Molecular Physics and Chemistry in Membranes: The Java Environment for Nature-Inspired Approaches (JENA)

Biological information processing is based on natural laws at a molecular level. Resulting principles make use of dedicated chemical reactions, mechanisms for transportation of biomolecules, and forces among molecules and their environment mainly induced by electric charges and by movement in local space. Since these interactions are typically located in a liquid surrounded by a membrane or a barrier, a dynamical molecular system emerges whose behavior follows the elementary rules of thermodynamics and molecular mechanics. For fine-grained modelling and simulation of processes and implementations of membrane computing, we strive for a corresponding software tool able to manage a multiple particle system in time and space at a medium level of abstraction and with no need of abstract parameter fitting. To this end, we provide the Java Environment for Nature-inspired Approaches (JENA) as a modular, configurable, and extendable platform toward a virtual laboratory and a virtual cell complementing more abstract and more idealized approaches in membrane computing. We give an introduction to JENA and its features and capabilities from the user’s perspective and from a technical point of view. Four illustrative case studies (chemical Lotka-Volterra oscillator, electrophoresis, centrifugation, neural signal transduction across synaptic cleft) demonstrate JENA’s practicability and descriptive capacity.