Molecular automata modeling in structural biology

Publisher Summary This chapter discusses molecular automata modeling in structural biology. Dynamic activities within living cells rest on biomolecular systems organized into cellular structures and organelles. A common motivation of computer simulation in the past decade has been to understand cellular complexity by developing models from which to derive powerful unifying generalizations and predictions of cell dynamics. However, the modeling and simulation of cell dynamics present a host of theoretical and practical challenges. These challenges involve the need to achieve some level of competence in cellular and molecular principles (i.e., enzymology, polymerization, self-assembly) as well as familiarity with computer simulation and mathematical methods (i.e., programming, graphics rendering, differential equations, numerical analysis). Cellular automata are discrete space and time models that have been used to model biological systems. A cellular automaton in two dimensions, roughly speaking, is a checkerboard, where each cell is called a “finite automaton” because the cell is in any of a finite number of states.