| NSF Org: |
CCF Division of Computing and Communication Foundations |
| Recipient: |
|
| Initial Amendment Date: | May 31, 2016 |
| Latest Amendment Date: | June 28, 2016 |
| Award Number: | 1619343 |
| Award Instrument: | Standard Grant |
| Program Manager: |
Mitra Basu
mbasu@nsf.gov (703)292-8649 CCF Division of Computing and Communication Foundations CSE Directorate for Computer and Information Science and Engineering |
| Start Date: | June 1, 2016 |
| End Date: | May 31, 2020 (Estimated) |
| Total Intended Award Amount: | $250,000.00 |
| Total Awarded Amount to Date: | $266,000.00 |
| Funds Obligated to Date: |
|
| History of Investigator: |
|
| Recipient Sponsored Research Office: |
1850 RESEARCH PARK DR STE 300 DAVIS CA US 95618-6153 (530)754-7700 |
| Sponsor Congressional District: |
|
| Primary Place of Performance: |
One Shields Ave Davis CA US 95616-5270 |
| Primary Place of
Performance Congressional District: |
|
| Unique Entity Identifier (UEI): |
|
| Parent UEI: |
|
| NSF Program(s): | Software & Hardware Foundation |
| Primary Program Source: |
|
| Program Reference Code(s): |
|
| Program Element Code(s): |
|
| Award Agency Code: | 4900 |
| Fund Agency Code: | 4900 |
| Assistance Listing Number(s): | 47.070 |
ABSTRACT
Biology is replete with smart molecular systems that perform nanoscale assembly, sense environmental stimuli, create chemical signals, and produce physical motion - each of these tasks coordinated by information processing circuits implemented with chemical reactions. Learning how to build artificial chemicals that compute autonomously in complex environments would bring about groundbreaking advances in manufacturing, chemical sensing, and medicine. The theory of computation has proven invaluable in enabling information processing in electronic man-made systems, and much-studied algorithms underlie the behavior of everything from communication networks to video games. However, a thorough understanding of the principles of chemical computation is still lacking. The goal of this proposal is to use rigorous mathematical models to investigate the capabilities and limitations of chemical information processing.
The proposed research will bring the fields of physics, chemistry, biology, and computer science closer intellectually and mutually enrich them. For example, conceptual frameworks and mathematical tools capturing the manipulation of information at the molecular level may yield critical insights into the design principles of evolved biological regulatory networks. Further, understanding how information processing is possible in the disordered world of chemistry could result in error-robust electronic computing. The project will also contribute to the development of undergraduate and graduate courses, which will train students to apply the principles of computer science and electrical engineering in traditionally incompatible domains. This will encourage the next generation of scientists to break through traditional disciplinary barriers and create the scientific and engineering fields of tomorrow.
This proposal will answer foundational questions about the computational power of chemical kinetics (chemical reaction networks). How can chemicals be programmed to have desired behaviors? How much molecular energy does such computation consume? How much "more computation" does every additional chemical reaction enable? Recent advances in DNA nanotechnology (strand displacement cascades) demonstrate that molecular systems of complex functionality can be designed and constructed from the ground up. This proposal will help precisely delineate the capabilities and limitations of this technology, resulting in smaller, simpler DNA-based circuits. This proposal also introduces a new paradigm, based on the laws of thermodynamics, for programming DNA-DNA interactions. As chemical and biological systems are comprised of molecules that are inherently information-rich and programmable, principles of computer science will help design smart molecules.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
Note:
When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external
site maintained by the publisher. Some full text articles may not yet be available without a
charge during the embargo (administrative interval).
Some links on this page may take you to non-federal websites. Their policies may differ from
this site.
PROJECT OUTCOMES REPORT
Disclaimer
This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.
Biology is replete with smart molecular systems that perform nanoscale assembly, sense environmental stimuli, effect physical motion, etc., each of these tasks coordinated by chemical information processing circuits. If we can learn how to rationally engineer molecular systems of similar complexity, we could achieve great breakthroughs in manufacturing, chemical sensing, and medicine. For example, "smart drugs" that target drug activity to disease cells and activate in response to specific molecular clues would have minimal side effects and improve therapeutic outcomes. Such tasks require molecular information processing systems that operate autonomously in complex environments.
Intellectual Merit
The intellectual merit of this award was in advancing our understanding of computation as embedded in the chemical world. In support of this goal, we outlined foundational theoretical challenges in three aims: (1) formal chemical kinetics, (2) strand displacement reactions in DNA nanotechnology, (3) thermodynamic equilibrium of molecular binding.
Over the lifetime of the award, concrete conjectures for aims (1) and (3) were proven to be true. Many additional questions, which had not be concretely formulated by the time the proposal was written, were also answered. We were not able to make as much progress on the questions posed in aim (2), but our understanding of these systems has been refined since the proposal was written.
Broader Impact
Two master's students were trained and graduated. One is a women now employed in a Silicon valley startup, and the other is currently a Ph.D. student at the University of Maryland.
Additionally, three other Ph.D. students were trained (currently not graduated), one of them a woman who has published two papers with the PI and co-authored a third current in submission.
The work was disseminated to the broader community through published conference and journal papers.
Last Modified: 06/22/2020
Modified by: David S Doty
Please report errors in award information by writing to: awardsearch@nsf.gov.
