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Computational
Biophysical Chemistry of Homeostasis and Adaptation
in Mammalian Cells
This project proposes to integrate the known literature
into a computer model of mammalian cellular signal transduction
and transcriptional regulation, then to test and refine
this model based on data. One goal is to accurately
predict cellular mRNA concentrations based on the thermodynamics
of molecular interactions. Since the fundamental laws
of thermodynamics, particularly Gibbs energy and equilibrium
constants, regulate all reactions, a model rooted in
the laws of thermodynamics is needed to accurately simulate
cellular homeostasis and adaptation. The original target
for confirming a working cellular and molecular biology
model will focus on modeling mammalian cells during
development and carcinogenesis induced by Ras. Ras signal
transduction through Raf-MEK-Erk to induce elk-SRF transcription
factor stimulation of early response genes such as fos
was chosen due to the central role in development and
cancer and the availability of data.
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