Biosciences and Biotechnology Division

Synthetic Biology Group

About us
Research and capabilities
In the news
Our team
Our publications

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.

Dante Ricci
Christina Kang-Yun
Ziye “Jesse” Dong
Group of researchers
Jennifer Chlebek
Patrick Diep
Scientists working

Our research and capabilities

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

In the news

Our team

Park, Dan Mcfarland
Dan Park
Group Leader
Chlebek, Jennifer Lynn
Jennifer Chlebek
Staff Scientist
Diep, Patrick
Patrick Diep
Diplock, Nathan Zeiben
Nathan Diplock
Dong, Ziye
Ziye Dong
Postdoctoral Researcher
Kang-Yun, Christina Sora
Christina Kang-Yun
Leonard, Sean Patrick
Sean Leonard
Lim, Bentley
Bentley Lim
Seidel, Jeremy Allen
Jeremy Seidel
Uychoco, Patricia Faye Valerio
Patricia Faye Uychoco
Zhong, Ziwei
Ziwei Zhong

Select publications

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

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

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

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

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