Delayed clearance of the pro-carcinogen benzo[a]pyrene in PLHC-1 cells when co-exposed to the antifungal drug clotrimazole and effects on the CYP1A biomarker.

Cytochrome P450 1 A (CYP1A) is a key enzyme in the metabolism of the polycyclic aromatic hydrocarbon (PAH) benzo[a]pyrene (BaP) in animals, and a biomarker for environmental PAH exposure. The common antimycotic imidazole drug clotrimazole (CLO) has been detected in the aquatic environment and likely co-exists with BaP. Like BaP, CLO can bind to CYP1A enzymes and can act as a CYP1A inhibitor. Co-exposure of BaP with CLO significantly delayed BaP elimination in a fish liver cell line (PLHC-1). Intracellular BaP concentration was 2.4 times higher after 6 h in co-exposed cells, compared to cells exposed to BaP alone. Higher BaP concentrations in cells co-exposed to CLO positively correlated with CLO dose, indicating CLO-mediated delays in BaP clearance. After 24 h, BaP was undetectable irrespective of CLO co-exposure. In contrast, intracellular CLO concentrations remained constant over the 72 h experimental period. Co-exposure of BaP with CLO caused synergistic and time-dependent increases on the CYP1A biomarker both on CYP1A mRNA levels and on CYP1A enzyme activity, in accordance with an apparent delayed BaP elimination in the presence of CLO. These results indicate a toxicokinetic interaction between BaP and CLO on the CYP1A enzyme that delays metabolic clearance of BaP.

QuantumATK: an integrated platform of electronic and atomic-scale modelling tools.

QuantumATK is an integrated set of atomic-scale modelling tools developed since 2003 by professional software engineers in collaboration with academic researchers. While different aspects and individual modules of the platform have been previously presented, the purpose of this paper is to give a general overview of the platform. The QuantumATK simulation engines enable electronic-structure calculations using density functional theory or tight-binding model Hamiltonians, and also offers bonded or reactive empirical force fields in many different parametrizations. Density functional theory is implemented using either a plane-wave basis or expansion of electronic states in a linear combination of atomic orbitals. The platform includes a long list of advanced modules, including Green's-function methods for electron transport simulations and surface calculations, first-principles electron-phonon and electron-photon couplings, simulation of atomic-scale heat transport, ion dynamics, spintronics, optical properties of materials, static polarization, and more. Seamless integration of the different simulation engines into a common platform allows for easy combination of different simulation methods into complex workflows. Besides giving a general overview and presenting a number of implementation details not previously published, we also present four different application examples. These are calculations of the phonon-limited mobility of Cu, Ag and Au, electron transport in a gated 2D device, multi-model simulation of lithium ion drift through a battery cathode in an external electric field, and electronic-structure calculations of the composition-dependent band gap of SiGe alloys.

Properties of homo- and hetero-Schottky junctions from first principle calculations.

Electronic structure calculations for a homo-material semimetal (thick Sn)/semiconductor (thin Sn) heterodimensional junction and two conventional metal (Ag or Pt)/silicon hetero-material junctions are performed. Charge distributions and local density of states are examined to compare the physics of junctions formed by quantum confinement in a homo-material, heterodimensional semimetal junction with that of conventional Schottky hetero-material junctions. Relative contributions to the Schottky barrier heights are described in terms of the interface dipoles arising due to charge transfer at the interface and the effects of metal induced gap states extending into the semiconducting regions. Although the importance of these physical mechanisms vary for the three junctions, a single framework describing the junction energetics captures the behaviors of both the heterodimensional semimetal junction and the more conventional metal/semiconductor junctions.

Effect of iron doping on protein molecular conductance.

Protein molecular conductance has attracted attention from researchers for the possibility of constructing innovative flexible biocompatible nanoscale electronic devices and smart hybrid materials. Due to protein complexity, most evaluations of protein conductivity are based on the simple estimation of protein's molecular orbital energy levels and spatial distributions without analysing its protein interaction with electrodes and the calculation of the rates of electron transfer (ET). In the present work, we included in our density functional theory (DFT) analysis an approach based on the non-equilibrium Green's function (NEGF) allowing for calculation from the first principles the molecular interaction with electrodes and thus the role of electrode materials, Fermi level, the thermal distribution of electronic energy levels, and the coupling efficiency between the molecule and the electrodes. Compared to proteins studied so far, mainly artificial peptides, heme-containing cytochromes, and bacterial pili, we choose rubredoxin for our calculation. Rubredoxin contains a non-heme iron that, as we have discovered recently, can be involved in extracellular ET in electroactive bacterial biofilms (Yates et al., Energy Environ. Sci., 2016, 9, 3544-3558). Our calculations show that an iron atom incorporated into the protein structure as an iron-sulfur cluster opens a transmission path at the energy corresponding to the Fermi level of the electrodes. This allows the protein to become an extremely efficient conductor at very low bias voltages (<±350 mV). Calculation of the role of protein amino acids based on the local density of states and electron transfer paths reveals that neither aromatic amino acid Tyr nor Phe at any ring orientation participates in coherent ET through the FeS cluster of the protein. Moreover, direct ET through surrounding amino acids, bypassing FeS, is possible only at biases ±1.5 to ±2 V. The polar amino acid Asn might participate in ET at these bias voltages. The conductivity of the protein core substantially depends on the polarity of the applied electric field, allowing for unidirectional ET and operation of the protein as a molecular rectifier. These results can be used for a wise de novo design of proteins for molecular electronics and cellular energy converting devices, particularly for utilization of iron doping in the construction of conductive protein wires.