2026-10-13T18:31:16Z https://api.figshare.com/v2/oai

oai:figshare.com:article/34034034 2026-09-30T16:30:35Z category_873 category_133 category_135 portal_63 item_type_6 month_year_09_2026

Quantifying Directedness in Chemical Reaction Networks Using Assembly Theory Michael Jirasek (4581718) Abhishek Sharma (144862) Mary Wong (25144905) Jennifer Munro (20283021) Leroy Cronin (538206) Chemical Sciences not elsewhere classified Plant Biology Computational Biology quantities distinguish undirected observed copy number experimentally tractable metrics diverse polymerization conditions general experimental framework molecular assembly index results establish er 77 – 0 51 – 0 chemical reaction networks quantitative framework chemical systems chemical evolution ensemble assembly assembly theory assembly space whereas sequence transitions associated resolved data relevant temporal quantitative measure network analysis matched controls exploration ratio er measures directed exploration determining whether combinatorial synthesis causal context acid combinations 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. 2026-09-30T00:00:00Z Text Journal contribution 10.1021/acscentsci.6c00618.s001 https://figshare.com/articles/journal_contribution/Quantifying_Directedness_in_Chemical_Reaction_Networks_Using_Assembly_Theory/34034034 CC BY-NC 4.0