Synthetic Biology Group

The Synthetic Biology Group designs proteins, microbes, and microbial communities for clean energy, manufacturing, agriculture, and human health.

Our group applies systems biology approaches to develop a predictive understanding of complex biological systems and uncover the foundational design principles that govern their behavior. We integrate computational modeling, synthetic biology, and biochemical methods to redesign proteins and microbial pathways capable of sequestering and separating critical metals, resisting mutational inactivation, and producing strategically valuable compounds. By leveraging engineering and materials science principles, we transform fundamental scientific discoveries into platform technologies that advance national security.

Our major research areas include:

Developing protein and microbe-based rare earth element extraction and separation approaches
Developing biocontainment strategies for environmental biotechnology
Redesigning bacterial proteins and navigating uncharted sequence and fitness landscapes
Leveraging artificial intelligence (AI) for the rapid and effective de novo design of antibodies and antibody-like molecules

Our capabilities include:

Advanced genetic engineering of model and non-model microbes
Metalloprotein engineering
AI/machine learning based protein (re)design
Metal ion separations and biomining
Process engineering
First principles modeling
High throughput experimentation and automation
Adaptive laboratory evolution

Dan Park

Group Leader

Dante Ricci

Staff Scientist

Christa Manning

Jonathan Bethke

Jennifer Chlebek

Staff Scientist

Patrick Diep

Nathan Diplock

Ziye Dong

Postdoctoral Researcher

Christina Kang-Yun

Sean Leonard

Bentley Lim

Jeremy Seidel

Patricia Faye Uychoco

Xun Wang

Ziwei Zhong

2025

Computationally Derived Structural Insights into Rare Earth Selectivity in Lanmodulin and its Variants
Computational and Structural Biotechnology Journal
K.A. Sajeevan, B. Acharya, S. Ferdous, D.M. Park, J.A. Cotruvo Jr, R. Chowdhury

Recovery of Rare Earth Elements Using Lanmodulin
Lanthanides in Enzymology and Microbiology
D. M. Park, P. Diep, Z. Dong, Y. Jiao

2024

Creating Overlapping Genes by Alternate-Frame Insertion
BioRxiv
S. P. Leonard, T. Halvorsen, B. Lim, D. M. Park, Y. Jiao, M. Yung, D. Ricci

Toxin-Antitoxin Systems Reflect Community Interactions Through Horizontal Gene Transfer
Molecular Biology and Evolution
J. H. Bethke, J. A. Kimbrel, Y. Jiao, D. Ricci

EF-Hand Battle Royale: Hetero-ion Complexation in Lanmodulin
JACS Au
J. Seidel, P. Diep, Z. Dong, J. A. Cotruvo Jr., D. M. Park

Beneficiation of REE: Prospects for Biotechnology Deployment
Rare Earth Elements: Sustainable Recovery, Processing, and Purification
Y. Fujita, D. M. Park, M. Lencka, A. Anderko, D. Reed, V. Thompson, G. Das, A. Eslamimanesh, Y. Jiao

Protein-Based Approach for High-Purity Sc, Y, and Grouped Lanthanide Separation
Separation and Purification Technology
Z. Dong, J. A. Mattocks, J. A. Seidel, J. A. Cotruvo Jr., D. M. Park

2023

A Scalable and Consolidated Microbial Platform for Rare Earth Element Leaching and Recovery from Waste Sources
Environmental Science and Technology
N. Good, C. S. Kang-Yun, E. Skovran, D. M. Park, N. C. Martinez-Gomez

Prolonging Genetic Circuit Stability Through Adaptive Evolution of Overlapping Genes
Nucleic Acids
J. L. Chlebek, S. P. Leonard, C. S. Kang-Yun, M. C. Yung, D. P. Ricci, Y. Jiao, D. M. Park

Enhanced Rare-Earth Separation with a Metal-Sensitive Lanmodulin Dimer
Nature
J. A. Mattocks, J. J. Jung, C.-Y. Lin, Z. Dong, N. H. Yennawar, E. R. Featherston, C. S. Kang-Yun, T. A. Hamilton, D. M. Park, A. K. Boal, J. A. Cotruvo

2022

Comparison of Kill Switch Toxins in Plant-Beneficial Pseudomonas fluorescens Reveals Drivers of Lethality, Stability, and Escape
ACS Synthetic Biology
T. M. Halvorsen, D. P. Ricci, D. M. Park, Y. Jiao, M. C. Yung

Microbial Carbonation of Monocalcium Silicate
ACS Omega
M. S. Guzman, J. Iyer, P. Kim, D. Kopp, Z. Dong, P. Foroughi, M. C. Yung, R. E. Riman, Y. Jiao

Complete Genome Sequence of Acidithiobacillus ferriphilus GT2, Isolated from Gold Mill Tailings
Microbiology Resource Announcements
M. Guzman, D. Reed, Y. Fujita, Y. Jiao, D. M. Park

2021 and earlier

Capturing an Elusive but Critical Element: Natural Protein Enables Actinium Chemistry
Science Advances
G. J.-P. Deblonde, J. Mattocks, Z. Dong, P. Wooddy, J. Cotruvo Jr., M. Zavarin

Bridging Hydrometallurgy and Biochemistry: A Protein-Based Process for Recovery and Separation of Rare Earth Elements
ACS Central Science
Z. Dong, J. A. Mattocks, G. J.-P. Deblonde, D. Hu, Y. Jiao, J. A. Cotruvo, D. M. Park

Microbe-Encapsulated Silica Gel Biosorbents for Selective Extraction of Scandium from Coal Byproducts
Environmental Science and Technology
Z. Dong, G. J.-P. Deblonde, A. Middleton, D. Hu, A. Dohnalkova, L. Kovarik, O. Qafoku, V. Shutthanandan, H. Jin, H. Hsu-Kim, N. Theaker, Y. Jiao, D. M. Park

Projection Microstereolithographic Microbial Bioprinting for Engineered Biofilms
Nano Letters
K. Dubbin, Z. Dong, D. M. Park, J. Alvarado, J. Su, E. Wasson, C. Robertson, J. Jackson, A. Bose, M. Moya, Y. Jiao, W. F. Hynes

A Biosorption-Based Approach for Selective Extraction of Rare Earth Elements from Coal Byproducts
Separation and Purification Technology, 2020
D. M. Park, A. Middleton, R. Smith, G. Deblonde, D. Laudal, N. Theaker, H. Hsu-Kim, Y. Jiao

Selective and Efficient Biomacromolecular Extraction of Rare-Earth Elements Using Lanmodulin
ACS Inorganic Chemistry, 2020
G. J.-P. Deblonde, J. A. Mattocks, D. M. Park, D. W. Reed, J. A. Cotruvo, Y. Jiao

Selective Biosorption of Valuable Rare Earth Elements Among Co-occurring Lanthanides
Environmental Engineering Science, 2020
E. Chang, A. W. Brewer, D. M. Park, Y. Jiao, L. N. Lammers

Major Element Composition Controls Rare Earth Element Solubility During Leaching of Coal Fly Ash and Coal By-products
International Journal of Coal Geology, 2020
A. Middleton, D. M. Park, Y. Jiao, H. Hsu-Kim

Techno-economic and Life Cycle Assessments for Sustainable Rare Earth Recovery from Coal Byproducts Using Biosorption
ACS Sustainable Chemistry and Engineering, 2020
M. Alipanah, D. M. Park, A. Middleton, Z. Dong, H. Hsu-Kim, Y. Jiao, H. Jin

Surface Complexation Model of Rare Earth Element Adsorption onto Bacterial Surfaces with Lanthanide Binding Tags
Applied Chemistry, 2020
E. Chang, A. Brewer, D. M. Park, Y. Jiao, L. N. Lammers

Synthetic Biology Group

Our research and capabilities

In the news

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2025

2024

2023

2022

2021 and earlier