2020 Fiscal Year Research-status Report
Optimal information processing in biophysical networks
| Project/Area Number |
18K03473
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| Research Institution | Okinawa Institute of Science and Technology Graduate University |
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Principal Investigator |
PIGOLOTTI Simone 沖縄科学技術大学院大学, 生物複雑性ユニット, 准教授 (30812193)
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| Co-Investigator(Kenkyū-buntansha) |
CHIUCHIU Davide 沖縄科学技術大学院大学, 生物複雑性ユニット, 研究員 (40817491) [Withdrawn]
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| Project Period (FY) |
2018-04-01 – 2022-03-31
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| Keywords | Information processing / Polymerization / Kinetic Proofreading / Speed-error tradeoff / Chemical networks / Information theory |
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| Outline of Annual Research Achievements |
In the third year of the project, we worked on characterizing the tradeoffs between speed, error, and dissipation in biological error correction. These results will permit to understand how close biological systems are to optimality, which is the main research question of the project.
To achieve this goal, we developed a computational optimization scheme using state of the art numerical algorithms and high-performance computers supported by the project. Thanks to these tools, we were able to characterize the "front" of optimal solutions (in terms of speed, error, and dissipation) for biological error correction.
The PI of the project has also been working on a collaborative Perspective article which explores cellular energetics and, in particular, the energetics of information processing.
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| Current Status of Research Progress |
Current Status of Research Progress
3: Progress in research has been slightly delayed.
Reason
The numerical code for characterizing optimal error correction is now functioning and the vast majority of the results have been already obtained. The project has slowed down due COVID and due to the departure of the co-PI (Davide Chiuchiu) who left OIST a few months ago. Given the advanced status of the project, we are confident that will be able to finish it within FY2021.
The perspective paper on cellular energetics has been already submitted and we expect to have it published during this fiscal year.
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| Strategy for Future Research Activity |
The plan for this fiscal year is to run additional numerical simulations to complement the results for the optimal error correction (in particular for the protein translation model), write and submit a paper with the results, and present the results at international conferences.
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| Causes of Carryover |
The remaining budget will be used for publication expenses, to publish our results in a broad audience, open-access journal. Additional, we plan to disseminate our results at international conferences (either in person or virtually, depending on the evolution of the COVID pandemic).
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