Quantifying Directedness in Chemical Reaction Networks Using Assembly Theory
- 1The University of Glasgow , , University Avenue , ,
Abstract
There is currently no general experimental framework for determining whether an open-ended reaction network explores chemical space undirectedly or with some level of directedness. Assembly Theory (AT) provides a quantitative framework for mapping experimentally observed molecular ensembles into assembly space. Here we show that directedness in chemical systems can be quantified using two experimentally accessible observables, the exploration ratio (ER) and ensemble assembly (A). ER measures the fraction of the inferred joint assembly space sampled, while A integrates the molecular assembly index with the observed copy number. Together, these quantities distinguish undirected from directed exploration and, when applied to time-resolved data or matched controls, provide a quantitative measure of transitions associated with selection. By analyzing peptide ensembles generated under diverse polymerization conditions, we find that nonspecific activation conditions yield exploration ratios of 0.77–0.96, whereas sequence-selective proteases yield lower ratios of 0.51–0.75 and elevated A. These differences are consistent across multiple environments and amino-acid combinations. The results establish ER and A as experimentally tractable metrics for directedness in chemical reaction networks and provide a route to quantify selection when the relevant temporal or causal context is defined, with implications for reaction-network analysis, combinatorial synthesis, and chemical evolution.
Related
- EDGE-INFERNO: The chemical signatures of assembly history in reionization fossils
- The assembly history of NGC 1365 through chemical archaeology
- EDGE-INFERNO: The chemical signatures of assembly history in reionization fossils
- Accelerating Chemical Kinetics for Exoplanet Atmospheres using Neural Networks
- Quantifying and testing the evidence for a phantom crossing
BibTeX
@article{jirasek2026quantifying,
title = {{Quantifying Directedness in Chemical Reaction Networks Using Assembly Theory}},
author = {Michael Jirasek and Abhishek Sharma and Mary Wong and Jennifer Munro and Leroy Cronin},
journal = {ACS Central Science},
year = {2026},
month = sep,
doi = {10.1021/acscentsci.6c00618},
url = {https://pubs.acs.org/acscii/article/12/10/1601/5442620/Quantifying-Directedness-in-Chemical-Reaction},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Quantifying Directedness in Chemical Reaction Networks Using Assembly Theory
AU - Michael Jirasek
AU - Abhishek Sharma
AU - Mary Wong
AU - Jennifer Munro
AU - Leroy Cronin
PY - 2026
DA - 2026/09/30
JO - ACS Central Science
DO - 10.1021/acscentsci.6c00618
UR - https://pubs.acs.org/acscii/article/12/10/1601/5442620/Quantifying-Directedness-in-Chemical-Reaction
AB - There is currently no general experimental framework for determining whether an open-ended reaction network explores chemical space undirectedly or with some level of directedness. Assembly Theory (AT) provides a quantitative framework for mapping experimentally observed molecular ensembles into assembly space. Here we show that directedness in chemical systems can be quantified using two experimentally accessible observables, the exploration ratio (ER) and ensemble assembly (A). ER measures the fraction of the inferred joint assembly space sampled, while A integrates the molecular assembly index with the observed copy number. Together, these quantities distinguish undirected from directed exploration and, when applied to time-resolved data or matched controls, provide a quantitative measure of transitions associated with selection. By analyzing peptide ensembles generated under diverse polymerization conditions, we find that nonspecific activation conditions yield exploration ratios of 0.77–0.96, whereas sequence-selective proteases yield lower ratios of 0.51–0.75 and elevated A. These differences are consistent across multiple environments and amino-acid combinations. The results establish ER and A as experimentally tractable metrics for directedness in chemical reaction networks and provide a route to quantify selection when the relevant temporal or causal context is defined, with implications for reaction-network analysis, combinatorial synthesis, and chemical evolution.
SN - 2374-7943
SN - 2374-7951
ER -