Monthly reports to the consortium coordinator ^{(internal access only)}

Informal interim reports to the EC ^{(internal access only)}

• month 1-6
• month 7-12

Formal reports to the EC ^{(internal access only)}

• month 1-18:
  scientific report
  management report
  deliverables:
  • 1. Refinements of existing measures of landscape structure
  • 2. Novel definitions of quantitative measures and qualitative properties of landscapes that have not been investigated systematically to-date
  • 3. Efficient algorithms for estimating and/or approximating the measures in independent simulations and "on flight" from trajectories
  • 4. New types of swarm algorithms to determine landscape measures that change the search landscape
  • 9. Extension of existing constraint-based approach to enumerate the lower energy part of lattice protein landscapes
  • 18. Implementation of efficient (parallel) codes able to identify saddles and minima in the energy landscape for off-lattice models
  • 27. Report on hierarchical structure of relaxation processes in protein folding kinetics
  • 39. Delivery of the first trajectory of a peptide showing reversible folding
• month 19-40:
  scientific report
  publishable final activity report
  deliverables:
  • 5. Application of the developed measures and the corresponding algorithms within the project
  • 6. Theoretical results on properties of energy landscapes with respect to the new measures
  • 7. Algorithms for steering dynamical simulations so as to make them computationally more efficient
  • 8. Algorithms for predicting foldability of biopolymer from partial trajectories of dynamical simulations
  • 10. Methods to enumerate this part satisfying additional properties (like minimal distance to other found conformations etc.)
  • 11. Combined stochastic and constraint-based methods
  • 12. Improved methods for the simulation and analysis of folding kinetics
  • 13. Algorithms to investigate kinetic folding of the growing RNA chain during transcription
  • 14. Algorithms for the prediction of the hybridization dynamics and the resulting equilibrium structure between two or more RNA molecules
  • 15. Novel algorithms for the "de-novo" design of RNA molecules with predefined kinetic and thermodynamic properties
  • 16. Detection of sequence and structure motifs that promote efficient folding
  • 17. Criteria for the classification of families of sequences exhibiting specific kinetic properties
  • 19. Implementation of numerical codes to characterize the connectivity graph and generally the properties of the landscape in terms of topological and geometrical indicators
  • 20. Results on the dependence of the landscape properties on the number of residues in the chain (chain length)
  • 21. Results on the differences between good and bad folders
  • 22. Results on the geometric and topologic quantities measured for protein landscapes
  • 23. New experimental setup in a AFM lab with pulsed-force setting
  • 24. Reports on the experimental results for titin
  • 25. Reports on the experimental results for elastin
  • 26. Reports on simulations for simplified models as well as all-atom models in the AFM experimental geometry
  • 28. Comparative study of computational mechanics techniques versus dynamical hierarchies in molecular systems
  • 29. Report on dynamical hierarchies as a model reduction technique for protein folding
  • 30. A robust spectral method for finding meta stable states and lumping in non-reversible Markov chains
  • 31. Report on information-theoretic characterisation of self-organisation in biomolecular systems
  • 32. Report on information theory bridging the transition between microscopic and macroscopic systems
  • 33. Report presenting a unified framework of dynamical hierarchies and information
  • 34. A theoretical framework for computing statistical complexity of the dynamics of molecular systems
  • 35. Parameters of dynamic complexity of simple model self-organising and non-self-organising molecular systems
  • 36. Numerical characteristics in terms of dynamic complexity of a realistic protein simulated at all-atom level in explicit solvent
  • 37. Description of the connection between the statistical complexity and information flow in molecular systems
  • 38. Development of Simulation Techniques at Different Scales in Molecular Systems
  • 40. Delivery of full trajectories of peptides showing multiple folding/unfolding events
  • 41. Completion of the phosphoglycerate kinase under native and non-native conditions
  • 42. Creating and maintaining the website describing the complexity measures for molecular systems
  • 43. Organising a workshop for all the participants of the project