Abstract
A language of formal proteins, theκ-calculus, is introduced. Interactions are modeled at the domain level, bonds are represented by means of shared names, and reactions are required to satisfy a causality requirement of monotonicity.
An example of a simplified signalling pathway is introduced to illustrate how standard biological events can be expressed in our protein language. A more comprehensive example, the lactose operon, is also developed, bringing some confidence in the formalism considered as a modeling language.
Then a finer-grained concurrent model, the mκ-calculus, is considered, where interactions have to be at most binary. We show how to embed the coarser-grained language in the latter, a property which we call self-assembly.
Finally we show how the finer-grained language can itself be encoded in π-calculus, a standard foundational language for concurrency theory.
An example of a simplified signalling pathway is introduced to illustrate how standard biological events can be expressed in our protein language. A more comprehensive example, the lactose operon, is also developed, bringing some confidence in the formalism considered as a modeling language.
Then a finer-grained concurrent model, the mκ-calculus, is considered, where interactions have to be at most binary. We show how to embed the coarser-grained language in the latter, a property which we call self-assembly.
Finally we show how the finer-grained language can itself be encoded in π-calculus, a standard foundational language for concurrency theory.
| Original language | English |
|---|---|
| Pages (from-to) | 69 - 110 |
| Number of pages | 42 |
| Journal | Theoretical Computer Science |
| Volume | 325 |
| Issue number | 1 |
| DOIs | |
| Publication status | Published - Sept 2004 |