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Developing a novel fine-grained (CHARMM) force field for
protonated PEI
rigorously derived from high-quality ab initio calculations,
using very recent software packages and technologies. We
will define specific residues and optimize atomic charges,
as well as bond, angle, and dihedral parameters.
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Fine-grained MD investigation of dynamic structuring of
solvated PEI
in terms of gyration radius, end-to-end distance, persistence
length, radial distribution functions, coordination,
diffusion coefficients, and chain rigidity.
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Developing a novel coarse-grained (MARTINI) force
field for protonated PEI
by mapping entire CHARMM residues to coarse-grained (CG) beads and adjusting
their interaction parameters using as reference the
atomistic FF and MD simulations. The CG simulations will use
tenfold time steps for significantly larger solvated PEI
systems.
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Fine- and coarse-grained MD investigations of DNA
condensation
aiming at enhanced efficiency of condensation/transfection
processes. Using the developed CHARMM and MARTINI FFs, we
will simulate DNA/PEI condensation under diverse conditions.
Topological and energetic correlations of the charged
interactions sites of DNA and PEI will corroborate the DNA
size reduction to provide estimates for optimal protonation
ratios of PEI.
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