Biological processes most obey the laws of physics, but are also subject to functional requirements and shaped by the forces of evolution. Our group is interested in how functional requirements are implemented within the given physical constraints. To that end, we develop theoretical tools to describe complex regulatory systems and their coupling to the cellular context. Topics of specific interest are molecular machines, gene regulation and cell growth as well as (bacterial) cell motility.
Active matter and motilityMany 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).
Stochastic dynamics in cellsMany 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).
Gene regulation, cell growth, and population dynamicsMany 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).