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Role of the Subunits Interactions in the Conformational Transitions in Adult Human Hemoglobin: an Explicit Solvent Molecular Dynamics Study
Olaniyi K. Yusuff, Jonathan O. Babalola, Giovanni Bussi +1
Hemoglobin exhibits allosteric structural changes upon ligand binding due to the dynamic interactions between the ligand binding sites, the amino acids residues and some other solu…
Ab initio complex band structure of conjugated polymers: Effects of hydrid DFT and GW schemes
Andrea Ferretti, Giuseppe Mallia, Layla Martin-Samos +4
The non-resonant tunneling regime for charge transfer across nanojunctions is critically dependent on the so-called β parameter, governing the exponential decay of the current as t…
Metadynamics with adaptive Gaussians
Davide Branduardi, Giovanni Bussi, Michele Parrinello
Metadynamics is an established sampling method aimed at reconstructing the free-energy surface relative to a set of appropriately chosen collective variables. In standard metadynam…
Colored-noise thermostats à la carte
Michele Ceriotti, Giovanni Bussi, Michele Parrinello
Recently, we have shown how a colored-noise Langevin equation can be used in the context of molecular dynamics as a tool to obtain dynamical trajectories whose properties are tailo…
RNA unwinding from reweighted pulling simulations
Francesco Colizzi, Giovanni Bussi
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps…