology. Due to the large system …

The success of new scientific areas can be assessed by their potential in contributing to new
theoretical approaches and in applications to real-world problems. Complex networks have …

The eigenvalues and eigenvectors of the molecular dynamics propagator (or transfer
operator) contain the essential information about the molecular thermodynamics and …

Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

A fast community detection algorithm based on aq-state Potts model is presented.
Communities (groups of densely interconnected nodes that are only loosely connected to …