Publications

You can also find my articles on my Google Scholar profile.

Preprints

1. "Systematic Analysis of Biomolecular Conformational Ensembles with PENSA"
   M. Vögele, N. J. Thomson, S. T. Truong, J. McAvity, U. Zachariae, R. O. Dror
   arXiv:2212.02714 [q-bio.BM] 2022

Research Articles

1. "Is the Functional Response of a Receptor Determined by the Thermodynamics of Ligand Binding?"
   M. Vögele, B. W. Zhang, J. Kaindl, L. Wang
   J. Chem. Theory Comput. 2023, 19, 22, 8414–8422; ChemRxiv:2023-p1507
2. "Nanoporous Membranes of Densely Packed Carbon Nanotubes Formed by Lipid-Mediated Self-Assembly"
   M. Vögele, J. Köfinger, G. Hummer
   ACS Appl. Bio Mater. 2022
3. "Euclidean Transformers for Macromolecular Structures: Lessons Learned"
   D. D. Liu, L. Melo, A. Costa, M. Vögele, R. J. L. Townshend, R. O. Dror
   ICML Computational Biology 2022
4. "Atypical structural snapshots of human cytomegalovirus GPCR interactions with host G proteins"
   N. Tsutsumi*, S. Maeda*, Q. Qu*, M. Vögele*, K. M. Jude, C.-M. Suomivuori, O. Panova, D. Waghray, H. E. Kato, A. Velasco, R. O. Dror, G. Skiniotis, B. K. Kobilka, K. C. Garcia
   Sci. Adv. 2022, 8(3):eabl5442
5. "ATOM3D: Tasks On Molecules in Three Dimensions"
   R. J. L. Townshend, M. Vögele*, P. Suriana*, A. Derry*, A. Powers, Y. Laloudakis, S. Balachandar, B. Jing, B. Anderson, S. Eismann, R. Kondor, R. B. Altman, R. O. Dror
   NeurIPS Datasets and Benchmarks 2021 (Best Paper Award); arXiv:2012.04035
6. "PDADMAC/PSS Oligoelectrolyte Multilayers: Internal Structure and Hydration Properties at Early Growth Stages from Atomistic Simulations"
   P. A. Sánchez, M. Vögele, J. Smiatek, B. Qiao, M. Sega, C. Holm
   Molecules 2020, 25, 1848
7. "Atomistic simulation of PDADMAC/PSS oligoelectrolyte multilayers: overall comparison of tri- and tetra-layer systems"
   P. A. Sánchez, M. Vögele, J. Smiatek, B. Qiao, M. Sega, C. Holm
   Soft Matter 2019, 15, 9437-9451; arXiv:1910.14506
8. "Finite-Size-Corrected Rotational Diffusion Coefficients of Membrane Proteins and Carbon Nanotubes from Molecular Dynamics Simulations"
   M. Vögele, J. Köfinger, G. Hummer
   J. Phys. Chem. B 2019, 123, 5099−5106
9. "Membrane perforation by the pore-forming toxin pneumolysin"
   M. Vögele, R. M. Bhaskara, E. Mulvihill, K. van Pee, Ö. Yildiz, W. Kühlbrandt, D. J. Müller, G. Hummer
   Proc. Natl. Acad. Sci. U.S.A 2019, 116(27), 13352–13357
10. "Molecular dynamics simulations of carbon nanotube porins in lipid bilayers"
    M. Vögele, J. Köfinger, G. Hummer
    Faraday Discuss. 2018, 209, 341
11. "Hydrodynamics of Diffusion in Lipid Membrane Simulations"
    M. Vögele, J. Köfinger, G. Hummer
    Phys. Rev. Lett. 2018, 120, 268104; arXiv:1803.04714
12. "Carbon Nanotubes Mediate Fusion of Lipid Vesicles"
    R. M. Bhaskara, S. M. Linker, M. Vögele, J. Köfinger, G. Hummer
    ACS Nano 2017, 11(2), 1273–1280
13. "Divergent Diffusion Coefficients in Simulations of Fluids and Lipid Membranes"
    M. Vögele, G. Hummer
    J. Phys. Chem. B 2016, 120(33), 8722–8732
14. "Coarse-grained simulations of polyelectrolyte complexes: MARTINI models for poly(styrene sulfonate) and poly(diallyldimethylammonium)"
    M. Vögele, C. Holm, J. Smiatek
    J. Chem. Phys. 2015, 143, 243151
15. "Properties of the polarizable MARTINI water model: A comparative study for aqueous electrolyte solutions"
    M. Vögele, C. Holm, J. Smiatek
    J. Mol. Liq. 2015, 212, 103-110

Public Reports

1. "Max Planck PhDNet Survey Report 2018"
   B. Regler, L. Einhorn, J. Lasser, M. Vögele, S. Elizarova, F. Bäuerle, C. Wu, S. Förste, J. Shenolikar
   (PDF at MPG Pure)

Discussions and Opinion

1. "Reply to Desikan et al.: Micelle formation among various mechanisms of toxin pore formation"
   M. Vögele, R. M. Bhaskara, E. Mulvihill, K. van Pee, Ö. Yildiz, W. Kühlbrandt, D. J. Müller, G. Hummer
   Proc. Natl. Acad. Sci. U.S.A 2020, 117(10), 5109–5110
2. "Perceptions of publication pressure in the Max Planck Society"
   C. M. Wu, B. Regler, F. K. Bäuerle, M. Vögele, L. Einhorn, S. Elizarova, S. Förste, J. Shenolikar, J. Lasser
   Nat. Hum. Behav. 2019, 3, 1029–1030
3. "The modelling and enhancement of water hydrodynamics: general discussion"
   M. Baaden, M. P. Borthakur, S. Casanova, R. Coalson, V. Freger, M. Gonzalez, A. Góra, B. Hinds, W. Hirunpinyopas, G. Hummer, M. Kumar, C. Lynch, S. Murail, A. Noy, M. Sansom, Q. Song, H. Vashisth, M. Vögele
   Faraday Discuss. 2018, 209, 273
4. "Biomimetic water channels: general discussion"
   M. Baaden, M. Barboiu, R. M. Bill, C.-L. Chen, J. Davis, M. Di Vincenzo, V. Freger, M. Fröba, P. A. Gale, B. Gong, C. Hélix-Nielsen, R. Hickey, B. Hinds, J.-L. Hou, G. Hummer, M. Kumar, Y.-M. Legrand, M. Lokesh, B. Mi, S. Murail, P. Pohl, M. Sansom, Q. Song, W. Song, S. Törnroth-Horsefield, H. Vashisth, M. Vögele
   Faraday Discuss. 2018, 209, 205