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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] 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)
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)
We describe a systematic and efficient method of determining pseudo-atom positions and potentials for use in nano-structure 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)
Researchers at the National Renewable Energy Laboratory and their collaborators have developed over the past ∼10 years a set of algorithms for an atomistic description of the electronic structure of nanostructures, based on plane-wave pseudopotentials and configuration-interaction. The present contribution describes the first step in assembling these(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)
We use pseudopotential theory to provide ͑1͒ the band offsets of strained GaAs and InAs on various substrates and ͑2͒ the energies E v (x) and E c (x) of the valence and conduction bands of In x Ga 1Ϫx As alloy, as a function of composition. Results are presented for both the bulk alloy and for the alloy strained on InP or GaAs. We predict that while E c(More)