(4qa) Experimental studies and AI modeling of engineered microbes and microbial interactions for a sustainable circular economy in waste management and bioproduct production

Bioproducts derived from microorganisms can serve as essential resources for food, feed, medicine, biofuels, cosmetics, etc., fulfilling the increasing demands of humanity. Microorganisms possess the unique ability to grow on waste-derived nutrients, producing bioproducts as part of a circular economy, which offers significant potential in reducing the impacts of climate change. A deeper understanding of the molecular mechanisms and environmental factors regulating microbial metabolism is crucial for directing metabolic processes toward specific outcomes, particularly the production of certain bioproducts. The fields of synthetic biology and genetic engineering offer powerful resources for identifying key components of metabolic pathways and steering organisms toward desired metabolic outcomes. Furthermore, microbial communities have demonstrated enhanced stability and sustainability, making the design of efficient synthetic microbial communities under optimized environmental conditions a pivotal element for achieving specific bioproducts and economic feasibility. Additionally, we can use mathematical models, which have been invaluable in predicting metabolic activities/pathways and cellular behavior, to streamline the research process to save both time and energy. My research interests lie at the intersections of artificial intelligence, bioengineering, chemical engineering, and biology, with the goal of integrating scientific knowledge and molecular technologies with engineering strategies to design end-to-end systems that leverage biological processes for the benefit of humanity.

Research Interests

I envision a future where bioengineering technologies harness the full potential of microorganisms, transforming them into engineered, controlled machines. Throughout my PhD programs in Chemical Engineering, Biotechnology, and Biosciences, and during my postdoctoral research, I have acquired expertise in applying molecular techniques to explore cell metabolism, characterize protein activities and their subcellular locations, genetically engineer cells, and design synthetic microbial communities. My work has focused on understanding key factors governing alga-bacteria interactions and linking their functions to waste-based growth, contributing to a sustainable circular economy with multi-faceted benefits such as bio-hydrogen production and biomass valorization. Chalmydomonas reinhardtii, the well-known green microalga and more than ten different bacteria including Escherichia, Pseudomonas, Rhizobium, Microbacterium, Bacillus and Stenotrophomonas were used as the alga and bacteria systems in my research. Recently, I initiated a project as co-PI that applies machine learning to predict dual-targeted proteins in cells. Based on my research background and professional interests, my key objectives for the future include:

1. Further uncovering biochemical principles governing microbial (algae-bacteria) metabolism at molecular and physiological levels through genetic engineering, synthetic biology, and omics analysis.
2. Developing reliable, practical models that capture the interplay among microorganisms and the impact of the environment on the associations, revealing beneficial interactions that enable community members to thrive in challenging conditions and drive synergetic network metabolism.
3. Creating AI-based models capable of predicting the behavior of individual cells in virtual environments when genetically engineered or when interacting with other cells. These goals will be pursued through multidisciplinary project designs, involving high-throughput experiments and comprehensive literature reviews to generate sufficient data for training AI models. The insights gained will enable my research group to engineer microbes and develop synthetic microbial communities, including algae and bacteria, to enhance the circular economy through waste management and bioproduct production, ultimately addressing critical human health, environmental, and ecological challenges.

Teaching Interests

Teaching and mentoring have always been passions of mine, and I see them as integral to academic life. Since my school years, I have been dedicated to developing my skills as an educator and mentor, aiming to foster self-development, critical thinking, creative problem-solving, and deep learning in my students. My broad educational background in Chemical Engineering, Biotechnology, and Biosciences allows me to effectively teach a wide range of courses at both the undergraduate and graduate levels. These include reaction kinetics, bioreactor design, transport phenomena (in both chemical and biological systems), thermodynamics, engineering mathematics, microbiology, biochemistry, bioprocess engineering, general chemistry, and introductory courses in Chemical and Biological Engineering. Drawing from my own research experience, I am enthusiastic about designing a graduate-level course that focuses on biology for engineers, genetic engineering, microbial communities, and the application of AI in Chemical and Biological Engineering. Additionally, I am deeply invested in outreach activities, particularly those that engage younger generations and the broader public, to raise awareness about pressing global challenges and the cutting-edge technologies being developed in our fields. I believe that fostering societal awareness will help younger generations identify their interests and consider future needs, while also empowering the public to better care for themselves and their environment.