Daniel Merkle

With Johannes B. S. Petersen, Akbar Davoodi, Christoph Flamm, and Peter F. Stadler · Under review

Explainable annotation of mass spectra

Instead of assigning an MS/MS peak only by a database score, we ask for a chemically admissible sequence of bond changes from the precursor to the observed ion. The result is an explicit fragment structure and a multi-step explanation that can be inspected, compared, or rejected. A public software release of DeclarION is in preparation.

With Rebecca Holzschuh, Christoph Flamm, and Peter F. Stadler

Half-edge graphs and executable electron movement

Lewis structures and electron-pushing diagrams are usually treated as separate notations. Half-edge graphs provide one formal representation in which electron pairs, radicals, bonds, and their movement can be handled consistently. We are now making this representation executable so that mechanistic electron-pushing steps can be used directly in graph-rewrite rules.

ChemRxiv preprintRepository

With Addie Jordon and Juri Kolčák · Revised manuscript

Continuous Petri nets beyond steady-state flux balance

Flux balance analysis identifies steady-state fluxes that satisfy stoichiometry, but does not by itself establish that the reactions can be ordered from a finite stock of molecules. Continuous Petri-net reachability keeps the same stoichiometric backbone while also testing causal fireability, distinguishing finite from limit reachability, and allowing non-steady endpoints. The revised work compares these views on the E. coli core network and the pentose-phosphate pathway.

arXivRepository

With Casper Asbjørn Eriksen

Analytic combinatorics for chemical structures

We translate chemically meaningful structure classes into compact combinatorial specifications. This gives exact counting sequences and direct samplers for branched molecules with stereochemical constraints, without hard-coding a separate generator for each class. The accompanying CombOL library has been accepted at ICMS 2026.

CombOL paperRepository

With Johann E. Kufs (Bielefeld University) and Juri Kolčak

Mass spectra and secondary metabolites of Dictyostelium

Here we connect our work on mechanistic MS/MS interpretation with the secondary metabolites produced by Dictyostelium discoideum. Given precursor mass, elemental constraints, and fragmentation evidence, we enumerate chemically admissible candidate structures and identify which observations each candidate can explain. Current work focuses on PKS-derived metabolites and feeds promising candidates back into detailed fragment annotation.

CollaborationRepository

With Marcel Friedrichs · Revised manuscript submitted

Exact atom provenance by saturation

This work takes a step beyond our earlier semigroup approach to atom tracing: it can preserve which source atoms occur together in a product and can handle several copies of the same compound in one reaction. Saturation expands only the labeling configurations reachable from the selected inputs, producing exact and inspectable isotope traces for pathway analysis and experimental design. An updated manuscript and software release are forthcoming.

Current arXiv version