The calculation of free‐energy differences is one of the main challenges in computational
biology and biochemistry. Umbrella sampling, biased molecular dynamics (MD), is one of …

A novel variational method for construction of free energy profiles from molecular simulation
data is presented. The variational free energy profile (VFEP) method uses the maximum …

The variational free energy profile (vFEP) method is extended to two dimensions and tested
with molecular simulation applications. The proposed 2D-vFEP approach effectively …

We examine the capabilities and foundations of three landmark rate theories: harmonic
transition state theory, classical nucleation theory, and the Marcus theory of electron transfer …

Umbrella integration is a method to analyze umbrella sampling simulations by calculating
and integrating the mean force. Here, the method is extended to multidimensional reaction …

The zinc sensing transcriptional repressor Staphylococcus aureus CzrA represents an
excellent model system to understand how metal sensor proteins maintain cellular metal …

The free energy difference is the key role to predict reaction rates of solid phase transition.
Umbrella sampling is an effective method for enhanced sampling, especially in the region …

Correctly calculating the structure of metal coordination sites in a protein during the process
of nuclear magnetic resonance (NMR) structure determination and refinement continues to …

A metal-mediated interprotomer hydrogen bond has been implicated in the allosteric
mechanism of DNA operator binding in several metal-sensing proteins. Using computational …

Hybrid quantum/classical molecular dynamics simulations of the two proton transfer
reactions catalyzed by ketosteroid isomerase are presented. The potential energy surfaces …