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

Within the context of the European Horizon 2020 project ACDC, we intend to develop a probabilistic chemical compiler, to aid the construction of three-dimensional agglomerations of artificial hierarchical cellular constructs. These programmable discrete units offer a wide variety of technical innovations, like a portable biochemical laboratory that e.g. produces macromolecular medicine on demand. For this purpose, we have to investigate the agglomeration process of droplets and vesicles under proposed constraints, like confinement. This paper focuses on the influence of the geometry of the initialization and of the container on the agglomeration

Paths in a network of polydisperse spherical droplets

We simulate the movement and agglomeration of oil droplets in water under constraints, like confinement, using a simplified stochastic-hydrodynamic model. In the analysis of the network created by the droplets in the agglomeration, we focus on the paths between pairs of droplets and compare the computational results for various system sizes

Percolation breakdown in binary and ternary monodisperse and polydisperse systems of spherical particles

We perform computer simulations of an agglomeration process for monodisperse and polydisperse systems of spherical particles in a cylindrical container, using a simplified stochastic-hydrodynamic model. We consider a ternary system with three particle types A, B, and C, in which only connections of the type can be forged, while any other connections with particles of the same type or with C-particles are forbidden, and for comparison a binary system with two particle types A and C, in which only connections of the type can be formed. We study the breakdown of the percolation in the agglomeration at the bottom of the cylinder with an increasing fraction of C-particles

Kauffman Model with spatially separated ligation and cleavage reactions

One of the open questions regarding the origin of life is the problem how macromolecules could be created. One possible answer is the existence of autocatalytic sets in which some macromolecules mutually catalyze each other’s formation. This mechanism is theoretically described in the Kauffman model. We introduce and simulate an extension of the Kauffman model, in which ligation and cleavage reactions are spatially separated in different containers connected by diffusion, and provide computational results for instances with and without autocatalytic sets, focusing on the time evolution of the densities of the various molecules. Furthermore, we study the rich behavior of a randomly generated instance containing an autocatalytic metabolism, in which molecules are created by ligation processes and destroyed by cleavage processes and vice versa or generated and destroyed both by ligation processes

Geometric restrictions to the agglomeration of spherical particles

Within the scope of the European Horizon 2020 project ACDC – Artificial Cells with Distributed Cores to Decipher Protein Function, we aim at the development of a chemical compiler governing the three-dimensional arrangement of droplets, which are filled with various chemicals. Neighboring droplets form bilayers containing pores through which chemicals can move from one droplet to its neighbors. When achieving a desired three-dimensional configuration of droplets, we can thus enable gradual biochemical reaction schemes for various purposes, e.g., for the production of some desired macromolecules for pharmaceutical purposes. In this paper, we focus on geometric restrictions to possible arrangements of droplets. We present analytic results for the buttercup problem and a heuristic optimization method for the kissing number problem, which we then apply to find (quasi) optimum values for a bidisperse kissing number problem, in which the center sphere exhibits a larger radius