Publications

Journal Article (76)

1.
Journal Article
Bonazzi, F.; Hall, C.; Weikl, T. R.: Membrane morphologies induced by mixtures of arc-shaped particles with opposite curvature. Soft Matter 17 (2), pp. 268 - 275 (2021)
2.
Journal Article
Kav, B.; Grafmüller, A.; Schneck, E.; Weikl, T. R.: Weak carbohydrate-carbohydrate interactions in membrane adhesion are fuzzy and generic. Nanoscale 12 (33), pp. 17342 - 17353 (2020)
3.
Journal Article
Weikl, T. R.; Hemmateenejad, B.: Accessory mutations balance the marginal stability of the HIV-1 protease in drug resistance. Proteins: Structure, Function, and Bioinformatics 88 (3), pp. 476 - 484 (2020)
4.
Journal Article
Antila, H.; Buslaev, P.; Favela-Rosales, F.; Mendes Ferreira, T.; Gushchin, I.; Javanainen, M.; Kav, B.; Madsen, J. J.; Melcr, J.; Miettinen, M. S. et al.; Määttä, J.; Nencini, R.; Ollila, O.H. S.; Piggot, T. J.: Headgroup Structure and Cation Binding in Phosphatidylserine Lipid Bilayers. The Journal of Physical Chemistry B 123 (43), pp. 9066 - 9079 (2019)
5.
Journal Article
Bonazzi, F.; Weikl, T. R.: Membrane morphologies induced by arc-shaped scaffolds are determined by arc angle and coverage. Biophysical Journal 116 (7), pp. 1239 - 1247 (2019)
6.
Journal Article
Mobaraki, N.; Hemmateenejad, B.; Weikl, T. R.; Sakhteman, A.: On the relationship between docking scores and protein conformational changes in HIV-1 protease. Journal of molecular graphics and modelling 91, pp. 186 - 193 (2019)
7.
Journal Article
Steinkühler, J.; Różycki, B.; Alvey, C.; Lipowsky, R.; Weikl, T. R.; Dimova, R.; Discher, D. E.: Membrane fluctuations and acidosis regulate cooperative binding of “marker of self” CD47 with macrophage checkpoint receptor SIRPα. Journal of Cell Science 132 (4), JCS216770 (2019)
8.
Journal Article
Bahrami, A. H.; Weikl, T. R.: Curvature-mediated assembly of Janus nanoparticles on membrane vesicles. Nano Letters 18 (2), pp. 1259 - 1263 (2018)
9.
Journal Article
Bassereau, P.; Jin, R.; Baumgart, T.; Deserno, M.; Dimova, R.; Frolov, V. A.; Bashkirov, P. V.; Grubmüller, H.; Jahn, R.; Risselada, H. J. et al.; Johannes, L.; Kozlov, M. M.; Lipowsky, R.; Pucadyil, T. J.; Zeno, W. F.; Stachowiak, J. C.; Stamou, D.; Breuer, A.; Lauritsen, L.; Simon, C.; Sykes, C.; Voth, G. A.; Weikl, T. R.: The 2018 biomembrane curvature and remodeling roadmap. Journal of Physics D: Applied Physics 51 (34), 343001 (2018)
10.
Journal Article
Paul, F.; Noé, F.; Weikl, T. R.: Identifying conformational-selection and induced-fit aspects in the binding-induced folding of PMI from Markov state modeling of atomistic simulations. Journal of Physical Chemistry B 122 (21), pp. 5649 - 5656 (2018)
11.
Journal Article
Sadeghi, M.; Weikl, T. R.; Noe, F.: Particle-based membrane model for mesoscopic simulation of cellular dynamics. The Journal of Chemical Physics 148 (4), 044901 (2018)
12.
Journal Article
Weikl, T. R.: Membrane-mediated cooperativity of proteins. Annual Review of Physical Chemistry 69, pp. 521 - 539 (2018)
13.
Journal Article
Meurer, A.; Smith, C. P.; Paprocki, M.; Čertík, O.; Kirpichev, S. B.; Rocklin, M.; Kumar, A.; Ivanov, S.; Moore, J. K.; Singh, S. et al.; Rathnayake, T.; Vig, S.; Granger, B. E.; Muller, R. P.; Bonazzi, F.; Gupta, H.; Vats, S.; Johansson, F.; Pedregosa, F.; Curry, M. J.; Terrel, A. R.; Roučka, Š.; Saboo, A.; Fernando, I.; Kulal, S.; Cimrman, R.; Scopatz, A.: SymPy: symbolic computing in Python. PeerJ Computer Science 3, e103 (2017)
14.
Journal Article
Paul, F.; Wehmeyer, C.; Abualrous, E. T.; Wu, H.; Crabtree, M. D.; Schöneberg, J.; Clarke, J.; Freund, C.; Weikl, T. R.; Noé, F.: Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nature Communications 8, 1095 (2017)
15.
Journal Article
Raatz, M.; Weikl, T. R.: Membrane tubulation by elongated and patchy nanoparticles. Advanced Materials Interfaces 4 (1), 1600325 (2017)
16.
Journal Article
Bahrami, A. H.; Lipowsky, R.; Weikl, T. R.: The role of membrane curvature for the wrapping of nanoparticles. Soft Matter 12 (2), pp. 581 - 587 (2016)
17.
Journal Article
Kav, B.; Ozturk, M.; Kabakcioglu, A.: Function changing mutations in glucocorticoid receptor evolution correlate with their relevance to mode coupling. Proteins: Structure, Function, and Bioinformatics 84 (5), pp. 655 - 665 (2016)
18.
Journal Article
Paul, F.; Weikl, T. R.: How to distinguish conformational selection and induced fit based on chemical relaxation rates. PLoS Computational Biology 12 (9), e1005067 (2016)
19.
Journal Article
Sadeghi, J.; Khurshudyan, M.; Farahani, H.: Phenomenological varying modified chaplygin gas with variable G and Λ: toy models for our universe. International Journal of Theoretical Physics, Group Theory and Nonlinear Optics 55 (1), pp. 81 - 97 (2016)
20.
Journal Article
Weikl, T. R.; Hu, J.; Xu, G.-K.; Lipowsky, R.: Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: insights from computational model systems and theory. Cell Adhesion and Migration 10 (5), pp. 576 - 589 (2016)
21.
Journal Article
Curtis, E. M.; Bahrami, A. H.; Weikl, T. R.; Hall, C. K.: Modeling nanoparticle wrapping or translocation in bilayer membranes. Nanoscale 7 (34), pp. 14505 - 14514 (2015)
22.
Journal Article
Hu, J.; Xu, G.-K.; Lipowsky, R.; Weikl, T. R.: Binding kinetics of membrane-anchored receptors and ligands: molecular dynamics simulations and theory. The Journal of Chemical Physics 143 (24), 243137 (2015)
23.
Journal Article
Xu, G.-K.; Hu, J.; Lipowsky, R.; Weikl, T. R.: Binding constants of membrane-anchored receptors and ligands: a general theory corroborated by Monte Carlo simulations. The Journal of Chemical Physics 143 (24), 243136 (2015)
24.
Journal Article
Bahrami, A. H.; Raatz, M.; Agudo-Canalejo, J.; Michel, R.; Curtis, E. M.; Hall, C. K.; Gradzielski, M.; Lipowsky, R.; Weikl, T. R.: Wrapping of nanoparticles by membranes. Advances in Colloid and Interface Science 208, pp. 214 - 224 (2014)
25.
Journal Article
Raatz, M.; Lipowsky, R.; Weikl, T. R.: Cooperative wrapping of nanoparticles by membrane tubes. Soft Matter 10 (20), pp. 3570 - 3577 (2014)
26.
Journal Article
Weikl, T. R.; Paul, F.: Conformational selection in protein binding and function. Protein Science 23 (11), pp. 1508 - 1518 (2014)
27.
Journal Article
Bahrami, A. H.: Orientational changes and impaired internalization of ellipsoidal nanoparticles by vesicle membranes. Soft Matter 9 (36), pp. 8642 - 8646 (2013)
28.
Journal Article
Hu, J. L.; Lipowsky, R.; Weikl, T. R.: Binding constants of membrane-anchored receptors and ligands depend strongly on the nanoscale roughness of membranes. Proceedings of the National Academy of Sciences of the United States of America 110 (38), pp. 15283 - 15288 (2013)
29.
Journal Article
Lipowsky, R.; Rouhiparkouhi, T.; Discher, D. E.; Weikl, T. R.: Domain formation in cholesterol-phospholipid membranes exposed to adhesive surfaces or environments. Soft Matter 9 (35), pp. 8438 - 8453 (2013)
30.
Journal Article
Neuman, B. W.; Kiss, G.; Al-Mulla, H. M. N.; Dokland, T.; Buchmeier, M. J.; Weikl, T.; Schley, D.: Direct observation of membrane insertion by enveloped virus matrix proteins by phosphate displacement. PLoS One 8 (2), e57916 (2013)
31.
Journal Article
Perez-Hernandez, G.; Paul, F.; Giorgino, T.; De Fabritiis, G.; Noe, F.: Identification of slow molecular order parameters for Markov model construction. The Journal of Chemical Physics 139 (1), 015102 (2013)
32.
Journal Article
Rouhiparkouhi, T.; Weikl, T. R.; Discher, D. E.; Lipowsky, R.: Adhesion-Induced Phase Behavior of Two-Component Membranes and Vesicles. International Journal of Molecular Sciences 14 (1), pp. 2203 - 2229 (2013)
33.
Journal Article
Weikl, T. R.; Hemmateenejad, B.: How conformational changes can affect catalysis, inhibition and drug resistance of enzymes with induced-fit binding mechanism such as the HIV-1 protease. Biochimica et Biophysica Acta: Proteins and Proteomics 1834 (5), pp. 867 - 873 (2013)
34.
Journal Article
Bahrami, A. H.; Lipowsky, R.; Weikl, T. R.: Tubulation and aggregation of spherical nanoparticles adsorbed on vesicles. Physical Review Letters 109 (18), 188102 (2012)
35.
Journal Article
Stieger, T.; Schoen, M.; Weikl, T. R.: Adhesion of surfaces mediated by adsorbed particles: Monte Carlo simulations and a general relationship between adsorption isotherms and effective adhesion energies. Soft Matter 8, pp. 11737 - 11745 (2012)
36.
Journal Article
Weikl, T. R.; Boehr, D. D.: Conformational selection and induced changes along the catalytic cycle of Escherichia coli dihydrofolate reductase. Proteins: Structure, Function, and Bioinformatics 80 (10), pp. 2369 - 2383 (2012)
37.
Journal Article
Hu, J. L.; Weikl, T.; Lipowsky, R.: Vesicles with multiple membrane domains. Soft Matter 7 (13), pp. 6092 - 6102 (2011)
38.
Journal Article
Krobath, H.; Rózycki, B.; Lipowsky, R.; Weikl, T. R.: Line tension and stability of domains in cell-adhesion zones mediated by long and short receptor-ligand complexes. PLoS One 6 (8), e23284 (2011)
39.
Journal Article
Rózycki, B.; Lipowsky, R.; Weikl, T. R.: Segregation of receptor-ligand complexes in cell adhesion zones: phase diagrams and the role of thermal membrane roughness. New Journal of Physics 12, 095003 (2010)
40.
Journal Article
Weikl, T. R.: Transition states in protein folding. Communications in Computational Physics 7 (2 Sp. Iss.), pp. 283 - 300 (2010)
41.
Journal Article
Krobath, H.; Rózycki, B.; Lipowsky, R.; Weikl, T. R.: Binding cooperativity of membrane adhesion receptors. Soft Matter 5 (17), pp. 3354 - 3361 (2009)
42.
Journal Article
Noe, F.; Schütte, C.; Vanden-Eijnden, E.; Reich, L.; Weikl, T. R.: Constructing the equilibrium ensemble of folding pathways from short off-equilibrium simulations. Proceedings of the National Academy of Sciences of the United States of America 106 (45), pp. 19011 - 19016 (2009)
43.
Journal Article
Reich, L.; Becker, M.; Seckler, R.; Weikl, T. R.: In vivo folding efficiencies for mutants of the P22 tailspike beta-helix protein correlate with predicted stability changes. Biophysical Chemistry 141 (2-3), pp. 186 - 192 (2009)
44.
Journal Article
Różycki, B.; Lipowsky, R.; Weikl, T. R.: Adhesion of surfaces via particle adsorption: exact results for a lattice of fluid columns. Journal of Statistical Mechanics: Theory and Experiment (11), P11006 (2009)
45.
Journal Article
Weikl, T. R.; Asfaw, M.; Krobath, H.; Rózycki, B.; Lipowsky, R.: Adhesion of membranes via receptor-ligand complexes: domain formation, binding cooperativity, and active processes. Soft Matter 5 (17), pp. 3213 - 3224 (2009)
46.
Journal Article
Weikl, T. R.; Deuster, C. v.: Selected-fit versus induced-fit protein binding: kinetic differences and mutational analysis. Proteins: Structure, Function, and Bioinformatics 75 (1), pp. 104 - 110 (2009)
47.
Journal Article
Dill, K. A.; Ozkan, S. B.; Shell, M. S.; Weikl, T. R.: The protein folding problem. Annual Review of Biophysics 37, pp. 289 - 316 (2008)
48.
Journal Article
Różycki, B.; Lipowsky, R.; Weikl, T.: Effective surface interactions mediated by adhesive particles. EPL 84 (2), 26004 (2008)
49.
Journal Article
Różycki, B.; Weikl, T. R.; Lipowsky, R.: Stable patterns of membrane domains at corrugated substrates. Physical Review Letters 100 (9), 098103 (2008)
50.
Journal Article
Weikl, T. R.: Transition states in protein folding kinetics: modeling Phi-Values of small beta-sheet proteins. Biophysical Journal 94 (3), pp. 929 - 937 (2008)
51.
Journal Article
Weikl, T. R.: Loop-closure principles in protein folding. Archives of Biochemistry and Biophysics 469 (1), pp. 67 - 75 (2008)
52.
Journal Article
Dill, K. A.; Ozkan, S. B.; Weikl, T. R.; Chodera, J. D.; Voelz, V. A.: The protein folding problem: when will it be solved? Current Opinion in Structural Biology 17 (3), pp. 342 - 346 (2007)
53.
Journal Article
Krobath, H.; Schütz, G. J.; Lipowsky, R.; Weikl, T. R.: Lateral diffusion of receptor-ligand bonds in membrane adhesion zones: effect of thermal membrane roughness. EPL 78 (3), 38003 (2007)
54.
Journal Article
Różycki, B.; Weikl, T. R.; Lipowsky, R.: Stochastic resonance for adhesion of membranes with active stickers. European Physical Journal E 22 (1), pp. 97 - 106 (2007)
55.
Journal Article
Weikl, T. R.; Dill, K. A.: Transition-states in protein folding kinetics: the structural interpretation of phi values. Journal of Molecular Biology (London) 365 (5), pp. 1578 - 1586 (2007)
56.
Journal Article
Asfaw, M.; Różycki, B.; Lipowsky, R.; Weikl, T. R.: Membrane adhesion via competing receptor/ligand bonds. EPL 76 (4), pp. 703 - 709 (2006)
57.
Journal Article
Dixit, P. D.; Weikl, T. R.: A simple measure of native-state topology and chain connectivity predicts the folding rates of two-state proteins with and without crosslinks. Proteins: Structure, Function, and Bioinformatics 64 (1), pp. 193 - 197 (2006)
58.
Journal Article
Reich, L.; Weikl, T. R.: Substructural cooperativity and parallel versus sequential events during protein unfolding. Proteins: Structure, Function, and Bioinformatics 63 (4), pp. 1052 - 1058 (2006)
59.
Journal Article
Różycki, B.; Lipowsky, R.; Weikl, T. R.: Adhesion of membranes with active stickers. Physical Review Letters 96 (4), 048101 (2006)
60.
Journal Article
Różycki, B.; Weikl, T. R.; Lipowsky, R.: Adhesion of membranes via switchable molecules. Physical Review E 73 (6), 061908 (2006)
61.
Journal Article
Weikl, T. R.: Wie Proteine ihre dreidimensionale Struktur finden. Bioforum 29, pp. 40 - 41 (2006)
62.
Journal Article
Merlo, C.; Dill, K. A.; Weikl, T. R.: phi values in protein-folding kinetics have energetic and structural components. Proceedings of the National Academy of Sciences of the United States of America 102 (29), pp. 10171 - 10175 (2005)
63.
Journal Article
Weikl, T. R.: Loop-closure events during protein folding: Rationalizing the shape of Phi-value distributions. Proteins: Structure, Function, and Genetics 60 (4), pp. 701 - 711 (2005)
64.
Journal Article
Weikl, T. R.; Lipowsky, R.: Pattern formation during T-cell adhesion. Biophysical Journal 87 (6), pp. 3665 - 3678 (2004)
65.
Journal Article
Weikl, T. R.; Palassini, M.; Dill, K. A.: Cooperativity in two-state protein folding kinetics. Protein Science 13 (3), pp. 822 - 829 (2004)
66.
Journal Article
Weikl, T. R.: Indirect interactions of membrane-adsorbed cylinders. European Physical Journal E 12 (2), pp. 265 - 273 (2003)
67.
Journal Article
Weikl, T. R.; Dill, K. A.: Folding rates and low-entropy-loss routes of two-state proteins. Journal of Molecular Biology (London) 329 (3), pp. 585 - 598 (2003)
68.
Journal Article
Weikl, T. R.; Dill, K. A.: Folding kinetics of two-state proteins: Effect of circularization, permutation, and crosslinks. Journal of Molecular Biology (London) 332 (4), pp. 953 - 963 (2003)
69.
Journal Article
Weikl, T. R.: Dynamic phase separation of fluid membranes with rigid inclusions. Physical Review E 66 (6), 061915, p. 061915 (2002)
70.
Journal Article
Weikl, T. R.; Andelman, D.; Komura, S.; Lipowsky, R.: Adhesion of membranes with competing specific and generic interactions. European Physical Journal E 8 (1), pp. 59 - 66 (2002)
71.
Journal Article
Weikl, T. R.; Groves, J. T.; Lipowsky, R.: Pattern formation during adhesion of multicomponent membranes. EPL 59 (6), pp. 916 - 922 (2002)
72.
Journal Article
Helfrich, W.; Weikl, T. R.: Two direct methods to calculate fluctuation forces between rigid objects embedded in fluid membranes. European Physical Journal E 5 (4), pp. 423 - 439 (2001)
73.
Journal Article
Weikl, T. R.; Lipowsky, R.: Adhesion-induced phase behavior of multicomponent membranes. Physical Review E 64 (1), 011903 (2001)
74.
Journal Article
Weikl, T. R.; Lipowsky, R.: Local adhesion of membranes to striped surface domains. Langmuir 16, pp. 9338 - 9346 (2000)
75.
Journal Article
Weikl, T. R.; Netz, R. R.; Lipowsky, R.: Unbinding transitions and phase separation of multicomponent membranes. Physical Review E 62, pp. R 45 - R 48 (2000)
76.
Journal Article
Weikl, T. R.; Kozlov, M. M.; Helfrich, W.: Interaction of conical membrane inclusions - effect of lateral tension. Physical Review E 57 (6), pp. 6988 - 6995 (1998)

Book Chapter (3)

77.
Book Chapter
Weikl, T. R.; Hu, J.; Kav, B.; Różycki, B.: Binding and segregation of proteins in membrane adhesion: theory, modeling, and simulations. In: Advances in Biomembranes and Lipid Self-Assembly, Vol. 30, pp. 159 - 194 (Ed. Lipowsky, R.) (2019)
78.
Book Chapter
Weikl, T. R.; Hu, J.; Kav, B.; Różycki, B.: Binding and segregation of proteins in membrane adhesion: theory, modeling, and simulations. In: Advances in Biomembranes and Lipid Self-Assembly, Vol. 30, pp. 159 - 194 (2019)
79.
Book Chapter
Weikl, T. R.; Lipowsky, R.: Membrane adhesion and domain formation. In: Advances in Planar Lipid Bilayers and Liposomes, Vol. 5, pp. 63 - 127 (2007)

Meeting Abstract (1)

80.
Meeting Abstract
Merlo, C.; Weikl, T. R.: The structural interpretation of phi-values in protein folding kinetics. In Biophysical Journal, 88 (1), p. 213A - 213A. (2005)

Thesis - PhD (5)

81.
Thesis - PhD
Kav, B.: Membrane adhesion mediated via lipid-anchored saccharides. Dissertation, 125 pp., Universität Potsdam, Potsdam (2019)
82.
Thesis - PhD
Bonazzi, F.: Shaping of membranes by arc-like particles. Dissertation, Technische Universität, Berlin (2018)
83.
Thesis - PhD
Paul, F.: Markov State Modeling of Binding and Conformational Changes of Proteins. Dissertation, 112 pp., Universität Potsdam, Potsdam (2017)
84.
Thesis - PhD
Bahrami, A. H.: Vesicles interacting with nanoparticles. Dissertation, 86 pp., Technische Universität, Berlin (2013)
85.
Thesis - PhD
Weikl, T.: Adhäsion von mehrkomponentigen Membranen. Dissertation, Universität Potsdam, Potsdam (1999)

Thesis - Habilitation (1)

86.
Thesis - Habilitation
Weikl, T.: Transition states and loop-closure principles in protein folding. Habilitation, Universität Potsdam, Potsdam (2007)

Editorial (1)

87.
Editorial
Zhou, R.; Weikl, T. R.; Ma, Y.-q.: Theoretical modeling of interactions at the bio-nano interface. Nanoscale 12 (19), pp. 10426 - 10429 (2020)
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