Final Activity Report Summary - MOLDY (Molecular dynamics simulation tools) The aim of the project was to develop and apply molecular dynamics simulation to bio-materials and nano-materials. By employing expertise from across Europe the project was able to implement existing best practice in molecular dynamics, develop new algorithms for molecular dynamics, apply molecular dynamics to a range of nano- and bio-material applications and validate the results against experimental data. The examination of the best practice showed considerable variation in the efficiency of molecular dynamics which was particularly acute with respect to the networking in parallel computers. A novel time integration algorithm, the Omelyan algorithm, was developed, tested and integrated into a number of molecular dynamics codes. The results of the best practice analysis, the analysis of the Omelyan algorithm and the results from the validation research were made available to the community through the MOLDY web pages. Three primary molecular dynamics research projects, one on nano materials and two bio-materials, were developed to test the molecular dynamics approach primarily by comparison to experiment data. Nano materials simulation of thin films was performed and compared to known structures. The two bio-materials projects were to develop and test new models for lipid membranes which formed the walls of cells and to simulate the structure and dynamics of the beta-2 adrenoceptor which was one of the only membrane bound proteins for which the structure was known. All three of these projects gave rise to novel results and provided a significant improvement on previous attempts to model similar systems. Of particular significance was the bio-materials modelling which showed that our models were able to model cell lipid walls considerably better than previous models and that this had significant impact on the dynamics, i.e. motion, and conformation, i.e. shape, of the beta 2 adrenoceptor. This was significant as the beta 2 adrenocpetor was a critical protein in asthma and the conformation adopted by the protein in a significant part of its function and of the way in which drug design could be used to improve medicines. In addition to their own research the Marie Curie fellows established a number of collaborations with a number of researchers from Trinity College Dublin on joint research projects in both nano-materials and bio-materials resulting in joint publications. Six papers in total, three with external researchers from the project, were published or were in preparation by the time of the project completion. The results were also presented through posters and talks at scientific conferences. With the expertise of the incoming Marie Curie fellows they developed a series of modules for teaching aspects of molecular dynamics simulation and analysis for both undergraduate and postgraduate students to enhance the student teaching programmes at Trinity College Dublin. These modules, which included basic molecular dynamics, forcefields for bio and nano-materials and conformational analysis were integrated into chemistry with molecular modelling degree and the high performance computing Masters course. In addition the Marie Curie fellow involved in the algorithm development developed a software engineering course for scientists who were familiar with programming but had limited experience of best practice in software development. Transfer of knowledge to the Marie Curie fellows was developed in a number of ways including scientific meetings, discussion with academics and other researchers, attendance at courses run by both the School of Chemistry and the Trinity Centre for High Performance Computing, attendance at conferences and project meetings, including discussions between the fellows and the principal investigator (PI). The project overall was a great success with a new algorithm being developed, best practice examined and a range of novel research in molecular dynamics carried out. In addition there was significant knowledge transfer both the institution and to Marie Curie fellows.
