Research

The chemical side of omics data

My science research develops computational approaches to understanding geosphere-biosphere coevolution. This includes building software tools for thermodynamic calculations and analyzing DNA and protein sequences to explore how life responds to environmental changes at evolutionary time scales.

💻 Software & Methods

chem16S: Chemical metrics for exploring genomic adaptation

Bioinformatics (2023) 📊 Vignette

Developed a method to quantify community-level genomic differences using chemical variables. Key finding: distinct chemical signatures differentiate microbial communities across redox and salinity gradients, revealing how environmental chemistry shapes genomic composition. Technical approach: R package implementation with visualization tools for analyzing 16S rRNA datasets.

CHNOSZ: Thermodynamic calculations and diagrams for geochemistry

Frontiers in Earth Science (2019) 📊 Vignette

Developed and maintain CHNOSZ, an open-source R package for thermodynamic calculations with applications to geochemistry, materials science, and microbiology. The software integrates extensive thermodynamic databases with functions to calculate chemical affinities, standard molal properties, and generate high-quality Eh-pH and other types of chemical activity diagrams. Technical features: Continuously updated since 2009, includes comprehensive documentation (help pages, demos, vignettes), enables computational reproducibility in geochemical modeling.

Diagrams with multiple metals in CHNOSZ

Applied Computing and Geosciences (2021) 📊 Vignette

Extended CHNOSZ capabilities to handle multi-metal systems using the mosaic stacking technique. This methodological advancement enables construction of equilibrium diagrams for bimetallic minerals (e.g., Fe-V, Cu-Fe systems). Applications: Hydrothermal geochemistry, materials science, ore deposit modeling, corrosion prediction.

🧬 Genome Evolution and the Environment

Community- and genome-based evidence for redox influence on protein evolution

mSystems (2023) 📊 Vignette

Demonstrated global- and local-scale correlations between environmental redox potential (Eh) and carbon oxidation state of proteins from microbial genomes. This work shows that environmental redox conditions leave quantifiable signatures in genomic sequences.

Thermodynamic approach to geochemical information from genomes

Geobiology (2023) 📊 Vignette

Thermodynamic analysis of genomic data for extracting geochemical features (redox, pH, and temperatures), with applications to deciphering environmental settings of past evolutionary transitions.

Water activity and redox potential in evolution and development

Journal of Molecular Evolution (2022) 📊 Vignette

Applied thermodynamic modeling to protein sequences across different gene ages, reconstructing redox conditions favoring protein formation through deep time. Results support the hypothesis of life originating in reducing environments and provide a quantitative framework for linking sequence data to ancient environmental chemistry. Technical contribution: Integration of thermodynamic calculations with comparative genomics.

🦠 Human Body Chemistry: Microbiomes and Proteomes

Chemical features of proteins in microbial genomes associated with body sites and gut inflammation

Biomedical Informatics (2025) 📊 Vignette

Applied computational analysis combining reference genomes with microbial abundances to quantify water and oxygen content of proteins at the community level. Key findings: (1) gut bacterial proteins have systematically lower water content compared to other body sites, indicating site-specific evolutionary adaptations, and (2) obligate anaerobes (e.g., Faecalibacterium) have more oxidized proteins than aerotolerant bacteria, favoring survival during inflammatory oxidative stress. Data: Multi-omics datasets including metagenomics, metatranscriptomics, and metaproteomics.

Water as a reactant in differential protein expression in cancer

Computational and Systems Oncology (2021) 📊 Vignette

Analyzed hundreds of proteomic datasets to quantify stoichiometric hydration state (nH₂O) in protein expression changes. Found systematically higher values in cancer tissue compared to healthy tissue, suggesting a physicochemical link between protein expression patterns and elevated cellular water content in tumors. Methods: Large-scale analysis of chemical features in cancer proteomics datasets.

🤝 Collaborative Research

Growth and stability of stratiform carrollite (CuCo₂S₄) in the Tenke-Fungurume ore district, Central African Copperbelt

von der Heyden, Dick, Rosenfels, Carlton, Lilova, Navrotsky, Subramani, Woodfield & Gibson
The Canadian Journal of Mineralogy and Petrology (2024) 📊 Vignette

Integrated multiple data sources to develop the first comprehensive thermodynamic dataset for carrollite, the main ore mineral of cobalt for battery applications. Combined heat capacity measurements and oxide melt solution calorimetry with trace element analysis to constrain mineral stability and substitution mechanisms. Key findings: Carrollite stability between 211-438°C, with temperature-dependent zonation patterns in ore deposits. Models predict mineral assemblages and metal solubility under varying pH, temperature, and redox conditions.

Physicochemical constraints on the abiotic polymerization of nucleotides into RNA

LaRowe & Dick
Journal of Geophysical Research: Biogeosciences (2025) 💾 Model code on Zenodo

Quantified energetic controls on RNA formation from nucleotides across diverse environmental conditions relevant to the origin of life. Used Gibbs energy calculations to predict nucleotide polymerization probability and RNA length distributions as functions of temperature, pressure, pH, and composition. Computational framework: CHNOSZ mosaic() function to handle complex speciation of ionizable compounds (phosphate, nucleotides) across temperature-pressure-pH space. This approach accounts for all possible charge states and their equilibrium proportions in solution. Open science: Model code publicly archived, enabling experimental validation and application to other planetary environments