Artificial intelligence exploration of unstable protocells leads to predictable properties and discovery of collective behavior

Abstract

Protocell models are used to investigate how cells might have first assembled on Earth. Some, like oil-in-water droplets, can be seemingly simple models, while able to exhibit complex and unpredictable behaviors. How such simple oil-in-water systems can come together to yield complex and life-like behaviors remains a key question. Herein, we illustrate how the combination of automated experimentation and image processing, physicochemical analysis, and machine learning allows significant advances to be made in understanding the driving forces behind oil-in-water droplet behaviors. Utilizing >7,000 experiments collected using an autonomous robotic platform, we illustrate how smart automation cannot only help with exploration, optimization, and discovery of new behaviors, but can also be core to developing fundamental understanding of such systems. Using this process, we were able to relate droplet formulation to behavior via predicted physical properties, and to identify and predict more occurrences of a rare collective droplet behavior, droplet swarming. Proton NMR spectroscopic and qualitative pH methods enabled us to better understand oil dissolution, chemical change, phase transitions, and droplet and aqueous phase flows, illustrating the utility of the combination of smart-automation and traditional analytical chemistry techniques. We further extended our study for the simultaneous exploration of both the oil and aqueous phases using a robotic platform. Overall, this work shows that the combination of chemistry, robotics, and artificial intelligence enables discovery, prediction, and mechanistic understanding in ways that no one approach could achieve alone.

A curious formulation robot enables the discovery of a novel protocell behavior

“…The temperature in the room might have changed between the second and the third repeat. However, as in all previous reported work on this droplet system (24,26), the temperature was neither recorded nor controlled, and all experiments were performed at room temperature. A new set of questions emerged: (i) Can a change of only a few degrees Celsius really affect our droplet system?…”

“…Oil dissolution into the aqueous phase is hypothesized to play a major role in the observed droplet behaviors (27,29), with oil dissolution affecting the interfacial tension, leading to droplet motion induced by Marangoni instabilities. We used a previously reported 1 H nuclear magnetic resonance (NMR) spectroscopic method (24) to quantify the aqueous phase oil concentration during droplet motion at 22.4° ± 0.2°C and 27.7° ± 0.2°C (see the " 1 H NMR oil dissolution analysis" section in the Supplementary Materials). A 5°C temperature increase is seen to accelerate the dissolution of all oils (Fig.…”

“…We tested our approach on dynamic oil-in-water droplets-promising protocell models (21,22) displaying an astonishing range of lifelike behaviors, including movement, division, fusion, and chemotaxis (23)(24)(25)(26). Although these droplets are thought to be driven by Marangoni instabilities originating from surface tension asymmetry (27), to date, the understanding of even the most simple systems remains limited (28,29).…”

“…To perform the experiment, we designed a new high-throughput droplet dispensing robot with parallel operations ( Fig. 2 and movie S1; see the "Robotic platform: Dropfactory" section in the Supplementary Materials) that can complete more than 30 experiments per hour, a six-time throughput increase from previously reported platforms (24,26). Our CA-robot can perform droplet experiments, record and analyze the droplets' behaviors, and select the next experiments in full closed-loop autonomy.…”

Distributed DNA-based Communication in Populations of Synthetic Protocells

“…Due to their minimalistic design, engineering distributed information processing functions in fully synthetic multicellular communities has several advantages including a high degree of control and reduced design-build-test cycles. Abiotic protocellular consortia, based on lipid or non-lipid compartments and wired by orthogonal information channels, would thus present a versatile technology for the bottom-up construction of complex cell-population behaviors 18,19,20 . Although some elegant strategies to achieve one-way intercellular communication in fully synthetic protocellular systems have been reported 21,22,23,24 , a scalable methodology for implementing distributed functions involving bidirectional communication across populations of protocells is currently lacking.Here, we present Biomolecular Implementation of Protocellular Communication (BIO-PC), a highly programmable protocellular messaging system that enables the construction of biochemical communication devices with collective…”