Mathis-Group Arizona State University

Highlighted Publications

Self-organization in computation and chemistry: Return to AlChemy
Self-organization in computation and chemistry: Return to AlChemy
Cole Mathis, Devansh Patel, Westley Weimer, Stephanie Forrest
Chaos: An Interdisciplinary Journal of Nonlinear Science  ·  01 Sep 2024  ·  doi:10.1063/5.0207358
Life detection in a universe of false positives
Life detection in a universe of false positives
Harrison B. Smith, Cole Mathis
BioEssays  ·  11 Oct 2023  ·  doi:10.1002/bies.202300050
Identifying molecules as biosignatures with assembly theory and mass spectrometry
Identifying molecules as biosignatures with assembly theory and mass spectrometry
Stuart M. Marshall, Cole Mathis, Emma Carrick, Graham Keenan, Geoffrey J. T. Cooper, …, Matthew Craven, Piotr S. Gromski, Douglas G. Moore, Sara. I. Walker, Leroy Cronin
Nature Communications  ·  24 May 2021  ·  doi:10.1038/s41467-021-23258-x

Software

See our GitHub profile for access to software we’ve developed and scripts to reproduce our work.

All Publications

2026

assembly-theory: Open, Reproducible Calculation of Assembly Indices
assembly-theory: Open, Reproducible Calculation of Assembly Indices
Devansh Vimal, Garrett Parzych, Olivia M. Smith, Devendra Parkar, Holly Bergen, Joshua J. Daymude, Cole Mathis
Journal of Open Source Software  ·  06 Jan 2026  ·  doi:10.21105/joss.09318

2025

Convergent Functional Constraints Make Biochemical Reaction Diversity Predictable
Convergent Functional Constraints Make Biochemical Reaction Diversity Predictable
Veronica V. Mierzejewski, Cole Mathis, Christopher P. Kempes, Sara I. Walker
Cold Spring Harbor Laboratory  ·  22 Jun 2025  ·  doi:10.1101/2025.06.20.660822
The Emergence of Chirality from Metabolism
The Emergence of Chirality from Metabolism
John F. Malloy, Camerian Millsaps, Kamesh Narasimhan, Louie Slocombe, Cole Mathis, Leroy Cronin, Sara Imari Walker
arXiv  ·  01 Jan 2025  ·  doi:10.48550/arXiv.2505.01056
Open, Reproducible Calculation of Assembly Indices
Open, Reproducible Calculation of Assembly Indices
Devansh Vimal, Garrett Parzych, Olivia M. Smith, Devendra Parkar, Sean Bergen, Joshua J. Daymude, Cole Mathis
arXiv  ·  01 Jan 2025  ·  doi:10.48550/arXiv.2507.08852
Historical Contingencies Steer the Topology of Randomly Assembled Graphs
Historical Contingencies Steer the Topology of Randomly Assembled Graphs
Cole Mathis, Harrison B. Smith
arXiv  ·  01 Jan 2025  ·  doi:10.48550/arXiv.2507.00335
Challenge-Based Funding to Spark Origins Breakthroughs
Challenge-Based Funding to Spark Origins Breakthroughs
Cole Mathis, Harrison B. Smith
arXiv  ·  01 Jan 2025  ·  doi:10.48550/arXiv.2507.00106

2024

Experimentally measured assembly indices are required to determine the threshold for life
Experimentally measured assembly indices are required to determine the threshold for life
Sara I. Walker, Cole Mathis, Stuart Marshall, Leroy Cronin
Journal of The Royal Society Interface  ·  01 Nov 2024  ·  doi:10.1098/rsif.2024.0367
Self-organization in computation and chemistry: Return to AlChemy
Self-organization in computation and chemistry: Return to AlChemy
Cole Mathis, Devansh Patel, Westley Weimer, Stephanie Forrest
Chaos: An Interdisciplinary Journal of Nonlinear Science  ·  01 Sep 2024  ·  doi:10.1063/5.0207358
Investigating and Quantifying Molecular Complexity Using Assembly Theory and Spectroscopy
Investigating and Quantifying Molecular Complexity Using Assembly Theory and Spectroscopy
Michael Jirasek, Abhishek Sharma, Jessica R. Bame, S. Hessam M. Mehr, Nicola Bell, …, Alasdair MacLeod, Geoffrey J. T. Cooper, Marcel Swart, Rosa Mollfulleda, Leroy Cronin
ACS Central Science  ·  18 Apr 2024  ·  doi:10.1021/acscentsci.4c00120
Self-Organization in Computation & Chemistry: Return to AlChemy
Self-Organization in Computation & Chemistry: Return to AlChemy
Cole Mathis, Devansh Patel, Westley Weimer, Stephanie Forrest
arXiv  ·  01 Jan 2024  ·  doi:10.48550/arXiv.2408.12137
Experimental Measurement of Assembly Indices are Required to Determine The Threshold for Life
Experimental Measurement of Assembly Indices are Required to Determine The Threshold for Life
Sara I. Walker, Cole Mathis, Stuart Marshall, Leroy Cronin
arXiv  ·  01 Jan 2024  ·  doi:10.48550/arXiv.2406.06826

2023

False Positives and the Challenge of Testing the Alien Hypothesis
False Positives and the Challenge of Testing the Alien Hypothesis
Searra Foote, Pritvik Sinhadc, Cole Mathis, Sara Imari Walker
Astrobiology  ·  01 Nov 2023  ·  doi:10.1089/ast.2023.0005
Life detection in a universe of false positives
Life detection in a universe of false positives
Harrison B. Smith, Cole Mathis
BioEssays  ·  11 Oct 2023  ·  doi:10.1002/bies.202300050
What it takes to solve the Origin(s) of Life: An integrated review of techniques
What it takes to solve the Origin(s) of Life: An integrated review of techniques
OoLEN, Silke Asche, Carla Bautista, David Boulesteix, Alexandre Champagne-Ruel, …, Loraine Schwander, Siddhant Sharma, Harrison B. Smith, Andrey Vieira, Joana C. Xavier
arXiv  ·  01 Jan 2023  ·  doi:10.48550/arXiv.2308.11665
Determining Molecular Complexity using Assembly Theory and Spectroscopy
Determining Molecular Complexity using Assembly Theory and Spectroscopy
Michael Jirasek, Abhishek Sharma, Jessica R. Bame, S. Hessam M. Mehr, Nicola Bell, …, Alasdair Macleod, Geoffrey J. T. Cooper, Marcel Swart, Rosa Mollfulleda, Leroy Cronin
arXiv  ·  01 Jan 2023  ·  doi:10.48550/arXiv.2302.13753

2022

The Futility of Exoplanet Biosignatures
The Futility of Exoplanet Biosignatures
Harrison B. Smith, Cole Mathis
arXiv  ·  01 Jan 2022  ·  doi:10.48550/arXiv.2205.07921
Investigating the autocatalytically driven formation of Keggin-based polyoxometalate clusters
Investigating the autocatalytically driven formation of Keggin-based polyoxometalate clusters
David Lockey, Cole Mathis, Haralampos N. Miras, Leroy Cronin
Matter  ·  01 Jan 2022  ·  doi:10.1016/j.matt.2021.11.030
False positives and the challenge of testing the alien hypothesis
False positives and the challenge of testing the alien hypothesis
Searra Foote, Pritvik Sinhadc, Cole Mathis, Sara Imari Walker
arXiv  ·  01 Jan 2022  ·  doi:10.48550/arXiv.2207.00634

2021

Exploring the sequence space of unknown oligomers and polymers
Exploring the sequence space of unknown oligomers and polymers
David Doran, Emma Clarke, Graham Keenan, Emma Carrick, Cole Mathis, Leroy Cronin
Cell Reports Physical Science  ·  01 Dec 2021  ·  doi:10.1016/j.xcrp.2021.100685
Exploring and mapping chemical space with molecular assembly trees
Exploring and mapping chemical space with molecular assembly trees
Yu Liu, Cole Mathis, Michał Dariusz Bajczyk, Stuart M. Marshall, Liam Wilbraham, Leroy Cronin
Science Advances  ·  24 Sep 2021  ·  doi:10.1126/sciadv.abj2465
A robotic prebiotic chemist probes long term reactions of complexifying mixtures
A robotic prebiotic chemist probes long term reactions of complexifying mixtures
Silke Asche, Geoffrey J. T. Cooper, Graham Keenan, Cole Mathis, Leroy Cronin
Nature Communications  ·  10 Jun 2021  ·  doi:10.1038/s41467-021-23828-z
Identifying molecules as biosignatures with assembly theory and mass spectrometry
Identifying molecules as biosignatures with assembly theory and mass spectrometry
Stuart M. Marshall, Cole Mathis, Emma Carrick, Graham Keenan, Geoffrey J. T. Cooper, …, Matthew Craven, Piotr S. Gromski, Douglas G. Moore, Sara. I. Walker, Leroy Cronin
Nature Communications  ·  24 May 2021  ·  doi:10.1038/s41467-021-23258-x
Exploring and Mapping Chemical Space with Molecular Assembly Trees
Exploring and Mapping Chemical Space with Molecular Assembly Trees
Yu Liu, Cole Mathis, stuart Marshall, Michał Dariusz Bajczyk, Liam Wilbraham, Leroy Cronin
American Chemical Society (ACS)  ·  05 May 2021  ·  doi:10.26434/chemrxiv.13476597

2020

Identifying Molecules as Biosignatures with Assembly Theory and Mass Spectrometry
Identifying Molecules as Biosignatures with Assembly Theory and Mass Spectrometry
stuart Marshall, Cole Mathis, Emma Carrick, Graham Keenan, Geoffrey Cooper, …, Piotr S. Gromski, Marcel Swart, Douglas G. Moore, Sara Walker, Leroy Cronin
American Chemical Society (ACS)  ·  16 Nov 2020  ·  doi:10.26434/chemrxiv.13227881.v1
A Universal Sequencing System for Unknown Oligomers
A Universal Sequencing System for Unknown Oligomers
David Doran, Emma Clarke, Graham Keenan, Emma Carrick, Cole Mathis, Leroy Cronin
American Chemical Society (ACS)  ·  09 Nov 2020  ·  doi:10.26434/chemrxiv.13202969.v1
Spontaneous formation of autocatalytic sets with self-replicating inorganic metal oxide clusters
Spontaneous formation of autocatalytic sets with self-replicating inorganic metal oxide clusters
Haralampos N. Miras, Cole Mathis, Weimin Xuan, De-Liang Long, Robert Pow, Leroy Cronin
Proceedings of the National Academy of Sciences  ·  05 May 2020  ·  doi:10.1073/pnas.1921536117

2019

Spontaneous Formation of Autocatalytic Sets with Self-Replicating Inorganic Metal Oxide Clusters
Spontaneous Formation of Autocatalytic Sets with Self-Replicating Inorganic Metal Oxide Clusters
Haralampos N. Miras, Cole Mathis, Weimin Xuan, De-Liang Long, Robert Pow, Leroy Cronin
American Chemical Society (ACS)  ·  14 Aug 2019  ·  doi:10.26434/chemrxiv.9598442.v1
Individual perception dynamics in drunk games
Individual perception dynamics in drunk games
Alberto Antonioni, Luis A. Martinez-Vaquero, Cole Mathis, Leto Peel, Massimo Stella
Physical Review E  ·  28 May 2019  ·  doi:10.1103/PhysRevE.99.052311
Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions
Environmental control programs the emergence of distinct functional ensembles from unconstrained chemical reactions
Andrew J. Surman, Marc Rodriguez-Garcia, Yousef M. Abul-Haija, Geoffrey J. T. Cooper, Piotr S. Gromski, Rebecca Turk-MacLeod, Margaret Mullin, Cole Mathis, Sara I. Walker, Leroy Cronin
Proceedings of the National Academy of Sciences  ·  06 Mar 2019  ·  doi:10.1073/pnas.1813987116
Universal scaling across biochemical networks on Earth
Universal scaling across biochemical networks on Earth
Hyunju Kim, Harrison B. Smith, Cole Mathis, Jason Raymond, Sara I. Walker
Science Advances  ·  04 Jan 2019  ·  doi:10.1126/sciadv.aau0149

2018

Environmental Control Programs the Emergence of Distinct Product Ensembles from Unconstrained Chemical Reaction Networks
Environmental Control Programs the Emergence of Distinct Product Ensembles from Unconstrained Chemical Reaction Networks
Andrew J. Surman, , Marc Rodriguez Garcia, Yousef Abul-Haija, Geoffrey Cooper, …, Rebecca Turk-MacLeod, Margaret Mullin, Cole Mathis, Sara Walker, Leroy Cronin
American Chemical Society (ACS)  ·  14 Aug 2018  ·  doi:10.26434/chemrxiv.6962813.v1
Individual perception dynamics in drunk games
Individual perception dynamics in drunk games
Alberto Antonioni, Luis A. Martinez-Vaquero, Cole Mathis, Leto Peel, Massimo Stella
arXiv  ·  01 Jan 2018  ·  doi:10.48550/arxiv.1807.08635

2017

Universal scaling across biochemical networks on Earth
Universal scaling across biochemical networks on Earth
Hyunju Kim, Harrison B. Smith, Cole Mathis, Jason Raymond, Sara I. Walker
Cold Spring Harbor Laboratory  ·  31 Oct 2017  ·  doi:10.1101/212118
Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation
Prebiotic RNA Network Formation: A Taxonomy of Molecular Cooperation
Cole Mathis, Sanjay Ramprasad, Sara Walker, Niles Lehman
Life  ·  16 Oct 2017  ·  doi:10.3390/life7040038
The Emergence of Life as a First-Order Phase Transition
The Emergence of Life as a First-Order Phase Transition
Cole Mathis, Tanmoy Bhattacharya, Sara Imari Walker
Astrobiology  ·  01 Mar 2017  ·  doi:10.1089/ast.2016.1481