Multi-scale simulations: development

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.

PeopleMargherita Bini, Luca Bellucci, Giorgia Brancolini, Ciro Cecconi, Stefano Corni, Rosa Di Felice, Daniele Montepietra, Riccardo Nifosì, Giuseppe Sacco, Valentina Tozzini*, Laura Zanetti Polzi
KeywordsMolecular Dynamics simulations, ab initio calculations, Coarse grained models, Force Field developments, clustering methods, advanced sampling, machine learning, bio-quantum computing
Publications
V Tozzini, C Giulivi Editorial: Revolutionizing Life Sciences: The Nobel Leap in Artificial Intelligence-Driven Biomodeling Front Mol Biosci 2024
M Bini, V Tozzini, G Brancolini Deconstructing Electrostatics of Functionalized Metal Nanoparticlesfrom Molecular Dynamics Simulations J Phys Chem B 2023
L Marchetti, R Nifosì, PL Martelli, E Da Pozzo, V Cappello, F Banterle, ML Trincavelli, C Martini, M D’Elia Quantum computing algorithms: getting closer to critical problems in computational biology Briefings in Bioinformatics 2022
S Ozden, S Monti, V Tozzini, NS Dutta, S Gili, N Caggiano, AJ Link, N Pugno, J Higgins, R Priestley, C Arnold Egg protein derived ultralightweight hybrid monolithic aerogel for water purification Mater Today 2022
M Bini, G Brancolini, V Tozzini Aggregation behavior of nanoparticles: Revisiting the phase diagram of colloids Front Mol Biosci 2022
G Palermo, AMJJ Bonvin, M Dal Peraro, RE Amaro, V Tozzini Multiscale Modeling from Macromolecules to Cell: Opportunities and Challenges of Biomolecular Simulations Front Mol Biosci 2020
G Brancolini, V Tozzini Multi-scale modeling of Proteins interactions with functionalized Nanoparticles Curr Opin Coll Int Sci 2019
F Delfino, Y Porozov, E Stepanov, G Tamazian, V Tozzini Evolutionary Switches Structural Transitions via Coarse-Grained Models J Comp Biol 2019
F Delfino, Y Porozov, E Stepanov, G Tamazian, V Tozzini Structural Transition States Explored With Minimalist Coarse Grained Models: Applications to Calmodulin Front Mol Biosci 2019
Giorgia Brancolini, Luca Bellucci, Maria Celeste Maschio, Rosa Di Felice, Stefano Corni, The interaction of peptides and proteins with nanostructures surfaces: a challenge for nanoscience, Curr Opin Coll Int Sci 2019
P Mereghetti, G Maccari, GLB Spampinato, V Tozzini Optimization of Analytical Potentials for Coarse-Grained Biopolymers Models J Phys Chem B 2016
F Trovato, V Tozzini Diffusion within the cytoplasm: a mesoscale model of interacting macromolecules Biophys J 2014
*Contact person: valentina.tozzini@nano.cnr.it