Two Yale researchers have received funding awards from the U.S. Department of Energy’s (DOE) Genesis Mission, a national initiative that aims to build the world’s most powerful integrated science discovery platform.
Sarah Demers, a professor of physics and chair of Yale’s Department of Physics, and Farren Isaacs, a professor of molecular, cellular and development biology and of Biomedical Engineering, will receive Phase 1 RFA awards, which are designed to identify promising pathways toward transformative scientific capabilities and establish a foundation for future investment and trade. Demers and Isaacs are members of Yale’s Faculty of Arts and Sciences (FAS). Isaacs also has an appointment in the Yale School of Engineering & Applied Science.
Project teams will design and demonstrate research workflows that integrate AI with scientific investigation, while evaluating whether those approaches can accelerate discovery, improve predictive capabilities, enhance experimentation, or generate new scientific insights, according to the DOE.
The two projects are among 278 projects to receive awards, the DOE announced today during the Genesis Mission summit in Washington, D.C. They were selected from more than 5,000 proposals submitted following a request for applications. Among projects selected, 168 are led by universities, 87 are led by DOE and National Nuclear Security Administration National Laboratories, 19 are led by companies, and four are led by nonprofit organizations.
The Genesis Mission, a national initiative led by DOE and its 17 National Laboratories, unites government, industry, academia, and philanthropists to accelerate breakthroughs in energy, scientific discovery, and national security through a new platform that combines AI, supercomputing, quantum systems, and advanced scientific instruments.
“We are delighted that the U.S. Department of Energy has selected two research projects involving Yale researchers,” said Ronald Breaker, the FAS dean of science. “The innovative synthetic biology and AI technologies emerging from the Isaacs laboratory have the potential to transform engineered microbes into miniature biological factories capable of producing valuable materials and advancing a more sustainable bioeconomy. At the same time, the Demers laboratory is exploring the fundamental nature of particles and forces, pursuing discoveries that could reshape our understanding of the universe through entirely new physics.
“These projects exemplify the breadth and impact of Yale research,” Breaker added. “I am also excited about the opportunities they will create for our students and trainees, who will gain invaluable experience working on ambitious, collaborative research with the potential for far-reaching scientific and societal impact.
Demers said her lab will use the DOE funding for its work on the Mu2e experiment at Fermilab, which is based in Illinois and looks for particle physics discoveries beyond the Standard Model.
“We will search for charged-lepton flavor violation [a rare type of particle interaction], motivated by many possible extensions to the standard model of particle physics that would answer some of our current open questions,” she said. “We are set to begin data-taking over the upcoming few years, with the experiment currently in commissioning using cosmic rays, and we will move to a muon beam soon.”
The Mu2e tracking detector that Sarah Demers and her team at Fermilab helped assemble, test, and install.
The new funding also will help to achieve complete, automated investigation of every Cosmic Ray Run dataset, Demers added, reducing anomaly diagnosis time for a detected anomaly from hours to minutes and freeing expert shifters for scientific judgment. “This is particularly important for the Yale trigger work, where the data quality monitoring will be integrated to help us find and adjust to any problems quickly so that we do not lose data.”
Isaacs’ team, which is in the Systems Biology Institute at Yale’s West Campus, will work on developing a generative AI platform that advances the design of synthetic genomes — the cell’s operating system — that would bolster applications central to the department’s Bio Design mission for advancing the biotechnology revolution.
A team led by Yale’s Farren Isaacs will develop a generative AI genome design platform they hope can be utilized for a host of applications, including synthesizing advanced materials and chemicals, engineering programmable cells for remediation, and extracting rare earth elements.
Living organisms, Isaacs says, are endowed with an extraordinary reservoir of biosynthetic and molecular capabilities that remain largely untapped for these kinds of applications, such as synthesizing advanced materials and chemicals, engineering programmable cells for remediation, or extracting rare earth elements. The group’s generative AI technology will aim to transform the laborious “Design-Build-Test-Learning” (DBTL) cycle into a “Design-Build” (DB) paradigm that is capable of synthesizing novel genomes with predictable functions in DOE-relevant organisms.
The group will also generate species-specific libraries of synthetic genomic regions, generating “omics” data — massive biological datasets created by DNA sequencing, mass spectrometry, and other high-throughput technologies — to train AI-generative models for predictable synthetic genome design.
“By delivering programmable, predictable, and economically viable microorganisms, this work aims to displace tedious strain-engineering campaigns, enhancing the bio-based production of chemicals, materials, and enzymes.” Isaacs says. “Ultimately, this project will establish new frameworks to predict and engineer life at the genome scale, advancing DOE’s mission in programmable biology and sustainable biomanufacturing, ensuring environmental sustainability and energy security.”
