23 citations · 44 across the 4 of their papers we have counts for
4 papers
Lost in Projection? Gaussian Filtering Recovers Hidden Conformational States
Sofia Sartore, Daniel Nagel, Georg Diez +1
To interpret molecular dynamics (MD) simulations, it is common practice to reduce the dimensionality of the molecular coordinates to a low-dimensional collective variable . Proj…
Fokker-Planck Score Learning: Efficient Free-Energy Estimation under Periodic Boundary Conditions
Daniel Nagel, Tristan Bereau
Accurate free-energy estimation is essential in molecular simulation, yet the periodic boundary conditions (PBC) commonly used in computer simulations have rarely been explicitly e…
Accurate estimation of the normalized mutual information of multidimensional data
Daniel Nagel, Georg Diez, Gerhard Stock
While the linear Pearson correlation coefficient represents a well-established normalized measure to quantify the interrelation of two stochastic variables and , it fails fo…
Towards a Benchmark for Markov State Models: The Folding of HP35
Daniel Nagel, Sofia Sartore, Gerhard Stock
Adopting a s-long molecular dynamics (MD) trajectory of the reversible folding of villin headpiece (HP35) published by D. E. Shaw Research, we recently constructed a Mark…