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The school will commence at 4pm on Monday, 26th July, and will conclude at lunchtime on Friday, 30th July.

Molsim2010 program

Scientific lunch breaks

Tuesday: Graphene Under Strain.

Prof. Luciano Colombo

Graphene, a one-atom-thick sheet of carbon atoms arranged onto a honeycomb lattice with a gapless electronic structure, is the mother structure of most carbon-based nanomaterials central to modern nanoscience. Fullerenes, nanotubes, and multi-sheet graphite-like nanosystems are in fact obtained by wrapping, rolling or stacking a graphene monolayer. Graphene has been experimentally produced under controlled conditions only few years ago. Since then it has attracted a huge amount of experimental and theoretical investigations addressed to its unique physical properties, which are interesting from a fundamental research perspective, as well as for potential technological applications in nanoelectronics. Typically, when graphene nanoribbons are used as nano-contacts to transfer charge carriers or as nano-mechanical resonators or as heat nano-sinks, they must work in strained conditions. Therefore, any further fundamental understing of the physics and chemistry of graphene does require the proper  modelling of its elastic properties. In this work I address the above issue by combining continuum elasticity to tight-binding molecular dynamics. I work out the stress-strain constitutive equation of graphene in both the linear and nonlinera regime; I discuss the relevand elastic moduli; I provide evidence about the elecrton energy gap opening in graphene by strain engineering.

Wednesday: Molecular Modelling of Poly-anionic Carbohydrates and their Interactions with Proteins.

Ms Neha Gandhi

Sulphated glycosaminoglycans (GAGs) are glycans found on all cell surfaces which act by binding selectively to a variety of proteins and pathogens and are critically relevant to many disease processes such as inflammation, neurodegeneration, angiogenesis, cardiovascular disorders, cancer and infectious disease. Heparin/heparan sulphate (HS) are GAGs consisting of 1-4 linked uronic acid and glucosamine and encompassing varying degree of sulphation are mainly involved in many of these activities. GAGs such as heparin/HS are challenging from a molecular modelling perspective because of their high negative charge density and their conformational flexibility. The monosaccharide 2-O-sulfo-α-L-iduronic acid (IdoA2S) is one of the major components of heparin/HS. The ability of molecular mechanics force fields to reproduce ring-puckering conformational equilibrium and glycosidic torsions are important for the successful prediction of the free energies of interaction of these carbohydrates with proteins, however most of these force fields lack parameters for sulphates. Our results of several nanoseconds long atomistic MD simulations showed that the GROMOS96 force field can predict successfully the dominant skew-boat to chair conformational transition of the IdoA2S monosaccharide in aqueous solution whereas GLYCAM06 force field sampled transitional conformations. In addition, I will be discussing the application of computational techniques such as sequence analysis, homology modelling, molecular docking, explicit molecular dynamics (MD) simulations and free energy calculations using MM-PBSA to elucidate the three-dimensional features of GAGs and their interactions with proteins such as PECAM-1, IL-8 and heparanase.

Thursday: Exploring the Free Energy Landscapes of Chemical Reactions and Other Rare Events.

Dr Bernd Ensing

Although computer simulations of molecular systems can provide unique insight into the behavior of the atoms a molecules, a major hurdle is that many interesting phenomena take place on a time scale that is much longer than the typical simulation time that can be computed. Most chemical reactions, for example, are considered "rare events" in first-principles molecular dynamics simulations. In this talk, I will present some of the progress that has been made with advanced simulation techniques, such as transition path sampling and metadynamics, to overcome the rare event problem. We can now compute and visualize multi-dimensional free energy landscapes and locate the reaction pathways and transition states as  function of the relevant order parameters. A recent advancement made in our group, path-metadynamics, allows us to probe simultaneously the reaction mechanism and the free energy profile. The methods are illustrated by Car-Parrinello molecular dynamics simulations of organic chemical reactions, chemical transitions in the photocycle of the photactive yellow protein and classical molecular dynamics calculations of the alanine dipeptide.