Ultrafast Primary Reactions in the Photosystems of Oxygen-Evolving Organisms

NASA Astrophysics Data System (ADS)

Holzwarth, A. R.

In oxygen-evolving photosynthetic organisms (plants, green algae, cyanobacteria), the primary steps of photosynthesis occur in two membrane-bound protein supercomplexes, Photosystem I (PS I) and Photosystem II (PS II), located in the thylakoid membrane (c.f. Fig. 7.1) along with two other important protein complexes, the cytochrome b6/f complex and the ATP-synthase [1]. Each of the photosystems consists of a reaction center (RC) where the photoinduced early electron transfer processes occur, of a so-called core antenna consisting of chlorophyll (Chl) protein complexes responsible for light absorption and ultrafast energy transfer to the RC pigments, and additional peripheral antenna complexes of various kinds that increase the absorption cross-section. The peripheral complexes are Chl a/b-protein complexes in higher plants and green algae (LHC I or LHC II for PS I or PS II, respectively) and so-called phycobilisomes in cyanobacteria and red algae [2-4]. The structures and light-harvesting functions of these antenna systems have been extensively reviewed [2, 5-9]. Recently, X-ray structures of both PS I and PS II antenna/RC complexes have been determined, some to atomic resolution. Although many details of the pigment content and organization of the RCs and antenna systems of PS I and PS II have been known before, the high resolution structures of the integral complexes allow us for the first time to try to understand structure/function relationships in detail. This article covers our present understanding of the ultrafast energy transfer and early electron transfer processes occurring in the photosystems of oxygen-evolving organisms. The main emphasis will be on the electron transfer processes. However, in both photosystems the kinetics of the energy transfer processes in the core antennae is intimately interwoven with the kinetics of the electron transfer steps. Since both types of processes occur on a similar time scale, their kinetics cannot be considered separately in any experiment and consequently they have to be discussed together.

Propagation of eigenmodes and transfer functions in waveguide WDM structures

NASA Astrophysics Data System (ADS)

Mashkov, Vladimir A.; Francoeur, S.; Geuss, U.; Neiser, K.; Temkin, Henryk

1998-02-01

A method of propagation functions and transfer amplitudes suitable for the design of integrated optical circuits is presented. The method is based on vectorial formulation of electrodynamics: the distributions and propagation of electromagnetic fields in optical circuits is described by equivalent surface sources. This approach permits a division of complex optical waveguide structures into sets of primitive blocks and to separately calculate the transfer function and the transfer amplitude for each block. The transfer amplitude of the entire optical system is represented by a convolution of transfer amplitudes of its primitive blocks. The eigenvalues and eigenfunctions of arbitrary waveguide structure are obtained in the WKB approximation and compared with other methods. The general approach is illustrated with the transfer amplitude calculations for Dragone's star coupler and router.

Charge-transfer optical absorption mechanism of DNA:Ag-nanocluster complexes

NASA Astrophysics Data System (ADS)

Longuinhos, R.; Lúcio, A. D.; Chacham, H.; Alexandre, S. S.

2016-05-01

Optical properties of DNA:Ag-nanoclusters complexes have been successfully applied experimentally in Chemistry, Physics, and Biology. Nevertheless, the mechanisms behind their optical activity remain unresolved. In this work, we present a time-dependent density functional study of optical absorption in DNA:Ag4. In all 23 different complexes investigated, we obtain new absorption peaks in the visible region that are not found in either the isolated Ag4 or isolated DNA base pairs. Absorption from red to green are predominantly of charge-transfer character, from the Ag4 to the DNA fragment, while absorption in the blue-violet range are mostly associated to electronic transitions of a mixed character, involving either DNA-Ag4 hybrid orbitals or intracluster orbitals. We also investigate the role of exchange-correlation functionals in the calculated optical spectra. Significant differences are observed between the calculations using the PBE functional (without exact exchange) and the CAM-B3LYP functional (which partly includes exact exchange). Specifically, we observe a tendency of charge-transfer excitations to involve purines bases, and the PBE spectra error is more pronounced in the complexes where the Ag cluster is bound to the purines. Finally, our results also highlight the importance of adding both the complementary base pair and the sugar-phosphate backbone in order to properly characterize the absorption spectrum of DNA:Ag complexes.

Charge-transfer optical absorption mechanism of DNA:Ag-nanocluster complexes.

PubMed

Longuinhos, R; Lúcio, A D; Chacham, H; Alexandre, S S

2016-05-01

Optical properties of DNA:Ag-nanoclusters complexes have been successfully applied experimentally in Chemistry, Physics, and Biology. Nevertheless, the mechanisms behind their optical activity remain unresolved. In this work, we present a time-dependent density functional study of optical absorption in DNA:Ag_{4}. In all 23 different complexes investigated, we obtain new absorption peaks in the visible region that are not found in either the isolated Ag_{4} or isolated DNA base pairs. Absorption from red to green are predominantly of charge-transfer character, from the Ag_{4} to the DNA fragment, while absorption in the blue-violet range are mostly associated to electronic transitions of a mixed character, involving either DNA-Ag_{4} hybrid orbitals or intracluster orbitals. We also investigate the role of exchange-correlation functionals in the calculated optical spectra. Significant differences are observed between the calculations using the PBE functional (without exact exchange) and the CAM-B3LYP functional (which partly includes exact exchange). Specifically, we observe a tendency of charge-transfer excitations to involve purines bases, and the PBE spectra error is more pronounced in the complexes where the Ag cluster is bound to the purines. Finally, our results also highlight the importance of adding both the complementary base pair and the sugar-phosphate backbone in order to properly characterize the absorption spectrum of DNA:Ag complexes.

Excitation energy transfer in the photosystem I

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

Webber, Andrew N

2012-09-25

Photosystem I is a multimeric pigment protein complex in plants, green alage and cyanobacteria that functions in series with Photosystem II to use light energy to oxidize water and reduce carbon dioxide. The Photosystem I core complex contains 96 chlorophyll a molecules and 22 carotenoids that are involved in light harvesting and electron transfer. In eucaryotes, PSI also has a peripheral light harvesting complex I (LHCI). The role of specific chlorophylls in excitation and electron transfer are still unresolved. In particular, the role of so-called bridging chlorophylls, located between the bulk antenna and the core electron transfer chain, in themore » transfer of excitation energy to the reaction center are unknown. During the past funding period, site directed mutagenesis has been used to create mutants that effect the physical properties of these key chlorophylls, and to explore how this alters the function of the photosystem. Studying these mutants using ultrafast absorption spectroscopy has led to a better understanding of the process by which excitation energy is transferred from the antenna chlorophylls to the electron transfer chain chlorophylls, and what the role of connecting chlorophylls and A_0 chlorophylls is in this process. We have also used these mutants to investigate whch of the central group of six chlorophylls are involved in the primary steps of charge separation and electron transfer.« less

Aerobic metabolism underlies complexity and capacity

PubMed Central

Koch, Lauren G; Britton, Steven L

2008-01-01

The evolution of biological complexity beyond single-celled organisms was linked temporally with the development of an oxygen atmosphere. Functionally, this linkage can be attributed to oxygen ranking high in both abundance and electronegativity amongst the stable elements of the universe. That is, reduction of oxygen provides for close to the largest possible transfer of energy for each electron transfer reaction. This suggests the general hypothesis that the steep thermodynamic gradient of an oxygen environment was permissive for the development of multicellular complexity. A corollary of this hypothesis is that aerobic metabolism underwrites complex biological function mechanistically at all levels of organization. The strong contemporary functional association of aerobic metabolism with both physical capacity and health is presumably a product of the integral role of oxygen in our evolutionary history. Here we provide arguments from thermodynamics, evolution, metabolic network analysis, clinical observations and animal models that are in accord with the centrality of oxygen in biology. PMID:17947307

Förster resonance energy transfer studies of luminescent gold nanoparticles functionalized with ruthenium(II) and rhenium(I) complexes: modulation via esterase hydrolysis.

PubMed

Leung, Frankie Chi-Ming; Tam, Anthony Yiu-Yan; Au, Vonika Ka-Man; Li, Mei-Jin; Yam, Vivian Wing-Wah

2014-05-14

A number of ruthenium(II) and rhenium(I) bipyridine complexes functionalized with lipoic acid moieties have been synthesized and characterized. Functionalization of gold nanoparticles with these chromophoric ruthenium(II) and rhenium(I) complexes has resulted in interesting supramolecular assemblies with Förster resonance energy transfer (FRET) properties that could be modulated via esterase hydrolysis. The luminescence of the metal complex chromophores was turned on upon cleavage of the ester bond linkage by esterase to reduce the efficiency of FRET quenching. The prepared nanoassembly conjugates have been characterized by transmission electron microscopy (TEM), energy-dispersive X-ray analysis (EDX), Fourier transform infrared spectroscopy (FTIR), dynamic light scattering (DLS), UV-visible spectroscopy, and emission spectroscopy. The quenching mechanism has also been studied by transient absorption and time-resolved emission decay measurements. The FRET efficiencies were found to vary with the nature of the chromophores and the length of the spacer between the donor (transition metal complexes) and the acceptor (gold nanoparticles).

Transfer functions for protein signal transduction: application to a model of striatal neural plasticity.

PubMed

Scheler, Gabriele

2013-01-01

We present a novel formulation for biochemical reaction networks in the context of protein signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select a set of "source" species, which are interpreted as input signals. Signals are transmitted to all other species in the system (the "target" species) with a specific delay and with a specific transmission strength. The delay is computed as the maximal reaction time until a stable equilibrium for the target species is reached, in the context of all other reactions in the system. The transmission strength is the concentration change of the target species. The computed input-output transfer functions can be stored in a matrix, fitted with parameters, and even recalled to build dynamical models on the basis of state changes. By separating the temporal and the magnitudinal domain we can greatly simplify the computational model, circumventing typical problems of complex dynamical systems. The transfer function transformation of biochemical reaction systems can be applied to mass-action kinetic models of signal transduction. The paper shows that this approach yields significant novel insights while remaining a fully testable and executable dynamical model for signal transduction. In particular we can deconstruct the complex system into local transfer functions between individual species. As an example, we examine modularity and signal integration using a published model of striatal neural plasticity. The modularizations that emerge correspond to a known biological distinction between calcium-dependent and cAMP-dependent pathways. Remarkably, we found that overall interconnectedness depends on the magnitude of inputs, with higher connectivity at low input concentrations and significant modularization at moderate to high input concentrations. This general result, which directly follows from the properties of individual transfer functions, contradicts notions of ubiquitous complexity by showing input-dependent signal transmission inactivation.

A mechanistic study and computational prediction of iron, cobalt and manganese cyclopentadienone complexes for hydrogenation of carbon dioxide.

PubMed

Ge, Hongyu; Chen, Xiangyang; Yang, Xinzheng

2016-10-13

A series of cobalt and manganese cyclopentadienone complexes are proposed and examined computationally as promising catalysts for hydrogenation of CO 2 to formic acid with total free energies as low as 20.0 kcal mol -1 in aqueous solution. Density functional theory study of the newly designed cobalt and manganese complexes and experimentally reported iron cyclopentadienone complexes reveals a stepwise hydride transfer mechanism with a water or a methanol molecule assisted proton transfer for the cleavage of H 2 as the rate-determining step.

Energy transfer between surface-immobilized light-harvesting chlorophyll a/b complex (LHCII) studied by surface plasmon field-enhanced fluorescence spectroscopy (SPFS).

PubMed

Lauterbach, Rolf; Liu, Jing; Knoll, Wolfgang; Paulsen, Harald

2010-11-16

The major light-harvesting chlorophyll a/b complex (LHCII) of the photosynthetic apparatus in green plants can be viewed as a protein scaffold binding and positioning a large number of pigment molecules that combines rapid and efficient excitation energy transfer with effective protection of its pigments from photobleaching. These properties make LHCII potentially interesting as a light harvester (or a model thereof) in photoelectronic applications. Most of such applications would require the LHCII to be immobilized on a solid surface. In a previous study we showed the immobilization of recombinant LHCII on functionalized gold surfaces via a 6-histidine tag (His tag) in the protein moiety. In this work the occurrence and efficiency of Förster energy transfer between immobilized LHCII on a functionalized surface have been analyzed by surface plasmon field-enhanced fluorescence spectroscopy (SPFS). A near-infrared dye was attached to some but not all of the LHC complexes, serving as an energy acceptor to chlorophylls. Analysis of the energy transfer from chlorophylls to this acceptor dye yielded information about the extent of intercomplex energy transfer between immobilized LHCII.

The transfer functions of cardiac tissue during stochastic pacing.

PubMed

de Lange, Enno; Kucera, Jan P

2009-01-01

The restitution properties of cardiac action potential duration (APD) and conduction velocity (CV) are important factors in arrhythmogenesis. They determine alternans, wavebreak, and the patterns of reentrant arrhythmias. We developed a novel approach to characterize restitution using transfer functions. Transfer functions relate an input and an output quantity in terms of gain and phase shift in the complex frequency domain. We derived an analytical expression for the transfer function of interbeat intervals (IBIs) during conduction from one site (input) to another site downstream (output). Transfer functions can be efficiently obtained using a stochastic pacing protocol. Using simulations of conduction and extracellular mapping of strands of neonatal rat ventricular myocytes, we show that transfer functions permit the quantification of APD and CV restitution slopes when it is difficult to measure APD directly. We find that the normally positive CV restitution slope attenuates IBI variations. In contrast, a negative CV restitution slope (induced by decreasing extracellular [K(+)]) amplifies IBI variations with a maximum at the frequency of alternans. Hence, it potentiates alternans and renders conduction unstable, even in the absence of APD restitution. Thus, stochastic pacing and transfer function analysis represent a powerful strategy to evaluate restitution and the stability of conduction.

Synthesis, spectroscopic, thermal and electrical conductivity studies of three charge transfer complexes formed between 1,3-di[( E)-1-(2-hydroxyphenyl)methylideneamino]-2-propanol Schiff base and different acceptors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Ibrahim, Mohamed M.; Moussa, Mohamed A. A.

2012-01-01

Charge-transfer complexes (CTC) resulting from interactions of 1,3-di[( E)-1-(2-hydroxyphenyl) methylideneamino]-2-propanol Schiff base with some acceptors such as iodine (I2), bromine (Br2), and picric acid (PiA) have been isolated in the solid state in a chloroform solvent at room temperature. Based on elemental analysis, UV-Vis, infrared, and 1H NMR spectra, and thermogravimetric analysis (TG/DTG) of the solid CTC, [(Schiff)(I2)] (1), [(Schiff)(Br2)] complexes with a ratio of 1:1 and [(Schiff)(PiA)3] complexes with 1:3 have been prepared. In the picric acid complex, infrared and 1H NMR spectroscopic data indicate that the charge-transfer interaction is associated with a hydrogen bonding, whereas the iodine and bromine complexes were interpreted in terms of the formation of dative ion pairs [Schiff+, I{2/•-}] and [Schiff+, Br{2/•-}], respectively. Kinetic parameters were obtained for each stage of thermal degradation of the CT complexes using Coats-Redfern and Horowitz-Metzger methods. DC electrical properties as a function of temperature of these charge transfer complexes have been studied.

Palladium pincer complex catalyzed stannyl and silyl transfer to propargylic substrates: synthetic scope and mechanism.

PubMed

Kjellgren, Johan; Sundén, Henrik; Szabó, Kálmán J

2005-02-16

Pincer complex catalyzed substitution of various propargylic substrates could be achieved using tin- and silicon-based dimetallic reagents to obtain propargyl- and allenylstannanes and silanes. These reactions involving chloride, mesylate, and epoxide substrates could be carried out under mild conditions, and therefore many functionalities (such as COOEt, OR, OH, NR, and NAc) are tolerated. It was shown that pincer catalysts with electron-supplying ligands, such as NCN, SCS, and SeCSe complexes, display the highest catalytic activity. The catalytic substitution of secondary propargyl chlorides and primary propargyl chlorides with electron-withdrawing substituents proceeds with high regioselectivity providing the allenyl product. Opening of the propargyl epoxides takes place with an excellent stereo- and regioselectivity to give stereodefined allenylstannanes. Silylstannanes as dimetallic reagents undergo an exclusive silyl transfer to the propargylic substrate affording allenylsilanes with high regioselectivity. According to our mechanistic studies, the key intermediate of the reaction is an organostannane (or silane)-coordinated pincer complex, which is formed from the dimetallic reagent and the corresponding pincer complex catalyst. DFT modeling studies have shown that the trimethylstannyl functionality is transferred to the propargylic substrate in a single reaction step with high allenyl selectivity. Inspection of the TS structures reveals that the trimethylstannyl group transfer is initiated by the attack of the palladium-tin sigma-bond electrons on the propargylic substrate. This is a novel mechanism in palladium chemistry, which is based on the unique topology of the pincer complex catalysts.

Electronic structure and charge transfer excited states of endohedral fullerene containing electron donoracceptor complexes utilized in organic photovoltaics

NASA Astrophysics Data System (ADS)

Amerikheirabadi, Fatemeh

Organic Donor-Acceptor complexes form the main component of the organic photovoltaic devices (OPVs). The open circuit voltage of OPVs is directly related to the charge transfer excited state energies of these complexes. Currently a large number of different molecular complexes are being tested for their efficiency in photovoltaic devices. In this work, density functional theory as implemented in the NRLMOL code is used to investigate the electronic structure and related properties of these donor-acceptor complexes. The charge transfer excitation energies are calculated using the perturbative delta self-consistent field method recently developed in our group as the standard time dependent density functional approaches fail to accurately provide them. The model photovoltaics systems analyzed are as follows: Sc3N C 80--ZnTPP, Y3 N C80-- ZnTPP and Sc3 N C80-- ZnPc. In addition, a thorough analysis of the isolated donor and acceptor molecules is also provided. The studied acceptors are chosen from a class of fullerenes named trimetallic nitride endohedral fullerenes. These molecules have shown to possess advantages as acceptors such as long lifetimes of the charge-separated states.

Cyclodextrin-enhanced extraction and energy transfer of carcinogens in complex oil environments.

PubMed

Serio, Nicole; Chanthalyma, Chitapom; Prignano, Lindsey; Levine, Mindy

2013-11-27

Reported herein is the use of γ-cyclodextrin for two tandem functions: (a) the extraction of carcinogenic polycyclic aromatic hydrocarbons (PAHs) from oil samples into aqueous solution and (b) the promotion of highly efficient energy transfer from the newly extracted PAHs to a high-quantum-yield fluorophore. The extraction proceeded in moderate to good efficiencies, and the resulting cyclodextrin-promoted energy transfer led to a new, brightly fluorescent signal in aqueous solution. The resulting dual-function system (extraction followed by energy transfer) has significant relevance in the environmental detection and cleanup of oil-spill-related carcinogens.

Real-Time Kinetic Probes Support Monothiol Glutaredoxins As Intermediate Carriers in Fe-S Cluster Biosynthetic Pathways.

PubMed

Vranish, James N; Das, Deepika; Barondeau, David P

2016-11-18

Iron-sulfur (Fe-S) clusters are protein cofactors that are required for many essential cellular functions. Fe-S clusters are synthesized and inserted into target proteins by an elaborate biosynthetic process. The insensitivity of most Fe-S assembly and transfer assays requires high concentrations for components and places major limits on reaction complexity. Recently, fluorophore labels were shown to be effective at reporting cluster content for Fe-S proteins. Here, the incorporation of this labeling approach allowed the design and interrogation of complex Fe-S cluster biosynthetic reactions that mimic in vivo conditions. A bacterial Fe-S assembly complex, composed of the cysteine desulfurase IscS and scaffold protein IscU, was used to generate [2Fe-2S] clusters for transfer to mixtures of putative intermediate carrier and acceptor proteins. The focus of this study was to test whether the monothiol glutaredoxin, Grx4, functions as an obligate [2Fe-2S] carrier protein in the Fe-S cluster distribution network. Interestingly, [2Fe-2S] clusters generated by the IscS-IscU complex transferred to Grx4 at rates comparable to previous assays using uncomplexed IscU as a cluster source in chaperone-assisted transfer reactions. Further, we provide evidence that [2Fe-2S]-Grx4 delivers clusters to multiple classes of Fe-S targets via direct ligand exchange in a process that is both dynamic and reversible. Global fits of cluster transfer kinetics support a model in which Grx4 outcompetes terminal target proteins for IscU-bound [2Fe-2S] clusters and functions as an intermediate cluster carrier. Overall, these studies demonstrate the power of chemically conjugated fluorophore reporters for unraveling mechanistic details of biological metal cofactor assembly and distribution networks.

Optimisation of stability and charge transferability of ferrocene-encapsulated carbon nanotubes

NASA Astrophysics Data System (ADS)

Prajongtat, Pongthep; Sriyab, Suwannee; Zentgraf, Thomas; Hannongbua, Supa

2018-01-01

Ferrocene-encapsulated carbon nanotubes (Fc@CNTs) became promising nanocomposite materials for a wide range of applications due to their superior catalytic, mechanical and electronic properties. To open up new windows of applications, the highly stable and charge transferable encapsulation complexes are required. In this work, we designed the new encapsulation complexes formed from ferrocene derivatives (FcR, where R = -CHO, -CH2OH, -CON3 and -PCl2) and single-walled carbon nanotubes (SWCNTs). The influence of diameter and chirality of the nanotubes on the stability, charge transferability and electronic properties of such complexes has been investigated using density functional theory. The calculations suggest that the encapsulation stability and charge transferability of the encapsulation complexes depend on the size and chirality of the nanotubes. FcR@SWCNTs are more stable than Fc@SWCNTs at the optimum tube diameter. The greatest charge transfer was observed for FcCH2OH@SWCNTs and Fc@SWCNTs since the Fe d levels of FcCH2OH and Fc are nearly equal and close to the Fermi energy level of the nanotubes. The obtained results pave the way to the design of new encapsulated ferrocene derivatives which can give rise to higher stability and charge transferability of the encapsulation complexes.

Optical properties, excitation energy and primary charge transfer in photosystem II: theory meets experiment.

PubMed

Renger, Thomas; Schlodder, Eberhard

2011-01-01

In this review we discuss structure-function relationships of the core complex of photosystem II, as uncovered from analysis of optical spectra of the complex and its subunits. Based on descriptions of optical difference spectra including site directed mutagenesis we propose a revision of the multimer model of the symmetrically arranged reaction center pigments, described by an asymmetric exciton Hamiltonian. Evidence is provided for the location of the triplet state, the identity of the primary electron donor, the localization of the cation and the secondary electron transfer pathway in the reaction center. We also discuss the stationary and time-dependent optical properties of the CP43 and CP47 subunits and the excitation energy transfer and trapping-by-charge-transfer kinetics in the core complex. Copyright © 2011 Elsevier B.V. All rights reserved.

Regulation of human Nfu activity in Fe-S cluster delivery-characterization of the interaction between Nfu and the HSPA9/Hsc20 chaperone complex.

PubMed

Wachnowsky, Christine; Liu, Yushi; Yoon, Taejin; Cowan, J A

2018-01-01

Iron-sulfur cluster biogenesis is a complex, but highly regulated process that involves de novo cluster formation from iron and sulfide ions on a scaffold protein, and subsequent delivery to final targets via a series of Fe-S cluster-binding carrier proteins. The process of cluster release from the scaffold/carrier for transfer to the target proteins may be mediated by a dedicated Fe-S cluster chaperone system. In human cells, the chaperones include heat shock protein HSPA9 and the J-type chaperone Hsc20. While the role of chaperones has been somewhat clarified in yeast and bacterial systems, many questions remain over their functional roles in cluster delivery and interactions with a variety of human Fe-S cluster proteins. One such protein, Nfu, has recently been recognized as a potential interaction partner of the chaperone complex. Herein, we examined the ability of human Nfu to function as a carrier by interacting with the human chaperone complex. Human Nfu is shown to bind to both chaperone proteins with binding affinities similar to those observed for IscU binding to the homologous HSPA9 and Hsc20, while Nfu can also stimulate the ATPase activity of HSPA9. Additionally, the chaperone complex was able to promote Nfu function by enhancing the second-order rate constants for Fe-S cluster transfer to target proteins and providing directionality in cluster transfer from Nfu by eliminating promiscuous transfer reactions. Together, these data support a hypothesis in which Nfu can serve as an alternative carrier protein for chaperone-mediated cluster release and delivery in Fe-S cluster biogenesis and trafficking. © 2017 Federation of European Biochemical Societies.

Policy Transfer via Markov Logic Networks

NASA Astrophysics Data System (ADS)

Torrey, Lisa; Shavlik, Jude

We propose using a statistical-relational model, the Markov Logic Network, for knowledge transfer in reinforcement learning. Our goal is to extract relational knowledge from a source task and use it to speed up learning in a related target task. We show that Markov Logic Networks are effective models for capturing both source-task Q-functions and source-task policies. We apply them via demonstration, which involves using them for decision making in an initial stage of the target task before continuing to learn. Through experiments in the RoboCup simulated-soccer domain, we show that transfer via Markov Logic Networks can significantly improve early performance in complex tasks, and that transferring policies is more effective than transferring Q-functions.

Density functional study of the electronic structure of dye-functionalized fullerenes and their model donor-acceptor complexes containing P3HT

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

Baruah, Tunna; Garnica, Amanda; Paggen, Marina

2016-04-14

We study the electronic structure of C{sub 60} fullerenes functionalized with a thiophene-diketo-pyrrolopyrrole-thiophene based chromophore using density functional theory combined with large polarized basis sets. As the attached chromophore has electron donor character, the functionalization of the fullerene leads to a donor-acceptor (DA) system. We examine in detail the effect of the linker and the addition site on the electronic structure of the functionalized fullerenes. We further study the electronic structure of these DA complexes with a focus on the charge transfer excitations. Finally, we examine the interface of the functionalized fullerenes with the widely used poly(3-hexylthiophene-2,5-diyl) (P3HT) donor. Ourmore » results show that all functionalized fullerenes with an exception of the C{sub 60}-pyrrolidine [6,6], where the pyrrolidine is attached at a [6,6] site, have larger electron affinities relative to the pristine C{sub 60} fullerene. We also estimate the quasi-particle gap, lowest charge transfer excitation energy, and the exciton binding energies of the functionalized fullerene-P3MT model systems. Results show that the exciton binding energies in these model complexes are slightly smaller compared to a similarly prepared phenyl-C{sub 61}-butyric acid methyl ester (PCBM)-P3MT complex.« less

Structure-Function of the Cytochrome b 6f Complex of Oxygenic Photosynthesis

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

Cramer, W. A.; Yamashita, E.; Baniulis, D.

2014-03-20

Structure–function of the major integral membrane cytochrome b 6f complex that functions in cyanobacteria, algae, and green plants to transfer electrons between the two reaction center complexes in the electron transport chain of oxygenic photosynthesis is discussed in the context of recently obtained crystal structures of the complex and soluble domains of cytochrome f and the Rieske iron–sulfur protein. The energy-transducing function of the complex, generation of the proton trans-membrane electrochemical potential gradient, centers on the oxidation/reduction pathways of the plastoquinol/plastoquinone (QH 2/Q), the proton donor/acceptor within the complex. These redox reactions are carried out by five redox prosthetic groupsmore » embedded in each monomer, the high potential two iron–two sulfur cluster and the heme of cytochrome f on the electropositive side (p) of the complex, two noncovalently bound b-type hemes that cross the complex and the membrane, and a covalently bound c-type heme (c n) on the electronegative side (n). These five redox-active groups are organized in high- (cyt f/[2Fe–2S] and low-potential (hemes b p, b n, c n) electron transport pathways that oxidize and reduce the quinol and quinone on the p- and n-sides in a Q-cycle-type mechanism, while translocating as many as 2 H + to the p-side aqueous side for every electron transferred through the high potential chain to the photosystem I reaction center. The presence of heme c n and the connection of the n-side of the membrane and b 6f complex to the cyclic electron transport chain indicate that the Q cycle in the oxygenic photosynthetic electron transport chain differs from those connected to the bc 1 complex in the mitochondrial respiratory chain and the chain in photosynthetic bacteria. Inferences from the structure and C2 symmetry of the complex for the pathway of QH 2/Q transfer within the complex, problems posed by the presence of lipid in the inter-monomer cavity, and the narrow portal for QH2 passage through the p-side oxidation site proximal to the [2Fe–2S] cluster are discussed.« less

Intramolecular allyl transfer reaction from allyl ether to aldehyde groups: experimental and theoretical studies.

PubMed

Franco, Delphine; Wenger, Karine; Antonczak, Serge; Cabrol-Bass, Daniel; Duñach, Elisabet; Rocamora, Mercè; Gomez, Montserrat; Muller, Guillermo

2002-02-02

The intramolecular transfer of the allyl group of functionalized allyl aryl ethers to an aldehyde group in the presence of Ni0 complexes was studied from chemical, electrochemical and theoretical points of view. The chemical reaction involves the addition of Ni0 to the allyl ether followed by stoichiometric allylation. The electrochemical process is catalytic in nickel and involves the reduction of intermediate eta3-allylnickel(II) complexes.

Modelling and Order of Acoustic Transfer Functions Due to Reflections from Augmented Objects

NASA Astrophysics Data System (ADS)

Kuster, Martin; de Vries, Diemer

2006-12-01

It is commonly accepted that the sound reflections from real physical objects are much more complicated than what usually is and can be modelled by room acoustics modelling software. The main reason for this limitation is the level of detail inherent in the physical object in terms of its geometrical and acoustic properties. In the present paper, the complexity of the sound reflections from a corridor wall is investigated by modelling the corresponding acoustic transfer functions at several receiver positions in front of the wall. The complexity for different wall configurations has been examined and the changes have been achieved by altering its acoustic image. The results show that for a homogenous flat wall, the complexity is significant and for a wall including various smaller objects, the complexity is highly dependent on the position of the receiver with respect to the objects.

Prokaryotic Gene Clusters: A Rich Toolbox for Synthetic Biology

PubMed Central

Fischbach, Michael; Voigt, Christopher A.

2014-01-01

Bacteria construct elaborate nanostructures, obtain nutrients and energy from diverse sources, synthesize complex molecules, and implement signal processing to react to their environment. These complex phenotypes require the coordinated action of multiple genes, which are often encoded in a contiguous region of the genome, referred to as a gene cluster. Gene clusters sometimes contain all of the genes necessary and sufficient for a particular function. As an evolutionary mechanism, gene clusters facilitate the horizontal transfer of the complete function between species. Here, we review recent work on a number of clusters whose functions are relevant to biotechnology. Engineering these clusters has been hindered by their regulatory complexity, the need to balance the expression of many genes, and a lack of tools to design and manipulate DNA at this scale. Advances in synthetic biology will enable the large-scale bottom-up engineering of the clusters to optimize their functions, wake up cryptic clusters, or to transfer them between organisms. Understanding and manipulating gene clusters will move towards an era of genome engineering, where multiple functions can be “mixed-and-matched” to create a designer organism. PMID:21154668

Centralized PI control for high dimensional multivariable systems based on equivalent transfer function.

PubMed

Luan, Xiaoli; Chen, Qiang; Liu, Fei

2014-09-01

This article presents a new scheme to design full matrix controller for high dimensional multivariable processes based on equivalent transfer function (ETF). Differing from existing ETF method, the proposed ETF is derived directly by exploiting the relationship between the equivalent closed-loop transfer function and the inverse of open-loop transfer function. Based on the obtained ETF, the full matrix controller is designed utilizing the existing PI tuning rules. The new proposed ETF model can more accurately represent the original processes. Furthermore, the full matrix centralized controller design method proposed in this paper is applicable to high dimensional multivariable systems with satisfactory performance. Comparison with other multivariable controllers shows that the designed ETF based controller is superior with respect to design-complexity and obtained performance. Copyright © 2014 ISA. Published by Elsevier Ltd. All rights reserved.

DFT/TDDFT investigation on the photophysical properties of a series of phosphorescent cyclometalated complexes based on the benchmark complex FIrpic

NASA Astrophysics Data System (ADS)

Han, Deming; Gong, Ping; Lv, Shuhui; Zhao, Lihui; Zhao, Henan

2018-05-01

The photophysical properties of four Ir(III) complexes have been investigated by means of the density functional theory/time-dependent density functional theory (DFT/TDDFT). The effect of the electron-withdrawing and electron-donating substituents on charge injection, transport, absorption and phosphorescent properties has been studied. The theoretical calculation shows that the lowest-lying singlet absorptions for complexes 1-4 are located at 387, 385, 418 and 386 nm, respectively. For 1-4, the phosphorescence at 465, 485, 494 and 478 nm is mainly attributed to the LUMO → HOMO and LUMO → HOMO-1 transition configurations characteristics. In addition, ionisation potential (IP), electron affinities (EAs) and reorganisation energy have been investigated to evaluate the charge transfer and balance properties between hole and electron. The balance of the reorganisation energies for complex 3 is better than others. The difference between hole transport and electron transport for complex 3 is the smallest among these complexes, which is beneficial to achieve the hole and electron transfer balance in emitting layer.

Filtering Non-Linear Transfer Functions on Surfaces.

PubMed

Heitz, Eric; Nowrouzezahrai, Derek; Poulin, Pierre; Neyret, Fabrice

2014-07-01

Applying non-linear transfer functions and look-up tables to procedural functions (such as noise), surface attributes, or even surface geometry are common strategies used to enhance visual detail. Their simplicity and ability to mimic a wide range of realistic appearances have led to their adoption in many rendering problems. As with any textured or geometric detail, proper filtering is needed to reduce aliasing when viewed across a range of distances, but accurate and efficient transfer function filtering remains an open problem for several reasons: transfer functions are complex and non-linear, especially when mapped through procedural noise and/or geometry-dependent functions, and the effects of perspective and masking further complicate the filtering over a pixel's footprint. We accurately solve this problem by computing and sampling from specialized filtering distributions on the fly, yielding very fast performance. We investigate the case where the transfer function to filter is a color map applied to (macroscale) surface textures (like noise), as well as color maps applied according to (microscale) geometric details. We introduce a novel representation of a (potentially modulated) color map's distribution over pixel footprints using Gaussian statistics and, in the more complex case of high-resolution color mapped microsurface details, our filtering is view- and light-dependent, and capable of correctly handling masking and occlusion effects. Our approach can be generalized to filter other physical-based rendering quantities. We propose an application to shading with irradiance environment maps over large terrains. Our framework is also compatible with the case of transfer functions used to warp surface geometry, as long as the transformations can be represented with Gaussian statistics, leading to proper view- and light-dependent filtering results. Our results match ground truth and our solution is well suited to real-time applications, requires only a few lines of shader code (provided in supplemental material, which can be found on the Computer Society Digital Library at http://doi.ieeecomputersociety.org/10.1109/TVCG.2013.102), is high performance, and has a negligible memory footprint.

Transferring the entatic-state principle to copper photochemistry

NASA Astrophysics Data System (ADS)

Dicke, B.; Hoffmann, A.; Stanek, J.; Rampp, M. S.; Grimm-Lebsanft, B.; Biebl, F.; Rukser, D.; Maerz, B.; Göries, D.; Naumova, M.; Biednov, M.; Neuber, G.; Wetzel, A.; Hofmann, S. M.; Roedig, P.; Meents, A.; Bielecki, J.; Andreasson, J.; Beyerlein, K. R.; Chapman, H. N.; Bressler, C.; Zinth, W.; Rübhausen, M.; Herres-Pawlis, S.

2018-03-01

The entatic state denotes a distorted coordination geometry of a complex from its typical arrangement that generates an improvement to its function. The entatic-state principle has been observed to apply to copper electron-transfer proteins and it results in a lowering of the reorganization energy of the electron-transfer process. It is thus crucial for a multitude of biochemical processes, but its importance to photoactive complexes is unexplored. Here we study a copper complex—with a specifically designed constraining ligand geometry—that exhibits metal-to-ligand charge-transfer state lifetimes that are very short. The guanidine-quinoline ligand used here acts on the bis(chelated) copper(I) centre, allowing only small structural changes after photoexcitation that result in very fast structural dynamics. The data were collected using a multimethod approach that featured time-resolved ultraviolet-visible, infrared and X-ray absorption and optical emission spectroscopy. Through supporting density functional calculations, we deliver a detailed picture of the structural dynamics in the picosecond-to-nanosecond time range.

Theoretical study on interaction of cytochrome f and plastocyanin complex by a simple coarse-grained model with molecular crowding effect

NASA Astrophysics Data System (ADS)

Nakagawa, Satoshi; Kurniawan, Isman; Kodama, Koichi; Arwansyah, Muhammad Saleh; Kawaguchi, Kazutomo; Nagao, Hidemi

2018-03-01

We present a simple coarse-grained model with the molecular crowding effect in solvent to investigate the structure and dynamics of protein complexes including association and/or dissociation processes and investigate some physical properties such as the structure and the reaction rate from the viewpoint of the hydrophobic intermolecular interactions of protein complex. In the present coarse-grained model, a function depending upon the density of hydrophobic amino acid residues in a binding area of the complex is introduced, and the function involves the molecular crowding effect for the intermolecular interactions of hydrophobic amino acid residues between proteins. We propose a hydrophobic intermolecular potential energy between proteins by using the density-dependent function. The present coarse-grained model is applied to the complex of cytochrome f and plastocyanin by using the Langevin dynamics simulation to investigate some physical properties such as the complex structure, the electron transfer reaction rate constant from plastocyanin to cytochrome f and so on. We find that for proceeding the electron transfer reaction, the distance between metals in their active sites is necessary within about 18 Å. We discuss some typical complex structures formed in the present simulation in relation to the molecular crowding effect on hydrophobic interactions.

Band Alignment and Charge Transfer in Complex Oxide Interfaces

NASA Astrophysics Data System (ADS)

Zhong, Zhicheng; Hansmann, Philipp

2017-01-01

The synthesis of transition metal heterostructures is currently one of the most vivid fields in the design of novel functional materials. In this paper, we propose a simple scheme to predict band alignment and charge transfer in complex oxide interfaces. For semiconductor heterostructures, band-alignment rules like the well-known Anderson or Schottky-Mott rule are based on comparison of the work function or electron affinity of the bulk components. This scheme breaks down for oxides because of the invalidity of a single work-function approximation as recently shown in [Phys. Rev. B 93, 235116 (2016), 10.1103/PhysRevB.93.235116; Adv. Funct. Mater. 26, 5471 (2016), 10.1002/adfm.201600243]. Here, we propose a new scheme that is built on a continuity condition of valence states originating in the compounds' shared network of oxygen. It allows for the prediction of sign and relative amplitude of the intrinsic charge transfer, taking as input only information about the bulk properties of the components. We support our claims by numerical density functional theory simulations as well as (where available) experimental evidence. Specific applications include (i) controlled doping of SrTiO3 layers with the use of 4 d and 5 d transition metal oxides and (ii) the control of magnetic ordering in manganites through tuned charge transfer.

High Pressure Optical Studies of the Thallous Halides and of Charge-Transfer Complexes

NASA Astrophysics Data System (ADS)

Jurgensen, Charles Willard

High pressure was used to study the insulator -to-metal transition in sulfur and the thallous halides and to study the intermolecular interactions in charge -transfer complexes. The approach to the band overlap insulator -to-metal transition was studied in three thallous halides and sulfur by optical absorption measurements of the band gap as a function of pressure. The band gap of sulfur continuously decreases with pressure up to the insulator -to-metal transition which occurs between 450 and 485 kbars. The results on the thallous halides indicate that the indirect gap decreases more rapidly than the direct gap; the closing of the indirect gap is responsible for the observed insulator -to-metal transitions. High pressure electronic and vibrational spectroscopic measurements on the solid-state complexes of HMB-TCNE were used to study the intermolecular interactions of charge -transfer complexes. The vibrational frequency shifts indicate that the degree of charge transfer increases with pressure which is independently confirmed by an increase in the molar absorptivity of the electronic charge-transfer peak. Induction and dispersion forces contribute towards a red shift of the charge-transfer peak; however, charge-transfer resonance contributes toward a blue shift and this effect is dominant for the HMB-TCNE complexes. High pressure electronic spectra were used to study the effect of intermolecular interactions on the electronic states of TCNQ and its complexes. The red shifts with pressure of the electronic spectra of TCNQ and (TCNQ)(' -) in polymer media and of crystalline TCNQ can be understood in terms of Van der Waals interactions. None of the calculations which considered intradimer distance obtained the proper behavior for either the charge-transfer of the locally excited states of the complexes. The qualitative behavior of both states can be interpreted as the effect of increased mixing of the locally excited and charge transfer states.

UV-Vis spectroscopy and density functional study of solvent effect on the charge transfer band of the n → σ* complexes of 2-Methylpyridine and 2-Chloropyridine with molecular iodine

NASA Astrophysics Data System (ADS)

Gogoi, Pallavi; Mohan, Uttam; Borpuzari, Manash Protim; Boruah, Abhijit; Baruah, Surjya Kumar

2017-03-01

UV-Vis spectroscopy has established that Pyridine substitutes form n→σ* charge transfer (CT) complexes with molecular Iodine. This study is a combined approach of purely experimental UV-Vis spectroscopy, Multiple linear regression theory and Computational chemistry to analyze the effect of solvent upon the charge transfer band of 2-Methylpyridine-I2 and 2-Chloropyridine-I2 complexes. Regression analysis verifies the dependence of the CT band upon different solvent parameters. Dielectric constant and refractive index are considered among the bulk solvent parameters and Hansen, Kamlet and Catalan parameters are taken into consideration at the molecular level. Density Functional Theory results explain well the blue shift of the CT bands in polar medium as an outcome of stronger donor acceptor interaction. A logarithmic relation between the bond length of the bridging atoms of the donor and the acceptor with the dielectric constant of the medium is established. Tauc plot and TDDFT study indicates a non-vertical electronic transition in the complexes. Buckingham and Lippert Mataga equations are applied to check the Polarizability effect on the CT band.

Single crystal functional oxides on silicon

PubMed Central

Bakaul, Saidur Rahman; Serrao, Claudy Rayan; Lee, Michelle; Yeung, Chun Wing; Sarker, Asis; Hsu, Shang-Lin; Yadav, Ajay Kumar; Dedon, Liv; You, Long; Khan, Asif Islam; Clarkson, James David; Hu, Chenming; Ramesh, Ramamoorthy; Salahuddin, Sayeef

2016-01-01

Single-crystalline thin films of complex oxides show a rich variety of functional properties such as ferroelectricity, piezoelectricity, ferro and antiferromagnetism and so on that have the potential for completely new electronic applications. Direct synthesis of such oxides on silicon remains challenging because of the fundamental crystal chemistry and mechanical incompatibility of dissimilar interfaces. Here we report integration of thin (down to one unit cell) single crystalline, complex oxide films onto silicon substrates, by epitaxial transfer at room temperature. In a field-effect transistor using a transferred lead zirconate titanate layer as the gate insulator, we demonstrate direct reversible control of the semiconductor channel charge with polarization state. These results represent the realization of long pursued but yet to be demonstrated single-crystal functional oxides on-demand on silicon. PMID:26853112

Protein-induced geometric constraints and charge transfer in bacteriochlorophyll-histidine complexes in LH2.

PubMed

Wawrzyniak, Piotr K; Alia, A; Schaap, Roland G; Heemskerk, Mattijs M; de Groot, Huub J M; Buda, Francesco

2008-12-14

Bacteriochlorophyll-histidine complexes are ubiquitous in nature and are essential structural motifs supporting the conversion of solar energy into chemically useful compounds in a wide range of photosynthesis processes. A systematic density functional theory study of the NMR chemical shifts for histidine and for bacteriochlorophyll-a-histidine complexes in the light-harvesting complex II (LH2) is performed using the BLYP functional in combination with the 6-311++G(d,p) basis set. The computed chemical shift patterns are consistent with available experimental data for positive and neutral(tau) (N(tau) protonated) crystalline histidines. The results for the bacteriochlorophyll-a-histidine complexes in LH2 provide evidence that the protein environment is stabilizing the histidine close to the Mg ion, thereby inducing a large charge transfer of approximately 0.5 electronic equivalent. Due to this protein-induced geometric constraint, the Mg-coordinated histidine in LH2 appears to be in a frustrated state very different from the formal neutral(pi) (N(pi) protonated) form. This finding could be important for the understanding of basic functional mechanisms involved in tuning the electronic properties and exciton coupling in LH2.

Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm

NASA Astrophysics Data System (ADS)

Fu, Jinglin; Yang, Yuhe Renee; Johnson-Buck, Alexander; Liu, Minghui; Liu, Yan; Walter, Nils G.; Woodbury, Neal W.; Yan, Hao

2014-07-01

Swinging arms are a key functional component of multistep catalytic transformations in many naturally occurring multi-enzyme complexes. This arm is typically a prosthetic chemical group that is covalently attached to the enzyme complex via a flexible linker, allowing the direct transfer of substrate molecules between multiple active sites within the complex. Mimicking this method of substrate channelling outside the cellular environment requires precise control over the spatial parameters of the individual components within the assembled complex. DNA nanostructures can be used to organize functional molecules with nanoscale precision and can also provide nanomechanical control. Until now, protein-DNA assemblies have been used to organize cascades of enzymatic reactions by controlling the relative distance and orientation of enzymatic components or by facilitating the interface between enzymes/cofactors and electrode surfaces. Here, we show that a DNA nanostructure can be used to create a multi-enzyme complex in which an artificial swinging arm facilitates hydride transfer between two coupled dehydrogenases. By exploiting the programmability of DNA nanostructures, key parameters including position, stoichiometry and inter-enzyme distance can be manipulated for optimal activity.

Multi-enzyme complexes on DNA scaffolds capable of substrate channelling with an artificial swinging arm.

PubMed

Fu, Jinglin; Yang, Yuhe Renee; Johnson-Buck, Alexander; Liu, Minghui; Liu, Yan; Walter, Nils G; Woodbury, Neal W; Yan, Hao

2014-07-01

Swinging arms are a key functional component of multistep catalytic transformations in many naturally occurring multi-enzyme complexes. This arm is typically a prosthetic chemical group that is covalently attached to the enzyme complex via a flexible linker, allowing the direct transfer of substrate molecules between multiple active sites within the complex. Mimicking this method of substrate channelling outside the cellular environment requires precise control over the spatial parameters of the individual components within the assembled complex. DNA nanostructures can be used to organize functional molecules with nanoscale precision and can also provide nanomechanical control. Until now, protein-DNA assemblies have been used to organize cascades of enzymatic reactions by controlling the relative distance and orientation of enzymatic components or by facilitating the interface between enzymes/cofactors and electrode surfaces. Here, we show that a DNA nanostructure can be used to create a multi-enzyme complex in which an artificial swinging arm facilitates hydride transfer between two coupled dehydrogenases. By exploiting the programmability of DNA nanostructures, key parameters including position, stoichiometry and inter-enzyme distance can be manipulated for optimal activity.

Variable-Domain Displacement Transfer Functions for Converting Surface Strains into Deflections for Structural Deformed Shape Predictions

NASA Technical Reports Server (NTRS)

Ko, William L.; Fleischer, Van Tran

2015-01-01

Variable-Domain Displacement Transfer Functions were formulated for shape predictions of complex wing structures, for which surface strain-sensing stations must be properly distributed to avoid jointed junctures, and must be increased in the high strain gradient region. Each embedded beam (depth-wise cross section of structure along a surface strain-sensing line) was discretized into small variable domains. Thus, the surface strain distribution can be described with a piecewise linear or a piecewise nonlinear function. Through discretization, the embedded beam curvature equation can be piece-wisely integrated to obtain the Variable-Domain Displacement Transfer Functions (for each embedded beam), which are expressed in terms of geometrical parameters of the embedded beam and the surface strains along the strain-sensing line. By inputting the surface strain data into the Displacement Transfer Functions, slopes and deflections along each embedded beam can be calculated for mapping out overall structural deformed shapes. A long tapered cantilever tubular beam was chosen for shape prediction analysis. The input surface strains were analytically generated from finite-element analysis. The shape prediction accuracies of the Variable- Domain Displacement Transfer Functions were then determined in light of the finite-element generated slopes and deflections, and were fofound to be comparable to the accuracies of the constant-domain Displacement Transfer Functions

Nominal and functional task difficulty in skill acquisition: Effects on performance in two tests of transfer.

PubMed

Sanli, Elizabeth A; Lee, Timothy D

2015-06-01

The influence of nominal and functional task difficulty during the acquisition of a motor skill was examined in two tests of transfer of learning. The task involved a ballistic, target-directed, finger action. Nominal task difficulty was defined as the distance of the target from the home position. Functional task difficulty was created by manipulating the progression of target distances during practice. Based on the challenge point framework (Guadagnoli & Lee, 2004), we predicted that practice with a set of targets farther away from the performer would benefit from less functional task difficulty, while practice with a closer set of targets would benefit from more functional task difficulty. In single-task transfer tests, learners who practiced using the high nominal task difficulty targets benefitted in terms of persistence of performance over time. In dual-task transfer tests, groups with an intermediate combined (nominal and functional) task difficulty performed with greater persistence over time on tests of transfer than those who practiced with the highest or lowest combined difficulty. Together these findings suggest that the influences of nominal and functional task difficulty during acquisition are weighted differentially depending upon the transfer test context. The challenge point framework does not accurately capture this complex relationship in its current form. Copyright © 2015 Elsevier B.V. All rights reserved.

Carotenoids and Photosynthesis.

PubMed

Hashimoto, Hideki; Uragami, Chiasa; Cogdell, Richard J

2016-01-01

Carotenoids are ubiquitous and essential pigments in photosynthesis. They absorb in the blue-green region of the solar spectrum and transfer the absorbed energy to (bacterio-)chlorophylls, and so expand the wavelength range of light that is able to drive photosynthesis. This is an example of singlet-singlet energy transfer, and so carotenoids serve to enhance the overall efficiency of photosynthetic light reactions. Carotenoids also act to protect photosynthetic organisms from the harmful effects of excess exposure to light. Triplet-triplet energy transfer from chlorophylls to carotenoids plays a key role in this photoprotective reaction. In the light-harvesting pigment-protein complexes from purple photosynthetic bacteria and chlorophytes, carotenoids have an additional role of structural stabilization of those complexes. In this article we review what is currently known about how carotenoids discharge these functions. The molecular architecture of photosynthetic systems will be outlined first to provide a basis from which to describe carotenoid photochemistry, which underlies most of their important functions in photosynthesis.

Resolving the excited state equilibrium of peridinin in solution.

PubMed

Papagiannakis, Emmanouil; Larsen, Delmar S; van Stokkum, Ivo H M; Vengris, Mikas; Hiller, Roger G; van Grondelle, Rienk

2004-12-14

The carotenoid peridinin is abundant in the biosphere, as it is the main pigment bound by the light-harvesting complexes of dinoflagellates, where it collects blue and green sunlight and transfers energy to chlorophyll a with high efficiency. Its molecular structure is particularly complex, giving rise to an intricate excited state manifold, which includes a state with charge-transfer character. To disentangle the excited states of peridinin and understand their function in vivo, we applied dispersed pump-probe and pump-dump-probe spectroscopy. The preferential depletion of population from the intramolecular charge transfer state by the dump pulse demonstrates that the S(1) and this charge transfer state are distinct entities. The ensuing dump-induced dynamics illustrates the equilibration of the two states which occurs on the time scale of a few picoseconds. Additionally, the dump pulse populates a short-lived ground state intermediate, which is suggestive of a complex relaxation pathway, probably including structural reorientation or solvation of the ground state. These findings indicate that the unique intramolecular charge transfer state of peridinin is an efficient energy donor to chlorophyll a in the peridinin-chlorophyll-protein complex and thus plays a significant role in global light harvesting.

Theory after experiment on sensing mechanism of a newly developed sensor molecule: Converging or diverging?

NASA Astrophysics Data System (ADS)

Paul, Suvendu; Karar, Monaj; Das, Biswajit; Mallick, Arabinda; Majumdar, Tapas

2017-12-01

Fluoride ion sensing mechanism of 3,3‧-bis(indolyl)-4-chlorophenylmethane has been analyzed with density functional and time-dependent density functional theories. Extensive theoretical calculations on molecular geometry & energy, charge distribution, orbital energies & electronic distribution, minima on potential energy surface confirmed strong hydrogen bonded sensor-anion complex with incomplete proton transfer in S0. In S1, strong hydrogen bonding extended towards complete ESDPT. The distinct and single minima on the PES of the sensor-anion complex for both ground and first singlet excited states confirmed the concerted proton transfer mechanism. Present study well reproduced the experimental spectroscopic data and provided ESDPT as probable fluoride sensing mechanism.

Transfer function of analog fiber-optic systems driven by Fabry-Perot lasers: comment

NASA Astrophysics Data System (ADS)

Gyula, Veszely

2006-10-01

A bad notation makes difficult the understanding of the paper of Capmany et al. [J. Opt. Soc. Am. B22, 2099 (2005)]. The reason is that the real time function and the complex time function run into one another.

Order reduction of z-transfer functions via multipoint Jordan continued-fraction expansion

NASA Technical Reports Server (NTRS)

Lee, Ying-Chin; Hwang, Chyi; Shieh, Leang S.

1992-01-01

The order reduction problem of z-transfer functions is solved by using the multipoint Jordan continued-fraction expansion (MJCFE) technique. An efficient algorithm that does not require the use of complex algebra is presented for obtaining an MJCFE from a stable z-transfer function with expansion points selected from the unit circle and/or the positive real axis of the z-plane. The reduced-order models are exactly the multipoint Pade approximants of the original system and, therefore, they match the (weighted) time-moments of the impulse response and preserve the frequency responses of the system at some characteristic frequencies, such as gain crossover frequency, phase crossover frequency, bandwidth, etc.

End-Functionalized Palladium SCS Pincer Polymers via Controlled Radical Polymerizations.

PubMed

Lye, Diane S; Cohen, Aaron E; Wong, Madeleine Z; Weck, Marcus

2017-07-01

A direct and facile route toward semitelechelic polymers, end-functionalized with palladated sulfur-carbon-sulfur pincer (Pd II -pincer) complexes is reported that avoids any post-polymerization step. Key to our methodology is the combination of reversible addition-fragmentation chain-transfer (RAFT) polymerization with functionalized chain-transfer agents. This strategy yields Pd end-group-functionalized materials with monomodal molar mass dispersities (Đ) of 1.18-1.44. The RAFT polymerization is investigated using a Pd II -pincer chain-transfer agent for three classes of monomers: styrene, tert-butyl acrylate, and N-isopropylacrylamide. The ensuing Pd II -pincer end-functionalized polymers are analyzed using 1 H NMR spectroscopy, gel-permeation chromatography, and elemental analysis. The RAFT polymerization methodology provides a direct pathway for the fabrication of Pd II -pincer functionalized polymers with complete end-group functionalization. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nature and potency interactions of the hydrogen bond through the NBO analysis for charge transfer complex between 2-amino-4-hydroxy-6-methylpyrimidine and 2,3-pyrazinedicarboxylic acid

NASA Astrophysics Data System (ADS)

Faizan, Mohd; Afroz, Ziya; Alam, Mohammad Jane; Bhat, Sheeraz Ahmad; Ahmad, Shabbir; Ahmad, Afaq

2018-05-01

The intermolecular interactions in complex formation between 2-amino-4-hydroxy-6-methylpyrimidine (AHMP) and 2,3-pyrazinedicarboxylicacid (PDCA) have been explored using density functional theory calculations. The isolated 1:1 molecular geometry of proton transfer (PT) complex between AHMP and PDCA has been optimized on a counterpoise corrected potential energy surface (PES) at DFT-B3LYP/6-31G(d,p) level of theory in the gaseous phase. Further, the formation of hydrogen bonded charge transfer (HBCT) complex between PDCA and AHMP has been also discussed. PT energy barrier between two extremes is calculated using potential energy surface (PES) scan by varying bond length. The intermolecular interactions have been analyzed from theoretical perspective of natural bond orbital (NBO) analysis. In addition, the interaction energy between molecular fragments involved in the complex formation has been also computed by counterpoise procedure at same level of theory.

Synthesis, structural, spectroscopic and optical studies of charge transfer complex salts.

PubMed

Manikandan, Maruthappan; Mahalingam, Thaiyan; Hayakawa, Yasuhiro; Ravi, Ganesan

2013-01-15

New charge transfer molecular complex adducts of picric acid (C6H3N3O7) with triethylamine (C6H15N) and dimethylformamide (HCON(CH3)2) were synthesized successfully for the first time. Chemical composition and stoichiometry of the synthesized complex salts were verified by CHN elemental analysis. Solubility of the complex salts have been determined by gravimetric method and single crystals of two new salts were grown by low temperature solution growth technique. Crystal system, crystalline nature and cell parameters of the grown crystals were determined by single crystal X-ray diffraction (SXRD) and powder X-ray diffraction (PXRD) analyses. The formations of the charge-transfer complex, functional groups and the modes of vibrations have been confirmed by Fourier transform infrared (FTIR) spectroscopy. In order to know the linear and nonlinear optical suitability for device fabrication, UV-Vis (UV) spectral analysis and relative second harmonic generation (SHG) efficiency test were performed for the grown crystals. Copyright © 2012 Elsevier B.V. All rights reserved.

A mixed valence zinc dithiolene system with spectator metal and reactor ligands.

PubMed

Ratvasky, Stephen C; Mogesa, Benjamin; van Stipdonk, Michael J; Basu, Partha

2016-08-16

Neutral complexes of zinc with N,N'-diisopropylpiperazine-2,3-dithione ( i Pr 2 Dt 0 ) and N,N'-dimethylpiperazine-2,3-dithione (Me 2 Dt 0 ) with chloride or maleonitriledithiolate (mnt 2- ) as coligands have been synthesized and characterized. The molecular structures of these zinc complexes have been determined using single crystal X-ray diffractometry. Complexes recrystallize in monoclinic P type systems with zinc adopting a distorted tetrahedral geometry. Two zinc complexes with mixed-valent dithiolene ligands exhibit ligand-to-ligand charge transfer bands. Optimized geometries, molecular vibrations and electronic structures of charge-transfer complexes were calculated using density functional theory (B3LYP/6-311G+(d,p) level). Redox orbitals are shown to be almost exclusively ligand in nature, with a HOMO based heavily on the electron-rich maleonitriledithiolate ligand, and a LUMO comprised mostly of the electron-deficient dithione ligand. Charge transfer is thus believed to proceed from dithiolate HOMO to dithione LUMO, showing ligand-to-ligand redox interplay across a d 10 metal.

Synthesis, structural, spectroscopic and optical studies of charge transfer complex salts

NASA Astrophysics Data System (ADS)

Manikandan, Maruthappan; Mahalingam, Thaiyan; Hayakawa, Yasuhiro; Ravi, Ganesan

2013-01-01

New charge transfer molecular complex adducts of picric acid (C6H3N3O7) with triethylamine (C6H15N) and dimethylformamide (HCON(CH3)2) were synthesized successfully for the first time. Chemical composition and stoichiometry of the synthesized complex salts were verified by CHN elemental analysis. Solubility of the complex salts have been determined by gravimetric method and single crystals of two new salts were grown by low temperature solution growth technique. Crystal system, crystalline nature and cell parameters of the grown crystals were determined by single crystal X-ray diffraction (SXRD) and powder X-ray diffraction (PXRD) analyses. The formations of the charge-transfer complex, functional groups and the modes of vibrations have been confirmed by Fourier transform infrared (FTIR) spectroscopy. In order to know the linear and nonlinear optical suitability for device fabrication, UV-Vis (UV) spectral analysis and relative second harmonic generation (SHG) efficiency test were performed for the grown crystals.

Dynamic Stiffness Transfer Function of an Electromechanical Actuator Using System Identification

NASA Astrophysics Data System (ADS)

Kim, Sang Hwa; Tahk, Min-Jea

2018-04-01

In the aeroelastic analysis of flight vehicles with electromechanical actuators (EMAs), an accurate prediction of flutter requires dynamic stiffness characteristics of the EMA. The dynamic stiffness transfer function of the EMA with brushless direct current (BLDC) motor can be obtained by conducting complicated mathematical calculations of control algorithms and mechanical/electrical nonlinearities using linearization techniques. Thus, system identification approaches using experimental data, as an alternative, have considerable advantages. However, the test setup for system identification is expensive and complex, and experimental procedures for data collection are time-consuming tasks. To obtain the dynamic stiffness transfer function, this paper proposes a linear system identification method that uses information obtained from a reliable dynamic stiffness model with a control algorithm and nonlinearities. The results of this study show that the system identification procedure is compact, and the transfer function is able to describe the dynamic stiffness characteristics of the EMA. In addition, to verify the validity of the system identification method, the simulation results of the dynamic stiffness transfer function and the dynamic stiffness model were compared with the experimental data for various external loads.

A charge transfer amplified fluorescent Hg2+ complex for detection of picric acid and construction of logic functions.

PubMed

Kumar, Manoj; Reja, Shahi Imam; Bhalla, Vandana

2012-12-07

A chemosensor 3 based on the N,N-dimethylaminocinnamaldehyde has been synthesized which shows fluorescence turn-on response with Hg(2+) ions, and the in situ prepared 3-Hg(2+) complex has been used for detection of picric acid via electrostatic interaction and construction of a combinatorial logic circuit with NOR and INHIBIT logic functions.

[Hand reconstruction by microsurgical free toe transfer].

PubMed

Stamate, T; Budurcă, A R; Hermeziu, Oana

2003-01-01

Reconstruction of complex hand mutilations with multi-digital or thumb amputations are best treated with microsurgical toe transfers. We present the results of the first 15 cases operated by the first author, of which 12 are thumb reconstructions (6 great toe and 6 second toe transfers) and 3 long fingers reconstructions with combined second and third toe transfers. There were no microsurgical complications. Cortical integration and functional integration was achieved for all transferred toes, with discriminatory sensibility (m2PD between 5 and 13 mm) and active mobility range between 30 and 60 degrees.

Genetic code expansion for multiprotein complex engineering.

PubMed

Koehler, Christine; Sauter, Paul F; Wawryszyn, Mirella; Girona, Gemma Estrada; Gupta, Kapil; Landry, Jonathan J M; Fritz, Markus Hsi-Yang; Radic, Ksenija; Hoffmann, Jan-Erik; Chen, Zhuo A; Zou, Juan; Tan, Piau Siong; Galik, Bence; Junttila, Sini; Stolt-Bergner, Peggy; Pruneri, Giancarlo; Gyenesei, Attila; Schultz, Carsten; Biskup, Moritz Bosse; Besir, Hueseyin; Benes, Vladimir; Rappsilber, Juri; Jechlinger, Martin; Korbel, Jan O; Berger, Imre; Braese, Stefan; Lemke, Edward A

2016-12-01

We present a baculovirus-based protein engineering method that enables site-specific introduction of unique functionalities in a eukaryotic protein complex recombinantly produced in insect cells. We demonstrate the versatility of this efficient and robust protein production platform, 'MultiBacTAG', (i) for the fluorescent labeling of target proteins and biologics using click chemistries, (ii) for glycoengineering of antibodies, and (iii) for structure-function studies of novel eukaryotic complexes using single-molecule Förster resonance energy transfer as well as site-specific crosslinking strategies.

Structure and Electronic Spectra of Purine-Methyl Viologen Charge Transfer Complexes

PubMed Central

Jalilov, Almaz S.; Patwardhan, Sameer; Singh, Arunoday; Simeon, Tomekia; Sarjeant, Amy A.; Schatz, George C.; Lewis, Frederick D.

2014-01-01

The structure and properties of the electron donor-acceptor complexes formed between methyl viologen (MV) and purine nucleosides and nucleotides in water and the solid state have been investigated using a combination of experimental and theoretical methods. Solution studies were performed using UV-vis and 1H NMR spectroscopy. Theoretical calculations were performed within the framework of density functional theory (DFT). Energy decomposition analysis indicates that dispersion and induction (charge-transfer) interactions dominate the total binding energy, whereas electrostatic interactions are largely repulsive. The appearance of charge transfer bands in the absorption spectra of the complexes are well described by time-dependent (TD) DFT and are further explained in terms of the redox properties of purine monomers and solvation effects. Crystal structures are reported for complexes of methyl viologen with the purines 2′-deoxyguanosine 3′-monophosphate GMP (DAD′DAD′ type) and 7-deazaguanosine zG (DAD′ADAD′ type). Comparison of the structures determined in the solid state and by theoretical methods in solution provides valuable insights into the nature of charge-transfer interactions involving purine bases as electron donors. PMID:24294996

Complexes of DNA bases and Watson-Crick base pairs interaction with neutral silver Agn (n = 8, 10, 12) clusters: a DFT and TDDFT study.

PubMed

Srivastava, Ruby

2018-03-01

We study the binding of the neutral Ag n (n = 8, 10, 12) to the DNA base-adenine (A), guanine (G) and Watson-Crick -adenine-thymine, guanine-cytosine pairs. Geometries of complexes were optimized at the DFT level using the hybrid B3LYP functional. LANL2DZ effective core potential was used for silver and 6-31 + G ** was used for all other atoms. NBO charges were analyzed using the Natural population analysis. The absorption properties of Ag n -A,G/WC complexes were also studied using time-dependent density functional theory. The absorption spectra for these complexes show wavelength in the visible region. It was revealed that silver clusters interact more strongly with WC pairs than with isolated DNA complexes. Furthermore, it was found that the electronic charge transferred from silver to isolated DNA clusters are less than the electronic charge transferred from silver to the Ag n -WC complexes. The vertical ionization potential, vertical electron affinity, hardness, and electrophilicity index of Ag n -DNA/WC complexes have also been discussed.

The free-energy barrier to hydride transfer across a dipalladium complex

DOE PAGES

Ramirez-Cuesta, Anibal J.

2015-01-01

We use density-functional theory molecular dynamics (DFT-MD) simulations to determine the hydride transfer coordinate between palladium centres of the crystallographically observed terminal hydride locations, Pd-Pd-H, originally postulated for the solution dynamics of the complex bis-NHC dipalladium hydride [{(MesIm)(2)CH2}(2)Pd2H][PF6], and then calculate the free-energy along this coordinate. We estimate the transfer barrier-height to be about 20 kcal mol(-1) with a hydride transfer rate in the order of seconds at room temperature. We validate our DFT-MD modelling using inelastic neutron scattering which reveals anharmonicity of the hydride environment that is so pronounced that there is complete failure of the harmonic model formore » the hydride ligand. The simulations are extended to high temperature to bring the H-transfer to a rate that is accessible to the simulation technique.« less

Sam37 is crucial for formation of the mitochondrial TOM-SAM supercomplex, thereby promoting β-barrel biogenesis.

PubMed

Wenz, Lena-Sophie; Ellenrieder, Lars; Qiu, Jian; Bohnert, Maria; Zufall, Nicole; van der Laan, Martin; Pfanner, Nikolaus; Wiedemann, Nils; Becker, Thomas

2015-09-28

Biogenesis of mitochondrial β-barrel proteins requires two preprotein translocases, the general translocase of the outer membrane (TOM) and the sorting and assembly machinery (SAM). TOM and SAM form a supercomplex that promotes transfer of β-barrel precursors. The SAM core complex contains the channel protein Sam50, which cooperates with Sam35 in precursor recognition, and the peripheral membrane protein Sam37. The molecular function of Sam37 has been unknown. We report that Sam37 is crucial for formation of the TOM-SAM supercomplex. Sam37 interacts with the receptor domain of Tom22 on the cytosolic side of the mitochondrial outer membrane and links TOM and SAM complexes. Sam37 thus promotes efficient transfer of β-barrel precursors to the SAM complex. We conclude that Sam37 functions as a coupling factor of the translocase supercomplex of the mitochondrial outer membrane. © 2015 Wenz et al.

Instantaneous Transfer Entropy for the Study of Cardiovascular and Cardiorespiratory Nonstationary Dynamics.

PubMed

Valenza, Gaetano; Faes, Luca; Citi, Luca; Orini, Michele; Barbieri, Riccardo

2018-05-01

Measures of transfer entropy (TE) quantify the direction and strength of coupling between two complex systems. Standard approaches assume stationarity of the observations, and therefore are unable to track time-varying changes in nonlinear information transfer with high temporal resolution. In this study, we aim to define and validate novel instantaneous measures of TE to provide an improved assessment of complex nonstationary cardiorespiratory interactions. We here propose a novel instantaneous point-process TE (ipTE) and validate its assessment as applied to cardiovascular and cardiorespiratory dynamics. In particular, heartbeat and respiratory dynamics are characterized through discrete time series, and modeled with probability density functions predicting the time of the next physiological event as a function of the past history. Likewise, nonstationary interactions between heartbeat and blood pressure dynamics are characterized as well. Furthermore, we propose a new measure of information transfer, the instantaneous point-process information transfer (ipInfTr), which is directly derived from point-process-based definitions of the Kolmogorov-Smirnov distance. Analysis on synthetic data, as well as on experimental data gathered from healthy subjects undergoing postural changes confirms that ipTE, as well as ipInfTr measures are able to dynamically track changes in physiological systems coupling. This novel approach opens new avenues in the study of hidden, transient, nonstationary physiological states involving multivariate autonomic dynamics in cardiovascular health and disease. The proposed method can also be tailored for the study of complex multisystem physiology (e.g., brain-heart or, more in general, brain-body interactions).

High-level user interfaces for transfer function design with semantics.

PubMed

Salama, Christof Rezk; Keller, Maik; Kohlmann, Peter

2006-01-01

Many sophisticated techniques for the visualization of volumetric data such as medical data have been published. While existing techniques are mature from a technical point of view, managing the complexity of visual parameters is still difficult for non-expert users. To this end, this paper presents new ideas to facilitate the specification of optical properties for direct volume rendering. We introduce an additional level of abstraction for parametric models of transfer functions. The proposed framework allows visualization experts to design high-level transfer function models which can intuitively be used by non-expert users. The results are user interfaces which provide semantic information for specialized visualization problems. The proposed method is based on principal component analysis as well as on concepts borrowed from computer animation.

Influence of Proton Acceptors on the Proton-Coupled Electron Transfer Reaction Kinetics of a Ruthenium-Tyrosine Complex.

PubMed

Lennox, J Christian; Dempsey, Jillian L

2017-11-22

A polypyridyl ruthenium complex with fluorinated bipyridine ligands and a covalently bound tyrosine moiety was synthesized, and its photo-induced proton-coupled electron transfer (PCET) reactivity in acetonitrile was investigated with transient absorption spectroscopy. Using flash-quench methodology with methyl viologen as an oxidative quencher, a Ru 3+ species is generated that is capable of initiating the intramolecular PCET oxidation of the tyrosine moiety. Using a series of substituted pyridine bases, the reaction kinetics were found to vary as a function of proton acceptor concentration and identity, with no significant H/D kinetic isotope effect. Through analysis of the kinetics traces and comparison to a control complex without the tyrosine moiety, PCET reactivity was found to proceed through an equilibrium electron transfer followed by proton transfer (ET-PT) pathway in which irreversible deprotonation of the tyrosine radical cation shifts the ET equilibrium, conferring a base dependence on the reaction. Comprehensive kinetics modeling allowed for deconvolution of complex kinetics and determination of rate constants for each elementary step. Across the five pyridine bases explored, spanning a range of 4.2 pK a units, a linear free-energy relationship was found for the proton transfer rate constant with a slope of 0.32. These findings highlight the influence that proton transfer driving force exerts on PCET reaction kinetics.

Extensive domain motion and electron transfer in the human electron transferring flavoprotein.medium chain Acyl-CoA dehydrogenase complex.

PubMed

Toogood, Helen S; van Thiel, Adam; Basran, Jaswir; Sutcliffe, Mike J; Scrutton, Nigel S; Leys, David

2004-07-30

The crystal structure of the human electron transferring flavoprotein (ETF).medium chain acyl-CoA dehydrogenase (MCAD) complex reveals a dual mode of protein-protein interaction, imparting both specificity and promiscuity in the interaction of ETF with a range of structurally distinct primary dehydrogenases. ETF partitions the functions of partner binding and electron transfer between (i) the recognition loop, which acts as a static anchor at the ETF.MCAD interface, and (ii) the highly mobile redox active FAD domain. Together, these enable the FAD domain of ETF to sample a range of conformations, some compatible with fast interprotein electron transfer. Disorders in amino acid or fatty acid catabolism can be attributed to mutations at the protein-protein interface. Crucially, complex formation triggers mobility of the FAD domain, an induced disorder that contrasts with general models of protein-protein interaction by induced fit mechanisms. The subsequent interfacial motion in the MCAD.ETF complex is the basis for the interaction of ETF with structurally diverse protein partners. Solution studies using ETF and MCAD with mutations at the protein-protein interface support this dynamic model and indicate ionic interactions between MCAD Glu(212) and ETF Arg alpha(249) are likely to transiently stabilize productive conformations of the FAD domain leading to enhanced electron transfer rates between both partners.

Discontinuous Galerkin finite element methods for radiative transfer in spherical symmetry

NASA Astrophysics Data System (ADS)

Kitzmann, D.; Bolte, J.; Patzer, A. B. C.

2016-11-01

The discontinuous Galerkin finite element method (DG-FEM) is successfully applied to treat a broad variety of transport problems numerically. In this work, we use the full capacity of the DG-FEM to solve the radiative transfer equation in spherical symmetry. We present a discontinuous Galerkin method to directly solve the spherically symmetric radiative transfer equation as a two-dimensional problem. The transport equation in spherical atmospheres is more complicated than in the plane-parallel case owing to the appearance of an additional derivative with respect to the polar angle. The DG-FEM formalism allows for the exact integration of arbitrarily complex scattering phase functions, independent of the angular mesh resolution. We show that the discontinuous Galerkin method is able to describe accurately the radiative transfer in extended atmospheres and to capture discontinuities or complex scattering behaviour which might be present in the solution of certain radiative transfer tasks and can, therefore, cause severe numerical problems for other radiative transfer solution methods.

Influence of Humic Acid Complexation with Metal Ions on Extracellular Electron Transfer Activity.

PubMed

Zhou, Shungui; Chen, Shanshan; Yuan, Yong; Lu, Qin

2015-11-23

Humic acids (HAs) can act as electron shuttles and mediate biogeochemical cycles, thereby influencing the transformation of nutrients and environmental pollutants. HAs commonly complex with metals in the environment, but few studies have focused on how these metals affect the roles of HAs in extracellular electron transfer (EET). In this study, HA-metal (HA-M) complexes (HA-Fe, HA-Cu, and HA-Al) were prepared and characterized. The electron shuttle capacities of HA-M complexes were experimentally evaluated through microbial Fe(III) reduction, biocurrent generation, and microbial azoreduction. The results show that the electron shuttle capacities of HAs were enhanced after complexation with Fe but were weakened when using Cu or Al. Density functional theory calculations were performed to explore the structural geometry of the HA-M complexes and revealed the best binding sites of the HAs to metals and the varied charge transfer rate constants (k). The EET activity of the HA-M complexes were in the order HA-Fe > HA-Cu > HA-Al. These findings have important implications for biogeochemical redox processes given the ubiquitous nature of both HAs and various metals in the environment.

Rotordynamic analysis using the Complex Transfer Matrix: An application to elastomer supports using the viscoelastic correspondence principle

NASA Astrophysics Data System (ADS)

Varney, Philip; Green, Itzhak

2014-11-01

Numerous methods are available to calculate rotordynamic whirl frequencies, including analytic methods, finite element analysis, and the transfer matrix method. The typical real-valued transfer matrix (RTM) suffers from several deficiencies, including lengthy computation times and the inability to distinguish forward and backward whirl. Though application of complex coordinates in rotordynamic analysis is not novel per se, specific advantages gained from using such coordinates in a transfer matrix analysis have yet to be elucidated. The present work employs a complex coordinate redefinition of the transfer matrix to obtain reduced forms of the elemental transfer matrices in inertial and rotating reference frames, including external stiffness and damping. Application of the complex-valued state variable redefinition results in a reduction of the 8×8 RTM to the 4×4 Complex Transfer Matrix (CTM). The CTM is advantageous in that it intrinsically separates forward and backward whirl, eases symbolic manipulation by halving the transfer matrices’ dimension, and provides significant improvement in computation time. A symbolic analysis is performed on a simple overhung rotor to demonstrate the mathematical motivation for whirl frequency separation. The CTM's utility is further shown by analyzing a rotordynamic system supported by viscoelastic elastomer rings. Viscoelastic elastomer ring supports can provide significant damping while reducing the cost and complexity associated with conventional components such as squeeze film dampers. The stiffness and damping of a viscoelastic damper ring are determined herein as a function of whirl frequency using the viscoelastic correspondence principle and a constitutive fractional calculus viscoelasticity model. The CTM is then employed to obtain the characteristic equation, where the whirl frequency dependent stiffness and damping of the elastomer supports are included. The Campbell diagram is shown, demonstrating the CTM's ability to intrinsically separate synchronous whirl direction for a non-trivial rotordynamic system. Good agreement is found between the CTM results and previously obtained analytic and experimental results for the elastomer ring supported rotordynamic system.

Transfer function modeling of damping mechanisms in viscoelastic plates

NASA Technical Reports Server (NTRS)

Slater, J. C.; Inman, D. J.

1991-01-01

This work formulates a method for the modeling of material damping characteristics in plates. The Sophie German equation of classical plate theory is modified to incorporate hysteresis effects represented by complex stiffness using the transfer function approach proposed by Golla and Hughes, (1985). However, this procedure is not limited to this representation. The governing characteristic equation is decoupled through separation of variables, yielding a solution similar to that of undamped classical plate theory, allowing solution of the steady state as well as the transient response problem.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms

NASA Astrophysics Data System (ADS)

Mohamed, Gehad G.; Hamed, Maher M.; Zaki, Nadia G.; Abdou, Mohamed M.; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-01

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100 μg mL- 1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase.

Melatonin charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone: Molecular structure, DFT studies, thermal analyses, evaluation of biological activity and utility for determination of melatonin in pure and dosage forms.

PubMed

Mohamed, Gehad G; Hamed, Maher M; Zaki, Nadia G; Abdou, Mohamed M; Mohamed, Marwa El-Badry; Abdallah, Abanoub Mosaad

2017-07-05

A simple, accurate and fast spectrophotometric method for the quantitative determination of melatonin (ML) drug in its pure and pharmaceutical forms was developed based on the formation of its charge transfer complex with 2,3-dichloro-5,6-dicyano-1,4-benzoquinone (DDQ) as an electron acceptor. The different conditions for this method were optimized accurately. The Lambert-Beer's law was found to be valid over the concentration range of 4-100μgmL -1 ML. The solid form of the CT complex was structurally characterized by means of different spectral methods. Density functional theory (DFT) and time-dependent density functional theory (TD-DFT) calculations were carried out. The different quantum chemical parameters of the CT complex were calculated. Thermal properties of the CT complex and its kinetic thermodynamic parameters were studied, as well as its antimicrobial and antifungal activities were investigated. Molecular docking studies were performed to predict the binding modes of the CT complex components towards E. coli bacterial RNA and the receptor of breast cancer mutant oxidoreductase. Copyright © 2017 Elsevier B.V. All rights reserved.

The Alternative complex III: properties and possible mechanisms for electron transfer and energy conservation.

PubMed

Refojo, Patrícia N; Teixeira, Miguel; Pereira, Manuela M

2012-10-01

Alternative complexes III (ACIII) are recently identified membrane-bound enzymes that replace functionally the cytochrome bc(1/)b(6)f complexes. In general, ACIII are composed of four transmembrane proteins and three peripheral subunits that contain iron-sulfur centers and C-type hemes. ACIII are built by a combination of modules present in different enzyme families, namely the complex iron-sulfur molybdenum containing enzymes. In this article a historical perspective on the investigation of ACIII is presented, followed by an overview of the present knowledge on these enzymes. Electron transfer pathways within the protein are discussed taking into account possible different locations (cytoplasmatic or periplasmatic) of the iron-sulfur containing protein and their contribution to energy conservation. In this way several hypotheses for energy conservation modes are raised including linear and bifurcating electron transfer pathways. This article is part of a Special Issue entitled: 17th European Bioenergetics Conference (EBEC 2012). Copyright © 2012 Elsevier B.V. All rights reserved.

High sensitization efficiency and energy transfer routes for population inversion at low pump intensity in Er organic complexes for IR amplification.

PubMed

Hu, J X; Karamshuk, S; Gorbaciova, J; Ye, H Q; Lu, H; Zhang, Y P; Zheng, Y X; Liang, X; Hernández, I; Wyatt, P B; Gillin, W P

2018-02-19

Organic erbium complexes have long been of interest due to their potential for using the strong absorption into the organic to sensitise the erbium emission. Despite this interest there is remarkably little quantitative information on how effective the approach is and the discussion of the energy transfer mechanism is generally vague. Here we accurately quantify the sensitisation as a function of excitation pump density and model it using a rate equation approach. As a result, we can calculate the degree of population inversion for the erbium ions as a function of the pump intensity. We demonstrate that even when we increase the erbium concentration in the films from ~10 to ~80% we find a relatively small decrease in the sensitisation which we attribute to the large (>20 Å) Förster radius for the sensitisation process. We show that we can obtain population inversion in our films at very low pump powers ~600 mW/cm 2 . The calculated Förster radius for the organic erbium complexes suggests design rules for energy transfer between antennas and erbium ions in molecular systems and hybrid organic-inorganic nanoparticles.

Algebraic Functions, Computer Programming, and the Challenge of Transfer

ERIC Educational Resources Information Center

Schanzer, Emmanuel Tanenbaum

2015-01-01

Students' struggles with algebra are well documented. Prior to the introduction of functions, mathematics is typically focused on applying a set of arithmetic operations to compute an answer. The introduction of functions, however, marks the point at which mathematics begins to focus on building up abstractions as a way to solve complex problems.…

Role of Tim50 in the Transfer of Precursor Proteins from the Outer to the Inner Membrane of Mitochondria

PubMed Central

Sichting, Martin; Popov-Čeleketić, Dušan; Mapa, Koyeli; Gevorkyan-Airapetov, Lada; Zohary, Keren; Hell, Kai; Azem, Abdussalam

2009-01-01

Transport of essentially all matrix and a number of inner membrane proteins is governed, entirely or in part, by N-terminal presequences and requires a coordinated action of the translocases of outer and inner mitochondrial membranes (TOM and TIM23 complexes). Here, we have analyzed Tim50, a subunit of the TIM23 complex that is implicated in transfer of precursors from TOM to TIM23. Tim50 is recruited to the TIM23 complex via Tim23 in an interaction that is essentially independent of the rest of the translocase. We find Tim50 in close proximity to the intermembrane space side of the TOM complex where it recognizes both types of TIM23 substrates, those that are to be transported into the matrix and those destined to the inner membrane, suggesting that Tim50 recognizes presequences. This function of Tim50 depends on its association with TIM23. We conclude that the efficient transfer of precursors between TOM and TIM23 complexes requires the concerted action of Tim50 with Tim23. PMID:19144822

Role of Tim50 in the transfer of precursor proteins from the outer to the inner membrane of mitochondria.

PubMed

Mokranjac, Dejana; Sichting, Martin; Popov-Celeketić, Dusan; Mapa, Koyeli; Gevorkyan-Airapetov, Lada; Zohary, Keren; Hell, Kai; Azem, Abdussalam; Neupert, Walter

2009-03-01

Transport of essentially all matrix and a number of inner membrane proteins is governed, entirely or in part, by N-terminal presequences and requires a coordinated action of the translocases of outer and inner mitochondrial membranes (TOM and TIM23 complexes). Here, we have analyzed Tim50, a subunit of the TIM23 complex that is implicated in transfer of precursors from TOM to TIM23. Tim50 is recruited to the TIM23 complex via Tim23 in an interaction that is essentially independent of the rest of the translocase. We find Tim50 in close proximity to the intermembrane space side of the TOM complex where it recognizes both types of TIM23 substrates, those that are to be transported into the matrix and those destined to the inner membrane, suggesting that Tim50 recognizes presequences. This function of Tim50 depends on its association with TIM23. We conclude that the efficient transfer of precursors between TOM and TIM23 complexes requires the concerted action of Tim50 with Tim23.

Effects of distributions of energy of transfer rates on spectral hole burning in photosynthetic pigment-protein complexes

NASA Astrophysics Data System (ADS)

Ahmouda, Somaya

To perform photosynthesis, plants, algae and bacteria possess well organized and closely coupled photosynthetic pigment-protein complexes. Information on energy transfer in photosynthetic complexes is important to understand their functioning and possibly to design new and improved photovoltaic devices. The information on energy transfer processes contained in the narrow zero-phonon lines at low temperatures is hidden under the inhomogeneous broadening. Thus, it has been proven difficult to analyze the spectroscopic properties of these complexes in sufficient detail by conventional spectroscopy methods. In this context the high resolution spectroscopy techniques such as Spectral Hole Burning are powerful tools designed to get around the inhomogeneous broadening. Spectral Hole Burning involves selective excitation by a laser which removes molecules with the zero-phonon transitions resonant with this laser. This thesis focuses on the effects of the distributions of the energy transfer rates (homogeneous line widths) on the evolution of spectral holes. These distributions are a consequence of the static disorder in the photosynthetic pigment-protein complexes. The qualitative effects of different types of the line width distributions on the evolution of spectral holes have been and explored by numerical simulations, an example of analysis of the original experimental data has been presented as well.

Photoprotection and triplet energy transfer in higher plants: the role of electronic and nuclear fluctuations.

PubMed

Cupellini, Lorenzo; Jurinovich, Sandro; Prandi, Ingrid G; Caprasecca, Stefano; Mennucci, Benedetta

2016-04-28

Photosynthetic organisms employ several photoprotection strategies to avoid damage due to the excess energy in high light conditions. Among these, quenching of triplet chlorophylls by neighboring carotenoids (Cars) is fundamental in preventing the formation of singlet oxygen. Cars are able to accept the triplets from chlorophylls by triplet energy transfer (TET). We have here studied TET rates in CP29, a minor light-harvesting complex (LHC) of the Photosystem II in plants. A fully atomistic strategy combining classical molecular dynamics of the LHC in its natural environment with a hybrid time-dependent density functional theory/polarizable MM description of the TET is used. We find that the structural fluctuations of the pigment-protein complex can largely enhance the transfer rates with respect to those predicted using the crystal structure, reducing the triplet quenching times in the subnanosecond scale. These findings add a new perspective for the interpretation of the photoprotection function and its relation with structural motions of the LHC.

Robust and stretchable indium gallium zinc oxide-based electronic textiles formed by cilia-assisted transfer printing

PubMed Central

Yoon, Jongwon; Jeong, Yunkyung; Kim, Heeje; Yoo, Seonggwang; Jung, Hoon Sun; Kim, Yonghun; Hwang, Youngkyu; Hyun, Yujun; Hong, Woong-Ki; Lee, Byoung Hun; Choa, Sung-Hoon; Ko, Heung Cho

2016-01-01

Electronic textile (e-textile) allows for high-end wearable electronic devices that provide easy access for carrying, handling and using. However, the related technology does not seem to be mature because the woven fabric hampers not only the device fabrication process directly on the complex surface but also the transfer printing of ultrathin planar electronic devices. Here we report an indirect method that enables conformal wrapping of surface with arbitrary yet complex shapes. Artificial cilia are introduced in the periphery of electronic devices as adhesive elements. The cilia also play an important role in confining a small amount of glue and damping mechanical stress to maintain robust electronic performance under mechanical deformation. The example of electronic applications depicts the feasibility of cilia for ‘stick-&-play' systems, which provide electronic functions by transfer printing on unconventional complex surfaces. PMID:27248982

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.

Extension of Light-Harvesting Ability of Photosynthetic Light-Harvesting Complex 2 (LH2) through Ultrafast Energy Transfer from Covalently Attached Artificial Chromophores.

PubMed

Yoneda, Yusuke; Noji, Tomoyasu; Katayama, Tetsuro; Mizutani, Naoto; Komori, Daisuke; Nango, Mamoru; Miyasaka, Hiroshi; Itoh, Shigeru; Nagasawa, Yutaka; Dewa, Takehisa

2015-10-14

Introducing appropriate artificial components into natural biological systems could enrich the original functionality. To expand the available wavelength range of photosynthetic bacterial light-harvesting complex 2 (LH2 from Rhodopseudomonas acidophila 10050), artificial fluorescent dye (Alexa Fluor 647: A647) was covalently attached to N- and C-terminal Lys residues in LH2 α-polypeptides with a molar ratio of A647/LH2 ≃ 9/1. Fluorescence and transient absorption spectroscopies revealed that intracomplex energy transfer from A647 to intrinsic chromophores of LH2 (B850) occurs in a multiexponential manner, with time constants varying from 440 fs to 23 ps through direct and B800-mediated indirect pathways. Kinetic analyses suggested that B800 chromophores mediate faster energy transfer, and the mechanism was interpretable in terms of Förster theory. This study demonstrates that a simple attachment of external chromophores with a flexible linkage can enhance the light harvesting activity of LH2 without affecting inherent functions of energy transfer, and can achieve energy transfer in the subpicosecond range. Addition of external chromophores, thus, represents a useful methodology for construction of advanced hybrid light-harvesting systems that afford solar energy in the broad spectrum.

Insight into the kinetics and thermodynamics of the hydride transfer reactions between quinones and lumiflavin: a density functional theory study.

PubMed

Reinhardt, Clorice R; Jaglinski, Tanner C; Kastenschmidt, Ashly M; Song, Eun H; Gross, Adam K; Krause, Alyssa J; Gollmar, Jonathan M; Meise, Kristin J; Stenerson, Zachary S; Weibel, Tyler J; Dison, Andrew; Finnegan, Mackenzie R; Griesi, Daniel S; Heltne, Michael D; Hughes, Tom G; Hunt, Connor D; Jansen, Kayla A; Xiong, Adam H; Hati, Sanchita; Bhattacharyya, Sudeep

2016-09-01

The kinetics and equilibrium of the hydride transfer reaction between lumiflavin and a number of substituted quinones was studied using density functional theory. The impact of electron withdrawing/donating substituents on the redox potentials of quinones was studied. In addition, the role of these substituents on the kinetics of the hydride transfer reaction with lumiflavin was investigated in detail under the transition state (TS) theory assumption. The hydride transfer reactions were found to be more favorable for an electron-withdrawing substituent. The activation barrier exhibited a quadratic relationship with the driving force of these reactions as derived under the formalism of modified Marcus theory. The present study found a significant extent of electron delocalization in the TS that is stabilized by enhanced electrostatic, polarization, and exchange interactions. Analysis of geometry, bond-orders, and energetics revealed a predominant parallel (Leffler-Hammond) effect on the TS. Closer scrutiny reveals that electron-withdrawing substituents, although located on the acceptor ring, reduce the N-H bond order of the donor fragment in the precursor complex. Carried out in the gas-phase, this is the first ever report of a theoretical study of flavin's hydride transfer reactions with quinones, providing an unfiltered view of the electronic effect on the nuclear reorganization of donor-acceptor complexes.

Hybrid mesoporous-silica materials functionalized by Pt(II) complexes: correlation between the spatial distribution of the active center, photoluminescence emission, and photocatalytic activity.

PubMed

Mori, Kohsuke; Watanabe, Kentaro; Terai, Yoshikazu; Fujiwara, Yasufumi; Yamashita, Hiromi

2012-09-03

[Pt(tpy)Cl]Cl (tpy: terpyridine) was successfully anchored to a series of mesoporous-silica materials that were modified with (3-aminopropyl)triethoxysilane with the aim of developing new inorganic-organic hybrid photocatalysts. Herein, the relationship between the luminescence characteristics and photocatalytic activities of these materials is examined as a function of Pt loading to define the spatial distribution of the Pt complex in the mesoporous channel. At low Pt loading, the Pt complex is located as an isolated species and exhibits strong photoluminescence emission at room temperature owing to metal-to-ligand charge-transfer ((3)MLCT) transitions (at about 530 nm). Energy- and/or electron-transfer from (3)MLCT to O(2) generate potentially active oxygen species, which are capable of promoting the selective photooxidation of styrene derivatives. On the other hand, short Pt···Pt interactions are prominent at high loading and the metal-metal-to-ligand charge-transfer ((3)MMLCT) transition is at about 620 nm. Such Pt complexes, which are situated close to each other, efficiently catalyze H(2)-evolution reactions in aqueous media in the presence of a sacrificial electron donor (EDTA) under visible-light irradiation. This study also investigates the effect of nanoconfinement on anchored guest complexes by considering the differences between the pore dimensions and structures of mesoporous-silica materials. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fluorescence "turn on" detection of mercuric ion based on bis(dithiocarbamato)copper(II) complex functionalized carbon nanodots.

PubMed

Yuan, Chao; Liu, Bianhua; Liu, Fei; Han, Ming-Yong; Zhang, Zhongping

2014-01-21

A new "turn on" fluorescence nanosensor for selective Hg(2+) determination is reported based on bis(dithiocarbamato)copper(II) functionalized carbon nanodots (CuDTC2-CDs). The CuDTC2 complex was conjugated to the prepared amine-coated CDs by the condensation of carbon disulfide onto the nitrogen atoms in the surface amine groups, followed by the coordination of copper(II) to the resulting dithiocarbamate groups (DTC) and finally by the additional coordination of ammonium N-(dithicarbaxy) sarcosine (DTCS) to form the CuDTC2-complexing CDs. The CuDTC2 complex at surface strongly quenched the bright-blue fluorescence of the CDs by a combination of electron transfer and energy transfer mechanism. Hg(2+) could immediately switch on the fluorescence of the CuDTC2-CDs by promptly displacing the Cu(2+) in the CuDTC2 complex and thus shutting down the energy transfer pathway, in which the sensitive limit for Hg(2+) as low as 4 ppb was reached. Moreover, a paper-based sensor has been fabricated by printing the CuDTC2-CDs probe ink on a piece of cellulose acetate paper using a commercial inkjet printer. The fluorescence "turn on" on the paper provided the most conveniently visual detection of aqueous Hg(2+) ions by the observation with naked eye. The very simple and effective strategy reported here facilitates the development of portable and reliable fluorescence nanosensors for the determination of Hg(2+) in real samples.

Tetrapeptide-coumarin conjugate 3D networks based on hydrogen-bonded charge transfer complexes: gel formation and dye release.

PubMed

Guo, Zongxia; Gong, Ruiying; Jiang, Yi; Wan, Xiaobo

2015-08-14

Oligopeptide-based derivatives are important synthons for bio-based functional materials. In this article, a Gly-(L-Val)-Gly-(L-Val)-coumarin (GVGV-Cou) conjugate was synthesized, which forms 3D networks in ethanol. The gel nanostructures were characterized by UV-vis spectroscopy, FT-IR spectroscopy, X-ray diffraction (XRD), SEM and TEM. It is suggested that the formation of charge transfer (CT) complexes between the coumarin moieties is the main driving force for the gel formation. The capability of the gel to encapsulate and release dyes was explored. Both Congo Red (CR) and Methylene Blue (MB) can be trapped in the CT gel matrix and released over time. The present gel might be used as a functional soft material for guest encapsulation and release.

Geometrical optical transfer function: is it worth calculating?

PubMed

Díaz, José A; Mahajan, Virendra N

2017-10-01

In this paper, we explore the merit of calculating the geometrical optical transfer function (GOTF) in optical design by comparing the time to calculate it with the time to calculate the diffraction optical transfer function (DOTF). We determine the DOTF by numerical integration of the pupil function autocorrelation (that reduces to an integration of a complex exponential of the aberration difference function), 2D digital autocorrelation of the pupil function, and the Fourier transform (FT) of the point-spread function (PSF); and we determine the GOTF by the FT of the geometrical PSF (that reduces to an integration over the pupil plane of a complex exponential that is a scalar product of the spatial frequency and transverse ray aberration vectors) and the FT of the spot diagram. Our starting point for calculating the DOTF is the wave aberrations of the system in its pupil plane, and the transverse ray aberrations in the image plane for the GOTF. Numerical results for primary aberrations and some typical imaging systems show that the direct numerical integrations are slow, but the GOTF calculation by a FT of the spot diagram is two or even three times slower than the DOTF calculation by an FT of the PSF, depending on the aberration. We conclude that the calculation of GOTF is, at best, an approximation of the DOTF and only for large aberrations; GOTF does not offer any advantage in the optical design process, and hence negates its utility.

Symbolic Dynamics and Grammatical Complexity

NASA Astrophysics Data System (ADS)

Hao, Bai-Lin; Zheng, Wei-Mou

The following sections are included: * Formal Languages and Their Complexity * Formal Language * Chomsky Hierarchy of Grammatical Complexity * The L-System * Regular Language and Finite Automaton * Finite Automaton * Regular Language * Stefan Matrix as Transfer Function for Automaton * Beyond Regular Languages * Feigenbaum and Generalized Feigenbaum Limiting Sets * Even and Odd Fibonacci Sequences * Odd Maximal Primitive Prefixes and Kneading Map * Even Maximal Primitive Prefixes and Distinct Excluded Blocks * Summary of Results

Energy transfer in light-harvesting complexes LHCII and CP29 of spinach studied with three pulse echo peak shift and transient grating.

PubMed

Salverda, Jante M; Vengris, Mikas; Krueger, Brent P; Scholes, Gregory D; Czarnoleski, Adam R; Novoderezhkin, Vladimir; van Amerongen, Herbert; van Grondelle, Rienk

2003-01-01

Three pulse echo peak shift and transient grating (TG) measurements on the plant light-harvesting complexes LHCII and CP29 are reported. The LHCII complex is by far the most abundant light-harvesting complex in higher plants and fulfills several important physiological functions such as light-harvesting and photoprotection. Our study is focused on the light-harvesting function of LHCII and the very similar CP29 complex and reveals hitherto unresolved excitation energy transfer processes. All measurements were performed at room temperature using detergent isolated complexes from spinach leaves. Both complexes were excited in their Chl b band at 650 nm and in the blue shoulder of the Chl a band at 670 nm. Exponential fits to the TG and three pulse echo peak shift decay curves were used to estimate the timescales of the observed energy transfer processes. At 650 nm, the TG decay can be described with time constants of 130 fs and 2.2 ps for CP29, and 300 fs and 2.8 ps for LHCII. At 670 nm, the TG shows decay components of 230 fs and 6 ps for LHCII, and 300 fs and 5 ps for CP29. These time constants correspond to well-known energy transfer processes, from Chl b to Chl a for the 650 nm TG and from blue (670 nm) Chl a to red (680 nm) Chl a for the 670 nm TG. The peak shift decay times are entirely different. At 650 nm we find times of 150 fs and 0.5-1 ps for LHCII, and 360 fs and 3 ps for CP29, which we can associate mainly with Chl b <--> Chl b energy transfer. At 670 nm we find times of 140 fs and 3 ps for LHCII, and 3 ps for CP29, which we can associate with fast (only in LHCII) and slow transfer between relatively blue Chls a or Chl a states. From the occurrence of both fast Chl b <--> Chl b and fast Chl b --> Chl a transfer in CP29, we conclude that at least two mixed binding sites are present in this complex. A detailed comparison of our observed rates with exciton calculations on both CP29 and LHCII provides us with more insight in the location of these mixed sites. Most importantly, for CP29, we find that a Chl b pair must be present in some, but not all, complexes, on sites A(3) and B(3). For LHCII, the observed rates can best be understood if the same pair, A(3) and B(3), is involved in both fast Chl b <--> Chl b and fast Chl a <--> Chl a transfer. Hence, it is likely that mixed sites also occur in the native LHCII complex. Such flexibility in chlorophyll binding would agree with the general flexibility in aggregation form and xanthophyll binding of the LHCII complex and could be of use for optimizing the role of LHCII under specific circumstances, for example under high-light conditions. Our study is the first to provide spectroscopic evidence for mixed binding sites, as well as the first to show their existence in native complexes.

Selective Co-Encapsulation Inside an M6 L4 Cage.

PubMed

Leenders, Stefan H A M; Becker, René; Kumpulainen, Tatu; de Bruin, Bas; Sawada, Tomohisa; Kato, Taito; Fujita, Makoto; Reek, Joost N H

2016-10-17

There is broad interest in molecular encapsulation as such systems can be utilized to stabilize guests, facilitate reactions inside a cavity, or give rise to energy-transfer processes in a confined space. Detailed understanding of encapsulation events is required to facilitate functional molecular encapsulation. In this contribution, it is demonstrated that Ir and Rh-Cp-type metal complexes can be encapsulated inside a self-assembled M 6 L 4 metallocage only in the presence of an aromatic compound as a second guest. The individual guests are not encapsulated, suggesting that only the pair of guests can fill the void of the cage. Hence, selective co-encapsulation is observed. This principle is demonstrated by co-encapsulation of a variety of combinations of metal complexes and aromatic guests, leading to several ternary complexes. These experiments demonstrate that the efficiency of formation of the ternary complexes depends on the individual components. Moreover, selective exchange of the components is possible, leading to formation of the most favorable complex. Besides the obvious size effect, a charge-transfer interaction may also contribute to this effect. Charge-transfer bands are clearly observed by UV/Vis spectrophotometry. A change in the oxidation potential of the encapsulated electron donor also leads to a shift in the charge-transfer energy bands. As expected, metal complexes with a higher oxidation potential give rise to a higher charge-transfer energy and a larger hypsochromic shift in the UV/Vis spectrum. These subtle energy differences may potentially be used to control the binding and reactivity of the complexes bound in a confined space. © 2016 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Status of Therapeutic Gene Transfer to Treat Cardiovascular Disease in Dogs and Cats.

PubMed

Sleeper, Meg M

2017-09-01

Gene therapy is a procedure resulting in the transfer of a gene into an individual's cells to treat a disease. One goal of gene transfer is to express a functional gene when the endogenous gene is inactive. However, because heart failure is a complex disease characterized by multiple abnormalities at the cellular level, an alternate gene delivery approach is to alter myocardial protein levels to improve function. This article discusses background information on gene delivery, including packaging, administration, and a brief discussion of some of the candidate transgenes likely to alter the progression of naturally occurring heart disease in dogs and cats. Copyright © 2017 Elsevier Inc. All rights reserved.

Electronic structures of tris(dioxolene)chromium and tris(dithiolene)chromium complexes of the electron-transfer series [Cr(dioxolene)(3)](z) and [Cr(dithiolene)(3)](z) (z = 0, 1-, 2-, 3-). A combined experimental and density functional theoretical study.

PubMed

Kapre, Ruta R; Bothe, Eberhard; Weyhermüller, Thomas; George, Serena Debeer; Muresan, Nicoleta; Wieghardt, Karl

2007-09-17

From the reaction mixture of 3,6-di-tert-butylcatechol, H2[3,6L(cat)], [CrCl3(thf)3], and NEt3 in CH3CN in the presence of air, the neutral complex [CrIII(3,6L*(sq))3] (S = 0) (1) was isolated. Reduction of 1 with [Co(Cp)2] in CH2Cl2 yielded microcrystals of [Co(Cp)2][CrIII(3,6L*(sq))2(3,6L(cat))] (S = 1/2) (2) where (3,6L*(sq)(1-) is the pi-radical monoanionic o-semiquinonate of the catecholate dianion (3,6Lcat)(2-). Electrochemistry demonstrated that both species are members of the electron-transfer series [Cr(3,6LO,O)]z (z = 0, 1-, 2-, 3-). The corresponding tris(benzo-1,2-dithiolato)chromium complex [N(n-Bu)4][CrIII(3,5L*S,S)2(3,5LS,S)] (S = 1/2) (3) has also been isolated; (3,5LS,S)(2-) represents the closed-shell dianion 3,5-di-tert-butylbenzene-1,2-dithiolate(2-), and (3,5L*S,S)(1-) is its monoanionic pi radical. Complex 3 is a member of the electron-transfer series [Cr(3,5L(S,S))3]z (z = 0, 1-, 2-, 3-). It is shown by Cr K-edge and S K-edge X-ray absorption, UV-vis, and EPR spectroscopies, as well as X-ray crystallography, of 1 and 3 that the oxidation state of the central Cr ion in each member of both electron-transfer series remains the same (+III) and that all redox processes are ligand-based. These experimental results have been corroborated by broken symmetry density functional theoretical calculations by using the B3LYP functional.

The thermochromic behavior of aromatic amine-SO2 charge transfer complexes

NASA Astrophysics Data System (ADS)

Monezi, Natália M.; Borin, Antonio C.; Santos, Paulo S.; Ando, Rômulo A.

2017-02-01

The distinct thermochromism observed in solutions containing N,N-dimethylaniline (DMA) and N,N-diethylaniline (DEA) and SO2 was investigated by resonance Raman spectroscopy in a wide range of temperatures. The results indicate in addition to the charge transfer (CT) complexes DMA-SO2 and DEA-SO2, the presence of collision complexes involving the CT complexes and excess DMA and DEA molecules. The latter in fact is the chromophore responsible for the long wavelength absorption originating the color. The Raman signature of the collision complex was attributed to the distinct enhancement of a band at 1140 cm- 1 assigned to νs(SO2), in contrast to the same mode in the 1:1 complex at 1115 cm- 1. The intensity of such band, assigned to the collision complex is favored at high temperatures and depends on the steric hindrance associated to amines, as well as the SO2 molar fraction. Quantum chemical calculations based on time-dependent density functional theory (TDDFT) support the proposed interpretation.

WHEAT GERM CELL-FREE TRANSLATION, PURIFICATION, AND ASSEMBLY OF A FUNCTIONAL HUMAN STEAROYL-COA DESATURASE COMPLEX

PubMed Central

Goren, Michael A.; Fox, Brian G.

2008-01-01

A wheat germ cell-free extract was used to perform in vitro translation of human stearoyl-CoA desaturase in the presence of unilamelar liposomes, and near complete transfer of the expressed integral membrane protein into the liposome was observed. Moreover, co-translation of the desaturase along with human cytochrome b5 led to transfer of both membrane proteins into the liposomes. A simple, single step purification via centrifugation in a density gradient yielded proteoliposomes with the desaturase in high purity as judged by capillary electrophoresis. After in vitro reconstitution of the non-heme iron and heme active sites, the function of the reconstituted enzyme complex was demonstrated by conversion of stearoyl-CoA to oleoyl-CoA. This simple translation approach obviates the use of detergents or other lipids to stabilize and isolate a catalytically active integral membrane enzyme. The applicability of cell-free translation to the assembly and purification of other integral membrane protein complexes is discussed. PMID:18765284

Wheat germ cell-free translation, purification, and assembly of a functional human stearoyl-CoA desaturase complex.

PubMed

Goren, Michael A; Fox, Brian G

2008-12-01

A wheat germ cell-free extract was used to perform in vitro translation of human stearoyl-CoA desaturase in the presence of unilamelar liposomes, and near complete transfer of the expressed integral membrane protein into the liposome was observed. Moreover, co-translation of the desaturase along with human cytochrome b(5) led to transfer of both membrane proteins into the liposomes. A simple, single step purification via centrifugation in a density gradient yielded proteoliposomes with the desaturase in high purity as judged by capillary electrophoresis. After in vitro reconstitution of the non-heme iron and heme active sites, the function of the reconstituted enzyme complex was demonstrated by conversion of stearoyl-CoA to oleoyl-CoA. This simple translation approach obviates the use of detergents or other lipids to stabilize and isolate a catalytically active integral membrane enzyme. The applicability of cell-free translation to the assembly and purification of other integral membrane protein complexes is discussed.

Construction and Structural Analysis of Tethered Lipid Bilayer Containing Photosynthetic Antenna Proteins for Functional Analysis

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

Sumino, Ayumi; Dewa, Takehisa; Takeuchi, Toshikazu

2011-07-11

The construction and structural analysis of a tethered planar lipid bilayer containing bacterial photosynthetic membrane proteins, light-harvesting complex 2 (LH2), and light-harvesting core complex (LH1-RC) is described and establishes this system as an experimental platform for their functional analysis. The planar lipid bilayer containing LH2 and/or LH1-RC complexes was successfully formed on an avidin-immobilized coverglass via an avidin-biotin linkage. Atomic force microscopy (AFM) showed that a smooth continuous membrane was formed there. Lateral diffusion of these membrane proteins, observed by a fluorescence recovery after photobleaching (FRAY), is discussed in terms of the membrane architecture. Energy transfer from LH2 to LH1-RCmore » within the tethered membrane architecture. Energy transfer from LH2 to LH1-RC within the tethered membrane was observed by steady-state fluorescence spectroscopy, indicating that the tethered membrane can mimic the natural situation.« less

Structural basis of intramitochondrial phosphatidic acid transport mediated by Ups1-Mdm35 complex.

PubMed

Yu, Fang; He, Fangyuan; Yao, Hongyan; Wang, Chengyuan; Wang, Jianchuan; Li, Jianxu; Qi, Xiaofeng; Xue, Hongwei; Ding, Jianping; Zhang, Peng

2015-07-01

Ups1 forms a complex with Mdm35 and is critical for the transport of phosphatidic acid (PA) from the mitochondrial outer membrane to the inner membrane. We report the crystal structure of the Ups1-Mdm35-PA complex and the functional characterization of Ups1-Mdm35 in PA binding and transfer. Ups1 features a barrel-like structure consisting of an antiparallel β-sheet and three α-helices. Mdm35 adopts a three-helical clamp-like structure to wrap around Ups1 to form a stable complex. The β-sheet and α-helices of Ups1 form a long tunnel-like pocket to accommodate the substrate PA, and a short helix α2 acts as a lid to cover the pocket. The hydrophobic residues lining the pocket and helix α2 are critical for PA binding and transfer. In addition, a hydrophilic patch on the surface of Ups1 near the PA phosphate-binding site also plays an important role in the function of Ups1-Mdm35. Our study reveals the molecular basis of the function of Ups1-Mdm35 and sheds new light on the mechanism of intramitochondrial phospholipid transport by the MSF1/PRELI family proteins. © 2015 The Authors.

Crustal Properties Across the Mid-Continent Rift via Transfer Function Analysis

NASA Astrophysics Data System (ADS)

Frederiksen, A. W.; Tyomkin, Y.; Campbell, R.; van der Lee, S.; Zhang, H.

2015-12-01

The Mid-Continent Rift (MCR), a failed Proterozoic rift structure in central North America, is a dominant feature of North American gravity maps. The rift underwent a combination of extension, magmatism, and later compression, and it is difficult to predict how these events affected the overall crustal thickness and bulk composition in the vicinity of the rift axis, though the associated gravity high indicates that large-volume mafic magmatism took place. The Superior Province Rifting Earthscope Experiment (SPREE) project instrumented the MCR with Flexible Array broadband seismographs from 2011 through 2013 in Minnesota and Wisconsin, along two lines crossing the rift axis as well as a line following the axis. We examine teleseismic P-coda data from SPREE and nearby Transportable Array instruments using a new technique: transfer-function analysis. In this approach, possible models of crustal structure are used to generate a predicted transfer function relating the radial and vertical components of the P coda at a particular site. The transfer function then allows generation of a misfit (between the true radial component and a synthetic radial component predicted from the vertical trace) without the need to perform receiver-function deconvolution, thus avoiding the deconvolution problems encountered with receiver functions in sedimentary basins. We use the transfer-function approach to perform a grid search over three crustal properties: crustal thickness, crustal P/S velocity ratio, and the thickness of an overlying sedimentary basin. Results for our SPREE/TA data set indicate that the crust is significantly thickened along the rift axis, with maximum thicknesses approaching 50 km; the crust is thinner (ca. 40 km) outside of the rift zone. The crustal thickness structure is particularly complex beneath southeastern Minnesota, where very strong Moho topography is present, as well as up to 2 km of sediment; further north, the Moho is smoother and the basin is not present. P/S ratio varies along the rift axis, suggesting a higher mafic component (higher ratio) in southern Minnesota. The complexity we see along the MCR is consistent with the results obtained by Zhang et al. (this conference) using receiver function analysis.

Self-optimizing charge-transfer energy phenomena in metallosupramolecular complexes by dynamic constitutional self-sorting.

PubMed

Legrand, Yves-Marie; van der Lee, Arie; Barboiu, Mihail

2007-11-12

In this paper we report an extended series of 2,6-(iminoarene)pyridine-type ZnII complexes [(Lii)2Zn]II, which were surveyed for their ability to self-exchange both their ligands and their aromatic arms and to form different homoduplex and heteroduplex complexes in solution. The self-sorting of heteroduplex complexes is likely to be the result of geometric constraints. Whereas the imine-exchange process occurs quantitatively in 1:1 mixtures of [(Lii)2Zn]II complexes, the octahedral coordination process around the metal ion defines spatial-frustrated exchanges that involve the selective formation of heterocomplexes of two, by two different substituents; the bulkiest ones (pyrene in principle) specifically interact with the pseudoterpyridine core, sterically hindering the least bulky ones, which are intermolecularly stacked with similar ligands of neighboring molecules. Such a self-sorting process defined by the specific self-constitution of the ligands exchanging their aromatic substituents is self-optimized by a specific control over their spatial orientation around a metal center within the complex. They ultimately show an improved charge-transfer energy function by virtue of the dynamic amplification of self-optimized heteroduplex architectures. These systems therefore illustrate the convergence of the combinatorial self-sorting of the dynamic combinatorial libraries (DCLs) strategy and the constitutional self-optimized function.

The Use of Dispersion Relations For The Geomagnetic Transfer Functions

NASA Astrophysics Data System (ADS)

Marcuello, A.; Queralt, P.; Ledo, J. J.

The magnetotelluric responses are complex magnitudes, where real and imaginary parts contain the same information on the geoelectrical structure. It seems possible, from very general hypotheses on the geoelectrical models (causality, stability and passivity), to apply the Kramers-Krönig dispersion relations to the magnetotelluric responses (impedance, geomagnetic transfer functions,...). In particular, the applica- bility of these relations to the impedance is a current point of discussion, but there are not many examples of their application to the geomagnetic transfer functions (tipper). The aim of this paper is to study how the relations of dispersion are applied to the real and imaginary part of the geomagnetic transfer functions, and to check its validity. For this reason, we have considered data (or responses) from two- and three-dimensional structures, and for these data, we have taken two situations: 1.- Responses that have been synthetically generated from numerical modelling, that allows us to control the quality of the data. 2.- Responses obtained from fieldwork, that are affected by exper- imental error. Additionally, we have also explored the use of these relations to extrap- olate the geomagnetic transfer functions outside the interval of measured frequencies, in order to obtain constrains on the values of these extrapolated data. The results have shown that the dispersion relations are accomplished for the geomag- netic transfer functions, and they can offer information about how these responses are behaved outside (but near) the range of measured frequencies.

Solid-state acid-base interactions in complexes of heterocyclic bases with dicarboxylic acids: crystallography, hydrogen bond analysis, and 15N NMR spectroscopy.

PubMed

Li, Z Jane; Abramov, Yuriy; Bordner, Jon; Leonard, Jason; Medek, Ales; Trask, Andrew V

2006-06-28

A cancer candidate, compound 1, is a weak base with two heterocyclic basic nitrogens and five hydrogen-bonding functional groups, and is sparingly soluble in water rendering it unsuitable for pharmaceutical development. The crystalline acid-base pairs of 1, collectively termed solid acid-base complexes, provide significant increases in the solubility and bioavailability compared to the free base, 1. Three dicarboxylic acid-base complexes, sesquisuccinate 2, dimalonate 3, and dimaleate 4, show the most favorable physicochemical profiles and are studied in greater detail. The structural analyses of the three complexes using crystal structure and solid-state NMR reveal that the proton-transfer behavior in these organic acid-base complexes vary successively correlating with Delta pKa. As a result, 2 is a neutral complex, 3 is a mixed ionic and zwitterionic complex and 4 is an ionic salt. The addition of the acidic components leads to maximized hydrogen bond interactions forming extended three-dimensional networks. Although structurally similar, the packing arrangements of the three complexes are considerably different due to the presence of multiple functional groups and the flexible backbone of 1. The findings in this study provide insight into the structural characteristics of complexes involving heterocyclic bases and carboxylic acids, and demonstrate that X-ray crystallography and 15N solid-state NMR are truly complementary in elucidating hydrogen bonding interactions and the degree of proton transfer of these complexes.

Single-Molecule Interfacial Electron Transfer

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

Lu, H. Peter

This project is focused on the use of single-molecule high spatial and temporal resolved techniques to study molecular dynamics in condensed phase and at interfaces, especially, the complex reaction dynamics associated with electron and energy transfer rate processes. The complexity and inhomogeneity of the interfacial ET dynamics often present a major challenge for a molecular level comprehension of the intrinsically complex systems, which calls for both higher spatial and temporal resolutions at ultimate single-molecule and single-particle sensitivities. Combined single-molecule spectroscopy and electrochemical atomic force microscopy approaches are unique for heterogeneous and complex interfacial electron transfer systems because the static andmore » dynamic inhomogeneities can be identified and characterized by studying one molecule at a specific nanoscale surface site at a time. The goal of our project is to integrate and apply these spectroscopic imaging and topographic scanning techniques to measure the energy flow and electron flow between molecules and substrate surfaces as a function of surface site geometry and molecular structure. We have been primarily focusing on studying interfacial electron transfer under ambient condition and electrolyte solution involving both single crystal and colloidal TiO 2 and related substrates. The resulting molecular level understanding of the fundamental interfacial electron transfer processes will be important for developing efficient light harvesting systems and broadly applicable to problems in fundamental chemistry and physics. We have made significant advancement on deciphering the underlying mechanism of the complex and inhomogeneous interfacial electron transfer dynamics in dyesensitized TiO 2 nanoparticle systems that strongly involves with and regulated by molecule-surface interactions. We have studied interfacial electron transfer on TiO 2 nanoparticle surfaces by using ultrafast single-molecule spectroscopy and electrochemical AFM metal tip scanning microscopy, focusing on understanding the interfacial electron transfer dynamics at specific nanoscale electron transfer sites with high-spatially and temporally resolved topographic-and-spectroscopic characterization at individual molecule basis, characterizing single-molecule rate processes, reaction driving force, and molecule-substrate electronic coupling. One of the most significant characteristics of our new approach is that we are able to interrogate the complex interfacial electron transfer dynamics by actively pin-point energetic manipulation of the surface interaction and electronic couplings, beyond the conventional excitation and observation.« less

OPTICAL INFORMATION PROCESSING: Modulation—spectral analysis of an image transmitted across a distorting medium

NASA Astrophysics Data System (ADS)

Zubov, Vladimir A.; Mironova, T. V.

1998-05-01

The task of simultaneous determination of the structure and characteristics of a two-dimensional amplitude—phase signal and a two-dimensional complex transfer or instrumental function is considered. The solution is based on determination of four independent intensity distributions of spectral representations of the signal Isr(ωx, ωy) subjected to the action of the transfer function, of the signal Ismr(ωx, ωy which) has experienced additional modulation applied in a certain manner and the action of the transfer function, of the signal Isrn(ωx, ωy) representing the signal Isr(ωx, ωy) with certain additional modulation at the output, and of the signal Ismrn(ωx, ωy) which is the signal Ismr(ωx, ωy) with certain additional modulation at the output. These intensity distributions make it possible to calculate the amplitude and phase components of the image being analysed and of the transfer function. Additional modulations should in some way ensure visualisation of the phase information. A specific type of additional spatial modulation, in the form of linear amplitude, is discussed.

Semantic layers for illustrative volume rendering.

PubMed

Rautek, Peter; Bruckner, Stefan; Gröller, Eduard

2007-01-01

Direct volume rendering techniques map volumetric attributes (e.g., density, gradient magnitude, etc.) to visual styles. Commonly this mapping is specified by a transfer function. The specification of transfer functions is a complex task and requires expert knowledge about the underlying rendering technique. In the case of multiple volumetric attributes and multiple visual styles the specification of the multi-dimensional transfer function becomes more challenging and non-intuitive. We present a novel methodology for the specification of a mapping from several volumetric attributes to multiple illustrative visual styles. We introduce semantic layers that allow a domain expert to specify the mapping in the natural language of the domain. A semantic layer defines the mapping of volumetric attributes to one visual style. Volumetric attributes and visual styles are represented as fuzzy sets. The mapping is specified by rules that are evaluated with fuzzy logic arithmetics. The user specifies the fuzzy sets and the rules without special knowledge about the underlying rendering technique. Semantic layers allow for a linguistic specification of the mapping from attributes to visual styles replacing the traditional transfer function specification.

Using social media to facilitate knowledge transfer in complex engineering environments: a primer for educators

NASA Astrophysics Data System (ADS)

Murphy, Glen; Salomone, Sonia

2013-03-01

While highly cohesive groups are potentially advantageous they are also often correlated with the emergence of knowledge and information silos based around those same functional or occupational clusters. Consequently, an essential challenge for engineering organisations wishing to overcome informational silos is to implement mechanisms that facilitate, encourage and sustain interactions between otherwise disconnected groups. This paper acts as a primer for those seeking to gain an understanding of the design, functionality and utility of a suite of software tools generically termed social media technologies in the context of optimising the management of tacit engineering knowledge. Underpinned by knowledge management theory and using detailed case examples, this paper explores how social media technologies achieve such goals, allowing for the transfer of knowledge by tapping into the tacit and explicit knowledge of disparate groups in complex engineering environments.

Efficient algorithms for the simulation of non-adiabatic electron transfer in complex molecular systems: application to DNA.

PubMed

Kubař, Tomáš; Elstner, Marcus

2013-04-28

In this work, a fragment-orbital density functional theory-based method is combined with two different non-adiabatic schemes for the propagation of the electronic degrees of freedom. This allows us to perform unbiased simulations of electron transfer processes in complex media, and the computational scheme is applied to the transfer of a hole in solvated DNA. It turns out that the mean-field approach, where the wave function of the hole is driven into a superposition of adiabatic states, leads to over-delocalization of the hole charge. This problem is avoided using a surface hopping scheme, resulting in a smaller rate of hole transfer. The method is highly efficient due to the on-the-fly computation of the coarse-grained DFT Hamiltonian for the nucleobases, which is coupled to the environment using a QM/MM approach. The computational efficiency and partial parallel character of the methodology make it possible to simulate electron transfer in systems of relevant biochemical size on a nanosecond time scale. Since standard non-polarizable force fields are applied in the molecular-mechanics part of the calculation, a simple scaling scheme was introduced into the electrostatic potential in order to simulate the effect of electronic polarization. It is shown that electronic polarization has an important effect on the features of charge transfer. The methodology is applied to two kinds of DNA sequences, illustrating the features of transfer along a flat energy landscape as well as over an energy barrier. The performance and relative merit of the mean-field scheme and the surface hopping for this application are discussed.

Understanding large multiprotein complexes: applying a multiple allosteric networks model to explain the function of the Mediator transcription complex.

PubMed

Lewis, Brian A

2010-01-15

The regulation of transcription and of many other cellular processes involves large multi-subunit protein complexes. In the context of transcription, it is known that these complexes serve as regulatory platforms that connect activator DNA-binding proteins to a target promoter. However, there is still a lack of understanding regarding the function of these complexes. Why do multi-subunit complexes exist? What is the molecular basis of the function of their constituent subunits, and how are these subunits organized within a complex? What is the reason for physical connections between certain subunits and not others? In this article, I address these issues through a model of network allostery and its application to the eukaryotic RNA polymerase II Mediator transcription complex. The multiple allosteric networks model (MANM) suggests that protein complexes such as Mediator exist not only as physical but also as functional networks of interconnected proteins through which information is transferred from subunit to subunit by the propagation of an allosteric state known as conformational spread. Additionally, there are multiple distinct sub-networks within the Mediator complex that can be defined by their connections to different subunits; these sub-networks have discrete functions that are activated when specific subunits interact with other activator proteins.

Complex logic functions implemented with quantum dot bionanophotonic circuits.

PubMed

Claussen, Jonathan C; Hildebrandt, Niko; Susumu, Kimihiro; Ancona, Mario G; Medintz, Igor L

2014-03-26

We combine quantum dots (QDs) with long-lifetime terbium complexes (Tb), a near-IR Alexa Fluor dye (A647), and self-assembling peptides to demonstrate combinatorial and sequential bionanophotonic logic devices that function by time-gated Förster resonance energy transfer (FRET). Upon excitation, the Tb-QD-A647 FRET-complex produces time-dependent photoluminescent signatures from multi-FRET pathways enabled by the capacitor-like behavior of the Tb. The unique photoluminescent signatures are manipulated by ratiometrically varying dye/Tb inputs and collection time. Fluorescent output is converted into Boolean logic states to create complex arithmetic circuits including the half-adder/half-subtractor, 2:1 multiplexer/1:2 demultiplexer, and a 3-digit, 16-combination keypad lock.

Site Transfer Functions of Three-Component Ground Motion in Western Turkey

NASA Astrophysics Data System (ADS)

Ozgur Kurtulmus, Tevfik; Akyol, Nihal; Camyildiz, Murat; Gungor, Talip

2015-04-01

Because of high seismicity accommodating crustal deformation and deep graben structures, on which have, urbanized and industrialized large cities in western Turkey, the importance of site-specific seismic hazard assessments becomes more crucial. Characterizing source, site and path effects is important for both assessing the seismic hazard in a specific region and generation of the building codes/or renewing previous ones. In this study, we evaluated three-component recordings for micro- and moderate-size earthquakes with local magnitudes ranging between 2.0 and 5.6. This dataset is used for site transfer function estimations, utilizing two different spectral ratio approaches 'Standard Spectral Ratio-(SSR)' and 'Horizontal to Vertical Spectral Ratio-(HVSR)' and a 'Generalized Inversion Technique-(GIT)' to highlight site-specific seismic hazard potential of deep basin structures of the region. Obtained transfer functions revealed that the sites located near the basin edges are characterized by broader HVSR curves. Broad HVSR peaks could be attributed to the complexity of wave propagation related to significant 2D/3D velocity variations at the sediment-bedrock interface near the basin edges. Comparison of HVSR and SSR estimates for the sites located on the grabens showed that SSR estimates give larger values at lower frequencies which could be attributed to lateral variations in regional velocity and attenuation values caused by basin geometry and edge effects. However, large amplitude values of vertical component GIT site transfer functions were observed at varying frequency ranges for some of the stations. These results imply that vertical component of ground motion is not amplification free. Contamination of HVSR site transfer function estimates at different frequency bands could be related to complexities in the wave field caused by deep or shallow heterogeneities in the region such as differences in the basin geometries, fracturing and fluid saturation along different propagation paths. The results also show that, even if the site is located on a horst, the presence of weathered zones near the surface could cause moderate frequency dependent site effects.

Selective CO2 reduction conjugated with H2O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

NASA Astrophysics Data System (ADS)

Morikawa, T.; Sato, S.; Arai, T.; Uemura, K.; Yamanaka, K. I.; Suzuki, T. M.; Kajino, T.; Motohiro, T.

2013-12-01

We developed a new hybrid photocatalyst for CO2 reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (ECBM) of the semiconductor and the CO2 reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO2 to formate using water as an electron donor and a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO2 reduction with a TiO2 photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.

A review of the source and function of microbiota in breast milk.

PubMed

Latuga, M Susan; Stuebe, Alison; Seed, Patrick C

2014-01-01

Breast milk contains a rich microbiota composed of viable skin and non-skin bacteria. The extent of the breast milk microbiota diversity has been revealed through new culture-independent studies using microbial DNA signatures. However, the extent to which the breast milk microbiota are transferred from mother to infant and the function of these breast milk microbiota for the infant are only partially understood. Here, we appraise hypotheses regarding the formation of breast milk microbiota, including retrograde infant-to-mother transfer and enteromammary trafficking, and we review current knowledge of mechanisms determining the extent of breast milk microbiota transfer from mother to infant. We highlight known functions of constituents in the breast milk microbiota-to enhance immunity, liberate nutrients, synergize with breast milk oligosaccharides to enhance intestinal barrier function, and strengthen a functional gut-brain axis. We also consider the pathophysiology of maternal mastitis with respect to a dysbiosis or abnormal shift in the breast milk microbiota. In conclusion, through a complex, highly evolved process in the early stages of discovery, mothers transfer the breast milk microbiota to their infants to impact infant growth and development. Thieme Medical Publishers 333 Seventh Avenue, New York, NY 10001, USA.

A quantitative structure–function relationship for the Photosystem II reaction center: Supermolecular behavior in natural photosynthesis

PubMed Central

Barter, Laura M. C.; Durrant, James R.; Klug, David R.

2003-01-01

Light-induced charge separation is the primary photochemical event of photosynthesis. Efficient charge separation in photosynthetic reaction centers requires the balancing of electron and excitation energy transfer processes, and in Photosystem II (PSII), these processes are particularly closely entangled. Calculations that treat the cofactors of the PSII reaction center as a supermolecular complex allow energy and electron transfer reactions to be described in a unified way. This calculational approach is shown to be in good agreement with experimentally observed energy and electron transfer dynamics. This supermolecular view also correctly predicts the effect of changing the redox potentials of cofactors by site-directed mutagenesis, thus providing a unified and quantitative structure–function relationship for the PSII reaction center. PMID:12538865

Cytochrome bc1-cy Fusion Complexes Reveal the Distance Constraints for Functional Electron Transfer Between Photosynthesis Components*

PubMed Central

Lee, Dong-Woo; Öztürk, Yavuz; Osyczka, Artur; Cooley, Jason W.; Daldal, Fevzi

2008-01-01

Photosynthetic (Ps) growth of purple non-sulfur bacteria such as Rhodobacter capsulatus depends on the cyclic electron transfer (ET) between the ubihydroquinone (QH2): cytochrome (cyt) c oxidoreductases (cyt bc1 complex), and the photochemical reaction centers (RC), mediated by either a membrane-bound (cyt cy) or a freely diffusible (cyt c2) electron carrier. Previously, we constructed a functional cyt bc1-cy fusion complex that supported Ps growth solely relying on membrane-confined ET (Lee, D.-W., Ozturk, Y., Mamedova, A., Osyczka, A., Cooley, J. W., and Daldal, F. (2006) Biochim. Biophys. Acta1757 ,346 -35216781662). In this work, we further characterized this cyt bc1-cy fusion complex, and used its derivatives with shorter cyt cy linkers as “molecular rulers” to probe the distances separating the Ps components. Comparison of the physicochemical properties of both membrane-embedded and purified cyt bc1-cy fusion complexes established that these enzymes were matured and assembled properly. Light-activated, time-resolved kinetic spectroscopy analyses revealed that their variants with shorter cyt cy linkers exhibited fast, native-like ET rates to the RC via the cyt bc1. However, shortening the length of the cyt cy linker decreased drastically this electronic coupling between the cyt bc1-cy fusion complexes and the RC, thereby limiting Ps growth. The shortest and still functional cyt cy linker was about 45 amino acids long, showing that the minimal distance allowed between the cyt bc1-cy fusion complexes and the RC and their surrounding light harvesting proteins was very short. These findings support the notion that membrane-bound Ps components form large, active structural complexes that are “hardwired” for cyclic ET. PMID:18343816

Risk Management in Biologics Technology Transfer.

PubMed

Toso, Robert; Tsang, Jonathan; Xie, Jasmina; Hohwald, Stephen; Bain, David; Willison-Parry, Derek

Technology transfer of biological products is a complex process that is important for product commercialization. To achieve a successful technology transfer, the risks that arise from changes throughout the project must be managed. Iterative risk analysis and mitigation tools can be used to both evaluate and reduce risk. The technology transfer stage gate model is used as an example tool to help manage risks derived from both designed process change and unplanned changes that arise due to unforeseen circumstances. The strategy of risk assessment for a change can be tailored to the type of change. In addition, a cross-functional team and centralized documentation helps maximize risk management efficiency to achieve a successful technology transfer. © PDA, Inc. 2016.

Mechanisms of proton transfer in Nafion: elementary reactions at the sulfonic acid groups.

PubMed

Sagarik, Kritsana; Phonyiem, Mayuree; Lao-ngam, Charoensak; Chaiwongwattana, Sermsiri

2008-04-21

Proton transfer reactions at the sulfonic acid groups in Nafion were theoretically studied, using complexes formed from triflic acid (CF3SO3H), H3O+ and H2O, as model systems. The investigations began with searching for potential precursors and transition states at low hydration levels, using the test-particle model (T-model), density functional theory (DFT) and ab initio calculations. They were employed as starting configurations in Born-Oppenheimer molecular dynamics (BOMD) simulations at 298 K, from which elementary reactions were analyzed and categorized. For the H3O+-H2O complexes, BOMD simulations suggested that a quasi-dynamic equilibrium could be established between the Eigen and Zundel complexes, and that was considered to be one of the most important elementary reactions in the proton transfer process. The average lifetime of H3O+ obtained from BOMD simulations is close to the lowest limit, estimated from low-frequency vibrational spectroscopy. It was demonstrated that proton transfer reactions at -SO3H are not concerted, due to the thermal energy fluctuation and the existence of various quasi-dynamic equilibria, and -SO3H could directly and indirectly mediate proton transfer reactions through the formation of proton defects, as well as the -SO3- and -SO3H2+ transition states.

Unsteady aerodynamic modeling and active aeroelastic control

NASA Technical Reports Server (NTRS)

Edwards, J. W.

1977-01-01

Unsteady aerodynamic modeling techniques are developed and applied to the study of active control of elastic vehicles. The problem of active control of a supercritical flutter mode poses a definite design goal stability, and is treated in detail. The transfer functions relating the arbitrary airfoil motions to the airloads are derived from the Laplace transforms of the linearized airload expressions for incompressible two dimensional flow. The transfer function relating the motions to the circulatory part of these loads is recognized as the Theodorsen function extended to complex values of reduced frequency, and is termed the generalized Theodorsen function. Inversion of the Laplace transforms yields exact transient airloads and airfoil motions. Exact root loci of aeroelastic modes are calculated, providing quantitative information regarding subcritical and supercritical flutter conditions.

A Unified Theory for the Blue- and Red-Shifting Phenomena in Hydrogen and Halogen Bonds.

PubMed

Wang, Changwei; Danovich, David; Shaik, Sason; Mo, Yirong

2017-04-11

Typical hydrogen and halogen bonds exhibit red-shifts of their vibrational frequencies upon the formation of hydrogen and halogen bonding complexes (denoted as D···Y-A, Y = H and X). The finding of blue-shifts in certain complexes is of significant interest, which has led to numerous studies of the origins of the phenomenon. Because charge transfer mixing (i.e., hyperconjugation in bonding systems) has been regarded as one of the key forces, it would be illuminating to compare the structures and vibrational frequencies in bonding complexes with the charge transfer effect "turned on" and "turned off". Turning off the charge transfer mixing can be achieved by employing the block-localized wave function (BLW) method, which is an ab initio valence bond (VB) method. Further, with the BLW method, the overall stability gained in the formation of a complex can be analyzed in terms of a few physically meaningful terms. Thus, the BLW method provides a unified and physically lucid way to explore the nature of red- and blue-shifting phenomena in both hydrogen and halogen bonding complexes. In this study, a direct correlation between the total stability and the variation of the Y-A bond length is established based on our BLW computations, and the consistent roles of all energy components are clarified. The n(D) → σ*(Y-A) electron transfer stretches the Y-A bond, while the polarization due to the approach of interacting moieties reduces the HOMO-LUMO gap and results in a stronger orbital mixing within the YA monomer. As a consequence, both the charge transfer and polarization stabilize bonding systems with the Y-A bond stretched and red-shift the vibrational frequency of the Y-A bond. Notably, the energy of the frozen wave function is the only energy component which prefers the shrinking of the Y-A bond and thus is responsible for the associated blue-shifting. The total variations of the Y-A bond length and the corresponding stretching vibrational frequency are thus determined by the competition between the frozen-energy term and the sum of polarization and charge transfer energy terms. Because the frozen energy is composed of electrostatic and Pauli exchange interactions and frequency shifting is a long-range phenomenon, we conclude that long-range electrostatic interaction is the driving force behind the frozen energy term.

Separate Fe-S Scaffold And Carrier Functions For SufB2C2 And SufA During In Vitro Maturation Of [2Fe-2S] Fdx

PubMed Central

Chahal, Harsimranjit K.; Outten, F. Wayne

2012-01-01

Iron-sulfur (Fe-S) clusters are inorganic cofactors required for a variety of biological processes. In vivo biogenesis of Fe-S clusters proceeds via complex pathways involving multiple protein complexes. In the Suf Fe-S cluster biogenesis system, SufB may be a scaffold for nascent Fe-S cluster assembly whereas SufA is proposed to act as either a scaffold or an Fe-S cluster carrier from the scaffold to target apo-proteins. However, SufB can form multiple stable complexes with other Suf proteins, such as SufB2C2 and SufBC2D and the specific functions of these complexes in Fe-S cluster assembly are not clear. Here we compare the ability of the SufB2C2 and SufBC2D complexes as well as SufA to promote in vitro maturation of the [2Fe-2S] ferredoxin (Fdx). We found that SufB2C2 was most proficient as a scaffold for de novo assembly of holo-Fdx using sulfide and iron as freely available building blocks while SufA was best at direct transfer of a pre-formed Fe-S cluster to Fdx. Furthermore, cluster transfer from [4Fe-4S] SufB2C2 or SufBC2D to Fdx will proceed through a SufA intermediate to Fdx is SufA is present. Finally, addition of ATP repressed cluster transfer from [4Fe-4S] SufB2C2 to Fdx and from SufBC2D to [2Fe-2S] SufA or Fdx. These studies indicate that SufB2C2 can serve as a terminal scaffold to load the SufA Fe-S cluster carrier for in vitro maturation of [2Fe-2S] enzymes like Fdx. This work is the first to systematically compare the cluster transfer rates of a scaffold (SufB) to the transfer rates of a carrier (SufA) under the same conditions to the same target enzyme and is also the first to reconstitute the full transfer pathway (from scaffold to carrier to target enzyme) in a single reaction. PMID:23018275

Theoretical Investigation of OCN(-) Charge Transfer Complexes in Condensed Phase Media: Spectroscopic Properties in Amorphous Ice

NASA Technical Reports Server (NTRS)

Park, Jin-Young; Woon, David E.

2004-01-01

Density functional theory (DFT) calculations of cyanate (OCN(-)) charge-transfer complexes were performed to model the "XCN" feature observed in interstellar icy grain mantles. OCN(-) charge-transfer complexes were formed from precursor combinations of HNCO or HOCN with either NH3 or H2O. Three different solvation strategies for realistically modeling the ice matrix environment were explored, including (1) continuum solvation, (2) pure DFT cluster calculations, and (3) an ONIOM DFT/PM3 cluster calculation. The model complexes were evaluated by their ability to reproduce seven spectroscopic measurements associated with XCN: the band origin of the OCN(-) asymmetric stretching mode, shifts in that frequency due to isotopic substitutions of C, N, O, and H, plus two weak features. The continuum solvent field method produced results consistent with some of the experimental data but failed to account for other behavior due to its limited capacity to describe molecular interactions with solvent. DFT cluster calculations successfully reproduced the available spectroscopic measurements very well. In particular, the deuterium shift showed excellent agreement in complexes where OCN(-) was fully solvated. Detailed studies of representative complexes including from two to twelve water molecules allowed the exploration of various possible solvation structures and provided insights into solvation trends. Moreover, complexes arising from cyanic or isocyanic acid in pure water suggested an alternative mechanism for the formation of OCN(-) charge-transfer complexes without the need for a strong base such as NH3 to be present. An extended ONIOM (B3LYP/PM3) cluster calculation was also performed to assess the impact of a more realistic environment on HNCO dissociation in pure water.

Waste-Heat-Driven Cooling Using Complex Compound Sorbents

NASA Technical Reports Server (NTRS)

Rocketfeller, Uwe; Kirol, Lance; Khalili, Kaveh

2004-01-01

Improved complex-compound sorption pumps are undergoing development for use as prime movers in heat-pump systems for cooling and dehumidification of habitats for humans on the Moon and for residential and commercial cooling on Earth. Among the advantages of sorption heat-pump systems are that they contain no moving parts except for check valves and they can be driven by heat from diverse sources: examples include waste heat from generation of electric power, solar heat, or heat from combustion of natural gas. The use of complex compound sorbents in cooling cycles is not new in itself: Marketing of residential refrigerators using SrCl2 was attempted in the 1920s and 30s and was abandoned because heat- and mass-transfer rates of the sorbents were too low. Addressing the issue that gave rise to the prior abandonment of complex compound sorption heat pumps, the primary accomplishment of the present development program thus far has been the characterization of many candidate sorption media, leading to large increases in achievable heat- and mass-transfer rates. In particular, two complex compounds (called "CC260-1260" and "CC260-2000") were found to be capable of functioning over the temperature range of interest for the lunar-habitat application and to offer heat- and mass-transfer rates and a temperature-lift capability adequate for that application. Regarding the temperature range: A heat pump based on either of these compounds is capable of providing a 95-K lift from a habitable temperature to a heat-rejection (radiator) temperature when driven by waste heat at an input temperature .500 K. Regarding the heat- and mass-transfer rates or, more precisely, the power densities made possible by these rates: Power densities observed in tests were 0.3 kilowatt of cooling per kilogram of sorbent and 2 kilowatts of heating per kilogram of sorbent. A prototype 1-kilowatt heat pump based on CC260-2000 has been built and demonstrated to function successfully.

Structural insights into electron transfer in caa3-type cytochrome oxidase

PubMed Central

Lyons, Joseph A.; Aragão, David; Slattery, Orla; Pisliakov, Andrei V.; Soulimane, Tewfik; Caffrey, Martin

2012-01-01

Summary Paragraph Cytochrome c oxidase is a member of the heme copper oxidase superfamily (HCO)1. HCOs function as the terminal enzymes in the respiratory chain of mitochondria and aerobic prokaryotes, coupling molecular oxygen reduction to transmembrane proton pumping. Integral to the enzyme’s function is the transfer of electrons from cytochrome c to the oxidase via a transient association of the two proteins. Electron entry and exit are proposed to occur from the same site on cytochrome c2–4. Here we report the crystal structure of the caa3-type cytochrome oxidase from Thermus thermophilus, which has a covalently tethered cytochrome c domain. Crystals were grown in a bicontinuous mesophase using a synthetic short-chain monoacylglycerol as the hosting lipid. From the electron density map, at 2.36 Å resolution, a novel integral membrane subunit and a native glycoglycerophospholipid embedded in the complex were identified. Contrary to previous electron transfer mechanisms observed for soluble cytochrome c, the structure reveals the architecture of the electron transfer complex for the fused cupredoxin/cytochrome c domain which implicates different sites on cytochrome c for electron entry and exit. Support for an alternative to the classical proton gate characteristic of this HCO class is presented. PMID:22763450

Energy transfer in light-adapted photosynthetic membranes: from active to saturated photosynthesis.

PubMed

Fassioli, Francesca; Olaya-Castro, Alexandra; Scheuring, Simon; Sturgis, James N; Johnson, Neil F

2009-11-04

In bacterial photosynthesis light-harvesting complexes, LH2 and LH1 absorb sunlight energy and deliver it to reaction centers (RCs) with extraordinarily high efficiency. Submolecular resolution images have revealed that both the LH2:LH1 ratio, and the architecture of the photosynthetic membrane itself, adapt to light intensity. We investigate the functional implications of structural adaptations in the energy transfer performance in natural in vivo low- and high-light-adapted membrane architectures of Rhodospirillum photometricum. A model is presented to describe excitation migration across the full range of light intensities that cover states from active photosynthesis, where all RCs are available for charge separation, to saturated photosynthesis where all RCs are unavailable. Our study outlines three key findings. First, there is a critical light-energy density, below which the low-light adapted membrane is more efficient at absorbing photons and generating a charge separation at RCs, than the high-light-adapted membrane. Second, connectivity of core complexes is similar in both membranes, suggesting that, despite different growth conditions, a preferred transfer pathway is through core-core contacts. Third, there may be minimal subareas on the membrane which, containing the same LH2:LH1 ratio, behave as minimal functional units as far as excitation transfer efficiency is concerned.

Sensor Authentication: Embedded Processor Code

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

Svoboda, John

2012-09-25

Described is the c code running on the embedded Microchip 32bit PIC32MX575F256H located on the INL developed noise analysis circuit board. The code performs the following functions: Controls the noise analysis circuit board preamplifier voltage gains of 1, 10, 100, 000 Initializes the analog to digital conversion hardware, input channel selection, Fast Fourier Transform (FFT) function, USB communications interface, and internal memory allocations Initiates high resolution 4096 point 200 kHz data acquisition Computes complex 2048 point FFT and FFT magnitude. Services Host command set Transfers raw data to Host Transfers FFT result to host Communication error checking

The ring structure and organization of light harvesting 2 complexes in a reconstituted lipid bilayer, resolved by atomic force microscopy.

PubMed

Stamouli, Amalia; Kafi, Sidig; Klein, Dionne C G; Oosterkamp, Tjerk H; Frenken, Joost W M; Cogdell, Richard J; Aartsma, Thijs J

2003-04-01

The main function of the transmembrane light-harvesting complexes in photosynthetic organisms is the absorption of a light quantum and its subsequent rapid transfer to a reaction center where a charge separation occurs. A combination of freeze-thaw and dialysis methods were used to reconstitute the detergent-solubilized Light Harvesting 2 complex (LH2) of the purple bacterium Rhodopseudomonas acidophila strain 10050 into preformed egg phosphatidylcholine liposomes, without the need for extra chemical agents. The LH2-containing liposomes opened up to a flat bilayer, which were imaged with tapping and contact mode atomic force microscopy under ambient and physiological conditions, respectively. The LH2 complexes were packed in quasicrystalline domains. The endoplasmic and periplasmic sides of the LH2 complexes could be distinguished by the difference in height of the protrusions from the lipid bilayer. The results indicate that the complexes entered in intact liposomes. In addition, it was observed that the most hydrophilic side, the periplasmic, enters first in the membrane. In contact mode the molecular structure of the periplasmic side of the transmembrane pigment-protein complex was observed. Using Föster's theory for describing the distance dependent energy transfer, we estimate the dipole strength for energy transfer between two neighboring LH2s, based on the architecture of the imaged unit cell.

[Microsurgical 2nd toe transfer for catastrophic hand reconstruction].

PubMed

Placer, A; Lozano, Ja

2007-01-01

The correct reconstruction of the catastrophic hand requires complex surgical techniques. The microsurgical transference of a toe is indicated when all other reconstructive options are shown to be useless for the reconstruction of the required clamp function. In this clinical note we set out the case of a 32 year old man, who came to our accident and emergency department after suffering a traffic accident. After exploration the diagnosis was that of catastrophic left hand, among other policontusions. Urgent surgery was carried out, saving the maximum possible viable structures. The immediate result of this surgery was a hand with 1st, 4th and 5th functional fingers. As the essential clamp function between the 1st and 4th or 5th fingers was not totally satisfactory, we decided to reconstruct the 3rd finger of his hand with his ipsilateral 2nd toe. All pertinent studies to determine vascularisation of the flap were carried out in planning the surgery, and the microsurgical transfer was then realized, which was successful. Today, after a suitable rehabilitation, the patient has recovered a satisfactory function of heavy and fine clamp in the operated hand. Toe to hand transfer is a good option for finger reconstruction and its function. Rehabilitation is the key to functional recovery.

Sulfur K-edge XAS of WV=O vs. MoV=O Bis(dithiolene) Complexes: Contributions of Relativistic Effects to Electronic Structure and Reactivity of Tungsten Enzymes†

PubMed Central

Tenderholt, Adam L.; Szilagyi, Robert K.; Holm, Richard H.; Hodgson, Keith O.; Hedman, Britt; Solomon, Edward I.

2009-01-01

Molybdenum- or tungsten-containing enzymes catalyze oxygen atom transfer reactions involved in carbon, sulfur, or nitrogen metabolism. It has been observed that reduction potentials and oxygen atom transfer rates are different for W relative to Mo enzymes and the isostructural Mo/W complexes. Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations on [MoVO(bdt)2]− and [WVO(bdt)2]−, where bdt = benzene-1,2-dithiolate(2−), have been used to determine that the energies of the half-filled redox-active orbital, and thus the reduction potentials and M=O bond strengths, are different for these complexes due to relativistic effects in the W sites. PMID:17720249

The structure of a ring-opened proliferating cell nuclear antigen-replication factor C complex revealed by fluorescence energy transfer.

PubMed

Zhuang, Zhihao; Yoder, Bonita L; Burgers, Peter M J; Benkovic, Stephen J

2006-02-21

Numerous proteins that function in DNA metabolic pathways are known to interact with the proliferating cell nuclear antigen (PCNA). The important function of PCNA in stimulating various cellular activities requires its topological linkage with DNA. Loading of the circular PCNA onto duplex DNA requires the activity of a clamp-loader [replication factor C (RFC)] complex and the energy derived from ATP hydrolysis. The mechanistic and structural details regarding PCNA loading by the RFC complex are still developing. In particular, the positive identification of a long-hypothesized structure of an open clamp-RFC complex as an intermediate in loading has remained elusive. In this study, we capture an open yeast PCNA clamp in a complex with RFC through fluorescence energy transfer experiments. We also follow the topological transitions of PCNA in the various steps of the clamp-loading pathway through both steady-state and stopped-flow fluorescence studies. We find that ATP effectively drives the clamp-loading process to completion with the formation of the closed PCNA bound to DNA, whereas ATPgammaS cannot. The information derived from this work complements that obtained from previous structural and mechanistic studies and provides a more complete picture of a eukaryotic clamp-loading pathway using yeast as a paradigm.

The nature of the interaction of dimethylselenide with IIIA group element compounds.

PubMed

Madzhidov, Timur I; Chmutova, Galina A

2013-05-16

The first systematic theoretical study of the nature of intermolecular bonding of dimethylselenide as donor and IIIA group element halides as acceptors was made with the help of the approach of Quantum Theory of Atoms in Molecules. Density Functional Theory with "old" Sapporo triple-ζ basis sets was used to calculate geometry, thermodynamics, and wave function of Me2Se···AX3 complexes. The analysis of the electron density distribution and the Laplacian of the electron density allowed us to reveal and explain the tendencies in the influence of the central atom (A = B, Al, Ga, In) and halogen (X = F, Cl, Br, I) on the nature of Se···A bonding. Significant changes in properties of the selenium lone pair upon complexation were described by means of the analysis of the Laplacian of the charge density. Charge transfer characteristics and the contributions to it from electron localization and delocalization were analyzed in terms of localization and delocalization indexes. Common features of the complexation and differences in the nature of bonding were revealed. Performed analysis evidenced that gallium and indium halide complexes can be attributed to charge transfer-driven complexes; aluminum halides complexes seem to be mainly of an electrostatic nature. The nature of bonding in different boron halides essentially varies; these complexes are stabilized mainly by covalent Se···B interaction. In all the complexes under study covalence of the Se···A interaction is rather high.

Multilayer-MCTDH approach to the energy transfer dynamics in the LH2 antenna complex

NASA Astrophysics Data System (ADS)

Shibl, Mohamed F.; Schulze, Jan; Al-Marri, Mohammed J.; Kühn, Oliver

2017-09-01

The multilayer multiconfiguration time-dependent Hartree method is used to study the coupled exciton-vibrational dynamics in a high-dimensional nonameric model of the LH2 antenna complex of purple bacteria. The exciton-vibrational coupling is parametrized within the Huang-Rhys model according to phonon and intramolecular vibrational modes derived from an experimental bacteriochlorophyll spectral density. In contrast to reduced density matrix approaches, the Schrödinger equation is solved explicitly, giving access to the full wave function. This facilitates an unbiased analysis in terms of the coupled dynamics of excitonic and vibrational degrees of freedom. For the present system, we identify spectator modes for the B800 to B800 transfer and we find a non-additive effect of phonon and intramolecular vibrational modes on the B800 to B850 exciton transfer.

Studies on the weak interactions and CT complex formations between chloranilic acid, 2,3-dichloro-5,6-dicyano-p-benzoquinone, tetracyanoethylene and papaverine in acetonitrile and their thermodynamic properties, theoretically, spectrophotometrically aided by FTIR

NASA Astrophysics Data System (ADS)

Datta, Asim Sagar; (Chattaraj), Seema Bagchi; Chakrabortty, Ashutosh; Lahiri, Sujit Chandra

2015-07-01

Spectrophotometric, FTIR and theoretical studies of the charge-transfer complexes between mild narcotic drug papaverine and the acceptors chloranilic acid (Cl-A), 2,3-dichloro-5,6-dicyano-p-benzoquinone (DDQ) and tetracyanoethylene (TCNE) in acetonitrile, their association constants, thermodynamic (ΔG0, ΔH0 and ΔS0) and other related properties had been described. Papaverine was found to form colored charge-transfer complexes with Cl-A, DDQ and TCNE in acetonitrile. The absorption maxima of the complexes were 518.5, 584.0 and 464.0 nm for Cl-A complex, DDQ complex, and TCNE complex respectively. The compositions of the papaverine complexes were determined to be 1:1 from Job's method of continuous variation. Solid complexes formed between papaverine and the acceptors were isolated. Comparison of the FTIR spectra of the solid complexes between papaverine and the acceptors and their constituents showed considerable shift in absorption peaks, changes in intensities of the peaks and formation of the new bands on complexation. However, no attempt has been made to purify the complexes and study the detailed spectra both theoretically and experimentally. The energies hνCT of the charge-transfer complexes were compared with the theoretical values of hνCT of the complexes obtained from HOMO and LUMO of the donor and the acceptors. The reasons for the differences in hνCT values were explained. Density function theory was used for calculation. hνCT (experimental) values of the transition energies of the complexes in acetonitrile differed from hνCT (theoretical) values. IDV value of papaverine was calculated. Charge-transfer complexes were assumed to be partial electrovalent compounds with organic dative ions D+ and A- (in the excited state) and attempts had been made to correlate the energy changes for the formation of the complexes with the energy changes for the formation of electrovalent compounds between M+ and X- ions.

Multi-step optimization strategy for fuel-optimal orbital transfer of low-thrust spacecraft

NASA Astrophysics Data System (ADS)

Rasotto, M.; Armellin, R.; Di Lizia, P.

2016-03-01

An effective method for the design of fuel-optimal transfers in two- and three-body dynamics is presented. The optimal control problem is formulated using calculus of variation and primer vector theory. This leads to a multi-point boundary value problem (MPBVP), characterized by complex inner constraints and a discontinuous thrust profile. The first issue is addressed by embedding the MPBVP in a parametric optimization problem, thus allowing a simplification of the set of transversality constraints. The second problem is solved by representing the discontinuous control function by a smooth function depending on a continuation parameter. The resulting trajectory optimization method can deal with different intermediate conditions, and no a priori knowledge of the control structure is required. Test cases in both the two- and three-body dynamics show the capability of the method in solving complex trajectory design problems.

Modeling Electronic-Nuclear Interactions for Excitation Energy Transfer Processes in Light-Harvesting Complexes.

PubMed

Lee, Mi Kyung; Coker, David F

2016-08-18

An accurate approach for computing intermolecular and intrachromophore contributions to spectral densities to describe the electronic-nuclear interactions relevant for modeling excitation energy transfer processes in light harvesting systems is presented. The approach is based on molecular dynamics (MD) calculations of classical correlation functions of long-range contributions to excitation energy fluctuations and a separate harmonic analysis and single-point gradient quantum calculations for electron-intrachromophore vibrational couplings. A simple model is also presented that enables detailed analysis of the shortcomings of standard MD-based excitation energy fluctuation correlation function approaches. The method introduced here avoids these problems, and its reliability is demonstrated in accurate predictions for bacteriochlorophyll molecules in the Fenna-Matthews-Olson pigment-protein complex, where excellent agreement with experimental spectral densities is found. This efficient approach can provide instantaneous spectral densities for treating the influence of fluctuations in environmental dissipation on fast electronic relaxation.

Glutathione-complexed [2Fe-2S] clusters function in Fe-S cluster storage and trafficking.

PubMed

Fidai, Insiya; Wachnowsky, Christine; Cowan, J A

2016-10-01

Glutathione-coordinated [2Fe-2S] complex is a non-protein-bound [2Fe-2S] cluster that is capable of reconstituting the human iron-sulfur cluster scaffold protein IscU. This complex demonstrates physiologically relevant solution chemistry and is a viable substrate for iron-sulfur cluster transport by Atm1p exporter protein. Herein, we report on some of the possible functional and physiological roles for this novel [2Fe-2S](GS4) complex in iron-sulfur cluster biosynthesis and quantitatively characterize its role in the broader network of Fe-S cluster transfer reactions. UV-vis and circular dichroism spectroscopy have been used in kinetic studies to determine second-order rate constants for [2Fe-2S] cluster transfer from [2Fe-2S](GS4) complex to acceptor proteins, such as human IscU, Schizosaccharomyces pombe Isa1, human and yeast glutaredoxins (human Grx2 and Saccharomyces cerevisiae Grx3), and human ferredoxins. Second-order rate constants for cluster extraction from these holo proteins were also determined by varying the concentration of glutathione, and a likely common mechanism for cluster uptake was determined by kinetic analysis. The results indicate that the [2Fe-2S](GS4) complex is stable under physiological conditions, and demonstrates reversible cluster exchange with a wide range of Fe-S cluster proteins, thereby supporting a possible physiological role for such centers.

Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells.

PubMed

Dong, Lan-Feng; Kovarova, Jaromira; Bajzikova, Martina; Bezawork-Geleta, Ayenachew; Svec, David; Endaya, Berwini; Sachaphibulkij, Karishma; Coelho, Ana R; Sebkova, Natasa; Ruzickova, Anna; Tan, An S; Kluckova, Katarina; Judasova, Kristyna; Zamecnikova, Katerina; Rychtarcikova, Zuzana; Gopalan, Vinod; Andera, Ladislav; Sobol, Margarita; Yan, Bing; Pattnaik, Bijay; Bhatraju, Naveen; Truksa, Jaroslav; Stopka, Pavel; Hozak, Pavel; Lam, Alfred K; Sedlacek, Radislav; Oliveira, Paulo J; Kubista, Mikael; Agrawal, Anurag; Dvorakova-Hortova, Katerina; Rohlena, Jakub; Berridge, Michael V; Neuzil, Jiri

2017-02-15

Recently, we showed that generation of tumours in syngeneic mice by cells devoid of mitochondrial (mt) DNA (ρ 0 cells) is linked to the acquisition of the host mtDNA. However, the mechanism of mtDNA movement between cells remains unresolved. To determine whether the transfer of mtDNA involves whole mitochondria, we injected B16ρ 0 mouse melanoma cells into syngeneic C57BL/6N su9-DsRed2 mice that express red fluorescent protein in their mitochondria. We document that mtDNA is acquired by transfer of whole mitochondria from the host animal, leading to normalisation of mitochondrial respiration. Additionally, knockdown of key mitochondrial complex I (NDUFV1) and complex II (SDHC) subunits by shRNA in B16ρ 0 cells abolished or significantly retarded their ability to form tumours. Collectively, these results show that intact mitochondria with their mtDNA payload are transferred in the developing tumour, and provide functional evidence for an essential role of oxidative phosphorylation in cancer.

Ribosome binding induces repositioning of the signal recognition particle receptor on the translocon

PubMed Central

Kuhn, Patrick; Draycheva, Albena; Vogt, Andreas; Petriman, Narcis-Adrian; Sturm, Lukas; Drepper, Friedel; Warscheid, Bettina; Wintermeyer, Wolfgang

2015-01-01

Cotranslational protein targeting delivers proteins to the bacterial cytoplasmic membrane or to the eukaryotic endoplasmic reticulum membrane. The signal recognition particle (SRP) binds to signal sequences emerging from the ribosomal tunnel and targets the ribosome-nascent-chain complex (RNC) to the SRP receptor, termed FtsY in bacteria. FtsY interacts with the fifth cytosolic loop of SecY in the SecYEG translocon, but the functional role of the interaction is unclear. By using photo-cross-linking and fluorescence resonance energy transfer measurements, we show that FtsY–SecY complex formation is guanosine triphosphate independent but requires a phospholipid environment. Binding of an SRP–RNC complex exposing a hydrophobic transmembrane segment induces a rearrangement of the SecY–FtsY complex, which allows the subsequent contact between SecY and ribosomal protein uL23. These results suggest that direct RNC transfer to the translocon is guided by the interaction between SRP and translocon-bound FtsY in a quaternary targeting complex. PMID:26459600

Transport dynamics in membranes of photosynthetic purple bacteria

NASA Astrophysics Data System (ADS)

Caycedo, Felipe; Rodriguez, Ferney; Quiroga, Luis; Fassioli, Francesca; Johnson, Neil

2007-03-01

Photo-Syntethic Unit (PSU) of purple bacteria is conformed by three basic constituents: Light Harvesting Complex 2 (LH2) antenna complexes, where chromophores are distributed in a ring in close contact with caroteniods with a function of collecting light; LH1s, ring shaped structures of chromophores which harvest and funnel excitations to the Reaction Centre (RC), where phtosynthesis takes place. Studies concerning a single PSU have been capable of reproducing experimental transfer times, but incapable of explaining the fact that architecture LH2-LH1-RC of phototosynthetic membranes changes as light intensity conditions vary. The organization of antenna complexes in the membranes that support PSU seems to have its own functionality. A hopping model where excitations are transferred within a membrane is used, and populations of RC, LH1 and LH2 are investigated. Different statistics concerning arrival times of excitations that excite a single PSU are considered and compared with the global model where coordinates of a great portion of a membrane are included. The model permits in a classical basis to understand which parameters make photosynthesis in purple bateria efficient and reliable.

A detailed study of intermolecular interactions, electronic and vibrational properties of the metal complex bis(uracilato)diammine copper(ii) dihydrate

NASA Astrophysics Data System (ADS)

Gramajo Feijoo, M.; Fernández-Liencres, M. P.; Gil, D. M.; Gómez, M. I.; Ben Altabef, A.; Navarro, A.; Tuttolomondo, M. E.

2018-03-01

Density Functional Theory (DFT) calculations were performed with the aim of investigating the vibrational, electronic and structural properties of [Cu(uracilato-N1)2 (NH3)2]ṡ2H2O complex. The IR and Raman spectra were recorded leading to a complete analysis of the normal modes of vibration of the metal complex. A careful study of the intermolecular interactions observed in solid state was performed by using the Hirshfeld surface analysis and their associated 2D fingerprint plots. The results indicated that the crystal packing is stabilized by Nsbnd H⋯O hydrogen bonds and π-stacking interactions. In addition, Csbnd H···π interactions were also observed. Time-dependent density functional theory (TD-DFT) calculations revealed that all the low-lying electronic states correspond to a mixture of intraligand charge transfer (ILCT) and ligand-to-metal charge transfer (LMCT) transitions. Finally, Natural Bond Orbital (NBO) and Atoms in Molecules (AIM) analysis were performed to shed light on the intermolecular interactions in the coordination sphere.

Suppression of BRCA2 by Mutant Mitochondrial DNA in Prostate Cancer

DTIC Science & Technology

2011-05-01

Briefly, the electron transfer activities of complex I/III (NADH dehydrogenase/cytochrome bc1 complex: catalyzes the electron transfer from NADH to...ferricytochrome c) and complex II/III (succinate dehydrogenase/cytochrome bc1 complex: catalyzes the electron transfer from succinate to ferricytochrome...The electron transfer activity of complex IV (cytochrome c oxidase: catalyzes the final step of the respiratory chain by transferring electrons from

Novel Zn(II) complexes of 1,3-diphenyl-4-(arylazo)pyrazol-5-one derivatives: Synthesis, spectroscopic properties, DFT calculations and first order nonlinear optical properties

NASA Astrophysics Data System (ADS)

Abdel-Latif, Samir A.; Mohamed, Adel A.

2018-03-01

Eight novel Zn(II) complexes with substituted 1,3-diphenyl-4-(arylazo)pyrazol-5-one (L1-L4) derivatives have been synthesized and elucidated using various physicochemical techniques. Quantum mechanical calculations of energies, geometries were done by DFT using B3LYP/GEN functional combined with 6.311G (d,p) and LAN2DZ basis sets. The analyses of HOMO and LUMO have been used to explain the charge transfer within the ligands and complexes. The calculated small energy gap between HOMO and LUMO energies shows that the charge transfer occurs within Zn(II) complexes. Geometrical parameters, molecular electrostatic potential maps (MEP) and total electron densities analyses of the ligands and their Zn complexes have been carried out. Molecular stability, hyperconjugative interactions, intramolecular charge transfer (ICT) and bond strength has been investigated by the applying of natural bond orbital (NBO) analysis. Total static dipole moment (μ), the mean polarizability (<α>), the anisotropy of the polarizability (Δα), the mean first-order hyperpolarizability (<β>) have been also performed. The obtained values show that Zn(II) complexes is brilliant candidate to NLO materials. The analyses of the 1:1 complexes indicate that the Zn(II) ion is five-coordinated with water molecules at axial position in case of L1, L2 and L4 whereas, six-coordinated with L3 and non-electrolytic behaviour of complexes indicates the absence of counter ion.

The solvation of the ground and transition states in the reaction of ortho-palladized acetanilide with styrene in organic solvents

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

Sakodynskaya, I.K.; Neverov, A.A; Ryabov, A.D.

1986-07-01

The rate of the reaction of di-mu-chlorobis(acetanilidato-2C, 0) dipalladium(II) with styrene leading to 2-acetaminostilbene was found in 11 organic solvents. In all media, the reaction has second-order kinetics. The free energy, enthalpy and entropy of activation were determined in each solvent. The data for the solubility of the starting Pd(II) complex were used to determine the free energy for the transfer of the ground state of this reaction from a standard solvent (heptane) to the other solvents. The analogous transfer functions were calculated for the transition state. The correlation of the transfer functions of the starting and transition states ofmore » this reaction with empirical solvent parameters was examined.« less

Interfacial charge separation and recombination in InP and quasi-type II InP/CdS core/shell quantum dot-molecular acceptor complexes.

PubMed

Wu, Kaifeng; Song, Nianhui; Liu, Zheng; Zhu, Haiming; Rodríguez-Córdoba, William; Lian, Tianquan

2013-08-15

Recent studies of group II-VI colloidal semiconductor heterostuctures, such as CdSe/CdS core/shell quantum dots (QDs) or dot-in-rod nanorods, show that type II and quasi-type II band alignment can facilitate electron transfer and slow down charge recombination in QD-molecular electron acceptor complexes. To explore the general applicability of this wave function engineering approach for controlling charge transfer properties, we investigate exciton relaxation and dissociation dynamics in InP (a group III-V semiconductor) and InP/CdS core/shell (a heterostructure beween group III-V and II-VI semiconductors) QDs by transient absorption spectroscopy. We show that InP/CdS QDs exhibit a quasi-type II band alignment with the 1S electron delocalized throughout the core and shell and the 1S hole confined in the InP core. In InP-methylviologen (MV(2+)) complexes, excitons in the QD can be dissociated by ultrafast electron transfer to MV(2+) from the 1S electron level (with an average time constant of 11.4 ps) as well as 1P and higher electron levels (with a time constant of 0.39 ps), which is followed by charge recombination to regenerate the complex in its ground state (with an average time constant of 47.1 ns). In comparison, InP/CdS-MV(2+) complexes show similar ultrafast charge separation and 5-fold slower charge recombination rates, consistent with the quasi-type II band alignment in these heterostructures. This result demonstrates that wave function engineering in nanoheterostructures of group III-V and II-VI semiconductors provides a promising approach for optimizing their light harvesting and charge separation for solar energy conversion applications.

Direct transfer of subwavelength plasmonic nanostructures on bioactive silk films.

PubMed

Lin, Dianmin; Tao, Hu; Trevino, Jacob; Mondia, Jessica P; Kaplan, David L; Omenetto, Fiorenzo G; Dal Negro, Luca

2012-11-27

By a reusable transfer fabrication technique, we demonstrate high-fidelity fabrication of metal nanoparticles, optical nanoantennas, and nanohole arrays directly on a functional silk biopolymer. The ability to reproducibly pattern silk biopolymers with arbitrarily complex plasmonic arrays is of importance for a variety of applications in optical biosensing, tissue engineering, cell biology, and the development of novel bio-optoelectronic medical devices. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SAM-based Cell Transfer to Photopatterned Hydrogels for Microengineering Vascular-Like Structures

PubMed Central

Sadr, Nasser; Zhu, Mojun; Osaki, Tatsuya; Kakegawa, Takahiro; Yang, Yunzhi; Moretti, Matteo; Fukuda, Junji; Khademhosseini, Ali

2011-01-01

A major challenge in tissue engineering is to reproduce the native 3D microvascular architecture fundamental for in vivo functions. Current approaches still lack a network of perfusable vessels with native 3D structural organization. Here we present a new method combining self-assembled monolayer (SAM)-based cell transfer and gelatin methacrylate hydrogel photopatterning techniques for microengineering vascular structures. Human umbilical vein cell (HUVEC) transfer from oligopeptide SAM-coated surfaces to the hydrogel revealed two SAM desorption mechanisms: photoinduced and electrochemically triggered. The former, occurs concomitantly to hydrogel photocrosslinking, and resulted in efficient (>97%) monolayer transfer. The latter, prompted by additional potential application, preserved cell morphology and maintained high transfer efficiency of VE-cadherin positive monolayers over longer culture periods. This approach was also applied to transfer HUVECs to 3D geometrically defined vascular-like structures in hydrogels, which were then maintained in perfusion culture for 15 days. As a step toward more complex constructs, a cell-laden hydrogel layer was photopatterned around the endothelialized channel to mimic the vascular smooth muscle structure of distal arterioles. This study shows that the coupling of the SAM-based cell transfer and hydrogel photocrosslinking could potentially open up new avenues in engineering more complex, vascularized tissue constructs for regenerative medicine and tissue engineering applications. PMID:21802723

Computational studies of molecular charge transfer complexes of heterocyclic 4-methylepyridine-2-azomethine-p-benzene derivatives with picric acid and m-dinitrobenzene.

PubMed

Al-Harbi, L M; El-Mossalamy, E H; Obaid, A Y; Al-Jedaani, A H

2014-01-01

Charge transfer complexes of substituted aryl Schiff bases as donors with picric acid and m-dinitrobenzene as acceptors were investigated by using computational analysis calculated by Configuration Interaction Singles Hartree-Fock (CIS-HF) at standard 6-31G∗ basis set and Time-Dependent Density-Functional Theory (TD-DFT) levels of theory at standard 6-31G∗∗ basis set, infrared spectra, visible and nuclear magnetic resonance spectra are investigated. The optimized geometries and vibrational frequencies were evaluated. The energy and oscillator strength were calculated by Configuration Interaction Singles Hartree-Fock method (CIS-HF) and the Time-Dependent Density-Functional Theory (TD-DFT) results. Electronic properties, such as HOMO and LUMO energies and band gaps of CTCs set, were studied by the Time-Dependent density functional theory with Becke-Lee-Young-Parr (B3LYP) composite exchange correlation functional and by Configuration Interaction Singles Hartree-Fock method (CIS-HF). The ionization potential Ip and electron affinity EA were calculated by PM3, HF and DFT methods. The columbic force was calculated theoretically by using (CIS-HF and TD-DFT) methods. This study confirms that the theoretical calculation of vibrational frequencies for (aryl Schiff bases--(m-dinitrobenzene and picric acid)) complexes are quite useful for the vibrational assignment and for predicting new vibrational frequencies. Copyright © 2013 Elsevier B.V. All rights reserved.

Exercise in claudicants increase or decrease walking ability and the response relates to mitochondrial function.

PubMed

van Schaardenburgh, Michel; Wohlwend, Martin; Rognmo, Øivind; Mattsson, Erney J R

2017-06-07

Exercise of patients with intermittent claudication improves walking performance. Exercise does not usually increase blood flow, but seems to increase muscle mitochondrial enzyme activities. Although exercise is beneficial in most patients, it might be harmful in some. The mitochondrial response to exercise might therefore differ between patients. Our hypothesis was that changes in walking performance relate to changes in mitochondrial function after 8 weeks of exercise. At a subgroup level, negative responders decrease and positive responders increase mitochondrial capacity. Two types of exercise were studied, calf raising and walking (n = 28). We wanted to see whether there were negative and positive responders, independent of type of exercise. Measurements of walking performance, peripheral hemodynamics, mitochondrial respiration and content (citrate synthase activity) were obtained on each patient before and after the intervention period. Multiple linear regression was used to test whether changes in peak walking time relate to mitochondrial function. Subgroups of negative (n = 8) and positive responders (n = 8) were defined as those that either decreased or increased peak walking time following exercise. Paired t test and analysis of covariance was used to test changes within and between subgroups. Changes in peak walking time were related to changes in mitochondrial respiration supported by electron transferring flavoprotein (ETF + CI) P (p = 0.004), complex I (CI + ETF) P (p = 0.003), complex I + complex II (CI + CII + ETF) P (p = 0.037) and OXPHOS coupling efficiency (p = 0.046) in the whole group. Negative responders had more advanced peripheral arterial disease. Mitochondrial respiration supported by electron transferring flavoprotein (ETF + CI) P (p = 0.0013), complex I (CI + ETF) P (p = 0.0005), complex I + complex II (CI + CII + ETF) P (p = 0.011) and electron transfer system capacity (CI + CII + ETF) E (p = 0.021) and OXPHOS coupling efficiency decreased in negative responders (p = 0.0007) after exercise. Positive responders increased citrate synthase activity (p = 0.010). Changes in walking performance seem to relate to changes in mitochondrial function after exercise. Negative responders have more advanced peripheral arterial disease and decrease, while positive responders increase mitochondrial capacity. Trial registration ClinicalTrials.gov ID: NCT023110256.

Selective CO{sub 2} reduction conjugated with H{sub 2}O oxidation utilizing semiconductor/metal-complex hybrid photocatalysts

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

Morikawa, T., E-mail: morikawa@mosk.tytlabs.co.jp; Sato, S., E-mail: morikawa@mosk.tytlabs.co.jp; Arai, T., E-mail: morikawa@mosk.tytlabs.co.jp

2013-12-10

We developed a new hybrid photocatalyst for CO{sub 2} reduction, which is composed of a semiconductor and a metal complex. In the hybrid photocatalyst, ΔG between the position of conduction band minimum (E{sub CBM}) of the semiconductor and the CO{sub 2} reduction potential of the complex is an essential factor for realizing fast electron transfer from the conduction band of semiconductor to metal complex leading to high photocatalytic activity. On the basis of this concept, the hybrid photocatalyst InP/Ru-complex, which functions in aqueous media, was developed. The photoreduction of CO{sub 2} to formate using water as an electron donor andmore » a proton source was successfully achieved as a Z-scheme system by functionally conjugating the InP/Ru-complex photocatalyst for CO{sub 2} reduction with a TiO{sub 2} photocatalyst for water oxidation. The conversion efficiency from solar energy to chemical energy was ca. 0.04%, which approaches that for photosynthesis in a plant. Because this system can be applied to many other inorganic semiconductors and metal-complex catalysts, the efficiency and reaction selectivity can be enhanced by optimization of the electron transfer process including the energy-band configurations, conjugation conformations, and catalyst structures. This electrical-bias-free reaction is a huge leap forward for future practical applications of artificial photosynthesis under solar irradiation to produce organic species.« less

MICOS and phospholipid transfer by Ups2-Mdm35 organize membrane lipid synthesis in mitochondria.

PubMed

Aaltonen, Mari J; Friedman, Jonathan R; Osman, Christof; Salin, Bénédicte; di Rago, Jean-Paul; Nunnari, Jodi; Langer, Thomas; Tatsuta, Takashi

2016-06-06

Mitochondria exert critical functions in cellular lipid metabolism and promote the synthesis of major constituents of cellular membranes, such as phosphatidylethanolamine (PE) and phosphatidylcholine. Here, we demonstrate that the phosphatidylserine decarboxylase Psd1, located in the inner mitochondrial membrane, promotes mitochondrial PE synthesis via two pathways. First, Ups2-Mdm35 complexes (SLMO2-TRIAP1 in humans) serve as phosphatidylserine (PS)-specific lipid transfer proteins in the mitochondrial intermembrane space, allowing formation of PE by Psd1 in the inner membrane. Second, Psd1 decarboxylates PS in the outer membrane in trans, independently of PS transfer by Ups2-Mdm35. This latter pathway requires close apposition between both mitochondrial membranes and the mitochondrial contact site and cristae organizing system (MICOS). In MICOS-deficient cells, limiting PS transfer by Ups2-Mdm35 and reducing mitochondrial PE accumulation preserves mitochondrial respiration and cristae formation. These results link mitochondrial PE metabolism to MICOS, combining functions in protein and lipid homeostasis to preserve mitochondrial structure and function. © 2016 Aaltonen et al.

Frenkel and Charge-Transfer Excitations in Donor-acceptor Complexes from Many-Body Green's Functions Theory.

PubMed

Baumeier, Björn; Andrienko, Denis; Rohlfing, Michael

2012-08-14

Excited states of donor-acceptor dimers are studied using many-body Green's functions theory within the GW approximation and the Bethe-Salpeter equation. For a series of prototypical small-molecule based pairs, this method predicts energies of local Frenkel and intermolecular charge-transfer excitations with the accuracy of tens of meV. Application to larger systems is possible and allowed us to analyze energy levels and binding energies of excitons in representative dimers of dicyanovinyl-substituted quarterthiophene and fullerene, a donor-acceptor pair used in state of the art organic solar cells. In these dimers, the transition from Frenkel to charge transfer excitons is endothermic and the binding energy of charge transfer excitons is still of the order of 1.5-2 eV. Hence, even such an accurate dimer-based description does not yield internal energetics favorable for the generation of free charges either by thermal energy or an external electric field. These results confirm that, for qualitative predictions of solar cell functionality, accounting for the explicit molecular environment is as important as the accurate knowledge of internal dimer energies.

Acquisition of a Complex Basketball-Dribbling Task in School Children as a Function of Bilateral Practice Order

ERIC Educational Resources Information Center

Stockel, Tino; Weigelt, Matthias; Krug, Jurgen

2011-01-01

The purpose of this study was to investigate order-of-practice effects for the acquisition of a complex basketball skill in a bilateral transfer paradigm. The task required participants to dribble as fast as possible in slalom-like movements across six javelins and return to the initial position. Fifty-two right-handed school children (M age =…

Extracellular vesicle-mediated transfer of donor genomic DNA to recipient cells is a novel mechanism for genetic influence between cells

PubMed Central

Cai, Jin; Han, Yu; Ren, Hongmei; Chen, Caiyu; He, Duofen; Zhou, Lin; Eisner, Gilbert M.; Asico, Laureano D.; Jose, Pedro A.; Zeng, Chunyu

2013-01-01

Extracellular vesicles (EVs) carry signals within or at their limiting membranes, providing a mechanism by which cells can exchange more complex information than what was previously thought. In addition to mRNAs and microRNAs, there are DNA fragments in EVs. Solexa sequencing indicated the presence of at least 16434 genomic DNA (gDNA) fragments in the EVs from human plasma. Immunofluorescence study showed direct evidence that acridine orange-stained EV DNAs could be transferred into the cells and localize to and inside the nuclear membrane. However, whether the transferred EV DNAs are functional or not is not clear. We found that EV gDNAs could be homologously or heterologously transferred from donor cells to recipient cells, and increase gDNA-coding mRNA, protein expression, and function (e.g. AT1 receptor). An endogenous promoter of the AT1 receptor, NF-κB, could be recruited to the transferred DNAs in the nucleus, and increase the transcription of AT1 receptor in the recipient cells. Moreover, the transferred EV gDNAs have pathophysiological significance. BCR/ABL hybrid gene, involved in the pathogenesis of chronic myeloid leukemia, could be transferred from K562 EVs to HEK293 cells or neutrophils. Our present study shows that the gDNAs transferred from EVs to cells have physiological significance, not only to increase the gDNA-coding mRNA and protein levels, but also to influence function in recipient cells. PMID:23580760

Spectroscopic and Computational Investigations of a Mononuclear Manganese(IV)-Oxo Complex Reveal Electronic Structure Contributions to Reactivity

DOE PAGES

Leto, Domenick F.; Massie, Allyssa A.; Rice, Derek B.; ...

2016-11-01

The mononuclear Mn(IV)-oxo complex [Mn IV(O)(N4py)] 2+, where N4py is the pentadentate ligand N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine, we propose to attack C–H bonds by an excited-state reactivity pattern [Cho, K.-B.; Shaik, S.; Nam, W. J. Phys. Chem. Lett. 2012, 3, 2851-2856 (DOI: 10.1021/jz301241z)]. In this model, a 4E excited state is utilized to provide a lower-energy barrier for hydrogen-atom transfer. This proposal is intriguing, as it offers both a rationale for the relatively high hydrogen-atom-transfer reactivity of [Mn IV(O)(N4py)] 2+ and a guideline for creating more reactive complexes through ligand modification. Here we employ a combination of electronic absorption and variable-temperature magnetic circularmore » dichroism (MCD) spectroscopy to experimentally evaluate this excited-state reactivity model. Using these spectroscopic methods, in conjunction with time-dependent density functional theory (TD-DFT) and complete-active space self-consistent-field calculations (CASSCF), we define the ligand-field and charge-transfer excited states of [MnIV(O)(N4py)]2+. Through a graphical analysis of the signs of the experimental C-term MCD signals, we unambiguously assign a low-energy MCD feature of [Mn IV(O)(N4py)] 2+ as the 4E excited state predicted to be involved in hydrogen-atom-transfer reactivity. The CASSCF calculations predict enhanced Mn III-oxyl character on the excited-state 4E surface, consistent with previous DFT calculations. Potential-energy surfaces, developed using the CASSCF methods, are used to determine how the energies and wave functions of the ground and excited states evolved as a function of Mn=O distance. Furthermore, the unique insights into ground- and excited-state electronic structure offered by these spectroscopic and computational studies are harmonized with a thermodynamic model of hydrogen-atom-transfer reactivity, which predicts a correlation between transition-state barriers and driving force« less

Spectroscopic and Computational Investigations of a Mononuclear Manganese(IV)-Oxo Complex Reveal Electronic Structure Contributions to Reactivity

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

Leto, Domenick F.; Massie, Allyssa A.; Rice, Derek B.

The mononuclear Mn(IV)-oxo complex [Mn IV(O)(N4py)] 2+, where N4py is the pentadentate ligand N,N-bis(2-pyridylmethyl)-N-bis(2-pyridyl)methylamine, we propose to attack C–H bonds by an excited-state reactivity pattern [Cho, K.-B.; Shaik, S.; Nam, W. J. Phys. Chem. Lett. 2012, 3, 2851-2856 (DOI: 10.1021/jz301241z)]. In this model, a 4E excited state is utilized to provide a lower-energy barrier for hydrogen-atom transfer. This proposal is intriguing, as it offers both a rationale for the relatively high hydrogen-atom-transfer reactivity of [Mn IV(O)(N4py)] 2+ and a guideline for creating more reactive complexes through ligand modification. Here we employ a combination of electronic absorption and variable-temperature magnetic circularmore » dichroism (MCD) spectroscopy to experimentally evaluate this excited-state reactivity model. Using these spectroscopic methods, in conjunction with time-dependent density functional theory (TD-DFT) and complete-active space self-consistent-field calculations (CASSCF), we define the ligand-field and charge-transfer excited states of [MnIV(O)(N4py)]2+. Through a graphical analysis of the signs of the experimental C-term MCD signals, we unambiguously assign a low-energy MCD feature of [Mn IV(O)(N4py)] 2+ as the 4E excited state predicted to be involved in hydrogen-atom-transfer reactivity. The CASSCF calculations predict enhanced Mn III-oxyl character on the excited-state 4E surface, consistent with previous DFT calculations. Potential-energy surfaces, developed using the CASSCF methods, are used to determine how the energies and wave functions of the ground and excited states evolved as a function of Mn=O distance. Furthermore, the unique insights into ground- and excited-state electronic structure offered by these spectroscopic and computational studies are harmonized with a thermodynamic model of hydrogen-atom-transfer reactivity, which predicts a correlation between transition-state barriers and driving force« less

Mitochondrial transfer from Wharton's jelly-derived mesenchymal stem cells to mitochondria-defective cells recaptures impaired mitochondrial function.

PubMed

Lin, Hung-Yu; Liou, Chia-Wei; Chen, Shang-Der; Hsu, Te-Yao; Chuang, Jiin-Haur; Wang, Pei-Wen; Huang, Sheng-Teng; Tiao, Mao-Meng; Chen, Jin-Bor; Lin, Tsu-Kung; Chuang, Yao-Chung

2015-05-01

Adult mesenchymal stem cell (MSC)-conducted mitochondrial transfer has been recently shown to rescue cellular bioenergetics and prevent cell death caused by mitochondrial dysfunction. Wharton's jelly-derived MSCs (WJMSCs) harvested from postpartum umbilical cords are an accessible and abundant source of stem cells. This study aimed to determine the capability of WJMSCs to transfer their own mitochondria and rescue impaired oxidative phosphorylation (OXPHOS) and bioenergetics caused by mitochondrial DNA defects. To do this, WJMSCs were co-cultured with mitochondrial DNA (mtDNA)-depleted ρ(0) cells and the recapture of mitochondrial function was evaluated. WJMSCs were shown to be capable of transferring their own mitochondria into ρ(0) cells and underwent interorganellar mixture within these cells. Permissive culture media (BrdU-containing and pyruvate- and uridine-free) sieved out a survival cell population from the co-cultured WJMSCs (BrdU-sensitive) and ρ(0) cells (pyruvate/uridine-free). The survival cells had mtDNA identical to that of WJMSCs, whereas they expressed cellular markers identical to that of ρ(0) cells. Importantly, these ρ(0)-plus -WJMSC-mtDNA (ρ(+W)) cells recovered the expression of mtDNA-encoded proteins and exhibited functional oxygen consumption and respiratory control, as well as the activity of electron transport chain (ETC) complexes I, II, III and IV. In addition, ETC complex V-inhibitor-sensitive ATP production and metabolic shifting were also recovered. Furthermore, cellular behaviors including attachment-free proliferation, aerobic viability and OXPHOS-reliant cellular motility were also regained after mitochondrial transfer by WJMSCs. The therapeutic effect of WJMSCs-derived mitochondrial transfer was able to stably sustain for at least 45 passages. In conclusion, this study suggests that WJMSCs may serve as a potential therapeutic strategy for diseases linked to mitochondrial dysfunction through the donation of healthy mitochondria to cells with genetic mitochondrial defects. Copyright © 2015 Elsevier B.V. All rights reserved.

A Mononuclear Nonheme Iron(V)-Imido Complex

DOE PAGES

Hong, Seungwoo; Sutherlin, Kyle D.; Vardhaman, Anil Kumar; ...

2017-06-19

Mononuclear nonheme iron(V)-oxo complexes have been reported previously. Herein, we report the first example of a mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [(TAML)Fe V(NTs)] – . The spectroscopic characterization of 1 revealed an S = 1/2 Fe(V) oxidation state, an Fe—N bond length of 1.65(4) Å, and an Fe—N vibration at 817 cm –1. In conclusion, the reactivity of 1 was demonstrated in C—H bond functionalization and nitrene transfer reactions.

A Mononuclear Nonheme Iron(V)-Imido Complex

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

Hong, Seungwoo; Sutherlin, Kyle D.; Vardhaman, Anil Kumar

Mononuclear nonheme iron(V)-oxo complexes have been reported previously. Herein, we report the first example of a mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [(TAML)Fe V(NTs)] – . The spectroscopic characterization of 1 revealed an S = 1/2 Fe(V) oxidation state, an Fe—N bond length of 1.65(4) Å, and an Fe—N vibration at 817 cm –1. In conclusion, the reactivity of 1 was demonstrated in C—H bond functionalization and nitrene transfer reactions.

Charge Transfer Effect on Raman and Surface Enhanced Raman Spectroscopy of Furfural Molecules.

PubMed

Wan, Fu; Shi, Haiyang; Chen, Weigen; Gu, Zhaoliang; Du, Lingling; Wang, Pinyi; Wang, Jianxin; Huang, Yingzhou

2017-08-02

The detection of furfural in transformer oil through surface enhanced Raman spectroscopy (SERS) is one of the most promising online monitoring techniques in the process of transformer aging. In this work, the Raman of individual furfural molecules and SERS of furfural-M x (M = Ag, Au, Cu) complexes are investigated through density functional theory (DFT). In the Raman spectrum of individual furfural molecules, the vibration mode of each Raman peak is figured out, and the deviation from experimental data is analyzed by surface charge distribution. In the SERS of furfural-M x complexes, the influence of atom number and species on SERS chemical enhancement factors (EFs) are studied, and are further analyzed by charge transfer effect. Our studies strengthen the understanding of charge transfer effect in the SERS of furfural molecules, which is important in the online monitoring of the transformer aging process through SERS.

Charge Transfer Effect on Raman and Surface Enhanced Raman Spectroscopy of Furfural Molecules

PubMed Central

Wan, Fu; Shi, Haiyang; Chen, Weigen; Gu, Zhaoliang; Du, Lingling; Wang, Pinyi; Wang, Jianxin

2017-01-01

The detection of furfural in transformer oil through surface enhanced Raman spectroscopy (SERS) is one of the most promising online monitoring techniques in the process of transformer aging. In this work, the Raman of individual furfural molecules and SERS of furfural-Mx (M = Ag, Au, Cu) complexes are investigated through density functional theory (DFT). In the Raman spectrum of individual furfural molecules, the vibration mode of each Raman peak is figured out, and the deviation from experimental data is analyzed by surface charge distribution. In the SERS of furfural-Mx complexes, the influence of atom number and species on SERS chemical enhancement factors (EFs) are studied, and are further analyzed by charge transfer effect. Our studies strengthen the understanding of charge transfer effect in the SERS of furfural molecules, which is important in the online monitoring of the transformer aging process through SERS. PMID:28767053

The structure of control and data transfer management system for the GAMMA-400 scientific complex

NASA Astrophysics Data System (ADS)

Arkhangelskiy, A. I.; Bobkov, S. G.; Serdin, O. V.; Gorbunov, M. S.; Topchiev, N. P.

2016-02-01

A description of the control and data transfer management system for scientific instrumentation involved in the GAMMA-400 space project is given. The technical capabilities of all specialized equipment to provide the functioning of the scientific instrumentation and satellite support systems are unified in a single structure. Control of the scientific instruments is maintained using one-time pulse radio commands, as well as program commands in the form of 16-bit code words, which are transmitted via onboard control system and scientific data acquisition system. Up to 100 GByte of data per day can be transferred to the ground segment of the project. The correctness of the proposed and implemented structure, engineering solutions and electronic elemental base selection has been verified by the experimental working-off of the prototype of the GAMMA-400 scientific complex in laboratory conditions.

Kinetic studies on the oxidation of cytochrome b(5) Phe35 mutants with cytochrome c, plastocyanin and inorganic complexes.

PubMed

Yao, Ping; Wang, Yun-Hua; Sun, Bing-Yun; Xie, Yi; Hirota, Shun; Yamauchi, Osamu; Huang, Zhong-Xian

2002-04-01

To illustrate the functions of the aromatic residue Phe35 of cytochrome b(5) and to give further insight into the roles of the Phe35-containing hydrophobic patch and/or aromatic channel of cytochrome b(5), we studied electron transfer reactions of cytochrome b(5) and its Phe35Tyr and Phe35Leu variants with cytochrome c, with the wild-type and Tyr83Phe and Tyr83Leu variants of plastocyanin, and with the inorganic complexes [Fe(EDTA)](-), [Fe(CDTA)](-) and [Ru(NH(3))(6)](3+). The changes at Phe35 of cytochrome b(5) and Tyr83 of plastocyanin do not affect the second-order rate constants for the electron transfer reactions. These results show that the invariant aromatic residues and aromatic patch/channel are not essential for electron transfer in these systems.

Membrane Contact Sites: Complex Zones for Membrane Association and Lipid Exchange

PubMed Central

Quon, Evan; Beh, Christopher T.

2015-01-01

Lipid transport between membranes within cells involves vesicle and protein carriers, but as agents of nonvesicular lipid transfer, the role of membrane contact sites has received increasing attention. As zones for lipid metabolism and exchange, various membrane contact sites mediate direct associations between different organelles. In particular, membrane contact sites linking the plasma membrane (PM) and the endoplasmic reticulum (ER) represent important regulators of lipid and ion transfer. In yeast, cortical ER is stapled to the PM through membrane-tethering proteins, which establish a direct connection between the membranes. In this review, we consider passive and facilitated models for lipid transfer at PM–ER contact sites. Besides the tethering proteins, we examine the roles of an additional repertoire of lipid and protein regulators that prime and propagate PM–ER membrane association. We conclude that instead of being simple mediators of membrane association, regulatory components of membrane contact sites have complex and multilayered functions. PMID:26949334

Mechanical system diagnostics using vibration testing techniques

NASA Technical Reports Server (NTRS)

Mcleod, Catherine D.; Raju, P. K.; Crocker, M. J.

1990-01-01

The 'Cepstrum' technique of vibration-path identification allows the recovery of the transfer function of a system with little knowledge as to its excitation force, by means of a mathematical manipulation of the system output in conjunction with subtraction of part of the output and suitable signal processing. An experimental program has been conducted to evaluate the usefulness of this technique in the cases of simple, cantilever-beam and free-free plate structures as well as in that of a complex mechanical system. On the basis of the transfer functions thus recovered, it was possible to evaluate the shifts in the resonance frequencies of a structure due to the presence of defects.

Functional-Group-Tolerant, Silver-Catalyzed N-N Bond Formation by Nitrene Transfer to Amines.

PubMed

Maestre, Lourdes; Dorel, Ruth; Pablo, Óscar; Escofet, Imma; Sameera, W M C; Álvarez, Eleuterio; Maseras, Feliu; Díaz-Requejo, M Mar; Echavarren, Antonio M; Pérez, Pedro J

2017-02-15

Silver(I) promotes the highly chemoselective N-amidation of tertiary amines under catalytic conditions to form aminimides by nitrene transfer from PhI═NTs. Remarkably, this transformation proceeds in a selective manner in the presence of olefins and other functional groups without formation of the commonly observed aziridines or C-H insertion products. The methodology can be applied not only to rather simple tertiary amines but also to complex natural molecules such as brucine or quinine, where the products derived from N-N bond formation were exclusively formed. Theoretical mechanistic studies have shown that this selective N-amidation reaction proceeds through triplet silver nitrenes.

Photoinduced electron transfer process on emission spectrum of N,N‧-bis(salicylidene)-1,2-phenylenediamine as a Mg2+ cation chemosensor: A first principle DFT and TDDFT study

NASA Astrophysics Data System (ADS)

Taherpour, Avat (Arman); Jamshidi, Morteza; Rezaei, Omid; Belverdi, Ali Rezaei

2018-06-01

The electronic and optical properties of N,N‧-bis(salicylidene)-1,2-phenylenediamine (SPDA) ligand were studied as a chemical sensor of Mg2+ cation in two solvents (water and DMSO) using the ab initio theory through Density Functional Theory (DFT) and Time Dependent Density Functional theory (TDDFT) methods. The results show that the SPDA ligand has a high ability for chemical sensing of Mg2+. The results has also represented that HOMO-LUMO energy gap decreases 0.941 eV after the complex formation between SPDA and Mg2+. In addition, obvious changes are found in the UV-Vis absorption spectrum, optical analyses SPDA ligand and [SPDA.Mg]2+ complex, which it has the capability of detecting Mg2+ via the adsorptive UV-Vis and colorimetric methods. Emission spectrum calculations and photoinduced electron transfer (PET) process in water solution shows different wavelength emission spectrum in amount of 4.6 nm. An analysis of NBO (natural bond orbital) data indicates tangible changes in the electron transfers data from the electron pairs of ligand to the conjugated system, both prior and subsequent to Mg2+addition.

Functional brain activation associated with working memory training and transfer.

PubMed

Clark, Cameron M; Lawlor-Savage, Linette; Goghari, Vina M

2017-09-15

While behavioural trials of working memory (WM) training have received much attention in recent years, a lesser explored parallel approach is functional neuroimaging. A small literature has suggested a complex time course for functional activation pattern changes following WM training (i.e. not simply increasing or decreasing due to training); however, no study to date has examined such neuroplastic effects in both the training task (dual n-back) and the fluid intelligence transfer task to which the training is purported to transfer (Raven's Matrices). This study investigated neural correlates of WM training in healthy young adults randomized to six weeks of WM training, or an active control condition (processing speed training) with a pre- and post-training fMRI design. Results indicated significant reductions in activation for the WM trained group in key WM-task related areas for trained WM tasks after training compared to the processing speed active control group. The same pattern of training related decreases in activation for the WM trained group was not observed for the transfer task, which is consistent with null results for all cognitive outcomes of the present trial. The observed pattern of results suggests that repetitive practice with a complex task does indeed lead to neuroplastic processes that very likely represent the reduced demand for attentional control while sub-components of the task become more routinized with practice. We suggest that future research investigate neural correlates of WM training in populations for which WM itself is impaired and/or behavioural trials of WM training have returned more promising results. Copyright © 2017 Elsevier B.V. All rights reserved.

Insights on the interaction of Zn2 + cation with triazoles: Structures, bonding, electronic excitation and applications

NASA Astrophysics Data System (ADS)

Dahmani, R.; Ben Yaghlane, S.; Boughdiri, S.; Mogren Al-Mogren, M.; Prakash, M.; Hochlaf, M.

2018-03-01

At present, we investigate the structures, the stability, the bonding and the spectroscopy of the Zn2 +-triazole complexes (Zn2 +-Tz), which are subunits of triazolate based porous materials and Zn-enzymes. This theoretical work is performed using ab initio methods and density functional theory (DFT) where dispersion correction is included. Through these benchmarks, we establish the ability and reliability of M05-2X + D3 and PBE0 + D3 functionals for the correct description of Zn2 +-Tz bond since these DFTs lead to close agreement with post Hartree-Fock methods. Therefore, M05-2X + D3 and PBE0 + D3 functionals are recommended for the characterization of larger organometallic complexes formed by Zn and N-rich linkers. For Zn2 +-Tz, we found two stable σ-type complexes: (i) a planar structure where Zn2 + links to unprotonated nitrogen and (ii) an out-of-plane cluster where carbon interacts with Zn2 +. The most stable isomers consist on a coordinated covalent bond between the lone pair of unprotonated nitrogen and the vacant 4 s orbital of Zn2 +. The roles of covalent interactions within these complexes are discussed after vibrational, NBO, NPA charges and orbital analyses. The bonding is dominated by charge transfer from Zn2 + to Tz and intramolecular charge transfer, which plays a vital role for the catalytic activity of these complexes. These findings are important to understand, at the microscopic level, the structure and the bonding within triazolate based macromolecular porous materials and Zn-enzymes.

Transfer printing techniques for materials assembly and micro/nanodevice fabrication.

PubMed

Carlson, Andrew; Bowen, Audrey M; Huang, Yonggang; Nuzzo, Ralph G; Rogers, John A

2012-10-09

Transfer printing represents a set of techniques for deterministic assembly of micro-and nanomaterials into spatially organized, functional arrangements with two and three-dimensional layouts. Such processes provide versatile routes not only to test structures and vehicles for scientific studies but also to high-performance, heterogeneously integrated functional systems, including those in flexible electronics, three-dimensional and/or curvilinear optoelectronics, and bio-integrated sensing and therapeutic devices. This article summarizes recent advances in a variety of transfer printing techniques, ranging from the mechanics and materials aspects that govern their operation to engineering features of their use in systems with varying levels of complexity. A concluding section presents perspectives on opportunities for basic and applied research, and on emerging use of these methods in high throughput, industrial-scale manufacturing. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Information thermodynamics of near-equilibrium computation

NASA Astrophysics Data System (ADS)

Prokopenko, Mikhail; Einav, Itai

2015-06-01

In studying fundamental physical limits and properties of computational processes, one is faced with the challenges of interpreting primitive information-processing functions through well-defined information-theoretic as well as thermodynamic quantities. In particular, transfer entropy, characterizing the function of computational transmission and its predictability, is known to peak near critical regimes. We focus on a thermodynamic interpretation of transfer entropy aiming to explain the underlying critical behavior by associating information flows intrinsic to computational transmission with particular physical fluxes. Specifically, in isothermal systems near thermodynamic equilibrium, the gradient of the average transfer entropy is shown to be dynamically related to Fisher information and the curvature of system's entropy. This relationship explicitly connects the predictability, sensitivity, and uncertainty of computational processes intrinsic to complex systems and allows us to consider thermodynamic interpretations of several important extreme cases and trade-offs.

Quantitative Analysis of HIV-1 Preintegration Complexes

PubMed Central

Engelman, Alan; Oztop, Ilker; Vandegraaff, Nick; Raghavendra, Nidhanapati K.

2009-01-01

Retroviral replication proceeds through the formation of a provirus, an integrated DNA copy of the viral RNA genome. The linear cDNA product of reverse transcription is the integration substrate and two different integrase activities, 3′ processing and DNA strand transfer, are required for provirus formation. Integrase nicks the cDNA ends adjacent to phylogenetically-conserved CA dinucleotides during 3′ processing. After nuclear entry and locating a suitable chromatin acceptor site, integrase joins the recessed 3′-OHs to the 5′-phosphates of a double-stranded staggered cut in the DNA target. Integrase functions in the context of a large nucleoprotein complex, called the preintegration complex (PIC), and PICs are analyzed to determine levels of integrase 3′ processing and DNA strand transfer activities that occur during acute virus infection. Denatured cDNA end regions are monitored by indirect end-labeling to measure the extent of 3′ processing. Native PICs can efficiently integrate their viral cDNA into exogenously added target DNA in vitro, and Southern blotting or nested PCR assays are used to quantify the resultant DNA strand transfer activity. This study details HIV-1 infection, PIC extraction, partial purification, and quantitative analyses of integrase 3′ processing and DNA strand transfer activities. PMID:19233280

Reactions of guanine with methyl chloride and methyl bromide: O6-methylation versus charge transfer complex formation

NASA Astrophysics Data System (ADS)

Shukla, P. K.; Mishra, P. C.; Suhai, S.

Density functional theory (DFT) at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels was employed to study O6-methylation of guanine due to its reactions with methyl chloride and methyl bromide and to obtain explanation as to why the methyl halides cause genotoxicity and possess mutagenic and carcinogenic properties. Geometries of the various isolated species involved in the reactions, reactant complexes (RCs), and product complexes (PCs) were optimized in gas phase. Transition states connecting the reactant complexes with the product complexes were also optimized in gas phase at the same levels of theory. The reactant complexes, product complexes, and transition states were solvated in aqueous media using the polarizable continuum model (PCM) of the self-consistent reaction field theory. Zero-point energy (ZPE) correction to total energy and the corresponding thermal energy correction to enthalpy were made in each case. The reactant complexes of the keto form of guanine with methyl chloride and methyl bromide in water are appreciably more stable than the corresponding complexes involving the enol form of guanine. The nature of binding in the product complexes was found to be of the charge transfer type (O6mG+ · X-, X dbond Cl, Br). Binding of HCl, HBr, and H2O molecules to the PCs obtained with the keto form of guanine did not alter the positions of the halide anions in the PCs, and the charge transfer character of the PCs was also not modified due to this binding. Further, the complexes obtained due to the binding of HCl, HBr, and H2O molecules to the PCs had greater stability than the isolated PCs. The reaction barriers involved in the formation of PCs were found to be quite high (?50 kcal/mol). Mechanisms of genotoxicity, mutagenesis and carcinogenesis caused by the methyl halides appear to involve charge transfer-type complex formation. Thus the mechanisms of these processes involving the methyl halides appear to be quite different from those that involve the other strongly carcinogenic methylating agents.

Parameter identification for nonlinear aerodynamic systems

NASA Technical Reports Server (NTRS)

Pearson, Allan E.

1990-01-01

Parameter identification for nonlinear aerodynamic systems is examined. It is presumed that the underlying model can be arranged into an input/output (I/O) differential operator equation of a generic form. The algorithm estimation is especially efficient since the equation error can be integrated exactly given any I/O pair to obtain an algebraic function of the parameters. The algorithm for parameter identification was extended to the order determination problem for linear differential system. The degeneracy in a least squares estimate caused by feedback was addressed. A method of frequency analysis for determining the transfer function G(j omega) from transient I/O data was formulated using complex valued Fourier based modulating functions in contrast with the trigonometric modulating functions for the parameter estimation problem. A simulation result of applying the algorithm is given under noise-free conditions for a system with a low pass transfer function.

Frequency analysis via the method of moment functionals

NASA Technical Reports Server (NTRS)

Pearson, A. E.; Pan, J. Q.

1990-01-01

Several variants are presented of a linear-in-parameters least squares formulation for determining the transfer function of a stable linear system at specified frequencies given a finite set of Fourier series coefficients calculated from transient nonstationary input-output data. The basis of the technique is Shinbrot's classical method of moment functionals using complex Fourier based modulating functions to convert a differential equation model on a finite time interval into an algebraic equation which depends linearly on frequency-related parameters.

Using a Full Complex Site Transfer Function to Estimate Strong Ground Motion in Port-au-Prince (Haiti).

NASA Astrophysics Data System (ADS)

ST Fleur, S.; Courboulex, F.; Bertrand, E.; Mercier De Lepinay, B. F.; Hough, S. E.; Boisson, D.; Momplaisir, R.

2017-12-01

To assess the possible impact of a future earthquake in the urban area of Port-au-Prince (Haiti), we have implemented a simulation approach for complex ground motions produced by an earthquake. To this end, we have integrated local site effect in the prediction of strong ground motions in Port-au-Prince using the complex transfer functions method, which takes into account amplitude changes as well as phase changes. This technique is particularly suitable for basins where a conventional 1D digital approach proves inadequate, as is the case in Port-au-Prince. To do this, we use the results of the Standard Spectral Ratio (SSR) approach of St Fleur et al. (2016) to estimate the amplitude of the response of the site to a nearby rock site. Then, we determine the phase difference between sites, interpreted as changes in the phase of the signal related to local site conditions, using the signals of the 2010 earthquake aftershocks records. Finally, the accelerogram of the simulated earthquake is obtain using the technique of the inverse Fourier transform. The results of this study showed that the strongest soil motions are expected in neighborhoods of downtown Port-au-Prince and adjacent hills. In addition, this simulation method by complex transfer functions was validated by comparison with recorded actual data. Our simulated response spectra reproduce very well both the amplitude and the shape of the response spectra of recorded earthquakes. This new approach allowed to reproduce the lengthening of the signal that could be generated by surface waves at certain stations in the city of Port-au-Prince. However, two points of vigilance must be considered: (1) a good signal-to-noise ratio is necessary to obtain a robust estimate of the site-reference phase shift (ratio at least equal to 10); (2) unless the amplitude and phase changes are measured on strong motion records, this technique does not take non-linear effects into account.

Real-Time Parameter Estimation Method Applied to a MIMO Process and its Comparison with an Offline Identification Method

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

Kaplanoglu, Erkan; Safak, Koray K.; Varol, H. Selcuk

2009-01-12

An experiment based method is proposed for parameter estimation of a class of linear multivariable systems. The method was applied to a pressure-level control process. Experimental time domain input/output data was utilized in a gray-box modeling approach. Prior knowledge of the form of the system transfer function matrix elements is assumed to be known. Continuous-time system transfer function matrix parameters were estimated in real-time by the least-squares method. Simulation results of experimentally determined system transfer function matrix compare very well with the experimental results. For comparison and as an alternative to the proposed real-time estimation method, we also implemented anmore » offline identification method using artificial neural networks and obtained fairly good results. The proposed methods can be implemented conveniently on a desktop PC equipped with a data acquisition board for parameter estimation of moderately complex linear multivariable systems.« less

Using Neural Networks to Improve the Performance of Radiative Transfer Modeling Used for Geometry Dependent Surface Lambertian-Equivalent Reflectivity Calculations

NASA Technical Reports Server (NTRS)

Fasnacht, Zachary; Qin, Wenhan; Haffner, David P.; Loyola, Diego; Joiner, Joanna; Krotkov, Nickolay; Vasilkov, Alexander; Spurr, Robert

2017-01-01

Surface Lambertian-equivalent reflectivity (LER) is important for trace gas retrievals in the direct calculation of cloud fractions and indirect calculation of the air mass factor. Current trace gas retrievals use climatological surface LER's. Surface properties that impact the bidirectional reflectance distribution function (BRDF) as well as varying satellite viewing geometry can be important for retrieval of trace gases. Geometry Dependent LER (GLER) captures these effects with its calculation of sun normalized radiances (I/F) and can be used in current LER algorithms (Vasilkov et al. 2016). Pixel by pixel radiative transfer calculations are computationally expensive for large datasets. Modern satellite missions such as the Tropospheric Monitoring Instrument (TROPOMI) produce very large datasets as they take measurements at much higher spatial and spectral resolutions. Look up table (LUT) interpolation improves the speed of radiative transfer calculations but complexity increases for non-linear functions. Neural networks perform fast calculations and can accurately predict both non-linear and linear functions with little effort.

Adaptation of light-harvesting functions of unicellular green algae to different light qualities.

PubMed

Ueno, Yoshifumi; Aikawa, Shimpei; Kondo, Akihiko; Akimoto, Seiji

2018-05-28

Oxygenic photosynthetic organisms perform photosynthesis efficiently by distributing captured light energy to photosystems (PSs) at an appropriate balance. Maintaining photosynthetic efficiency under changing light conditions requires modification of light-harvesting and energy-transfer processes. In the current study, we examined how green algae regulate their light-harvesting functions in response to different light qualities. We measured low-temperature time-resolved fluorescence spectra of unicellular green algae Chlamydomonas reinhardtii and Chlorella variabilis cells grown under different light qualities. By observing the delayed fluorescence spectra, we demonstrated that both types of green algae primarily modified the associations between light-harvesting chlorophyll protein complexes (LHCs) and PSs (PSII and PSI). Under blue light, Chlamydomonas transferred more energy from LHC to chlorophyll (Chl) located far from the PSII reaction center, while energy was transferred from LHC to PSI via different energy-transfer pathways in Chlorella. Under green light, both green algae exhibited enhanced energy transfer from LHCs to both PSs. Red light induced fluorescence quenching within PSs in Chlamydomonas and LHCs in Chlorella. In Chlorella, energy transfer from PSII to PSI appears to play an important role in balancing excitation between PSII and PSI.

Regulation of cargo transfer between ESCRT-0 and ESCRT-I complexes by flotillin-1 during endosomal sorting of ubiquitinated cargo

PubMed Central

Meister, M; Bänfer, S; Gärtner, U; Koskimies, J; Amaddii, M; Jacob, R; Tikkanen, R

2017-01-01

Ubiquitin-dependent sorting of membrane proteins in endosomes directs them to lysosomal degradation. In the case of receptors such as the epidermal growth factor receptor (EGFR), lysosomal degradation is important for the regulation of downstream signalling. Ubiquitinated proteins are recognised in endosomes by the endosomal sorting complexes required for transport (ESCRT) complexes, which sequentially interact with the ubiquitinated cargo. Although the role of each ESCRT complex in sorting is well established, it is not clear how the cargo is passed on from one ESCRT to the next. We here show that flotillin-1 is required for EGFR degradation, and that it interacts with the subunits of ESCRT-0 and -I complexes (hepatocyte growth factor-regulated tyrosine kinase substrate (Hrs) and Tsg101). Flotillin-1 is required for cargo recognition and sorting by ESCRT-0/Hrs and for its interaction with Tsg101. In addition, flotillin-1 is also required for the sorting of human immunodeficiency virus 1 Gag polyprotein, which mimics ESCRT-0 complex during viral assembly. We propose that flotillin-1 functions in cargo transfer between ESCRT-0 and -I complexes. PMID:28581508

Reversing Conventional Reactivity of Mixed Oxo/Alkyl Rare-Earth Complexes: Non-Redox Oxygen Atom Transfer.

PubMed

Hong, Jianquan; Tian, Haiwen; Zhang, Lixin; Zhou, Xigeng; Del Rosal, Iker; Weng, Linhong; Maron, Laurent

2018-01-22

The preferential substitution of oxo ligands over alkyl ones of rare-earth complexes is commonly considered as "impossible" due to the high oxophilicity of metal centers. Now, it has been shown that simply assembling mixed methyl/oxo rare-earth complexes to a rigid trinuclear cluster framework cannot only enhance the activity of the Ln-oxo bond, but also protect the highly reactive Ln-alkyl bond, thus providing a previously unrecognized opportunity to selectively manipulate the oxo ligand in the presence of numerous reactive functionalities. Such trimetallic cluster has proved to be a suitable platform for developing the unprecedented non-redox rare-earth-mediated oxygen atom transfer from ketones to CS 2 and PhNCS. Controlled experiments and computational studies shed light on the driving force for these reactions, emphasizing the importance of the sterical accessibility and multimetallic effect of the cluster framework in promoting reversal of reactivity of rare-earth oxo complexes. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

SAM-based cell transfer to photopatterned hydrogels for microengineering vascular-like structures.

PubMed

Sadr, Nasser; Zhu, Mojun; Osaki, Tatsuya; Kakegawa, Takahiro; Yang, Yunzhi; Moretti, Matteo; Fukuda, Junji; Khademhosseini, Ali

2011-10-01

A major challenge in tissue engineering is to reproduce the native 3D microvascular architecture fundamental for in vivo functions. Current approaches still lack a network of perfusable vessels with native 3D structural organization. Here we present a new method combining self-assembled monolayer (SAM)-based cell transfer and gelatin methacrylate hydrogel photopatterning techniques for microengineering vascular structures. Human umbilical vein cell (HUVEC) transfer from oligopeptide SAM-coated surfaces to the hydrogel revealed two SAM desorption mechanisms: photoinduced and electrochemically triggered. The former, occurs concomitantly to hydrogel photocrosslinking, and resulted in efficient (>97%) monolayer transfer. The latter, prompted by additional potential application, preserved cell morphology and maintained high transfer efficiency of VE-cadherin positive monolayers over longer culture periods. This approach was also applied to transfer HUVECs to 3D geometrically defined vascular-like structures in hydrogels, which were then maintained in perfusion culture for 15 days. As a step toward more complex constructs, a cell-laden hydrogel layer was photopatterned around the endothelialized channel to mimic the vascular smooth muscle structure of distal arterioles. This study shows that the coupling of the SAM-based cell transfer and hydrogel photocrosslinking could potentially open up new avenues in engineering more complex, vascularized tissue constructs for regenerative medicine and tissue engineering applications. Copyright © 2011 Elsevier Ltd. All rights reserved.

Bio-Inspired In-Air Sonar Localization: What Artificial Pinnae do for Robotic Bats

NASA Astrophysics Data System (ADS)

Schillebeeckx, Filips

This dissertation investigates the hypothesis that binaural spectral cues, as generated by biomimetic microphone-baffle shapes in a suitable configuration, are both a sufficient and efficient means to realize real-time 3D localization capabilities for an in-air sonar system. We demonstrate 3D localization of real reflectors under realistic noise conditions, a task previously not performed successfully with a single binaural sonar measurement. The principal driving force behind this new approach is the use of two complex artificial pinna structures acting as complex direction-dependent spectral filters on the returning echoes. The technique makes use of broadband spectral cues in the received echoes only. Experiments with complex reflectors illustrate that the active head-related transfer function dominates the echo spectrum, allowing 3D localization in the presence of spectrum distortions caused by unknown reflector filtering. Also, experimental results in which multiple targets are localized simultaneously are presented. It is then investigated how binaural sonar system configuration choices affect 3D spectrum-based reflector localization. The proposed model demonstrates the limits of the spectral cue information provided by conventional transducers. Configurations composed of conventional receivers are evaluated as a function of unknown reflection strength and compared with a system with artificial pinnae receivers. Localization performance is quantified by an information theoretic performance criterion expressing the mutual information carried by a binaural spectrum on the corresponding 3D reflector location. Optimal configurations with conventional transducers are shown to be a function of echo reflection strength and the specific region of interest. The more complex spatial sensitivity patterns of organic pinna forms such as that of the Phyllostomus discolor bat species provide additional spectral cues that greatly improve localization information transfer compared to conventional transducers. Results indicate that the varying acoustic axis in the head-related transfer function of the pinna and even more so the higher peripheral sensitivity around the varying acoustic axis are the driving forces behind the artificial pinna's superior localization performance. Finally, it is shown that technical antennas that do not reproduce all the structural details seen in natural biosonar antennas can be suitable and robust design alternatives for in-air sonar systems intended for use on autonomous robots.

Horizontal transfer of whole mitochondria restores tumorigenic potential in mitochondrial DNA-deficient cancer cells

PubMed Central

Dong, Lan-Feng; Kovarova, Jaromira; Bajzikova, Martina; Bezawork-Geleta, Ayenachew; Svec, David; Endaya, Berwini; Sachaphibulkij, Karishma; Coelho, Ana R; Sebkova, Natasa; Ruzickova, Anna; Tan, An S; Kluckova, Katarina; Judasova, Kristyna; Zamecnikova, Katerina; Rychtarcikova, Zuzana; Gopalan, Vinod; Andera, Ladislav; Sobol, Margarita; Yan, Bing; Pattnaik, Bijay; Bhatraju, Naveen; Truksa, Jaroslav; Stopka, Pavel; Hozak, Pavel; Lam, Alfred K; Sedlacek, Radislav; Oliveira, Paulo J; Kubista, Mikael; Agrawal, Anurag; Dvorakova-Hortova, Katerina; Rohlena, Jakub; Berridge, Michael V; Neuzil, Jiri

2017-01-01

Recently, we showed that generation of tumours in syngeneic mice by cells devoid of mitochondrial (mt) DNA (ρ0 cells) is linked to the acquisition of the host mtDNA. However, the mechanism of mtDNA movement between cells remains unresolved. To determine whether the transfer of mtDNA involves whole mitochondria, we injected B16ρ0 mouse melanoma cells into syngeneic C57BL/6Nsu9-DsRed2 mice that express red fluorescent protein in their mitochondria. We document that mtDNA is acquired by transfer of whole mitochondria from the host animal, leading to normalisation of mitochondrial respiration. Additionally, knockdown of key mitochondrial complex I (NDUFV1) and complex II (SDHC) subunits by shRNA in B16ρ0 cells abolished or significantly retarded their ability to form tumours. Collectively, these results show that intact mitochondria with their mtDNA payload are transferred in the developing tumour, and provide functional evidence for an essential role of oxidative phosphorylation in cancer. DOI: http://dx.doi.org/10.7554/eLife.22187.001 PMID:28195532

Computational Confirmation of the Carrier for the ``XCN'' Interstellar Ice Band: OCN- Charge Transfer Complexes

NASA Astrophysics Data System (ADS)

Park, Jin-Young; Woon, David E.

2004-01-01

Recent experimental studies provide evidence that the carrier for the so-called XCN feature at 2165 cm-1 (4.62 μm) in young stellar objects is an OCN-/NH+4 charge transfer (CT) complex that forms in energetically processed interstellar icy grain mantles. Although other RCN nitriles and RNC isonitriles have been considered, Greenberg's conjecture that OCN- is associated with the XCN feature has persisted for over 15 years. In this work, we report a computational investigation that thoroughly confirms the hypothesis that the XCN feature observed in laboratory studies can result from OCN-/NH+4 CT complexes arising from HNCO and NH3 in a water ice environment. Density functional theory calculations with HNCO, NH3, and up to 12 waters reproduce seven spectroscopic measurements associated with XCN: the band origin of the asymmetric stretching mode of OCN-, shifts due to isotopic substitutions of C, N, O, and H, and two weak features. However, very similar values are also found for the OCN-/NH+4 CT complex arising from HOCN and NH3. In both cases, the complex forms by barrierless proton transfer from HNCO or HOCN to NH3 during the optimization of the solvated system. Scaled B3LYP/6-31+G** harmonic frequencies for the HNCO and HOCN cases are 2181 and 2202 cm-1, respectively.

Computational Confirmation of the Carrier for the "XCN" Interstellar Ice Bank: OCN(-) Charge Transfer Complexes

NASA Technical Reports Server (NTRS)

Park, J.-Y.; Woon, D. E.

2004-01-01

Recent experimental studies provide evidence that carrier for the so-called XCN feature at 2165 cm(exp -1) (4.62 micron) in young stellar objects is an OCN(-)/NH4(+) charge transfer (CT) complex that forms in energetically processed interstellar icy grain mantles. Although other RCN nitriles and RCN iosonitriles have been considered, Greenberg's conjecture that OCN(-) is associated with the XCN feature has persisted for over 15 years. In this work we report a computational investigation that thoroughly confirms the hypothesis that the XCN feature observed in laboratory studies can result from OCN(-)/NH4(+) CT complexes arising from HNCO and NH3, in a water ice environment. Density functional theory calculations with theory calculations with HNCO, NH3, and up to 12 waters reproduce seven spectroscopic measurements associated with XCN: the band origin of the asymmetric stretching mode of OCN(-), shifts due to isotopic substitutions of C, N, O, and H, and two weak features. However, very similar values are also found for the OCN(-)/NH4(+) CT complex arising from HOCN and NH3. In both cases, the complex forms by barrierless proton transfer from HNCO or HOCN to NH3 during the optimization of the solvated system. Scaled B3LYP/6-31+G** harmonic frequencies for HNCO and HOCN cases are 2181 and 2202 cm(exp -1), respectively.

Coherent transport and energy flow patterns in photosynthesis under incoherent excitation.

PubMed

Pelzer, Kenley M; Can, Tankut; Gray, Stephen K; Morr, Dirk K; Engel, Gregory S

2014-03-13

Long-lived coherences have been observed in photosynthetic complexes after laser excitation, inspiring new theories regarding the extreme quantum efficiency of photosynthetic energy transfer. Whether coherent (ballistic) transport occurs in nature and whether it improves photosynthetic efficiency remain topics of debate. Here, we use a nonequilibrium Green's function analysis to model exciton transport after excitation from an incoherent source (as opposed to coherent laser excitation). We find that even with an incoherent source, the rate of environmental dephasing strongly affects exciton transport efficiency, suggesting that the relationship between dephasing and efficiency is not an artifact of coherent excitation. The Green's function analysis provides a clear view of both the pattern of excitonic fluxes among chromophores and the multidirectionality of energy transfer that is a feature of coherent transport. We see that even in the presence of an incoherent source, transport occurs by qualitatively different mechanisms as dephasing increases. Our approach can be generalized to complex synthetic systems and may provide a new tool for optimizing synthetic light harvesting materials.

Quantifying cadherin mechanotransduction machinery assembly/disassembly dynamics using fluorescence covariance analysis.

PubMed

Vedula, Pavan; Cruz, Lissette A; Gutierrez, Natasha; Davis, Justin; Ayee, Brian; Abramczyk, Rachel; Rodriguez, Alexis J

2016-06-30

Quantifying multi-molecular complex assembly in specific cytoplasmic compartments is crucial to understand how cells use assembly/disassembly of these complexes to control function. Currently, biophysical methods like Fluorescence Resonance Energy Transfer and Fluorescence Correlation Spectroscopy provide quantitative measurements of direct protein-protein interactions, while traditional biochemical approaches such as sub-cellular fractionation and immunoprecipitation remain the main approaches used to study multi-protein complex assembly/disassembly dynamics. In this article, we validate and quantify multi-protein adherens junction complex assembly in situ using light microscopy and Fluorescence Covariance Analysis. Utilizing specific fluorescently-labeled protein pairs, we quantified various stages of adherens junction complex assembly, the multiprotein complex regulating epithelial tissue structure and function following de novo cell-cell contact. We demonstrate: minimal cadherin-catenin complex assembly in the perinuclear cytoplasm and subsequent localization to the cell-cell contact zone, assembly of adherens junction complexes, acto-myosin tension-mediated anchoring, and adherens junction maturation following de novo cell-cell contact. Finally applying Fluorescence Covariance Analysis in live cells expressing fluorescently tagged adherens junction complex proteins, we also quantified adherens junction complex assembly dynamics during epithelial monolayer formation.

Carbohydrase Systems of Saccharophagus degradans Degrading Marine Complex Polysaccharides

PubMed Central

Hutcheson, Steven W.; Zhang, Haitao; Suvorov, Maxim

2011-01-01

Saccharophagus degradans 2–40 is a γ-subgroup proteobacterium capable of using many of the complex polysaccharides found in the marine environment for growth. To utilize these complex polysaccharides, this bacterium produces a plethora of carbohydrases dedicated to the processing of a carbohydrate class. Aiding in the identification of the contributing genes and enzymes is the known genome sequence for this bacterium. This review catalogs the genes and enzymes of the S. degradans genome that are likely to function in the systems for the utilization of agar, alginate, α- and β-glucans, chitin, mannans, pectins, and xylans and discusses the cell biology and genetics of each system as it functions to transfer carbon back to the bacterium. PMID:21731555

[Results of revision after failed surgical treatment for traumatic anterior shoulder instability].

PubMed

Lópiz-Morales, Y; Alcobe-Bonilla, J; García-Fernández, C; Francés-Borrego, A; Otero-Fernández, R; Marco-Martínez, F

2013-01-01

Persistent or recurrent glenohumeral instability after a previous operative stabilization can be a complex problem. Our aim is to establish the incidence of recurrence and its revision surgery, and to analyse the functional results of the revision instability surgery, as well as to determine surgical protocols to perform it. A retrospective analysis was conducted on 16 patients with recurrent instability out of 164 patients operated on between 1999 and 2011. The mean follow-up was 57 months and the mean age was 29 years. To evaluate functional outcome we employed Constant, Rowe, UCLA scores and the visual analogue scale. Of the 12 patients who failed the initial arthroscopic surgery, 6 patients underwent an arthroscopic antero-inferior labrum repair technique, 4 using open labrum repair techniques, and 2 coracoid transfer. The two cases of open surgery with recurrences underwent surgery for coracoid transfer. Results of the Constant score were excellent or good in 64% of patients. Surgical revision of instability is a complex surgery essentially for two reasons: the difficulty in recognising the problem, and the technical demand (greater variety and the increasingly complex techniques). Copyright © 2012 SECOT. Published by Elsevier Espana. All rights reserved.

Competitive Energy and Electron Transfer in β-Functionalized Free-Base Porphyrin-Zinc Porphyrin Dimer Axially Coordinated to C60 : Synthesis, Supramolecular Formation and Excited-State Processes.

PubMed

Hu, Yi; Thomas, Michael B; Jinadasa, R G Waruna; Wang, Hong; D'Souza, Francis

2017-09-18

Simultaneous occurrence of energy and electron transfer events involving different acceptor sites in a newly assembled supramolecular triad comprised of covalently linked free-base porphyrin-zinc porphyrin dyad, H 2 P-ZnP axially coordinated to electron acceptor fullerene, has been successfully demonstrated. The dyad was connected through the β-pyrrole positions of the porphyrin macrocycle instead of the traditionally used meso-positions for better electronic communication. Interestingly, the β-pyrrole functionalization modulated the optical properties to such an extent that it was possible to almost exclusively excite the zinc porphyrin entity in the supramolecular triad. The measured binding constant for the complex with 1:1 molecular stoichiometry was in the order of 10 4  m -1 revealing moderately stable complex formation. An energy level diagram constructed using optical, electrochemical and computational results suggested that both the anticipated energy and electron events are thermodynamically feasible in the triad. Consequently, it was possible to demonstrate occurrence of excited state energy transfer to the covalently linked H 2 P, and electron transfer to the coordinated ImC 60 from studies involving steady-state and time-resolved emission, and femto- and nanosecond transient absorption studies. The estimated energy transfer was around 67 % in the dyad with a rate constant of 1.1×10 9  s -1 . In the supramolecular triad, the charge separated state was rather long-lived although it was difficult to arrive the exact lifetime of charge separated state from nanosecond transient spectral studies due to overlap of strong triplet excited signals of porphyrin in the monitoring wavelength window. Nevertheless, simultaneous occurrence of energy and electron transfer in the appropriately positioned energy and electron acceptor entities in a supramolecular triad was possible to demonstrate in the present study, a step forward to unraveling the complex photochemical events occurring in natural photosynthesis and its implications in building light energy harvesting devices. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Time-resolved and steady-state fluorescence studies of excited-state proton-transfer reactions of proflavine

NASA Astrophysics Data System (ADS)

De Silvestri, S.; Laporta, P.

1984-01-01

Time-resolved and steady-state fluorescence studies of proflavine in aqueous solution are presented. The observation of a monoexponential fluorescence decay with a time constant decreasing with increasing pH and the presence of an anomalous red-shift in the fluorescence spectrum as a function of pH indicate the existence of a complex proton-transfer mechanism in the excited state. A reaction scheme is proposed and the corresponding proton-transfer rates are evaluated. An excited-state pK value of 12.85 is obtained for the equilibrium between the cationic form of proflavine and the same form dissociated at an amino group.

Reconstruction of a Three-Dimensional Transonic Rotor Flow Field from Holographical Interferogram Data.

DTIC Science & Technology

1985-03-01

interferometry and computer- R - spanwise coordinate, ft assisted tomography ( CAT ) are used to determine the transonic velocity field of a model rotor...and extracting fringe-order functions, the c data are transferred to a CAT code.- The CAT code Ui transmitted wave complex amplitude then calculates...the perturbation velocity in sev- eral planes above the blade surface. The values Ur reference wave complex amplitude from the holography- CAT method

Toward simulating complex systems with quantum effects

NASA Astrophysics Data System (ADS)

Kenion-Hanrath, Rachel Lynn

Quantum effects like tunneling, coherence, and zero point energy often play a significant role in phenomena on the scales of atoms and molecules. However, the exact quantum treatment of a system scales exponentially with dimensionality, making it impractical for characterizing reaction rates and mechanisms in complex systems. An ongoing effort in the field of theoretical chemistry and physics is extending scalable, classical trajectory-based simulation methods capable of capturing quantum effects to describe dynamic processes in many-body systems; in the work presented here we explore two such techniques. First, we detail an explicit electron, path integral (PI)-based simulation protocol for predicting the rate of electron transfer in condensed-phase transition metal complex systems. Using a PI representation of the transferring electron and a classical representation of the transition metal complex and solvent atoms, we compute the outer sphere free energy barrier and dynamical recrossing factor of the electron transfer rate while accounting for quantum tunneling and zero point energy effects. We are able to achieve this employing only a single set of force field parameters to describe the system rather than parameterizing along the reaction coordinate. Following our success in describing a simple model system, we discuss our next steps in extending our protocol to technologically relevant materials systems. The latter half focuses on the Mixed Quantum-Classical Initial Value Representation (MQC-IVR) of real-time correlation functions, a semiclassical method which has demonstrated its ability to "tune'' between quantum- and classical-limit correlation functions while maintaining dynamic consistency. Specifically, this is achieved through a parameter that determines the quantumness of individual degrees of freedom. Here, we derive a semiclassical correction term for the MQC-IVR to systematically characterize the error introduced by different choices of simulation parameters, and demonstrate the ability of this approach to optimize MQC-IVR simulations.

How Phosphotransferase System-Related Protein Phosphorylation Regulates Carbohydrate Metabolism in Bacteria†

PubMed Central

Deutscher, Josef; Francke, Christof; Postma, Pieter W.

2006-01-01

The phosphoenolpyruvate(PEP):carbohydrate phosphotransferase system (PTS) is found only in bacteria, where it catalyzes the transport and phosphorylation of numerous monosaccharides, disaccharides, amino sugars, polyols, and other sugar derivatives. To carry out its catalytic function in sugar transport and phosphorylation, the PTS uses PEP as an energy source and phosphoryl donor. The phosphoryl group of PEP is usually transferred via four distinct proteins (domains) to the transported sugar bound to the respective membrane component(s) (EIIC and EIID) of the PTS. The organization of the PTS as a four-step phosphoryl transfer system, in which all P derivatives exhibit similar energy (phosphorylation occurs at histidyl or cysteyl residues), is surprising, as a single protein (or domain) coupling energy transfer and sugar phosphorylation would be sufficient for PTS function. A possible explanation for the complexity of the PTS was provided by the discovery that the PTS also carries out numerous regulatory functions. Depending on their phosphorylation state, the four proteins (domains) forming the PTS phosphorylation cascade (EI, HPr, EIIA, and EIIB) can phosphorylate or interact with numerous non-PTS proteins and thereby regulate their activity. In addition, in certain bacteria, one of the PTS components (HPr) is phosphorylated by ATP at a seryl residue, which increases the complexity of PTS-mediated regulation. In this review, we try to summarize the known protein phosphorylation-related regulatory functions of the PTS. As we shall see, the PTS regulation network not only controls carbohydrate uptake and metabolism but also interferes with the utilization of nitrogen and phosphorus and the virulence of certain pathogens. PMID:17158705

Laser induced forward transfer of SnO2 for sensing applications using different precursors systems

NASA Astrophysics Data System (ADS)

Mattle, Thomas; Hintennach, Andreas; Lippert, Thomas; Wokaun, Alexander

2013-02-01

This paper presents the transfer of SnO2 by laser induced forward transfer (LIFT) for gas sensor applications. Different donor substrates of SnO2 with and without triazene polymer (TP) as a dynamic release layer were prepared. Transferring these films under different conditions were evaluated by optical microscopy and functionality. Transfers of sputtered SnO2 films do not lead to satisfactory results and transfers of SnO2 nanoparticles are difficult. Transfers of SnO2 nanoparticles can only be achieved when applying a second laser pulse to the already transferred material, which improves the adhesion resulting in a complete pixel. A new approach of decomposing the transfer material during LIFT transfer was developed. Donor films based on UV absorbing metal complex precursors namely, SnCl2(acac)2 were prepared and transferred using the LIFT technique. Transfer conditions were optimized for the different systems, which were deposited onto sensor-like microstructures. The conductivity of the transferred material at temperatures of about 400 ∘C are in a range usable for SnO2 gas sensors. First sensing tests were carried out and the transferred material proved to change conductivity when exposed to ethanol, acetone, and methane.

NEW MODEL AND MEASUREMENT PRINCIPLE OF FLOWING AND HEAT TRANSFER CHARACTERISTICS OF REGENERATOR

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

Chen, Y. Y.; Graduate University of the Chinese Academy of Sciences, Beijing, 100049; Luo, E. C.

2008-03-16

Regenerators play key role in oscillating-flow cryocoolers or thermoacoustic heat engine systems. However, their flowing and heat transfer mechanism is still not well understood. The complexities of the oscillating flow regenerator make traditional method of heat transfer research become difficult or helpless. In this paper, a model for porous media regenerator was given based on the linear thermoacoustic theory. Then the correlations for characteristic parameters were obtained by deducing universal expressions for thermoacoustic viscous function F{sub v} and thermal function F{sub T}. A simple acoustical method and experimental system to get F{sub v} and F{sub T} via measurements of isothermalmore » regenerators were presented. Some measurements of packed stainless screen regenerators were performed, and preliminary experimental results for flow and convective coefficients were derived, which showing flowing friction factor is approximately within 132/Re to 173/Re.« less

High-Tc Superconducting Bolometer Noise Measurement Using Low Noise Transformers - Theory and Optimization

NASA Technical Reports Server (NTRS)

Aslam, Shahid; Jones, Hollis H.

2011-01-01

Care must always be taken when performing noise measurements on high-Tc superconducting materials to ensure that the results are not from the measurement system itself. One situation likely to occur is with low noise transformers. One of the least understood devices, it provides voltage gain for low impedance inputs (< 100 ), e.g., YBaCuO and GdBaCuO thin films, with comparatively lower noise levels than other devices for instance field effect and bipolar junction transistors. An essential point made in this paper is that because of the complex relationships between the transformer ports, input impedance variance alters the transformer s transfer function in particular, the low frequency cutoff shift. The transfer of external and intrinsic transformer noise to the output along with optimization and precautions are treated; all the while, we will cohesively connect the transfer function shift, the load impedance, and the actual noise at the transformer output.

Properties of electronically excited states of four squaraine dyes and their complexes with fullerene C70: A theoretical investigation

NASA Astrophysics Data System (ADS)

Zhang, Jian; Li, Tingyu

2017-09-01

Solar cells sensitized by polypyridyl Ru(II) complexes exhibit relatively high efficiency, however those photo-sensitizers did not absorb the photons in the far-red and near-infrared region. At present, squaraine dyes have received considerable attention as their attractively intrinsic red light absorption and unusual high molar extinction coefficient. Here we applied density functional theory and time dependent density functional theory to investigate the properties of electronically excited states of four squaraine dyes and their complexes with fullerene C70. The influences of different functionals, basis sets and solvent effects are evaluated. To understand the photophysical properties, the investigations are basing on a classification method which splits the squaraine dyes and their complexes with fullerene C70 into two units to characterize the intramolecular density distribution. We present the signatures of their electronically excited states which are characterized as local excitation or charge-transfer excitation. The relationship between open-circuit voltage and the number of intramolecular hydrogen bonds in squaraine dyes are discussed.

Health worker posting and transfer at primary level in Tamil Nadu: Governance of a complex health system function

PubMed Central

Garimella, Surekha; Sheikh, Kabir

2016-01-01

Background: Posting and transfer (PT) of health personnel – placing the right health workers in the right place at the right time – is a core function of any large-scale health service. In the context of government health services, this may be seen as a simple process of bureaucratic governance and implementation of the rule of law. However the literature from India and comparable low and middle-income country health systems suggests that in reality PT is a contested domain, driven by varied expressions of private and public interest throughout the chain of implementation. Objective: To investigate policymaking for PT in the government health sector and implementation of policies as experienced by different health system actors and stakeholders at primary health care level. Methodology: We undertook an empirical case study of a PT reform policy at primary health care level in Tamil Nadu State, to understand how different groups of health systems actors experience PT. In-depth qualitative methods were undertaken to study processes of implementation of PT policies enacted through ‘counselling’ of health workers (individualized consultations to determine postings and transfers). Results: PT emerges as a complex phenomenon, shaped partially by the laws of the state and partially as a parallel system of norms and incentives requiring consideration and coordination of the interests of different groups. Micro-practices of governance represent homegrown coping mechanisms of health administrators that reconcile public and private interests and sustain basic health system functions. Beyond a functional perspective of PT, it also reflects justice and fairness as it plays out in the health system. It signifies how well a system treats its employees, and by inference, is an index of the overall health of the system. Conclusions: For a complex governance function such as PT, the roles of private actors and private interests are not easily separable from the public, but rather are intertwined within the complexities of delivery of a public service. This complexity blurs conventional boundaries of private and public ownership and behaviour, and raises critical questions for the interpretation of coordinated governance. Hence, the imperative of enforcing rules may need to be complemented with bottom-up policy approaches, including treating PT not merely as system dysfunction, but also as a potential instrument of governance innovations, procedural justice and the accountability of health services to communities they seek to serve. PMID:28217602

High Throughput Engineering to Revitalize a Vestigial Electron Transfer Pathway in Bacterial Photosynthetic Reaction Centers*

PubMed Central

Faries, Kaitlyn M.; Kressel, Lucas L.; Wander, Marc J.; Holten, Dewey; Laible, Philip D.; Kirmaier, Christine; Hanson, Deborah K.

2012-01-01

Photosynthetic reaction centers convert light energy into chemical energy in a series of transmembrane electron transfer reactions, each with near 100% yield. The structures of reaction centers reveal two symmetry-related branches of cofactors (denoted A and B) that are functionally asymmetric; purple bacterial reaction centers use the A pathway exclusively. Previously, site-specific mutagenesis has yielded reaction centers capable of transmembrane charge separation solely via the B branch cofactors, but the best overall electron transfer yields are still low. In an attempt to better realize the architectural and energetic factors that underlie the directionality and yields of electron transfer, sites within the protein-cofactor complex were targeted in a directed molecular evolution strategy that implements streamlined mutagenesis and high throughput spectroscopic screening. The polycistronic approach enables efficient construction and expression of a large number of variants of a heteroligomeric complex that has two intimately regulated subunits with high sequence similarity, common features of many prokaryotic and eukaryotic transmembrane protein assemblies. The strategy has succeeded in the discovery of several mutant reaction centers with increased efficiency of the B pathway; they carry multiple substitutions that have not been explored or linked using traditional approaches. This work expands our understanding of the structure-function relationships that dictate the efficiency of biological energy-conversion reactions, concepts that will aid the design of bio-inspired assemblies capable of both efficient charge separation and charge stabilization. PMID:22247556

Electron transfer and conformational change in complexes of trimethylamine dehydrogenase and electron transferring flavoprotein.

PubMed

Jones, Matthew; Talfournier, Francois; Bobrov, Anton; Grossmann, J Günter; Vekshin, Nikolai; Sutcliffe, Michael J; Scrutton, Nigel S

2002-03-08

The trimethylamine dehydrogenase-electron transferring flavoprotein (TMADH.ETF) electron transfer complex has been studied by fluorescence and absorption spectroscopies. These studies indicate that a series of conformational changes occur during the assembly of the TMADH.ETF electron transfer complex and that the kinetics of assembly observed with mutant TMADH (Y442F/L/G) or ETF (alpha R237A) complexes are much slower than are the corresponding rates of electron transfer in these complexes. This suggests that electron transfer does not occur in the thermodynamically most favorable state (which takes too long to form), but that one or more metastable states (which are formed more rapidly) are competent in transferring electrons from TMADH to ETF. Additionally, fluorescence spectroscopy studies of the TMADH.ETF complex indicate that ETF undergoes a stable conformational change (termed structural imprinting) when it interacts transiently with TMADH to form a second, distinct, structural form. The mutant complexes compromise imprinting of ETF, indicating a dependence on the native interactions present in the wild-type complex. The imprinted form of semiquinone ETF exhibits an enhanced rate of electron transfer to the artificial electron acceptor, ferricenium. Overall molecular conformations as probed by small-angle x-ray scattering studies are indistinguishable for imprinted and non-imprinted ETF, suggesting that changes in structure likely involve confined reorganizations within the vicinity of the FAD. Our results indicate a series of conformational events occur during the assembly of the TMADH.ETF electron transfer complex, and that the properties of electron transfer proteins can be affected lastingly by transient interaction with their physiological redox partners. This may have significant implications for our understanding of biological electron transfer reactions in vivo, because ETF encounters TMADH at all times in the cell. Our studies suggest that caution needs to be exercised in extrapolating the properties of in vitro interprotein electron transfer reactions to those occurring in vivo.

Interactive Acoustic Simulation in Urban and Complex Environments

DTIC Science & Technology

2015-03-21

and validity of the solution given by the two methods. Transfer functions are used to model two-way couplings to allow multiple orders of acoustic...Function ( BRDF )[79, 137]. The ray models have also been applied to inhomogeneous outdoor media by numerical integration of the differential ray...surface, the interaction can be modeled by specular reflection, Snell’s law refraction, or BRDF -based reflection, depending on the surface properties

Solving the inverse scattering problem in reflection-mode dynamic speckle-field phase microscopy (Conference Presentation)

NASA Astrophysics Data System (ADS)

Zhou, Renjie; So, Peter T. C.; Yaqoob, Zahid; Jin, Di; Hosseini, Poorya; Kuang, Cuifang; Singh, Vijay Raj; Kim, Yang-Hyo; Dasari, Ramachandra R.

2017-02-01

Most of the quantitative phase microscopy systems are unable to provide depth-resolved information for measuring complex biological structures. Optical diffraction tomography provides a non-trivial solution to it by 3D reconstructing the object with multiple measurements through different ways of realization. Previously, our lab developed a reflection-mode dynamic speckle-field phase microscopy (DSPM) technique, which can be used to perform depth resolved measurements in a single shot. Thus, this system is suitable for measuring dynamics in a layer of interest in the sample. DSPM can be also used for tomographic imaging, which promises to solve the long-existing "missing cone" problem in 3D imaging. However, the 3D imaging theory for this type of system has not been developed in the literature. Recently, we have developed an inverse scattering model to rigorously describe the imaging physics in DSPM. Our model is based on the diffraction tomography theory and the speckle statistics. Using our model, we first precisely calculated the defocus response and the depth resolution in our system. Then, we further calculated the 3D coherence transfer function to link the 3D object structural information with the axially scanned imaging data. From this transfer function, we found that in the reflection mode excellent sectioning effect exists in the low lateral spatial frequency region, thus allowing us to solve the "missing cone" problem. Currently, we are working on using this coherence transfer function to reconstruct layered structures and complex cells.

Next Generation Tissue Engineering of Orthopedic Soft Tissue-to-Bone Interfaces.

PubMed

Boys, Alexander J; McCorry, Mary Clare; Rodeo, Scott; Bonassar, Lawrence J; Estroff, Lara A

2017-09-01

Soft tissue-to-bone interfaces are complex structures that consist of gradients of extracellular matrix materials, cell phenotypes, and biochemical signals. These interfaces, called entheses for ligaments, tendons, and the meniscus, are crucial to joint function, transferring mechanical loads and stabilizing orthopedic joints. When injuries occur to connected soft tissue, the enthesis must be re-established to restore function, but due to structural complexity, repair has proven challenging. Tissue engineering offers a promising solution for regenerating these tissues. This prospective review discusses methodologies for tissue engineering the enthesis, outlined in three key design inputs: materials processing methods, cellular contributions, and biochemical factors.

Next Generation Tissue Engineering of Orthopedic Soft Tissue-to-Bone Interfaces

PubMed Central

Boys, Alexander J.; McCorry, Mary Clare; Rodeo, Scott; Bonassar, Lawrence J.; Estroff, Lara A.

2017-01-01

Soft tissue-to-bone interfaces are complex structures that consist of gradients of extracellular matrix materials, cell phenotypes, and biochemical signals. These interfaces, called entheses for ligaments, tendons, and the meniscus, are crucial to joint function, transferring mechanical loads and stabilizing orthopedic joints. When injuries occur to connected soft tissue, the enthesis must be re-established to restore function, but due to structural complexity, repair has proven challenging. Tissue engineering offers a promising solution for regenerating these tissues. This prospective review discusses methodologies for tissue engineering the enthesis, outlined in three key design inputs: materials processing methods, cellular contributions, and biochemical factors. PMID:29333332

A bioinspired redox relay that mimics radical interactions of the Tyr-His pairs of photosystem II

NASA Astrophysics Data System (ADS)

Megiatto, Jackson D., Jr.; Méndez-Hernández, Dalvin D.; Tejeda-Ferrari, Marely E.; Teillout, Anne-Lucie; Llansola-Portolés, Manuel J.; Kodis, Gerdenis; Poluektov, Oleg G.; Rajh, Tijana; Mujica, Vladimiro; Groy, Thomas L.; Gust, Devens; Moore, Thomas A.; Moore, Ana L.

2014-05-01

In water-oxidizing photosynthetic organisms, light absorption generates a powerfully oxidizing chlorophyll complex (P680•+) in the photosystem II reaction centre. This is reduced via an electron transfer pathway from the manganese-containing water-oxidizing catalyst, which includes an electron transfer relay comprising a tyrosine (Tyr)-histidine (His) pair that features a hydrogen bond between a phenol group and an imidazole group. By rapidly reducing P680•+, the relay is thought to mitigate recombination reactions, thereby ensuring a high quantum yield of water oxidation. Here, we show that an artificial reaction centre that features a benzimidazole-phenol model of the Tyr-His pair mimics both the short-internal hydrogen bond in photosystem II and, using electron paramagnetic resonance spectroscopy, the thermal relaxation that accompanies proton-coupled electron transfer. Although this artificial system is much less complex than the natural one, theory suggests that it captures the essential features that are important in the function of the relay.

Coherence and population dynamics of chlorophyll excitations in FCP complex: Two-dimensional spectroscopy study

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

Butkus, Vytautas; Gelzinis, Andrius; Valkunas, Leonas

2015-06-07

Energy transfer processes and coherent phenomena in the fucoxanthin–chlorophyll protein complex, which is responsible for the light harvesting function in marine algae diatoms, were investigated at 77 K by using two-dimensional electronic spectroscopy. Experiments performed on femtosecond and picosecond timescales led to separation of spectral dynamics, witnessing evolutions of coherence and population states of the system in the spectral region of Q{sub y} transitions of chlorophylls a and c. Analysis of the coherence dynamics allowed us to identify chlorophyll (Chl) a and fucoxanthin intramolecular vibrations dominating over the first few picoseconds. Closer inspection of the spectral region of the Q{submore » y} transition of Chl c revealed previously not identified, mutually non-interacting chlorophyll c states participating in femtosecond or picosecond energy transfer to the Chl a molecules. Consideration of separated coherent and incoherent dynamics allowed us to hypothesize the vibrations-assisted coherent energy transfer between Chl c and Chl a and the overall spatial arrangement of chlorophyll molecules.« less

Tandem catalysis of ring-closing metathesis/atom transfer radical reactions with homobimetallic ruthenium–arene complexes

PubMed Central

Borguet, Yannick; Sauvage, Xavier; Zaragoza, Guillermo; Demonceau, Albert

2010-01-01

Summary The tandem catalysis of ring-closing metathesis/atom transfer radical reactions was investigated with the homobimetallic ruthenium–indenylidene complex [(p-cymene)Ru(μ-Cl)3RuCl(3-phenyl-1-indenylidene)(PCy3)] (1) to generate active species in situ. The two catalytic processes were first carried out independently in a case study before the whole sequence was optimized and applied to the synthesis of several polyhalogenated bicyclic γ-lactams and lactones from α,ω-diene substrates bearing trihaloacetamide or trichloroacetate functionalities. The individual steps were carefully monitored by 1H and 31P NMR spectroscopies in order to understand the intimate details of the catalytic cycles. Polyhalogenated substrates and the ethylene released upon metathesis induced the clean transformation of catalyst precursor 1 into the Ru(II)–Ru(III) mixed-valence compound [(p-cymene)Ru(μ-Cl)3RuCl2(PCy3)], which was found to be an efficient promoter for atom transfer radical reactions under the adopted experimental conditions. PMID:21160564

Diffusion or advection? Mass transfer and complex boundary layer landscapes of the brown alga Fucus vesiculosus.

PubMed

Lichtenberg, Mads; Nørregaard, Rasmus Dyrmose; Kühl, Michael

2017-03-01

The role of hyaline hairs on the thallus of brown algae in the genus Fucus is long debated and several functions have been proposed. We used a novel motorized set-up for two-dimensional and three-dimensional mapping with O 2 microsensors to investigate the spatial heterogeneity of the diffusive boundary layer (DBL) and O 2 flux around single and multiple tufts of hyaline hairs on the thallus of Fucus vesiculosus. Flow was a major determinant of DBL thickness, where higher flow decreased DBL thickness and increased O 2 flux between the algal thallus and the surrounding seawater. However, the topography of the DBL varied and did not directly follow the contour of the underlying thallus. Areas around single tufts of hyaline hairs exhibited a more complex mass-transfer boundary layer, showing both increased and decreased thickness when compared with areas over smooth thallus surfaces. Over thallus areas with several hyaline hair tufts, the overall effect was an apparent increase in the boundary layer thickness. We also found indications for advective O 2 transport driven by pressure gradients or vortex shedding downstream from dense tufts of hyaline hairs that could alleviate local mass-transfer resistances. Mass-transfer dynamics around hyaline hair tufts are thus more complex than hitherto assumed and may have important implications for algal physiology and plant-microbe interactions. © 2017 The Author(s).

Diffusion or advection? Mass transfer and complex boundary layer landscapes of the brown alga Fucus vesiculosus

PubMed Central

Nørregaard, Rasmus Dyrmose

2017-01-01

The role of hyaline hairs on the thallus of brown algae in the genus Fucus is long debated and several functions have been proposed. We used a novel motorized set-up for two-dimensional and three-dimensional mapping with O2 microsensors to investigate the spatial heterogeneity of the diffusive boundary layer (DBL) and O2 flux around single and multiple tufts of hyaline hairs on the thallus of Fucus vesiculosus. Flow was a major determinant of DBL thickness, where higher flow decreased DBL thickness and increased O2 flux between the algal thallus and the surrounding seawater. However, the topography of the DBL varied and did not directly follow the contour of the underlying thallus. Areas around single tufts of hyaline hairs exhibited a more complex mass-transfer boundary layer, showing both increased and decreased thickness when compared with areas over smooth thallus surfaces. Over thallus areas with several hyaline hair tufts, the overall effect was an apparent increase in the boundary layer thickness. We also found indications for advective O2 transport driven by pressure gradients or vortex shedding downstream from dense tufts of hyaline hairs that could alleviate local mass-transfer resistances. Mass-transfer dynamics around hyaline hair tufts are thus more complex than hitherto assumed and may have important implications for algal physiology and plant–microbe interactions. PMID:28330986

An oxadiazole-functionalized ligand and its yellow-emitting Re(I) complex for organoelectronic application

NASA Astrophysics Data System (ADS)

Hu, Ge; Guo, Lei; Wei, Sheng; Zhang, Shuang

2012-06-01

A Re(I) complex of Re(CO)3(PTO)Br with 2-(pyridin-2-yl)-5-p-tolyl-1,3,4-oxadiazole (PTO) as the diamine ligand is synthesized, resulting in a phosphorescent emitter which contains oxadiazole functional moiety. Single crystal analysis confirms that oxadiazole moiety of PTO ligand participates in the coordination with Re center. Coordination ability difference between N atom from pyridine ring and that from oxadiazole moiety is found. Density functional theory calculation on the crystal suggests that the onset electronic transition owns a mixed character of metal-to-ligand-charge-transfer and ligand-to-ligand-charge-transfer. Upon photon excitation, Re(CO)3(PTO)Br exhibits a yellow emission peaking at 549 nm with a short excited state lifetime of 0.15 μs. Further measurements suggest that Re(CO)3(PTO)Br owns HOMO and LUMO energy levels of -5.79 V and -3.49 V and a high decomposition temperature of 322 °C. The optimal electroluminescence device using Re(CO)3(PTO)Br as the emitting dopant shows an orange light of 598 nm, with a maximum luminance of 4600 cd/m2 and a maximum current efficiency of 11.5 cd/A.

Self-assembled diatom substrates with plasmonic functionality

NASA Astrophysics Data System (ADS)

Kwon, Sun Yong; Park, Sehyun; Nichols, William T.

2014-04-01

Marine diatoms have an exquisitely complex exoskeleton that is promising for engineered surfaces such as sensors and catalysts. For such applications, creating uniform arrays of diatom frustules across centimeter scales will be necessary. Here, we present a simple, low-cost floating interface technique to self-assemble the diatom frustules. We show that well-prepared diatoms form floating hexagonal close-packed arrays at the air-water interface that can be transferred directly to a substrate. We functionalize the assembled diatom surfaces with gold and characterize the plasmonic functionality by using surface enhanced Raman scattering (SERS). Thin gold films conform to the complex, hierarchical diatom structure and produce a SERS enhancement factor of 2 × 104. Small gold nanoparticles attached to the diatom's surface produce a higher enhancement of 7 × 104 due to stronger localization of the surface plasmons. Taken together, the large-scale assembly and plasmonic functionalization represent a promising platform to control the energy and the material flows at a complex surface for applications such as sensors and plasmonic enhanced catalysts.

A Review of the Literature on Training Simulators: Translators: Transfer of Training and Simulator Fidelity.

DTIC Science & Technology

1984-04-01

Noise is distracting especially in complex tasks that require close attention and concentration (Finkelman 1975). Improper lighting (Tinker 1943...before coping with . the entire systemi. However, the functional fidelity may be affected due to the isolation of a £ articular subsystem. Curry (1981

Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes

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

Spero, Melanie A.; Brickner, Joshua R.; Mollet, Jordan T.

NADH:quinone oxidoreductase (complex I) is a bioenergetic enzyme that transfers electrons from NADH to quinone, conserving the energy of this reaction by contributing to the proton motive force. While the importance of NADH oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex I to bacterial electron transport chains has been tested in only a few species. Here, we analyze the function of two phylogenetically distinct complex I isozymes in Rhodobacter sphaeroides, an alphaproteobacterium that contains well-characterized electron transport chains. We found that R. sphaeroides complex I activity is important for aerobic respiration and required for anaerobic dimethylmore » sulfoxide (DMSO) respiration (in the absence of light), photoautotrophic growth, and photoheterotrophic growth (in the absence of an external electron acceptor). Our data also provide insight into the functions of the phylogenetically distinct R. sphaeroides complex I enzymes (complex I A and complex I E) in maintaining a cellular redox state during photoheterotrophic growth. We propose that the function of each isozyme during photoheterotrophic growth is either NADH synthesis (complex I A) or NADH oxidation (complex I E). The canonical alphaproteobacterial complex I isozyme (complex I A) was also shown to be important for routing electrons to nitrogenase-mediated H 2 production, while the horizontally acquired enzyme (complex I E) was dispensable in this process. Unlike the singular role of complex I in mitochondria, we predict that the phylogenetically distinct complex I enzymes found across bacterial species have evolved to enhance the functions of their respective electron transport chains. Cells use a proton motive force (PMF), NADH, and ATP to support numerous processes. In mitochondria, complex I uses NADH oxidation to generate a PMF, which can drive ATP synthesis. This study analyzed the function of complex I in bacteria, which contain more-diverse and more-flexible electron transport chains than mitochondria. We tested complex I function in Rhodobacter sphaeroides, a bacterium predicted to encode two phylogenetically distinct complex I isozymes. R. sphaeroides cells lacking both isozymes had growth defects during all tested modes of growth, illustrating the important function of this enzyme under diverse conditions. We conclude that the two isozymes are not functionally redundant and predict that phylogenetically distinct complex I enzymes have evolved to support the diverse lifestyles of bacteria.« less

Different Functions of Phylogenetically Distinct Bacterial Complex I Isozymes

DOE PAGES

Spero, Melanie A.; Brickner, Joshua R.; Mollet, Jordan T.; ...

2016-02-01

NADH:quinone oxidoreductase (complex I) is a bioenergetic enzyme that transfers electrons from NADH to quinone, conserving the energy of this reaction by contributing to the proton motive force. While the importance of NADH oxidation to mitochondrial aerobic respiration is well documented, the contribution of complex I to bacterial electron transport chains has been tested in only a few species. Here, we analyze the function of two phylogenetically distinct complex I isozymes in Rhodobacter sphaeroides, an alphaproteobacterium that contains well-characterized electron transport chains. We found that R. sphaeroides complex I activity is important for aerobic respiration and required for anaerobic dimethylmore » sulfoxide (DMSO) respiration (in the absence of light), photoautotrophic growth, and photoheterotrophic growth (in the absence of an external electron acceptor). Our data also provide insight into the functions of the phylogenetically distinct R. sphaeroides complex I enzymes (complex I A and complex I E) in maintaining a cellular redox state during photoheterotrophic growth. We propose that the function of each isozyme during photoheterotrophic growth is either NADH synthesis (complex I A) or NADH oxidation (complex I E). The canonical alphaproteobacterial complex I isozyme (complex I A) was also shown to be important for routing electrons to nitrogenase-mediated H 2 production, while the horizontally acquired enzyme (complex I E) was dispensable in this process. Unlike the singular role of complex I in mitochondria, we predict that the phylogenetically distinct complex I enzymes found across bacterial species have evolved to enhance the functions of their respective electron transport chains. Cells use a proton motive force (PMF), NADH, and ATP to support numerous processes. In mitochondria, complex I uses NADH oxidation to generate a PMF, which can drive ATP synthesis. This study analyzed the function of complex I in bacteria, which contain more-diverse and more-flexible electron transport chains than mitochondria. We tested complex I function in Rhodobacter sphaeroides, a bacterium predicted to encode two phylogenetically distinct complex I isozymes. R. sphaeroides cells lacking both isozymes had growth defects during all tested modes of growth, illustrating the important function of this enzyme under diverse conditions. We conclude that the two isozymes are not functionally redundant and predict that phylogenetically distinct complex I enzymes have evolved to support the diverse lifestyles of bacteria.« less

Sulfur K-edge X-ray absorption spectroscopy and density functional theory calculations on monooxo Mo(IV) and bisoxo Mo(VI) bis-dithiolenes: insights into the mechanism of oxo transfer in sulfite oxidase and its relation to the mechanism of DMSO reductase.

PubMed

Ha, Yang; Tenderholt, Adam L; Holm, Richard H; Hedman, Britt; Hodgson, Keith O; Solomon, Edward I

2014-06-25

Sulfur K-edge X-ray absorption spectroscopy (XAS) and density functional theory (DFT) calculations have been used to determine the electronic structures of two complexes [Mo(IV)O(bdt)2](2-) and [Mo(VI)O2(bdt)2](2-) (bdt = benzene-1,2-dithiolate(2-)) that relate to the reduced and oxidized forms of sulfite oxidase (SO). These are compared with those of previously studied dimethyl sulfoxide reductase (DMSOr) models. DFT calculations supported by the data are extended to evaluate the reaction coordinate for oxo transfer to a phosphite ester substrate. Three possible transition states are found with the one at lowest energy, stabilized by a P-S interaction, in good agreement with experimental kinetics data. Comparison of both oxo transfer reactions shows that in DMSOr, where the oxo is transferred from the substrate to the metal ion, the oxo transfer induces electron transfer, while in SO, where the oxo transfer is from the metal site to the substrate, the electron transfer initiates oxo transfer. This difference in reactivity is related to the difference in frontier molecular orbitals (FMO) of the metal-oxo and substrate-oxo bonds. Finally, these experimentally related calculations are extended to oxo transfer by sulfite oxidase. The presence of only one dithiolene at the enzyme active site selectively activates the equatorial oxo for transfer, and allows facile structural reorganization during turnover.

Structure, function and regulation of plant photosystem I.

PubMed

Jensen, Poul Erik; Bassi, Roberto; Boekema, Egbert J; Dekker, Jan P; Jansson, Stefan; Leister, Dario; Robinson, Colin; Scheller, Henrik Vibe

2007-05-01

Photosystem I (PSI) is a multisubunit protein complex located in the thylakoid membranes of green plants and algae, where it initiates one of the first steps of solar energy conversion by light-driven electron transport. In this review, we discuss recent progress on several topics related to the functioning of the PSI complex, like the protein composition of the complex in the plant Arabidopsis thaliana, the function of these subunits and the mechanism by which nuclear-encoded subunits can be inserted into or transported through the thylakoid membrane. Furthermore, the structure of the native PSI complex in several oxygenic photosynthetic organisms and the role of the chlorophylls and carotenoids in the antenna complexes in light harvesting and photoprotection are reviewed. The special role of the 'red' chlorophylls (chlorophyll molecules that absorb at longer wavelength than the primary electron donor P700) is assessed. The physiology and mechanism of the association of the major light-harvesting complex of photosystem II (LHCII) with PSI during short term adaptation to changes in light quality and quantity is discussed in functional and structural terms. The mechanism of excitation energy transfer between the chlorophylls and the mechanism of primary charge separation is outlined and discussed. Finally, a number of regulatory processes like acclimatory responses and retrograde signalling is reviewed with respect to function of the thylakoid membrane. We finish this review by shortly discussing the perspectives for future research on PSI.

TDDFT study of twisted intramolecular charge transfer and intermolecular double proton transfer in the excited state of 4‧-dimethylaminoflavonol in ethanol solvent

NASA Astrophysics Data System (ADS)

Wang, Ye; Shi, Ying; Cong, Lin; Li, Hui

2015-02-01

Time-dependent density functional theory method at the def-TZVP/B3LYP level was employed to investigate the intramolecular and intermolecular hydrogen bonding dynamics in the first excited (S1) state of 4‧-dimethylaminoflavonol (DMAF) monomer and in ethanol solution. In the DMAF monomer, we demonstrated that the intramolecular charge transfer (ICT) takes place in the S1 state. This excited state ICT process was followed by intramolecular proton transfer. Our calculated results are in good agreement with the mechanism proposed in experimental work. For the hydrogen-bonded DMAF-EtOH complex, it was demonstrated that the intermolecular hydrogen bonds can induce the formation of the twisted intramolecular charge transfer (TICT) state and the conformational twisting is along the C3-C4 bond. Moreover, the intermolecular hydrogen bonds can also facilitate the intermolecular double proton transfer in the TICT state. A stepwise intermolecular double proton transfer process was revealed. Therefore, the intermolecular hydrogen bonds can alter the mechanism of intramolecular charge transfer and proton transfer in the excited state for the DMAF molecule.

Reactivity of a Cobalt(III)–Hydroperoxo Complex in Electrophilic Reactions

DOE PAGES

Shin, Bongki; Sutherlin, Kyle D.; Ohta, Takehiro; ...

2016-11-15

The reactivity of mononuclear metal-hydroperoxo adducts has fascinated researchers in many areas due to their diverse biological and catalytic processes. In this study, a mononuclear cobalt(III)-peroxo complex bearing a tetradentate macrocyclic ligand, [Co III(Me 3-TPADP)(O 2)] + (Me 3-TPADP = 3,6,9-trimethyl-3,6,9-triaza-1(2,6)-pyridinacyclodecaphane), was prepared by reacting [Co II(Me 3-TPADP)(CH 3CN) 2] 2+ with H 2O 2 in the presence of triethylamine. Upon protonation, the cobalt(III)- peroxo intermediate was converted into a cobalt(III)-hydroperoxo complex, [Co III(Me 3-TPADP)(O 2H)(CH 3CN)] 2+. The mononuclear cobalt(III)-peroxo and -hydroperoxo intermediates were characterized by a variety of physicochemical methods. Results of electrospray ionization mass spectrometry clearly showmore » the transformation of the intermediates: the peak at m/z 339.2 assignable to the cobalt(III)-peroxo species disappears with concomitant growth of the peak at m/z 190.7 corresponding to the cobalt(III)-hydroperoxo complex (with bound CH 3CN). Isotope labeling experiments further support the existence of the cobalt(III)-peroxo and -hydroperoxo complexes. In particular, the O-O bond stretching frequency of the cobalt(III)-hydroperoxo complex was determined to be 851 cm -1 for 16O 2H samples (803 cm -1 for 18O 2H samples) and its Co-O vibrational energy was observed at 571 cm -1 for 16O 2H samples (551 cm -1 for 18O 2H samples; 568 cm -1 for 16O 2 2H samples) by resonance Raman spectroscopy. Reactivity studies performed with the cobalt(III)-peroxo and -hydroperoxo complexes in organic functionalizations reveal that the latter is capable of conducting oxygen atom transfer with an electrophilic character, whereas the former exhibits no oxygen atom transfer reactivity under the same reaction conditions. Alternatively, the cobalt(III)-hydroperoxo complex does not perform hydrogen atom transfer reactions, while analogous low-spin Fe(III)-hydroperoxo complexes are capable of this reactivity. Density function theory calculations indicate that this lack of reactivity is due to the high free energy cost of O-O bond homolysis that would be required to produce the hypothetical Co(IV)-oxo product.« less

Reactivity of a Cobalt(III)–Hydroperoxo Complex in Electrophilic Reactions

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

Shin, Bongki; Sutherlin, Kyle D.; Ohta, Takehiro

The reactivity of mononuclear metal-hydroperoxo adducts has fascinated researchers in many areas due to their diverse biological and catalytic processes. In this study, a mononuclear cobalt(III)-peroxo complex bearing a tetradentate macrocyclic ligand, [Co III(Me 3-TPADP)(O 2)] + (Me 3-TPADP = 3,6,9-trimethyl-3,6,9-triaza-1(2,6)-pyridinacyclodecaphane), was prepared by reacting [Co II(Me 3-TPADP)(CH 3CN) 2] 2+ with H 2O 2 in the presence of triethylamine. Upon protonation, the cobalt(III)- peroxo intermediate was converted into a cobalt(III)-hydroperoxo complex, [Co III(Me 3-TPADP)(O 2H)(CH 3CN)] 2+. The mononuclear cobalt(III)-peroxo and -hydroperoxo intermediates were characterized by a variety of physicochemical methods. Results of electrospray ionization mass spectrometry clearly showmore » the transformation of the intermediates: the peak at m/z 339.2 assignable to the cobalt(III)-peroxo species disappears with concomitant growth of the peak at m/z 190.7 corresponding to the cobalt(III)-hydroperoxo complex (with bound CH 3CN). Isotope labeling experiments further support the existence of the cobalt(III)-peroxo and -hydroperoxo complexes. In particular, the O-O bond stretching frequency of the cobalt(III)-hydroperoxo complex was determined to be 851 cm -1 for 16O 2H samples (803 cm -1 for 18O 2H samples) and its Co-O vibrational energy was observed at 571 cm -1 for 16O 2H samples (551 cm -1 for 18O 2H samples; 568 cm -1 for 16O 2 2H samples) by resonance Raman spectroscopy. Reactivity studies performed with the cobalt(III)-peroxo and -hydroperoxo complexes in organic functionalizations reveal that the latter is capable of conducting oxygen atom transfer with an electrophilic character, whereas the former exhibits no oxygen atom transfer reactivity under the same reaction conditions. Alternatively, the cobalt(III)-hydroperoxo complex does not perform hydrogen atom transfer reactions, while analogous low-spin Fe(III)-hydroperoxo complexes are capable of this reactivity. Density function theory calculations indicate that this lack of reactivity is due to the high free energy cost of O-O bond homolysis that would be required to produce the hypothetical Co(IV)-oxo product.« less

Role of Surface-Capping Ligands in Photoexcited Electron Transfer between CdS Nanorods and [FeFe] Hydrogenase and the Subsequent H 2 Generation

DOE PAGES

Wilker, Molly B.; Utterback, James K.; Greene, Sophie; ...

2017-12-08

Complexes of CdS nanorods and [FeFe] hydrogenase from Clostridium acetobutylicum have been shown to photochemically produce H 2. This study examines the role of the ligands that passivate the nanocrystal surfaces in the electron transfer from photoexcited CdS to hydrogenase and the H 2 generation that follows. We functionalized CdS nanorods with a series of mercaptocarboxylate surface-capping ligands of varying lengths and measured their photoexcited electron relaxation by transient absorption (TA) spectroscopy before and after hydrogenase adsorption. Rate constants for electron transfer from the nanocrystals to the enzyme, extracted by modeling of TA kinetics, decrease exponentially with ligand length, suggestingmore » that the ligand layer acts as a barrier to charge transfer and controls the degree of electronic coupling. Relative light-driven H 2 production efficiencies follow the relative quantum efficiencies of electron transfer, revealing the critical role of surface-capping ligands in determining the photochemical activity of these nanocrystal-enzyme complexes. Our results suggest that the H 2 production in this system could be maximized with a choice of a surface-capping ligand that decreases the distance between the nanocrystal surface and the electron injection site of the enzyme.« less

Experiments and Analyses of Data Transfers Over Wide-Area Dedicated Connections

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

Rao, Nageswara S.; Liu, Qiang; Sen, Satyabrata

Dedicated wide-area network connections are increasingly employed in high-performance computing and big data scenarios. One might expect the performance and dynamics of data transfers over such connections to be easy to analyze due to the lack of competing traffic. However, non-linear transport dynamics and end-system complexities (e.g., multi-core hosts and distributed filesystems) can in fact make analysis surprisingly challenging. We present extensive measurements of memory-to-memory and disk-to-disk file transfers over 10 Gbps physical and emulated connections with 0–366 ms round trip times (RTTs). For memory-to-memory transfers, profiles of both TCP and UDT throughput as a function of RTT show concavemore » and convex regions; large buffer sizes and more parallel flows lead to wider concave regions, which are highly desirable. TCP and UDT both also display complex throughput dynamics, as indicated by their Poincare maps and Lyapunov exponents. For disk-to-disk transfers, we determine that high throughput can be achieved via a combination of parallel I/O threads, parallel network threads, and direct I/O mode. Our measurements also show that Lustre filesystems can be mounted over long-haul connections using LNet routers, although challenges remain in jointly optimizing file I/O and transport method parameters to achieve peak throughput.« less

On Data Transfers Over Wide-Area Dedicated Connections

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

Rao, Nageswara S.; Liu, Qiang

Dedicated wide-area network connections are employed in big data and high-performance computing scenarios, since the absence of cross-traffic promises to make it easier to analyze and optimize data transfers over them. However, nonlinear transport dynamics and end-system complexity due to multi-core hosts and distributed file systems make these tasks surprisingly challenging. We present an overview of methods to analyze memory and disk file transfers using extensive measurements over 10 Gbps physical and emulated connections with 0–366 ms round trip times (RTTs). For memory transfers, we derive performance profiles of TCP and UDT throughput as a function of RTT, which showmore » concave regions in contrast to entirely convex regions predicted by previous models. These highly desirable concave regions can be expanded by utilizing large buffers and more parallel flows. We also present Poincar´e maps and Lyapunov exponents of TCP and UDT throughputtraces that indicate complex throughput dynamics. For disk file transfers, we show that throughput can be optimized using a combination of parallel I/O and network threads under direct I/O mode. Our initial throughput measurements of Lustre filesystems mounted over long-haul connections using LNet routers show convex profiles indicative of I/O limits.« less

Role of Surface-Capping Ligands in Photoexcited Electron Transfer between CdS Nanorods and [FeFe] Hydrogenase and the Subsequent H 2 Generation

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

Wilker, Molly B.; Utterback, James K.; Greene, Sophie

Complexes of CdS nanorods and [FeFe] hydrogenase from Clostridium acetobutylicum have been shown to photochemically produce H 2. This study examines the role of the ligands that passivate the nanocrystal surfaces in the electron transfer from photoexcited CdS to hydrogenase and the H 2 generation that follows. We functionalized CdS nanorods with a series of mercaptocarboxylate surface-capping ligands of varying lengths and measured their photoexcited electron relaxation by transient absorption (TA) spectroscopy before and after hydrogenase adsorption. Rate constants for electron transfer from the nanocrystals to the enzyme, extracted by modeling of TA kinetics, decrease exponentially with ligand length, suggestingmore » that the ligand layer acts as a barrier to charge transfer and controls the degree of electronic coupling. Relative light-driven H 2 production efficiencies follow the relative quantum efficiencies of electron transfer, revealing the critical role of surface-capping ligands in determining the photochemical activity of these nanocrystal-enzyme complexes. Our results suggest that the H 2 production in this system could be maximized with a choice of a surface-capping ligand that decreases the distance between the nanocrystal surface and the electron injection site of the enzyme.« less

Tests of Exoplanet Atmospheric Radiative Transfer Codes

NASA Astrophysics Data System (ADS)

Harrington, Joseph; Challener, Ryan; DeLarme, Emerson; Cubillos, Patricio; Blecic, Jasmina; Foster, Austin; Garland, Justin

2016-10-01

Atmospheric radiative transfer codes are used both to predict planetary spectra and in retrieval algorithms to interpret data. Observational plans, theoretical models, and scientific results thus depend on the correctness of these calculations. Yet, the calculations are complex and the codes implementing them are often written without modern software-verification techniques. In the process of writing our own code, we became aware of several others with artifacts of unknown origin and even outright errors in their spectra. We present a series of tests to verify atmospheric radiative-transfer codes. These include: simple, single-line line lists that, when combined with delta-function abundance profiles, should produce a broadened line that can be verified easily; isothermal atmospheres that should produce analytically-verifiable blackbody spectra at the input temperatures; and model atmospheres with a range of complexities that can be compared to the output of other codes. We apply the tests to our own code, Bayesian Atmospheric Radiative Transfer (BART) and to several other codes. The test suite is open-source software. We propose this test suite as a standard for verifying current and future radiative transfer codes, analogous to the Held-Suarez test for general circulation models. This work was supported by NASA Planetary Atmospheres grant NX12AI69G and NASA Astrophysics Data Analysis Program grant NNX13AF38G.

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

Sharma, Amrish, E-mail: amrish99@gmail.com; Kaur, Sandeep, E-mail: sipusukhn@gmail.com; Mudahar, Isha, E-mail: isha@pbi.ac.in

We have investigated the structural and electronic properties of carbon nanotube with small fullerene halves C{sub n} (n ≤ 40) which are covalently bonded to the side wall of an armchair single wall carbon nanotube (SWCNT) using first principle method based on density functional theory. The fullerene size results in weak bonding between fullerene halves and carbon nanotube (CNT). Further, it was found that the C-C bond distance that attaches the fullerene half and CNT is of the order of 1.60 Å. The calculated binding energies indicate the stability of the complexes formed. The HOMO-LUMO gaps and electron density ofmore » state plots points towards the metallicity of the complex formed. Our calculations on charge transfer reveal that very small amount of charge is transferred from CNT to fullerene halves.« less

Conformational fluctuation of Synaptotagmin-1 observed with single molecule fluorescence resonance energy transfer (smFRET)

NASA Astrophysics Data System (ADS)

Choi, Ucheor; Weninger, Keith

2008-10-01

Calcium dependent neurotransmitter release at the synapses involves a synaptic vesicle protein synaptotagmin-1, a calcium sensor, to regulate exocytosis. It has been known that Synaptotagmin-1 interacts with assembled SNARE complexes, but it is unclear how their molecular mechanisms are coupled. X-ray studies in the absence of calcium revealed a closed conformation of synaptotagmin-1 and with calcium bound to the C2 domains of synaptotagmin-3 found extensive interactions holding the domains open. Suggesting the two conformations can be the key to the two functions of synaptotagmin in regulating neurotransmission. Here we use single molecule fluorescence resonance energy transfer (smFRET) to study synaptotagmin interactions with SNARE complexes and the spontaneous conformational changes of synaptotagmin-1 when calcium is induced.

Three-Dimensional Reconstruction of Nuclear Envelope Architecture Using Dual-Color Metal-Induced Energy Transfer Imaging.

PubMed

Chizhik, Anna M; Ruhlandt, Daja; Pfaff, Janine; Karedla, Narain; Chizhik, Alexey I; Gregor, Ingo; Kehlenbach, Ralph H; Enderlein, Jörg

2017-12-26

The nuclear envelope, comprising the inner and the outer nuclear membrane, separates the nucleus from the cytoplasm and plays a key role in cellular functions. Nuclear pore complexes (NPCs), which are embedded in the nuclear envelope, control transport of macromolecules between the two compartments. Here, using dual-color metal-induced energy transfer (MIET), we determine the axial distance between Lap2β and Nup358 as markers for the inner nuclear membrane and the cytoplasmic side of the NPC, respectively. Using MIET imaging, we reconstruct the 3D profile of the nuclear envelope over the whole basal area, with an axial resolution of a few nanometers. This result demonstrates that optical microscopy can achieve nanometer axial resolution in biological samples and without recourse to complex interferometric approaches.

Quantum transport in the FMO photosynthetic light-harvesting complex.

PubMed

Karafyllidis, Ioannis G

2017-06-01

The very high light-harvesting efficiency of natural photosynthetic systems in conjunction with recent experiments, which showed quantum-coherent energy transfer in photosynthetic complexes, raised questions regarding the presence of non-trivial quantum effects in photosynthesis. Grover quantum search, quantum walks, and entanglement have been investigated as possible effects that lead to this efficiency. Here we explain the near-unit photosynthetic efficiency without invoking non-trivial quantum effects. Instead, we use non-equilibrium Green's functions, a mesoscopic method used to study transport in nano-conductors to compute the transmission function of the Fenna-Matthews-Olson (FMO) complex using an experimentally derived exciton Hamiltonian. The chlorosome antenna and the reaction center play the role of input and output contacts, connected to the FMO complex. We show that there are two channels for which the transmission is almost unity. Our analysis also revealed a dephasing-driven regulation mechanism that maintains the efficiency in the presence of varying dephasing potentials.

Synthesis and characterization of highly conductive charge-transfer complexes using positron annihilation spectroscopy

NASA Astrophysics Data System (ADS)

Adam, Abdel Majid A.; Refat, Moamen S.; Sharshar, T.; Heiba, Z. K.

Molecular charge-transfer complexes of the tetramethylethylenediamine (TMEDA) with picric acid (Pi-OH), benzene-1,4-diol (QL), tin(IV) tetrachloride (SnCl4), iodine, bromine, and zinc chloride (ZnCl2) have been synthesized and investigated by elemental and thermal analysis, electronic, infrared, Raman and proton-NMR, energy-dispersive X-ray spectroscopy, X-ray powder diffraction and positron annihilation lifetime spectroscopy, and scanning electron microscopy. In this work, three types of acceptors π-acceptors (Pi-OH and QL), σ-acceptors (iodine and bromine), and vacant orbital acceptors (SnCl4 and ZnCl2) were covered. The results of elemental analysis indicated that the CT complexes were formed with ratios 1:1 and 1:2 for QL, SnCl4, and ZnCl2 acceptors and iodine, Pi-OH, and Br2 acceptors, respectively. The type of chelating between the TMEDA donor and the mentioned acceptors depends upon the behavior of both items. The positron annihilation lifetime parameters were found to be dependent on the structure, electronic configuration, and the power of acceptors. The correlation between these parameters and the molecular weight and biological activities of studied complexes was also observed. Regarding the electrical properties, the AC conductivity and the dielectric coefficients were measured as a function of frequency at room temperature. The TMEDA charge-transfer complexes were screened against antibacterial (Escherichia coli, Staphylococcus aureus, Bacillus subtilis, and Pseudomonas aeruginosa) and antifungal (Aspergillus flavus and Candida albicans) activities.

Actuator and aerodynamic modeling for high-angle-of-attack aeroservoelasticity

NASA Technical Reports Server (NTRS)

Brenner, Martin J.

1993-01-01

Accurate prediction of airframe/actuation coupling is required by the imposing demands of modern flight control systems. In particular, for agility enhancement at high angle of attack and low dynamic pressure, structural integration characteristics such as hinge moments, effective actuator stiffness, and airframe/control surface damping can have a significant effect on stability predictions. Actuator responses are customarily represented with low-order transfer functions matched to actuator test data, and control surface stiffness is often modeled as a linear spring. The inclusion of the physical properties of actuation and its installation on the airframe is therefore addressed in this paper using detailed actuator models which consider the physical, electrical, and mechanical elements of actuation. The aeroservoelastic analysis procedure is described in which the actuators are modeled as detailed high-order transfer functions and as approximate low-order transfer functions. The impacts of unsteady aerodynamic modeling on aeroservoelastic stability are also investigated in this paper by varying the order of approximation, or number of aerodynamic lag states, in the analysis. Test data from a thrust-vectoring configuration of an F/A-18 aircraft are compared to predictions to determine the effects on accuracy as a function of modeling complexity.

Actuator and aerodynamic modeling for high-angle-of-attack aeroservoelasticity

NASA Technical Reports Server (NTRS)

Brenner, Martin J.

1993-01-01

Accurate prediction of airframe/actuation coupling is required by the imposing demands of modern flight control systems. In particular, for agility enhancement at high angle of attack and low dynamic pressure, structural integration characteristics such as hinge moments, effective actuator stiffness, and airframe/control surface damping can have a significant effect on stability predictions. Actuator responses are customarily represented with low-order transfer functions matched to actuator test data, and control surface stiffness is often modeled as a linear spring. The inclusion of the physical properties of actuation and its installation on the airframe is therefore addressed using detailed actuator models which consider the physical, electrical, and mechanical elements of actuation. The aeroservoelastic analysis procedure is described in which the actuators are modeled as detailed high-order transfer functions and as approximate low-order transfer functions. The impacts of unsteady aerodynamic modeling on aeroservoelastic stability are also investigated by varying the order of approximation, or number of aerodynamic lag states, in the analysis. Test data from a thrust-vectoring configuration of an F/A-l8 aircraft are compared to predictions to determine the effects on accuracy as a function of modeling complexity.

De novo design and engineering of functional metal and porphyrin-binding protein domains

NASA Astrophysics Data System (ADS)

Everson, Bernard H.

In this work, I describe an approach to the rational, iterative design and characterization of two functional cofactor-binding protein domains. First, a hybrid computational/experimental method was developed with the aim of algorithmically generating a suite of porphyrin-binding protein sequences with minimal mutual sequence information. This method was explored by generating libraries of sequences, which were then expressed and evaluated for function. One successful sequence is shown to bind a variety of porphyrin-like cofactors, and exhibits light- activated electron transfer in mixed hemin:chlorin e6 and hemin:Zn(II)-protoporphyrin IX complexes. These results imply that many sophisticated functions such as cofactor binding and electron transfer require only a very small number of residue positions in a protein sequence to be fixed. Net charge and hydrophobic content are important in determining protein solubility and stability. Accordingly, rational modifications were made to the aforementioned design procedure in order to improve its overall success rate. The effects of these modifications are explored using two `next-generation' sequence libraries, which were separately expressed and evaluated. Particular modifications to these design parameters are demonstrated to effectively double the purification success rate of the procedure. Finally, I describe the redesign of the artificial di-iron protein DF2 into CDM13, a single chain di-Manganese four-helix bundle. CDM13 acts as a functional model of natural manganese catalase, exhibiting a kcat of 0.08s-1 under steady-state conditions. The bound manganese cofactors have a reduction potential of +805 mV vs NHE, which is too high for efficient dismutation of hydrogen peroxide. These results indicate that as a high-potential manganese complex, CDM13 may represent a promising first step toward a polypeptide model of the Oxygen Evolving Complex of the photosynthetic enzyme Photosystem II.

The algorithmic details of polynomials application in the problems of heat and mass transfer control on the hypersonic aircraft permeable surfaces

NASA Astrophysics Data System (ADS)

Bilchenko, G. G.; Bilchenko, N. G.

2018-03-01

The hypersonic aircraft permeable surfaces heat and mass transfer effective control mathematical modeling problems are considered. The analysis of the control (the blowing) constructive and gasdynamical restrictions is carried out for the porous and perforated surfaces. The functions classes allowing realize the controls taking into account the arising types of restrictions are suggested. Estimates of the computational complexity of the W. G. Horner scheme application in the case of using the C. Hermite interpolation polynomial are given.

Study of intermediates from transition metal excited-state electron-transfer reactions

NASA Astrophysics Data System (ADS)

Hoffman, M. Z.

1984-03-01

Attention during the past year focused on MV(+)., the reduced methyl viologen radical cation, which is a precursor to the formation of H2 in the photosensitized reduction of water. Through the use of photochemical and radiation chemical techniques, the efficiency of interaction of MV(+). with colloidal Pt, the stability of MV(+). as a function of pH, the quantum yield of formation of MV(+). in the Ru(bpy)3(2+)/MV(2+)/EDTA system, and the formation of photoactive charge-transfer complexes between MV(2+) and sacrificial electron donors were studied.

Non-vascularized free toe phalanx transfers in congenital hand deformities--the Great Ormond Street experience.

PubMed

Cavallo, A V; Smith, P J; Morley, S; Morsi, A W

2003-12-01

Many options of varying complexity are available for the management of congenital short digits resulting from aphalangia in symbrachydactyly and constriction ring syndrome. We have used non-vascularized free toe phalanx transfers for these children when a vascularized toe transfer has been contraindicated. We describe our technique and experience with 22 children who underwent a total of 64 transfers of the proximal (35) or middle (29) toe phalanges (average 3 per child). The mean age at initial surgery was 15 months, and the mean follow-up was 5 years. Duration of time until epiphyseal closure could not be determined accurately, but total digital elongation averaged 6mm. Complications of this technique include joint instability, premature epiphyseal closure and, in one patient, infection and graft loss. Donor site deformity was determined according to measured growth deficit and toe function. This technique is a simple option for digital elongation and, if performed in the appropriate age group in short fingered and monodactylous subtypes of symbrachydactyly, has the potential to allow growth and function with minimal donor site deficit.

Constrained subsystem density functional theory.

PubMed

Ramos, Pablo; Pavanello, Michele

2016-08-03

Constrained Subsystem Density Functional Theory (CSDFT) allows to compute diabatic states for charge transfer reactions using the machinery of the constrained DFT method, and at the same time is able to embed such diabatic states in a molecular environment via a subsystem DFT scheme. The CSDFT acronym is chosen to reflect the fact that on top of the subsystem DFT approach, a constraining potential is applied to each subsystem. We show that CSDFT can successfully tackle systems as complex as single stranded DNA complete of its backbone, and generate diabatic states as exotic as a hole localized on a phosphate group as well as on the nucleobases. CSDFT will be useful to investigators needing to evaluate the environmental effect on charge transfer couplings for systems in condensed phase environments.

Achieving One-Electron Oxidation of a Mononuclear Nonheme Iron(V)-Imido Complex

DOE PAGES

Hong, Seungwoo; Lu, Xiaoyan; Lee, Yong -Min; ...

2017-09-29

Here, a mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [Fe V(NTs)(TAML)] – (1), was oxidized by one-electron oxidants, affording formation of an iron(V)-imido TAML cation radical species, [Fe V(NTs)(TAML +•)] (2); 2 is a diamagnetic (S = 0) complex, resulting from the antiferromagnetic coupling of the low-spin iron(V) ion (S = 1/2) with the one-electron oxidized ligand (TAML +•). 2 is a competent oxidant in C–H bond functionalization and nitrene transfer reaction, showing that the reactivity of 2 is greater than that of 1.

Hyphal formation of Candida albicans is controlled by electron transfer system

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

Watanabe, Toshihiko; Ogasawara, Ayako; Mikami, Takeshi

2006-09-15

Most Candida albicans cells cultured in RPMI1640 medium at 37 deg. C grow in hyphal form in aerobic conditions, but they grow in yeast form in anaerobic conditions. The hyphal growth of C. albicans was inhibited in glucose-deficient conditions. Malonic acid, an inhibitor of succinate dehydrogenase, enhanced the yeast proliferation of C. albicans, indicating that the hyphal-formation signal was derived from the glycolysis system and the signal was transmitted to the electron transfer system via the citric acid cycle. Thenoyl trifluoro acetone (TTFA), an inhibitor of the signal transmission between complex II and Co Q, significantly inhibited the hyphal growthmore » of C. albicans. Antimycin, KCN, and oligomycin, inhibitors of complex III, IV, and V, respectively, did not inhibit the hyphal growth of C. albicans. The production of mRNAs for the hyphal formation signal was completely inhibited in anaerobic conditions. These results indicate that the electron transfer system functions upstream of the RAS1 signal pathway and activates the expression of the hyphal formation signal. Since the electron transfer system is inactivated in anaerobic conditions, C. albicans grew in yeast form in this condition.« less

Copper(II) complex with 6-methylpyridine-2-carboxyclic acid: Experimental and computational study on the XRD, FT-IR and UV-Vis spectra, refractive index, band gap and NLO parameters

NASA Astrophysics Data System (ADS)

Altürk, Sümeyye; Avcı, Davut; Başoğlu, Adil; Tamer, Ömer; Atalay, Yusuf; Dege, Necmi

2018-02-01

Crystal structure of the synthesized copper(II) complex with 6-methylpyridine-2-carboxylic acid, [Cu(6-Mepic)2·H2O]·H2O, was determined by XRD, FT-IR and UV-Vis spectroscopic techniques. Furthermore, the geometry optimization, harmonic vibration frequencies for the Cu(II) complex were carried out by using Density Functional Theory calculations with HSEh1PBE/6-311G(d,p)/LanL2DZ level. Electronic absorption wavelengths were obtained by using TD-DFT/HSEh1PBE/6-311G(d,p)/LanL2DZ level with CPCM model and major contributions were determined via Swizard/Chemissian program. Additionally, the refractive index, linear optical (LO) and non-nonlinear optical (NLO) parameters of the Cu(II) complex were calculated at HSEh1PBE/6-311G(d,p) level. The experimental and computed small energy gap shows the charge transfer in the Cu(II) complex. Finally, the hyperconjugative interactions and intramolecular charge transfer (ICT) were studied by performing of natural bond orbital (NBO) analysis.

Copper(II) complex with 6-methylpyridine-2-carboxyclic acid: Experimental and computational study on the XRD, FT-IR and UV-Vis spectra, refractive index, band gap and NLO parameters.

PubMed

Altürk, Sümeyye; Avcı, Davut; Başoğlu, Adil; Tamer, Ömer; Atalay, Yusuf; Dege, Necmi

2018-02-05

Crystal structure of the synthesized copper(II) complex with 6-methylpyridine-2-carboxylic acid, [Cu(6-Mepic) 2 ·H 2 O]·H 2 O, was determined by XRD, FT-IR and UV-Vis spectroscopic techniques. Furthermore, the geometry optimization, harmonic vibration frequencies for the Cu(II) complex were carried out by using Density Functional Theory calculations with HSEh1PBE/6-311G(d,p)/LanL2DZ level. Electronic absorption wavelengths were obtained by using TD-DFT/HSEh1PBE/6-311G(d,p)/LanL2DZ level with CPCM model and major contributions were determined via Swizard/Chemissian program. Additionally, the refractive index, linear optical (LO) and non-nonlinear optical (NLO) parameters of the Cu(II) complex were calculated at HSEh1PBE/6-311G(d,p) level. The experimental and computed small energy gap shows the charge transfer in the Cu(II) complex. Finally, the hyperconjugative interactions and intramolecular charge transfer (ICT) were studied by performing of natural bond orbital (NBO) analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

Differential identity of Filopodia and Tunneling Nanotubes revealed by the opposite functions of actin regulatory complexes.

PubMed

Delage, Elise; Cervantes, Diégo Cordero; Pénard, Esthel; Schmitt, Christine; Syan, Sylvie; Disanza, Andrea; Scita, Giorgio; Zurzolo, Chiara

2016-12-23

Tunneling Nanotubes (TNTs) are actin enriched filopodia-like protrusions that play a pivotal role in long-range intercellular communication. Different pathogens use TNT-like structures as "freeways" to propagate across cells. TNTs are also implicated in cancer and neurodegenerative diseases, making them promising therapeutic targets. Understanding the mechanism of their formation, and their relation with filopodia is of fundamental importance to uncover their physiological function, particularly since filopodia, differently from TNTs, are not able to mediate transfer of cargo between distant cells. Here we studied different regulatory complexes of actin, which play a role in the formation of both these structures. We demonstrate that the filopodia-promoting CDC42/IRSp53/VASP network negatively regulates TNT formation and impairs TNT-mediated intercellular vesicle transfer. Conversely, elevation of Eps8, an actin regulatory protein that inhibits the extension of filopodia in neurons, increases TNT formation. Notably, Eps8-mediated TNT induction requires Eps8 bundling but not its capping activity. Thus, despite their structural similarities, filopodia and TNTs form through distinct molecular mechanisms. Our results further suggest that a switch in the molecular composition in common actin regulatory complexes is critical in driving the formation of either type of membrane protrusion.

Latissimus Dorsi Transfer in Posterior Irreparable Rotator Cuff Tears

PubMed Central

Anastasopoulos, Panagiotis P.; Alexiadis, George; Spyridonos, Sarantis; Fandridis, Emmanouil

2017-01-01

Background: Massive rotator cuff tears pose a difficult and complex challenge even for the experienced surgeon; inability to repair these tears by conventional means designates them as irreparable, while management becomes quite taxing. Several operative options have been suggested for the management of such lesions with varying degrees of success, while it is imperative to match patient demands and expectations to the predicted outcome. Methods: Research articles are examined and key concepts are discussed, in order to provide an evidence based review of the available literature. The anatomy and pathomechanics along with the indications, contraindications and surgical techniques are reported. Results: Transfer of the Latissimus dorsi has been used with success to restore shoulder function in deficits of the posterior rotator cuff. Although it can be used in a variety of settings, the ideal patient for a Latissimus dorsi tendon transfer is a young and active individual, with no glenohumeral osteoarthritis that has a severe disability and weakness related to an irreparable posterior cuff tear. Conclusion: Tendon transfers have proved to be a successful treatment option in salvaging this difficult problem, providing pain relief and restoring shoulder function. Despite the excellent functional outcomes and pain suppression following operation, a variety of factors may affect the outcome; thus making indications and preoperative assessment a valuable component. PMID:28400877

Latissimus Dorsi Transfer in Posterior Irreparable Rotator Cuff Tears.

PubMed

Anastasopoulos, Panagiotis P; Alexiadis, George; Spyridonos, Sarantis; Fandridis, Emmanouil

2017-01-01

Massive rotator cuff tears pose a difficult and complex challenge even for the experienced surgeon; inability to repair these tears by conventional means designates them as irreparable, while management becomes quite taxing. Several operative options have been suggested for the management of such lesions with varying degrees of success, while it is imperative to match patient demands and expectations to the predicted outcome. Research articles are examined and key concepts are discussed, in order to provide an evidence based review of the available literature. The anatomy and pathomechanics along with the indications, contraindications and surgical techniques are reported. Transfer of the Latissimus dorsi has been used with success to restore shoulder function in deficits of the posterior rotator cuff. Although it can be used in a variety of settings, the ideal patient for a Latissimus dorsi tendon transfer is a young and active individual, with no glenohumeral osteoarthritis that has a severe disability and weakness related to an irreparable posterior cuff tear. Tendon transfers have proved to be a successful treatment option in salvaging this difficult problem, providing pain relief and restoring shoulder function. Despite the excellent functional outcomes and pain suppression following operation, a variety of factors may affect the outcome; thus making indications and preoperative assessment a valuable component.

Structural insights into RNA processing by the human RISC-loading complex.

PubMed

Wang, Hong-Wei; Noland, Cameron; Siridechadilok, Bunpote; Taylor, David W; Ma, Enbo; Felderer, Karin; Doudna, Jennifer A; Nogales, Eva

2009-11-01

Targeted gene silencing by RNA interference (RNAi) requires loading of a short guide RNA (small interfering RNA (siRNA) or microRNA (miRNA)) onto an Argonaute protein to form the functional center of an RNA-induced silencing complex (RISC). In humans, Argonaute2 (AGO2) assembles with the guide RNA-generating enzyme Dicer and the RNA-binding protein TRBP to form a RISC-loading complex (RLC), which is necessary for efficient transfer of nascent siRNAs and miRNAs from Dicer to AGO2. Here, using single-particle EM analysis, we show that human Dicer has an L-shaped structure. The RLC Dicer's N-terminal DExH/D domain, located in a short 'base branch', interacts with TRBP, whereas its C-terminal catalytic domains in the main body are proximal to AGO2. A model generated by docking the available atomic structures of Dicer and Argonaute homologs into the RLC reconstruction suggests a mechanism for siRNA transfer from Dicer to AGO2.

Biophotonic logic devices based on quantum dots and temporally-staggered Förster energy transfer relays

NASA Astrophysics Data System (ADS)

Claussen, Jonathan C.; Algar, W. Russ; Hildebrandt, Niko; Susumu, Kimihiro; Ancona, Mario G.; Medintz, Igor L.

2013-11-01

Integrating photonic inputs/outputs into unimolecular logic devices can provide significantly increased functional complexity and the ability to expand the repertoire of available operations. Here, we build upon a system previously utilized for biosensing to assemble and prototype several increasingly sophisticated biophotonic logic devices that function based upon multistep Förster resonance energy transfer (FRET) relays. The core system combines a central semiconductor quantum dot (QD) nanoplatform with a long-lifetime Tb complex FRET donor and a near-IR organic fluorophore acceptor; the latter acts as two unique inputs for the QD-based device. The Tb complex allows for a form of temporal memory by providing unique access to a time-delayed modality as an alternate output which significantly increases the inherent computing options. Altering the device by controlling the configuration parameters with biologically based self-assembly provides input control while monitoring changes in emission output of all participants, in both a spectral and temporal-dependent manner, gives rise to two input, single output Boolean Logic operations including OR, AND, INHIBIT, XOR, NOR, NAND, along with the possibility of gate transitions. Incorporation of an enzymatic cleavage step provides for a set-reset function that can be implemented repeatedly with the same building blocks and is demonstrated with single input, single output YES and NOT gates. Potential applications for these devices are discussed in the context of their constituent parts and the richness of available signal.

Biophotonic logic devices based on quantum dots and temporally-staggered Förster energy transfer relays.

PubMed

Claussen, Jonathan C; Algar, W Russ; Hildebrandt, Niko; Susumu, Kimihiro; Ancona, Mario G; Medintz, Igor L

2013-12-21

Integrating photonic inputs/outputs into unimolecular logic devices can provide significantly increased functional complexity and the ability to expand the repertoire of available operations. Here, we build upon a system previously utilized for biosensing to assemble and prototype several increasingly sophisticated biophotonic logic devices that function based upon multistep Förster resonance energy transfer (FRET) relays. The core system combines a central semiconductor quantum dot (QD) nanoplatform with a long-lifetime Tb complex FRET donor and a near-IR organic fluorophore acceptor; the latter acts as two unique inputs for the QD-based device. The Tb complex allows for a form of temporal memory by providing unique access to a time-delayed modality as an alternate output which significantly increases the inherent computing options. Altering the device by controlling the configuration parameters with biologically based self-assembly provides input control while monitoring changes in emission output of all participants, in both a spectral and temporal-dependent manner, gives rise to two input, single output Boolean Logic operations including OR, AND, INHIBIT, XOR, NOR, NAND, along with the possibility of gate transitions. Incorporation of an enzymatic cleavage step provides for a set-reset function that can be implemented repeatedly with the same building blocks and is demonstrated with single input, single output YES and NOT gates. Potential applications for these devices are discussed in the context of their constituent parts and the richness of available signal.

Students Fail to Transfer Knowledge of Chromosome Structure to Topics Pertaining to Cell Division

ERIC Educational Resources Information Center

Newman, Dina L.; Catavero, Christina M.; Wright, L. Kate

2012-01-01

Cellular processes that rely on knowledge of molecular behavior are difficult for students to comprehend. For example, thorough understanding of meiosis requires students to integrate several complex concepts related to chromosome structure and function. Using a grounded theory approach, we have unified classroom observations, assessment data, and…

Using Social Media to Facilitate Knowledge Transfer in Complex Engineering Environments: A Primer for Educators

ERIC Educational Resources Information Center

Murphy, Glen; Salomone, Sonia

2013-01-01

While highly cohesive groups are potentially advantageous they are also often correlated with the emergence of knowledge and information silos based around those same functional or occupational clusters. Consequently, an essential challenge for engineering organisations wishing to overcome informational silos is to implement mechanisms that…

Analytical model and figures of merit for filtered Microwave Photonic Links.

PubMed

Gasulla, Ivana; Capmany, José

2011-09-26

The concept of filtered Microwave Photonic Links is proposed in order to provide the most general and versatile description of complex analog photonic systems. We develop a field propagation model where a global optical filter, characterized by its optical transfer function, embraces all the intermediate optical components in a linear link. We assume a non-monochromatic light source characterized by an arbitrary spectral distribution which has a finite linewidth spectrum and consider both intensity modulation and phase modulation with balanced and single detection. Expressions leading to the computation of the main figures of merit concerning the link gain, noise and intermodulation distortion are provided which, to our knowledge, are not available in the literature. The usefulness of this derivation resides in the capability to directly provide performance criteria results for complex links just by substituting in the overall closed-form formulas the numerical or measured optical transfer function characterizing the link. This theory is presented thus as a potential tool for a wide range of relevant microwave photonic application cases which is extendable to multiport radio over fiber systems. © 2011 Optical Society of America

Frequency domain system identification of helicopter rotor dynamics incorporating models with time periodic coefficients

NASA Astrophysics Data System (ADS)

Hwang, Sunghwan

1997-08-01

One of the most prominent features of helicopter rotor dynamics in forward flight is the periodic coefficients in the equations of motion introduced by the rotor rotation. The frequency response characteristics of such a linear time periodic system exhibits sideband behavior, which is not the case for linear time invariant systems. Therefore, a frequency domain identification methodology for linear systems with time periodic coefficients was developed, because the linear time invariant theory cannot account for sideband behavior. The modulated complex Fourier series was introduced to eliminate the smearing effect of Fourier series expansions of exponentially modulated periodic signals. A system identification theory was then developed using modulated complex Fourier series expansion. Correlation and spectral density functions were derived using the modulated complex Fourier series expansion for linear time periodic systems. Expressions of the identified harmonic transfer function were then formulated using the spectral density functions both with and without additive noise processes at input and/or output. A procedure was developed to identify parameters of a model to match the frequency response characteristics between measured and estimated harmonic transfer functions by minimizing an objective function defined in terms of the trace of the squared frequency response error matrix. Feasibility was demonstrated by the identification of the harmonic transfer function and parameters for helicopter rigid blade flapping dynamics in forward flight. This technique is envisioned to satisfy the needs of system identification in the rotating frame, especially in the context of individual blade control. The technique was applied to the coupled flap-lag-inflow dynamics of a rigid blade excited by an active pitch link. The linear time periodic technique results were compared with the linear time invariant technique results. Also, the effect of noise processes and initial parameter guess on the identification procedure were investigated. To study the effect of elastic modes, a rigid blade with a trailing edge flap excited by a smart actuator was selected and system parameters were successfully identified, but with some expense of computational storage and time. Conclusively, the linear time periodic technique substantially improved the identified parameter accuracy compared to the linear time invariant technique. Also, the linear time periodic technique was robust to noises and initial guess of parameters. However, an elastic mode of higher frequency relative to the system pumping frequency tends to increase the computer storage requirement and computing time.

High fluorescence emission of carboxylic acid functionalized polystyrene/BaTiO{sub 3} nanocomposites and rare earth metal complexes: Preparation and characterization

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

Cao, X. T.; Showkat, A. M.; Wang, Z.

2015-03-30

Noble fluorescence nanocomposite compound based on barium titanate nanoparticles (BTO), polystyrene (PSt), and terbium ion (Tb{sup 3+}) was synthesized by a combination of surface-initiated reversible addition-fragmentation chain transfer (RAFT) polymerization, Friedel-Crafts alkylation reaction and coordinate chemistry. Initially, a modification of surface of BTO was conducted by an exchange process with S-benzyl S’-trimethoxysilylpropyltrithiocarbonate to create macro-initiator for polymerization of styrene. Subsequently, aryl carboxylic acid functionalized polystyrene grafted barium titanate (BTO-g-PSt-COOH) was generated by substitution reaction between 4-(Chloromethyl) benzoic acid and PSt chains. The coordination of the nanohybrids with Tb{sup 3+} ions afforded fluorescent Tb{sup 3+} tagged aryl carboxylic acid functionalized polystyrenemore » grafted barium titanate (BTO-g-PSt-Tb{sup 3+}) complexes. Structure, morphology, and fluorescence properties of nanohybrid complexes were investigated by respective physical and spectral studies. FT-IR and SEM analyses confirmed the formation of BTO-g-PSt-Tb{sup 3+}nanohybrids. Furthermore, TGA profiles demonstrated the grafting of aryl carboxylic acid functionalized polystyrene on BTO surface. Optical properties of BTO-g-PSt-Tb{sup 3+} complexes were investigated by fluorescence spectroscopy.« less

What is microbial community ecology?

PubMed

Konopka, Allan

2009-11-01

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbes possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered as a community property.

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

Konopka, Allan

The activities of complex communities of microbes affect biogeochemical transformations in natural, managed and engineered ecosystems. Meaningfully defining what constitutes a community of interacting microbial populations is not trivial, but is important for rigorous progress in the field. Important elements of research in microbial community ecology include the analysis of functional pathways for nutrient resource and energy flows, mechanistic understanding of interactions between microbial populations and their environment, and the emergent properties of the complex community. Some emergent properties mirror those analyzed by community ecologists who study plants and animals: biological diversity, functional redundancy and system stability. However, because microbesmore » possess mechanisms for the horizontal transfer of genetic information, the metagenome may also be considered a community property.« less

Asymmetric Catalysis with bis(hydroxyphenyl)diamides/rare-earth metal complexes.

PubMed

Kumagai, Naoya; Shibasaki, Masakatsu

2013-01-02

A series of asymmetric catalysts composed of conformationally flexible amide-based chiral ligands and rare-earth metals was developed for proton-transfer catalysis. These ligands derived from amino acids provide an intriguing chiral platform for the formation of asymmetric catalysts upon complexation with rare-earth metals. The scope of this arsenal of catalysts was further broadened by the development of heterobimetallic catalytic systems. The cooperative function of hydrogen bonding and metal coordination resulted in intriguing substrate specificity and stereocontrol, and the dynamic nature of the catalysts led to a switch of their function. Herein, we summarize our recent exploration of this class of catalysts. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Cellular complexity in subcortical white matter: a distributed control circuit?

PubMed

Colombo, Jorge A

2018-03-01

The subcortical white matter (SWM) has been traditionally considered as a site for passive-neutral-information transfer through cerebral cortex association and projection fibers. Yet, the presence of subcortical neuronal and glial "interstitial" cells expressing immunolabelled neurotransmitters/neuromodulators and synaptic vesicular proteins, and recent immunohistochemical and electrophysiological observations on the rat visual cortex as well as interactive regulation of myelinating processes support the possibility that SWM nests subcortical, regionally variable, distributed neuronal-glial circuits, that could influence information transfer. Their hypothetical involvement in regulating the timing and signal transfer probability at the SWM axonal components ought to be considered and experimentally analysed. Thus, the "interstitial" neuronal cells-associated with local glial cells-traditionally considered to be vestigial and functionally inert under normal conditions, they may well turn to be critical in regulating information transfer at the SWM.

Phylogeny of Rieske/cytb Complexes with a Special Focus on the Haloarchaeal Enzymes

PubMed Central

Baymann, Frauke; Schoepp-Cothenet, Barbara; Lebrun, Evelyne; van Lis, Robert; Nitschke, Wolfgang

2012-01-01

Rieske/cytochrome b (Rieske/cytb) complexes are proton pumping quinol oxidases that are present in most bacteria and Archaea. The phylogeny of their subunits follows closely the 16S-rRNA phylogeny, indicating that chemiosmotic coupling was already present in the last universal common ancestor of Archaea and bacteria. Haloarchaea are the only organisms found so far that acquired Rieske/cytb complexes via interdomain lateral gene transfer. They encode two Rieske/cytb complexes in their genomes; one of them is found in genetic context with nitrate reductase genes and has its closest relatives among Actinobacteria and the Thermus/Deinococcus group. It is likely to function in nitrate respiration. The second Rieske/cytb complex of Haloarchaea features a split cytochrome b sequence as do Cyanobacteria, chloroplasts, Heliobacteria, and Bacilli. It seems that Haloarchaea acquired this complex from an ancestor of the above-mentioned phyla. Its involvement in the bioenergetic reaction chains of Haloarchaea is unknown. We present arguments in favor of the hypothesis that the ancestor of Haloarchaea, which relied on a highly specialized bioenergetic metabolism, that is, methanogenesis, and was devoid of quinones and most enzymes of anaerobic or aerobic bioenergetic reaction chains, integrated laterally transferred genes into its genome to respond to a change in environmental conditions that made methanogenesis unfavorable. PMID:22798450

Definition of an intramolecular Eu-to-Eu energy transfer within a discrete [Eu2L] complex in solution.

PubMed

Nonat, Aline; Regueiro-Figueroa, Martín; Esteban-Gómez, David; de Blas, Andrés; Rodríguez-Blas, Teresa; Platas-Iglesias, Carlos; Charbonnière, Loïc J

2012-06-25

Ligand L, based on two do3a moieties linked by the methylene groups of 6,6'-dimethyl-2,2'-bipyridine, was synthesized and characterized. The addition of Ln salts to an aqueous solution of L (0.01 M Tris-HCl, pH 7.4) led to the successive formation of [LnL] and [Ln(2)L] complexes, as evidenced by UV/Vis and fluorescence titration experiments. Homodinuclear [Ln(2)L] complexes (Ln = Eu, Gd, Tb, Yb, and Lu) were prepared and characterized. The (1)H and (13)C NMR spectra of the Lu and Yb complexes in D(2)O solution (pD = 7.0) showed C(1) symmetry of these species in solution, pointing to two different chemical environments for the two lanthanide cations. The analysis of the chemical shifts of the Yb complex indicated that the two coordination sites present square antiprismatic (SAP) coordination environments around the metal ions. The spectroscopic properties of the [Tb(2)L] complex upon ligand excitation revealed conventional behavior with τ(H2O) = 2.05(1) ms and ϕ(H2O) = 51%, except for the calculation of the hydration number obtained from the luminescent lifetimes in H(2)O and D(2)O, which pointed to a non-integer value of 0.6 water molecules per Tb(III) ion. In contrast, the Eu complex revealed surprising features such as: 1) the presence of two and up to five components in the (5)D(0)→(7)F(0) and (5)D(0)→(7)F(1) emission bands, respectively; 2) marked differences between the normalized spectra obtained in H(2)O and D(2)O solutions; and 3) unconventional temporal evolution of the luminescence intensity at certain wavelengths, the intensity profile first displaying a rising step before the occurrence of the expected decay. Additional spectroscopic experiments performed on [Gd(2-x)Eu(x)L] complexes (x = 0.1 and 1.9) confirmed the presence of two distinct Eu sites with hydration numbers of 0 (site I) and 2 (site II), and showed that the unconventional temporal evolution of the emission intensity is the result of an unprecedented intramolecular Eu-to-Eu energy-transfer process. A mathematical model was developed to interpret the experimental data, leading to energy-transfer rates of 0.98 ms(-1) for the transfer from the site with q=0 to that with q=2 and vice versa. Hartree-Fock (HF) and density functional theory (DFT) calculations performed at the B3LYP level were used to investigate the conformation of the complex in solution, and to estimate the intermetallic distance, which provided Förster radii (R(0)) values of 8.1 Å for the energy transfer from site I to site II, and 6.8 Å for the reverse energy transfer. These results represent the first evidence of an intramolecular energy-transfer equilibrium between two identical lanthanide cations within a discrete molecular complex in solution. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Compression of head-related transfer function using autoregressive-moving-average models and Legendre polynomials.

PubMed

Shekarchi, Sayedali; Hallam, John; Christensen-Dalsgaard, Jakob

2013-11-01

Head-related transfer functions (HRTFs) are generally large datasets, which can be an important constraint for embedded real-time applications. A method is proposed here to reduce redundancy and compress the datasets. In this method, HRTFs are first compressed by conversion into autoregressive-moving-average (ARMA) filters whose coefficients are calculated using Prony's method. Such filters are specified by a few coefficients which can generate the full head-related impulse responses (HRIRs). Next, Legendre polynomials (LPs) are used to compress the ARMA filter coefficients. LPs are derived on the sphere and form an orthonormal basis set for spherical functions. Higher-order LPs capture increasingly fine spatial details. The number of LPs needed to represent an HRTF, therefore, is indicative of its spatial complexity. The results indicate that compression ratios can exceed 98% while maintaining a spectral error of less than 4 dB in the recovered HRTFs.

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.

Voltage and frequency dependence of prestin-associated charge transfer

PubMed Central

Sun, Sean X.; Farrell, Brenda; Chana, Matthew S.; Oster, George; Brownell, William E.; Spector, Alexander A.

2009-01-01

Membrane protein prestin is a critical component of the motor complex that generates forces and dimensional changes in cells in response to changes in the cell membrane potential. In its native cochlear outer hair cell, prestin is crucial to the amplification and frequency selectivity of the mammalian ear up to frequencies of tens of kHz. Other cells transfected with prestin acquire voltage-dependent properties similar to those of the native cell. The protein performance is critically dependent on chloride ions, and intrinsic protein charges also play a role. We propose an electro-diffusion model to reveal the frequency and voltage dependence of electric charge transfer by prestin. The movement of the combined charge (i.e., anion and protein charges) across the membrane is described with a Fokker-Planck equation coupled to a kinetic equation that describes the binding of chloride ions to prestin. We found a voltage-and frequency-dependent phase shift between the transferred charge and the applied electric field that determines capacitive and resistive components of the transferred charge. The phase shift monotonically decreases from zero to -90 degree as a function of frequency. The capacitive component as a function of voltage is bell-shaped, and decreases with frequency. The resistive component is bell-shaped for both voltage and frequency. The capacitive and resistive components are similar to experimental measurements of charge transfer at high frequencies. The revealed nature of the transferred charge can help reconcile the high-frequency electrical and mechanical observations associated with prestin, and it is important for further analysis of the structure and function of this protein. PMID:19490917

Spectroscopic characterization and reactivity studies of a mononuclear nonheme Mn(III)-hydroperoxo complex.

PubMed

So, Hee; Park, Young Jun; Cho, Kyung-Bin; Lee, Yong-Min; Seo, Mi Sook; Cho, Jaeheung; Sarangi, Ritimukta; Nam, Wonwoo

2014-09-03

We report the first example of a mononuclear nonheme manganese(III)-hydroperoxo complex derived from protonation of an isolated manganese(III)-peroxo complex bearing an N-tetramethylated cyclam (TMC) ligand, [Mn(III)(TMC)(OOH)](2+). The Mn(III)-hydroperoxo intermediate is characterized with various spectroscopic methods as well as with density functional theory (DFT) calculations, showing the binding of a hydroperoxide ligand in an end-on fashion. The Mn(III)-hydroperoxo species is a competent oxidant in oxygen atom transfer (OAT) reactions, such as the oxidation of sulfides. The electrophilic character of the Mn(III)-hydroperoxo complex is demonstrated unambiguously in the sulfoxidation of para-substituted thioanisoles.

Rational engineering of Geobacter sulfurreducens electron transfer components: A foundation for building improved Geobacter-based bioelectrochemical technologies

DOE PAGES

Dantas, Joana M.; Morgado, Leonor; Aklujkar, Muktak; ...

2015-07-30

Multiheme cytochromes have been implicated in Geobacter sulfurreducens extracellular electron transfer (EET). These proteins are potential targets to improve EET and enhance bioremediation and electrical current production by G. sulfurreducens. However, the functional characterization of multiheme cytochromes is particularly complex due to the co-existence of several microstates in solution, connecting the fully reduced and fully oxidized states. Throughout the last decade, new strategies have been developed to characterize multiheme redox proteins functionally and structurally. These strategies were used to reveal the functional mechanism of G. sulfurreducens multiheme cytochromes and also to identify key residues in these proteins for EET. Inmore » previous studies, we set the foundations for enhancement of the EET abilities of G. sulfurreducens by characterizing a family of five triheme cytochromes (PpcA-E). These periplasmic cytochromes are implicated in electron transfer between the oxidative reactions of metabolism in the cytoplasm and the reduction of extracellular terminal electron acceptors at the cell's outer surface. The results obtained suggested that PpcA can couple e -/H + transfer, a property that might contribute to the proton electrochemical gradient across the cytoplasmic membrane for metabolic energy production. The structural and functional properties of PpcA were characterized in detail and used for rational design of a family of 23 single site PpcA mutants. In this review, we summarize the functional characterization of the native and mutant proteins. Mutants that retain the mechanistic features of PpcA and adopt preferential e -/H + transfer pathways at lower reduction potential values compared to the wild-type protein were selected for in vivo studies as the best candidates to increase the electron transfer rate of G. sulfurreducens. For the first time G. sulfurreducens strains have been manipulated by the introduction of mutant forms of essential proteins with the aim to develop and improve bioelectrochemical technologies.« less

Relationship between femtosecond-picosecond dynamics to enzyme catalyzed H-transfer

PubMed Central

Cheatum, Christopher M.; Kohen, Amnon

2015-01-01

At physiological temperatures, enzymes exhibit a broad spectrum of conformations, which interchange via thermally activated dynamics. These conformations are sampled differently in different complexes of the protein and its ligands, and the dynamics of exchange between these conformers depends on the mass of the group that is moving and the length scale of the motion, as well as restrictions imposed by the globular fold of the enzymatic complex. Many of these motions have been examined and their role in the enzyme function illuminated, yet most experimental tools applied so far have identified dynamics at time scales of seconds to nanoseconds, which are much slower than the time scale for H-transfer between two heavy atoms. This chemical conversion and other processes involving cleavage of covalent bonds occur on picosecond to femtosecond time scales, where slower processes mask both the kinetics and dynamics. Here we present a combination of kinetic and spectroscopic methods that may enable closer examination of the relationship between enzymatic C-H→C transfer and the dynamics of the active site environment at the chemically relevant time scale. These methods include kinetic isotope effects and their temperature dependence, which are used to study the kinetic nature of the H-transfer, and 2D IR spectroscopy, which is used to study the dynamics of transition-state- and ground-state-analog complexes. The combination of these tools is likely to provide a new approach to examine the protein dynamics that directly influence the chemical conversion catalyzed by enzymes. PMID:23539379

Multiscale model of light harvesting by photosystem II in plants

DOE PAGES

Amarnath, Kapil; Bennett, Doran I. G.; Schneider, Anna R.; ...

2016-01-19

The first step of photosynthesis in plants is the absorption of sunlight by pigments in the antenna complexes of photosystem II (PSII), followed by transfer of the nascent excitation energy to the reaction centers, where long-term storage as chemical energy is initiated. Quantum mechanical mechanisms must be invoked to explain the transport of excitation within individual antenna. However, it is unclear how these mechanisms influence transfer across assemblies of antenna and thus the photochemical yield at reaction centers in the functional thylakoid membrane. In this paper, we model light harvesting at the several-hundred-nanometer scale of the PSII membrane, while preservingmore » the dominant quantum effects previously observed in individual complexes. We show that excitation moves diffusively through the antenna with a diffusion length of 50 nm until it reaches a reaction center, where charge separation serves as an energetic trap. The diffusion length is a single parameter that incorporates the enhancing effect of excited state delocalization on individual rates of energy transfer as well as the complex kinetics that arise due to energy transfer and loss by decay to the ground state. The diffusion length determines PSII’s high quantum efficiency in ideal conditions, as well as how it is altered by the membrane morphology and the closure of reaction centers. Finally, we anticipate that the model will be useful in resolving the nonphotochemical quenching mechanisms that PSII employs in conditions of high light stress.« less

Testing complex animal cognition: Concept learning, proactive interference, and list memory.

PubMed

Wright, Anthony A

2018-01-01

This article describes an approach for assessing and comparing complex cognition in rhesus monkeys and pigeons by training them in a sequence of synergistic tasks, each yielding a whole function for enhanced comparisons. These species were trained in similar same/different tasks with expanding training sets (8, 16, 32, 64, 128 … 1024 pictures) followed by novel-stimulus transfer eventually resulting in full abstract-concept learning. Concept-learning functions revealed better rhesus transfer throughout and full concept learning at the 128 set, versus pigeons at the 256 set. They were then tested in delayed same/different tasks for proactive interference by inserting occasional tests within trial-unique sessions where the test stimulus matched a previous sample stimulus (1, 2, 4, 8, 16 trials prior). Proactive-interference functions revealed time-based interference for pigeons (1, 10 s delays), but event-based interference for rhesus (no effect of 1, 10, 20 s delays). They were then tested in list-memory tasks by expanding the sample to four samples in trial-unique sessions (minimizing proactive interference). The four-item, list-memory functions revealed strong recency memory at short delays, gradually changing to strong primacy memory at long delays over 30 s for rhesus, and 10 s for pigeons. Other species comparisons and future directions are discussed. © 2018 Society for the Experimental Analysis of Behavior.

Biodiversity in a complex world: consolidation and progress in functional biodiversity research.

PubMed

Hillebrand, Helmut; Matthiessen, Birte

2009-12-01

The global decline of biodiversity caused by human domination of ecosystems worldwide is supposed to alter important process rates and state variables in these ecosystems. However, there is considerable debate on the prevalence and importance of biodiversity effects on ecosystem function (BDEF). Here, we argue that much of the debate stems from two major shortcomings. First, most studies do not directly link the traits leading to increased or decreased function to the traits needed for species coexistence and dominance. We argue that implementing a trait-based approach and broadening the perception of diversity to include trait dissimilarity or trait divergence will result in more realistic predictions on the consequences of altered biodiversity. Second, the empirical and theoretical studies do not reflect the complexity of natural ecosystems, which makes it difficult to transfer the results to natural situations of species loss. We review how different aspects of complexity (trophic structure, multifunctionality, spatial or temporal heterogeneity, and spatial population dynamics) alter our perception of BDEF. We propose future research avenues concisely testing whether acknowledging this complexity will strengthen the observed biodiversity effects. Finally, we propose that a major future task is to disentangle biodiversity effects on ecosystem function from direct changes in function due to human alterations of abiotic constraints.

Enantio-Relay Catalysis Constructs Chiral Biaryl Alcohols over Cascade Suzuki Cross-Coupling-Asymmetric Transfer Hydrogenation

NASA Astrophysics Data System (ADS)

Zhang, Dacheng; Gao, Xiaoshuang; Cheng, Tanyu; Liu, Guohua

2014-05-01

The construction of chiral biaryl alcohols using enantio-relay catalysis is a particularly attractive synthetic method in organic synthesis. However, overcoming the intrinsic incompatibility of distinct organometallic complexes and the reaction conditions used are significant challenges in asymmetric catalysis. To overcome these barriers, we have taken advantage of an enantio-relay catalysis strategy and a combined dual-immobilization approach. We report the use of an imidazolium-based organopalladium-functionalized organic-inorganic hybrid silica and ethylene-coated chiral organoruthenium-functionalized magnetic nanoparticles to catalyze a cascade Suzuki cross-coupling-asymmetric transfer hydrogenation reaction to prepare chiral biaryl alcohols in a two-step, one-pot process. As expected, the site-isolated active species, salient imidazolium phase-transfer character and high ethylene-coated hydrophobicity can synergistically boost the catalytic performance. Furthermore, enantio-relay catalysis has the potential to efficiently prepare a variety of chiral biaryl alcohols. Our synthetic strategy is a general method that shows the potential of developing enantio-relay catalysis towards environmentally benign and sustainable organic synthesis.

Status of therapeutic gene transfer to treat cardiovascular disease in dogs and cats.

PubMed

Sleeper, Meg; Bish, Lawrence T; Haskins, Mark; Ponder, Katherine P; Sweeney, H Lee

2011-06-01

Gene therapy is a procedure resulting in the transfer of a gene(s) into an individual's cells to treat a disease, which is designed to produce a protein or functional RNA (the gene product). Although most current gene therapy clinical trials focus on cancer and inherited diseases, multiple studies have evaluated the efficacy of gene therapy to abrogate various forms of heart disease. Indeed, human clinical trials are currently underway. One goal of gene transfer may be to express a functional gene when the endogenous gene is inactive. Alternatively, complex diseases such as end stage heart failure are characterized by a number of abnormalities at the cellular level, many of which can be targeted using gene delivery to alter myocardial protein levels. This review will discuss issues related to gene vector systems, gene delivery strategies and two cardiovascular diseases in dogs successfully treated with therapeutic gene delivery. Copyright © 2011 Elsevier B.V. All rights reserved.

Analysis of a Range of Catabolic Mutants Provides Evidence That Phytanoyl-Coenzyme A Does Not Act as a Substrate of the Electron-Transfer Flavoprotein/Electron-Transfer Flavoprotein:Ubiquinone Oxidoreductase Complex in Arabidopsis during Dark-Induced Senescence1[W][OA

PubMed Central

Araújo, Wagner L.; Ishizaki, Kimitsune; Nunes-Nesi, Adriano; Tohge, Takayuki; Larson, Tony R.; Krahnert, Ina; Balbo, Ilse; Witt, Sandra; Dörmann, Peter; Graham, Ian A.; Leaver, Christopher J.; Fernie, Alisdair R.

2011-01-01

The process of dark-induced senescence in plants is not fully understood, however, the functional involvement of an electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO), has been demonstrated. Recent studies have revealed that the enzymes isovaleryl-coenzyme A (CoA) dehydrogenase and 2-hydroxyglutarate dehydrogenase act as important electron donors to this complex. In addition both enzymes play a role in the breakdown of cellular carbon storage reserves with isovaleryl-CoA dehydrogenase being involved in degradation of the branched-chain amino acids, phytol, and lysine while 2-hydroxyglutarate dehydrogenase is exclusively involved in lysine degradation. Given that the chlorophyll breakdown intermediate phytanoyl-CoA accumulates dramatically both in knockout mutants of the ETF/ETFQO complex and of isovaleryl-CoA dehydrogenase following growth in extended dark periods we have investigated the direct importance of chlorophyll breakdown for the supply of carbon and electrons during this process. For this purpose we isolated three independent Arabidopsis (Arabidopsis thaliana) knockout mutants of phytanoyl-CoA 2-hydroxylase and grew them under the same extended darkness regime as previously used. Despite the fact that these mutants accumulated phytanoyl-CoA and also 2-hydroxyglutarate they exhibited no morphological changes in comparison to the other mutants previously characterized. These results are consistent with a single entry point of phytol breakdown into the ETF/ETFQO system and furthermore suggest that phytol is not primarily metabolized by this pathway. Furthermore analysis of isovaleryl-CoA dehydrogenase/2-hydroxyglutarate dehydrogenase double mutants generated here suggest that these two enzymes essentially account for the entire electron input via the ETF complex. PMID:21788362

Designing interfaces of hydrogenase-nanomaterial hybrids for efficient solar conversion.

PubMed

King, Paul W

2013-01-01

The direct conversion of sunlight into biofuels is an intriguing alternative to a continued reliance on fossil fuels. Natural photosynthesis has long been investigated both as a potential solution, and as a model for utilizing solar energy to drive a water-to-fuel cycle. The molecules and organizational structure provide a template to inspire the design of efficient molecular systems for photocatalysis. A clear design strategy is the coordination of molecular interactions that match kinetic rates and energetic levels to control the direction and flow of energy from light harvesting to catalysis. Energy transduction and electron-transfer reactions occur through interfaces formed between complexes of donor-acceptor molecules. Although the structures of several of the key biological complexes have been solved, detailed descriptions of many electron-transfer complexes are lacking, which presents a challenge to designing and engineering biomolecular systems for solar conversion. Alternatively, it is possible to couple the catalytic power of biological enzymes to light harvesting by semiconductor nanomaterials. In these molecules, surface chemistry and structure can be designed using ligands. The passivation effect of the ligand can also dramatically affect the photophysical properties of the semiconductor, and energetics of external charge-transfer. The length, degree of bond saturation (aromaticity), and solvent exposed functional groups of ligands can be manipulated to further tune the interface to control molecular assembly, and complex stability in photocatalytic hybrids. The results of this research show how ligand selection is critical to designing molecular interfaces that promote efficient self-assembly, charge-transfer and photocatalysis. This article is part of a Special Issue entitled: Metals in Bioenergetics and Biomimetics Systems. Copyright © 2013 Elsevier B.V. All rights reserved.

An assessment on convective and radiative heat transfer modelling in tubular solid oxide fuel cells

NASA Astrophysics Data System (ADS)

Sánchez, D.; Muñoz, A.; Sánchez, T.

Four models of convective and radiative heat transfer inside tubular solid oxide fuel cells are presented in this paper, all of them applicable to multidimensional simulations. The work is aimed at assessing if it is necessary to use a very detailed and complicated model to simulate heat transfer inside this kind of device and, for those cases when simple models can be used, the errors are estimated and compared to those of the more complex models. For the convective heat transfer, two models are presented. One of them accounts for the variation of film coefficient as a function of local temperature and composition. This model gives a local value for the heat transfer coefficients and establishes the thermal entry length. The second model employs an average value of the transfer coefficient, which is applied to the whole length of the duct being studied. It is concluded that, unless there is a need to calculate local temperatures, a simple model can be used to evaluate the global performance of the cell with satisfactory accuracy. For the radiation heat transfer, two models are presented again. One of them considers radial radiation exclusively and, thus, radiative exchange between adjacent cells is neglected. On the other hand, the second model accounts for radiation in all directions but increases substantially the complexity of the problem. For this case, it is concluded that deviations between both models are higher than for convection. Actually, using a simple model can lead to a not negligible underestimation of the temperature of the cell.

Expeditious diastereoselective synthesis of elaborated ketones via remote Csp3-H functionalization

NASA Astrophysics Data System (ADS)

Shu, Wei; Lorente, Adriana; Gómez-Bengoa, Enrique; Nevado, Cristina

2017-01-01

The quest for selective C-H functionalization reactions, able to provide new strategic opportunities for the rapid assembly of molecular complexity, represents a major focus of the chemical community. Examples of non-directed, remote Csp3-H activation to forge complex carbon frameworks remain scarce due to the kinetic stability and thus intrinsic challenge associated to the chemo-, regio- and stereoselective functionalization of aliphatic C-H bonds. Here we describe a radical-mediated, directing-group-free regioselective 1,5-hydrogen transfer of unactivated Csp3-H bonds followed by a second Csp2-H functionalization to produce, with exquisite stereoselectivity, a variety of elaborated fused ketones. This study demonstrates that aliphatic acids can be strategically harnessed as 1,2-diradical synthons and that secondary aliphatic C-H bonds can be engaged in stereoselective C-C bond-forming reactions, highlighting the potential of this protocol for target-oriented natural product and pharmaceutical synthesis.

Short-term Music Training Enhances Complex, Distributed Neural Communication during Music and Linguistic Tasks

PubMed Central

Carpentier, Sarah M.; Moreno, Sylvain; McIntosh, Anthony R.

2016-01-01

Musical training is frequently associated with benefits to linguistic abilities, and recent focus has been placed on possible benefits of bilingualism to lifelong executive functions; however, the neural mechanisms for such effects are unclear. The aim of this study was to gain better understanding of the whole-brain functional effects of music and second-language training that could support such previously observed cognitive transfer effects. We conducted a 28-day longitudinal study of monolingual English-speaking 4- to 6-year-old children randomly selected to receive daily music or French language training, excluding weekends. Children completed passive EEG music note and French vowel auditory oddball detection tasks before and after training. Brain signal complexity was measured on source waveforms at multiple temporal scales as an index of neural information processing and network communication load. Comparing pretraining with posttraining, musical training was associated with increased EEG complexity at coarse temporal scales during the music and French vowel tasks in widely distributed cortical regions. Conversely, very minimal decreases in complexity at fine scales and trends toward coarse-scale increases were displayed after French training during the tasks. Spectral analysis failed to distinguish between training types and found overall theta (3.5–7.5 Hz) power increases after all training forms, with spatially fewer decreases in power at higher frequencies (>10 Hz). These findings demonstrate that musical training increased diversity of brain network states to support domain-specific music skill acquisition and music-to-language transfer effects. PMID:27243611

Short-term Music Training Enhances Complex, Distributed Neural Communication during Music and Linguistic Tasks.

PubMed

Carpentier, Sarah M; Moreno, Sylvain; McIntosh, Anthony R

2016-10-01

Musical training is frequently associated with benefits to linguistic abilities, and recent focus has been placed on possible benefits of bilingualism to lifelong executive functions; however, the neural mechanisms for such effects are unclear. The aim of this study was to gain better understanding of the whole-brain functional effects of music and second-language training that could support such previously observed cognitive transfer effects. We conducted a 28-day longitudinal study of monolingual English-speaking 4- to 6-year-old children randomly selected to receive daily music or French language training, excluding weekends. Children completed passive EEG music note and French vowel auditory oddball detection tasks before and after training. Brain signal complexity was measured on source waveforms at multiple temporal scales as an index of neural information processing and network communication load. Comparing pretraining with posttraining, musical training was associated with increased EEG complexity at coarse temporal scales during the music and French vowel tasks in widely distributed cortical regions. Conversely, very minimal decreases in complexity at fine scales and trends toward coarse-scale increases were displayed after French training during the tasks. Spectral analysis failed to distinguish between training types and found overall theta (3.5-7.5 Hz) power increases after all training forms, with spatially fewer decreases in power at higher frequencies (>10 Hz). These findings demonstrate that musical training increased diversity of brain network states to support domain-specific music skill acquisition and music-to-language transfer effects.

Mars Observer data production, transfer, and archival: The data production assembly line

NASA Technical Reports Server (NTRS)

Childs, David B.

1993-01-01

This paper describes the data production, transfer, and archival process designed for the Mars Observer Flight Project. It addresses the developmental and operational aspects of the archive collection production process. The developmental aspects cover the design and packaging of data products for archival and distribution to the planetary community. Also discussed is the design and development of a data transfer and volume production process capable of handling the large throughput and complexity of the Mars Observer data products. The operational aspects cover the main functions of the process: creating data and engineering products, collecting the data products and ancillary products in a central repository, producing archive volumes, validating volumes, archiving, and distributing the data to the planetary community.

Tethered orbital propellant depot

NASA Technical Reports Server (NTRS)

Fester, D. A.; Rudolph, L. K.; Kiefel, E. R.

1985-01-01

A planned function of the Space Station is to refurbish and refuel an advanced space-based LO2/LH2 orbit transfer vehicle. An alternative to propellant storage at the station is to use a remote facility tied to the station with a log tether. Preliminary design of such a facility is described with emphasis on fluid transfer and storage requirements. Using tether lengths of at least 300 ft, gravity gradient forces will dominate surface tension in such a system. Although gravity given transfer is difficult because of line pressure drops, fluid settling over the tank outlet greatly alleviates acquisition concerns and will facilitate vented tank fills. The major concern with a tethered orbital refueling facility is its considerable operational complexity including transport of the OTV to and from the facility.

Rapid Transfer of Abstract Rules to Novel Contexts in Human Lateral Prefrontal Cortex

PubMed Central

Cole, Michael W.; Etzel, Joset A.; Zacks, Jeffrey M.; Schneider, Walter; Braver, Todd S.

2011-01-01

Flexible, adaptive behavior is thought to rely on abstract rule representations within lateral prefrontal cortex (LPFC), yet it remains unclear how these representations provide such flexibility. We recently demonstrated that humans can learn complex novel tasks in seconds. Here we hypothesized that this impressive mental flexibility may be possible due to rapid transfer of practiced rule representations within LPFC to novel task contexts. We tested this hypothesis using functional MRI and multivariate pattern analysis, classifying LPFC activity patterns across 64 tasks. Classifiers trained to identify abstract rules based on practiced task activity patterns successfully generalized to novel tasks. This suggests humans can transfer practiced rule representations within LPFC to rapidly learn new tasks, facilitating cognitive performance in novel circumstances. PMID:22125519

Simulating Ru L3-edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers

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

Van Kuiken, Benjamin E.; Valiev, Marat; Daifuku, Stephanie L.

2013-05-01

Ruthenium L2,3-edge X-ray absorption (XA) spectroscopy probes transitions from core 2p orbitals to the 4d levels of the atom and is a powerful tool for interrogating the local electronic and molecular structure around the metal atom. However, a molecular-level interpretation of the Ru L2,3-edge spectral lineshapes is often complicated by spin–orbit coupling (SOC) and multiplet effects. In this study, we develop spin-free time-dependent density functional theory (TDDFT) as a viable and predictive tool to simulate the Ru L3-edge spectra. We successfully simulate and analyze the ground state Ru L3-edge XA spectra of a series of RuII and RuIII complexes: [Ru(NH3)6]2+/3+,more » [Ru(CN)6]4-/3-, [RuCl6]4-/3-, and the ground (1A1) and photoexcited (3MLCT) transient states of [Ru(bpy)3]2+ and Ru(dcbpy)2(NCS)2 (termed N3). The TDDFT simulations reproduce all the experimentally observed features in Ru L3-edge XA spectra. The advantage of using TDDFT to assign complicated Ru L3-edge spectra is illustrated by its ability to identify ligand specific charge transfer features in complex molecules. We conclude that the B3LYP functional is the most reliable functional for accurately predicting the location of charge transfer features in these spectra. Experimental and simulated Ru L3-edge XA spectra are presented for the transition metal mixed-valence dimers [(NC)5MII-CN-RuIII(NH3)5]- (where M = Fe or Ru) dissolved in water. We explore the spectral signatures of electron delocalization in Ru L3-edge XA spectroscopy and our simulations reveal that the inclusion of explicit solvent molecules is crucial for reproducing the experimentally determined valencies, highlighting the importance of the role of the solvent in transition metal charge transfer chemistry.« less

Multiple hydrogen bonding in excited states of aminopyrazine in methanol solution: time-dependent density functional theory study.

PubMed

Chai, Shuo; Yu, Jie; Han, Yong-Chang; Cong, Shu-Lin

2013-11-01

Aminopyrazine (AP) and AP-methanol complexes have been theoretically studied by using density functional theory (DFT) and time-dependent density functional theory (TDDFT). The excited-state hydrogen bonds are discussed in detail. In the ground state the intermolecular multiple hydrogen bonds can be formed between AP molecule and protic solvents. The AP monomer and hydrogen-bonded complex of AP with one methanol are photoexcited initially to the S2 state, and then transferred to the S1 state via internal conversion. However the complex of AP with two methanol molecules is directly excited to the S1 state. From the calculated electronic excited energies and simulated absorption spectra, we find that the intermolecular hydrogen bonds are strengthened in the electronic excited states. The strengthening is confirmed by the optimized excited-state geometries. The photochemical processes in the electronic excited states are significantly influenced by the excited-state hydrogen bond strengthening. Copyright © 2013 Elsevier B.V. All rights reserved.

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe–S Assembly Complex

PubMed Central

Fox, Nicholas G.; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A.; Barondeau, David P.

2015-01-01

Iron–sulfur (Fe–S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe–S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe–S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe–S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe–S assembly complex. Here the kinetics of Fe–S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe–S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe–S assembly complex. PMID:26016518

Frataxin Accelerates [2Fe-2S] Cluster Formation on the Human Fe-S Assembly Complex.

PubMed

Fox, Nicholas G; Das, Deepika; Chakrabarti, Mrinmoy; Lindahl, Paul A; Barondeau, David P

2015-06-30

Iron-sulfur (Fe-S) clusters function as protein cofactors for a wide variety of critical cellular reactions. In human mitochondria, a core Fe-S assembly complex [called SDUF and composed of NFS1, ISD11, ISCU2, and frataxin (FXN) proteins] synthesizes Fe-S clusters from iron, cysteine sulfur, and reducing equivalents and then transfers these intact clusters to target proteins. In vitro assays have relied on reducing the complexity of this complicated Fe-S assembly process by using surrogate electron donor molecules and monitoring simplified reactions. Recent studies have concluded that FXN promotes the synthesis of [4Fe-4S] clusters on the mammalian Fe-S assembly complex. Here the kinetics of Fe-S synthesis reactions were determined using different electron donation systems and by monitoring the products with circular dichroism and absorbance spectroscopies. We discovered that common surrogate electron donor molecules intercepted Fe-S cluster intermediates and formed high-molecular weight species (HMWS). The HMWS are associated with iron, sulfide, and thiol-containing proteins and have properties of a heterogeneous solubilized mineral with spectroscopic properties remarkably reminiscent of those of [4Fe-4S] clusters. In contrast, reactions using physiological reagents revealed that FXN accelerates the formation of [2Fe-2S] clusters rather than [4Fe-4S] clusters as previously reported. In the preceding paper [Fox, N. G., et al. (2015) Biochemistry 54, DOI: 10.1021/bi5014485], [2Fe-2S] intermediates on the SDUF complex were shown to readily transfer to uncomplexed ISCU2 or apo acceptor proteins, depending on the reaction conditions. Our results indicate that FXN accelerates a rate-limiting sulfur transfer step in the synthesis of [2Fe-2S] clusters on the human Fe-S assembly complex.

Investigation of Stability of Photosynthetic Reaction Center and Quantum Dot Hybrid Films.

PubMed

Lukashev, E P; Knox, P P; Oleinikov, I P; Seifullina, N Kh; Grishanova, N P

2016-01-01

The efficiency of interaction (efficiency of energy transfer) between various quantum dots (QDs) and photosynthetic reaction centers (RCs) from the purple bacterium Rhodobacter sphaeroides and conditions of long-term stability of functioning of such hybrid complexes in film preparations were investigated. It was found that dry films containing RCs and QDs and maintained at atmospheric humidity are capable to keep their functional activity for at least some months as judging by results of measurement of their spectral characteristics, efficiency of energy transfer from QDs to RCs, and RC electron-transport activity. Addition of trehalose to the films giving them still greater stability is especially expressed for films maintained at low humidity. These stable hybrid film structures are promising for further biotechnological studies for developing new phototransformation devices.

Proton transfer complexes based on some π-acceptors having acidic protons with 3-amino-6-[2-(2-thienyl)vinyl]-1,2,4-triazin-5(4 H)-one donor: Synthesis and spectroscopic characterizations

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2011-05-01

Charge transfer complexes based on 3-amino-6-[2-(2-thienyl)vinyl]-1,2,4-triazin-5(4 H)-one (ArNH 2) organic basic donor and pi-acceptors having acidic protons such as picric acid (PiA), hydroquinone (Q(OH) 2) and 3,5-dinitrobenzene (DNB) have been synthesized and spectroscopically studied. The sbnd NH3+ ammonium ion was formed under the acid-base theory through proton transfer from an acidic to basic centers in all charge transfer complexes resulted. The values of formation constant ( KCT) and molar extinction coefficient ( ɛCT) which were estimated from the spectrophotometric studies have a dramatic effect for the charge transfer complexes with differentiation of pi-acceptors. For further studies the vibrational spectroscopy of the [( ArNH3+)(PiA -)] (1), [( ArNH3+)(Q (OH)2-)] (2) and [( ArNH3+)(DNB -)] (3) of (1:1) charge transfer complexes of (donor: acceptor) were characterized by elemental analysis, infrared spectra, Raman spectra, 1H and 13CNMR spectra. The experimental data of elemental analyses of the charge transfer complexes (1), (2) and (3) were in agreement with calculated data. The IR and Raman spectra of (1), (2) and (3) are indicated to the presence of bands around 3100 and 1600 cm -1 distinguish to sbnd NH3+. The thermogravimetric analysis (TG) and differential scanning calorimetry (DSC) techniques were performed to give knowledge about thermal stability behavior of the synthesized charge transfer complexes. The morphological features of start materials and charge transfer complexes were investigated using scanning electron microscopy (SEM) and optical microscopy.

Ferrocene/fullerene hybrids showing large second-order nonlinear optical activities: impact of the cage unit size.

PubMed

Wang, Wen-Yong; Wang, Li; Ma, Na-Na; Zhu, Chang-Li; Qiu, Yong-Qing

2015-06-07

The electron donor-acceptor complexes, which undergo intramolecular charge transfer under external stimulus, are an emerging class of materials showing important application in nonlinear optics. Synthesizing ferrocene/fullerene complexes through face-to-face fusion would enjoy the merits of both ferrocene and fullerene due to their strong donor-acceptor interactions. Four ferrocene/fullerene hybrid complexes with the gradual extension of fullerene cage size, including CpFe(C60H5), CpFe(C66H5), CpFe(C70H5), and CpFe(C80H5) (Cp is cyclopentadienyl), have been investigated by density functional theory. These hybrid molecules give eclipsed and staggered isomers. The main reason that the eclipsed isomer is stable is that the eclipsed structure possesses large CpFefullerene bonding energy. The CpFefullerene interaction is smaller than that of CpFefullerene, which must come from two different interfaces. The presence of covalent bond character between CpFe and fullerene is supported by the localized orbital locator, deformation of electron density distribution and energy decomposition analysis. Significantly, the absorption bands and first hyperpolarizabilities of these hybrid complexes are strongly sensitive to the fullerene cage size, which is ascribed to a change in the charge transfer pattern, especially for CpFe(C80H5), which displays reverse π → π* charge transfer from bottom to top cage, leading to notable hyperpolarizability. Investigation of the structure-property relationship at the molecular level can benefit the design and preparation of such hybrid complexes in chemistry and materials science.

Chemical and physical investigations on the charge transfer interaction of organic donors with iodine and its application as non-traditional organic conductors

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Sharshar, T.; Adam, Abdel Majid A.; Elsabawy, Khaled M.; Hemeda, O. M.

2014-09-01

The iso-leucine-iodide and methionine-iodide charge-transfer complexes were prepared and characterized using different spectroscopic techniques. The iodide charge-transfer complexes were synthesized by grinding KI-I2-amino acid with 1:1:1 M ratio in presence of few drops of methanol solvent. The structures of both solid amino acid iodide charge-transfer complexes are discussed with the help of the obtained results of the infrared and Raman laser spectra, Uv-vis. electronic spectra and thermal analyses. The electrical properties (AC resistivity and dielectric constant) of both complexes were investigated. The positron annihilation Doppler broadening (PADB) spectroscopies were also used to probe the structural changes of both complexes. The PADB line-shape parameters (S and W) were found to be dependent on the structure, electronic configuration of the charge transfer complex. The PADB technique is a powerful tool to probe the structural features of the KI-I2-amino acid complexes.

Electron transfer function versus oxygen delivery: a comparative study for several hexacoordinated globins across the animal kingdom.

PubMed

Kiger, Laurent; Tilleman, Lesley; Geuens, Eva; Hoogewijs, David; Lechauve, Christophe; Moens, Luc; Dewilde, Sylvia; Marden, Michael C

2011-01-01

Caenorhabditis elegans globin GLB-26 (expressed from gene T22C1.2) has been studied in comparison with human neuroglobin (Ngb) and cytoglobin (Cygb) for its electron transfer properties. GLB-26 exhibits no reversible binding for O(2) and a relatively low CO affinity compared to myoglobin-like globins. These differences arise from its mechanism of gaseous ligand binding since the heme iron of GLB-26 is strongly hexacoordinated in the absence of external ligands; the replacement of this internal ligand, probably the E7 distal histidine, is required before binding of CO or O(2) as for Ngb and Cygb. Interestingly the ferrous bis-histidyl GLB-26 and Ngb, another strongly hexacoordinated globin, can transfer an electron to cytochrome c (Cyt-c) at a high bimolecular rate, comparable to those of inter-protein electron transfer in mitochondria. In addition, GLB-26 displays an unexpectedly rapid oxidation of the ferrous His-Fe-His complex without O(2) actually binding to the iron atom, since the heme is oxidized by O(2) faster than the time for distal histidine dissociation. These efficient mechanisms for electron transfer could indicate a family of hexacoordinated globin which are functionally different from that of pentacoordinated globins.

Density functional theory study on the influence of pyrrolidine substituent of C60 bisadduct on its supramolecular interaction with porphine

NASA Astrophysics Data System (ADS)

Zhao, Li-Hong; Weng, Jun-Ying; Zhao, Wei; Ruan, Wen-Juan; Xin, Fei; Zhang, Ying-Hui

2013-09-01

Calculation using three kinds of density functional theory (DFT) methods revealed that the nonbonded interaction of pyrrolidine-functionalized C60 bisadducts with porphine derivatives (MP: M = Zn, 2H) was significantly affected by pyrrolidine substituents. Several types of the stable interaction configurations of trans-3 C60 bisadduct/ZnP complex (abbreviated as tran-3/ZnP) were compared. The association energy predicted by the wB97XD method was larger than that predicted by CAM-B3LYP and BHandH functionals. The results showed that the closer approach of porphine ring to the two pyrrolidine substituents, the larger the association energy of the complex. This trend was ascribed to the additional C-H⋯π interaction between the pyrrolidine and porphine rings. The natural bond orbital analysis proved the existence of an additional charge transfer process between the porphine and pyrrolidine rings for the t-I type of trans-3/porphine complexes. The red shift of absorption peaks of porphine were predicted in consistent with general experimental results.

Formation of stable and functional HIV-1 nucleoprotein complexes in vitro.

PubMed

Tanchou, V; Gabus, C; Rogemond, V; Darlix, J L

1995-10-06

HIV genomic RNA resides within the nucleocapsid, in the interior of the virus, which serves to protect the RNA against nuclease degradation and to promote its reverse transcription. To investigate the role of nucleocapsid protein (NCp7) in the stability and replication of genomic RNA within the nucleocapsid, we used NCp7, reverse transcriptase (RT) and RNAs representing the 5' and 3' regions of the genome to reconstitute functional HIV-1 nucleocapsids. The nucleoprotein complexes generated in vitro were found to be stable, which, according to biochemical and genetic data, probably results from the tight binding of NCp7 molecules to the RNA and strong NCp7/NCp7 interactions. The nucleoprotein complexes efficiently protected viral RNA against RNase degradation and, at the same time, promoted viral DNA synthesis by RT. DNA strand transfer from the 5' to the 3' RNA template was very efficient in nucleoprotein complexes formed in the presence of both RNAs, but not when the RNAs were in separate complexes. These results indicate that the in vitro reconstituted HIV-1 nucleoprotein complexes function like virion nucleocapsids and thus provide a way to study at the molecular level this viral substructure and the synthesis of proviral DNA, and to search for new anti-HIV agents.

Electronic connection between the quinone and cytochrome C redox pools and its role in regulation of mitochondrial electron transport and redox signaling.

PubMed

Sarewicz, Marcin; Osyczka, Artur

2015-01-01

Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria. Copyright © 2015 the American Physiological Society.

Electronic Connection Between the Quinone and Cytochrome c Redox Pools and Its Role in Regulation of Mitochondrial Electron Transport and Redox Signaling

PubMed Central

Sarewicz, Marcin; Osyczka, Artur

2015-01-01

Mitochondrial respiration, an important bioenergetic process, relies on operation of four membranous enzymatic complexes linked functionally by mobile, freely diffusible elements: quinone molecules in the membrane and water-soluble cytochromes c in the intermembrane space. One of the mitochondrial complexes, complex III (cytochrome bc1 or ubiquinol:cytochrome c oxidoreductase), provides an electronic connection between these two diffusible redox pools linking in a fully reversible manner two-electron quinone oxidation/reduction with one-electron cytochrome c reduction/oxidation. Several features of this homodimeric enzyme implicate that in addition to its well-defined function of contributing to generation of proton-motive force, cytochrome bc1 may be a physiologically important point of regulation of electron flow acting as a sensor of the redox state of mitochondria that actively responds to changes in bioenergetic conditions. These features include the following: the opposing redox reactions at quinone catalytic sites located on the opposite sides of the membrane, the inter-monomer electronic connection that functionally links four quinone binding sites of a dimer into an H-shaped electron transfer system, as well as the potential to generate superoxide and release it to the intermembrane space where it can be engaged in redox signaling pathways. Here we highlight recent advances in understanding how cytochrome bc1 may accomplish this regulatory physiological function, what is known and remains unknown about catalytic and side reactions within the quinone binding sites and electron transfers through the cofactor chains connecting those sites with the substrate redox pools. We also discuss the developed molecular mechanisms in the context of physiology of mitochondria. PMID:25540143

Ecological networks to unravel the routes to horizontal transposon transfers.

PubMed

Venner, Samuel; Miele, Vincent; Terzian, Christophe; Biémont, Christian; Daubin, Vincent; Feschotte, Cédric; Pontier, Dominique

2017-02-01

Transposable elements (TEs) represent the single largest component of numerous eukaryotic genomes, and their activity and dispersal constitute an important force fostering evolutionary innovation. The horizontal transfer of TEs (HTT) between eukaryotic species is a common and widespread phenomenon that has had a profound impact on TE dynamics and, consequently, on the evolutionary trajectory of many species' lineages. However, the mechanisms promoting HTT remain largely unknown. In this article, we argue that network theory combined with functional ecology provides a robust conceptual framework and tools to delineate how complex interactions between diverse organisms may act in synergy to promote HTTs.

Mechanistic insights into iron catalyzed dehydrogenation of formic acid: β-hydride elimination vs. direct hydride transfer.

PubMed

Yang, Xinzheng

2013-09-07

Density functional theory calculations reveal a complete reaction mechanism with detailed energy profiles and transition state structures for the dehydrogenation of formic acid catalyzed by an iron complex, [P(CH2CH2PPh2)3FeH](+). In the cationic reaction pathway, a β-hydride elimination process is confirmed to be the rate-determining step in this catalytic reaction. A potential reaction pathway starting with a direct hydride transfer from HCOO(-) to Fe is found to be possible, but slightly less favorable than the catalytic cycle with a β-hydride elimination step.

Functional analogue reaction systems of the DMSO reductase isoenzyme family: probable mechanism of S-oxide reduction in oxo transfer reactions mediated by bis(dithiolene)-tungsten(IV,VI) complexes.

PubMed

Sung, Kie-Moon; Holm, R H

2002-04-24

The recent development of structural and functional analogues of the DMSO reductase family of isoenzymes allows mechanistic examination of the minimal oxygen atom transfer paradigm M(IV) + QO M(VI) O + Q with the biological metals M = Mo and W. Systematic variation of the electronic environment at the WIV center of desoxo bis(dithiolene) complexes is enabled by introduction of para-substituted phenyl groups in the equatorial (eq) dithiolene ligand and the axial (ax) phenolate ligand. The compounds [W(CO)2(S2C2(C6H4-p-X)2)2] (54-60%) have been prepared by ligand transfer from [Ni(S2C2(C6H4-p-X)2)2] to [W(CO)3(MeCN)3]. A series of 25 complexes [W(IV)(OC6H4-p-X')(S2C2(C6H4-p-X)2)2]1- ([X4,X'], X = Br, F, H, Me, OMe; X' = CN, Br, H, Me, NH2; 41-53%) has been obtained by ligand substitution of five dicarbonyl complexes with five phenolate ligands. Linear free energy relationships between E1/2 and Hammett constant p for the electron-transfer series [Ni(S2C2(C6H4-p-X)2)2]0,1-,2- and [W(CO)2(S2C2(C6H4-p-X)2)2]0,1-,2- demonstrate a substituent influence on electron density distribution at the metal center. The reactions [WIV(OC6H4-p-X')(S2C2(C6H4-p-X)2)2]1- + (CH2)4SO [W(VI)O(OC6H4-p-X')(S2C2(C6H4-p-X)2)2]1- + (CH2)4S with constant substrate are second order with large negative activation entropies indicative of an associative transition state. Rate constants at 298 K adhere to the Hammett equations log(k([X4,X']/k[X4,H]) = rho(ax)sigma(p) and log(k[X4,X']/k([H4,X']) = 4rho(eq)sigma(p). Electron-withdrawing groups (EWG) and electron-donating groups (EDG) have opposite effects on the rate such that k(EWG) > k(EDG). The effects of X' on reactivity are found to be approximately 5 times greater than that of X (rho(ax) = 2.1, rho(eq) = 0.44) in the Hammett equation. Using these and other findings, a stepwise oxo transfer reaction pathway is proposed in which an early transition state, of primary W(IV)-O(substrate) bond-making character, is rate-limiting. This is followed by a six-coordinate substrate complex and a second transition state proposed to involve atom and electron transfer leading to the development of the W(VI)=O group. This work is the most detailed mechanistic investigation of oxo transfer mediated by a biological metal.

Linear control theory for gene network modeling.

PubMed

Shin, Yong-Jun; Bleris, Leonidas

2010-09-16

Systems biology is an interdisciplinary field that aims at understanding complex interactions in cells. Here we demonstrate that linear control theory can provide valuable insight and practical tools for the characterization of complex biological networks. We provide the foundation for such analyses through the study of several case studies including cascade and parallel forms, feedback and feedforward loops. We reproduce experimental results and provide rational analysis of the observed behavior. We demonstrate that methods such as the transfer function (frequency domain) and linear state-space (time domain) can be used to predict reliably the properties and transient behavior of complex network topologies and point to specific design strategies for synthetic networks.

Impacts of natural disturbance on soil carbon dynamics in forest ecosystems

Treesearch

Steven T. Overby; Stephen C. Hart; Daniel G. Neary

2002-01-01

Forest soils are entities within themselves, self-organized and highly resilient over time. The transfer of energy bound in carbon (C) molecules drives the organization and functions of this biological system (Fisher and Binkley, 2000; Paul and Clark, 1996). Photosynthetic organisms reduce atmospheric C and store energy from solar radiation in the formation of complex...

Hydrogeologic controls on summer stream temperatures in the McKenzie River basin, Oregon

Treesearch

Christina Tague; Michael Farrell; Gordon Grant; Sarah Lewis; Serge Rey

2007-01-01

Stream temperature is a complex function of energy inputs including solar radiation and latent and sensible heat transfer. In streams where groundwater inputs are significant, energy input through advection can also be an important control on stream temperature. For an individual stream reach, models of stream temperature can take advantage of direct measurement or...

Infrared spectra of proton transfer complexes of the cycleanine alkaloid in solid state

NASA Astrophysics Data System (ADS)

Kasende, Okuma E.; de Waal, D.

2003-01-01

Proton transfer complexes obtained between the cycleanine alkaloid and hydrogen chloride, hydrogen bromide and nitric acids have been investigated by infrared spectroscopic technique between 4000 and 400 cm -1 in KBr. The vibrational perturbations brought about by proton transfer complex formation, discussed in terms of preferred site of interaction, show that the proton of the inorganic acids is transferred to cycleanine through one of its N sites.

C-PCM based calculation of energy profiles for proton transfer in phosphorus-containing acid- N, N-dimethylformamide complexes

NASA Astrophysics Data System (ADS)

Fedorova, I. V.; Khatuntseva, E. A.; Krest'yaninov, M. A.; Safonova, L. P.

2016-02-01

Proton transfer along the hydrogen bond in complexes of DMF with H3PO4, H3PO3, CH3H2PO3, and their dimers has been investigated by the B3LYP/6-31++G** method in combination with the C-PCM model. When the Oacid···ODMF distance ( R) in the scanning procedure is not fixed, the energy profile in all cases has a single well. When this distance is fixed, there can be a proton transfer in all of the complexes in the gas phase at R > 2.6 Å; if solvation is taken into account, proton transfer can take place at R > 2.4 Å ( R > 2.5 Å for DMF complexes with CH3H2PO3 and its dimer). The height of the energy barrier to proton transfer increases with increasing R. Proton transfer is energetically most favorable in the DMF-phosphoric acid complexes. The structural and energetic characteristics of the hydrogen-bonded complexes calculated on the basis of the solvation model are compared with the same parameters for the complexes in the gas phase.

Synthesis and electrochemical studies of charge-transfer complexes of thiazolidine-2,4-dione with σ and π acceptors

NASA Astrophysics Data System (ADS)

Singh, Prashant; Kumar, Pradeep; Katyal, Anju; Kalra, Rashmi; Dass, Sujata K.; Prakash, Satya; Chandra, Ramesh

2010-03-01

In the present work, we report the synthesis and characterization of novel charge-transfer complexes of thiazolidine-2,4-dione (TZD) with sigma acceptor (iodine) and pi acceptors (chloranil, dichlorodicyanoquinone, picric acid and duraquinone). We also evaluated their thermal and electrochemical properties and we conclude that these complexes are frequency dependent. Charge-transfer complex between thiazolidine-2,4-dione and iodine give best conductivity. In conclusion, complex with sigma acceptors are more conducting than with pi acceptors.

Are Model Transferability And Complexity Antithetical? Insights From Validation of a Variable-Complexity Empirical Snow Model in Space and Time

NASA Astrophysics Data System (ADS)

Lute, A. C.; Luce, Charles H.

2017-11-01

The related challenges of predictions in ungauged basins and predictions in ungauged climates point to the need to develop environmental models that are transferable across both space and time. Hydrologic modeling has historically focused on modelling one or only a few basins using highly parameterized conceptual or physically based models. However, model parameters and structures have been shown to change significantly when calibrated to new basins or time periods, suggesting that model complexity and model transferability may be antithetical. Empirical space-for-time models provide a framework within which to assess model transferability and any tradeoff with model complexity. Using 497 SNOTEL sites in the western U.S., we develop space-for-time models of April 1 SWE and Snow Residence Time based on mean winter temperature and cumulative winter precipitation. The transferability of the models to new conditions (in both space and time) is assessed using non-random cross-validation tests with consideration of the influence of model complexity on transferability. As others have noted, the algorithmic empirical models transfer best when minimal extrapolation in input variables is required. Temporal split-sample validations use pseudoreplicated samples, resulting in the selection of overly complex models, which has implications for the design of hydrologic model validation tests. Finally, we show that low to moderate complexity models transfer most successfully to new conditions in space and time, providing empirical confirmation of the parsimony principal.

GW-BSE approach on S1 vertical transition energy of large charge transfer compounds: A performance assessment.

PubMed

Ziaei, Vafa; Bredow, Thomas

2016-11-07

In this work, we apply many-body perturbation theory (MBPT) on large critical charge transfer (CT) complexes to assess its performance on the S 1 excitation energy. Since the S 1 energy of CT compounds is heavily dependent on the Hartree-Fock (HF) exchange fraction in the reference density functional, MBPT opens a new way for reliable prediction of CT S 1 energy without explicit knowledge of suitable amount of HF-exchange, in contrary to the time-dependent density functional theory (TD-DFT), where depending on various functionals, large errors can arise. Thus, simply by starting from a (semi-)local reference functional and performing update of Kohn-Sham (KS) energies in the Green's function G while keeping dynamical screened interaction (W(ω)) frozen to the mean-field level, we obtain impressingly highly accurate S 1 energy at slightly higher computational cost in comparison to TD-DFT. However, this energy-only updating mechanism in G fails to work if the initial guess contains a fraction or 100% HF-exchange, and hence considerably inaccurate S 1 energy is predicted. Furthermore, eigenvalue updating both in G and W(ω) overshoots the S 1 energy due to enhanced underscreening of W(ω), independent of the (hybrid-)DFT starting orbitals. A full energy-update on top of HF orbitals even further overestimates the S 1 energy. An additional update of KS wave functions within the Quasi-Particle Self-Consistent GW (QSGW) deteriorates results, in stark contrast to the good results obtained from QSGW for periodic systems. For the sake of transferability, we further present data of small critical non-charge transfer systems, confirming the outcomes of the CT-systems.

Analysis of transition-metal acetylacetonate complexes by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Wyatt, Mark F; Havard, Stephen; Stein, Bridget K; Brenton, A Gareth

2008-01-01

Transition-metal acetylacetonate complexes of the form Metal(acac)(2), where Metal = Fe(II), Co(II), Ni(II), Cu(II), and Zn(II), and Metal(acac)(3), where Metal = V(III), Cr(III), Mn(III), Fe(III), and Co(III), were investigated by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOFMS). The data was acquired using the aprotic, electron transfer matrix, 2-[(2E)-3-(4-tert-butylphenyl)-2-methylprop-2-enylidene]malononitrile (DCTB), and the observation of positive radical ions is shown clearly to depend on the metal element and the oxidation state it occupies. The ionization energy of DCTB was calculated to be 8.08 eV by density functional theory methods, which is notably lower than the experimental value, but within the range of other computational values. This value is very close to those of the analytes, so the existing electron transfer mechanism which is based on the ionization energies of the matrix and analyte, cannot be used predictively. Similarly, the data neither proves nor disproves the validity of the existing electron transfer ionization mechanism, with respect to metal coordination complexes without strong chromophores. In this case, periodic trends may be more useful in explaining the observed species and the prediction of species from sets of similar complexes. The addition of a sodium salt benefits the MALDI-TOFMS characterization of certain compounds studied, but the benefit of the addition of ammonium or silver salts is negligible.

Horizontally transferred genes in the genome of Pacific white shrimp, Litopenaeus vannamei

PubMed Central

2013-01-01

Background In recent years, as the development of next-generation sequencing technology, a growing number of genes have been reported as being horizontally transferred from prokaryotes to eukaryotes, most of them involving arthropods. As a member of the phylum Arthropoda, the Pacific white shrimp Litopenaeus vannamei has to adapt to the complex water environments with various symbiotic or parasitic microorganisms, which provide a platform for horizontal gene transfer (HGT). Results In this study, we analyzed the genome-wide HGT events in L. vannamei. Through homology search and phylogenetic analysis, followed by experimental PCR confirmation, 14 genes with HGT event were identified: 12 of them were transferred from bacteria and two from fungi. Structure analysis of these genes showed that the introns of the two fungi-originated genes were substituted by shrimp DNA fragment, two genes transferred from bacteria had shrimp specific introns inserted in them. Furthermore, around other three bacteria-originated genes, there were three large DNA segments inserted into the shrimp genome. One segment was a transposon that fully transferred, and the other two segments contained only coding regions of bacteria. Functional prediction of these 14 genes showed that 6 of them might be related to energy metabolism, and 4 others related to defense of the organism. Conclusions HGT events from bacteria or fungi were happened in the genome of L. vannamei, and these horizontally transferred genes can be transcribed in shrimp. This is the first time to report the existence of horizontally transferred genes in shrimp. Importantly, most of these genes are exposed to a negative selection pressure and appeared to be functional. PMID:23914989

Oxoiron(IV) Tetramethylcyclam Complexes with Axial Carboxylate Ligands: Effect of Tethering the Carboxylate on Reactivity.

PubMed

Bigelow, Jennifer O; England, Jason; Klein, Johannes E M N; Farquhar, Erik R; Frisch, Jonathan R; Martinho, Marlène; Mandal, Debasish; Münck, Eckard; Shaik, Sason; Que, Lawrence

2017-03-20

Oxoiron(IV) species are implicated as reactive intermediates in nonheme monoiron oxygenases, often acting as the agent for hydrogen-atom transfer from substrate. A histidine is the most likely ligand trans to the oxo unit in most enzymes characterized thus far but is replaced by a carboxylate in the case of isopenicillin N synthase. As the effect of a trans carboxylate ligand on the properties of the oxoiron(IV) unit has not been systematically studied, we have synthesized and characterized four oxoiron(IV) complexes supported by the tetramethylcyclam (TMC) macrocycle and having a carboxylate ligand trans to the oxo unit. Two complexes have acetate or propionate axial ligands, while the other two have the carboxylate functionality tethered to the macrocyclic ligand framework by one or two methylene units. Interestingly, these four complexes exhibit substrate oxidation rates that differ by more than 100-fold, despite having E p,c values for the reduction of the Fe═O unit that span a range of only 130 mV. Eyring parameters for 1,4-cyclohexadiene oxidation show that reactivity differences originate from differences in activation enthalpy between complexes with tethered carboxylates and those with untethered carboxylates, in agreement with computational results. As noted previously for the initial subset of four complexes, the logarithms of the oxygen atom transfer rates of 11 complexes of the Fe IV (O)TMC(X) series increase linearly with the observed E p,c values, reflecting the electrophilicity of the Fe═O unit. In contrast, no correlation with E p,c values is observed for the corresponding hydrogen atom transfer (HAT) reaction rates; instead, the HAT rates increase as the computed triplet-quintet spin state gap narrows, consistent with Shaik's two-state-reactivity model. In fact, the two complexes with untethered carboxylates are among the most reactive HAT agents in this series, demonstrating that the axial ligand can play a key role in tuning the HAT reactivity in a nonheme iron enzyme active site.

Electrocatalysis of borohydride oxidation: a review of density functional theory approach combined with experimental validation.

PubMed

Escaño, Mary Clare Sison; Arevalo, Ryan Lacdao; Gyenge, Elod; Kasai, Hideaki

2014-09-03

The electrocatalysis of borohydride oxidation is a complex, up-to-eight-electron transfer process, which is essential for development of efficient direct borohydride fuel cells. Here we review the progress achieved by density functional theory (DFT) calculations in explaining the adsorption of BH4(-) on various catalyst surfaces, with implications for electrocatalyst screening and selection. Wherever possible, we correlate the theoretical predictions with experimental findings, in order to validate the proposed models and to identify potential directions for further advancements.

Electrocatalysis of borohydride oxidation: a review of density functional theory approach combined with experimental validation

NASA Astrophysics Data System (ADS)

Sison Escaño, Mary Clare; Lacdao Arevalo, Ryan; Gyenge, Elod; Kasai, Hideaki

2014-09-01

The electrocatalysis of borohydride oxidation is a complex, up-to-eight-electron transfer process, which is essential for development of efficient direct borohydride fuel cells. Here we review the progress achieved by density functional theory (DFT) calculations in explaining the adsorption of BH4- on various catalyst surfaces, with implications for electrocatalyst screening and selection. Wherever possible, we correlate the theoretical predictions with experimental findings, in order to validate the proposed models and to identify potential directions for further advancements.

Ground state intermolecular proton transfer in the supersystems thymine-(H2O)n and thymine-(CH3OH)n, n = 1,2: a theoretical study.

PubMed

Delchev, Vassil B; Shterev, Ivan G

2009-04-01

Twelve binary and eight ternary supersystems between thymine and methanol, and water were investigated in the ground state at the B3LYP and MP2 levels of theory using B3LYP/6-311 + + G(d,p) basis functions. The thermodynamics of complex formations and the mechanisms of intermolecular proton transfers were clarified in order to find out the most stable H-boned system. It was established that the energy barriers of the water/methanol-assisted proton transfers are several times lower than those of the intramolecular proton transfers in the DNA/RNA bases. The X-ray powder spectra of thymine, and this precrystallized from water and methanol showed that water molecules are incorporated in the crystal lattice of thymine forming H-bridges between thymine molecules.

Improvements to Fidelity, Generation and Implementation of Physics-Based Lithium-Ion Reduced-Order Models

NASA Astrophysics Data System (ADS)

Rodriguez Marco, Albert

Battery management systems (BMS) require computationally simple but highly accurate models of the battery cells they are monitoring and controlling. Historically, empirical equivalent-circuit models have been used, but increasingly researchers are focusing their attention on physics-based models due to their greater predictive capabilities. These models are of high intrinsic computational complexity and so must undergo some kind of order-reduction process to make their use by a BMS feasible: we favor methods based on a transfer-function approach of battery cell dynamics. In prior works, transfer functions have been found from full-order PDE models via two simplifying assumptions: (1) a linearization assumption--which is a fundamental necessity in order to make transfer functions--and (2) an assumption made out of expedience that decouples the electrolyte-potential and electrolyte-concentration PDEs in order to render an approach to solve for the transfer functions from the PDEs. This dissertation improves the fidelity of physics-based models by eliminating the need for the second assumption and, by linearizing nonlinear dynamics around different constant currents. Electrochemical transfer functions are infinite-order and cannot be expressed as a ratio of polynomials in the Laplace variable s. Thus, for practical use, these systems need to be approximated using reduced-order models that capture the most significant dynamics. This dissertation improves the generation of physics-based reduced-order models by introducing different realization algorithms, which produce a low-order model from the infinite-order electrochemical transfer functions. Physics-based reduced-order models are linear and describe cell dynamics if operated near the setpoint at which they have been generated. Hence, multiple physics-based reduced-order models need to be generated at different setpoints (i.e., state-of-charge, temperature and C-rate) in order to extend the cell operating range. This dissertation improves the implementation of physics-based reduced-order models by introducing different blending approaches that combine the pre-computed models generated (offline) at different setpoints in order to produce good electrochemical estimates (online) along the cell state-of-charge, temperature and C-rate range.

Transfer function for vital infrasound pressures between the carotid artery and the tympanic membrane.

PubMed

Furihata, Kenji; Yamashita, Masato

2013-02-01

While occupational injury is associated with numerous individual and work-related risk factors, including long working hours and short sleep duration, the complex mechanisms causing such injuries are not yet fully understood. The relationship between the infrasound pressures of the tympanic membrane [ear canal pressure (ECP)], detected using an earplug embedded with a low-frequency microphone, and the carotid artery [carotid artery pressure (CAP)], detected using a stethoscope fitted with the same microphone, can be quantitatively characterized using systems analysis. The transfer functions of 40 normal workers (19 to 57 years old) were characterized, involving the analysis of 446 data points. The ECP waveform exhibits a pulsatile character with a slow respiratory component, which is superimposed on a biphasic recording that is synchronous with the cardiac cycle. The respiratory ECP waveform correlates with the instantaneous heart rate. The results also revealed that various fatigue-related risk factors may affect the mean magnitudes of the measured pressures and the delay transfer functions between CAP and ECP in the study population; these factors include systolic blood pressure, salivary amylase activity, age, sleep duration, postural changes, chronic fatigue, and pulse rate.

The mitochondrial electron transfer flavoprotein complex is essential for survival of Arabidopsis in extended darkness.

PubMed

Ishizaki, Kimitsune; Schauer, Nicolas; Larson, Tony R; Graham, Ian A; Fernie, Alisdair R; Leaver, Christopher J

2006-09-01

In mammals, the electron transfer flavoprotein (ETF) is a heterodimeric protein composed of two subunits, alpha and beta, that is responsible for the oxidation of at least nine mitochondrial matrix flavoprotein dehydrogenases. Electrons accepted by ETF are further transferred to the main respiratory chain via the ETF ubiquinone oxide reductase (ETFQO). Sequence analysis of the unique Arabidopsis homologues of two subunits of ETF revealed their high similarity to both subunits of the mammalian ETF. Yeast two-hybrid experiments showed that the Arabidopsis ETFalpha and ETFbeta can form a heteromeric protein. Isolation and characterization of two independent T-DNA insertional Arabidopsis mutants of the ETFbeta gene revealed accelerated senescence and early death compared to wild-type during extended darkness. Furthermore in contrast to wild-type, the etfb mutants demonstrated a significant accumulation of several amino acids, isovaleryl CoA and phytanoyl CoA during dark-induced carbohydrate deprivation. These phenotypic characteristics of etfb mutants are broadly similar to those that we observed previously in Arabidopsis etfqo mutants, suggesting functional association between ETF and ETFQO in Arabidopsis, and confirming the essential roles of the ETF/ETFQO electron transfer complex in the catabolism of leucine and involvement in the chlorophyll degradation pathway activated during dark-induced carbohydrate deprivation.

Simulating Ru L 3 -Edge X-ray Absorption Spectroscopy with Time-Dependent Density Functional Theory: Model Complexes and Electron Localization in Mixed-Valence Metal Dimers

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

Van Kuiken, Benjamin E.; Valiev, Marat; Daifuku, Stephanie L.

2013-05-30

Ruthenium L3-edge X-ray absorption (XA) spectroscopy probes unoccupied 4d orbitals of the metal atom and is increasingly being used to investigate the local electronic structure in ground and excited electronic states of Ru complexes. The simultaneous development of computational tools for simulating Ru L3-edge spectra is crucial for interpreting the spectral features at a molecular level. This study demonstrates that time-dependent density functional theory (TDDFT) is a viable and predictive tool for simulating ruthenium L3-edge XA spectroscopy. We systematically investigate the effects of exchange correlation functional and implicit and explicit solvent interactions on a series of RuII and RuIII complexesmore » in their ground and electronic excited states. The TDDFT simulations reproduce all of the experimentally observed features in Ru L3-edge XA spectra within the experimental resolution (0.4 eV). Our simulations identify ligand-specific charge transfer features in complicated Ru L3-edge spectra of [Ru(CN)6]4- and RuII polypyridyl complexes illustrating the advantage of using TDDFT in complex systems. We conclude that the B3LYP functional most accurately predicts the transition energies of charge transfer features in these systems. We use our TDDFT approach to simulate experimental Ru L3-edge XA spectra of transition metal mixed-valence dimers of the form [(NC)5MII-CN-RuIII(NH3)5] (where M = Fe or Ru) dissolved in water. Our study determines the spectral signatures of electron delocalization in Ru L3-edge XA spectra. We find that the inclusion of explicit solvent molecules is necessary for reproducing the spectral features and the experimentally determined valencies in these mixed-valence complexes. This study validates the use of TDDFT for simulating Ru 2p excitations using popular quantum chemistry codes and providing a powerful interpretive tool for equilibrium and ultrafast Ru L3-edge XA spectroscopy.« less

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

Hong, Seungwoo; Lu, Xiaoyan; Lee, Yong -Min

Here, a mononuclear nonheme iron(V)-imido complex bearing a tetraamido macrocyclic ligand (TAML), [Fe V(NTs)(TAML)] – (1), was oxidized by one-electron oxidants, affording formation of an iron(V)-imido TAML cation radical species, [Fe V(NTs)(TAML +•)] (2); 2 is a diamagnetic (S = 0) complex, resulting from the antiferromagnetic coupling of the low-spin iron(V) ion (S = 1/2) with the one-electron oxidized ligand (TAML +•). 2 is a competent oxidant in C–H bond functionalization and nitrene transfer reaction, showing that the reactivity of 2 is greater than that of 1.

An anionic rhodium eta4-quinonoid complex as a multifunctional catalyst for the arylation of aldehydes with arylboronic acids.

PubMed

Son, Seung Uk; Kim, Sang Bok; Reingold, Jeffrey A; Carpenter, Gene B; Sweigart, Dwight A

2005-09-07

The pi-bonded rhodium quinonoid complex, K+[(1,4-benzoquinone)Rh(COD)]-, functions as a good catalyst for the coupling of arylboronic acid and aldehydes to afford diaryl alcohols. The catalysis is heterobimetallic in that both the transition metal and concomitant alkali metal counterion play an integral part in the reaction. In addition, the anionic quinonoid catalyst itself plays a bifunctional role by acting as a ligand to the boronic acid and as a Lewis acid receptor site for the transferring aryl group.

The effect of substituted moiety on the optoelectronic and photophysical properties of tris (phenylbenzimidazolinato) Ir (III) carbene complexes and the OLED performance: a theoretical study

NASA Astrophysics Data System (ADS)

Srivastava, Ruby

2015-06-01

Density functional theory (DFT) and time-dependent density functional theory (TDDFT) are used to analyse theoretically the optoelectronic, photophysical properties and organic light-emitting diode performance of a series of fac-mer blue-emitting Iridium (III) carbene complexes. Swain-Lupton constant is used to discuss the substituents effect. 5d-orbital splitting and d-d* transitions are calculated to assess the efficiency of the studied complexes. The reorganisation energies (λ), transfer integrals, mobilities, radiative decay rate (kr), and triplet exciton generation fraction (χT) are also calculated. Due to the higher χT of these complexes, the formation of triplet exciton will be more and it will cause a faster intersystem crossing. Two host materials are proposed and host-guest match (Dexter-Förster energy) is also discussed. We hope that this unified work will surely help to design new blue-emitting phosphorescent materials in future.

Minimal Model of Quantum Kinetic Clusters for the Energy-Transfer Network of a Light-Harvesting Protein Complex.

PubMed

Wu, Jianlan; Tang, Zhoufei; Gong, Zhihao; Cao, Jianshu; Mukamel, Shaul

2015-04-02

The energy absorbed in a light-harvesting protein complex is often transferred collectively through aggregated chromophore clusters. For population evolution of chromophores, the time-integrated effective rate matrix allows us to construct quantum kinetic clusters quantitatively and determine the reduced cluster-cluster transfer rates systematically, thus defining a minimal model of energy-transfer kinetics. For Fenna-Matthews-Olson (FMO) and light-havrvesting complex II (LCHII) monomers, quantum Markovian kinetics of clusters can accurately reproduce the overall energy-transfer process in the long-time scale. The dominant energy-transfer pathways are identified in the picture of aggregated clusters. The chromophores distributed extensively in various clusters can assist a fast and long-range energy transfer.

Simulation-Based Approach to Determining Electron Transfer Rates Using Square-Wave Voltammetry.

PubMed

Dauphin-Ducharme, Philippe; Arroyo-Currás, Netzahualcóyotl; Kurnik, Martin; Ortega, Gabriel; Li, Hui; Plaxco, Kevin W

2017-05-09

The efficiency with which square-wave voltammetry differentiates faradic and charging currents makes it a particularly sensitive electroanalytical approach, as evidenced by its ability to measure nanomolar or even picomolar concentrations of electroactive analytes. Because of the relative complexity of the potential sweep it uses, however, the extraction of detailed kinetic and mechanistic information from square-wave data remains challenging. In response, we demonstrate here a numerical approach by which square-wave data can be used to determine electron transfer rates. Specifically, we have developed a numerical approach in which we model the height and the shape of voltammograms collected over a range of square-wave frequencies and amplitudes to simulated voltammograms as functions of the heterogeneous rate constant and the electron transfer coefficient. As validation of the approach, we have used it to determine electron transfer kinetics in both freely diffusing and diffusionless surface-tethered species, obtaining electron transfer kinetics in all cases in good agreement with values derived using non-square-wave methods.

Toward understanding as photosynthetic biosignatures: light harvesting and energy transfer calculation

NASA Astrophysics Data System (ADS)

Komatsu, Y.; Umemura, M.; Shoji, M.; Shiraishi, K.; Kayanuma, M.; Yabana, K.

2014-03-01

Among several proposed biosignatures, red edge is a direct evidence of photosynthetic life if it is detected (Kiang et al 2007). Red edge is a sharp change in reflectance spectra of vegetation in NIR region (about 700-750 nm). The sign of red edge is observed by Earthshine or remote sensing (Wolstencroft & Raven 2002, Woolf et al 2002). But, why around 700-750 nm? The photosynthetic organisms on Earth have evolved to optimize the sunlight condition. However, if we consider about photosynthetic organism on extrasolar planets, they should have developed to utilize the spectra of its principal star. Thus, it is not strange even if it shows different vegetation spectra. In this study, we focused on the light absorption mechanism of photosynthetic organisms on Earth and investigated the fundamental properties of the light harvesting mechanisms, which is the first stage for the light absorption. Light harvesting complexes contain photosynthetic pigments like chlorophylls. Effective light absorption and the energy transfer are accomplished by the electronic excitations of collective photosynthetic pigments. In order to investigate this mechanism, we constructed an energy transfer model by using a dipole-dipole approximation for the interactions between electronic excitations. Transition moments and transition energies of each pigment are calculated at the time-dependent density functional theory (TDDFT) level (Marques & Gross 2004). Quantum dynamics simulation for the excitation energy transfer was calculated by the Liouvelle's equation. We adopted the model to purple bacteria, which has been studied experimentally and known to absorb lower energy. It is meaningful to focus on the mechanism of this bacteria, since in the future mission, M planets will become a important target. We calculated the oscillator strengths in one light harvesting complex and confirmed the validity by comparing to the experimental data. This complex is made of an inner and an outer ring. The energy transfer from the outer to the inner ring can be reproduced. To deal with a realistic system, we calculated at a macro structural model. The energy transfer between light harvesting complexes is accomplished rapidly via inner rings. By exchange the original pigment to a pigment absorb lower energy, faster energy transfer occurs and the density was trapped in pigment having lower energy. We will compare the result of purple bacteria, which is considered to show longer red edge, cyanobacteria and plants.

AIE active multianalyte fluorescent probe for the detection of Cu2+, Ni2+ and Hg2+ ions.

PubMed

Pannipara, Mehboobali; Al-Sehemi, Abdullah G; Irfan, Ahmad; Assiri, Mohammed; Kalam, Abul; Al-Ammari, Yahya S

2018-08-05

A novel pyrazolyl chromene derivative (Probe 1) displaying aggregation induced emission (AIE) properties that capable of sensing of multiple metal ions has been designed and synthesized. The multi analyte probe exhibits selective sensing for Cu 2+ and Ni 2+ ions via fluorescence turn-off mechanism and ratiometric selectivity for Hg 2+ ions in aqueous media. The extent of binding of the probe with sensitive metal ions has been demonstrated. The experimental results were further investigated by computational means by optimizing the ground state geometries of Probe 1 and its various metal complexes for Probe 1-Ni, Probe 1-Hg and Probe 1-Cu using density functional theory (DFT) at B3LYP/6-31+g(d,p) (LANL2DZ) level. On the basis of binding energies, the stability of metal complexes has been studied. In Probe 1-Ni and Probe 1-Cu complexes, charge transfer has been observed from Probe 1 to metal ions revealing ligand to metal charge transfer (LMCT) while in Probe1-Hg complex LMCT as well as intra-molecular charge tranfer (ICT) within Probe 1. Copyright © 2018 Elsevier B.V. All rights reserved.

Copper(II) adsorption on the kaolinite(001) surface: Insights from first-principles calculations and molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Kong, Xiang-Ping; Wang, Juan

2016-12-01

The adsorption behavior of Cu(II) on the basal hydroxylated kaolinite(001) surface in aqueous environment was investigated by first-principles calculations and molecular dynamics simulations. Structures of possible monodentate and bidentate inner-sphere adsorption complexes of Cu(II) were examined, and the charge transfer and bonding mechanism were analyzed. Combining the binding energy of complex, the radial distribution function of Cu(II) with oxygen and the extended X-ray absorption fine structure data, monodentate complex on site of surface oxygen with ;upright; hydrogen and bidentate complex on site of two oxygens (one with ;upright; hydrogen and one with ;lying; hydrogen) of single Al center have been found to be the major adsorption species of Cu(II). Both adsorption species are four-coordinated with a square planar geometry. The distribution of surface hydroxyls with ;lying; hydrogen around Cu(II) plays a key role in the structure and stability of adsorption complex. Upon the Mulliken population analysis and partial density of states, charge transfer occurs with Cu(II) accepting some electrons from both surface oxygens and aqua oxygens, and the bonding Cu 3d-O 2p state filling is primarily responsible for the strong covalent interaction of Cu(II) with surface oxygen.

Mitochondrial Protein Interaction Mapping Identifies Regulators of Respiratory Chain Function.

PubMed

Floyd, Brendan J; Wilkerson, Emily M; Veling, Mike T; Minogue, Catie E; Xia, Chuanwu; Beebe, Emily T; Wrobel, Russell L; Cho, Holly; Kremer, Laura S; Alston, Charlotte L; Gromek, Katarzyna A; Dolan, Brendan K; Ulbrich, Arne; Stefely, Jonathan A; Bohl, Sarah L; Werner, Kelly M; Jochem, Adam; Westphall, Michael S; Rensvold, Jarred W; Taylor, Robert W; Prokisch, Holger; Kim, Jung-Ja P; Coon, Joshua J; Pagliarini, David J

2016-08-18

Mitochondria are essential for numerous cellular processes, yet hundreds of their proteins lack robust functional annotation. To reveal functions for these proteins (termed MXPs), we assessed condition-specific protein-protein interactions for 50 select MXPs using affinity enrichment mass spectrometry. Our data connect MXPs to diverse mitochondrial processes, including multiple aspects of respiratory chain function. Building upon these observations, we validated C17orf89 as a complex I (CI) assembly factor. Disruption of C17orf89 markedly reduced CI activity, and its depletion is found in an unresolved case of CI deficiency. We likewise discovered that LYRM5 interacts with and deflavinates the electron-transferring flavoprotein that shuttles electrons to coenzyme Q (CoQ). Finally, we identified a dynamic human CoQ biosynthetic complex involving multiple MXPs whose topology we map using purified components. Collectively, our data lend mechanistic insight into respiratory chain-related activities and prioritize hundreds of additional interactions for further exploration of mitochondrial protein function. Copyright © 2016 Elsevier Inc. All rights reserved.

Tunable Crystallinity and Charge Transfer in Two-Dimensional G-Quadruplex Organic Frameworks.

PubMed

Wu, Yi-Lin; Bobbitt, N Scott; Logsdon, Jenna L; Powers-Riggs, Natalia E; Nelson, Jordan N; Liu, Xiaolong; Wang, Timothy C; Snurr, Randall Q; Hupp, Joseph T; Farha, Omar K; Hersam, Mark C; Wasielewski, Michael R

2018-04-03

DNA G-quadruplex structures were recently discovered to provide reliable scaffolding for two-dimensional organic frameworks due to the strong hydrogen-bonding ability of guanine. Herein, 2,7-diaryl pyrene building blocks with high HOMO energies and large optical gaps are incorporated into G-quadruplex organic frameworks. The adjustable substitution on the aryl groups provides an opportunity to elucidate the framework formation mechanism; molecular non-planarity is found to be beneficial for restricting interlayer slippage, and the framework crystallinity is highest when intermolecular interaction and non-planarity strike a fine balance. When guanine-functionalized pyrenes are co-crystallized with naphthalene diimide, charge-transfer (CT) complexes are obtained. The photophysical properties of the pyrene-only and CT frameworks are characterized by UV/Vis and steady-state and time-resolved photoluminescence spectroscopies, and by EPR spectroscopy for the CT complex frameworks. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A theoretical insight for solvent effect on myoglobin assay of W(CO)4L2 type novel complexes with DFT/TDDFT

NASA Astrophysics Data System (ADS)

Üstün, Elvan; Demi˙r, Serpil; Coşkun, Feyzullah; Kaloğlu, Murat; Şahi˙n, Onur; Büyükgüngör, Orhan; Özdemi˙r, İsmail

2016-11-01

Novel tetracarbonyl complexes of type W(CO)4L2 (L: 4-chlorobenzylimidazoline; 4-methylbenzylimidazoline; 3,5-dimethylbenzylimidazoline; 2,4,6-trimethylbenzylimidazoline; 2,3,5,6- tetramethylbenzylimidazoline) were synthesized. Then newly synthesized novel compounds were characterized by IR, 1H NMR, 13C NMR and LC-MS. The characterizations of two of the complexes have also been confirmed with single crystal X-Ray diffraction and DFT optimization results of these complexes have been compared with single crystal results. We have investigated the solvent effect on the structure and metal-to-ligand charge transfer (MLCT) transitions with DFT/TDDFT calculations with ORCA package program with BP86 functional.

Human frataxin activates Fe-S cluster biosynthesis by facilitating sulfur transfer chemistry.

PubMed

Bridwell-Rabb, Jennifer; Fox, Nicholas G; Tsai, Chi-Lin; Winn, Andrew M; Barondeau, David P

2014-08-05

Iron-sulfur clusters are ubiquitous protein cofactors with critical cellular functions. The mitochondrial Fe-S assembly complex, which consists of the cysteine desulfurase NFS1 and its accessory protein (ISD11), the Fe-S assembly protein (ISCU2), and frataxin (FXN), converts substrates l-cysteine, ferrous iron, and electrons into Fe-S clusters. The physiological function of FXN has received a tremendous amount of attention since the discovery that its loss is directly linked to the neurodegenerative disease Friedreich's ataxia. Previous in vitro results revealed a role for human FXN in activating the cysteine desulfurase and Fe-S cluster biosynthesis activities of the Fe-S assembly complex. Here we present radiolabeling experiments that indicate FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe-S clusters. Additional mutagenesis, enzyme kinetic, UV-visible, and circular dichroism spectroscopic studies suggest conserved ISCU2 residue C104 is critical for FXN activation, whereas C35, C61, and C104 are all essential for Fe-S cluster formation on the assembly complex. These results cannot be fully explained by the hypothesis that FXN functions as an iron donor for Fe-S cluster biosynthesis, and further support an allosteric regulator role for FXN. Together, these results lead to an activation model in which FXN accelerates persulfide formation on NFS1 and favors a helix-to-coil interconversion on ISCU2 that facilitates the transfer of sulfur from NFS1 to ISCU2 as an initial step in Fe-S cluster biosynthesis.

Human Frataxin Activates Fe–S Cluster Biosynthesis by Facilitating Sulfur Transfer Chemistry

PubMed Central

2015-01-01

Iron–sulfur clusters are ubiquitous protein cofactors with critical cellular functions. The mitochondrial Fe–S assembly complex, which consists of the cysteine desulfurase NFS1 and its accessory protein (ISD11), the Fe–S assembly protein (ISCU2), and frataxin (FXN), converts substrates l-cysteine, ferrous iron, and electrons into Fe–S clusters. The physiological function of FXN has received a tremendous amount of attention since the discovery that its loss is directly linked to the neurodegenerative disease Friedreich’s ataxia. Previous in vitro results revealed a role for human FXN in activating the cysteine desulfurase and Fe–S cluster biosynthesis activities of the Fe–S assembly complex. Here we present radiolabeling experiments that indicate FXN accelerates the accumulation of sulfur on ISCU2 and that the resulting persulfide species is viable in the subsequent synthesis of Fe–S clusters. Additional mutagenesis, enzyme kinetic, UV–visible, and circular dichroism spectroscopic studies suggest conserved ISCU2 residue C104 is critical for FXN activation, whereas C35, C61, and C104 are all essential for Fe–S cluster formation on the assembly complex. These results cannot be fully explained by the hypothesis that FXN functions as an iron donor for Fe–S cluster biosynthesis, and further support an allosteric regulator role for FXN. Together, these results lead to an activation model in which FXN accelerates persulfide formation on NFS1 and favors a helix-to-coil interconversion on ISCU2 that facilitates the transfer of sulfur from NFS1 to ISCU2 as an initial step in Fe–S cluster biosynthesis. PMID:24971490

Interfacial charge separation and photovoltaic efficiency in Fe(ii)-carbene sensitized solar cells.

PubMed

Pastore, Mariachiara; Duchanois, Thibaut; Liu, Li; Monari, Antonio; Assfeld, Xavier; Haacke, Stefan; Gros, Philippe C

2016-10-12

The first combined theoretical and photovoltaic characterization of both homoleptic and heteroleptic Fe(ii)-carbene sensitized photoanodes in working dye sensitized solar cells (DSSCs) has been performed. Three new heteroleptic Fe(ii)-NHC dye sensitizers have been synthesized, characterized and tested. Despite an improved interfacial charge separation in comparison to the homoleptic compounds, the heteroleptic complexes did not show boosted photovoltaic performances. The ab initio quantitative analysis of the interfacial electron and hole transfers and the measured photovoltaic data clearly evidenced fast recombination reactions for heteroleptics, even associated with un unfavorable directional electron flow, and hence slower injection rates, in the case of homoleptics. Notably, quantum mechanics calculations revealed that deprotonation of the not anchored carboxylic function in the homoleptic complex can effectively accelerate the electron injection rate and completely suppress the electron recombination to the oxidized dye. This result suggests that introduction of strong electron-donating substituents on the not-anchored carbene ligand in heteroleptic complexes, in such a way of mimicking the electronic effects of the carboxylate functionality, should yield markedly improved interfacial charge generation properties. The present results, providing for the first time a detailed understanding of the interfacial electron transfers and photovoltaic characterization in Fe(ii)-carbene sensitized solar cells, open the way to a rational molecular engineering of efficient iron-based dyes for photoelectrochemical applications.

Synthesis of Stable Interfaces on SnO2 Surfaces for Charge-Transfer Applications

NASA Astrophysics Data System (ADS)

Benson, Michelle C.

The commercial market for solar harvesting devices as an alternative energy source requires them to be both low-cost and efficient to replace or reduce the dependence on fossil fuel burning. Over the last few decades there has been promising efforts towards improving solar devices by using abundant and non-toxic metal oxide nanomaterials. One particular metal oxide of interest has been SnO2 due to its high electron mobility, wide-band gap, and aqueous stability. However SnO2 based solar cells have yet to reach efficiency values of other metal oxides, like TiO2. The advancement of SnO2 based devices is dependent on many factors, including improved methods of surface functionalization that can yield stable interfaces. This work explores the use of a versatile functionalization method through the use of the Cu(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction. The CuAAC reaction is capable of producing electrochemically, photochemically, and electrocatalytically active surfaces on a variety of SnO2 materials. The resulting charge-transfer characteristics were investigated as well as an emphasis on understanding the stability of the resulting molecular linkage. We determined the CuAAC reaction is able to proceed through both azide-modified and alkyne-modified surfaces. The resulting charge-transfer properties showed that the molecular tether was capable of supporting charge separation at the interface. We also investigated the enhancement of electron injection upon the introduction of an ultra-thin ZrO2 coating on SnO2. Several complexes were used to fully understand the charge-transfer capabilities, including model systems of ferrocene and a ruthenium coordination complex, a ruthenium mononuclear water oxidation catalyst, and a commercial ruthenium based dye.

Femtosecond dynamics of energy transfer in B800-850 light-harvesting complexes of Rhodobacter sphaeroides.

PubMed Central

Trautman, J K; Shreve, A P; Violette, C A; Frank, H A; Owens, T G; Albrecht, A C

1990-01-01

We report femtosecond transient absorption studies of energy transfer dynamics in the B800-850 light-harvesting complex (LHC) of Rhodobacter sphaeroides 2.4.1. For complexes solubilized in lauryldimethylamine-N-oxide (LDAO), the carotenoid to bacteriochlorophyll (Bchl) B800 and carotenoid to Bchl B850 energy transfer times are 0.34 and 0.20 ps, respectively. The B800 to B850 energy transfer time is 2.5 ps. For complexes treated with lithium dodecyl sulfate (LDS), a carotenoid to B850 energy transfer time of less than or equal to 0.2 ps is seen, and a portion of the total carotenoid population is decoupled from Bchl. In both LDAO-solubilized and LDS-treated complexes an intensity-dependent picosecond decay component of the excited B850 population is ascribed to excitation annihilation within minimal units of the LHC. PMID:2404276

Segregating the core computational faculty of human language from working memory.

PubMed

Makuuchi, Michiru; Bahlmann, Jörg; Anwander, Alfred; Friederici, Angela D

2009-05-19

In contrast to simple structures in animal vocal behavior, hierarchical structures such as center-embedded sentences manifest the core computational faculty of human language. Previous artificial grammar learning studies found that the left pars opercularis (LPO) subserves the processing of hierarchical structures. However, it is not clear whether this area is activated by the structural complexity per se or by the increased memory load entailed in processing hierarchical structures. To dissociate the effect of structural complexity from the effect of memory cost, we conducted a functional magnetic resonance imaging study of German sentence processing with a 2-way factorial design tapping structural complexity (with/without hierarchical structure, i.e., center-embedding of clauses) and working memory load (long/short distance between syntactically dependent elements; i.e., subject nouns and their respective verbs). Functional imaging data revealed that the processes for structure and memory operate separately but co-operatively in the left inferior frontal gyrus; activities in the LPO increased as a function of structural complexity, whereas activities in the left inferior frontal sulcus (LIFS) were modulated by the distance over which the syntactic information had to be transferred. Diffusion tensor imaging showed that these 2 regions were interconnected through white matter fibers. Moreover, functional coupling between the 2 regions was found to increase during the processing of complex, hierarchically structured sentences. These results suggest a neuroanatomical segregation of syntax-related aspects represented in the LPO from memory-related aspects reflected in the LIFS, which are, however, highly interconnected functionally and anatomically.

Multi-domain training in healthy old age: Hotel Plastisse as an iPad-based serious game to systematically compare multi-domain and single-domain training.

PubMed

Binder, Julia C; Zöllig, Jacqueline; Eschen, Anne; Mérillat, Susan; Röcke, Christina; Schoch, Sarah F; Jäncke, Lutz; Martin, Mike

2015-01-01

Finding effective training interventions for declining cognitive abilities in healthy aging is of great relevance, especially in view of the demographic development. Since it is assumed that transfer from the trained to untrained domains is more likely to occur when training conditions and transfer measures share a common underlying process, multi-domain training of several cognitive functions should increase the likelihood of such an overlap. In the first part, we give an overview of the literature showing that cognitive training using complex tasks, such as video games, leisure activities, or practicing a series of cognitive tasks, has shown promising results regarding transfer to a number of cognitive functions. These studies, however, do not allow direct inference about the underlying functions targeted by these training regimes. Custom-designed serious games allow to design training regimes according to specific cognitive functions and a target population's need. In the second part, we introduce the serious game Hotel Plastisse as an iPad-based training tool for older adults that allows the comparison of the simultaneous training of spatial navigation, visuomotor function, and inhibition to the training of each of these functions separately. Hotel Plastisse not only defines the cognitive functions of the multi-domain training clearly, but also implements training in an interesting learning environment including adaptive difficulty and feedback. We propose this novel training tool with the goal of furthering our understanding of how training regimes should be designed in order to affect cognitive functioning of older adults most broadly.

Multi-domain training in healthy old age: Hotel Plastisse as an iPad-based serious game to systematically compare multi-domain and single-domain training

PubMed Central

Binder, Julia C.; Zöllig, Jacqueline; Eschen, Anne; Mérillat, Susan; Röcke, Christina; Schoch, Sarah F.; Jäncke, Lutz; Martin, Mike

2015-01-01

Finding effective training interventions for declining cognitive abilities in healthy aging is of great relevance, especially in view of the demographic development. Since it is assumed that transfer from the trained to untrained domains is more likely to occur when training conditions and transfer measures share a common underlying process, multi-domain training of several cognitive functions should increase the likelihood of such an overlap. In the first part, we give an overview of the literature showing that cognitive training using complex tasks, such as video games, leisure activities, or practicing a series of cognitive tasks, has shown promising results regarding transfer to a number of cognitive functions. These studies, however, do not allow direct inference about the underlying functions targeted by these training regimes. Custom-designed serious games allow to design training regimes according to specific cognitive functions and a target population's need. In the second part, we introduce the serious game Hotel Plastisse as an iPad-based training tool for older adults that allows the comparison of the simultaneous training of spatial navigation, visuomotor function, and inhibition to the training of each of these functions separately. Hotel Plastisse not only defines the cognitive functions of the multi-domain training clearly, but also implements training in an interesting learning environment including adaptive difficulty and feedback. We propose this novel training tool with the goal of furthering our understanding of how training regimes should be designed in order to affect cognitive functioning of older adults most broadly. PMID:26257643

Graph theoretical analysis of complex networks in the brain

PubMed Central

Stam, Cornelis J; Reijneveld, Jaap C

2007-01-01

Since the discovery of small-world and scale-free networks the study of complex systems from a network perspective has taken an enormous flight. In recent years many important properties of complex networks have been delineated. In particular, significant progress has been made in understanding the relationship between the structural properties of networks and the nature of dynamics taking place on these networks. For instance, the 'synchronizability' of complex networks of coupled oscillators can be determined by graph spectral analysis. These developments in the theory of complex networks have inspired new applications in the field of neuroscience. Graph analysis has been used in the study of models of neural networks, anatomical connectivity, and functional connectivity based upon fMRI, EEG and MEG. These studies suggest that the human brain can be modelled as a complex network, and may have a small-world structure both at the level of anatomical as well as functional connectivity. This small-world structure is hypothesized to reflect an optimal situation associated with rapid synchronization and information transfer, minimal wiring costs, as well as a balance between local processing and global integration. The topological structure of functional networks is probably restrained by genetic and anatomical factors, but can be modified during tasks. There is also increasing evidence that various types of brain disease such as Alzheimer's disease, schizophrenia, brain tumours and epilepsy may be associated with deviations of the functional network topology from the optimal small-world pattern. PMID:17908336

Selective ligand activity at Nur/retinoid X receptor complexes revealed by dimer-specific bioluminescence resonance energy transfer-based sensors

PubMed Central

Giner, Xavier C; Cotnoir-White, David; Mader, Sylvie; Lévesque, Daniel

2017-01-01

Retinoid X receptors (RXR) play a role as master regulators due to their capacity to form heterodimers with other nuclear receptors. Accordingly, retinoid signaling is involved in multiple biological processes, including development, cell differentiation, metabolism and cell death. However, the role and functions of RXR in different heterodimer complexes remain unsolved, mainly because most RXR drugs (called rexinoids) are not selective to specific heterodimer complexes. This also strongly limits the use of rexinoids for specific therapeutic approaches. In order to better characterize rexinoids at specific nuclear receptor complexes, we have developed and optimized luciferase protein complementation-based Bioluminescence Resonance Energy Transfer (BRET) assays, which can directly measure recruitment of a co-activator motif fused to yellow fluorescent protein (YFP) by specific nuclear receptor dimers. To validate the assays, we compared rexinoid modulation of co-activator recruitment by RXR homodimer, and heterodimers Nur77/RXR and Nurr1/RXR. Results reveal that some rexinoids display selective co-activator recruitment activities with homo- or hetero-dimer complexes. In particular, SR11237 (BMS649) has increased potency for recruitment of co-activator motif and transcriptional activity with the Nur77/RXR heterodimer compared to other complexes. This technology should prove useful to identify new compounds with specificity for individual dimeric species formed by nuclear receptors. PMID:26148973

“Ping-Pong” Interactions between Mitochondrial tRNA Import Receptors within a Multiprotein Complex

PubMed Central

Bhattacharyya, Subhendra Nath; Chatterjee, Saibal; Goswami, Srikanta; Tripathi, Gayatri; Dey, Sailendra Nath; Adhya, Samit

2003-01-01

The mitochondrial genomes of a wide variety of species contain an insufficient number of functional tRNA genes, and translation of mitochondrial mRNAs is sustained by import of nucleus-encoded tRNAs. In Leishmania, transfer of tRNAs across the inner membrane can be regulated by positive and negative interactions between them. To define the factors involved in such interactions, a large multisubunit complex (molecular mass, ∼640 kDa) from the inner mitochondrial membrane of the kinetoplastid protozoon Leishmania, consisting of ∼130-Å particles, was isolated. The complex, when incorporated into phospholipid vesicles, induced specific, ATP- and proton motive force-dependent transfer of Leishmania tRNATyr as well as of oligoribonucleotides containing the import signal YGGYAGAGC. Moreover, allosteric interactions between tRNATyr and tRNAIle were observed in the RNA import complex-reconstituted system, indicating the presence of primary and secondary tRNA binding sites within the complex. By a combination of antibody inhibition, photochemical cross-linking, and immunoprecipitation, it was shown that binding of tRNAIle to a 21-kDa component of the complex is dependent upon tRNATyr, while binding of tRNATyr to a 45-kDa component is inhibited by tRNAIle. This “ping-pong” mechanism may be an effective means to maintain a balanced tRNA pool for mitochondrial translation. PMID:12861008

Studying Nuclear Receptor Complexes in the Cellular Environment.

PubMed

Schaufele, Fred

2016-01-01

The ligand-regulated structure and biochemistry of nuclear receptor complexes are commonly determined by in vitro studies of isolated receptors, cofactors, and their fragments. However, in the living cell, the complexes that form are governed not just by the relative affinities of isolated cofactors for the receptor but also by the cell-specific sequestration or concentration of subsets of competing or cooperating cofactors, receptors, and other effectors into distinct subcellular domains and/or their temporary diversion into other cellular activities. Most methods developed to understand nuclear receptor function in the cellular environment involve the direct tagging of the nuclear receptor or its cofactors with fluorescent proteins (FPs) and the tracking of those FP-tagged factors by fluorescence microscopy. One of those approaches, Förster resonance energy transfer (FRET) microscopy, quantifies the transfer of energy from a higher energy "donor" FP to a lower energy "acceptor" FP attached to a single protein or to interacting proteins. The amount of FRET is influenced by the ligand-induced changes in the proximities and orientations of the FPs within the tagged nuclear receptor complexes, which is an indicator of the structure of the complexes, and by the kinetics of the interaction between FP-tagged factors. Here, we provide a guide for parsing information about the structure and biochemistry of nuclear receptor complexes from FRET measurements in living cells.

Conformation-based signal transfer and processing at the single-molecule level

NASA Astrophysics Data System (ADS)

Li, Chao; Wang, Zhongping; Lu, Yan; Liu, Xiaoqing; Wang, Li

2017-11-01

Building electronic components made of individual molecules is a promising strategy for the miniaturization and integration of electronic devices. However, the practical realization of molecular devices and circuits for signal transmission and processing at room temperature has proven challenging. Here, we present room-temperature intermolecular signal transfer and processing using SnCl2Pc molecules on a Cu(100) surface. The in-plane orientations of the molecules are effectively coupled via intermolecular interaction and serve as the information carrier. In the coupled molecular arrays, the signal can be transferred from one molecule to another in the in-plane direction along predesigned routes and processed to realize logical operations. These phenomena enable the use of molecules displaying intrinsic bistable states as complex molecular devices and circuits with novel functions.

Radiative transfer of X-rays in the solar corona

NASA Technical Reports Server (NTRS)

Acton, L. W.

1978-01-01

The problem of resonance scattering of X-ray emission lines in the solar corona is investigated. For the resonance lines of some helium-like ions, significant optical depths are reached over distances small compared with the size of typical coronal features. A general integral equation for the transfer of resonance-line radiation under solar coronal conditions is derived. This expression is in a form useful for modeling the complex three-dimensional temperature and density structure of coronal active regions. The transfer equation is then cast in a form illustrating the terms which give rise to the attenuation or enhancement of the resonance-line intensity. The source function for helium-like oxygen (O VII) under coronal conditions is computed and discussed in terms of the relative importance of scattering.

A Space Station tethered orbital refueling facility

NASA Technical Reports Server (NTRS)

Fester, D. A.; Rudolph, L. K.; Kiefel, E. R.

1985-01-01

A planned function of the Space Station is to refurbish and refuel an advanced space-based LO2/LH2 orbit transfer vehicle. An alternative to propellant storage at the station is to use a remote facility tied to the station with a long tether. Preliminary design of such a facility is described with emphasis on fluid transfer and storage requirements. Using tether lengths of at least 300 ft, gravity gradient forces will dominate surface tension in such a system. Although gravity driven transfer is difficult because of line pressure drops, fluid settling over the tank outlet greatly alleviates acquisition concerns and will facilitate vented tank fills. The major concern with a tethered orbital refueling facility is its considerable operational complexity including transport of the OTV to and from the facility.

Evaluation of Several Two-Step Scoring Functions Based on Linear Interaction Energy, Effective Ligand Size, and Empirical Pair Potentials for Prediction of Protein-Ligand Binding Geometry and Free Energy

PubMed Central

Rahaman, Obaidur; Estrada, Trilce P.; Doren, Douglas J.; Taufer, Michela; Brooks, Charles L.; Armen, Roger S.

2011-01-01

The performance of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for “step 2 discrimination” were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only “interacting” ligand atoms as the “effective size” of the ligand, and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and five-fold cross validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new dataset (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ dataset where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand efficiencies is most relevant to real-world drug design efforts. PMID:21644546

Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

PubMed

Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

2011-09-26

The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand efficiencies is most relevant to real-world drug design efforts.

Purple-bacterial photosynthetic reaction centers and quantum-dot hybrid-assemblies in lecithin liposomes and thin films.

PubMed

Lukashev, Eugeny P; Knox, Petr P; Gorokhov, Vladimir V; Grishanova, Nadezda P; Seifullina, Nuranija Kh; Krikunova, Maria; Lokstein, Heiko; Paschenko, Vladimir Z

2016-11-01

Quantum dots (QDs) absorb ultraviolet and long-wavelength visible light energy much more efficiently than natural bacterial light-harvesting proteins and can transfer the excitation energy to photosynthetic reaction centers (RCs). Inclusion of RCs combined with QDs as antennae into liposomes opens new opportunities for using such hybrid systems as a basis for artificial energy-transforming devices that potentially can operate with greater efficiency and stability than devices based only on biological components or inorganic components alone. RCs from Rhodobacter sphaeroides and QDs (CdSe/ZnS with hydrophilic covering) were embedded in lecithin liposomes by extrusion of a solution of multilayer lipid vesicles through a polycarbonate membrane or by dialysis of lipids and proteins dispersed with excess detergent. The efficiency of RC and QD interaction within the liposomes was estimated using fluorescence excitation spectra of the photoactive bacteriochlorophyll of the RCs and by measuring the fluorescence decay kinetics of the QDs. The functional activity of the RCs in hybrid complexes was fully maintained, and their stability was even increased. The efficiency of energy transfer between QDs and RCs and conditions of long-term stability of function of such hybrid complexes in film preparations were investigated as well. It was found that dry films containing RCs and QDs, maintained at atmospheric humidity, are capable of maintaining their functional activity for at least some months as judged by measurements of their spectral characteristics, efficiency of energy transfer from QDs to RCs and RC electron transport activity. Addition of trehalose to the films increases the stability further, especially for films maintained at low humidity. These stable hybrid film structures are promising for further studies towards developing new phototransformation devices for biotechnological applications. Copyright © 2016 Elsevier B.V. All rights reserved.

Fluorescence resonance energy transfer analysis of escherichia coli RNA polymerase and polymerase-DNA complexes.

PubMed

Heyduk, T; Niedziela-Majka, A

Fluorescence resonance energy transfer (FRET) is a technique allowing measurements of atomic-scale distances in diluted solutions of macromolecules under native conditions. This feature makes FRET a powerful tool to study complicated biological assemblies. In this report we review the applications of FRET to studies of transcription initiation by Escherichia coli RNA polymerase. The versatility of FRET for studies of a large macromolecular assembly such as RNA polymerase is illustrated by examples of using FRET to address several different aspects of transcription initiation by polymerase. FRET has been used to determine the architecture of polymerase, its complex with single-stranded DNA, and the conformation of promoter fragment bound to polymerase. FRET has been also used as a binding assay to determine the thermodynamics of promoter DNA fragment binding to the polymerase. Functional conformational changes in the specificity subunit of polymerase responsible for the modulation of the promoter binding activity of the enzyme and the mechanistic aspects of the transition from the initiation to the elongation complex were also investigated. Copyright 2002 Wiley Periodicals, Inc.

Crystal structure of a transfer-ribonucleoprotein particle that promotes asparagine formation

PubMed Central

Blaise, Mickaël; Bailly, Marc; Frechin, Mathieu; Behrens, Manja Annette; Fischer, Frédéric; Oliveira, Cristiano L P; Becker, Hubert Dominique; Pedersen, Jan Skov; Thirup, Søren; Kern, Daniel

2010-01-01

Four out of the 22 aminoacyl-tRNAs (aa-tRNAs) are systematically or alternatively synthesized by an indirect, two-step route requiring an initial mischarging of the tRNA followed by tRNA-dependent conversion of the non-cognate amino acid. During tRNA-dependent asparagine formation, tRNAAsn promotes assembly of a ribonucleoprotein particle called transamidosome that allows channelling of the aa-tRNA from non-discriminating aspartyl-tRNA synthetase active site to the GatCAB amidotransferase site. The crystal structure of the Thermus thermophilus transamidosome determined at 3 Å resolution reveals a particle formed by two GatCABs, two dimeric ND-AspRSs and four tRNAsAsn molecules. In the complex, only two tRNAs are bound in a functional state, whereas the two other ones act as an RNA scaffold enabling release of the asparaginyl-tRNAAsn without dissociation of the complex. We propose that the crystal structure represents a transient state of the transamidation reaction. The transamidosome constitutes a transfer-ribonucleoprotein particle in which tRNAs serve the function of both substrate and structural foundation for a large molecular machine. PMID:20717102

Quaternary structure of a G-protein-coupled receptor heterotetramer in complex with Gi and Gs.

PubMed

Navarro, Gemma; Cordomí, Arnau; Zelman-Femiak, Monika; Brugarolas, Marc; Moreno, Estefania; Aguinaga, David; Perez-Benito, Laura; Cortés, Antoni; Casadó, Vicent; Mallol, Josefa; Canela, Enric I; Lluís, Carme; Pardo, Leonardo; García-Sáez, Ana J; McCormick, Peter J; Franco, Rafael

2016-04-05

G-protein-coupled receptors (GPCRs), in the form of monomers or homodimers that bind heterotrimeric G proteins, are fundamental in the transfer of extracellular stimuli to intracellular signaling pathways. Different GPCRs may also interact to form heteromers that are novel signaling units. Despite the exponential growth in the number of solved GPCR crystal structures, the structural properties of heteromers remain unknown. We used single-particle tracking experiments in cells expressing functional adenosine A1-A2A receptors fused to fluorescent proteins to show the loss of Brownian movement of the A1 receptor in the presence of the A2A receptor, and a preponderance of cell surface 2:2 receptor heteromers (dimer of dimers). Using computer modeling, aided by bioluminescence resonance energy transfer assays to monitor receptor homomerization and heteromerization and G-protein coupling, we predict the interacting interfaces and propose a quaternary structure of the GPCR tetramer in complex with two G proteins. The combination of results points to a molecular architecture formed by a rhombus-shaped heterotetramer, which is bound to two different interacting heterotrimeric G proteins (Gi and Gs). These novel results constitute an important advance in understanding the molecular intricacies involved in GPCR function.

Absorption spectrometric study of charge transfer complex formation between 4-acetamidophenol (paracetamol) and a series of quinones including Vitamin K 3

NASA Astrophysics Data System (ADS)

Saha, Avijit; Mukherjee, Asok K.

2004-07-01

The formation of charge transfer (CT) complexes of 4-acetamidophenol (commonly called 'paracetamol') and a series of quinones (including Vitamin K 3) has been studied spectrophotometrically in ethanol medium. The vertical ionisation potential of paracetamol and the degrees of charge transfer of the complexes in their ground state has been estimated from the trends in the charge transfer bands. The oscillator and transition dipole strengths of the complexes have been determined from the CT absorption spectra at 298 K. The complexes have been found by Job's method of continuous variation to have the uncommon 2:1 (paracetamol:quinone) stoichiometry in each case. The enthalpies and entropies of formation of the complexes have been obtained by determining their formation constants at five different temperatures.

Synthesis, characterization, and luminescent properties of Eu3+ dipyridophenazine functionalized complexes for potential bioimaging applications

NASA Astrophysics Data System (ADS)

Beasley, Jeremy

Luminescent properties of lanthanide complexes possess unique characteristics that make them good candidates for possible bioimaging agents and have inspired research initiatives to further explore these materials. However, the toxicity of these metals limits their applications as in-vivo bioimaging agents. One solution that eliminates the toxic effects is to encase these lanthanide complexes in silica. This project was designed to probe the variation in the fluorescence properties of a highly luminescent europium (III) complex, utilizing a fluorinated â-diketonate ligand (thenoyltrifluoroacetone (tta)), upon the substitution of the solvent molecules by various functionalized dipyrido[3,2-a:2',3'-c]phenazine (DPPZ) ligands. A method for covalently attaching, or occluding complexes in silica nanoparticles were also included in the project design. The structure and properties of the functionalized DPPZ ligands and their respective complexes were determined by FT-IR, 1H-NMR, UV-Vis, and fluorescence spectroscopy techniques. UV excitation of the complexes resulted in red luminescence (~ 614 nm) characteristic of trivalent europium ions. The differences in luminescence properties of the complexes are rationalized in terms of the electronic features of the different functionalized DPPZ ligands. The higher overall quantum yield of the un-functionalized DPPZ complex, Eu(tta)3DPPZ (Q.Y.= 7.68 +/- 0.06 %), and the low overall quantum yield observed for Eu(tta)3DPPZ-COOEt (Q.Y.= 1.08 +/- 0.05%), Eu(tta) 3DPPZ-Si (Q.Y.= 0.65+/- 0.04%), Eu(tta)3DPPZ-COOH (Q.Y.= 0.61+/- 0.07 %), Eu(tta)3DPPZ-CH3 (Q.Y.= 0.59+/-0.02 %) are rationalized in terms of how electron donating or withdrawing groups affect their respective ligand-to-metal energy transfer efficiencies. Eu(tta) 3DPPZ was the only complex to show enhanced luminescent properties capable of potential applications in biomedical imaging.

Interfacial hydration, dynamics and electron transfer: multi-scale ET modeling of the transient [myoglobin, cytochrome b5] complex.

PubMed

Keinan, Shahar; Nocek, Judith M; Hoffman, Brian M; Beratan, David N

2012-10-28

Formation of a transient [myoglobin (Mb), cytochrome b(5) (cyt b(5))] complex is required for the reductive repair of inactive ferri-Mb to its functional ferro-Mb state. The [Mb, cyt b(5)] complex exhibits dynamic docking (DD), with its cyt b(5) partner in rapid exchange at multiple sites on the Mb surface. A triple mutant (Mb(3M)) was designed as part of efforts to shift the electron-transfer process to the simple docking (SD) regime, in which reactive binding occurs at a restricted, reactive region on the Mb surface that dominates the docked ensemble. An electrostatically-guided brownian dynamics (BD) docking protocol was used to generate an initial ensemble of reactive configurations of the complex between unrelaxed partners. This ensemble samples a broad and diverse array of heme-heme distances and orientations. These configurations seeded all-atom constrained molecular dynamics simulations (MD) to generate relaxed complexes for the calculation of electron tunneling matrix elements (T(DA)) through tunneling-pathway analysis. This procedure for generating an ensemble of relaxed complexes combines the ability of BD calculations to sample the large variety of available conformations and interprotein distances, with the ability of MD to generate the atomic level information, especially regarding the structure of water molecules at the protein-protein interface, that defines electron-tunneling pathways. We used the calculated T(DA) values to compute ET rates for the [Mb(wt), cyt b(5)] complex and for the complex with a mutant that has a binding free energy strengthened by three D/E → K charge-reversal mutations, [Mb(3M), cyt b(5)]. The calculated rate constants are in agreement with the measured values, and the mutant complex ensemble has many more geometries with higher T(DA) values than does the wild-type Mb complex. Interestingly, water plays a double role in this electron-transfer system, lowering the tunneling barrier as well as inducing protein interface remodeling that screens the repulsion between the negatively-charged propionates of the two hemes.

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

Kaur, Sandeep, E-mail: sipusukhn@gmail.com; Sharma, Amrish; Mudahar, Isha, E-mail: isha@pbi.ac.in

First principle calculations based on density functional theory were performed to calculate the structural and electronic properties of C{sub 20}-N{sub m}@C{sub n} dimer complexes. The calculated binding energies of the complexes formed are comparable to C{sub 60} dimer which ensures their stability. The bond lengths of these dimer complexes were found to be nearly same as pure complexes C{sub 20}-C{sub n}. Further, nitrogen (N) atoms were encapsulated inside the secondary cage (C{sub n}) of dimer complexes and the number of N atoms depends on diameter of the cage. The HOMO-LUMO gaps of new proposed complexes indicate the increase in gapmore » as compared to pure complexes. Mulliken charge analysis of these complexes has been studied which shows the significant charge transfer from the N atoms to the secondary cage of these complexes. The study propose the formation of the new dimer complexes which are stable and are able to encapsulate atoms which are otherwise reactive in free space.« less

Plastic Surgery Challenges in War Wounded I: Flap-Based Extremity Reconstruction

PubMed Central

Sabino, Jennifer M.; Slater, Julia; Valerio, Ian L.

2016-01-01

Scope and Significance: Reconstruction of traumatic injuries requiring tissue transfer begins with aggressive resuscitation and stabilization. Systematic advances in acute casualty care at the point of injury have improved survival and allowed for increasingly complex treatment before definitive reconstruction at tertiary medical facilities outside the combat zone. As a result, the complexity of the limb salvage algorithm has increased over 14 years of combat activities in Iraq and Afghanistan. Problem: Severe poly-extremity trauma in combat casualties has led to a large number of extremity salvage cases. Advanced reconstructive techniques coupled with regenerative medicine applications have played a critical role in the restoration, recovery, and rehabilitation of functional limb salvage. Translational Relevance: The past 14 years of war trauma have increased our understanding of tissue transfer for extremity reconstruction in the treatment of combat casualties. Injury patterns, flap choice, and reconstruction timing are critical variables to consider for optimal outcomes. Clinical Relevance: Subacute reconstruction with specifically chosen flap tissue and donor site location based on individual injuries result in successful tissue transfer, even in critically injured patients. These considerations can be combined with regenerative therapies to optimize massive wound coverage and limb salvage form and function in previously active patients. Summary: Traditional soft tissue reconstruction is integral in the treatment of war extremity trauma. Pedicle and free flaps are a critically important part of the reconstructive ladder for salvaging extreme extremity injuries that are seen as a result of the current practice of war. PMID:27679751

Analysis of Photosynthetic Antenna Function in a Mutant of Arabidopsis thaliana (L.) Lacking trans-Hexadecenoic Acid 1

PubMed Central

McCourt, Peter; Browse, John; Watson, Jan; Arntzen, Charles J.; Somerville, Chris R.

1985-01-01

Several lines of evidence support the proposal that the unusual chloroplast-specific lipid acyl group Δ3,trans-hexadecenoic acid (trans-C16:1) stimulates the formation or maintenance of the oligomeric form of the light-harvesting chlorophyll a/b complex (LHCP). To assess the functional significance of this apparent association we have analyzed LHCP structure and function in a mutant of Arabidopsis thaliana (L.) which lacks trans-C16:1 by electrophoretic analysis of the protein-chlorophyll complexes and by measurements of chlorophyll fluorescence under a variety of conditions. By these criteria the putative oligomeric form of LHCP appears to be slightly more labile to detergent-mediated dissociation in the mutant. The oligomeric PSI chlorophyll-protein complex, associated with PSI, was also more labile to detergent-mediated dissociation in the mutant, suggesting a previously unsuspected association of trans-C16:1 with the PSI complex. However, no significant effect of the mutation on the efficiency of energy transfer from LHCP to the photochemical reaction centers was observed under any of the various conditions imposed. Also, the stability of the chlorophyll-protein complexes to temperature-induced dissociation was unaffected in the mutant. The role of trans-C16:1 is very subtle or is only conditionally expressed. Images Fig. 1 PMID:16664340

Time dependent-density functional theory (TD-DFT) and experimental studies of UV-Visible spectra and cyclic voltammetry for Cu(II) complex with Et2DTC

NASA Astrophysics Data System (ADS)

Valle, Eliana Maira A.; Maltarollo, Vinicius Gonçalves; Almeida, Michell O.; Honorio, Kathia Maria; dos Santos, Mauro Coelho; Cerchiaro, Giselle

2018-04-01

In this work, we studied the complexation mode between copper(II) ion and the specific ligand investigated as carriers of metals though biological membranes, diethyldithiocarbamate (Et2DTC). It is important to understand how this occurs because it is an important intracellular chelator with potential therapeutic applications. Theoretical and experimental UV visible studies were performed to investigate the complexation mode between copper and the ligand. Electrochemical studies were also performed to complement the spectroscopic analyses. According to the theoretical calculations, using TD-DFT (Time dependent density functional theory), with B3LYP functional and DGDVZP basis set, implemented in Gaussian 03 package, it was observed that the formation of the complex [Cu(Et2DTC)2] is favorable with higher electron density over the sulfur atoms of the ligand. UV/Vis spectra have a charge transfer band at 450 nm, with the DMSO-d6 band shift from 800 to 650 nm. The electrochemical experiments showed the formation of a new redox process, referring to the complex, where the reduction peak potential of copper is displaced to less positive region. Therefore, the results obtained from this study give important insights on possible mechanisms involved in several biological processes related to the studied system.

Ultrafast direct electron transfer at organic semiconductor and metal interfaces.

PubMed

Xiang, Bo; Li, Yingmin; Pham, C Huy; Paesani, Francesco; Xiong, Wei

2017-11-01

The ability to control direct electron transfer can facilitate the development of new molecular electronics, light-harvesting materials, and photocatalysis. However, control of direct electron transfer has been rarely reported, and the molecular conformation-electron dynamics relationships remain unclear. We describe direct electron transfer at buried interfaces between an organic polymer semiconductor film and a gold substrate by observing the first dynamical electric field-induced vibrational sum frequency generation (VSFG). In transient electric field-induced VSFG measurements on this system, we observe dynamical responses (<150 fs) that depend on photon energy and polarization, demonstrating that electrons are directly transferred from the Fermi level of gold to the lowest unoccupied molecular orbital of organic semiconductor. Transient spectra further reveal that, although the interfaces are prepared without deliberate alignment control, a subensemble of surface molecules can adopt conformations for direct electron transfer. Density functional theory calculations support the experimental results and ascribe the observed electron transfer to a flat-lying polymer configuration in which electronic orbitals are found to be delocalized across the interface. The present observation of direct electron transfer at complex interfaces and the insights gained into the relationship between molecular conformations and electron dynamics will have implications for implementing novel direct electron transfer in energy materials.

Assembly of functional photosystem complexes in Rhodobacter sphaeroides incorporating carotenoids from the spirilloxanthin pathway

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

Chi, Shuang C.; Mothersole, David J.; Dilbeck, Preston

Carotenoids protect the photosynthetic apparatus against harmful radicals arising from the presence of both light and oxygen. They also act as accessory pigments for harvesting solar energy, and are required for stable assembly of many light-harvesting complexes. In the phototrophic bacterium Rhodobacter (Rba.) sphaeroides phytoene desaturase (CrtI) catalyses three sequential desaturations of the colourless carotenoid phytoene, extending the number of conjugated carbon-carbon double bonds, N, from three to nine and producing the yellow carotenoid neurosporene; subsequent modifications produce the yellow/red carotenoids spheroidene/spheroidenone (N=10/11). Genomic crtI replacements were used to swap the native three-step Rba. sphaeroides CrtI for the four-step Pantoeamore » agglomerans enzyme, which re-routed carotenoid biosynthesis and culminated in the production of 2,2'-diketo-spirilloxanthin under semi-aerobic conditions. The new carotenoid pathway was elucidated using a combination of HPLC and mass spectrometry. Premature termination of this new pathway by inactivating crtC or crtD produced strains with lycopene or rhodopin as major carotenoids. All of the spirilloxanthin series carotenoids are accepted by the assembly pathways for LH2 and RC-LH1-PufX complexes. The efficiency of carotenoid-to-bacteriochlorophyll energy transfer for 2,2'-diketo-spirilloxanthin (15 conjugated CC bonds; N=15) in LH2 complexes is low, at 35%. High energy transfer efficiencies were obtained for neurosporene (N=9; 94%), spheroidene (N=10; 96%) and spheroidenone (N=11; 95%), whereas intermediate values were measured for lycopene (N=11; 64%), rhodopin (N=11; 62%) and spirilloxanthin (N=13; 39%). In conclusion, the variety and stability of these novel Rba. sphaeroides antenna complexes make them useful experimental models for investigating the energy transfer dynamics of carotenoids in bacterial photosynthesis.« less

Assembly of functional photosystem complexes in Rhodobacter sphaeroides incorporating carotenoids from the spirilloxanthin pathway

DOE PAGES

Chi, Shuang C.; Mothersole, David J.; Dilbeck, Preston; ...

2014-10-27

Carotenoids protect the photosynthetic apparatus against harmful radicals arising from the presence of both light and oxygen. They also act as accessory pigments for harvesting solar energy, and are required for stable assembly of many light-harvesting complexes. In the phototrophic bacterium Rhodobacter (Rba.) sphaeroides phytoene desaturase (CrtI) catalyses three sequential desaturations of the colourless carotenoid phytoene, extending the number of conjugated carbon-carbon double bonds, N, from three to nine and producing the yellow carotenoid neurosporene; subsequent modifications produce the yellow/red carotenoids spheroidene/spheroidenone (N=10/11). Genomic crtI replacements were used to swap the native three-step Rba. sphaeroides CrtI for the four-step Pantoeamore » agglomerans enzyme, which re-routed carotenoid biosynthesis and culminated in the production of 2,2'-diketo-spirilloxanthin under semi-aerobic conditions. The new carotenoid pathway was elucidated using a combination of HPLC and mass spectrometry. Premature termination of this new pathway by inactivating crtC or crtD produced strains with lycopene or rhodopin as major carotenoids. All of the spirilloxanthin series carotenoids are accepted by the assembly pathways for LH2 and RC-LH1-PufX complexes. The efficiency of carotenoid-to-bacteriochlorophyll energy transfer for 2,2'-diketo-spirilloxanthin (15 conjugated CC bonds; N=15) in LH2 complexes is low, at 35%. High energy transfer efficiencies were obtained for neurosporene (N=9; 94%), spheroidene (N=10; 96%) and spheroidenone (N=11; 95%), whereas intermediate values were measured for lycopene (N=11; 64%), rhodopin (N=11; 62%) and spirilloxanthin (N=13; 39%). In conclusion, the variety and stability of these novel Rba. sphaeroides antenna complexes make them useful experimental models for investigating the energy transfer dynamics of carotenoids in bacterial photosynthesis.« less

Dilemmas of Transfer Pricing Comparability Analysis in Manufacturing Entities. Polish-Czech Case Study

NASA Astrophysics Data System (ADS)

Sulik-Górecka, Aleksandra

2018-06-01

Modern manufacturing entities often operate in capital groups, and their role is sometimes limited to the function of cost centers. From the legal point of view, however, they are separate entities obliged to apply transfer pricing regulations. Meeting the requirements of the arm's length principle can be very difficult at this time, given the relationships and conflicts of interest in the capital group. Complexity increases in capital groups operating in different countries, due to differences in tax regulations. The main purpose of the paper is to demonstrate that the need to valuate the sale of finished goods to a manufacturing entity, which is a subject to a different tax jurisdiction, may lead to a problem of compliance with the arm's length principle. In addition, the paper proposes a methodology for comparability analysis that may be used by manufacturing entities to defend conditions of setting transfer pricing. The paper presents the different functional profiles of manufacturing entities and points out the difficulties that they may encounter when preparing the comparability analysis. It has also been noted that there are differences in transfer pricing regulations in different countries, for example by analyzing Polish and Czech regulations. The lack of uniform benchmarking legislation can cause inconsistencies in the selection of comparable data, resulting in differences in transfer pricing. The paper uses the method of legal regulation review and analysis of results of published studies concerning the scope of transfer pricing and comparability analysis. The paper also adopts a case study analysis.

Horizontal gene transfer of an entire metabolic pathway between a eukaryotic alga and its DNA virus

PubMed Central

Monier, Adam; Pagarete, António; de Vargas, Colomban; Allen, Michael J.; Read, Betsy; Claverie, Jean-Michel; Ogata, Hiroyuki

2009-01-01

Interactions between viruses and phytoplankton, the main primary producers in the oceans, affect global biogeochemical cycles and climate. Recent studies are increasingly revealing possible cases of gene transfers between cyanobacteria and phages, which might have played significant roles in the evolution of cyanobacteria/phage systems. However, little has been documented about the occurrence of horizontal gene transfer in eukaryotic phytoplankton/virus systems. Here we report phylogenetic evidence for the transfer of seven genes involved in the sphingolipid biosynthesis pathway between the cosmopolitan eukaryotic microalga Emiliania huxleyi and its large DNA virus EhV. PCR assays indicate that these genes are prevalent in E. huxleyi and EhV strains isolated from different geographic locations. Patterns of protein and gene sequence conservation support that these genes are functional in both E. huxleyi and EhV. This is the first clear case of horizontal gene transfer of multiple functionally linked enzymes in a eukaryotic phytoplankton–virus system. We examine arguments for the possible direction of the gene transfer. The virus-to-host direction suggests the existence of ancient viruses that controlled the complex metabolic pathway in order to infect primitive eukaryotic cells. In contrast, the host-to-virus direction suggests that the serial acquisition of genes involved in the same metabolic pathway might have been a strategy for the ancestor of EhVs to stay ahead of their closest relatives in the great evolutionary race for survival. PMID:19451591

Measuring Interference of Drug-Like Molecules with the Respiratory Chain: Toward the Early Identification of Mitochondrial Uncouplers in Lead Finding

PubMed Central

Matter, Hans; Diekert, Kerstin; Dörner, Wolfgang; Dröse, Stefan; Licher, Thomas

2013-01-01

Abstract The electron transport chain (ETC) couples electron transfer between donors and acceptors with proton transport across the inner mitochondrial membrane. The resulting electrochemical proton gradient is used to generate chemical energy in the form of adenosine triphosphate (ATP). Proton transfer is based on the activity of complex I–V proteins in the ETC. The overall electrical activity of these proteins can be measured by proton transfer using Solid Supported Membrane technology. We tested the activity of complexes I, III, and V in a combined assay, called oxidative phosphorylation assay (oxphos assay), by activating each complex with the corresponding substrate. The oxphos assay was used to test in-house substances from different projects and several drugs currently available on the market that have reported effects on mitochondrial functions. The resulting data were compared to the influence of the respective compounds on mitochondria as determined by oxygen consumption and to data generated with an ATP depletion assay. The comparison shows that the oxidative phosphorylation assay provides both a rapid approach for detecting interaction of compounds with respiratory chain proteins and information on their mode of interaction. Therefore, the oxphos assay is a useful tool to support structure activity relationship studies by allowing early identification of mitotoxicity and for analyzing the outcome of phenotypic screens that are susceptible to the generation of mitotoxicity-related artifacts. PMID:23992120

Atomistic determinants of co-enzyme Q reduction at the Qi-site of the cytochrome bc1 complex

NASA Astrophysics Data System (ADS)

Postila, Pekka A.; Kaszuba, Karol; Kuleta, Patryk; Vattulainen, Ilpo; Sarewicz, Marcin; Osyczka, Artur; Róg, Tomasz

2016-09-01

The cytochrome (cyt) bc1 complex is an integral component of the respiratory electron transfer chain sustaining the energy needs of organisms ranging from humans to bacteria. Due to its ubiquitous role in the energy metabolism, both the oxidation and reduction of the enzyme’s substrate co-enzyme Q has been studied vigorously. Here, this vast amount of data is reassessed after probing the substrate reduction steps at the Qi-site of the cyt bc1 complex of Rhodobacter capsulatus using atomistic molecular dynamics simulations. The simulations suggest that the Lys251 side chain could rotate into the Qi-site to facilitate binding of half-protonated semiquinone - a reaction intermediate that is potentially formed during substrate reduction. At this bent pose, the Lys251 forms a salt bridge with the Asp252, thus making direct proton transfer possible. In the neutral state, the lysine side chain stays close to the conserved binding location of cardiolipin (CL). This back-and-forth motion between the CL and Asp252 indicates that Lys251 functions as a proton shuttle controlled by pH-dependent negative feedback. The CL/K/D switching, which represents a refinement to the previously described CL/K pathway, fine-tunes the proton transfer process. Lastly, the simulation data was used to formulate a mechanism for reducing the substrate at the Qi-site.

Goal Management Training and Mindfulness Meditation improve executive functions and transfer to ecological tasks of daily life in polysubstance users enrolled in therapeutic community treatment.

PubMed

Valls-Serrano, Carlos; Caracuel, Alfonso; Verdejo-Garcia, Antonio

2016-08-01

We have previously shown that Goal Management Training+Mindfulness Meditation (GMT+MM) improves executive functions in polysubstance users enrolled in outpatient treatment. The aim of this study was to establish if GMT+MM has similar positive effects on executive functions in polysubstance users in residential treatment, and if executive functions' gains transfer to more ecologically valid goal-oriented tasks. Thirty-two polysbustance users were randomly allocated to eight weeks of GMT+MM (n=16) or control, i.e., no-intervention (n=16); both groups received treatment as usual. Outcome measures included performance in laboratory tasks of basic and complex executive functions (i.e., basic: working memory and inhibition; complex: planning and self-regulation) and in an ecological task of goal-directed behavior (the Multiple Errands Test - contextualized version, MET-CV) measured post-interventions. Results showed that GMT+MM was superior to control in improving basic measures of working memory (Letter-number sequencing; F=4.516, p=0.049) and reflection impulsivity (Information Sampling Test; F=6.217, p=0.018), along with initial thinking times during planning (Zoo Map Test; F=8.143, p=0.008). In addition, GMT+MM was superior to control in improving performance in the MET-CV (task failures; F=8.485, p=0.007). Our findings demonstrate that GMT+MM increases reflective processes and the achievement of goals in daily activities, furthermore ecological test can detects changes easily than laboratory tasks. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Origin of attraction in p-benzoquinone complexes with benzene and p-hydroquinone.

PubMed

Tsuzuki, Seiji; Uchimaru, Tadafumi; Ono, Taizo

2017-08-30

The origin of the attraction in charge-transfer complexes (a p-hydroquinone-p-benzoquinone complex and benzene complexes with benzoquinone, tetracyanoethylene and Br 2 ) was analyzed using distributed multipole analysis and symmetry-adapted perturbation theory. Both methods show that the dispersion interactions are the primary source of the attraction in these charge-transfer complexes followed by the electrostatic interactions. The natures of the intermolecular interactions in these complexes are close to the π/π interactions of neutral aromatic molecules. The electrostatic interactions play important roles in determining the magnitude of the attraction. The contribution of charge-transfer interactions to the attraction is not large compared with the dispersion interactions in these complexes.

Investigating the sources of variability in the dynamic response of built-up structures through a linear analytical model

NASA Astrophysics Data System (ADS)

Abolfathi, Ali; O'Boy, Dan J.; Walsh, Stephen J.; Fisher, Stephen A.

2017-01-01

It is well established that the dynamic response of a number of nominally identical built-up structures are often different and the variability increases with increasing complexity of the structure. Furthermore, the effects of the different parameters, for example the variation in joint locations or the range of the Young's modulus, on the dynamic response of the system are not the same. In this paper, the effects of different material and geometric parameters on the variability of a vibration transfer function are compared using an analytical model of a simple linear built-up structure that consist of two plates connected by a single mount. Similar results can be obtained if multiple mounts are used. The scope of this paper is limited to a low and medium frequency range where usually deterministic models are used for vibrational analysis. The effect of the mount position and also the global variation in the properties of the plate, such as modulus of elasticity or thickness, is higher on the variability of vibration transfer function than the effect of the mount properties. It is shown that the vibration transfer function between the plates is independent of the mount property if a stiff enough mount with a small mass is implemented. For a soft mount, there is a direct relationship between the mount impedance and the variation in the vibration transfer function. Furthermore, there are a range of mount stiffnesses between these two extreme cases at which the vibration transfer function is more sensitive to changes in the stiffness of the mount than when compared to a soft mount. It is found that the effect of variation in the mount damping and the mount mass on the variability is negligible. Similarly, the effect of the plate damping on the variability is not significant.

Quantum coherence spectroscopy reveals complex dynamics in bacterial light-harvesting complex 2 (LH2).

PubMed

Harel, Elad; Engel, Gregory S

2012-01-17

Light-harvesting antenna complexes transfer energy from sunlight to photosynthetic reaction centers where charge separation drives cellular metabolism. The process through which pigments transfer excitation energy involves a complex choreography of coherent and incoherent processes mediated by the surrounding protein and solvent environment. The recent discovery of coherent dynamics in photosynthetic light-harvesting antennae has motivated many theoretical models exploring effects of interference in energy transfer phenomena. In this work, we provide experimental evidence of long-lived quantum coherence between the spectrally separated B800 and B850 rings of the light-harvesting complex 2 (LH2) of purple bacteria. Spectrally resolved maps of the detuning, dephasing, and the amplitude of electronic coupling between excitons reveal that different relaxation pathways act in concert for optimal transfer efficiency. Furthermore, maps of the phase of the signal suggest that quantum mechanical interference between different energy transfer pathways may be important even at ambient temperature. Such interference at a product state has already been shown to enhance the quantum efficiency of transfer in theoretical models of closed loop systems such as LH2.

Quantum coherence spectroscopy reveals complex dynamics in bacterial light-harvesting complex 2 (LH2)

PubMed Central

Harel, Elad; Engel, Gregory S.

2012-01-01

Light-harvesting antenna complexes transfer energy from sunlight to photosynthetic reaction centers where charge separation drives cellular metabolism. The process through which pigments transfer excitation energy involves a complex choreography of coherent and incoherent processes mediated by the surrounding protein and solvent environment. The recent discovery of coherent dynamics in photosynthetic light-harvesting antennae has motivated many theoretical models exploring effects of interference in energy transfer phenomena. In this work, we provide experimental evidence of long-lived quantum coherence between the spectrally separated B800 and B850 rings of the light-harvesting complex 2 (LH2) of purple bacteria. Spectrally resolved maps of the detuning, dephasing, and the amplitude of electronic coupling between excitons reveal that different relaxation pathways act in concert for optimal transfer efficiency. Furthermore, maps of the phase of the signal suggest that quantum mechanical interference between different energy transfer pathways may be important even at ambient temperature. Such interference at a product state has already been shown to enhance the quantum efficiency of transfer in theoretical models of closed loop systems such as LH2. PMID:22215585

Stabilization of non-productive conformations underpins rapid electron transfer to electron-transferring flavoprotein.

PubMed

Toogood, Helen S; van Thiel, Adam; Scrutton, Nigel S; Leys, David

2005-08-26

Crystal structures of protein complexes with electron-transferring flavoprotein (ETF) have revealed a dual protein-protein interface with one region serving as anchor while the ETF FAD domain samples available space within the complex. We show that mutation of the conserved Glu-165beta in human ETF leads to drastically modulated rates of interprotein electron transfer with both medium chain acyl-CoA dehydrogenase and dimethylglycine dehydrogenase. The crystal structure of free E165betaA ETF is essentially identical to that of wild-type ETF, but the crystal structure of the E165betaA ETF.medium chain acyl-CoA dehydrogenase complex reveals clear electron density for the FAD domain in a position optimal for fast interprotein electron transfer. Based on our observations, we present a dynamic multistate model for conformational sampling that for the wild-type ETF. medium chain acyl-CoA dehydrogenase complex involves random motion between three distinct positions for the ETF FAD domain. ETF Glu-165beta plays a key role in stabilizing positions incompatible with fast interprotein electron transfer, thus ensuring high rates of complex dissociation.

Binding of 3O2 and 1O2 to dyes used in photodynamic therapy in gas phase and aqueous media

NASA Astrophysics Data System (ADS)

Kushwaha, P. S.; Mishra, P. C.

Density functional theory (DFT) was employed at the B3LYP/6-31+G* level to study complexes of 1O2 and 3O2 with the dye molecules proflavine, methylene blue, and acridine orange, which are useful in photodynamic therapy. It was found that the most stable complex between 1O2 and proflavine are formed when 1O2 is located above the central ring, while the most stable complex between 1O2 and methylene blue is formed when 1O2 is located above the molecular plane, but not above any of the rings, near the sulfur atom. 1O2 can make a stable complex with acridine orange, as it is located above the outer ring of the dye. The binding energies of the complexes of 1O2 with all three dyes are enhanced considerably in going from gas phase to aqueous media. The complexes of 3O2 with the dyes will be unstable in all cases, while those of 1O2 with the same will be quite stable and will not be dissociated due to thermal fluctuations at room temperature. In the complexes of 1O2 and 3O2 with the dyes, charge transfer occurs from the dyes to the O2 moiety, the amount of charge transfer being much more to 1O2 than to 3O2 in each case.

Tunable complex-valued multi-tap microwave photonic filter based on single silicon-on-insulator microring resonator.

PubMed

Lloret, Juan; Sancho, Juan; Pu, Minhao; Gasulla, Ivana; Yvind, Kresten; Sales, Salvador; Capmany, José

2011-06-20

A complex-valued multi-tap tunable microwave photonic filter based on single silicon-on-insulator microring resonator is presented. The degree of tunability of the approach involving two, three and four taps is theoretical and experimentally characterized, respectively. The constraints of exploiting the optical phase transfer function of a microring resonator aiming at implementing complex-valued multi-tap filtering schemes are also reported. The trade-off between the degree of tunability without changing the free spectral range and the number of taps is studied in-depth. Different window based scenarios are evaluated for improving the filter performance in terms of the side-lobe level.

Model of multistep electron transfer in a single-mode polar medium

NASA Astrophysics Data System (ADS)

Feskov, S. V.; Yudanov, V. V.

2017-09-01

A mathematical model of multistep photoinduced electron transfer (PET) in a polar medium with a single relaxation time (Debye solvent) is developed. The model includes the polarization nonequilibrity formed in the vicinity of the donor-acceptor molecular system at the initial steps of photoreaction and its influence on the subsequent steps of PET. It is established that the results from numerical simulation of transient luminescence spectra of photoexcited donor-acceptor complexes (DAC) conform to calculated data obtained on the basis of the familiar experimental technique used to measure the relaxation function of solvent polarization in the vicinity of DAC in the picosecond and subpicosecond ranges.

Two-Flux Green's Function Analysis for Transient Spectral Radiation in a Composite

NASA Technical Reports Server (NTRS)

Siegel, Robert

1996-01-01

An analysis is developed for obtaining transient temperatures in a two-layer semitransparent composite with spectrally dependent properties. Each external boundary of the composite is subjected to radiation and convection. The two-flux radiative transfer equations are solved by deriving a Green's function. This yields the local radiative heat source needed to numerically solve the transient energy equation. An advantage of the two-flux method is that isotropic scattering is included without added complexity. The layer refractive indices are larger than one. This produces internal reflections at the boundaries and the internal interface; the reflections are assumed diffuse. Spectral results using the Green's function method are verified by comparing with numerical solutions using the exact radiative transfer equations. Transient temperature distributions are given to illustrate the effect of radiative heating on one side of a composite with external convective cooling. The protection of a material from incident radiation is illustrated by adding scattering to the layer adjacent to the radiative source.

Relationships between the decoupled and coupled transfer functions: Theoretical studies and experimental validation

NASA Astrophysics Data System (ADS)

Wang, Zengwei; Zhu, Ping; Liu, Zhao

2018-01-01

A generalized method for predicting the decoupled transfer functions based on in-situ transfer functions is proposed. The method allows predicting the decoupled transfer functions using coupled transfer functions, without disassembling the system. Two ways to derive relationships between the decoupled and coupled transfer functions are presented. Issues related to immeasurability of coupled transfer functions are also discussed. The proposed method is validated by numerical and experimental case studies.

The electronically excited states of LH2 complexes from Rhodopseudomonas acidophila strain 10050 studied by time-resolved spectroscopy and dynamic Monte Carlo simulations. II. Homo-arrays of LH2 complexes reconstituted into phospholipid model membranes.

PubMed

Pflock, Tobias J; Oellerich, Silke; Krapf, Lisa; Southall, June; Cogdell, Richard J; Ullmann, G Matthias; Köhler, Jürgen

2011-07-21

We performed time-resolved spectroscopy on homoarrays of LH2 complexes from the photosynthetic purple bacterium Rhodopseudomonas acidophila. Variations of the fluorescence transients were monitored as a function of the excitation fluence and the repetition rate of the excitation. These parameters are directly related to the excitation density within the array and to the number of LH2 complexes that still carry a triplet state prior to the next excitation. Comparison of the experimental observations with results from dynamic Monte Carlo simulations for a model cluster of LH2 complexes yields qualitative agreement without the need for any free parameter and reveals the mutual relationship between energy transfer and annihilation processes.

The Multiple Origins of Complex Multicellularity

NASA Astrophysics Data System (ADS)

Knoll, Andrew H.

2011-05-01

Simple multicellularity has evolved numerous times within the Eukarya, but complex multicellular organisms belong to only six clades: animals, embryophytic land plants, florideophyte red algae, laminarialean brown algae, and two groups of fungi. Phylogeny and genomics suggest a generalized trajectory for the evolution of complex multicellularity, beginning with the co-optation of existing genes for adhesion. Molecular channels to facilitate cell-cell transfer of nutrients and signaling molecules appear to be critical, as this trait occurs in all complex multicellular organisms but few others. Proliferation of gene families for transcription factors and cell signals accompany the key functional innovation of complex multicellular clades: differentiated cells and tissues for the bulk transport of oxygen, nutrients, and molecular signals that enable organisms to circumvent the physical limitations of diffusion. The fossil records of animals and plants document key stages of this trajectory.

Large eddy simulation for predicting turbulent heat transfer in gas turbines

PubMed Central

Tafti, Danesh K.; He, Long; Nagendra, K.

2014-01-01

Blade cooling technology will play a critical role in the next generation of propulsion and power generation gas turbines. Accurate prediction of blade metal temperature can avoid the use of excessive compressed bypass air and allow higher turbine inlet temperature, increasing fuel efficiency and decreasing emissions. Large eddy simulation (LES) has been established to predict heat transfer coefficients with good accuracy under various non-canonical flows, but is still limited to relatively simple geometries and low Reynolds numbers. It is envisioned that the projected increase in computational power combined with a drop in price-to-performance ratio will make system-level simulations using LES in complex blade geometries at engine conditions accessible to the design process in the coming one to two decades. In making this possible, two key challenges are addressed in this paper: working with complex intricate blade geometries and simulating high-Reynolds-number (Re) flows. It is proposed to use the immersed boundary method (IBM) combined with LES wall functions. A ribbed duct at Re=20 000 is simulated using the IBM, and a two-pass ribbed duct is simulated at Re=100 000 with and without rotation (rotation number Ro=0.2) using LES with wall functions. The results validate that the IBM is a viable alternative to body-conforming grids and that LES with wall functions reproduces experimental results at a much lower computational cost. PMID:25024418

Theoretical studies of charge transfer and proton transfer complex formation between 3,5-dinitrobenzic acid and 1,2-dimethylimidazole

NASA Astrophysics Data System (ADS)

Afroz, Ziya; Faizan, Mohd.; Alam, Mohammad Jane; Ahmad, Shabbir; Ahmad, Afaq

2018-05-01

Natural atomic charge analysis and molecular electrostatic potential (MEP) surface analysis of hydrogen bonded charge transfer (HBCT) and proton transfer (PT) complex of 3,5-dinitrobenzoic acid (DNBA) and 1,2-dimethylimidazole (DMI) have been investigated by theoretical modelling using widely employed DFT/B3LYP/6-311G(d,p) level of theory. Along with this analysis, Hirshfeld surface study of the intermolecular interactions and associated 2D finger plot for reported PT complex between DNBA and DMI have been explored.

Simulation of the temperature distribution in crystals grown by Czochralski method

NASA Technical Reports Server (NTRS)

Dudokovic, M. P.; Ramachandran, P. A.

1985-01-01

Production of perfect crystals, free of residual strain and dislocations and with prescribed dopant concentration, by the Czochralski method is possible only if the complex, interacting phenomena that affect crystal growth in a Cz-puller are fully understood and quantified. Natural and forced convection in the melt, thermocapillary effect and heat transfer in and around the crystal affect its growth rate, the shape of the crystal-melt interface and the temperature gradients in the crystal. The heat transfer problem in the crystal and between the crystal and all other surfaces present in the crystal pulling apparatus are discussed at length. A simulation and computer algorithm are used, based on the following assumptions: (1) only conduction occurs in the crystal (experimentally determined conductivity as a function of temperature is used), (2) melt temperature and the melt-crystal heat transfer coefficient are available (either as constant values or functions of radial position), (3) pseudo-steady state is achieved with respect to temperature gradients, (4) crystal radius is fixed, and (5) both direct and reflected radiation exchange occurs among all surfaces at various temperatures in the crystal puller enclosure.

Assessment of the horizontal transfer of functional genes as a suitable approach for evaluation of the bioremediation potential of petroleum-contaminated sites: a mini-review.

PubMed

Shahi, Aiyoub; Ince, Bahar; Aydin, Sevcan; Ince, Orhan

2017-06-01

Petroleum sludge contains recalcitrant residuals. These compounds because of being toxic to humans and other organism are of the major concerns. Therefore, petroleum sludge should be safely disposed. Physicochemical methods which are used by this sector are mostly expensive and need complex devices. Bioremediation methods because of being eco-friendly and cost-effective overcome most of the limitations of physicochemical treatments. Microbial strains capable to degrade petroleum hydrocarbons are practically present in all soils and sediments and their population density increases in contact with contaminants. Bacterial strains cannot degrade alone all kinds of petroleum hydrocarbons, rather microbial consortium should collaborate with each other for degradation of petroleum hydrocarbon mixtures. Horizontal transfer of functional genes between bacteria plays an important role in increasing the metabolic potential of the microbial community. Therefore, selecting a suitable degrading gene and tracking its horizontal transfer would be a useful approach to evaluate the bioremediation process and to assess the bioremediation potential of contaminated sites.

Dendroclimatic transfer functions revisited: Little Ice Age and Medieval Warm Period summer temperatures reconstructed using artificial neural networks and linear algorithms

NASA Astrophysics Data System (ADS)

Helama, S.; Makarenko, N. G.; Karimova, L. M.; Kruglun, O. A.; Timonen, M.; Holopainen, J.; Meriläinen, J.; Eronen, M.

2009-03-01

Tree-rings tell of past climates. To do so, tree-ring chronologies comprising numerous climate-sensitive living-tree and subfossil time-series need to be "transferred" into palaeoclimate estimates using transfer functions. The purpose of this study is to compare different types of transfer functions, especially linear and nonlinear algorithms. Accordingly, multiple linear regression (MLR), linear scaling (LSC) and artificial neural networks (ANN, nonlinear algorithm) were compared. Transfer functions were built using a regional tree-ring chronology and instrumental temperature observations from Lapland (northern Finland and Sweden). In addition, conventional MLR was compared with a hybrid model whereby climate was reconstructed separately for short- and long-period timescales prior to combining the bands of timescales into a single hybrid model. The fidelity of the different reconstructions was validated against instrumental climate data. The reconstructions by MLR and ANN showed reliable reconstruction capabilities over the instrumental period (AD 1802-1998). LCS failed to reach reasonable verification statistics and did not qualify as a reliable reconstruction: this was due mainly to exaggeration of the low-frequency climatic variance. Over this instrumental period, the reconstructed low-frequency amplitudes of climate variability were rather similar by MLR and ANN. Notably greater differences between the models were found over the actual reconstruction period (AD 802-1801). A marked temperature decline, as reconstructed by MLR, from the Medieval Warm Period (AD 931-1180) to the Little Ice Age (AD 1601-1850), was evident in all the models. This decline was approx. 0.5°C as reconstructed by MLR. Different ANN based palaeotemperatures showed simultaneous cooling of 0.2 to 0.5°C, depending on algorithm. The hybrid MLR did not seem to provide further benefit above conventional MLR in our sample. The robustness of the conventional MLR over the calibration, verification and reconstruction periods qualified it as a reasonable transfer function for our forest-limit (i.e., timberline) dataset. ANN appears a potential tool for other environments and/or proxies having more complex and noisier climatic relationships.

The effects of video-game training on broad cognitive transfer in multiple sclerosis: A pilot randomized controlled trial.

PubMed

Janssen, Alisha; Boster, Aaron; Lee, HyunKyu; Patterson, Beth; Prakash, Ruchika Shaurya

2015-01-01

Multiple sclerosis (MS) is a neurodegenerative disease of the central nervous system that results in diffuse nerve damage and associated physical and cognitive impairments. Of the few comprehensive rehabilitation options that exist for populations with lower baseline cognitive functioning, those that have been successful at eliciting broad cognitive improvements have focused on a multimodal training approach, emphasizing complex cognitive processing that utilizes multiple domains simultaneously. The current study sought to determine the feasibility of an 8-week, hybrid-variable priority training (HVT) program, with a secondary aim to assess the success of this training paradigm at eliciting broad cognitive transfer effects. Capitalizing on the multimodal training modalities offered by the Space Fortress platform, we compared the HVT strategy-based intervention with a waitlist control group, to primarily assess skill acquisition and secondarily determine presence of cognitive transfer. Twenty-eight participants met inclusionary criteria for the study and were randomized to either training or waitlist control groups. To assess broad transfer effects, a battery of neuropsychological tests was administered pre- and post-intervention. The results indicated an overall improvement in skill acquisition and evidence for the feasibility of the intervention, but a lack of broad transfer to tasks of cognitive functioning. Participants in the training group, however, did show improvements on a measure of spatial short-term memory. The current investigation provided support for the feasibility of a multimodal training approach, using the HVT strategy, within the MS population, but lacked broad transfer to multiple domains of cognitive functioning. Future improvements to obtain greater cognitive transfer efficacy would include a larger sample size, a longer course of training to evoke greater game score improvement, the inclusion of only cognitively impaired individuals, and integration of subjective measures of improvement in addition to objective tests of cognitive performance.

On the need for widespread horizontal gene transfers under genome size constraint.

PubMed

Isambert, Hervé; Stein, Richard R

2009-08-25

While eukaryotes primarily evolve by duplication-divergence expansion (and reduction) of their own gene repertoire with only rare horizontal gene transfers, prokaryotes appear to evolve under both gene duplications and widespread horizontal gene transfers over long evolutionary time scales. But, the evolutionary origin of this striking difference in the importance of horizontal gene transfers remains by and large a mystery. We propose that the abundance of horizontal gene transfers in free-living prokaryotes is a simple but necessary consequence of two opposite effects: i) their apparent genome size constraint compared to typical eukaryote genomes and ii) their underlying genome expansion dynamics through gene duplication-divergence evolution, as demonstrated by the presence of many tandem and block repeated genes. In principle, this combination of genome size constraint and underlying duplication expansion should lead to a coalescent-like process with extensive turnover of functional genes. This would, however, imply the unlikely, systematic reinvention of functions from discarded genes within independent phylogenetic lineages. Instead, we propose that the long-term evolutionary adaptation of free-living prokaryotes must have resulted in the emergence of efficient non-phylogenetic pathways to circumvent gene loss. This need for widespread horizontal gene transfers due to genome size constraint implies, in particular, that prokaryotes must remain under strong selection pressure in order to maintain the long-term evolutionary adaptation of their "mutualized" gene pool, beyond the inevitable turnover of individual prokaryote species. By contrast, the absence of genome size constraint for typical eukaryotes has presumably relaxed their need for widespread horizontal gene transfers and strong selection pressure. Yet, the resulting loss of genetic functions, due to weak selection pressure and inefficient gene recovery mechanisms, must have ultimately favored the emergence of more complex life styles and ecological integration of many eukaryotes. This article was reviewed by Pierre Pontarotti, Eugene V Koonin and Sergei Maslov.

Photosensitization of Intact Heart Mitochondria by the Phthalocyanine Pc 4: Correlation of Structural and Functional Deficits with Cytochrome c Release

PubMed Central

Kim, Junhwan; Fujioka, Hisashi; Oleinick, Nancy L.; Anderson, Vernon E.

2010-01-01

Singlet oxygen is produced by absorption of red light by the phthalocyanine dye, Pc 4, followed by energy transfer to dissolved triplet oxygen. Mitochondria pre-incubated with Pc 4 were illuminated by red light and the damage to mitochondrial structure and function by the generated singlet oxygen was studied. At early illumination times (3–5 min. of red light exposure), state 3 respiration was inhibited (50%) while state 4 activity increased, resulting in effectively complete uncoupling. Individual complex activities were measured and only complex IV activity was significantly reduced and exhibited a dose response while the activities of electron transport complexes I, II and III were not significantly affected. Cyt c release was an increasing function of irradiation time with 30% being released following 5 min. of illumination. Mitochondrial expansion along with changes in the structure of the cristae were observed by transmission electron microscopy following 5 min. of irradiation with an increase of large vacuoles and membrane rupture occurring following more extensive exposures. PMID:20510354

A chloroplast "wake up" mechanism: Illumination with weak light activates the photosynthetic antenna function in dark-adapted plants.

PubMed

Janik, Ewa; Bednarska, Joanna; Zubik, Monika; Luchowski, Rafal; Mazur, Radoslaw; Sowinski, Karol; Grudzinski, Wojciech; Garstka, Maciej; Gruszecki, Wieslaw I

2017-03-01

The efficient and fluent operation of photosynthesis in plants relies on activity of pigment-protein complexes called antenna, absorbing light and transferring excitations toward the reaction centers. Here we show, based on the results of the fluorescence lifetime imaging analyses of single chloroplasts, that pigment-protein complexes, in dark-adapted plants, are not able to act effectively as photosynthetic antennas, due to pronounced, adverse excitation quenching. It appeared that the antenna function could be activated by a short (on a minute timescale) illumination with light of relatively low intensity, substantially below the photosynthesis saturation threshold. The low-light-induced activation of the antenna function was attributed to phosphorylation of the major accessory light-harvesting complex LHCII, based on the fact that such a mechanism was not observed in the stn7 Arabidopsis thaliana mutant, with impaired LHCII phosphorylation. It is proposed that the protein phosphorylation-controlled change in the LHCII clustering ability provides mechanistic background for this regulatory process. Copyright © 2016 Elsevier GmbH. All rights reserved.

Integrating some mind and brain views of transference: the phenomena.

PubMed

Levin, F M

1997-01-01

Because understanding the underpinnings of transferential learning allows the analyst to more effectively exploit transference in the clinical situation, as well as to advance psychoanalytic theory, the functions and mechanisms of transference phenomena in learning are subjected to an interdisciplinary analysis. Through transference the brain creates hierarchical databases that make emotional sense of the world, especially the world of human relationships. Transference plays a role in defense and resistance clinically; less explored but equally important is the adaptive potential of transference and its effect on an individual's readiness for structural change through the activation of working memory. Most investigators within psychoanalysis have not considered the importance of similarity judgments and memory priming, especially as these help to explain why transference and its proper handling are effective in treatment. Yet there are complex relationships among transference, similarity judgment, and memory priming that tie together psychoanalysis, cognitive psychology, and neurophysiology. Evidence increasingly suggests a relationship between transference and the transfer of knowledge between various content domains (databases) of mind and brain, which is essential to cognitive and emotional learning. There are indications as well that transference decisively facilitates learning readiness ("windows") in general by means of two of its components: free association and spontaneous (self-initiated) activity. The important question of which mind/brain mechanisms motivate transference is not yet understood comprehensively. However, Vygotsky's work on the zone of proximal development (ZPD), M.Stern's teleonomic theory, schema theory, and neural network theory offer further insights into what motivates transference.

Site-selective oxidation, amination and epimerization reactions of complex polyols enabled by transfer hydrogenation

NASA Astrophysics Data System (ADS)

Hill, Christopher K.; Hartwig, John F.

2017-12-01

Polyoxygenated hydrocarbons that bear one or more hydroxyl groups comprise a large set of natural and synthetic compounds, often with potent biological activity. In synthetic chemistry, alcohols are important precursors to carbonyl groups, which then can be converted into a wide range of oxygen- or nitrogen-based functionality. Therefore, the selective conversion of a single hydroxyl group in natural products into a ketone would enable the selective introduction of unnatural functionality. However, the methods known to convert a simple alcohol, or even an alcohol in a molecule that contains multiple protected functional groups, are not suitable for selective reactions of complex polyol structures. We present a new ruthenium catalyst with a unique efficacy for the selective oxidation of a single hydroxyl group among many in unprotected polyol natural products. This oxidation enables the introduction of nitrogen-based functional groups into such structures that lack nitrogen atoms and enables a selective alcohol epimerization by stepwise or reversible oxidation and reduction.

Strategies to enhance the excitation energy-transfer efficiency in a light-harvesting system using the intra-molecular charge transfer character of carotenoids

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

Yukihira, Nao; Sugai, Yuko; Fujiwara, Masazumi

Fucoxanthin is a carotenoid that is mainly found in light-harvesting complexes from brown algae and diatoms. Due to the presence of a carbonyl group attached to polyene chains in polar environments, excitation produces an excited intra-molecular charge transfer. This intra-molecular charge transfer state plays a key role in the highly efficient (~95%) energy-transfer from fucoxanthin to chlorophyllain the light-harvesting complexes from brown algae. In purple bacterial light-harvesting systems the efficiency of excitation energy-transfer from carotenoids to bacteriochlorophylls depends on the extent of conjugation of the carotenoids. In this study we were successful, for the first time, in incorporating fucoxanthin intomore » a light-harvesting complex 1 from the purple photosynthetic bacterium,Rhodospirillum rubrumG9+ (a carotenoidless strain). Femtosecond pump-probe spectroscopy was applied to this reconstituted light-harvesting complex in order to determine the efficiency of excitation energy-transfer from fucoxanthin to bacteriochlorophyllawhen they are bound to the light-harvesting 1 apo-proteins.« less

Direct Observation of Energy Detrapping in LH1-RC Complex by Two-Dimensional Electronic Spectroscopy.

PubMed

Ma, Fei; Yu, Long-Jiang; Hendrikx, Ruud; Wang-Otomo, Zheng-Yu; van Grondelle, Rienk

2017-01-18

The purple bacterial core light harvesting antenna-reaction center (LH1-RC) complex is the simplest system able to achieve the entire primary function of photosynthesis. During the past decade, a variety of photosynthetic proteins were studied by a powerful technique, two-dimensional electronic spectroscopy (2DES). However, little attention has been paid to LH1-RC, although its reversible uphill energy transfer, trapping, and backward detrapping processes, represent a crucial step in the early photosynthetic reaction dynamics. Thus, in this work, we employed 2DES to study two LH1-RC complexes of Thermochromatium (Tch.) tepidum. By direct observation of detrapping, the complex reversible process was clearly identified and an overall scheme of the excitation evolution in LH1-RC was obtained.

A Computerized Hospital Patient Information Management System

PubMed Central

Wig, Eldon D.

1982-01-01

The information processing needs of a hospital are many, with varying degrees of complexity. The prime concern in providing an integrated hospital information management system lies in the ability to process the data relating to the single entity for which every hospital functions - the patient. This paper examines the PRIMIS computer system developed to accommodate hospital needs with respect to a central patient registry, inpatients (i.e., Admission/Transfer/Discharge), and out-patients. Finally, the potential for expansion to permit the incorporation of more hospital functions within PRIMIS is examined.

Principles of Protein Recognition and Properties of Protein-protein Interfaces

NASA Astrophysics Data System (ADS)

Keskin, Ozlem; Gursoy, Attila; Nussinov, Ruth

In this chapter we address two aspects - the static physical interactions which allow the information transfer for the function to be performed; and the dynamic, i.e. how the information is transmitted between the binding sites in the single protein molecule and in the network. We describe the single protein molecules and their complexes; and the analogy between protein folding and protein binding. Eventually, to fully understand the interactome and how it performs the essential cellular functions, we have to put all together - and hierarchically progress through the system.

Modelling the bidirectional reflectance distribution function (BRDF) of seawater polluted by an oil film.

PubMed

Otremba, Zbigniew; Piskozub, Jacek

2004-04-19

The Bi-directional Reflectance Distribution Function (BRDF) of both clean seawaters and those polluted with oil film was determined using the Monte Carlo radiative transfer technique in which the spectrum of complex refractive index of Romashkino crude oil and the optical properties of case II water for chosen wavelengths was considered. The BRDF values were recorded for 1836 solid angular sectors of throughout the upper hemisphere. The visibility of areas polluted with oil observed from various directions and for various wavelengths is discussed.

Comparative analysis on flexibility requirements of typical Cryogenic Transfer lines

NASA Astrophysics Data System (ADS)

Jadon, Mohit; Kumar, Uday; Choukekar, Ketan; Shah, Nitin; Sarkar, Biswanath

2017-04-01

The cryogenic systems and their applications; primarily in large Fusion devices, utilize multiple cryogen transfer lines of various sizes and complexities to transfer cryogenic fluids from plant to the various user/ applications. These transfer lines are composed of various critical sections i.e. tee section, elbows, flexible components etc. The mechanical sustainability (under failure circumstances) of these transfer lines are primary requirement for safe operation of the system and applications. The transfer lines need to be designed for multiple design constraints conditions like line layout, support locations and space restrictions. The transfer lines are subjected to single load and multiple load combinations, such as operational loads, seismic loads, leak in insulation vacuum loads etc. [1]. The analytical calculations and flexibility analysis using professional software are performed for the typical transfer lines without any flexible component, the results were analysed for functional and mechanical load conditions. The failure modes were identified along the critical sections. The same transfer line was then refurbished with the flexible components and analysed for failure modes. The flexible components provide additional flexibility to the transfer line system and make it safe. The results obtained from the analytical calculations were compared with those obtained from the flexibility analysis software calculations. The optimization of the flexible component’s size and selection was performed and components were selected to meet the design requirements as per code.

A High-yield Two-step Transfer Printing Method for Large-scale Fabrication of Organic Single-crystal Devices on Arbitrary Substrates

PubMed Central

Deng, Wei; Zhang, Xiujuan; Pan, Huanhuan; Shang, Qixun; Wang, Jincheng; Zhang, Xiaohong; Zhang, Xiwei; Jie, Jiansheng

2014-01-01

Single-crystal organic nanostructures show promising applications in flexible and stretchable electronics, while their applications are impeded by the large incompatibility with the well-developed photolithography techniques. Here we report a novel two-step transfer printing (TTP) method for the construction of organic nanowires (NWs) based devices onto arbitrary substrates. Copper phthalocyanine (CuPc) NWs are first transfer-printed from the growth substrate to the desired receiver substrate by contact-printing (CP) method, and then electrode arrays are transfer-printed onto the resulting receiver substrate by etching-assisted transfer printing (ETP) method. By utilizing a thin copper (Cu) layer as sacrificial layer, microelectrodes fabricated on it via photolithography could be readily transferred to diverse conventional or non-conventional substrates that are not easily accessible before with a high transfer yield of near 100%. The ETP method also exhibits an extremely high flexibility; various electrodes such as Au, Ti, and Al etc. can be transferred, and almost all types of organic devices, such as resistors, Schottky diodes, and field-effect transistors (FETs), can be constructed on planar or complex curvilinear substrates. Significantly, these devices can function properly and exhibit closed or even superior performance than the device counterparts fabricated by conventional approach. PMID:24942458

Lambda Red-mediated mutagenesis and efficient large scale affinity purification of the Escherichia coli NADH:ubiquinone oxidoreductase (complex I).

PubMed

Pohl, Thomas; Uhlmann, Mareike; Kaufenstein, Miriam; Friedrich, Thorsten

2007-09-18

The proton-pumping NADH:ubiquinone oxidoreductase, the respiratory complex I, couples the transfer of electrons from NADH to ubiquinone with the translocation of protons across the membrane. The Escherichia coli complex I consists of 13 different subunits named NuoA-N (from NADH:ubiquinone oxidoreductase), that are coded by the genes of the nuo-operon. Genetic manipulation of the operon is difficult due to its enormous size. The enzymatic activity of variants is obscured by an alternative NADH dehydrogenase, and purification of the variants is hampered by their instability. To overcome these problems the entire E. coli nuo-operon was cloned and placed under control of the l-arabinose inducible promoter ParaBAD. The exposed N-terminus of subunit NuoF was chosen for engineering the complex with a hexahistidine-tag by lambda-Red-mediated recombineering. Overproduction of the complex from this construct in a strain which is devoid of any membrane-bound NADH dehydrogenase led to the assembly of a catalytically active complex causing the entire NADH oxidase activity of the cytoplasmic membranes. After solubilization with dodecyl maltoside the engineered complex binds to a Ni2+-iminodiacetic acid matrix allowing the purification of approximately 11 mg of complex I from 25 g of cells. The preparation is pure and monodisperse and comprises all known subunits and cofactors. It contains more lipids than earlier preparations due to the gentle and fast purification procedure. After reconstitution in proteoliposomes it couples the electron transfer with proton translocation in an inhibitor sensitive manner, thus meeting all prerequisites for structural and functional studies.

Reconstruction of Complex Facial Defects Using Cervical Expanded Flap Prefabricated by Temporoparietal Fascia Flap.

PubMed

Zhang, Ling; Yang, Qinghua; Jiang, Haiyue; Liu, Ge; Huang, Wanlu; Dong, Weiwei

2015-09-01

Reconstruction of complex facial defects using cervical expanded flap prefabricated by temporoparietal fascia flap. Complex facial defects are required to restore not only function but also aesthetic appearance, so it is vital challenge for plastic surgeons. Skin grafts and traditional flap transfer cannot meet the reconstructive requirements of color and texture with recipient. The purpose of this sturdy is to create an expanded prefabricated temporoparietal fascia flap to repair complex facial defects. Two patients suffered severe burns on the face underwent complex facial resurfacing with prefabricated cervical flap. The vasculature of prefabricated flap, including the superficial temporal vessel and surrounding fascia, was used as the vascular carrier. The temporoparietal fascia flap was sutured underneath the cervical subcutaneous tissue, and expansion was begun in postoperative 1 week. After 4 to 6 months of expansion, the expander was removed, facial scars were excised, and cervical prefabricated flap was elevated and transferred to repair the complex facial defects. Two complex facial defects were repaired successfully by prefabricated temporoparietal fascia flap, and prefabricated flaps survived completely. On account of donor site's skin was thinner and expanded too fast, 1 expanded skin flap was rupture during expansion, but necrosis was not occurred after the 2nd operation. Venous congestion was observed in 1 patient, but after dressing, flap necrosis was not happened. Donor site was closed primarily. Postoperative follow-up 6 months, the color, texture of prefabricated flap was well-matched with facial skin. This method of expanded prefabricated flap may provide a reliable solution to the complex facial resurfacing.

Materials for Fluorescence Resonance Energy Transfer Analysis: Beyond Traditional Donor-Acceptor Combinations

DTIC Science & Technology

2006-01-01

a variety of surface functionalities (e.g., biotin, avidin, collagen , amines, alde- hydes, sulfates, and carboxylates) that allow facile bioconju...relative expression level.[14,20,21] The green fluorescent protein (GFP; Figure 9) derived from the jellyfish Aequorea victoria is the prototypical...derived from jellyfish , is a Ca2+-sensitive bioluminescent photoprotein consisting of the luciferase apoaequorin complexed to its coelenterazine

Optimal File-Distribution in Heterogeneous and Asymmetric Storage Networks

NASA Astrophysics Data System (ADS)

Langner, Tobias; Schindelhauer, Christian; Souza, Alexander

We consider an optimisation problem which is motivated from storage virtualisation in the Internet. While storage networks make use of dedicated hardware to provide homogeneous bandwidth between servers and clients, in the Internet, connections between storage servers and clients are heterogeneous and often asymmetric with respect to upload and download. Thus, for a large file, the question arises how it should be fragmented and distributed among the servers to grant "optimal" access to the contents. We concentrate on the transfer time of a file, which is the time needed for one upload and a sequence of n downloads, using a set of m servers with heterogeneous bandwidths. We assume that fragments of the file can be transferred in parallel to and from multiple servers. This model yields a distribution problem that examines the question of how these fragments should be distributed onto those servers in order to minimise the transfer time. We present an algorithm, called FlowScaling, that finds an optimal solution within running time {O}(m log m). We formulate the distribution problem as a maximum flow problem, which involves a function that states whether a solution with a given transfer time bound exists. This function is then used with a scaling argument to determine an optimal solution within the claimed time complexity.

Preparation and spectroscopic studies on charge-transfer complexes of 2,2'-bipyridine with picric and chloranilic acids

NASA Astrophysics Data System (ADS)

Teleb, Said M.; Gaballa, Akmal S.

2005-11-01

Charge-transfer (CT) complexes formed on the reaction of 2,2'-bipyridine with some acceptors such as picric acid (HPA) and chloranilic acid (H 2CA) have been studied in CHCl 3 and MeOH at room temperature. Based on elemental analysis and IR spectra of the solid CT complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge-transfer complexes [(bpyH)(PA)] and [(bpyH 2)(CA)], respectively. The infrared and 1H NMR spectroscopic data indicate a charge-transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding. The formation constants ( KC) for the complexes were shown to be dependent on the structure of the electron acceptors used.

Preparation and spectroscopic studies on charge-transfer complexes of 2,2'-bipyridine with picric and chloranilic acids.

PubMed

Teleb, Said M; Gaballa, Akmal S

2005-11-01

Charge-transfer (CT) complexes formed on the reaction of 2,2'-bipyridine with some acceptors such as picric acid (HPA) and chloranilic acid (H(2)CA) have been studied in CHCl(3) and MeOH at room temperature. Based on elemental analysis and IR spectra of the solid CT complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge-transfer complexes [(bpyH)(PA)] and [(bpyH(2))(CA)], respectively. The infrared and (1)H NMR spectroscopic data indicate a charge-transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding. The formation constants (K(C)) for the complexes were shown to be dependent on the structure of the electron acceptors used.

Molecular dynamics simulation and TDDFT study of the structures and UV-vis absorption spectra of MCT-β-CD and its inclusion complexes.

PubMed

Lu, Huijuan; Wang, Yujiao; Xie, Xiaomei; Chen, Feifei; Li, Wei

2015-01-01

In this research, the inclusion ratios and inclusion constants of MCT-β-CD/PERM and MCT-β-CD/CYPERM inclusion complexes were measured by UV-vis and fluorescence spectroscopy. The inclusion ratios are both 1:1, and the inclusion constants are 60 and 342.5 for MCT-β-CD/PERM and MCT-β-CD/CYPERM, respectively. The stabilities of inclusion complexes were investigated by MD simulation. MD shows that VDW energy plays a vital role in the stability of inclusion complex, and the destruction of inclusion complex is due to the increasing temperature. The UV-vis absorption spectra of MCT-β-CD and its inclusion complexes were studied by time-dependent density functional theory (TDDFT) method employing BLYP-D3, B3LYP-D3 and M06-2X-D3 functionals. BLYP-D3 well reproduces the UV-vis absorption spectrum and reveals that the absorption bands of MCT-β-CD mainly arise from n→π(∗) and n→σ(∗) transition, and those of inclusion complexes mainly arise from intramolecular charge transfer (ICT). ICT results in the shift of main absorption bands of MCT-β-CD. Copyright © 2015 Elsevier B.V. All rights reserved.

Segregating the core computational faculty of human language from working memory

PubMed Central

Makuuchi, Michiru; Bahlmann, Jörg; Anwander, Alfred; Friederici, Angela D.

2009-01-01

In contrast to simple structures in animal vocal behavior, hierarchical structures such as center-embedded sentences manifest the core computational faculty of human language. Previous artificial grammar learning studies found that the left pars opercularis (LPO) subserves the processing of hierarchical structures. However, it is not clear whether this area is activated by the structural complexity per se or by the increased memory load entailed in processing hierarchical structures. To dissociate the effect of structural complexity from the effect of memory cost, we conducted a functional magnetic resonance imaging study of German sentence processing with a 2-way factorial design tapping structural complexity (with/without hierarchical structure, i.e., center-embedding of clauses) and working memory load (long/short distance between syntactically dependent elements; i.e., subject nouns and their respective verbs). Functional imaging data revealed that the processes for structure and memory operate separately but co-operatively in the left inferior frontal gyrus; activities in the LPO increased as a function of structural complexity, whereas activities in the left inferior frontal sulcus (LIFS) were modulated by the distance over which the syntactic information had to be transferred. Diffusion tensor imaging showed that these 2 regions were interconnected through white matter fibers. Moreover, functional coupling between the 2 regions was found to increase during the processing of complex, hierarchically structured sentences. These results suggest a neuroanatomical segregation of syntax-related aspects represented in the LPO from memory-related aspects reflected in the LIFS, which are, however, highly interconnected functionally and anatomically. PMID:19416819

Structure of a HOIP/E2~ubiquitin complex reveals RBR E3 ligase mechanism and regulation

PubMed Central

Lechtenberg, Bernhard C.; Rajput, Akhil; Sanishvili, Ruslan; Dobaczewska, Małgorzata K.; Ware, Carl F.; Mace, Peter D.; Riedl, Stefan J.

2015-01-01

Ubiquitination is a central process affecting all facets of cellular signaling and function1. A critical step in ubiquitination is the transfer of ubiquitin from an E2 ubiquitin-conjugating enzyme to a substrate or a growing ubiquitin chain, which is mediated by E3 ubiquitin ligases. RING-type E3 ligases typically facilitate the transfer of ubiquitin from the E2 directly to the substrate2,3. The RBR family of RING-type E3 ligases, however, breaks this paradigm by forming a covalent intermediate with ubiquitin similarly to HECT-type E3 ligases4–6. The RBR family includes Parkin4 and HOIP, the central catalytic factor of the linear ubiquitin chain assembly complex (LUBAC)7. While structural insights into the RBR E3 ligases Parkin and HHARI in their overall autoinhibited forms are available8–13, no structures exist of intact fully active RBR E3 ligases or any of their complexes. Thus, the RBR mechanism of action has remained largely enigmatic. Here we present the first structure of the fully active HOIP-RBR in its transfer complex with an E2~ubiquitin conjugate, which elucidates the intricate nature of RBR E3 ligases. The active HOIP-RBR adopts a conformation markedly different from that of autoinhibited RBRs. HOIP-RBR binds the E2~ubiquitin conjugate in an elongated fashion, with the E2 and E3 catalytic centers ideally aligned for ubiquitin transfer, which structurally both requires and enables a HECT-like mechanism. In addition, surprisingly, three distinct helix–IBR-fold motifs inherent to RBRs form ubiquitin-binding regions that engage the activated ubiquitin of the E2~Ub conjugate as well as an additional regulatory ubiquitin molecule. The features uncovered reveal critical states of the HOIP-RBR E3 ligase cycle, and comparison with Parkin and HHARI suggests a general mechanism for RBR E3 ligases. PMID:26789245

Towards a functional model of mental disorders incorporating the laws of thermodynamics.

PubMed

Murray, George C; McKenzie, Karen

2013-05-01

The current paper presents the hypothesis that the understanding of mental disorders can be advanced by incorporating the laws of thermodynamics, specifically relating to energy conservation and energy transfer. These ideas, along with the introduction of the notion that entropic activities are symptomatic of inefficient energy transfer or disorder, were used to propose a model of understanding mental ill health as resulting from the interaction of entropy, capacity and work (environmental demands). The model was applied to Attention Deficit Hyperactivity Disorder, and was shown to be compatible with current thinking about this condition, as well as emerging models of mental disorders as complex networks. A key implication of the proposed model is that it argues that all mental disorders require a systemic functional approach, with the advantage that it offers a number of routes into the assessment, formulation and treatment for mental health problems. Copyright © 2013 Elsevier Ltd. All rights reserved.

Dynamics of energy transfer from lycopene to bacteriochlorophyll in genetically-modified LH2 complexes of Rhodobacter sphaeroides.

PubMed

Hörvin Billsten, H; Herek, J L; Garcia-Asua, G; Hashøj, L; Polívka, T; Hunter, C N; Sundström, V

2002-03-26

LH2 complexes from Rb. sphaeroides were modified genetically so that lycopene, with 11 saturated double bonds, replaced the native carotenoids which contain 10 saturated double bonds. Tuning the S1 level of the carotenoid in LH2 in this way affected the dynamics of energy transfer within LH2, which were investigated using both steady-state and time-resolved techniques. The S1 energy of lycopene in n-hexane was determined to be approximately 12 500 +/- 150 cm(-1), by direct measurement of the S1-S2 transient absorption spectrum using a femtosecond IR-probing technique, thus placing an upper limit on the S1 energy of lycopene in the LH2 complex. Fluorescence emission and excitation spectra demonstrated that energy can be transferred from lycopene to the bacteriochlorophyll molecules within this LH2 complex. The energy-transfer dynamics within the mutant complex were compared to wild-type LH2 from Rb. sphaeroides containing the carotenoid spheroidene and from Rs. molischianum, in which lycopene is the native carotenoid. The results show that the overall efficiency for Crt --> B850 energy transfer is approximately 80% in lyco-LH2 and approximately 95% in WT-LH2 of Rb. sphaeroides. The difference in overall Crt --> BChl transfer efficiency of lyco-LH2 and WT-LH2 mainly relates to the low efficiency of the Crt S(1) --> BChl pathway for complexes containing lycopene, which was 20% in lyco-LH2. These results show that in an LH2 complex where the Crt S1 energy is sufficiently high to provide efficient spectral overlap with both B800 and B850 Q(y) states, energy transfer via the Crt S1 state occurs to both pigments. However, the introduction of lycopene into the Rb. sphaeroides LH2 complex lowers the S1 level of the carotenoid sufficiently to prevent efficient transfer of energy to the B800 Q(y) state, leaving only the Crt S1 --> B850 channel, strongly suggesting that Crt S1 --> BChl energy transfer is controlled by the relative Crt S1 and BChl Q(y) energies.

Metabolites from invasive pests inhibit mitochondrial complex II: A potential strategy for the treatment of human ovarian carcinoma?

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

Ferramosca, Alessandra, E-mail: alessandra.ferramosca@unisalento.it; Conte, Annalea; Guerra, Flora

The red pigment caulerpin, a secondary metabolite from the marine invasive green algae Caulerpa cylindracea can be accumulated and transferred along the trophic chain, with detrimental consequences on biodiversity and ecosystem functioning. Despite increasing research efforts to understand how caulerpin modifies fish physiology, little is known on the effects of algal metabolites on mammalian cells. Here we report for the first time the mitochondrial targeting activity of both caulerpin, and its closely related derivative caulerpinic acid, by using as experimental model rat liver mitochondria, a system in which bioenergetics mechanisms are not altered. Mitochondrial function was tested by polarographic andmore » spectrophotometric methods. Both compounds were found to selectively inhibit respiratory complex II activity, while complexes I, III, and IV remained functional. These results led us to hypothesize that both algal metabolites could be used as antitumor agents in cell lines with defects in mitochondrial complex I. Ovarian cancer cisplatin-resistant cells are a good example of cell lines with a defective complex I function on which these molecules seem to have a toxic effect on proliferation. This provided novel insight toward the potential use of metabolites from invasive Caulerpa species for the treatment of human ovarian carcinoma cisplatin-resistant cells. -- Highlights: •Novel insight toward the potential use of the algal metabolites for the treatment of human diseases. •Caulerpin and caulerpinic acid inhibit respiratory complex II activity. •Both algal metabolites could be used as antitumor agents in ovarian cancer cisplatin-resistant cells.« less

Unraveling the evolutionary history of the phosphoryl-transfer chain of the phosphoenolpyruvate:phosphotransferase system through phylogenetic analyses and genome context

PubMed Central

2008-01-01

Background The phosphoenolpyruvate phosphotransferase system (PTS) plays a major role in sugar transport and in the regulation of essential physiological processes in many bacteria. The PTS couples solute transport to its phosphorylation at the expense of phosphoenolpyruvate (PEP) and it consists of general cytoplasmic phosphoryl transfer proteins and specific enzyme II complexes which catalyze the uptake and phosphorylation of solutes. Previous studies have suggested that the evolution of the constituents of the enzyme II complexes has been driven largely by horizontal gene transfer whereas vertical inheritance has been prevalent in the general phosphoryl transfer proteins in some bacterial groups. The aim of this work is to test this hypothesis by studying the evolution of the phosphoryl transfer proteins of the PTS. Results We have analyzed the evolutionary history of the PTS phosphoryl transfer chain (PTS-ptc) components in 222 complete genomes by combining phylogenetic methods and analysis of genomic context. Phylogenetic analyses alone were not conclusive for the deepest nodes but when complemented with analyses of genomic context and functional information, the main evolutionary trends of this system could be depicted. Conclusion The PTS-ptc evolved in bacteria after the divergence of early lineages such as Aquificales, Thermotogales and Thermus/Deinococcus. The subsequent evolutionary history of the PTS-ptc varied in different bacterial lineages: vertical inheritance and lineage-specific gene losses mainly explain the current situation in Actinobacteria and Firmicutes whereas horizontal gene transfer (HGT) also played a major role in Proteobacteria. Most remarkably, we have identified a HGT event from Firmicutes or Fusobacteria to the last common ancestor of the Enterobacteriaceae, Pasteurellaceae, Shewanellaceae and Vibrionaceae. This transfer led to extensive changes in the metabolic and regulatory networks of these bacteria including the development of a novel carbon catabolite repression system. Hence, this example illustrates that HGT can drive major physiological modifications in bacteria. PMID:18485189

Role of Nfu1 and Bol3 in iron-sulfur cluster transfer to mitochondrial clients

PubMed Central

Melber, Andrew; Na, Un; Vashisht, Ajay; Weiler, Benjamin D; Lill, Roland; Wohlschlegel, James A; Winge, Dennis R

2016-01-01

Iron-sulfur (Fe-S) clusters are essential for many cellular processes, ranging from aerobic respiration, metabolite biosynthesis, ribosome assembly and DNA repair. Mutations in NFU1 and BOLA3 have been linked to genetic diseases with defects in mitochondrial Fe-S centers. Through genetic studies in yeast, we demonstrate that Nfu1 functions in a late step of [4Fe-4S] cluster biogenesis that is of heightened importance during oxidative metabolism. Proteomic studies revealed Nfu1 physical interacts with components of the ISA [4Fe-4S] assembly complex and client proteins that need [4Fe-4S] clusters to function. Additional studies focused on the mitochondrial BolA proteins, Bol1 and Bol3 (yeast homolog to human BOLA3), revealing that Bol1 functions earlier in Fe-S biogenesis with the monothiol glutaredoxin, Grx5, and Bol3 functions late with Nfu1. Given these observations, we propose that Nfu1, assisted by Bol3, functions to facilitate Fe-S transfer from the biosynthetic apparatus to the client proteins preventing oxidative damage to [4Fe-4S] clusters. DOI: http://dx.doi.org/10.7554/eLife.15991.001 PMID:27532773

Electron transfer across multiple hydrogen bonds: the case of ureapyrimidinedione-substituted vinyl ruthenium and osmium complexes.

PubMed

Pichlmaier, Markus; Winter, Rainer F; Zabel, Manfred; Zális, Stanislav

2009-04-08

Ruthenium and osmium complexes 2a,b and 3a,b featuring the N-4,6-dioxo-5,5-dibutyl- or the N-4,6-dioxo-5,5-di-(2-propenyl)-1,4,5,6-tetrahydropyrimidin-2-yl-N'(4-ethenylphenyl)-urea ligand dimerize by a self-complementary quadruply hydrogen-bonding donor/donor/acceptor/acceptor (DDAA) motif. We provide evidence that the dimeric structures are maintained in nonpolar solvents and in 0.1 M NBu(4)PF(6)/CH(2)Cl(2) supporting electrolyte solution. All complexes are reversibly oxidized in two consecutive two-electron oxidations (DeltaE(1/2) approximately = 500 mV) without any discernible potential splitting for the oxidation of the individual hydrogen-bridged redox active moieties. IR and UV/vis/NIR spectroelectrochemistry show a one-step conversion of the neutral to the dication without any discernible features of an intermediate monooxidized radical cation. Oxidation-induced IR changes of the NH and CO groups that are involved in hydrogen bonding are restricted to the styryl-bonded urea NH function. IR band assignments are aided by quantum chemical calculations. Our experimental findings clearly show that, at least in the present systems, the ureapyrimidinedione (Upy) DDAA hydrogen-bonding motif does not support electron transfer. The apparent reason is that neither of the hydrogen-bonding functionalities contributes to the occupied frontier levels. This results in nearly degenerate pairs of MOs representing the in-phase and out-of-phase combinations of the individual monomeric building blocks.

Identification of the 2-Hydroxyglutarate and Isovaleryl-CoA Dehydrogenases as Alternative Electron Donors Linking Lysine Catabolism to the Electron Transport Chain of Arabidopsis Mitochondria[W][OA

PubMed Central

Araújo, Wagner L.; Ishizaki, Kimitsune; Nunes-Nesi, Adriano; Larson, Tony R.; Tohge, Takayuki; Krahnert, Ina; Witt, Sandra; Obata, Toshihiro; Schauer, Nicolas; Graham, Ian A.; Leaver, Christopher J.; Fernie, Alisdair R.

2010-01-01

The process of dark-induced senescence in plants is relatively poorly understood, but a functional electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) complex, which supports respiration during carbon starvation, has recently been identified. Here, we studied the responses of Arabidopsis thaliana mutants deficient in the expression of isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase to extended darkness and other environmental stresses. Evaluations of the mutant phenotypes following carbon starvation induced by extended darkness identify similarities to those exhibited by mutants of the ETF/ETFQO complex. Metabolic profiling and isotope tracer experimentation revealed that isovaleryl-CoA dehydrogenase is involved in degradation of the branched-chain amino acids, phytol, and Lys, while 2-hydroxyglutarate dehydrogenase is involved exclusively in Lys degradation. These results suggest that isovaleryl-CoA dehydrogenase is the more critical for alternative respiration and that a series of enzymes, including 2-hydroxyglutarate dehydrogenase, plays a role in Lys degradation. Both physiological and metabolic phenotypes of the isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase mutants were not as severe as those observed for mutants of the ETF/ETFQO complex, indicating some functional redundancy of the enzymes within the process. Our results aid in the elucidation of the pathway of plant Lys catabolism and demonstrate that both isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase act as electron donors to the ubiquinol pool via an ETF/ETFQO-mediated route. PMID:20501910

Identification of the 2-hydroxyglutarate and isovaleryl-CoA dehydrogenases as alternative electron donors linking lysine catabolism to the electron transport chain of Arabidopsis mitochondria.

PubMed

Araújo, Wagner L; Ishizaki, Kimitsune; Nunes-Nesi, Adriano; Larson, Tony R; Tohge, Takayuki; Krahnert, Ina; Witt, Sandra; Obata, Toshihiro; Schauer, Nicolas; Graham, Ian A; Leaver, Christopher J; Fernie, Alisdair R

2010-05-01

The process of dark-induced senescence in plants is relatively poorly understood, but a functional electron-transfer flavoprotein/electron-transfer flavoprotein:ubiquinone oxidoreductase (ETF/ETFQO) complex, which supports respiration during carbon starvation, has recently been identified. Here, we studied the responses of Arabidopsis thaliana mutants deficient in the expression of isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase to extended darkness and other environmental stresses. Evaluations of the mutant phenotypes following carbon starvation induced by extended darkness identify similarities to those exhibited by mutants of the ETF/ETFQO complex. Metabolic profiling and isotope tracer experimentation revealed that isovaleryl-CoA dehydrogenase is involved in degradation of the branched-chain amino acids, phytol, and Lys, while 2-hydroxyglutarate dehydrogenase is involved exclusively in Lys degradation. These results suggest that isovaleryl-CoA dehydrogenase is the more critical for alternative respiration and that a series of enzymes, including 2-hydroxyglutarate dehydrogenase, plays a role in Lys degradation. Both physiological and metabolic phenotypes of the isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase mutants were not as severe as those observed for mutants of the ETF/ETFQO complex, indicating some functional redundancy of the enzymes within the process. Our results aid in the elucidation of the pathway of plant Lys catabolism and demonstrate that both isovaleryl-CoA dehydrogenase and 2-hydroxyglutarate dehydrogenase act as electron donors to the ubiquinol pool via an ETF/ETFQO-mediated route.

Copolymers of poly-L-lysine with serine and tryptophan form stable DNA vectors: implications for receptor-mediated gene transfer.

PubMed

Gómez-Valadés, A G; Molas, M; Vidal-Alabró, A; Bermúdez, J; Bartrons, R; Perales, J C

2005-01-20

Inefficient gene transfer and poor stability in physiological medium are important shortcomings for receptor-mediated gene transfer vectors. Here, we evaluate vectors formulated with random copolymers of L-lysine/L-serine (3:1) and L-lysine/L-tryptophan (4:1), focusing on both their biophysical and functional characterization. By means of dynamic light scattering (DLS) and transmission electron microscopy (TEM), we demonstrate that poly-L-lysine (pK), poly-L-lysine-L-tryptophan (pKW) and poly-L-lysine-L-serine (pKS) are able to form compacted, small particles when mixed with plasmid DNA in the absence of salt. Upon dilution in physiological medium, copolymers of both lys/ser and lys/trp do not aggregate, in contrast with poly-L-lysine DNA complexes as determined by scattering, DLS and TEM measurements. Tight packing, as demonstrated by resistance to heparin, SDS and trypsin treatments, is also featured in tryptophan-containing complexes. Successful receptor-mediated endocytosis gene transfer using galactosylated copolymers into cells expressing the asiagloglycoprotein receptor correlated with lack of aggregation. Particles obtained using galactosylated poly-L-lysine-L-tryptophan (Gal-pKW) copolymer demonstrated specific receptor-mediated gene transfer since reporter gene activity dropped in the presence of an excess ligand in the culture medium during transfection. Although copolymers of galactosylated poly-L-lysine-L-serine (Gal-pKS) do not aggregate in the presence of salt, they are not able to internalize in a specific receptor-mediated endocytosis fashion. The introduction of bulky aromatic/hydrophobic (tryptophan) or hydrophillic (serine) moieties into the positively charged vectors allows the compacted particles to disperse into salt-containing medium avoiding salt-induced aggregation. Moreover, tryptophan-containing particles are able to mediate specific gene transfer via receptor-mediated endocytosis.

Dangers and uses of cross-correlation in analyzing time series in perception, performance, movement, and neuroscience: The importance of constructing transfer function autoregressive models.

PubMed

Dean, Roger T; Dunsmuir, William T M

2016-06-01

Many articles on perception, performance, psychophysiology, and neuroscience seek to relate pairs of time series through assessments of their cross-correlations. Most such series are individually autocorrelated: they do not comprise independent values. Given this situation, an unfounded reliance is often placed on cross-correlation as an indicator of relationships (e.g., referent vs. response, leading vs. following). Such cross-correlations can indicate spurious relationships, because of autocorrelation. Given these dangers, we here simulated how and why such spurious conclusions can arise, to provide an approach to resolving them. We show that when multiple pairs of series are aggregated in several different ways for a cross-correlation analysis, problems remain. Finally, even a genuine cross-correlation function does not answer key motivating questions, such as whether there are likely causal relationships between the series. Thus, we illustrate how to obtain a transfer function describing such relationships, informed by any genuine cross-correlations. We illustrate the confounds and the meaningful transfer functions by two concrete examples, one each in perception and performance, together with key elements of the R software code needed. The approach involves autocorrelation functions, the establishment of stationarity, prewhitening, the determination of cross-correlation functions, the assessment of Granger causality, and autoregressive model development. Autocorrelation also limits the interpretability of other measures of possible relationships between pairs of time series, such as mutual information. We emphasize that further complexity may be required as the appropriate analysis is pursued fully, and that causal intervention experiments will likely also be needed.

Facile Synthesis of Multivalent Folate-Block Copolymer Conjugates via Aqueous RAFT Polymerization: Targeted Delivery of siRNA and Subsequent Gene Suppression†

PubMed Central

York, Adam W.; Zhang, Yilin; Holley, Andrew C.; Guo, Yanlin; Huang, Faqing; McCormick, Charles L.

2009-01-01

Cell specific delivery of small interfering ribonucleic acid (siRNA) using well-defined multivalent folate-conjugated block copolymers is reported. Primary amine functional, biocompatible, hydrophilic-block-cationic copolymers were synthesized via aqueous reversible addition-fragmentation chain transfer (RAFT) polymerization. N-(2-hydroxypropyl)methacrylamide) (HPMA), a permanently hydrophilic monomer, was copolymerized with a primary amine containing monomer, N-(3-aminopropyl)methacrylamide (APMA). Poly(HPMA) confers biocompatibility while APMA provides amine functionality allowing conjugation of folate derivatives. (HPMA-stat-APMA) was chain extended with a cationic block, poly(N-[3-(dimethylamino)propyl]methacrylamide) in order to promote electrostatic complexation between the copolymer and the negatively charged phosphate backbone of siRNA. Notably, poly(HPMA) stabilizes the neutral complexes in aqueous solution while APMA allows the conjugation of a targeting moiety, thus, dually circumventing problems associated with the delivery of genes via cationically charged complexes (universal transfection). Fluorescence microscopy and gene down-regulation studies indicate that these neutral complexes can be specifically delivered to cancer cells that over-express folate receptors. PMID:19290625

Combined effects of metal complexation and size expansion in the electronic structure of DNA base pairs

NASA Astrophysics Data System (ADS)

Brancolini, Giorgia; Di Felice, Rosa

2011-05-01

Novel DNA derivatives have been recently investigated in the pursuit of modified DNA duplexes to tune the electronic structure of DNA-based assemblies for nanotechnology applications. Size-expanded DNAs (e.g., xDNA) and metalated DNAs (M-DNA) may enhance stacking interactions and induce metallic conductivity, respectively. Here we explore possible ways of tailoring the DNA electronic structure by combining the aromatic size expansion with the metal-doping. We select the salient structures from our recent study on natural DNA pairs complexed with transition metal ions and consider the equivalent model configurations for xDNA pairs. We present the results of density functional theory electronic structure calculations of the metalated expanded base-pairs with various localized basis sets and exchange-correlation functionals. Implicit solvent and coordination water molecules are also included. Our results indicate that the effect of base expansion is largest in Ag-xGC complexes, while Cu-xGC complexes are the most promising candidates for nanowires with enhanced electron transfer and also for on-purpose modification of the DNA double-helix for signal detection.

A scalable plant-resolving radiative transfer model based on optimized GPU ray tracing

USDA-ARS?s Scientific Manuscript database

A new model for radiative transfer in participating media and its application to complex plant canopies is presented. The goal was to be able to efficiently solve complex canopy-scale radiative transfer problems while also representing sub-plant heterogeneity. In the model, individual leaf surfaces ...

Structural complexity and molecular heterogeneity of a butterfly ejaculate reflect a complex history of selection

PubMed Central

Cherwin, Tamara S.; Plakke, Melissa S.; Hill, Jason; Small, Brandon S.; Goetz, Breanna J.; Wheat, Christopher W.; Morehouse, Nathan I.

2017-01-01

Male ejaculates are often structurally complex, and this complexity is likely to influence key reproductive interactions between males and females. However, despite its potential evolutionary significance, the molecular underpinnings of ejaculate structural complexity have received little empirical attention. To address this knowledge gap, we sought to understand the biochemical and functional properties of the structurally complex ejaculates of Pieris rapae butterflies. Males in this species produce large ejaculates called spermatophores composed of an outer envelope, an inner matrix, and a bolus of sperm. Females are thought to benefit from the nutrition contained in the soluble inner matrix through increases in longevity and fecundity. However, the indigestible outer envelope of the spermatophore delays female remating, allowing males to monopolize paternity for longer. Here, we show that these two nonsperm-containing spermatophore regions, the inner matrix and the outer envelope, differ in their protein composition and functional properties. We also reveal how these divergent protein mixtures are separately stored in the male reproductive tract and sequentially transferred to the female reproductive tract during spermatophore assembly. Intriguingly, we discovered large quantities of female-derived proteases in both spermatophore regions shortly after mating, which may contribute to spermatophore digestion and hence, female control over remating rate. Finally, we report evidence of past selection on these spermatophore proteins and female proteases, indicating a complex evolutionary history. Our findings illustrate how structural complexity of ejaculates may allow functionally and/or spatially associated suites of proteins to respond rapidly to divergent selective pressures, such as sexual conflict or reproductive cooperation. PMID:28630352

Ab initio study of charge transfer between lithium and aromatic hydrocarbons. Can the results be directly transferred to the lithium-graphene interaction?

PubMed

Sadlej-Sosnowska, N

2014-08-28

We have used electronic density calculations to study neutral complexes of Li with aromatic hydrocarbons. The charge transferred between a Li atom and benzene, coronene, circumcoronene, and circumcircumcoronene has been studied by ab initio methods (at the HF and MP2 level). Toward this aim, the method of integrating electron density in two cuboid fragments of space was applied. One of the fragments was constructed so that it enclosed the bulk of the electron density of lithium; the second, the bulk of the electron density of hydrocarbon. It was found that for each complex two conformations were identified: the most stable with a greater vertical Li-hydrocarbon distance, on the order of 2.5 Å, and another of higher energy with a corresponding distance less than 2 Å. In all cases the transfer of a fractional number, 0.1-0.3 electrons, between Li and hydrocarbon was found; however, the direction of the transfer was not the same in all complexes investigated. The structures of complexes of the first configuration could be represented as Li(σ-)···AH(σ+), whereas the opposite direction of charge transfer was found for complexes of the second configuration, with higher energy. The directions of the dipole moments in the complexes supported these conclusions because they directly measure the redistribution of electron density in a complex with respect to substrates.

Optimizing the wireless power transfer over MIMO Channels

NASA Astrophysics Data System (ADS)

Wiedmann, Karsten; Weber, Tobias

2017-09-01

In this paper, the optimization of the power transfer over wireless channels having multiple-inputs and multiple-outputs (MIMO) is studied. Therefore, the transmitter, the receiver and the MIMO channel are modeled as multiports. The power transfer efficiency is described by a Rayleigh quotient, which is a function of the channel's scattering parameters and the incident waves from both transmitter and receiver side. This way, the power transfer efficiency can be maximized analytically by solving a generalized eigenvalue problem, which is deduced from the Rayleigh quotient. As a result, the maximum power transfer efficiency achievable over a given MIMO channel is obtained. This maximum can be used as a performance bound in order to benchmark wireless power transfer systems. Furthermore, the optimal operating point which achieves this maximum will be obtained. The optimal operating point will be described by the complex amplitudes of the optimal incident and reflected waves of the MIMO channel. This supports the design of the optimal transmitter and receiver multiports. The proposed method applies for arbitrary MIMO channels, taking transmitter-side and/or receiver-side cross-couplings in both near- and farfield scenarios into consideration. Special cases are briefly discussed in this paper in order to illustrate the method.

Microbial Biofilm Voltammetry: Direct Electrochemical Characterization of Catalytic Electrode-Attached Biofilms▿ †

PubMed Central

Marsili, Enrico; Rollefson, Janet B.; Baron, Daniel B.; Hozalski, Raymond M.; Bond, Daniel R.

2008-01-01

While electrochemical characterization of enzymes immobilized on electrodes has become common, there is still a need for reliable quantitative methods for study of electron transfer between living cells and conductive surfaces. This work describes growth of thin (<20 μm) Geobacter sulfurreducens biofilms on polished glassy carbon electrodes, using stirred three-electrode anaerobic bioreactors controlled by potentiostats and nondestructive voltammetry techniques for characterization of viable biofilms. Routine in vivo analysis of electron transfer between bacterial cells and electrodes was performed, providing insight into the main redox-active species participating in electron transfer to electrodes. At low scan rates, cyclic voltammetry revealed catalytic electron transfer between cells and the electrode, similar to what has been observed for pure enzymes attached to electrodes under continuous turnover conditions. Differential pulse voltammetry and electrochemical impedance spectroscopy also revealed features that were consistent with electron transfer being mediated by an adsorbed catalyst. Multiple redox-active species were detected, revealing complexity at the outer surfaces of this bacterium. These techniques provide the basis for cataloging quantifiable, defined electron transfer phenotypes as a function of potential, electrode material, growth phase, and culture conditions and provide a framework for comparisons with other species or communities. PMID:18849456

Electron-Transfer-Enhanced Cation-Cation Interactions in Homo- and Heterobimetallic Actinide Complexes: A Relativistic Density Functional Theory Study.

PubMed

Zheng, Ming; Chen, Fang-Yuan; Tian, Jia-Nan; Pan, Qing-Jiang

2018-04-02

To provide deep insight into cation-cation interactions (CCIs) involving hexavalent actinyl species that are major components in spent nuclear fuel and pose important implications for the effective removal of radiotoxic pollutants in the environment, a series of homo- and heterobimetallic actinide complexes supported by cyclopentadienyl (Cp) and polypyrrolic macrocycle (H 4 L) ligands were systematically investigated using relativistic density functional theory. The metal sort in both parts of (THF)(H 2 L)(OAn VI O) and (An') III Cp 3 from U to Np to Pu, as well as the substituent bonding to Cp from electron-donating Me to H to electron-withdrawing Cl, SiH 3 , and SiMe 3 , was changed. Over 0.70 electrons are unraveled to transfer from the electron-rich U III to the electron-deficient An VI of the actinyl moiety, leading to a more stable An V -U IV isomer; in contrast, uranylneptunium and uranylplutonium complexes behave as electron-resonance structures between VI-III and V-IV. These were further corroborated by geometrical and electronic structures. The energies of CCIs (i.e., O exo -An' bonds) were calculated to be -19.6 to -41.2 kcal/mol, affording those of OUO-Np (-23.9 kcal/mol) and OUO-Pu (-19.6 kcal/mol) with less electron transfer (ET) right at the low limit. Topological analyses of the electron density at the O exo -An' bond critical points demonstrate that the CCIs are ET or dative bonds in nature. A positive correlation has been built between the CCIs' strength and corresponding ET amount. It is concluded that the CCIs of O exo -An' are driven by the electrostatic attraction between the actinyl oxo atom (negative) and the actinide ion (positive) and enhanced by their ET. Finally, experimental syntheses of (THF)(H 2 L)(OU VI O)(An') III Cp 3 (An' = U and Np) were well reproduced by thermodynamic calculations that yielded negative free energies in a tetrahydrofuran solution but a positive one for their uranylplutonium analogue, which was synthetically inaccessible. So, our thermodynamics would provide implications for the synthetic possibility of other theoretically designed bimetallic actinide complexes.

Unravelling electronic and structural requisites of triplet-triplet energy transfer by advanced electron paramagnetic resonance and density functional theory

NASA Astrophysics Data System (ADS)

Di Valentin, M.; Salvadori, E.; Barone, V.; Carbonera, D.

2013-10-01

Advanced electron paramagnetic resonance (EPR) techniques, in combination with Density Functional theory (DFT), have been applied to the comparative study of carotenoid triplet states in two major photosynthetic antenna complexes, the Peridinin-chlorophyll a-protein of dinoflagellates and the light-harvesting complex II of higher plants. Carotenoid triplet states are populated by triplet-triplet energy transfer (TTET) from chlorophyll molecules to photoprotect the system from singlet oxygen formation under light-stress conditions. The TTET process is strongly dependent on the relative arrangement and on the electronic properties of the triplet states involved. The proposed spectroscopic approach exploits the concept of spin conservation during TTET, which leads to recognisable spin polarisation effects in the time-resolved and field-swept echo-detected EPR spectra. The electron spin polarisation produced at the carotenoid acceptor site depends on the initial polarisation of the chlorophyll donor and on the relative geometrical arrangement of the donor-acceptor zero-field splitting axes. We have demonstrated that a proper analysis of the spectra in the framework of spin angular momentum conservation allows to derive the pathways of TTET and to gain insight into the structural requirements of this mechanism for those antenna complexes, whose X-ray structure is available. We have further proved that this method, developed for natural antenna complexes of known X-ray structure, can be extended to systems lacking structural information in order to derive the relative arrangement of the partners in the energy transfer process. The structural requirements for efficient TTET, obtained from time-resolved and pulse EPR, have been complemented by a detailed description of the electronic structure of the carotenoid triplet state, provided by pulse Electron-Nuclear DOuble Resonance (ENDOR) experiments. Triplet-state hyperfine couplings of the α- and β-protons of the carotenoid conjugated chain have been assigned with the aid of quantum chemical calculation. DFT predictions of the electronic structure of the carotenoid triplet state, in terms of spin density distribution, frontier orbital description and orbital excitation represent suitable building blocks toward a deeper understanding of electronic requirements for efficient TTET.

Daclatasvir Prevents Hepatitis C Virus Infectivity by Blocking Transfer of the Viral Genome to Assembly Sites.

PubMed

Boson, Bertrand; Denolly, Solène; Turlure, Fanny; Chamot, Christophe; Dreux, Marlène; Cosset, François-Loïc

2017-03-01

Daclatasvir is a direct-acting antiviral agent and potent inhibitor of NS5A, which is involved in replication of the hepatitis C virus (HCV) genome, presumably via membranous web shaping, and assembly of new virions, likely via transfer of the HCV RNA genome to viral particle assembly sites. Daclatasvir inhibits the formation of new membranous web structures and, ultimately, of replication complex vesicles, but also inhibits an early assembly step. We investigated the relationship between daclatasvir-induced clustering of HCV proteins, intracellular localization of viral RNAs, and inhibition of viral particle assembly. Cell-culture-derived HCV particles were produced from Huh7.5 hepatocarcinoma cells in presence of daclatasvir for short time periods. Infectivity and production of physical particles were quantified and producer cells were subjected to subcellular fractionation. Intracellular colocalization between core, E2, NS5A, NS4B proteins, and viral RNAs was quantitatively analyzed by confocal microscopy and by structured illumination microscopy. Short exposure of HCV-infected cells to daclatasvir reduced viral assembly and induced clustering of structural proteins with non-structural HCV proteins, including core, E2, NS4B, and NS5A. These clustered structures appeared to be inactive assembly platforms, likely owing to loss of functional connection with replication complexes. Daclatasvir greatly reduced delivery of viral genomes to these core clusters without altering HCV RNA colocalization with NS5A. In contrast, daclatasvir neither induced clustered structures nor inhibited HCV assembly in cells infected with a daclatasvir-resistant mutant (NS5A-Y93H), indicating that daclatasvir targets a mutual, specific function of NS5A inhibiting both processes. In addition to inhibiting replication complex biogenesis, daclatasvir prevents viral assembly by blocking transfer of the viral genome to assembly sites. This leads to clustering of HCV proteins because viral particles and replication complex vesicles cannot form or egress. This dual mode of action of daclatasvir could explain its efficacy in blocking HCV replication in cultured cells and in treatment of patients with HCV infection. Copyright © 2017 AGA Institute. Published by Elsevier Inc. All rights reserved.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids

NASA Astrophysics Data System (ADS)

Refat, Moamen S.; Saad, Hosam A.; Adam, Abdel Majid A.

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA) 2] and [(o-TOL)(CA) 2] have been prepared. The 13C NMR, 1H NMR, 1H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH 2 groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic.

Intermolecular hydrogen bond complexes by in situ charge transfer complexation of o-tolidine with picric and chloranilic acids.

PubMed

Refat, Moamen S; Saad, Hosam A; Adam, Abdel Majid A

2011-08-01

A two new charge transfer complexes formed from the interactions between o-tolidine (o-TOL) and picric (PA) or chloranilic (CA) acids, with the compositions, [(o-TOL)(PA)(2)] and [(o-TOL)(CA)(2)] have been prepared. The (13)C NMR, (1)H NMR, (1)H-Cosy, and IR show that the charge-transfer chelation occurs via the formation of chain structures O-H⋯N intermolecular hydrogen bond between 2NH(2) groups of o-TOL molecule and OH group in each PA or CA units. Photometric titration measurements concerning the two reactions in methanol were performed and the measurements show that the donor-acceptor molar ratio was found to be 1:2 using the modified Benesi-Hildebrand equation. The spectroscopic data were discussed in terms of formation constant, molar extinction coefficient, oscillator strength, dipole moment, standard free energy, and ionization potential. Thermal behavior of both charge transfer complexes showed that the complexes were more stable than their parents. The thermodynamic parameters were estimated from the differential thermogravimetric curves. The results indicated that the formation of molecular charge transfer complexes is spontaneous and endothermic. Copyright © 2011 Elsevier B.V. All rights reserved.

Rupture Complexities of Fluid Induced Microseismic Events at the Basel EGS Project

NASA Astrophysics Data System (ADS)

Folesky, Jonas; Kummerow, Jörn; Shapiro, Serge A.; Häring, Markus; Asanuma, Hiroshi

2016-04-01

Microseismic data sets of excellent quality, such as the seismicity recorded in the Basel-1 enhanced geothermal system, Switzerland, in 2006-2007, provide the opportunity to analyse induced seismic events in great detail. It is important to understand in how far seismological insights on e.g. source and rupture processes are scale dependent and how they can be transferred to fluid induced micro-seismicity. We applied the empirical Green's function (EGF) method in order to reconstruct the relative source time functions of 195 suitable microseismic events from the Basel-1 reservoir. We found 93 solutions with a clear and consistent directivity pattern. The remaining events display either no measurable directivity, are unfavourably oriented or exhibit non consistent or complex relative source time functions. In this work we focus on selected events of M ˜ 1 which show possible rupture complexities. It is demonstrated that the EGF method allows to resolve complex rupture behaviour even if it is not directly identifiable in the seismograms. We find clear evidence of rupture directivity and multi-phase rupturing in the analysed relative source time functions. The time delays between consecutive subevents lies in the order of 10ms. Amplitudes of the relative source time functions of the subevents do not always show the same azimuthal dependence, indicating dissimilarity in the rupture directivity of the subevents. Our observations support the assumption that heterogeneity on fault surfaces persists down to small scale (few tens of meters).

Synthesis, crystal structure, antimicrobial activity and DNA-binding of hydrogen-bonded proton-transfer complex of 2,6-diaminopyridine with picric acid.

PubMed

Khan, Ishaat M; Ahmad, Afaq; Ullah, M F

2011-04-04

A proton-transfer (charge transfer) complex formed on the reaction between 2,6-diaminopyridine (donor) and picric acid (acceptor) was synthesized and characterized by FTIR, (1)H NMR, thermal and elemental analysis. The crystal structure determined by single-crystal X-ray diffraction indicates that cation and anion are joined together by strong N(+)-H- -O(-) type hydrogen bonds. The hydrogen-bonded charge transfer (HBCT) complex was screened for its pharmacology such as antimicrobial activity against various fungal and bacterial strains and Calf thymus DNA-binding. The results showed that HBCT complex (100μg/ml) exhibited good antibacterial antifungal activity as that of standard antibiotics Tetracycline and Nystatin. A molecular frame work through H-bonding interactions between neighboring moieties is found to be responsible for high melting point of resulting complex. This has been attributed to the formation of 1:1 HBCT complex. Copyright © 2011 Elsevier B.V. All rights reserved.

Spectrophotometric and spectroscopic studies of charge transfer complex of 1-Naphthylamine as an electron donor with picric acid as an electron acceptor in different polar solvents

NASA Astrophysics Data System (ADS)

Singh, Neeti; Ahmad, Afaq

2010-08-01

The charge transfer complex of 1-Naphthylamine as a donor with π-acceptor picric acid has been studied spectrophotometrically in different solvents at room temperature. The results indicate that the formation of charge transfer complex is high in less polar solvent. The stoichiometry of the complex was found to be 1:1 by straight line method. The data are analysed in terms of formation constant ( KCT), molar extinction coefficient ( ɛCT), standard free energy (Δ G o), oscillator strength ( ƒ), transition dipole moment ( μ EN), resonance energy ( R N) and ionization potential ( I D). It is concluded that the formation constant ( KCT) of the complex is found to be depends upon the nature of both electron acceptor and donor and also on the polarity of solvents. Further the charge transfer molecular complex between picric acid and 1-Naphthylamine is stabilized by hydrogen bonding.

Assessment of Ab Initio and Density Functional Theory Methods for the Excitations of Donor-Acceptor Complexes: The Case of the Benzene-Tetracyanoethylene Model.

PubMed

Xu, Peng; Zhang, Cai-Rong; Wang, Wei; Gong, Ji-Jun; Liu, Zi-Jiang; Chen, Hong-Shan

2018-04-10

The understanding of the excited-state properties of electron donors, acceptors and their interfaces in organic optoelectronic devices is a fundamental issue for their performance optimization. In order to obtain a balanced description of the different excitation types for electron-donor-acceptor systems, including the singlet charge transfer (CT), local excitations, and triplet excited states, several ab initio and density functional theory (DFT) methods for excited-state calculations were evaluated based upon the selected model system of benzene-tetracyanoethylene (B-TCNE) complexes. On the basis of benchmark calculations of the equation-of-motion coupled-cluster with single and double excitations method, the arithmetic mean of the absolute errors and standard errors of the electronic excitation energies for the different computational methods suggest that the M11 functional in DFT is superior to the other tested DFT functionals, and time-dependent DFT (TDDFT) with the Tamm-Dancoff approximation improves the accuracy of the calculated excitation energies relative to that of the full TDDFT. The performance of the M11 functional underlines the importance of kinetic energy density, spin-density gradient, and range separation in the development of novel DFT functionals. According to the TDDFT results, the performances of the different TDDFT methods on the CT properties of the B-TCNE complexes were also analyzed.

Molecular Level Design Principle behind Optimal Sizes of Photosynthetic LH2 Complex: Taming Disorder through Cooperation of Hydrogen Bonding and Quantum Delocalization.

PubMed

Jang, Seogjoo; Rivera, Eva; Montemayor, Daniel

2015-03-19

The light harvesting 2 (LH2) antenna complex from purple photosynthetic bacteria is an efficient natural excitation energy carrier with well-known symmetric structure, but the molecular level design principle governing its structure-function relationship is unknown. Our all-atomistic simulations of nonnatural analogues of LH2 as well as those of a natural LH2 suggest that nonnatural sizes of LH2-like complexes could be built. However, stable and consistent hydrogen bonding (HB) between bacteriochlorophyll and the protein is shown to be possible only near naturally occurring sizes, leading to significantly smaller disorder than for nonnatural ones. Extensive quantum calculations of intercomplex exciton transfer dynamics, sampled for a large set of disorder, reveal that taming the negative effect of disorder through a reliable HB as well as quantum delocalization of the exciton is a critical mechanism that makes LH2 highly functional, which also explains why the natural sizes of LH2 are indeed optimal.

Inheritance of yeast nuclear pore complexes requires the Nsp1p subcomplex

PubMed Central

Makio, Tadashi; Lapetina, Diego L.

2013-01-01

In the yeast Saccharomyces cerevisiae, organelles and macromolecular complexes are delivered from the mother to the emerging daughter during cell division, thereby ensuring progeny viability. Here, we have shown that during mitosis nuclear pore complexes (NPCs) in the mother nucleus are actively delivered through the bud neck and into the daughter cell concomitantly with the nuclear envelope. Furthermore, we show that NPC movement into the daughter cell requires members of an NPC subcomplex containing Nsp1p and its interacting partners. NPCs lacking these nucleoporins (Nups) were blocked from entry into the daughter by a putative barrier at the bud neck. This selection process could be observed within individual cells such that NPCs containing Nup82p (an Nsp1p-interacting Nup) were transferred to the daughter cells while functionally compromised NPCs lacking Nup82p were retained in the mother. This mechanism is proposed to facilitate the inheritance of functional NPCs by daughter cells. PMID:24165935

Improvement of gas-adsorption performances of Ag-functionalized monolayer MoS2 surfaces: A first-principles study

NASA Astrophysics Data System (ADS)

Song, Jian; Lou, Huan

2018-05-01

Investigations of the adsorptions of representative gases (NO2, NH3, H2S, SO2, CO, and HCHO) on different Ag-functionalized monolayer MoS2 surfaces were performed by first principles methods. The adsorption configurations, adsorption energies, electronic structure properties, and charge transfer were calculated, and the results show that the adsorption activities to gases of monolayer MoS2 are dramatically enhanced by the Ag-modification. The Ag-modified perfect MoS2 (Ag-P) and MoS2 with S-vacancy (Ag-Vs) substrates exhibit a more superior adsorption activity to NO2 than other gases, which is consistent with the experimental reports. The charge transfer processes of different molecules adsorbed on different surfaces exhibit various characteristics, with potential benefits to gas selectivity. For instance, the NO2 and SO2 obtain more electrons from both Ag-P and Ag-Vs substrates but the NH3 and H2S donate more electrons to materials than others. In addition, the CO and HCHO possess totally opposite charge transfer directs on both substrates, respectively. The BS and PDOS calculations show that semiconductor types of gas/Ag-MoS2 systems are more determined by the metal-functionalization of material, and the directs and numbers of charge transfer process between gases and adsorbents can cause the increase or decline of material resistance theoretically, which is helpful to gas detection and distinction. The further analysis indicates suitable co-operation between the gain-lost electron ability of gas and metallicity of featuring metal might adjust the resistivity of complex and contribute to new thought for metal-functionalization. Our works provide new valuable ideas and theoretical foundation for the potential improvement of MoS2-based gas sensor performances, such as sensitivity and selectivity.

Evolutionary and biogeographical implications of degraded LAGLIDADG endonuclease functionality and group I intron occurrence in stony corals (Scleractinia) and mushroom corals (Corallimorpharia).

PubMed

Celis, Juan Sebastián; Edgell, David R; Stelbrink, Björn; Wibberg, Daniel; Hauffe, Torsten; Blom, Jochen; Kalinowski, Jörn; Wilke, Thomas

2017-01-01

Group I introns and homing endonuclease genes (HEGs) are mobile genetic elements, capable of invading target sequences in intron-less genomes. LAGLIDADG HEGs are the largest family of endonucleases, playing a key role in the mobility of group I introns in a process known as 'homing'. Group I introns and HEGs are rare in metazoans, and can be mainly found inserted in the COXI gene of some sponges and cnidarians, including stony corals (Scleractinia) and mushroom corals (Corallimorpharia). Vertical and horizontal intron transfer mechanisms have been proposed as explanations for intron occurrence in cnidarians. However, the central role of LAGLIDADG motifs in intron mobility mechanisms remains poorly understood. To resolve questions regarding the evolutionary origin and distribution of group I introns and HEGs in Scleractinia and Corallimorpharia, we examined intron/HEGs sequences within a comprehensive phylogenetic framework. Analyses of LAGLIDADG motif conservation showed a high degree of degradation in complex Scleractinia and Corallimorpharia. Moreover, the two motifs lack the respective acidic residues necessary for metal-ion binding and catalysis, potentially impairing horizontal intron mobility. In contrast, both motifs are highly conserved within robust Scleractinia, indicating a fully functional endonuclease capable of promoting horizontal intron transference. A higher rate of non-synonymous substitutions (Ka) detected in the HEGs of complex Scleractinia and Corallimorpharia suggests degradation of the HEG, whereas lower Ka rates in robust Scleractinia are consistent with a scenario of purifying selection. Molecular-clock analyses and ancestral inference of intron type indicated an earlier intron insertion in complex Scleractinia and Corallimorpharia in comparison to robust Scleractinia. These findings suggest that the lack of horizontal intron transfers in the former two groups is related to an age-dependent degradation of the endonuclease activity. Moreover, they also explain the peculiar geographical patterns of introns in stony and mushroom corals.

Oscillatory bistability of real-space transfer in semiconductor heterostructures

NASA Astrophysics Data System (ADS)

Do˙ttling, R.; Scho˙ll, E.

1992-01-01

Charge transport parallel to the layers of a modulation-doped GaAs/AlxGa1-xAs heterostructure is studied theoretically. The heating of electrons by the applied electric field leads to real-space transfer of electrons from the GaAs into the adjacent AlxGa1-xAs layer. For sufficiently large dc bias, spontaneous periodic 100-GHz current oscillations, and bistability and hysteretic switching transitions between oscillatory and stationary states are predicted. We present a detailed investigation of complex bifurcation scenarios as a function of the bias voltage U0 and the load resistance RL. For large RL subcritical Hopf bifurcations and global bifurcations of limit cycles are displayed.

Locating CVBEM collocation points for steady state heat transfer problems

USGS Publications Warehouse

Hromadka, T.V.

1985-01-01

The Complex Variable Boundary Element Method or CVBEM provides a highly accurate means of developing numerical solutions to steady state two-dimensional heat transfer problems. The numerical approach exactly solves the Laplace equation and satisfies the boundary conditions at specified points on the boundary by means of collocation. The accuracy of the approximation depends upon the nodal point distribution specified by the numerical analyst. In order to develop subsequent, refined approximation functions, four techniques for selecting additional collocation points are presented. The techniques are compared as to the governing theory, representation of the error of approximation on the problem boundary, the computational costs, and the ease of use by the numerical analyst. ?? 1985.

The Cytochrome b 6 f Complex: Biophysical Aspects of Its Functioning in Chloroplasts.

PubMed

Tikhonov, Alexander N

2018-01-01

This chapter presents an overview of structural properties of the cytochrome (Cyt) b 6 f complex and its functioning in chloroplasts. The Cyt b 6 f complex stands at the crossroad of photosynthetic electron transport pathways, providing connectivity between Photosystem (PSI) and Photosysten II (PSII) and pumping protons across the membrane into the thylakoid lumen. After a brief review of the chloroplast electron transport chain, the consideration is focused on the structural organization of the Cyt b 6 f complex and its interaction with plastoquinol (PQH 2 , reduced form of plastoquinone), a mediator of electron transfer from PSII to the Cyt b 6 f complex. The processes of PQH 2 oxidation by the Cyt b 6 f complex have been considered within the framework of the Mitchell's Q-cycle. The overall rate of the intersystem electron transport is determined by PQH 2 turnover at the quinone-binding site Q o of the Cyt b 6 f complex. The rate of PQH 2 oxidation is controlled by the intrathylakoid pH in , which value determines the protonation/deprotonation events in the Q o -center. Two other regulatory mechanisms associated with the Cyt b 6 f complex are briefly overviewed: (i) redistribution of electron fluxes between alternative (linear and cyclic) pathways, and (ii) "state transitions" related to redistribution of solar energy between PSI and PSII.

Cyclopentadiene-mediated hydride transfer from rhodium complexes.

PubMed

Pitman, C L; Finster, O N L; Miller, A J M

2016-07-12

Attempts to generate a proposed rhodium hydride catalytic intermediate instead resulted in isolation of (Cp*H)Rh(bpy)Cl (1), a pentamethylcyclopentadiene complex, formed by C-H bond-forming reductive elimination from the fleeting rhodium hydride. The hydride transfer ability of diene 1 was explored through thermochemistry and hydride transfer reactions, including the reduction of NAD(+).

Horizontal gene transfer in an acid mine drainage microbial community.

PubMed

Guo, Jiangtao; Wang, Qi; Wang, Xiaoqi; Wang, Fumeng; Yao, Jinxian; Zhu, Huaiqiu

2015-07-04

Horizontal gene transfer (HGT) has been widely identified in complete prokaryotic genomes. However, the roles of HGT among members of a microbial community and in evolution remain largely unknown. With the emergence of metagenomics, it is nontrivial to investigate such horizontal flow of genetic materials among members in a microbial community from the natural environment. Because of the lack of suitable methods for metagenomics gene transfer detection, microorganisms from a low-complexity community acid mine drainage (AMD) with near-complete genomes were used to detect possible gene transfer events and suggest the biological significance. Using the annotation of coding regions by the current tools, a phylogenetic approach, and an approximately unbiased test, we found that HGTs in AMD organisms are not rare, and we predicted 119 putative transferred genes. Among them, 14 HGT events were determined to be transfer events among the AMD members. Further analysis of the 14 transferred genes revealed that the HGT events affected the functional evolution of archaea or bacteria in AMD, and it probably shaped the community structure, such as the dominance of G-plasma in archaea in AMD through HGT. Our study provides a novel insight into HGT events among microorganisms in natural communities. The interconnectedness between HGT and community evolution is essential to understand microbial community formation and development.

Modeling of the structure-specific kinetics of abiotic, dark reduction of Hg(II) complexed by O/N and S functional groups in humic acids while accounting for time-dependent structural rearrangement

USDA-ARS?s Scientific Manuscript database

Redox transformations involving electron transfer from natural organic matter (NOM) are important for the mercury (Hg) biogeochemical cycle. In the water column light drives the reduction of Hg(II) to Hg(0), whereas in soils and sediments dark reduction of Hg(II) is of greater importance. The object...

Polyamines: naturally occurring small molecule modulators of electrostatic protein-protein interactions.

PubMed

Berwanger, Anja; Eyrisch, Susanne; Schuster, Inge; Helms, Volkhard; Bernhardt, Rita

2010-02-01

Modulations of protein-protein interactions are a key step in regulating protein function, especially in networks. Modulators of these interactions are supposed to be candidates for the development of novel drugs. Here, we describe the role of the small, polycationic and highly abundant natural polyamines that could efficiently bind to charged spots at protein interfaces as modulators of such protein-protein interactions. Using the mitochondrial cytochrome P45011A1 (CYP11A1) electron transfer system as a model, we have analyzed the capability of putrescine, spermidine, and spermine at physiologically relevant concentrations to affect the protein-protein interactions between adrenodoxin reductase (AdR), adrenodoxin (Adx), and CYP11A1. The actions of polyamines on the individual components, on their association/dissociation, on electron transfer, and on substrate conversion were examined. These studies revealed modulating effects of polyamines on distinct interactions and on the entire system in a complex way. Modulation via changed protein-protein interactions appeared plausible from docking experiments that suggested favourable high-affinity binding sites of polyamines (spermine>spermidine>putrescine) at the AdR-Adx interface. Our findings imply for the first time that small endogenous compounds are capable of interfering with distinct components of transient protein complexes and might control protein functions by modulating electrostatic protein-protein interactions.

[Patient-centered approaches to understanding, transformation and solution of team conflicts in the psychiatric clinic within the scope of the Balint group concept].

PubMed

Drees, A

1987-08-01

The working climate and therapeutic possibilities in a hospital are determined, among other factors, by emotional processes in everyday ward routine. Team conflicts and their solution are not infrequently reflections of the open-mindedness of a hospital towards the complexity of these processes. However, the complex interlocking of transference processes with rôle-specific and personality-conditioned behaviour patterns makes it more difficult to understand and make use of these emotional processes within the team. We present a specific attempt to working up emotional conflicts in a patient-centred approach via focussing on self-rating of the team workers in respect of mood, feeling tone and imagination. Specific internal Balint groups are the fulcrum. To distinguish this method from the theory of object-directed transference of emotions and constructions of relations, the theoretical basis of this group method is seen in the systemic paradigm with which patient-focussed solution functions are obtained in respect of process orientation and instrumental part functions of the team workers. In this connection it was explored to what extent the following factors can be interpreted as patient-induced phenomena: therapeutic and rôle behaviour, hospital structures and administrative squabbles, internal and external walls of a mental hospital.

Dynamic aspects of antibody:oligosaccharide complexes characterized by molecular dynamics simulations and saturation transfer difference nuclear magnetic resonance.

PubMed

Theillet, François-Xavier; Frank, Martin; Vulliez-Le Normand, Brigitte; Simenel, Catherine; Hoos, Sylviane; Chaffotte, Alain; Bélot, Frédéric; Guerreiro, Catherine; Nato, Farida; Phalipon, Armelle; Mulard, Laurence A; Delepierre, Muriel

2011-12-01

Carbohydrates are likely to maintain significant conformational flexibility in antibody (Ab):carbohydrate complexes. As demonstrated herein for the protective monoclonal Ab (mAb) F22-4 recognizing the Shigella flexneri 2a O-antigen (O-Ag) and numerous synthetic oligosaccharide fragments thereof, the combination of molecular dynamics simulations and nuclear magnetic resonance saturation transfer difference experiments, supported by physicochemical analysis, allows us to determine the binding epitope and its various contributions to affinity without using any modified oligosaccharides. Moreover, the methods used provide insights into ligand flexibility in the complex, thus enabling a better understanding of the Ab affinities observed for a representative set of synthetic O-Ag fragments. Additionally, these complementary pieces of information give evidence to the ability of the studied mAb to recognize internal as well as terminal epitopes of its cognate polysaccharide antigen. Hence, we show that an appropriate combination of computational and experimental methods provides a basis to explore carbohydrate functional mimicry and receptor binding. The strategy may facilitate the design of either ligands or carbohydrate recognition domains, according to needed improvements of the natural carbohydrate:receptor properties. © The Author 2011. Published by Oxford University Press. All rights reserved.

The effect of intermolecular hydrogen bonding on the fluorescence of a bimetallic platinum complex.

PubMed

Zhao, Guang-Jiu; Northrop, Brian H; Han, Ke-Li; Stang, Peter J

2010-09-02

The bimetallic platinum complexes are known as unique building blocks and arewidely utilized in the coordination-driven self-assembly of functionalized supramolecular metallacycles. Hence, photophysical study of the bimetallic platinum complexes will be very helpful for the understanding on the optical properties and further applications of coordination-driven self-assembled supramolecular metallacycles. Herein, we report steady-state and time-resolved spectroscopic experiments as well as quantum chemistry calculations to investigate the significant intermolecular hydrogen bonding effects on the intramolecular charge transfer (ICT) fluorescence of a bimetallic platinum compound 4,4'-bis(trans-Pt(PEt(3))(2)OTf)benzophenone 3 in solution. We demonstrated that the fluorescent state of compound 3 can be assigned as a metal-to-ligand charge transfer (MLCT) state. Moreover, it was observed that the formation of intermolecular hydrogen bonds can effectively lengthen the fluorescence lifetime of 3 in alcoholic solvents compared with that in hexane solvent. At the same time, the electronically excited states of 3 in solution are definitely changed by intermolecular hydrogen bonding interactions. As a consequence, we propose a new fluorescence modulation mechanism by hydrogen bonding to explain different fluorescence emissions of 3 in hydrogen-bonding solvents and nonhydrogen-bonding solvents.

Nonlinear optical properties of rhenium(I) complexes: Influence of the extended π-conjugated connectors and proton abstraction.

PubMed

Yu, Hai-Ling; Hong, Bo; Yang, Ning; Zhao, Hong-Yan

2015-09-01

The photoinduced proton-coupled electron transfer chemistry is very crucial to the development of nonlinear optical (NLO) materials with large first hyperpolarizability contrast. We have performed a systematic investigation on the geometric structures, NLO switching, and simulated absorption spectra of rhenium(I) complexes via density functional theory (DFT). The results show that the first hyperpolarizabilities (βvec) increase remarkably with further extending of the organic connectors. In addition, the solvent leads to a slight enhancement of the hyperpolarizability and frequency dependent hyperpolarizability. Furthermore, the proton abstraction plays an important role in tuning the second-order NLO response. It is found that deprotonation not only increases the absolute value of βvec but also changes the sign of βvec from positive to negative. This different sign can be explained by the opposite dipole moments. The efficient enhancement of first hyperpolarizability is attributed to the better delocalization of the π-electron system and the more obvious degree of charge transfer. Therefore, these kinds of complexes might be promising candidates for designed as proton driven molecular second-order NLO switching. Copyright © 2015 Elsevier Inc. All rights reserved.

Fluorescence-excitation and emission spectra from LH2 antenna complexes of Rhodopseudomonas acidophila as a function of the sample preparation conditions.

PubMed

Kunz, Ralf; Timpmann, Kõu; Southall, June; Cogdell, Richard J; Köhler, Jürgen; Freiberg, Arvi

2013-10-10

The high sensitivity of optical spectra of pigment-protein complexes to temperature and pressure is well known. In the present study, we have demonstrated the significant influence of the environments commonly used in bulk and single-molecule spectroscopic studies at low temperatures on the LH2 photosynthetic antenna complex from Rhodopseudomonas acidophila. A transfer of this LH2 complex from a bulk-buffer solution into a spin-coated polymer film results in a 189 cm(-1) blue shift of the B850 excitonic absorption band at 5 K. Within the molecular exciton model, the origin of this shift could be disentangled into three parts, namely to an increase of the local site energies, a contraction of the exciton band, and a decrease of the displacement energy.

The origin of phosphorescence in Iridium (III) complexes. The role of relativistic effects

NASA Astrophysics Data System (ADS)

Cantero-López, Plinio; Páez-Hernández, Dayan; Arratia-Pérez, Ramiro

2017-10-01

A series of luminescent Ir(III) complexes of the type [Ir(F2ppy)2L] (where L = Lpytz , LOMe , Lbut) have been studied using relativistic two-component density functional theory considering the spin-orbit coupling. The absorption spectra of the three complexes were determined. The most important transition appears in the region between 250 and 350 nm, which is in good agreement with the experimental reports. The three complexes show phosphorescent properties due to a metal-ligand charge transfer (MLCT) process, where the spin-orbit coupling (SOC) plays a key role due to the introduction of a zero field splitting (ZFS) and the mixing of states with different spins which contributes to modify the emission selection rule. The lifetimes of the emission processes were calculated, and the values are in the same order of the experimental reports.

Path induced coherent energy transfer in light-harvesting complexes in purple bacteria

NASA Astrophysics Data System (ADS)

Sun, Kewei; Ye, Jun; Zhao, Yang

2014-09-01

Features of path dependent energy transfer in a dual-ring light-harvesting (LH2) complexes (B850) system have been examined in detail systematically. The Frenkel-Dirac time dependent variational method with the Davydov D1 Ansatz is employed with detailed evolution of polaron dynamics in real space readily obtained. It is found that the phase of the transmission amplitude through the LH2 complexes plays an important role in constructing the coherent excitonic energy transfer. It is also found that the symmetry breaking caused by the dimerization of bacteriochlorophylls and coherence or correlation between two rings will be conducive in enhancing the exciton transfer efficiency.

Group transfer and electron transfer reactions of organometallic complexes

NASA Astrophysics Data System (ADS)

Atwood, Jim D.

During 1994, despite the disruptions, the authors have made progress in several aspects of their research on electron transfer reactions between organometallic complexes. This summary covers three areas that are relatively complete: (1) reactions between metal carbonyl anions and metal carbonyl halides, (2) reactions of hydrido- and alkyl-containing anions (RFe(CO)4(-) and RW(CO)5(-) with metal carbonyl cations; and (3) reactions of a seventeen-electron complex (Cp* Cr(CO)3*) with metal carbonyl derivatives. Two areas of examination that have just begun (possible carbene transfer and the possible role of metal carbonyl anions in carbon-hydrogen bond activation) will also be described.

Energy transfer in purple bacterial photosynthetic units from cells grown in various light intensities.

PubMed

Niedzwiedzki, Dariusz M; Gardiner, Alastair T; Blankenship, Robert E; Cogdell, Richard J

2018-05-03

Three photosynthetic membranes, called intra-cytoplasmic membranes (ICMs), from wild-type and the ∆pucBA abce mutant of the purple phototrophic bacterium Rps. palustris were investigated using optical spectroscopy. The ICMs contain identical light-harvesting complex 1-reaction centers (LH1-RC) but have various spectral forms of light-harvesting complex 2 (LH2). Spectroscopic studies involving steady-state absorption, fluorescence, and femtosecond time-resolved absorption at room temperature and at 77 K focused on inter-protein excitation energy transfer. The studies investigated how energy transfer is affected by altered spectral features of the LH2 complexes as those develop under growth at different light conditions. The study shows that LH1 → LH2 excitation energy transfer is strongly affected if the LH2 complex alters its spectroscopic signature. The LH1 → LH2 excitation energy transfer rate modeled with the Förster mechanism and kinetic simulations of transient absorption of the ICMs demonstrated that the transfer rate will be 2-3 times larger for ICMs accumulating LH2 complexes with the classical B800-850 spectral signature (grown in high light) compared to the ICMs from the same strain grown in low light. For the ICMs from the ∆pucBA abce mutant, in which the B850 band of the LH2 complex is blue-shifted and almost degenerate with the B800 band, the LH1 → LH2 excitation energy transfer was not observed nor predicted by calculations.

Evolution of cytochrome bc complexes: from membrane-anchored dehydrogenases of ancient bacteria to triggers of apoptosis in vertebrates

PubMed Central

Dibrova, Daria V.; Cherepanov, Dmitry A.; Galperin, Michael Y.; Skulachev, Vladimir P.; Mulkidjanian, Armen Y.

2013-01-01

This review traces the evolution of the cytochrome bc complexes from their early spread among prokaryotic lineages and up to the mitochondrial cytochrome bc1 complex (complex III) and its role in apoptosis. The results of phylogenomic analysis suggest that the bacterial cytochrome b6f-type complexes with short cytochromes b were the ancient form that preceded in evolution the cytochrome bc1-type complexes with long cytochromes b. The common ancestor of the b6f-type and the bc1-type complexes probably resembled the b6f-type complexes found in Heliobacteriaceae and in some Planctomycetes. Lateral transfers of cytochrome bc operons could account for the several instances of acquisition of different types of bacterial cytochrome bc complexes by archaea. The gradual oxygenation of the atmosphere could be the key evolutionary factor that has driven further divergence and spread of the cytochrome bc complexes. On one hand, oxygen could be used as a very efficient terminal electron acceptor. On the other hand, auto-oxidation of the components of the bc complex results in the generation of reactive oxygen species (ROS), which necessitated diverse adaptations of the b6f-type and bc1-type complexes, as well as other, functionally coupled proteins. A detailed scenario of the gradual involvement of the cardiolipin-containing mitochondrial cytochrome bc1 complex into the intrinsic apoptotic pathway is proposed, where the functioning of the complex as an apoptotic trigger is viewed as a way to accelerate the elimination of the cells with irreparably damaged, ROS-producing mitochondria. PMID:23871937

Direct evidence of an elongation factor-Tu/Ts·GTP·Aminoacyl-tRNA quaternary complex.

PubMed

Burnett, Benjamin J; Altman, Roger B; Ferguson, Angelica; Wasserman, Michael R; Zhou, Zhou; Blanchard, Scott C

2014-08-22

During protein synthesis, elongation factor-Tu (EF-Tu) bound to GTP chaperones the entry of aminoacyl-tRNA (aa-tRNA) into actively translating ribosomes. In so doing, EF-Tu increases the rate and fidelity of the translation mechanism. Recent evidence suggests that EF-Ts, the guanosine nucleotide exchange factor for EF-Tu, directly accelerates both the formation and dissociation of the EF-Tu-GTP-Phe-tRNA(Phe) ternary complex (Burnett, B. J., Altman, R. B., Ferrao, R., Alejo, J. L., Kaur, N., Kanji, J., and Blanchard, S. C. (2013) J. Biol. Chem. 288, 13917-13928). A central feature of this model is the existence of a quaternary complex of EF-Tu/Ts·GTP·aa-tRNA(aa). Here, through comparative investigations of phenylalanyl, methionyl, and arginyl ternary complexes, and the development of a strategy to monitor their formation and decay using fluorescence resonance energy transfer, we reveal the generality of this newly described EF-Ts function and the first direct evidence of the transient quaternary complex species. These findings suggest that EF-Ts may regulate ternary complex abundance in the cell through mechanisms that are distinct from its guanosine nucleotide exchange factor functions. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Synthesis, photophysical properties, and computational studies of four-coordinate copper(I) complexes based on benzimidazolylidene N-heterocyclic carbene (NHC) ligands bearing aryl substituents

NASA Astrophysics Data System (ADS)

Xu, Shengxian; Wang, Jinglan; Liu, Shaobo; Zhao, Feng; Xia, Hongying; Wang, Yibo

2018-02-01

Three four-coordinate N-heterocyclic carbene (NHC) copper(I) complexes, [Cu(Ph-BenIm-Py)(POP)]PF6 (1), [Cu(Naph-BenIm-Py)(POP)]PF6 (2), and [Cu(Anthr-BenIm-Py)(POP)]PF6 (3) (Ph-BenIm-Py = 3-benzyl-1-(pyridin-2-yl)-1H-benzimidazolylidene, Naph-BenIm-Py = 3-(naphthalen-2-yl-1-(pyridin-2-yl)-1H- benzimidazolylidene, Anthr-BenIm-Py = 3-(anthracen-9-yl)-1-(pyridin-2-yl)-1H-benzimidazolylidene, and POP = bis[2-diphenylphosphino]-phenyl)ether) have been synthesized and characterized. The different aryl substituents (phenyl, naphthyl, and anthracyl groups) were introduced into NHC ligands and the corresponding photophysical properties of the complexes were systematically investigated. The absorption spectra of all NHCsbnd Cu(I) complexes show a characteristic feature of metal-to-ligand charge transfer (MLCT) in the lower-energy region. Complex 1 exhibited good photoluminescence (PL) properties companying with the high quantum yields and long excited-state lifetimes, whereas 2 and 3 with naphthyl and anthracyl groups show the low PL efficiency caused by the strong π-π stacking interactions. Density functional theory (DFT) and time dependent density functional theory (TDDFT) calculations were employed to rationalize the photophysical properties of the NHCsbnd Cu(I) complexes.

Impact of aryloxy initiators on the living and immortal polymerization of lactide.

PubMed

Chile, L-E; Ebrahimi, T; Wong, A; Aluthge, D C; Hatzikiriakos, S G; Mehrkhodavandi, P

2017-05-23

This report describes two different methodologies for the synthesis of aryl end-functionalized poly(lactide)s (PLAs) catalyzed by indium complexes. In the first method, a series of para-functionalized phenoxy-bridged dinuclear indium complexes [(NNO)InCl] 2 (μ-Cl)(μ-OPh R ) (R = OMe (1), Me (2), H (3), Br (4), NO 2 (5)) were synthesized and fully characterized. The solution and solid state structures of these complexes reflect the electronic differences between these initiators. The polymerization rates correlate with the electron donating ability of the phenoxy initiators: the para-nitro substituted complex 5 is essentially inactive. However, the para-methoxy variant, while less active than the ethoxy-bridged complex [(NNO)InCl] 2 (μ-Cl)(μ-OEt) (A), shows sufficient activity. Alternatively, aryl-capped PLAs were synthesized via immortal polymerization of PLA with A in the presence of a range of arylated chain transfer agents. Certain aromatic diols shut down polymerization by chelating one indium centre to form a stable metal complex. Immortal ROP was successful when using phenol, and 1,5-naphthalenediol. These polymers were analysed and chain end fidelity was confirmed using 1 H NMR spectroscopy, MALDI-TOF mass spectrometry, and UV-Vis spectroscopy. This study shed light on possible speciation when attempting to generate PLA-lignin copolymers.

Distributed Coding/Decoding Complexity in Video Sensor Networks

PubMed Central

Cordeiro, Paulo J.; Assunção, Pedro

2012-01-01

Video Sensor Networks (VSNs) are recent communication infrastructures used to capture and transmit dense visual information from an application context. In such large scale environments which include video coding, transmission and display/storage, there are several open problems to overcome in practical implementations. This paper addresses the most relevant challenges posed by VSNs, namely stringent bandwidth usage and processing time/power constraints. In particular, the paper proposes a novel VSN architecture where large sets of visual sensors with embedded processors are used for compression and transmission of coded streams to gateways, which in turn transrate the incoming streams and adapt them to the variable complexity requirements of both the sensor encoders and end-user decoder terminals. Such gateways provide real-time transcoding functionalities for bandwidth adaptation and coding/decoding complexity distribution by transferring the most complex video encoding/decoding tasks to the transcoding gateway at the expense of a limited increase in bit rate. Then, a method to reduce the decoding complexity, suitable for system-on-chip implementation, is proposed to operate at the transcoding gateway whenever decoders with constrained resources are targeted. The results show that the proposed method achieves good performance and its inclusion into the VSN infrastructure provides an additional level of complexity control functionality. PMID:22736972

Distributed coding/decoding complexity in video sensor networks.

PubMed

Cordeiro, Paulo J; Assunção, Pedro

2012-01-01

Video Sensor Networks (VSNs) are recent communication infrastructures used to capture and transmit dense visual information from an application context. In such large scale environments which include video coding, transmission and display/storage, there are several open problems to overcome in practical implementations. This paper addresses the most relevant challenges posed by VSNs, namely stringent bandwidth usage and processing time/power constraints. In particular, the paper proposes a novel VSN architecture where large sets of visual sensors with embedded processors are used for compression and transmission of coded streams to gateways, which in turn transrate the incoming streams and adapt them to the variable complexity requirements of both the sensor encoders and end-user decoder terminals. Such gateways provide real-time transcoding functionalities for bandwidth adaptation and coding/decoding complexity distribution by transferring the most complex video encoding/decoding tasks to the transcoding gateway at the expense of a limited increase in bit rate. Then, a method to reduce the decoding complexity, suitable for system-on-chip implementation, is proposed to operate at the transcoding gateway whenever decoders with constrained resources are targeted. The results show that the proposed method achieves good performance and its inclusion into the VSN infrastructure provides an additional level of complexity control functionality.

The excited states of a porphine-quinone complex under an external electrostatic field calculated by TDDFT

NASA Astrophysics Data System (ADS)

Aittala, Pekka J.; Cramariuc, Oana; Hukka, Terttu I.

2011-01-01

The potential energy curves (PECs) of the Q, B, and the lowest charge transfer (CT) states of a porphine-2,5-dimethyl-1,4-benzoquinone (PQ) complex have been studied by using the time-dependent density functional theory (TDDFT) with the CAM-B3LYP functional without and with the presence of an external electrostatic field. The PECs calculated using CAM-B3LYP with the original parameters α = 0.19, β = 0.65, and μ = 0.33 a0-1 are practically identical with those obtained using BH&HLYP. Applying of CAM-B3LYP with parameters α = 0.19, β = 0.81, and μ = 0.25 a0-1 yields PECs of the excited states that agree well with the PECs calculated previously using the CC2 method.

Complex and differential glial responses in Alzheimer's disease and ageing.

PubMed

Rodríguez, José J; Butt, Arthur M; Gardenal, Emanuela; Parpura, Vladimir; Verkhratsky, Alexei

2016-01-01

Glial cells and their association with neurones are fundamental for brain function. The emergence of complex neurone-glial networks assures rapid information transfer, creating a sophisticated circuitry where both types of neural cells work in concert, serving different activities. All glial cells, represented by astrocytes, oligodendrocytes, microglia and NG2-glia, are essential for brain homeostasis and defence. Thus, glia are key not only for normal central nervous system (CNS) function, but also to its dysfunction, being directly associated with all forms of neuropathological processes. Therefore, the progression and outcome of neurological and neurodegenerative diseases depend on glial reactions. In this review, we provide a concise account of recent data obtained from both human material and animal models demonstrating the pathological involvement of glia in neurodegenerative processes, including Alzheimer's disease (AD), as well as physiological ageing.

Stimulus-responsive light-harvesting complexes based on the pillararene-induced co-assembly of β-carotene and chlorophyll

NASA Astrophysics Data System (ADS)

Sun, Yan; Guo, Fang; Zuo, Tongfei; Hua, Jingjing; Diao, Guowang

2016-06-01

The locations and arrangements of carotenoids at the subcellular level are responsible for their designated functions, which reinforces the necessity of developing methods for constructing carotenoid-based suprastructures beyond the molecular level. Because carotenoids lack the binding sites necessary for controlled interactions, functional structures based on carotenoids are not easily obtained. Here, we show that carotene-based suprastructures were formed via the induction of pillararene through a phase-transfer-mediated host-guest interaction. More importantly, similar to the main component in natural photosynthesis, complexes could be synthesized after chlorophyll was introduced into the carotene-based suprastructure assembly process. Remarkably, compared with molecular carotene or chlorophyll, this synthesized suprastructure exhibits some photocatalytic activity when exposed to light, which can be exploited for photocatalytic reaction studies of energy capture and solar conversion in living organisms.

Preparation, spectroscopic and antibacterial studies on charge-transfer complexes of 2-hydroxypyridine with picric acid and 7,7‧,8,8‧-tetracyano-p-quinodimethane

NASA Astrophysics Data System (ADS)

Gaballa, Akmal S.; Amin, Alaa S.

2015-06-01

The reactions of electron acceptors such as picric acid (HPA) and 7,7‧,8,8‧-tetracyano-p-quinodimethane (TCNQ) with 2-hydroxypyridine (HPyO) have been investigated in EtOH at room temperature. Based on elemental analysis and IR spectra of the solid CT-complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge transfer complexes [(H2PyO)(PA)] and [(PyO)(HTCNQ)], respectively. The infrared and 1H NMR spectroscopic data indicate a charge transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding in [(H2PyO)(PA)] complex. Another charge transfer interaction was observed in [(PyO)(HTCNQ)] complex. The formation constants (KCT) for the CT-complexes are shown to be strongly dependent on the type and structure of the electron acceptors. Factors affecting the CT-processes and the kinetics of thermal decomposition of the complexes have been studied. The CT complexes were screened for their antibacterial activities against selected bacterial strains.

Preparation, spectroscopic and antibacterial studies on charge-transfer complexes of 2-hydroxypyridine with picric acid and 7,7',8,8'-tetracyano-p-quinodimethane.

PubMed

Gaballa, Akmal S; Amin, Alaa S

2015-06-15

The reactions of electron acceptors such as picric acid (HPA) and 7,7',8,8'-tetracyano-p-quinodimethane (TCNQ) with 2-hydroxypyridine (HPyO) have been investigated in EtOH at room temperature. Based on elemental analysis and IR spectra of the solid CT-complexes along with the photometric titration curves for the reactions, the data obtained indicate the formation of 1:1 charge transfer complexes [(H2PyO)(PA)] and [(PyO)(HTCNQ)], respectively. The infrared and (1)H NMR spectroscopic data indicate a charge transfer interaction associated with a proton migration from the acceptor to the donor followed by intramolecular hydrogen bonding in [(H2PyO)(PA)] complex. Another charge transfer interaction was observed in [(PyO)(HTCNQ)] complex. The formation constants (KCT) for the CT-complexes are shown to be strongly dependent on the type and structure of the electron acceptors. Factors affecting the CT-processes and the kinetics of thermal decomposition of the complexes have been studied. The CT complexes were screened for their antibacterial activities against selected bacterial strains. Copyright © 2015 Elsevier B.V. All rights reserved.

Heterologous production of an energy-conserving carbon monoxide dehydrogenase complex in the hyperthermophile Pyrococcus furiosus

DOE PAGES

Schut, Gerrit J.; Lipscomb, Gina L.; Nguyen, Diep M. N.; ...

2016-01-29

In this study, carbon monoxide (CO) is an important intermediate in anaerobic carbon fixation pathways in acetogenesis and methanogenesis. In addition, some anaerobes can utilize CO as an energy source. In the hyperthermophilic archaeon Thermococcus onnurineus, which grows optimally at 80°C, CO oxidation and energy conservation is accomplished by a respiratory complex encoded by a 16-gene cluster containing a CO dehydrogenase, a membrane-bound [NiFe]-hydrogenase and a Na +/H + antiporter module. This complex oxidizes CO, evolves CO 2 and H 2, and generates a Na+ motive force that is used to conserve energy by a Na+-dependent ATP synthase. Herein wemore » used a bacterial artificial chromosome to insert the 13.2 kb gene cluster encoding the CO-oxidizing respiratory complex of T. onnurineus into the genome of the heterotrophic archaeon, Pyrococcus furiosus, which grows optimally at 100° C. P. furiosus is normally unable to utilize CO, however, the recombinant strain readily oxidized CO and generated H 2 at 80° C. Moreover, CO also served as an energy source and allowed the P. furiosus strain to grow with a limiting concentration of sugar or with peptides as the carbon source. Moreover, CO oxidation by P. furiosus was also coupled to the re-utilization, presumably for biosynthesis, of acetate generated by fermentation. The functional transfer of CO utilization between Thermococcus and Pyrococcus species demonstrated herein is representative of the horizontal gene transfer of an environmentally relevant metabolic capability. The transfer of CO utilizing, hydrogen-producing genetic modules also has applications for biohydrogen production and a CO-based industrial platform for various thermophilic organisms.« less

Pnicogen bonds between X═PH3 (X = O, S, NH, CH2) and phosphorus and nitrogen bases.

PubMed

Alkorta, Ibon; Sánchez-Sanz, Goar; Elguero, José; Del Bene, Janet E

2014-02-27

Ab initio MP2/aug'-cc-pVTZ calculations have been carried out to investigate the pnicogen bonded complexes formed between the acids O═PH3, S═PH3, HN═PH3, and H2C═PH3 and the bases NH3, NCH, N2, PH3, and PCH. All nitrogen and phosphorus bases form complexes in which the bases are lone pair electron donors. The binding energies of complexes involving the stronger bases NH3, NCH, and PH3 differentiate among the acids, but the binding energies of complexes with the weaker bases do not. These complexes are stabilized by charge transfer from the lone pair orbital of N or P to the σ*P═A orbital of X═PH3, where A is the atom of X directly bonded to P. PCH also forms complexes with the X═PH3 acids as a π electron donor to the σ*P═A orbital. The binding energies and the charge-transfer energies of the π complexes are greater than those of the complexes in which PCH is a lone pair donor. Whether the positive charge on P increases, decreases, or remains the same upon complex formation, the chemical shieldings of (31)P decrease in the complexes relative to the corresponding monomers. (1p)J(P-N) and (1p)J(P-P) values correlate best with the corresponding P-N and P-P distances as a function of the nature of the base. (1)J(P-A) values do not correlate with P-A distances. Rather, the absolute values of (1)J(P-O), (1)J(P-S), and (1)J(P-N) decrease upon complexation. Decreasing (1)J(P-A) values correlate linearly with increasing complex binding energies. In contrast, (1)J(P-C) values increase upon complexation and correlate linearly with increasing binding energies.

Intermanual transfer and bilateral cortical plasticity is maintained in older adults after skilled motor training with simple and complex tasks

PubMed Central

Dickins, Daina S. E.; Sale, Martin V.; Kamke, Marc R.

2015-01-01

Intermanual transfer refers to the phenomenon whereby unilateral motor training induces performance gains in both the trained limb and in the opposite, untrained limb. Evidence indicates that intermanual transfer is attenuated in older adults following training on a simple ballistic movement task, but not after training on a complex task. This study investigated whether differences in plasticity in bilateral motor cortices underlie these differential intermanual transfer effects in older adults. Twenty young (<35 years-old) and older adults (>65 years) trained on a simple (repeated ballistic thumb abduction) and complex (sequential finger-thumb opposition) task in separate sessions. Behavioral performance was used to quantify intermanual transfer between the dominant (trained) and non-dominant (untrained) hands. The amplitude of motor-evoked potentials induced by single pulse transcranial magnetic stimulation was used to investigate excitability changes in bilateral motor cortices. Contrary to predictions, both age groups exhibited performance improvements in both hands after unilateral skilled motor training with simple and complex tasks. These performance gains were accompanied by bilateral increases in cortical excitability in both groups for the simple but not the complex task. The findings suggest that advancing age does not necessarily influence the capacity for intermanual transfer after training with the dominant hand. PMID:25999856

The dipole moment of the electron carrier adrenodoxin is not critical for redox partner interaction and electron transfer.

PubMed

Hannemann, Frank; Guyot, Arnaud; Zöllner, Andy; Müller, Jürgen J; Heinemann, Udo; Bernhardt, Rita

2009-07-01

Dipole moments of proteins arise from helical dipoles, hydrogen bond networks and charged groups at the protein surface. High protein dipole moments were suggested to contribute to the electrostatic steering between redox partners in electron transport chains of respiration, photosynthesis and steroid biosynthesis, although so far experimental evidence for this hypothesis was missing. In order to probe this assumption, we changed the dipole moment of the electron transfer protein adrenodoxin and investigated the influence of this on protein-protein interactions and electron transfer. In bovine adrenodoxin, the [2Fe-2S] ferredoxin of the adrenal glands, a dipole moment of 803 Debye was calculated for a full-length adrenodoxin model based on the Adx(4-108) and the wild type adrenodoxin crystal structures. Large distances and asymmetric distribution of the charged residues in the molecule mainly determine the observed high value. In order to analyse the influence of the resulting inhomogeneous electric field on the biological function of this electron carrier the molecular dipole moment was systematically changed. Five recombinant adrenodoxin mutants with successively reduced dipole moment (from 600 to 200 Debye) were analysed for their redox properties, their binding affinities to the redox partner proteins and for their function during electron transfer-dependent steroid hydroxylation. None of the mutants, not even the quadruple mutant K6E/K22Q/K24Q/K98E with a dipole moment reduced by about 70% showed significant changes in the protein function as compared with the unmodified adrenodoxin demonstrating that neither the formation of the transient complex nor the biological activity of the electron transfer chain of the endocrine glands was affected. This is the first experimental evidence that the high dipole moment observed in electron transfer proteins is not involved in electrostatic steering among the proteins in the redox chain.

Synthesis, characterization, crystal structure and solution studies of a novel proton transfer (charge transfer) complex of 2,2‧-dipyridylamine with 2,6-pyridine dicarboxylic acid

NASA Astrophysics Data System (ADS)

Ghasemi, Khaled; Rezvani, Ali Reza; Shokrollahi, Ardeshir; Zarghampour, Fereshteh; Moghimi, Abolghasem; García-Granda, Santiago; Mendoza-Meroño, Rafael

2015-06-01

Reaction between 2,2‧-dipyridylamine (DPA) and 2,6-pyridine dicarboxylic acid (dipicolinic acid, dipicH2), in water results in the formation of a proton transfer or charge transfer (CT) complex, (DPAH)+(dipicH)-·H2O, 1. The characterization was performed using 1H NMR and FTIR spectroscopy, elemental analysis and X-ray crystallography. The crystal system is triclinic with space group P1. The structural investigations exhibit that the hydrogen bonds and π-π stacking interactions stabilize the crystal structure of proton transfer complex. The protonation constants of 2,6-pyridine dicarboxylic acid, 2,2‧-dipyridylamine and the equilibrium constants for dipic-DPA (1:1) proton transfer system were calculated by potentiometric pH titration method using Hyperquad2008 program. The stoichiometries of the proton transfer species in solution was in agreement with the solid state result.

Charge transfer complex of some nervous and brain drugs - Part 1: Synthesis, spectroscopic, analytical and biological studies on the reaction between haloperidol antipsychotic drugs with π-acceptors

NASA Astrophysics Data System (ADS)

El-Habeeb, Abeer A.; Al-Saif, Foziah A.; Refat, Moamen S.

2013-02-01

Donor-acceptor interactions between the electron donor haloperidol (HPL) and π-acceptors like 7,7,8,8-tetracyanoquinodimethane (TCNQ) and picric acid (PA) have been studied spectrophotometrically in CH3OH solvent. The donor-acceptor (charge transfer complexes) were discussed in terms of formation constant (KCT), molar extinction coefficient (ɛCT), standard free energy (ΔGo), oscillator strength (ƒ), transition dipole moment (μ), resonance energy (RN) and ionization potential (ID). The stoichiometry of these complexes was found to be 1:1 M ratio and having the formulas [(HPL)(TCNQ)] and [(HPL)(PA)], respectively. The charge transfer interaction was successfully applied to determine of HPL drug using mentioned common π-acceptors also, the results obtained herein are satisfactory for estimation of HPL compound in the pharmaceutical form. The formed solid charge-transfer complexes were also isolated and characterized using elemental analysis, conductivity, (infrared, Raman, and 1H NMR) spectra and X-ray powder diffraction (XRD). The experimental data of elemental analyses are in agreement with calculated data. The infrared spectra of both HPL complexes are confirming the participation of sbnd OH of 4-hydroxy-1-piperidyl moiety in the donor-acceptor chelation. The morphological surface of the resulted charge transfer complexes were investigated using scanning electron microscopy (SEM). The thermogravimetric analysis (TG/DTG) and differential scanning calorimetry (DSC) techniques were performed to give knowledge about the thermal stability behavior of the synthesized charge transfer complexes. Thermodynamic parameters were computed from the thermal decomposition data. These complexes were also tested for their antimicrobial activity against six different microorganisms, and the results were compared with the parent drug.

Microparticle-mediated transfer of the viral receptors CAR and CD46, and the CFTR channel in a CHO cell model confers new functions to target cells.

PubMed

Gonzalez, Gaëlle; Vituret, Cyrielle; Di Pietro, Attilio; Chanson, Marc; Boulanger, Pierre; Hong, Saw-See

2012-01-01

Cell microparticles (MPs) released in the extracellular milieu can embark plasma membrane and intracellular components which are specific of their cellular origin, and transfer them to target cells. The MP-mediated, cell-to-cell transfer of three human membrane glycoproteins of different degrees of complexity was investigated in the present study, using a CHO cell model system. We first tested the delivery of CAR and CD46, two monospanins which act as adenovirus receptors, to target CHO cells. CHO cells lack CAR and CD46, high affinity receptors for human adenovirus serotype 5 (HAdV5), and serotype 35 (HAdV35), respectively. We found that MPs derived from CHO cells (MP-donor cells) constitutively expressing CAR (MP-CAR) or CD46 (MP-CD46) were able to transfer CAR and CD46 to target CHO cells, and conferred selective permissiveness to HAdV5 and HAdV35. In addition, target CHO cells incubated with MP-CD46 acquired the CD46-associated function in complement regulation. We also explored the MP-mediated delivery of a dodecaspanin membrane glycoprotein, the CFTR to target CHO cells. CFTR functions as a chloride channel in human cells and is implicated in the genetic disease cystic fibrosis. Target CHO cells incubated with MPs produced by CHO cells constitutively expressing GFP-tagged CFTR (MP-GFP-CFTR) were found to gain a new cellular function, the chloride channel activity associated to CFTR. Time-course analysis of the appearance of GFP-CFTR in target cells suggested that MPs could achieve the delivery of CFTR to target cells via two mechanisms: the transfer of mature, membrane-inserted CFTR glycoprotein, and the transfer of CFTR-encoding mRNA. These results confirmed that cell-derived MPs represent a new class of promising therapeutic vehicles for the delivery of bioactive macromolecules, proteins or mRNAs, the latter exerting the desired therapeutic effect in target cells via de novo synthesis of their encoded proteins.

Massive Gene Transfer and Extensive RNA Editing of a Symbiotic Dinoflagellate Plastid Genome

PubMed Central

Mungpakdee, Sutada; Shinzato, Chuya; Takeuchi, Takeshi; Kawashima, Takeshi; Koyanagi, Ryo; Hisata, Kanako; Tanaka, Makiko; Goto, Hiroki; Fujie, Manabu; Lin, Senjie; Satoh, Nori; Shoguchi, Eiichi

2014-01-01

Genome sequencing of Symbiodinium minutum revealed that 95 of 109 plastid-associated genes have been transferred to the nuclear genome and subsequently expanded by gene duplication. Only 14 genes remain in plastids and occur as DNA minicircles. Each minicircle (1.8–3.3 kb) contains one gene and a conserved noncoding region containing putative promoters and RNA-binding sites. Nine types of RNA editing, including a novel G/U type, were discovered in minicircle transcripts but not in genes transferred to the nucleus. In contrast to DNA editing sites in dinoflagellate mitochondria, which tend to be highly conserved across all taxa, editing sites employed in DNA minicircles are highly variable from species to species. Editing is crucial for core photosystem protein function. It restores evolutionarily conserved amino acids and increases peptidyl hydropathy. It also increases protein plasticity necessary to initiate photosystem complex assembly. PMID:24881086

Magnetohydrodynamics effect on convective boundary layer flow and heat transfer of viscoelastic micropolar fluid past a sphere

NASA Astrophysics Data System (ADS)

Amera Aziz, Laila; Kasim, Abdul Rahman Mohd; Zuki Salleh, Mohd; Syahidah Yusoff, Nur; Shafie, Sharidan

2017-09-01

The main interest of this study is to investigate the effect of MHD on the boundary layer flow and heat transfer of viscoelastic micropolar fluid. Governing equations are transformed into dimensionless form in order to reduce their complexity. Then, the stream function is applied to the dimensionless equations to produce partial differential equations which are then solved numerically using the Keller-box method in Fortran programming. The numerical results are compared to published study to ensure the reliability of present results. The effects of selected physical parameters such as the viscoelastic parameter, K, micropolar parameter, K1 and magnetic parameter, M on the flow and heat transfer are discussed and presented in tabular and graphical form. The findings from this study will be of critical importance in the fields of medicine, chemical as well as industrial processes where magnetic field is involved.

A Biomimetic-Computational Approach to Optimizing the Quantum Efficiency of Photovoltaics

NASA Astrophysics Data System (ADS)

Perez, Lisa M.; Holzenburg, Andreas

The most advanced low-cost organic photovoltaic cells have a quantum efficiency of 10%. This is in stark contrast to plant/bacterial light-harvesting systems which offer quantum efficiencies close to unity. Of particular interest is the highly effective quantum coherence-enabled energy transfer (Fig. 1). Noting that quantum coherence is promoted by charged residues and local dielectrics, classical atomistic simulations and time-dependent density functional theory (DFT) are used to identify charge/dielectric patterns and electronic coupling at exactly defined energy transfer interfaces. The calculations make use of structural information obtained on photosynthetic protein-pigment complexes while still in the native membrane making it possible to establish a link between supramolecular organization and quantum coherence in terms of what length scales enable fast energy transport and prevent quenching. Calculating energy transfer efficiencies between components based on different proximities will permit the search for patterns that enable defining material properties suitable for advanced photovoltaics.

Charge transfer mechanism for the formation of metallic states at the KTaO3/SrTiO3 interface

NASA Astrophysics Data System (ADS)

Nazir, S.; Singh, N.; Schwingenschlögl, U.

2011-03-01

The electronic and optical properties of the KTaO3/SrTiO3 heterointerface are analyzed by the full-potential linearized augmented plane-wave approach of density functional theory. Optimization of the atomic positions points at subordinate changes in the crystal structure and chemical bonding near the interface, which is due to a minimal lattice mismatch. The creation of metallic interface states thus is not affected by structural relaxation but can be explained by charge transfer between transition metal and oxygen atoms. It is to be expected that a charge transfer is likewise important for related interfaces such as LaAlO3/SrTiO3. The KTaO3/SrTiO3 system is ideal for disentangling the complex behavior of metallic interface states, since almost no structural relaxation takes place.

Thermal design, rating and second law analysis of shell and tube condensers based on Taguchi optimization for waste heat recovery based thermal desalination plants

NASA Astrophysics Data System (ADS)

Chandrakanth, Balaji; Venkatesan, G; Prakash Kumar, L. S. S; Jalihal, Purnima; Iniyan, S

2018-03-01

The present work discusses the design and selection of a shell and tube condenser used in Low Temperature Thermal Desalination (LTTD). To optimize the key geometrical and process parameters of the condenser with multiple parameters and levels, a design of an experiment approach using Taguchi method was chosen. An orthogonal array (OA) of 25 designs was selected for this study. The condenser was designed, analysed using HTRI software and the heat transfer area with respective tube side pressure drop were computed using the same, as these two objective functions determine the capital and running cost of the condenser. There was a complex trade off between the heat transfer area and pressure drop in the analysis, however second law analysis was worked out for determining the optimal heat transfer area vs pressure drop for condensing the required heat load.

Large eddy simulation for predicting turbulent heat transfer in gas turbines.

PubMed

Tafti, Danesh K; He, Long; Nagendra, K

2014-08-13

Blade cooling technology will play a critical role in the next generation of propulsion and power generation gas turbines. Accurate prediction of blade metal temperature can avoid the use of excessive compressed bypass air and allow higher turbine inlet temperature, increasing fuel efficiency and decreasing emissions. Large eddy simulation (LES) has been established to predict heat transfer coefficients with good accuracy under various non-canonical flows, but is still limited to relatively simple geometries and low Reynolds numbers. It is envisioned that the projected increase in computational power combined with a drop in price-to-performance ratio will make system-level simulations using LES in complex blade geometries at engine conditions accessible to the design process in the coming one to two decades. In making this possible, two key challenges are addressed in this paper: working with complex intricate blade geometries and simulating high-Reynolds-number (Re) flows. It is proposed to use the immersed boundary method (IBM) combined with LES wall functions. A ribbed duct at Re=20 000 is simulated using the IBM, and a two-pass ribbed duct is simulated at Re=100 000 with and without rotation (rotation number Ro=0.2) using LES with wall functions. The results validate that the IBM is a viable alternative to body-conforming grids and that LES with wall functions reproduces experimental results at a much lower computational cost. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Intergenic Transcriptional Interference Is Blocked by RNA Polymerase III Transcription Factor TFIIIB in Saccharomyces cerevisiae

PubMed Central

Korde, Asawari; Rosselot, Jessica M.; Donze, David

2014-01-01

The major function of eukaryotic RNA polymerase III is to transcribe transfer RNA, 5S ribosomal RNA, and other small non-protein-coding RNA molecules. Assembly of the RNA polymerase III complex on chromosomal DNA requires the sequential binding of transcription factor complexes TFIIIC and TFIIIB. Recent evidence has suggested that in addition to producing RNA transcripts, chromatin-assembled RNA polymerase III complexes may mediate additional nuclear functions that include chromatin boundary, nucleosome phasing, and general genome organization activities. This study provides evidence of another such “extratranscriptional” activity of assembled RNA polymerase III complexes, which is the ability to block progression of intergenic RNA polymerase II transcription. We demonstrate that the RNA polymerase III complex bound to the tRNA gene upstream of the Saccharomyces cerevisiae ATG31 gene protects the ATG31 promoter against readthrough transcriptional interference from the upstream noncoding intergenic SUT467 transcription unit. This protection is predominately mediated by binding of the TFIIIB complex. When TFIIIB binding to this tRNA gene is weakened, an extended SUT467–ATG31 readthrough transcript is produced, resulting in compromised ATG31 translation. Since the ATG31 gene product is required for autophagy, strains expressing the readthrough transcript exhibit defective autophagy induction and reduced fitness under autophagy-inducing nitrogen starvation conditions. Given the recent discovery of widespread pervasive transcription in all forms of life, protection of neighboring genes from intergenic transcriptional interference may be a key extratranscriptional function of assembled RNA polymerase III complexes and possibly other DNA binding proteins. PMID:24336746

Oxygen-atom transfer reactivity of axially ligated Mn(V)-oxo complexes: evidence for enhanced electrophilic and nucleophilic pathways.

PubMed

Neu, Heather M; Yang, Tzuhsiung; Baglia, Regina A; Yosca, Timothy H; Green, Michael T; Quesne, Matthew G; de Visser, Sam P; Goldberg, David P

2014-10-01

Addition of anionic donors to the manganese(V)-oxo corrolazine complex Mn(V)(O)(TBP8Cz) has a dramatic influence on oxygen-atom transfer (OAT) reactivity with thioether substrates. The six-coordinate anionic [Mn(V)(O)(TBP8Cz)(X)](-) complexes (X = F(-), N3(-), OCN(-)) exhibit a ∼5 cm(-1) downshift of the Mn-O vibrational mode relative to the parent Mn(V)(O)(TBP8Cz) complex as seen by resonance Raman spectroscopy. Product analysis shows that the oxidation of thioether substrates gives sulfoxide product, consistent with single OAT. A wide range of OAT reactivity is seen for the different axial ligands, with the following trend determined from a comparison of their second-order rate constants for sulfoxidation: five-coordinate ≈ thiocyanate ≈ nitrate < cyanate < azide < fluoride ≪ cyanide. This trend correlates with DFT calculations on the binding of the axial donors to the parent Mn(V)(O)(TBP8Cz) complex. A Hammett study was performed with p-X-C6H4SCH3 derivatives and [Mn(V)(O)(TBP8Cz)(X)](-) (X = CN(-) or F(-)) as the oxidant, and unusual "V-shaped" Hammett plots were obtained. These results are rationalized based upon a change in mechanism that hinges on the ability of the [Mn(V)(O)(TBP8Cz)(X)](-) complexes to function as either an electrophilic or weak nucleophilic oxidant depending upon the nature of the para-X substituents. For comparison, the one-electron-oxidized cationic Mn(V)(O)(TBP8Cz(•+)) complex yielded a linear Hammett relationship for all substrates (ρ = -1.40), consistent with a straightforward electrophilic mechanism. This study provides new, fundamental insights regarding the influence of axial donors on high-valent Mn(V)(O) porphyrinoid complexes.

Carotenoid-to-bacteriochlorophyll energy transfer through vibronic coupling in LH2 from Phaeosprillum molischianum.

PubMed

Thyrhaug, Erling; Lincoln, Craig N; Branchi, Federico; Cerullo, Giulio; Perlík, Václav; Šanda, František; Lokstein, Heiko; Hauer, Jürgen

2018-03-01

The peripheral light-harvesting antenna complex (LH2) of purple photosynthetic bacteria is an ideal testing ground for models of structure-function relationships due to its well-determined molecular structure and ultrafast energy deactivation. It has been the target for numerous studies in both theory and ultrafast spectroscopy; nevertheless, certain aspects of the convoluted relaxation network of LH2 lack a satisfactory explanation by conventional theories. For example, the initial carotenoid-to-bacteriochlorophyll energy transfer step necessary on visible light excitation was long considered to follow the Förster mechanism, even though transfer times as short as 40 femtoseconds (fs) have been observed. Such transfer times are hard to accommodate by Förster theory, as the moderate coupling strengths found in LH2 suggest much slower transfer within this framework. In this study, we investigate LH2 from Phaeospirillum (Ph.) molischianum in two types of transient absorption experiments-with narrowband pump and white-light probe resulting in 100 fs time resolution, and with degenerate broadband 10 fs pump and probe pulses. With regard to the split Q x band in this system, we show that vibronically mediated transfer explains both the ultrafast carotenoid-to-B850 transfer, and the almost complete lack of transfer to B800. These results are beyond Förster theory, which predicts an almost equal partition between the two channels.

Users manual for program ADMIT: Admittance and pressure transfer function developed for use on a PC computer

NASA Technical Reports Server (NTRS)

Armstrong, Wilbur C.

1992-01-01

The piping in a liquid rocket can assume complex configurations due to multiple tanks, multiple engines, and structures that must be piped around. The capability to handle some of these complex configurations have been incorporated into the ADMIT code. The capability to modify the input on line has been implemented. The configurations allowed include multiple tanks, multiple engines, the splitting of a pipe into unequal segments going to different (or the same) engines. This program will handle the following type elements: straight pipes, bends, inline accumulators, tuned stub accumulators, Helmholtz resonators, parallel resonators, pumps, split pipes, multiple tanks, and multiple engines.

Synthetic analog computation in living cells.

PubMed

Daniel, Ramiz; Rubens, Jacob R; Sarpeshkar, Rahul; Lu, Timothy K

2013-05-30

A central goal of synthetic biology is to achieve multi-signal integration and processing in living cells for diagnostic, therapeutic and biotechnology applications. Digital logic has been used to build small-scale circuits, but other frameworks may be needed for efficient computation in the resource-limited environments of cells. Here we demonstrate that synthetic analog gene circuits can be engineered to execute sophisticated computational functions in living cells using just three transcription factors. Such synthetic analog gene circuits exploit feedback to implement logarithmically linear sensing, addition, ratiometric and power-law computations. The circuits exhibit Weber's law behaviour as in natural biological systems, operate over a wide dynamic range of up to four orders of magnitude and can be designed to have tunable transfer functions. Our circuits can be composed to implement higher-order functions that are well described by both intricate biochemical models and simple mathematical functions. By exploiting analog building-block functions that are already naturally present in cells, this approach efficiently implements arithmetic operations and complex functions in the logarithmic domain. Such circuits may lead to new applications for synthetic biology and biotechnology that require complex computations with limited parts, need wide-dynamic-range biosensing or would benefit from the fine control of gene expression.

Calculation of photoelectron spectra of molybdenum and tungsten complexes using Green's functions methods.

PubMed

Bayse, Craig A; Ortwine, Kristine N

2007-08-16

Green's functions calculations are presented for several complexes of molybdenum and tungsten, two metals that are similar structurally but display subtle, but significant, differences in electronic structure. Outer valence Green's functions IPs for M(CO)6, M(Me)6, MH6, [MCl4O](-), and [MO4](-) (M = Mo, W) are generally within +/-0.2 eV of available experimental photoelectron spectra. The calculations show that electrons in M-L bonding orbitals are ejected at lower energies for Mo while the detachment energy for electrons in d orbitals varies with metal and complex. For the metal carbonyls, the quasiparticle picture assumed in OVGF breaks down for the inner valence pi CO molecular orbitals due to the coupling of two-hole-one-particle charge transfer states to the one-hole states. Incorporation of the 2h1p states through a Tamm-Dancoff approximation calculation accurately represents the band due to detachment from these molecular orbitals. Though the ordering of IPs for Green's functions methods and DFT Koopmans' theorem IPs is similar for the highest IPs for most compounds considered, the breakdown of the quasiparticle picture for the metal carbonyls suggests that scaling of the latter values may result in a fortuitous or incorrect assignment of experimental VDEs.

Contact infection of infectious disease onboard a cruise ship.

PubMed

Zhang, Nan; Miao, Ruosong; Huang, Hong; Chan, Emily Y Y

2016-12-08

Cruise tourism has become more popular. Long-term personal contact, complex population flows, a lack of medical care facilities, and defective infrastructure aboard most cruise ships is likely to result in the ship becoming an incubator for infectious diseases. In this paper, we use a cruise ship as a research scenario. Taking into consideration personal behavior, the nature and transfer route of the virus across different surfaces, virus reproduction, and disinfection, we studied contact infection of infectious disease on a cruise ship. Using gastroenteritis caused by the norovirus as an example, we analyzed the characteristics of infectious disease propagation based on simulation results under different conditions. We found hand washing are the most important factors affecting virus propagation and passenger infection. It also decides either the total number of virus microorganisms or the virus distribution in different functional areas. The transfer rate between different surfaces is a key factor influencing the concentricity of the virus. A high transfer rate leads to high concentricity. In addition, the risk of getting infected is effectively reduced when the disinfection frequency is above a certain threshold. The efficiency of disinfection of functional areas is determined by total virus number and total contact times of surfaces.

Contact infection of infectious disease onboard a cruise ship

PubMed Central

Zhang, Nan; Miao, Ruosong; Huang, Hong; Chan, Emily Y. Y.

2016-01-01

Cruise tourism has become more popular. Long-term personal contact, complex population flows, a lack of medical care facilities, and defective infrastructure aboard most cruise ships is likely to result in the ship becoming an incubator for infectious diseases. In this paper, we use a cruise ship as a research scenario. Taking into consideration personal behavior, the nature and transfer route of the virus across different surfaces, virus reproduction, and disinfection, we studied contact infection of infectious disease on a cruise ship. Using gastroenteritis caused by the norovirus as an example, we analyzed the characteristics of infectious disease propagation based on simulation results under different conditions. We found hand washing are the most important factors affecting virus propagation and passenger infection. It also decides either the total number of virus microorganisms or the virus distribution in different functional areas. The transfer rate between different surfaces is a key factor influencing the concentricity of the virus. A high transfer rate leads to high concentricity. In addition, the risk of getting infected is effectively reduced when the disinfection frequency is above a certain threshold. The efficiency of disinfection of functional areas is determined by total virus number and total contact times of surfaces. PMID:27929141

Contact infection of infectious disease onboard a cruise ship

NASA Astrophysics Data System (ADS)

Zhang, Nan; Miao, Ruosong; Huang, Hong; Chan, Emily Y. Y.

2016-12-01

Cruise tourism has become more popular. Long-term personal contact, complex population flows, a lack of medical care facilities, and defective infrastructure aboard most cruise ships is likely to result in the ship becoming an incubator for infectious diseases. In this paper, we use a cruise ship as a research scenario. Taking into consideration personal behavior, the nature and transfer route of the virus across different surfaces, virus reproduction, and disinfection, we studied contact infection of infectious disease on a cruise ship. Using gastroenteritis caused by the norovirus as an example, we analyzed the characteristics of infectious disease propagation based on simulation results under different conditions. We found hand washing are the most important factors affecting virus propagation and passenger infection. It also decides either the total number of virus microorganisms or the virus distribution in different functional areas. The transfer rate between different surfaces is a key factor influencing the concentricity of the virus. A high transfer rate leads to high concentricity. In addition, the risk of getting infected is effectively reduced when the disinfection frequency is above a certain threshold. The efficiency of disinfection of functional areas is determined by total virus number and total contact times of surfaces.

An approach to efficient mobility management in intelligent networks

NASA Technical Reports Server (NTRS)

Murthy, K. M. S.

1995-01-01

Providing personal communication systems supporting full mobility require intelligent networks for tracking mobile users and facilitating outgoing and incoming calls over different physical and network environments. In realizing the intelligent network functionalities, databases play a major role. Currently proposed network architectures envision using the SS7-based signaling network for linking these DB's and also for interconnecting DB's with switches. If the network has to support ubiquitous, seamless mobile services, then it has to support additionally mobile application parts, viz., mobile origination calls, mobile destination calls, mobile location updates and inter-switch handovers. These functions will generate significant amount of data and require them to be transferred between databases (HLR, VLR) and switches (MSC's) very efficiently. In the future, the users (fixed or mobile) may use and communicate with sophisticated CPE's (e.g. multimedia, multipoint and multisession calls) which may require complex signaling functions. This will generate volumness service handling data and require efficient transfer of these message between databases and switches. Consequently, the network providers would be able to add new services and capabilities to their networks incrementally, quickly and cost-effectively.

Charge transfer complex between 2,3-diaminopyridine with chloranilic acid. Synthesis, characterization and DFT, TD-DFT computational studies

NASA Astrophysics Data System (ADS)

Al-Ahmary, Khairia M.; Habeeb, Moustafa M.; Al-Obidan, Areej H.

2018-05-01

New charge transfer complex (CTC) between the electron donor 2,3-diaminopyridine (DAP) with the electron acceptor chloranilic (CLA) acid has been synthesized and characterized experimentally and theoretically using a variety of physicochemical techniques. The experimental work included the use of elemental analysis, UV-vis, IR and 1H NMR studies to characterize the complex. Electronic spectra have been carried out in different hydrogen bonded solvents, methanol (MeOH), acetonitrile (AN) and 1:1 mixture from AN-MeOH. The molecular composition of the complex was identified to be 1:1 from Jobs and molar ratio methods. The stability constant was determined using minimum-maximum absorbances method where it recorded high values confirming the high stability of the formed complex. The solid complex was prepared and characterized by elemental analysis that confirmed its formation in 1:1 stoichiometric ratio. Both IR and NMR studies asserted the existence of proton and charge transfers in the formed complex. For supporting the experimental results, DFT computations were carried out using B3LYP/6-31G(d,p) method to compute the optimized structures of the reactants and complex, their geometrical parameters, reactivity parameters, molecular electrostatic potential map and frontier molecular orbitals. The analysis of DFT results strongly confirmed the high stability of the formed complex based on existing charge transfer beside proton transfer hydrogen bonding concordant with experimental results. The origin of electronic spectra was analyzed using TD-DFT method where the observed λmax are strongly consisted with the computed ones. TD-DFT showed the contributed states for various electronic transitions.

Functional Assembly of Soluble and Membrane Recombinant Proteins of Mammalian NADPH Oxidase Complex.

PubMed

Souabni, Hajer; Ezzine, Aymen; Bizouarn, Tania; Baciou, Laura

2017-01-01

Activation of phagocyte cells from an innate immune system is associated with a massive consumption of molecular oxygen to generate highly reactive oxygen species (ROS) as microbial weapons. This is achieved by a multiprotein complex, the so-called NADPH oxidase. The activity of phagocyte NADPH oxidase relies on an assembly of more than five proteins, among them the membrane heterodimer named flavocytochrome b 558 (Cytb 558 ), constituted by the tight association of the gp91 phox (also named Nox2) and p22 phox proteins. The Cytb 558 is the membrane catalytic core of the NADPH oxidase complex, through which the reducing equivalent provided by NADPH is transferred via the associated prosthetic groups (one flavin and two hemes) to reduce dioxygen into superoxide anion. The other major proteins (p47 phox , p67 phox , p40 phox , Rac) requisite for the complex activity are cytosolic proteins. Thus, the NADPH oxidase functioning relies on a synergic multi-partner assembly that in vivo can be hardly studied at the molecular level due to the cell complexity. Thus, a cell-free assay method has been developed to study the NADPH oxidase activity that allows measuring and eventually quantifying the ROS generation based on optical techniques following reduction of cytochrome c. This setup is a valuable tool for the identification of protein interactions, of crucial components and additives for a functional enzyme. Recently, this method was improved by the engineering and the production of a complete recombinant NADPH oxidase complex using the combination of purified proteins expressed in bacterial and yeast host cells. The reconstitution into artificial membrane leads to a fully controllable system that permits fine functional studies.

Designing Artificial Neural Networks Using Particle Swarm Optimization Algorithms

PubMed Central

Vázquez, Roberto A.

2015-01-01

Artificial Neural Network (ANN) design is a complex task because its performance depends on the architecture, the selected transfer function, and the learning algorithm used to train the set of synaptic weights. In this paper we present a methodology that automatically designs an ANN using particle swarm optimization algorithms such as Basic Particle Swarm Optimization (PSO), Second Generation of Particle Swarm Optimization (SGPSO), and a New Model of PSO called NMPSO. The aim of these algorithms is to evolve, at the same time, the three principal components of an ANN: the set of synaptic weights, the connections or architecture, and the transfer functions for each neuron. Eight different fitness functions were proposed to evaluate the fitness of each solution and find the best design. These functions are based on the mean square error (MSE) and the classification error (CER) and implement a strategy to avoid overtraining and to reduce the number of connections in the ANN. In addition, the ANN designed with the proposed methodology is compared with those designed manually using the well-known Back-Propagation and Levenberg-Marquardt Learning Algorithms. Finally, the accuracy of the method is tested with different nonlinear pattern classification problems. PMID:26221132

The Rieske Iron-Sulfur Protein: Import and Assembly into the Cytochrome bc(1) Complex of Yeast Mitochondria.

PubMed

Conte, Laura; Zara, Vincenzo

2011-01-01

The Rieske iron-sulfur protein, one of the catalytic subunits of the cytochrome bc(1) complex, is involved in electron transfer at the level of the inner membrane of yeast mitochondria. The Rieske iron-sulfur protein is encoded by nuclear DNA and, after being synthesized in the cytosol, is imported into mitochondria with the help of a cleavable N-terminal presequence. The imported protein, besides incorporating the 2Fe-2S cluster, also interacts with other catalytic and non-catalytic subunits of the cytochrome bc(1) complex, thereby assembling into the mature and functional respiratory complex. In this paper, we summarize the most recent findings on the import and assembly of the Rieske iron-sulfur protein into Saccharomyces cerevisiae mitochondria, also discussing a possible role of this protein both in the dimerization of the cytochrome bc(1) complex and in the interaction of this homodimer with other complexes of the mitochondrial respiratory chain.

The Rieske Iron-Sulfur Protein: Import and Assembly into the Cytochrome bc 1 Complex of Yeast Mitochondria

PubMed Central

Conte, Laura; Zara, Vincenzo

2011-01-01

The Rieske iron-sulfur protein, one of the catalytic subunits of the cytochrome bc 1 complex, is involved in electron transfer at the level of the inner membrane of yeast mitochondria. The Rieske iron-sulfur protein is encoded by nuclear DNA and, after being synthesized in the cytosol, is imported into mitochondria with the help of a cleavable N-terminal presequence. The imported protein, besides incorporating the 2Fe-2S cluster, also interacts with other catalytic and non-catalytic subunits of the cytochrome bc 1 complex, thereby assembling into the mature and functional respiratory complex. In this paper, we summarize the most recent findings on the import and assembly of the Rieske iron-sulfur protein into Saccharomyces cerevisiae mitochondria, also discussing a possible role of this protein both in the dimerization of the cytochrome bc 1 complex and in the interaction of this homodimer with other complexes of the mitochondrial respiratory chain. PMID:21716720

"Non-Toxic" Proteins of the Botulinum Toxin Complex Exert In-vivo Toxicity.

PubMed

Miyashita, Shin-Ichiro; Sagane, Yoshimasa; Suzuki, Tomonori; Matsumoto, Takashi; Niwa, Koichi; Watanabe, Toshihiro

2016-08-10

The botulinum neurotoxin (BoNT) causes muscle paralysis and is the most potent toxin in nature. BoNT is associated with a complex of auxiliary "Non-Toxic" proteins, which constitute a large-sized toxin complex (L-TC). However, here we report that the "Non-Toxic" complex of serotype D botulinum L-TC, when administered to rats, exerts in-vivo toxicity on small-intestinal villi. Moreover, Serotype C and D of the "Non-Toxic" complex, but not BoNT, induced vacuole-formation in a rat intestinal epithelial cell line (IEC-6), resulting in cell death. Our results suggest that the vacuole was formed in a manner distinct from the mechanism by which Helicobacter pylori vacuolating toxin (VacA) and Vibrio cholerae haemolysin induce vacuolation. We therefore hypothesise that the serotype C and D botulinum toxin complex is a functional hybrid of the neurotoxin and vacuolating toxin (VT) which arose from horizontal gene transfer from an ancestral BoNT-producing bacterium to a hypothetical VT-producing bacterium.

Role of B800 in carotenoid-bacteriochlorophyll energy and electron transfer in LH2 complexes from the purple bacterium Rhodobacter sphaeroides.

PubMed

Polívka, Tomas; Niedzwiedzki, Dariusz; Fuciman, Marcel; Sundström, Villy; Frank, Harry A

2007-06-28

The role of the B800 in energy and electron transfer in LH2 complexes has been studied using femtosecond time-resolved transient absorption spectroscopy. The B800 site was perturbed by application of lithium dodecyl sulfate (LDS), and comparison of treated and untreated LH2 complexes from Rhodobacter sphaeroides incorporating carotenoids neurosporene, spheroidene, and spheroidenone was used to explore the role of B800 in carotenoid to bacteriochlorophyll-a (BChla) energy transfer and carotenoid radical formation. Efficiencies of the S1-mediated energy transfer in the LDS-treated complexes were 86, 61, and 57% in the LH2 complexes containing neurosporene, spheroidene, and spheroidenone, respectively. Analysis of the carotenoid S1 lifetimes in solution, LDS-treated, and untreated LH2 complexes allowed determination of B800/B850 branching ratio in the S1-mediated energy transfer. It is shown that B800 is a major acceptor, as approximately 60% of the energy from the carotenoid S1 state is accepted by B800. This value is nearly independent of conjugation length of the carotenoid. In addition to its role in energy transfer, the B800 BChla is the only electron acceptor in the event of charge separation between carotenoid and BChla in LH2 complexes, which is demonstrated by prevention of carotenoid radical formation in the LDS-treated LH2 complexes. In the untreated complexes containing neurosporene and spheroidene, the carotenoid radical is formed with a time constant of 300-400 fs. Application of different excitation wavelengths and intensity dependence of the carotenoid radical formation showed that the carotenoid radical can be formed only after excitation of the S2 state of carotenoid, although the S2 state itself is not a precursor of the charge-separated state. Instead, either a hot S1 state or a charge-transfer state lying between S2 and S1 states of the carotenoid are discussed as potential precursors of the charge-separated state.

Individual differences in learning and transfer: stable tendencies for learning exemplars versus abstracting rules.

PubMed

McDaniel, Mark A; Cahill, Michael J; Robbins, Mathew; Wiener, Chelsea

2014-04-01

We hypothesize that during training some learners may focus on acquiring the particular exemplars and responses associated with the exemplars (termed exemplar learners), whereas other learners attempt to abstract underlying regularities reflected in the particular exemplars linked to an appropriate response (termed rule learners). Supporting this distinction, after training (on a function-learning task), participants displayed an extrapolation profile reflecting either acquisition of the trained cue-criterion associations (exemplar learners) or abstraction of the function rule (rule learners; Studies 1a and 1b). Further, working memory capacity (measured by operation span [Ospan]) was associated with the tendency to rely on rule versus exemplar processes. Studies 1c and 2 examined the persistence of these learning tendencies on several categorization tasks. Study 1c showed that rule learners were more likely than exemplar learners (indexed a priori by extrapolation profiles) to resist using idiosyncratic features (exemplar similarity) in generalization (transfer) of the trained category. Study 2 showed that the rule learners but not the exemplar learners performed well on a novel categorization task (transfer) after training on an abstract coherent category. These patterns suggest that in complex conceptual tasks, (a) individuals tend to either focus on exemplars during learning or on extracting some abstraction of the concept, (b) this tendency might be a relatively stable characteristic of the individual, and (c) transfer patterns are determined by that tendency.

Individual Differences in Learning and Transfer: Stable Tendencies for Learning Exemplars versus Abstracting Rules

PubMed Central

McDaniel, Mark A.; Cahill, Michael J.; Robbins, Mathew; Wiener, Chelsea

2013-01-01

We hypothesize that during training some learners may focus on acquiring the particular exemplars and responses associated with the exemplars (termed exemplar learners), whereas other learners attempt to abstract underlying regularities reflected in the particular exemplars linked to an appropriate response (termed rule learners). Supporting this distinction, after training (on a function-learning task), participants either displayed an extrapolation profile reflecting acquisition of the trained cue-criterion associations (exemplar learners) or abstraction of the function rule (rule learners; Studies 1a and 1b). Further, working memory capacity (measured by Ospan) was associated with the tendency to rely on rule versus exemplar processes. Studies 1c and 2 examined the persistence of these learning tendencies on several categorization tasks. Study 1c showed that rule learners were more likely than exemplar learners (indexed a priori by extrapolation profiles) to resist using idiosyncratic features (exemplar similarity) in generalization (transfer) of the trained category. Study 2 showed that the rule learners but not the exemplar learners performed well on a novel categorization task (transfer) after training on an abstract coherent category. These patterns suggest that in complex conceptual tasks, (a) individuals tend to either focus on exemplars during learning or on extracting some abstraction of the concept, (b) this tendency might be a relatively stable characteristic of the individual, and (c) transfer patterns are determined by that tendency. PMID:23750912

Imaging protein complex formation in the autophagy pathway: analysis of the interaction of LC3 and Atg4BC74A in live cells using Förster resonance energy transfer and fluorescence recovery after photobleaching

NASA Astrophysics Data System (ADS)

Kraft, Lewis J.; Kenworthy, Anne K.

2012-01-01

The protein microtubule-associated protein 1, light chain 3 (LC3) functions in autophagosome formation and plays a central role in the autophagy pathway. Previously, we found LC3 diffuses more slowly in cells than is expected for a freely diffusing monomer, suggesting it may constitutively associate with a macromolecular complex containing other protein components of the pathway. In the current study, we used Förster resonance energy transfer (FRET) microscopy and fluorescence recovery after photobleaching (FRAP) to investigate the interactions of LC3 with Atg4BC74A, a catalytically inactive mutant of the cysteine protease involved in lipidation and de-lipidation of LC3, as a model system to probe protein complex formation in the autophagy pathway. We show Atg4BC74A is in FRET proximity with LC3 in both the cytoplasm and nucleus of living cells, consistent with previous biochemical evidence that suggests these proteins directly interact. In addition, overexpressed Atg4BC74A diffuses significantly more slowly than predicted based on its molecular weight, and its translational diffusion coefficient is significantly slowed upon coexpression with LC3 to match that of LC3 itself. Taken together, these results suggest Atg4BC74A and LC3 are contained within the same multiprotein complex and that this complex exists in both the cytoplasm and nucleoplasm of living cells.