Forschung
Biologische Prozesse müssen den Gesetzen der Physik befolgen, unterliegen aber ausserdem auch funktionalen Bedingungen und Kräften der Evolution. Wir interessieren uns dafür, wie biologische Funktionen im Rahmen der physikalischen Zwangsbedingungen implementiert sind. Dafür entwickeln wir Methoden, um komplexe Regulationssysteme und deren Wechselwirkung mit ihrem zellulären Kontext theoretisch zu beschreiben. Im Zentrum unseres Interesses stehen molekulare Maschinen, Genregulation und Zellwachstum sowie Zellbewegungen.
Aktive Materie und Motilität
Many biological systems are driven by a coupling to an internal driving force (eventually fueled by a metabolism), which gives rise to active behaviors such as self-propulsion and growth. Self-propulsion poses a number of interesting questions such as: How do self-propelled particles (e.g. cells, but also micro-robots) navigate complex environments? How can they be controlled? What collective behaviors emerge in systems of many such particles? What is the interplay of activity and density of particles? Our work in this area focuses in particular on magnetotaxis in magnetotactic bacteria and on self-propelled filaments.
- A. Codutti, M. A. Charsooghi, E. Cerdá-Doñate, H. M. Taïeb, T. Robinson, D. Faivre, S. Klumpp, Single-cell motion of magnetotactic bacteria in microfluidic confinement: interplay between surface interaction and magnetic torque, bioRxiv 2021.03.27.437322 (2021).
- V. Telezki and S. Klumpp, Simulations of structure formation by confined dipolar active particles, Soft Matter 16, 10537-10547 (2020).
- S. Klumpp, C. T. Lefèvre, M. Bennet, D. Faivre, Swimming with magnets: from biological organisms to synthetic devices, Phys. Rep. 789, 1-54 (2019).
Stochastische Dynamik in Zellen
Many biological processes are inherently stochastic. We are interested in how stochasticity shapes the material properties and the function of biologic systems beyond acting as a perturbation. Our interest is in specific systems as well as general questions, e.g. related to the coarse-graining of stochastic dynamics.
- L. Schaedel, C. Lorenz, A. V. Schepers, S. Klumpp, and S. Köster, Vimentin Intermediate Filaments Stabilize Dynamic Microtubules by Direct Interactions, Nature Commun. 12, 3799 (2021).
- D. Seiferth, P. Sollich, and S. Klumpp, Coarse graining of biochemical systems described by discrete stochastic dynamics, Phys. Rev. E 102, 062149 (2020).
Genregulation, Zellwachstum und Populationsdynamik
Many cellular processes, in particular gene expression, are coupled to cell growth. This coupling gives rise to interesting problems related to the control of gene expression and often results in complex population dynamics with heterogeneous populations
- A. Roy and S. Klumpp, Simulating genetic circuits in bacterial populations with growth heterogeneity, Biophys. J. 114, 484-492 (2018).
- P. Patra and S. Klumpp, Emergence of phenotype switching through continuous and discontinuous evolutionary transitions, Phys. Biol. 12, 046004 (2015).
- S. Klumpp and T. Hwa, Bacterial growth: global effects on gene expression, growth feedback and proteome partition, Curr. Opin. Biotech. 28, 96-102 (2014).