Jordan C Atlas Current Research
Research Focus
A "minimal cell" is defined as a prokaryote with the minimum number of genes for growth and replication in an environment with ample nutritional resources. The overall goal of my research is to complete a genomically-detailed Minimal Cell Model (MCM) that addresses all the metabolic and non-metabolic features of a chemoheterotrophic bacterial cell. The project proposed here includes two main parts: 1) Development of novel algorithms that facilitate rapid addition of chemically detailed modules to the MCM, and 2) Utilization of a statistical mechanics method for parameter estimation that takes advantage of high-performance computation. While the original MCM used chemically lumped pseudospecies, the complete MCM will use concentrations of individual chemical species and mass balances on each species based on known biochemical reaction data. The MCM was shown to be "modular" by adding chemical detail to a previously lumped component. If the remaining model expansion is to be successful, it will be necessary to devise a modeling method that allows the user to specify a cell reaction network at run time. The process of model building is facilitated if modules can be attacked in parallel and then combined into a complete whole cell model.
Current Projects
Bacterial Cell Modelling
A "minimal cell" is defined as a prokaryote with the minimum number of genes for growth and replication in an environment with ample nutritional resources. The overall goal of our research is to complete a genomically-detailed Minimal Cell Model (MCM) that addresses all the metabolic and non-metabolic features of a chemoheterotrophic bacterial cell. The project proposed here includes two main parts: 1) Development of novel algorithms that facilitate rapid addition of chemically detailed modules to the MCM, and 2) Utilization of a statistical mechanics method for parameter estimation that takes advantage of high-performance computation. While the original MCM used chemically lumped pseudospecies, the complete MCM will use concentrations of individual chemical species and mass balances on each species based on known biochemical reaction data. The MCM was shown to be "modular" by adding chemical detail to a previously lumped component. If the remaining model expansion is to be successful, it will be necessary to devise a modeling method that allows the user to specify a cell reaction network at run time. The process of model building is facilitated if modules can be attacked in parallel and then combined into a complete whole cell model.
Contact Information
| 224 Olin Hall Cornell University Ithaca, NY 14853 |
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| Phone: | 607-255-5240 |
| Fax: | |
| Email: | jca33@cornell.edu |