Zooming in on Solvation Free Energy Surfaces in Atomistic Simulations

Free-energy landscape of protein oligomerization from atomistic simulations.

In the realm of protein-protein interactions, the assembly process of homooligomers plays a fundamental role because the majority of proteins fall into this category. A comprehensive understanding of this multistep process requires the characterization of the driving molecular interactions and the transient intermediate species. The latter are often short-lived and thus remain elusive to most e...

Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibra...

Escorted free energy simulations.

We describe a strategy to improve the efficiency of free energy estimates by reducing dissipation in nonequilibrium Monte Carlo simulations. This strategy generalizes the targeted free energy perturbation approach [C. Jarzynski, Phys. Rev. E 65, 046122 (2002)] to nonequilibrium switching simulations, and involves generating artificial, "escorted" trajectories by coupling the evolution of the sy...

Zooming in on 3D magnetized plasmas with grid-adaptive simulations

the impact of e-readiness on ec success in public sector in iran the impact of e-readiness on ec success in public sector in iran

acknowledge the importance of e-commerce to their countries and to survival of their businesses and in creating and encouraging an atmosphere for the wide adoption and success of e-commerce in the long term. the investment for implementing e-commerce in the public sector is one of the areas which is focused in government‘s action plan for cross-disciplinary it development and e-readiness in go...