Publications of the Department (MPG.PuRe list)

Gomez, A.; Erb, T. J.; Grubmüller, H.; Vöhringer-Martinez, E.: Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO₂ Fixation. Journal of Chemical Information and Modeling 63 (24), pp. 7807 - 7815 (2023)

Heinz, L.; Grubmüller, H.: Why Solvent Response Contributions to Solvation Free Energies Are Compatible with Ben-Naim’s Theorem. Journal of Chemical Theory and Computation 19 (22), pp. 8013 - 8019 (2023)

Dieball, C.; Wellecke, G.; Godec, A.: Asymmetric thermal relaxation in driven systems: Rotations go opposite ways. Physical Review Research 5 (4), L042030 (2023)

Motycka, B.; Csarman, F.; Rupp, M.; Schnabel, K.; Nagy, G.; Karnpakdee, K.; Scheiblbrandner, S.; Tscheliessnig, R.; Oostenbrink, C.; Hammel, M. et al.; Ludwig, R.: Amino Acid Residues Controlling Domain Interaction and Interdomain Electron Transfer in Cellobiose Dehydrogenase. ChemBioChem: A European Journal of Chemical Biology 24 (22), e202300431 (2023)

Wilson, C.J.; Karttunen, M.; de Groot, B. L.; Gapsys, V.: Accurately Predicting Protein pK_a Values Using Nonequilibrium Alchemy. Journal of Chemical Theory and Computation 19 (21), pp. 7833 - 7845 (2023)

Eltzner, B.; Hansen, P. E. H.; Huckemann, S. F.; Sommer, S.: Diffusion means in geometric spaces. Bernoulli 29 (4), pp. 3141 - 3170 (2023)

Kozlowski, N.; Grubmüller, H.: Uncertainties in Markov State Models of Small Proteins. Journal of Chemical Theory and Computation 19 (16), pp. 5516 - 5524 (2023)

Hartich, D.; Godec, A.: Violation of local detailed balance upon lumping despite a clear timescale separation. Physical Review Research 5 (3), L032017 (2023)

Paternoga, H.; Crowe-McAuliffe, C.; Bock, L. V.; Koller, T. O.; Morici, M.; Beckert, B.; Myasnikov, A. G.; Grubmüller, H.; Nováček, J.; Wilson, D. N.: Structural conservation of antibiotic interaction with ribosomes. Nature Structural & Molecular Biology 30, pp. 1380 - 1392 (2023)

Wiechers, H.; Kehl, A.; Hiller, M.; Eltzner, B.; Huckemann, S.F.; Meyer, A.; Tkach, I.; Bennati, M.; Pokern, Y.: Bayesian optimization to estimate hyperfine couplings from ¹⁹F ENDOR spectra. Journal of Magnetic Resonance 353, 107491 (2023)

Kopec, W.; Thomson, A. S.; de Groot, B. L.; Rothberg, B. S.: Interactions between selectivity filter and pore helix control filter gating in the MthK channel. Journal of General Physiology 155 (8), e202213166 (2023)

Boothroyd, S.; Behara, P. K.; Madin, O. C.; Hahn, D. F.; Jang, H.; Gapsys, V.; Wagner, J. R.; Horton, J. T.; Dotson, D. L.; Thompson, M. W. et al.; Maat, J.; Gokey, T.; Wang, L.-P.; Cole, D. J.; Gilson, M. K.; Chodera, J. D.; Bayly, C. I.; Shirts, M. R.; Mobley, D. L.: Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field. Journal of Chemical Theory and Computation 19 (11), pp. 3251 - 3275 (2023)

Lam, C. K.; de Groot, B. L.: Ion Conduction Mechanisms in Potassium Channels Revealed by Permeation Cycles. Journal of Chemical Theory and Computation 19 (9), pp. 2574 - 2589 (2023)

Bock, L. V.; Gabrielli, S.; Kolář, M. H.; Grubmüller, H.: Simulation of Complex Biomolecular Systems: The Ribosome Challenge. Annual Review of Biophysics 52, pp. 361 - 390 (2023)

Moore, J. H.; Margreitter, C.; Janet, J. P.; Engkvist, O.; de Groot, B. L.; Gapsys, V.: Automated relative binding free energy calculations from SMILES to ΔΔG. Communications Chemistry 6, 82 (2023)

Gu, R.-X.; de Groot, B. L.: Central cavity dehydration as a gating mechanism of potassium channels. Nature Communications 14 (1), 2178 (2023)

Matthes, D.; de Groot, B. L.: Molecular dynamics simulations reveal the importance of amyloid-beta oligomer β-sheet edge conformations in membrane permeabilization. The Journal of Biological Chemistry 299 (4), 103034 (2023)

Pan, Y.; Pohjolainen, E.; Schmidpeter, P. A. M.; Vaiana, A. C.; Nimigean, C. M.; Grubmüller, H.; Scheuring, S.: Discrimination between cyclic nucleotides in a cyclic nucleotide-gated ion channel. Nature Structural and Molecular Biology 30, pp. 512 - 520 (2023)

Wiechers, H.; Eltzner, B.; Mardia, K. V.; Huckemann, S. F.: Learning torus PCA-based classification for multiscale RNA correction with application to SARS-CoV-2. Journal of the Royal Statistical Society - Series C: Applied Statistics 72 (2), pp. 271 - 293 (2023)

Dieball, C.; Godec, A.: Feynman-Kac theory of time-integrated functionals: Itô versus functional calculus. Journal of Physics A 56 (15), 155002 (2023)

Dieball, C.; Godec, A.: Direct Route to Thermodynamic Uncertainty Relations and Their Saturation. Physical Review Letters 130 (8), 087101 (2023)

Blom, K.; Ziethen, N.; Zwicker, D.; Godec, A.: Thermodynamically consistent phase-field theory including nearest-neighbor pair correlations. Physical Review Research 5 (1), 013135 (2023)

Badocha, M.; Wieczór, M.; Marciniak, A.; Kleist, C.; Grubmüller, H.; Czub, J.: Molecular mechanism and energetics of coupling between substrate binding and product release in the F₁-ATPase catalytic cycle. Proceedings of the National Academy of Sciences of the United States of America 120 (8), e2215650120 (2023)

Hauke, L.; Primeßnig, A.; Eltzner, B.; Radwitz, J.; Huckemann, S. F.; Rehfeldt, F.: FilamentSensor 2.0: An open-source modular toolbox for 2D/3D cytoskeletal filament tracking. PLoS One 18 (2), e0279336 (2023)

Godec, A.; Makarov, D. E.: Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories. The Journal of Physical Chemistry Letters 14 (1), pp. 49 - 56 (2023)

Bebon, R.; Godec, A.: Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime. Physical Review Letters 131 (23), 237101 (2023)

Wieczor, M.; Genna, V.; Aranda, J.; Badia, R. M.; Lluis Gelpi, J.; Gapsys, V.; de Groot, B. L.; Lindahl, E.; Municoy, M.; Hospital, A. et al.; Orozco, M.: Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case. Wiley Interdisciplinary Reviews: Computational Molecular Science 13 (1), e1622 (2023)

Schultze, S.; Grubmüller, H.: Bayesian structure determination of multiple conformational structures from single-molecule X-ray scattering images. (2023)

Dieball, C.; Godec, A.: Direct Route to Thermodynamic Uncertainty Relations and Their Saturation. (2023)