ABSTRACT Combining Analysis and Synthesis in a Model of a Biological Cell

We have previously described a top-down analytical approach

Combining analysis and synthesis in a model of a biological cell

We have previously described a top-down analytical approach, Cell Assembly Kit (CellAK), based on the object-oriented (00) paradigm and the Unified Modeling Language (UML) and Real-Time Object-Oriented Methodology (ROOM) formalisms, for developing models and simulations of cells and other biological entities. In this approach, models consist of a hierarchy of containers (ex: cytosol), active objects with behavior (ex: enzymes, lipid bilayers, transport proteins), and passive small molecules (ex: glucose, pyruvate). In this paper we describe the Substrate Catalyst Link (SCL) bottom-up synthesis approach [17], the concept of autopoiesis on which it is based, and what we have learned in trying to integrate this approach into CellAK. The enhanced CellAK architecture consists of a network of active objects (polymers), each of which has behavior that causally depends partly on its own fine-grained structure (monomers), where this structure is constantly changing through interaction with other active objects