Vol. 5 No. 1 (2025): Issue 5
Articles

Novel Genetic Circuits Design through Monte Carlo Simulation

Julien Lefevre
Molecular Biology Institute of Montauban, Montauban, 82000, France
Camille Dubois
Bioengineering and Synthesis Laboratory, Université de Bourgogne Franche-Comté, Besançon, 25000, France
Antoine Moreau
Applied Systems Biology Research Group, University of La Rochelle, La Rochelle, 17000, France

Published 2025-02-20

Keywords

  • Genetic Circuits,
  • Synthetic Biology,
  • Monte Carlo Simulation,
  • Probabilistic Modeling,
  • Circuit Optimization

How to Cite

Lefevre, J., Dubois, C., & Moreau, A. (2025). Novel Genetic Circuits Design through Monte Carlo Simulation. Optimizations in Applied Machine Learning, 5(1). https://doi.org/10.71070/oaml.v5i1.93

Abstract

Novel genetic circuits design is crucial for advancing synthetic biology applications. Currently, the design of genetic circuits faces challenges in achieving optimal functionality and efficiency due to the complexity of biological systems. This paper addresses the limitations in existing research by proposing a novel approach using Monte Carlo simulation. By utilizing Monte Carlo simulation, this study offers a new perspective on genetic circuits design, allowing for the exploration of a wider design space and the identification of more robust and efficient circuit configurations. The innovative aspect of this work lies in its integration of probabilistic modeling to optimize genetic circuits performance, paving the way for the development of more advanced and reliable synthetic biological systems.

References

  1. J. Lei, "Efficient Strategies on Supply Chain Network Optimization for Industrial Carbon Emission Reduction," arXiv preprint arXiv:2404.16863, 2024.
  2. J. Lei and A. Nisar, "Investigating the Influence of Green Technology Innovations on Energy Consumption and Corporate Value: Empirical Evidence from Chemical Industries of China," Innovations in Applied Engineering and Technology, pp. 1-16, 2023.
  3. P.-M. Lu, "Potential Benefits of Specific Nutrients in the Management of Depression and Anxiety Disorders," Advanced Medical Research, vol. 3, no. 1, pp. 1-10, 2024.
  4. L. Buecherl and C. J. Myers, "Engineering genetic circuits: advancements in genetic design automation tools and standards for synthetic biology," Current opinion in microbiology, vol. 68, p. 102155, 2022.
  5. J. Hasty, D. McMillen, and J. J. Collins, "Engineered gene circuits," Nature, vol. 420, no. 6912, pp. 224-230, 2002.
  6. Y. Park, A. Espah Borujeni, T. E. Gorochowski, J. Shin, and C. A. Voigt, "P recision design of stable genetic circuits carried in highly‐insulated E. coli genomic landing pads," Molecular systems biology, vol. 16, no. 8, p. e9584, 2020.
  7. C. D. McBride, T. W. Grunberg, and D. Del Vecchio, "Design of genetic circuits that are robust to resource competition," Current Opinion in Systems Biology, vol. 28, p. 100357, 2021.
  8. X. Lv et al., "New synthetic biology tools for metabolic control," Current Opinion in Biotechnology, vol. 76, p. 102724, 2022.
  9. T. Nguyen et al., "Design of asynchronous genetic circuits," Proceedings of the IEEE, vol. 107, no. 7, pp. 1356-1368, 2019.
  10. G. Menon and J. Krishnan, "Design principles for compartmentalization and spatial organization of synthetic genetic circuits," ACS Synthetic Biology, vol. 8, no. 7, pp. 1601-1619, 2019.
  11. K. L. Nylund, T. Asparouhov, and B. O. Muthén, "Deciding on the number of classes in latent class analysis and growth mixture modeling: A Monte Carlo simulation study," Structural equation modeling: A multidisciplinary Journal, vol. 14, no. 4, pp. 535-569, 2007.
  12. Y.-S. Cheng, P.-M. Lu, C.-Y. Huang, and J.-J. Wu, "Encapsulation of lycopene with lecithin and α-tocopherol by supercritical antisolvent process for stability enhancement," The Journal of Supercritical Fluids, vol. 130, pp. 246-252, 2017.
  13. P.-M. Lu and Z. Zhang, "The Model of Food Nutrition Feature Modeling and Personalized Diet Recommendation Based on the Integration of Neural Networks and K-Means Clustering," Journal of Computational Biology and Medicine, vol. 5, no. 1, 2025.
  14. W. W. Chin, B. L. Marcolin, and P. R. Newsted, "A partial least squares latent variable modeling approach for measuring interaction effects: Results from a Monte Carlo simulation study and an electronic-mail emotion/adoption study," Information systems research, vol. 14, no. 2, pp. 189-217, 2003.
  15. R. Y. Rubinstein, "Simulation and the Monte Carlo method," in Wiley series in probability and mathematical statistics, 1981.
  16. N. C. Grassly, J. Adachj, and A. Rambaut, "PSeq-Gen: an application for the Monte Carlo simulation of protein sequence evolution along phylogenetic trees," Bioinformatics, vol. 13, no. 5, pp. 559-560, 1997.
  17. I. Kawrakow, E. Mainegra-Hing, and F. Tessier, "The EGSnrc Code System: Monte Carlo Simulation of Electron and Photon Transport," 2016.
  18. M. G. Arend and T. Schäfer, "Statistical power in two-level models: A tutorial based on Monte Carlo simulation," Psychological methods, vol. 24, no. 1, p. 1, 2019.
  19. B. Echard, N. Gayton, and M. Lemaire, "AK-MCS: an active learning reliability method combining Kriging and Monte Carlo simulation," Structural safety, vol. 33, no. 2, pp. 145-154, 2011.
  20. J. Odentrantz, "Markov chains: Gibbs fields, Monte Carlo simulation, and queues," ed: Taylor & Francis, 2000.