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We report on a computational investigation of the passive transport of H2 and O2 between the external solution and the hydrogen-producing active site of CpI [FeFe]-hydrogenase from Clostridium pasteurianum. Two distinct methodologies for studying gas access are discussed and applied: (1) temperature-controlled locally enhanced sampling, and (2) volumetric(More)
The [FeFe] hydrogenases HydA1 and HydA2 in the green alga Chlamydomonas reinhardtii catalyze the final reaction in a remarkable metabolic pathway allowing this photosynthetic organism to produce H(2) from water in the chloroplast. A [2Fe-2S] ferredoxin is a critical branch point in electron flow from Photosystem I toward a variety of metabolic fates,(More)
The [FeFe]-hydrogenases in the green alga Chlamydomonas reinhardtii utilize photogenerated electrons to reduce protons into hydrogen gas. The electrons are supplied from photosystem I and transferred to the [FeFe]-hydrogenase through specific hydrogenase-ferredoxin association. To understand how structural and kinetic factors control the association better,(More)
The [FeFe] hydrogenase from the green alga Chlamydomonas reinhardtii can catalyze the reduction of protons to hydrogen gas using electrons supplied from photosystem I and transferred via ferredoxin. To better understand the association of the hydrogenase and the ferredoxin, we have simulated the process over multiple timescales. A Brownian dynamics(More)
We describe a systematic and efficient method of determining pseudo-atom positions and potentials for use in nanostructure calculations based on bulk empirical pseudopotentials (EPMs). Given a bulk EPM for binary semiconductor X, we produce parameters for pseudo-atoms necessary to passivate a nanostructure of X in preparation for quantum mechanical(More)
The band-edge exciton fine structure of wurtzite CdSe nanocrystals is investigated by a plane-wave pseudopotential method that includes spin-orbit coupling, screened electron-hole Coulomb interactions, and exchange interactions. Large-scale, systematic simulations have been carried out on quantum dots, nanorods, nanowires, and nanodisks. The size and shape(More)
We have developed and tested molecular mechanics parameters for [FeS] clusters found in known [FeFe] hydrogenases. Bond stretching, angle bending, dihedral and improper torsion parameters for models of the oxidized and reduced catalytic H-cluster, [4Fe4S](+,2+)Cys4, [4Fe4S](+,2+)Cys3His, and [2Fe2S](+,2+)Cys4, were calculated solely from Kohn-Sham density(More)
Pi-conjugated dendrimers are an important class of materials for optoelectronic devices, especially for light-harvesting systems. We report here a theoretical investigation of the optical response and of the excited-state properties of three-arm and four-arm phenyl-cored dendrimers for photovoltaic applications. A variety of theoretical methods are used and(More)
We present here a theoretical methodology that exploits quantum mechanical calculations, molecular mechanics calculations, and Monte Carlo simulations to predict the time-of-flight measurement mobilities in films of phenyl-cored conjugated thiophene dendrimers. Our aim is to reveal structure-property relationships in amorphous films of organic pi-conjugated(More)