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Multi-scale models of whole cells: progress and challenges.
Konstantia Georgouli1, Jae-Seung Yeom2, Robert C Blake2
1Biosciences and Biotechnology Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, CA, United States.
Frontiers in Cell and Developmental Biology
|November 29, 2023
Summary
Whole-cell models (WCMs) are detailed simulations of cellular activity. Current WCMs are slow, highlighting the need for computational improvements and high-performance computing for complex biological systems.
Area of Science:
- Computational systems biology
- Biophysics
- Bioinformatics
Background:
- Whole-cell models (WCMs) represent a comprehensive approach in computational systems biology, aiming to simulate the activity of every molecule within a cell.
- These models integrate various system models using hybrid methods, employing appropriate mathematical techniques for diverse biological processes.
- The development and curation of WCMs are labor-intensive, resulting in a limited number of existing models.
Purpose of the Study:
- To review the progress and current state of whole-cell modeling.
- To discuss limitations and challenges in whole-cell model development and simulation.
- To identify areas for improvement in WCMs for enhanced biological insights.
Main Methods:
- Review of existing literature on whole-cell modeling.
- Analysis of hybrid modeling approaches for simulating cellular processes.
- Discussion of computational challenges and high-performance computing requirements.
Main Results:
- Whole-cell models offer significant biological insights and have identified novel phenomena.
- A key contribution of WCMs is revealing discrepancies in data for parametrization and validation.
- Current WCM simulators are slow, necessitating acceleration for complex or multicellular system simulations.
Conclusions:
- Whole-cell modeling is a powerful tool in systems biology, despite development challenges.
- Improvements in simulation speed and computational efficiency are crucial for advancing WCM applications.
- Future directions should focus on optimizing simulators and leveraging high-performance computing.
