Publications of the Department (MPG.PuRe list)

Journal Article

Rennekamp, B.; Grubmüller, H.; Gräter, F.: Hidden length lets collagen buffer mechanical and chemical stress. Physical Review E 110, 054408 (2024)

MPG.PuRe

Journal Article

Goswami, K.; Cherstvy, A. G.; Godec, A.; Metzler, R.: Anomalous diffusion of active Brownian particles in responsive elastic gels: Nonergodicity, non-Gaussianity, and distributions of trapping times. Physical Review E 110, 044609 (2024)

MPG.PuRe

Journal Article

Schultze, S.; Grubmüller, H.: Bayesian electron density determination from sparse and noisy single-molecule X-ray scattering images. Science Advances 10 (43), eadp4425 (2024)

MPG.PuRe

Journal Article

Hartich, D.; Godec, A.: Comment on “Inferring broken detailed balance in the absence of observable currents”. Nature Communications 15, 8678 (2024)

MPG.PuRe

Journal Article

Gapsys, V.; Kopec, W.; Matthes, D.; de Groot, B. L.: Biomolecular simulations at the exascale: From drug design to organelles and beyond. Current Opinion in Structural Biology 88, 102887 (2024)

MPG.PuRe

Journal Article

Mendez-Otalvaro, E.; Kopec, W.; de Groot, B. L.: Effect of two activators on the gating of a K_2P channel. Biophysical Journal 123 (19), pp. 3408 - 3420 (2024)

MPG.PuRe

Journal Article

Chiu, P.-L.; Orjuela, J. D.; de Groot, B. L.; Aponte Santamaría, C.; Walz, T.: Structure and dynamics of cholesterol-mediated aquaporin-0 arrays and implications for lipid rafts. eLife 12, RP90851 (2024)

MPG.PuRe

Journal Article

Nagy, G.; Hoffmann, S. V.; Jones, N. C.; Grubmüller, H.: Reference Data Set for Circular Dichroism Spectroscopy Comprised of Validated Intrinsically Disordered Protein Models. Applied Spectroscopy 78 (9), pp. 897 - 911 (2024)

MPG.PuRe

10.

Journal Article

Vollmar, L.; Bebon, R.; Schimpf, J.; Flietel, B.; Celiksoy, S.; Sönnichsen, C.; Godec, A.; Hugel, T.: Model-free inference of memory in conformational dynamics of a multi-domain protein. Journal of Physics A 57 (36), 365001 (2024)

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11.

Journal Article

Dieball, C.; Godec, A.: Thermodynamic Bounds on Generalized Transport: From Single-Molecule to Bulk Observables. Physical Review Letters 133 (6), 067101 (2024)

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12.

Journal Article

Konold, P. E.; Monrroy, L.; Bellisario, A.; Filipe, D.; Adams, P.; Alvarez, R.; Bean, R.; Bielecki, J.; Bódizs, S.; Ducrocq, G. et al.; Grubmüller, H.; Kirian, R. A.; Kloos, M.; Koliyadu, J. C. P.; Koua, F. H. M.; Larkiala, T.; Letrun, R.; Lindsten, F.; Maihöfer, M.; Martin, A. V.; Mészáros, P.; Mutisya, J.; Nimmrich, A.; Okamoto, K.; Round, A.; Sato, T.; Valerio, J.; Westphal, D.; Wollter, A.; Yenupuri, T. V.; You, T.; Maia, F.; Westenhoff, S.: Microsecond time-resolved X-ray scattering by utilizing MHz repetition rate at second-generation XFELs. Nature Methods 21, pp. 1608 - 1611 (2024)

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13.

Journal Article

Mironenko, A.; de Groot, B. L.; Kopec, W.: Selectivity filter mutations shift ion permeation mechanism in potassium channels. PNAS Nexus 3 (7), pgae272 (2024)

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14.

Journal Article

Dunlop, J.; Cerisola, F.; Tabanera-Bravo, J.; Anders, J.: Thermodynamically optimal protocols for dual-purpose qubit operations. Physical Review Research 6 (3), 033005 (2024)

MPG.PuRe

15.

Journal Article

Lawson, C. L.; Kryshtafovych, A.; Pintilie, G. D.; Burley, S. K.; Černý, J.; Chen, V. B.; Emsley, P.; Gobbi, A.; Joachimiak, A.; Noreng, S. et al.; Prisant, M. G.; Read, R. J.; Richardson, J. S.; Rohou, A. L.; Schneider, B.; Sellers, B. D.; Shao, C.; Sourial, E.; Williams, C. I.; Williams, C. J.; Yang, Y.; Abbaraju, V.; Afonine, P. V.; Baker, M. L.; Bond, P. S.; Blundell, T. L.; Burnley, T.; Campbell, A.; Cao, R.; Cheng, J.; Chojnowski, G.; Cowtan, K. D.; DiMaio, F.; Esmaeeli, R.; Giri, N.; Grubmüller, H.; Hoh, S. W.; Hou, J.; Hryc, C. F.; Hunte, C.; Igaev, M.; Joseph, A. P.; Kao, W.-C.; Kihara, D.; Kumar, D.; Lang, L.; Lin, S.; Subramaniya, S. R. M. V.; Mittal, S.; Mondal, A.; Moriarty, N. W.; Muenks, A.; Murshudov, G. N.; Nicholls, R. A.; Olek, M.; Palmer, C. M.; Perez, A.; Pohjolainen, E.; Pothula, K. R.; Rowley, C. N.; Sarkar, D.; Schäfer, L. U.; Schlicksup, C. J.; Schröder, G. F.; Shekhar, M.; Si, D.; Singharoy, A.; Sobolev, O. V.; Terashi, G.; Vaiana, A. C.; Vedithi, S. C.; Verburgt, J.; Wang, X.; Warshamanage, R.; Winn, M. D.; Weyand, S.; Yamashita, K.; Zhao, M.; Schmid, M. F.; Berman, H. M.; Chiu, W.: Outcomes of the EMDataResource cryo-EM Ligand Modeling Challenge. Nature Methods 21, pp. 1340 - 1348 (2024)

MPG.PuRe

16.

Journal Article

Wilson, C. J.; de Groot, B. L.; Gapsys, V.: Resolving coupled pH titrations using alchemical free energy calculations. Journal of Computational Chemistry 45 (17), pp. 1444 - 1455 (2024)

MPG.PuRe

17.

Journal Article

Hahn, D. F.; Gapsys, V.; de Groot, B. L.; Mobley, D. L.; Tresadern, G.: Current State of Open Source Force Fields in Protein–Ligand Binding Affinity Predictions. Journal of Chemical Information and Modeling 64 (13), pp. 5063 - 5076 (2024)

MPG.PuRe

18.

Journal Article

Bock, L. V.; Igaev, M.; Grubmüller, H.: Single-particle Cryo-EM and molecular dynamics simulations: A perfect match. Current Opinion in Structural Biology 86, 102825 (2024)

MPG.PuRe

19.

Journal Article

Vanegas, L. J.; Eltzner, B.; Rudolf, D.; Dura, M.; Lehnart, S. E.; Munk, A.: Analyzing cross-talk between superimposed signals: Vector norm dependent hidden Markov models and applications to ion channels. The Annals of Applied Statistics 18 (2), pp. 1445 - 1470 (2024)

MPG.PuRe

20.

Journal Article

Lauer, S.M.; Reepmeyer, M.; Berendes, O.; Klepacki, D.; Gasse, J.; Gabrielli, S.; Grubmüller, H.; Bock, L. V.; Krizsan, A.; Nikolay, R. et al.; Spahn, C.M.T.; Hoffmann, R.: Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88. Nature Communications 15, 3945 (2024)

MPG.PuRe

21.

Journal Article

Blom, K.; Song, K.; Vouga, E.; Godec, A.; Makarov, D. E.: Milestoning estimators of dissipation in systems observed at a coarse resolution. PNAS 121 (17), e2318333121 (2024)

MPG.PuRe

22.

Journal Article

Miao, M.; Makarov, D. E.; Blom, K.: Nonequilibrium statistical mechanics of money/energy exchange models. Journal of Physics A 57 (15), 155003 (2024)

MPG.PuRe

23.

Journal Article

Zhao, X.; Hartich, D.; Godec, A.: Emergence of Memory in Equilibrium versus Nonequilibrium Systems. Physical Review Letters 132 (14), 147101 (2024)

MPG.PuRe

24.

Journal Article

Gersteuer, F.; Morici, M.; Gabrielli, S.; Fujiwara, K.; Safdari, H. A.; Paternoga, H.; Bock, L. V.; Chiba, S.; Wilson, D. N.: The SecM arrest peptide traps a pre-peptide bond formation state of the ribosome. Nature Communications 15, 2431 (2024)

MPG.PuRe

Full

25.

Journal Article

Morici, M.; Gabrielli, S.; Fujiwara, K.; Paternoga, H.; Beckert, B.; Bock, L. V.; Chiba, S.; Wilson, D. N.: RAPP-containing arrest peptides induce translational stalling by short circuiting the ribosomal peptidyltransferase activity. Nature Communications 15, 2432 (2024)

MPG.PuRe

26.

Journal Article

Gomez, A.; Tinzl, M.; Stoffel, G.; Westedt, H.; Grubmüller, H.; Erb, T.J.; Vöhringer-Martinez, E.; Stripp, S.T.: Infrared spectroscopy reveals metal-independent carbonic anhydrase activity in crotonyl-CoA carboxylase/reductase. Chemical Science 15, pp. 4960 - 4968 (2024)

MPG.PuRe

27.

Journal Article

Huang, P.; Abacka, H.; Wilson, C. J.; Wind, M. L.; Rutzler, M.; Hagstroem-Andersson, A.; Gourdon, P.; de Groot, B. L.; Venskutonyte, R.; Lindkvist-Petersson, K.: Molecular basis for human aquaporin inhibition. PNAS 121 (7), e2319682121 (2024)

MPG.PuRe

28.

Journal Article

Petrov, D.; Perthold, J.W.; Oostenbrink, C.; de Groot, B. L.; Gapsys, V.: Guidelines for Free-Energy Calculations Involving Charge Changes. Journal of Chemical Theory and Computation 20 (2), pp. 914 - 925 (2024)

MPG.PuRe

29.

Journal Article

Ibáñez, M.; Dieball, C.; Lasanta, A.; Godec, A.; Rica, R. A.: Heating and cooling are fundamentally asymmetric and evolve along distinct pathways. Nature Physics 20, pp. 135 - 141 (2024)

MPG.PuRe

Book Chapter (1)

30.

Book Chapter

Bebon, R.; Godec, A.: Concentration of Empirical First-Passage Times. In: Target Search Problems, pp. 31 - 53 (Eds. Grebenkov, D.; Metzler, R.; Oshanin, G.). Springer Nature Switzerland, Cham (2024)

MPG.PuRe

Preprint (4)

31.

Preprint

Kalutskii, M.; Grubmüller, H.; Volkov, V. A.; Igaev, M.: Microtubule dynamics are defined by conformations and stability of clustered protofilaments. bioRxiv (2024)

MPG.PuRe

32.

Preprint

Otteson, L.; Nagy, G.; Kunkel, J.; Kodis, G.; Zheng, W.; Bignon, C.; Longhi, S.; Grubmüller, H.; Vaiana, A. C.; Vaiana, S. M.: Transient Non-local Interactions Dominate the Dynamics of Measles Virus N_TAIL. bioRxiv (2024)

MPG.PuRe

33.

Preprint

Griesinger, C.; Sant, V.; Matthes, D.; Mazal, H.; Antonschmidt, L.; Wieser, F.; Tekwani Movellan, K.; Xue, K.; Nimerovsky, E.; Stampolaki, M. et al.; Nathan, M.; Riedel, D.; Becker, S.; Sandoghdar, V.; de Groot, B. L.; Andreas, L. B.: Lipidic folding pathway of α-Synuclein via a toxic oligomer. Research Square (2024)

MPG.PuRe

34.

Preprint

Luke, D. R.; Schultze, S.; Grubmüller, H.: Stochastic Algorithms for Large-Scale Composite Optimization: the Case of Single-Shot X-FEL Imaging. arXiv (2024)

MPG.PuRe