Zeitschriftenartikel (1006)

2014
Zeitschriftenartikel
Stefaniu, C.; Vilotijevic, I.; Santer, M.; Brezesinski, G.; Seeberger, P. H.; Silva, D. V.: Versatility of a glycosylphosphatidylinositol fragment in forming highly ordered polymorphs. Langmuir 30 (18), S. 5185 - 5192 (2014)
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Valleriani, A.; Li, X.; Kolomeisky, A. B.: Unveiling the hidden structure of complex stochastic biochemical networks. The Journal of Chemical Physics 140 (6), 064101 (2014)
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Weikl, T. R.; Paul, F.: Conformational selection in protein binding and function. Protein Science 23 (11), S. 1508 - 1518 (2014)
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Yuzenkova, Y.; Gamba, P.; Herber, M.; Attaiech, L.; Shafeeq, S.; Kuipers, O. P.; Klumpp, S.; Zenkin, N.; Veening, J.-W.: Control of transcription elongation by GreA determines rate of gene expression in Streptococcus pneumoniae. Nucleic Acids Research 42 (17), S. 10987 - 10999 (2014)
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Ziobrowski, P.; Andrzejewska, E.; Szybowicz, M.; Nowicka, A.; Sadej-Bajerlein, M.; Gojzewski, H.; Drozdowski, M.: Particle clustering in photocurable nanocomposites: dependence of curing kinetics and viscoelastic properties. Journal of Applied Polymer Science 131 (4), 39895 (2014)
2013
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Awasthi, N.; Ritschel, T.; Lipowsky, R.; Knecht, V.: Standard Gibbs energies of formation and equilibrium constants from ab-initio calculations: covalent dimerization of NO2 and synthesis of NH3. The Journal of Chemical Thermodynamics 62, S. 211 - 221 (2013)
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Bahrami, A. H.: Orientational changes and impaired internalization of ellipsoidal nanoparticles by vesicle membranes. Soft Matter 9 (36), S. 8642 - 8646 (2013)
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Berger, F.; Keller, C.; Lipowsky, R.; Klumpp, S.: Elastic coupling effects in cooperative transport by a pair of molecular motors. Cellular and Molecular Bioengineering 6 (1 SI), S. 48 - 64 (2013)
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Bezlyepkina, N.; Gracia, R. S.; Shchelokovskyy, P.; Lipowsky, R.; Dimova, R.: Phase diagram and tie-line determination for the ternary mixture DOPC/eSM/cholesterol. Biophysical Journal 104 (7), S. 1456 - 1464 (2013)
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Bierbaum, V.; Lipowsky, R.: Dwell time distributions of the molecular motor myosin V. PLoS One 8 (2), e55366 (2013)
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Cupelli, C.; Borchardt, T.; Steiner, T.; Paust, N.; Zengerle, R.; Santer, M.: Leukocyte enrichment based on a modified pinched flow fractionation approach. Microfluidics and Nanofluidics 14 (3-4), S. 551 - 563 (2013)
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Deneke, C.; Lipowsky, R.; Valleriani, A.: Effect of ribosome shielding on mRNA stability. Physical Biology 10 (4), 046008 (2013)
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Deneke, C.; Lipowsky, R.; Valleriani, A.: Complex degradation processes lead to non-exponential decay patterns and age-dependent decay rates of messenger RNA. PLoS One 8 (2), e55442 (2013)
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Dong, J. J.; Klumpp, S.; Zia, R. K. P.: Mass transport perspective on an accelerated exclusion process: Analysis of augmented current and unit-velocity phases. Physical Review E 87 (2), 022146 (2013)
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Faber, M.; Klumpp, S.: Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models. PHYSICAL REVIEW E 88 (5), 052701 (2013)
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Grafmüller, A.; Lipowsky, R.; Knecht, V.: Effect of tension and curvature on the chemical potential of lipids in lipid aggregates. Physical Chemistry Chemical Physics 15 (3), S. 876 - 881 (2013)
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Grafmüller, A.; Noya, E. G.; Voth, G. A.: Nucleotide-dependent lateral and longitudinal interactions in microtubules. Journal of Molecular Biology (London) 425 (12), S. 2232 - 2246 (2013)
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Hintsche, M.; Klumpp, S.: Dilution and the theoretical description of growth-rate dependent gene expression. Journal of Biological Engineering 7 (1), 22 (2013)
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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), S. 15283 - 15288 (2013)
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Irudayam, S. J.; Pobandt, T.; Berkowitz, M. L.: Free energy barrier for melittin reorientation from a membrane-bound state to a transmembrane state. The Journal of Physical Chemistry B 117 (43), S. 13457 - 13463 (2013)
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Jégou, A.; Niedermayer, T.; Lipowsky, R.; Carlier, M.-F.; Romet-Lemonne, G.: On Phosphate Release in Actin Filaments. Biophysical Journal 104 (12), S. 2778 - 2779 (2013)
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Kang, Y.; Barbiz, S.; Lipowsky, R.; Santer, M.: Conformational insights into recognition mechanism of O-antigen polysaccharides by tailspike protein. European Biophysics Journal with Biophysics Letters 42 (Suppl. 1), S. S112 - S112 (2013)
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Kar, P.; Lipowsky, R.; Knecht, V.: Importance of polar solvation and configurational entropy for design of antiretroviral drugs targeting HIV-1 protease. The Journal of Physical Chemistry B 117 (19), S. 5793 - 5805 (2013)
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Keller, C.; Berger, F.; Liepelt, S.; Lipowsky, R.: Network complexity and parametric simplicity for cargo transport by two molecular motors. Journal of Statistical Physics 150 (2), S. 205 - 234 (2013)
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Klumpp, S.: A Superresolution Census of RNA Polymerase. Biophysical Journal 105 (12), S. 2613 - 2614 (2013)
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Klumpp, S.; Scott, M.; Pedersen, S.; Hwa, T.: Molecular crowding limits translation and cell growth. Proceedings of the National Academy of Sciences of the United States of America 110 (42), S. 16754 - 16759 (2013)
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Knecht, V.; Klasczyk, B.: Specific binding of chloride ions to lipid vesicles and implications at molecular scale. Biophysical Journal 104 (4), S. 818 - 824 (2013)
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Knecht, V.; Klasczyk, B.; Dimova, R.: Macro- versus microscopic view on the electrokinetics of a water-membrane interface. Langmuir 29 (25), S. 7939 - 7948 (2013)
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Li, X.; Lipowsky, R.; Kierfeld, J.: Bifurcation of velocity distributions in cooperative transport of filaments by fast and slow motors. Biophysical Journal 104 (3), S. 666 - 676 (2013)
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Lipowsky, R.: Spontaneous tubulation of membranes and vesicles reveals membrane tension generated by spontaneous curvature. Faraday Discussions 161, S. 305 - 331 (2013)
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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), S. 8438 - 8453 (2013)
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Mertins, O.; Dimova, R.: Insights on the interactions of chitosan with phospholipid vesicles. Part I: effect of polymer deprotonation. Langmuir 29 (47), S. 14545 - 14551 (2013)
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Mertins, O.; Dimova, R.: insights on the interactions of chitosan with phospholipid vesicles. Part II: membrane stiffening and pore formation. Langmuir 29 (47), S. 14552 - 14559 (2013)
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Minh Dang, T.; Vila Verde, A.; Van Nguyen, D.; Bolhuis, P. G.; Schall, P.: Temperature-sensitive colloidal phase behavior induced by critical Casimir forces. JOURNAL OF CHEMICAL PHYSICS 139 (9), 094903 (2013)
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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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Patra, P.; Klumpp, S.: Population dynamics of bacterial persistence. PLoS One 8 (5), e62814 (2013)
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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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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), S. 2203 - 2229 (2013)
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Sahoo, M.; Klumpp, S.: Backtracking dynamics of RNA polymerase: pausing and error correction. Journal of Physics: Condensed Matter 25 (37), 374104 (2013)
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Shapovalov, V. L.; Möhwald, H.; Konovalov, O. V.; Knecht, V.: Negligible water surface charge determined using Kelvin probe and total reflection X-ray fluorescence techniques. Physical Chemistry Chemical Physics 15 (33), S. 13991 - 13998 (2013)
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Smirnova, Y. G.; Aeffner, S.; Risselada, H. J.; Salditt, T.; Marrink, S. J.; Müller, M.; Knecht, V.: Interbilayer repulsion forces between tension-free lipid bilayers from simulation. Soft Matter 9 (45), S. 10705 - 10718 (2013)
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Sosale, N.; Rouhi, T.; Lipowsky, R.; Discher, D. E.: 'Marker of self', CD47, modulates mechanical forces imposed by macrophages during phagocytosis. Biophysical Journal 104 (2 Suppl. 1), S. 480A - 480A (2013)
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Suraniti, E.; Kanoufi, F.; Gosse, C.; Zhao, X.; Dimova, R.; Pouligny, B.; Sojic, N.: Electrochemical Detection of Single Microbeads Manipulated by Optical Tweezers in the Vicinity of Ultramicroelectrodes. Analytical Chemistry 85 (19), S. 8902 - 8909 (2013)
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Tong, Y.; Vila Verde, A.; Campen, K.: The Free OD at the Air/D2O Interface is Structurally and Dynamically Heterogeneous. The Journal of Physical Chemistry B 117 (39), S. 11753 - 11764 (2013)
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Vach, P. J.; Brun, N.; Bennet, M.; Bertinetti, L.; Widdrat, M.; Baumgartner, J.; Klumpp, S.; Fratzl, P.; Faivre, D.: Selecting for function: solution synthesis of magnetic nanopropellers. Nano Letters 13 (11), S. 5373 - 5378 (2013)
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Vila Verde, A.; Lipowsky, R.: Cooperative slowdown of water rotation near densely charged ions is intense but short-ranged. The Journal of Physical Chemistry B 117, S. 10556 - 10566 (2013)
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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), S. 867 - 873 (2013)
2012
Zeitschriftenartikel
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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Brilliantov, N. V.; Seidel, C.: Grafted polyelectrolyte in strong electric field under load: field-regulated force and chain contraction. EPL 97 (2), 28006 (2012)
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Casse, O.; Shkilnyy, A.; Linders, J.; Mayer, C.; Haussinger, D.; Völkel, A.; Thünemann, A. F.; Dimova, R.; Cölfen, H.; Meier, W. et al.; Schlaad, H.; Taubert, A.: Solution behavior of double-hydrophilic block copolymers in dilute aqueous solution. Macromolecules 45 (11), S. 4772 - 4777 (2012)
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Deneke, C.; Rudorf, S.; Valleriani, A.: Transient Phenomena in Gene Expression after Induction of Transcription. PLoS One 7 (4), e35044 (2012)
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Dimova, R.: Giant vesicles: a biomimetic tool for membrane characterization. Advances in Planar Lipid Bilayers and Liposomes 16, S. 1 - 50 (2012)
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Dimova, R.; Lipowsky, R.: Lipid membranes in contact with aqueous phases of polymer solutions. Soft Matter 8 (24), S. 2409 - 2415 (2012)
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Dong, J. J.; Klumpp, S.; Zia, R. K. P.: Entrainment and unit velocity: surprises in an accelerated exclusion process. Physical Review Letters 109 (13), 130602 (2012)
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Fedyunin, I.; Lehnhardt, L.; Böhmer, N.; Kaufmann, P.; Zhang, G.; Ignatova, Z.: tRNA concentration fine tunes protein solubility. FEBS Letters 586 (19), S. 3336 - 3340 (2012)
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Garz, A.; Sandmann, M.; Rading, M.; Ramm, S.; Menzel, R.; Steup, M.: Cell-to-cell diversity in a synchronized Chlamydomonas culture as revealed by single-cell analyses. Biophysical Journal 103 (5), S. 1078 - 1086 (2012)
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Guskova, O. A.; Seidel, C.: Assembly of nano-particles on diblock copolymer brushes: toward laterally nano-structured composites. Soft Matter 8 (10), S. 2833 - 2843 (2012)
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Hausmann, R.; Grepl, M.; Knecht, V.; Moeller, M. J.: The glomerular filtration barrier function: new concepts. Current Opinion in Nephrology and Hypertension 21 (4), S. 441 - 449 (2012)
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Kar, P.; Knecht, V.: Energetics of mutation-induced changes in potency of lersivirine against HIV-1 reverse transcriptase. Journal of Physical Chemistry B 116 (22), S. 6269 - 6278 (2012)
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Kar, P.; Knecht, V.: Mutation-induced loop opening and energetics for binding of tamiflu to influenza N8 neuraminidase. Journal of Physical Chemistry B 116 (21), S. 6137 - 6149 (2012)
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Kar, P.; Knecht, V.: Origin of decrease in potency of darunavir and two related antiviral inhibitors against HIV-2 compared to HIV-1 protease. Journal of Physical Chemistry B 116 (8), S. 2605 - 2614 (2012)
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Kar, P.; Knecht, V.: Energetic basis for drug resistance of HIV-1 protease mutants against amprenavir. Journal of Computer-Aided Molecular Design 26 (2), S. 215 - 232 (2012)
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Keller, P.; Valleriani, A.: Single-molecule stochastic times in a reversible bimolecular reaction. The Journal of Chemical Physics 137 (8), 084106 (2012)
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Klumpp, S.: Mechanisms and economy of molecular machines. Physica Scripta T151, 014066 (2012)
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Klumpp, S.; Dong, J. J.; Hwa, T.: On ribosome load, codon usage and protein abundance. PLoS One 7, e48542 (2012)
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Klumpp, S.; Faivre, D.: Interplay of magnetic interactions and active movements in the formation of magnetosome chains. PLoS One 7 (3), e33562 (2012)
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Knorr, R. L.; Dimova, R.; Lipowsky, R.: Curvature of double-membrane organelles generated by changes in membrane size and composition. PLoS One 7 (3), e32753 (2012)
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Kusumaatmaja, H.; Lipowsky, R.; Jin, C.; Mutihac, R. C.; Riegler, H.: Nonisomorphic nucleation pathways arising from morphological transitions of liquid channels. Physical Review Letters 108 (12), 126102 (2012)
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Lechner, S.; Patra, P.; Klumpp, S.; Bertram, R.: Interplay between population dynamics and drug tolerance in Staphylococcus aureus persister cells. Journal of Molecular Microbiology and Biotechnology 22, S. 381 - 391 (2012)
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Li, X.; Lipowsky, R.; Kierfeld, J.: Critical motor number for fractional steps of cytoskeletal filaments in gliding assays. PLoS One 7 (8), e43219 (2012)
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Li, Y. H.; Kusumaatmaja, H.; Lipowsky, R.; Dimova, R.: Wetting-induced budding of vesicles in contact with several aqueous phases. The Journal of Physical Chemistry B 116 (6), S. 1819 - 1823 (2012)
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Liu, Y.; Lipowsky, R.; Dimova, R.: Concentration dependence of the interfacial tension for aqueous two-phase polymer solutions of dextran and polyethylene glycol. Langmuir 28 (8), S. 3831 - 3839 (2012)
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Marathe, R.; Bierbaum, V.; Gomez, D.; Klumpp, S.: Deterministic and stochastic descriptions of gene expression dynamics. Journal of Statistical Physics 148 (4), S. 607 - 626 (2012)
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Marathe, R.; Gomez, D.; Klumpp, S.: Sources of stochasticity in constitutive and autoregulated gene expression. Physica Scripta T151, 014068 (2012)
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Miettinen, M. S.; Knecht, V.; Monticelli, L.; Ignatova, Z.: Assessing polyglutamine conformation in the nucleating event by molecular dynamics simulations. The Journal of Physical Chemistry B 116 (34), S. 10259 - 10265 (2012)
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Niedermayer, T.; Jégou, A.; Chieze, L.; Guichard, B.; Helfer, E.; Romet-Lemonne, G.; Carlier, M. F.; Lipowsky, R.: Intermittent depolymerization of actin filaments is caused by photo-induced dimerization of actin protomers. Proceedings of the National Academy of Sciences of the United States of America 109 (27), S. 10769 - 10774 (2012)
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Rózycki, B.; Boura, E.; Hurley, J. H.; Hummer, G.: Membrane-elasticity model of coatless vesicle budding induced by ESCRT complexes. PLoS Computational Biology 8 (10), e1002736 (2012)
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Rudorf, S.; Rädler, J. O.: Self-assembly of stable monomolecular nucleic acid lipid particles with a size of 30 nm. Journal of the American Chemical Society 134 (28), S. 11652 - 11658 (2012)
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Rusconi, M.; Valleriani, A.; Dunlop, J. W. C.; Kurths, J.; Weinkamer, R.: Quantitative approach to the stochastics of bone remodeling. EPL 97 (2), 28009 (2012)
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Salipante, P. F.; Knorr, R. L.; Dimova, R.; Vlahovska, P. M.: Electrodeformation method for measuring the capacitance of bilayer membranes. Soft Matter 8 (14), S. 3810 - 3816 (2012)
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Stefaniu, C.; Vilotijevic, I.; Santer, M.; Varón Silva, D.; Brezesinski, G.; Seeberger, P. H.: Subgel phase structure in monolayers of glycosylphosphatidylinositol glycolipids. Angewandte Chemie International Edition 51, S. 12874 - 12878 (2012)
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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, S. 11737 - 11745 (2012)
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Verde, A. V.; Bolhuis, P. G.; Campen, R. K.: Statics and dynamics of free and hydrogen-bonded OH groups at the air/water interface. The Journal of Physical Chemistry B 116 (31), S. 9467 - 9481 (2012)
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von Deuster, C. I. E.; Knecht, V.: Antimicrobial selectivity based on zwitterionic lipids and underlying balance of interactions. Biochimica et Biophysica Acta: BBA 1818 (9), S. 2192 - 2201 (2012)
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Wehle, M.; Vilotijevic, I.; Lipowsky, R.; Seeberger, P. H.; Varón Silva, D.; Santer, M.: Mechanical compressibility of the glycosylphosphatidylinositol (GPI) anchor backbone governed by independent glycosidic linkages. Journal of the American Chemical Society 134 (46), S. 18964 - 18972 (2012)
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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), S. 2369 - 2383 (2012)
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Zhang, G.; Fedyunin, I.; Kirchner, S.; Xiao, C. L.; Valleriani, A.; Ignatova, Z.: FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads. Nucleic Acids Research (London) 40 (11), e83 (2012)
2011
Zeitschriftenartikel
Berger, F.; Keller, C.; Müller, M. J. I.; Klumpp, S.; Lipowsky, R.: Co-operative transport by molecular motors. Biochemical Society Transactions 39 (5), S. 1211 - 1215 (2011)
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Bierbaum, V.; Lipowsky, R.: Chemomechanical coupling and motor cycles of myosin V. Biophysical Journal 100 (7), S. 1747 - 1755 (2011)
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Guo, K. K.; Xiao, W. J.; Qiu, D.: Polymerization of actin filaments coupled with adenosine triphosphate hydrolysis: brownian dynamics and theoretical analysis. The Journal of Chemical Physics 135 (10), 105101 (2011)
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Guskova, O. A.; Seidel, C.: Mesoscopic simulations of morphological transitions of stimuli-responsive diblock copolymer brushes. Macromolecules 44 (3), S. 671 - 682 (2011)
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Hu, J. L.; Weikl, T.; Lipowsky, R.: Vesicles with multiple membrane domains. Soft Matter 7 (13), S. 6092 - 6102 (2011)
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Hundertmark, M.; Dimova, R.; Lengefeld, J.; Seckler, R.; Hincha, D. K.: The intrinsically disordered late embryogenesis abundant protein LEA18 from Arabidopsis thaliana modulates membrane stability through binding and folding. Biochimica et Biophysica Acta: BBA 1808 (1), S. 446 - 453 (2011)
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Jégou, A.; Niedermayer, T.; Lipowsky, R.; Carlier, M.-F.; Romet-Lemonne, G.: Observation of Individual Actin Filaments Reveals that ATP Hydrolysis is a Random Mechanism. Observation of Individual Actin Filaments Reveals that ATP Hydrolysis is a Random Mechanism 100 (3 Suppl 1,2), S. 33a - 34a (2011)
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Jegou, A.; Niedermayer, T.; Orban, J.; Didry, D.; Lipowsky, R.; Carlier, M. F.; Romet-Lemonne, G.: Individual actin filaments in a microfluidic flow reveal the mechanism of ATP hydrolysis and give insight into the properties of profilin. PLoS Biology 9 (9), e1001161 (2011)
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Kar, P.; Lipowsky, R.; Knecht, V.: Importance of polar solvation for cross-reactivity of antibody and its variants with steroids. The Journal of Physical Chemistry B 115 (23), S. 7661 - 7669 (2011)
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Klasczyk, B.; Knecht, V.: Validating affinities for ion-lipid association from simulation against experiment. Journal of Physical Chemistry A 115 (38), S. 10587 - 10595 (2011)
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Klumpp, S.: Growth-rate dependence reveals design principles of plasmid copy number control. PLoS One 6 (5), e20403 (2011)
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Klumpp, S.: Pausing and backtracking in transcription under dense traffic conditions. Journal of Statistical Physics 142 (6), S. 1252 - 1267 (2011)
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