The author of this web content is a programmer and cell biology enthusiast who has embarked on a journey to simulate the simplest cell using TypeScript. The simulation is based on a paper that creates a model of a minimal cell and runs a simulation to observe processes such as DNA replication, metabolism, and protein synthesis. The simulation focuses on the well-stirred model, which represents the whole cell as a single homogeneous mixture. The minimal cell used in the simulation, JCVI-syn3A, has been created by removing genes from a bacterial cell until it can no longer survive. The simulation relies on genomic data and kinetic parameters stored in files. The genetic systems are simulated using the chemical master equation, which involves randomly choosing reactions to execute based on their propensity. The metabolic reactions, on the other hand, are calculated deterministically using ordinary differential equations. The simulation produces results that are validated against the results in the paper. The performance of the simulation is quite good, and there are possibilities for future research in exploring cell cycle mechanics, scaling up to more complicated cells, and conducting full molecular dynamics simulations of entire cells. The complete source code for the project is publicly available on the author’s GitHub page.
https://technistuff.com/posts/simulating-a-minimal-cell/