Liquid Journal of Complex Systems

Article #4, version 9 March 2012, state: Liquid turbulent

A Success Story in the Science of Complex Systems: Emergent Organisation in Complex Biomolecular Systems

Authors: Robert C. Glen and the EMBIO team

Abstract

The EMBIO project aimed to develop and apply mathematical and computational approaches that identify principles governing the emergent organisation of self-organising biomolecular systems. The goal of the project was to quantify the complexity associated with self-organization in bio-molecular systems as a means to understand complex phenomena in systems that exhibit spontaneous emergence. Specific achievements, allowing EMBIO to be considered a success story, were:

- to monitor the process of emergent complexity by performing all-atom simulations of peptide/protein folding and lipid membrane self-assembly in explicit water;

- to obtain detailed, all-atom data on representative regions of the free energy landscape (folding funnel) by simulating biopolymers (proteins and/or RNA) in their denatured and native forms;

- to investigate the sequence space of RNA molecular models and its effect on the kinetics of folding;

- to study topological, statistical and dynamic properties of generic potential energy and fitness surfaces in models of polypeptides and in RNA during self-organization;

- to find and characterize the features of the free energy funnel for simplified protein-in-water dynamic models in order to distinguish between “good” and “bad” folders;

- to define and describe parameters of the folding-unfolding pathways on the free energy funnel through the experimental mechanical stretching of giant single molecular proteins;

- to reconstruct dynamic hierarchies in a model bio-polymer system thus directly detecting the emergence of the dynamic forms and information flow at different scales in the system;

- to calculate the dynamic complexity of the system’s trajectories in different regions of the energy funnel as well as the folding process as a whole.

The project collected approaches and algorithms for quantitative estimation of complexity of a general multidimensional dynamic system. These can now be applied to a large variety of complex systems in any branch of natural and social sciences.

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Received: 9 March 2012 | Updated: 9 March 2012 | Liquid turbulent since: 9 March 2012

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