Bacterial chemotaxis control process analysis with SysML

Abstract

AbstractThis paper looks at the bacteria chemotaxis control process utilizing the System Modeling Language (SysML) to leverage well‐defined and proven engineering tools for architecting, analyzing, and refining complex systems. It proposes a new methodology called reverse‐engineering object‐oriented systems engineering method (RE‐OOSEM) that converts descriptive biology research information into descriptive systems engineering information. It utilizes SysML and model‐based systems engineering (MBSE) to capture system architecture from biological system knowledge and inputs them into systems engineering tools. From an engineering point of view, this allows greater insight into how biological systems operate and suggests how much model detail is required to uncover a top‐down system understanding. RE‐OOSEM methodology guides the SysML chemotaxis control capture process. SysML syntax is used instead of biological syntax to facilitate biological chemotaxis control system analysis from an engineered system point of view. The model can act as a scaffolding to help uncover system function, the relationships of system components and processes, and bioinformatic phenotype and genotype correlation. An executable MathWorks Stateflow chemotaxis control process model based on the SysML architectural model is included. The results show the following engineering perspective observations. (1) Several control components are not dedicated but are available and utilized when needed. (2) Individual chemoreceptors act together as a sensor array. (3) Phosphate groups act as a signaling mechanism. (4) Methylation via CH3 groups of the chemoreceptor results in sensitivity adaptation. (5) Closed‐loop control collaboratively utilizes ligand bonding, phosphorylation, and methylation. (6) Timing relationships of the control subprocesses give insight into the system's architecture.