rutger_hermsen_b

Dr. Rutger Hermsen
Theoretical Biology & Bioinformatics
Department of Biology
Faculty of Science, Utrecht University
Kruytgebouw, room Z510
Padualaan 8, 3584 CH Utrecht
The Netherlands
Tel.: +31 (0)30 2533637
Fax.: +31 (0)30 2513655
e-mail: r.hermsen@uu.nl

Curriculum Vitae

Rutger Hermsen studied Theoretical Physics and Philosophy of the Exact Sciences in Utrecht. In 2004, he joined Prof. ten Wolde’s Biochemical Network Group at FOM Institute AMOLF in Amsterdam. He obtained his PhD in 2008 at the Free University (VU) in Amsterdam. Subsequently, he started his postdoctoral work with Prof. Terence Hwa in the Center for Theoretical Biological Physics at UC San Diego. In 2012, a NWO “Veni” grant allowed him to continue his research as an independent postdoc in the Bionanoscience Department at the TU Delft, supported by Prof. Cees Dekker. In September 2013, he became an Assistant Professor (Tenure Track) at Utrecht University, in the Theoretical Biology division lead by Prof. Rob de Boer.

Research summary

Currently, our research focuses on two rather distinct domains of theoretical biology.

Evolution in heterogeneous environments

First, we are interested in fundamental questions concerning biological evolution in heterogeneous environments, which we address by studying theoretical (mathematical) models. In particular, we explore the simple idea that genetic mutations may not only affect an organism’s fitness in its current habitat, but could also alter its spatial range. Examples of such processes are viruses that adapt to a different host species, or bacteria that develop antibiotic resistance in an environment that contains concentration gradients.

Despite the simplicity of this idea, little has been done to establish minimal models of the emerging evolutionary “modes”, in which adaptation and range expansion go hand in hand. We have made some progress by analyzing stochastic models of populations evolving in source-sink ecologies (Hermsen, 2010) or one-dimensional gradients (Hermsen, 2012) – but many directions remain unexplored. The formalisms we employ in these projects are often borrowed from physics (stochastic processes, front propagation, first-passage theory) and the models tend to be strongly simplified. This project is supported by a NWO “Veni” grant.

figuur

Simulation of a population of bacteria evolving in a one-dimensional array of compartments (horizontal axis) containing, from left to right, an increasing concentration of antibiotic. In time, the population (gray shading) expands in real space while evolving in genotype space (vertical axis). (Hermsen, 2012)

Bacterial growth physiology and biochemical networks

Second, we aim to understand the growth of bacterial cultures on mixed-substrate media based on coarse-grained, systems-level constraints and principles. Recently, fundamentally new insights into the classical phenomenon of catabolite repression have thrown new light on the regulation of carbon catabolic processes in Escherichia coli. We have shown that these insights permit quantitative predictions of, among others, substrate consumption patterns and steady-state growth rates. This line of work is developed in collaboration with Prof. Terence Hwa and his lab members at UC San Diego.

Lab members

PhD students
Hilje Doekes
Laurens Krah

Postdocs
Michael (Misha) Sheinman

Publications

Hermsen, R (2016). The adaptation rate of a quantitative trait in an environmental gradient. Physical Biology, 13 (6), (pp. 065003).

Hermsen, R; Okano, Hiro;  You, Conghui; Werner, Nicole & Hwa, Terence (2015). A growth-rate composition formula for the growth of E.coli on co-utilized carbon substrates. Molecular Systems Biology, 11 (4)

J. B. Deris, M. Kim, Z. Zhang, H. Okano, R. Hermsen, A. Groisman, and T. Hwa (2013) ‘The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria’ Science 342 (6162) p. 1068
Highlighted in ScienceDaily News
Highlighted in Inside Science News

R. Hermsen, J. B. Deris, and T. Hwa (2012) ‘On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient’ Proc. Natl. Acad. Sci. 109: 10775-10780
Highlighted in Proc. Natl. Acad. Sci.
Highlighted in Physics Today Update
UC Health News
Viewpoint in Physics

R. Hermsen, D.W. Erickson, and T. Hwa (2011) ‘Speed, sensitivity, and bistability in auto-activating signaling circuits’ PLoS Comput. Biol. 7: e1002265

R. Hermsen and T. Hwa (2010) ‘Sources and Sinks: a stochastic model of evolution in heterogeneous environments’ Physical Review Letters, 105 (24), p. 248104
Marked as Editor’s Suggestion by PRL
Synopsis on the APS Physics website

R. Hermsen, B. Ursem, and P. R. ten Wolde (2010) ‘Combinatorial gene regulation using autoregulation’ PLoS Computational Biology, 6 (6), p. e1000813

R. Hermsen, S.A. Teichmann, P. R. ten Wolde (2008) ‘Chance and necessity in chromosomal gene distributions’ trends in Genetics, 24 (5), p. 216—219

R. Hermsen, S. Tans, P. R. ten Wolde (2006) ‘Transcription regulation by competing transcription factor modules’ PLoS Computational Biology, 2 (12)
Highlighted in Nature Reviews Genetics