If you would like to acknowledge funding provided by M3ODEL, please include the following statement:
"X.X. acknowledges funding from the Mainz Institute of Multiscale Modeling, M3ODEL".
If the research fits within our scope, but didn't get financial support, you can still acknowledge M3ODEL with:
"This study contributes to research done in the Mainz Institute of Multiscale Modeling, M3ODEL".
Our research covers many fields. To highlight those, we use a color code by field, based on the main affiliation of the PIs. The fields are:
A: Atmospheric Physics; B: Biology/Bioinformatics; C: Chemistry; G: Geosciences; I: Informatics; M: Mathematics; P: Physics
A: Atmospheric Physics; B: Biology/Bioinformatics; C: Chemistry; G: Geosciences; I: Informatics; M: Mathematics; P: Physics
PIs in bold; students & post-docs in bold and italics
2025
[47] Zippo E., D. Dormann, T. Speck, L. Stelzl. Molecular simulations of enzymatic phosphorylation of disordered proteins and their condensates. Nature Communications 16, 4649 (2025). doi:10.1038/s41467-025-59676-4
[46] Alagna N., J. Spangenberg, S. Mündnich, A. Busch, S. Pastore, A. Wierczeiko, W. Goettsch, V. Dietrich, L. Pryszcz, S. Cruciani, E.M. Novoa, K. Joshi, R. Perera, S. Di Giorgio, P. Arrubarrena, I. Tellioglu, C.-L. Poon, Y. Wan, J. Göke, A. Hildebrand, C. Dieterich, M. Helm, M. Marz, S. Gerber. Predicting RNA modifications by nanopore sequencing: The RMaP challenge. Communications Chemistry, accepted (2025)
[45] Pastore S., P. Hillenbrand, N. Molnar, I. Kovlyagina, M. Chanu Chongtham, S. Sys, B. Lutz, M. Tevosian, S. Gerber. ClearFinder: a Python GUI for annotating cells in cleared mouse brain. BMC Bioinformatics 26 (24) (2025). doi:10.1186/s12859-025-06039-x
2024
[44] Hewel C., [...], S. Sys, T. Butto, N. Paul, J. Koch, F. Lyko, F. Kraft, S. Schweiger, E.A. Lemke, M. Helm, M. Linke, S. Gerber. Direct RNA sequencing (RNA004) allows for improved transcriptome assessment and near real-time tracking of methylation for medical applications. bioRxiv (2024). doi:10.1101/2024.07.25.605188
[43] Sys S.J., A. Ceron-Noriega, A. Kerber, S. Weissbach, S. Schweiger, M. Wand, K. Everschor-Sitte, S. Gerber. Chromatin Capture Upsampling Toolbox - CCUT: A Versatile and unified Framework to Train Your Chromatin Capture Deep Learning Models. bioRxiv (2024). doi:10.1101/2024.05.29.596528
[42] Boisserée S., E. Moulas, M. Bachmayr. Fluid flow channeling and mass transport with discontinuous porosity distribution. arXiv:2411.14211 (2024). doi:10.48550/arXiv.2411.14211
[41] Franzen D., J. Disselhoff, D. Hartmann. The LMM ARChitect: Solving ARC-AGI Is a Matter of Perspective. (2024). https://arcprize.org/2024-results
[40] Christian H.X., A. Mehmeti-Göpel, M. Wand. On the Weight Dynamics of Deep Normalized Networks. Proceedings of the 41st International Conference on Machine Learning, PMLR 235:992-1007 Volume 235, 21-27 July 2024, Vienna, Austria. https://proceedings.mlr.press/v235/ali-mehmeti-gopel24a.html
[39] Niebler S., B. Schmidt, P. Spichtinger, H. Tost. Scalable GPU-enabled creation of three dimensional weather fronts. Proceedings of the Platform for Advanced Scientific Computing (PASC) Conference 2024, 2, 1-12 (2024). doi:10.1145/3659914.3659916
[38] Lukacova-Medvid'ova M., S. Schneider. Estimatable variation neural networks and their application to ODEs and scalar hyperbolic conservation laws. arXiv:2409.08909 (2024). doi:10.48550/arXiv.2409.08909
[37] Gonçalves-Kulik M., L. A. Baptista, F. Schmid, M.A. Andrade-Navarro. Assessing the helical stability of polyXYs at the boundaries of Intrinsically Disordered Regions with MD simulations. bioRxiv 2024.11.16.623902 (2024). doi:10.1101/2024.11.16.623902
[36] Kaus B.J.P., M. Thielmann, P. Aellig, L. de Siena, J. Frasunkiewicz, L. Fuchs, A. Piccolo, H. Ranocha, N. Riel, A. Spang, T. Weiler. GeophysicalModelGenerator.jl: A Julia package to visualise geoscientific data and create numerical model setups. Journal of Open Source Software 9, 6763 (2024). doi:10.21105/joss.06763.
[35] Changiarath A., D. Flores-Solis, J. Michels, R.H. Rodriguez, S.M. Hanson, F. Schmid, M. Zweckstetter, J. Padeken, L.S. Stelzl. Promoter and Gene-Body RNA-Polymerase II co-exist in partial demixed condensates. bioRxiv 2024, 2024.03.16.585180 (2024). doi:10.1101/2024.03.16.585180.
[34] Mazzucchelli M., E. Moulas, B.J.P. Kaus, T. Speck. Fluid-mineral equilibrium under nonhydrostatics stress: Insight from molecular dynamics. American Journal of Science 324, 2 (2024). doi:10.2475/001c.92881
[33] Zhang Y., A. Stovas, L. de Siena. Wavefield simulation and reverse time migration for acoustic TTI media. Geophysics 89 (2024). doi:10.1190/geo2023-0137.1
[32] Changiarath A., J. Michels, R. Herrera Rodriguez, S.M. Hanson, F. Schmid, J. Padeken, L.S. Stelzl. Conditions for the co-existence of promoter and gene-body condensates. BioRxiv 2024.03.16.585180 (2024). doi:10.1101/2024.03.16.585180
[31] Krüger M., A. Mishra, P. Spichtinger, U. Pöschl, T. Berkemeier. A numerical compass for experiment design in chemical kinetics and molecular property estimation. Journal of Cheminformatics 16, 34 (2024). doi:10.1186/s13321-024-00825-0
2023
[30] Bachmayr M., S. Boisserée, L.M. Kreusser. Analysis of nonlinear poroviscoelastic flows with discontinuous porosities. Nonlinearity 36 (12) (2023). doi:10.1088/1361-6544/ad0871
[29] King T., L. De Siena, Y. Zhang, N. Nakata, P. Bensons, S. Vinciguerra. Mapping faults in the laboratory with seismic scattering 2: the modelling perspective. Geophysical Journal International 234(2) (2023). doi:10.1093/gji/ggad100
[28] Gonçalves-Kulik M., F. Schmid, M.A. Andrade-Navarro. One Step Closer to the Understanding of the Relationship IDR-LCR-Structure. Genes. 14(9), 1711 (2023). doi:10.3390/genes14091711
[27] Flores-Solis D., I.P. Lushpinskaia, A.A. Polyansky, A. Changiarath, M. Boehning, M. Mirkovic, J. Walshe, L.M. Pietrek, P. Cramer, L.S. Stelzl, B. Zagrovic, M. Zweckstetter. Driving forces behind phase separation of the carboxy-terminal domain of RNA polymerase II. Nature Communications 14, 5979 (2023). doi:10.1038/s41467-023-41633-8
[26] Lemcke S., J.H. Appeldorn, M. Wand, T. Speck. Toward a structural identification of metastable molecular conformations. The Journal of Chemical Physics 159 (11), 114106 (2023). doi:10.1063/5.0164145
[25] Sourpis A.I., N.C. Forero-Martinez, F. Schmid. The Effect of Electric Fields on the Structure of Water/Acetonitrile Mixtures. The Journal of the Electrochemical Society 170(8), 083508. doi:10.1149/1945-7111/acef61
2022
[24] Gerber S., L. Pospisil, S. Sys, C. Hewel, A. Torkamani, I. Horenko. Co-inference of data mislabelings reveals improved models in genomics and breast cancer diagnostics. Frontiers in Artificial Intelligence 4 (2022). doi:10.3389/frai.2021.739432
[23] Sys S., S. Weißbach, L. Jakob, S. Gerber, C. Schneider. CollembolAI, a macrophotography and computer vision workflow to digitize and characterize samples of soil invertebrate communities preserved in fluid. Methods in Ecology and Evolution 13, 2729-2742 (2022). doi:10.1111/2041-210X.14001
[22] Feireisl E., M. Lukáčová-Medvidova, S. Schneider, B. She. Approximating viscosity solutions of the Euler system. Mathematics of Computation 91, 2129-2164 (2022). doi:10.1090/mcom/3738
[21] Gonçalves-Kulik M., P. Mier, K. Kastano, J. Cortés, P. Bernadó, F. Schmid, M.A. Andrade-Navarro. Low Complexity Induces Structure in Protein Regions Predicted as Intrinsically Disordered. Biomolecules 12, 1098 (2022). doi:10.3390/biom12081098
[20] Bauer D.J., L. Stelzl, A. Nikoubashman. Single-chain and condensed-state behavior of hnRNPA1 from molecular simulations. J. Chem. Phys. 157, 154903 (2022). doi:10.1063/5.0105540
[19] Niebler S., A. Miltenberger, B. Schmidt, P. Spichtinger. Automated detection and classification of synoptic scale fronts from atmospheric data grids. Weather and Climate Dynamics 3, 113-137 (2022). doi:10.5194/wcd-3-113-2022
[18] Moulas E., B.J.P. Kaus, B. Jamtveit. Dynamic Pressure Variations in the Lower Crust Caused by Localized Fluid-Induced Weakening. Communications Earth and Environment 3:157, 1-7 (2022). doi:10.1038/s43247-022-00478-7
[17] Di Martino M.P., L. De Siena, N. Tisato. Pore Space Topology Controls Ultrasonic Waveforms in Dry Volcanic Rocks. Geophysical Research Letters 49 (2022). doi:10.1029/2022GL100310
2021
[16] Chen C., M.K. Singh, K. Wunderlich, S. Harvey, C. Whitfield, Z. Zhou, M. Wagner, K. Landfester, I. Lieberwirth, G. Fytas, K. Kremer, D. Mukherji, D.Y.W. Ng, T. Weil. Polymer cyclization for the emergence of hierarchical nanostructures. Nature Communications 12, 3959 (2021). doi:10.1038/s41467-021-24222-5
[15] Weißbach S., S. Sys, C. Hewel, H. Todorov, S. Schweiger, J. Winter, M. Pfenninger, A. Torkamani, D. Evans, J. Burger, K. Everschor-Sitte, H. May-Simera, S. Gerber. Reliability of genomic variants across different next-generation sequencing platforms and bioinformatic processing pipelines. BMC Genomics 22, 62 (2021). doi:10.1186/s12864-020-07362-8
[14] Rodrigues D.R., K. Everschor-Sitte, S. Gerber, I. Horenko. A deeper look into natural sciences with physics-based and data-driven measures. iScience 24, 3 (2021). doi:10.1016/j.isci.2021.102171
[13] Li B., K. Daoulas, F. Schmid. Dynamic coarse-graining of polymer systems using mobility functions. Journal of Physics: Condensed Matter 33, 194004 (2021). doi:10.1088/1361-648X/abed1b
[12] Datta R., L. Yelash, F. Schmid, F. Kummer, M. Oberlack, M. Lukáčová-Medvidova, P. Virnau. Shear-thinning in oligomer melts-molecular origin and applications. Polymers 13(16), 2806 (2021). doi:10.3390/polym13162806
[11] Bockius N., J. Shea, G. Jung, F. Schmid, M. Hanke. Model reduction techniques for the computation of extended Markov parameterizations for generalized Langevin equations. Journal of Physics: Condensed Matter 33, 214003 (2021). doi:10.1088/1361-648X/abe6df
[10] Grulich L., R. Weigel, A. Hildebrandt, M. Wand, P. Spichtinger. Automatic shape detection of ice crystals. Journal of Computational Science, 54, 101429 (2021). doi: 10.1016/j.jocs.2021.101429
[9] Kottwitz M.O., A.A. Popov, S. Abe, B.J.P. Kaus. Investigating the effects of intersection flow localization in equivalent-continuum-based upscaling of flow in discrete fracture networks. Solid Earth 12, 2235–2254 (2021). doi:10.5194/se-12-2235-2021
[8] G.S. Reuber. Statistical and deterministic inverse methods in the geosciences: introduction, review, and application to the nonlinear diffusion equation. GEM International Journal on Geomathematics 12:19 (2021). doi:10.1007/s13137-021-00186-y
2020
[7] G.S. Reuber, L. Holbach, A.A. Popov, M. Hanke, B.J.P. Kaus. Inferring rheology and geometry of subsurface structures by adjoint-based inversion of principal stress directions. Geophys. J. International 223.2 (2020): 851-861. doi:10.1093/gji/ggaa344
[6] Jangizehi A., F. Schmid, P. Besenius, K. Kremer, S. Seiffert. Defects and defect engineering in soft matter. Soft Matter 16, 10809-10859 (2020). doi:10.1039/d0sm01371d
[5] Fischer A., F. Schmid, T. Speck. Quorum-sensing active particles with discontinuous motility. Physical Review E 101, 012601 (2020). doi:10.1103/PhysRevE.101.012601
[4] Stieffenhofer M., M. Wand, T. Bereau. Adversarial reverse mapping of equilibrated condensed-phase molecular structures. Machine Learning: Science and Technology 1 (4), 045014 (2020). doi:10.1088/2632-2153/abb6d4
[3] Rosemeier J., P. Spichtinger. Pattern formation in clouds via Turing instabilities. Mathematics of Climate and Weather Forecasting 6, 75-96 (2020). doi:10.1515/mcwf-2020-0104
2019
[2] Chertock A., A. Kurganov, M. Lukáčová-Medvidova, P. Spichtinger, B. Wiebe. Stochastic Galerkin method for cloud simulation. Mathematics of Climate and Weather Forecasting 5, 65-106 (2019). doi:10.1515/mcwf-2019-0005
[1] Baumgartner M., M. Sagebaum, N. Gauger, P. Spichtinger, A. Brinkmann. Algorithmic differentiation for cloud schemes (IFS Cy43r3) using CoDiPack (v1.8.1). Geoscientific Model Development 12, 5197-5212 (2019). doi:10.5194/gmd-12-5197-2019