36 citations · 123 across the 14 of their papers we have counts for
15 papers
From Knowledge to Action: Outcomes of the 2025 Large Language Model (LLM) Hackathon for Applications in Materials Science and Chemistry
Aritra Roy, Kevin Shen, Andrew MacBride +350
Large language models (LLMs) are rapidly changing how researchers in materials science and chemistry discover, organize, and act on scientific knowledge. This paper analyzes a broa…
Structure and dynamics of ionic liquids under shear flow
Abbas Gholami, Sebastian Kloth, Zhen-Hao Xu +4
We investigate the intrinsic behavior of ionic liquids under shear flow, using a coarse-grained model of C4mim-PF6 as a prototypical example. The importance of long-ranged electros…
The 2025 Roadmap to Ultrafast Dynamics: Frontiers of Theoretical and Computational Modelling
Fabio Caruso, Michael A. Sentef, Claudio Attaccalite +27
The exploration of ultrafast phenomena is a frontier of condensed matter research, where the interplay of theory, computation, and experiment is unveiling new opportunities for und…
Martignac: Computational workflows for reproducible, traceable, and composable coarse-grained Martini simulations
Tristan Bereau, Luis J. Walter, Joseph F. Rudzinski
Despite their wide use and far-reaching implications, molecular dynamics (MD) simulations suffer from a lack of both traceability and reproducibility. We introduce Martignac: compu…
Broad chemical transferability in structure-based coarse-graining
Kiran H. Kanekal, Joseph F. Rudzinski, Tristan Bereau
Compared to top-down coarse-grained (CG) models, bottom-up approaches are capable of offering higher structural fidelity. This fidelity results from the tight link to a higher-reso…
Finite-size scaling and thermodynamics of model supercooled liquids: Long-range concentration fluctuations and the role of attractive interactions
Atreyee Banerjee, Mauricio Sevilla, Joseph F. Rudzinski +1
We compute partial structure factors, Kirkwood-Buff integrals (KBIs) and chemical potentials of model supercooled liquids with and without attractive interactions. We aim at invest…
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.…
Accurate structure-based coarse-graining leads to consistent barrier-crossing dynamics
Tristan Bereau, Joseph F. Rudzinski
Structure-based coarse graining of molecular systems offers a systematic route to reproduce the many-body potential of mean force. Unfortunately, common strategies are inherently l…
Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields
Joseph F. Rudzinski, Tristan Bereau
The parametrization of coarse-grained (CG) simulation models for molecular systems often aims at reproducing static properties alone. The reduced molecular friction of the CG repre…
Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information
Joseph F. Rudzinski, Kurt Kremer, Tristan Bereau
Molecular simulations can provide microscopic insight into the physical and chemical driving forces of complex molecular processes. Despite continued advancement of simulation meth…