Publications
No matching items
| Title | authors | Description | Date |
|---|---|---|---|
| Neural Thermodynamic Integration: Free Energies from Energy-Based Diffusion Models | Máté, Fleuret, Bereau | J. Phys. Chem. Lett. None (2024) | 2024-11-06 |
| Robust and efficient reranking in crystal structure prediction: a data driven method for real-life molecules | Anelli, Dietrich, Ectors, Stowasser, Bereau, Neumann, Van Den Ende | CrystEngComm 26 (2024) | 2024-10-04 |
| EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning | Gryn’Ova, Bereau, Müller, Friederich, Wade, Nunes-Alves, Soares, Merz, Jr. | J. Chem. Inf. Model. 64 (2024) | 2024-08-12 |
| Roadmap on data-centric materials science | Bauer, Benner, Bereau, Blum, Boley, Carbogno, Catlow, Dehm, Eibl, Ernstorfer, Fekete, Foppa, Fratzl, Freysoldt, Gault, Ghiringhelli, Giri, Gladyshev, Goyal, Hattrick-Simpers, Kabalan, Karpov, Khorrami, Koch, Kokott, Kosch, Kowalec, Kremer, Leitherer, Li, Liebscher, Logsdail, Lu, Luong, Marek, Merz, R. Mianroodi, Neugebauer, Pei, Purcell, Raabe, Rampp, Rossi, Rost, Saal, Saalmann, Sasidhar, Saxena, Sbailò, Scheidgen, Schloz, Schmidt, Teshuva, Trunschke, Wei, Weikum, Xian, Yao, Yin, Zhao, Scheffler | Modelling Simul. Mater. Sci. Eng. 32 (2024) | 2024-05-17 |
| Shared metadata for data-centric materials science | Ghiringhelli, Baldauf, Bereau, Brockhauser, Carbogno, Chamanara, Cozzini, Curtarolo, Draxl, Dwaraknath, Fekete, Kermode, Koch, Kühbach, Ladines, Lambrix, Himmer, Levchenko, Oliveira, Michalchuk, Miller, Onat, Pavone, Pizzi, Regler, Rignanese, Schaarschmidt, Scheidgen, Schneidewind, Sheveleva, Su, Usvyat, Valsson, Wöll, Scheffler | Sci Data 10 (2023) | 2023-09-14 |
| Data-mining unveils structure–property–activity correlation of viral infectivity enhancing self-assembling peptides | Kaygisiz, Rauch-Wirth, Dutta, Yu, Nagata, Bereau, Münch, Synatschke, Weil | Nat Commun 14 (2023) | 2023-08-23 |
| Condensed-Phase Molecular Representation to Link Structure and Thermodynamics in Molecular Dynamics | Mohr, Van Der Mast, Bereau | J. Chem. Theory Comput. None (2023) | 2023-07-03 |
| Inverse design of viral infectivity-enhancing peptide fibrils from continuous protein-vector embeddings | Kaygisiz, Dutta, Rauch-Wirth, Synatschke, Münch, Bereau, Weil | Biomater. Sci. None (2023) | 2023-06-15 |
| Induced asymmetries in membranes | Girard, Bereau | Biophysical Journal 122 (2022) | 2022-12-06 |
| Identifying Sequential Residue Patterns in Bitter and Umami Peptides | Dutta, Bereau, Vilgis | ACS Food Sci. Technol. 2 (2022) | 2022-11-09 |
| Benchmarking coarse-grained models of organic semiconductors via deep backmapping | Stieffenhofer, Scherer, May, Bereau, Andrienko | Front. Chem. 10 (2022) | 2022-09-09 |
| Broad chemical transferability in structure-based coarse-graining | Kanekal, Rudzinski, Bereau | J. Chem. Phys. 157 (2022) | 2022-08-12 |
| CLiB – a novel cardiolipin-binder isolated via data-driven and in vitro screening | Kleinwächter, Mohr, Joppe, Hellmann, Bereau, Osiewacz, Schneider | RSC Chem. Biol. 3 (2022) | 2022-06-10 |
| FAIR data enabling new horizons for materials research | Scheffler, Aeschlimann, Albrecht, Bereau, Bungartz, Felser, Greiner, Groß-Klußmann, Koch, Kremer, Nagel, Scheidgen, Wöll, Draxl | Nature 604 (2022) | 2022-04-27 |
| Data-driven discovery of cardiolipin-selective small molecules by computational active learning | Mohr, Shmilovich, Kleinwächter, Schneider, Ferguson, Bereau | Chem. Sci. 13 (2022) | 2022-03-02 |
| Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer | Mondal, Cazade, Das, Bereau, Meuwly | J. Phys. Chem. B 125 (2021) | 2021-09-24 |
| Publisher’s Note: “Data-driven equation for drug–membrane permeability across drugs and membranes” [J. Chem. Phys. 154, 244114 (2021)] | Dutta, Vreeken, Ghiringhelli, Bereau | The Journal of Chemical Physics 155 (2021) | 2021-07-19 |
| Data-driven equation for drug–membrane permeability across drugs and membranes | Dutta, Vreeken, Ghiringhelli, Bereau | The Journal of Chemical Physics 154 (2021) | 2021-06-29 |
| Finite-size transitions in complex membranes | Girard, Bereau | Biophysical Journal 120 (2021) | 2021-05-04 |
| Computer simulations of lipid regulation by molecular semigrand canonical ensembles | Girard, Bereau | Biophysical Journal 120 (2021) | 2021-05-01 |
| Reweighting non-equilibrium steady-state dynamics along collective variables | Bause, Bereau | J. Chem. Phys. 154 (2021) | 2021-04-01 |
| The Bacteriostatic Activity of 2-Phenylethanol Derivatives Correlates with Membrane Binding Affinity | Kleinwächter, Pannwitt, Centi, Hellmann, Thines, Bereau, Schneider | Membranes 11 (2021) | 2021-03-31 |
| Adversarial reverse mapping of condensed-phase molecular structures: Chemical transferability | Stieffenhofer, Bereau, Wand | APL Materials 9 (2021) | 2021-03-12 |
| Dynamical properties across different coarse-grained models for ionic liquids | Rudzinski, Kloth, Wörner, Pal, Kremer, Bereau, Vogel | J. Phys.: Condens. Matter 33 (2021) | 2021-02-16 |
| Coarse-grained conformational surface hopping: Methodology and transferability | Rudzinski, Bereau | The Journal of Chemical Physics 153 (2020) | 2020-12-04 |
| Computational compound screening of biomolecules and soft materials by molecular simulations | Bereau | Modelling Simul. Mater. Sci. Eng. 29 (2020) | 2020-12-03 |
| Adversarial reverse mapping of equilibrated condensed-phase molecular structures | Stieffenhofer, Wand, Bereau | Mach. Learn.: Sci. Technol. 1 (2020) | 2020-09-09 |
| Free-energy landscape of polymer-crystal polymorphism | Liu, Brandenburg, Valsson, Kremer, Bereau | Soft Matter 16 (2020) | 2020-09-03 |
| Regulating Lipid Composition Rationalizes Acyl Tail Saturation Homeostasis in Ectotherms | Girard, Bereau | Biophysical Journal 119 (2020) | 2020-08-06 |
| Hydration free energies from kernel-based machine learning: Compound-database bias | Rauer, Bereau | The Journal of Chemical Physics 153 (2020) | 2020-07-01 |
| Designing exceptional gas-separation polymer membranes using machine learning | Barnett, Bilchak, Wang, Benicewicz, Murdock, Bereau, Kumar | Sci. Adv. 6 (2020) | 2020-05-15 |
| Kernel-Based Machine Learning for Efficient Simulations of Molecular Liquids | Scherer, Scheid, Andrienko, Bereau | J. Chem. Theory Comput. 16 (2020) | 2020-04-13 |
| Interpretable embeddings from molecular simulations using Gaussian mixture variational autoencoders | Bozkurt Varolgunes, Bereau, Rudzinski | Mach. Learn.: Sci. Technol. 1 (2020) | 2020-03-18 |
| Molecular dynamics trajectories for 630 coarse-grained drug-membrane permeations | Hoffmann, Centi, Menichetti, Bereau | Sci Data 7 (2020) | 2020-02-13 |
| Inserting Small Molecules across Membrane Mixtures: Insight from the Potential of Mean Force | Centi, Dutta, Parekh, Bereau | Biophysical Journal 118 (2020) | 2020-02-05 |
| Probing Nanoparticle/Membrane Interactions by Combining Amphiphilic Diblock Copolymer Assembly and Plasmonics | Koch, Morsbach, Bereau, Lévêque, Butt, Deserno, Landfester, Fytas | J. Phys. Chem. B 124 (2020) | 2020-01-17 |
| Direct route to reproducing pair distribution functions with coarse-grained models via transformed atomistic cross correlations | Wörner, Bereau, Kremer, Rudzinski | J. Chem. Phys. 151 (2019) | 2019-12-26 |
| Microscopic reweighting for nonequilibrium steady-state dynamics | Bause, Wittenstein, Kremer, Bereau | Phys. Rev. E 100 (2019) | 2019-12-19 |
| Resolution limit of data-driven coarse-grained models spanning chemical space | Kanekal, Bereau | J. Chem. Phys. 151 (2019) | 2019-10-22 |
| Controlled exploration of chemical space by machine learning of coarse-grained representations | Hoffmann, Menichetti, Kanekal, Bereau | Phys. Rev. E 100 (2019) | 2019-09-04 |
| Hoobas: A highly object-oriented builder for molecular dynamics | Girard, Ehlen, Shakya, Bereau, De La Cruz | Computational Materials Science 167 (2019) | 2019-05-20 |
| Sequence‐Optimized Peptide Nanofibers as Growth Stimulators for Regeneration of Peripheral Neurons | Schilling, Mack, Lickfett, Sieste, Ruggeri, Sneideris, Dutta, Bereau, Naraghi, Sinske, Knowles, Synatschke, Weil, Knöll | Adv. Funct. Mater. 29 (2019) | 2019-04-15 |
| Revisiting the Meyer-Overton rule for drug-membrane permeabilities | Menichetti, Bereau | Molecular Physics 117 (2019) | 2019-04-08 |
| Drug–Membrane Permeability across Chemical Space | Menichetti, Kanekal, Bereau | ACS Cent. Sci. 5 (2019) | 2019-01-09 |
| Automated detection of many-particle solvation states for accurate characterizations of diffusion kinetics | Rudzinski, Radu, Bereau | The Journal of Chemical Physics 150 (2019) | 2019-01-08 |
| Accurate Structure-Based Coarse Graining Leads to Consistent Barrier-Crossing Dynamics | Bereau, Rudzinski | Phys. Rev. Lett. 121 (2018) | 2018-12-21 |
| Structural-kinetic-thermodynamic relationships identified from physics-based molecular simulation models | Rudzinski, Bereau | The Journal of Chemical Physics 148 (2018) | 2018-05-30 |
| Polymorphism of Syndiotactic Polystyrene Crystals from Multiscale Simulations | Liu, Kremer, Bereau | Adv. Theory Simul. 1 (2018) | 2018-05-16 |
| Engineering Proteins at Interfaces: From Complementary Characterization to Material Surfaces with Designed Functions | Morsbach, Gonella, Mailänder, Wegner, Wu, Weidner, Berger, Koynov, Vollmer, Encinas, Kuan, Bereau, Kremer, Weil, Bonn, Butt, Landfester | Angew. Chem. Int. Ed. 57 (2018) | 2018-04-17 |
| Non-covalent interactions across organic and biological subsets of chemical space: Physics-based potentials parametrized from machine learning | Bereau, Distasio, Tkatchenko, Von Lilienfeld | The Journal of Chemical Physics 148 (2018) | 2018-03-15 |
| The Role of Conformational Entropy in the Determination of Structural-Kinetic Relationships for Helix-Coil Transitions | Rudzinski, Bereau | Computation 6 (2018) | 2018-02-27 |
| In silico screening of drug-membrane thermodynamics reveals linear relations between bulk partitioning and the potential of mean force | Menichetti, Kanekal, Kremer, Bereau | The Journal of Chemical Physics 147 (2017) | 2017-09-25 |
| Efficient potential of mean force calculation from multiscale simulations: Solute insertion in a lipid membrane | Menichetti, Kremer, Bereau | Biochemical and Biophysical Research Communications 498 (2017) | 2017-09-07 |
| Nitrated Fatty Acids Modulate the Physical Properties of Model Membranes and the Structure of Transmembrane Proteins | Franz, Bereau, Pannwitt, Anbazhagan, Lehr, Nubbemeyer, Dietz, Bonn, Weidner, Schneider | Chem. Eur. J. 23 (2017) | 2017-05-15 |
| Concurrent parametrization against static and kinetic information leads to more robust coarse-grained force fields | Rudzinski, Bereau | Eur. Phys. J. Spec. Top. 225 (2016) | 2016-07-15 |
| An in-silico walker | Xiao, Chen, Bereau, Shi | Chemical Physics Letters 659 (2016) | 2016-06-11 |
| Impact of Quadrupolar Electrostatics on Atoms Adjacent to the Sigma-Hole in Condensed-Phase Simulations | El Hage, Bereau, Jakobsen, Meuwly | J. Chem. Theory Comput. 12 (2016) | 2016-05-09 |
| Protein-Backbone Thermodynamics across the Membrane Interface | Bereau, Kremer | J. Phys. Chem. B 120 (2016) | 2016-05-03 |
| Research Update: Computational materials discovery in soft matter | Bereau, Andrienko, Kremer | APL Materials 4 (2016) | 2016-03-15 |
| Communication: Consistent interpretation of molecular simulation kinetics using Markov state models biased with external information | Rudzinski, Kremer, Bereau | The Journal of Chemical Physics 144 (2016) | 2016-02-05 |
| Folding and insertion thermodynamics of the transmembrane WALP peptide | Bereau, Bennett, Pfaendtner, Deserno, Karttunen | The Journal of Chemical Physics 143 (2015) | 2015-11-13 |
| Multi-timestep Integrator for the Modified Andersen Barostat | Bereau | Physics Procedia 68 (2015) | 2015-08-28 |
| Better Together: Lipopeptide Micelle Formation Enhances Antimicrobial Selectivity | Bereau | Biophysical Journal 109 (2015) | 2015-08-18 |
| Transferable Atomic Multipole Machine Learning Models for Small Organic Molecules | Bereau, Andrienko, Von Lilienfeld | J. Chem. Theory Comput. 11 (2015) | 2015-05-21 |
| Automated Parametrization of the Coarse-Grained Martini Force Field for Small Organic Molecules | Bereau, Kremer | J. Chem. Theory Comput. 11 (2015) | 2015-04-28 |
| Solvation of fluoro-acetonitrile in water by 2D-IR spectroscopy: A combined experimental-computational study | Cazade, Tran, Bereau, Das, Kläsi, Hamm, Meuwly | The Journal of Chemical Physics 142 (2015) | 2015-04-07 |
| Multipolar Force Fields and Their Effects on Solvent Dynamics around Simple Solutes | Jakobsen, Bereau, Meuwly | J. Phys. Chem. B 119 (2015) | 2015-01-13 |
| Enhanced Sampling of Coarse-Grained Transmembrane-Peptide Structure Formation from Hydrogen-Bond Replica Exchange | Bereau, Deserno | J Membrane Biol 248 (2014) | 2014-10-13 |
| Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion | Bereau, Von Lilienfeld | The Journal of Chemical Physics 141 (2014) | 2014-07-16 |
| Computational Two-Dimensional Infrared Spectroscopy without Maps: N-Methylacetamide in Water | Cazade, Bereau, Meuwly | J. Phys. Chem. B 118 (2014) | 2014-03-31 |
| More than the sum of its parts: Coarse-grained peptide-lipid interactions from a simple cross-parametrization | Bereau, Wang, Deserno | The Journal of Chemical Physics 140 (2014) | 2014-03-18 |
| Deriving Static Atomic Multipoles from the Electrostatic Potential | Kramer, Bereau, Spinn, Liedl, Gedeck, Meuwly | J. Chem. Inf. Model. 53 (2013) | 2013-12-05 |
| Leveraging Symmetries of Static Atomic Multipole Electrostatics in Molecular Dynamics Simulations | Bereau, Kramer, Meuwly | J. Chem. Theory Comput. 9 (2013) | 2013-11-05 |
| Scoring Multipole Electrostatics in Condensed-Phase Atomistic Simulations | Bereau, Kramer, Monnard, Nogueira, Ward, Meuwly | J. Phys. Chem. B 117 (2013) | 2013-04-05 |
| Coarse-Grained and Atomistic Simulations of the Salt-Stable Cowpea Chlorotic Mottle Virus (SS-CCMV) Subunit 26–49: β-Barrel Stability of the Hexamer and Pentamer Geometries | Bereau, Globisch, Deserno, Peter | J. Chem. Theory Comput. 8 (2012) | 2012-04-23 |
| Structural Basis of Folding Cooperativity in Model Proteins: Insights from a Microcanonical Perspective | Bereau, Deserno, Bachmann | Biophysical Journal 100 (2011) | 2011-06-18 |
| Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity | Bereau, Bachmann, Deserno | J. Am. Chem. Soc. 132 (2010) | 2010-09-07 |
| Generic coarse-grained model for protein folding and aggregation | Bereau, Deserno | The Journal of Chemical Physics 130 (2009) | 2009-06-18 |
| Optimized convergence for multiple histogram analysis | Bereau, Swendsen | Journal of Computational Physics 228 (2009) | 2009-05-19 |