Title authors Description Date
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
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