8 papers
Dynamical properties across different coarse-grained models for ionic liquids
Joseph F. Rudzinski, Sebastian Kloth, Svenja Wörner +4
Room-temperature ionic liquids (RTILs) stand out among molecular liquids for their rich physicochemical characteristics, including structural and dynamic heterogeneity. The signifi…
Coarse-grained conformational surface hopping: Methodology and transferability
Joseph F. Rudzinski, Tristan Bereau
Coarse-grained (CG) conformational surface hopping (SH) adapts the concept of multisurface dynamics, initially developed to describe electronic transitions in chemical reactions, t…
Interpretable Embeddings From Molecular Simulations Using Gaussian Mixture Variational Autoencoders
Yasemin Bozkurt Varolgunes, Tristan Bereau, Joseph F. Rudzinski
Extracting insight from the enormous quantity of data generated from molecular simulations requires the identification of a small number of collective variables whose corresponding…
Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations
Svenja J. Woerner, Tristan Bereau, Kurt Kremer +1
Coarse-grained (CG) models are often parametrized to reproduce one-dimensional structural correlation functions of an atomically-detailed model along the degrees of freedom governi…
Recent progress towards chemically-specific coarse-grained simulation models with consistent dynamical properties
Joseph F. Rudzinski
Coarse-grained (CG) models can provide computationally efficient and conceptually simple characterizations of soft matter systems. While generic models probe the underlying physics…
Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics
Joseph F. Rudzinski, Marc Radu, Tristan Bereau
Discrete-space kinetic models, i.e., Markov state models, have emerged as powerful tools for reducing the complexity of trajectories generated from molecular dynamics simulations.…