Publications

Adhikari, U.; Goliaei, A.; Tsereteli, L.; Berkowitz, M. L.: Properties of poloxamer molecules and poloxamer micelles dissolved in water and next to lipid bilayers: results from computer simulations. The Journal of Physical Chemistry B 120 (26), pp. 5823 - 5830 (2016)

Agudo-Canalejo, J.; Lipowsky, R.: Stabilization of membrane necks by adhesive particles, substrate surfaces, and constriction forces. Soft Matter 12 (39), pp. 8155 - 8166 (2016)

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)

Bartholomäus, A.; Fedyunin, I.; Feist, P.; Sin, C.; Zhang, G.; Valleriani, A.; Ignatova, Z.: Bacteria differently regulate mRNA abundance to specifically respond to various stresses. Philosophical Transactions of the Royal Society of London - Series A: Mathematical Physical and Engineering Sciences 374 (2063), 20150069 (2016)

Bhatia, T.; Cornelius, F.; Brewer, J.; Bagatolli, L. A.; Simonsen, A. C.; Ipsen, J. H.; Mouritsen, O. G.: Spatial distribution and activity of Na ⁺/K ⁺-ATPase in lipid bilayer membranes with phase boundaries. Biochimica et Biophysica Acta (BBA) - Biomembranes 1858 (6), pp. 1390 - 1399 (2016)

Brilliantov, N. V.; Budkov, Y. A.; Seidel, C.: Generation of mechanical force by grafted polyelectrolytes in an electric field. Physical Review E 93 (3), 032505 (2016)

Brilliantov, N. V.; Budkov, Y. A.; Seidel, C.: Generation of mechanical force by grafted polyelectrolytes in an electric field: application to polyelectrolyte-based nano-devices. Philosophical Transactions of the Royal Society of London - Series A: Mathematical Physical and Engineering Sciences 374 (2080), 20160143 (2016)

Canto, A. M.T.M. d.; Robalo, J. R.; Santos, P. D.; Carvalho, A. J. P.; Ramalho, J.P. P.; Loura, L. M.S.: Diphenylhexatriene membrane probes DPH and TMA-DPH: a comparative molecular dynamics simulation study. Biochimica et Biophysica Acta - Biomembranes 1858 (11), pp. 2647 - 2661 (2016)

Catte, A.; Girych, M.; Javanainen, M.; Loison, C.; Melcr, J.; Miettinen, M. S.; Monticelli, L.; Maatta, J.; Oganesyan, V. S.; Ollila, O. H. S. et al.; Tynkkynen, J.; Vilov, S.: Molecular electrometer and binding of cations to phospholipid bilayers. Physical Chemistry Chemical Physics 18 (47), pp. 32560 - 32569 (2016)

Derakhshani-Molayousefi, M.; Kashefolgheta, S.; Eilers, J. E.; Lu, Y.: Computational replication of the primary isotope dependence of secondary kinetic isotope effects in solution hydride transfer reactions: supporting the isotopically different tunneling ready state conformations. The Journal of Physical Chemistry A 120 (25), pp. 4277 - 4284 (2016)

Feldmann, D.; Maduar, S. R.; Santer, M.; Lomadze, N.; Vinogradova, O. I.; Santer, S.: Manipulation of small particles at solid liquid interface: light driven diffusioosmosis. Scientific Reports 6, 36443 (2016)

Fricke, N.; Dimova, R.: GM1 softens POPC membranes and induces the formation of micron-sized domains. Biophysical Journal 111 (9), pp. 1935 - 1945 (2016)

Gomez, D.; Klumpp, S.: Facilitated diffusion in the presence of obstacles on the DNA. Physical Chemistry Chemical Physics 18 (16), pp. 11184 - 11192 (2016)

Jin, C.; Riegler, H.: Morphological transitions during melting of small cylindrical aggregates. The Journal of Physical Chemistry C 120 (30), pp. 16815 - 16821 (2016)

Kang, Y.; Gohlke, U.; Engström, O.; Hamark, C.; Scheidt, T.; Kunstmann, S.; Heinemann, U.; Widmalm, G.; Santer, M.; Barbirz, S.: Bacteriophage tailspikes and bacterial O-antigens as a model system to study weak-affinity protein–polysaccharide interactions. Journal of the American Chemical Society 138 (29), pp. 9109 - 9118 (2016)

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)

Klumpp, S.; Faivre, D.: Magnetotactic bacteria: magnetic navigation on the microscale. European Physical Journal - Special Topics 225 (11), pp. 2173 - 2188 (2016)

Krepel, D.; Gomez, D.; Klumpp, S.; Levy, Y.: Mechanism of facilitated diffusion during a DNA search in crowded environments. The Journal of Physical Chemistry B 120 (43), pp. 11113 - 11122 (2016)

Kubsch, B.; Robinson, T.; Lipowsky, R.; Dimova, R.: Solution asymmetry and salt expand fluid-fluid coexistence regions of charged membranes. Biophysical Journal 110 (12), pp. 2581 - 2584 (2016)

Lawatscheck, C.; Pickhardt, M.; Wieczorek, S.; Grafmüller, A.; Mandelkow, E.; Börner, H. G.: Generalizing the concept of specific compound formulation additives towards non-fluorescent drugs: a solubilization study on potential anti-Alzheimer-active small-molecule compounds. Angewandte Chemie International Edition 55 (30), pp. 8752 - 8756 (2016)

Lira, R. B. d.; Steinkühler, J.; Knorr, R. L.; Dimova, R.; Riske, K. A.: Posing for a picture: vesicle immobilization in agarose gel. Scientific Reports 6, 25254 (2016)

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)

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

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)

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)

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)

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)

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)

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)

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)

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)

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)

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

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)

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)

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)

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)

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)

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

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

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

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)

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

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

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)

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)

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)

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)

Dimova, R.; Riske, K. A.: Electrodeformation, Electroporation, and Electrofusion of Giant Unilamellar Vesicles. In: Handbook of Electroporation (Ed. Miklavcic, D.). Springer International Publishing, Cham (2016)

Kubsch, B.; Robinson, T.; Lipowsky, R.; Dimova, R.: Presence of Salt and Solution Asymmetry Across Charged Membranes Influences Their Phase State. In Biophysical Journal, 110 (3) Supplement 1 Ed., 2045-Pos , p. 413a. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, February 27, 2016 - March 02, 2016. Biophysical Society, Bethesda, MD (2016)

Rey, U.; Ucar, M.; Lipowsky, R.; Sigrist, S.: Aplip1 Controls the Processivity of Neurexin Axonal Transport. In Biophysical Journal, 110 (3) Supplement 1 Ed., 2279-Pos , p. 463a. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, February 27, 2016 - March 02, 2016. Biophysical Society, Bethesda, MD (2016)

Robinson, T.; Kubsch, B.; Bastiaens, P.; Lipowsky, R.; Dimova, R.: Membrane Fusion via Snare Mimetics Spatially Confined to Intramembrane Domains. In Biophysical Journal (Annual Meeting Abstracts), 110 (3) Supplement 1 Ed., 1242-Pos, pp. 249a - 250a. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, February 27, 2016 - March 02, 2016. Biophysical Society, Bethesda, MD (2016)

Steinkühler, J.; Alvey, C.; Lipowsky, R.; Dimova, R.; Discher, D.: Specific Adhesion of Giant Plasma Membrane Vesicles to Surface- Immobilized SIRPα by Membrane Reconstituted ‘‘Marker of Self’’ Signaling Protein CD47. In Biophysical Journal (Annual Meeting Abstracts), 110 (3) Supplement 1 Ed., 2814-Pos, pp. 569a - 570a. 60th Annual Meeting of the Biophysical-Society, Los Angeles, CA, February 27, 2016 - March 02, 2016. Biophysical Society, Bethesda, MD (2016)

Różycki, .; Lipowsky, R.: Spontaneous curvature of biomembranes from molecular simulations. Biomembrane Days 2016, Berlin (2016)

Agudo-Canalejo, J.: Effects of bilayer asymmetry on nanotube formation and particle engulfment by biomembranes and vesicles. Dissertation, 119 pp., Technische Universität Berlin, Berlin (2016)

Gomez, D.: Mechanisms of biochemical reactions within crowded environments. Dissertation, Universität, Potsdam (2016)

Sin, C.: Post-transcriptional control of gene expression. Dissertation, 238 pp., Universität Potsdam, Potsdam (2016)

Steinkühler, J.: Partitioning of membrane components in adhering vesicles. Dissertation, Technische Universität, Berlin (2016)