Paper Citing NAMD - Abstract
Gillet, Jean-Numa
Ultrafast molecular dynamics of biofuel extraction for microalgae and bacteria milking: blocking membrane folding pathways to damaged lipid-bilayer conformations with nanomicelles
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 33:690-705, APR 3 2015
Cell milking is a 100% renewable green energy for CO2 by extraction of biofuels inside the cytosol of photosynthetic micro-organisms as microalgae and bacteria. The cells are exposed to a hydrophobic solvent forming holes and cracks through their membranes from which the biofuels can leak out. In protein folding, the goal would be to find pathways to the unique functional protein conformer. However, in the lipid-bilayer interaction with the solvent for milking, the objective is to block the pathways for damaged membrane conformations of low free energy with undesired nanostructures, using the solvent properties, as shown with an ab initio structural bioinformatic model. Statistical thermodynamics is used to compute the free energy (including entropy) from the molecular dynamics trajectory of the biomolecular system with many conformational changes. This model can be extended to the general problem of biomolecules folding as for proteins and nucleic acids. Using an adaptation of the Einstein diffusion law, the conformational change dynamics of the lipid bilayer depends on the two diffusion coefficients of the solvent: D-1 before the irreversible folding transition time and the much smaller D-2 thereafter. In contrast to the n-hexane and n-heptane hydrocarbons of smaller size, the residual D-2 = 4.7 x 10(-7) cm(2)/s of the n-decane solvent, with the highest partition coefficient among the three extractors, is the only to present a D-2 value that is significantly below the critical threshold of 10(-6) cm(2)/s. Therefore, the membrane would resist to long hydrocarbons and the exposed cells would remain viable for milking.
