Department of Chemical Engineering & Biomolecular Science and Engineering 
Institute for Collaborative Biotechnologies
University of California, Santa Barbara, CA

Project 1: Network Inference and Properties of a Steroidogenesis Metabolic 
This proposal seeks to understand complex systems by examining how a model 
biological network responds to, compensates for, and fails when exposed to 
different stressors.  The susceptibility of a network to failure is 
greatly dependent upon how the different elements are controlled and 
connected, otherwise known as the network architecture.  We propose to 
study the architecture and modularity of the steroidogenesis metabolic 
network for synthesis of estradiol from cholesterol in fish ovaries. To 
understand the role of architecture in network fragility, we will 
investigate how the transcriptional or gene regulatory layer of control is 
integrated into the steroidogenesis network to create a robust 
architecture. This project is a collaborative endeavor with Chemical 
Engineers, Molecular Biologists and Ecologists.

Project 2: Signal Integration in Control of Coral Lifescycles as a Model 
for Engineering Networks
We aim to build mathematical models that describe the phenomena of 
reproduction in coral as well as larval metamorphosis, that account for 
both the response to global signals (solar and lunar cues), as well as 
local (chemical and neuronal signaling cues between individual corals in a 
population and between individual polyps in a colony). This integrated 
biological system exhibits striking parallels to the multi-scale networks 
required for engineering applications. The resulting multi-scale model to 
be derived from the proposed work will span from the molecular details of 
intra-colony and inter-colony signaling and the corresponding regulation 
of key genes and proteins to the coordinated yet disseminated interaction 
between the network of individuals and the local- and global-scale 
environment. This project is a collaborative endeavor with Chemical 
Engineers, Marine Biologists and Ecologists.

Project 3: Systems Approach to the Neuronally Controlled Adaptive Optical 
Output in Cephalopods
The nervous systems of cephalopods (octopi, squid and cuttlefish) are 
capable of driving adaptive changes in the color, reflectance and optical 
appearance of the skin within milliseconds.  The nervous systems of these 
animals already have provided highly tractable models for experimental 
analyses of neuronal structure and mechanisms of action for more than 50 
years; the mechanism of neuronal conduction and the action potential were 
discovered in studies of the giant nerve cells of the squid. In a project 
that bridges the established strengths of systems engineers and molecular 
biologists, this project seeks to analyze the systems-level control of the 
dynamic, neuronally mediated control of the optical patterns of the skin 
in squid. In particular, we will develop a detailed signal transduction 
network model that relates the cue to the cellular response. This project 
is a collaborative endeavor with Chemical Engineers, Molecular Biologists 
and Marine Biologists.

The project openings are in the laboratory of Prof. Frank Doyle, and would 
entail, primarily, the computational modeling and systems analysis of the 
respective organisms.

	The ideal candidate(s) would have experience in mathematical 
modeling of biological systems and would have sufficient background in the 
biosciences to interact with molecular biologists, marine biologists 
and/or ecologists.  Interested candidates should send their CVs, including 
contact information for references, to Professor Doyle 
([log in to unmask]).