SnO Nanostructured Thin Films for Room-Temperature Gas Sensing of Volatile Organic Compounds.

We demonstrated room-temperature gas sensing of volatile organic compounds (VOCs) using SnO nanostructured thin films grown via the aerosol chemical vapor deposition process at deposition temperatures ranging from 450 to 600 °C. We investigated the film's sensing response to the presence of three classes of VOCs: apolar, monopolar, and biopolar. The synthesis process was optimized, with the most robust response observed for films grown at 550 °C as compared to other temperatures.

Improving the Carrier Lifetime of Tin Sulfide via Prediction and Mitigation of Harmful Point Defects.

Tin monosulfide (SnS) is an emerging thin-film absorber material for photovoltaics. An outstanding challenge is to improve carrier lifetimes to >1 ns, which should enable >10% device efficiencies. However, reported results to date have only demonstrated lifetimes at or below 100 ps.

Wide bandgap BaSnO films with room temperature conductivity exceeding 10 S cm.

Wide bandgap perovskite oxides with high room temperature conductivities and structural compatibility with a diverse family of organic/inorganic perovskite materials are of significant interest as transparent conductors and as active components in power electronics. Such materials must also possess high room temperature mobility to minimize power consumption and to enable high-frequency applications. Here, we report n-type BaSnO films grown using hybrid molecular beam epitaxy with room temperature conductivity exceeding 10 S cm.

BoostGAPFILL: improving the fidelity of metabolic network reconstructions through integrated constraint and pattern-based methods.

Motivation: Metabolic network reconstructions are often incomplete. Constraint-based and pattern-based methodologies have been used for automated gap filling of these networks, each with its own strengths and weaknesses. Moreover, since validation of hypotheses made by gap filling tools require experimentation, it is challenging to benchmark performance and make improvements other than that related to speed and scalability.

Investigating the role of biofilms in trihalomethane formation in water distribution systems with a multicomponent model.

Biofilms are ubiquitous in the pipes of drinking water distribution systems (DWDSs), and recent experimental studies revealed that the chlorination of the microbial carbon associated with the biofilm contributes to the total disinfection by-products (DBPs) formation with distinct mechanisms from those formed from precursors derived from natural organic matter (NOM). A multiple species reactive-transport model was developed to explain the role of biofilms in DBPs formation by accounting for the simultaneous transport and interactions of disinfectants, organic compounds, and biomass. Using parameter values from experimental studies in the literature, the model equations were solved to predict chlorine decay and microbial regrowth dynamics in an actual DWDS, and trihalomethanes (THMs) formation in a pilot-scale distribution system simulator.

Mechanistic and microkinetic analysis of CO2 hydrogenation on ceria.

We use density functional theory (DFT) calculations to investigate the mechanism of CO2 hydrogenation to methanol on a reduced ceria (110) catalyst, which has previously been shown to activate CO2. Two reaction channels to methanol are identified: (1) COOH pathway via a carboxyl intermediate and (2) HCOO pathway via a formate intermediate. While formaldehyde (H2CO) appears to be the key intermediate for methanol synthesis, other intermediates, including carbine diol, formic acid and methanol, are not feasible due to their high formation energies.

Water quality modeling in the dead end sections of drinking water distribution networks.

Dead-end sections of drinking water distribution networks are known to be problematic zones in terms of water quality degradation. Extended residence time due to water stagnation leads to rapid reduction of disinfectant residuals allowing the regrowth of microbial pathogens. Water quality models developed so far apply spatial aggregation and temporal averaging techniques for hydraulic parameters by assigning hourly averaged water demands to the main nodes of the network.

Distortions of the Xanthophylls Caused by Interactions with Neighboring Pigments and the LHCII Protein Are Crucial for Studying Energy Transfer Pathways within the Complex.

It has been proposed that photoprotective non-photochemical quenching (NPQ) in higher plants arises from a conformational change in the antenna which alters pigment-pigment interactions. This brings about the formation of energy quenching "traps" that capture and dissipate excitation energy as heat. We have used the semiempirical AM1-CAS-CI method combined with the transition density cube (TDC) approach to model chlorophyll (Chl) to xanthophyll (Xanth) resonant Coulomb couplings in the crystal structure of LHCII.

Non-radiative relaxation of photoexcited chlorophylls: theoretical and experimental study.

Nonradiative relaxation of high-energy excited states to the lowest excited state in chlorophylls marks the first step in the process of photosynthesis. We perform ultrafast transient absorption spectroscopy measurements, that reveal this internal conversion dynamics to be slightly slower in chlorophyll B than in chlorophyll A. Modeling this process with non-adiabatic excited state molecular dynamics simulations uncovers a critical role played by the different side groups in the two molecules in governing the intramolecular redistribution of excited state wavefunction, leading, in turn, to different time-scales.

Oligomerization state and pigment binding strength of the peridinin-Chl a-protein.

The peridinin-chlorophyll a-protein (PCP) is one of the major light harvesting complexes (LHCs) in photosynthetic dinoflagellates. We analyzed the oligomeric state of PCP isolated from the dinoflagellate Symbiodinium, which has received increasing attention in recent years because of its role in coral bleaching. Size-exclusion chromatography (SEC) and small angle neutron scattering (SANS) analysis indicated PCP exists as monomers.

An 'all pigment' model of excitation quenching in LHCII.

The rapid, photoprotective down-regulation of plant light-harvesting in bright light proceeds via the non-photochemical quenching of chlorophyll excitation energy in the major photosystem II light-harvesting complex LHCII. However, there is currently no consensus regarding the precise mechanism by which excess energy is quenched. Current X-ray structures of this complex correspond to a dissipative conformation and therefore correct microscopic theoretical modelling should capture this property.

Efficient pathways of excitation energy transfer from delocalized S2 excitons in the peridinin-chlorophyll a-protein complex.

Excitation energy transfer (EET) in peridinin-chlorophyll-protein (PCP) complexes is dominated by the S1 → Qy pathway, but the high efficiencies cannot be solely explained by this one pathway. We postulate that EET from peridinin S2 excitons may also be important. We use complete active space configuration interaction calculations and the transition density cube method to calculate Coulombic couplings between peridinin and chlorophyll a in the PCP complex of the dinoflagellate Amphidinium carterae and compare monomeric and dimeric delocalized peridinin S2 excited states.

First principles study of defect formation in thermoelectric zinc antimonide, β-Zn4Sb3.

Understanding the formation of various point defects in the promising thermoelectric material, β-Zn(4)Sb(3), is crucial for theoretical determination of the origins of its p-type behavior and considerations of potential n-type dopability. While n-type conductivity has been fleetingly observed in Te:ZnSb, there have been no reports, to the best of our knowledge, of stable n-type behavior in β-Zn(4)Sb(3). To understand the origin of this difficulty, we investigated the formation of intrinsic point defects in β-Zn(4)Sb(3) density functional theory calculations.

Enhanced thermoelectric efficiency via orthogonal electrical and thermal conductances in phosphorene.

Thermoelectric devices that utilize the Seebeck effect convert heat flow into electrical energy and are highly desirable for the development of portable, solid state, passively powered electronic systems. The conversion efficiencies of such devices are quantified by the dimensionless thermoelectric figure of merit (ZT), which is proportional to the ratio of a device's electrical conductance to its thermal conductance. In this paper, a recently fabricated two-dimensional (2D) semiconductor called phosphorene (monolayer black phosphorus) is assessed for its thermoelectric capabilities.

Evidence of functional trimeric chlorophyll a/c2-peridinin proteins in the dinoflagellate Symbiodinium.

The chlorophyll a-chlorophyll c2-peridinin-protein (apcPC), a major light harvesting component in peridinin-containing dinoflagellates, is an integral membrane protein complex. We isolated functional acpPC from the dinoflagellate Symbiodinium. Both SDS-PAGE and electrospray ionization mass spectrometry (ESI-MS) analysis quantified the denatured subunit polypeptide molecular weight (MW) as 18kDa.

Excitation energy transfer in the peridinin-chlorophyll a-protein complex modeled using configuration interaction.

We modeled excitation energy transfer (EET) in the peridinin-chlorophyll a-protein (PCP) complex of dinoflagellate Amphidinium carterae to determine which pathways contribute dominantly to the high efficiency of this process. We used complete active space configuration interaction (CAS-CI) to calculate electronic structure properties of the peridinin (PID) and chlorophyll a (CLA) pigments in PCP and the transition density cube (TDC) method to calculate Coulombic couplings between energy transfer donors and acceptors. Our calculations show that the S1 → Qy EET pathway from peridinin to chlorophyll a is the dominant energy transfer pathway in PCP, with two sets of interactions-between PID612 and CLA601 and between PID622 and CLA602-contributing most strongly.

Computational determination of the pigment binding motif in the chlorosome protein a of green sulfur bacteria.

We present a molecular-scale model of Bacteriochlorophyll a (BChl a) binding to the chlorosome protein A (CsmA) of Chlorobaculum tepidum, and the aggregated pigment–protein dimer, as determined from protein–ligand docking and quantum chemistry calculations. Our calculations provide strong evidence that the BChl a molecule is coordinated to the His25 residue of CsmA, with the magnesium center of the bacteriochlorin ring situated\3 A° from the imidazole nitrogen atom of the histidine sidechain, and the phytyl tail aligned along the nonpolar residues of the a-helix of CsmA. We also confirm that the Qy band in the absorption spectra of BChl a experiences a large (?16 to ?43 nm) redshift when aggregated with another BChl a molecule in the CsmA dimer, compared to the BChl a in solvent; this redshift has been previously established by experimental researchers.

Low-temperature spectroscopic properties of the peridinin-chlorophyll a-protein (PCP) complex from the coral symbiotic dinoflagellate Symbiodinium.

The spectroscopic properties of the peridinin-chlorophyll a-protein (PCP) from the coral symbiotic dinoflagellate Symbiodinium have been characterized by application of various ultrafast optical spectroscopies including femto- and nanosecond time-resolved absorption and picosecond time-resolved fluorescence (TRF) at 77 K. Excited state properties of peridinin and Chl a and their intramolecular interaction characteristics have been obtained from global fitting analysis and directed kinetic modeling of the data sets and compared to their counterparts known for the PCP from Amphidinium carterae. The lifetimes of the excited state of peridinin show close agreement with those known for the counterpart PCP, demonstrating that molecular interactions have the same characteristics in both complexes.

Spectroscopic properties of the Chlorophyll a-Chlorophyll c 2-Peridinin-Protein-Complex (acpPC) from the coral symbiotic dinoflagellate Symbiodinium.

Femtosecond time-resolved transient absorption spectroscopy was performed on the chlorophyll a-chlorophyll c 2-peridinin-protein-complex (acpPC), a major light-harvesting complex of the coral symbiotic dinoflagellate Symbiodinium. The measurements were carried out on the protein as well on the isolated pigments in the visible and the near-infrared region at 77 K. The data were globally fit to establish inter-pigment energy transfer paths within the scaffold of the complex.

Carbon dioxide activation and dissociation on ceria (110): a density functional theory study.

Ceria (CeO(2)) is a promising catalyst for the reduction of carbon dioxide (CO(2)) to liquid fuels and commodity chemicals, in part because of its high oxygen storage capacity, yet the fundamentals of CO(2) adsorption, activation, and reduction on ceria surfaces remain largely unknown. We use density functional theory, corrected for onsite Coulombic interactions (GGA+U), to explore various adsorption sites and configurations for CO(2) on stoichiometric and reduced ceria (110), the latter with either an in-plane oxygen vacancy or a split oxygen vacancy. We find that CO(2) adsorption on both reduced ceria (110) surfaces is thermodynamically favored over the corresponding adsorption on stoichiometric ceria (110), but the most stable adsorption configuration consists of CO(2) adsorbed parallel to the reduced ceria (110) surface at a split oxygen vacancy.

Characterization of the peridinin-chlorophyll a-protein complex in the dinoflagellate Symbiodinium.

The water-soluble peridinin-chlorophyll a-proteins (PCPs) are one of the major light harvesting complexes in photosynthetic dinoflagellates. PCP contains the carotenoid peridinin as its primary pigment. In this study, we identified and characterized the PCP protein and the PCP gene organization in Symbiodinium sp.

Probing the photothermal effect of gold-based nanocages with surface-enhanced Raman scattering (SERS).

The conformation of molecules on a metallic nanoparticle’s surface is sensitive to temperature variations and can be easily monitored by SERS. Excitation of the metallic nanoparticle for SERS can concurrently induce a photothermal effect whereby the light absorbed by the nanoparticle is released as heat. From the SERS spectra, we could derive the changes in temperature at the surface of a nanoparticle during the photothermal effect.

EMG wavelet analysis of quadriceps muscle during repeated knee extension movement.

Purpose: Wavelet transform is a time-frequency analysis method that quantifies temporal changes of the frequency content of nonstationary signals without losing resolution in time or frequency. It may be used to analyze surface EMG (sEMG) signals under dynamic conditions. However, this method is difficult to apply clinically because it generates large quantity of data in a very short time, and the change in muscle fiber length and diameter during dynamic contraction induces a large variability of the data at various wavelet domains and joint positions.