journal article·2025-09Open access

Programmable DNA‐Based Molecular Neural Network Biocomputing Circuits for Solving Partial Differential Equations

Yijun Xiao, Alfonso Rodríguez‐Patón, Jianmin Wang, Pan Zheng, Tongmao Ma, Tao Song

Advanced Science· Volume 12· Issue 33

Abstract

Abstract Partial differential equations, essential for modeling dynamic systems, persistently confront computational complexity bottlenecks in high‐dimensional problems, yet DNA‐based parallel computing architectures, leveraging their discrete mathematics merits, provide transformative potential by harnessing inherent molecular parallelism. This research introduces an augmented matrix‐based DNA molecular neural network to achieve molecular‐level solving of biological Brusselator PDEs. Two crucial innovations address existing technological constraints: (i) an augmented matrix‐based error‐feedback DNA molecular neural network, enabling multidimensional parameter integration through DNA strand displacement cascades and iterative weight optimization; (ii) incorporating membrane diffusion theory with division operation principles into DNA circuits to develop partial differential calculation modules. Simulation results demonstrate that the augmented matrix‐based DNA neural network efficiently and accurately learns target functions; integrating the proposed partial derivative computation strategy, this architecture solves the biological Brusselator PDE numerically with errors below 0.02 within 12,500 s. This work establishes a novel intelligent non‐silicon‐based computational framework, providing theoretical foundations and potential implementation paradigms for future bio‐inspired computing and unconventional computing devices in life science research.
Source: crossref · Quality: baseline

Research context

OpenAlex topics: Advanced biosensing and bioanalysis techniques · Quantum-Dot Cellular Automata · Nanopore and Nanochannel Transport Studies

SciVX discovery tags are terminology-based. OpenAlex topics are source-provided classifications.

Affiliations

Qingdao Institute of Software, College of Computer Science and Technology China University of Petroleum Qingdao 266580 China

Departamento de Inteligencia Artificial, ETSIINF Universidad Politécnica de Madrid Madrid 28040 Spain

Department of Integrative Biotechnology Yonsei University Incheon 03722 Korea (the Republic of)

Information Systems Group University of Canterbury Christchurch 8041 New Zealand

Funding

National Natural Science Foundation of China

References (28)

Show source-provided references
1. Brunton S. L. · Comput. Sci. · 2024 · 4 · 483
2. 10.1038/s42256-024-00897-510.1038/s42256-024-00897-5 ↗
3. 10.1016/j.jtbi.2024.11173210.1016/j.jtbi.2024.111732 ↗
4. Fan D. · Sci. · 2020 · 7
5. Zhao H. · Sci. · 2025
6. Wang L. · Sci. · 2024 · 11
7. 10.1126/science.aal205210.1126/science.aal2052 ↗
8. M.Hemery F.Fages International Conference on Computational Methods in Systems Biology Springer2023 pp.78–96.10.1007/978-3-031-42697-1_6 ↗
9. Li J. · Chem. · 2017 · 9 · 1056
10. Li Z. · ACM/JMS Journal of Data Science · 2024 · 1 · 1
11. 10.1016/j.jcp.2018.10.04510.1016/j.jcp.2018.10.045 ↗
12. 10.1038/s41586-024-08040-510.1038/s41586-024-08040-5 ↗
13. 10.1038/s41586-023-06484-910.1038/s41586-023-06484-9 ↗
14. 10.1038/s41586-018-0289-610.1038/s41586-018-0289-6 ↗
15. 10.1039/D1NR06861J10.1039/D1NR06861J ↗
16. 10.1109/TCBB.2020.304556710.1109/TCBB.2020.3045567 ↗
17. 10.1039/D3CP02811A10.1039/D3CP02811A ↗
18. 10.1038/s42256-022-00502-710.1038/s42256-022-00502-7 ↗
19. 10.1038/nnano.2013.18910.1038/nnano.2013.189 ↗
20. Shah S. · J. Am. Chem. Soc. · 2020 · 142 · 9587
21. 10.1109/TNB.2021.312839310.1109/TNB.2021.3128393 ↗
22. 10.3390/cimb4404011910.3390/cimb44040119 ↗
23. 10.1038/s41467-019-13980-y10.1038/s41467-019-13980-y ↗
24. 10.1038/s41570-024-00576-410.1038/s41570-024-00576-4 ↗
25. 10.1109/TNB.2023.327457310.1109/TNB.2023.3274573 ↗
26. 10.1002/adbi.20220020310.1002/adbi.202200203 ↗
27. 10.1088/0957-4484/17/2/R0110.1088/0957-4484/17/2/R01 ↗
28. 10.1021/sb400169s10.1021/sb400169s ↗