A coarse graining method for the identification of transition rates between molecular conformations.

By S. Kube, Marcus Weber. 2007

121 citations recorded by the source corpus.

Subfields: Atomic and Molecular Physics, and Optics, Molecular Biology, Spectroscopy

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Citations in the corpus

Deep Generative Markov State Models (2018, background): “As a result, the proposed models have a structural advantage over other high-accuracy Markov state modeling approaches that define metastable states in a fuzzy or probabilistic manner but do not guarantee a valid transition matrix [12, 15] (See Supplementary Material for more details.”
CellRank for directed single-cell fate mapping (2020, unknown): “By applying an invariant subspace projection, the projection error vanishes and the coarse-graining operation commutes with the propagation operation 20,87 .”
Identification of slow molecular order parameters for Markov model construction. (2013, background): “• From the largest m Eigenvalues and their associated Eigenfunctions, a rank-m propagator can be assembled that can describe the dynamics slower than timescale t m [46].”
An Introduction to Markov State Models and Their Application to Long Timescale Molecular Simulation (2014, methodology): “generated by replicaexchange [24] or well-converged meta-dynamics [13] simulations) or utilizing a potential energy bias Ubias(x) = −kBT lnμi(x) to rapidly equilibrate a simulation within the state before removing the biasing potential to generate unbiased dynamical trajectories [21].”
Fuzzy spectral clustering by PCCA+: application to Markov state models and data classification (2013, background): “The question at hand has been examined in detail by Kube and Weber (2006, 2007).”
Markov models of molecular kinetics: generation and validation. (2011, background): “In principle, the full dynamical information of the discretized system can be obtained by initiating trajectories of length τ out of each state i as long as we draw the starting points of these simulations from a local equilibrium density μi(x) [42, 43, 67].”