Search results for "Co diffusion"
showing 2 items of 2 documents
Mapping the network of pathways of CO diffusion in myoglobin.
2010
The pathways of diffusion of a CO molecule inside a myoglobin protein and toward the solvent are investigated. Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO molecule position inside the protein is calculated by using the single-sweep method in concert with fully resolved atomistic simulations in explicit solvent. The results are interpreted under the assumption that the diffusion of the ligand can be modeled as a navigation on the PMF in which the ligand hops between the PMF local minima following the minimum free energy paths (MFEPs) with rates set by the free energy barriers that need to be crossed. Here, all the local minima of the PMF, the MF…
Mapping CO diffusion paths in Myoglobin with the Single Sweep Method
2010
The pathways of diffusion and escape of a CO molecule inside and out a myoglobin protein are investigated. Specifically, the three-dimensional potential of mean force (PMF or free energy) of the CO molecule position inside the protein is calculated by using the single-sweep method in concert with fully resolved atomistic simulations in explicit solvent.The results are interpreted under the assumption that the diffusion of the ligand can be modeled as a navigation on the PMF in which the ligand hops between the PMF local minima following the minimum free energy paths (MFEPs) with rates set by the free energy barriers that need to be crossed. We calculate all these quantities --local minima, …