Ehud Shapiro
My research, carried out in part at
the Department of Biological Chemistry, explores the use of computer science
concepts and tools in molecular biology. One research area is the development
of a computer made of biological molecules. The research started with a conceptual
model of a Turing machine, suitable for biomolecular implementation, and its
mechanical realization. The next step (Nature 2001) was the development of an
autonomous programmable molecular finite automaton. In this two-state, two symbol
automaton the input and software were made of DNA, and the hardware consisted
of DNA manipulating enzymes. A subsequent version of the automaton used only
a single enzyme as hardware, and obtained all the necessary fuel for its operation
from the cleavage of its input DNA molecule in the normal course of the computation
(PNAS 2003). The automaton was then shown to be capable of stochastic computing.
We controlled transition probabilities by varying the relative concentration
of software molecules encoding for competing transitions (PNAS, in press). Recently,
we augmented the stochastic molecular automaton with an input module, capable
of sensing molecular disease symptoms, and an output module, capable of releasing
a drug molecule in a controlled fashion. We programmed the computer to sense
and diagnose molecular symptoms for prostate cancer and for small-cell lung
cancer and to release, upon diagnosis, a molecule purported to be a drug for
cancer.
Recent Publications
- [with Y. Benenson, T. Paz-Elizur, R. Adar, Z. Livneh and E. Keinan] Programmable and autonomous computing machine made of biomolecules. Nature 414 (2001) 430-434.
- [with Y. Benenson, R. Adar, T. Paz-Elizur and Z. Livneh] DNA molecule provides a computing machine with both data and fuel. Proc. Natl. Acad. Sci. USA 100 (2003) 2191-2196.
- [with R. Adar, Y. Benenson, G. Linshiz, A. Rosner and N. Tishbi] Stochastic computing with biomolecular automata. Proc. Natl. Acad. Sci. USA, in press.