Publications

Journal Article

Liu, Y.; Agudo-Canalejo, J.; Grafmüller, A.; Dimova, R.; Lipowsky, R.: Patterns of flexible nanotubes formed by liquid-ordered and liquid-disordered membranes. ACS Nano 10 (1), pp. 463 - 474 (2016)

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Luo, C.; Kröger, M.; Sommer, J.-U.: Entanglements and crystallization of concentrated polymer solutions: molecular dynamics simulations. Macromolecules 49 (23), pp. 9017 - 9025 (2016)

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McShane, E.; Sin, C.; Zauber, H.; Wells, J.; Donnelly, N.; Wang, X.; Hou, J.; Chen, W.; Storchova, Z.; Marsh, J. et al.; Valleriani, A.; Selbach, M.: Kinetic analysis of protein stability reveals age-dependent degradation. Cell 167 (3), pp. 803 - 815.e21 (2016)

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Journal Article

Memczak, H.; Lauster, D.; Kar, P.; Di Lella, S.; Volkmer, R.; Knecht, V.; Herrmann, A.; Ehrentreich-Förster, E.; Bier, F. F.; Stöcklein, W. F. M.: Anti-hemagglutinin antibody derived lead peptides for inhibitors of influenza virus binding. PLoS One 11 (7), e0159074 (2016)

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Molcan, M.; Gojzewski, H.; Skumiel, A.; Dutz, S.; Kovac, J.; Kubovcikova, M.; Kopcansky, P.; Vekas, L.; Timko, M.: Energy losses in mechanically modified bacterial magnetosomes. Journal of Physics D: Applied Physics 49 (36), 365002 (2016)

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Mousavi, M. P. S.; Kashef Ol Gheta, S.; Stein, A.; Bühlmann, P.: Electrochemical stability of quaternary ammonium cations: an experimental and computational study. Journal of the Electrochemical Society 163 (2), pp. H74 - H80 (2016)

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Mousavi, M. P. S.; Wilson, B. E.; Kashefolgheta, S.; Anderson, E.; He, S.; Bühlmann, P.; Stein, A.: Ionic liquids as electrolytes for electrochemical double-layer capacitors: structures that optimize specific energy. ACS Applied Materials and Interfaces 8 (5), pp. 3396 - 3406 (2016)

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Olarte, C.; Chiarugi, D.; Falaschi, M.; Hermith, D.: A proof theoretic view of spatial and temporal dependencies in biochemical systems. Theoretical Computer Science 641, pp. 25 - 42 (2016)

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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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Reinhardt, A.; Wehle, M.; Geißner, A.; Crouch, E. C.; Kang, Y.; Yang, Y.; Chakkumkal, A.; Santer, M.; Seeberger, P. H.: Structure binding relationship of human surfactant protein D and various lipopolysaccharide inner core structures. Journal of Structural Biology 195 (3), pp. 387 - 395 (2016)

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Journal Article

Różycki, B.; Lipowsky, R.: Membrane curvature generated by asymmetric depletion layers of ions, small molecules, and nanoparticles. The Journal of Chemical Physics 145 (7), 074117 (2016)

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Rusconi, M.; Valleriani, A.: Predict or classify: the deceptive role of time-locking in brain signal classification. Scientific Reports 6, 28236 (2016)

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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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Journal Article

Sadej, M.; Gojzewski, H.; Andrzejewska, E.: Photocurable polymethacrylate-silica nanocomposites: correlation between dispersion stability, curing kinetics, morphology and properties. Journal of Polymer Research 23 (6), 116 (2016)

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Sahoo, M.; Klumpp, S.: Asymmetric exclusion process with a dynamic roadblock and open boundaries. Journal of Physics A: Mathematical and Theoretical 49 (31), 315001 (2016)

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Sauter, J.; Grafmüller, A.: Predicting chemical potential and osmotic pressure of polysaccharide solutions by molecular simulations. Journal of Chemical Theory and Computation 12 (9), pp. 4375 - 4384 (2016)

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Schimka, S.; Santer, S. A.; Mujkic-Ninnemann, N.; Bléger, D.; Hartmann, L.; Wehle, M.; Lipowsky, R.; Santer, M.: Photosensitive peptidomimetic for light-controlled, reversible DNA compaction. Biomacromolecules 17 (6), pp. 1959 - 1968 (2016)

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Sin, C.; Chiarugi, D.; Valleriani, A.: Quantitative assessment of ribosome drop-off in E. coli. Nucleic Acids Research 44 (6), pp. 2528 - 2537 (2016)

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Sin, C.; Chiarugi, D.; Valleriani, A.: Degradation parameters from pulse-chase experiments. PLoS One 11 (5), e0155028 (2016)

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Journal Article

Steinkühler, J.; Agudo-Canalejo, J.; Lipowsky, R.; Dimova, R.: Modulating vesicle adhesion by electric fields. Biophysical Journal 111 (7), pp. 1454 - 1464 (2016)

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Journal Article

Toro-Nahuelpan, M.; Müller, F. D.; Klumpp, S.; Plitzko, J. M.; Bramkamp, M.; Schüler, D.: Segregation of prokaryotic magnetosomes organelles is driven by treadmilling of a dynamic actin-like MamK filament. BMC Biology 14, 14:88 (2016)

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Vach, P. J.; Klumpp, S.; Faivre, D.: Steering magnetic micropropellers along independent trajectories. Journal of Physics D: Applied Physics 49, 065003 (2016)

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External

Journal Article

Valleriani, A.: A conditional likelihood is required to estimate the selection coefficient in ancient DNA. Scientific Reports 6, 31561 (2016)

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Vila Verde, A.; Frenkel, D.: Kinetics of formation of bile salt micelles from coarse-grained Langevin Dynamics simulations. Soft Matter 12 (23), pp. 5172 - 5179 (2016)

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Vila Verde, A.; Santer, M.; Lipowsky, R.: Solvent-shared pairs of densely charged ions induce intense but short-range supra-additive slowdown of water rotation. Physical Chemistry Chemical Physics 18 (3), pp. 1918 - 1930 (2016)

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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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Journal Article

Zhao, Z.; Li, Q.; Ji, X.; Dimova, R.; Lipowsky, R.; Liu, Y.: Molar mass fractionation in aqueous two-phase polymer solutions of dextran and poly(ethylene glycol). Journal of Chromatography A 1452, pp. 107 - 115 (2016)

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2015

Journal Article

Agudo-Canalejo, J.; Lipowsky, R.: Critical particle sizes for the engulfment of nanoparticles by membranes and vesicles with bilayer asymmetry. ACS Nano 9 (4), pp. 3704 - 3720 (2015)

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Agudo-Canalejo, J.; Lipowsky, R.: Adhesive nanoparticles as local probes of membrane curvature. Nano Letters 15 (10), pp. 7168 - 7173 (2015)

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Journal Article

Bennet, M.; Bertinetti, L.; Neely, R. K.; Schertel, A.; Körnig, A.; Flors, C.; Müller, F. D.; Schüler, D.; Klumpp, S.; Faivre, D.: Biologically controlled synthesis and assembly of magnetite nanoparticles. Faraday Discussions 181, pp. 71 - 83 (2015)

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Journal Article

Berger, F.; Keller, C.; Klumpp, S.; Lipowsky, R.: External forces influence the elastic coupling effects during cargo transport by molecular motors. Physical Review E 91 (2), 022701 (2015)

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Bierbaum, V.; Klumpp, S.: Impact of the cell division cycle on gene circuits. Physical Biology 12 (6), 066003 (2015)

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Bodei, C.; Bortolussi, L.; Chiarugi, D.; Guerriero, M. L.; Policriti, A.; Romanel, A.: On the impact of discreteness and abstractions on modelling noise in gene regulatory networks. Computational Biology and Chemistry 56, pp. 98 - 108 (2015)

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Journal Article

Chiarugi, D.; Falaschi, M.; Hermith, D.; Olarte, C.: Verification of spatial and temporal modalities in biochemical systems. Electronic Notes in Theoretical Computer Science 316, pp. 29 - 44 (2015)

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Chiarugi, D.; Falaschi, M.; Hermith, D.; Olarte, C.; Torella, L.: Modelling non-Markovian dynamics in biochemical reactions. BMC Systems Biology 9 (Suppl 3), S8 (2015)

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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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Journal Article

Dontsova, D.; Pronkin, S.; Wehle, M.; Chen, Z.; Fettkenhauer, C.; Clavel, G.; Antonietti, M.: Triazoles: a new class of precursors for the synthesis of negatively charged carbon nitride derivatives. Chemistry of Materials 27 (15), pp. 5170 - 5179 (2015)

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Journal Article

Ghani, F.; Gojzewski, H.; Riegler, H.: Nucleation and growth of copper phthalocyanine aggregates deposited from solution on planar surfaces. Applied Surface Science 351, pp. 969 - 976 (2015)

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Journal Article

Gomez, D.; Klumpp, S.: Biochemical reactions in crowded environments: revisiting the effects of volume exclusion with simulations. Frontiers in Physics 3, 45 (2015)

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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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Journal Article

Jehannin, M.; Charton, S.; Karpitschka, S.; Zemb, T.; Möhwald, H.; Riegler, H.: Periodic precipitation patterns during coalescence of reacting sessile droplets. Langmuir 31 (42), pp. 11484 - 11490 (2015)

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External

Journal Article

Karpitschka, S.; Weber, C. M.; Riegler, H.: Spin casting of dilute solutions: vertical composition profile during hydrodynamic-evaporative film thinning. Chemical Engineering Science 129, pp. 243 - 248 (2015)

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Journal Article

Keller, P.; Rœlly, S.; Valleriani, A.: A quasi random walk to model a biological transport process. Methodology and Computing in Applied Probability 17 (1), pp. 125 - 137 (2015)

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Keller, P.; Rœlly, S.; Valleriani, A.: On time duality for Markov chains. Stochastic Models 31 (1), pp. 98 - 118 (2015)

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Journal Article

Kiani, B.; Faivre, D.; Klumpp, S.: Elastic properties of magnetosome chains. New Journal of Physics 17 (4), 043007 (2015)

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Klumpp, S.; Kiani, B.; Vach, P. J.; Faivre, D.: Navigation with magnetic nanoparticles: magnetotactic bacteria and magnetic micro-robots. Physica Scripta 2015 (T165), 014044 (2015)

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Journal Article

Knorr, R. L.; Lipowsky, R.; Dimova, R.: Autophagosome closure requires membrane scission. Autophagy 11 (11), pp. 2134 - 2137 (2015)

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Journal Article

Lefèvre, C. T.; Bennet, M.; Klumpp, S.; Faivre, D.: Positioning the flagellum at the center of a dividing cell to combine bacterial division with magnetic polarity. mBio 6 (2), e02286-14 (2015)

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Journal Article

Nicholas, M. P.; Berger, F.; Rao, L.; Brenner, S.; Cho, C.; Gennerich, A.: Cytoplasmic dynein regulates its attachment to microtubules via nucleotide state-switched mechanosensing at multiple AAA domains. Proceedings of the National Academy of Sciences of the United States of America 112 (20), pp. 6371 - 6376 (2015)

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Journal Article

Niedermayer, T.; Lipowsky, R.: Association-dissociation process with aging subunits: recursive solution. Physical Review E 92 (5), 052137 (2015)

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Journal Article

Paradisi, P.; Allegrini, P.; Chiarugi, D.: A renewal model for the emergence of anomalous solute crowding in liposomes. BMC Systems Biology 9 (Suppl 3), S7 (2015)

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Journal Article

Patra, P.; Klumpp, S.: Emergence of phenotype switching through continuous and discontinuous evolutionary transitions. Physical Biology 12 (4), 046004 (2015)

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Journal Article

Pinchasik, B.-E. S.; Steinkühler, J.; Wuytens, P. C.; Skirtach, A. G.; Fratzl, P.; Möhwald, H.: From beetles in nature to the lab: actuating underwater locomotion on hydrophobic surfaces. Langmuir 31 (51), pp. 13734 - 13742 (2015)

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External

Journal Article

Pithan, L.; Meister, E.; Jin, C.; Weber, C.; Zykov, A.; Sauer, K.; Brütting, W.; Riegler, H.; Opitz, A.; Kowarik, S.: Thermally driven smoothening of molecular thin films: structural transitions in n-alkane layers studied in real-time. The Journal of Chemical Physics 143 (16), 164707 (2015)

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Journal Article

Rading, M. M.; Sandmann, M.; Steup, M.; Chiarugi, D.; Valleriani, A.: Weak correlation of starch and volume in synchronized photosynthetic cells. Physical Review E 91 (1), 012711 (2015)

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Journal Article

Robalo, J. R.; Ramalho, J. P. P.; Huster, D.; Loura, L. M. S.: Influence of the sterol aliphatic side chain on membrane properties: a molecular dynamics study. Physical Chemistry Chemical Physics 17 (35), pp. 22736 - 22748 (2015)

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Journal Article

Różycki, B.; Lipowsky, R.: Spontaneous curvature of bilayer membranes from molecular simulations: asymmetric lipid densities and asymmetric adsorption. The Journal of Chemical Physics 142 (5), 054101 (2015)

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Journal Article

Rudorf, S.; Lipowsky, R.: Protein synthesis in E. coli: dependence of codon-specific elongation on tRNA concentration and codon usage. PLoS One 10 (8), e0134994 (2015)

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Journal Article

Sahoo, M.; Dong, J.; Klumpp, S.: Dynamic blockage in an exclusion process. Journal of Physics A: Mathematical and Theoretical 48 (1), 015007 (2015)

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Sauter, J.; Grafmüller, A.: Solution properties of hemicellulose polysaccharides with four common carbohydrate force fields. Journal of Chemical Theory and Computation 11 (4), pp. 1765 - 1774 (2015)

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Journal Article

Siebert, M.; Böhme, M. A.; Driller, J. H.; Babikir, H.; Mampell, M. M.; Rey, U.; Ramesh, N.; Matkovic, T.; Holton, N.; Reddy-Alla, S. et al.; Göttfert, F.; Kamin, D.; Quentin, C.; Klinedinst, S.; Andlauer, T. F.; Hell, S. W.; Collins, C. A.; Wahl, M. C.; Loll, B.; Sigrist, S. J.: A high affinity RIM-binding protein/Aplip1 interaction prevents the formation of ectopic axonal active zones. eLife 4, e06935 (2015)

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Sin, C.; Chiarugi, D.; Valleriani, A.: Single-molecule modeling of mRNA degradation by miRNA: lessons from data. BMC Systems Biology 9 (Suppl 3), S2 (2015)

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Journal Article

Sosale, N. G.; Rouhiparkouhi, T.; Bradshaw, A. M.; Dimova, R.; Lipowsky, R.; Discher, D. E.: Cell rigidity and shape override CD47's "sell"-signaling in phagocytosis by hyperactivating myosin-II. Blood 125 (3), pp. 542 - 552 (2015)

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Journal Article

Soulié, V.; Karpitschka, S.; Lequien, F.; Prene, P.; Zemb, T.; Möhwald, H.; Riegler, H.: The evaporation behavior of sessile droplets from aqueous saline solutions. Physical Chemistry Chemical Physics 17 (34), pp. 22296 - 22303 (2015)

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Journal Article

Vach, P. J.; Fratzl, P.; Klumpp, S.; Faivre, D.: Fast magnetic micropropellers with random shapes. Nano Letters 15, pp. 7064 - 7070 (2015)

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Journal Article

Valleriani, A.: Circular analysis in complex stochastic systems. Scientific Reports 5, 17986 (2015)

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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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Journal Article

Yu, M.; Lira, R. B.; Riske, K. A.; Dimova, R.; Lin, H.: Ellipsoidal relaxation of deformed vesicles. Physical Review Letters 115 (12), 128303 (2015)

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Journal Article

Zhao, Z.; Ji, X.; Dimova, R.; Lipowsky, R.; Liu, Y.: Viscoelasticity of poly(ethylene glycol) solutions on supported lipid bilayers via quartz crystal microbalance with dissipation. Macromolecules 48 (6), pp. 1824 - 1831 (2015)

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2014

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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Journal Article

Bennet, M.; McCarthy, A.; Fix, D.; Edwards, M. R.; Repp, F.; Vach, P.; Dunlop, J. W. C.; Sitti, M.; Buller, G. S.; Klumpp, S. et al.; Faivre, D.: Influence of magnetic fields on magneto-aerotaxis. PLoS One 9 (7), e101150 (2014)

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Journal Article

Dasgupta, R.; Dimova, R.: Inward and outward membrane tubes pulled from giant vesicles. Journal of Physics D: Applied Physics 47 (28), 282001 (2014)

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Dimova, R.: Recent developments in the field of bending rigidity measurements on membranes. Advances in Colloid and Interface Science 208, pp. 225 - 234 (2014)

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Journal Article

Gomez, D.; Marathe, R.; Bierbaum, V.; Klumpp, S.: Modeling stochastic gene expression in growing cells. Journal of Theoretical Biology 348, pp. 1 - 11 (2014)

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Journal Article

Grafmüller, A.; Knecht, V.: The free energy of nanopores in tense membranes. Physical Chemistry Chemical Physics 16 (23), pp. 11270 - 11278 (2014)

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Journal Article

Guskova, O. A.; Seidel, C.: Nanoparticle droplets at the polymer brush/solvent interface. Vestnik Tverskovo Gossudarstvenowa Universiteta. Seriya: Khimiyaa (1), pp. 44 - 55 (2014)

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Journal Article

Kang, Y.; Barbirz, S.; Lipowsky, R.; Santer, M.: Conformational diversity of O-antigen polysaccharides of the Gram-negative bacterium Shigella flexneri serotype Y. Journal of Physical Chemistry B 118 (9), pp. 2523 - 2534 (2014)

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Journal Article

Karpitschka, S.; Hanske, C.; Fery, A.; Riegler, H.: Coalescence and noncoalescence of sessile drops: impact of surface forces. Langmuir 30 (23), pp. 6826 - 6830 (2014)

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Journal Article

Karpitschka, S.; Riegler, H.: Sharp transition between coalescence and non-coalescence of sessile drops. Journal of Fluid Mechanics 743, R1 (2014)

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Journal Article

Klumpp, S.: The secret life of a cellular business. LaboratoryNews (1), pp. 20 - 21 (2014)

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Klumpp, S.; Hwa, T.: Bacterial growth: global effects on gene expression, growth feedback and proteome partition. Current Opinion in Biotechnology 28, pp. 96 - 102 (2014)

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Journal Article

Knorr, R. L.; Nakatogawa, H.; Ohsumi, Y.; Lipowsky, R.; Baumgart, T.; Dimova, R.: Membrane morphology is actively transformed by covalent binding of the protein Atg8 to PE-lipids. PLoS One 9 (12), e115357 (2014)

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Journal Article

Körnig, A.; Dong, J.; Bennet, M.; Widdrat, M.; Andert, J.; Müller, F. D.; Schüler, D.; Klumpp, S.; Faivre, D.: Probing the mechanical properties of magnetosome chains in living magnetotactic bacteria. Nano Letters 14 (8), pp. 4653 - 4659 (2014)

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Journal Article

Krukau, A.; Knecht, V.; Lipowsky, R.: Allosteric control of kinesin's motor domain by tubulin: a molecular dynamics study. Physical Chemistry Chemical Physics 16 (13), pp. 6189 - 6198 (2014)

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Journal Article

Lefèvre, C. T.; Bennet, M.; Landau, L.; Vach, P.; Pignol, D.; Bazylinski, D. A.; Frankel, R. B.; Klumpp, S.; Faivre, D.: Diversity of magneto-aerotactic behaviors and oxygen sensing mechanisms in cultured magnetotactic bacteria. Biophysical Journal 107 (2), pp. 527 - 538 (2014)

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Li, X.; Kolomeisky, A. B.; Valleriani, A.: Pathway structure determination in complex stochastic networks with non-exponential dwell times. The Journal of Chemical Physics 140 (18), 84102 (2014)

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Li, X.; Kolomeisky, A. B.; Valleriani, A.: Stochastic kinetics on networks: when slow is fast. Journal of Physical Chemistry B 118 (35), pp. 10419 - 10425 (2014)

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Journal Article

Lipowsky, R.: Remodeling of membrane compartments: some consequences of membrane fluidity. Biological Chemistry 395 (3), pp. 253 - 274 (2014)

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Journal Article

Lipowsky, R.: Coupling of bending and stretching deformations in vesicle membranes. Advances in Colloid and Interface Science 208, pp. 14 - 24 (2014)

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Journal Article

Lira, R. d.; Dimova, R.; Riske, K. A.: Giant unilamellar vesicles formed by hybrid films of agarose and lipids display altered mechanical properties. Biophysical Journal 107 (7), pp. 1609 - 1619 (2014)

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Journal Article

Lutz, B.; Faber, M.; Verma, A.; Klumpp, S.; Schug, A.: Differences between cotranscriptional and free riboswitch folding. Nucleic Acids Research 42 (4), pp. 2687 - 2696 (2014)

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Journal Article

Marathe, R.; Meel, C.; Schmidt, N. C.; Dewenter, L.; Kurre, R.; Greune, L.; Schmidt, M. A.; Müller, M. J. I.; Lipowsky, R.; Maier, B. et al.; Klumpp, S.: Bacterial twitching motility is coordinated by a two-dimensional tug-of-war with directional memory. Nature Communications 5, p. 3759 - 3759 (2014)

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Mauri, M.; Klumpp, S.: A model for sigma factor competition in bacterial cells. PLoS Computational Biology 10 (10), e1003845 (2014)

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Miettinen, M. S.; Monticelli, L.; Nedumpully-Govindan, P.; Knecht, V.; Ignatova, Z.: Stable polyglutamine dimers can contain β-hairpins with interdigitated side chains but not α-helices, β-nanotubes, β-pseudohelices, or steric zippers. Biophysical Journal 106 (8), pp. 1721 - 1728 (2014)

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Molcan, M.; Hashim, A.; Kovac, J.; Rajnak, M.; Kopcansky, P.; Makowski, M.; Gojzewski, H.; Molokac, M.; Hvizdak, L.; Timko, M.: Characterization of magnetosomes after exposure to the effect of the sonication and ultracentrifugation. Acta Physica Polonica A 126 (1), pp. 198 - 199 (2014)

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Pataraia, S.; Liu, Y.; Lipowsky, R.; Dimova, R.: Effect of cytochrome c on the phase behavior of charged multicomponent lipid membranes. Biochimica et Biophysica Acta 1838 (8), pp. 2036 - 2045 (2014)

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Patra, P.; Klumpp, S.: Phenotypically heterogeneous populations in spatially heterogeneous environments. Physical Review E 89 (3), 030702 (2014)

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Pobandt, T.; Knecht, V.: Free energy of lipid bilayer defects affected by Alzheimer's disease-associated amyloid-ß₄₂ monomers. The Journal of Physical Chemistry B 118 (13), pp. 3507 - 3516 (2014)

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