Combining analysis and synthesis in a model of a biological cell

for ideas, and then abstract away from these ideas to produce algorithmic processes that can create problem solutions in a bottom-up manner. We have previously described a top-down analytical approach, Cell Assembly Kit (CellAK), based on the object-oriented (OO) paradigm and the Unified Modeling Language (UML) and RealTime 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 ca...

• Type: Conference
• Year: 2004
• Where: SAC
• Authors: Ken Webb, Tony White
• Keywords: Active Objects, Applied Computing, Bottom-up Synthesis Approach, SAC 2004, Top-down Analytical Approach