Biophysical processes occurr on scales spanning over twelve order of magnitude in lengths and nearly fifteen in time. Therefore, a number of different methodological approaches must be combined in a coherent way to give a comprehensive representation. This is the so called multi-scale simulations paradigm, developed since the seventies of the last century, consisting in combining different resolution representations from the atomistic to supermolecular meso-scale models, passing through super-atomistic coarse grained models.
This approach allows reaching in silico the macroscopic time scales by a controlled reduction of the degrees of freedom, but at the same time requires a big effort in the coherent parameterization of the empirical force fields at the different resolutions. This is achieved with a combined bottom-up – top-down strategy, using both data obtained with simulations at higher resolution levels and experimental data, which also ensures adherence of models to the experimental observation.
The expertise of the bio-modeling scientists at NANO encompasses ab initio Density Functional Theory calculations, atomistic molecular dynamics, reactive force fields, and coarse grained and mesoscale models development, hybrid simulations (e.g. QM/MM or atomistic/CG), advanced sampling techniques, machine learning and genetic algorithms. These are applied to a number of different systems, involving proteins, nucleic acids, biofunctionalized nanoparticles, even in interaction with non biological surfaces, and to a number of different studies, such as amyloid related diseases, intra-cellular or diagnostic sensors, systems for drug delivery, systems for advanced radiotherapy.
Molecular Dynamics simulations, ab initio calculations, Coarse grained models, Force Field developments, clustering methods, advanced sampling, machine learning, bio-quantum computing
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