Origin of life research takes various forms but in general tries to understand how organic organization can bootstrap from inorganic structures or constraints, or how more sophisticated protocellular structures can bootstrap from more primitive forms. The demonstration of these transitions can be difficult to implement in the real world. Here we focus on how inorganic structures, formed in the presence of simple organics, can lead to novel hybrid inorganic-organic 3D architectures that support simple membrane formation. We analyzed both the mineral and hybrid structures, and vesicle formation in the presence of these geochemical surfaces using different physio-chemical techniques. This study shows a potential route that the first cellular structures could have taken through their interaction with hybrid organic-inorganic abiotic structures in their environment. Such model systems can also be insightful for artificial life studies regarding the importance of self-assembly promoted between two different systems: inorganic and organic.

As part of the European Horizon 2020 project ACDC, a chemical compiler is being developed that allows the self-assembly of artificial, three-dimensional, vesicular structures to be first simulated and then translated into reality. This work reports on simulations that shed light on an important aspect: How to disentangle inter-vesicular connections?

The phosphate economy in cells is essential in many biochemical processes from signal transduction, to energy metabolism to DNA and RNA synthesis. All living systems therefore acquire and regulate phosphate in order to survive and reproduce. E. coli , for example, regulate the inorganic phosphate ( P i ) uptake in order to survive under phosphate-limiting conditions. To achieve this, E. coli have developed an accurate control mechanism, Pho regulon, to adapt to environmental perturbations of P i , controlled by the PhoR/PhoB two-component regulatory system (TCS). The signalling of the TCS is delivered by interactions with the ABC transporter via PhoU. However, the exact mechanisms of interaction are unknown. Here, we propose mechanistic explanations for these mechanisms via a quantitative computational analysis, whereby we model plausible ABC and TCS state transitions. We analyse the interaction mechanism and the dynamic behaviour of TCS system deactivation in relation to the external P i levels. We show that the behaviour of this system depends on the network structure. In particular, we use alternative models to demonstrate that variation in interaction patterns affect the response time of the system. Overall we show how to model a system where some key interactions are as yet unknown and to provide testable predictions that can easily be verified in the lab. This way, modelling is being used to increase our mechanistic understanding of important biological systems by defining and driving wet lab experiments and to increase our biological understanding of the often complex relationship between an organism and its environment.

There is increasing interest in using technological interfaces to explore and expand the capabilities of artificial life research. We are beginning to see systems that exploit the integration of wetware, software and hardware. Here we focus on the overall architecture for real-time model-based control of thermocapillary motion of droplets in a liquid layer with a low power laser beam on a modular robotic platform. We developed a control-oriented class of models using a closed-loop system architecture, that is characterized by state estimation, parameter identification and control. This results in a fast and potentially robust system for the manipulation of far from equilibrium droplet systems in real time.

The bacteria E. coli have developed one of the most efficient regulatory response to phosphate starvation that is known in detail. Achieving a mechanistic understanding of this system, realized by Pho regulon at the genetic level, has implications for applications in artificial life and for others in biotechnology that exploit such mechanisms. To this end, we present a dynamical model of Pho regulon, coupled with a layered description of its regulation in the experimental conditions of phosphate starvation. The model describes the dynamics of two-component regulatory system together with the key regulatory promoter PhoB and experimental data on promoter PhoA. The model is parameterized according to the feasible range given in the literature, and fitted to the dynamic response of our experimental data on alkaline phosphatase production, coded as Gfp. Sensitivity analysis demonstrates that the rate of Pho transcription has a significant influence over the expression of Pho-controlled genes. Variations in the transcription rates alter the sensitivity of the phosphate starvation response to external phosphate concentration, whereas variations in the translation rates affect the gain of the system. Our model provides a dynamic description of the core determinants of Pho regulon and promoter activities and their response to the change of external phosphate level. As the model architecture is intrinsically open to integrate supplementary layers, together with experimental findings, it should provide insights in investigations on engineering new dynamic sensors and regulators for living technologies.