Molecular automata assembly: principles and simulation of bacterial membrane construction
In order to understand the basic rules and principles governing molecular self-
'Evolving hardware' as model of enzyme evolution
Organism growth and survival is based on thousands of enzymes organized in networks. The motivation to understand how a large number of enzymes evolved so fast inside cells may be relevant to explaining the origin and maintenance of life on Earth. We introduced electronic circuits called ‘electronic enzymes’ that model the catalytic function performed by biological enzymes .
Electronic enzymes are the hardware realization of enzymes defined as molecular automata with a finite number of internal conformational states and a set of Boolean operators modelling the active groups of the active site. One of the main features of electronic enzymes is the possibility of evolution finding the proper active site by means of a genetic algorithm yielding a metabolic ring or k-
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-