Publications

Journal Article

Kav, B.; Weikl, T. R.; Schneck, E.: Measuring pico-Newton forces with lipid anchors as force sensors in molecular dynamics simulations. The Journal of Physical Chemistry B 127 (18), pp. 4081 - 4089 (2023)

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Journal Article

Castillo, S. R.; Rickeard, B. W.; DiPasquale, M.; Nguyen, M. H. L.; Lewis-Laurent, A.; Doktorova, M.; Kav, B.; Miettinen, M. S.; Nagao, M.; Kelley, E. G. et al.; Marquardt, D.: Probing the link between pancratistatin and mitochondrial apoptosis through changes in the membrane dynamics on the nanoscale. Molecular Pharmaceutics 19 (6), pp. 1839 - 1852 (2022)

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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)

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Journal Article

Kav, B.; Demé, B.; Gege, C.; Tanaka, M.; Schneck, E.; Weikl, T. R.: Interplay of trans- and cis-interactions of glycolipids in membrane adhesion. Frontiers in Molecular Biosciences 8 (1047), 754654 (2021)

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Journal Article

Pandey, P. R.; Różycki, B.; Lipowsky, R.; Weikl, T. R.: Structural variability and concerted motions of the T cell receptor - CD3 complex. eLife 10, e67195 (2021)

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External

Journal Article

Różycki, B.; Weikl, T. R.: Cooperative stabilization of close-contact zones leads to sensitivity and selectivity in T-cell recognition. Cells 10 (5), 1023 (2021)

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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)

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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)

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10.

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)

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11.

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)

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12.

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)

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13.

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)

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External

14.

Journal Article

Weikl, T. R.; Hu, J.; Kav, B.; Różycki, B.: Binding and segregation of proteins in membrane adhesion: theory, modeling, and simulations. Advances in Biomembranes and Lipid Self-Assembly 30, pp. 159 - 194 (2019)

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15.

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)

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16.

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)

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17.

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)

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18.

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)

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pre-print

19.

Journal Article

Weikl, T. R.: Membrane-mediated cooperativity of proteins. Annual Review of Physical Chemistry 69, pp. 521 - 539 (2018)

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20.

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)

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21.

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)

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External

22.

Journal Article

Raatz, M.; Weikl, T. R.: Membrane tubulation by elongated and patchy nanoparticles. Advanced Materials Interfaces 4 (1), 1600325 (2017)

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23.

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)

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24.

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)

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25.

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)

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26.

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)

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27.

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)

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28.

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)

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29.

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)

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30.

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)

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31.

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)

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32.

Journal Article

Raatz, M.; Lipowsky, R.; Weikl, T. R.: Cooperative wrapping of nanoparticles by membrane tubes. Soft Matter 10 (20), pp. 3570 - 3577 (2014)

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33.

Journal Article

Weikl, T. R.; Paul, F.: Conformational selection in protein binding and function. Protein Science 23 (11), pp. 1508 - 1518 (2014)

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34.

Journal Article

Bahrami, A. H.: Orientational changes and impaired internalization of ellipsoidal nanoparticles by vesicle membranes. Soft Matter 9 (36), pp. 8642 - 8646 (2013)

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35.

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)

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36.

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)

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37.

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)

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38.

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)

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39.

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)

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40.

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)

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41.

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)

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42.

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)

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43.

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)

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44.

Journal Article

Hu, J. L.; Weikl, T.; Lipowsky, R.: Vesicles with multiple membrane domains. Soft Matter 7 (13), pp. 6092 - 6102 (2011)

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45.

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)

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46.

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)

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47.

Journal Article

Weikl, T. R.: Transition states in protein folding. Communications in Computational Physics 7 (2 Sp. Iss.), pp. 283 - 300 (2010)

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48.

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)

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49.

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)

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50.

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)

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51.

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)

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52.

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)

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53.

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)

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54.

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)

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55.

Journal Article

Różycki, B.; Lipowsky, R.; Weikl, T.: Effective surface interactions mediated by adhesive particles. EPL 84 (2), 26004 (2008)

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56.

Journal Article

Różycki, B.; Weikl, T. R.; Lipowsky, R.: Stable patterns of membrane domains at corrugated substrates. Physical Review Letters 100 (9), 098103 (2008)

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57.

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)

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58.

Journal Article

Weikl, T. R.: Loop-closure principles in protein folding. Archives of Biochemistry and Biophysics 469 (1), pp. 67 - 75 (2008)

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59.

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)

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60.

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)

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61.

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)

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62.

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)

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63.

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)

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64.

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)

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65.

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)

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66.

Journal Article

Różycki, B.; Lipowsky, R.; Weikl, T. R.: Adhesion of membranes with active stickers. Physical Review Letters 96 (4), 048101 (2006)

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67.

Journal Article

Różycki, B.; Weikl, T. R.; Lipowsky, R.: Adhesion of membranes via switchable molecules. Physical Review E 73 (6), 061908 (2006)

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68.

Journal Article

Weikl, T. R.: Wie Proteine ihre dreidimensionale Struktur finden. Bioforum 29, pp. 40 - 41 (2006)

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69.

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)

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70.

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)

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71.

Journal Article

Weikl, T. R.; Lipowsky, R.: Pattern formation during T-cell adhesion. Biophysical Journal 87 (6), pp. 3665 - 3678 (2004)

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72.

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)

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73.

Journal Article

Weikl, T. R.: Indirect interactions of membrane-adsorbed cylinders. European Physical Journal E 12 (2), pp. 265 - 273 (2003)

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74.

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)

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75.

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)

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76.

Journal Article

Weikl, T. R.: Dynamic phase separation of fluid membranes with rigid inclusions. Physical Review E 66 (6), 061915, p. 061915 (2002)

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77.

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)

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78.

Journal Article

Weikl, T. R.; Groves, J. T.; Lipowsky, R.: Pattern formation during adhesion of multicomponent membranes. EPL 59 (6), pp. 916 - 922 (2002)

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79.

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)

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80.

Journal Article

Weikl, T. R.: Fluctuation-induced aggregation of rigid membrane inclusions. EPL (Europhysics Letters) 54 (4), 547 (2001)

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81.

Journal Article

Weikl, T. R.; Lipowsky, R.: Adhesion-induced phase behavior of multicomponent membranes. Physical Review E 64 (1), 011903 (2001)

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82.

Journal Article

Weikl, T. R.; Lipowsky, R.: Local adhesion of membranes to striped surface domains. Langmuir 16, pp. 9338 - 9346 (2000)

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83.

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)

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84.

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)

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Book Chapter (1)

85.

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)

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