Life Sciences - Research Group of Sebastian Thallmair
Publications
Preprints
4. P. C. T. Souza*, L. Borges-Araújo, C. Brasnett, R. A. Moreira, F. Grünewald, P. Park, L. Wang, H. Razmazma, A. C. Borges-Araújo, L. F. Cofas-Vargas, L. Monticelli, R. Mera-Adasme, M. N. Melo, S. Wu, S. J. Marrink*, A. B. Poma*, S. Thallmair*
GōMartini 3: From large conformational changes in proteins to environmental bias corrections
bioRxiv (2024).
3. C. Gil Herrero, S. Thallmair*
GPCR Surface Creates a Favorable Pathway for Membrane Permeation of Drug Molecules
bioRxiv (2024).
2. V. Thallmair, L. Schultz, S. Evers, C. Goecke, S. Thallmair, M. G. Leitner, D. Oliver*
Local PI(4,5)P2 Pool Dynamics Detected by the Coincidence Biosensor TubbyCT Maintain the Integrity of ER-PM Junctions During PLC Signaling
bioRxiv (2020).
1. J. P. P. Zauleck, S. Thallmair, R. de Vivie-Riedle*
Revisiting an Approximation in the Wilson G-matrix Formalism and Its Impact on Molecular Quantum Dynamics
arXiv (2017).
Public Outreach
5. S. Thallmair
Wie Lichtschalter in Medikamenten der Zukunft eingesetzt werden können
FIAS Forum Lecture Series, FIAS, Frankfurt am Main, Germany, 07/03/2024.
4. A. Störiko, S. Thallmair
Sensor enables analysis of an important cellular scavenger
FIAS News (13/07/2023).
3. A. Störiko, S. Thallmair
New binding site to cell membrane identified
FIAS News and Press Release (07/09/2022).
2. S. Thallmair
Warum brauchen Pflanzen keine Sonnencreme?
public evening talk at the Nationalpark Haus St. Peter-Ording, Germany, 27/07/2019.
1. P. E. C. Melis, S. J. Marrink, S. Thallmair, A. Blass, V. Spandan Arza, J. Nijkamp, N. Janssen, G. Závodszky
On the Use of 3D Printing for Scientific Visualization
3D printing project for scientific and public outreach, 05/2017 – 06/2018.
Publications
50. L. Borges-Araújo, A. Borges-Araújo, T. Ozturk, D. P. Ramirez-Echemendia, B. Fábián, T. S. Carpenter, S. Thallmair, J. Barnoud, H. I. Ingólfsson, G. Hummer, D. P. Tieleman, S. J. Marrink, P. C. T. Souza*, M. N. Melo*
Martini 3 Coarse-Grained Force Field for Cholesterol
J. Chem. Theory Comput. 19, 7387 (2023).
49. V. Thallmair, L. Schultz, S. Evers, T. Jolie, C. Goecke, M. G. Leitner, S. Thallmair, D. Oliver*
Localization of the Tubby Domain, a PI(4,5)P2 Biosensor, to E-Syt3-rich ER-PM Junctions
J. Cell Sci. 136, jcs260848 (2023).
48. S. Emmert, G. Quargnali, S. Thallmair, P. Rivera-Fuentes*
A Locally Activatable Sensor for Robust Quantification of Organellar Glutathion
Nat. Chem. 15, 1415 (2023).
47. B. Fábián*, S. Thallmair, G. Hummer
Optimal bond-constraint topology for molecular dynamics simulations of cholesterol
J. Chem. Theory Comput. 19, 1592 (2023).
46. R. Alessandri, S. Thallmair, C. Gil Herrero, R. Mera-Adasme, S. J. Marrink, P. C. T. Souza
A Practical Introduction to Martini 3 and its Application to Protein-Ligand Binding Simulations
in "A Practical Guide to Recent Advances in Multiscale Modeling and Simulation of Biomolecules" edited by Y. Wang, R. Zhou, AIP Publishing, Melville, New York, pp. 1-1—1-34 (2023).
45. V. Thallmair, L. Schultz, W. Zhao, S. J. Marrink, D. Oliver*, S. Thallmair*
Two Cooperative Binding Sites Sensitize PI(4,5)P2 Recognition by the Tubby Domain
Sci. Adv. 8, eabp9471 (2022).
44. J. Volarić, S. Thallmair, B. L. Feringa*, W. Szymanski*
Photoswitchable, Water-soluble Bis-azobenzene Cross-linkers with Enhanced Properties for Biological Applications
ChemPhotoChem 6, e202200170 (2022).
43. B. Fábián*, S. Thallmair, G. Hummer
Small Ionic Radii Limit Time Step in Martini 3 Molecular Dynamics Simulations
J. Chem. Phys. 157, 034101 (2022).
42. J. Losa, S. Leupold, D. Alonso-Martinez, P. Vainikka, S. Thallmair, K. M. Tych, S. J. Marrink, M. Heinemann*
Perspective: A Stirring Role for Metabolism in Cells
Mol. Syst. Biol. 18, e10822 (2022).
41. P. Kobauri, N. S. Galenkamp, A. M. Schulte, J. de Vries, N. A. Simeth, G. Maglia, S. Thallmair, D. Kolarski, W. Szymanski*, B. L. Feringa*
Hypothesis-Driven, Structure-Based Design in Photopharmacology: The Case of eDHFR Inhibitors
J. Med. Chem. 65, 4798 (2022).
40. F. Azadi-Chegeni, S. Thallmair, M. E. Ward, G. Perin, S. J. Marrink, M. Baldus, T. Morosinotto, A. Pandit*
Protein Dynamics and Lipid Affinity of Monomeric Zeaxanthin-Binding LHCII in Thylakoid Membranes
Biophys. J. 121, 396 (2022).
39. P. A. Vainikka, S. Thallmair, P. C. T. Souza, S. J. Marrink*
Martini 3 Coarse-Grained Model for Type III Deep Eutectic Solvents: Thermodynamic, Structural, and Extraction Properties
ACS Sustainable Chem. Eng. 9, 17338 (2021).
38. C. Ramírez-Palacios, H. J. Wijma, S. Thallmair, S. J. Marrink, D. B. Janssen*
Computational Prediction of ω-Transaminase Specificity by a Combination of Docking and Molecular Dynamics Simulations
J. Chem. Inf. Model. 61, 5569 (2021).
37. S. Thallmair†*, M. Javanainen†*, B. Fábián, H. Martinez-Seara, S. J. Marrink
Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations
J. Phys. Chem. B 125, 9537 (2021).
36. Q. Meng†, C. Ramírez-Palacios†, N. Capra, M. E. Hooghwinkel, S. Thallmair, H. J. Rozeboom, A.-M. W. H. Thunnissen, H. J. Wijma, S. J. Marrink, D. B. Janssen*
Computational Redesign of an ω-Transaminase from Pseudomonas jessenii for Asymmetric Synthesis of Enantiopure Bulky Amines
ACS Catal. 11, 10733 (2021).
35. P. C. T. Souza*, R. Alessandri, J. Barnoud, S. Thallmair, I. Faustino, F. Grünewald, I. Patmanidis, H. Abdizadeh, B. M. H. Bruininks, T. A. Wassenaar, P. C. Kroon, J. Melcr, V. Nieto, V. Corradi, H. M. Khan, J. Domanski, M. Javanainen, H. Martinez-Seara, N. Reuter, R. B. Best, I. Vattulainen, L. Monticelli, X. Periole, D. P. Tielemann, A. H. de Vries, S. J. Marrink*
Martini 3: A General Purpose Force Field for Coarse-Grained Molecular Dynamics
Nat. Methods 18, 382 (2021).
34. P. Kobauri, W. Szymanski*, F. Cao, S. Thallmair, S. J. Marrink, M. D. Witte, F. J. Dekker*, B. L. Feringa*
Biaryl Sulfonamides as cisoid Azosteres for Photopharmacology
Chem. Commun. 57, 4126 (2021).
33. S. Schönfeld, W. Bauer, S. Thallmair, G. Hörner*, B. Weber*
Running in the Family: Molecular Factors Controlling Spin Crossover of Iron(II) Complexes with Schiff‐base Like Ligands
Z. Anorg. Allg. Chem. 647, 905 (2021).
32. P. C. T. Souza†*, S. Thallmair†, P. Conflitti, J. C. Ramírez Palacios, R. Alessandri, S. Raniolo, V. Limongelli, S. J. Marrink*
Protein-Ligand Binding with the Coarse-Grained Martini Model
Nat. Commun. 11, 3714 (2020).
31. N. Liguori†*, R. Croce, S. J. Marrink, S. Thallmair†*
Molecular Dynamics Simulations in Photosynthesis
Photosynth. Res. 144, 273 (2020).
30. H. M. Khan*, P. C. T. Souza, S. Thallmair, J. Barnoud, A. H. De Vries, S. J. Marrink, N. Reuter*
Capturing choline-aromatics cation-π interactions in the MARTINI force field
J. Chem. Theory Comput. 16, 2550 (2020).
29. Q. Zhou, J. Chen, Y. Luan, P. A. Vainikka, S. Thallmair, S. J. Marrink, B. L. Feringa*, P. van Rijn*
Unidirectional Rotating Molecular Motors Dynamically Interact with Adsorbed Proteins to Direct the Fate of Mesenchymal Stem Cells
Sci. Adv. 6, eaay2756 (2020).
28. P. C. T. Souza, S. Thallmair, S. J. Marrink*, R. Mera-Adasme*
An Allosteric Pathway in SOD1 Unravels the Molecular Mechanism of the G93A ALS-Linked Mutation
J. Phys. Chem. Lett. 10, 7740 (2019).
27. R. Alessandri, P. C. T. Souza, S. Thallmair, M. N. Melo, A. H. De Vries, S. J. Marrink*
Pitfalls of the Martini Model
J. Chem. Theory Comput. 15, 5448 (2019).
26. S. Thallmair*, P. A. Vainikka, S. J. Marrink*
Lipid fingerprint and cofactor dynamcis of light-harvesting complex II in different membranes
Biophys. J. 116, 1446 (2019).
25. S. Thallmair*, S. J. Marrink
Chromophore arrangement in light-harvesting complex II influenced by the protein dynamics on the microsecond time scale
EPJ Web Conf. 205, 09039 (2019).
24. S. Thallmair*, H. I. Ingólfsson, S. J. Marrink*
Cholesterol Flip-Flop Impacts Domain Registration in Plasma Membrane Models
J. Phys. Chem. Lett. 9, 5527 (2018).
23. J. P. P. Zauleck, M. T. Peschel, F. Rott, S. Thallmair, R. de Vivie-Riedle*
Ultrafast reactive quantum dynamics coupled to classical solvent dynamics using an Ehrenfest approach
J. Phys. Chem. A 122, 2849 (2018).
22. S. Thallmair*, P. A. Vainikka, S. J. Marrink
Molecular dynamcis of light-harvesting complex II embedded in the thylakoid membrane
Biophys. J. 114, 522a (2018).
21. E. Riedle*, M. K. Roos, S. Thallmair, C. F. Sailer, N. Krebs, B. P. Fingerhut, R. de Vivie-Riedle*
Ultrafast photochemistry with two product channels: wavepacket motion through two distinct conical intersections
Chem. Phys. Lett. 683, 128-134 (2017).
20. D. Keefer†, S. Thallmair†, S. Matsika, R. de Vivie-Riedle*
Controlling photorelaxation in uracil with shaped laser pulses: A theoretical assessment
J. Am. Chem. Soc. 139, 5061-5066 (2017).
19. S. Thallmair, D. Keefer, F. M. Rott, R. de Vivie-Riedle*
Simulating the control of molecular reactions via modulated light fields: From gas phase to solution
J. Phys. B: At. Mol. Opt. Phys. 50, 082001 (2017).
18. J. P. P. Zauleck, S. Thallmair, M. Loipersberger, R. de Vivie-Riedle*
Two new methods to generate internal coordinates for molecular wave packet dynamics in reduced dimensions
J. Chem. Theory Comput. 12, 5698-5708 (2016).
17. D. Keefer*, S. Thallmair, S. Matsika, R. de Vivie-Riedle
How to Control the Ultrafast Dynamics of Uracil with Shaped Laser Pulses: Theoretical Insights
in International Conference on Ultrafast Phenomena, Optical Society of America (2016), paper UTh3B.2.
16. D. Keefer*, S. Thallmair, J. P. P. Zauleck, R. de Vivie-Riedle
Optimal Control Theory for Molecular Reactions in Atomistic Surroundings
in International Conference on Ultrafast Phenomena, Optical Society of America (2016), paper UTh3B.5.
15. S. Thallmair, M. K. Roos, R. de Vivie-Riedle*
Design of specially adapted reactive coordinates to economically compute potential and kinetic energy operators including geometry relaxation
J. Chem. Phys. 144, 234104 (2016).
14. S. Thallmair, M. K. Roos, R. de Vivie-Riedle*
Molecular features in complex environment: Cooperative team players during excited state bond cleavage
Struct. Dyn. 3, 023601 (2016).
13. D. Keefer, S. Thallmair, J. P. P. Zauleck, R. de Vivie-Riedle*
A Multi Target Approach to Control Chemical Reactions in Their Inhomogeneous Solvent Environment
J. Phys. B: At. Mol. Opt. Phys. 48, 234003 (2015).
12. S. Thallmair, J. P. P. Zauleck, R. de Vivie-Riedle*
Quantum Dynamics in an Explicit Solvent Environment: A Photochemical Bond Cleavage Treated with a Combined QD/MD Approach
J. Chem. Theory Comput. 11, 1987-1995 (2015).
11. S. Thallmair*, J. P. P. Zauleck, R. de Vivie-Riedle
Quantum Dynamics of Molecular Reactions Directed by Explicit Solvent Environment
in: Ultrafast Phenomena XIX, K. Yamanouchi, S. Cundiff, R. de Vivie- Riedle, M. Kuwata-Gonokami, L. S. DiMauro (Eds.), Springer, 2015, 373-377.
10. S. Thallmair, M. Kowalewski, J. P. P. Zauleck, M. K. Roos, R. de Vivie-Riedle*
Quantum Dynamics of a Photochemical Bond Cleavage Influenced by the Solvent Environment: A Dynamic Continuum Approach
J. Phys. Chem. Lett. 5, 3480-3485 (2014).
9. S. Thallmair, R. Siemering, P. Kölle, M. Kling, M. Wollenhaupt, T. Baumert, R. de Vive-Riedle*
The Interplay of Nuclear and Electronic Motion in the Control of Molecular Processes: A Theoretical Perspective
in: Molecular Quantum Dynamics – from Theory to Applications, F. Gatti (Ed.), Springer, 2014, 213-248.
8. S. Thallmair, B. P. Fingerhut, R. de Vivie-Riedle*
Ground and Excited State Surfaces for the Bond Cleavage in Phenylmethylphenylphosphonium Ions
J. Phys. Chem. A 117, 10626-10633 (2013).
7. J. Ammer*, C. Nolte, K. Karagiosoff*, S. Thallmair, P. Mayer, R. de Vivie-Riedle, H. Mayr
Ion-Pairing of Phosphonium Salts in Solution: C–H∙∙∙Halogen and C–H∙∙∙π Hydrogen Bonds
Chem. Eur. J. 19, 14612-14630 (2013).
6. S. Thallmair*, M. Kowalewski, B. P. Fingerhut, C. F. Sailer, R. de Vivie-Riedle
Molecular Wave Packet Dynamics Decelerated by Solvent Environment: A Theoretical Approach
in: Ultrafast Phenomena XVIII, M. Chergui, S. Cundiff, A. Taylor, R. de Vivie-Riedle, K. Yamanouchi (Eds.), EPJ Web of Conferences 41, 05043 (2013).
5. C. F. Sailer, S. Thallmair, B. P. Fingerhut, C. Nolte, J. Ammer, H. Mayr, I. Pugliesi, R. de Vivie-Riedle, E. Riedle*
A Comprehensive Microscopic Picture of the Benzhydryl Radical and Cation Photogeneration and Interconversion Through Electron Transfer
Chem. Phys. Chem. 14, 1423-1437 (2013).
4. P. von den Hoff, S. Thallmair, M. Kowalewski, R. Siemering, R. de Vivie-Riedle*
Optimal Control Theory – Closing the Gap Between Theory and Experiment
Phys. Chem. Chem. Phys. 14, 14460-14485 (2012).
3. T. M. Pfaffeneder, S. Thallmair, W. Bauer, B. Weber*
Complete and Incomplete Spin Transitions in 1D Chain Iron(II) Compounds
New J. Chem. 35, 691-700 (2010).
2. C. Gollub, M. Kowalewski, S. Thallmair, R. de Vivie-Riedle*
Chemoselective Quantum Control of Carbonyl Bonds in Grignard Reactions Using Shaped Laser Pulses
Phys. Chem. Chem. Phys. 12, 15780-15787 (2010).
1. S. Thallmair, W. Bauer, B. Weber*
Strategies towards the Purposeful Design of Long-Range Ferromagnetic Ordering Due to Spin Canting
Polyhedron 28, 1796-1801 (2009).
†these authors contributed equally
*(co)corresponding author