ArticleThe journal of physical chemistry. B2017
Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations.
Article in The journal of physical chemistry. B, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- A scoping study of the whole-cell imaging literature as a foundation for the emerging field of cell anatomy.BMC biology · 2026Article
- Assembly of Macromolecular Complexes in the Whole-Cell Model of a Minimal Cell.The journal of physical chemistry. B · 2026Article
- Visualizing Cell Structures with Minecraft.Biophysicist (Rockville, Md.) · 2025Article
- A scoping study of the whole-cell imaging literature: a foundational corpus, potential for mesoscale data synthesis, and implications for standardization of an emerging field.bioRxiv : the preprint server for biology · 2025Article
- Intelligent resolution: Integrating Cryo-EM with AI-driven multi-resolution simulations to observe the severe acute respiratory syndrome coronavirus-2 replication-transcription machinery in action.The international journal of high performance computing applications · 2022Article
- Integrative modeling of the cell.Acta biochimica et biophysica Sinica · 2022Review
- The correlation between cell and nucleus size is explained by an eukaryotic cell growth model.PLoS computational biology · 2022Article
- Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps.Frontiers in molecular biosciences · 2021Article
- Art and Science of the Cellular Mesoscale.Trends in biochemical sciences · 2020Review
- Securing the future of research computing in the biosciences.PLoS computational biology · 2019Article
- Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.Nature reviews. Chemistry · 2018Article
- Review
- Molecular simulations of cellular processes.Biophysical reviews · 2017Review
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Authors and funding
7 authors.
Funding
Abstract
Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved stochastic simulations of whole cells has arisen, allowing the simulation of complex biochemical networks over cell cycle time scales using data taken from -omics, single molecule experiments, and in vitro kinetics. By using real cell geometry derived from cryo-ET data, we have the opportunity to imbue these highly detailed structural data-frozen in time-with realistic biochemical dynamics and investigate how cell structure affects the behavior of the embedded chemical reaction network. Here we present two examples to illustrate the challenges and techniques involved in integrating structural data into stochastic simulations. First, a tomographic reconstruction of Saccharomyces cerevisiae is used to construct the geometry of an entire cell through which a simple stochastic model of an inducible genetic switch is studied. Second, a tomogram of the nuclear periphery in a HeLa cell is converted directly to the simulation geometry through which we study the effects of cellular substructure on the stochastic dynamics of gene repression. These simple chemical models allow us to illustrate how to build whole-cell simulations using cryo-ET derived geometry and the challenges involved in such a process.
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