
Simone Furini
(PhD in Bioengineering) is active at the University of Siena. His main area of expertise is the simulation of biological systems at the molecular level. More
Free-energy profiles and number of permeation ions
When calculating the free-energy of ions permeating membrane proteins, an initial decision to make is how many ions needs to be included in the calculation. This decision is usually based on previous knowledge (both experiments and simulations), and on the intuition of the researcher. But intuition might be wrong… And taking the number of ions wrong might render free-energy profiles that are ...
Concentration gradients in simulations with PBC
Selectivity in bacterial Na+ channels
Molecular Dynamics simulations reveal how K+-channels might conduct K+ ions at high speed
The selectivity of ion channels to different ion species is crucial for important biological processes, as nerve transmission and muscular contraction. Thanks to the availability of experimental atomic structures of several ion channels, including K+-channels, Na+-channels and Ca2+-channels, it is now possible to investigate the microscopic details of conduction ...
Molecular Dynamics simulations can analyze how protein might move along DNA sequences
The binding of proteins to DNA controls many cellular events, including gene expression. In order to work properly, DNA binding proteins need to find their target sequences on DNA with high speed and accuracy. The recognition of the specific DNA binding site requires intimate contacts between the protein and the DNA molecule. However, strong atomic interactions between the two molecules are ...