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qDNA Research Group Awarded $5M Renewal Grant from the Department of Energy

Nano Group of Researchers

Composed of five research teams, Boise State’s Quantum DNA (qDNA) Research Group does not shy away from a challenge. In the fall of 2019, the group was in the early stages of implementing two new, large grants: one from the Office of Naval Research (ONR; $3.7 million over three years) to study quantum computing and one from the Department of Energy (DOE), Basic Energy Science’s (BES) Established Program to Stimulate Competitive Research (EPSCoR) to study quantum entanglement. The latter grant was structured to be executed in phases, with the initial phase funded at $3 million over two years and two subsequent phases (up to $5 million over two years each) funded based on performance and competitive renewal proposals. Following external peer review of a completely new Phase II proposal, DOE recently announced that Boise State was selected to receive its Phase II renewal grant of $5 million as part of a broader announcement of funded energy-related research projects.

“Spooky action at a distance”

Albert Einstein’s famous quote relates to the field of quantum physics (versus Isaac Newton’s classical physics) and its ability to show theoretically that two objects can affect each other’s behavior instantaneously, even across long distances. The qDNA Research Group is pioneering the use of deoxyribonucleic acid (DNA)—the building block of life on our planet—as a programmable, self-assembling architecture that organizes light-absorbing dye molecules to achieve quantum information science (QIS) applications. QIS is a recognized Industry of the Future. One such application is quantum entanglement, which explicitly involves Einstein’s “spooky action at a distance.”

qDNA researchers use various modifications of the DNA architecture to bring dye molecules close together so that they work collectively (i.e., they form an aggregate within which energy exchange between dyes can occur) to promote basic aspects of entanglement in dye aggregates. Aggregating the dyes enables absorbed light energy to be shared (delocalized) between the dyes, an essential element of entanglement, by the creation of an exciton. An exciton is an electrically neutral quasiparticle consisting of an electron (negatively charged) and hole (positively charged), whose excited-state energy (from the absorbed light) is shared between dyes. The strength, or rate, of sharing is determined by how rapidly the dyes exchange energy and how they orient relative to each other. Entanglement occurs when the excited state of one dye in the aggregate cannot be described independent of the excited state of another dye and is due to this collective interaction.

The DOE EPSCoR Phase I award advanced our understanding of novel dye materials useful for pursuing entanglement, design rules for manipulation of dye, dye aggregate, and DNA-templated dye structure-property relationships, and the theoretical, computational, instrument, and methodological advances needed to create, measure, and control quantum entanglement. Dr. Bernard Yurke, a Distinguish Research Fellow at Boise State in the Micron School of Materials Science and Engineering (MSMSE) and Department of Electrical and Computer Engineering (ECE), Co-Lead of the qDNA Research Group, and Co-Investigator on the Phase II award, expands on the preceding in this way. “The Phase I award facilitated extending our studies of exciton delocalization in aggregates employing dyes beyond those commercially available off-the-shelf to custom dyes of our own design that enables us to build a knowledge base by which dyes most suitable for studies of exciton entanglement can be identified. A highlight of the investigations was the identification of DNA-assembled squaraine rotaxane dyes that, by DNA assembly, would form aggregates ideally suited for the study of exciton behavior.”

The group’s Phase II research efforts are ambitious with the overarching goals of (1) establishing dye aggregates with desirable structure-property relationships that enable realizing entangled states and (2) exploring theoretically complementary approaches for measuring entanglement. In a truly integrated, transdisciplinary approach, each one of the five research teams will play a vital role.

Phase II funding will enable the Dye Synthesis Team and DNA Construct Synthesis Team to pursue a two-prong strategy for developing new candidate dye materials and their attachment to different DNA scaffolds that maintains a key industry collaboration with SETA BioMedicals, while enabling Boise State to further develop its own in-house dye synthesis capabilities geared toward mimicking nature’s dyes: chlorophylls. According to Co-Investigator and Dye Synthesis Team Lead Dr. Olga Mass (MSMSE), “Embedded into a protein scaffold, chlorophylls constitute the green leaf’s photosynthetic apparatus where quantum entanglement has been observed at room temperature. Our team is going to synthesize stable mimics of natural chlorophylls with photophysical properties fine-tuned for achieving and detecting entanglement. Unlike the green leaf, the synthetic chlorophylls will be organized into aggregates with the help of a DNA scaffold.”

In addition, the DNA Construct Synthesis Team, working in collaboration with SETA Biomedicals, will investigate the effects of dye and nucleic acid properties on quantum behavior using steady-state optical spectroscopy techniques. “We are using DNA,” observed Associate Professor of MSMSE and the Department of Chemistry and Biochemistry, Co-Investigator, and DNA Construct Synthesis Team Lead Jeunghoon Lee, “to precisely place the dyes and to control their quantum mechanical properties. Using DNA is currently the best way to manipulate the molecular orientation of the dyes down to the 2 nm scale.

The Ultrafast Spectroscopy Team will examine exciton properties and time evolution (on the femtosecond and picosecond timescale) of exciton lifetimes (i.e., how long do the dyes continue to exchange energy or maintain “coherence”) via advanced ultrafast nonlinear spectroscopies. Coherence, then, can be thought of the dyes in an aggregate maintaining a relationship of their states over a period of time in which they cannot be perturbed independent of the other. Maintaining coherence over a sufficient period of time is an essential ingredient for quantum computing and entanglement. “Boise State’s one-of-a-kind femtosecond laser light sources,” said Co-Investigator and Ultrafast Spectroscopy Team Lead Dr. Ryan Pensack (MSMSE), “will enable us to both generate coherences and directly measure them, including their important properties such as rates of sharing and dephasing. In coordination with our four additional research teams, these results will be part of a feedback loop designed to enhance these properties and ultimately realize the ability to create, control, and measure quantum entanglement.”

The Single Molecule Characterization Team will determine DNA-templated dye placement precision, an important validation step to confirm design control. Typically, millions of aggregates are synthesized in a water-based solution and their optical properties measured as an average. The Single Molecule Characterization Team can measure the properties of single aggregates using super-resolved fluorescence microscopy—a technique that received the 2014 Nobel Prize in Chemistry. Associate Professor Wan Kuang of ECE, Co-Investigator, and Single Molecule Characterization Team Lead said, “The Phase II award allows us to enhance the technique to capture time transients of molecules at microseconds resolution.”

The Theory and Simulation Team will continue to advance theoretical modeling of DNA-templated dye aggregates and computational methods that integrate and validate experimental results from the other teams and to guide experiments. “Dye aggregates and DNA are complex and challenging for traditional modeling methods to simulate,” noted Associate Professor of MSMSE, Co-Investigator, and Theory and Simulation Team Lead, Lan Li. “We will combine data-driven and multiscale modeling methods to accelerate predicting dye structures, properties, and interactions with DNA. Such integrated methods will select dye candidates with desired properties for the other teams and develop design rules to guide their experiments.”

Finally, the qDNA group will continue to develop quantum molecular theory and ultimately (1) define design rules for a pathway to create, measure, and control entanglement and (2) develop the theory to enable the measurement of entanglement. “The Phase II award,” said Yurke, “enables the further theoretical investigations of the physical chemistry and photochemistry of dyes and dye aggregates. In addition, it enables the development of theoretical foundations of new femtosecond spectroscopy techniques for the investigation of circular dichroism and exciton-exciton interactions, as well as for the development of novel techniques to measure entanglement.”

Success is dependent on a strong research team and institutional commitment

To successfully receive its Phase II DOE BES EPSCoR funding, the qDNA group had to quickly ramp up its research and research management capacity, in terms of both staffing and infrastructure, weather the non-trivial impacts of COVID-19 that shut down laboratory access for long periods of time, navigate a building move, adapt to supply chain issues when purchasing materials and instrumentation, and produce and publish rigorous and innovative science over a short time period. Moreover, the scientific understanding gained had to form the basis for a Phase II renewal proposal that would push the science forward even more.

The result: a research group that spans multiple departments and colleges at Boise State, involves five research teams, and has doubled in size in less than two years, involving now almost 30 faculty, professional staff, and students. The added staffing has introduced new disciplinary skill sets and a diversity of backgrounds and work experiences that enhances transdisciplinary research and provides an interactive environment that cultivates teaching and learning via research. Such an environment is emblematic of Boise State and, for our undergraduate and graduate students, will serve them well throughout their professional careers. Phase II funding will fuel additional growth in resources and staffing and associated educational opportunities.

The combination of ONR funding, previous awards, and DOE’s Phase I funding also has enabled the qDNA group to build significant infrastructure capabilities in areas of ultrafast laser spectroscopy, dye synthesis, and single molecule characterization. These capabilities are now housed in the state-of-the-art Micron Center for Materials Research (MCMR) building. These infrastructure capabilities, along with current personnel and future planned hirings, are positioning Boise State as a leader in using DNA-templated dye aggregates as a basis for accomplishing quantum entanglement, as well as quantum computing. “The external reviews that led to this award were the best our qDNA group has ever received,” stated Bill Knowlton, Professor of MSMSE and ECE and Principal Investigator of the grant. “It is a tribute to the diverse expertise and educational backgrounds of the students, research staff, and faculty that fuel an outstanding level of communication and collaboration.”

The preceding has required strong commitment from Boise State to leverage these grants with its own resources. The College of Engineering and MSMSE commitment to provide the necessary laboratory space and support, principally in the new MCMR, provides the qDNA group with state-of-the-art facilities to pursue their research. “The College of Engineering is happy to support the efforts of the Quantum DNA Research Group, led by Dr. Bill Knowlton,” said Dr. JoAnn Lighty, Dean of the College of Engineering. “The group continues to contribute at a national and international level to the much-needed engineering and science research in quantum entanglement, as recognized by this new Phase II award.”

The Division of Research and Economic Development’s contribution over the long run to meet the increased administrative and research staffing needs needed to support large grants and their management has played a prominent role in the success of the qDNA group. As Dr. Nancy Glenn, Interim Vice-President of Research and Economic Development states: “We are so pleased with this new award. The Quantum DNA Research Group is doing fascinating research using DNA to template dye molecules to advance the understanding of quantum entanglement at room temperature, with ultimate applications in quantum information systems. They have assembled an ultra-talented group of students, postdocs, staff and faculty that exemplifies what is possible at Boise State University and its ‘blue turf thinking’. Further, the federal investment affirms Quantum DNA’s excellence and Boise State’s growing national and competitive research profile.”