Publikationen

Zeitschriftenartikel (88)

  1. 1.
    Zeitschriftenartikel
    Bachmann, F.; Giltinan, J.; Codutti, A.; Klumpp, S.; Sitti, M.; Faivre, D.: Selection for function: from chemically synthesized prototypes to 3D-printed microdevices. Advanced Intelligent Systems, 2000078 (2020)
  2. 2.
    Zeitschriftenartikel
    Codutti, A.; Bente, K.; Faivre, D.; Klumpp, S.: Chemotaxis in external fields: simulations for active magnetic biological matter. PLoS Computational Biology 15 (12), e1007548 (2019)
  3. 3.
    Zeitschriftenartikel
    Gomez, D.; Huber, K.; Klumpp, S.: On protein folding in crowded conditions. The Journal of Physical Chemistry Letters 10 (24), S. 7650 - 7656 (2019)
  4. 4.
    Zeitschriftenartikel
    Klumpp, S.; Lefevre, C. T.; Bennet, M. A.; Faivre, D.: Swimming with magnets: From biological organisms to synthetic devices. Physics Reports: Review Section of Physics Letters 789, S. 1 - 54 (2019)
  5. 5.
    Zeitschriftenartikel
    Pohl, A.; Berger, F.; Sullan, R. M.; Valverde-Tercedor, C.; Freindl, K.; Spiridis, N.; Lefevre, C.; Menguy, N.; Klumpp, S.; Blank, K. G. et al.; Faivre, D.: Decoding biomineralization: interaction of a Mad10 derived-peptide with magnetite thin films. Nano Letters 19 (11), S. 8207 - 8215 (2019)
  6. 6.
    Zeitschriftenartikel
    Sumi, T.; Klumpp, S.: Is F1-ATPase a rotary motor with nearly 100% efficiency? Quantitative analysis of chemomechanical coupling and mechanical slip. Nano Letters 19 (5), S. 3370 - 3378 (2019)
  7. 7.
    Zeitschriftenartikel
    Codutti, A.; Bachmann, F.; Faivre, D.; Klumpp, S.: Bead-based hydrodynamic simulations of rigid magnetic micropropellers. Frontiers in Robotics and AI 5, 109 (2018)
  8. 8.
    Zeitschriftenartikel
    Roy, A.; Klumpp, S.: Simulating Genetic Circuits in Bacterial Populations with Growth Heterogeneity. Biophysical Journal 114 (2), S. 484 - 492 (2018)
  9. 9.
    Zeitschriftenartikel
    Kiani, B.; Faivre, D.; Klumpp, S.: Self-organization and stability of magnetosome chains—A simulation study. PLoS One 13 (1), e0190265 (2018)
  10. 10.
    Zeitschriftenartikel
    Ghaisari, S.; Winklhofer, M.; Strauch, P.; Klumpp, S.; Faivre, D.: Magnetosome Organization in Magnetotactic Bacteria Unraveled by Ferromagnetic Resonance Spectroscopy. Biophysical Journal 113 (3), S. 637 - 644 (2017)
  11. 11.
    Zeitschriftenartikel
    Gong, C. C.; Klumpp, S.: Modeling sRNA-Regulated Plasmid Maintenance. PLoS One 12 (1), e0169703 (2017)
  12. 12.
    Zeitschriftenartikel
    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), S. 11113 - 11122 (2016)
  13. 13.
    Zeitschriftenartikel
    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)
  14. 14.
    Zeitschriftenartikel
    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)
  15. 15.
    Zeitschriftenartikel
    Gomez, D.; Klumpp, S.: Facilitated diffusion in the presence of obstacles on the DNA. Physical Chemistry Chemical Physics 18 (16), S. 11184 - 11192 (2016)
  16. 16.
    Zeitschriftenartikel
    Klumpp, S.; Faivre, D.: Magnetotactic bacteria Magnetic navigation on the microscale. European Physical Journal - Special Topics 225 (11), S. 2173 - 2188 (2016)
  17. 17.
    Zeitschriftenartikel
    Vach, P. J.; Klumpp, S.; Faivre, D.: Steering magnetic micropropellers along independent trajectories. Journal of Physics D: Applied Physics 49, 065003 (2016)
  18. 18.
    Zeitschriftenartikel
    Kiani, B.; Faivre, D.; Klumpp, S.: Elastic properties of magnetosome chains. New Journal of Physics 17 (4), 043007 (2015)
  19. 19.
    Zeitschriftenartikel
    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, S. 71 - 83 (2015)
  20. 20.
    Zeitschriftenartikel
    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)
  21. 21.
    Zeitschriftenartikel
    Bierbaum, V.; Klumpp, S.: Impact of the cell division cycle on gene circuits. Physical Biology 12 (6), 066003 (2015)
  22. 22.
    Zeitschriftenartikel
    Gomez, D.; Klumpp, S.: Biochemical reactions in crowded environments: Revisiting the effects of volume exclusion with simulations. Frontiers in Physics 3, 45 (2015)
  23. 23.
    Zeitschriftenartikel
    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)
  24. 24.
    Zeitschriftenartikel
    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)
  25. 25.
    Zeitschriftenartikel
    Patra, P.; Klumpp, S.: Emergence of phenotype switching through continuous and discontinuous evolutionary transitions. Physical Biology 12 (4), 046004 (2015)
  26. 26.
    Zeitschriftenartikel
    Sahoo, M.; Dong, J.; Klumpp, S.: Dynamic blockage in an exclusion process. Journal of Physics A: Mathematical and Theoretical 48 (1), 015007 (2015)
  27. 27.
    Zeitschriftenartikel
    Vach, P. J.; Fratzl, P.; Klumpp, S.; Faivre, D.: Fast magnetic micropropellers with random shapes. Nano Letters 15, S. 7064 - 7070 (2015)
  28. 28.
    Zeitschriftenartikel
    Lutz, B.; Faber, M.; Verma, A.; Klumpp, S.; Schug, A.: Differences between cotranscriptional and free riboswitch folding. Nucleic Acids Research 42 (4), S. 2687 - 2696 (2014)
  29. 29.
    Zeitschriftenartikel
    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)
  30. 30.
    Zeitschriftenartikel
    Gomez, D.; Marathe, R.; Bierbaum, V.; Klumpp, S.: Modeling stochastic gene expression in growing cells. Journal of Theoretical Biology 348, S. 1 - 11 (2014)
  31. 31.
    Zeitschriftenartikel
    Klumpp, S.: The secret life of a cellular business. LaboratoryNews (1), S. 20 - 21 (2014)
  32. 32.
    Zeitschriftenartikel
    Klumpp, S.; Hwa, T.: Bacterial growth: global effects on gene expression, growth feedback and proteome partition. Current Opinion in Biotechnology 28, S. 96 - 102 (2014)
  33. 33.
    Zeitschriftenartikel
    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), S. 4653 - 4659 (2014)
  34. 34.
    Zeitschriftenartikel
    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), S. 527 - 538 (2014)
  35. 35.
    Zeitschriftenartikel
    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, S. 3759 - 3759 (2014)
  36. 36.
    Zeitschriftenartikel
    Mauri, M.; Klumpp, S.: A model for sigma factor competition in bacterial cells. PLoS Computational Biology 10 (10), e1003845 (2014)
  37. 37.
    Zeitschriftenartikel
    Patra, P.; Klumpp, S.: Phenotypically heterogeneous populations in spatially heterogeneous environments. Physical Review E 89 (3), 030702 (2014)
  38. 38.
    Zeitschriftenartikel
    Scott, M.; Klumpp, S.; Mateescu, E. M.; Hwa, T.: Emergence of robust growth laws from optimal regulation of ribosome synthesis. Molecular Systems Biology 10 (8), 747 (2014)
  39. 39.
    Zeitschriftenartikel
    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)
  40. 40.
    Zeitschriftenartikel
    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)
  41. 41.
    Zeitschriftenartikel
    Sahoo, M.; Klumpp, S.: Backtracking dynamics of RNA polymerase: pausing and error correction. Journal of Physics: Condensed Matter 25 (37), 374104 (2013)
  42. 42.
    Zeitschriftenartikel
    Patra, P.; Klumpp, S.: Population Dynamics of Bacterial Persistence. PLoS One 8 (5), e62814 (2013)
  43. 43.
    Zeitschriftenartikel
    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 Sp. Iss. SI), S. 48 - 64 (2013)
  44. 44.
    Zeitschriftenartikel
    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)
  45. 45.
    Zeitschriftenartikel
    Berger, F.; Keller, C.; Klumpp, S.; Lipowsky, R.: Distinct Transport Regimes of Two Elastically Coupled Molecular Motors. Biophysical Journal 104 (2 Suppl. 1), S. 325A - 325A (2013)
  46. 46.
    Zeitschriftenartikel
    Faber, M.; Klumpp, S.: Kinetic Monte Carlo approach to RNA folding dynamics using structure-based models. PHYSICAL REVIEW E 88 (5), 052701 (2013)
  47. 47.
    Zeitschriftenartikel
    Hintsche, M.; Klumpp, S.: Dilution and the theoretical description of growth-rate dependent gene expression. Journal of Biological Engineering 7 (1), 22 (2013)
  48. 48.
    Zeitschriftenartikel
    Klumpp, S.: A Superresolution Census of RNA Polymerase. Biophysical Journal 105 (12), S. 2613 - 2614 (2013)
  49. 49.
    Zeitschriftenartikel
    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)
  50. 50.
    Zeitschriftenartikel
    Klumpp, S.: Mechanisms and economy of molecular machines. Physica Scripta T151, 014066 (2012)
 
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