title: Surviving heat shock: control strategies for robustness and performance.
abstract: Molecular biology studies the cause-and-effect relationships among microscopic processes initiated by individual molecules within a cell and observes their macroscopic phenotypic effects on cells and organisms. These studies provide a wealth of information about the underlying networks and pathways responsible for the basic functionality and robustness of biological systems. At the same time, these studies create exciting opportunities for the development of quantitative and predictive models that connect the mechanism to its phenotype then examine various modular structures and the range of their dynamical behavior. The use of such models enables a deeper understanding of the design principles underlying biological organization and makes their reverse engineering and manipulation both possible and tractable The heat shock response presents an interesting mechanism where such an endeavor is possible. Using a model of heat shock, we extract the design motifs in the system and justify their existence in terms of various performance objectives. We also offer a modular decomposition that parallels that of traditional engineering control architectures.
authors.affiliation: Department of Mechanical and Environmental Engineering, University of California, Santa Barbara, CA 93106, USA.
authors.forename: H
authors.initials: H
authors.lastname: El-Samad
authors.forename: H
authors.initials: H
authors.lastname: Kurata
authors.forename: J C
authors.initials: JC
authors.lastname: Doyle
authors.forename: C A
authors.initials: CA
authors.lastname: Gross
authors.forename: M
authors.initials: M
authors.lastname: Khammash
mesh_terms: D004926:Escherichia coli / Q000502:physiology*; D029968:Escherichia coli Proteins / Q000032:analysis / Q000502:physiology; D005246:Feedback; D018840:HSP70 Heat-Shock Proteins / Q000032:analysis / Q000502:physiology; D006360:Heat-Shock Proteins / Q000032:analysis / Q000502:physiology; D018869:Heat-Shock Response; D008433:Mathematics; D008954:Models, Biological; D012808:Sigma Factor / Q000032:analysis / Q000502:physiology
chemical_list: D029968:Escherichia coli Proteins; D018840:HSP70 Heat-Shock Proteins; D006360:Heat-Shock Proteins; D012808:Sigma Factor; C069774:heat-shock sigma factor 32; C063842:dnaK protein, E coli