Peter Eggenberger Hotz

Specific and reversible DNA-directed self-assembly of oil-in-water emulsion droplets

Higher-order structures that originate from the specific and reversible DNA-directed self-assembly of microscopic building blocks hold great promise for future technologies. Here, we functionalized biotinylated soft colloid oil-in-water emulsion droplets with biotinylated single-stranded DNA oligonucleotides using streptavidin as an intermediary linker. We show the components of this modular linking system to be stable and to induce sequence-specific aggregation of binary mixtures of emulsion droplets. Three length scales were thereby involved: nanoscale DNA base pairing linking microscopic building blocks resulted in macroscopic aggregates visible to the naked eye. The aggregation process was reversible by changing the temperature and electrolyte concentration and by the addition of competing oligonucleotides. The system was reset and reused by subsequent refunctionalization of the emulsion droplets. DNA-directed self-assembly of oil-in-water emulsion droplets, therefore, offers a solid basis for programmable and recyclable soft materials that undergo structural rearrangements on demand and that range in application from information technology to medicine.

Genome-physics interaction as a new concept to reduce the number of genetic parameters in artificial evolution

This paper reports on investigations on the possible advantage of the coupling between genomes and physics of cells in artificial evolution. The idea is simple: evolution can rely on physical processes during development allowing to produce shapes without need to specify how exactly this shaping has to be done. Evolving a minimal energy surface such as soap bubbles would need only the specification of the boundary values and a homogenous interaction pattern between the cells. This paper shows that it is possible to link a genetic regulatory network to physics during development, that a reduction of parameters is indeed possible and that the understanding of what is going on in such a system is relatively easy to gain.

Hierarchical Unilamellar Vesicles of Controlled Compositional Heterogeneity

Eukaryotic life contains hierarchical vesicular architectures (i.e. organelles) that are crucial for material production and trafficking, information storage and access, as well as energy production. In order to perform specific tasks, these compartments differ among each other in their membrane composition and their internal cargo and also differ from the cell membrane and the cytosol. Man-made structures that reproduce this nested architecture not only offer a deeper understanding of the functionalities and evolution of organelle-bearing eukaryotic life but also allow the engineering of novel biomimetic technologies. Here, we show the newly developed vesicle-in-water-in-oil emulsion transfer preparation technique to result in giant unilamellar vesicles internally compartmentalized by unilamellar vesicles of different membrane composition and internal cargo, i.e. hierarchical unilamellar vesicles of controlled compositional heterogeneity. The compartmentalized giant unilamellar vesicles were subsequently isolated by a separation step exploiting the heterogeneity of the membrane composition and the encapsulated cargo. Due to the controlled, efficient, and technically straightforward character of the new preparation technique, this study allows the hierarchical fabrication of compartmentalized giant unilamellar vesicles of controlled compositional heterogeneity and will ease the development of eukaryotic cell mimics that resemble their natural templates as well as the fabrication of novel multi-agent drug delivery systems for combination therapies and complex artificial microreactors.

Comparing direct and developmental encoding schemes in artificial evolution: a case study in evolving lens shapes

In this paper, different evolutionary encoding schemes were compared. In a simulator for geometrical optics different lens shapes in three dimensions were evolved using direct and indirect encodings. Direct and indirect methods were compared for their precision, convergence and efficiency. The results showed that the indirect encoding schemes converged faster than the direct ones, needed less genetic parameters and scientifically most important, it could be understood why the indirect scheme outperformed the direct one.

Asymmetric cell division in artificial evolution

Increasingly often artificial evolutionary techniques are coupled with mechanisms abstracted from developmental biology. For instance, artificial cells endowed with genetic regulatory networks were used to evolve and develop simulated creatures. With the evolution of a simple vermicular structure it is shown that asymmetric cell division is useful for the positioning of cells and that this mechanism can be integrated with other developmental mechanisms such as genetic regulation and cell adhesion to get moving artificial creatures. Surprisingly, the movements were controlled by the genetic regulatory network alone without the need to evolve a neural structure.

Morphogenetic Evolution of 3D Sheets Exploiting a Spatial Constraint

In this paper we show how geometric constraints enable developmental processes to generate the morphology of three-dimensional folding sheets more easily. These sheets consist of artificial cells, which are connected and are able to exert forces on each other. To keep track of the complex pattern of connectivity, we introduce a cell connection map, which represents the internal states of the cells and is used to visualize these states. The performed simulations show that the system can easily produce some complicated morphogenetic forms and we show that the forms can be quantified as entropy by evaluating the cell connection map. This entropy was also used as a fitness function in order to evolve shapes. We would like to point out that once an adequate geometric constraint is given, the forms are generated by simple internal states and cell-cell interactions.