Studying and Simulating the Three-Dimensional Arrangement of Droplets

Abstract

We present some work in progress on the development of a probabilistic chemical compiler, being able to make a plan of how to create a three-dimensional agglomeration of artificial hierarchical cellular constructs. These programmable discrete units offer a wide variety of technical innovations, like a portable biochemical laboratory being able to e.g. produce macromolecular medicine on demand, and of scientific investigations, like contributions to questions regarding the origin of life. This paper focuses on one specific issue of developing such a compiler, namely the problem of simulating the experimentally observed spatial transition from an originally one-dimensional lineup of droplets into a three-dimensional, almost spherical arrangement, in which the droplets form a network via bilayers connecting them and in which they are contained within some outer hull. The network created by the bilayers allows the droplets to “communicate” (like agents in a multi agent system) with each other and to exchange chemicals contained within them, thus enabling a complex successive biochemical reaction scheme.

A Chemical Compiler for the Synthesis of Branched Oligomers on Standardized Chemical Reaction Structures

“…To showcase the leverage of our compiler, we use a simulator described by Schneider et al (2020Schneider et al ( , 2021Schneider et al ( , 2022 which simulates the assembly of a network of droplets and the subsequent reactions of the chemicals loaded into the droplets. In brief, 3000 spherical droplets with a radius of 30 µm are initialized within a cylinder of radius 1 mm and height of 4 mm so that they do not touch or intersect with the cylinder walls or with each other.…”

Geometric Restrictions to the Agglomeration of Spherical Particles

“…Thus, an agglomeration of droplets filled with various chemicals can form a bilayer network, allowing a gradual chemical reaction process. Our aim is to create a specific agglomeration of droplets in order to generate a desired gradual chemical reaction process for some purpose, like the generation of some desired macromolecule [18,17]. In order to reach this goal, we need to study the dynamics and outcome of agglomeration processes [20], but also to develop a chemical compiler [6,23], creating a plan of how to design an experiment leading to an appropriate agglomeration for a bilayer network for the desired gradual reaction processes.…”

Influence of the geometry on the agglomeration of a polydisperse binary system of spherical particles

“…In such bilayer networks, a controlled successive biochemical reaction scheme can be accomplished to produce the intended macromolecules. The main task of the theory and simulation group in Winterthur is to simulate the various agglomeration processes occurring in the experiments (Schneider et al, 2020b) and to investigate the properties of the resulting bilayer networks (Schneider et al, 2020a) in order to finally create a chemical compiler designing an experiment for producing a desired outcome with a specific agglomeration of droplets (Flumini et al, 2020;Weyland et al, 2020).…”