Featured & Joint Publications

Publications are color coded by fields:
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

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. doi:10.21105/joss.06763.

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; doi:10.1101/2024.03.16.585180.

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

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

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. doi:10.1101/2024.03.16.585180

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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