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PHYSICAL BIOSCIENCES DIVISION ONE STOP

Adam Arkin


Division Director
E.O. Lawrence Berkeley National Laboratory
Professor, University of California at Berkeley, Department of Bioengineering
Director, Berkeley Synthetic Biology Institute
PI and Co-Director, Virtual Institute of Microbial Stress and Survival
Investigator, Energy Biosciences Institute

Physical Biosciences Division

Contact info:


Lawrence Berkeley National Laboratory
Energy Biosciences Building (EBB)
2151 Berkeley Way, 5th Floor
Berkeley, CA 94704 USA

Mailing address:
E.O. Lawrence Berkeley National Laboratory
1 Cyclotron Road, MS 955-512L
Berkeley, CA 94720


Primary Phone: 510-495-2116
Fax: 510-486-6219
E-mail: APArkin@lbl.gov

Websites:


Computational and Theoretical Biology
Synthetic Biology


Research Emphasis:

The Arkin Lab works on detailed modeling of genetic and biochemical networks with emphasis on developmental systems. The laboratory creates custom genetic circuitry in Saccaromyces cerivisiae and multichannel, protein and small molecule biosensors. The Arkin Lab is interested in the detailed physical analysis of the network of biochemical and genetic reactions that govern cellular development. The goal is to divine the engineering principles of the control systems that determine cell behavior and differentiation in response to internal and external signals. Because of their simplicity (relative to eukaryotic cells), and because many bacterial genome sequencing projects have recently completed, we study mostly bacterial and viral circuitry. Particular biological systems currently under study in my lab include, l-phage/Escherichia coli interactions, the role of stochastic phase-variation of type-1 pili in uropathic E. coli virulence, and analysis of the sporulation initiation and germination pathways in Bacillus subtilis. As the basis for such analyses we examine the detailed mechanisms of the underlying chemical reactions. For example, a rigorous physical analysis of the mechanisms of prokaryotic gene expression revealed that the temporal pattern of protein production from a single gene is an erratic and bursty stochastic process. Analysis of networks of such genes responsible for developmental switches demonstrated that while some architectures generate deterministic outcomes despite this noise, others exploit the noise to produce population diversity to, for example, evade attack by the immune system. In addition to theoretical analyses, the laboratory has started experimental measurements on such systems and has begun design and implementation (in yeast and E. coli) of our own custom genetic circuitry. Thus, the laboratory applies theoretical and computational analyses from dynamical systems, stochastic processes, chemical kinetics and statistical mechanics and methods from molecular biology to determine the principles of cellular signal processing and to aid in design of custom cellular circuitry that may, for example, act as sensitive biosensors.