{"id":44621,"date":"2021-11-12T15:22:48","date_gmt":"2021-11-12T14:22:48","guid":{"rendered":"https:\/\/www.h-its.org\/de\/forschung\/simplaixnew-simpn-de\/publications-simpn\/"},"modified":"2023-08-04T11:49:44","modified_gmt":"2023-08-04T09:49:44","slug":"publikationen-simplaix","status":"publish","type":"page","link":"https:\/\/www.h-its.org\/de\/forschung\/simplaix\/publikationen-simplaix\/","title":{"rendered":"Publikationen SIMPLAIX"},"content":{"rendered":"\n  <div class=\"hits-blocks hits-publications-block\">\n\n      <div class=\"publications-list\">\n        <\/ul><h2 id=\"publication-year-2026\">2026<\/h2><ul class=\"publications-list\"><li>Soares TA, Nunes-Alves A, Bereau T, Friederich P, Gryn\u2019ova G, Mu\u0308ller C, Wade RC, Merz K (2026). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.6c01719\"><span class=\"publication-title\">Mapping the Molecular\nUniverse: Exploring Chemical\nCompound Space by Multiscale High-Throughput Screening and Machine\nLearning<\/span><\/a>, Journal of Chemical Information and Modeling 66(12):6809-6813. <span style=\"color:#ddd; font-size:12px\">2282<\/span><\/li><li>Sucerquia D, Farrugia M, Rennekamp B, Dreuw A, Gr\u00e4ter F (2026). <a href=\"https:\/\/doi.org\/10.1063\/5.0325167\"><span class=\"publication-title\">SITH: A quantum-chemical framework for predicting bond destabilization in stretched molecules<\/span><\/a>, The Journal of Chemical Physics 164(23):234103. <span style=\"color:#ddd; font-size:12px\">2273<\/span><\/li><li>Hartmann E, Buhr J, Riedmiller K, Ulanov E, Sch\u00fcpp BN, Kiesewetter D, Sucerquia D, Aponte-Santamar\u00eda C, Gr\u00e4ter F (2026). <a href=\"https:\/\/doi.org\/10.1038\/s41467-026-71955-2\"><span class=\"publication-title\">KIMMDY: A biomolecular reaction emulator<\/span><\/a>, Nature Communications, 17(1) <span style=\"color:#ddd; font-size:12px\">2259<\/span><\/li><li>Fedorov R, Nihei A, Gryn\u2019ova G (2026). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.5c01450\"><span class=\"publication-title\">Multi-Solvent Graph Neural Network for Reduction Potential Prediction Across the Chemical Space<\/span><\/a>, J. Chem. Inf. Model. 66(2):847-854. <span style=\"color:#ddd; font-size:12px\">2277<\/span><\/li><li>Neubert M, Reiser P, Gr\u00e4ter F, Friederich P (2026). <a href=\"https:\/\/doi.org\/10.1039\/d6dd00054a\"><span class=\"publication-title\">Learning potential energy surfaces of hydrogen atom transfer reactions in peptides<\/span><\/a>, Digital Discovery 5(4):1831-1844. <span style=\"color:#ddd; font-size:12px\">2275<\/span><\/li><li>Klockow MV, Ickler M, Lippmann P, Hamprecht FA (2026). <a href=\"https:\/\/proceedings.iclr.cc\/paper_files\/paper\/2026\/file\/718573eff1cb169316783d3e08514b5b-Paper-Conference.pdf\"><span class=\"publication-title\">A Function-Centric Graph Neural Network Approach for Predicting Electron Densities<\/span><\/a>, https:\/\/proceedings.iclr.cc\/paper_files\/paper\/2026\/file\/718573eff1cb169316783d3e08514b5b-Paper-Conference.pdf <span style=\"color:#ddd; font-size:12px\">2276<\/span><\/li><\/ul><h2 id=\"publication-year-2025\">2025<\/h2><ul class=\"publications-list\"><li>Ernst M, Fedorov R, Calzolari A, Mollart C, Grieser FF, Ber S, Gryn&#8217;ova G (2025). <a href=\"https:\/\/doi.org\/10.26434\/chemrxiv-2025-zbc8x-v2\"><span class=\"publication-title\">Fragment to Framework: Automatic Fragmentation of Covalent Organic Frameworks into Building Blocks for Band Gap Analysis<\/span><\/a>, Preprint. https:\/\/doi.org\/10.26434\/chemrxiv-2025-zbc8x-v2 <span style=\"color:#ddd; font-size:12px\">2278<\/span><\/li><li>Remme R, Kaczun T, Ebert T, Gehrig CA, Geng D, Gerhartz G, Ickler MK, Klockow MV, Lippmann P, Schmidt JS, Wagner S, Dreuw A, Hamprecht FA (2025). <a href=\"https:\/\/doi.org\/10.1021\/jacs.5c06219\"><span class=\"publication-title\">Stable and Accurate Orbital-Free Density Functional Theory Powered by Machine Learning<\/span><\/a>, J. Am. Chem. Soc. 147(32):28851-28859. <span style=\"color:#ddd; font-size:12px\">2231<\/span><\/li><li>Teuffel J, Mukherjee G, Han SB, Elstner M, Wade RC (2025). <a href=\"https:\/\/doi.org\/10.1063\/5.0248701\"><span class=\"publication-title\">On the determinants of electron transfer reorganization energy in a cytochrome P450: cytochrome b5 complex. A combined quantum mechanics and molecular dynamics simulation study<\/span><\/a>, The Journal of Chemical Physics 162(19):195101. <span style=\"color:#ddd; font-size:12px\">2064<\/span><\/li><li>Hoffmann DS, Dohmen PM, Sokolov M, Kleinekath\u00f6fer U, Elstner M (2025). <a href=\"https:\/\/doi.org\/10.1021\/acs.jpcb.5c00320\"><span class=\"publication-title\">Exciton Transfer Simulations in a Light-Harvesting 2 Complex Reveal the Transient Delocalization Mechanism<\/span><\/a>, J. Phys. Chem. B 129(13):3345-3365. <span style=\"color:#ddd; font-size:12px\">2082<\/span><\/li><li>Schopmans H, Friederich P (2025). <a href=\"https:\/\/arxiv.org\/abs\/2501.19077\"><span class=\"publication-title\">Temperature-Annealed Boltzmann Generators<\/span><\/a>, arXiv,cs.LG,2501.19077 <span style=\"color:#ddd; font-size:12px\">2060<\/span><\/li><li>Walter LJ, Bereau T (2025). <a href=\"https:\/\/doi.org\/10.1039\/D5SC03855C\"><span class=\"publication-title\">Navigating chemical space: multi-level Bayesian optimization with hierarchical coarse-graining<\/span><\/a>, Chem. Sci.,10.1039.D5SC03855C <span style=\"color:#ddd; font-size:12px\">2083<\/span><\/li><li>Hummerich S, Bereau T, K\u00f6the U (2025). <a href=\"https:\/\/doi.org\/10.48550\/arxiv.2511.01464\"><span class=\"publication-title\">Split-Flows: Measure Transport and Information Loss Across Molecular Resolutions<\/span><\/a>, arXiv. https:\/\/arxiv.org\/abs\/2511.01464. <span style=\"color:#ddd; font-size:12px\">2274<\/span><\/li><li>Viliuga V, Seute L, Wolf N, Wagner S, Elofsson A, St\u00fchmer J, Gr\u00e4ter F (2025). <a href=\"https:\/\/doi.org\/10.48550\/arxiv.2508.18211\"><span class=\"publication-title\">Flexibility-Conditioned Protein Structure Design with Flow Matching<\/span><\/a>, arXiv. https:\/\/arxiv.org\/abs\/2508.18211. <span style=\"color:#ddd; font-size:12px\">2283<\/span><\/li><\/ul><h2 id=\"publication-year-2024\">2024<\/h2><ul class=\"publications-list\"><li>Han SB, Teuffel J, Mukherjee G, Wade RC (2024). <a href=\"https:\/\/doi.org\/10.1002\/pro.5165\"><span class=\"publication-title\">Multiresolution molecular dynamics simulations reveal the interplay between conformational variability and functional interactions in membrane-bound cytochrome 2B4<\/span><\/a>, Protein Science 33(10),e5165 <span style=\"color:#ddd; font-size:12px\">1860<\/span><\/li><li>Gryn\u2019ova G, Bereau T, M\u00fcller C, Friederich P, Wade RC, Nunes-Alves A, Soares TA, Merz K (2024). <a href=\"https:\/\/doi.org\/10.1021\/acs.jcim.4c01300\"><span class=\"publication-title\">EDITORIAL: Chemical Compound Space Exploration by Multiscale High-Throughput Screening and Machine Learning<\/span><\/a>, J. Chem. Inf. Model. 2024, 64, 15, 5737\u20135738 <span style=\"color:#ddd; font-size:12px\">1856<\/span><\/li><li>Sokolov M, Hoffmann DS, Dohmen PM, Kr\u00e4mer M, H\u00f6fener S, Kleinekath\u00f6fer U, Elstner M (2024). <a href=\"https:\/\/doi.org\/10.1039\/D4CP02116A\"><span class=\"publication-title\">Non-adiabatic molecular dynamics simulations provide new insights into the exciton transfer in the Fenna\u2013Matthews\u2013Olson complex<\/span><\/a>, Phys. Chem. Chem. Phys., 2024,26, 19469-19496 <span style=\"color:#ddd; font-size:12px\">1857<\/span><\/li><li>Ghalami F, Dohmen PM, Kr\u00e4mer M, Elstner M, Xie W (2024). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.4c00220\"><span class=\"publication-title\">Nonadiabatic Simulation of Exciton Dynamics in Organic Semiconductors Using Neural Network-Based Frenkel Hamiltonian and Gradients<\/span><\/a>, J. Chem. Theory Comput. 2024, 20, 14, 6160\u20136174 <span style=\"color:#ddd; font-size:12px\">1858<\/span><\/li><li>Riedmiller K, Reiser P, Bobkova E, Maltsev K, Gryn\u2019ova G, Friederich P, Gr\u00e4ter F (2024). <a href=\"https:\/\/doi.org\/10.1039\/D3SC03922F\"><span class=\"publication-title\">Substituting density functional theory in reaction barrier calculations for hydrogen atom transfer in proteins<\/span><\/a>, Chem. Sci.,10.1039.D3SC03922F <span style=\"color:#ddd; font-size:12px\">1781<\/span><\/li><li>Zhou C, Neubert M, Koide Y, Zhang Y, Vuong V, Schl\u00f6der T, Dehnen S, Friederich P (2024). <a href=\"https:\/\/arxiv.org\/abs\/2412.00401\"><span class=\"publication-title\">PAL \u2013 Parallel active learning for machine-learned potentials<\/span><\/a>, arXiv,cs.LG,2412.00401 <span style=\"color:#ddd; font-size:12px\">2061<\/span><\/li><li>Galperin D, K\u00f6the U (2024). <a href=\"https:\/\/doi.org\/10.48550\/arxiv.2410.19426\"><span class=\"publication-title\">Analyzing Generative Models by Manifold Entropic Metrics<\/span><\/a>, arXiv. https:\/\/arxiv.org\/abs\/2410.19426. <span style=\"color:#ddd; font-size:12px\">2279<\/span><\/li><li>Wahl S, Rousselot A, Draxler F, Schopmans H, K\u00f6the U (2024). <a href=\"https:\/\/doi.org\/10.48550\/arxiv.2410.19492\"><span class=\"publication-title\">TRADE: Transfer of Distributions between External Conditions with Normalizing Flows<\/span><\/a>, arXiv. https:\/\/arxiv.org\/abs\/2410.19492. <span style=\"color:#ddd; font-size:12px\">2280<\/span><\/li><\/ul><h2 id=\"publication-year-2023\">2023<\/h2><ul class=\"publications-list\"><li>Remme R, Kaczun T, Scheurer M, Dreuw A, Hamprecht FA (2023). <a href=\"https:\/\/doi.org\/10.1063\/5.0158275\"><span class=\"publication-title\">KineticNet: Deep learning a transferable kinetic energy functional for orbital-free density functional theory<\/span><\/a>, The Journal of Chemical Physics 159(14),144113 <span style=\"color:#ddd; font-size:12px\">1822<\/span><\/li><li>Fedorov R, Gryn\u2019ova G (2023). <a href=\"https:\/\/doi.org\/10.1021\/acs.jctc.3c00355\"><span class=\"publication-title\">Unlocking the Potential: Predicting Redox Behavior of Organic Molecules, from Linear Fits to Neural Networks<\/span><\/a>, J. Chem. Theory Comput. 19(15):4796-4814 <span style=\"color:#ddd; font-size:12px\">1685<\/span><\/li><li>Ruff R, Reiser P, St\u00fchmer J, Friederich P (2023). <a href=\"https:\/\/doi.org\/10.48550\/arxiv.2302.14102\"><span class=\"publication-title\">Connectivity Optimized Nested Graph Networks for Crystal Structures<\/span><\/a>, arXiv. https:\/\/arxiv.org\/abs\/2302.14102. <span style=\"color:#ddd; font-size:12px\">2281<\/span><\/li><\/ul><h2 id=\"publication-year-2022\">2022<\/h2><ul class=\"publications-list\"><li>Reiser P, Neubert M, Eberhard A, Torresi L, Zhou C, Shao C, Metni H, Hoesel Cv, Schopmans H, Sommer T, Friederich P (2022). <a href=\"https:\/\/doi.org\/10.1038\/s43246-022-00315-6\"><span class=\"publication-title\">Graph neural networks for materials science and chemistry<\/span><\/a>, Commun Mater 3(1),93 <span style=\"color:#ddd; font-size:12px\">1686<\/span><\/li><li>Lippmann P, Sanmart\u00edn EF, Hamprecht FA (2022). <a href=\"https:\/\/doi.org\/10.48550\/arXiv.2210.07702\"><span class=\"publication-title\">Theory and Approximate Solvers for Branched Optimal Transport with Multiple Sources<\/span><\/a>, arXiv,cs.LG,2210.07702 <span style=\"color:#ddd; font-size:12px\">1689<\/span><\/li><\/ul>      <\/div>\n\n  <\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":107,"featured_media":44766,"parent":44617,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"page-templates\/group.php","meta":{"_acf_changed":false,"inline_featured_image":false,"footnotes":""},"hits-research-group":[1422],"class_list":["post-44621","page","type-page","status-publish","has-post-thumbnail","hentry","hits-research-group-simplaix"],"acf":[],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.7 - 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