Synthetic biology uses living cells as the substrate for performing human-defined computations. Many current implementations of cellular computing are based on the “genetic circuit” metaphor, an approximation of the operation of silicon-based computers. Although this conceptual mapping has been relatively successful, we argue that it fundamentally limits the types of computation that may be engineered inside the cell, and fails to exploit the rich and diverse functionality available in natural living systems. We propose the notion of “cellular supremacy” to focus attention on domains in which biocomputing might offer superior performance over traditional computers. We consider potential pathways toward cellular supremacy, and suggest application areas in which it may be found.
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 sequencespecific 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.C omplex higher-order structures that spontaneously arise from the specific and reversible self-assembly of simple building blocks hold great promise to become the foundation of tomorrow's technology (1). In the context of DNA-directed self-assembly of hard colloids and artificial vesicles, linear DNA oligonucleotides were shown to be adhesive elements that allowed the self-assembly process not only to be specific but also to be reversible by a variety of external stimuli such as temperature (2-4), changes in the electrolyte concentration (4, 5), addition of competing oligonucleotides (6), and exploitation of the secondary structure of DNA oligonucleotides (7).Oil-in-water (o/w) emulsion droplets (EDs) offer a robust, configurable, and recyclable soft-colloid system with interesting properties for the fabrication of new delivery systems and advanced synthetic materials with adaptable properties (8). By exploiting the well-characterized ligand-receptor pair biotin-streptavidin, EDs were immobilized on glass surfaces (9) and actively transported along microtubules (10). In the context of self-assembly, both polymer-mediated (11-13) and biotin-streptavidin-mediated aggregation of EDs was shown (14). Despite the advantages a combination of EDs as building blocks and DNA oligonucleotides as linking agent offers, a protocol for DNA-directed self-assembly of EDs is currently missing.To close this gap, here we prepared an o/w emulsion composed of heavier-than-water diethyl phthalate (DEP) dispersed in an aqueous medium, stabilized by phospholipids, and functionalized with single-stranded DNA (ssDNA) oligonucleotides. Palmitoyloleoyl phosphatidylcholine (POPC) and distearoylphosphatidyl ethanolamine (DSPE) in a 9:1 molar ratio were used to stabilize the EDs. The DSPE was grafted with flexible poly(ethylene glycol) (PEG) tethers with a molecular weight of 2,000 (DSPE-PEG...
Dissipative particle dynamics (DPD) is now a well-established method for simulating soft matter systems. However, its applicability was recently questioned because some investigations showed an upper coarse-graining limit that would prevent the applicability of the method to the whole mesoscopic range. This article aims to reestablish DPD as a truly scale-free method by analyzing the problems reported by other authors and by presenting a scaling scheme that allows one to gauge a DPD-simulation to any desired length scale.
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