Ribosomes are autocatalytic machines, and understanding the dynamics and strategies of how ribosomes allocate resources is a vital topic of molecular biology research.

2025 Winter

I joined Dr. Lin, Wei-Hsiang’s molecular biology lab in January of 2025, and was assigned a short project, which I completed while outside the country. This work is unfinished. In the work, I devise a recursive scheme for deriving arbitrarily accurate coarse-graining for a simple autocatalytic pathway (SAP), implying we can treat an autocatalytic linear reaction network (LNR) of arbitrary length as an equivalent circuit with length two, which admit an analytic expression. Note that, despite this, the analytic expressions are usually monstrous.

See my preliminary results here

2025 Spring

My project concerns the allocation of resources in a cell. The details are not disclosed, but you may see some pretty graphs from the research. Cells have to make more cells, and this is done through the help of ribosomes, which are thus autocatalytic machines, i.e. in addition to making proteins for the cell, they must also make themselves. The main topic of interest is how cells allocate their resources to optimize the efficiency of this autocatalytic process. This work is based on Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T. Interdependence of cell growth and gene expression: origins and consequences. Science. 2010 Nov 19;330(6007):1099-102. https://10.1126/science.1192588.

Presentations

  • 20250214: The paper discusses bounds on entropy production by a living organism. I presented a detailed study of entropy production in non-equilibrium and coarse-grained systems, and provided a mathematical viewpoint for entropy here. The main takeaway is that living things are out-of-equilibrium, and therefore break detailed balance.

  • 20250620: New paper Constraints on Metabolic Network Analysis in Bacterial Physiology by Matthew Scott et al. talks about the coarse-graining paradigm for cellular metabolism. Here are the BEAMER slides for my presentation. Interestingly, cellular metabolism may be interpreted as a modular bowtie, as introduced in the paper Bow ties, metabolism and disease by Marie Csete and John Doyle.