Paper Citing NAMD - Abstract
Jasinski, A.; Mikulska, K.; Krajnik, B.; Mackowski, S.; Nowak, W.
Dynamics of Protein Elements of Hybrid Nanostructures - Molecular Dynamics Simulations of Light Harvesting Peridinin-Chlorophyll a-Protein Model
ACTA PHYSICA POLONICA A, 122:284-288, AUG 2012
Hybrid nanostructures are often composed of inorganic parts and "biological" ones. Optimized through million years of evolution light harvesting proteins are hard to mimic synthetically. Promising strategy in search for efficient solar cells is an attachment of selected natural protein systems to inorganic quantum dots. Such experimental hybrid structures should have improved charge separation properties. Among the most promising proteins is peridinin-chlorophyll-protein from Amphidinium carterae (PCP). It has a wide absorption spectrum (420-550 nm), optimized for sunlight. The dynamics of this protein, used in modern nanotechnology has been not addressed yet. In this work we present results of PCP computer modeling using a well established molecular dynamics methodology. The CHARMM27 force field parameters were prepared for this protein and all chromophore components. The system was embedded in a box of water, with proper counter ions, and a number of 10 ns molecular dynamics simulations were run using the NAMD code. It has been found that peridinine chromophores exhibit substantial orientational flexibility but a pair Per612 and Per613 is more rigid than the remaining two carotenoids. Orientation and dynamics of absorption and emission electric dipole moments have been also analyzed. Apparently, the architecture of PCP is not optimized for efficient Per-Chl alpha energy transfer by the Forster mechanism. Several practical issues related to molecular dynamics simulation of similar hybrid nanostructures are discussed.
