Welcome to the Simmel lab - Systems Biophysics and Bionanotechnology

Our goal is the realization of self-organizing molecular systems that are able to respond to their environment, compute, move, take action. On the long term, we envision autonomous systems that are reconfigurable, that can evolve and develop.

Diffusive motion of a molecular robot arm
Single molecule studies on lithographically arranged DNA origami platforms
Dynamical diversity of a compartmentalized biochemical oscillator

Diffusive motion of a molecular robot arm. Fast and efficient transport of molecular cargoes along tracks or on supramolecular platforms is an important pre-requisite for the development of future nanorobotic systems and assembly lines. Here, we study the diffusive transport of DNA cargo strands bound to a supramolecular DNA origami structure via an extended tether arm. Our results suggest diffusive motion on a molecular tether as a highly efficient mechanism for fast transfer of cargoes over long distances.

E. Kopperger, T. Pirzer, F. C. Simmel, Diffusive transport of molecular cargo tethered to a DNA origami platform, Nano Letters 15, 2693–2699 (2015). http://dx.doi.org/10.1021/acs.nanolett.5b00351

Dynamical diversity of a compartmentalized biochemical oscillator: In this collaborative study performed with the groups of Erik Winfree (Caltech) and Elisa Franco (UC Riverside), we encapsulated a programmable biochemical feedback oscillator based on transcription reactions into microemulsion droplets with sizes in the range of 16 fL to 33 pL. We evaluated thousands of oscillator reactions from individual droplets and found large variability in the period and amplitude of the oscillations. The variations are much larger than expected from a simple Poisson-partitioning model and can be traced back to broader-than-Poisson variability in enzyme activity in the droplets.

M. Weitz, J. Kim, K. Kapsner, E. Winfree, E. Franco, F. C. Simmel, Diversity in the dynamical behaviour of a compartmentalized programmable biochemical oscillator, Nature Chemistry 6, 295-302 (2014). http://dx.doi.org/10.1038/nchem.1869 

Single molecule studies on lithographically arranged DNA origami platforms: By combining DNA self-assembly and electron-beam lithography on transparent glass substrates, we created a DNA origami microarray, which is compatible with the requirements of single molecule fluorescence and super-resolution microscopy. We utilized the microarray to characterize the performance of DNA strand displacement reactions localized on the DNA origami structures. We find considerable variability within the array, which results both from structural variations and stochastic reaction dynamics prevalent at the single molecule level.

M. Scheible, G. Pardatscher, A. Kuzyk, F. C. Simmel, Single Molecule Characterization of DNA Binding and Strand Displacement Reactions on Lithographic DNA Origami Microarrays, Nano Letters 14, 1627-1633 (2014). DOI: 10.1021/nl500092j

Communication and computation of bacteria in emulsion droplets: We describe the encapsulation of bacteria within spatially extended arrays of water-in-oil emulsion droplets. We find that chemical signals – genetic inducers – diffuse from droplet to droplet, and thus influence gene expression in the bacteria. As shown in the figure on the left, also computational receiver bacteria were engineered that integrate two chemical signals with a genetic AND-gate, and respond by GFP expression only in the neighborhood of two distinct types of reservoir droplets.

M. Weitz, A. Mückl, K. Kapsner, R. Berg, A. Meyer, F. C. Simmel, Communication and computation by bacteria compartmentalized within microemulsion droplets, Journal of the American Chemical Society 136, 72-75 (2014). dx.doi.org/10.1021/ja411132w