Computer modeling of electron and proton transport in chloroplasts.

PubMed

Tikhonov, Alexander N; Vershubskii, Alexey V

2014-07-01

Photosynthesis is one of the most important biological processes in biosphere, which provides production of organic substances from atmospheric CO2 and water at expense of solar energy. In this review, we contemplate computer models of oxygenic photosynthesis in the context of feedback regulation of photosynthetic electron transport in chloroplasts, the energy-transducing organelles of the plant cell. We start with a brief overview of electron and proton transport processes in chloroplasts coupled to ATP synthesis and consider basic regulatory mechanisms of oxygenic photosynthesis. General approaches to computer simulation of photosynthetic processes are considered, including the random walk models of plastoquinone diffusion in thylakoid membranes and deterministic approach to modeling electron transport in chloroplasts based on the mass action law. Then we focus on a kinetic model of oxygenic photosynthesis that includes key stages of the linear electron transport, alternative pathways of electron transfer around photosystem I (PSI), transmembrane proton transport and ATP synthesis in chloroplasts. This model includes different regulatory processes: pH-dependent control of the intersystem electron transport, down-regulation of photosystem II (PSII) activity (non-photochemical quenching), the light-induced activation of the Bassham-Benson-Calvin (BBC) cycle. The model correctly describes pH-dependent feedback control of electron transport in chloroplasts and adequately reproduces a variety of experimental data on induction events observed under different experimental conditions in intact chloroplasts (variations of CO2 and O2 concentrations in atmosphere), including a complex kinetics of P700 (primary electron donor in PSI) photooxidation, CO2 consumption in the BBC cycle, and photorespiration. Finally, we describe diffusion-controlled photosynthetic processes in chloroplasts within the framework of the model that takes into account complex architecture of

Model-based Confirmation of Alternative Substrates of Mitochondrial Electron Transport Chain

PubMed Central

Kleessen, Sabrina; Araújo, Wagner L.; Fernie, Alisdair R.; Nikoloski, Zoran

2012-01-01

Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data. PMID:22334689

Model-based confirmation of alternative substrates of mitochondrial electron transport chain.

PubMed

Kleessen, Sabrina; Araújo, Wagner L; Fernie, Alisdair R; Nikoloski, Zoran

2012-03-30

Discrimination of metabolic models based on high throughput metabolomics data, reflecting various internal and external perturbations, is essential for identifying the components that contribute to the emerging behavior of metabolic processes. Here, we investigate 12 different models of the mitochondrial electron transport chain (ETC) in Arabidopsis thaliana during dark-induced senescence in order to elucidate the alternative substrates to this metabolic pathway. Our findings demonstrate that the coupling of the proposed computational approach, based on dynamic flux balance analysis, with time-resolved metabolomics data results in model-based confirmations of the hypotheses that, during dark-induced senescence in Arabidopsis, (i) under conditions where the main substrate for the ETC are not fully available, isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase are able to donate electrons to the ETC, (ii) phytanoyl-CoA does not act even as an indirect substrate of the electron transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase complex, and (iii) the mitochondrial γ-aminobutyric acid transporter has functional significance in maintaining mitochondrial metabolism. Our study provides a basic framework for future in silico studies of alternative pathways in mitochondrial metabolism under extended darkness whereby the role of its components can be computationally discriminated based on available molecular profile data.

Contribution of Cyclic and Pseudo-cyclic Electron Transport to the Formation of Proton Motive Force in Chloroplasts.

PubMed

Shikanai, Toshiharu; Yamamoto, Hiroshi

2017-01-09

Photosynthetic electron transport is coupled to proton translocation across the thylakoid membrane, resulting in the formation of a trans-thylakoid proton gradient (ΔpH) and membrane potential (Δψ). Ion transporters and channels localized to the thylakoid membrane regulate the contribution of each component to the proton motive force (pmf). Although both ΔpH and Δψ contribute to ATP synthesis as pmf, only ΔpH downregulates photosynthetic electron transport via the acidification of the thylakoid lumen by inducing thermal dissipation of excessive absorbed light energy from photosystem II antennae and slowing down of the electron transport through the cytochrome b 6 f complex. To optimize the tradeoff between efficient light energy utilization and protection of both photosystems against photodamage, plants have to regulate the pmf amplitude and its components, ΔpH and Δψ. Cyclic electron transport around photosystem I (PSI) is a major regulator of the pmf amplitude by generating pmf independently of the net production of NADPH by linear electron transport. Chloroplast ATP synthase relaxes pmf for ATP synthesis, and its activity should be finely tuned for maintaining the size of the pmf during steady-state photosynthesis. Pseudo-cyclic electron transport mediated by flavodiiron protein (Flv) forms a large electron sink, which is essential for PSI photoprotection in fluctuating light in cyanobacteria. Flv is conserved from cyanobacteria to gymnosperms but not in angiosperms. The Arabidopsis proton gradient regulation 5 (pgr5) mutant is defective in the main pathway of PSI cyclic electron transport. By introducing Physcomitrella patens genes encoding Flvs, the function of PSI cyclic electron transport was substituted by that of Flv-dependent pseudo-cyclic electron transport. In transgenic plants, the size of the pmf was complemented to the wild-type level but the contribution of ΔpH to the total pmf was lower than that in the wild type. In the pgr5 mutant, the

Pivotal Role of Iron in the Regulation of Cyanobacterial Electron Transport.

PubMed

González, A; Sevilla, E; Bes, M T; Peleato, M L; Fillat, M F

2016-01-01

Iron-containing metalloproteins are the main cornerstones for efficient electron transport in biological systems. The abundance and diversity of iron-dependent proteins in cyanobacteria makes those organisms highly dependent of this micronutrient. To cope with iron imbalance, cyanobacteria have developed a survey of adaptation strategies that are strongly related to the regulation of photosynthesis, nitrogen metabolism and other central electron transfer pathways. Furthermore, either in its ferrous form or as a component of the haem group, iron plays a crucial role as regulatory signalling molecule that directly or indirectly modulates the composition and efficiency of cyanobacterial redox reactions. We present here the major mechanism used by cyanobacteria to couple iron homeostasis to the regulation of electron transport, making special emphasis in processes specific in those organisms. © 2016 Elsevier Ltd. All rights reserved.

Electronic Interactions of n-Doped Perylene Diimide Groups Appended to Polynorbornene Chains: Implications for Electron Transport in Organic Electronics.

PubMed

Nguyen, Minh T; Biberdorf, Joshua D; Holliday, Bradley J; Jones, Richard A

2017-11-01

A polymer consisting of a polynorbornene backbone with perylene diimide (PDI) pendant groups on each monomeric unit is synthesized via ring opening metathesis polymerization. The PDI pendant groups along the polymer backbone, studied by UV-vis absorption, fluorescence emission, and electron paramagnetic resonance spectroscopy in addition to electrochemical methods, show evidence of molecular aggregation and corresponding electronic coupling with neighboring groups, which forms pathways for efficient electron transport from one group to another in a specific reduced form. When n-doped, the title polymer shows redox conductivity of 5.4 × 10 -3 S cm -1 , comparable with crystalline PDI materials, and is therefore a promising material for use in organic electronics. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

[Pathways of lanthanum ion transport across the posterior epithelium of the cornea in rabbits].

PubMed

Virnik, V L

1985-11-01

Morphological estimation of the barrier-transport properties of the posterior epithelium in the donor cornea has been performed in the most early time of fanoxic lesions of the cells. Ionized lanthanum, as an effective inhibitor of oxidative phosphorylation and simultaneously--as a marker of transport pathways for particles similar in their size to water molecule, is used in the investigation. The concentration gradient of rare-earth ions is produced by vital injection of lanthanum trichloride into the proper substance (stroma) of the cornea. From the microinjection focus the electron opaque marker is transported through the substrate of the basal substance of the stroma to the posterior epithelium and further along its intercellular and transcellular pathways into the anterior chamber of the eye. The rare-earth ions freely penetrate through the gap and tight junctions. Transcellular transport of lanthanum in the contents of the plasmolemmal microvesicles, vital absorption of the marker on the lateral and luminal parts of the plasmolemma and on the intracellular membranes, lesions of mitochondria and canaliculi of the endoplasmic reticulum of the anoxic character are stated. A suggestion is made on structural preservation of the pathways of convective and dissipative transition of the substance through the posterior epithelium of the cornea during the earliest time of the experimental anoxia.

DNA replication depends on photosynthetic electron transport in cyanobacteria.

PubMed

Ohbayashi, Ryudo; Watanabe, Satoru; Kanesaki, Yu; Narikawa, Rei; Chibazakura, Taku; Ikeuchi, Masahiko; Yoshikawa, Hirofumi

2013-07-01

The freshwater cyanobacterium Synechococcus elongatus PCC 7942 exhibits light-dependent growth. Although it has been reported that DNA replication also depends on light irradiation in S. elongatus 7942, the involvement of the light in the regulation of DNA replication remains unclear. To elucidate the regulatory pathway of DNA replication by light, we studied the effect of several inhibitors, including two electron transport inhibitors, 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU) and 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone (DBMIB), on DNA replication in S. elongatus 7942. DCMU inhibited only DNA replication initiation, whereas DBMIB blocked both the initiation and progression of DNA replication. These results suggest that DNA replication depends on the photosynthetic electron transport activity and initiation and progression of DNA replication are regulated in different ways. © 2013 Federation of European Microbiological Societies. Published by John Wiley & Sons Ltd. All rights reserved.

Prediction of FAD binding sites in electron transport proteins according to efficient radial basis function networks and significant amino acid pairs.

PubMed

Le, Nguyen-Quoc-Khanh; Ou, Yu-Yen

2016-07-30

Cellular respiration is a catabolic pathway for producing adenosine triphosphate (ATP) and is the most efficient process through which cells harvest energy from consumed food. When cells undergo cellular respiration, they require a pathway to keep and transfer electrons (i.e., the electron transport chain). Due to oxidation-reduction reactions, the electron transport chain produces a transmembrane proton electrochemical gradient. In case protons flow back through this membrane, this mechanical energy is converted into chemical energy by ATP synthase. The convert process is involved in producing ATP which provides energy in a lot of cellular processes. In the electron transport chain process, flavin adenine dinucleotide (FAD) is one of the most vital molecules for carrying and transferring electrons. Therefore, predicting FAD binding sites in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. We used an independent data set to evaluate the performance of the proposed method, which had an accuracy of 69.84 %. We compared the performance of the proposed method in analyzing two newly discovered electron transport protein sequences with that of the general FAD binding predictor presented by Mishra and Raghava and determined that the accuracy of the proposed method improved by 9-45 % and its Matthew's correlation coefficient was 0.14-0.5. Furthermore, the proposed method enabled reducing the number of false positives significantly and can provide useful information for biologists. We developed a method that is based on PSSM profiles and SAAPs for identifying FAD binding sites in newly discovered electron transport protein sequences. This approach achieved a significant improvement after we added SAAPs to PSSM features to analyze FAD binding proteins in the electron transport chain. The proposed method can serve as an effective tool for predicting FAD binding sites in electron

Seychelles Fisheries Connectivity and Transport Pathways

DTIC Science & Technology

2015-09-30

1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. Seychelles Fisheries Connectivity and Transport Pathways...Plateau. • Identification of physical oceanographic controls on mass and momentum transport on scales that are relevant to local ecology and fisheries and...Development of basic regional modeling capacity that Seychelles managers and fisheries can use to guide decisions and improve community outreach and

Pathways of fluid transport and reabsorption across the peritoneal membrane.

PubMed

Asghar, R B; Davies, S J

2008-05-01

The three-pore model of peritoneal fluid transport predicts that once the osmotic gradient has dissipated, fluid reabsorption will be due to a combination of small-pore reabsorption driven by the intravascular oncotic pressure, and an underlying disappearance of fluid from the cavity by lymphatic drainage. Our study measured fluid transport by these pathways in the presence and absence of an osmotic gradient. Paired hypertonic and standard glucose-dwell studies were performed using radio-iodinated serum albumin as an intraperitoneal volume marker and changes in intraperitoneal sodium mass to determine small-pore versus transcellular fluid transport. Disappearance of iodinated albumin was considered to indicate lymphatic drainage. Variability in transcellular ultrafiltration was largely explained by the rate of small-solute transport across the membrane. In the absence of an osmotic gradient, fluid reabsorption occurred via the small-pore pathway, the rate being proportional to the small-solute transport characteristics of the membrane. In most cases, fluid removal from the peritoneal cavity by this pathway was faster than by lymphatic drainage. Our study shows that the three-pore model describes the pathways of peritoneal fluid transport well. In the presence of high solute transport, poor transcellular ultrafiltration was due to loss of the osmotic gradient and an enhanced small-pore reabsorption rate after this gradient dissipated.

Malate-aspartate shuttle and exogenous NADH/cytochrome c electron transport pathway as two independent cytosolic reducing equivalent transfer systems.

PubMed

Abbrescia, Daniela Isabel; La Piana, Gianluigi; Lofrumento, Nicola Elio

2012-02-15

In mammalian cells aerobic oxidation of glucose requires reducing equivalents produced in glycolytic phase to be channelled into the phosphorylating respiratory chain for the reduction of molecular oxygen. Data never presented before show that the oxidation rate of exogenous NADH supported by the malate-aspartate shuttle system (reconstituted in vitro with isolated liver mitochondria) is comparable to the rate obtained on activation of the cytosolic NADH/cytochrome c electron transport pathway. The activities of these two reducing equivalent transport systems are independent of each other and additive. NADH oxidation induced by the malate-aspartate shuttle is inhibited by aminooxyacetate and by rotenone and/or antimycin A, two inhibitors of the respiratory chain, while the NADH/cytochrome c system remains insensitive to all of them. The two systems may simultaneously or mutually operate in the transfer of reducing equivalents from the cytosol to inside the mitochondria. In previous reports we suggested that the NADH/cytochrome c system is expected to be functioning in apoptotic cells characterized by the presence of cytochrome c in the cytosol. As additional new finding the activity of reconstituted shuttle system is linked to the amount of α-ketoglutarate generated inside the mitochondria by glutamate dehydrogenase rather than by aspartate aminotransferase. Copyright © 2011 Elsevier Inc. All rights reserved.

A long-distance fluid transport pathway within fibrous connective tissues in patients with ankle edema.

PubMed

Li, Hongyi; Yang, Chongqing; Lu, Kuiyuan; Zhang, Liyang; Yang, Jiefu; Wang, Fang; Liu, Dongge; Cui, Di; Sun, Mingjun; Pang, Jianxin; Dai, Luru; Han, Dong; Liao, Fulong

2016-10-05

Although the microcirculatory dysfunctions of edema formation are well documented, the draining pattern of dermal edema lacks information. This study was to assess the potential drainage pathways of the interstitial fluid in patients with ankle edema using the anatomical and histological methods. Four amputees of lower leg participated in this study. Fluorescent imaging agent was injected into lateral ankle dermis in one volunteered patient before the amputation and three lower legs after the amputation. Physiologically in the volunteer or enhanced by cyclical compression on three amputated limbs, several fluorescent longitudinal pathways from ankle dermis to the broken end of the amputated legs were subsequently visualized and studied using histological methods, laser confocal microscopy and electron microscopy methods respectively. Interestingly, the fluorescent pathways confirmed to be fibrous connective tissues and the presence of two types: those of the cutaneous pathway (located in dermis or the interlobular septum among adipose tissues within the hypodermis) and those of the perivascular pathway (located in connective tissues surrounding the veins and the arteries). The intrinsic three-dimensional architecture of each fluorescent pathway was the longitudinally running and interconnected fibril bundles, upon which, an interfacial transport pathway within connective tissues was visualized by fluorescein. The current anatomical data suggested that a unique long-distance transport pathway composed of oriented fibrous connective tissues might play a pathophysiological role in draining dermal edema besides vascular circulations and provide novel understandings of general fibrous connective tissues in life science.

A common pathway for charge transport through voltage-sensing domains.

PubMed

Chanda, Baron; Bezanilla, Francisco

2008-02-07

Voltage-gated ion channels derive their voltage sensitivity from the movement of specific charged residues in response to a change in transmembrane potential. Several studies on mechanisms of voltage sensing in ion channels support the idea that these gating charges move through a well-defined permeation pathway. This gating pathway in a voltage-gated ion channel can also be mutated to transport free cations, including protons. The recent discovery of proton channels with sequence homology to the voltage-sensing domains suggests that evolution has perhaps exploited the same gating pathway to generate a bona fide voltage-dependent proton transporter. Here we will discuss implications of these findings on the mechanisms underlying charge (and ion) transport by voltage-sensing domains.

Kinesin molecular motors: Transport pathways, receptors, and human disease

NASA Astrophysics Data System (ADS)

Goldstein, Lawrence S. B.

2001-06-01

Kinesin molecular motor proteins are responsible for many of the major microtubule-dependent transport pathways in neuronal and non-neuronal cells. Elucidating the transport pathways mediated by kinesins, the identity of the cargoes moved, and the nature of the proteins that link kinesin motors to cargoes are areas of intense investigation. Kinesin-II recently was found to be required for transport in motile and nonmotile cilia and flagella where it is essential for proper left-right determination in mammalian development, sensory function in ciliated neurons, and opsin transport and viability in photoreceptors. Thus, these pathways and proteins may be prominent contributors to several human diseases including ciliary dyskinesias, situs inversus, and retinitis pigmentosa. Kinesin-I is needed to move many different types of cargoes in neuronal axons. Two candidates for receptor proteins that attach kinesin-I to vesicular cargoes were recently found. One candidate, sunday driver, is proposed to both link kinesin-I to an unknown vesicular cargo and to bind and organize the mitogen-activated protein kinase components of a c-Jun N-terminal kinase signaling module. A second candidate, amyloid precursor protein, is proposed to link kinesin-I to a different, also unknown, class of axonal vesicles. The finding of a possible functional interaction between kinesin-I and amyloid precursor protein may implicate kinesin-I based transport in the development of Alzheimer's disease.

Tunneling explains efficient electron transport via protein junctions.

PubMed

Fereiro, Jerry A; Yu, Xi; Pecht, Israel; Sheves, Mordechai; Cuevas, Juan Carlos; Cahen, David

2018-05-15

Metalloproteins, proteins containing a transition metal ion cofactor, are electron transfer agents that perform key functions in cells. Inspired by this fact, electron transport across these proteins has been widely studied in solid-state settings, triggering the interest in examining potential use of proteins as building blocks in bioelectronic devices. Here, we report results of low-temperature (10 K) electron transport measurements via monolayer junctions based on the blue copper protein azurin (Az), which strongly suggest quantum tunneling of electrons as the dominant charge transport mechanism. Specifically, we show that, weakening the protein-electrode coupling by introducing a spacer, one can switch the electron transport from off-resonant to resonant tunneling. This is a consequence of reducing the electrode's perturbation of the Cu(II)-localized electronic state, a pattern that has not been observed before in protein-based junctions. Moreover, we identify vibronic features of the Cu(II) coordination sphere in transport characteristics that show directly the active role of the metal ion in resonance tunneling. Our results illustrate how quantum mechanical effects may dominate electron transport via protein-based junctions.

Simulation of electron transport during electron-beam-induced deposition of nanostructures

PubMed Central

Jeschke, Harald O; Valentí, Roser

2013-01-01

Summary We present a numerical investigation of energy and charge distributions during electron-beam-induced growth of tungsten nanostructures on SiO2 substrates by using a Monte Carlo simulation of the electron transport. This study gives a quantitative insight into the deposition of energy and charge in the substrate and in the already existing metallic nanostructures in the presence of the electron beam. We analyze electron trajectories, inelastic mean free paths, and the distribution of backscattered electrons in different compositions and at different depths of the deposit. We find that, while in the early stages of the nanostructure growth a significant fraction of electron trajectories still interacts with the substrate, when the nanostructure becomes thicker the transport takes place almost exclusively in the nanostructure. In particular, a larger deposit density leads to enhanced electron backscattering. This work shows how mesoscopic radiation-transport techniques can contribute to a model that addresses the multi-scale nature of the electron-beam-induced deposition (EBID) process. Furthermore, similar simulations can help to understand the role that is played by backscattered electrons and emitted secondary electrons in the change of structural properties of nanostructured materials during post-growth electron-beam treatments. PMID:24367747

Monte Carlo Transport for Electron Thermal Transport

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Cao, Duc; Moses, Gregory

2015-11-01

The iSNB (implicit Schurtz Nicolai Busquet multigroup electron thermal transport method of Cao et al. is adapted into a Monte Carlo transport method in order to better model the effects of non-local behavior. The end goal is a hybrid transport-diffusion method that combines Monte Carlo Transport with a discrete diffusion Monte Carlo (DDMC). The hybrid method will combine the efficiency of a diffusion method in short mean free path regions with the accuracy of a transport method in long mean free path regions. The Monte Carlo nature of the approach allows the algorithm to be massively parallelized. Work to date on the method will be presented. This work was supported by Sandia National Laboratory - Albuquerque and the University of Rochester Laboratory for Laser Energetics.

Electron Transport in Hall Thrusters

NASA Astrophysics Data System (ADS)

McDonald, Michael Sean

Despite high technological maturity and a long flight heritage, computer models of Hall thrusters remain dependent on empirical inputs and a large part of thruster development to date has been heavily experimental in nature. This empirical approach will become increasingly unsustainable as new high-power thrusters tax existing ground test facilities and more exotic thruster designs stretch and strain the boundaries of existing design experience. The fundamental obstacle preventing predictive modeling of Hall thruster plasma properties and channel erosion is the lack of a first-principles description of electron transport across the strong magnetic fields between the cathode and anode. In spite of an abundance of proposed transport mechanisms, accurate assessments of the magnitude of electron current due to any one mechanism are scarce, and comparative studies of their relative influence on a single thruster platform simply do not exist. Lacking a clear idea of what mechanism(s) are primarily responsible for transport, it is understandably difficult for the electric propulsion scientist to focus his or her theoretical and computational tools on the right targets. This work presents a primarily experimental investigation of collisional and turbulent Hall thruster electron transport mechanisms. High-speed imaging of the thruster discharge channel at tens of thousands of frames per second reveals omnipresent rotating regions of elevated light emission, identified with a rotating spoke instability. This turbulent instability has been shown through construction of an azimuthally segmented anode to drive significant cross-field electron current in the discharge channel, and suggestive evidence points to its spatial extent into the thruster near-field plume as well. Electron trajectory simulations in experimentally measured thruster electromagnetic fields indicate that binary collisional transport mechanisms are not significant in the thruster plume, and experiments

Physiological Roles of Plant Post-Golgi Transport Pathways in Membrane Trafficking.

PubMed

Uemura, Tomohiro

2016-10-01

Membrane trafficking is the fundamental system through which proteins are sorted to their correct destinations in eukaryotic cells. Key regulators of this system include RAB GTPases and soluble N-ethylmaleimide sensitive factor attachment protein receptors (SNAREs). Interestingly, the numbers of RAB GTPases and SNAREs involved in post-Golgi transport pathways in plant cells are larger than those in animal and yeast cells, suggesting that plants have evolved unique and complex post-Golgi transport pathways. The trans-Golgi network (TGN) is an important organelle that acts as a sorting station in the post-Golgi transport pathways of plant cells. The TGN also functions as the early endosome, which is the first compartment to receive endocytosed proteins. Several endocytosed proteins on the plasma membrane (PM) are initially targeted to the TGN/EE, then recycled back to the PM or transported to the vacuole for degradation. The recycling and degradation of the PM localized proteins is essential for the development and environmental responses in plant. The present review describes the post-Golgi transport pathways that show unique physiological functions in plants. © The Author 2016. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Imaging axonal transport in the rat visual pathway.

PubMed

Abbott, Carla J; Choe, Tiffany E; Lusardi, Theresa A; Burgoyne, Claude F; Wang, Lin; Fortune, Brad

2013-02-01

A technique was developed for assaying axonal transport in retinal ganglion cells using 2 µl injections of 1% cholera toxin b-subunit conjugated to AlexaFluor488 (CTB). In vivo retinal and post-mortem brain imaging by confocal scanning laser ophthalmoscopy and post-mortem microscopy were performed. The transport of CTB was sensitive to colchicine, which disrupts axonal microtubules. The bulk rates of transport were determined to be approximately 80-90 mm/day (anterograde) and 160 mm/day (retrograde). Results demonstrate that axonal transport of CTB can be monitored in vivo in the rodent anterior visual pathway, is dependent on intact microtubules, and occurs by active transport mechanisms.

Nonequilibrium Transport and the Bernoulli Effect of Electrons in a Two-Dimensional Electron Gas

NASA Astrophysics Data System (ADS)

Kaya, Ismet I.

2013-02-01

Nonequilibrium transport of charged carriers in a two-dimensional electron gas is summarized from an experimental point of view. The transport regime in which the electron-electron interactions are enhanced at high bias leads to a range of striking effects in a two-dimensional electron gas. This regime of transport is quite different than the ballistic transport in which particles propagate coherently with no intercarrier energy transfer and the diffusive transport in which the momentum of the electron system is lost with the involvement of the phonons. Quite a few hydrodynamic phenomena observed in classical gasses have the electrical analogs in the current flow. When intercarrier scattering events dominate the transport, the momentum sharing via narrow angle scattering among the hot and cold electrons lead to negative resistance and electron pumping which can be viewed as the analog of the Bernoulli-Venturi effect observed classical gasses. The recent experimental findings and the background work in the field are reviewed.

Tracking of Short Distance Transport Pathways in Biological Tissues by Ultra-Small Nanoparticles

NASA Astrophysics Data System (ADS)

Segmehl, Jana S.; Lauria, Alessandro; Keplinger, Tobias; Berg, John K.; Burgert, Ingo

2018-03-01

In this work, ultra-small europium-doped HfO2 nanoparticles were infiltrated into native wood and used as trackers for studying penetrability and diffusion pathways in the hierarchical wood structure. The high electron density, laser induced luminescence, and crystallinity of these particles allowed for a complementary detection of the particles in the cellular tissue. Confocal Raman microscopy and high-resolution synchrotron scanning wide-angle X-ray scattering (WAXS) measurements were used to detect the infiltrated particles in the native wood cell walls. This approach allows for simultaneously obtaining chemical information of the probed biological tissue and the spatial distribution of the integrated particles. The in-depth information about particle distribution in the complex wood structure can be used for revealing transport pathways in plant tissues, but also for gaining better understanding of modification treatments of plant scaffolds aiming at novel functionalized materials.

Transport pathway and source area for Artemisia pollen in Beijing, China

NASA Astrophysics Data System (ADS)

Qin, Xiaoxin; Li, Yiyin; Sun, Xu; Meng, Ling; Wang, Xiaoke

2017-12-01

Artemisia pollen is an important allergen responsible for allergic rhinitis in Beijing, China. To explore the transport pathways and source areas of Artemisia pollen, we used Burkard 7-day traps to monitor daily pollen concentrations in 2016 in an urban and suburban locality. Backward trajectories of 24- and 96-h and their cluster analysis were performed to identify transport pathways of Artemisia pollen using the HYSPLIT model on 0.5° × 0.5° GADS meteorological data. The potential source contribution function (PSCF) and concentration weighted trajectory (CWT) were calculated to further identify the major potential source areas at local, regional, and long-range scales. Our results showed significant differences in Artemisia pollen concentration between urban and suburban areas, attributed to differences in plant distribution and altitude of the sampling locality. Such differences arisen from both pollen emission and air mass movements, hence pollen dispersal. At local or regional scales, source area of northwestern parts of Beijing City, Hebei Province and northern and northwestern parts of Inner Mongolia influenced the major transport pathways of Artemisia pollen. Transport pathway at a long-range scale and its corresponding source area extended to northwestern parts of Mongolia. The regional-scale transport affected by wind and altitude is more profound for Artemisia pollen at the suburban than at the urban station.

Electronic Transport in Two-Dimensional Materials

NASA Astrophysics Data System (ADS)

Sangwan, Vinod K.; Hersam, Mark C.

2018-04-01

Two-dimensional (2D) materials have captured the attention of the scientific community due to the wide range of unique properties at nanometer-scale thicknesses. While significant exploratory research in 2D materials has been achieved, the understanding of 2D electronic transport and carrier dynamics remains in a nascent stage. Furthermore, because prior review articles have provided general overviews of 2D materials or specifically focused on charge transport in graphene, here we instead highlight charge transport mechanisms in post-graphene 2D materials, with particular emphasis on transition metal dichalcogenides and black phosphorus. For these systems, we delineate the intricacies of electronic transport, including band structure control with thickness and external fields, valley polarization, scattering mechanisms, electrical contacts, and doping. In addition, electronic interactions between 2D materials are considered in the form of van der Waals heterojunctions and composite films. This review concludes with a perspective on the most promising future directions in this fast-evolving field.

Treating electron transport in MCNP{sup trademark}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hughes, H.G.

1996-12-31

The transport of electrons and other charged particles is fundamentally different from that of neutrons and photons. A neutron, in aluminum slowing down from 0.5 MeV to 0.0625 MeV will have about 30 collisions; a photon will have fewer than ten. An electron with the same energy loss will undergo 10{sup 5} individual interactions. This great increase in computational complexity makes a single- collision Monte Carlo approach to electron transport unfeasible for many situations of practical interest. Considerable theoretical work has been done to develop a variety of analytic and semi-analytic multiple-scattering theories for the transport of charged particles. Themore » theories used in the algorithms in MCNP are the Goudsmit-Saunderson theory for angular deflections, the Landau an theory of energy-loss fluctuations, and the Blunck-Leisegang enhancements of the Landau theory. In order to follow an electron through a significant energy loss, it is necessary to break the electron`s path into many steps. These steps are chosen to be long enough to encompass many collisions (so that multiple-scattering theories are valid) but short enough that the mean energy loss in any one step is small (for the approximations in the multiple-scattering theories). The energy loss and angular deflection of the electron during each step can then be sampled from probability distributions based on the appropriate multiple- scattering theories. This subsumption of the effects of many individual collisions into single steps that are sampled probabilistically constitutes the ``condensed history`` Monte Carlo method. This method is exemplified in the ETRAN series of electron/photon transport codes. The ETRAN codes are also the basis for the Integrated TIGER Series, a system of general-purpose, application-oriented electron/photon transport codes. The electron physics in MCNP is similar to that of the Integrated TIGER Series.« less

Connection between the membrane electron transport system and Hyn hydrogenase in the purple sulfur bacterium, Thiocapsa roseopersicina BBS.

PubMed

Tengölics, Roland; Mészáros, Lívia; Győri, E; Doffkay, Zsolt; Kovács, Kornél L; Rákhely, Gábor

2014-10-01

Thiocapsa. roseopersicina BBS has four active [NiFe] hydrogenases, providing an excellent opportunity to examine their metabolic linkages to the cellular redox processes. Hyn is a periplasmic membrane-associated hydrogenase harboring two additional electron transfer subunits: Isp1 is a transmembrane protein, while Isp2 is located on the cytoplasmic side of the membrane. In this work, the connection of HynSL to various electron transport pathways is studied. During photoautotrophic growth, electrons, generated from the oxidation of thiosulfate and sulfur, are donated to the photosynthetic electron transport chain via cytochromes. Electrons formed from thiosulfate and sulfur oxidation might also be also used for Hyn-dependent hydrogen evolution which was shown to be light and proton motive force driven. Hyn-linked hydrogen uptake can be promoted by both sulfur and nitrate. The electron flow from/to HynSL requires the presence of Isp2 in both directions. Hydrogenase-linked sulfur reduction could be inhibited by a QB site competitive inhibitor, terbutryne, suggesting a redox coupling between the Hyn hydrogenase and the photosynthetic electron transport chain. Based on these findings, redox linkages of Hyn hydrogenase are modeled. Copyright © 2014 Elsevier B.V. All rights reserved.

Biguanides sensitize leukemia cells to ABT-737-induced apoptosis by inhibiting mitochondrial electron transport

PubMed Central

Velez, Juliana; Pan, Rongqing; Lee, Jason T.C.; Enciso, Leonardo; Suarez, Marta; Duque, Jorge Eduardo; Jaramillo, Daniel; Lopez, Catalina; Morales, Ludis; Bornmann, William; Konopleva, Marina; Krystal, Gerald; Andreeff, Michael; Samudio, Ismael

2016-01-01

Metformin displays antileukemic effects partly due to activation of AMPK and subsequent inhibition of mTOR signaling. Nevertheless, Metformin also inhibits mitochondrial electron transport at complex I in an AMPK-independent manner, Here we report that Metformin and rotenone inhibit mitochondrial electron transport and increase triglyceride levels in leukemia cell lines, suggesting impairment of fatty acid oxidation (FAO). We also report that, like other FAO inhibitors, both agents and the related biguanide, Phenformin, increase sensitivity to apoptosis induction by the bcl-2 inhibitor ABT-737 supporting the notion that electron transport antagonizes activation of the intrinsic apoptosis pathway in leukemia cells. Both biguanides and rotenone induce superoxide generation in leukemia cells, indicating that oxidative damage may sensitize toABT-737 induced apoptosis. In addition, we demonstrate that Metformin sensitizes leukemia cells to the oligomerization of Bak, suggesting that the observed synergy with ABT-737 is mediated, at least in part, by enhanced outer mitochondrial membrane permeabilization. Notably, Phenformin was at least 10-fold more potent than Metformin in abrogating electron transport and increasing sensitivity to ABT-737, suggesting that this agent may be better suited for targeting hematological malignancies. Taken together, our results suggest that inhibition of mitochondrial metabolism by Metformin or Phenformin is associated with increased leukemia cell susceptibility to induction of intrinsic apoptosis, and provide a rationale for clinical studies exploring the efficacy of combining biguanides with the orally bioavailable derivative of ABT-737, Venetoclax. PMID:27283492

Biguanides sensitize leukemia cells to ABT-737-induced apoptosis by inhibiting mitochondrial electron transport.

PubMed

Velez, Juliana; Pan, Rongqing; Lee, Jason T C; Enciso, Leonardo; Suarez, Marta; Duque, Jorge Eduardo; Jaramillo, Daniel; Lopez, Catalina; Morales, Ludis; Bornmann, William; Konopleva, Marina; Krystal, Gerald; Andreeff, Michael; Samudio, Ismael

2016-08-09

Metformin displays antileukemic effects partly due to activation of AMPK and subsequent inhibition of mTOR signaling. Nevertheless, Metformin also inhibits mitochondrial electron transport at complex I in an AMPK-independent manner, Here we report that Metformin and rotenone inhibit mitochondrial electron transport and increase triglyceride levels in leukemia cell lines, suggesting impairment of fatty acid oxidation (FAO). We also report that, like other FAO inhibitors, both agents and the related biguanide, Phenformin, increase sensitivity to apoptosis induction by the bcl-2 inhibitor ABT-737 supporting the notion that electron transport antagonizes activation of the intrinsic apoptosis pathway in leukemia cells. Both biguanides and rotenone induce superoxide generation in leukemia cells, indicating that oxidative damage may sensitize toABT-737 induced apoptosis. In addition, we demonstrate that Metformin sensitizes leukemia cells to the oligomerization of Bak, suggesting that the observed synergy with ABT-737 is mediated, at least in part, by enhanced outer mitochondrial membrane permeabilization. Notably, Phenformin was at least 10-fold more potent than Metformin in abrogating electron transport and increasing sensitivity to ABT-737, suggesting that this agent may be better suited for targeting hematological malignancies. Taken together, our results suggest that inhibition of mitochondrial metabolism by Metformin or Phenformin is associated with increased leukemia cell susceptibility to induction of intrinsic apoptosis, and provide a rationale for clinical studies exploring the efficacy of combining biguanides with the orally bioavailable derivative of ABT-737, Venetoclax.

Paleoclassical transport explains electron transport barriers in RTP and TEXTOR

NASA Astrophysics Data System (ADS)

Hogeweij, G. M. D.; Callen, J. D.; RTP Team; TEXTOR Team

2008-06-01

The recently developed paleoclassical transport model sets the minimum level of electron thermal transport in a tokamak. This transport level has proven to be in good agreement with experimental observations in many cases when fluctuation-induced anomalous transport is small, i.e. in (near-)ohmic plasmas in small to medium size tokamaks, inside internal transport barriers (ITBs) or edge transport barriers (H-mode pedestal). In this paper predictions of the paleoclassical transport model are compared in detail with data from such kinds of discharges: ohmic discharges from the RTP tokamak, EC heated RTP discharges featuring both dynamic and shot-to-shot scans of the ECH power deposition radius and off-axis EC heated discharges from the TEXTOR tokamak. For ohmically heated RTP discharges the Te profiles predicted by the paleoclassical model are in reasonable agreement with the experimental observations, and various parametric dependences are captured satisfactorily. The electron thermal ITBs observed in steady state EC heated RTP discharges and transiently after switch-off of off-axis ECH in TEXTOR are predicted very well by the paleoclassical model.

Cerebrospinal and Interstitial Fluid Transport via the Glymphatic Pathway Modeled by Optimal Mass Transport

PubMed Central

Ratner, Vadim; Gao, Yi; Lee, Hedok; Elkin, Rena; Nedergaard, Maiken; Benveniste, Helene; Tannenbaum, Allen

2017-01-01

The glymphatic pathway is a system which facilitates continuous cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange and plays a key role in removing waste products from the rodent brain. Dysfunction of the glymphatic pathway may be implicated in the pathophysiology of Alzheimer's disease. Intriguingly, the glymphatic system is most active during deep wave sleep general anesthesia. By using paramagnetic tracers administered into CSF of rodents, we previously showed the utility of MRI in characterizing a macroscopic whole brain view of glymphatic transport but we have yet to define and visualize the specific flow patterns. Here we have applied an alternative mathematical analysis approach to a dynamic time series of MRI images acquired every 4 min over ∼3 hrs in anesthetized rats, following administration of a small molecular weight paramagnetic tracer into the CSF reservoir of the cisterna magna. We use Optimal Mass Transport (OMT) to model the glymphatic flow vector field, and then analyze the flow to find the network of CSF-ISF flow channels. We use 3D visualization computational tools to visualize the OMT defined network of CSF-ISF flow channels in relation to anatomical and vascular key landmarks from the live rodent brain. The resulting OMT model of the glymphatic transport network agrees largely with the current understanding of the glymphatic transport patterns defined by dynamic contrast-enhanced MRI revealing key CSF transport pathways along the ventral surface of the brain with a trajectory towards the pineal gland, cerebellum, hypothalamus and olfactory bulb. In addition, the OMT analysis also revealed some interesting previously unnoticed behaviors regarding CSF transport involving parenchymal streamlines moving from ventral reservoirs towards the surface of the brain, olfactory bulb and large central veins. PMID:28323163

Cerebrospinal and interstitial fluid transport via the glymphatic pathway modeled by optimal mass transport.

PubMed

Ratner, Vadim; Gao, Yi; Lee, Hedok; Elkin, Rena; Nedergaard, Maiken; Benveniste, Helene; Tannenbaum, Allen

2017-05-15

The glymphatic pathway is a system which facilitates continuous cerebrospinal fluid (CSF) and interstitial fluid (ISF) exchange and plays a key role in removing waste products from the rodent brain. Dysfunction of the glymphatic pathway may be implicated in the pathophysiology of Alzheimer's disease. Intriguingly, the glymphatic system is most active during deep wave sleep general anesthesia. By using paramagnetic tracers administered into CSF of rodents, we previously showed the utility of MRI in characterizing a macroscopic whole brain view of glymphatic transport but we have yet to define and visualize the specific flow patterns. Here we have applied an alternative mathematical analysis approach to a dynamic time series of MRI images acquired every 4min over ∼3h in anesthetized rats, following administration of a small molecular weight paramagnetic tracer into the CSF reservoir of the cisterna magna. We use Optimal Mass Transport (OMT) to model the glymphatic flow vector field, and then analyze the flow to find the network of CSF-ISF flow channels. We use 3D visualization computational tools to visualize the OMT defined network of CSF-ISF flow channels in relation to anatomical and vascular key landmarks from the live rodent brain. The resulting OMT model of the glymphatic transport network agrees largely with the current understanding of the glymphatic transport patterns defined by dynamic contrast-enhanced MRI revealing key CSF transport pathways along the ventral surface of the brain with a trajectory towards the pineal gland, cerebellum, hypothalamus and olfactory bulb. In addition, the OMT analysis also revealed some interesting previously unnoticed behaviors regarding CSF transport involving parenchymal streamlines moving from ventral reservoirs towards the surface of the brain, olfactory bulb and large central veins. Copyright © 2017. Published by Elsevier Inc.

Investigating dysregulated pathways in Staphylococcus aureus (SA) exposed macrophages based on pathway interaction network.

PubMed

Zhou, Wei; Zhang, Yan; Li, Yue-Hua; Wang, Shuang; Zhang, Jing-Jing; Zhang, Cui-Xia; Zhang, Zhi-Sheng

2017-02-01

This work aimed to identify dysregulated pathways for Staphylococcus aureus (SA) exposed macrophages based on pathway interaction network (PIN). The inference of dysregulated pathways was comprised of four steps: preparing gene expression data, protein-protein interaction (PPI) data and pathway data; constructing a PIN dependent on the data and Pearson correlation coefficient (PCC); selecting seed pathway from PIN by computing activity score for each pathway according to principal component analysis (PCA) method; and investigating dysregulated pathways in a minimum set of pathways (MSP) utilizing seed pathway and the area under the receiver operating characteristics curve (AUC) index implemented in support vector machines (SVM) model. A total of 20,545 genes, 449,833 interactions and 1189 pathways were obtained in the gene expression data, PPI data and pathway data, respectively. The PIN was consisted of 8388 interactions and 1189 nodes, and Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins was identified as the seed pathway. Finally, 15 dysregulated pathways in MSP (AUC=0.999) were obtained for SA infected samples, such as Respiratory electron transport and DNA Replication. We have identified 15 dysregulated pathways for SA infected macrophages based on PIN. The findings might provide potential biomarkers for early detection and therapy of SA infection, and give insights to reveal the molecular mechanism underlying SA infections. However, how these dysregulated pathways worked together still needs to be studied. Copyright © 2016 Elsevier Ltd. All rights reserved.

A deterministic model of electron transport for electron probe microanalysis

NASA Astrophysics Data System (ADS)

Bünger, J.; Richter, S.; Torrilhon, M.

2018-01-01

Within the last decades significant improvements in the spatial resolution of electron probe microanalysis (EPMA) were obtained by instrumental enhancements. In contrast, the quantification procedures essentially remained unchanged. As the classical procedures assume either homogeneity or a multi-layered structure of the material, they limit the spatial resolution of EPMA. The possibilities of improving the spatial resolution through more sophisticated quantification procedures are therefore almost untouched. We investigate a new analytical model (M 1-model) for the quantification procedure based on fast and accurate modelling of electron-X-ray-matter interactions in complex materials using a deterministic approach to solve the electron transport equations. We outline the derivation of the model from the Boltzmann equation for electron transport using the method of moments with a minimum entropy closure and present first numerical results for three different test cases (homogeneous, thin film and interface). Taking Monte Carlo as a reference, the results for the three test cases show that the M 1-model is able to reproduce the electron dynamics in EPMA applications very well. Compared to classical analytical models like XPP and PAP, the M 1-model is more accurate and far more flexible, which indicates the potential of deterministic models of electron transport to further increase the spatial resolution of EPMA.

Evidence of a sewer vapor transport pathway at the USEPA ...

EPA Pesticide Factsheets

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into the duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. These test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope. Highlights • The sewer line is an important pathway for VOC transport at the USEPA duplex. • The importance of this pathway was not identified during prior study of the duplex. • Sewer lines should be routinely evaluated

Nondispersive Electron Transport in Alq3

DTIC Science & Technology

2001-08-20

APPLIED PHYSICS LETTERS VOLUME 79, NUMBER 16 15 OCTOBER 2001Nondispersive electron transport in Alq3 George G. Malliaras,a) Yulong Shen, and David H...room temperature electron transport in amorphous films of tris ~8-hydroxyquinolinolato! aluminum ~III! ( Alq3 ) with the time-of-flight technique...We use the correlated disorder model to determine an effective dipole moment for Alq3 , and the corresponding meridional to facial isomeric ratio

Passive and iontophoretic transport through the skin polar pathway.

PubMed

Li, S K; Peck, K D

2013-01-01

The purpose of the present article is to briefly recount the contributions of Prof. William I. Higuchi to the area of skin transport. These contributions include developing fundamental knowledge of the barrier properties of the stratum corneum, mechanisms of skin transport, concentration gradient across skin in topical drug applications that target the viable epidermal layer, and permeation enhancement by chemical and electrical means. The complex and changeable nature of the skin barrier makes it difficult to assess and characterize the critical parameters that influence skin permeation. The systematic and mechanistic approaches taken by Dr. Higuchi in studying these parameters provided fundamental knowledge in this area and had a measured and lasting influence upon this field of study. This article specifically reviews the validation and characterization of the polar permeation pathway, the mechanistic model of skin transport, the influence of the dermis on the target skin concentration concept, and iontophoretic transport across the polar pathway of skin including the effects of electroosmosis and electropermeabilization. © 2013 S. Karger AG, Basel.

Theoretical investigations of molecular wires: Electronic spectra and electron transport

NASA Astrophysics Data System (ADS)

Palma, Julio Leopoldo

The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with

ETMB-RBF: discrimination of metal-binding sites in electron transporters based on RBF networks with PSSM profiles and significant amino acid pairs.

PubMed

Ou, Yu-Yen; Chen, Shu-An; Wu, Sheng-Cheng

2013-01-01

Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation-reduction reactions. In these oxidation-reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain. We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins. We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88. We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins.

ETMB-RBF: Discrimination of Metal-Binding Sites in Electron Transporters Based on RBF Networks with PSSM Profiles and Significant Amino Acid Pairs

PubMed Central

Ou, Yu-Yen; Chen, Shu-An; Wu, Sheng-Cheng

2013-01-01

Background Cellular respiration is the process by which cells obtain energy from glucose and is a very important biological process in living cell. As cells do cellular respiration, they need a pathway to store and transport electrons, the electron transport chain. The function of the electron transport chain is to produce a trans-membrane proton electrochemical gradient as a result of oxidation–reduction reactions. In these oxidation–reduction reactions in electron transport chains, metal ions play very important role as electron donor and acceptor. For example, Fe ions are in complex I and complex II, and Cu ions are in complex IV. Therefore, to identify metal-binding sites in electron transporters is an important issue in helping biologists better understand the workings of the electron transport chain. Methods We propose a method based on Position Specific Scoring Matrix (PSSM) profiles and significant amino acid pairs to identify metal-binding residues in electron transport proteins. Results We have selected a non-redundant set of 55 metal-binding electron transport proteins as our dataset. The proposed method can predict metal-binding sites in electron transport proteins with an average 10-fold cross-validation accuracy of 93.2% and 93.1% for metal-binding cysteine and histidine, respectively. Compared with the general metal-binding predictor from A. Passerini et al., the proposed method can improve over 9% of sensitivity, and 14% specificity on the independent dataset in identifying metal-binding cysteines. The proposed method can also improve almost 76% sensitivity with same specificity in metal-binding histidine, and MCC is also improved from 0.28 to 0.88. Conclusions We have developed a novel approach based on PSSM profiles and significant amino acid pairs for identifying metal-binding sites from electron transport proteins. The proposed approach achieved a significant improvement with independent test set of metal-binding electron transport proteins

Peritoneal fluid transport: mechanisms, pathways, methods of assessment.

PubMed

Waniewski, Jacek

2013-11-01

Fluid removal during peritoneal dialysis is controlled by many mutually dependent factors and therefore its analysis is more complex than that of the removal of small solutes used as markers of dialysis adequacy. Many new tests have been proposed to assess quantitatively different components of fluid transport (transcapillary ultrafiltration, peritoneal absorption, free water, etc.) and to estimate the factors that influence the rate of fluid transport (osmotic conductance). These tests provide detailed information about indices and parameters that describe fluid transport, especially those concerning the problem of the permanent loss of ultrafiltration capacity (ultrafiltration failure). Different theories and respective mathematical models of mechanisms and pathways of fluid transport are presently discussed and applied, and some fluid transport issues are still debated. Copyright © 2013 IMSS. Published by Elsevier Inc. All rights reserved.

Energy-filtered cold electron transport at room temperature.

PubMed

Bhadrachalam, Pradeep; Subramanian, Ramkumar; Ray, Vishva; Ma, Liang-Chieh; Wang, Weichao; Kim, Jiyoung; Cho, Kyeongjae; Koh, Seong Jin

2014-09-10

Fermi-Dirac electron thermal excitation is an intrinsic phenomenon that limits functionality of various electron systems. Efforts to manipulate electron thermal excitation have been successful when the entire system is cooled to cryogenic temperatures, typically <1 K. Here we show that electron thermal excitation can be effectively suppressed at room temperature, and energy-suppressed electrons, whose energy distribution corresponds to an effective electron temperature of ~45 K, can be transported throughout device components without external cooling. This is accomplished using a discrete level of a quantum well, which filters out thermally excited electrons and permits only energy-suppressed electrons to participate in electron transport. The quantum well (~2 nm of Cr2O3) is formed between source (Cr) and tunnelling barrier (SiO2) in a double-barrier-tunnelling-junction structure having a quantum dot as the central island. Cold electron transport is detected from extremely narrow differential conductance peaks in electron tunnelling through CdSe quantum dots, with full widths at half maximum of only ~15 mV at room temperature.

Energy-filtered cold electron transport at room temperature

PubMed Central

Bhadrachalam, Pradeep; Subramanian, Ramkumar; Ray, Vishva; Ma, Liang-Chieh; Wang, Weichao; Kim, Jiyoung; Cho, Kyeongjae; Koh, Seong Jin

2014-01-01

Fermi-Dirac electron thermal excitation is an intrinsic phenomenon that limits functionality of various electron systems. Efforts to manipulate electron thermal excitation have been successful when the entire system is cooled to cryogenic temperatures, typically <1 K. Here we show that electron thermal excitation can be effectively suppressed at room temperature, and energy-suppressed electrons, whose energy distribution corresponds to an effective electron temperature of ~45 K, can be transported throughout device components without external cooling. This is accomplished using a discrete level of a quantum well, which filters out thermally excited electrons and permits only energy-suppressed electrons to participate in electron transport. The quantum well (~2 nm of Cr2O3) is formed between source (Cr) and tunnelling barrier (SiO2) in a double-barrier-tunnelling-junction structure having a quantum dot as the central island. Cold electron transport is detected from extremely narrow differential conductance peaks in electron tunnelling through CdSe quantum dots, with full widths at half maximum of only ~15 mV at room temperature. PMID:25204839

Model Comparison for Electron Thermal Transport

NASA Astrophysics Data System (ADS)

Moses, Gregory; Chenhall, Jeffrey; Cao, Duc; Delettrez, Jacques

2015-11-01

Four electron thermal transport models are compared for their ability to accurately and efficiently model non-local behavior in ICF simulations. Goncharov's transport model has accurately predicted shock timing in implosion simulations but is computationally slow and limited to 1D. The iSNB (implicit Schurtz Nicolai Busquet electron thermal transport method of Cao et al. uses multigroup diffusion to speed up the calculation. Chenhall has expanded upon the iSNB diffusion model to a higher order simplified P3 approximation and a Monte Carlo transport model, to bridge the gap between the iSNB and Goncharov models while maintaining computational efficiency. Comparisons of the above models for several test problems will be presented. This work was supported by Sandia National Laboratory - Albuquerque and the University of Rochester Laboratory for Laser Energetics.

Pre-silencing of genes involved in the electron transport chain (ETC) pathway is associated with responsiveness to abatacept in rheumatoid arthritis.

PubMed

Derambure, C; Dzangue-Tchoupou, G; Berard, C; Vergne, N; Hiron, M; D'Agostino, M A; Musette, P; Vittecoq, O; Lequerré, T

2017-05-25

In the current context of personalized medicine, one of the major challenges in the management of rheumatoid arthritis (RA) is to identify biomarkers that predict drug responsiveness. From the European APPRAISE trial, our main objective was to identify a gene expression profile associated with responsiveness to abatacept (ABA) + methotrexate (MTX) and to understand the involvement of this signature in the pathophysiology of RA. Whole human genome microarrays (4 × 44 K) were performed from a first subset of 36 patients with RA. Data validation by quantitative reverse-transcription (qRT)-PCR was performed from a second independent subset of 32 patients with RA. Gene Ontology and WikiPathways database allowed us to highlight the specific biological mechanisms involved in predicting response to ABA/MTX. From the first subset of 36 patients with RA, a combination including 87 transcripts allowed almost perfect separation between responders and non-responders to ABA/MTX. Next, the second subset of patients 32 with RA allowed validation by qRT-PCR of a minimal signature with only four genes. This latter signature categorized 81% of patients with RA with 75% sensitivity, 85% specificity and 85% negative predictive value. This combination showed a significant enrichment of genes involved in electron transport chain (ETC) pathways. Seven transcripts from ETC pathways (NDUFA6, NDUFA4, UQCRQ, ATP5J, COX7A2, COX7B, COX6A1) were significantly downregulated in responders versus non-responders to ABA/MTX. Moreover, dysregulation of these genes was independent of inflammation and was specific to ABA response. Pre-silencing of ETC genes is associated with future response to ABA/MTX and might be a crucial key to susceptibility to ABA response.

Parameterizing the Transport Pathways for Cell Invasion in Complex Scaffold Architectures

PubMed Central

Ashworth, Jennifer C.; Mehr, Marco; Buxton, Paul G.; Best, Serena M.

2016-01-01

Interconnecting pathways through porous tissue engineering scaffolds play a vital role in determining nutrient supply, cell invasion, and tissue ingrowth. However, the global use of the term “interconnectivity” often fails to describe the transport characteristics of these pathways, giving no clear indication of their potential to support tissue synthesis. This article uses new experimental data to provide a critical analysis of reported methods for the description of scaffold transport pathways, ranging from qualitative image analysis to thorough structural parameterization using X-ray Micro-Computed Tomography. In the collagen scaffolds tested in this study, it was found that the proportion of pore space perceived to be accessible dramatically changed depending on the chosen method of analysis. Measurements of % interconnectivity as defined in this manner varied as a function of direction and connection size, and also showed a dependence on measurement length scale. As an alternative, a method for transport pathway parameterization was investigated, using percolation theory to calculate the diameter of the largest sphere that can travel to infinite distance through a scaffold in a specified direction. As proof of principle, this approach was used to investigate the invasion behavior of primary fibroblasts in response to independent changes in pore wall alignment and pore space accessibility, parameterized using the percolation diameter. The result was that both properties played a distinct role in determining fibroblast invasion efficiency. This example therefore demonstrates the potential of the percolation diameter as a method of transport pathway parameterization, to provide key structural criteria for application-based scaffold design. PMID:26888449

Electronic transport in smectic liquid crystals

NASA Astrophysics Data System (ADS)

Shiyanovskaya, I.; Singer, K. D.; Twieg, R. J.; Sukhomlinova, L.; Gettwert, V.

2002-04-01

Time-of-flight measurements of transient photoconductivity have revealed bipolar electronic transport in phenylnaphthalene and biphenyl liquid crystals (LC), which exhibit several smectic mesophases. In the phenylnaphthalene LC, the hole mobility is significantly higher than the electron mobility and exhibits different temperature and phase behavior. Electron mobility in the range ~10-5 cm2/V s is temperature activated and remains continuous at the phase transitions. However, hole mobility is nearly temperature independent within the smectic phases, but is very sensitive to smectic order, 10-3 cm2/V s in the smectic-B (Sm-B) and 10-4 cm2/V s in the smectic-A (Sm-A) mesophases. The different behavior for holes and electron transport is due to differing transport mechanisms. The electron mobility is apparently controlled by rate-limiting multiple shallow trapping by impurities, but hole mobility is not. To explain the lack of temperature dependence for hole mobility within the smectic phases we consider two possible polaron transport mechanisms. The first mechanism is based on the hopping of Holstein small polarons in the nonadiabatic limit. The polaron binding energy and transfer integral values, obtained from the model fit, turned out to be sensitive to the molecular order in smectic mesophases. A second possible scenario for temperature-independent hole mobility involves the competion between two different polaron mechanisms involving so-called nearly small molecular polarons and small lattice polarons. Although the extracted transfer integrals and binding energies are reasonable and consistent with the model assumptions, the limited temperature range of the various phases makes it difficult to distinguish between any of the models. In the biphenyl LCs both electron and hole mobilities exhibit temperature activated behavior in the range of 10-5 cm2/V s without sensitivity to the molecular order. The dominating transport mechanism is considered as multiple trapping

Phonon limited electronic transport in Pb

NASA Astrophysics Data System (ADS)

Rittweger, F.; Hinsche, N. F.; Mertig, I.

2017-09-01

We present a fully ab initio based scheme to compute electronic transport properties, i.e. the electrical conductivity σ and thermopower S, in the presence of electron-phonon interaction. We explicitly investigate the \

Elucidation of the glucose transport pathway in glucose transporter 4 via steered molecular dynamics simulations.

PubMed

Sheena, Aswathy; Mohan, Suma S; Haridas, Nidhina Pachakkil A; Anilkumar, Gopalakrishnapillai

2011-01-01

GLUT4 is a predominant insulin regulated glucose transporter expressed in major glucose disposal tissues such as adipocytes and muscles. Under the unstimulated state, GLUT4 resides within intracellular vesicles. Various stimuli such as insulin translocate this protein to the plasma membrane for glucose transport. In the absence of a crystal structure for GLUT4, very little is known about the mechanism of glucose transport by this protein. Earlier we proposed a homology model for GLUT4 and performed a conventional molecular dynamics study revealing the conformational rearrangements during glucose and ATP binding. However, this study could not explain the transport of glucose through the permeation tunnel. To elucidate the molecular mechanism of glucose transport and its energetic, a steered molecular dynamics study (SMD) was used. Glucose was pulled from the extracellular end of GLUT4 to the cytoplasm along the pathway using constant velocity pulling method. We identified several key residues within the tunnel that interact directly with either the backbone ring or the hydroxyl groups of glucose. A rotation of glucose molecule was seen near the sugar binding site facilitating the sugar recognition process at the QLS binding site. This study proposes a possible glucose transport pathway and aids the identification of several residues that make direct interactions with glucose during glucose transport. Mutational studies are required to further validate the observation made in this study.

Electronic transport in VO 2 —Experimentally calibrated Boltzmann transport modeling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kinaci, Alper; Kado, Motohisa; Rosenmann, Daniel

2015-12-28

Materials that undergo metal-insulator transitions (MITs) are under intense study because the transition is scientifically fascinating and technologically promising for various applications. Among these materials, VO2 has served as a prototype due to its favorable transition temperature. While the physical underpinnings of the transition have been heavily investigated experimentally and computationally, quantitative modeling of electronic transport in the two phases has yet to be undertaken. In this work, we establish a density-functional-theory (DFT)-based approach to model electronic transport properties in VO2 in the semiconducting and metallic regimes, focusing on band transport using the Boltzmann transport equations. We synthesized high qualitymore » VO2 films and measured the transport quantities across the transition, in order to calibrate the free parameters in the model. We find that the experimental calibration of the Hubbard correction term can efficiently and adequately model the metallic and semiconducting phases, allowing for further computational design of MIT materials for desirable transport properties.« less

Dissipationless transport of spin-polarized electrons and Cooper pairs in an electron waveguide

NASA Astrophysics Data System (ADS)

Levy, J.; Annadi, A.; Lu, S.; Cheng, G.; Tylan-Tyler, A.; Briggeman, M.; Tomczyk, M.; Huang, M.; Pekker, D.; Irvin, P.; Lee, H.; Lee, J.-W.; Eom, C.-B.

Electron systems undergo profound changes in their behavior when constrained to move along a single axis. To date, clean one-dimensional (1D) electron transport has only been observed in carbon-based nanotubes and nanoribbons, and compound semiconductor nanowires. Complex-oxide heterostructures can possess conductive two-dimensional (2D) interfaces with much richer chemistries and properties, e.g., superconductivity, but with mobilities that appear to preclude ballistic transport in 1D. Here we show that nearly ideal 1D electron waveguides exhibiting ballistic transport of electrons and non-superconducting Cooper pairs can be formed at the interface between the two band insulators LaAlO3 and SrTiO3. The electron waveguides possess gate and magnetic-field selectable spin and charge degrees of freedom, and can be tuned to the one-dimensional limit of a single spin-polarized quantum channel. The strong attractive electron-electron interactions enable a new mode of dissipationless transport of electron pairs that is not superconducting. The selectable spin and subband quantum numbers of these electron waveguides may be useful for quantum simulation, quantum informatio We gratefully acknowledge financial support from ONR N00014-15-1-2847 (JL), AFOSR (FA9550-15-1-0334 (CBE) and FA9550-12-1-0057 (JL, CBE)), AOARD FA2386-15-1-4046 (CBE) and NSF (DMR-1104191 (JL), DMR-1124131 (CBE, JL) and DMR-1234096 (CBE)).

Recent progress in understanding electron thermal transport in NSTX

DOE PAGES

Ren, Y.; Belova, E.; Gorelenkov, N.; ...

2017-03-10

The anomalous level of electron thermal transport inferred in magnetically confined configurations is one of the most challenging problems for the ultimate realization of fusion power using toroidal devices: tokamaks, spherical tori and stellarators. It is generally believed that plasma instabilities driven by the abundant free energy in fusion plasmas are responsible for the electron thermal transport. The National Spherical Torus eXperiment (NSTX) (Ono et al 2000 Nucl. Fusion 40 557) provides a unique laboratory for studying plasma instabilities and their relation to electron thermal transport due to its low toroidal field, high plasma beta, low aspect ratio and largemore » ExB flow shear. Recent findings on NSTX have shown that multiple instabilities are required to explain observed electron thermal transport, given the wide range of equilibrium parameters due to different operational scenarios and radial regions in fusion plasmas. Here we review the recent progresses in understanding anomalous electron thermal transport in NSTX and focus on mechanisms that could drive electron thermal transport in the core region. The synergy between experiment and theoretical/ numerical modeling is essential to achieving these progresses. The plans for newly commissioned NSTX-Upgrade will also be discussed.« less

Calculations of Electron Transport through Radicals

NASA Astrophysics Data System (ADS)

Smeu, Manuel; Dilabio, Gino

2010-03-01

Organic radicals are of interest in molecular electronics because a singly occupied molecular orbital (SOMO) would have a higher energy than its doubly occupied analog, suggesting they might make better conductors. The unpaired electron present in a radical leads to degeneracy splitting in other energy levels and such molecules may act as spin filters. Our study employs first principles transport calculations that are performed using a combination of density functional theory and a non-equilibrium Green's function technique. The conductance of 1,4-benzenediamine (BDA) molecules bridging two Au electrodes was modeled. These molecules were substituted in the 2-position with: -CH3, -NH2, and -OH; as well as with their radical analogs: -CH2, -NH, and -O, all of which have π-type SOMOs. The conductance of a radical with a σ-type SOMO was also calculated from a BDA molecule with the H atom in the 2-position removed. Comparing the transmission spectra for these species will yield insight into the nature of electron transport through radicals vs. transport through their reduced form as well as the nature of transport through π- and σ-type molecular orbitals.

Multiple Drug Transport Pathways through Human P-Glycoprotein.

PubMed

McCormick, James W; Vogel, Pia D; Wise, John G

2015-07-21

P-Glycoprotein (P-gp) is a plasma membrane efflux pump that is commonly associated with therapy resistances in cancers and infectious diseases. P-gp can lower the intracellular concentrations of many drugs to subtherapeutic levels by translocating them out of the cell. Because of the broad range of substrates transported by P-gp, overexpression of P-gp causes multidrug resistance. We reported previously on dynamic transitions of P-gp as it moved through conformations based on crystal structures of homologous ABCB1 proteins using in silico targeted molecular dynamics techniques. We expanded these studies here by docking transport substrates to drug binding sites of P-gp in conformations open to the cytoplasm, followed by cycling the pump through conformations that opened to the extracellular space. We observed reproducible transport of two substrates, daunorubicin and verapamil, by an average of 11-12 Å through the plane of the membrane as P-gp progressed through a catalytic cycle. Methylpyrophosphate, a ligand that should not be transported by P-gp, did not show this movement through P-gp. Drug binding to either of two subsites on P-gp appeared to determine the initial pathway used for drug movement through the membrane. The specific side-chain interactions with drugs within each pathway seemed to be, at least in part, stochastic. The docking and transport properties of a P-gp inhibitor, tariquidar, were also studied. A mechanism of inhibition by tariquidar that involves stabilization of an outward open conformation with tariquidar bound in intracellular loops or at the drug binding domain of P-gp is presented.

Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components

PubMed Central

Pirbadian, Sahand; Barchinger, Sarah E.; Leung, Kar Man; Byun, Hye Suk; Jangir, Yamini; Bouhenni, Rachida A.; Reed, Samantha B.; Romine, Margaret F.; Saffarini, Daad A.; Shi, Liang; Gorby, Yuri A.; Golbeck, John H.; El-Naggar, Mohamed Y.

2014-01-01

Bacterial nanowires offer an extracellular electron transport (EET) pathway for linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Despite the global, environmental, and technological consequences of this biotic–abiotic interaction, the composition, physiological relevance, and electron transport mechanisms of bacterial nanowires remain unclear. We report, to our knowledge, the first in vivo observations of the formation and respiratory impact of nanowires in the model metal-reducing microbe Shewanella oneidensis MR-1. Live fluorescence measurements, immunolabeling, and quantitative gene expression analysis point to S. oneidensis MR-1 nanowires as extensions of the outer membrane and periplasm that include the multiheme cytochromes responsible for EET, rather than pilin-based structures as previously thought. These membrane extensions are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and are consistent with bacterial nanowires that mediate long-range EET by the previously proposed multistep redox hopping mechanism. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution. PMID:25143589

Shewanella oneidensis MR-1 nanowires are outer membrane and periplasmic extensions of the extracellular electron transport components.

PubMed

Pirbadian, Sahand; Barchinger, Sarah E; Leung, Kar Man; Byun, Hye Suk; Jangir, Yamini; Bouhenni, Rachida A; Reed, Samantha B; Romine, Margaret F; Saffarini, Daad A; Shi, Liang; Gorby, Yuri A; Golbeck, John H; El-Naggar, Mohamed Y

2014-09-02

Bacterial nanowires offer an extracellular electron transport (EET) pathway for linking the respiratory chain of bacteria to external surfaces, including oxidized metals in the environment and engineered electrodes in renewable energy devices. Despite the global, environmental, and technological consequences of this biotic-abiotic interaction, the composition, physiological relevance, and electron transport mechanisms of bacterial nanowires remain unclear. We report, to our knowledge, the first in vivo observations of the formation and respiratory impact of nanowires in the model metal-reducing microbe Shewanella oneidensis MR-1. Live fluorescence measurements, immunolabeling, and quantitative gene expression analysis point to S. oneidensis MR-1 nanowires as extensions of the outer membrane and periplasm that include the multiheme cytochromes responsible for EET, rather than pilin-based structures as previously thought. These membrane extensions are associated with outer membrane vesicles, structures ubiquitous in Gram-negative bacteria, and are consistent with bacterial nanowires that mediate long-range EET by the previously proposed multistep redox hopping mechanism. Redox-functionalized membrane and vesicular extensions may represent a general microbial strategy for electron transport and energy distribution.

Endosymbiosis and the design of eukaryotic electron transport.

PubMed

Berry, Stephan

2003-09-30

The bioenergetic organelles of eukaryotic cells, mitochondria and chloroplasts, are derived from endosymbiotic bacteria. Their electron transport chains (ETCs) resemble those of free-living bacteria, but were tailored for energy transformation within the host cell. Parallel evolutionary processes in mitochondria and chloroplasts include reductive as well as expansive events: On one hand, bacterial complexes were lost in eukaryotes with a concomitant loss of metabolic flexibility. On the other hand, new subunits have been added to the remaining bacterial complexes, new complexes have been introduced, and elaborate folding patterns of the thylakoid and mitochondrial inner membranes have emerged. Some bacterial pathways were reinvented independently by eukaryotes, such as parallel routes for quinol oxidation or the use of various anaerobic electron acceptors. Multicellular organization and ontogenetic cycles in eukaryotes gave rise to further modifications of the bioenergetic organelles. Besides mitochondria and chloroplasts, eukaryotes have ETCs in other membranes, such as the plasma membrane (PM) redox system, or the cytochrome P450 (CYP) system. These systems have fewer complexes and simpler branching patterns than those in energy-transforming organelles, and they are often adapted to non-bioenergetic functions such as detoxification or cellular defense.

Electron transport in single molecules: from benzene to graphene.

PubMed

Chen, F; Tao, N J

2009-03-17

Electron movement within and between molecules--that is, electron transfer--is important in many chemical, electrochemical, and biological processes. Recent advances, particularly in scanning electrochemical microscopy (SECM), scanning-tunneling microscopy (STM), and atomic force microscopy (AFM), permit the study of electron movement within single molecules. In this Account, we describe electron transport at the single-molecule level. We begin by examining the distinction between electron transport (from semiconductor physics) and electron transfer (a more general term referring to electron movement between donor and acceptor). The relation between these phenomena allows us to apply our understanding of single-molecule electron transport between electrodes to a broad range of other electron transfer processes. Electron transport is most efficient when the electron transmission probability via a molecule reaches 100%; the corresponding conductance is then 2e(2)/h (e is the charge of the electron and h is the Planck constant). This ideal conduction has been observed in a single metal atom and a string of metal atoms connected between two electrodes. However, the conductance of a molecule connected to two electrodes is often orders of magnitude less than the ideal and strongly depends on both the intrinsic properties of the molecule and its local environment. Molecular length, means of coupling to the electrodes, the presence of conjugated double bonds, and the inclusion of possible redox centers (for example, ferrocene) within the molecular wire have a pronounced effect on the conductance. This complex behavior is responsible for diverse chemical and biological phenomena and is potentially useful for device applications. Polycyclic aromatic hydrocarbons (PAHs) afford unique insight into electron transport in single molecules. The simplest one, benzene, has a conductance much less than 2e(2)/h due to its large LUMO-HOMO gap. At the other end of the spectrum, graphene

Understanding the Contribution of Zinc Transporters in the Function of the Early Secretory Pathway

PubMed Central

Matsunaga, Mayu; Takeda, Taka-aki

2017-01-01

More than one-third of newly synthesized proteins are targeted to the early secretory pathway, which is comprised of the endoplasmic reticulum (ER), Golgi apparatus, and other intermediate compartments. The early secretory pathway plays a key role in controlling the folding, assembly, maturation, modification, trafficking, and degradation of such proteins. A considerable proportion of the secretome requires zinc as an essential factor for its structural and catalytic functions, and recent findings reveal that zinc plays a pivotal role in the function of the early secretory pathway. Hence, a disruption of zinc homeostasis and metabolism involving the early secretory pathway will lead to pathway dysregulation, resulting in various defects, including an exacerbation of homeostatic ER stress. The accumulated evidence indicates that specific members of the family of Zn transporters (ZNTs) and Zrt- and Irt-like proteins (ZIPs), which operate in the early secretory pathway, play indispensable roles in maintaining zinc homeostasis by regulating the influx and efflux of zinc. In this review, the biological functions of these transporters are discussed, focusing on recent aspects of their roles. In particular, we discuss in depth how specific ZNT transporters are employed in the activation of zinc-requiring ectoenzymes. The means by which early secretory pathway functions are controlled by zinc, mediated by specific ZNT and ZIP transporters, are also subjects of this review. PMID:29048339

Understanding the Contribution of Zinc Transporters in the Function of the Early Secretory Pathway.

PubMed

Kambe, Taiho; Matsunaga, Mayu; Takeda, Taka-Aki

2017-10-19

More than one-third of newly synthesized proteins are targeted to the early secretory pathway, which is comprised of the endoplasmic reticulum (ER), Golgi apparatus, and other intermediate compartments. The early secretory pathway plays a key role in controlling the folding, assembly, maturation, modification, trafficking, and degradation of such proteins. A considerable proportion of the secretome requires zinc as an essential factor for its structural and catalytic functions, and recent findings reveal that zinc plays a pivotal role in the function of the early secretory pathway. Hence, a disruption of zinc homeostasis and metabolism involving the early secretory pathway will lead to pathway dysregulation, resulting in various defects, including an exacerbation of homeostatic ER stress. The accumulated evidence indicates that specific members of the family of Zn transporters (ZNTs) and Zrt- and Irt-like proteins (ZIPs), which operate in the early secretory pathway, play indispensable roles in maintaining zinc homeostasis by regulating the influx and efflux of zinc. In this review, the biological functions of these transporters are discussed, focusing on recent aspects of their roles. In particular, we discuss in depth how specific ZNT transporters are employed in the activation of zinc-requiring ectoenzymes. The means by which early secretory pathway functions are controlled by zinc, mediated by specific ZNT and ZIP transporters, are also subjects of this review.

Preface: cardiac control pathways: signaling and transport phenomena.

PubMed

Sideman, Samuel

2008-03-01

Signaling is part of a complex system of communication that governs basic cellular functions and coordinates cellular activity. Transfer of ions and signaling molecules and their interactions with appropriate receptors, transmembrane transport, and the consequent intracellular interactions and functional cellular response represent a complex system of interwoven phenomena of transport, signaling, conformational changes, chemical activation, and/or genetic expression. The well-being of the cell thus depends on a harmonic orchestration of all these events and the existence of control mechanisms that assure the normal behavior of the various parameters involved and their orderly expression. The ability of cells to sustain life by perceiving and responding correctly to their microenvironment is the basis for development, tissue repair, and immunity, as well as normal tissue homeostasis. Natural deviations, or human-induced interference in the signaling pathways and/or inter- and intracellular transport and information transfer, are responsible for the generation, modulation, and control of diseases. The present overview aims to highlight some major topics of the highly complex cellular information transfer processes and their control mechanisms. Our goal is to contribute to the understanding of the normal and pathophysiological phenomena associated with cardiac functions so that more efficient therapeutic modalities can be developed. Our objective in this volume is to identify and enhance the study of some basic passive and active physical and chemical transport phenomena, physiological signaling pathways, and their biological consequences.

Transdermal transport pathway creation: Electroporation pulse order.

PubMed

Becker, Sid; Zorec, Barbara; Miklavčič, Damijan; Pavšelj, Nataša

2014-11-01

In this study we consider the physics underlying electroporation which is administered to skin in order to radically increase transdermal drug delivery. The method involves the application of intense electric fields to alter the structure of the impermeable outer layer, the stratum corneum. A generally held view in the field of skin electroporation is that the skin's drop in resistance (to transport) is proportional to the total power of the pulses (which may be inferred by the number of pulses administered). Contrary to this belief, experiments conducted in this study show that the application of high voltage pulses prior to the application of low voltage pulses result in lower transport than when low voltage pulses alone are applied (when less total pulse power is administered). In order to reconcile these unexpected experimental results, a computational model is used to conduct an analysis which shows that the high density distribution of very small aqueous pathways through the stratum corneum associated with high voltage pulses is detrimental to the evolution of larger pathways that are associated with low voltage pulses. Copyright © 2014 Elsevier Inc. All rights reserved.

Electron transport chains in organohalide-respiring bacteria and bioremediation implications.

PubMed

Wang, Shanquan; Qiu, Lan; Liu, Xiaowei; Xu, Guofang; Siegert, Michael; Lu, Qihong; Juneau, Philippe; Yu, Ling; Liang, Dawei; He, Zhili; Qiu, Rongliang

In situ remediation employing organohalide-respiring bacteria represents a promising solution for cleanup of persistent organohalide pollutants. The organohalide-respiring bacteria conserve energy by utilizing H 2 or organic compounds as electron donors and organohalides as electron acceptors. Reductive dehalogenase (RDase), a terminal reductase of the electron transport chain in organohalide-respiring bacteria, is the key enzyme that catalyzes halogen removal. Accumulating experimental evidence thus far suggests that there are distinct models for respiratory electron transfer in organohalide-respirers of different lineages, e.g., Dehalococcoides, Dehalobacter, Desulfitobacterium and Sulfurospirillum. In this review, to connect the knowledge in organohalide-respiratory electron transport chains to bioremediation applications, we first comprehensively review molecular components and their organization, together with energetics of the organohalide-respiratory electron transport chains, as well as recent elucidation of intramolecular electron shuttling and halogen elimination mechanisms of RDases. We then highlight the implications of organohalide-respiratory electron transport chains in stimulated bioremediation. In addition, major challenges and further developments toward understanding the organohalide-respiratory electron transport chains and their bioremediation applications are identified and discussed. Copyright © 2018 Elsevier Inc. All rights reserved.

Electronic transport in gadolinium atomic-size contacts

NASA Astrophysics Data System (ADS)

Olivera, B.; Salgado, C.; Lado, J. L.; Karimi, A.; Henkel, V.; Scheer, E.; Fernández-Rossier, J.; Palacios, J. J.; Untiedt, C.

2017-02-01

We report on the fabrication, transport measurements, and density functional theory (DFT) calculations of atomic-size contacts made of gadolinium (Gd). Gd is known to have local moments mainly associated with f electrons. These coexist with itinerant s and d bands that account for its metallic character. Here we explore whether and how the local moments influence electronic transport properties at the atomic scale. Using both scanning tunneling microscope and lithographic mechanically controllable break junction techniques under cryogenic conditions, we study the conductance of Gd when only few atoms form the junction between bulk electrodes made of the very same material. Thousands of measurements show that Gd has an average lowest conductance, attributed to single-atom contact, below 2/e2 h . Our DFT calculations for monostrand chains anticipate that the f bands are fully spin polarized and insulating and that the conduction may be dominated by s , p , and d bands. We also analyze the electronic transport for model nanocontacts using the nonequilibrium Green's function formalism in combination with DFT. We obtain an overall good agreement with the experimental results for zero bias and show that the contribution to the electronic transport from the f channels is negligible and that from the d channels is marginal.

Long-Range Superexchange in Electron Transport Proteins

NASA Astrophysics Data System (ADS)

Gruschus, James Michael

A new Hamiltonian model for the calculation of long-range electronic couplings in complex molecular systems is presented. These couplings make possible the electron transfers occurring at several critical steps in photosynthesis and respiration. The couplings studied are demonstrated to arise from a mechanism known as superexchange, where the electrons of the insulating medium are intimately involved in the delocalization of the donor wavefunction tail, allowing significant interaction with the acceptor at much greater separations than could be achieved were the medium absent. Superexchange phenomena in molecules of moderate complexity are first compared to couplings calculated with the model Hamiltonian, with very encouraging results. The method is then applied to several cytochrome c proteins where electron transfer has been measured between a zinc-substituted porphyrin and a ruthenium complex ligated to several sites at the protein surface. The calculated couplings are in unprecedented agreement with experiment. Novel, analytical derivatives of the superexchange coupling with respect to the orbital energies and interactions are then carried out on these proteins yielding the general, chemically relevant result that the entire three-dimensional zone between redox sites is important in mediating the superexchange coupling, in contrast to the prevailing assumption that the coupling can be characterized by a one-dimensional pathway consisting primarily of chains of bonded atoms. In addition, the derivatives provide the most comprehensive ever, atom-by -atom visualization of the superexchange process. Using AMBER molecular dynamics trajectories of the cytochrome c proteins, the effect of structural fluctuations on superexchange is examined. The calculated couplings show a substantial variability, a result contrary to the constant coupling implicit in most present-day transfer rate theory. Couplings are also calculated on surfaces enveloping several variants of

Ionic-Electronic Ambipolar Transport in Metal Halide Perovskites: Can Electronic Conductivity Limit Ionic Diffusion?

PubMed

Kerner, Ross A; Rand, Barry P

2018-01-04

Ambipolar transport describes the nonequilibrium, coupled motion of positively and negatively charged particles to ensure that internal electric fields remain small. It is commonly invoked in the semiconductor community where the motion of excess electrons and holes drift and diffuse together. However, the concept of ambipolar transport is not limited to semiconductor physics. Materials scientists working on ion conducting ceramics understand ambipolar transport dictates the coupled diffusion of ions and the rate is limited by the ion with the lowest diffusion coefficient. In this Perspective, we review a third application of ambipolar transport relevant to mixed ionic-electronic conducting materials for which the motion of ions is expected to be coupled to electronic carriers. In this unique situation, the ambipolar diffusion model has been successful at explaining the photoenhanced diffusion of metal ions in chalcogenide glasses and other properties of materials. Recent examples of photoenhanced phenomena in metal halide perovskites are discussed and indicate that mixed ionic-electronic ambipolar transport is similarly important for a deep understanding of these emerging materials.

Numerical solution of the electron transport equation

NASA Astrophysics Data System (ADS)

Woods, Mark

The electron transport equation has been solved many times for a variety of reasons. The main difficulty in its numerical solution is that it is a very stiff boundary value problem. The most common numerical methods for solving boundary value problems are symmetric collocation methods and shooting methods. Both of these types of methods can only be applied to the electron transport equation if the boundary conditions are altered with unrealistic assumptions because they require too many points to be practical. Further, they result in oscillating and negative solutions, which are physically meaningless for the problem at hand. For these reasons, all numerical methods for this problem to date are a bit unusual because they were designed to try and avoid the problem of extreme stiffness. This dissertation shows that there is no need to introduce spurious boundary conditions or invent other numerical methods for the electron transport equation. Rather, there already exists methods for very stiff boundary value problems within the numerical analysis literature. We demonstrate one such method in which the fast and slow modes of the boundary value problem are essentially decoupled. This allows for an upwind finite difference method to be applied to each mode as is appropriate. This greatly reduces the number of points needed in the mesh, and we demonstrate how this eliminates the need to define new boundary conditions. This method is verified by showing that under certain restrictive assumptions, the electron transport equation has an exact solution that can be written as an integral. We show that the solution from the upwind method agrees with the quadrature evaluation of the exact solution. This serves to verify that the upwind method is properly solving the electron transport equation. Further, it is demonstrated that the output of the upwind method can be used to compute auroral light emissions.

Nanoscale On-Silico Electron Transport via Ferritins.

PubMed

Bera, Sudipta; Kolay, Jayeeta; Banerjee, Siddhartha; Mukhopadhyay, Rupa

2017-02-28

Silicon is a solid-state semiconducting material that has long been recognized as a technologically useful one, especially in electronics industry. However, its application in the next-generation metalloprotein-based electronics approaches has been limited. In this work, the applicability of silicon as a solid support for anchoring the iron-storage protein ferritin, which has a semiconducting iron nanocore, and probing electron transport via the ferritin molecules trapped between silicon substrate and a conductive scanning probe has been investigated. Ferritin protein is an attractive bioelectronic material because its size (X-ray crystallographic diameter ∼12 nm) should allow it to fit well in the larger tunnel gaps (>5 nm), fabrication of which is relatively more established, than the smaller ones. The electron transport events occurring through the ferritin molecules that are covalently anchored onto the MPTMS-modified silicon surface could be detected at the molecular level by current-sensing atomic force spectroscopy (CSAFS). Importantly, the distinct electronic signatures of the metal types (i.e., Fe, Mn, Ni, and Au) within the ferritin nanocore could be distinguished from each other using the transport band gap analyses. The CSAFS measurements on holoferritin, apoferritin, and the metal core reconstituted ferritins reveal that some of these ferritins behave like n-type semiconductors, while the others behave as p-type semiconductors. The band gaps for the different ferritins are found to be within 0.8 to 2.6 eV, a range that is valid for the standard semiconductor technology (e.g., diodes based on p-n junction). The present work indicates effective on-silico integration of the ferritin protein, as it remains functionally viable after silicon binding and its electron transport activities can be detected. Potential use of the ferritin-silicon nanohybrids may therefore be envisaged in applications other than bioelectronics, too, as ferritin is a versatile

Spin-polarized electron transport in hybrid graphene-BN nanoribbons

NASA Astrophysics Data System (ADS)

Gao, Song; Lu, Wei; Zheng, Guo-Hui; Jia, Yalei; Ke, San-Huang

2017-05-01

The experimental realization of hybrid graphene and h-BN provides a new way to modify the electronic and transport properties of graphene-based materials. In this work, we investigate the spin-polarized electron transport in hybrid graphene-BN zigzag nanoribbons by performing first-principles nonequilibrium Green’s function method calculations. A 100% spin-polarized electron transport in a large energy window around the Fermi level is found and this behavior is independent of the ribbon width as long as there contain 3 zigzag carbon chains. This behavior may be useful in making perfect spin filters.

Sources and transport pathways of micropollutants into surface waters - an overview

NASA Astrophysics Data System (ADS)

Stamm, Christian

2017-04-01

Micropollutants reach water bodies from a large range of sources through different transport pathways. They consist of hundreds or thousands of compounds rendering exposure assessment an analytical challenge. Prominent examples of micropollutants are wastewater-born pharmaceuticals and hormones or plant protection products originating from diffuse agricultural sources. This presentation reviews the possible origin of micropollutants and their transport pathways. It demonstrates that considering municipal wastewater and agriculture may fall short of comprising all relevant source-pathway combination in a given watershed by providing examples from industry, animal production, or leaching to groundwater. The diversity of source-pathway leads on the one hand to a large number of possible chemicals to be considered including parent compounds of end products, their transformation products, legacy compounds but also intermediates used during industrial synthesis processes. On the other hand, it leads to a wide range of temporal dynamics by which these compounds reach streams and rivers. This combination makes a comprehensive exposure assessment for micropollutants a real scientific challenge. An outlook into new development in sampling and analytics will suggest possible solution for this challenge.

Quantum electron tunneling in respiratory complex I.

PubMed

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A

2011-05-12

We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. While the one-electron tunneling approximation is found to hold in electron tunneling between the antiferromagnetic binuclear and tetranuclear Fe/S clusters without major orbital or spin rearrangement of the core electrons, induced polarization of the core electrons contributes significantly to decrease the electron transfer rates to 19-56 %. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of the electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A signature of the wave properties of electrons is observed as distinct quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included is in good agreement with a reported phenomenological relation.

Unconventional aspects of electronic transport in delafossite oxides

NASA Astrophysics Data System (ADS)

Daou, Ramzy; Frésard, Raymond; Eyert, Volker; Hébert, Sylvie; Maignan, Antoine

2017-12-01

The electronic transport properties of the delafossite oxides ? are usually understood in terms of two well-separated entities, namely the triangular ? and (? layers. Here, we review several cases among this extensive family of materials where the transport depends on the interlayer coupling and displays unconventional properties. We review the doped thermoelectrics based on ? and ?, which show a high-temperature recovery of Fermi-liquid transport exponents, as well as the highly anisotropic metals ?, ?, and ?, where the sheer simplicity of the Fermi surface leads to unconventional transport. We present some of the theoretical tools that have been used to investigate these transport properties and review what can and cannot be learned from the extensive set of electronic structure calculations that have been performed.

An ab initio electronic transport database for inorganic materials.

PubMed

Ricci, Francesco; Chen, Wei; Aydemir, Umut; Snyder, G Jeffrey; Rignanese, Gian-Marco; Jain, Anubhav; Hautier, Geoffroy

2017-07-04

Electronic transport in materials is governed by a series of tensorial properties such as conductivity, Seebeck coefficient, and effective mass. These quantities are paramount to the understanding of materials in many fields from thermoelectrics to electronics and photovoltaics. Transport properties can be calculated from a material's band structure using the Boltzmann transport theory framework. We present here the largest computational database of electronic transport properties based on a large set of 48,000 materials originating from the Materials Project database. Our results were obtained through the interpolation approach developed in the BoltzTraP software, assuming a constant relaxation time. We present the workflow to generate the data, the data validation procedure, and the database structure. Our aim is to target the large community of scientists developing materials selection strategies and performing studies involving transport properties.

Quantum Electron Tunneling in Respiratory Complex I1

PubMed Central

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A.

2014-01-01

We have simulated the atomistic details of electronic wiring of all Fe/S clusters in complex I, a key enzyme in the respiratory electron transport chain. The tunneling current theory of many-electron systems is applied to the broken-symmetry (BS) states of the protein at the ZINDO level. One-electron tunneling approximation is found to hold in electron tunneling between the anti-ferromagnetic binuclear and tetranuclear Fe/S clusters with moderate induced polarization of the core electrons. Calculated tunneling energy is about 3 eV higher than Fermi level in the band gap of the protein, which supports that the mechanism of electron transfer is quantum mechanical tunneling, as in the rest of electron transport chain. Resulting electron tunneling pathways consist of up to three key contributing protein residues between neighboring Fe/S clusters. A distinct signature of the wave properties of electrons is observed as quantum interferences when multiple tunneling pathways exist. In N6a-N6b, electron tunnels along different pathways depending on the involved BS states, suggesting possible fluctuations of the tunneling pathways driven by the local protein environment. The calculated distance dependence of the electron transfer rates with internal water molecules included are in good agreement with a reported phenomenological relation. PMID:21495666

Electron-hole collision limited transport in charge-neutral bilayer graphene

NASA Astrophysics Data System (ADS)

Nam, Youngwoo; Ki, Dong-Keun; Soler-Delgado, David; Morpurgo, Alberto F.

2017-12-01

Ballistic transport occurs whenever electrons propagate without collisions deflecting their trajectory. It is normally observed in conductors with a negligible concentration of impurities, at low temperature, to avoid electron-phonon scattering. Here, we use suspended bilayer graphene devices to reveal a new regime, in which ballistic transport is not limited by scattering with phonons or impurities, but by electron-hole collisions. The phenomenon manifests itself in a negative four-terminal resistance that becomes visible when the density of holes (electrons) is suppressed by gate-shifting the Fermi level in the conduction (valence) band, above the thermal energy. For smaller densities, transport is diffusive, and the measured conductivity is reproduced quantitatively, with no fitting parameters, by including electron-hole scattering as the only process causing velocity relaxation. Experiments on a trilayer device show that the phenomenon is robust and that transport at charge neutrality is governed by the same physics. Our results provide a textbook illustration of a transport regime that had not been observed previously and clarify the nature of conduction through charge-neutral graphene under conditions in which carrier density inhomogeneity is immaterial. They also demonstrate that transport can be limited by a fully electronic mechanism, originating from the same microscopic processes that govern the physics of Dirac-like plasmas.

A Deterministic Computational Procedure for Space Environment Electron Transport

NASA Technical Reports Server (NTRS)

Nealy, John E.; Chang, C. K.; Norman, Ryan B.; Blattnig, Steve R.; Badavi, Francis F.; Adamcyk, Anne M.

2010-01-01

A deterministic computational procedure for describing the transport of electrons in condensed media is formulated to simulate the effects and exposures from spectral distributions typical of electrons trapped in planetary magnetic fields. The primary purpose for developing the procedure is to provide a means of rapidly performing numerous repetitive transport calculations essential for electron radiation exposure assessments for complex space structures. The present code utilizes well-established theoretical representations to describe the relevant interactions and transport processes. A combined mean free path and average trajectory approach is used in the transport formalism. For typical space environment spectra, several favorable comparisons with Monte Carlo calculations are made which have indicated that accuracy is not compromised at the expense of the computational speed.

Electron Transport Properties of Ge nanowires

NASA Astrophysics Data System (ADS)

Hanrath, Tobias; Khondaker, Saiful I.; Yao, Zhen; Korgel, Brian A.

2003-03-01

Electron Transport Properties of Ge nanowires Tobias Hanrath*, Saiful I. Khondaker, Zhen Yao, Brian A. Korgel* *Dept. of Chemical Engineering, Dept. of Physics, Texas Materials Institute, and Center for Nano- and Molecular Science and Technology University of Texas at Austin, Austin, Texas 78712-1062 e-mail: korgel@mail.che.utexas.edu Germanium (Ge) nanowires with diameters ranging from 6 to 50 nm and several micrometer in length were grown via a supercritical fluid-liquid-solid synthesis. Parallel electron energy loss spectroscopy (PEELS) was employed to study the band structure and electron density in the Ge nanowires. The observed increase in plasmon peak energy and peak width with decreasing nanowire diameter is attributed to quantum confinement effects. For electrical characterization, Ge nanowires were deposited onto a patterned Si/SiO2 substrate. E-beam lithography was then used to form electrode contacts to individual nanowires. The influence of nanowire diameter, surface chemistry and crystallographic defects on electron transport properties were investigated and the comparison of Ge nanowire conductivity with respect to bulk, intrinsic Ge will be presented.

Molecular electronics: Some views on transport junctions and beyond

PubMed Central

Joachim, Christian; Ratner, Mark A.

2005-01-01

The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of “conduction as scattering” generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions. PMID:15956192

Molecular electronics: some views on transport junctions and beyond.

PubMed

Joachim, Christian; Ratner, Mark A

2005-06-21

The field of molecular electronics comprises a fundamental set of issues concerning the electronic response of molecules as parts of a mesoscopic structure and a technology-facing area of science. We will overview some important aspects of these subfields. The most advanced ideas in the field involve the use of molecules as individual logic or memory units and are broadly based on using the quantum state space of the molecule. Current work in molecular electronics usually addresses molecular junction transport, where the molecule acts as a barrier for incoming electrons: This is the fundamental Landauer idea of "conduction as scattering" generalized to molecular junction structures. Another point of view in terms of superexchange as a guiding mechanism for coherent electron transfer through the molecular bridge is discussed. Molecules generally exhibit relatively strong vibronic coupling. The last section of this overview focuses on vibronic effects, including inelastic electron tunneling spectroscopy, hysteresis in junction charge transport, and negative differential resistance in molecular transport junctions.

Vertical electronic transport in van de waals heterostructures

NASA Astrophysics Data System (ADS)

Qiao, Zhenhua; Zhenhua Qiao's Group Team

In this work, we will introduce the theoretical investigation of the vertical electronic transport in various heterostructrues by using both tight-binding method and first-principles calculations. Counterintuitively, we find that the maximum electronic transport is achieved at very limited scattering regions but not at large overlapped catering regions. Based on this finding, we design a special setup to measure the tunneling effect in rotated bilayer systems.

An ab initio electronic transport database for inorganic materials

DOE PAGES

Ricci, Francesco; Chen, Wei; Aydemir, Umut; ...

2017-07-04

Electronic transport in materials is governed by a series of tensorial properties such as conductivity, Seebeck coefficient, and effective mass. These quantities are paramount to the understanding of materials in many fields from thermoelectrics to electronics and photovoltaics. Transport properties can be calculated from a material’s band structure using the Boltzmann transport theory framework. We present here the largest computational database of electronic transport properties based on a large set of 48,000 materials originating from the Materials Project database. Our results were obtained through the interpolation approach developed in the BoltzTraP software, assuming a constant relaxation time. We present themore » workflow to generate the data, the data validation procedure, and the database structure. In conclusion, our aim is to target the large community of scientists developing materials selection strategies and performing studies involving transport properties.« less

An ab initio electronic transport database for inorganic materials

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ricci, Francesco; Chen, Wei; Aydemir, Umut

Electronic transport in materials is governed by a series of tensorial properties such as conductivity, Seebeck coefficient, and effective mass. These quantities are paramount to the understanding of materials in many fields from thermoelectrics to electronics and photovoltaics. Transport properties can be calculated from a material’s band structure using the Boltzmann transport theory framework. We present here the largest computational database of electronic transport properties based on a large set of 48,000 materials originating from the Materials Project database. Our results were obtained through the interpolation approach developed in the BoltzTraP software, assuming a constant relaxation time. We present themore » workflow to generate the data, the data validation procedure, and the database structure. In conclusion, our aim is to target the large community of scientists developing materials selection strategies and performing studies involving transport properties.« less

Electron heat transport measured in a stochastic magnetic field.

PubMed

Biewer, T M; Forest, C B; Anderson, J K; Fiksel, G; Hudson, B; Prager, S C; Sarff, J S; Wright, J C; Brower, D L; Ding, W X; Terry, S D

2003-07-25

New profile measurements have allowed the electron thermal diffusivity profile to be estimated from power balance in the Madison Symmetric Torus where magnetic islands overlap and field lines are stochastic. The measurements show that (1) the electron energy transport is conductive not convective, (2) the measured thermal diffusivities are in good agreement with numerical simulations of stochastic transport, and (3) transport is greatly reduced near the reversal surface where magnetic diffusion is small.

Charge transport through DNA based electronic barriers

NASA Astrophysics Data System (ADS)

Patil, Sunil R.; Chawda, Vivek; Qi, Jianqing; Anantram, M. P.; Sinha, Niraj

2018-05-01

We report charge transport in electronic 'barriers' constructed by sequence engineering in DNA. Considering the ionization potentials of Thymine-Adenine (AT) and Guanine-Cytosine (GC) base pairs, we treat AT as 'barriers'. The effect of DNA conformation (A and B form) on charge transport is also investigated. Particularly, the effect of width of 'barriers' on hole transport is investigated. Density functional theory (DFT) calculations are performed on energy minimized DNA structures to obtain the electronic Hamiltonian. The quantum transport calculations are performed using the Landauer-Buttiker framework. Our main findings are contrary to previous studies. We find that a longer A-DNA with more AT base pairs can conduct better than shorter A-DNA with a smaller number of AT base pairs. We also find that some sequences of A-DNA can conduct better than a corresponding B-DNA with the same sequence. The counterions mediated charge transport and long range interactions are speculated to be responsible for counter-intuitive length and AT content dependence of conductance of A-DNA.

A Deterministic Transport Code for Space Environment Electrons

NASA Technical Reports Server (NTRS)

Nealy, John E.; Chang, C. K.; Norman, Ryan B.; Blattnig, Steve R.; Badavi, Francis F.; Adamczyk, Anne M.

2010-01-01

A deterministic computational procedure has been developed to describe transport of space environment electrons in various shield media. This code is an upgrade and extension of an earlier electron code. Whereas the former code was formulated on the basis of parametric functions derived from limited laboratory data, the present code utilizes well established theoretical representations to describe the relevant interactions and transport processes. The shield material specification has been made more general, as have the pertinent cross sections. A combined mean free path and average trajectory approach has been used in the transport formalism. Comparisons with Monte Carlo calculations are presented.

Electronic transport in torsional strained Weyl semimetals

NASA Astrophysics Data System (ADS)

Soto-Garrido, Rodrigo; Muñoz, Enrique

2018-05-01

In a recent paper (Muñoz and Soto-Garrido 2017 J. Phys.: Condens. Matter 29 445302) we have studied the effects of mechanical strain and magnetic field on the electronic transport properties in graphene. In this article we extended our work to Weyl semimetals (WSM). We show that although the WSM are 3D materials, most of the analysis done for graphene (2D material) can be carried out. In particular, we studied the electronic transport through a cylindrical region submitted to torsional strain and external magnetic field. We provide exact analytical expressions for the scattering cross section and the transmitted electronic current. In addition, we show the node-polarization effect on the current and propose a recipe to measure the torsion angle from transmission experiments.

Multiple Drug Transport Pathways through human P-Glycoprotein(†)

PubMed Central

McCormick, James W.; Vogel, Pia D.; Wise, John G.

2015-01-01

P-glycoprotein (P-gp) is a plasma membrane efflux pump that is commonly associated with therapy resistances in cancers and infectious diseases. P-gp can lower the intracellular concentrations of many drugs to subtherapeutic levels by translocating them out of the cell. Because of the broad range of substrates transported by P-gp, overexpression of P-gp causes multidrug resistance. We reported previously on dynamic transitions of P-gp as it moved through conformations based on crystal structures of homologous ABCB1 proteins using in silico targeted molecular dynamics techniques. We expanded these studies here by docking transport substrates to drug binding sites of P-gp in conformations open to the cytoplasm, followed by cycling the pump through conformations that opened to the extracellular space. We observed reproducible transport of two substrates, daunorubicin and verapamil, by an average of 11 to 12 Å through the plane of the membrane as P-gp progressed through a catalytic cycle. Methyl-pyrophosphate, a ligand that should not be transported by P-gp, did not show this movement through P-gp. Drug binding to either of two subsites on P-gp appeared to determine the initial pathway used for drug movement through the membrane. The specific side-chain interactions with drugs within each pathway seemed to be, at least in part, stochastic. The docking and transport properties of a P-gp inhibitor, tariquidar, were also studied. A mechanism of inhibition by tariquidar is presented that involves stabilization of an outward open conformation with tariquidar bound in intracellular loops or at the drug binding domain of P-gp. PMID:26125482

Preferential pathways in complex fracture systems and their influence on large scale transport

NASA Astrophysics Data System (ADS)

Willmann, M.; Mañé, R.; Tyukhova, A.

2017-12-01

Many subsurface applications in complex fracture systems require large-scale predictions. Precise predictions are difficult because of the existence of preferential pathways at different scales. The intrinsic complexity of fracture systems increases within fractured sedimentary formations, because also the coupling of fractures and matrix has to be taken into account. This interplay of fracture system and the sedimentary matrix is strongly controlled by the actual fracture aperture of an individual fracture. And an effective aperture cannot be easily be determined because of the preferential pathways along the fracture plane. We investigate the influence of these preferential pathways on large scale solute transport and upscale the aperture. By explicitly modeling flow and particle tracking in individual fractures, we develop a new effective transport aperture, which is weighted by the aperture along the preferential paths, a Lagrangian aperture. We show that this new aperture is consistently larger than existing definitions of effective flow and transport apertures. Finally, we apply our results to a fractured sedimentary formation in Northern Switzerland.

Transcellular Pathways in Lymphatic Endothelial Cells Regulate Changes in Solute Transport by Fluid Stress.

PubMed

Triacca, Valentina; Güç, Esra; Kilarski, Witold W; Pisano, Marco; Swartz, Melody A

2017-04-28

The transport of interstitial fluid and solutes into lymphatic vessels is important for maintaining interstitial homeostasis and delivering antigens and soluble factors to the lymph node for immune surveillance. Transendothelial transport across lymphatic endothelial cells (LECs) is commonly considered to occur paracellularly, or between cell-cell junctions, and driven by local pressure and concentration gradients. However, emerging evidence suggests that LECs also play active roles in regulating interstitial solute balance and can scavenge and store antigens, raising the possibility that vesicular or transcellular pathways may be important in lymphatic solute transport. The aim of this study was to determine the relative importance of transcellular (vesicular) versus paracellular transport pathways by LECs and how mechanical stress (ie, fluid flow conditioning) alters either pathway. We demonstrate that transcellular transport mechanisms substantially contribute to lymphatic solute transport and that solute uptake occurs in both caveolae- and clathrin-coated vesicles. In vivo, intracelluar uptake of fluorescently labeled albumin after intradermal injection by LECs was similar to that of dermal dendritic cells. In vitro, we developed a method to differentially quantify intracellular solute uptake versus transendothelial transport by LECs. LECs preconditioned to 1 µm/s transmural flow demonstrated increased uptake and basal-to-apical solute transport, which could be substantially reversed by blocking dynamin-dependent vesicle formation. These findings reveal the importance of intracellular transport in steady-state lymph formation and suggest that LECs use transcellular mechanisms in parallel to the well-described paracellular route to modulate solute transport from the interstitium according to biomechanical cues. © 2017 American Heart Association, Inc.

Electron transport in molecular wires with transition metal contacts

NASA Astrophysics Data System (ADS)

Dalgleish, Hugh

A molecular wire is an organic molecule that forms a conducting bridge between electronic contacts. Single molecules are likely to be the smallest entities to conduct electricity and thus molecular wires present many interesting challenges to fundamental science as well as enormous potential for nanoelectronic technological applications. A particular challenge stems from the realization that the properties of molecular wires are strongly influenced by the combined characteristics of the molecule and the metal contacts. While gold has been the most studied contact material to date, interest in molecular wires with transition metal contacts that are electronically more complex than gold is growing. This thesis presents a theoretical investigation of electron transport and associated phenomena in molecular wires with transition metal contacts. An appropriate methodology is developed on the basis of Landauer theory and ab initio and semi-empirical considerations and new, physically important systems are identified. Spin-dependent transport mechanisms and device characteristics are explored for molecular wires with ferromagnetic iron contacts, systems that have not been considered previously, either theoretically or experimentally. Electron transport between iron point contacts bridged by iron atoms is also investigated. Spin-dependent transport is also studied for molecules bridging nickel contacts and a possible explanation of some experimentally observed phenomena is proposed. A novel physical phenomenon termed strong spin current rectification and a new controllable negative differential resistance mechanism with potential applications for molecular electronic technology are introduced. The phenomena predicted in this thesis should be accessible to present day experimental techniques and this work is intended to stimulate experiments directed at observing them. Keywords. molecular electronics; spintronics; electron transport; interface states.

Insights into the post-transcriptional regulation of the mitochondrial electron transport chain.

PubMed

Sirey, Tamara M; Ponting, Chris P

2016-10-15

The regulation of the mitochondrial electron transport chain is central to the control of cellular homeostasis. There are significant gaps in our understanding of how the expression of the mitochondrial and nuclear genome-encoded components of the electron transport chain are co-ordinated, and how the assembly of the protein complexes that constitute the electron transport chain are regulated. Furthermore, the role post-transcriptional gene regulation may play in modulating these processes needs to be clarified. This review summarizes the current knowledge regarding the post-transcriptional gene regulation of the electron transport chain and highlights how noncoding RNAs may contribute significantly both to complex electron transport chain regulatory networks and to mitochondrial dysfunction. © 2016 The Author(s).

Aspects of electron transport in zigzag graphene nanoribbons

NASA Astrophysics Data System (ADS)

Bhalla, Pankaj; Pratap, Surender

2018-05-01

In this paper, we investigate the aspects of electron transport in the zigzag graphene nanoribbons (ZGNRs) using the nonequilibrium Green’s function (NEGF) formalism. The latter is an esoteric tool in mesoscopic physics. It is used to perform an analysis of ZGNRs by considering potential well. Within this potential, the dependence of transmission coefficient, local density of states (LDOS) and electron transport properties on number of atoms per unit cell is discussed. It is observed that there is an increment in electron and thermal conductance with increasing number of atoms. In addition to these properties, the dependence of same is also studied in figure of merit. The results infer that the contribution of electrons to enhance the figure of merit is important above the crossover temperature.

Electronic transport in graphene-based heterostructures

NASA Astrophysics Data System (ADS)

Tan, J. Y.; Avsar, A.; Balakrishnan, J.; Koon, G. K. W.; Taychatanapat, T.; O'Farrell, E. C. T.; Watanabe, K.; Taniguchi, T.; Eda, G.; Castro Neto, A. H.; Özyilmaz, B.

2014-05-01

While boron nitride (BN) substrates have been utilized to achieve high electronic mobilities in graphene field effect transistors, it is unclear how other layered two dimensional (2D) crystals influence the electronic performance of graphene. In this Letter, we study the surface morphology of 2D BN, gallium selenide (GaSe), and transition metal dichalcogenides (tungsten disulfide (WS2) and molybdenum disulfide (MoS2)) crystals and their influence on graphene's electronic quality. Atomic force microscopy analysis shows that these crystals have improved surface roughness (root mean square value of only ˜0.1 nm) compared to conventional SiO2 substrate. While our results confirm that graphene devices exhibit very high electronic mobility (μ) on BN substrates, graphene devices on WS2 substrates (G/WS2) are equally promising for high quality electronic transport (μ ˜ 38 000 cm2/V s at room temperature), followed by G/MoS2 (μ ˜ 10 000 cm2/V s) and G/GaSe (μ ˜ 2200 cm2/V s). However, we observe a significant asymmetry in electron and hole conduction in G/WS2 and G/MoS2 heterostructures, most likely due to the presence of sulphur vacancies in the substrate crystals. GaSe crystals are observed to degrade over time even under ambient conditions, leading to a large hysteresis in graphene transport making it a less suitable substrate.

Melatonin and the electron transport chain.

PubMed

Hardeland, Rüdiger

2017-11-01

Melatonin protects the electron transport chain (ETC) in multiple ways. It reduces levels of ·NO by downregulating inducible and inhibiting neuronal nitric oxide synthases (iNOS, nNOS), thereby preventing excessive levels of peroxynitrite. Both ·NO and peroxynitrite-derived free radicals, such as ·NO 2 , hydroxyl (·OH) and carbonate radicals (CO 3 · - ) cause blockades or bottlenecks in the ETC, by ·NO binding to irons, protein nitrosation, nitration and oxidation, changes that lead to electron overflow or even backflow and, thus, increased formation of superoxide anions (O 2 · - ). Melatonin improves the intramitochondrial antioxidative defense by enhancing reduced glutathione levels and inducing glutathione peroxidase and Mn-superoxide dismutase (Mn-SOD) in the matrix and Cu,Zn-SOD in the intermembrane space. An additional action concerns the inhibition of cardiolipin peroxidation. This oxidative change in the membrane does not only initiate apoptosis or mitophagy, as usually considered, but also seems to occur at low rate, e.g., in aging, and impairs the structural integrity of Complexes III and IV. Moreover, elevated levels of melatonin inhibit the opening of the mitochondrial permeability transition pore and shorten its duration. Additionally, high-affinity binding sites in mitochondria have been described. The assumption of direct binding to the amphipathic ramp of Complex I would require further substantiation. The mitochondrial presence of the melatonin receptor MT 1 offers the possibility that melatonin acts via an inhibitory G protein, soluble adenylyl cyclase, decreased cAMP and lowered protein kinase A activity, a signaling pathway shown to reduce Complex I activity in the case of a mitochondrial cannabinoid receptor.

Taking an electron-magnon duality shortcut from electron to magnon transport

NASA Astrophysics Data System (ADS)

Mook, Alexander; Göbel, Börge; Henk, Jürgen; Mertig, Ingrid

2018-04-01

The quasiparticles in insulating magnets are the charge-neutral magnons, whose magnetic moments couple to electromagnetic fields. For collinear easy-axis magnets, this coupling can be mapped elegantly onto the scenario of charged particles in electromagnetic fields. From this mapping we obtain equations of motion for magnon wave packets equal to those of electron wave packets in metals. Thus, well-established electronic transport phenomena can be carried over to magnons: this duality shortcut facilitates the discussion of magnon transport. We identify the magnon versions of normal and anomalous Hall, Nernst, Ettingshausen, and Righi-Leduc effects. They are discussed for selected types of easy-axis magnets: ferromagnets, antiferromagnets, and ferrimagnets. Besides a magnon Wiedemann-Franz law and the magnon counterpart of the negative magnetoresistance of electrons in Weyl semimetals, we predict that certain low-symmetry ferrimagnets exhibit a nonlinear version of the anomalous magnon Hall-effect family.

The Electron Transport Chain: An Interactive Simulation

ERIC Educational Resources Information Center

Romero, Chris; Choun, James

2014-01-01

This activity provides students an interactive demonstration of the electron transport chain and chemiosmosis during aerobic respiration. Students use simple, everyday objects as hydrogen ions and electrons and play the roles of the various proteins embedded in the inner mitochondrial membrane to show how this specific process in cellular…

Small substrate transport and mechanism of a molybdate ATP binding cassette transporter in a lipid environment.

PubMed

Rice, Austin J; Harrison, Alistair; Alvarez, Frances J D; Davidson, Amy L; Pinkett, Heather W

2014-05-23

Embedded in the plasma membrane of all bacteria, ATP binding cassette (ABC) importers facilitate the uptake of several vital nutrients and cofactors. The ABC transporter, MolBC-A, imports molybdate by passing substrate from the binding protein MolA to a membrane-spanning translocation pathway of MolB. To understand the mechanism of transport in the biological membrane as a whole, the effects of the lipid bilayer on transport needed to be addressed. Continuous wave-electron paramagnetic resonance and in vivo molybdate uptake studies were used to test the impact of the lipid environment on the mechanism and function of MolBC-A. Working with the bacterium Haemophilus influenzae, we found that MolBC-A functions as a low affinity molybdate transporter in its native environment. In periods of high extracellular molybdate concentration, H. influenzae makes use of parallel molybdate transport systems (MolBC-A and ModBC-A) to take up a greater amount of molybdate than a strain with ModBC-A alone. In addition, the movement of the translocation pathway in response to nucleotide binding and hydrolysis in a lipid environment is conserved when compared with in-detergent analysis. However, electron paramagnetic resonance spectroscopy indicates that a lipid environment restricts the flexibility of the MolBC translocation pathway. By combining continuous wave-electron paramagnetic resonance spectroscopy and substrate uptake studies, we reveal details of molybdate transport and the logistics of uptake systems that employ multiple transporters for the same substrate, offering insight into the mechanisms of nutrient uptake in bacteria. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Transport coefficients in nonequilibrium gas-mixture flows with electronic excitation.

PubMed

Kustova, E V; Puzyreva, L A

2009-10-01

In the present paper, a one-temperature model of transport properties in chemically nonequilibrium neutral gas-mixture flows with electronic excitation is developed. The closed set of governing equations for the macroscopic parameters taking into account electronic degrees of freedom of both molecules and atoms is derived using the generalized Chapman-Enskog method. The transport algorithms for the calculation of the thermal-conductivity, diffusion, and viscosity coefficients are proposed. The developed theoretical model is applied for the calculation of the transport coefficients in the electronically excited N/N(2) mixture. The specific heats and transport coefficients are calculated in the temperature range 50-50,000 K. Two sets of data for the collision integrals are applied for the calculations. An important contribution of the excited electronic states to the heat transfer is shown. The Prandtl number of atomic species is found to be substantially nonconstant.

State-specific transport properties of electronically excited Ar and C

NASA Astrophysics Data System (ADS)

Istomin, V. A.; Kustova, E. V.

2018-05-01

In the present study, a theoretical model of state-resolved transport properties in electronically excited atomic species developed earlier is applied to argon and carbon atomic species. It is shown that for Ar and C, similarly to the case of atomic nitrogen and oxygen, the Slater-like models can be applied to calculate diameters of electronically excited atoms. Using the Slater-like model it is shown that for half-filled N (2 px1py1pz1) and full-filled Ar (3 px2py2pz2) electronic shells the growth of atomic radius goes slowly compared to C (2 px1py1) and O (2 px2py1pz1). The effect of collision diameters on the transport properties of Ar and C is evaluated. The influence of accounted number of electronic levels on the transport coefficients is examined for the case of Boltzmann distributions over electronic energy levels. It is emphasized that in the temperature range 1000-14000 K, for Boltzmann-like distributions over electronic states the number of accounted electronic levels do not influence the transport coefficients. Contrary to this, for higher temperatures T > 14000 K this effect becomes of importance, especially for argon.

Kinetic theory of transport for inhomogeneous electron fluids

NASA Astrophysics Data System (ADS)

Lucas, Andrew; Hartnoll, Sean A.

2018-01-01

The interplay between electronic interactions and disorder is neglected in the conventional Boltzmann theory of transport, yet can play an essential role in determining the resistivity of unconventional metals. When quasiparticles are long lived, one can account for these intertwined effects by solving spatially inhomogeneous Boltzmann equations. Assuming smooth disorder and neglecting umklapp scattering, we solve these inhomogeneous kinetic equations and compute the electrical resistivity across the ballistic-to-hydrodynamic transition. An important consequence of electron-electron interactions is the modification of the momentum-relaxation time; this effect is ignored in the homogeneous theory. We characterize precisely when interactions enhance the momentum scattering rate, and when they decrease it. Our approach unifies existing semiclassical theories of transport, and explains how the resistivity can be proportional to the rate of momentum-conserving collisions without Baber scattering. We compare this result with existing transport mysteries, including the disorder-independent T2 resistivity of many Fermi liquids, and the linear-in-T "Planckian-limited" resistivity of many strange metals.

The Herbaspirillum seropedicae SmR1 Fnr orthologs controls the cytochrome composition of the electron transport chain.

PubMed

Batista, Marcelo B; Sfeir, Michelle Z T; Faoro, Helisson; Wassem, Roseli; Steffens, Maria B R; Pedrosa, Fábio O; Souza, Emanuel M; Dixon, Ray; Monteiro, Rose A

2013-01-01

The transcriptional regulatory protein Fnr, acts as an intracellular redox sensor regulating a wide range of genes in response to changes in oxygen levels. Genome sequencing of Herbaspirillum seropedicae SmR1 revealed the presence of three fnr-like genes. In this study we have constructed single, double and triple fnr deletion mutant strains of H. seropedicae. Transcriptional profiling in combination with expression data from reporter fusions, together with spectroscopic analysis, demonstrates that the Fnr1 and Fnr3 proteins not only regulate expression of the cbb3-type respiratory oxidase, but also control the cytochrome content and other component complexes required for the cytochrome c-based electron transport pathway. Accordingly, in the absence of the three Fnr paralogs, growth is restricted at low oxygen tensions and nitrogenase activity is impaired. Our results suggest that the H. seropedicae Fnr proteins are major players in regulating the composition of the electron transport chain in response to prevailing oxygen concentrations.

The Herbaspirillum seropedicae SmR1 Fnr orthologs controls the cytochrome composition of the electron transport chain

PubMed Central

Batista, Marcelo B.; Sfeir, Michelle Z. T.; Faoro, Helisson; Wassem, Roseli; Steffens, Maria B. R.; Pedrosa, Fábio O.; Souza, Emanuel M.; Dixon, Ray; Monteiro, Rose A.

2013-01-01

The transcriptional regulatory protein Fnr, acts as an intracellular redox sensor regulating a wide range of genes in response to changes in oxygen levels. Genome sequencing of Herbaspirillum seropedicae SmR1 revealed the presence of three fnr-like genes. In this study we have constructed single, double and triple fnr deletion mutant strains of H. seropedicae. Transcriptional profiling in combination with expression data from reporter fusions, together with spectroscopic analysis, demonstrates that the Fnr1 and Fnr3 proteins not only regulate expression of the cbb3-type respiratory oxidase, but also control the cytochrome content and other component complexes required for the cytochrome c-based electron transport pathway. Accordingly, in the absence of the three Fnr paralogs, growth is restricted at low oxygen tensions and nitrogenase activity is impaired. Our results suggest that the H. seropedicae Fnr proteins are major players in regulating the composition of the electron transport chain in response to prevailing oxygen concentrations. PMID:23996052

Requirement for Coenzyme Q in Plasma Membrane Electron Transport

NASA Astrophysics Data System (ADS)

Sun, I. L.; Sun, E. E.; Crane, F. L.; Morre, D. J.; Lindgren, A.; Low, H.

1992-12-01

Coenzyme Q is required in the electron transport system of rat hepatocyte and human erythrocyte plasma membranes. Extraction of coenzyme Q from the membrane decreases NADH dehydrogenase and NADH:oxygen oxidoreductase activity. Addition of coenzyme Q to the extracted membrane restores the activity. Partial restoration of activity is also found with α-tocopherylquinone, but not with vitamin K_1. Analogs of coenzyme Q inhibit NADH dehydrogenase and oxidase activity and the inhibition is reversed by added coenzyme Q. Ferricyanide reduction by transmembrane electron transport from HeLa cells is inhibited by coenzyme Q analogs and restored with added coenzyme Q10. Reduction of external ferricyanide and diferric transferrin by HeLa cells is accompanied by proton release from the cells. Inhibition of the reduction by coenzyme Q analogs also inhibits the proton release, and coenzyme Q10 restores the proton release activity. Trans-plasma membrane electron transport stimulates growth of serum-deficient cells, and added coenzyme Q10 increases growth of HeLa (human adenocarcinoma) and BALB/3T3 (mouse fibroblast) cells. The evidence is consistent with a function for coenzyme Q in a trans-plasma membrane electron transport system which influences cell growth.

Electron and hole transport in the organic small molecule α-NPD

NASA Astrophysics Data System (ADS)

Rohloff, R.; Kotadiya, N. B.; Crǎciun, N. I.; Blom, P. W. M.; Wetzelaer, G. A. H.

2017-02-01

Electron and hole transport properties of the organic small molecule N,N'-Di(1-naphthyl)-N,N'-diphenyl-(1,1'-biphenyl)-4,4'-diamine are investigated by space-charge-limited current measurements. The hole transport shows trap-free behavior with a mobility of 2.3 × 10-8 m2/Vs at vanishing carrier density and electric field. The electron transport, on the other hand, shows heavily trap-limited behavior, which leads to highly unbalanced transport. A trap concentration of 1.3 × 1024 m-3 was found by modeling the electron currents, similar to the universal trap concentration found in conjugated polymers. This indicates that electron trapping is a generic property of organic semiconductors, ranging from vacuum-deposited small-molecules to solution-processed conjugated polymers.

Kinetic Theory of Electronic Transport in Random Magnetic Fields

NASA Astrophysics Data System (ADS)

Lucas, Andrew

2018-03-01

We present the theory of quasiparticle transport in perturbatively small inhomogeneous magnetic fields across the ballistic-to-hydrodynamic crossover. In the hydrodynamic limit, the resistivity ρ generically grows proportionally to the rate of momentum-conserving electron-electron collisions at large enough temperatures T . In particular, the resulting flow of electrons provides a simple scenario where viscous effects suppress conductance below the ballistic value. This new mechanism for ρ ∝T2 resistivity in a Fermi liquid may describe low T transport in single-band SrTiO3 .

Kinetic Theory of Electronic Transport in Random Magnetic Fields.

PubMed

Lucas, Andrew

2018-03-16

We present the theory of quasiparticle transport in perturbatively small inhomogeneous magnetic fields across the ballistic-to-hydrodynamic crossover. In the hydrodynamic limit, the resistivity ρ generically grows proportionally to the rate of momentum-conserving electron-electron collisions at large enough temperatures T. In particular, the resulting flow of electrons provides a simple scenario where viscous effects suppress conductance below the ballistic value. This new mechanism for ρ∝T^{2} resistivity in a Fermi liquid may describe low T transport in single-band SrTiO_{3}.

Electron transport model of dielectric charging

NASA Technical Reports Server (NTRS)

Beers, B. L.; Hwang, H. C.; Lin, D. L.; Pine, V. W.

1979-01-01

A computer code (SCCPOEM) was assembled to describe the charging of dielectrics due to irradiation by electrons. The primary purpose for developing the code was to make available a convenient tool for studying the internal fields and charge densities in electron-irradiated dielectrics. The code, which is based on the primary electron transport code POEM, is applicable to arbitrary dielectrics, source spectra, and current time histories. The code calculations are illustrated by a series of semianalytical solutions. Calculations to date suggest that the front face electric field is insufficient to cause breakdown, but that bulk breakdown fields can easily be exceeded.

Response Matrix Monte Carlo for electron transport

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ballinger, C.T.; Nielsen, D.E. Jr.; Rathkopf, J.A.

1990-11-01

A Response Matrix Monte Carol (RMMC) method has been developed for solving electron transport problems. This method was born of the need to have a reliable, computationally efficient transport method for low energy electrons (below a few hundred keV) in all materials. Today, condensed history methods are used which reduce the computation time by modeling the combined effect of many collisions but fail at low energy because of the assumptions required to characterize the electron scattering. Analog Monte Carlo simulations are prohibitively expensive since electrons undergo coulombic scattering with little state change after a collision. The RMMC method attempts tomore » combine the accuracy of an analog Monte Carlo simulation with the speed of the condensed history methods. The combined effect of many collisions is modeled, like condensed history, except it is precalculated via an analog Monte Carol simulation. This avoids the scattering kernel assumptions associated with condensed history methods. Results show good agreement between the RMMC method and analog Monte Carlo. 11 refs., 7 figs., 1 tabs.« less

Hybrid transport and diffusion modeling using electron thermal transport Monte Carlo SNB in DRACO

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Moses, Gregory

2017-10-01

The iSNB (implicit Schurtz Nicolai Busquet) multigroup diffusion electron thermal transport method is adapted into an Electron Thermal Transport Monte Carlo (ETTMC) transport method to better model angular and long mean free path non-local effects. Previously, the ETTMC model had been implemented in the 2D DRACO multiphysics code and found to produce consistent results with the iSNB method. Current work is focused on a hybridization of the computationally slower but higher fidelity ETTMC transport method with the computationally faster iSNB diffusion method in order to maximize computational efficiency. Furthermore, effects on the energy distribution of the heat flux divergence are studied. Work to date on the hybrid method will be presented. This work was supported by Sandia National Laboratories and the Univ. of Rochester Laboratory for Laser Energetics.

Sediment Connectivity and Transport Pathways in Tidal Inlets: a Conceptual Framework with Application to Ameland Inlet

NASA Astrophysics Data System (ADS)

Pearson, S.; van Prooijen, B. C.; Zheng Bing, W.; Bak, J.

2017-12-01

Predicting the response of tidal inlets and adjacent coastlines to sea level rise and anthropogenic interventions (e.g. sand nourishments) requires understanding of sediment transport pathways. These pathways are strongly dependent on hydrodynamic forcing, grain size, underlying morphology, and the timescale considered. To map and describe these pathways, we considered the concept of sediment connectivity, which quantifies the degree to which sediment transport pathways link sources to receptors. In this study we established a framework for understanding sediment transport pathways in coastal environments, using Ameland Inlet in the Dutch Wadden Sea as a basis. We used the Delft3D morphodynamic model to assess the fate of sediment as it moved between specific morphological units defined in the model domain. Simulation data was synthesized in a graphical network and then graph theory used to analyze connectivity at different space and time scales. At decadal time scales, fine and very fine sand (<250μm) have greater connectivity with receptor areas further away from their sources. Conversely, medium sand (>250μm) shows lower connectivity, even in more energetic areas. Greater sediment connectivity was found under the influence of wind and waves when compared to purely tidal forcing. Connectivity shows considerable spatial variation in cross shore and alongshore directions, depending on proximity to the inlet and dominant wave direction. Furthermore, connectivity generally increases at longer timescales. Asymmetries in connectivity (i.e. unidirectional transport) can be used to explain long-term erosional or depositional trends. As such, an understanding of sediment connectivity as a function of grain size could yield useful insights for resolving sediment transport pathways and the fate of a nourishment in coastal environments.

Electronic transport properties of some liquid semiconductor

NASA Astrophysics Data System (ADS)

Sonvane, Y. A.; Thakor, P. B.; Jani, A. R.

2012-06-01

Electronic transport properties like electrical resistivity (ρ) and thermoelectric power (Q) of liquid semiconductor (Si, Ga, Ge, In, Sn, Tl and Bi) are calculated in the present study. Our well established single parametric model potential alongwith Percus Yevick hard sphere (PYHS) reference system are used to describe the structural information. To see the influence of exchange and correlation effect, Hartree, Taylor and Sarkar et al local field correlation functions are used. From present results, it is seen that good agreements between present results and experimental data have been achieved. Lastly we conclude that our model potential successfully produces the data of electronic transport properties for some liquid semiconductor (Si, Ga, Ge, In, Sn, Tl and Bi).

Modified Monte Carlo method for study of electron transport in degenerate electron gas in the presence of electron-electron interactions, application to graphene

NASA Astrophysics Data System (ADS)

Borowik, Piotr; Thobel, Jean-Luc; Adamowicz, Leszek

2017-07-01

Standard computational methods used to take account of the Pauli Exclusion Principle into Monte Carlo (MC) simulations of electron transport in semiconductors may give unphysical results in low field regime, where obtained electron distribution function takes values exceeding unity. Modified algorithms were already proposed and allow to correctly account for electron scattering on phonons or impurities. Present paper extends this approach and proposes improved simulation scheme allowing including Pauli exclusion principle for electron-electron (e-e) scattering into MC simulations. Simulations with significantly reduced computational cost recreate correct values of the electron distribution function. Proposed algorithm is applied to study transport properties of degenerate electrons in graphene with e-e interactions. This required adapting the treatment of e-e scattering in the case of linear band dispersion relation. Hence, this part of the simulation algorithm is described in details.

Intraflagellar transport protein 122 antagonizes Sonic Hedgehog signaling and controls ciliary localization of pathway components.

PubMed

Qin, Jian; Lin, Yulian; Norman, Ryan X; Ko, Hyuk W; Eggenschwiler, Jonathan T

2011-01-25

Primary cilia are required for proper Sonic Hedgehog (Shh) signaling in mammals. However, their role in the signal transduction process remains unclear. We have identified sister of open brain (sopb), a null allele of mouse Intraflagellar transport protein 122 (Ift122). IFT122 negatively regulates the Shh pathway in the cilium at a step downstream of the Shh ligand and the transmembrane protein Smoothened, but upstream of the Gli2 transcription factor. Ift122(sopb) mutants generate primary cilia, but they show features of defective retrograde intraflagellar transport. IFT122 controls the ciliary localization of Shh pathway regulators in different ways. Disruption of IFT122 leads to accumulation of Gli2 and Gli3 at cilia tips while blocking the ciliary localization of the antagonist TULP3. Suppressor of Fused and Smoothened localize to the cilium through an IFT122-independent mechanism. We propose that the balance between positive and negative regulators of the Shh pathway at the cilium tip controls the output of the pathway and that Shh signaling regulates this balance through intraflagellar transport.

Study on the Electronic Transport Properties of Zigzag GaN Nanotubes

NASA Astrophysics Data System (ADS)

Li, Enling; Wang, Xiqiang; Hou, Liping; Zhao, Danna; Dai, Yuanbin; Wang, Xuewen

2011-02-01

The electronic transport properties of zigzag GaN nanotubes (n, 0) (4 <= n <= 9) have been calculated using the density functional theory and non-equilibrium Green's functions method. Firstly, the density functional theory (DFT) is used to optimize and calculate the electronic structure of GaNNTs (n, 0) (4<=n<=9). Secondly, DFT and non-equilibrium Green function (NEGF) method are also used to predict the electronic transport properties of GaNNTs two-probe system. The results showed: there is a corresponding relation between the electronic transport properties and the valley of state density of each GaNNT. In addition, the volt-ampere curve of GaNNT is approximately linear.

Electron transport limitation in P3HT:CdSe nanorods hybrid solar cells.

PubMed

Lek, Jun Yan; Xing, Guichuan; Sum, Tze Chien; Lam, Yeng Ming

2014-01-22

Hybrid solar cells have the potential to be efficient solar-energy-harvesting devices that can combine the benefits of solution-processable organic materials and the extended absorption offered by inorganic materials. In this work, an understanding of the factors limiting the performance of hybrid solar cells is explored. Through photovoltaic-device characterization correlated with transient absorption spectroscopy measurements, it was found that the interfacial charge transfer between the organic (P3HT) and inorganic (CdSe nanorods) components is not the factor limiting the performance of these solar cells. The insulating original ligands retard the charge recombination between the charge-transfer states across the CdSe-P3HT interface, and this is actually beneficial for charge collection. These cells are, in fact, limited by the subsequent electron collection via CdSe nanoparticles to the electrodes. Hence, the design of a more continuous electron-transport pathway should greatly improve the performance of hybrid solar cells in the future.

Non-renewal statistics for electron transport in a molecular junction with electron-vibration interaction

NASA Astrophysics Data System (ADS)

Kosov, Daniel S.

2017-09-01

Quantum transport of electrons through a molecule is a series of individual electron tunneling events separated by stochastic waiting time intervals. We study the emergence of temporal correlations between successive waiting times for the electron transport in a vibrating molecular junction. Using the master equation approach, we compute the joint probability distribution for waiting times of two successive tunneling events. We show that the probability distribution is completely reset after each tunneling event if molecular vibrations are thermally equilibrated. If we treat vibrational dynamics exactly without imposing the equilibration constraint, the statistics of electron tunneling events become non-renewal. Non-renewal statistics between two waiting times τ1 and τ2 means that the density matrix of the molecule is not fully renewed after time τ1 and the probability of observing waiting time τ2 for the second electron transfer depends on the previous electron waiting time τ1. The strong electron-vibration coupling is required for the emergence of the non-renewal statistics. We show that in the Franck-Condon blockade regime, extremely rare tunneling events become positively correlated.

Localization of a GABA transporter to glial cells in the developing and adult olfactory pathway of the moth Manduca sexta1

PubMed Central

Oland, Lynne A; Gibson, Nicholas J; Tolbert, Leslie P

2010-01-01

Glial cells have several critical roles in the developing and adult olfactory (antennal) lobe of the moth Manduca sexta. Early in development, glial cells occupy discrete regions of the developing olfactory pathway and processes of GABAergic neurons extend into some of these regions. Because GABA is known to have developmental effects in a variety of systems, we explored the possibility that the glial cells express a GABA transporter that could regulate GABA levels to which olfactory neurons and glial cells are exposed. Using an antibody raised against a characterized high-affinity M. sexta GABA transporter with high sequence homology to known mammalian GABA transporters (Mbungu et al., 1995; Umesh and Gill, 2002), we found that the GABA transporter is localized to subsets of centrally derived glial cells during metamorphic adult development. The transporter persists into adulthood in a subset of the neuropil-associated glial cells, but its distribution pattern as determined by light- and electron-microscopic-level immunocytochemistry indicates that it could not serve to regulate GABA concentration in the synaptic cleft. Rather its role is more likely to regulate extracellular GABA levels within the glomerular neuropil. Expression in the sorting zone glial cells disappears after the period of olfactory receptor axon ingrowth, but may be important during ingrowth if GABA regulates axon growth. Glial cells take up GABA, and that uptake can be blocked by DABA. This is the first molecular evidence that the central glial cell population in this pathway is heterogeneous. PMID:20058309

Electron temperature critical gradient and transport stiffness in DIII-D

DOE PAGES

Smith, Sterling P.; Petty, Clinton C.; White, Anne E.; ...

2015-07-06

The electron energy flux has been probed as a function of electron temperature gradient on the DIII-D tokamak, in a continuing effort to validate turbulent transport models. In the scan of gradient, a critical electron temperature gradient has been found in the electron heat fluxes and stiffness at various radii in L-mode plasmas. The TGLF reduced turbulent transport model [G.M. Staebler et al, Phys. Plasmas 14, 055909 (2007)] and full gyrokinetic GYRO model [J. Candy and R.E. Waltz, J. Comput. Phys. 186, 545 (2003)] recover the general trend of increasing electron energy flux with increasing electron temperature gradient scale length,more » but they do not predict the absolute level of transport at all radii and gradients. Comparing the experimental observations of incremental (heat pulse) diffusivity and stiffness to the models’ reveals that TGLF reproduces the trends in increasing diffusivity and stiffness with increasing electron temperature gradient scale length with a critical gradient behavior. Furthermore, the critical gradient of TGLF is found to have a dependence on q 95, contrary to the independence of the experimental critical gradient from q 95.« less

Molecular electronics: insight from first-principles transport simulations.

PubMed

Paulsson, Magnus; Frederiksen, Thomas; Brandbyge, Mads

2010-01-01

Conduction properties of nanoscale contacts can be studied using first-principles simulations. Such calculations give insight into details behind the conductance that is not readily available in experiments. For example, we may learn how the bonding conditions of a molecule to the electrodes affect the electronic transport. Here we describe key computational ingredients and discuss these in relation to simulations for scanning tunneling microscopy (STM) experiments with C60 molecules where the experimental geometry is well characterized. We then show how molecular dynamics simulations may be combined with transport calculations to study more irregular situations, such as the evolution of a nanoscale contact with the mechanically controllable break-junction technique. Finally we discuss calculations of inelastic electron tunnelling spectroscopy as a characterization technique that reveals information about the atomic arrangement and transport channels.

Electron capture and transport mediated by lattice solitons

NASA Astrophysics Data System (ADS)

Hennig, D.; Chetverikov, A.; Velarde, M. G.; Ebeling, W.

2007-10-01

We study electron transport in a one-dimensional molecular lattice chain. The molecules are linked by Morse interaction potentials. The electronic degree of freedom, expressed in terms of a tight binding system, is coupled to the longitudinal displacements of the molecules from their equilibrium positions along the axis of the lattice. More specifically, the distance between two sites influences in an exponential fashion the corresponding electronic transfer matrix element. We demonstrate that when an electron is injected in the undistorted lattice it causes a local deformation such that a compression results leading to a lowering of the electron’s energy below the lower edge of the band of linear states. This corresponds to self-localization of the electron due to a polaronlike effect. Then, if a traveling soliton lattice deformation is launched a distance apart from the electron’s position, upon encountering the polaronlike state it captures the latter dragging it afterwards along its path. Strikingly, even when the electron is initially uniformly distributed over the lattice sites a traveling soliton lattice deformation gathers the electronic amplitudes during its traversing of the lattice. Eventually, the electron state is strongly localized and moves coherently in unison with the soliton lattice deformation. This shows that for the achievement of coherent electron transport we need not start with the polaronic effect.

Transport of secondary electrons and reactive species in ion tracks

NASA Astrophysics Data System (ADS)

Surdutovich, Eugene; Solov'yov, Andrey V.

2015-08-01

The transport of reactive species brought about by ions traversing tissue-like medium is analysed analytically. Secondary electrons ejected by ions are capable of ionizing other molecules; the transport of these generations of electrons is studied using the random walk approximation until these electrons remain ballistic. Then, the distribution of solvated electrons produced as a result of interaction of low-energy electrons with water molecules is obtained. The radial distribution of energy loss by ions and secondary electrons to the medium yields the initial radial dose distribution, which can be used as initial conditions for the predicted shock waves. The formation, diffusion, and chemical evolution of hydroxyl radicals in liquid water are studied as well. COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy.

Does menaquinone participate in brain astrocyte electron transport?

PubMed

Lovern, Douglas; Marbois, Beth

2013-10-01

Quinone compounds act as membrane resident carriers of electrons between components of the electron transport chain in the periplasmic space of prokaryotes and in the mitochondria of eukaryotes. Vitamin K is a quinone compound in the human body in a storage form as menaquinone (MK); distribution includes regulated amounts in mitochondrial membranes. The human brain, which has low amounts of typical vitamin K dependent function (e.g., gamma carboxylase) has relatively high levels of MK, and different regions of brain have different amounts. Coenzyme Q (Q), is a quinone synthesized de novo, and the levels of synthesis decline with age. The levels of MK are dependent on dietary intake and generally increase with age. MK has a characterized role in the transfer of electrons to fumarate in prokaryotes. A newly recognized fumarate cycle has been identified in brain astrocytes. The MK precursor menadione has been shown to donate electrons directly to mitochondrial complex III. Vitamin K compounds function in the electron transport chain of human brain astrocytes. Copyright © 2013 Elsevier Ltd. All rights reserved.

Diffusive vs. impulsive energetic electron transport during radiation belt storms

NASA Astrophysics Data System (ADS)

Vassiliadis, D.; Koepke, M.; Tornquist, M.

2008-12-01

Earth's electron radiation belts are continually replenished by inward particle transport (as well as other, local acceleration processes) taking place during radiation belt storms. For some storms the radial transport is primarily diffusive while for others it is impulsive, or characterized by injections. To distinguish between these types of inward transport, we first use a dynamic model of the phase-space density as measured by POLAR/HIST and expressed in terms of adiabatic invariants [Green and Kivelson, 2004]. In a review of storms from 1997 to 2004 the coefficients of the model are peaked at characteristic temporal and phase- space (mu, k, L*) scales during specific storms. The transport is quantified in terms of those invariants which are violated and identified with peaks of the electron distribution in invariant space. Second, we run guiding- center simulations in wave fields fitted to in situ measurements complemented at low and high L by ground ULF pulsations. The modes of response identified in earlier studies from SAMPEX and POLAR electron flux measurements are now associated with primarily diffusive transport in the central range of the outer belt, L=4-8, and primarily impulsive transport near the plasmapause boundary, L=3-4.

CAVER 3.0: A Tool for the Analysis of Transport Pathways in Dynamic Protein Structures

PubMed Central

Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

2012-01-01

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz. PMID:23093919

CAVER 3.0: a tool for the analysis of transport pathways in dynamic protein structures.

PubMed

Chovancova, Eva; Pavelka, Antonin; Benes, Petr; Strnad, Ondrej; Brezovsky, Jan; Kozlikova, Barbora; Gora, Artur; Sustr, Vilem; Klvana, Martin; Medek, Petr; Biedermannova, Lada; Sochor, Jiri; Damborsky, Jiri

2012-01-01

Tunnels and channels facilitate the transport of small molecules, ions and water solvent in a large variety of proteins. Characteristics of individual transport pathways, including their geometry, physico-chemical properties and dynamics are instrumental for understanding of structure-function relationships of these proteins, for the design of new inhibitors and construction of improved biocatalysts. CAVER is a software tool widely used for the identification and characterization of transport pathways in static macromolecular structures. Herein we present a new version of CAVER enabling automatic analysis of tunnels and channels in large ensembles of protein conformations. CAVER 3.0 implements new algorithms for the calculation and clustering of pathways. A trajectory from a molecular dynamics simulation serves as the typical input, while detailed characteristics and summary statistics of the time evolution of individual pathways are provided in the outputs. To illustrate the capabilities of CAVER 3.0, the tool was applied for the analysis of molecular dynamics simulation of the microbial enzyme haloalkane dehalogenase DhaA. CAVER 3.0 safely identified and reliably estimated the importance of all previously published DhaA tunnels, including the tunnels closed in DhaA crystal structures. Obtained results clearly demonstrate that analysis of molecular dynamics simulation is essential for the estimation of pathway characteristics and elucidation of the structural basis of the tunnel gating. CAVER 3.0 paves the way for the study of important biochemical phenomena in the area of molecular transport, molecular recognition and enzymatic catalysis. The software is freely available as a multiplatform command-line application at http://www.caver.cz.

Distribution of tunnelling times for quantum electron transport.

PubMed

Rudge, Samuel L; Kosov, Daniel S

2016-03-28

In electron transport, the tunnelling time is the time taken for an electron to tunnel out of a system after it has tunnelled in. We define the tunnelling time distribution for quantum processes in a dissipative environment and develop a practical approach for calculating it, where the environment is described by the general Markovian master equation. We illustrate the theory by using the rate equation to compute the tunnelling time distribution for electron transport through a molecular junction. The tunnelling time distribution is exponential, which indicates that Markovian quantum tunnelling is a Poissonian statistical process. The tunnelling time distribution is used not only to study the quantum statistics of tunnelling along the average electric current but also to analyse extreme quantum events where an electron jumps against the applied voltage bias. The average tunnelling time shows distinctly different temperature dependence for p- and n-type molecular junctions and therefore provides a sensitive tool to probe the alignment of molecular orbitals relative to the electrode Fermi energy.

Transport and transportation pathways of hazardous chemicals from solid waste disposal.

PubMed Central

Van Hook, R I

1978-01-01

To evaluate the impact of hazardous chemicals in solid wastes on man and other organisms, it is necessary to have information about amounts of chemical present, extent of exposure, and chemical toxicity. This paper addresses the question of organism exposure by considering the major physical and biological transport pathways and the physicochemical and biochemical transformations that may occur in sediments, soils, and water. Disposal of solid wastes in both terrestrial and oceanic environments is considered. Atmospheric transport is considered for emissions from incineration of solid wastes and for wind resuspension of particulates from surface waste deposits. Solid wastes deposited in terrestrial environments are subject to leaching by surface and ground waters. Leachates may then be transported to other surface waters and drinking water aquifers through hydrologic transport. Leachates also interact with natural organic matter, clays, and microorganisms in soils and sediments. These interactions may render chemical constituents in leachates more or less mobile, possibly change chemical and physical forms, and alter their biological activity. Oceanic waste disposal practices result in migration through diffusion and ocean currents. Surface area-to-volume ratios play a major role in the initial distributions of chemicals in the aquatic environment. Sediments serve as major sources and sinks of chemical contaminants. Food chain transport in both aquatic and terrestrial environments results in the movement of hazardous chemicals from lower to higher positions in the food web. Bioconcentration is observed in both terrestrial and aquatic food chains with certain elements and synthetic organics. Bioconcentration factors tend to be higher for synthetic organics, and higher in aquatic than in terrestrial systems. Biodilution is not atypical in terrestrial environments. Synergistic and antagonistic actions are common occurrences among chemical contaminants and can be

Low energy electron transport in furfural

NASA Astrophysics Data System (ADS)

Lozano, Ana I.; Krupa, Kateryna; Ferreira da Silva, Filipe; Limão-Vieira, Paulo; Blanco, Francisco; Muñoz, Antonio; Jones, Darryl B.; Brunger, Michael J.; García, Gustavo

2017-09-01

We report on an initial investigation into the transport of electrons through a gas cell containing 1 mTorr of gaseous furfural. Results from our Monte Carlo simulation are implicitly checked against those from a corresponding electron transmission measurement. To enable this simulation a self-consistent cross section data base was constructed. This data base is benchmarked through new total cross section measurements which are also described here. In addition, again to facilitate the simulation, our preferred energy loss distribution function is presented and discussed.

Rewiring the reductive tricarboxylic acid pathway and L-malate transport pathway of Aspergillus oryzae for overproduction of L-malate.

PubMed

Liu, Jingjing; Xie, Zhipeng; Shin, Hyun-Dong; Li, Jianghua; Du, Guocheng; Chen, Jian; Liu, Long

2017-07-10

Aspergillus oryzae finds wide application in the food, feed, and wine industries, and is an excellent cell factory platform for production of organic acids. In this work, we achieved the overproduction of L-malate by rewiring the reductive tricarboxylic acid (rTCA) pathway and L-malate transport pathway of A. oryzae NRRL 3488. First, overexpression of native pyruvate carboxylase and malate dehydrogenase in the rTCA pathway improved the L-malate titer from 26.1gL -1 to 42.3gL -1 in shake flask culture. Then, the oxaloacetate anaplerotic reaction was constructed by heterologous expression of phosphoenolpyruvate carboxykinase and phosphoenolpyruvate carboxylase from Escherichia coli, increasing the L-malate titer to 58.5gL -1 . Next, the export of L-malate from the cytoplasm to the external medium was strengthened by overexpression of a C4-dicarboxylate transporter gene from A. oryzae and an L-malate permease gene from Schizosaccharomyces pombe, improving the L-malate titer from 58.5gL -1 to 89.5gL -1 . Lastly, guided by transcription analysis of the expression profile of key genes related to L-malate synthesis, the 6-phosphofructokinase encoded by the pfk gene was identified as a potential limiting step for L-malate synthesis. Overexpression of pfk with the strong sodM promoter increased the L-malate titer to 93.2gL -1 . The final engineered A. oryzae strain produced 165gL -1 L-malate with a productivity of 1.38gL -1 h -1 in 3-L fed-batch culture. Overall, we constructed an efficient L-malate producer by rewiring the rTCA pathway and L-malate transport pathway of A. oryzae NRRL 3488, and the engineering strategy adopted here may be useful for the construction of A. oryzae cell factories to produce other organic acids. Copyright © 2017 Elsevier B.V. All rights reserved.

Vibronic coupling effect on the electron transport through molecules

NASA Astrophysics Data System (ADS)

Tsukada, Masaru; Mitsutake, Kunihiro

2007-03-01

Electron transport through molecular bridges or molecular layers connected to nano-electrodes is determined by the combination of coherent and dissipative processes, controlled by the electron-vibron coupling, transfer integrals between the molecular orbitals, applied electric field and temperature. We propose a novel theoretical approach, which combines ab initio molecular orbital method with analytical many-boson model. As a case study, the long chain model of the thiophene oligomer is solved by a variation approach. Mixed states of moderately extended molecular orbital states mediated and localised by dress of vibron cloud are found as eigen-states. All the excited states accompanied by multiple quanta of vibration can be solved, and the overall carrier transport properties including the conductance, mobility, dissipation spectra are analyzed by solving the master equation with the transition rates estimated by the golden rule. We clarify obtained in a uniform systematic way, how the transport mode changes from a dominantly coherent transport to the dissipative hopping transport.

Simulation of electron beam formation and transport in a gas-filled electron-optical system with a plasma emitter

DOE Office of Scientific and Technical Information (OSTI.GOV)

Grishkov, A. A.; Kornilov, S. Yu., E-mail: kornilovsy@gmail.com; Rempe, N. G.

2016-07-15

The results of computer simulations of the electron-optical system of an electron gun with a plasma emitter are presented. The simulations are performed using the KOBRA3-INP, XOOPIC, and ANSYS codes. The results describe the electron beam formation and transport. The electron trajectories are analyzed. The mechanisms of gas influence on the energy inhomogeneity of the beam and its current in the regions of beam primary formation, acceleration, and transport are described. Recommendations for optimizing the electron-optical system with a plasma emitter are presented.

Electron transport property of tetrathiafulvalene molecule

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mondal, Rajkumar; Bhattacharya, Barnali; Deb, Jyotirmoy

2016-05-23

We have investigated electron transport behavior of tetrathiafulvalene molecule connected with zigzag graphene nanoribbon (zGNR) using density functional theory combined with non-equilibrium Green’s function method. We have reported the transmission coefficient of the scattering region at different bias voltage to explain the nature of the current.

Theoretical modeling of electronic transport in molecular devices

NASA Astrophysics Data System (ADS)

Piccinin, Simone

In this thesis a novel approach for simulating electronic transport in nanoscale structures is introduced. We consider an open quantum system (the electrons of structure) accelerated by an external electromotive force and dissipating energy through inelastic scattering with a heat bath (phonons) acting on the electrons. This method can be regarded as a quantum-mechanical extension of the semi-classical Boltzmann transport equation. We use periodic boundary conditions and employ Density Functional Theory to recast the many-particle problem in an effective single-particle mean-field problem. By explicitly treating the dissipation in the electrodes, the behavior of the potential is an outcome of our method, at variance with the scattering approaches based on the Landauer formalism. We study the self-consistent steady-state solution, analyzing the out-of-equilibrium electron distribution, the electrical characteristics, the behavior of the self-consistent potential and the density of states of the system. We apply the method to the study of electronic transport in several molecular devices, consisting of small organic molecules or atomic wires sandwiched between gold surfaces. For gold wires we recover the experimental evidence that transport in short wires is ballistic, independent of the length of the wire and with conductance of one quantum. In benzene-1,4-dithiol we find that the delocalization of the frontier orbitals of the molecule is responsible for the high value of conductance and that, by inserting methylene groups to decouple the sulfur atoms from the carbon ring, the current is reduced, in agreement with the experimental measurements. We study the effect a geometrical distortion in a molecular device, namely the relative rotation of the carbon rings in a biphenyl-4,4'-dithiol molecule. We find that the reduced coupling between pi orbitals of the rings induced by the rotation leads to a reduction of the conductance and that this behavior is captured by a

Electron Transport Modeling of Molecular Nanoscale Bridges Used in Energy Conversion Schemes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunietz, Barry D

2016-08-09

The goal of the research program is to reliably describe electron transport and transfer processes at the molecular level. Such insight is essential for improving molecular applications of solar and thermal energy conversion. We develop electronic structure models to study (1) photoinduced electron transfer and transport processes in organic semiconducting materials, and (2) charge and heat transport through molecular bridges. We seek fundamental understanding of key processes, which lead to design new experiments and ultimately to achieve systems with improved properties.

Copper-transporting P-type ATPases use a unique ion-release pathway

PubMed Central

Andersson, Magnus; Mattle, Daniel; Sitsel, Oleg; Nielsen, Anna Marie; White, Stephen H.; Nissen, Poul; Gourdon, Pontus

2014-01-01

Heavy metals in cells are typically regulated by PIB-type ATPases such as the copper transporting Cu+-ATPases. The first crystal structure of a Cu+-ATPase (LpCopA) was trapped in a transition state of dephosphorylation (E2.Pi) and inferred to be occluded. The structure revealed a PIB-specific topology and suggested a copper transport pathway across the membrane. Here we show by molecular dynamics (MD) simulations that extracellular water solvates the transmembrane (TM) domain, indicative of a pathway for Cu+ release. Furthermore, a new LpCopA crystal structure determined at 2.8 Å resolution, trapped in the E2P state (which is associated with extracellular exchange in PII-type ATPases), delineates the same conduit as also further supported by site-directed mutagenesis. The E2P and E2.Pi states therefore appear equivalent and open to the extracellular side, in contrast to PII-type ATPases where the E2.Pi state is occluded. This indicates that Cu+-ATPases couple dephosphorylation differently to the conformational changes associated with ion extrusion. The ion pathway may explain why Menkes’ and Wilson’s disease mutations at the extracellular side impair protein function, and points to an accessible site for novel inhibitors targeting Cu+-ATPases of pathogens. PMID:24317491

Accessible triple-phase boundary length: A performance metric to account for transport pathways in heterogeneous electrochemical materials

NASA Astrophysics Data System (ADS)

Nakajo, A.; Cocco, A. P.; DeGostin, M. B.; Peracchio, A. A.; Cassenti, B. N.; Cantoni, M.; Van herle, J.; Chiu, W. K. S.

2016-09-01

The performance of materials for electrochemical energy conversion and storage depends upon the number of electrocatalytic sites available for reaction and their accessibility by the transport of reactants and products. For solid oxide fuel/electrolysis cell materials, standard 3-D measurements such as connected triple-phase boundary (TPB) length and effective transport properties partially inform on how local geometry and network topology causes variability in TPB accessibility. A new measurement, the accessible TPB, is proposed to quantify these effects in detail and characterize material performance. The approach probes the reticulated pathways to each TPB using an analytical electrochemical fin model applied to a 3-D discrete representation of the heterogeneous structure provided by skeleton-based partitioning. The method is tested on artificial and real structures imaged by 3-D x-ray and electron microscopy. The accessible TPB is not uniform and the pattern varies depending upon the structure. Connected TPBs can be even passivated. The sensitivity to manipulations of the local 3-D geometry and topology that standard measurements cannot capture is demonstrated. The clear presence of preferential pathways showcases a non-uniform utilization of the 3-D structure that potentially affects the performance and the resilience to alterations due to degradation phenomena. The concepts presented also apply to electrochemical energy storage and conversion devices such as other types of fuel cells, electrolyzers, batteries and capacitors.

Balance-Equation Approach to Nonuniform Electron Transport in Nonparabolic Semiconductors

NASA Astrophysics Data System (ADS)

Cao, Juncheng; Lei, Xiaolin

1998-10-01

On the basis of the Lei-Ting balance-equation transport theory recently developed for nonparabolic energy band, we propose a hydrodynamic approach to the spatially inhomogeneous electron transport in semiconductor devices. In the present approach, the momentum and energy collision terms are expressed by two nonlinear functions, the frictional acceleration and energy-loss rate, which give a detailed scattering-process-level description of nonstationary and nonlocal charge transport in the system. This approach allows one to calculate selfconsistently the transport parameters within the model itself based on the primary material data (band structure, deformation potential constant, etc.), thus it minimizes the uncertainty associated with the use of some empirical relations for transport coefficients. As a demonstration of the approach, we have carried out a numerical calculation for a submicrometer Si n^+nn^+ diode by assuming an isotropic Kane-type energy band. The results for electron velocity and energy, obtained at much less computing cost than the Monte-Carlo (MC) method, are in good agreement with MC prediction. The influence of heat-flow term on electron transport behaviour, especially on velocity overshoot, is also investigated. The project supported by National Natural Science Foundation of China, National and Shanghai Municipal Commission of Science and Technology, and the Shanghai Foundation for Research and Development of Applied Materials

Steepest entropy ascent quantum thermodynamic model of electron and phonon transport

NASA Astrophysics Data System (ADS)

Li, Guanchen; von Spakovsky, Michael R.; Hin, Celine

2018-01-01

An advanced nonequilibrium thermodynamic model for electron and phonon transport is formulated based on the steepest-entropy-ascent quantum thermodynamics framework. This framework, based on the principle of steepest entropy ascent (or the equivalent maximum entropy production principle), inherently satisfies the laws of thermodynamics and mechanics and is applicable at all temporal and spatial scales even in the far-from-equilibrium realm. Specifically, the model is proven to recover the Boltzmann transport equations in the near-equilibrium limit and the two-temperature model of electron-phonon coupling when no dispersion is assumed. The heat and mass transport at a temperature discontinuity across a homogeneous interface where the dispersion and coupling of electron and phonon transport are both considered are then modeled. Local nonequilibrium system evolution and nonquasiequilibrium interactions are predicted and the results discussed.

Identifying the molecular functions of electron transport proteins using radial basis function networks and biochemical properties.

PubMed

Le, Nguyen-Quoc-Khanh; Nguyen, Trinh-Trung-Duong; Ou, Yu-Yen

2017-05-01

The electron transport proteins have an important role in storing and transferring electrons in cellular respiration, which is the most proficient process through which cells gather energy from consumed food. According to the molecular functions, the electron transport chain components could be formed with five complexes with several different electron carriers and functions. Therefore, identifying the molecular functions in the electron transport chain is vital for helping biologists understand the electron transport chain process and energy production in cells. This work includes two phases for discriminating electron transport proteins from transport proteins and classifying categories of five complexes in electron transport proteins. In the first phase, the performances from PSSM with AAIndex feature set were successful in identifying electron transport proteins in transport proteins with achieved sensitivity of 73.2%, specificity of 94.1%, and accuracy of 91.3%, with MCC of 0.64 for independent data set. With the second phase, our method can approach a precise model for identifying of five complexes with different molecular functions in electron transport proteins. The PSSM with AAIndex properties in five complexes achieved MCC of 0.51, 0.47, 0.42, 0.74, and 1.00 for independent data set, respectively. We suggest that our study could be a power model for determining new proteins that belongs into which molecular function of electron transport proteins. Copyright © 2017 Elsevier Inc. All rights reserved.

Electron transport parameters in NF3

NASA Astrophysics Data System (ADS)

Lisovskiy, V.; Yegorenkov, V.; Ogloblina, P.; Booth, J.-P.; Martins, S.; Landry, K.; Douai, D.; Cassagne, V.

2014-03-01

We present electron transport parameters (the first Townsend coefficient, the dissociative attachment coefficient, the fraction of electron energy lost by collisions with NF3 molecules, the average and characteristic electron energy, the electron mobility and the drift velocity) in NF3 gas calculated from published elastic and inelastic electron-NF3 collision cross-sections using the BOLSIG+ code. Calculations were performed for the combined RB (Rescigno 1995 Phys. Rev. E 52 329, Boesten et al 1996 J. Phys. B: At. Mol. Opt. Phys. 29 5475) momentum-transfer cross-section, as well as for the JB (Joucoski and Bettega 2002 J. Phys. B: At. Mol. Opt. Phys. 35 783) momentum-transfer cross-section. In addition, we have measured the radio frequency (rf) breakdown curves for various inter-electrode gaps and rfs, and from these we have determined the electron drift velocity in NF3 from the location of the turning point in these curves. These drift velocity values are in satisfactory agreement with those calculated by the BOLSIG+ code employing the JB momentum-transfer cross-section.

Electron Transport through Porphyrin Molecular Junctions

NASA Astrophysics Data System (ADS)

Zhou, Qi

The goal of this work is to study the properties that would affect the electron transport through a porphyrin molecular junction. This work contributes to the field of electron transport in molecular junctions in the following 3 aspects. First of all, by carrying out experiments comparing the conductance of the iron (III) porphyrin (protected) and the free base porphyrin (protected), it is confirmed that the molecular energy level broadening and shifting occurs for porphyrin molecules when coupled with the metal electrodes, and this level broadening and shifting plays an important role in the electron transport through molecular junctions. Secondly, by carrying out an in-situ deprotection of the acetyl-protected free base porphyrin molecules, it is found out that the presence of acetyl groups reduces the conductance. Thirdly, by incorporating the Matrix-assisted laser desorption/ionization (MALDI) spectrum and the in-situ deprotection prior to formation of molecular junctions, it allows a more precise understanding of the molecules involved in the formation of molecular junctions, and therefore allows an accurate analysis of the conductance histogram. The molecules are prepared by self-assembly and the junctions are formed using a Scanning Tunneling Microscopy (STM) molecular break junction technique. The porphyrin molecules are characterized by MALDI in solution before self-assembly to a gold/mica substrate. The self-assembled monolayers (SAMs) of porphyrins on gold are characterized by Ultraviolet-visible (UV-Vis) reflection spectroscopy to confirm that the molecules are attached to the substrate. The SAMs are then characterized by Angle-Resolved X-ray photoelectron spectroscopy (ARXPS) to determine the thickness and the average molecular orientation of the molecular layer. The electron transport is measured by conductance-displacement (G-S) experiments under a given bias (-0.4V). The conductance value of a single molecule is identified by a statistical analysis

Substrate transport pathway inside outward open conformation of EmrD: a molecular dynamics simulation study.

PubMed

Xianwei, Tan; Diannan, Lu; Boxiong, Wang

2016-07-19

The EmrD transporter, which is a classical major facilitator superfamily (MFS) protein, can extrude a range of drug molecules out of E. coil. The drug molecules transport through the channel of MFS in an outward open state, an important issue in research about bacterial drug resistance, which however, is still unknown. In this paper, we construct a starting outward-open model of the EmrD transporter using a state transition method. The starting model is refined by a conventional molecular dynamics simulation. Locally enhanced sampling simulation (LES) is used to validate the outward-open model of EmrD. In the locally enhanced sampling simulation, ten substrates are placed along the channel of the outward-open EmrD, and these substrates are sampled in the outward-open center cavity. It is found that the translocation pathway of these substrates from the inside to the outside of the cell through the EmrD transporter is composed of two sub-pathways, one sub-pathway, including H2, H4, and H5, and another sub-pathway, including H8, H10, and H11. The results give us have a further insight to the ways of substrate translocation of an MFS protein. The model method is based on common features of an MFS protein, so this modeling method can be used to construct various MFS protein models which have a desired state with other conformations not known in the alternating-access mechanism.

Cellular Assays for Ferredoxins: A Strategy for Understanding Electron Flow through Protein Carriers That Link Metabolic Pathways.

PubMed

Atkinson, Joshua T; Campbell, Ian; Bennett, George N; Silberg, Jonathan J

2016-12-27

The ferredoxin (Fd) protein family is a structurally diverse group of iron-sulfur proteins that function as electron carriers, linking biochemical pathways important for energy transduction, nutrient assimilation, and primary metabolism. While considerable biochemical information about individual Fd protein electron carriers and their reactions has been acquired, we cannot yet anticipate the proportion of electrons shuttled between different Fd-partner proteins within cells using biochemical parameters that govern electron flow, such as holo-Fd concentration, midpoint potential (driving force), molecular interactions (affinity and kinetics), conformational changes (allostery), and off-pathway electron leakage (chemical oxidation). Herein, we describe functional and structural gaps in our Fd knowledge within the context of a sequence similarity network and phylogenetic tree, and we propose a strategy for improving our understanding of Fd sequence-function relationships. We suggest comparing the functions of divergent Fds within cells whose growth, or other measurable output, requires electron transfer between defined electron donor and acceptor proteins. By comparing Fd-mediated electron transfer with biochemical parameters that govern electron flow, we posit that models that anticipate energy flow across Fd interactomes can be built. This approach is expected to transform our ability to anticipate Fd control over electron flow in cellular settings, an obstacle to the construction of synthetic electron transfer pathways and rational optimization of existing energy-conserving pathways.

[The H+/e- ratio in the photosynthetic electron transport chain].

PubMed

Ivanov, B N; Shmeleva, V L; Ovchinnikova, V I

1983-06-01

The number of protons adsorbed by tylakoids during one electron passage along the photosynthetic electron transport chain (i.e. the H+/e- ratio) was measured in isolated pea chloroplasts upon continuous illumination. Methylviologen was used as electron acceptor on the reducing side of PS I. It was found that at pH 6.0 upon illumination with red light (lambda greater than 620 nm) at an intensity of 2 . 10(5) erg/cm2 . s ("intensive" light) the H+/e- ratio is equal to 3. Upon illumination of dark-adapted chloroplasts with a "weak" light (900 erg/cm2 . s) the H+/e- ratio is equal to 2. Upon illumination of the chloroplasts with a "weak" after "intensive" light the value of this ratio is close to 3. Azide when added to the reaction mixture may interfere with the accuracy of measurements of the value of the H+/e- ratio by affecting proton exchange. Based on the changes in the H+/e- ratio induced by illumination it was assumed that at saturating intensity of the illuminating light the electron transport chain passes into a so-called "light" state when the mechanisms of proton-electron coupling differing from those of rare electron transfer ("weak" light, flashes) are triggered on. At pH 6.0 the "light" state of the electron transport chain is maintained for some time in the dark.

Electron transport through a spin crossover junction. Perspectives from a wavefunction-based approach

NASA Astrophysics Data System (ADS)

Vela, Sergi; Verot, Martin; Fromager, Emmanuel; Robert, Vincent

2017-02-01

The present paper reports the application of a computational framework, based on the quantum master equation, the Fermi's golden Rule, and conventional wavefunction-based methods, to describe electron transport through a spin crossover molecular junction (Fe(bapbpy) (NCS)2, 1, bapbpy = N-(6-(6-(Pyridin-2-ylamino)pyridin-2-yl)pyridin-2-yl)-pyridin-2-amine). This scheme is an alternative to the standard approaches based on the relative position and nature of the frontier orbitals, as it evaluates the junction's Green's function by means of accurate state energies and wavefunctions. In the present work, those elements are calculated for the relevant states of the high- and low-spin species of 1, and they are used to evaluate the output conductance within a given range of bias- and gate-voltages. The contribution of the ground and low-lying excited states to the current is analyzed, and inspected in terms of their 2S + 1 Ms-states. In doing so, it is shown the relevance of treating not only the ground state in its maximum-Ms projection, as usually done in most computational-chemistry packages, but the whole spectrum of low-energy states of the molecule. Such improved representation of the junction has a notable impact on the total conductivity and, more importantly, it restores the equivalence between alpha and beta transport, which means that no spin polarization is observed in the absence of Zeeman splitting. Finally, this work inspects the strong- and weak-points of the suggested theoretical framework to understand electron transport through molecular switchable materials, identifies a pathway for future improvement, and offers a new insight into concepts that play a key role in spintronics.

Transport of Space Environment Electrons: A Simplified Rapid-Analysis Computational Procedure

NASA Technical Reports Server (NTRS)

Nealy, John E.; Anderson, Brooke M.; Cucinotta, Francis A.; Wilson, John W.; Katz, Robert; Chang, C. K.

2002-01-01

A computational procedure for describing transport of electrons in condensed media has been formulated for application to effects and exposures from spectral distributions typical of electrons trapped in planetary magnetic fields. The procedure is based on earlier parameterizations established from numerous electron beam experiments. New parameterizations have been derived that logically extend the domain of application to low molecular weight (high hydrogen content) materials and higher energies (approximately 50 MeV). The production and transport of high energy photons (bremsstrahlung) generated in the electron transport processes have also been modeled using tabulated values of photon production cross sections. A primary purpose for developing the procedure has been to provide a means for rapidly performing numerous repetitive calculations essential for electron radiation exposure assessments for complex space structures. Several favorable comparisons have been made with previous calculations for typical space environment spectra, which have indicated that accuracy has not been substantially compromised at the expense of computational speed.

A long way to the electrode: how do Geobacter cells transport their electrons?

PubMed

Bonanni, Pablo Sebastián; Schrott, Germán David; Busalmen, Juan Pablo

2012-12-01

The mechanism of electron transport in Geobacter sulfurreducens biofilms is a topic under intense study and debate. Although some proteins were found to be essential for current production, the specific role that each one plays in electron transport to the electrode remains to be elucidated and a consensus on the mechanism of electron transport has not been reached. In the present paper, to understand the state of the art in the topic, electron transport from inside of the cell to the electrode in Geobacter sulfurreducens biofilms is analysed, reviewing genetic studies, biofilm conductivity assays and electrochemical and spectro-electrochemical experiments. Furthermore, crucial data still required to achieve a deeper understanding are highlighted.

Diverse mutational pathways converge on saturable chloroquine transport via the malaria parasite’s chloroquine resistance transporter

PubMed Central

Summers, Robert L.; Dave, Anurag; Dolstra, Tegan J.; Bellanca, Sebastiano; Marchetti, Rosa V.; Nash, Megan N.; Richards, Sashika N.; Goh, Valerie; Schenk, Robyn L.; Stein, Wilfred D.; Kirk, Kiaran; Sanchez, Cecilia P.; Lanzer, Michael; Martin, Rowena E.

2014-01-01

Mutations in the chloroquine resistance transporter (PfCRT) are the primary determinant of chloroquine (CQ) resistance in the malaria parasite Plasmodium falciparum. A number of distinct PfCRT haplotypes, containing between 4 and 10 mutations, have given rise to CQ resistance in different parts of the world. Here we present a detailed molecular analysis of the number of mutations (and the order of addition) required to confer CQ transport activity upon the PfCRT as well as a kinetic characterization of diverse forms of PfCRT. We measured the ability of more than 100 variants of PfCRT to transport CQ when expressed at the surface of Xenopus laevis oocytes. Multiple mutational pathways led to saturable CQ transport via PfCRT, but these could be separated into two main lineages. Moreover, the attainment of full activity followed a rigid process in which mutations had to be added in a specific order to avoid reductions in CQ transport activity. A minimum of two mutations sufficed for (low) CQ transport activity, and as few as four conferred full activity. The finding that diverse PfCRT variants are all limited in their capacity to transport CQ suggests that resistance could be overcome by reoptimizing the CQ dosage. PMID:24728833

Carbon Nanotube-Based Membrane for Light-Driven, Simultaneous Proton and Electron Transport

DOE PAGES

Pilgrim, Gregory A.; Amori, Amanda R.; Hou, Zhentao; ...

2016-12-07

Here we discuss the photon driven transport of protons and electrons over hundreds of microns through a membrane based on vertically aligned single walled carbon nanotubes (SWNTs). Electrons are photogenerated in colloidal CdSe quantum dots that have been noncovalently attached to the carbon nanotube membrane and can be delivered at potentials capable of reducing earth-abundant molecular catalysts that perform proton reduction. Proton transport is driven by the electron photocurrent and is shown to be faster through the SWNT based membrane than through the commercial polymer Nafion. Furthermore, the potential utility of SWNT membranes for solar water splitting applications is demonstratedmore » through their excellent proton and electron transport properties as well as their ability to interact with other components of water splitting systems, such as small molecule electron acceptors.« less

Investigating the Contribution of the Phosphate Transport Pathway to Arsenic Accumulation in Rice1[W

PubMed Central

Wu, Zhongchang; Ren, Hongyan; McGrath, Steve P.; Wu, Ping; Zhao, Fang-Jie

2011-01-01

Arsenic (As) accumulation in rice (Oryza sativa) may pose a significant health risk to consumers. Plants take up different As species using various pathways. Here, we investigated the contribution of the phosphate (Pi) transport pathway to As accumulation in rice grown hydroponically or under flooded soil conditions. In hydroponic experiments, a rice mutant defective in OsPHF1 (for phosphate transporter traffic facilitator1) lost much of the ability to take up Pi and arsenate and to transport them from roots to shoots, whereas transgenic rice overexpressing either the Pi transporter OsPht1;8 (OsPT8) or the transcription factor OsPHR2 (for phosphate starvation response2) had enhanced abilities of Pi and arsenate uptake and translocation. OsPT8 was found to have a high affinity for both Pi and arsenate, and its overexpression increased the maximum influx by 3- to 5-fold. In arsenate-treated plants, both arsenate and arsenite were detected in the xylem sap, with the proportion of the latter increasing with the exposure time. Under the flooded soil conditions, the phf1 mutant took up less Pi whereas the overexpression lines took up more Pi. But there were no similar effects on As accumulation and distribution. Rice grain contained predominantly dimethylarsinic acid and arsenite, with arsenate being a minor species. These results suggest that the Pi transport pathway contributed little to As uptake and transport to grain in rice plants grown in flooded soil. Transgenic approaches to enhance Pi acquisition from paddy soil through the overexpression of Pi transporters may not increase As accumulation in rice grain. PMID:21715673

Helium, Iron and Electron Particle Transport and Energy Transport Studies on the TFTR Tokamak

DOE R&D Accomplishments Database

Synakowski, E. J.; Efthimion, P. C.; Rewoldt, G.; Stratton, B. C.; Tang, W. M.; Grek, B.; Hill, K. W.; Hulse, R. A.; Johnson, D .W.; Mansfield, D. K.; McCune, D.; Mikkelsen, D. R.; Park, H. K.; Ramsey, A. T.; Redi, M. H.; Scott, S. D.; Taylor, G.; Timberlake, J.; Zarnstorff, M. C. (Princeton Univ., NJ (United States). Plasma Physics Lab.); Kissick, M. W. (Wisconsin Univ., Madison, WI (United States))

1993-03-01

Results from helium, iron, and electron transport on TFTR in L-mode and Supershot deuterium plasmas with the same toroidal field, plasma current, and neutral beam heating power are presented. They are compared to results from thermal transport analysis based on power balance. Particle diffusivities and thermal conductivities are radially hollow and larger than neoclassical values, except possibly near the magnetic axis. The ion channel dominates over the electron channel in both particle and thermal diffusion. A peaked helium profile, supported by inward convection that is stronger than predicted by neoclassical theory, is measured in the Supershot The helium profile shape is consistent with predictions from quasilinear electrostatic drift-wave theory. While the perturbative particle diffusion coefficients of all three species are similar in the Supershot, differences are found in the L-Mode. Quasilinear theory calculations of the ratios of impurity diffusivities are in good accord with measurements. Theory estimates indicate that the ion heat flux should be larger than the electron heat flux, consistent with power balance analysis. However, theoretical values of the ratio of the ion to electron heat flux can be more than a factor of three larger than experimental values. A correlation between helium diffusion and ion thermal transport is observed and has favorable implications for sustained ignition of a tokamak fusion reactor.

Characteristics of electron transport chain and affecting factors for thiosulfate-driven perchlorate reduction.

PubMed

Zhang, Chao; Guo, Jianbo; Lian, Jing; Lu, Caicai; Ngo, Huu Hao; Guo, Wenshan; Song, Yuanyuan; Guo, Yankai

2017-10-01

The mechanism for perchlorate reduction was investigated using thiosulfate-driven (T-driven) perchlorate reduction bacteria. The influences of various environmental conditions on perchlorate reduction, including pH, temperature and electron acceptors were examined. The maximum perchlorate removal rate was observed at pH 7.5 and 40 °C. Perchlorate reduction was delayed due to the coexistence of perchlorate-chlorate and perchlorate-nitrate. The mechanism of the T-driven perchlorate reduction electron transport chain (ETC) was also investigated by utilizing different inhibitors. The results were as follows: firstly, the NADH dehydrogenase was not involved in the ETC; secondly, the FAD dehydrogenase and quinone loop participated in the ETC; and thirdly, cytochrome oxidase was the main pathway in the ETC. Meanwhile, microbial consortium structure analysis indicated that Sulfurovum which can oxidize sulfur compounds coupled to the reduction of nitrate or perchlorate was the primary bacterium in the T-driven and sulfur-driven consortium. This study generates a better understanding of the mechanism of T-driven perchlorate reduction. Copyright © 2017 Elsevier Ltd. All rights reserved.

Balanced electron-hole transport in spin-orbit semimetal SrIrO3 heterostructures

NASA Astrophysics Data System (ADS)

Manca, Nicola; Groenendijk, Dirk J.; Pallecchi, Ilaria; Autieri, Carmine; Tang, Lucas M. K.; Telesio, Francesca; Mattoni, Giordano; McCollam, Alix; Picozzi, Silvia; Caviglia, Andrea D.

2018-02-01

Relating the band structure of correlated semimetals to their transport properties is a complex and often open issue. The partial occupation of numerous electron and hole bands can result in properties that are seemingly in contrast with one another, complicating the extraction of the transport coefficients of different bands. The 5 d oxide SrIrO3 hosts parabolic bands of heavy holes and light electrons in gapped Dirac cones due to the interplay between electron-electron interactions and spin-orbit coupling. We present a multifold approach relying on different experimental techniques and theoretical calculations to disentangle its complex electronic properties. By combining magnetotransport and thermoelectric measurements in a field-effect geometry with first-principles calculations, we quantitatively determine the transport coefficients of different conduction channels. Despite their different dispersion relationships, electrons and holes are found to have strikingly similar transport coefficients, yielding a holelike response under field-effect and thermoelectric measurements and a linear electronlike Hall effect up to 33 T.

Evidence for a Hydrogenosomal-Type Anaerobic ATP Generation Pathway in Acanthamoeba castellanii

PubMed Central

Gray, Michael W.; Roger, Andrew J.

2013-01-01

Diverse, distantly-related eukaryotic lineages have adapted to low-oxygen environments, and possess mitochondrion-related organelles that have lost the capacity to generate adenosine triphosphate (ATP) through oxidative phosphorylation. A subset of these organelles, hydrogenosomes, has acquired a set of characteristic ATP generation enzymes commonly found in anaerobic bacteria. The recipient of these enzymes could not have survived prior to their acquisition had it not still possessed the electron transport chain present in the ancestral mitochondrion. In the divergence of modern hydrogenosomes from mitochondria, a transitional organelle must therefore have existed that possessed both an electron transport chain and an anaerobic ATP generation pathway. Here, we report a modern analog of this organelle in the habitually aerobic opportunistic pathogen, Acanthamoeba castellanii. This organism possesses a complete set of enzymes comprising a hydrogenosome-like ATP generation pathway, each of which is predicted to be targeted to mitochondria. We have experimentally confirmed the mitochondrial localizations of key components of this pathway using tandem mass spectrometry. This evidence is the first supported by localization and proteome data of a mitochondrion possessing both an electron transport chain and hydrogenosome-like energy metabolism enzymes. Our work provides insight into the first steps that might have occurred in the course of the emergence of modern hydrogenosomes. PMID:24086244

Understanding charge transport in molecular electronics.

PubMed

Kushmerick, J J; Pollack, S K; Yang, J C; Naciri, J; Holt, D B; Ratner, M A; Shashidhar, R

2003-12-01

For molecular electronics to become a viable technology the factors that control charge transport across a metal-molecule-metal junction need to be elucidated. We use an experimentally simple crossed-wire tunnel junction to interrogate how factors such as metal-molecule coupling, molecular structure, and the choice of metal electrode influence the current-voltage characteristics of a molecular junction.

Decoupled electron and phonon transports in hexagonal boron nitride-silicene bilayer heterostructure

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cai, Yongqing; Pei, Qing-Xiang, E-mail: peiqx@ihpc.a-star.edu.sg, E-mail: zhangg@ihpc.a-star.edu.sg; Zhang, Gang, E-mail: peiqx@ihpc.a-star.edu.sg, E-mail: zhangg@ihpc.a-star.edu.sg

2016-02-14

Calculations based on the density functional theory and empirical molecular dynamics are performed to investigate interlayer interaction, electronic structure and thermal transport of a bilayer heterostructure consisting of silicene and hexagonal boron nitride (h-BN). In this heterostructure, the two layers are found to interact weakly via a non-covalent binding. As a result, the Dirac cone of silicene is preserved with the Dirac cone point being located exactly at the Fermi level, and only a small amount of electrons are transferred from h-BN to silicene, suggesting that silicene dominates the electronic transport. Molecular dynamics calculation results demonstrate that the heat currentmore » along h-BN is six times of that along silicene, suggesting that h-BN dominates the thermal transport. This decoupled role of h-BN and silicene in thermal and electronic transport suggests that the BN-silicene bilayer heterostructure is promising for thermoelectric applications.« less

Breaking the barriers of all-polymer solar cells: Solving electron transporter and morphology problems

NASA Astrophysics Data System (ADS)

Gavvalapalli, Nagarjuna

All-polymer solar cells (APSC) are a class of organic solar cells in which hole and electron transporting phases are made of conjugated polymers. Unlike polymer/fullerene solar cell, photoactive material of APSC can be designed to have hole and electron transporting polymers with complementary absorption range and proper frontier energy level offset. However, the highest reported PCE of APSC is 5 times less than that of polymer/fullerene solar cell. The low PCE of APSC is mainly due to: i) low charge separation efficiency; and ii) lack of optimal morphology to facilitate charge transfer and transport; and iii) lack of control over the exciton and charge transport in each phase. My research work is focused towards addressing these issues. The charge separation efficiency of APSC can be enhanced by designing novel electron transporting polymers with: i) broad absorption range; ii) high electron mobility; and iii) high dielectric constant. In addition to with the above parameters chemical and electronic structure of the repeating unit of conjugated polymer also plays a role in charge separation efficiency. So far only three classes of electron transporting polymers, CN substituted PPV, 2,1,3-benzothiadiazole derived polymers and rylene diimide derived polymers, are used in APSC. Thus to enhance the charge separation efficiency new classes of electron transporting polymers with the above characteristics need to be synthesized. I have developed a new straightforward synthetic strategy to rapidly generate new classes of electron transporting polymers with different chemical and electronic structure, broad absorption range, and high electron mobility from readily available electron deficient monomers. In APSCs due to low entropy of mixing, polymers tend to micro-phase segregate rather than forming the more useful nano-phase segregation. Optimizing the polymer blend morphology to obtain nano-phase segregation is specific to the system under study, time consuming, and not

Effect of electron-electron scattering on the conductance of a quantum wire studied with the Boltzman transport equation

NASA Astrophysics Data System (ADS)

Lyo, S. K.; Huang, Danhong

2006-05-01

Electron-electron scattering conserves total momentum and does not dissipate momentum directly in a low-density system where the umklapp process is forbidden. However, it can still affect the conductance through the energy relaxation of the electrons. We show here that this effect can be studied with arbitrary accuracy in a multisublevel one-dimensional (1D) single quantum wire system in the presence of roughness and phonon scattering using a formally exact solution of the Boltzmann transport equation. The intrasubband electron-electron scattering is found to yield no net effect on the transport of electrons in 1D with only one sublevel occupied. For a system with a multilevel occupation, however, we find a significant effect of intersublevel electron-electron scattering on the temperature and density dependence of the resistance at low temperatures.

Electronic transport properties of nanostructured MnSi-films

NASA Astrophysics Data System (ADS)

Schroeter, D.; Steinki, N.; Scarioni, A. Fernández; Schumacher, H. W.; Süllow, S.; Menzel, D.

2018-05-01

MnSi, which crystallizes in the cubic B20 structure, shows intriguing magnetic properties involving the existence of skyrmions in the magnetic phase diagram. Bulk MnSi has been intensively investigated and thoroughly characterized, in contrast to MnSi thin film, which exhibits widely varying properties in particular with respect to electronic transport. In this situation, we have set out to reinvestigate the transport properties in MnSi thin films by means of studying nanostructure samples. In particular, Hall geometry nanostructures were produced to determine the intrinsic transport properties.

Giant electron-hole transport asymmetry in ultra-short quantum transistors.

PubMed

McRae, A C; Tayari, V; Porter, J M; Champagne, A R

2017-05-31

Making use of bipolar transport in single-wall carbon nanotube quantum transistors would permit a single device to operate as both a quantum dot and a ballistic conductor or as two quantum dots with different charging energies. Here we report ultra-clean 10 to 100 nm scale suspended nanotube transistors with a large electron-hole transport asymmetry. The devices consist of naked nanotube channels contacted with sections of tube under annealed gold. The annealed gold acts as an n-doping top gate, allowing coherent quantum transport, and can create nanometre-sharp barriers. These tunnel barriers define a single quantum dot whose charging energies to add an electron or a hole are vastly different (e-h charging energy asymmetry). We parameterize the e-h transport asymmetry by the ratio of the hole and electron charging energies η e-h . This asymmetry is maximized for short channels and small band gap tubes. In a small band gap device, we demonstrate the fabrication of a dual functionality quantum device acting as a quantum dot for holes and a much longer quantum bus for electrons. In a 14 nm-long channel, η e-h reaches up to 2.6 for a device with a band gap of 270 meV. The charging energies in this device exceed 100 meV.

Giant electron-hole transport asymmetry in ultra-short quantum transistors

PubMed Central

McRae, A. C.; Tayari, V.; Porter, J. M.; Champagne, A. R.

2017-01-01

Making use of bipolar transport in single-wall carbon nanotube quantum transistors would permit a single device to operate as both a quantum dot and a ballistic conductor or as two quantum dots with different charging energies. Here we report ultra-clean 10 to 100 nm scale suspended nanotube transistors with a large electron-hole transport asymmetry. The devices consist of naked nanotube channels contacted with sections of tube under annealed gold. The annealed gold acts as an n-doping top gate, allowing coherent quantum transport, and can create nanometre-sharp barriers. These tunnel barriers define a single quantum dot whose charging energies to add an electron or a hole are vastly different (e−h charging energy asymmetry). We parameterize the e−h transport asymmetry by the ratio of the hole and electron charging energies ηe−h. This asymmetry is maximized for short channels and small band gap tubes. In a small band gap device, we demonstrate the fabrication of a dual functionality quantum device acting as a quantum dot for holes and a much longer quantum bus for electrons. In a 14 nm-long channel, ηe−h reaches up to 2.6 for a device with a band gap of 270 meV. The charging energies in this device exceed 100 meV. PMID:28561024

Electron heat transport comparison in the Large Helical Device and TJ-II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Garcia, J.; Dies, J.; Castejon, F.

2007-10-15

The electron heat transport in the Large Helical Device (LHD) [K. Ida, T. Shimozuma, H. Funaba et al., Phys. Rev. Lett. 91, 085003 (2003)] and TJ-II [F. Castejon, V. Tribaldos, I. Garcia-Cortes, E. de la Luna, J. Herranz, I. Pastor, T. Estrada, and TJ-II Team, Nucl. Fusion 42, 271 (2002)] is analyzed by means of the TOTAL [K. Yamazaki and T. Amano, Nucl. Fusion 32, 4 (1992)] and PRETOR-Stellarator [J. Dies, F. Castejon, J. M. Fontdecaba, J. Fontanet, J. Izquierdo, G. Cortes, and C. Alejaldre, Proceedings of the 29th European Physical Society Conference on Plasma Physics and Controlled Fusion, Montreux,more » 2002, Europhysics Conference Abstracts, 2004, Vol. 26B, P-5.027] plasma simulation codes and assuming a global transport model mixing GyroBohm-like drift wave model and other drift wave model with shorter wavelength. The stabilization of the GyroBohm-like model by the ExB shear has been also taken into account. Results show how such kind of electron heat transport can simulate experimental evidence in both devices, leading to the electron internal transport barrier (eITB) formation in the LHD and to the so-called 'enhanced heat confinement regimes' in TJ-II when electron density is low enough. Therefore, two sources for the anomalous electron heat transport can coexist in plasmas with eITB; however, for each device the relative importance of anomalous and neoclassical transport can be different.« less

Visualization of three pathways for macromolecule transport across cultured endothelium and their modification by flow.

PubMed

Ghim, Mean; Alpresa, Paola; Yang, Sung-Wook; Braakman, Sietse T; Gray, Stephen G; Sherwin, Spencer J; van Reeuwijk, Maarten; Weinberg, Peter D

2017-11-01

Transport of macromolecules across vascular endothelium and its modification by fluid mechanical forces are important for normal tissue function and in the development of atherosclerosis. However, the routes by which macromolecules cross endothelium, the hemodynamic stresses that maintain endothelial physiology or trigger disease, and the dependence of transendothelial transport on hemodynamic stresses are controversial. We visualized pathways for macromolecule transport and determined the effect on these pathways of different types of flow. Endothelial monolayers were cultured under static conditions or on an orbital shaker producing different flow profiles in different parts of the wells. Fluorescent tracers that bound to the substrate after crossing the endothelium were used to identify transport pathways. Maps of tracer distribution were compared with numerical simulations of flow to determine effects of different shear stress metrics on permeability. Albumin-sized tracers dominantly crossed the cultured endothelium via junctions between neighboring cells, high-density lipoprotein-sized tracers crossed at tricellular junctions, and low-density lipoprotein-sized tracers crossed through cells. Cells aligned close to the angle that minimized shear stresses across their long axis. The rate of paracellular transport under flow correlated with the magnitude of these minimized transverse stresses, whereas transport across cells was uniformly reduced by all types of flow. These results contradict the long-standing two-pore theory of solute transport across microvessel walls and the consensus view that endothelial cells align with the mean shear vector. They suggest that endothelial cells minimize transverse shear, supporting its postulated proatherogenic role. Preliminary data show that similar tracer techniques are practicable in vivo. NEW & NOTEWORTHY Solutes of increasing size crossed cultured endothelium through intercellular junctions, through tricellular

Electron Trapping and Charge Transport by Large Amplitude Whistlers

NASA Technical Reports Server (NTRS)

Kellogg, P. J.; Cattell, C. A.; Goetz, K.; Monson, S. J.; Wilson, L. B., III

2010-01-01

Trapping of electrons by magnetospheric whistlers is investigated using data from the Waves experiment on Wind and the S/WAVES experiment on STEREO. Waveforms often show a characteristic distortion which is shown to be due to electrons trapped in the potential of the electrostatic part of oblique whistlers. The density of trapped electrons is significant, comparable to that of the unperturbed whistler. Transport of these trapped electrons to new regions can generate potentials of several kilovolts, Trapping and the associated potentials may play an important role in the acceleration of Earth's radiation belt electrons.

Squeezing at Entrance of Proton Transport Pathway in Proton-translocating Pyrophosphatase upon Substrate Binding*

PubMed Central

Huang, Yun-Tzu; Liu, Tseng-Huang; Lin, Shih-Ming; Chen, Yen-Wei; Pan, Yih-Jiuan; Lee, Ching-Hung; Sun, Yuh-Ju; Tseng, Fan-Gang; Pan, Rong-Long

2013-01-01

Homodimeric proton-translocating pyrophosphatase (H+-PPase; EC 3.6.1.1) is indispensable for many organisms in maintaining organellar pH homeostasis. This unique proton pump couples the hydrolysis of PPi to proton translocation across the membrane. H+-PPase consists of 14–16 relatively hydrophobic transmembrane domains presumably for proton translocation and hydrophilic loops primarily embedding a catalytic site. Several highly conserved polar residues located at or near the entrance of the transport pathway in H+-PPase are essential for proton pumping activity. In this investigation single molecule FRET was employed to dissect the action at the pathway entrance in homodimeric Clostridium tetani H+-PPase upon ligand binding. The presence of the substrate analog, imidodiphosphate mediated two sites at the pathway entrance moving toward each other. Moreover, single molecule FRET analyses after the mutation at the first proton-carrying residue (Arg-169) demonstrated that conformational changes at the entrance are conceivably essential for the initial step of H+-PPase proton translocation. A working model is accordingly proposed to illustrate the squeeze at the entrance of the transport pathway in H+-PPase upon substrate binding. PMID:23720778

Simulation of electron transport in quantum well devices

NASA Technical Reports Server (NTRS)

Miller, D. R.; Gullapalli, K. K.; Reddy, V. R.; Neikirk, D. P.

1992-01-01

Double barrier resonant tunneling diodes (DBRTD) have received much attention as possible terahertz devices. Despite impressive experimental results, the specifics of the device physics (i.e., how the electrons propagate through the structure) are only qualitatively understood. Therefore, better transport models are warranted if this technology is to mature. In this paper, the Lattice Wigner function is used to explain the important transport issues associated with DBRTD device behavior.

Benchmark solution for the Spencer-Lewis equation of electron transport theory

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ganapol, B.D.

As integrated circuits become smaller, the shielding of these sensitive components against penetrating electrons becomes extremely critical. Monte Carlo methods have traditionally been the method of choice in shielding evaluations primarily because they can incorporate a wide variety of relevant physical processes. Recently, however, as a result of a more accurate numerical representation of the highly forward peaked scattering process, S/sub n/ methods for one-dimensional problems have been shown to be at least as cost-effective in comparison with Monte Carlo methods. With the development of these deterministic methods for electron transport, a need has arisen to assess the accuracy ofmore » proposed numerical algorithms and to ensure their proper coding. It is the purpose of this presentation to develop a benchmark to the Spencer-Lewis equation describing the transport of energetic electrons in solids. The solution will take advantage of the correspondence between the Spencer-Lewis equation and the transport equation describing one-group time-dependent neutron transport.« less

Transmembrane transporter expression regulated by the glucosylceramide pathway in Cryptococcus neoformans.

PubMed

Singh, Arpita; Rella, Antonella; Schwacke, John; Vacchi-Suzzi, Caterina; Luberto, Chiara; Del Poeta, Maurizio

2015-11-16

The sphingolipid glucosylceramide (GlcCer) and factors involved in the fungal GlcCer pathways were shown earlier to be an integral part of fungal virulence, especially in fungal replication at 37 °C, in neutral/alkaline pH and 5 % CO2 environments (e.g. alveolar spaces). Two mutants, ∆gcs 1 lacking glucosylceramide synthase 1 gene (GCS1) which catalyzes the formation of sphingolipid GlcCer from the C9-methyl ceramide and ∆smt1 lacking sphingolipid C9 methyltransferase gene (SMT1), which adds a methyl group to position nine of the sphingosine backbone of ceramide, of this pathway were attenuated in virulence and have a growth defect at the above-mentioned conditions. These mutants with either no or structurally modified GlcCer located on the cell-membrane have reduced membrane rigidity, which may have altered not only the physical location of membrane proteins but also their expression, as the pathogen's mode of adaptation to changing need. Importantly, pathogens are known to adapt themselves to the changing host environments by altering their patterns of gene expression. By transcriptional analysis of gene expression, we identified six genes whose expression was changed from their wild-type counterpart grown in the same conditions, i.e. they became either down regulated or up regulated in these two mutants. The microarray data was validated by real-time PCR, which confirmed their fold change in gene expression. All the six genes we identified, viz siderochrome-iron transporter (CNAG_02083), monosaccharide transporter (CNAG_05340), glucose transporter (CNAG_03772), membrane protein (CNAG_03912), membrane transport protein (CNAG_00539), and sugar transporter (CNAG_06963), are membrane-localized and have significantly altered gene expression levels. Therefore, we hypothesize that these genes function either independently or in tandem with a structurally modified cell wall/plasma membrane resulting from the modifications of the GlcCer pathway and thus possibly

Intrachain versus interchain electron transport in poly(fluorene-alt-benzothiadiazole): a quantum-chemical insight.

PubMed

Van Vooren, Antoine; Kim, Ji-Seon; Cornil, Jérôme

2008-05-16

Poly(9,9-di-n-octylfluorene-alt-benzothiadiazole) [F8BT], displays very different charge-transport properties for holes versus electrons when comparing annealed and pristine thin films and transport parallel (intrachain) and perpendicular (interchain) to the polymer axes. The present theoretical contribution focuses on the electron-transport properties of F8BT chains and compares the efficiency of intrachain versus interchain transport in the hopping regime. The theoretical results rationalize significantly lowered electron mobility in annealed F8BT thin films and the smaller mobility anisotropy (mu( parallel)/mu( perpendicular)) measured for electrons in aligned films (i.e. 5-7 compared to 10-15 for holes).

Diffusive transport of energetic electrons in the solar corona: X-ray and radio diagnostics

NASA Astrophysics Data System (ADS)

Musset, S.; Kontar, E. P.; Vilmer, N.

2018-02-01

Context. Imaging spectroscopy in X-rays with RHESSI provides the possibility to investigate the spatial evolution of X-ray emitting electron distribution and therefore, to study transport effects on energetic electrons during solar flares. Aims: We study the energy dependence of the scattering mean free path of energetic electrons in the solar corona. Methods: We used imaging spectroscopy with RHESSI to study the evolution of energetic electrons distribution in various parts of the magnetic loop during the 2004 May 21 flare. We compared these observations with the radio observations of the gyrosynchrotron radiation of the same flare and with the predictions of a diffusive transport model. Results: X-ray analysis shows a trapping of energetic electrons in the corona and a spectral hardening of the energetic electron distribution between the top of the loop and the footpoints. Coronal trapping of electrons is stronger for radio-emitting electrons than for X-ray-emitting electrons. These observations can be explained by a diffusive transport model. Conclusions: We show that the combination of X-ray and radio diagnostics is a powerful tool to study electron transport in the solar corona in different energy domains. We show that the diffusive transport model can explain our observations, and in the range 25-500 keV, the scattering mean free path of electrons decreases with electron energy. We can estimate for the first time the scattering mean free path dependence on energy in the corona.

Electron Tunneling, a Quantum Probe for the Quantum World of Nanotechnology

ERIC Educational Resources Information Center

Hipps, K. W.; Scudiero, L.

2005-01-01

A quantum-mechanical probe is essential to study the quantum world, which is provided by electron tunneling. A spectroscopic mapping to image the electron-transport pathways on a sub-molecular scale is used.

Electronic structure and transport properties of quasi-one-dimensional carbon nanomaterials

NASA Astrophysics Data System (ADS)

Wu, Y. N.; Cheng, P.; Wu, M. J.; Zhu, H.; Xiang, Q.; Ni, J.

2017-09-01

Based on the density functional theory combined with the nonequilibrium Green's function, the influence of the wrinkle on the electronic structures and transport properties of quasi-one-dimensional carbon nanomaterials have been investigated, in which the wrinkled armchair graphene nanoribbons (wAGNRs) and the composite of AGNRs and single walled carbon nanotubes (SWCNTs) were considered with different connection of ripples. The wrinkle adjusts the electronic structures and transport properties of AGNRs. With the change of the strain, the wAGNRs for three width families reveal different electrical behavior. The band gap of AGNR(6) increases in the presence of the wrinkle, which is opposite to that of AGNR(5) and AGNR(7). The transport of AGNRs with the widths 6 or 7 has been modified by the wrinkle, especially by the number of isolated ripples, but it is insensitive to the strain. The nanojunctions constructed by AGNRs and SWCNTs can form the quantum wells, and some specific states are confined in wAGNRs. Although these nanojunctions exhibit the metallic, they have poor conductance due to the wrinkle. The filling of C20 into SWCNT has less influence on the electronic structure and transport of the junctions. The width and connection type of ripples have greatly influenced on the electronic structures and transport properties of quasi-one-dimensional nanomaterials.

Ocean Transport Pathways to a World Heritage Fringing Coral Reef: Ningaloo Reef, Western Australia.

PubMed

Xu, Jiangtao; Lowe, Ryan J; Ivey, Gregory N; Jones, Nicole L; Zhang, Zhenlin

2016-01-01

A Lagrangian particle tracking model driven by a regional ocean circulation model was used to investigate the seasonally varying connectivity patterns within the shelf circulation surrounding the 300 km long Ningaloo Reef in Western Australia (WA) during 2009-2010. Forward-in-time simulations revealed that surface water was transported equatorward and offshore in summer due to the upwelling-favorable winds. In winter, however, water was transported polewards down the WA coast due to the seasonally strong Leeuwin Current. Using backward-in-time simulations, the subsurface transport pathways revealed two main source regions of shelf water reaching Ningaloo Reef: (1) a year-round source to the northeast in the upper 100 m of water column; and (2) during the summer, an additional source offshore and to the west of Ningaloo in depths between ~30 and ~150 m. Transient wind-driven coastal upwelling, onshore geostrophic transport and stirring by offshore eddies were identified as the important mechanisms influencing the source water origins. The identification of these highly time-dependent transport pathways and source water locations is an essential step towards quantifying how key material (e.g., nutrients, larvae, contaminants, etc.) is exchanged between Ningaloo Reef and the surrounding shelf ocean, and how this is mechanistically coupled to the complex ocean dynamics in this region.

Ocean Transport Pathways to a World Heritage Fringing Coral Reef: Ningaloo Reef, Western Australia

PubMed Central

Xu, Jiangtao; Lowe, Ryan J.; Ivey, Gregory N.; Jones, Nicole L.; Zhang, Zhenlin

2016-01-01

A Lagrangian particle tracking model driven by a regional ocean circulation model was used to investigate the seasonally varying connectivity patterns within the shelf circulation surrounding the 300 km long Ningaloo Reef in Western Australia (WA) during 2009–2010. Forward-in-time simulations revealed that surface water was transported equatorward and offshore in summer due to the upwelling-favorable winds. In winter, however, water was transported polewards down the WA coast due to the seasonally strong Leeuwin Current. Using backward-in-time simulations, the subsurface transport pathways revealed two main source regions of shelf water reaching Ningaloo Reef: (1) a year-round source to the northeast in the upper 100 m of water column; and (2) during the summer, an additional source offshore and to the west of Ningaloo in depths between ~30 and ~150 m. Transient wind-driven coastal upwelling, onshore geostrophic transport and stirring by offshore eddies were identified as the important mechanisms influencing the source water origins. The identification of these highly time-dependent transport pathways and source water locations is an essential step towards quantifying how key material (e.g., nutrients, larvae, contaminants, etc.) is exchanged between Ningaloo Reef and the surrounding shelf ocean, and how this is mechanistically coupled to the complex ocean dynamics in this region. PMID:26790154

Blue emitting 1,8-naphthalimides with electron transport properties for organic light emitting diode applications

NASA Astrophysics Data System (ADS)

Ulla, Hidayath; Kiran, M. Raveendra; Garudachari, B.; Ahipa, T. N.; Tarafder, Kartick; Adhikari, Airody Vasudeva; Umesh, G.; Satyanarayan, M. N.

2017-09-01

In this article, the synthesis, characterization and use of two novel naphthalimides as electron-transporting emitter materials for organic light emitting diode (OLED) applications are reported. The molecules were obtained by substituting electron donating chloro-phenoxy group at the C-4 position. A detailed optical, thermal, electrochemical and related properties were systematically studied. Furthermore, theoretical calculations (DFT) were performed to get a better understanding of the electronic structures. The synthesized molecules were used as electron transporters and emitters in OLEDs with three different device configurations. The devices with the molecules showed blue emission with efficiencies of 1.89 cdA-1, 0.98 lmW-1, 0.71% at 100 cdm-2. The phosphorescent devices with naphthalimides as electron transport materials displayed better performance in comparison to the device without any electron transporting material and were analogous with the device using standard electron transporting material, Alq3. The results demonstrate that the naphthalimides could play a significant part in the progress of OLEDs.

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology

PubMed Central

Latendresse, Mario; Paley, Suzanne M.; Krummenacker, Markus; Ong, Quang D.; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M.; Caspi, Ron

2016-01-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. PMID:26454094

Electron transport in biomolecular gaseous and liquid systems: theory, experiment and self-consistent cross-sections

NASA Astrophysics Data System (ADS)

White, R. D.; Cocks, D.; Boyle, G.; Casey, M.; Garland, N.; Konovalov, D.; Philippa, B.; Stokes, P.; de Urquijo, J.; González-Magaña, O.; McEachran, R. P.; Buckman, S. J.; Brunger, M. J.; Garcia, G.; Dujko, S.; Petrovic, Z. Lj

2018-05-01

Accurate modelling of electron transport in plasmas, plasma-liquid and plasma-tissue interactions requires (i) the existence of accurate and complete sets of cross-sections, and (ii) an accurate treatment of electron transport in these gaseous and soft-condensed phases. In this study we present progress towards the provision of self-consistent electron-biomolecule cross-section sets representative of tissue, including water and THF, by comparison of calculated transport coefficients with those measured using a pulsed-Townsend swarm experiment. Water–argon mixtures are used to assess the self-consistency of the electron-water vapour cross-section set proposed in de Urquijo et al (2014 J. Chem. Phys. 141 014308). Modelling of electron transport in liquids and soft-condensed matter is considered through appropriate generalisations of Boltzmann’s equation to account for spatial-temporal correlations and screening of the electron potential. The ab initio formalism is applied to electron transport in atomic liquids and compared with available experimental swarm data for these noble liquids. Issues on the applicability of the ab initio formalism for krypton are discussed and addressed through consideration of the background energy of the electron in liquid krypton. The presence of self-trapping (into bubble/cluster states/solvation) in some liquids requires a reformulation of the governing Boltzmann equation to account for the combined localised–delocalised nature of the resulting electron transport. A generalised Boltzmann equation is presented which is highlighted to produce dispersive transport observed in some liquid systems.

Probing the electronic transport on the reconstructed Au/Ge(001) surface

PubMed Central

Krok, Franciszek; Kaspers, Mark R; Bernhart, Alexander M; Nikiel, Marek; Jany, Benedykt R; Indyka, Paulina; Wojtaszek, Mateusz; Möller, Rolf

2014-01-01

Summary By using scanning tunnelling potentiometry we characterized the lateral variation of the electrochemical potential µec on the gold-induced Ge(001)-c(8 × 2)-Au surface reconstruction while a lateral current flows through the sample. On the reconstruction and across domain boundaries we find that µec shows a constant gradient as a function of the position between the contacts. In addition, nanoscale Au clusters on the surface do not show an electronic coupling to the gold-induced surface reconstruction. In combination with high resolution scanning electron microscopy and transmission electron microscopy, we conclude that an additional transport channel buried about 2 nm underneath the surface represents a major transport channel for electrons. PMID:25247129

Electronic SSKIN pathway: reducing device-related pressure ulcers.

PubMed

Campbell, Natalie

2016-08-11

This article describes how an interprofessional project in a London NHS Foundation Trust was undertaken to develop an intranet-based medical device-related pressure ulcer prevention and management pathway for clinical staff working across an adult critical care directorate, where life-threatening events require interventions using medical devices. The aim of this project was to improve working policies and processes to define key prevention strategies and provide clinicians with a clear, standardised approach to risk and skin assessment, equipment use, documentation and reporting clinical data using the Trust's CareVue (electronic medical records), Datix (incident reporting and risk-management tool) and eTRACE (online clinical protocol ordering) systems. The process included the development, trial and local implementation of the pathway using collaborative teamwork and the SSKIN care bundle tool. The experience of identifying issues, overcoming challenges, defining best practice and cascading SSKIN awareness training is shared.

Electron transporting water-gated thin film transistors

NASA Astrophysics Data System (ADS)

Al Naim, Abdullah; Grell, Martin

2012-10-01

We demonstrate an electron-transporting water-gated thin film transistor, using thermally converted precursor-route zinc-oxide (ZnO) intrinsic semiconductors with hexamethyldisilazene (HMDS) hydrophobic surface modification. Water gated HMDS-ZnO thin film transistors (TFT) display low threshold and high electron mobility. ZnO films constitute an attractive alternative to organic semiconductors for TFT transducers in sensor applications for waterborne analytes. Despite the use of an electrolyte as gate medium, the gate geometry (shape of gate electrode and distance between gate electrode and TFT channel) is relevant for optimum performance of water-gated TFTs.

Preliminary observations on high energy phosphates and metabolic pathway and transporter potentials in extensor carpi radialis brevis and trapezius muscles of women with work-related myalgia.

PubMed

Green, Howard J; Ranney, Don; Burnett, Margaret; Galvin, Patti; Kyle, Natasha; Lounsbury, David; Ouyang, Jing; Smith, Ian C; Stewart, Riley; Tick, Heather; Tupling, A Russell

2014-11-01

This study compared both the extensor carpi radialis brevis (ECRB) and the trapezius (TRAP) muscles of women with work-related myalgia (WRM) with healthy controls (CON) to determine whether abnormalities existed in cellular energy status and the potentials of the various metabolic pathways and segments involved in energy production and substrate transport. For both the ECRB (CON, n = 6-9; WRM, n = 13) and the TRAP (CON, n = 6-7; WRM, n = 10), no differences (P > 0.05) were found for the concentrations (in millimoles per kilogram of dry mass) of ATP, PCr, lactate, and glycogen. Similarly, with one exception, the maximal activities (in moles per milligram of protein per hour) of mitochondrial enzymes representative of the citric acid cycle (CAC), the electron transport chain (ETC), and β-oxidation, as well as the cytosolic enzymes involved in high energy phosphate transfer, glycogenolysis, glycolysis, lactate oxidation, and glucose phosphorylation were not different (P > 0.05). The glucose transporters GLUT1 and GLUT4, and the monocarboxylate transporters MCT1 and MCT4, were also normal in WRM. It is concluded that, in general, abnormalities in the resting energy and substrate state, the potential of the different metabolic pathways and segments, as well as the glucose and monocarboxylate transporters do not appear to be involved in the cellular pathophysiology of WRM.

Alternative oxidase: a respiratory electron transport chain pathway essential for maintaining photosynthetic performance during drought stress.

PubMed

Vanlerberghe, Greg C; Martyn, Greg D; Dahal, Keshav

2016-07-01

Photosynthesis and respiration are the hubs of energy metabolism in plants. Drought strongly perturbs photosynthesis as a result of both diffusive limitations resulting from stomatal closure, and in some cases biochemical limitations that are associated with a reduced abundance of key photosynthetic components. The effects of drought on respiration, particularly respiration in the light (RL ), are less understood. The plant mitochondrial electron transport chain includes a non-energy conserving terminal oxidase called alternative oxidase (AOX). Several studies have shown that drought increases AOX transcript, protein and maximum capacity. Here we review recent studies comparing wild-type (WT) tobacco to transgenic lines with altered AOX protein amount. Specifically during drought, RL was compromised in AOX knockdown plants and enhanced in AOX overexpression plants, compared with WT. Significantly, these differences in RL were accompanied by dramatic differences in photosynthetic performance. Knockdown of AOX increased the susceptibility of photosynthesis to drought-induced biochemical limitations, while overexpression of AOX delayed the development of such biochemical limitations, compared with WT. Overall, the results indicate that AOX is essential to maintaining RL during drought, and that this non-energy conserving respiration maintains photosynthesis during drought by promoting energy balance in the chloroplast. This review also outlines several areas for future research, including the possibility that enhancement of non-energy conserving respiratory electron sinks may be a useful biotechnological approach to increase plant performance during stress. © 2016 Scandinavian Plant Physiology Society.

Intestinal Lymphatic Transport: an Overlooked Pathway for Understanding Absorption of Plant Secondary Compounds in Vertebrate Herbivores.

PubMed

Kohl, Kevin D; Dearing, M Denise

2017-03-01

Herbivores employ numerous strategies to reduce their exposure to toxic plant secondary chemicals (PSCs). However, the physiological mechanisms of PSC absorption have not been extensively explored. In particular, the absorption of PSCs via intestinal lymphatic absorption has been largely overlooked in herbivores, even though this pathway is well recognized for pharmaceutical uptake. Here, we investigated for the first time whether PSCs might be absorbed by lymphatic transport. We fed woodrats (Neotoma albigula) diets with increasing concentrations of terpene-rich juniper (Juniperus monosperma) either with or without a compound that blocks intestinal lymphatic absorption (Pluronic L-81). Woodrats consuming diets that contained the intestinal lymphatic absorption blocker exhibited increased food intakes and maintained higher body masses on juniper diets. Our study represents the first demonstration that PSCs may be absorbed by intestinal lymphatic absorption. This absorption pathway has numerous implications for the metabolism and distribution of PSCs in the systemic circulation, given that compounds absorbed via lymphatic transport bypass first-pass hepatic metabolism. The area of lymphatic transport of PSCs represents an understudied physiological pathway in plant-herbivore interactions.

Study of transport of laser-driven relativistic electrons in solid materials

NASA Astrophysics Data System (ADS)

Leblanc, Philippe

With the ultra intense lasers available today, it is possible to generate very hot electron beams in solid density materials. These intense laser-matter interactions result in many applications which include the generation of ultrashort secondary sources of particles and radiation such as ions, neutrons, positrons, x-rays, or even laser-driven hadron therapy. For these applications to become reality, a comprehensive understanding of laser-driven energy transport including hot electron generation through the various mechanisms of ionization, and their subsequent transport in solid density media is required. This study will focus on the characterization of electron transport effects in solid density targets using the state-of- the-art particle-in-cell code PICLS. A number of simulation results will be presented on the topics of ionization propagation in insulator glass targets, non-equilibrium ionization modeling featuring electron impact ionization, and electron beam guiding by the self-generated resistive magnetic field. An empirically derived scaling relation for the resistive magnetic in terms of the laser parameters and material properties is presented and used to derive a guiding condition. This condition may prove useful for the design of future laser-matter interaction experiments.

Simulations of electron transport and ignition for direct-drive fast-ignition targets

NASA Astrophysics Data System (ADS)

Solodov, A. A.; Anderson, K. S.; Betti, R.; Gotcheva, V.; Myatt, J.; Delettrez, J. A.; Skupsky, S.; Theobald, W.; Stoeckl, C.

2008-11-01

The performance of high-gain, fast-ignition fusion targets is investigated using one-dimensional hydrodynamic simulations of implosion and two-dimensional (2D) hybrid fluid-particle simulations of hot-electron transport, ignition, and burn. The 2D/3D hybrid-particle-in-cell code LSP [D. R. Welch et al., Nucl. Instrum. Methods Phys. Res. A 464, 134 (2001)] and the 2D fluid code DRACO [P. B. Radha et al., Phys. Plasmas 12, 056307 (2005)] are integrated to simulate the hot-electron transport and heating for direct-drive fast-ignition targets. LSP simulates the transport of hot electrons from the place where they are generated to the dense fuel core where their energy is absorbed. DRACO includes the physics required to simulate compression, ignition, and burn of fast-ignition targets. The self-generated resistive magnetic field is found to collimate the hot-electron beam, increase the coupling efficiency of hot electrons with the target, and reduce the minimum energy required for ignition. Resistive filamentation of the hot-electron beam is also observed. The minimum energy required for ignition is found for hot electrons with realistic angular spread and Maxwellian energy-distribution function.

Stepping stones in the electron transport from cells to electrodes in Geobacter sulfurreducens biofilms.

PubMed

Bonanni, Pablo Sebastián; Massazza, Diego; Busalmen, Juan Pablo

2013-07-07

Geobacter sulfurreducens bacteria grow on biofilms and have the particular ability of using polarized electrodes as the final electron acceptor of their respiratory chain. In these biofilms, electrons are transported through distances of more than 50 μm before reaching the electrode. The way in which electrons are transported across the biofilm matrix through such large distances remains under intense discussion. None of the two mechanisms proposed for explaining the process, electron hopping through outer membrane cytochromes and metallic like conduction through conductive PilA filaments, can account for all the experimental evidence collected so far. Aiming at providing new elements for understanding the basis for electron transport, in this perspective article we present a modelled structure of Geobacter pilus. Its analysis in combination with already existing experimental evidence gives support to the proposal of the "stepping stone" mechanism, in which the combined action of pili and cytochromes allows long range electron transport through the biofilm.

Experimental Studies of Lateral Electron Transport in Gallium Arsenide-Aluminum Gallium Arsenide Heterostructures.

DTIC Science & Technology

1982-12-01

AD-A125 858 EXPERIMENTAL STUDIES OF LATERAL ELECTRON TRANSPORT IN 1/3 GALLIUM ARSENIDE-RL..(U) ILLINOIS UNIV AT URBANA COORDINATED SCIENCE LAB N R...EXPERIMENTAL STUDIES OF LATERALXILECTRON TRANSPORT ,:g IN GALLIUM ARSENIDE -ALUMINUM GALLIUM ARSENIDE- -HETEROSTRUCTURES APRVE O PUBLICRLEAS.DSRBUINULMTE. 2...EXPERIMENTAL STUDIES OF LATERAL ELECTRON TRANSPORT IN GALLIUM ARSENIDE-ALUMINUM GALLIUM ARSENIDE Technical Report R-975 HETEROSTRUCTURES 6. PERFORMING ONG

Inelastic transport and low-bias rectification in a single-molecule diode.

PubMed

Hihath, Joshua; Bruot, Christopher; Nakamura, Hisao; Asai, Yoshihiro; Díez-Pérez, Ismael; Lee, Youngu; Yu, Luping; Tao, Nongjian

2011-10-25

Designing, controlling, and understanding rectification behavior in molecular-scale devices has been a goal of the molecular electronics community for many years. Here we study the transport behavior of a single molecule diode, and its nonrectifying, symmetric counterpart at low temperatures, and at both low and high biases to help elucidate the electron-phonon interactions and transport mechanisms in the rectifying system. We find that the onset of current rectification occurs at low biases, indicating a significant change in the elastic transport pathway. However, the peaks in the inelastic electron tunneling (IET) spectrum are antisymmetric about zero bias and show no significant changes in energy or intensity in the forward or reverse bias directions, indicating that despite the change in the elastic transmission probability there is little impact on the inelastic pathway. These results agree with first principles calculations performed to evaluate the IETS, which also allow us to identify which modes are active in the single molecule junction.

Quantum transport through disordered 1D wires: Conductance via localized and delocalized electrons

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gopar, Víctor A.

Coherent electronic transport through disordered systems, like quantum wires, is a topic of fundamental and practical interest. In particular, the exponential localization of electron wave functions-Anderson localization-due to the presence of disorder has been widely studied. In fact, Anderson localization, is not an phenomenon exclusive to electrons but it has been observed in microwave and acoustic experiments, photonic materials, cold atoms, etc. Nowadays, many properties of electronic transport of quantum wires have been successfully described within a scaling approach to Anderson localization. On the other hand, anomalous localization or delocalization is, in relation to the Anderson problem, a less studiedmore » phenomenon. Although one can find signatures of anomalous localization in very different systems in nature. In the problem of electronic transport, a source of delocalization may come from symmetries present in the system and particular disorder configurations, like the so-called Lévy-type disorder. We have developed a theoretical model to describe the statistical properties of transport when electron wave functions are delocalized. In particular, we show that only two physical parameters determine the complete conductance distribution.« less

Color stable white phosphorescent organic light emitting diodes with red emissive electron transport layer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wook Kim, Jin; Yoo, Seung Il; Sung Kang, Jin

2015-06-28

We analyzed the performance of multi-emissive white phosphorescent organic light-emitting diodes (PHOLEDs) in relation to various red emitting sites of hole and electron transport layers (HTL and ETL). The shift of the recombination zone producing stable white emission in PHOLEDs was utilized as luminance was increased with red emission in its electron transport layer. Multi-emissive white PHOLEDs including the red light emitting electron transport layer yielded maximum external quantum efficiency of 17.4% with CIE color coordinates (−0.030, +0.001) shifting only from 1000 to 10 000 cd/m{sup 2}. Additionally, we observed a reduction of energy loss in the white PHOLED via Ir(piq){submore » 3} as phosphorescent red dopant in electron transport layer.« less

Fused electron deficient semiconducting polymers for air stable electron transport.

PubMed

Onwubiko, Ada; Yue, Wan; Jellett, Cameron; Xiao, Mingfei; Chen, Hung-Yang; Ravva, Mahesh Kumar; Hanifi, David A; Knall, Astrid-Caroline; Purushothaman, Balaji; Nikolka, Mark; Flores, Jean-Charles; Salleo, Alberto; Bredas, Jean-Luc; Sirringhaus, Henning; Hayoz, Pascal; McCulloch, Iain

2018-01-29

Conventional semiconducting polymer synthesis typically involves transition metal-mediated coupling reactions that link aromatic units with single bonds along the backbone. Rotation around these bonds contributes to conformational and energetic disorder and therefore potentially limits charge delocalisation, whereas the use of transition metals presents difficulties for sustainability and application in biological environments. Here we show that a simple aldol condensation reaction can prepare polymers where double bonds lock-in a rigid backbone conformation, thus eliminating free rotation along the conjugated backbone. This polymerisation route requires neither organometallic monomers nor transition metal catalysts and offers a reliable design strategy to facilitate delocalisation of frontier molecular orbitals, elimination of energetic disorder arising from rotational torsion and allowing closer interchain electronic coupling. These characteristics are desirable for high charge carrier mobilities. Our polymers with a high electron affinity display long wavelength NIR absorption with air stable electron transport in solution processed organic thin film transistors.

Electronic and transport properties of Cobalt-based valence tautomeric molecules and polymers

NASA Astrophysics Data System (ADS)

Chen, Yifeng; Calzolari, Arrigo; Buongiorno Nardelli, Marco

2011-03-01

The advancement of molecular spintronics requires further understandings of the fundamental electronic structures and transport properties of prototypical spintronics molecules and polymers. Here we present a density functional based theoretical study of the electronic structures of Cobalt-based valence tautomeric molecules Co III (SQ)(Cat)L Co II (SQ)2 L and their polymers, where SQ refers to the semiquinone ligand, and Cat the catecholate ligand, while L is a redox innocent backbone ligand. The conversion from low-spin Co III ground state to high-spin Co II excited state is realized by imposing an on-site potential U on the Co atom and elongating the Co-N bond. Transport properties are subsequently calculated by extracting electronic Wannier functions from these systems and computing the charge transport in the ballistic regime using a Non-Equilibrium Green's Function (NEGF) approach. Our transport results show distinct charge transport properties between low-spin ground state and high-spin excited state, hence suggesting potential spintronics devices from these molecules and polymers such as spin valves.

Cation-limited kinetic model for microbial extracellular electron transport via an outer membrane cytochrome C complex

PubMed Central

Okamoto, Akihiro; Tokunou, Yoshihide; Saito, Junki

2016-01-01

Outer-membrane c-type cytochrome (OM c-Cyt) complexes in several genera of iron-reducing bacteria, such as Shewanella and Geobacter, are capable of transporting electrons from the cell interior to extracellular solids as a terminal step of anaerobic respiration. The kinetics of this electron transport has implications for controlling the rate of microbial electron transport during bioenergy or biochemical production, iron corrosion, and natural mineral cycling. Herein, we review the findings from in-vivo and in-vitro studies examining electron transport kinetics through single OM c-Cyt complexes in Shewanella oneidensis MR-1. In-vitro electron flux via a purified OM c-Cyt complex, comprised of MtrA, B, and C proteins from S. oneidensis MR-1, embedded in a proteoliposome system is reported to be 10- to 100-fold faster compared with in-vivo estimates based on measurements of electron flux per cell and OM c-Cyts density. As the proteoliposome system is estimated to have 10-fold higher cation flux via potassium channels than electrons, we speculate that the slower rate of electron-coupled cation transport across the OM is responsible for the significantly lower electron transport rate that is observed in-vivo. As most studies to date have primarily focused on the energetics or kinetics of interheme electron hopping in OM c-Cyts in this microbial electron transport mechanism, the proposed model involving cation transport provides new insight into the rate detemining step of EET, as well as the role of self-secreted flavin molecules bound to OM c-Cyt and proton management for energy conservation and production in S. oneidensis MR-1. PMID:27924259

Effect of Phase-Breaking Events on Electron Transport in Mesoscopic and Nanodevices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meunier, Vincent; Mintmire, John W; Thushari, Jayasekera

2008-01-01

Existing ballistic models for electron transport in mesoscopic and nanoscale systems break down as the size of the device becomes longer than the phase coherence length of electrons in the system. Krstic et al. experimentally observed that the current in single-wall carbon nanotube systems can be regarded as a combination of a coherent part and a noncoherent part. In this article, we discuss the use of Buettiker phase-breaking technique to address partially coherent electron transport, generalize that to a multichannel problem, and then study the effect of phase-breaking events on the electron transport in two-terminal graphene nanoribbon devices. We alsomore » investigate the difference between the pure-phase randomization and phase/momentum randomization boundary conditions. While momentum randomization adds an extra resistance caused by backward scattering, pure-phase randomization smooths the conductance oscillations because of interference.« less

Nonequilibrium distribution functions in electron transport: decoherence, energy redistribution and dissipation

NASA Astrophysics Data System (ADS)

Stegmann, Thomas; Ujsághy, Orsolya; Wolf, Dietrich E.

2018-04-01

A new statistical model for the combined effects of decoherence, energy redistribution and dissipation on electron transport in large quantum systems is introduced. The essential idea is to consider the electron phase information to be lost only at randomly chosen regions with an average distance corresponding to the decoherence length. In these regions the electron's energy can be unchanged or redistributed within the electron system or dissipated to a heat bath. The different types of scattering and the decoherence leave distinct fingerprints in the energy distribution functions. They can be interpreted as a mixture of unthermalized and thermalized electrons. In the case of weak decoherence, the fraction of thermalized electrons show electrical and thermal contact resistances. In the regime of incoherent transport the proposed model is equivalent to a Boltzmann equation. The model is applied to experiments with carbon nanotubes. The excellent agreement of the model with the experimental data allows to determine the scattering lengths of the system.

From hopping to ballistic transport in graphene-based electronic devices

NASA Astrophysics Data System (ADS)

Taychatanapat, Thiti

This thesis describes electronic transport experiments in graphene from the hopping to the ballistic regime. The first experiment studies dual-gated bilayer graphene devices. By applying an electric field with these dual gates, we can open a band gap in bilayer graphene and observe an increase in resistance of over six orders of magnitude as well as a strongly non-linear behavior in the transport characteristics. A temperature-dependence study of resistance at large electric field at the charge neutrality point shows the change in the transport mechanism from a hopping dominated regime at low temperature to a diffusive regime at high temperature. The second experiment examines electronic properties of Bernal-stacked trilayer graphene. Due to the low mobility of trilayer graphene on SiO 2substrates, we employ hexagonal boron nitride as a local substrate to improve its mobility. This led us to observe a quantum Hall effect with multiple Landau level crossings, proving the coexistence of massless and massive Dirac fermions in Bernal-stacked trilayer graphene. From the position of these crossing points in magnetic field and electron density, we can deduce the band parameters used to model its band structure. At high magnetic field, we observe broken symmetry states via Landau level splittings as well as crossings among these broken-symmetry states. In the third experiment, we investigate transverse magnetic focusing (TMF) in mono-, bi-, and tri-layer graphene. The ability to tune density allows us to electronically modify focal points and investigate TMF continuously from hole to electron regimes. This also allows us to observe the change in band structure of trilayer graphene as a function of applied electric field. Finally, we also observe TMF at room temperature in monolayer graphene which unambiguously proves the existence of ballistic transport at room temperature.

Copper silicide/silicon nanowire heterostructures: in situ TEM observation of growth behaviors and electron transport properties.

PubMed

Chiu, Chung-Hua; Huang, Chun-Wei; Chen, Jui-Yuan; Huang, Yu-Ting; Hu, Jung-Chih; Chen, Lien-Tai; Hsin, Cheng-Lun; Wu, Wen-Wei

2013-06-07

Copper silicide has been studied in the applications of electronic devices and catalysts. In this study, Cu3Si/Si nanowire heterostructures were fabricated through solid state reaction in an in situ transmission electron microscope (TEM). The dynamic diffusion of the copper atoms in the growth process and the formation mechanism are characterized. We found that two dimensional stacking faults (SF) may retard the growth of Cu3Si. Due to the evidence of the block of edge-nucleation (heterogeneous) by the surface oxide, center-nucleation (homogeneous) is suggested to dominate the silicidation. Furthermore, the electrical transport properties of various silicon channel length with Cu3Si/Si heterostructure interfaces and metallic Cu3Si NWs have been investigated. The observations not only provided an alternative pathway to explore the formation mechanisms and interface properties of Cu3Si/Si, but also suggested the potential application of Cu3Si at nanoscale for future processing in nanotechnology.

Increased expression of electron transport chain genes in uterine leiomyoma.

PubMed

Tuncal, Akile; Aydin, Hikmet Hakan; Askar, Niyazi; Ozkaya, Ali Burak; Ergenoglu, Ahmet Mete; Yeniel, Ahmet Ozgur; Akdemir, Ali; Ak, Handan

2014-01-01

The etiology and pathophysiology of uterine leiomyomas, benign smooth muscle tumors of the uterus, are not well understood. To evaluate the role of mitochondria in uterine leiomyoma, we compared electron transport gene expressions of uterine leiomyoma tissue with myometrium tissue in six uterine leiomyoma patients by RT-PCR array. Our results showed an average of 1.562 (±0.445) fold increase in nuclear-encoded electron transport genes. These results might suggest an increase in size, number, or activity of mitochondria in uterine leiomyoma that, to our knowledge, has not been previously reported. © 2014 by the Association of Clinical Scientists, Inc.

Spatial interferences in the electron transport of heavy-fermion materials

NASA Astrophysics Data System (ADS)

Zhang, Shu-feng; Liu, Yu; Song, Hai-Feng; Yang, Yi-feng

2016-08-01

The scanning tunneling microscopy/spectroscopy and the point contact spectroscopy represent major progress in recent heavy-fermion research. Both have revealed important information on the composite nature of the emergent heavy-electron quasiparticles. However, a detailed and thorough microscopic understanding of the similarities and differences in the underlying physical processes of these techniques is still lacking. Here we study the electron transport in the normal state of the periodic Anderson lattice by using the Keldysh nonequilibrium Green's function technique. In addition to the well-known Fano interference between the conduction and f -electron channels, our results further reveal the effect of spatial interference between different spatial paths at the interface on the differential conductance and their interesting interplay with the band features such as the hybridization gap and the Van Hove singularity. We find that the spatial interference leads to a weighted average in the momentum space for the electron transport and could cause suppression of the electronic band features under certain circumstances. In particular, it reduces the capability of probing the f -electron spectral weight near the edges of the hybridization gap for large interface depending on the Fermi surface of the lead. Our results indicate an intrinsic inefficiency of the point contact spectroscopy in probing the f electrons.

Correlating electronic transport to atomic structures in self-assembled quantum wires.

PubMed

Qin, Shengyong; Kim, Tae-Hwan; Zhang, Yanning; Ouyang, Wenjie; Weitering, Hanno H; Shih, Chih-Kang; Baddorf, Arthur P; Wu, Ruqian; Li, An-Ping

2012-02-08

Quantum wires, as a smallest electronic conductor, are expected to be a fundamental component in all quantum architectures. The electronic conductance in quantum wires, however, is often dictated by structural instabilities and electron localization at the atomic scale. Here we report on the evolutions of electronic transport as a function of temperature and interwire coupling as the quantum wires of GdSi(2) are self-assembled on Si(100) wire-by-wire. The correlation between structure, electronic properties, and electronic transport are examined by combining nanotransport measurements, scanning tunneling microscopy, and density functional theory calculations. A metal-insulator transition is revealed in isolated nanowires, while a robust metallic state is obtained in wire bundles at low temperature. The atomic defects lead to electron localizations in isolated nanowire, and interwire coupling stabilizes the structure and promotes the metallic states in wire bundles. This illustrates how the conductance nature of a one-dimensional system can be dramatically modified by the environmental change on the atomic scale. © 2012 American Chemical Society

Out-of-plane electron transport in finite layer MoS2

NASA Astrophysics Data System (ADS)

Holzapfel, R.; Weber, J.; Lukashev, P. V.; Stollenwerk, A. J.

2018-05-01

Ballistic electron emission microscopy (BEEM) has been used to study the processes affecting electron transport along the [0001] direction of finite layer MoS2 flakes deposited onto the surface of Au/Si(001) Schottky diodes. Prominent features present in the differential spectra from the MoS2 flakes are consistent with the density of states of finite layer MoS2 calculated using density functional theory. The ability to observe the electronic structure of the MoS2 appears to be due to the relatively smooth density of states of Si in this energy range and a substantial amount of elastic or quasi-elastic scattering along the MoS2/Au/Si(001) path. Demonstration of these measurements using BEEM suggests that this technique could potentially be used to study electron transport through van der Waals heterostructures, with applications in a number of electronic devices.

Telegraph noise in Markovian master equation for electron transport through molecular junctions

NASA Astrophysics Data System (ADS)

Kosov, Daniel S.

2018-05-01

We present a theoretical approach to solve the Markovian master equation for quantum transport with stochastic telegraph noise. Considering probabilities as functionals of a random telegraph process, we use Novikov's functional method to convert the stochastic master equation to a set of deterministic differential equations. The equations are then solved in the Laplace space, and the expression for the probability vector averaged over the ensemble of realisations of the stochastic process is obtained. We apply the theory to study the manifestations of telegraph noise in the transport properties of molecular junctions. We consider the quantum electron transport in a resonant-level molecule as well as polaronic regime transport in a molecular junction with electron-vibration interaction.

The vacuole system is a significant intracellular pathway for longitudinal solute transport in basidiomycete fungi.

PubMed

Darrah, P R; Tlalka, M; Ashford, A; Watkinson, S C; Fricker, M D

2006-07-01

Mycelial fungi have a growth form which is unique among multicellular organisms. The data presented here suggest that they have developed a unique solution to internal solute translocation involving a complex, extended vacuole. In all filamentous fungi examined, this extended vacuole forms an interconnected network, dynamically linked by tubules, which has been hypothesized to act as an internal distribution system. We have tested this hypothesis directly by quantifying solute movement within the organelle by photobleaching a fluorescent vacuolar marker. Predictive simulation models were then used to determine the transport characteristics over extended length scales. This modeling showed that the vacuolar organelle forms a functionally important, bidirectional diffusive transport pathway over distances of millimeters to centimeters. Flux through the pathway is regulated by the dynamic tubular connections involving homotypic fusion and fission. There is also a strongly predicted interaction among vacuolar organization, predicted diffusion transport distances, and the architecture of the branching colony margin.

Electronic transport behavior of diameter-graded Ag nanowires

NASA Astrophysics Data System (ADS)

Wang, Xue Wei; Yuan, Zhi Hao

2010-05-01

Ag nanowires with a graded diameter in anodic aluminum oxide (AAO) membranes were fabricated by the direct-current electrodeposition. The Ag nanowires have a graded-change in diameter from 8 to 32 nm, which is matched with the graded-change of the AAO pore diameter. Electronic transport measurements show that there is a transport behavior similar to that of a metal-semiconductor junction along the axial direction in the diameter-graded Ag nanowires. Such a novel homogeneous nanojunction will be of great fundamental and practical significance.

Electron effects in the Neutralized Transport Experiment (NTX)

NASA Astrophysics Data System (ADS)

Eylon, S.; Henestroza, E.; Roy, P. K.; Yu, S. S.

2005-05-01

The Neutralized Transport Experiment (NTX) at the Heavy Ion Fusion Virtual National Laboratory is exploring the performance of neutralized final focus systems for high-perveance heavy ion beams. To focus a high-intensity beam to a small spot requires a high-brightness beam. In the NTX experiment, a potassium ion beam of up to 400 keV and 80 mA is generated in a Pierce-type diode. At the diode exit, an aperture with variable opening provides the capability to vary the beam perveance. The beam is transported through four quadrupole magnets to a distance of 2.5 m. The beam can be neutralized and focused using a MEVVA plasma plug and a RF plasma source. We shall report on the measurement of the electron effects and the ways to mitigate the effects. Furthermore, we shall present the results of EGUN calculations consistent with the measurements effects of the electrons.

RECOVERY ACT - Thylakoid Assembly and Folded Protein Transport by the Tat Pathway

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dabney-Smith, Carole

Assembly of functional photosystems complete with necessary intrinsic (membrane-bound) and extrinsic proteins requires the function of at least 3 protein transport pathways in thylakoid membranes. Our research focuses on one of those pathways, a unique and essential protein transport pathway found in the chloroplasts of plants, bacteria, and some archaebacteria, the Twin arginine translocation (Tat) system. The chloroplast Tat (cpTat) system is thought to be responsible for the proper location of ~50% of thylakoid lumen proteins, several of which are necessary for proper photosystem assembly, maintenance, and function. Specifically, cpTat systems are unique because they transport fully folded and assembledmore » proteins across ion tight membranes using only three membrane components, Tha4, Hcf106, and cpTatC, and the protonmotive force generated by photosynthesis. Despite the importance of the cpTat system in plants, the mechanism of transport of a folded precursor is not well known. Our long-term goal is to investigate the role protein transport systems have on organelle biogenesis, particularly the assembly of membrane protein complexes in thylakoids of chloroplasts. The objective of this proposal is to correlate structural changes in the membrane-bound cpTat component, Tha4, to the mechanism of translocation of folded-precursor substrates across the membrane bilayer by using a cysteine accessibility and crosslinking approach. Our central hypothesis is that the precursor passes through a proteinaceous pore of assembled Tha4 protomers that have undergone a conformational or topological change in response to transport. This research is predicated upon the observations that Tha4 exists in molar excess in the membrane relative to the other cpTat components; its regulated assembly to the precursor-bound receptor; and our data showing oligomerization of Tha4 into very large complexes in response to transport. Our rationale for these studies is that understanding cp

Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology.

PubMed

Karp, Peter D; Latendresse, Mario; Paley, Suzanne M; Krummenacker, Markus; Ong, Quang D; Billington, Richard; Kothari, Anamika; Weaver, Daniel; Lee, Thomas; Subhraveti, Pallavi; Spaulding, Aaron; Fulcher, Carol; Keseler, Ingrid M; Caspi, Ron

2016-09-01

Pathway Tools is a bioinformatics software environment with a broad set of capabilities. The software provides genome-informatics tools such as a genome browser, sequence alignments, a genome-variant analyzer and comparative-genomics operations. It offers metabolic-informatics tools, such as metabolic reconstruction, quantitative metabolic modeling, prediction of reaction atom mappings and metabolic route search. Pathway Tools also provides regulatory-informatics tools, such as the ability to represent and visualize a wide range of regulatory interactions. This article outlines the advances in Pathway Tools in the past 5 years. Major additions include components for metabolic modeling, metabolic route search, computation of atom mappings and estimation of compound Gibbs free energies of formation; addition of editors for signaling pathways, for genome sequences and for cellular architecture; storage of gene essentiality data and phenotype data; display of multiple alignments, and of signaling and electron-transport pathways; and development of Python and web-services application programming interfaces. Scientists around the world have created more than 9800 Pathway/Genome Databases by using Pathway Tools, many of which are curated databases for important model organisms. © The Author 2015. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Theory of Electron, Phonon and Spin Transport in Nanoscale Quantum Devices.

PubMed

Sadeghi, Hatef

2018-06-21

At the level of fundamental science, it was recently demonstrated that molecular wires can mediate long-range phase-coherent tunnelling with remarkably low attenuation over a few nanometre even at room temperature. Furthermore, a large mean free path has been observed in graphene and other graphene-like two-dimensional materials. These create the possibility of using quantum and phonon interference to engineer electron and phonon transport for wide range of applications such as molecular switches, sensors, piezoelectricity, thermoelectricity and thermal management. To understand transport properties of such devices, it is crucial to calculate their electronic and phononic transmission coefficients. The aim of this tutorial article is to review the state-of-art theoretical and mathematical techniques to treat electron, phonon and spin transport in nanoscale molecular junctions. This helps not only to explain new phenomenon observed experimentally but also provides a vital design tool to develop novel nanoscale quantum devices. © 2018 IOP Publishing Ltd.

Dispersive electron transport in tris(8-hydroxyquinoline) aluminum (Alq3) probed by impedance spectroscopy.

PubMed

Berleb, Stefan; Brütting, Wolfgang

2002-12-31

Electron transport in tris(8-hydroxyquinoline) aluminum (Alq3) is investigated by impedance spectroscopy under conditions of space-charge limited conduction (SCLC). Existing SCLC models are extended to include the field dependence of the charge carrier mobility and energetically distributed trap states. The dispersive nature of electron transport is revealed by a frequency-dependent mobility with a dispersion parameter alpha in the range 0.4-0.5, independent of temperature. This indicates that positional rather than energetic disorder is the dominant mechanism for the dispersive transport of electrons in Alq3.

Using Adobe Flash Animations of Electron Transport Chain to Teach and Learn Biochemistry

ERIC Educational Resources Information Center

Teplá, Milada; Klímová, Helena

2015-01-01

Teaching the subject of the electron transport chain is one of the most challenging aspects of the chemistry curriculum at the high school level. This article presents an educational program called "Electron Transport Chain" which consists of 14 visual animations including a biochemistry quiz. The program was created in the Adobe Flash…

Electronic Structure and Transport in Solids from First Principles

NASA Astrophysics Data System (ADS)

Mustafa, Jamal Ibrahim

The focus of this dissertation is the determination of the electronic structure and trans- port properties of solids. We first review some of the theory and computational methodology used in the calculation of electronic structure and materials properties. Throughout the dissertation, we make extensive use of state-of-the-art software packages that implement density functional theory, density functional perturbation theory, and the GW approximation, in addition to specialized methods for interpolating matrix elements for extremely accurate results. The first application of the computational framework introduced is the determination of band offsets in semiconductor heterojunctions using a theory of quantum dipoles at the interface. This method is applied to the case of heterojunction formed between a new metastable phase of silicon, with a rhombohedral structure, and cubic silicon. Next, we introduce a novel method for the construction of localized Wannier functions, which we have named the optimized projection functions method (OPFM). We illustrate the method on a variety of systems and find that it can reliably construct localized Wannier functions with minimal user intervention. We further develop the OPFM to investigate a class of materials called topological insulators, which are insulating in the bulk but have conductive surface states. These properties are a result of a nontrivial topology in their band structure, which has interesting effects on the character of the Wannier functions. In the last sections of the main text, the noble metals are studied in great detail, including their electronic properties and carrier dynamics. In particular, we investigate, the Fermi surface properties of the noble metals, specifically electron-phonon scattering lifetimes, and subsequently the transport properties determined by carriers on the Fermi surface. To achieve this, a novel sampling technique is developed, with wide applicability to transport calculations

Structural control of mixed ionic and electronic transport in conducting polymers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rivnay, Jonathan; Inal, Sahika; Collins, Brian A.

Poly(3,4-ethylenedioxythiophene) doped with poly(styrenesulfonate), PEDOT:PSS, has been utilized for over two decades as a stable, solution-processable hole conductor. While its hole transport properties have been the subject of intense investigation, recent work has turned to PEDOT:PSS as a mixed ionic/electronic conductor in applications including bioelectronics, energy storage and management, and soft robotics. Conducting polymers can efficiently transport both holes and ions when sufficiently hydrated, however, little is known about the role of morphology on mixed conduction. Here, we show that bulk ionic and electronic mobilities are simultaneously affected by processing-induced changes in nano- and meso-scale structure in PEDOT:PSS films. Wemore » quantify domain composition, and find that domain purification on addition of dispersion co-solvents limits ion mobility, even while electronic conductivity improves. We show that an optimal morphology allows for the balanced ionic and electronic transport that is critical for prototypical mixed conductor devices. As a result, these findings may pave the way for the rational design of polymeric materials and processing routes to enhance devices reliant on mixed conduction.« less

Structural control of mixed ionic and electronic transport in conducting polymers

DOE PAGES

Rivnay, Jonathan; Inal, Sahika; Collins, Brian A.; ...

2016-04-19

Poly(3,4-ethylenedioxythiophene) doped with poly(styrenesulfonate), PEDOT:PSS, has been utilized for over two decades as a stable, solution-processable hole conductor. While its hole transport properties have been the subject of intense investigation, recent work has turned to PEDOT:PSS as a mixed ionic/electronic conductor in applications including bioelectronics, energy storage and management, and soft robotics. Conducting polymers can efficiently transport both holes and ions when sufficiently hydrated, however, little is known about the role of morphology on mixed conduction. Here, we show that bulk ionic and electronic mobilities are simultaneously affected by processing-induced changes in nano- and meso-scale structure in PEDOT:PSS films. Wemore » quantify domain composition, and find that domain purification on addition of dispersion co-solvents limits ion mobility, even while electronic conductivity improves. We show that an optimal morphology allows for the balanced ionic and electronic transport that is critical for prototypical mixed conductor devices. As a result, these findings may pave the way for the rational design of polymeric materials and processing routes to enhance devices reliant on mixed conduction.« less

The CHC22 Clathrin-GLUT4 Transport Pathway Contributes to Skeletal Muscle Regeneration

PubMed Central

Griffin, Christine A.; Esk, Christopher; Torres, Jorge A.; Ohkoshi, Norio; Ishii, Akiko; Tamaoka, Akira; Funke, Birgit H.; Kucherlapati, Raju; Margeta, Marta; Rando, Thomas A.; Brodsky, Frances M.

2013-01-01

Mobilization of the GLUT4 glucose transporter from intracellular storage vesicles provides a mechanism for insulin-responsive glucose import into skeletal muscle. In humans, clathrin isoform CHC22 participates in formation of the GLUT4 storage compartment in skeletal muscle and fat. CHC22 function is limited to retrograde endosomal sorting and is restricted in its tissue expression and species distribution compared to the conserved CHC17 isoform that mediates endocytosis and several other membrane traffic pathways. Previously, we noted that CHC22 was expressed at elevated levels in regenerating rat muscle. Here we investigate whether the GLUT4 pathway in which CHC22 participates could play a role in muscle regeneration in humans and we test this possibility using CHC22-transgenic mice, which do not normally express CHC22. We observed that GLUT4 expression is elevated in parallel with that of CHC22 in regenerating skeletal muscle fibers from patients with inflammatory and other myopathies. Regenerating human myofibers displayed concurrent increases in expression of VAMP2, another regulator of GLUT4 transport. Regenerating fibers from wild-type mouse skeletal muscle injected with cardiotoxin also showed increased levels of GLUT4 and VAMP2. We previously demonstrated that transgenic mice expressing CHC22 in their muscle over-sequester GLUT4 and VAMP2 and have defective GLUT4 trafficking leading to diabetic symptoms. In this study, we find that muscle regeneration rates in CHC22 mice were delayed compared to wild-type mice, and myoblasts isolated from these mice did not proliferate in response to glucose. Additionally, CHC22-expressing mouse muscle displayed a fiber type switch from oxidative to glycolytic, similar to that observed in type 2 diabetic patients. These observations implicate the pathway for GLUT4 transport in regeneration of both human and mouse skeletal muscle, and demonstrate a role for this pathway in maintenance of muscle fiber type. Extrapolating

Electronic transport characterization of silicon wafers by spatially resolved steady-state photocarrier radiometric imaging

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Qian; University of the Chinese Academy of Sciences, Beijing 100039; Li, Bincheng, E-mail: bcli@ioe.ac.cn

2015-09-28

Spatially resolved steady-state photocarrier radiometric (PCR) imaging technique is developed to characterize the electronic transport properties of silicon wafers. Based on a nonlinear PCR theory, simulations are performed to investigate the effects of electronic transport parameters (the carrier lifetime, the carrier diffusion coefficient, and the front surface recombination velocity) on the steady-state PCR intensity profiles. The electronic transport parameters of an n-type silicon wafer are simultaneously determined by fitting the measured steady-state PCR intensity profiles to the three-dimensional nonlinear PCR model. The determined transport parameters are in good agreement with the results obtained by the conventional modulated PCR technique withmore » multiple pump beam radii.« less

Towards greener environment: Energy efficient pathways for the transportation sector in Malaysia

NASA Astrophysics Data System (ADS)

Indati, M. S.; Ghate, A. T.; Leong, Y. P.

2013-06-01

Transportation sector is the second most energy consuming sector after industrial sector, accounting for 40% of total energy consumption in Malaysia. The transportation sector is one of the most energy intensive sectors in the country and relies primarily on petroleum products, which in total account for nearly 98% of the total consumption in the sector. Since it is heavily reliant on petroleum based fuels, the sector contributes significantly to the greenhouse gas (GHG) emissions. The need to reduce the greenhouse gas emission is paramount as Malaysia at Conference of the Parties (COP15) pledged to reduce its carbon intensity by 40% by 2020 from 2005 level subject to availability of technology and finance. Transport sector will be among the first sectors that need to be addressed to achieve this goal, as two-thirds of the emissions come from fuel combustion in transport sector. This paper will analyse the factors influencing the transport sector's growth and energy consumption trends and discuss the key issues and challenges for greener environment and sustainable transportation in Malaysia. The paper will also discuss the policy and strategic options aimed towards energy efficient pathways in Malaysia.

Alternative ground states enable pathway switching in biological electron transfer

DOE PAGES

Abriata, Luciano A.; Alvarez-Paggi, Damian; Ledesma, Gabirela N.; ...

2012-10-10

Electron transfer is the simplest chemical reaction and constitutes the basis of a large variety of biological processes, such as photosynthesis and cellular respiration. Nature has evolved specific proteins and cofactors for these functions. The mechanisms optimizing biological electron transfer have been matter of intense debate, such as the role of the protein milieu between donor and acceptor sites. Here we propose a mechanism regulating long-range electron transfer in proteins. Specifically, we report a spectroscopic, electrochemical, and theoretical study on WT and single-mutant CuA redox centers from Thermus thermophilus, which shows that thermal fluctuations may populate two alternative ground-state electronicmore » wave functions optimized for electron entry and exit, respectively, through two different and nearly perpendicular pathways. In conclusion, these findings suggest a unique role for alternative or “invisible” electronic ground states in directional electron transfer. Moreover, it is shown that this energy gap and, therefore, the equilibrium between ground states can be fine-tuned by minor perturbations, suggesting alternative ways through which protein–protein interactions and membrane potential may optimize and regulate electron–proton energy transduction.« less

Electron transport in ferromagnetic nanostructures

NASA Astrophysics Data System (ADS)

Lee, Sungbae

As the size of a physical system decreases toward the nanoscale, quantum mechanical effects such as the discretization of energy levels and the interactions of the electronic spins become readily observable. To understand what happens within submicrometer scale samples is one of the goals of modern condensed matter physics. Electron transport phenomena drew a lot of attention over the past two decades or so, not only because quantum corrections to the classical transport theory, but also they allow us to probe deeply into the microscopic nature of the system put to test. Although a significant amount of research was done in the past and thus extended our understanding in this field, most of these works were concentrated on simpler examples. Electron transport in strongly correlated systems is still a field that needs to be explored more thoroughly. In fact, experimental works that have been done so far to characterize coherence physics in correlated systems such as ferromagnetic metals are far from conclusive. One reason ferromagnetic samples draw such attention is that there exist correlations that lead to excitations (e.g. spin waves, domain wall motions) not present in normal metals, and these new environmental degrees of freedom can have profound effects on decoherence processes. In this thesis, three different types of magnetic samples were examined: a band ferromagnetism based metallic ferromagnet, permalloy, a III-V diluted ferromagnetic semiconductor with ferromagnetism from a hole-mediated exchange interaction, and magnetite nanocrystals and films. The first observation of time-dependent universal conductance fluctuations (TD-UCF) in permalloy is presented and our observations lead to three major conclusions. First, the cooperon contribution to the conductance is suppressed in this material. This is consistent with some theoretical expectations, and implies that weak localization will be suppressed as well. Second, we see evidence that domain wall motion

Electron transport in gold colloidal nanoparticle-based strain gauges.

PubMed

Moreira, Helena; Grisolia, Jérémie; Sangeetha, Neralagatta M; Decorde, Nicolas; Farcau, Cosmin; Viallet, Benoit; Chen, Ke; Viau, Guillaume; Ressier, Laurence

2013-03-08

A systematic approach for understanding the electron transport mechanisms in resistive strain gauges based on assemblies of gold colloidal nanoparticles (NPs) protected by organic ligands is described. The strain gauges were fabricated from parallel micrometer wide wires made of 14 nm gold (Au) colloidal NPs on polyethylene terephthalate substrates, elaborated by convective self-assembly. Electron transport in such devices occurs by inter-particle electron tunneling through the tunnel barrier imposed by the organic ligands protecting the NPs. This tunnel barrier was varied by changing the nature of organic ligands coating the nanoparticles: citrate (CIT), phosphines (BSPP, TDSP) and thiols (MPA, MUDA). Electro-mechanical tests indicate that only the gold NPs protected by phosphine and thiol ligands yield high gauge sensitivity. Temperature-dependent resistance measurements are explained using the 'regular island array model' that extracts transport parameters, i.e., the tunneling decay constant β and the Coulomb charging energy E(C). This reveals that the Au@CIT nanoparticle assemblies exhibit a behavior characteristic of a strong-coupling regime, whereas those of Au@BSPP, Au@TDSP, Au@MPA and Au@MUDA nanoparticles manifest a weak-coupling regime. A comparison of the parameters extracted from the two methods indicates that the most sensitive gauges in the weak-coupling regime feature the highest β. Moreover, the E(C) values of these 14 nm NPs cannot be neglected in determining the β values.

Electron transport in gold colloidal nanoparticle-based strain gauges

NASA Astrophysics Data System (ADS)

Moreira, Helena; Grisolia, Jérémie; Sangeetha, Neralagatta M.; Decorde, Nicolas; Farcau, Cosmin; Viallet, Benoit; Chen, Ke; Viau, Guillaume; Ressier, Laurence

2013-03-01

A systematic approach for understanding the electron transport mechanisms in resistive strain gauges based on assemblies of gold colloidal nanoparticles (NPs) protected by organic ligands is described. The strain gauges were fabricated from parallel micrometer wide wires made of 14 nm gold (Au) colloidal NPs on polyethylene terephthalate substrates, elaborated by convective self-assembly. Electron transport in such devices occurs by inter-particle electron tunneling through the tunnel barrier imposed by the organic ligands protecting the NPs. This tunnel barrier was varied by changing the nature of organic ligands coating the nanoparticles: citrate (CIT), phosphines (BSPP, TDSP) and thiols (MPA, MUDA). Electro-mechanical tests indicate that only the gold NPs protected by phosphine and thiol ligands yield high gauge sensitivity. Temperature-dependent resistance measurements are explained using the ‘regular island array model’ that extracts transport parameters, i.e., the tunneling decay constant β and the Coulomb charging energy EC. This reveals that the Au@CIT nanoparticle assemblies exhibit a behavior characteristic of a strong-coupling regime, whereas those of Au@BSPP, Au@TDSP, Au@MPA and Au@MUDA nanoparticles manifest a weak-coupling regime. A comparison of the parameters extracted from the two methods indicates that the most sensitive gauges in the weak-coupling regime feature the highest β. Moreover, the EC values of these 14 nm NPs cannot be neglected in determining the β values.

The Impacts of Phosphorus Deficiency on the Photosynthetic Electron Transport Chain.

PubMed

Carstensen, Andreas; Herdean, Andrei; Schmidt, Sidsel Birkelund; Sharma, Anurag; Spetea, Cornelia; Pribil, Mathias; Husted, Søren

2018-05-01

Phosphorus (P) is an essential macronutrient, and P deficiency limits plant productivity. Recent work showed that P deficiency affects electron transport to photosystem I (PSI), but the underlying mechanisms are unknown. Here, we present a comprehensive biological model describing how P deficiency disrupts the photosynthetic machinery and the electron transport chain through a series of sequential events in barley ( Hordeum vulgare ). P deficiency reduces the orthophosphate concentration in the chloroplast stroma to levels that inhibit ATP synthase activity. Consequently, protons accumulate in the thylakoids and cause lumen acidification, which inhibits linear electron flow. Limited plastoquinol oxidation retards electron transport to the cytochrome b 6 f complex, yet the electron transfer rate of PSI is increased under steady-state growth light and is limited under high-light conditions. Under P deficiency, the enhanced electron flow through PSI increases the levels of NADPH, whereas ATP production remains restricted and, hence, reduces CO 2 fixation. In parallel, lumen acidification activates the energy-dependent quenching component of the nonphotochemical quenching mechanism and prevents the overexcitation of photosystem II and damage to the leaf tissue. Consequently, plants can be severely affected by P deficiency for weeks without displaying any visual leaf symptoms. All of the processes in the photosynthetic machinery influenced by P deficiency appear to be fully reversible and can be restored in less than 60 min after resupply of orthophosphate to the leaf tissue. © 2018 American Society of Plant Biologists. All Rights Reserved.

Advanced electronic displays and their potential in future transport aircraft

NASA Technical Reports Server (NTRS)

Hatfield, J. J.

1981-01-01

It is pointed out that electronic displays represent one of the keys to continued integration and improvement of the effectiveness of avionic systems in future transport aircraft. An employment of modern electronic display media and generation has become vital in connection with the increases in modes and functions of modern aircraft. Requirements for electronic systems of future transports are examined, and a description is provided of the tools which are available for cockpit integration, taking into account trends in information processing and presentation, trends in integrated display devices, and trends concerning input/output devices. Developments related to display media, display generation, and I/O devices are considered, giving attention to a comparison of CRT and flat-panel display technology, advanced HUD technology and multifunction controls. Integrated display formats are discussed along with integrated systems and cockpit configurations.

Unravelling the progressive role of rattlers in thermoelectric clathrate and strategies for performance improvement: Concurrently enhancing electronic transport and blocking phononic transport

NASA Astrophysics Data System (ADS)

Yang, Jia-Yue; Cheng, Long; Hu, Ming

2017-12-01

Intermetallic clathrates, one class of guest-host systems with perfectly crystalline structures, hold great potential to be the "phonon glass - electron crystal" thermoelectric materials. Previous studies focus on revealing the atomistic origins of blocked phononic transport, yet little attention is drawn to the enhanced electronic transport. In this work, we investigate the binary type-I M8Si46 (M = Sr, Ba, Tl, and Pb) clathrates and unravel how rattlers concurrently block phononic transport and enhance electronic transport from first-principles. By comparing the empty and filled clathrates, the lattice thermal conductivity is greatly reduced by a factor of 21 due to the decrease in phonon relaxation time for propagative phonons over 0-6 THz by 1.5 orders of magnitude. On the other hand, rattlers bridge charge gaps among cages by donating electrons and thus drastically increase electrical conductivity. The concurrent realization of blocked phononic transport and enhanced electronic transport boosts the figure-of-merit (ZT) of empty clathrate by 4 orders of magnitude. Furthermore, by manipulating metallic rattlers and n-type doping, the power factor is markedly improved and ZT can reach 0.55 at 800 K. These results provide a quantitative description of the guest-host interaction and coupling dynamics from first-principles. The proposed strategy of manipulating ratting atoms and in-situ doping offers important guidance to engineer clathrates with high thermoelectric performance.

Electronic thermal transport in strongly correlated multilayered nanostructures

NASA Astrophysics Data System (ADS)

Freericks, J. K.; Zlatić, V.; Shvaika, A. M.

2007-01-01

The formalism for a linear-response many-body treatment of the electronic contributions to thermal transport is developed for multilayered nanostructures. By properly determining the local heat-current operator, it is possible to show that the Jonson-Mahan theorem for the bulk can be extended to inhomogeneous problems, so the various thermal-transport coefficient integrands are related by powers of frequency (including all effects of vertex corrections when appropriate). We illustrate how to use this formalism by showing how it applies to measurements of the Peltier effect, the Seebeck effect, and the thermal conductance.

Electron Transfer Pathways Facilitating U(VI) Reduction by Fe(II) on Al- vs Fe-Oxides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taylor, S. D.; Becker, U.; Rosso, K. M.

This study continues mechanistic development of heterogeneous electron transfer (ET) pathways at mineral surfaces in aquatic environments that enable the reduction U(VI) by surface-associated Fe(II). Using computational molecular simulation within the framework of Marcus Theory, our findings highlight the importance of the configurations and interaction of the electron donor and acceptor species with the substrate, with respect to influencing its electronic structure and thereby the ability of semiconducting minerals to facilitate ET. U(VI) reduction by surface-associated Fe(II) (adsorbed or structurally incorporated into the lattice) on an insulating, corundum (001) surface (α-Al2O3) occurs when proximal inner-sphere (IS) surface complexes are formed,more » such that ET occurs through a combination of direct exchange (i.e., Fe d- and U f-orbitals overlap through space) and superexchange via intervening surface oxygen atoms. U(VI) reduction by coadsorbed Fe(II) on the isostructural semiconducting hematite (α-Fe2O3) basal surface requires either their direct electronic interaction (e.g., IS complexation) or mediation of this interaction indirectly through the surface via an intrasurface pathway. Conceptually possible longer-range ET by charge-hopping through surface Fe atoms was investigated to determine whether this indirect pathway is competitive with direct ET. The calculations show that energy barriers are large for this conduction-based pathway; interfacial ET into the hematite surface is endothermic (+80.1 kJ/mol) and comprises the rate-limiting step (10–6 s–1). The presence of the IS adsorbates appears to weaken the electronic coupling between underlying Fe ions within the surface, resulting in slower intra-surface ET (10–5 s–1) than expected in the bulk basal plane. Our findings lay out first insights into donor-acceptor communication via a charge-hopping pathway through the surface for heterogeneous reduction of U(VI) by Fe(II) and help provide

Bubble bursting as an aerosol generation mechanism during an oil spill in the deep-sea environment: laboratory experimental demonstration of the transport pathway.

PubMed

Ehrenhauser, Franz S; Avij, Paria; Shu, Xin; Dugas, Victoria; Woodson, Isaiah; Liyana-Arachchi, Thilanga; Zhang, Zenghui; Hung, Francisco R; Valsaraj, Kalliat T

2014-01-01

Oil spills in the deep-sea environment such as the 2010 Deep Water Horizon oil spill in the Gulf of Mexico release vast quantities of crude oil into the sea-surface environment. Various investigators have discussed the marine transport and fate of the oil into different environmental compartments (air, water, sediment, and biota). The transport of the oil into the atmosphere in these previous investigations has been limited to only evaporation, a volatility dependent pathway. In this work, we studied the aerosolization of oil spill matter via bursting bubbles as they occur during whitecaps in a laboratory aerosolization reactor. By evaluating the alkane content in oil mousse, crude oil, the gas phase, and particulate matter we clearly demonstrate that aerosolization via bursting bubbles is a solubility and volatility independent transport pathway for alkanes. The signature of alkane fractions in the native oil and aerosolized matter matched well especially for the less volatile alkanes (C20-C29). Scanning electron microscope interfaced with energy dispersive X-ray images identified the carbon fractions associated with salt particles of aerosols. Theoretical molecular dynamics simulations in the accompanying paper lend support to the observed propensity for alkanes at air-salt water interfaces of breaking bubbles and the produced droplets. The presence of a dispersant in the aqueous phase increased the oil ejection rate at the surface especially for the C20-C29 alkanes. The information presented here emphasizes the need to further study sea-spray aerosols as a possible transport vector for spilled oil in the sea surface environment.

Using Adobe Flash animations of electron transport chain to teach and learn biochemistry.

PubMed

Teplá, Milada; Klímová, Helena

2015-01-01

Teaching the subject of the electron transport chain is one of the most challenging aspects of the chemistry curriculum at the high school level. This article presents an educational program called "Electron Transport Chain" which consists of 14 visual animations including a biochemistry quiz. The program was created in the Adobe Flash CS3 Professional animation program and is designed for high school chemistry students. Our goal is to develop educational materials that facilitate the comprehension of this complex subject through dynamic animations which show the course of the electron transport chain and simultaneously explain its nature. We record the process of the electron transport chain, including connections with oxidative phosphorylation, in such a way as to minimize the occurrence of discrepancies in interpretation. The educational program was evaluated in high schools through the administration of a questionnaire, which contained 12 opened-ended items and which required participants to evaluate the graphics of the animations, chemical content, student preferences, and its suitability for high school biochemistry teaching. © 2015 The International Union of Biochemistry and Molecular Biology.

Geometric effects in the electronic transport of deformed nanotubes

NASA Astrophysics Data System (ADS)

Santos, Fernando; Fumeron, Sébastien; Berche, Bertrand; Moraes, Fernando

2016-04-01

Quasi-two-dimensional systems may exibit curvature, which adds three-dimensional influence to their internal properties. As shown by da Costa (1981 Phys. Rev. A 23 1982-7), charged particles moving on a curved surface experience a curvature-dependent potential which greatly influence their dynamics. In this paper, we study the electronic ballistic transport in deformed nanotubes. The one-electron Schrödinger equation with open boundary conditions is solved numerically with a flexible MAPLE code made available as supplementary data. We find that the curvature of the deformations indeed has strong effects on the electron dynamics, suggesting its use in the design of nanotube-based electronic devices.

Reactive transport simulations of alternative flow pathways in the ambient unsaturated zone at Yucca Mountain, Nevada

NASA Astrophysics Data System (ADS)

Browning, L.; Murphy, W.; Manepally, C.; Fedors, R.

2003-04-01

Uncertainties in simulated ambient system unsaturated zone flow could have a significant impact on performance evaluations of the proposed nuclear waste repository at Yucca Mountain, Nevada. In addition to determining variations in the quantity of water available to corrode engineered materials and transport radionuclides, model assumptions regarding flow pathways may significantly affect estimates of groundwater chemistry. The manner and extent to which groundwater compositions evolve along a flow pathway are determined mainly by thermohydrologic conditions, the types of reactive materials encountered, and the interaction times with those materials. Simulated groundwater compositions can thus vary significantly depending on whether or not the flow model includes lateral diversion of infiltrating waters, or preferential flow pathways in variably-saturated materials. To assist a regulatory review of a potential license application for a geologic repository for high-level waste, we developed a reactive transport model for the ambient hydrogeochemical system at Yucca Mountain. The model simulates two phase, nonisothermal, advective and diffusive flow and transport through a one dimensional, matrix and fracture continua (dual permeability) containing ten kinetically reactive hydrostatigraphic layers in the vicinity of the SD-9 borehole at Yucca Mountain. In this presentation, we describe how the model was used to evaluate alternative ambient unsaturated zone flow pathways proposed by the U.S. Department of Energy. This abstract is an independent product of the CNWRA and does not necessarily reflect the views or regulatory position of the NRC.

Plasmonic hot electron transport drives nano-localized chemistry

PubMed Central

Cortés, Emiliano; Xie, Wei; Cambiasso, Javier; Jermyn, Adam S.; Sundararaman, Ravishankar; Narang, Prineha; Schlücker, Sebastian; Maier, Stefan A.

2017-01-01

Nanoscale localization of electromagnetic fields near metallic nanostructures underpins the fundamentals and applications of plasmonics. The unavoidable energy loss from plasmon decay, initially seen as a detriment, has now expanded the scope of plasmonic applications to exploit the generated hot carriers. However, quantitative understanding of the spatial localization of these hot carriers, akin to electromagnetic near-field maps, has been elusive. Here we spatially map hot-electron-driven reduction chemistry with 15 nm resolution as a function of time and electromagnetic field polarization for different plasmonic nanostructures. We combine experiments employing a six-electron photo-recycling process that modify the terminal group of a self-assembled monolayer on plasmonic silver nanoantennas, with theoretical predictions from first-principles calculations of non-equilibrium hot-carrier transport in these systems. The resulting localization of reactive regions, determined by hot-carrier transport from high-field regions, paves the way for improving efficiency in hot-carrier extraction science and nanoscale regio-selective surface chemistry. PMID:28348402

Electronic and transport properties of BCN alloy nanoribbons

NASA Astrophysics Data System (ADS)

Darvishi Gilan, Mahdi; Chegel, Raad

2018-03-01

The dependence of the carbon (C) concentration on the electronic and transport properties of boron carbonitride (BCN) alloy nanoribbons have been investigated using surface Green's functions technique and random Hamiltonian model by considering random hopping parameters including first and second nearest neighbors. Our calculations indicate that substituting boron (nitrogen) sites with carbon atoms induces a new band close to conduction (valence) band and carbon atoms behave like a donor (acceptor) dopants. Also, while both nitrogen and boron sites are substituted randomly by carbon atoms, new bands are induced close to both valence and conduction bands. The band gap decreases with C substituting and the number of charge carriers increases in low bias voltage. Far from Fermi level in the higher range of energy, transmission coefficient and current of the system are reduced by increasing the C concentration. Based on our results, tuning the electronic and transport properties of BCN alloy nanoribbons by random carbon dopants could be applicable to design nanoelectronics devices.

Defect control of conventional and anomalous electron transport at complex oxide interfaces

DOE PAGES

Gunkel, F.; Bell, Chris; Inoue, Hisashi; ...

2016-08-30

Using low-temperature electrical measurements, the interrelation between electron transport, magnetic properties, and ionic defect structure in complex oxide interface systems is investigated, focusing on NdGaO 3/SrTiO 3 (100) interfaces. Field-dependent Hall characteristics (2–300 K) are obtained for samples grown at various growth pressures. In addition to multiple electron transport, interfacial magnetism is tracked exploiting the anomalous Hall effect (AHE). These two properties both contribute to a nonlinearity in the field dependence of the Hall resistance, with multiple carrier conduction evident below 30 K and AHE at temperatures ≲10 K. Considering these two sources of nonlinearity, we suggest a phenomenological modelmore » capturing the complex field dependence of the Hall characteristics in the low-temperature regime. Our model allows the extraction of the conventional transport parameters and a qualitative analysis of the magnetization. The electron mobility is found to decrease systematically with increasing growth pressure. This suggests dominant electron scattering by acceptor-type strontium vacancies incorporated during growth. The AHE scales with growth pressure. In conclusion, the most pronounced AHE is found at increased growth pressure and, thus, in the most defective, low-mobility samples, indicating a correlation between transport, magnetism, and cation defect concentration.« less

Modeling Electronic Quantum Transport with Machine Learning

DOE PAGES

Lopez Bezanilla, Alejandro; von Lilienfeld Toal, Otto A.

2014-06-11

We present a machine learning approach to solve electronic quantum transport equations of one-dimensional nanostructures. The transmission coefficients of disordered systems were computed to provide training and test data sets to the machine. The system’s representation encodes energetic as well as geometrical information to characterize similarities between disordered configurations, while the Euclidean norm is used as a measure of similarity. Errors for out-of-sample predictions systematically decrease with training set size, enabling the accurate and fast prediction of new transmission coefficients. The remarkable performance of our model to capture the complexity of interference phenomena lends further support to its viability inmore » dealing with transport problems of undulatory nature.« less

Charge transport and electron-hole asymmetry in low-mobility graphene/hexagonal boron nitride heterostructures

NASA Astrophysics Data System (ADS)

Li, Jiayu; Lin, Li; Huang, Guang-Yao; Kang, N.; Zhang, Jincan; Peng, Hailin; Liu, Zhongfan; Xu, H. Q.

2018-02-01

Graphene/hexagonal boron nitride (G/h-BN) heterostructures offer an excellent platform for developing nanoelectronic devices and for exploring correlated states in graphene under modulation by a periodic superlattice potential. Here, we report on transport measurements of nearly 0 ° -twisted G/h-BN heterostructures. The heterostructures investigated are prepared by dry transfer and thermally annealing processes and are in the low mobility regime (approximately 3000 cm2 V-1 s-1 at 1.9 K). The replica Dirac spectra and Hofstadter butterfly spectra are observed on the hole transport side, but not on the electron transport side, of the heterostructures. We associate the observed electron-hole asymmetry with the presence of a large difference between the opened gaps in the conduction and valence bands and a strong enhancement in the interband contribution to the conductivity on the electron transport side in the low-mobility G/h-BN heterostructures. We also show that the gaps opened at the central Dirac point and the hole-branch secondary Dirac point are large, suggesting the presence of strong graphene-substrate interaction and electron-electron interaction in our G/h-BN heterostructures. Our results provide additional helpful insight into the transport mechanism in G/h-BN heterostructures.

Non-local electron transport validation using 2D DRACO simulations

NASA Astrophysics Data System (ADS)

Cao, Duc; Chenhall, Jeff; Moll, Eli; Prochaska, Alex; Moses, Gregory; Delettrez, Jacques; Collins, Tim

2012-10-01

Comparison of 2D DRACO simulations, using a modified versionfootnotetextprivate communications with M. Marinak and G. Zimmerman, LLNL. of the Schurtz, Nicolai and Busquet (SNB) algorithmfootnotetextSchurtz, Nicolai and Busquet, ``A nonlocal electron conduction model for multidimensional radiation hydrodynamics codes,'' Phys. Plasmas 7, 4238(2000). for non-local electron transport, with direct drive shock timing experimentsfootnotetextT. Boehly, et. al., ``Multiple spherically converging shock waves in liquid deuterium,'' Phys. Plasmas 18, 092706(2011). and with the Goncharov non-local modelfootnotetextV. Goncharov, et. al., ``Early stage of implosion in inertial confinement fusion: Shock timing and perturbation evolution,'' Phys. Plasmas 13, 012702(2006). in 1D LILAC will be presented. Addition of an improved SNB non-local electron transport algorithm in DRACO allows direct drive simulations with no need for an electron conduction flux limiter. Validation with shock timing experiments that mimic the laser pulse profile of direct drive ignition targets gives a higher confidence level in the predictive capability of the DRACO code. This research was supported by the University of Rochester Laboratory for Laser Energetics.

Quantum control via a genetic algorithm of the field ionization pathway of a Rydberg electron

NASA Astrophysics Data System (ADS)

Gregoric, Vincent C.; Kang, Xinyue; Liu, Zhimin Cheryl; Rowley, Zoe A.; Carroll, Thomas J.; Noel, Michael W.

2017-08-01

Quantum control of the pathway along which a Rydberg electron field ionizes is experimentally and computationally demonstrated. Selective field ionization is typically done with a slowly rising electric field pulse. The (1/n*)4 scaling of the classical ionization threshold leads to a rough mapping between arrival time of the electron signal and principal quantum number of the Rydberg electron. This is complicated by the many avoided level crossings that the electron must traverse on the way to ionization, which in general leads to broadening of the time-resolved field ionization signal. In order to control the ionization pathway, thus directing the signal to the desired arrival time, a perturbing electric field produced by an arbitrary wave-form generator is added to a slowly rising electric field. A genetic algorithm evolves the perturbing field in an effort to achieve the target time-resolved field ionization signal.

Dependence of magnetic field and electronic transport of Mn4 Single-molecule magnet in a Single-Electron Transistor

NASA Astrophysics Data System (ADS)

Rodriguez, Alvar; Singh, Simranjeet; Haque, Firoze; Del Barco, Enrique; Nguyen, Tu; Christou, George

2012-02-01

Dependence of magnetic field and electronic transport of Mn4 Single-molecule magnet in a Single-Electron Transistor A. Rodriguez, S. Singh, F. Haque and E. del Barco Department of Physics, University of Central Florida, 4000 Central Florida Blvd., Orlando, Florida 32816 USA T. Nguyen and G. Christou Department of Chemistry, University of Florida, Gainesville, Florida 32611 USA Abstract We have performed single-electron transport measurements on a series of Mn-based low-nuclearity single-molecule magnets (SMM) observing Coulomb blockade. SMMs with well isolated and low ground spin states, i.e. S = 9/2 (Mn4) and S = 6 (Mn3) were chosen for these studies, such that the ground spin multiplet does not mix with levels of other excited spin states for the magnetic fields (H = 0-8 T) employed in the experiments. Different functionalization groups were employed to change the mechanical, geometrical and transport characteristics of the molecules when deposited from liquid solution on the transistors. Electromigration-broken three-terminal single-electron transistors were used. Results obtained at temperatures down to 240 mK and in the presence of high magnetic fields will be shown.

Patterning of leaf vein networks by convergent auxin transport pathways.

PubMed

Sawchuk, Megan G; Edgar, Alexander; Scarpella, Enrico

2013-01-01

The formation of leaf vein patterns has fascinated biologists for centuries. Transport of the plant signal auxin has long been implicated in vein patterning, but molecular details have remained unclear. Varied evidence suggests a central role for the plasma-membrane (PM)-localized PIN-FORMED1 (PIN1) intercellular auxin transporter of Arabidopsis thaliana in auxin-transport-dependent vein patterning. However, in contrast to the severe vein-pattern defects induced by auxin transport inhibitors, pin1 mutant leaves have only mild vein-pattern defects. These defects have been interpreted as evidence of redundancy between PIN1 and the other four PM-localized PIN proteins in vein patterning, redundancy that underlies many developmental processes. By contrast, we show here that vein patterning in the Arabidopsis leaf is controlled by two distinct and convergent auxin-transport pathways: intercellular auxin transport mediated by PM-localized PIN1 and intracellular auxin transport mediated by the evolutionarily older, endoplasmic-reticulum-localized PIN6, PIN8, and PIN5. PIN6 and PIN8 are expressed, as PIN1 and PIN5, at sites of vein formation. pin6 synthetically enhances pin1 vein-pattern defects, and pin8 quantitatively enhances pin1pin6 vein-pattern defects. Function of PIN6 is necessary, redundantly with that of PIN8, and sufficient to control auxin response levels, PIN1 expression, and vein network formation; and the vein pattern defects induced by ectopic PIN6 expression are mimicked by ectopic PIN8 expression. Finally, vein patterning functions of PIN6 and PIN8 are antagonized by PIN5 function. Our data define a new level of control of vein patterning, one with repercussions on other patterning processes in the plant, and suggest a mechanism to select cell files specialized for vascular function that predates evolution of PM-localized PIN proteins.

Nonadiabatic small-polaron hopping electron transport in diphenoquinone-doped polycarbonate

NASA Astrophysics Data System (ADS)

Yamaguchi, Yasuhiro; Yokoyama, Masaaki

1991-10-01

The dependences of electron mobility on the electric field F, temperature T, and hopping site distance R have been characterized in 3,5-dimethyl-3',5'-di-tert-butyl-4,4'-diphenoquinone dispersed molecularly in a polycarbonate according to Schein's analytical technique. The electron mobility can be described in the form a0R2 exp(-2R/R0) exp(-E0/kT) × exp[β(1/kT-1/kT0)F1/2], where a0, R0, β, and T0 are constants. Moreover, it is found that the zero-field activation energy E0 is independent of R. The invariable E0 and the exponential dependence of the Arrhenius prefactor on R strongly suggest that the electron transport therein is due to nonadiabatic small-polaron hopping. Based on the small-polaron theory, the transport properties are qualitatively discussed in terms of molecular properties.

Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea

PubMed Central

Duszenko, Nikolas

2017-01-01

ABSTRACT Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli. We found the quantity of MPh per cell increases as cultures transition from exponential growth to stationary phase, and absolute quantities of MPh were 3-fold higher in M. acetivorans than in M. barkeri. The concentration of MPh suggests the cell membrane of M. acetivorans, but not of M. barkeri, is electrically quantized as if it were a single conductive metal sheet and near optimal for rate of electron transport. Similarly, stationary (but not exponentially growing) E. coli cells also have electrically quantized membranes on the basis of quinone content. Consistent with our hypothesis, we demonstrated that the exogenous addition of phenazine increases the growth rate of M. barkeri three times that of M. acetivorans. Our work suggests electron flux through MPh is naturally higher in M. acetivorans than in M. barkeri and that hydrogen cycling is less efficient at conserving energy than scalar proton translocation using MPh. IMPORTANCE Can we grow more from less? The ability to optimize and manipulate metabolic efficiency in cells is the difference between commercially viable and nonviable renewable technologies. Much can be learned from methane-producing archaea (methanogens) which evolved a successful metabolic lifestyle under extreme thermodynamic constraints. Methanogens use highly efficient electron transport

Electron/Ion Transport Enhancer in High Capacity Li-Ion Battery Anodes

DOE PAGES

Kwon, Yo Han; Minnici, Krysten; Huie, Matthew M.; ...

2016-08-30

In this paper, magnetite (Fe 3O 4) was used as a model high capacity metal oxide active material to demonstrate advantages derived from consideration of both electron and ion transport in the design of composite battery electrodes. The conjugated polymer, poly[3-(potassium-4-butanoate) thiophene] (PPBT), was introduced as a binder component, while polyethylene glycol (PEG) was coated onto the surface of Fe 3O 4 nanoparticles. The introduction of PEG reduced aggregate size, enabled effective dispersion of the active materials and facilitated ionic conduction. As a binder for the composite electrode, PPBT underwent electrochemical doping which enabled the formation of effective electrical bridgesmore » between the carbon and Fe 3O 4 components, allowing for more efficient electron transport. Additionally, the PPBT carboxylic moieties effect a porous structure, and stable electrode performance. Finally, the methodical consideration of both enhanced electron and ion transport by introducing a carboxylated PPBT binder and PEG surface treatment leads to effectively reduced electrode resistance, which improved cycle life performance and rate capabilities.« less

Microbial electron transport and energy conservation – the foundation for optimizing bioelectrochemical systems

PubMed Central

Kracke, Frauke; Vassilev, Igor; Krömer, Jens O.

2015-01-01

Microbial electrochemical techniques describe a variety of emerging technologies that use electrode–bacteria interactions for biotechnology applications including the production of electricity, waste and wastewater treatment, bioremediation and the production of valuable products. Central in each application is the ability of the microbial catalyst to interact with external electron acceptors and/or donors and its metabolic properties that enable the combination of electron transport and carbon metabolism. And here also lies the key challenge. A wide range of microbes has been discovered to be able to exchange electrons with solid surfaces or mediators but only a few have been studied in depth. Especially electron transfer mechanisms from cathodes towards the microbial organism are poorly understood but are essential for many applications such as microbial electrosynthesis. We analyze the different electron transport chains that nature offers for organisms such as metal respiring bacteria and acetogens, but also standard biotechnological organisms currently used in bio-production. Special focus lies on the essential connection of redox and energy metabolism, which is often ignored when studying bioelectrochemical systems. The possibility of extracellular electron exchange at different points in each organism is discussed regarding required redox potentials and effect on cellular redox and energy levels. Key compounds such as electron carriers (e.g., cytochromes, ferredoxin, quinones, flavins) are identified and analyzed regarding their possible role in electrode–microbe interactions. This work summarizes our current knowledge on electron transport processes and uses a theoretical approach to predict the impact of different modes of transfer on the energy metabolism. As such it adds an important piece of fundamental understanding of microbial electron transport possibilities to the research community and will help to optimize and advance bioelectrochemical

Mechanisms of electron transport and recombination in ZnO nanostructures for dye-sensitized solar cells.

PubMed

Vega-Poot, Alberto G; Macías-Montero, Manuel; Idígoras, Jesus; Borrás, Ana; Barranco, Angel; Gonzalez-Elipe, Agustín R; Lizama-Tzec, Francisco I; Oskam, Gerko; Anta, Juan A

2014-04-14

ZnO is an attractive material for applications in dye-sensitized solar cells and related devices. This material has excellent electron-transport properties in the bulk but its electron diffusion coefficient is much smaller in mesoporous films. In this work the electron-transport properties of two different kinds of dye-sensitized ZnO nanostructures are investigated by small-perturbation electrochemical techniques. For nanoparticulate ZnO photoanodes prepared via a wet-chemistry technique, the diffusion coefficient is found to reproduce the typical behavior predicted by the multiple-trapping and the hopping models, with an exponential increase with respect to the applied bias. In contrast, in ZnO nanostructured thin films of controlled texture and crystallinity prepared via a plasma chemical vapor deposition method, the diffusion coefficient is found to be independent of the electrochemical bias. This observation suggests a different transport mechanism not controlled by trapping and electron accumulation. In spite of the quite different transport features, the recombination kinetics, the electron-collection efficiency and the photoconversion efficiency are very similar for both kinds of photoanodes, an observation that indicates that surface properties rather than electron transport is the main efficiency-determining factor in solar cells based on ZnO nanostructured photoanodes. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Discrete Diffusion Monte Carlo for Electron Thermal Transport

NASA Astrophysics Data System (ADS)

Chenhall, Jeffrey; Cao, Duc; Wollaeger, Ryan; Moses, Gregory

2014-10-01

The iSNB (implicit Schurtz Nicolai Busquet electron thermal transport method of Cao et al. is adapted to a Discrete Diffusion Monte Carlo (DDMC) solution method for eventual inclusion in a hybrid IMC-DDMC (Implicit Monte Carlo) method. The hybrid method will combine the efficiency of a diffusion method in short mean free path regions with the accuracy of a transport method in long mean free path regions. The Monte Carlo nature of the approach allows the algorithm to be massively parallelized. Work to date on the iSNB-DDMC method will be presented. This work was supported by Sandia National Laboratory - Albuquerque.

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex

EPA Science Inventory

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampl...

Photosensitized electron transport across lipid vesicle walls: quantum yield dependence on sensitizer concentration.

PubMed Central

Ford, W E; Otvos, J W; Calvin, M

1979-01-01

An amphiphilic tris(2,2'-bipyridine)ruthenium(2+) derivative that is incorporated into the walls of phosphatidylcholine vesicles photosensitizes the irreversible oxidation of ethylenediaminetetraacetate(3-) dissolved in the inner aqueous compartments of the vesicle suspension and the one-electron reduction of heptylviologen(2+) dissolved in the continuous aqueous phase. The quantum yield of viologen radical production depends on the phospholipid-to-ruthenium complex mole ratios. A kinetic model is used to derive an order-of-magnitude estimate for the rate constant of electron transport across the vesicle walls. The results are inconsistent with a diffusional mechanism for electron transport and are interpreted in terms of electron exchange. PMID:291027

Electronic transport properties of graphene doped by gallium.

PubMed

Mach, J; Procházka, P; Bartošík, M; Nezval, D; Piastek, J; Hulva, J; Švarc, V; Konečný, M; Kormoš, L; Šikola, T

2017-10-13

In this work we present the effect of low dose gallium (Ga) deposition (<4 ML) performed in UHV (10 -7 Pa) on the electronic doping and charge carrier scattering in graphene grown by chemical vapor deposition. In situ graphene transport measurements performed with a graphene field-effect transistor structure show that at low Ga coverages a graphene layer tends to be strongly n-doped with an efficiency of 0.64 electrons per one Ga atom, while the further deposition and Ga cluster formation results in removing electrons from graphene (less n-doping). The experimental results are supported by the density functional theory calculations and explained as a consequence of distinct interaction between graphene and Ga atoms in case of individual atoms, layers, or clusters.

Electronic transport properties of graphene doped by gallium

NASA Astrophysics Data System (ADS)

Mach, J.; Procházka, P.; Bartošík, M.; Nezval, D.; Piastek, J.; Hulva, J.; Švarc, V.; Konečný, M.; Kormoš, L.; Šikola, T.

2017-10-01

In this work we present the effect of low dose gallium (Ga) deposition (<4 ML) performed in UHV (10-7 Pa) on the electronic doping and charge carrier scattering in graphene grown by chemical vapor deposition. In situ graphene transport measurements performed with a graphene field-effect transistor structure show that at low Ga coverages a graphene layer tends to be strongly n-doped with an efficiency of 0.64 electrons per one Ga atom, while the further deposition and Ga cluster formation results in removing electrons from graphene (less n-doping). The experimental results are supported by the density functional theory calculations and explained as a consequence of distinct interaction between graphene and Ga atoms in case of individual atoms, layers, or clusters.

Alcohol-Soluble Electron-Transport Materials for Fully Solution-Processed Green PhOLEDs.

PubMed

Chen, Fudong; Wang, Shirong; Xiao, Yin; Peng, Feng; Zhou, Nonglin; Ying, Lei; Li, Xianggao

2018-05-18

Two alcohol-soluble electron-transport materials (ETMs), diphenyl(4-(1-phenyl-1H-benzo[d]imidazol-2-yl)phenyl)phosphine oxide (pPBIPO) and (3,5-bis(1-phenyl-1H-benzo[d]imidazol-2-yl)phenyl)diphenylphosphine oxide (mBPBIPO), have been synthesized. The physical properties of these ETMs were investigated and they both exhibited high electron-transport mobilities (1.67×10 -4 and 2.15×10 -4  cm 2  V -1  s -1 ), high glass-transition temperatures (81 and 110 °C), and low LUMO energy levels (-2.87 and -2.82 eV, respectively). The solubility of PBIPO in n-butyl alcohol was more than 20 mg mL -1 , which meets the requirement for fully solution-processed organic light-emitting diodes (OLEDs). Fully solution-processed green-phosphorescent OLEDs were fabricated by using alcohol-soluble PBIPO as electron-transport layers (ETLs), and they exhibited high current efficiencies, power efficiencies, and external quantum efficiencies of up to 38.43 cd A -1 , 26.64 lm W -1 , and 10.87 %, respectively. Compared with devices that did not contain PBIPO as an ETM, the performance of these devices was much improved, which indicated the excellent electron-transport properties of PBIPO. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Managing care pathways combining SNOMED CT, archetypes and an electronic guideline system.

PubMed

Bernstein, Knut; Andersen, Ulrich

2008-01-01

Today electronic clinical guideline systems exist, but they are not well integrated with electronic health records. This paper thus proposes that the patient's "position" in the pathway during the patient journey should be made visible to all involved healthcare parties and the patient. This requires that the generic knowledge, which is represented in the guidelines, is combined with the patient specific information - and then made accessible for all relevant parties. In addition to the decision support provided by the guideline system documentation support can be provided by templates based on archetypes. This paper provides a proposal for how the guideline system and the EHR can be integrated by the use of archetypes and SNOMED CT. SNOMED CT provides the common reference terminology and the semantic links between the systems. The proposal also includes the use of a National Patient Index for storing data about the patient's position in the pathway and for sharing this information by all involved parties.

Electron transport fluxes in potato plateau regime

NASA Astrophysics Data System (ADS)

Shaing, K. C.; Hazeltine, R. D.

1997-12-01

Electron transport fluxes in the potato plateau regime are calculated from the solutions of the drift kinetic equation and fluid equations. It is found that the bootstrap current density remains finite in the region close to the magnetic axis, although it decreases with increasing collision frequency. This finite amount of the bootstrap current in the relatively collisional regime is important in modeling tokamak startup with 100% bootstrap current.

Influence of low-temperature resistivity on fast electron transport in solids: scaling to fast ignition electron beam parameters

NASA Astrophysics Data System (ADS)

McKenna, P.; MacLellan, D. A.; Butler, N. M. H.; Dance, R. J.; Gray, R. J.; Robinson, A. P. L.; Neely, D.; Desjarlais, M. P.

2015-06-01

The role of low-temperature electrical resistivity in defining the transport properties of mega-Ampere currents of fast (MeV) electrons in solids is investigated using 3D hybrid particle-in-cell (PIC) simulations. By considering resistivity profiles intermediate to the ordered (lattice) and disordered forms of two example materials, lithium and silicon, it is shown that both the magnitude of the resistivity and the shape of the resistivity-temperature profile at low temperatures strongly affect the self-generated resistive magnetic fields and the onset of resistive instabilities, and thus the overall fast electron beam transport pattern. The scaling of these effects to the giga-Ampere electron currents required for the fast ignition scheme for inertial fusion is also explored.

Evidence of a gustatory-vestibular pathway for protein transport.

PubMed

Gacek, Richard; Lyon, Michael J

2010-02-01

To demonstrate anatomically a pathway for protein transport from the palate to the vestibular system. The vestibulofacial anastomosis and associated ganglion cells were identified in a collection of 160 horizontally sectioned human temporal bones that had been stained with hematoxylin and eosin. Wheat germ agglutinin-horseradish peroxidase (HRP) was applied to the greater superficial petrosal nerve in 4 Sprague-Dawley rats. After 30 hours, the rats were killed by intracardiac perfusion, and the seventh and eighth nerves with adjacent brainstem removed. Frozen sections cut at 30 mum through this block were then reacted for HRP, counterstained with neutral red, and mounted on slides for examination in the light microscope. Thirty-two of the 160 human temporal bones contained sections through the vestibulofacial anastomosis and its ganglion. In all cases, the ganglion was incorporated into the vestibular ganglion (VG) adjacent to the nervus intermedius. In all 4 experimental rats, HRP reaction product labeled a small number of ganglion cells in the VG adjacent to the nervus intermedius and facial nerve. These observations support the presence of a pathway from receptors in the palate to the VG.

Tuning electronic transport in epitaxial graphene-based van der Waals heterostructures

NASA Astrophysics Data System (ADS)

Lin, Yu-Chuan; Li, Jun; de La Barrera, Sergio C.; Eichfeld, Sarah M.; Nie, Yifan; Addou, Rafik; Mende, Patrick C.; Wallace, Robert M.; Cho, Kyeongjae; Feenstra, Randall M.; Robinson, Joshua A.

2016-04-01

Two-dimensional tungsten diselenide (WSe2) has been used as a component in atomically thin photovoltaic devices, field effect transistors, and tunneling diodes in tandem with graphene. In some applications it is necessary to achieve efficient charge transport across the interface of layered WSe2-graphene, a semiconductor to semimetal junction with a van der Waals (vdW) gap. In such cases, band alignment engineering is required to ensure a low-resistance, ohmic contact. In this work, we investigate the impact of graphene electronic properties on the transport at the WSe2-graphene interface. Electrical transport measurements reveal a lower resistance between WSe2 and fully hydrogenated epitaxial graphene (EGFH) compared to WSe2 grown on partially hydrogenated epitaxial graphene (EGPH). Using low-energy electron microscopy and reflectivity on these samples, we extract the work function difference between the WSe2 and graphene and employ a charge transfer model to determine the WSe2 carrier density in both cases. The results indicate that WSe2-EGFH displays ohmic behavior at small biases due to a large hole density in the WSe2, whereas WSe2-EGPH forms a Schottky barrier junction.Two-dimensional tungsten diselenide (WSe2) has been used as a component in atomically thin photovoltaic devices, field effect transistors, and tunneling diodes in tandem with graphene. In some applications it is necessary to achieve efficient charge transport across the interface of layered WSe2-graphene, a semiconductor to semimetal junction with a van der Waals (vdW) gap. In such cases, band alignment engineering is required to ensure a low-resistance, ohmic contact. In this work, we investigate the impact of graphene electronic properties on the transport at the WSe2-graphene interface. Electrical transport measurements reveal a lower resistance between WSe2 and fully hydrogenated epitaxial graphene (EGFH) compared to WSe2 grown on partially hydrogenated epitaxial graphene (EGPH). Using low

ecode - Electron Transport Algorithm Testing v. 1.0

DOE Office of Scientific and Technical Information (OSTI.GOV)

Franke, Brian C.; Olson, Aaron J.; Bruss, Donald Eugene

2016-10-05

ecode is a Monte Carlo code used for testing algorithms related to electron transport. The code can read basic physics parameters, such as energy-dependent stopping powers and screening parameters. The code permits simple planar geometries of slabs or cubes. Parallelization consists of domain replication, with work distributed at the start of the calculation and statistical results gathered at the end of the calculation. Some basic routines (such as input parsing, random number generation, and statistics processing) are shared with the Integrated Tiger Series codes. A variety of algorithms for uncertainty propagation are incorporated based on the stochastic collocation and stochasticmore » Galerkin methods. These permit uncertainty only in the total and angular scattering cross sections. The code contains algorithms for simulating stochastic mixtures of two materials. The physics is approximate, ranging from mono-energetic and isotropic scattering to screened Rutherford angular scattering and Rutherford energy-loss scattering (simple electron transport models). No production of secondary particles is implemented, and no photon physics is implemented.« less

Electronic transport in disordered MoS2 nanoribbons

NASA Astrophysics Data System (ADS)

Ridolfi, Emilia; Lima, Leandro R. F.; Mucciolo, Eduardo R.; Lewenkopf, Caio H.

2017-01-01

We study the electronic structure and transport properties of zigzag and armchair monolayer molybdenum disulfide nanoribbons using an 11-band tight-binding model that accurately reproduces the material's bulk band structure near the band gap. We study the electronic properties of pristine zigzag and armchair nanoribbons, paying particular attention to the edges states that appear within the MoS2 bulk gap. By analyzing both their orbital composition and their local density of states, we find that in zigzag-terminated nanoribbons these states can be localized at a single edge for certain energies independent of the nanoribbon width. We also study the effects of disorder in these systems using the recursive Green's function technique. We show that for the zigzag nanoribbons, the conductance due to the edge states is strongly suppressed by short-range disorder such as vacancies. In contrast, the local density of states still shows edge localization. We also show that long-range disorder has a small effect on the transport properties of nanoribbons within the bulk gap energy window.

Electron and hole relaxation pathways in semiconductor quantum dots

DOE Office of Scientific and Technical Information (OSTI.GOV)

Klimov, V.I.; McBranch, D.W.; Leatherdale, C.A.

1999-11-01

Femtosecond (fs) broad-band transient absorption (TA) is used to study the intraband relaxation and depopulation dynamics of electron and hole quantized states in CdSe nanocrystals (NC{close_quote}s) with a range of surface properties. Instead of the drastic reduction in the energy relaxation rate expected due to a {open_quotes}phonon bottleneck,{close_quotes} we observe a fast subpicosecond 1P-to-1S electron relaxation, with the rate exceeding that due to phonon emission in bulk semiconductors. The energy relaxation is enhanced with reducing the NC{close_quote}s radius, and does not show any dependence on the NC surface properties (quality of the surface passivation). These data indicate that electron energymore » relaxation occurs by neither multiphonon emission nor by coupling to surface defects, but is likely meditated by Auger-type electron-hole energy transfer. We use fs infrared TA to probe electron and hole intraband transitions, which allows us to distinguish between electron and hole relaxation pathways leading to the depopulation of NC quantized states. In contrast to the electron relaxation, which is controlled by NC surface passivation, the depopulation of hole quantized states is extremely fast (sub-ps-to-ps time scales) in all types of samples, independent of NC surface treatment (including NC{close_quote}s overcoated with a ZnS layer). Our results indicate that ultrafast hole dynamics are not due to trapping at localized surface defects such as a vacancy, but rather arise from relaxation into intrinsic NC states or intrinsically unpassivated interface states. {copyright} {ital 1999} {ital The American Physical Society}« less

Long-distance electron transport occurs globally in marine sediments

NASA Astrophysics Data System (ADS)

Burdorf, Laurine D. W.; Tramper, Anton; Seitaj, Dorina; Meire, Lorenz; Hidalgo-Martinez, Silvia; Zetsche, Eva-Maria; Boschker, Henricus T. S.; Meysman, Filip J. R.

2017-02-01

Recently, long filamentous bacteria have been reported conducting electrons over centimetre distances in marine sediments. These so-called cable bacteria perform an electrogenic form of sulfur oxidation, whereby long-distance electron transport links sulfide oxidation in deeper sediment horizons to oxygen reduction in the upper millimetres of the sediment. Electrogenic sulfur oxidation exerts a strong impact on the local sediment biogeochemistry, but it is currently unknown how prevalent the process is within the seafloor. Here we provide a state-of-the-art assessment of its global distribution by combining new field observations with previous reports from the literature. This synthesis demonstrates that electrogenic sulfur oxidation, and hence microbial long-distance electron transport, is a widespread phenomenon in the present-day seafloor. The process is found in coastal sediments within different climate zones (off the Netherlands, Greenland, the USA, Australia) and thrives on a range of different coastal habitats (estuaries, salt marshes, mangroves, coastal hypoxic basins, intertidal flats). The combination of a widespread occurrence and a strong local geochemical imprint suggests that electrogenic sulfur oxidation could be an important, and hitherto overlooked, component of the marine cycle of carbon, sulfur and other elements.

A residence-time-based transport approach for the groundwater pathway in performance assessment models

NASA Astrophysics Data System (ADS)

Robinson, Bruce A.; Chu, Shaoping

2013-03-01

This paper presents the theoretical development and numerical implementation of a new modeling approach for representing the groundwater pathway in risk assessment or performance assessment model of a contaminant transport system. The model developed in the present study, called the Residence Time Distribution (RTD) Mixing Model (RTDMM), allows for an arbitrary distribution of fluid travel times to be represented, to capture the effects on the breakthrough curve of flow processes such as channelized flow and fast pathways and complex three-dimensional dispersion. Mathematical methods for constructing the model for a given RTD are derived directly from the theory of residence time distributions in flowing systems. A simple mixing model is presented, along with the basic equations required to enable an arbitrary RTD to be reproduced using the model. The practical advantages of the RTDMM include easy incorporation into a multi-realization probabilistic simulation; computational burden no more onerous than a one-dimensional model with the same number of grid cells; and straightforward implementation into available flow and transport modeling codes, enabling one to then utilize advanced transport features of that code. For example, in this study we incorporated diffusion into the stagnant fluid in the rock matrix away from the flowing fractures, using a generalized dual porosity model formulation. A suite of example calculations presented herein showed the utility of the RTDMM for the case of a radioactive decay chain, dual porosity transport and sorption.

Physiological Evidence for Isopotential Tunneling in the Electron Transport Chain of Methane-Producing Archaea.

PubMed

Duszenko, Nikolas; Buan, Nicole R

2017-09-15

Many, but not all, organisms use quinones to conserve energy in their electron transport chains. Fermentative bacteria and methane-producing archaea (methanogens) do not produce quinones but have devised other ways to generate ATP. Methanophenazine (MPh) is a unique membrane electron carrier found in Methanosarcina species that plays the same role as quinones in the electron transport chain. To extend the analogy between quinones and MPh, we compared the MPh pool sizes between two well-studied Methanosarcina species, Methanosarcina acetivorans C2A and Methanosarcina barkeri Fusaro, to the quinone pool size in the bacterium Escherichia coli We found the quantity of MPh per cell increases as cultures transition from exponential growth to stationary phase, and absolute quantities of MPh were 3-fold higher in M. acetivorans than in M. barkeri The concentration of MPh suggests the cell membrane of M. acetivorans , but not of M. barkeri , is electrically quantized as if it were a single conductive metal sheet and near optimal for rate of electron transport. Similarly, stationary (but not exponentially growing) E. coli cells also have electrically quantized membranes on the basis of quinone content. Consistent with our hypothesis, we demonstrated that the exogenous addition of phenazine increases the growth rate of M. barkeri three times that of M. acetivorans Our work suggests electron flux through MPh is naturally higher in M. acetivorans than in M. barkeri and that hydrogen cycling is less efficient at conserving energy than scalar proton translocation using MPh. IMPORTANCE Can we grow more from less? The ability to optimize and manipulate metabolic efficiency in cells is the difference between commercially viable and nonviable renewable technologies. Much can be learned from methane-producing archaea (methanogens) which evolved a successful metabolic lifestyle under extreme thermodynamic constraints. Methanogens use highly efficient electron transport systems and

SU-E-T-489: Quantum versus Classical Trajectory Monte Carlo Simulations of Low Energy Electron Transport.

PubMed

Thomson, R; Kawrakow, I

2012-06-01

Widely-used classical trajectory Monte Carlo simulations of low energy electron transport neglect the quantum nature of electrons; however, at sub-1 keV energies quantum effects have the potential to become significant. This work compares quantum and classical simulations within a simplified model of electron transport in water. Electron transport is modeled in water droplets using quantum mechanical (QM) and classical trajectory Monte Carlo (MC) methods. Water droplets are modeled as collections of point scatterers representing water molecules from which electrons may be isotropically scattered. The role of inelastic scattering is investigated by introducing absorption. QM calculations involve numerically solving a system of coupled equations for the electron wavefield incident on each scatterer. A minimum distance between scatterers is introduced to approximate structured water. The average QM water droplet incoherent cross section is compared with the MC cross section; a relative error (RE) on the MC results is computed. RE varies with electron energy, average and minimum distances between scatterers, and scattering amplitude. The mean free path is generally the relevant length scale for estimating RE. The introduction of a minimum distance between scatterers increases RE substantially (factors of 5 to 10), suggesting that the structure of water must be modeled for accurate simulations. Inelastic scattering does not improve agreement between QM and MC simulations: for the same magnitude of elastic scattering, the introduction of inelastic scattering increases RE. Droplet cross sections are sensitive to droplet size and shape; considerable variations in RE are observed with changing droplet size and shape. At sub-1 keV energies, quantum effects may become non-negligible for electron transport in condensed media. Electron transport is strongly affected by the structure of the medium. Inelastic scatter does not improve agreement between QM and MC simulations of low

Study of electron transport in a Hall thruster by axial–radial fully kinetic particle simulation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Shinatora, E-mail: choh.shinatora@jaxa.jp; Kubota, Kenichi; Funaki, Ikkoh

2015-10-15

Electron transport across a magnetic field in a magnetic-layer-type Hall thruster was numerically investigated for the future predictive modeling of Hall thrusters. The discharge of a 1-kW-class magnetic-layer-type Hall thruster designed for high-specific-impulse operation was modeled using an r-z two-dimensional fully kinetic particle code with and without artificial electron-diffusion models. The thruster performance results showed that both electron transport models captured the experimental result within discrepancies less than 20% in thrust and discharge current for all the simulated operation conditions. The electron cross-field transport mechanism of the so-called anomalous diffusion was self-consistently observed in the simulation without artificial diffusion models;more » the effective electron mobility was two orders of magnitude higher than the value obtained using the classical diffusion theory. To account for the self-consistently observed anomalous transport, the oscillation of plasma properties was speculated. It was suggested that the enhanced random-walk diffusion due to the velocity oscillation of low-frequency electron flow could explain the observed anomalous diffusion within an order of magnitude. The dominant oscillation mode of the electron flow velocity was found to be 20 kHz, which was coupled to electrostatic oscillation excited by global ionization instability.« less

Specific Interaction between Redox Phospholipid Polymers and Plastoquinone in Photosynthetic Electron Transport Chain.

PubMed

Tanaka, Kenya; Kaneko, Masahiro; Ishikawa, Masahito; Kato, Souichiro; Ito, Hidehiro; Kamachi, Toshiaki; Kamiya, Kazuhide; Nakanishi, Shuji

2017-04-19

Redox phospholipid polymers added in culture media are known to be capable of extracting electrons from living photosynthetic cells across bacterial cell membranes with high cytocompatibility. In the present study, we identify the intracellular redox species that transfers electrons to the polymers. The open-circuit electrochemical potential of an electrolyte containing the redox polymer and extracted thylakoid membranes shift to positive (or negative) under light irradiation, when an electron transport inhibitor specific to plastoquinone is added upstream (or downstream) in the photosynthetic electron transport chain. The same trend is also observed for a medium containing living photosynthetic cells of Synechococcus elongatus PCC7942. These results clearly indicate that the phospholipid redox polymers extract photosynthetic electrons mainly from plastoquinone. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron transport in doped fullerene molecular junctions

NASA Astrophysics Data System (ADS)

Kaur, Milanpreet; Sawhney, Ravinder Singh; Engles, Derick

The effect of doping on the electron transport of molecular junctions is analyzed in this paper. The doped fullerene molecules are stringed to two semi-infinite gold electrodes and analyzed at equilibrium and nonequilibrium conditions of these device configurations. The contemplation is done using nonequilibrium Green’s function (NEGF)-density functional theory (DFT) to evaluate its density of states (DOS), transmission coefficient, molecular orbitals, electron density, charge transfer, current, and conductance. We conclude from the elucidated results that Au-C16Li4-Au and Au-C16Ne4-Au devices behave as an ordinary p-n junction diode and a Zener diode, respectively. Moreover, these doped fullerene molecules do not lose their metallic nature when sandwiched between the pair of gold electrodes.

Basic concepts of quantum interference and electron transport in single-molecule electronics.

PubMed

Lambert, C J

2015-02-21

This tutorial outlines the basic theoretical concepts and tools which underpin the fundamentals of phase-coherent electron transport through single molecules. The key quantity of interest is the transmission coefficient T(E), which yields the electrical conductance, current-voltage relations, the thermopower S and the thermoelectric figure of merit ZT of single-molecule devices. Since T(E) is strongly affected by quantum interference (QI), three manifestations of QI in single-molecules are discussed, namely Mach-Zehnder interferometry, Breit-Wigner resonances and Fano resonances. A simple MATLAB code is provided, which allows the novice reader to explore QI in multi-branched structures described by a tight-binding (Hückel) Hamiltonian. More generally, the strengths and limitations of materials-specific transport modelling based on density functional theory are discussed.

The Role of Diffusion in the Transport of Energetic Electrons during Solar Flares

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bian, Nicolas H.; Kontar, Eduard P.; Emslie, A. Gordon, E-mail: nicolas.bian@glasgow.gla.ac.uk, E-mail: emslieg@wku.edu

2017-02-01

The transport of the energy contained in suprathermal electrons in solar flares plays a key role in our understanding of many aspects of flare physics, from the spatial distributions of hard X-ray emission and energy deposition in the ambient atmosphere to global energetics. Historically the transport of these particles has been largely treated through a deterministic approach, in which first-order secular energy loss to electrons in the ambient target is treated as the dominant effect, with second-order diffusive terms (in both energy and angle) generally being either treated as a small correction or even neglected. Here, we critically analyze thismore » approach, and we show that spatial diffusion through pitch-angle scattering necessarily plays a very significant role in the transport of electrons. We further show that a satisfactory treatment of the diffusion process requires consideration of non-local effects, so that the electron flux depends not just on the local gradient of the electron distribution function but on the value of this gradient within an extended region encompassing a significant fraction of a mean free path. Our analysis applies generally to pitch-angle scattering by a variety of mechanisms, from Coulomb collisions to turbulent scattering. We further show that the spatial transport of electrons along the magnetic field of a flaring loop can be modeled rather effectively as a Continuous Time Random Walk with velocity-dependent probability distribution functions of jump sizes and occurrences, both of which can be expressed in terms of the scattering mean free path.« less

First principles studies of electron tunneling in proteins

PubMed Central

Hayashi, Tomoyuki; Stuchebrukhov, Alexei A.

2014-01-01

A first principles study of electronic tunneling along the chain of seven Fe/S clusters in respiratory complex I, a key enzyme in the respiratory electron transport chain, is described. The broken-symmetry states of the Fe/S metal clusters calculated at both DFT and semi-empirical ZINDO levels were utilized to examine both the extremely weak electronic couplings between Fe/S clusters and the tunneling pathways, which provide a detailed atomistic-level description of the charge transfer process in the protein. One-electron tunneling approximation was found to hold within a reasonable accuracy, with only a moderate induced polarization of the core electrons. The method is demonstrated to be able to calculate accurately the coupling matrix elements as small as 10−4 cm−1. A distinct signature of the wave properties of electrons is observed as quantum interferences of multiple tunneling pathways. PMID:25383312

Vertical electron transport in van der Waals heterostructures with graphene layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ryzhii, V., E-mail: v-ryzhii@riec.tohoku.ac.jp; Center for Photonics and Infrared Engineering, Bauman Moscow State Technical University and Institute of Ultra High Frequency Semiconductor Electronics of RAS, Moscow 111005; Otsuji, T.

We propose and analyze an analytical model for the self-consistent description of the vertical electron transport in van der Waals graphene-layer (GL) heterostructures with the GLs separated by the barriers layers. The top and bottom GLs serve as the structure emitter and collector. The vertical electron transport in such structures is associated with the propagation of the electrons thermionically emitted from GLs above the inter-GL barriers. The model under consideration describes the processes of the electron thermionic emission from and the electron capture to GLs. It accounts for the nonuniformity of the self-consistent electric field governed by the Poisson equationmore » which accounts for the variation of the electron population in GLs. The model takes also under consideration the cooling of electrons in the emitter layer due to the Peltier effect. We find the spatial distributions of the electric field and potential with the high-electric-field domain near the emitter GL in the GL heterostructures with different numbers of GLs. Using the obtained spatial distributions of the electric field, we calculate the current-voltage characteristics. We demonstrate that the Peltier cooling of the two-dimensional electron gas in the emitter GL can strongly affect the current-voltage characteristics resulting in their saturation. The obtained results can be important for the optimization of the hot-electron bolometric terahertz detectors and different devices based on GL heterostructures.« less

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex.

PubMed

McHugh, Thomas; Beckley, Lila; Sullivan, Terry; Lutes, Chris; Truesdale, Robert; Uppencamp, Rob; Cosky, Brian; Zimmerman, John; Schumacher, Brian

2017-11-15

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into the duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. These test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope. Copyright © 2017 Elsevier B.V. All rights reserved.

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex

DOE PAGES

McHugh, Thomas; Beckley, Lila; Sullivan, Terry; ...

2017-04-26

We report the role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into themore » duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. Finally, these test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope.« less

Evidence of a sewer vapor transport pathway at the USEPA vapor intrusion research duplex

DOE Office of Scientific and Technical Information (OSTI.GOV)

McHugh, Thomas; Beckley, Lila; Sullivan, Terry

We report the role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into themore » duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. Finally, these test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope.« less

Eolian sand transport pathways in the southwestern United States: Importance of the Colorado River and local sources

USGS Publications Warehouse

Muhs, D.R.; Reynolds, R.L.; Been, J.; Skipp, G.

2003-01-01

Geomorphologists have long recognized that eolian sand transport pathways extend over long distances in desert regions. Along such pathways, sediment transport by wind can surmount topographic obstacles and cross major drainages. Recent studies have suggested that three distinct eolian sand transport pathways exist (or once existed) in the Mojave and Sonoran Desert regions of the southwestern United States. One hypothesized pathway is colian sand transport from the eastern Mojave Desert of California into western Arizona, near Parker, and would require sand movement across what must have been at least a seasonally dry Colorado River valley. We tested this hypothesis by mineralogical, geochemical and magnetic analyses of eolian sands on both sides of the Colorado River, as well as sediment from the river itself. Results indicate that dunes on opposite sides of the Colorado River are mineralogically distinct: eastern California dunes are feldspar-rich whereas western Arizona dunes are quartz-rich, derived from quartz-rich Colorado River sediments. Because of historic vegetation changes, little new sediment from the Colorado River is presently available to supply the Parker dunes. Based on this study and previous work, the Colorado River is now known to be the source of sand for at least three of the major dune fields of the Sonoran Desert of western Arizona and northern Mexico. On the other hand, locally derived alluvium appears to be a more important source of dune fields in the Mojave Desert of California. Although many geomorphologists have stressed the importance of large fluvial systems in the origin of desert dune fields, few empirical data actually exist to support this theory. The results presented here demonstrate that a major river system in the southwestern United States is a barrier to the migration of some dune fields, but essential to the origin of others. Published by Elsevier Science Ltd.

Development and application of a 2-electron reduced density matrix approach to electron transport via molecular junctions

NASA Astrophysics Data System (ADS)

Hoy, Erik P.; Mazziotti, David A.; Seideman, Tamar

2017-11-01

Can an electronic device be constructed using only a single molecule? Since this question was first asked by Aviram and Ratner in the 1970s [Chem. Phys. Lett. 29, 277 (1974)], the field of molecular electronics has exploded with significant experimental advancements in the understanding of the charge transport properties of single molecule devices. Efforts to explain the results of these experiments and identify promising new candidate molecules for molecular devices have led to the development of numerous new theoretical methods including the current standard theoretical approach for studying single molecule charge transport, i.e., the non-equilibrium Green's function formalism (NEGF). By pairing this formalism with density functional theory (DFT), a wide variety of transport problems in molecular junctions have been successfully treated. For some systems though, the conductance and current-voltage curves predicted by common DFT functionals can be several orders of magnitude above experimental results. In addition, since density functional theory relies on approximations to the exact exchange-correlation functional, the predicted transport properties can show significant variation depending on the functional chosen. As a first step to addressing this issue, the authors have replaced density functional theory in the NEGF formalism with a 2-electron reduced density matrix (2-RDM) method, creating a new approach known as the NEGF-RDM method. 2-RDM methods provide a more accurate description of electron correlation compared to density functional theory, and they have lower computational scaling compared to wavefunction based methods of similar accuracy. Additionally, 2-RDM methods are capable of capturing static electron correlation which is untreatable by existing NEGF-DFT methods. When studying dithiol alkane chains and dithiol benzene in model junctions, the authors found that the NEGF-RDM predicts conductances and currents that are 1-2 orders of magnitude below

Copper transport into the secretory pathway is regulated by oxygen in macrophages

PubMed Central

White, Carine; Kambe, Taiho; Fulcher, Yan G.; Sachdev, Sherri W.; Bush, Ashley I.; Fritsche, Kevin; Lee, Jaekwon; Quinn, Thomas P.; Petris, Michael J.

2009-01-01

Summary Copper is an essential nutrient for a variety of biochemical processes; however, the redox properties of copper also make it potentially toxic in the free form. Consequently, the uptake and intracellular distribution of this metal is strictly regulated. This raises the issue of whether specific pathophysiological conditions can promote adaptive changes in intracellular copper distribution. In this study, we demonstrate that oxygen limitation promotes a series of striking alterations in copper homeostasis in RAW264.7 macrophage cells. Hypoxia was found to stimulate copper uptake and to increase the expression of the copper importer, CTR1. This resulted in increased copper delivery to the ATP7A copper transporter and copper-dependent trafficking of ATP7A to cytoplasmic vesicles. Significantly, the ATP7A protein was required to deliver copper into the secretory pathway to ceruloplasmin, a secreted copperdependent enzyme, the expression and activity of which were stimulated by hypoxia. However, the activities of the alternative targets of intracellular copper delivery, superoxide dismutase and cytochrome c oxidase, were markedly reduced in response to hypoxia. Collectively, these findings demonstrate that copper delivery into the biosynthetic secretory pathway is regulated by oxygen availability in macrophages by a selective increase in copper transport involving ATP7A. PMID:19351718

Spatio-temporal modelling of the NF-κB intracellular signalling pathway: the roles of diffusion, active transport, and cell geometry.

PubMed

Terry, Alan J; Chaplain, Mark A J

2011-12-07

The nuclear factor kappa B (NF-κB) intracellular signalling pathway is central to many stressful, inflammatory, and innate immune responses. NF-κB proteins themselves are transcription factors for hundreds of genes. Experiments have shown that the NF-κB pathway can exhibit oscillatory dynamics-a negative feedback loop causes oscillatory nuclear-cytoplasmic translocation of NF-κB. Given that cell size and shape are known to influence intracellular signal transduction, we consider a spatio-temporal model of partial differential equations for the NF-κB pathway, where we model molecular movement by diffusion and, for several key species including NF-κB, by active transport as well. Through numerical simulations we find values for model parameters such that sustained oscillatory dynamics occur. Our spatial profiles and animations bear a striking resemblance to experimental images and movie clips employing fluorescent fusion proteins. We discover that oscillations in nuclear NF-κB may occur when active transport is across the nuclear membrane only, or when no species are subject to active transport. However, when active transport is across the nuclear membrane and NF-κB is additionally actively transported through the cytoplasm, oscillations are lost. Hence transport mechanisms in a cell will influence its response to activation of its NF-κB pathway. We also demonstrate that sustained oscillations in nuclear NF-κB are somewhat robust to changes in the shape of the cell, or the shape, location, and size of its nucleus, or the location of ribosomes. Yet if the cell is particularly flat or the nucleus sufficiently small, then oscillations are lost. Thus the geometry of a cell may partly determine its response to NF-κB activation. The NF-κB pathway is known to be constitutively active in several human cancers. Our spatially explicit modelling approach will allow us, in future work, to investigate targeted drug therapy of tumours. Copyright © 2011 Elsevier Ltd

Extensive electron transport and energization via multiple, localized dipolarizing flux bundles

NASA Astrophysics Data System (ADS)

Gabrielse, Christine; Angelopoulos, Vassilis; Harris, Camilla; Artemyev, Anton; Kepko, Larry; Runov, Andrei

2017-05-01

Using an analytical model of multiple dipolarizing flux bundles (DFBs) embedded in earthward traveling bursty bulk flows, we demonstrate how equatorially mirroring electrons can travel long distances and gain hundreds of keV from betatron acceleration. The model parameters are constrained by four Time History of Events and Macroscale Interactions during Substorms satellite observations, putting limits on the DFBs' speed, location, and magnetic and electric field magnitudes. We find that the sharp, localized peaks in magnetic field have such strong spatial gradients that energetic electrons ∇B drift in closed paths around the peaks as those peaks travel earthward. This is understood in terms of the third adiabatic invariant, which remains constant when the field changes on timescales longer than the electron's drift timescale: An energetic electron encircles a sharp peak in magnetic field in a closed path subtending an area of approximately constant flux. As the flux bundle magnetic field increases the electron's drift path area shrinks and the electron is prevented from escaping to the ambient plasma sheet, while it continues to gain energy via betatron acceleration. When the flux bundles arrive at and merge with the inner magnetosphere, where the background field is strong, the electrons suddenly gain access to previously closed drift paths around the Earth. DFBs are therefore instrumental in transporting and energizing energetic electrons over long distances along the magnetotail, bringing them to the inner magnetosphere and energizing them by hundreds of keV.