252 citations · 1k across the 43 of their papers we have counts for
19 papers · 1 filter
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…
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…
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…
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…
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…
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…
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…
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…
Hydration free energies from kernel-based machine learning: Compound-database bias
Clemens Rauer, Tristan Bereau
We consider the prediction of a basic thermodynamic property---hydration free energies---across a large subset of the chemical space of small organic molecules. Our in silico study…
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…
Resolution limit of data-driven coarse-grained models spanning chemical space
Kiran H. Kanekal, Tristan Bereau
Increasing the efficiency of materials design and discovery remains a significant challenge, especially given the prohibitively large size of chemical compound space. The use of a…
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.…
Drug-membrane permeability across chemical space
Roberto Menichetti, Kiran H. Kanekal, Tristan Bereau
Unraveling the relation between the chemical structure of small drug-like compounds and their rate of passive permeation across lipid membranes is of fundamental importance for pha…
Efficient potential of mean force calculation from multiscale simulations: solute insertion in a lipid membrane
Roberto Menichetti, Kurt Kremer, Tristan Bereau
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multisc…
Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning
Tristan Bereau, Robert A. DiStasio, Alexandre Tkatchenko +1
Classical intermolecular potentials typically require an extensive parametrization procedure for any new compound considered. To do away with prior parametrization, we propose a co…
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…
Transferable atomic multipole machine learning models for small organic molecules
Tristan Bereau, Denis Andrienko, O. Anatole von Lilienfeld
Accurate representation of the molecular electrostatic potential, which is often expanded in distributed multipole moments, is crucial for an efficient evaluation of intermolecular…
Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion
Tristan Bereau, O. Anatole von Lilienfeld
We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resultin…