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Found 3 papers, 1 papers with code
The mechanism of RNA base fraying: molecular dynamics simulations analyzed with core-set Markov state models
We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA fraying and its sequence and direction dependence.
Computational Physics Statistical Mechanics Biological Physics Chemical Physics Biomolecules
Variational Selection of Features for Molecular Kinetics
The modeling of atomistic biomolecular simulations using kinetic models such as Markov state models (MSMs) has had many notable algorithmic advances in recent years.
Variational Koopman models: slow collective variables and molecular kinetics from short off-equilibrium simulations
Recently, a powerful generalization of MSMs has been introduced, the variational approach (VA) of molecular kinetics and its special case the time-lagged independent component analysis (TICA), which allow us to approximate slow collective variables and molecular kinetics by linear combinations of smooth basis functions or order parameters.
