Joshua Atkinson

About

Joshua Atkinson is an Assistant Professor of Civil and Environmental Engineering and a member of the Omenn-Darling Bioengineering Institute at Princeton University. He earned his PhD in Systems, Synthetic, and Physical Biology from Rice University in 2019 and his BS in Microbiology from the University of Michigan in 2012. His research focuses on using approaches from synthetic biology, protein engineering, biophysics, and electrochemistry to understand and control how microbes and proteins transport electrons. The Atkinson Lab aims to elucidate the critical role of electron transport in energy and information processing within cells and microbial communities, with the goal of engineering new biotechnologies to address societal challenges related to sustainability, environmental monitoring and remediation, chemical synthesis, and resource recovery and extraction. His work emphasizes developing design rules for microbial electron transfer regulation, understanding how electron flows influence microbial community structures and geochemical cycles, and creating living electronic materials that integrate biological information processing with electrochemical devices.

Research topics

• Computer Science
• Nanotechnology
• Materials science
• Computational biology
• Chemistry
• Artificial Intelligence
• Biology
• Environmental chemistry
• Biochemical engineering
• Composite material

Selected publications

• Red-Light-Induced Genetic System for Control of Extracellular Electron Transfer

  ACS Synthetic Biology · 2024-05-02 · 9 citations

  article

  Optogenetics is a powerful tool for spatiotemporal control of gene expression. Several light-inducible gene regulators have been developed to function in bacteria, and these regulatory circuits have been ported to new host strains. Here, we developed and adapted a red-light-inducible transcription factor for Shewanella oneidensis. This regulatory circuit is based on the iLight optogenetic system, which controls gene expression using red light. A thermodynamic model and promoter engineering were…

  PublisherDOI

• Inter-kingdom electromechanical communication

  Nature Chemical Biology · 2024-07-19 · 2 citations

  article1st authorCorresponding
  PublisherDOI

• Artificial sediments enable reproducible cultivation and recapitulate ecological interactions of cable bacteria

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-04-16

  articleSenior author

  Abstract Cable bacteria are filamentous microbes that couple sulfide oxidation to oxygen reduction over centimeter distances via long-distance electron transport. While their activity creates characteristic biogeochemical gradients that shape sediment ecology, the study of cable bacteria has been constrained by the chemical and physical heterogeneity of the natural sediments they inhabit. To date, laboratory cultivation efforts have relied on these undefined environmental matrices. Here, we esta…

  PublisherDOI

• Biofilm Patterning Reveals the Functional Contributions of Periplasmic Cytochromes to the Electrochemical Activity of <i>Shewanella oneidensis</i>

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-01-08

  articleOpen access

  Abstract Shewanella oneidensis MR-1 is a model electroactive bacterium whose extracellular electron transfer (EET) pathway includes a sequential network of c -type cytochromes that span the inner membrane, periplasm, and outer membrane. While electrochemical studies revealed the critical role of outer-membrane cytochromes in mediating both outward EET from cells to external surfaces and lateral biofilm conduction across cells, the specific functional role of the periplasmic cytochromes in these…

  PublisherOA PDFDOI

• The Internet of Biofilm Living AI Devices

  IEEE Communications Magazine · 2025-07-28

  article

  As the world searches for groundbreaking, unconventional computing technologies, especially for intelligent edge applications, biological AI is emerging as an energy-efficient, robust, and reliable alternative. Researchers have unveiled the immense computing capacity inherent in biocomputing elements such as bacterial cells. The computing power of bacteria can be harnessed through Gene Regulatory Neural Networks (GRNNs). Biofilms, acting as sophisticated collections of GRNNs, leverage the natura…

  PublisherDOI

Recent grants

• NSF Postdoctoral Fellowship in Biology FY 2020

  NSF · $276k · 2020–2024

Frequent coauthors

• Jonathan J. Silberg

  Rice University

  31 shared

• Ian Campbell

  University of Washington

  12 shared

• Jeffrey A. Gralnick

  Biotechnology Institute

  10 shared

• George N. Bennett

  9 shared

• Vikas Nanda

  Johnson University

  8 shared

• Benjamin M. Bonis

  University of Minnesota

  8 shared

• Lin Su

  Southeast University

  7 shared

• Caroline M. Ajo‐Franklin

  6 shared

Labs

• Atkinson LabPI

  Focuses on using protein engineering and synthetic biology approaches to program electroactive proteins and cells to interface bacteria with electronic devices and control geochemical cycles by altering how electrons flow through microbial ecosystems.

Awards & honors

• NSF Postdoctoral Research Fellowship in Biology - Integrativ…
• Best Presentation – International Society of Microbial Elect…
• Lodieska Stockbridge Vaughn Fellowship (2018)
• DOE Office of Science Graduate Research Fellowship (2017)
• NSF Graduate Research Fellowship (2014)

Similar researchers at Princeton University

• Glaucio H Paulinoh-84
• Denise Mauzerallh-83
• Amilcare Porporatoh-82