3 papers
cond-mat.soft2026
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…
cond-mat.stat-mech2025
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…
physics.data-an2024
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…