Ehud Y. Shapiro

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Biomolecular systems, composed of networks of proteins, underlie the major functions of living cells. Compartments are key to the organization of such systems. We have previously developed an abstraction for biomolecular systems using the πcalculus process algebra, which successfully handled their molecular and biochemical aspects, but provided only a(More)
Concurrent logic languages are high-level programming languages for parallel and distributed systems that offer a wide range of both known and novel concurrent programming techniques. Being logic programming languages, they preserve many advantages of the abstract logic programming model, including the logical reading of programs and computations, the(More)
We describe a novel application of a stochastic name-passing calculus for the study of biomolecular systems. We specify the structure and dynamics of biochemical networks in a variant of the stochastic π-calculus, yielding a model which is mathematically well-defined and biologically faithful. We adapt the operational semantics of the calculus to account(More)
Despite the rapidly accumulating body of knowledge about protein networks, there is currently no convenient way of sharing and manipulation of such information. We suggest that a formal computer language for describing the biomolecular processes underlying protein networks is essential for rapid advancement in this field. We propose to model biomolecular(More)
Early biomolecular computer research focused on laboratory-scale, human-operated computers for complex computational problems. Recently, simple molecular-scale autonomous programmable computers were demonstrated allowing both input and output information to be in molecular form. Such computers, using biological molecules as input data and biologically(More)