252 citations · 1k across the 43 of their papers we have counts for
45 papers
Recovering molecules from coarse-grained beads: free-energy-conditioned generative backmapping across chemical space
Luis Itza Vazquez-Salazar, Tristan Bereau
Transferable coarse-grained (CG) force fields compress chemical space: by aggregating atoms into a reduced set of interaction beads, models such as MARTINI reduce the number of dis…
ESPResSo++: A Fast and Extensible Molecular Simulation Package for Coarse-Grained Models
Zhen-Hao Xu, James Vance, Nikita Tretyakov +9
ESPResSo++ is an open-source software package for molecular dynamics (MD) simulations with a particular emphasis on coarse-grained (CG) models of soft matter systems. Written in C+…
Protein Dynamics Beyond Structure Prediction
Juliette Griffié, Sviatlana Shashkova, Antonio Ciarlo +41
The ability to predict protein three-dimensional structures from amino acid sequences is a landmark achievement in molecular biology, where recent deep learning approaches such as…
Data-Efficient Multidimensional Free Energy Estimation via Physics-Informed Score Learning
Daniel Nagel, Tristan Bereau
Many biological processes involve numerous coupled degrees of freedom, yet free-energy estimation is often restricted to one-dimensional profiles to mitigate the high computational…
Split-Flows: Measure Transport and Information Loss Across Molecular Resolutions
Sander Hummerich, Tristan Bereau, Ullrich Köthe
By reducing resolution, coarse-grained models greatly accelerate molecular simulations, unlocking access to long-timescale phenomena, though at the expense of microscopic informati…
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…
Navigating Chemical Space: Multi-Level Bayesian Optimization with Hierarchical Coarse-Graining
Luis J. Walter, Tristan Bereau
Molecular discovery within the vast chemical space remains a significant challenge due to the immense number of possible molecules and limited scalability of conventional screening…
Solvation Free Energies from Neural Thermodynamic Integration
Bálint Máté, François Fleuret, Tristan Bereau
We present a method for computing free-energy differences using thermodynamic integration with a neural network potential that interpolates between two target Hamiltonians. The int…
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…
Neural Thermodynamic Integration: Free Energies from Energy-based Diffusion Models
Bálint Máté, François Fleuret, Tristan Bereau
Thermodynamic integration (TI) offers a rigorous method for estimating free-energy differences by integrating over a sequence of interpolating conformational ensembles. However, TI…
Roadmap on Data-Centric Materials Science
Stefan Bauer, Peter Benner, Tristan Bereau +58
Science is and always has been based on data, but the terms "data-centric" and the "4th paradigm of" materials research indicate a radical change in how information is retrieved, h…
Condensed-phase molecular representation to link structure and thermodynamics in molecular dynamics
Bernadette Mohr, Diego van der Mast, Tristan Bereau
Molecular design requires systematic and broadly applicable methods to extract structure-property relationships. The focus of this study is on learning thermodynamic properties fro…
Identifying sequential residue patterns in bitter and umami peptides
Arghya Dutta, Tristan Bereau, Thomas A. Vilgis
The primary structures of peptides, originating from food proteins, affect their taste. Connecting primary structure to taste, however, is difficult because the size of the peptide…
Shared Metadata for Data-Centric Materials Science
Luca M. Ghiringhelli, Carsten Baldauf, Tristan Bereau +32
The expansive production of data in materials science, their widespread sharing and repurposing requires educated support and stewardship. In order to ensure that this need helps r…
FAIR data enabling new horizons for materials research
Matthias Scheffler, Martin Aeschlimann, Martin Albrecht +11
The prosperity and lifestyle of our society are very much governed by achievements in condensed matter physics, chemistry and materials science, because new products for sectors su…
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…
Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine-Trimer
Padmabati Mondal, Pierre-André Cazade, Akshaya K. Das +2
The dynamics and spectroscopy of N-methyl-acetamide (NMA) and trialanine in solution is characterized from molecular dynamics (MD) simulations using different energy functions, inc…
Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability
Marc Stieffenhofer, Tristan Bereau, Michael Wand
Switching between different levels of resolution is essential for multiscale modeling, but restoring details at higher resolution remains challenging. In our previous study we have…
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…
Reweighting non-equilibrium steady-state dynamics along collective variables
Marius Bause, Tristan Bereau
Computer simulations generate microscopic trajectories of complex systems at a single thermodynamic state point. We recently introduced a Maximum Caliber (MaxCal) approach for dyna…
Data-driven equation for drug-membrane permeability across drugs and membranes
Arghya Dutta, Jilles Vreeken, Luca M. Ghiringhelli +1
Drug efficacy depends on its capacity to permeate across the cell membrane. We consider the prediction of passive drug-membrane permeability coefficients. Beyond the widely recogni…
Computational compound screening of biomolecules and soft materials by molecular simulations
Tristan Bereau
Decades of hardware, methodological, and algorithmic development have propelled molecular dynamics (MD) simulations to the forefront of materials-modeling techniques, bridging the…
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…
Free-energy landscape of polymer-crystal polymorphism
Chan Liu, Jan Gerit Brandenburg, Omar Valsson +2
Polymorphism rationalizes how processing can control the final structure of a material. The rugged free-energy landscape and exceedingly slow kinetics in the solid state have so fa…