The effect of plasmon silver and exiton semiconductor nanoparticles on the bacteriorhodopsin photocycle in Halobacterium salinarum membranes

NASA Astrophysics Data System (ADS)

Oleinikov, V. A.; Lukashev, E. P.; Zaitsev, S. Yu.; Chistyakov, A. A.; Solovyeva, D. O.; Mochalov, K. E.; Nabiev, I.

2017-01-01

The interaction of semiconductor quantum dots and silver nanoparticles (AgNPs) with bacteriorhodopsin (BR), a membrane protein contained in the purple membrane (PM) of Halobacterium salinarum, is studied. It is shown that both types of nanoparticles are adsorbed efficiently on the surface of the purple membranes, modulating the parameters of the bacteriorhodopsin photocycle. Electrostatic interactions are found to be the main cause of the effect of nanoparticles on the bacteriorhodopsin photocycle. These results explain our earlier data on the "fixation" of the bacteriorhodopsin photocycle for protein molecules trapped after incubation of the purple membranes with silver nanoparticles near the location of the "hot spots" of the effect of surface-enhanced Raman scattering (SERS). It is demonstrated that exposure of silver nanoparticles with bacteriorhodopsin in SERS-active regions lowers the amount of bacteriorhodopsin molecules involved in phototransformations.

Optical Logarithmic Transformation of Speckle Images with Bacteriorhodopsin Films

NASA Technical Reports Server (NTRS)

Downie, John D.

1995-01-01

The application of logarithmic transformations to speckle images is sometimes desirable in converting the speckle noise distribution into an additive, constant-variance noise distribution. The optical transmission properties of some bacteriorhodopsin films are well suited to implement such a transformation optically in a parallel fashion. I present experimental results of the optical conversion of a speckle image into a transformed image with signal-independent noise statistics, using the real-time photochromic properties of bacteriorhodopsin. The original and transformed noise statistics are confirmed by histogram analysis.

Application of bacteriorhodopsin films in an adaptive-focusing schlieren system

NASA Astrophysics Data System (ADS)

Downie, John D.

1995-09-01

The photochromic property of bacteriorhodopsin films is exploited in the application of a focusing schlieren optical system for the visualization of optical phase information. By encoding an image on the film with light of one wavelength and reading out with a different wavelength, the readout beam can effectively see the photographic negative of the original image. The potential advantage of this system over previous focusing schlieren systems is that the updatable nature of the bacteriorhodopsin film allows system adaptation. I discuss two image encoding and readout techniques for the bacteriorhodopsin and use film transmission characteristics to choose the more appropriate method. I demonstrate the system principle with experimental results using argon-ion and He-Cd lasers as the two light sources of different wavelengths, and I discuss current limitations to implementation with a white-light source.

Application of Bacteriorhodopsin Films in an Adaptive-Focusing Schlieren System

NASA Technical Reports Server (NTRS)

Downie, John D.

1995-01-01

The photochromic property of bacteriorhodopsin films is exploited in the application of a focusing schlieren optical system for the visualization of optical phase information. By encoding an image on the film with light of one wavelength and reading out with a different wavelength, the readout beam can effectively see the photographic negative of the original image. The potential advantage of this system over previous focusing schlieren systems is that the updatable nature of the bacteriorhodopsin film allows system adaptation. I discuss two image encoding and readout techniques for the bacteriorhodopsin and use film transmission characteristics to choose the more appropriate method. I demonstrate the system principle with experimental results using argon-ion and He-Cd lasers as the two light sources of different wavelengths, and I discuss current limitations to implementation with a white-light source.

Multiplexed Holographic Data Storage in Bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Mehrl, David J.; Krile, Thomas F.

1999-01-01

Biochrome photosensitive films in particular Bacteriorhodopsin exhibit features which make these materials an attractive recording medium for optical data storage and processing. Bacteriorhodopsin films find numerous applications in a wide range of optical data processing applications; however the short-term memory characteristics of BR limits their applications for holographic data storage. The life-time of the BR can be extended using cryogenic temperatures [1], although this method makes the system overly complicated and unstable. Longer life-times can be provided in one modification of BR - the "blue" membrane BR [2], however currently available films are characterized by both low diffraction efficiency and difficulties in providing photoreversible recording. In addition, as a dynamic recording material, the BR requires different wavelengths for recording and reconstructing of optical data in order to prevent the information erasure during its readout. This fact also put constraints on a BR-based Optical Memory, due to information loss in holographic memory systems employing the two-lambda technique for reading-writing thick multiplexed holograms.

Conformational Change of Bacteriorhodopsin Quantitatively Monitored by Microcantilever Sensors

PubMed Central

Braun, Thomas; Backmann, Natalija; Vögtli, Manuel; Bietsch, Alexander; Engel, Andreas; Lang, Hans-Peter; Gerber, Christoph; Hegner, Martin

2006-01-01

Bacteriorhodopsin proteoliposomes were used as a model system to explore the applicability of micromechanical cantilever arrays to detect conformational changes in membrane protein patches. The three main results of our study concern: 1), reliable functionalization of micromechanical cantilever arrays with proteoliposomes using ink jet spotting; 2), successful detection of the prosthetic retinal removal (bleaching) from the bacteriorhodopsin protein by measuring the induced nanomechanical surface stress change; and 3), the quantitative response thereof, which depends linearly on the amount of removed retinal. Our results show this technique to be a potential tool to measure membrane protein-based receptor-ligand interactions and conformational changes. PMID:16443650

Spectroscopic studies of bacteriorhodopsin fragments dissolved in organic solution.

PubMed Central

Torres, J; Padrós, E

1995-01-01

Fourier transform infrared and UV fourth-derivative spectroscopies were used to study the secondary structure of bacteriorhodopsin and its chymotryptic and one of the sodium borohydride fragments dissolved in chloroform-methanol (1:1, v/v), 0.1 M LiClO4. The C1 fragment (helices C, D, E, F, and G) showed an alpha-helical content of about 53%, whereas C2 (helices A and B) had about 60%, and B2 (helices F and G) about 65% alpha-helix. The infrared main band indicated differences in alpha-helical properties between these fragments. These techniques were also used to obtain information on the interactions among helices. According to the results obtained from the hydrogen/deuterium exchange kinetics, about 40% of the amide protons of C2 are particularly protected against exchange, whereas for the C1 fragment this process is unexpectedly fast. UV fourth-derivative spectra of these samples were used to obtain information about the environment of Trp side chains. The results showed that the Trp residues of C2 are more shielded from the solvent than those of C1 or B2. The results of this work indicate that the specific interactions existing between the transmembrane segments induce different types of helical conformations in native bacteriorhodopsin. PMID:7612847

Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.

PubMed

Woolf, T B

1997-11-01

Understanding the role of the lipid bilayer in membrane protein structure and dynamics is needed for tertiary structure determination methods. However, the molecular details are not well understood. Molecular dynamics computer calculations can provide insight into these molecular details of protein:lipid interactions. This paper reports on 10 simulations of individual alpha-helices in explicit lipid bilayers. The 10 helices were selected from the bacteriorhodopsin structure as representative alpha-helical membrane folding components. The bilayer is constructed of dimyristoyl phosphatidylcholine molecules. The only major difference between simulations is the primary sequence of the alpha-helix. The results show dramatic differences in motional behavior between alpha-helices. For example, helix A has much smaller root-mean-squared deviations than does helix D. This can be understood in terms of the presence of aromatic residues at the interface for helix A that are not present in helix D. Additional motions are possible for the helices that contain proline side chains relative to other amino acids. The results thus provide insight into the types of motion and the average structures possible for helices within the bilayer setting and demonstrate the strength of molecular simulations in providing molecular details that are not directly visualized in experiments.

Monolithically integrated bacteriorhodopsin-GaAs/GaAlAs phototransceiver.

PubMed

Shin, Jonghyun; Bhattacharya, Pallab; Xu, Jian; Váró, György

2004-10-01

A monolithically integrated bacteriorhodopsin-semiconductor phototransceiver is demonstrated for the first time to the authors' knowledge. In this novel biophotonic optical interconnect, the input photoexcitation is detected by bacteriorhodopsin (bR) that has been selectively deposited onto the gate of a GaAs-based field-effect transistor. The photovoltage developed across the bR is converted by the transistor into an amplified photocurrent, which drives an integrated light-emitting diode with a Ga0.37Al0.63As active region. Advantage is taken of the high-input impedance of the field-effect transistor, which matches the high internal resistance of bR. The input and output wavelengths are 594 and 655 nm, respectively. The transient response of the optoelectronic circuit to modulated input light has also been studied.

Introduction to electron crystallography.

PubMed

Kühlbrandt, Werner

2013-01-01

From the earliest work on regular arrays in negative stain, electron crystallography has contributed greatly to our understanding of the structure and function of biological macromolecules. The development of electron cryo-microscopy (cryo-EM) then lead to the first groundbreaking atomic models of the membrane proteins bacteriorhodopsin and light harvesting complex II within lipid bilayers. Key contributions towards cryo-EM and electron crystallography methods included specimen preparation and vitrification, liquid-helium cooling, data collection, and image processing. These methods are now applied almost routinely to both membrane and soluble proteins. Here we outline the advances and the breakthroughs that paved the way towards high-resolution structures by electron crystallography, both in terms of methods development and biological milestones.

Crystal structures of different substrates of bacteriorhodopsin's M intermediate at various pH levels.

PubMed

Yamamoto, Masataka; Hayakawa, Naoki; Murakami, Midori; Kouyama, Tsutomu

2009-10-30

The hexagonal P622 crystal of bacteriorhodopsin, which is made up of stacked membranes, is stable provided that the precipitant concentration in the soaking solution is higher than a critical value (i.e., 1.5 M ammonium sulfate). Diffraction data showed that the crystal lattice shrank linearly with increasing precipitant concentration, due primarily to narrowing of intermembrane spaces. Although the crystal shrinkage did not affect the rate of formation of the photoreaction M intermediate, its lifetime increased exponentially with the precipitant concentration. It was suggested that the energetic barrier of the M-to-N transition becomes higher when the motional freedom of the EF loop is reduced by crystal lattice force. As a result of this property, the M state accumulated predominantly when the crystal that was soaked at a high precipitant concentration was illuminated at room temperature. Structural data obtained at various pH levels showed that the overall structure of M is not strongly dependent on pH, except that Glu194 and Glu204 in the proton release complex are more separated at pH 7 than at pH 4.4. This result suggests that light-induced disruption of the paired structure of Glu194 and Glu204 is incomplete when external pH is lower than the pK(a) value of the proton release group in the M state.

Modeling Current-Voltage Charateristics of Proteorhodopsin and Bacteriorhodopsin: Towards an Optoelectronics Based on Proteins.

PubMed

Alfinito, Eleonora; Reggiani, Lino

2016-10-01

Current-voltage characteristics of metal-protein-metal structures made of proteorhodopsin and bacteriorhodopsin are modeled by using a percolation-like approach. Starting from the tertiary structure pertaining to the single protein, an analogous resistance network is created. Charge transfer inside the network is described as a sequential tunneling mechanism and the current is calculated for each value of the given voltage. The theory is validated with available experiments, in dark and light. The role of the tertiary structure of the single protein and of the mechanisms responsible for the photo-activity is discussed.

Electron crystallography and aquaporins.

PubMed

Schenk, Andreas D; Hite, Richard K; Engel, Andreas; Fujiyoshi, Yoshinori; Walz, Thomas

2010-01-01

Electron crystallography of two-dimensional (2D) crystals can provide information on the structure of membrane proteins at near-atomic resolution. Originally developed and used to determine the structure of bacteriorhodopsin (bR), electron crystallography has recently been applied to elucidate the structure of aquaporins (AQPs), a family of membrane proteins that form pores mostly for water but also other solutes. While electron crystallography has made major contributions to our understanding of the structure and function of AQPs, structural studies on AQPs, in turn, have fostered a number of technical developments in electron crystallography. In this contribution, we summarize the insights electron crystallography has provided into the biology of AQPs, and describe technical advancements in electron crystallography that were driven by structural studies on AQP 2D crystals. In addition, we discuss some of the lessons that were learned from electron crystallographic work on AQPs. Copyright © 2010 Elsevier Inc. All rights reserved.

Multiplexed Holographic Optical Data Storage In Thick Bacteriorhodopsin Films

NASA Technical Reports Server (NTRS)

Downie, John D.; Timucin, Dogan A.; Gary, Charles K.; Ozcan, Meric; Smithey, Daniel T.; Crew, Marshall

1998-01-01

The optical data storage capacity of photochromic bacteriorhodopsin films is investigated by means of theoretical calculations, numerical simulations, and experimental measurements on sequential recording of angularly multiplexed diffraction gratings inside a thick D85N BR film.

Nonlinear coherent optical image processing using logarithmic transmittance of bacteriorhodopsin films

NASA Astrophysics Data System (ADS)

Downie, John D.

1995-08-01

The transmission properties of some bacteriorhodopsin-film spatial light modulators are uniquely suited to allow nonlinear optical image-processing operations to be applied to images with multiplicative noise characteristics. A logarithmic amplitude-transmission characteristic of the film permits the conversion of multiplicative noise to additive noise, which may then be linearly filtered out in the Fourier plane of the transformed image. I present experimental results demonstrating the principle and the capability for several different image and noise situations, including deterministic noise and speckle. The bacteriorhodopsin film studied here displays the logarithmic transmission response for write intensities spanning a dynamic range greater than 2 orders of magnitude.

Nonlinear Coherent Optical Image Processing Using Logarithmic Transmittance of Bacteriorhodopsin Films

NASA Technical Reports Server (NTRS)

Downie, John D.

1995-01-01

The transmission properties of some bacteriorhodopsin-film spatial light modulators are uniquely suited to allow nonlinear optical image-processing operations to be applied to images with multiplicative noise characteristics. A logarithmic amplitude-transmission characteristic of the film permits the conversion of multiplicative noise to additive noise, which may then be linearly filtered out in the Fourier plane of the transformed image. I present experimental results demonstrating the principle and the capability for several different image and noise situations, including deterministic noise and speckle. The bacteriorhodopsin film studied here displays the logarithmic transmission response for write intensities spanning a dynamic range greater than 2 orders of magnitude.

Progress toward an explicit mechanistic model for the light-driven pump, bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1999-01-01

Recent crystallographic information about the structure of bacteriorhodopsin and some of its photointermediates, together with a large amount of spectroscopic and mutational data, suggest a mechanistic model for how this protein couples light energy to the translocation of protons across the membrane. Now nearing completion, this detailed molecular model will describe the nature of the steric and electrostatic conflicts at the photoisomerized retinal, as well as the means by which it induces proton transfers in the two half-channels leading to the two membrane surfaces, thereby causing unidirectional, uphill transport.

Unraveling the mechanism of proton translocation in the extracellular half-channel of bacteriorhodopsin.

PubMed

Ge, Xiaoxia; Gunner, M R

2016-05-01

Bacteriorhodopsin, a light activated protein that creates a proton gradient in halobacteria, has long served as a simple model of proton pumps. Within bacteriorhodopsin, several key sites undergo protonation changes during the photocycle, moving protons from the higher pH cytoplasm to the lower pH extracellular side. The mechanism underlying the long-range proton translocation between the central (the retinal Schiff base SB216, D85, and D212) and exit clusters (E194 and E204) remains elusive. To obtain a dynamic view of the key factors controlling proton translocation, a systematic study using molecular dynamics simulation was performed for eight bacteriorhodopsin models varying in retinal isomer and protonation states of the SB216, D85, D212, and E204. The side-chain orientation of R82 is determined primarily by the protonation states of the residues in the EC. The side-chain reorientation of R82 modulates the hydrogen-bond network and consequently possible pathways of proton transfer. Quantum mechanical intrinsic reaction coordinate calculations of proton-transfer in the methyl guanidinium-hydronium-hydroxide model system show that proton transfer via a guanidinium group requires an initial geometry permitting proton donation and acceptance by the same amine. In all the bacteriorhodopsin models, R82 can form proton wires with both the CC and the EC connected by the same amine. Alternatively, rare proton wires for proton transfer from the CC to the EC without involving R82 were found in an O' state where the proton on D85 is transferred to D212. © 2016 Wiley Periodicals, Inc.

Mechanisms responsible for the photocurrent in bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Alfinito, Eleonora; Reggiani, Lino

2015-03-01

Recently, there has been growing interest in the electrical properties of bacteriorhodopsin (bR), a protein belonging to the transmembrane protein family. Several experiments pointed out the role of green light in enhancing the current flow in nanolayers of bR, thus confirming potential applications of this protein in the field of optoelectronics. By contrast, the mechanisms underlying the charge transfer and the associated photocurrent are still far from being understood at a microscopic level. To take into account the structure-dependent nature of the current, in a previous set of papers we suggested a mechanism of sequential tunneling among neighboring amino acids. As a matter of fact, when irradiated with green light, bR undergoes a conformational change at a molecular level. Thus, the role played by the protein tertiary-structure in modeling the charge transfer cannot be neglected. The aim of this paper is to go beyond previous models, in the framework of a new branch of electronics we call proteotronics, which exploits the ability of using proteins as reliable, well-understood materials for the development of novel bioelectronic devices. In particular, the present approach assumes that the conformational change is not the unique transformation the protein undergoes when irradiated by light. Instead, the light can also promote an increase of the protein state free energy that, in turn, should modify its internal degree of connectivity. This phenomenon is here described by the change of the value of an interaction radius associated with the physical interactions among amino acids. The implemented model enables us to achieve a better agreement between theory and experiments in the region of a low applied bias by preserving the level of agreement at high values of applied bias. Furthermore, results provide new insights on the mechanisms responsible for bR photoresponse.

A spectroscopic investigation of the Schiff base reprotonation mechanism of bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Russell, Terence Stephen

This thesis reports time-resolved visible spectroscopy experiments performed on the light-driven proton pumping protein, bacteriorhodopsin (bR), and a number of artificially produced analogs. These analogs comprise a variety of single and double amino acid substitutions produced in several of the residues previously implicated in proton transport in bR. Also addressed are the results of resonance Raman and FTIR difference spectroscopy which provide information about the vibrational modes of the protein. The results from these experiments confirm aspects of both structural and functional models of bR based on previous electron diffraction and spectroscopic data. During a phase of the proton pumping photocycle in bR known as Schiff base reprotonation (also referred to as M intermediate decay), a proton is transferred over a 12 A distance from a proton donor residue (Asp-96) to the light-absorbing active site. The behavior of the M intermediate was monitored by time-resolved visible spectroscopy. In the single substitution known as D96N, the Asp-96 residue was replaced with a less efficient proton donor, asparagine. This mutant exhibited an M intermediate which decayed slowly in comparison to that of wild-type bR. However, this effect was reversed with the double substitution, T46D/D96N. This result indicates that the proton donor group can be moved to another nearby location and still yield a system functionally similar to the native protein. Replacement of the donor group with a histidine, His-96, resulted in a photocycle similar to D96N above pH 7. However, below this pH, the M intermediate is not detected. FTIR difference spectroscopy indicates that the protonation state of the substituted His-96 residue influences the structure of the active site of bR which suggests that a proton that is associated with His-96 may move towards the active site and thereby block M intermediate formation. Finally, the residue Thr-89 was replaced with an asparagine. This

Optical Processing of Speckle Images with Bacteriorhodopsin for Pattern Recognition

NASA Technical Reports Server (NTRS)

Downie, John D.; Tucker, Deanne (Technical Monitor)

1994-01-01

Logarithmic processing of images with multiplicative noise characteristics can be utilized to transform the image into one with an additive noise distribution. This simplifies subsequent image processing steps for applications such as image restoration or correlation for pattern recognition. One particularly common form of multiplicative noise is speckle, for which the logarithmic operation not only produces additive noise, but also makes it of constant variance (signal-independent). We examine the optical transmission properties of some bacteriorhodopsin films here and find them well suited to implement such a pointwise logarithmic transformation optically in a parallel fashion. We present experimental results of the optical conversion of speckle images into transformed images with additive, signal-independent noise statistics using the real-time photochromic properties of bacteriorhodopsin. We provide an example of improved correlation performance in terms of correlation peak signal-to-noise for such a transformed speckle image.

Photonic switching based on the photoinduced birefringence in bacteriorhodopsin films

NASA Astrophysics Data System (ADS)

Huang, Yuhua; Wu, Shin-Tson; Zhao, Youyuan

2004-03-01

Photoinduced birefringence in bacteriorhodopsin films was investigated using pump-probe method and its application for photonic switching explored. A diode-pumped second-harmonic YAG laser was used as a pumping beam and a diode laser at λ=660 nm was used as a probing beam. The pump and probe beams overlap at the sample. Without the pumping beam, the probing light cannot transmit the analyzer to the detector. However, due to the photoinduced anisotropy, a portion of the probing light is detected when the pumping beam is present. Since λ=660 nm is far from the absorption peak (˜570 nm) of the ground state, the photoinduced birefringence predominates. Using the intensity-dependent photoinduced birefringence in a bacteriorhodopsin film, we have demonstrated a photonic switch with ˜1000:1 contrast ratio, ˜0.6 s rise time and ˜1.5 s decay time.

Retinal isomerization in bacteriorhodopsin captured by a femtosecond x-ray laser.

PubMed

Nogly, Przemyslaw; Weinert, Tobias; James, Daniel; Carbajo, Sergio; Ozerov, Dmitry; Furrer, Antonia; Gashi, Dardan; Borin, Veniamin; Skopintsev, Petr; Jaeger, Kathrin; Nass, Karol; Båth, Petra; Bosman, Robert; Koglin, Jason; Seaberg, Matthew; Lane, Thomas; Kekilli, Demet; Brünle, Steffen; Tanaka, Tomoyuki; Wu, Wenting; Milne, Christopher; White, Thomas; Barty, Anton; Weierstall, Uwe; Panneels, Valerie; Nango, Eriko; Iwata, So; Hunter, Mark; Schapiro, Igor; Schertler, Gebhard; Neutze, Richard; Standfuss, Jörg

2018-06-14

Ultrafast isomerization of retinal is the primary step in photoresponsive biological functions including vision in humans and ion-transport across bacterial membranes. We studied the sub-picosecond structural dynamics of retinal isomerization in the light-driven proton pump bacteriorhodopsin using an x-ray laser. A series of structural snapshots with near-atomic spatial and temporal resolution in the femtosecond regime show how the excited all- trans retinal samples conformational states within the protein binding pocket prior to passing through a twisted geometry and emerging in the 13 -cis conformation. Our findings suggest ultrafast collective motions of aspartic acid residues and functional water molecules in the proximity of the retinal Schiff base as a key ingredient for this stereo-selective and efficient photochemical reaction. Copyright © 2018, American Association for the Advancement of Science.

Multifunctional optical security features based on bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Hampp, Norbert A.; Neebe, Martin; Juchem, Thorsten; Wolperdinger, Markus; Geiger, Markus; Schmuck, Arno

2004-06-01

Bacteriorhodopsin (BR), a photochromic retinal protein, has been developed into a new materials platform for applications in anti-counterfeiting. The combination of three different properties of the material on its molecular level, a light-inducible color change, photochemical data storage and traceability of the protein due to molecular marker sequences make this protein a promising material for security applications. The crystalline structure of the biopigment combines these properties with high stability. As BR is a biological material specialized knowledge for modification, cost- effective production and suitable processing of the material is required. Photochromic BR-based inks have been developed for screen printing, pad printing and ink jet printing. These prints show a high photochromic sensitivity towards variation of illumination. For this reason it is not possible to reproduce the dynamic color by photocopying. In addition to such visual inspection the printed symbols offer the possibility for digital write-once-read-many (WORM) data storage. Photochemical recording is accomplished by a two-photon process. Recording densities in a range from 106 bit/cm2 to 108 bit/cm2 have been achieved. Data structures are stored in a polarization sensitive mode which allows an easy and efficient data encryption.

White Light Schlieren Optics Using Bacteriorhodopsin as an Adaptive Image Grid

NASA Technical Reports Server (NTRS)

Peale, Robert; Ruffin, Boh; Donahue, Jeff; Barrett, Carolyn

1996-01-01

A Schlieren apparatus using a bacteriorhodopsin film as an adaptive image grid with white light illumination is demonstrated for the first time. The time dependent spectral properties of the film are characterized. Potential applications include a single-ended Schlieren system for leak detection.

An Observation of Diamond-Shaped Particle Structure in a Soya Phosphatidylcohline and Bacteriorhodopsin Composite Langmuir Blodgett Film Fabricated by Multilayer Molecular Thin Film Method

NASA Astrophysics Data System (ADS)

Tsujiuchi, Y.; Makino, Y.

A composite film of soya phosphatidylcohline (soya PC) and bacteriorhodopsin (BR) was fabricated by the multilayer molecular thin film method using fatty acid and lipid on a quartz substrate. Direct Force Microscopy (DFM), UV absorption spectra and IR absorption spectra of the film were characterized on the detail of surface structure of the film. The DFM data revealed that many rhombus (diamond-shaped) particles were observed in the film. The spectroscopic data exhibited the yield of M-intermediate of BR in the film. On our modelling of molecular configuration indicate that the coexistence of the strong inter-molecular interaction and the strong inter-molecular interaction between BR trimmers attributed to form the particles.

Light as an Energy Source in Continuous Cultures of Bacteriorhodopsin-Containing Halobacteria

PubMed Central

Rodriguez-Valera, F.; Nieto, J. J.; Ruiz-Berraquero, F.

1983-01-01

The role of light as an energy source for slightly aereated cultures of halobacteria was studied, using continuous cultures with low nutrient concentrations and a low oxygen supply. A series of experiments were carried out with non-illuminated and differently illuminated cultures and with different oxygen transfer rates. Under low oxygen availability, light proved to be a decisively important energy source that allowed the populations to reach higher growth rates and much higher population densities. Oxygen influenced the growth over only a minimal level, below which neither the illuminated nor the dark cultures were affected by the oxygen transfer rate. From these results, it appears that the bacteriorhodopsin-mediated energy supply could have a very important role for the ecology of halobacteria in their microaerophilic habitats. In the illuminated cultures, cells that originated purple colonies on plates appeared. These cells, which could be bacteriorhodopsin-constitutive mutants, are now being studied. PMID:16346250

Fourier Transform Infrared and Resonance Raman Spectroscopic Studies of Bacteriorhodopsin.

NASA Astrophysics Data System (ADS)

Earnest, Thomas Nixon

Fourier transform infrared and resonance Raman spectroscopy were used to investigate the structure and function of the light-activated, transmembrane proton pump, bacteriorhodopsin, from the purple membrane of Halobacterium halobium. Bacteriorhodopsin (bR) is a 27,000 dalton integral membrane protein consisting of 248 amino acids with a retinylidene chromophore. Absorption of a photon leads to the translocation of one or two protons from the inside of the cell to the outside. Resonance Raman spectroscopy allows for the study of the configuration of retinal in bR and its photointermediates by the selective enhancement of vibrational modes of the chromophore. This technique was used to determine that the chromophore is attached to lysine-216 in both the bR _{570} and the M _{412} intermediates. In bR with tyrosine-64 selectively nitrated or aminated, the chromophore appears to have the same configuration in that bR _{570} (all- trans) and M _{412} (13- cis) states as it does in unmodified bR. Polarized Fourier transform infrared spectroscopy (FTIR) permits the study of the direction of transition dipole moments arising from molecular vibrations of the protein and the retinal chromophore. The orientation of alpha helical and beta sheet components was determined for bR with the average helical tilt found to lie mostly parallel to the membrane normal. The beta sheet structures also exhibit an IR linear dichroism for the amide I and amide II bands which suggest that the peptide backbone is mostly perpendicular to the membrane plane although it is difficult to determine whether the bands originate from sheet or turn components. The orientation of secondary structure components of the C-1 (residues 72-248) and C-2 (residues 1-71) fragments were also investigated to determine the structure of these putative membrane protein folding intermediates. Polarized, low temperature FTIR -difference spectroscopy was then used to investigate the structure of bR as it undergoes

Evidence of multipolar response of Bacteriorhodopsin by noncollinear second harmonic generation.

PubMed

Bovino, F A; Larciprete, M C; Sibilia, C; Váró, G; Gergely, C

2012-06-18

Noncollinear second harmonic generation from a Bacteriorhodopsin (BR) oriented multilayer film was systematically investigated by varying the polarization state of both fundamental beams. Both experimental results and theoretical simulations, show that the resulting polarization mapping is an useful tool to put in evidence the optical chirality of the investigated film as well as the corresponding multipolar contributions to the nonlinear.

Time-resolved resonance Raman spectroscopy of intermediates of bacteriorhodopsin: The bK(590) intermediate.

PubMed

Terner, J; Hsieh, C L; Burns, A R; El-Sayed, M A

1979-07-01

We have combined microbeam and flow techniques with computer subtraction methods to obtain the resonance Raman spectrum of the short lived batho-intermediate (bK(590)) of bacteriorhodopsin. Comparison of the spectra obtained in (1)H(2)O and (2)H(2)O, as well as the fact that the bK(590) intermediate shows large optical red shifts, suggests that the Schiff base linkage of this intermediate is protonated. The fingerprint region of the spectrum of bK(590), sensitive to the isomeric configuration of the retinal chromophore, does not resemble the corresponding region of the parent bR(570) form. The resonance Raman spectrum of bK(590) as well as the spectra of all of the other main intermediates in the photoreaction cycle of bacteriorhodopsin are discussed and compared with resonance Raman spectra of published model compounds.

Determination of retinal chromophore structure in bacteriorhodopsin with resonance Raman spectroscopy.

PubMed

Smith, S O; Lugtenburg, J; Mathies, R A

1985-01-01

The analysis of the vibrational spectrum of the retinal chromophore in bacteriorhodopsin with isotopic derivatives provides a powerful "structural dictionary" for the translation of vibrational frequencies and intensities into structural information. Of importance for the proton-pumping mechanism is the unambiguous determination of the configuration about the C13=C14 and C=N bonds, and the protonation state of the Schiff base nitrogen. Vibrational studies have shown that in light-adapted BR568 the Schiff base nitrogen is protonated and both the C13=C14 and C=N bonds are in a trans geometry. The formation of K625 involves the photochemical isomerization about only the C13=C14 bond which displaces the Schiff base proton into a different protein environment. Subsequent Schiff base deprotonation produces the M412 intermediate. Thermal reisomerization of the C13=C14 bond and reprotonation of the Schiff base occur in the M412------O640 transition, resetting the proton-pumping mechanism. The vibrational spectra can also be used to examine the conformation about the C--C single bonds. The frequency of the C14--C15 stretching vibration in BR568, K625, L550 and O640 argues that the C14--C15 conformation in these intermediates is s-trans. Conformational distortions of the chromophore have been identified in K625 and O640 through the observation of intense hydrogen out-of-plane wagging vibrations in the Raman spectra (see Fig. 2). These two intermediates are the direct products of chromophore isomerization. Thus it appears that following isomerization in a tight protein binding pocket, the chromophore cannot easily relax to a planar geometry. The analogous observation of intense hydrogen out-of-plane modes in the primary photoproduct in vision (Eyring et al., 1982) suggests that this may be a general phenomenon in protein-bound isomerizations. Future resonance Raman studies should provide even more details on how bacterio-opsin and retinal act in concert to produce an

The role of proline residues in the dynamics of transmembrane helices: the case of bacteriorhodopsin.

PubMed

Perálvarez-Marín, Alex; Bourdelande, José-Luis; Querol, Enric; Padrós, Esteve

2006-01-01

Proline residues in transmembrane helices have been found to have important roles in the functioning of membrane proteins. Moreover, Pro residues occur with high frequency in transmembrane alpha-helices, as compared to alpha-helices for soluble proteins. Here, we report several properties of the bacteriorhodopsin mutants P50A (helix B), P91A (helix C) and P186A (helix F). Compared to wild type, strongly perturbed behaviour has been found for these mutants. In the resting state, increased hydroxylamine accessibility and altered Asp-85 pKa and light-dark adaptation were observed. On light activation, hydroxylamine accessibility was increased and proton transport activity, M formation kinetics and FTIR difference spectra of M and N intermediates showed clear distortions. On the basis of these alterations and the near identity of the crystalline structures of mutants with that of wild type, we conclude that the transmembrane proline residues of bacteriorhodopsin fulfil a dynamic role in both the resting and the light-activated states. Our results are consistent with the notion that mutation of Pro to Ala allows the helix to increase its flexibility towards the direction originally hindered by the steric clash between the ring Cgamma and the carbonyl O of the i-4 residue, at the same time decreasing the mobility towards the opposite direction. Due to their properties, transmembrane Pro residues may serve as transmission elements of conformational changes during the transport process. We propose that these concepts can be extended to other transmembrane proteins.

Bacteriorhodopsin as a chemical and biological sensor

NASA Astrophysics Data System (ADS)

Heeg, Bauke; Needleman, Richard; Khizhnyak, Anatoliy; L'Esperance, Drew M.; Scott, Eddie; Markov, Vladimir B.; Trolinger, James D.

2003-08-01

Bacteriorhodopsin (bR) is a small protein containing the chromophore retinal, and resides in the membrane of the Halobacterium salinarium. When the retinal absorbs a photon, a cycle of structural changes is triggered resulting in a cross-membrane proton transfer, which is used to generate energy for the organism. Many studies have been conducted to elucidate the dynamical structure - optical property relations, and the overall mechanism of photo-induced proton transport in bR is now well understood. On the other hand, site selective mutagenesis allows engineering of the original ("wild-type") bR, such that the protein can be made sensitive to specific chemicals or biological structures that consequently induce changes in the proton-transport. As such, bR provides a unique molecular platform onto which various functional elements can be built: peptide receptors for molecular recognition of pathogens (e.g. viruses, cancer cells, spores, bacteria, bio-toxins), fluorescent tags (using the inherent optical transduction mechanism of bR), and chemical anchors for capturing target cells. In particular, the stability of bR in extreme environments (pH range of 1 - 11, temperatures up to 110 °C) allows for optical detection under a large range of environmental conditions. In this paper we present and discuss experimental data of several bR mutants and their potential as chemical and biological sensors. In particular, the optical changes associated with metal ligand binding are discussed for two mutants, 170C and 169C/96N, as well as the optical changes associated with streptavidin-coated beads bound to bR with strep II tags inserted in the E/F loop.

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy.

PubMed

Heenan, Patrick R; Yu, Hao; Siewny, Matthew G W; Perkins, Thomas T

2018-03-28

Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG 0 ) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG 0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy

NASA Astrophysics Data System (ADS)

Heenan, Patrick R.; Yu, Hao; Siewny, Matthew G. W.; Perkins, Thomas T.

2018-03-01

Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG0) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

Direct Measurement of the Photoelectric Response Time of Bacteriorhodopsin via Electro-Optic Sampling

PubMed Central

Xu, J.; Stickrath, A. B.; Bhattacharya, P.; Nees, J.; Váró, G.; Hillebrecht, J. R.; Ren, L.; Birge, R. R.

2003-01-01

The photovoltaic signal associated with the primary photochemical event in an oriented bacteriorhodopsin film is measured by directly probing the electric field in the bacteriorhodopsin film using an ultrafast electro-optic sampling technique. The inherent response time is limited only by the laser pulse width of 500 fs, and permits a measurement of the photovoltage with a bandwidth of better than 350 GHz. All previous published studies have been carried out with bandwidths of 50 GHz or lower. We observe a charge buildup with an exponential formation time of 1.68 ± 0.05 ps and an initial decay time of 31.7 ps. Deconvolution with a 500-fs Gaussian excitation pulse reduces the exponential formation time to 1.61 ± 0.04 ps. The photovoltaic signal continues to rise for 4.5 ps after excitation, and the voltage profile corresponds well with the population dynamics of the K state. The origin of the fast photovoltage is assigned to the partial isomerization of the chromophore and the coupled motion of the Arg-82 residue during the primary event. PMID:12885657

Functional and evolutionary relationships between bacteriorhodopsin and halorhodopsin in the archaebacterium, halobacterium halobium

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1986-01-01

The archaebacteria occupy a unique place in phylogenetic trees constructed from analyses of sequences from key informational macromolecules, and their study continues to yield interesting ideas on the early evolution and divergence of biological forms. It is now known that the halobacteria among these species contain various retinal-proteins, resembling eukaryotic rhodopsins, but with different functions. Two of these pigments, located in the cytoplasmic membranes of the bacteria, are bacteriorhodopsin (a light-driven proton pump) and halorhodopsin (a light-driven chloride pump). Comparison of these systems is expected to reveal structure/function relationships in these simple (primitive?) energy transducing membrane components and evolutionary relationships which had produced the structural features which allow the divergent functions. Findings indicate that very different primary structures are needed for these proteins to accomplish their different functions. Indeed, analysis of partial amino acid sequences from halo-opsin shows already that few if any long segments exist which are homologous to bacterio-opsin. Either these proteins diverged a very long time ago to allow for the observed differences, or the evolutionary clock in the halobacteria runs faster than usual.

Enhanced photocurrent in engineered bacteriorhodopsin monolayer.

PubMed

Patil, Amol V; Premaruban, Thenhuan; Berthoumieu, Olivia; Watts, Anthony; Davis, Jason J

2012-01-12

The integration of the transmembrane protein bacteriorhodopsin (BR) with man-made electrode surfaces has attracted a great deal of interest for some two decades or more and holds significant promise from the perspective of derived photoresponse or energy capture interfaces. Here we demonstrate that a novel and strategically engineered cysteine site (M163C) can be used to intimately and effectively couple delipidated BR to supporting metallic electrode surfaces. By virtue of the combined effects of the greater surface molecular density afforded by delipidation, and the vicinity of the electrostatic changes associated with proton pumping to the transducing metallic continuum, the resulting films generate a considerably greater photocurrent density on wavelength-selective illumination than previously achievable with monolayers of BR. Given the uniquely photoresponsive, wavelength-selective, and photostable characteristics of this protein, the work has implications for utilization in solar energy capture and photodetector devices.

Pathways of proton release in the bacteriorhodopsin photocycle

NASA Technical Reports Server (NTRS)

Zimanyi, L.; Varo, G.; Chang, M.; Ni, B.; Needleman, R.; Lanyi, J. K.

1992-01-01

The pH dependencies of the rate constants in the photocycles of recombinant D96N and D115N/D96N bacteriorhodopsins were determined from time-resolved difference spectra between 70 ns and 420 ms after photoexcitation. The results were consistent with the model suggested earlier for proteins containing D96N substitution: BR hv----K----L----M1----M2----BR. Only the M2----M1 back-reaction was pH-dependent: its rate increased with increasing [H+] between pH 5 and 8. We conclude from quantitative analysis of this pH dependency that its reverse, the M1----M2 reaction, is linked to the release of a proton from a group with a pKa = 5.8. This suggests a model for wild-type bacteriorhodopsin in which at pH greater than 5.8 the transported proton is released on the extracellular side from this as yet unknown group and on the 100-microseconds time scale, but at pH less than 5.8, the proton release occurs from another residue and later in the photocycle most likely directly from D85 during the O----BR reaction. We postulate, on the other hand, that proton uptake on the cytoplasmic side will be by D96 and during the N----O reaction regardless of pH. The proton kinetics as measured with indicator dyes confirmed the unique prediction of this model: at pH greater than 6, proton release preceded proton uptake, but at pH less than 6, the release was delayed until after the uptake. The results indicated further that the overall M1----M2 reaction includes a second kinetic step in addition to proton release; this is probably the earlier postulated extracellular-to-cytoplasmic reorientation switch in the proton pump.

Forster Resonance Energy Transfer Between Core/Shell Quantum Dots and Bacteriorhodopsin

DTIC Science & Technology

2012-01-01

through 1 -ethyl- 3 -( 3 - dimethylaminopropyl ) carbodiimide hydrochloride (EDC) linker techniques. An amide linkage between the carboxyl- QD and bR amino...Förster Resonance Energy Transfer between Core/Shell QuantumDots and Bacteriorhodopsin Mark H. Griep, 1 , 2, 3 Eric M.Winder,2, 4 Donald R. Lueking,2, 4...failing to comply with a collection of information if it does not display a currently valid OMB control number. 1 . REPORT DATE 2012 2. REPORT TYPE 3

Recent Advances in the Field of Bionanotechnology: An Insight into Optoelectric Bacteriorhodopsin, Quantum Dots, and Noble Metal Nanoclusters

PubMed Central

Knoblauch, Christopher; Griep, Mark; Friedrich, Craig

2014-01-01

Molecular sensors and molecular electronics are a major component of a recent research area known as bionanotechnology, which merges biology with nanotechnology. This new class of biosensors and bioelectronics has been a subject of intense research over the past decade and has found application in a wide variety of fields. The unique characteristics of these biomolecular transduction systems has been utilized in applications ranging from solar cells and single-electron transistors (SETs) to fluorescent sensors capable of sensitive and selective detection of a wide variety of targets, both organic and inorganic. This review will discuss three major systems in the area of molecular sensors and electronics and their application in unique technological innovations. Firstly, the synthesis of optoelectric bacteriorhodopsin (bR) and its application in the field of molecular sensors and electronics will be discussed. Next, this article will discuss recent advances in the synthesis and application of semiconductor quantum dots (QDs). Finally, this article will conclude with a review of the new and exciting field of noble metal nanoclusters and their application in the creation of a new class of fluorescent sensors. PMID:25340449

Efficient production and purification of functional bacteriorhodopsin with a wheat-germ cell-free system and a combination of Fos-choline and CHAPS detergents.

PubMed

Genji, Takahisa; Nozawa, Akira; Tozawa, Yuzuru

2010-10-01

Cell-free translation is one potential approach to the production of functional transmembrane proteins. We have now examined various detergents as supplements to a wheat-germ cell-free system in order to optimize the production and subsequent purification of a functional model transmembrane protein, bacteriorhodopsin. We found that Fos-choline and CHAPS detergents counteracted each other's inhibitory effects on cell-free translation activity and thereby allowed the efficient production and subsequent purification of functional bacteriorhodopsin in high yield. Copyright © 2010 Elsevier Inc. All rights reserved.

Bacteriorhodopsin Material and Film Fabrication Issues for Holographic Applications

NASA Technical Reports Server (NTRS)

Downie, John D.; Timucin, Dogan A.; Smithey, Daniel T.; Crew, Marshall; Rayfield, George W.; Lan, Sonie (Technical Monitor)

1998-01-01

We discuss issues associated with bacteriorhodopsin (BR) materials and films that affect optical performance in holographic applications. For the D85N variant, some critical parameters include degree of hydration and recording wavelength. The quantum efficiency of the molecular state transition is observed to be apparently dependent on the illumination wavelength. We explain this effect by modeling the photo-activity of the D85N variant as two competing photocycles between the 9-cis and 13-cis retinal configurations. We are able to determine the pure excited P-state absorbance spectrum from the ground state spectrum and mixed population spectra obtained by bleaching to steady-state conditions.

Resonance Raman spectra of bacteriorhodopsin's primary photoproduct: evidence for a distorted 13-cis retinal chromophore.

PubMed Central

Braiman, M; Mathies, R

1982-01-01

We have obtained the resonance Raman spectrum of bacteriorhodopsin's primary photoproduct K with a novel low-temperature spinning sample technique. Purple membrane at 77 K is illuminated with spatially separated actinic (pump) and probe laser beams. The 514-nm pump beam produces a photostationary steady-state mixture of bacteriorhodopsin and K. This mixture is then rotated through the red (676 nm) probe beam, which selectively enhances the Raman scattering from K. The essential advantage of our successive pump-and-probe technique is that it prevents the fluorescence excited by the pump beam from masking the red probe Raman scattering. K exhibits strong Raman lines at 1516, 1294, 1194, 1012, 957, and 811 cm-1. The effects of C15 deuteration on K's fingerprint lines correlate well with those seen in 13-cis model compounds, indicating that K has a 13-cis chromophore. However, the presence of unusually strong "low-wavenumber" lines at 811 and 957 cm-1, attributable to hydrogen out-of-plane wags, indicates that the protein holds the chromophore in a distorted conformation after trans leads to cis isomerization. PMID:6281770

Bacteriorhodopsin films for optical signal processing and data storage

NASA Technical Reports Server (NTRS)

Walkup, John F. (Principal Investigator); Mehrl, David J. (Principal Investigator)

1996-01-01

This report summarizes the research results obtained on NASA Ames Grant NAG 2-878 entitled 'Investigations of Bacteriorhodopsin Films for Optical Signal Processing and Data Storage.' Specifically we performed research, at Texas Tech University, on applications of Bacteriorhodopisin film to both (1) dynamic spatial filtering and (2) holographic data storage. In addition, measurements of the noise properties of an acousto-optical matrix-vestor multiplier built for NASA Ames by Photonic Systems Inc. were performed at NASA Ames' Photonics Laboratory. This research resulted in two papers presented at major optical data processing conferences and a journal paper which is to appear in APPLIED OPTICS. A new proposal for additional BR research has recently been submitted to NASA Ames Research Center.

Directed evolution of bacteriorhodopsin for applications in bioelectronics

PubMed Central

Wagner, Nicole L.; Greco, Jordan A.; Ranaghan, Matthew J.; Birge, Robert R.

2013-01-01

In nature, biological systems gradually evolve through complex, algorithmic processes involving mutation and differential selection. Evolution has optimized biological macromolecules for a variety of functions to provide a comparative advantage. However, nature does not optimize molecules for use in human-made devices, as it would gain no survival advantage in such cooperation. Recent advancements in genetic engineering, most notably directed evolution, have allowed for the stepwise manipulation of the properties of living organisms, promoting the expansion of protein-based devices in nanotechnology. In this review, we highlight the use of directed evolution to optimize photoactive proteins, with an emphasis on bacteriorhodopsin (BR), for device applications. BR, a highly stable light-activated proton pump, has shown great promise in three-dimensional optical memories, real-time holographic processors and artificial retinas. PMID:23676894

Pathways of proton transfer in the light-driven pump bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1993-01-01

The mechanism of proton transport in the light-driven pump bacteriorhodopsin is beginning to be understood. Light causes the all-trans to 13-cis isomerization of the retinal chromophore. This sets off a sequential and directed series of transient decreases in the pKa's of a) the retinal Schiff base, b) an extracellular proton release complex which includes asp-85, and c) a cytoplasmic proton uptake complex which includes asp-96. The timing of these pKa changes during the photoreaction cycle causes sequential proton transfers which result in the net movement of a proton across the protein, from the cytoplasmic to the extracellular surface.

Vibrational motions associated with primary processes in bacteriorhodopsin studied by coherent infrared emission spectroscopy.

PubMed

Groma, Géza I; Colonna, Anne; Martin, Jean-Louis; Vos, Marten H

2011-03-16

The primary energetic processes driving the functional proton pump of bacteriorhodopsin take place in the form of complex molecular dynamic events after excitation of the retinal chromophore into the Franck-Condon state. These early events include a strong electronic polarization, skeletal stretching, and all-trans-to-13-cis isomerization upon formation of the J intermediate. The effectiveness of the photoreaction is ensured by a conical intersection between the electronic excited and ground states, providing highly nonadiabatic coupling to nuclear motions. Here, we study real-time vibrational coherences associated with these motions by analyzing light-induced infrared emission from oriented purple membranes in the 750-1400 cm(-)(1) region. The experimental technique applied is based on second-order femtosecond difference frequency generation on macroscopically ordered samples that also yield information on phase and direction of the underlying motions. Concerted use of several analysis methods resulted in the isolation and characterization of seven different vibrational modes, assigned as C-C stretches, out-of-plane methyl rocks, and hydrogen out-of-plane wags, whereas no in-plane H rock was found. Based on their lifetimes and several other criteria, we deduce that the majority of the observed modes take place on the potential energy surface of the excited electronic state. In particular, the direction sensitivity provides experimental evidence for large intermediate distortions of the retinal plane during the excited-state isomerization process. Copyright © 2011 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Low-power bacteriorhodopsin-silicon n-channel metal-oxide field-effect transistor photoreceiver.

PubMed

Shin, Jonghyun; Bhattacharya, Pallab; Yuan, Hao-Chih; Ma, Zhenqiang; Váró, György

2007-03-01

A bacteriorhodopsin (bR)-silicon n-channel metal-oxide field-effect transistor (NMOSFET) monolithically integrated photoreceiver is demonstrated. The bR film is selectively formed on an external gate electrode of the transistor by electrophoretic deposition. A modified biasing circuit is incorporated, which helps to match the resistance of the bR film to the input impedance of the NMOSFET and to shift the operating point of the transistor to coincide with the maximum gain. The photoreceiver exhibits a responsivity of 4.7 mA/W.

Chromophore orientation in bacteriorhodopsin determined from the angular dependence of deuterium nuclear magnetic resonance spectra of oriented purple membranes.

PubMed

Moltke, S; Nevzorov, A A; Sakai, N; Wallat, I; Job, C; Nakanishi, K; Heyn, M P; Brown, M F

1998-08-25

The orientation of prosthetic groups in membrane proteins is of considerable importance in understanding their functional role in energy conversion, signal transduction, and ion transport. In this work, the orientation of the retinylidene chromophore of bacteriorhodopsin (bR) was investigated using 2H NMR spectroscopy. Bacteriorhodopsin was regenerated with all-trans-retinal stereospecifically deuterated in one of the geminal methyl groups on C1 of the cyclohexene ring. A highly oriented sample, which is needed to obtain individual bond orientations from 2H NMR, was prepared by forming hydrated lamellar films of purple membranes on glass slides. A Monte Carlo method was developed to accurately simulate the 2H NMR line shape due to the distribution of bond angles and the orientational disorder of the membranes. The number of free parameters in the line shape simulation was reduced by independent measurements of the intrinsic line width (1.6 kHz from T2e experiments) and the effective quadrupolar coupling constant (38. 8-39.8 kHz from analysis of the line shape of a powder-type sample). The angle between the C1-(1R)-1-CD3 bond and the purple membrane normal was determined with high accuracy from the simultaneous analysis of a series of 2H NMR spectra recorded at different inclinations of the uniaxially oriented sample in the magnetic field at 20 and -50 degrees C. The value of 68.7 +/- 2.0 degrees in dark-adapted bR was used, together with the previously determined angle of the C5-CD3 bond, to calculate the possible orientations of the cyclohexene ring in the membrane. The solutions obtained from 2H NMR were then combined with additional constraints from linear dichroism and electron cryomicroscopy to obtain the allowed orientations of retinal in the noncentrosymmetric membrane structure. The combined data indicate that the methyl groups on the polyene chain point toward the cytoplasmic side of the membrane and the N-H bond of the Schiff base to the extracellular

Steady-State Characterization of Bacteriorhodopsin-D85N Photocycle

NASA Technical Reports Server (NTRS)

Timucin, Dogan A.; Downie, John D.; Norvig, Peter (Technical Monitor)

1999-01-01

An operational characterization of the photocycle of the genetic mutant D85N of bacteriorhodopsin, BR-D85N, is presented. Steady-state bleach spectra and pump-probe absorbance data are obtained with thick hydrated films containing BR-D85N embedded in a gelatin host. Simple two- and three-state models are used to analyze the photocycle dynamics and extract relevant information such as pure-state absorption spectra, photochemical-transition quantum efficiencies, and thermal lifetimes of dominant states appearing in the photocycle, the knowledge of which should aid in the analysis of optical recording and retrieval of data in films incorporating this photochromic material. The remarkable characteristics of this material and their implications from the viewpoint of optical data storage and processing are discussed.

Cryo-electron microscopy of membrane proteins.

PubMed

Goldie, Kenneth N; Abeyrathne, Priyanka; Kebbel, Fabian; Chami, Mohamed; Ringler, Philippe; Stahlberg, Henning

2014-01-01

Electron crystallography is used to study membrane proteins in the form of planar, two-dimensional (2D) crystals, or other crystalline arrays such as tubular crystals. This method has been used to determine the atomic resolution structures of bacteriorhodopsin, tubulin, aquaporins, and several other membrane proteins. In addition, a large number of membrane protein structures were studied at a slightly lower resolution, whereby at least secondary structure motifs could be identified.In order to conserve the structural details of delicate crystalline arrays, cryo-electron microscopy (cryo-EM) allows imaging and/or electron diffraction of membrane proteins in their close-to-native state within a lipid bilayer membrane.To achieve ultimate high-resolution structural information of 2D crystals, meticulous sample preparation for electron crystallography is of outmost importance. Beam-induced specimen drift and lack of specimen flatness can severely affect the attainable resolution of images for tilted samples. Sample preparations that sandwich the 2D crystals between symmetrical carbon films reduce the beam-induced specimen drift, and the flatness of the preparations can be optimized by the choice of the grid material and the preparation protocol.Data collection in the cryo-electron microscope using either the imaging or the electron diffraction mode has to be performed applying low-dose procedures. Spot-scanning further reduces the effects of beam-induced drift. Data collection using automated acquisition schemes, along with improved and user-friendlier data processing software, is increasingly being used and is likely to bring the technique to a wider user base.

Picosecond molecular motions in bacteriorhodopsin from neutron scattering.

PubMed Central

Fitter, J; Lechner, R E; Dencher, N A

1997-01-01

The characteristics of internal molecular motions of bacteriorhodopsin in the purple membrane have been studied by quasielastic incoherent neutron scattering. Because of the quasihomogeneous distribution of hydrogen atoms in biological molecules, this technique enables one to study a wide variety of intramolecular motions, especially those occurring in the picosecond to nanosecond time scale. We performed measurements at different energy resolutions with samples at various hydration levels within a temperature range of 10-300 K. The analysis of the data revealed a dynamical transition at temperatures Td between 180 K and 220 K for all motions resolved at time scales ranging from 0.1 to a few hundred picoseconds. Whereas below Td the motions are purely vibrational, they are predominantly diffusive above Td, characterized by an enormously broad distribution of correlation times. The variation of the hydration level, on the other hand, mainly affects motions slower than a few picoseconds. PMID:9336208

Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity*

PubMed Central

Hsu, Min-Feng; Fu, Hsu-Yuan; Cai, Chun-Jie; Yi, Hsiu-Pin; Yang, Chii-Shen; Wang, Andrew H.-J.

2015-01-01

Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg82 and Thr201, linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg82–Thr201 hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping. PMID:26483542

The bacteriorhodopsin model membrane system as a prototype molecular computing element.

PubMed

Hong, F T

1986-01-01

The quest for more sophisticated integrated circuits to overcome the limitation of currently available silicon integrated circuits has led to the proposal of using biological molecules as computational elements by computer scientists and engineers. While the theoretical aspect of this possibility has been pursued by computer scientists, the research and development of experimental prototypes have not been pursued with an equal intensity. In this survey, we make an attempt to examine model membrane systems that incorporate the protein pigment bacteriorhodopsin which is found in Halobacterium halobium. This system was chosen for several reasons. The pigment/membrane system is sufficiently simple and stable for rigorous quantitative study, yet at the same time sufficiently complex in molecular structure to permit alteration of this structure in an attempt to manipulate the photosignal. Several methods of forming the pigment/membrane assembly are described and the potential application to biochip design is discussed. Experimental data using these membranes and measured by a tunable voltage clamp method are presented along with a theoretical analysis based on the Gouy-Chapman diffuse double layer theory to illustrate the usefulness of this approach. It is shown that detailed layouts of the pigment/membrane assembly as well as external loading conditions can modify the time course of the photosignal in a predictable manner. Some problems that may arise in the actual implementation and manufacturing, as well as the use of existing technology in protein chemistry, immunology, and recombinant DNA technology are discussed.

Photolytic interruptions of the bacteriorhodopsin photocycle examined by time-resolved resonance raman spectroscopy.

PubMed

Grieger, I; Atkinson, G H

1985-09-24

An investigation of the photolytic conditions used to initiate and spectroscopically monitor the bacteriorhodopsin (BR) photocycle utilizing time-resolved resonance Raman (TR3) spectroscopy has revealed and characterized two photoinduced reactions that interrupt the thermal pathway. One reaction involves the photolytic interconversion of M-412 and M', and the other involves the direct photolytic conversion of the BR-570/K-590 photostationary mixture either to M-412 and M' or to M-like intermediates within 10 ns. The photolytic threshold conditions describing both reactions have been quantitatively measured and are discussed in terms of experimental parameters.

Structural and Functional Studies of a Newly Grouped Haloquadratum walsbyi Bacteriorhodopsin Reveal the Acid-resistant Light-driven Proton Pumping Activity.

PubMed

Hsu, Min-Feng; Fu, Hsu-Yuan; Cai, Chun-Jie; Yi, Hsiu-Pin; Yang, Chii-Shen; Wang, Andrew H-J

2015-12-04

Retinal bound light-driven proton pumps are widespread in eukaryotic and prokaryotic organisms. Among these pumps, bacteriorhodopsin (BR) proteins cooperate with ATP synthase to convert captured solar energy into a biologically consumable form, ATP. In an acidic environment or when pumped-out protons accumulate in the extracellular region, the maximum absorbance of BR proteins shifts markedly to the longer wavelengths. These conditions affect the light-driven proton pumping functional exertion as well. In this study, wild-type crystal structure of a BR with optical stability under wide pH range from a square halophilic archaeon, Haloquadratum walsbyi (HwBR), was solved in two crystal forms. One crystal form, refined to 1.85 Å resolution, contains a trimer in the asymmetric unit, whereas another contains an antiparallel dimer was refined at 2.58 Å. HwBR could not be classified into any existing subgroup of archaeal BR proteins based on the protein sequence phylogenetic tree, and it showed unique absorption spectral stability when exposed to low pH values. All structures showed a unique hydrogen-bonding network between Arg(82) and Thr(201), linking the BC and FG loops to shield the retinal-binding pocket in the interior from the extracellular environment. This result was supported by R82E mutation that attenuated the optical stability. The negatively charged cytoplasmic side and the Arg(82)-Thr(201) hydrogen bond may play an important role in the proton translocation trend in HwBR under acidic conditions. Our findings have unveiled a strategy adopted by BR proteins to solidify their defenses against unfavorable environments and maintain their optical properties associated with proton pumping. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.

Production of functional bacteriorhodopsin by an Escherichia coli cell-free protein synthesis system supplemented with steroid detergent and lipid.

PubMed

Shimono, Kazumi; Goto, Mie; Kikukawa, Takashi; Miyauchi, Seiji; Shirouzu, Mikako; Kamo, Naoki; Yokoyama, Shigeyuki

2009-10-01

Cell-free expression has become a highly promising tool for the efficient production of membrane proteins. In this study, we used a dialysis-based Escherichia coli cell-free system for the production of a membrane protein actively integrated into liposomes. The membrane protein was the light-driven proton pump bacteriorhodopsin, consisting of seven transmembrane alpha-helices. The cell-free expression system in the dialysis mode was supplemented with a combination of a detergent and a natural lipid, phosphatidylcholine from egg yolk, in only the reaction mixture. By examining a variety of detergents, we found that the combination of a steroid detergent (digitonin, cholate, or CHAPS) and egg phosphatidylcholine yielded a large amount (0.3-0.7 mg/mL reaction mixture) of the fully functional bacteriorhodopsin. We also analyzed the process of functional expression in our system. The synthesized polypeptide was well protected from aggregation by the detergent-lipid mixed micelles and/or lipid disks, and was integrated into liposomes upon detergent removal by dialysis. This approach might be useful for the high yield production of functional membrane proteins.

The two consecutive M substates in the photocycle of bacteriorhodopsin are affected specifically by the D85N and D96N residue replacements

NASA Technical Reports Server (NTRS)

Zimanyi, L.; Cao, Y.; Chang, M.; Ni, B.; Needleman, R.; Lanyi, J. K.

1992-01-01

The photocycle of the proton pump bacteriorhodopsin contains two consecutive intermediates in which the retinal Schiff base is unprotonated; the reaction between these states, termed M1 and M2, was suggested to be the switch in the proton transport which reorients the Schiff base from D85 on the extracellular side to D96 on the cytoplasmic side (Varo and Lanyi, Biochemistry 30, 5016-5022, 1991). At pH 10 the absorption maxima of both M1 and M2 could be determined in the recombinant D96N protein. We find that M1 absorbs at 411 nm as do M1 and M2 in wild-type bacteriorhodopsin, but M2 absorbs at 404 nm. Thus, in M2 but not M1 the unprotonated Schiff base is affected by the D96N residue replacement. The connectivity of the Schiff base to D96 in the detected M2 state, but not in M1, is thereby established. On the other hand, the photostationary state which develops during illumination of D85N bacteriorhodopsin contains an M state corresponding to M1 with an absorption maximum shifted to 400 nm, suggesting that this species in turn is affected by D85. These results are consistent with the suggestion that M1 and M2 are pre-switch and post-switch states, respectively.

Pressure dependence of the photocycle kinetics of bacteriorhodopsin.

PubMed Central

Klink, B U; Winter, R; Engelhard, M; Chizhov, I

2002-01-01

The pressure dependence of the photocycle kinetics of bacteriorhodopsin from Halobacterium salinarium was investigated at pressures up to 4 kbar at 25 degrees C and 40 degrees C. The kinetics can be adequately modeled by nine apparent rate constants, which are assigned to irreversible transitions of a single relaxation chain of nine kinetically distinguishable states P(1) to P(9). All states except P(1) and P(9) consist of two or more spectral components. The kinetic states P(2) to P(6) comprise only the two fast equilibrating spectral states L and M. From the pressure dependence, the volume differences DeltaV(o)(LM) between these two spectral states could be determined that range from DeltaV(o)(LM) = -11.4 +/- 0.7 ml/mol (P(2)) to DeltaV(o)(LM) = 14.6 +/- 2.8 mL/mol (P(6)). A model is developed that explains the dependence of DeltaV(o)(LM) on the kinetic state by the electrostriction effect of charges, which are formed and neutralized during the L/M transition. PMID:12496115

Multiplexed Holographic Data Storage in Bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Mehrl, David J.; Krile, Thomas F.

1997-01-01

High density optical data storage, driven by the information revolution, remains at the forefront of current research areas. Much of the current research has focused on photorefractive materials (SBN and LiNbO3) and polymers, despite various problems with expense, durability, response time and retention periods. Photon echo techniques, though promising, are questionable due to the need for cryogenic conditions. Bacteriorhodopsin (BR) films are an attractive alternative recording medium. Great strides have been made in refining BR, and materials with storage lifetimes as long as 100 days have recently become available. The ability to deposit this robust polycrystalline material as high quality optical films suggests the use of BR as a recording medium for commercial optical disks. Our own recent research has demonstrated the suitability of BR films for real time spatial filtering and holography. We propose to fully investigate the feasibility of performing holographic mass data storage in BR. Important aspects of the problem to be investigated include various data multiplexing techniques (e.g. angle- amplitude- and phase-encoded multiplexing, and in particular shift-multiplexing), multilayer recording techniques, SLM selection and data readout using crossed polarizers for noise rejection. Systems evaluations of storage parameters, including access times, memory refresh constraints, erasure, signal-to-noise ratios and bit error rates, will be included in our investigations.

Reaction cycle and thermodynamics in bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Lanyi, J. K.

1992-01-01

Light causes the all-trans to 13-cis isomerization of the retinal in bacteriorhodopsin; the thermal relaxation leading back to the initial state drives proton transport first via proton transfer between the retinal Schiff base and D85 and then between the Schiff base and D96. The reaction sequence and thermodynamics of this photocycle are described by measuring time-resolved absorption changes with a gated multichannel analyzer between 100 ns and 100 ms, at six temperatures between 5 degrees C and 30 degrees C. Analysis of the energetics of the chromophore reaction sequence is on the basis of a recently proposed model (Varo & Lanyi, Biochemistry 30, 5016-5022, 1991) which consists of a single cycle and many reversible reactions: BR -hv-->K<==>L<==>M1-->M2<==>N<==>O-->BR. The existence of the M1-->M2 reaction, which functions as the switch in the proton transfer, is confirmed by spectroscopic evidence. The calculated thermodynamic parameters indicate that the exchange of free energy between the protein and the protons is at the switch step. Further, a large entropy decrease at this reaction suggests a protein conformation change which will conserve delta G for driving the completion of the reaction cycle. The results provide insights to mechanism and energy coupling in this system, with possible relevance to the general question of how ion pumps function.

Systems Issues Pertaining to Holographic Optical Data Storage in Thick Bacteriorhodopsin Films

NASA Technical Reports Server (NTRS)

Downie, John D.; Timucin, Dogan A.; Gary, Charles K.; Oezcan, Meric; Smithey, Daniel T.; Crew, Marshall; Lau, Sonie (Technical Monitor)

1998-01-01

The optical data storage capacity and raw bit-error-rate achievable with thick photochromic bacteriorhodopsin (BR) films are investigated for sequential recording and read- out of angularly- and shift-multiplexed digital holograms inside a thick blue-membrane D85N BR film. We address the determination of an exposure schedule that produces equal diffraction efficiencies among each of the multiplexed holograms. This exposure schedule is determined by numerical simulations of the holographic recording process within the BR material, and maximizes the total grating strength. We also experimentally measure the shift selectivity and compare the results to theoretical predictions. Finally, we evaluate the bit-error-rate of a single hologram, and of multiple holograms stored within the film.

Refractive index of dark-adapted bacteriorhodopsin and tris(hydroxymethyl)aminomethane buffer between 390 and 880 nm.

PubMed

Heiner, Zsuzsanna; Osvay, Károly

2009-08-10

The refractivity of wild-type bacteriorhodopsin (bR(WT)) suspended in tris(hydroxymethyl)aminomethane (TRIS) buffer has been measured in the spectral range of 390-840 nm by the method of angle of minimal deviation with the use of a hollow glass prism. The refractive indices of pure bR(WT) as well as of TRIS buffer have been determined from the concentration dependent refraction values. Sellmeier-type dispersion equations have been fitted for both the TRIS buffer and pure bR(WT).

Bacteriorhodopsin-based photo-electrochemical cell.

PubMed

Chu, Li-Kang; Yen, Chun-Wan; El-Sayed, Mostafa A

2010-10-15

A simple solution-based electrochemical cell has been constructed and successfully employed in the detection of the photoelectric response upon photoexcitation of bacteriorhodopsin (bR) without external bias. Commercially-available indium tin oxide (ITO) glasses served as the optical windows and electrodes. Small amounts of bR suspensions (∼100 μL) were utilized as the photovoltaic medium to generate the proton gradient between two half-cells separated by a molecular porous membrane. Continuous broadband visible light (λ>380 nm) and a short-pulse 532-nm laser were employed for the photoexcitation of bR. Upon the modulated cw broadband irradiation, an instantaneous rise and decay of the current was observed. Our observations of the pH-dependent photocurrent are consistent with previous reports in a bR thin film configuration, which also showed a polarity inversion at pH 5-6. This is due to the change of the priority of the proton release and proton uptake in the photocycle of bR. Studies on the ionic strength effect were also carried out at different KCl concentrations, which resulted in the acceleration of the rise and decay of the photoelectric response. This was accompanied by a decrease in the stationary photocurrent at higher KCl concentrations in the broadband excitation experiments. The solution-based electrochemical cell uses aqueous medium, which is required for the completion of the bR proton pumping function. Due to the generation of the stationary current, it is advantageous to convert solar energy into electricity without the need of film-based photovoltaic devices with external bias. Copyright © 2010 Elsevier B.V. All rights reserved.

Control of retinal isomerization in bacteriorhodopsin in the high-intensity regime

PubMed Central

Florean, Andrei C.; Cardoza, David; White, James L.; Lanyi, J. K.; Sension, Roseanne J.; Bucksbaum, Philip H.

2009-01-01

A learning algorithm was used to manipulate optical pulse shapes and optimize retinal isomerization in bacteriorhodopsin, for excitation levels up to 1.8 × 1016 photons per square centimeter. Below 1/3 the maximum excitation level, the yield was not sensitive to pulse shape. Above this level the learning algorithm found that a Fourier-transform-limited (TL) pulse maximized the 13-cis population. For this optimal pulse the yield increases linearly with intensity well beyond the saturation of the first excited state. To understand these results we performed systematic searches varying the chirp and energy of the pump pulses while monitoring the isomerization yield. The results are interpreted including the influence of 1-photon and multiphoton transitions. The population dynamics in each intermediate conformation and the final branching ratio between the all-trans and 13-cis isomers are modified by changes in the pulse energy and duration. PMID:19564608

Time-resolved structural studies with serial crystallography: A new light on retinal proteins

PubMed Central

Panneels, Valérie; Wu, Wenting; Tsai, Ching-Ju; Nogly, Przemek; Rheinberger, Jan; Jaeger, Kathrin; Cicchetti, Gregor; Gati, Cornelius; Kick, Leonhard M.; Sala, Leonardo; Capitani, Guido; Milne, Chris; Padeste, Celestino; Pedrini, Bill; Li, Xiao-Dan; Standfuss, Jörg; Abela, Rafael; Schertler, Gebhard

2015-01-01

Structural information of the different conformational states of the two prototypical light-sensitive membrane proteins, bacteriorhodopsin and rhodopsin, has been obtained in the past by X-ray cryo-crystallography and cryo-electron microscopy. However, these methods do not allow for the structure determination of most intermediate conformations. Recently, the potential of X-Ray Free Electron Lasers (X-FELs) for tracking the dynamics of light-triggered processes by pump-probe serial femtosecond crystallography has been demonstrated using 3D-micron-sized crystals. In addition, X-FELs provide new opportunities for protein 2D-crystal diffraction, which would allow to observe the course of conformational changes of membrane proteins in a close-to-physiological lipid bilayer environment. Here, we describe the strategies towards structural dynamic studies of retinal proteins at room temperature, using injector or fixed-target based serial femtosecond crystallography at X-FELs. Thanks to recent progress especially in sample delivery methods, serial crystallography is now also feasible at synchrotron X-ray sources, thus expanding the possibilities for time-resolved structure determination. PMID:26798817

Engineering a Robust Photovoltaic Device with Quantum Dots and Bacteriorhodopsin

PubMed Central

2015-01-01

We present a route toward a radical improvement in solar cell efficiency using resonant energy transfer and sensitization of semiconductor metal oxides with a light-harvesting quantum dot (QD)/bacteriorhodopsin (bR) layer designed by protein engineering. The specific aims of our approach are (1) controlled engineering of highly ordered bR/QD complexes; (2) replacement of the liquid electrolyte by a thin layer of gold; (3) highly oriented deposition of bR/QD complexes on a gold layer; and (4) use of the Forster resonance energy transfer coupling between bR and QDs to achieve an efficient absorbing layer for dye-sensitized solar cells. This proposed approach is based on the unique optical characteristics of QDs, on the photovoltaic properties of bR, and on state-of-the-art nanobioengineering technologies. It permits spatial and optical coupling together with control of hybrid material components on the bionanoscale. This method paves the way to the development of the solid-state photovoltaic device with the efficiency increased to practical levels. PMID:25383133

Mechanism by which Untwisting of Retinal Leads to Productive Bacteriorhodopsin Photocycle States

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

Wolter, Tino; Elstner, Marcus; Fischer, Stefan

2014-01-01

Relaxation of the twisted-retinal photoproduct state triggers proton-coupled reaction cycle in retinal proteins. A key open question is whether the retinal relaxation path is governed by the intrinsic torsional properties of the retinal or rather by the interactions of the retinal with protein and water groups, given the crowded protein environments in which the retinal resides. We address this question by performing systematic quantum mechanical/molecular mechanical molecular dynamics computations of retinal dynamics in bacteriorhodopsin at different temperatures, reaction path computations, and assessment of the vibrational fingerprints of the retinal molecule. Our results demonstrate a complex dependence of the retinal dynamicsmore » and preferred geometry on temperature. As the temperature increases, the retinal dihedral angle samples values largely determined by its internal conformational energy. The protein environment shapes the energetics of retinal relaxation and provides hydrogen-bonding partners that stabilize the retinal geometry.« less

The effect of charged lipids on bacteriorhodopsin membrane reconstitution and its photochemical activities

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

Wang Zhen; Bai Jing; Xu Yuhong

2008-07-11

Bacteriorhodopsin (BR) was reconstituted into artificial lipid membrane containing various charged lipid compositions. The proton pumping activity of BR under flash and continuous illumination, proton permeability across membrane, as well as the decay kinetics of the photocycle intermediate M{sub 412} were studied. The results showed that lipid charges would significantly affect the orientation of BR inserted into lipid membranes. In liposomes containing anionic lipids, BRs were more likely to take natural orientation as in living cells. In neutral or positively charged liposomes, most BRs were reversely assembled, assuming an inside out orientation. Moreover, the lipids charges also affect BR's Mmore » intermediate kinetics, especially the slow component in M intermediate decay. The half-life M{sub 412s} increased significantly in BRs in liposomes containing cationic lipids, while decreased in those in anionic liposomes.« less

Hydrogen exchange mass spectrometry of bacteriorhodopsin reveals light-induced changes in the structural dynamics of a biomolecular machine.

PubMed

Pan, Yan; Brown, Leonid; Konermann, Lars

2011-12-21

Many proteins act as molecular machines that are fuelled by a nonthermal energy source. Examples include transmembrane pumps and stator-rotor complexes. These systems undergo cyclic motions (CMs) that are being driven along a well-defined conformational trajectory. Superimposed on these CMs are thermal fluctuations (TFs) that are coupled to stochastic motions of the solvent. Here we explore whether the TFs of a molecular machine are affected by the occurrence of CMs. Bacteriorhodopsin (BR) is a light-driven proton pump that serves as a model system in this study. The function of BR is based on a photocycle that involves trans/cis isomerization of a retinal chromophore, as well as motions of transmembrane helices. Hydrogen/deuterium exchange (HDX) mass spectrometry was used to monitor the TFs of BR, focusing on the monomeric form of the protein. Comparative HDX studies were conducted under illumination and in the dark. The HDX kinetics of BR are dramatically accelerated in the presence of light. The isotope exchange rates and the number of backbone amides involved in EX2 opening transitions increase roughly 2-fold upon illumination. In contrast, light/dark control experiments on retinal-free protein produced no discernible differences. It can be concluded that the extent of TFs in BR strongly depends on photon-driven CMs. The light-induced differences in HDX behavior are ascribed to protein destabilization. Specifically, the thermodynamic stability of the dark-adapted protein is estimated to be 5.5 kJ mol(-1) under the conditions of our work. This value represents the free energy difference between the folded state F and a significantly unfolded conformer U. Illumination reduces the stability of F by 2.2 kJ mol(-1). Mechanical agitation caused by isomerization of the chromophore is transferred to the surrounding protein scaffold, and subsequently, the energy dissipates into the solvent. Light-induced retinal motions therefore act analogously to an internal heat

Combined optical and photoelectric study of the photocycle of 13-cis bacteriorhodopsin.

PubMed Central

Gergely, C; Ganea, C; Váró, G

1994-01-01

The photocycle of the 13-cis retinal containing bacteriorhodopsin was studied by three different techniques. The optical multichannel analyzer monitored the spectral changes during the photocycle and gave information about the number and the spectrum of the intermediates. The absorption kinetic measurements provided the possibility of following the absorbance changes at several characteristic wavelengths. The electric signal provided information about the charge motions during the photocycle. The results reveal the existence of two intermediates in the 13-cis photocycle, one with a short lifetime having an average of 1.7 microseconds and an absorption maximum at 620 nm. The other, a long-living intermediate, has a lifetime of about 50 ms and an absorption maximum around 585 nm. The data analysis suggests that these intermediates are in two parallel branches of the photocycle, and branching from the intermediate with the shorter lifetime might be responsible for the light-adaptation process. PMID:7948698

Cooperativity-regulated parallel pathways of the bacteriorhodopsin photocycle.

PubMed

Tokaji, Z

1995-01-03

The paper demonstrates that the actinic light density dependence of the millisecond part of the bacteriorhodopsin (BR) photocycle at high pH predicts a model, which is the same in the sequence of the intermediates as concluded previously on the basis of double flash experiments [1992, FEBS Lett. 311, 267-270]. This model consists of the Mf-->N-->BR and M(s)-->BR parallel pathways, the relative yields of which are regulated by cooperative interaction of the BR molecules. The decay of M(s) is always slower than the decay of Mf and described as a direct reprotonation of the Schiff-base from the bulk, and the recovery of the ground-state nearly at the same time. M(s) is decomposed into M'f and M's. The first does not reprotonate, and similarly to Mf, it is suggested to be before the conformational change (switch), which latter process would be just before the decay of Mf. A simple way for the determination of the kinetics is also used. This confirms that the amount of N decreases with increasing fraction cycling and shows that the decay rate of N is independent of the fraction cycling. The differences in the kinetics are compared to each other, and they seem to allow a new way of kinetic evaluation at least under special conditions. The aim of this paper was briefly explained in my poster presented on the VIth International Conference on Retinal Protein (see [14]).

Photoisomerization in bacteriorhodopsin studied by FTIR, linear dichroism and photoselection experiments combined with quantum chemical theoretical analysis

NASA Astrophysics Data System (ADS)

Fahmy, K.; Siebert, F.; Großjean, M. F.; Tavan, P.

1989-12-01

Orientations of IR transition moments of the retinal chromophore of bacteriorhodopsin (BR) and of the apo-protein are investigated by FTIR linear dichroism and photoselection measurements. Low temperature difference spectra for the photoinduced transitions of BR to its photocycle intermediates K and L are evaluated using improved methods. Quantum chemical calculations of directions of IR and electronic transition moments of model chromophores are employed to analyze corresponding observations. The chromophore of light-adapted BR 568 is shown to exhibit small (15-30°) twists around the CC single bonds of retinals polyene chain but no large overall helicity (⩽15°). The average retinal plane is demonstrated to form an angle of 90±20° with the plane of the purple membrane. The C 9C 10 double bond of retinal is found approximately parallel to the plane of the membrane. Upon photoisomerization the orientation of the chromophore moiety from C 1 to C 13 is estimated to be largely conserved. The single bond twists of the chromophore in L are shown to be larger than those in BR 568. This result is in agreement with the previous prediction of increased single bond twists in L, which can cause a p K decrease of the chromophore and, thereby, enforce its deprotonation in the L→M transition [Schulten and Tavan, Nature, 272 (1978) 85].

Structured electronic physiotherapy records.

PubMed

Buyl, Ronald; Nyssen, Marc

2009-07-01

With the introduction of the electronic health record, physiotherapists too are encouraged to store their patient records in a structured digital format. The typical nature of a physiotherapy treatment requires a specific record structure to be implemented, with special attention to user-friendliness and communication with other healthcare providers. The objective of this study was to establish a framework for the electronic physiotherapy record and to define a model for the interoperability with the other healthcare providers involved in the patients' care. Although we started from the Belgian context, we used a generic approach so that the results can easily be extrapolated to other countries. The framework we establish here defines not only the different building blocks of the electronic physiotherapy record, but also describes the structure and the content of the exchanged data elements. Through a combined effort by all involved parties, we elaborated an eight-level structure for the electronic physiotherapy record. Furthermore we designed a server-based model for the exchange of data between electronic record systems held by physicians and those held by physiotherapists. Two newly defined XML messages enable data interchange: the physiotherapy prescription and the physiotherapy report. We succeeded in defining a solid, structural model for electronic physiotherapist record systems. Recent wide scale implementation of operational elements such as the electronic registry has proven to make the administrative work easier for the physiotherapist. Moreover, within the proposed framework all the necessary building blocks are present for further data exchange and communication with other healthcare parties in the future. Although we completed the design of the structure and already implemented some new aspects of the electronic physiotherapy record, the real challenge lies in persuading the end-users to start using these electronic record systems. Via a quality label

Nanosecond retinal structure changes in K-590 during the room-temperature bacteriorhodopsin photocycle: picosecond time-resolved coherent anti-stokes Raman spectroscopy.

PubMed

Weidlich, O; Ujj, L; Jäger, F; Atkinson, G H

1997-05-01

Time-resolved vibrational spectra are used to elucidate the structural changes in the retinal chromophore within the K-590 intermediate that precedes the formation of the L-550 intermediate in the room-temperature (RT) bacteriorhodopsin (BR) photocycle. Measured by picosecond time-resolved coherent anti-Stokes Raman scattering (PTR/CARS), these vibrational data are recorded within the 750 cm-1 to 1720 cm-1 spectral region and with time delays of 50-260 ns after the RT/BR photocycle is optically initiated by pulsed (< 3 ps, 1.75 nJ) excitation. Although K-590 remains structurally unchanged throughout the 50-ps to 1-ns time interval, distinct structural changes do appear over the 1-ns to 260-ns period. Specifically, comparisons of the 50-ps PTR/CARS spectra with those recorded with time delays of 1 ns to 260 ns reveal 1) three types of changes in the hydrogen-out-of-plane (HOOP) region: the appearance of a strong, new feature at 984 cm-1; intensity decreases for the bands at 957 cm-1, 952 cm-1, and 939 cm-1; and small changes intensity and/or frequency of bands at 855 cm-1 and 805 cm-1; and 2) two types of changes in the C-C stretching region: the intensity increase in the band at 1196 cm-1 and small intensity changes and/or frequency shifts for bands at 1300 cm-1 and 1362 cm-1. No changes are observed in the C = C stretching region, and no bands assignable to the Schiff base stretching mode (C = NH+) mode are found in any of the PTR/CARS spectra assignable to K-590. These PTR/CARS data are used, together with vibrational mode assignments derived from previous work, to characterize the retinal structural changes in K-590 as it evolves from its 3.5-ps formation (ps/K-590) through the nanosecond time regime (ns/K-590) that precedes the formation of L-550. The PTR/CARS data suggest that changes in the torsional modes near the C14-C15 = N bonds are directly associated with the appearance of ns/K-590, and perhaps with the KL intermediate proposed in earlier studies. These

Nonlinear Optical Properties of Bacteriorhodopsin and Retinal Chromophores and Their Applications for Optical Information Storage and Processing.

NASA Astrophysics Data System (ADS)

Chen, Zhongping

Retinal, a conjugated polyene, plays a crucial role in biology. Both the visual pigments and the energy transducing protein, bacteriorhodopsin (BR) have a form of retinal as their chromophores. Because visual excitation and energy transduction in these systems is initiated by the promotion of retinal to an excited electronic state, information about the excited-state structure of retinal and the effect of chromophore/protein interactions on this structure are essential to understanding the functions of these systems. In this thesis, surface second harmonic (SH) generation is used to measure the light-induced dipole moment changes of a series of retinal derivatives that were designed and synthesized to model specific components of chromophore/protein interactions. In addition, we report an in situ probe of the dipole moment change of the retinal chromophore bound in BR by SH generation from oriented purple membranes. The dipole moment changes of various forms of BR, including light-adapted, dark-adapted, blue, and acid purple membrane, were measured and compared. These results, combined with the results from model compounds, elucidate the effects of the chromophore/protein interactions on light-induced charge redistribution and give insight on the fundamental nature of light excitation and energy storage in SR and rhodopsin. Furthermore, the dependence of the molecular hyperpolarizability of the conjugated molecules on donor/acceptor strength, protonation, conjugate length, planarity, and nonconjugate charges is investigated. Our study shows for the first time that nonconjugated charges have a very large effect on the nonlinear optical properties of conjugated molecules. BR has interesting photochromic characteristics, very large optical nonlinearities, and a unique optoelectrical property where the polarity of the photovoltage depends on both its photochromic state and the excitation wavelength. These unique characteristics coupled with its high stability make BR

The Integration of Bacteriorhodopsin Proteins with Semiconductor Heterostructure Devices

NASA Astrophysics Data System (ADS)

Xu, Jian

2008-03-01

Bioelectronics has emerged as one of the most rapidly developing fields among the active frontiers of interdisciplinary research. A major thrust in this field is aimed at the coupling of the technologically-unmatched performance of biological systems, such as neural and sensing functions, with the well developed technology of microelectronics and optoelectronics. To this end we have studied the integration of a suitably engineered protein, bacteriorhodopsin (BR), with semiconductor optoelectronic devices and circuits. Successful integration will potentially lead to ultrasensitive sensors with polarization selectivity and built-in preprocessing capabilities that will be useful for high speed tracking, motion and edge detection, biological detection, and artificial vision systems. In this presentation we will summarize our progresses in this area, which include fundamental studies on the transient dynamics of photo-induced charge shift in BR and the coupling mechanism at protein-semiconductor interface for effective immobilizing and selectively integrating light sensitive proteins with microelectronic devices and circuits, and the device engineering of BR-transistor-integrated optical sensors as well as their applications in phototransceiver circuits. Work done in collaboration with Pallab Bhattacharya, Jonghyun Shin, Department of Electrical Engineering and Computer Science, University of Michigan, Ann Arbor, MI; Robert R. Birge, Department of Chemistry, University of Connecticut, Storrs, CT 06269; and György V'ar'o, Institute of Biophysics, Biological Research Center of the Hungarian Academy of Science, H-6701 Szeged, Hungary.

FTIR Studies of Internal Water Molecules of Bacteriorhodopsin: Structural Analysis of Halide-bound D85S and D212N Mutants in the Schiff Base Region

NASA Astrophysics Data System (ADS)

Shibata, Mikihiro; Kandori, Hideki

2007-12-01

Bacteriorhodopsin (BR), a membrane protein found in Halobacterium salinarum, functions as a light-driven proton pump. The Schiff base region has a quadropolar structure with positive charges located at the protonated Schiff base and Arg82, and counterbalancing negative charges located at Asp85 and Asp212 (Figure 1A). It is known that BR lacks a proton-pumping activity if Asp85 or Asp212 is neutralized by mutation. On the other hand, binding of C1- brings different effects for pumping functions in mutants at D85 and D212 position. While C1--bound D85T and D85S pump C1-, photovoltage measurements suggested that C1--bound D212N pumps protons at low pH. In this study, we measured low-temperature FTIR spectra of D85S and D212N containing various halides to compare the halide binding site of both proteins. In the case of D85S, the N-D stretching vibrations of the Schiff base were halide-dependent. This result suggests that the halide is a hydrogen-bond acceptor of the Schiff base, being consistent with the X-ray crystal structure. On the other hand, no halide dependence was observed for vibrational bands of the retinal skeleton and the Schiff base in the D212N mutant. This result suggests that the halide does not form a hydrogen bond with the Schiff base directly, unlike the mutation at D85 position. Halide-dependent water bands in the Schiff base region also differ between D85S and D212N. From these results, halide binding site of both proteins and role of two negative charges in BR will be discussed.

Spontaneous stacking of purple membranes during immobilization with physical cross-linked poly(vinyl alcohol) hydrogel with retaining native-like functionality of bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Yokoyama, Yasunori; Tanaka, Hikaru; Yano, Shunsuke; Takahashi, Hiroshi; Kikukawa, Takashi; Sonoyama, Masashi; Takenaka, Koshi

2017-05-01

We previously discovered the correlation between light-induced chromophore color change of a photo-receptor membrane protein bacteriorhodopsin (bR) and its two-dimensional crystalline state in the membrane. To apply this phenomenon to a novel optical memory device, it is necessary that bR molecules are immobilized as maintaining their structure and functional properties. In this work, a poly(vinyl alcohol) (PVA) hydrogel with physical cross-linkages (hydrogen bonds between PVA chains) that resulted from repeated freezing-and-thawing (FT) cycles was used as an immobilization medium. To investigate the effects of physically cross-linked PVA gelation on the structure and function of bR in purple membranes (PMs), spectroscopic techniques were employed against PM/PVA immobilized samples prepared with different FT cycle numbers. Visible circular dichroism spectroscopy strongly suggested PM stacking during gelation. X-ray diffraction data also indicated the PM stacking as well as its native-like crystalline lattice even after gelation. Time-resolved absorption spectroscopy showed that bR photocycle behaviors in PM/PVA immobilized samples were almost identical to that in suspension. These results suggested that a physically cross-linked PVA hydrogel is appropriate for immobilizing membrane proteins in terms of maintaining their structure and functionality.

Rapid pH change due to bacteriorhodopsin measured with a tin-oxide electrode.

PubMed Central

Robertson, B; Lukashev, E P

1995-01-01

The photocurrent transient generated by bacteriorhodopsin (bR) on a tin-oxide electrode is due to pH change and not to charge displacement as previously assumed. Films of either randomly oriented or highly oriented purple membranes were deposited on transparent electrodes made of tin-oxide-coated glass. The membranes contained either wild-type or D96N-mutant bR. When excited with yellow light through the glass, the bR pumps protons across the membrane. The result is a rapid local pH change as well as a charge displacement. Experiments with these films show that it is the pH change rather than the displacement that produces the current transient. The calibration for the transient pH measurement is given. The sensitivity of a tin-oxide electrode to a transient pH change is very much larger than its sensitivity to a steady-state pH change. PMID:7787036

Thermal transfer structures coupling electronics card(s) to coolant-cooled structure(s)

DOEpatents

David, Milnes P; Graybill, David P; Iyengar, Madhusudan K; Kamath, Vinod; Kochuparambil, Bejoy J; Parida, Pritish R; Schmidt, Roger R

2014-12-16

Cooling apparatuses and coolant-cooled electronic systems are provided which include thermal transfer structures configured to engage with a spring force one or more electronics cards with docking of the electronics card(s) within a respective socket(s) of the electronic system. A thermal transfer structure of the cooling apparatus includes a thermal spreader having a first thermal conduction surface, and a thermally conductive spring assembly coupled to the conduction surface of the thermal spreader and positioned and configured to reside between and physically couple a first surface of an electronics card to the first surface of the thermal spreader with docking of the electronics card within a socket of the electronic system. The thermal transfer structure is, in one embodiment, metallurgically bonded to a coolant-cooled structure and facilitates transfer of heat from the electronics card to coolant flowing through the coolant-cooled structure.

Vibrational spectrum of the K-590 intermediate in the bacteriorhodopsin photocycle at room temperature: picosecond time-resolved resonance coherent anti-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Ujj, L.; Jäger, F.; Popp, A.; Atkinson, G. H.

1996-12-01

The vibrational spectrum of the K-590 intermediate, thought to contribute significantly to the energy storage and transduction mechanism in the bacteriorhodopsin (BR) photocycle, is measured at room temperature using picosecond time-resolved resonance coherent anti-Stokes Raman scattering (PTR/CARS). The room-temperature BR photocycle is initiated by the 3 ps, 570 nm excitation of the ground-state species, BR-570, prepared in both H 2O and D 2O suspensions of BR. PTR/CARS data, recorded 50 ps after BR-570 excitation, at which time only BR-570 and K-590 are present, have an excellent S/N which provides a significantly more detailed view of the K-590 vibrational degrees of freedom than previously available. Two picosecond (6 ps FWHM) laser pulses, ω1 (633.4 nm) and ωS (675-700 nm), are used to record PTR/CARS data via electronic resonance enhancement in both BR-570 and K-590, each of which contains a distinct retinal structure (assigned as 13- rans, 15- anti, 13- cis, respectively). To obtain the vibrational spectrum of K-590 separately, the PTR/CARS spectra from the mixture of isomeric retinals is quantitatively analyzed in terms of third-order susceptibility ( η(3)) relationships. PTR/CARS spectra of K-590 recorded from both H 2O and D 2O suspensions of BR are compared with the analogous vibrational data obtained via spontaneous resonance Raman (RR) scattering at both low (77 K) and room temperature. Analyses of these vibrational spectra identify temperature-dependent effects and changes assignable to the substitution of deuterium at the Schiff-base nitrogen not previously reported.

Structures of aspartic acid-96 in the L and N intermediates of bacteriorhodopsin: analysis by Fourier transform infrared spectroscopy

NASA Technical Reports Server (NTRS)

Maeda, A.; Sasaki, J.; Shichida, Y.; Yoshizawa, T.; Chang, M.; Ni, B.; Needleman, R.; Lanyi, J. K.

1992-01-01

The light-induced difference Fourier transform infrared spectrum between the L or N intermediate minus light-adapted bacteriorhodopsin (BR) was measured in order to examine the protonated states and the changes in the interactions of carboxylic acids of Asp-96 and Asp-115 in these intermediates. Vibrational bands due to the protonated and unprotonated carboxylic acid were identified by isotope shift and band depletion upon substitution of Asp-96 or -115 by asparagine. While the signal due to the deprotonation of Asp-96 was clearly observed in the N intermediate, this residue remained protonated in L. Asp-115 was partially deprotonated in L. The C = O stretching vibration of protonated Asp-96 of L showed almost no shift upon 2H2O substitution, in contrast to the corresponding band of Asp-96 or Asp-115 of BR, which shifted by 9-12 cm-1 under the same conditions. In the model system of acetic acid in organic solvents, such an absence of the shift of the C = O stretching vibration of the protonated carboxylic acid upon 2H2O substitution was seen only when the O-H of acetic acid is hydrogen-bonded. The non-hydrogen-bonded monomer showed the 2H2O-dependent shift. Thus, the O-H bond of Asp-96 enters into hydrogen bonding upon conversion of BR to L. Its increased hydrogen bonding in L is consistent with the observed downshift of the O-H stretching vibration of the carboxylic acid of Asp-96.

Studying the spatial organization of membrane proteins by means of tritium stratigraphy: bacteriorhodopsin in purple membrane.

PubMed

Shishkov, A V; Ksenofontov, A L; Bogacheva, E N; Kordyukova, L V; Badun, G A; Alekseevsky, A V; Tsetlin, V I; Baratova, L A

2002-05-15

The topography of bacteriorhodopsin (bR) in situ was earlier studied by using the tritium bombardment approach [Eur. J. Biochem. 178 (1988) 123]. Now, having the X-ray crystallography data of bR at atom resolution [Proc. Natl. Acad. Sci. 95 (1998) 11673], we estimated the influence of membrane environment (lipid and protein) on tritium incorporation into amino acid residues forming transmembrane helices. We have determined the tritium flux attenuation coefficients for residues 10-29 of helix A. They turned out to be low (0.04+/-0.02 A(-1)) for residues adjacent to the lipid matrix, and almost fourfold higher (0.15+/-0.05 A(-1)) for those oriented to the neighboring transmembrane helices. We believe that tritium incorporation data could help modeling transmembrane segment arrangement in the membrane.

Time-resolved absorbance changes induced by fast acidification of bacteriorhodopsin in vesicle systems.

PubMed Central

Druckmann, S; Ottolenghi, M; Korenstein, R

1985-01-01

The direction of the accessibility to protons of the binding site in bacteriorhodopsin is of primary importance in elucidating the proton-pump mechanism. The problem is approached via the pH-dependent equilibrium bR560 in equilibrium bR605 in vesicles with preferentially oriented purple membranes. Fast acidification (stopped-flow) experiments with inside-out, monomeric, bR vesicles were carried out with and without a buffer enclosed in the vesicle interior. The results, showing a buffer-induced delay in the formation of bR605, indicate that the binding site is accessible to protons from the inside of the vesicles. We arrive at this conclusion also by working with inside-out trimeric vesicles in the presence and in the absence of H+ (and K+) ionophores. The results suggest that in Halobacterium halobium, the binding site and thus the retinal Schiff base are exposed to the outside of the cell. This conclusion is consistent with a pumping mechanism based on a light-induced pK change. PMID:3978185

Using Haloarcula marismortui Bacteriorhodopsin as a Fusion Tag for Enhancing and Visible Expression of Integral Membrane Proteins in Escherichia coli

PubMed Central

Hsu, Min-Feng; Yu, Tsung-Fu; Chou, Chia-Cheng; Fu, Hsu-Yuan; Yang, Chii-Shen; Wang, Andrew H. J.

2013-01-01

Membrane proteins are key targets for pharmacological intervention because of their vital functions. Structural and functional studies of membrane proteins have been severely hampered because of the difficulties in producing sufficient quantities of properly folded and biologically active proteins. Here we generate a high-level expression system of integral membrane proteins in Escherichia coli by using a mutated bacteriorhodopsin (BR) from Haloarcula marismortui (HmBRI/D94N) as a fusion partner. A purification strategy was designed by incorporating a His-tag on the target membrane protein for affinity purification and an appropriate protease cleavage site to generate the final products. The fusion system can be used to detect the intended target membrane proteins during overexpression and purification either with the naked eye or by directly monitoring their characteristic optical absorption. In this study, we applied this approach to produce two functional integral membrane proteins, undecaprenyl pyrophosphate phosphatase and carnitine/butyrobetaine antiporter with significant yield enhancement. This technology could facilitate the development of a high-throughput strategy to screen for conditions that improve the yield of correctly folded target membrane proteins. Other robust BRs can also be incorporated in this system. PMID:23457558

FTIR spectroscopic study on individual amino acid residues in the proton pumping process of bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Liu, Xiaomei

1998-05-01

My thesis project has concentrated on clarifying the role of individual amino acids such as tyrosine, arginine and threonine in the active proton transferring process of Bacteriorhodopsin(bR). BR is a protein found in the purple membrane of Halobacteria salinarium. The main function of bR is to transfer a proton from the interior side of the cell to the external medium upon illumination by visible light. BR belongs to a family of retinal- containing membrane proteins which includes rhodopsin, a visual receptor found in the eye, and sensory rhodopsin I, a light receptor for phototaxis found in H. salinarium. Complete understanding of the proton transferring mechanism of bR can help explain the energy transduction and active ion transport in biological systems. This information also provides insight into other members of the retinal-containing protein family. To study the behavior of a single amino acid in a protein which consists of 248 amino acids, I employed the Fourier transform infrared (FTIR) difference spectroscopy technique. This was combined with the recently developed genetic engineering method of site directed isotope labeling (SDIL). As complementary work, I also characterized the vibrational properties of individual amino acids in various environments. Because of the high resolution and sensitivity of FTIR difference spectroscopy, along with the ability of SDIL to detect structural changes at the single amino acid level, we are able to determine changes in the structure of specific amino acids at different steps in bR photocycle. My research results provide strong evidence for a proton pump model. This model predicts the participation of tyrosine 185 and one or more threonines in a hydrogen bonded chain which can transfer proton across the membrane. My data also suggest a more accurate model for the proton release step which involves arginine 82.

Electronics for Piezoelectric Smart Structures

NASA Technical Reports Server (NTRS)

Warkentin, D. J.; Tani, J.

1997-01-01

This paper briefly presents work addressing some of the basic considerations for the electronic components used in smart structures incorporating piezoelectric elements. After general remarks on the application of piezoelectric elements to the problem of structural vibration control, three main topics are described. Work to date on the development of techniques for embedding electronic components within structural parts is presented, followed by a description of the power flow and dissipation requirements of those components. Finally current work on the development of electronic circuits for use in an 'active wall' for acoustic noise is introduced.

Photochemical cycle of bacteriorhodopsin studied by resonance Raman spectroscopy.

PubMed

Stockburger, M; Klusmann, W; Gattermann, H; Massig, G; Peters, R

1979-10-30

Individual species of the photochemical cycle of bacteriorhodopsin, a retinal-protein complex of Halobacteria, were studied in aqueous suspensions of the "purple membrane" at room temperature by resonance Raman (RR) spectroscopy with flow systems. Two pronounced deuterium shifts were found in the RR spectra of the all-trans complex BR-570 in H2O-D2O suspensions. The first is ascribed to C=NH+ (C=ND+) stretching vibrations of the protonated Schiff base which links retinal to opsin. The second is assigned tentatively to an "X-H" ("X-D") bending mode, where "X" is an atom which carries an exchangeable proton. A RR spectrum of the 13-cis-retinal complex "BR-548" could be deduced from spectra of the dark-adapted purple membrane. The RR spectrum of the M-412 intermediate was monitored in a double-beam pump-probe experiment. The main vibrational features of the intermediate M' in the reaction M-412 in equilibrium hv M' leads to delta BR-570 could be deduced from a photostationary mixture of M-412 and M'. Difference procedures were applied to obtain RR spectra of the L-550 intermediate and of two new long-lived species, R1'-590 and R2-550. From kinetic data it is suggested that T1'-590 links the proton-translocating cycle to the "13-cis" cycle of BR-548. The protonation and isomeric states of the different species are discussed in light of the new spectroscopic and kinetic data. It is found that conformational changes during the photochemical cycle play an important role.

Fingerprint-Based Structure Retrieval Using Electron Density

PubMed Central

Yin, Shuangye; Dokholyan, Nikolay V.

2010-01-01

We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo-electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to simple fingerprint comparison. Using this approach, we are able to screen the entire Protein Data Bank and identify structures that fit two experimental electron densities determined by cryo-electron microscopy. PMID:21287628

Characterization and photochemistry of 13-desmethyl bacteriorhodopsin.

PubMed

Gillespie, Nathan B; Ren, Lei; Ramos, Lavoisier; Daniell, Heather; Dews, Deborah; Utzat, Karissa A; Stuart, Jeffrey A; Buck, Charles H; Birge, Robert R

2005-08-25

The photochemistry of the 13-desmethyl (DM) analogue of bacteriorhodopsin (BR) is examined by using spectroscopy, molecular orbital theory, and chromophore extraction followed by conformational analysis. The removal of the 13-methyl group permits the direct photochemical formation of a thermally stable, photochemically reversible state, P1(DM) (lambda(max) = 525 nm), which can be generated efficiently by exciting the resting state, bR(DM) with yellow or red light (lambda > 590 nm). Chromophore extraction analysis reveals that the retinal configuration in P1(DM) is 9-cis, identical to that of the retinal configuration in the native BR P1 state. Fourier transform infrared and Raman experiments on P1(DM) indicate an anti configuration around the C15=N bond, as would be expected of an O-state photoproduct. However, low-temperature spectroscopy and ambient, time-resolved studies indicate that the P1(DM) state forms primarily via thermal relaxation from the L(D)(DM) state. Theoretical studies on the BR binding site show that 13-dm retinal is capable of isomerizing into a 9-cis configuration with minimal steric hindrance from surrounding residues, in contrast to the native chromophore in which surrounding residues significantly obstruct the corresponding motion. Analysis of the photokinetic experiments indicates that the Arrhenius activation energy of the bR(DM) --> P1(DM) transition in 13-dm-BR is less than 0.6 kcal/mol (vs 22 +/-5 kcal/mol measured for the bR --> P (P1 and P2) reaction in 85:15 glycerol:water suspensions of wild type). Consequently, the P1(DM) state in 13-dm-BR can form directly from all-trans, 15-anti intermediates (bR(DM) and O(DM)) or all-trans, 15-syn (K(D)(DM)/L(D)(DM)) intermediates. This study demonstrates that the 13-methyl group, and its interactions with nearby binding site residues, is primarily responsible for channeling one-photon photochemical and thermal reactions and is limited to the all-trans and 13-cis species interconversions in the

Fingerprint-based structure retrieval using electron density.

PubMed

Yin, Shuangye; Dokholyan, Nikolay V

2011-03-01

We present a computational approach that can quickly search a large protein structural database to identify structures that fit a given electron density, such as determined by cryo-electron microscopy. We use geometric invariants (fingerprints) constructed using 3D Zernike moments to describe the electron density, and reduce the problem of fitting of the structure to the electron density to simple fingerprint comparison. Using this approach, we are able to screen the entire Protein Data Bank and identify structures that fit two experimental electron densities determined by cryo-electron microscopy. Copyright © 2010 Wiley-Liss, Inc.

Transient Fourier holography with bacteriorhodopsin films for breast cancer diagnostics

NASA Astrophysics Data System (ADS)

Rao, Devulapalli; Kothapalli, Sri-Rajasekar; Wu, Pengfei; Yelleswarapu, Chandra

X-ray mammography is the current gold standard for breast cancer screening. Microcalcifications and other features which are helpful to the radiologist for early diagnostics are often buried in the noise generated by the surrounding dense tissue. So image processing techniques are required to enhance these important features to improve the sensitivity of detection. An innovative technique is demonstrated for recording a hologram of the mammogram. It is recorded on a thin polymer film of Bacteriorhodopsin (bR) as photo induced isomerization grating containing the interference pattern between the object beam containing the Fourier spatial frequency components of the mammogram and a reference beam. The hologram contains all the enhanced features of the mammogram. A significant innovation of the technique is that the enhanced components in the processed image can be viewed by the radiologist in time scale. A technician can record the movie and when the radiologist looks at the movie at his convenience, freezing the frame as and when desired, he would see the microcalcifications as the brightest and last long in time. He would also observe lesions with intensity decreasing as their size increases. The same bR film can be used repeatedly for recording holograms with different mammograms. The technique is versatile and a different frequency band can be chosen to be optimized by changing the reference beam intensity. The experimental arrangement can be used for mammograms in screen film or digital format.

Effects of tyrosine-26 and tyrosine-64 nitration on the photoreactions of bacteriorhodopsin

NASA Technical Reports Server (NTRS)

Scherrer, P.; Stoeckenius, W.

1985-01-01

The photoreactions of nitrated bacteriorhodopsin (bR) are examined. Flash-induced difference spectra of bR, bR with aminotyrosine in position 26 (bR-N26R) and bR with aminotyrosine in position 64 are analyzed. It is observed that changes in the actinic wavelength (from 520 to 500 or 580 nm) have no affect on the shape of the spectra and the formation and decay kinetics of the O and M intermediates. Nitration of tyrosine-64 decreases the chromophore absorbance, shifts the absorption maximum to 535 nm, and affects photocycle kinetics independent of the pK of its phenolic group. Light-dark adaptation spectra for bR are studied. The kinetics of the M and O intermediates in bR with nitrotyrosine in position 64 (bR-N64) and bR with aminotyrosine in position 64 and bR with nitrotyrosine in position 26 and bR-N26R are described and compared to bR; the pH dependence and M and O decay rates are considered. The deprotonation of bR-N64 during the photoreaction cycle and the effects of nitration on the activity of proton pumping are investigated.

All-optical switching based on optical fibre long period gratings modified bacteriorhodopsin

NASA Astrophysics Data System (ADS)

Korposh, S.; James, S.; Partridge, M.; Sichka, M.; Tatam, R.

2018-05-01

All-optical switching using an optical fibre long-period gating (LPG) modified with bacteriorhodopsin (bR) is demonstrated. The switching process is based on the photo-induced RI change of bR, which in turn changes the phase matching conditions of the mode coupling by the LPG, leading to modulation of the propagating light. The effect was studied with an LPG immersed into a bR solution and with LPGs coated with the bR films, deposited onto the LPGs using the layer-by-layer electrostatic self-assembly (LbL) method. The dependence of the all-optical switching efficiency upon the concentration of the bR solution and on the grating period of the LPG was also studied. In addition, an in-fibre Mach-Zehnder interferometer (MZI) composed of a cascaded LPG pair separated by 30 mm and modified with bR was used to enhance the wavelength range of all-optical switching. The switching wavelength is determined by the grating period of the LPG. Switching efficiencies of 16% and 35% were observed when an LPG and an MZI were immersed into bR solutions, respectively. The switching time for devices coated with bR-films was within 1 s, 10 times faster than that observed for devices immersed into bR solution.

Electronic Structure of Semiconductor Interfaces.

DTIC Science & Technology

1984-11-01

Workshop on Effective One-Electron Potentials In Real Materials, Ossining , New York, Mar. 21-22, 1980 Member, Organizing Committee, Annual Conferences on...Workshop on Effective One-Electron Potentials in Real Materials, Ossining , New York, Mar. 21-22, 1980 (Invited Paper) Electronic Structure of

Structural changes due to the deprotonation of the proton release group in the M-photointermediate of bacteriorhodopsin as revealed by time-resolved FTIR spectroscopy.

PubMed

Morgan, Joel E; Vakkasoglu, Ahmet S; Lugtenburg, Johan; Gennis, Robert B; Maeda, Akio

2008-11-04

One of the steps in the proton pumping cycle of bacteriorhodopsin (BR) is the release of a proton from the proton-release group (PRG) on the extracellular side of the Schiff base. This proton release takes place shortly after deprotonation of the Schiff base (L-to-M transition) and results in an increase in the pKa of Asp85, which is a crucial mechanistic step for one-way proton transfer for the entire photocycle. Deprotonation of the PRG can also be brought about without photoactivation, by raising the pH of the enzyme (pKa of PRG; approximately 9). Thus, comparison of the FTIR difference spectrum for formation of the M intermediate (M minus initial unphotolyzed BR state) at pH 7 to the corresponding spectrum generated at pH 10 may reveal structural changes specifically associated with deprotonation of the PRG. Vibrational bands of BR that change upon M formation are distributed across a broad region between 2120 and 1685 cm(-1). This broad band is made up of two parts. The band above 1780 cm(-1), which is insensitive to C15-deuteration of the retinal, may be due to a proton delocalized in the PRG. The band between 1725 and 1685 cm(-1), on the lower frequency side of the broad band, is sensitive to C15-deuteration. This band may arise from transition dipole coupling of the vibrations of backbone carbonyl groups in helix G with the side chain of Tyr57 and with the C15H of the Schiff base. In M, these broad bands are abolished, and the 3657 cm(-1) band, which is due to the disruption of the hydrogen bonding of a water molecule, probably with Arg82, appears. Loss of the interaction of the backbone carbonyl groups in helix G with Tyr57 and the Schiff base, and separation of Tyr57 from Arg82, may be causes of these spectral changes, leading to the stabilization of the protonated Asp85 in M.

Proteins as "dopable" bio-electronic materials

NASA Astrophysics Data System (ADS)

Cahen, David

2013-02-01

Proteins are surprisingly good solid-state electronic conductors. This holds also for proteins without any known biological electron transfer function. How do they do it? To answer this question we measure solid-state electron transport (ETp) across proteins that are "dry" (only tightly bound water, to retain the conformation, still present). We compare results for the electron transfer (ET) protein, Azurin (Az), the proton-pumping membrane protein Bacteriorhodopsin (bR), and for Human and Bovine Serum Albumin (HSA and BSA). Clear differences between these proteins are seen, which preserve their structure in the solid state measurement configuration. Importantly for future bioelectronics, the results are sensitive to protein modification, e.g., removing or disconnecting the retinal in bR and removing or replacing the Cu redox centre in Az. These cofactors can thus be viewed as natural dopants for proteins. Insight in the ETp mechanism comes from temperature-dependent studies. Az shows 40-360K temperature-independent ETp across its 3.5 nm long axis, until its denaturation temperature, indicative of tunneling. Cu removal, replacement (by Zn) or deuteration changes this to thermally activated ETp. This suggests hopping and involvement of the amide backbone in the ETp. The latter, which rhymes with indications from ETp experiments on oligopeptide and simulations of ET in proteins, opens the way for modeling what otherwise is an awfully complex system. Below 200K all proteins and their variants show temperature-independent ETp. We can furthermore make a totally electrically inactive protein, HSA, into an efficient ETp medium by doping it with natural poly-ene. Putting our data in perspective by comparing them to all known protein ETp data in the literature, we conclude that, in general, proteins are well described as dopable molecular wires.

Defect Induced Electronic Structure of Uranofullerene

PubMed Central

Dai, Xing; Cheng, Cheng; Zhang, Wei; Xin, Minsi; Huai, Ping; Zhang, Ruiqin; Wang, Zhigang

2013-01-01

The interaction between the inner atoms/cluster and the outer fullerene cage is the source of various novel properties of endohedral metallofullerenes. Herein, we introduce an adatom-type spin polarization defect on the surface of a typical endohedral stable U2@C60 to predict the associated structure and electronic properties of U2@C61 based on the density functional theory method. We found that defect induces obvious changes in the electronic structure of this metallofullerene. More interestingly, the ground state of U2@C61 is nonet spin in contrast to the septet of U2@C60. Electronic structure analysis shows that the inner U atoms and the C ad-atom on the surface of the cage contribute together to this spin state, which is brought about by a ferromagnetic coupling between the spin of the unpaired electrons of the U atoms and the C ad-atom. This discovery may provide a possible approach to adapt the electronic structure properties of endohedral metallofullerenes. PMID:23439318

Coordinating the Structural Rearrangements Associated with Unidirectional Proton Transfer in the Bacteriorhodopsin Photocycle Induced by Deprotonation of the Proton-Release Group: A Time-Resolved Difference FTIR Spectroscopic Study†

PubMed Central

Morgan, Joel E.; Vakkasoglu, Ahmet S.; Lanyi, Janos K.; Gennis, Robert B.; Maeda, Akio

2014-01-01

In the photocycle of bacteriorhodopsin at pH 7, proton release from the proton releasing group (PRG) to the extracellular medium occurs during formation of the M intermediate. This proton release is inhibited at acidic pH, below the pKa of the PRG, ∼6 in M, and instead occurs later in the cycle as the initial state is restored from the O intermediate. Here, structural changes related to deprotonation of the PRG have been investigated by time-resolved FTIR spectroscopy at 25°C. The vibrational features at 2100-1790 cm-1, 1730-1685 cm-1, 1661 cm-1, and 1130-1045 cm-1 have greater negative intensity in the pure M-minus-BR spectrum and even in the M-minus-BR spectrum, that is present earlier together with the L-minus-BR spectrum, at pH 7, than in the corresponding M-minus-BR spectra at pH 5 or pH 4. The D212N mutation abolishes the decreases in the intensities of the broad feature between 1730 and 1685 cm-1 and the band at 1661 cm-1. The 1730-1685 cm-1 feature may arise from transition dipole coupling of the backbone carbonyl groups of Glu204, Phe208, Asp212 and Lys216 interacting with Tyr57 and C15-H of the chromophore. The 1661 cm-1 band, which is insensitive to D2O substitution, may arise by interaction of the backbone carbonyl of Asp212 with C15-H. The 2100-1790 cm-1 feature with a trough at 1885 cm-1 could be due to a water cluster. Depletion of these bands upon deprotonation of the PRG is attributable to disruption of a coordinated structure, held in place by interactions of Asp212. Deprotonation of the PRG is accompanied also by disruption of the interaction of the water molecule near Arg82. The liberated Asp212 may stabilize the protonated state of Asp85, and thus confer uni-directionality to the transport. PMID:20232848

Electronic structure of lead pyrophosphate

NASA Astrophysics Data System (ADS)

Suewattana, Malliga; Singh, David

2007-03-01

Lead Pyrophosphate Pb2P2O7 is of interest for potential radiation detection applications and use in long term waste storage. It forms in triclinic P1 crystals and can also be grown as glasses. We performed electronic structure calculations using the crystal structure which determined by Mullica et. al (J. Solid State Chem (1986)) using x-ray diffraction and found large forces on atoms suggesting that the refined atomic positions were not fully correct. Here we report first principles structure relaxation and a revised crystal structure for this compound. We analyze the resulting structure using pair distribution functions and discuss the implications for the electronic properties. This work was supported by DOE NA22 and the Office of Naval Research.

The CECAM Electronic Structure Library: community-driven development of software libraries for electronic structure simulations

NASA Astrophysics Data System (ADS)

Oliveira, Micael

The CECAM Electronic Structure Library (ESL) is a community-driven effort to segregate shared pieces of software as libraries that could be contributed and used by the community. Besides allowing to share the burden of developing and maintaining complex pieces of software, these can also become a target for re-coding by software engineers as hardware evolves, ensuring that electronic structure codes remain at the forefront of HPC trends. In a series of workshops hosted at the CECAM HQ in Lausanne, the tools and infrastructure for the project were prepared, and the first contributions were included and made available online (http://esl.cecam.org). In this talk I will present the different aspects and aims of the ESL and how these can be useful for the electronic structure community.

Deriving the intermediate spectra and photocycle kinetics from time-resolved difference spectra of bacteriorhodopsin. The simpler case of the recombinant D96N protein

NASA Technical Reports Server (NTRS)

Zimanyi, L.; Lanyi, J. K.

1993-01-01

The bacteriorhodopsin photocycle contains more than five spectrally distinct intermediates, and the complexity of their interconversions has precluded a rigorous solution of the kinetics. A representation of the photocycle of mutated D96N bacteriorhodopsin near neutral pH was given earlier (Varo, G., and J. K. Lanyi. 1991. Biochemistry. 30:5008-5015) as BRhv-->K<==>L<==>M1-->M2--> BR. Here we have reduced a set of time-resolved difference spectra for this simpler system to three base spectra, each assumed to consist of an unknown mixture of the pure K, L, and M difference spectra represented by a 3 x 3 matrix of concentration values between 0 and 1. After generating all allowed sets of spectra for K, L, and M (i.e., M1 + M2) at a 1:50 resolution of the matrix elements, invalid solutions were eliminated progressively in a search based on what is expected, empirically and from the theory of polyene excited states, for rhodopsin spectra. Significantly, the average matrix values changed little after the first and simplest of the search criteria that disallowed negative absorptions and more than one maximum for the M intermediate. We conclude from the statistics that during the search the solutions strongly converged into a narrow region of the multidimensional space of the concentration matrix. The data at three temperatures between 5 and 25 degrees C yielded a single set of spectra for K, L, and M; their fits are consistent with the earlier derived photocycle model for the D96N protein.

Scattering of an electronic wave packet by a one-dimensional electron-phonon-coupled structure

NASA Astrophysics Data System (ADS)

Brockt, C.; Jeckelmann, E.

2017-02-01

We investigate the scattering of an electron by phonons in a small structure between two one-dimensional tight-binding leads. This model mimics the quantum electron transport through atomic wires or molecular junctions coupled to metallic leads. The electron-phonon-coupled structure is represented by the Holstein model. We observe permanent energy transfer from the electron to the phonon system (dissipation), transient self-trapping of the electron in the electron-phonon-coupled structure (due to polaron formation and multiple reflections at the structure edges), and transmission resonances that depend strongly on the strength of the electron-phonon coupling and the adiabaticity ratio. A recently developed TEBD algorithm, optimized for bosonic degrees of freedom, is used to simulate the quantum dynamics of a wave packet launched against the electron-phonon-coupled structure. Exact results are calculated for a single electron-phonon site using scattering theory and analytical approximations are obtained for limiting cases.

Light energy transduction by the purple membrane of halophilic bacteria; Proceedings of the Symposium, San Francisco, Calif., June 6, 1976

NASA Technical Reports Server (NTRS)

1977-01-01

Several aspects of bacteriorhodopsin, the retinal protein component of the purple membranes of Halobacterium halobium, are discussed. Structural studies are presented. Photochemical properties of the protein complex and of its chromophore are described. Proton translocation of bacteriorhodopsin is compared to that of a protein from a thermophilic bacterium. Ionophore activity of bacteriorhodopsin is considered with attention to conformational changes, light dependency, and electrical potential. Amino acid transport is also examined and the light-energy budget is investigated. Bacteriorhodopsin is of interest because of its similarity to rhodopsin, which plays a major role in mammalian vision, and also because its attainability and distinctive characteristics will facilitate studies of certain bacterial physiological functions, such as ion transport and membrane organization.

Charge displacement in bacteriorhodopsin during the forward and reverse bR-K phototransition.

PubMed Central

Groma, G I; Hebling, J; Ludwig, C; Kuhl, J

1995-01-01

Dried oriented purple membrane samples of Halobacterium salinarium were excited by 150 fs laser pulses of 620 nm with a 7 kHz repetition rate. An unusual complex picosecond electric response signal consisting of a positive and a negative peak was detected by a sampling oscilloscope. The ratio of the two peaks was changed by 1) reducing the repetition rate, 2) varying the intensity of the excitation beam, and 3) applying background illumination by light of 647 nm or 511 nm. All of these features can be explained by the simultaneous excitation of the bacteriorhodopsin ground form and the K intermediate. The latter was populated by the (quasi)continuous excitation attributable to its prolonged lifetime in a dehydrated state. Least-square analysis resulted in a 5 ps upper and 2.5 ps lower limit for the time constant of the charge displacement process, corresponding to the forward reaction. That is in good agreement with the formation time of K. The charge separation driven by the reverse phototransition was faster, having a time constant of a 3.5 ps upper limit. The difference in the rates indicates the existence of different routes for the forward and the reverse photoreactions. PMID:8580349

Study of the electronic structure of electron accepting cyano-films: TCNQversusTCNE.

PubMed

Capitán, Maria J; Álvarez, Jesús; Navio, Cristina

2018-04-18

In this article, we perform systematic research on the electronic structure of two closely related organic electron acceptor molecules (TCNQ and TCNE), which are of technological interest due to their outstanding electronic properties. These studies have been performed from the experimental point of view by the use electron spectroscopies (XPS and UPS) and supported theoretically by the use of ab-initio DFT calculations. The cross-check between both molecules allows us to identify the characteristic electronic features of each part of the molecules and their contribution to the final electronic structure. We can describe the nature of the band gap of these materials, and we relate this with the appearance of the shake-up features in the core level spectra. A band bending and energy gap reduction of the aforementioned electronic structure in contact with a metal surface are seen in the experimental results as well in the theoretical calculations. This behavior implies that the TCNQ thin film accepts electrons from the metal substrate becoming a Schottky n-junction.

Graph-based linear scaling electronic structure theory.

PubMed

Niklasson, Anders M N; Mniszewski, Susan M; Negre, Christian F A; Cawkwell, Marc J; Swart, Pieter J; Mohd-Yusof, Jamal; Germann, Timothy C; Wall, Michael E; Bock, Nicolas; Rubensson, Emanuel H; Djidjev, Hristo

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Graph-based linear scaling electronic structure theory

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

Niklasson, Anders M. N., E-mail: amn@lanl.gov; Negre, Christian F. A.; Cawkwell, Marc J.

2016-06-21

We show how graph theory can be combined with quantum theory to calculate the electronic structure of large complex systems. The graph formalism is general and applicable to a broad range of electronic structure methods and materials, including challenging systems such as biomolecules. The methodology combines well-controlled accuracy, low computational cost, and natural low-communication parallelism. This combination addresses substantial shortcomings of linear scaling electronic structure theory, in particular with respect to quantum-based molecular dynamics simulations.

Embedded electronics for intelligent structures

NASA Astrophysics Data System (ADS)

Warkentin, David J.; Crawley, Edward F.

The signal, power, and communications provisions for the distributed control processing, sensing, and actuation of an intelligent structure could benefit from a method of physically embedding some electronic components. The preliminary feasibility of embedding electronic components in load-bearing intelligent composite structures is addressed. A technique for embedding integrated circuits on silicon chips within graphite/epoxy composite structures is presented which addresses the problems of electrical, mechanical, and chemical isolation. The mechanical and chemical isolation of test articles manufactured by this technique are tested by subjecting them to static and cyclic mechanical loads and a temperature/humidity/bias environment. The likely failure modes under these conditions are identified, and suggestions for further improvements in the technique are discussed.

Infrared and Visible Absolute and Difference Spectra of Bacteriorhodopsin Photocycle Intermediates

PubMed Central

Hendler, Richard W.; Meuse, Curtis W.; Braiman, Mark S.; Smith, Paul D.; Kakareka, John W.

2014-01-01

We have used new kinetic fitting procedures to obtain IR absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear algebra-based procedures of Hendler et al. (2001) J. Phys. Chem. B, 105, 3319–3228, for obtaining clean absolute visible spectra of bR photocycle intermediates, were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its MF and MS components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm−1 for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the MF pathway of the parallel cycles model of the photocycle. PMID:21929858

Picosecond time-resolved fluorescence spectroscopy of K-590 in the bacteriorhodopsin photocycle.

PubMed Central

Atkinson, G H; Blanchard, D; Lemaire, H; Brack, T L; Hayashi, H

1989-01-01

The fluorescence spectrum of a distinct isometric and conformational intermediate formed on the 10(-11) s time scale during the bacteriorhodopsin (BR) photocycle is observed at room temperature using a two laser, pump-probe technique with picosecond time resolution. The BR photocycle is initiated by pulsed (8 ps) excitation at 565 nm, whereas the fluorescence is generated by 4-ps laser pulses at 590 nm. The unstructured fluorescence extends from 650 to 880 nm and appears in the same general spectral region as the fluorescence spectrum assigned to BR-570. The transient fluorescence spectrum can be distinguished from that assigned to BR-570 by a larger emission quantum yield (approximately twice that of BR-570) and by a maximum intensity near 731 nm (shifted 17 nm to higher energy from the maximum of the BR-570 fluorescence spectrum). The fluorescence spectrum of BR-570 only is measured with low energy, picosecond pulsed excitation at 590 nm and is in good agreement with recent data in the literature. The assignment of the transient fluorescence spectrum to the K-590 intermediate is based on its appearance at time delays longer than 40 ps. The K-590 fluorescence spectrum remains unchanged over the entire 40-100-ps interval. The relevance of these fluorescence data with respect to the molecular mechanism used to model the primary processes in the BR photocycle also is discussed. PMID:2713439

Probing Actinide Electronic Structure through Pu Cluster Calculations

DOE PAGES

Ryzhkov, Mickhail V.; Mirmelstein, Alexei; Yu, Sung-Woo; ...

2013-02-26

The calculations for the electronic structure of clusters of plutonium have been performed, within the framework of the relativistic discrete-variational method. Moreover, these theoretical results and those calculated earlier for related systems have been compared to spectroscopic data produced in the experimental investigations of bulk systems, including photoelectron spectroscopy. Observation of the changes in the Pu electronic structure as a function of size provides powerful insight for aspects of bulk Pu electronic structure.

Electronic structures of elements according to ionization energies.

PubMed

Zadeh, Dariush H

2017-11-28

The electronic structures of elements in the periodic table were analyzed using available experimental ionization energies. Two new parameters were defined to carry out the study. The first parameter-apparent nuclear charge (ANC)-quantified the overall charge of the nucleus and inner electrons observed by an outer electron during the ionization process. This parameter was utilized to define a second parameter, which presented the shielding ability of an electron against the nuclear charge. This second parameter-electron shielding effect (ESE)-provided an insight into the electronic structure of atoms. This article avoids any sort of approximation, interpolation or extrapolation. First experimental ionization energies were used to obtain the two aforementioned parameters. The second parameter (ESE) was then graphed against the electron number of each element, and was used to read the corresponding electronic structure. The ESE showed spikes/peaks at the end of each electronic shell, providing insight into when an electronic shell closes and a new one starts. The electronic structures of elements in the periodic table were mapped using this methodology. These graphs did not show complete agreement with the previously known "Aufbau" filling rule. A new filling rule was suggested based on the present observations. Finally, a new way to organize elements in the periodic table is suggested. Two earlier topics of effective nuclear charge, and shielding factor were also briefly discussed and compared numerically to demonstrate the capability of the new approach.

Infrared and visible absolute and difference spectra of bacteriorhodopsin photocycle intermediates.

PubMed

Hendler, Richard W; Meuse, Curtis W; Braiman, Mark S; Smith, Paul D; Kakareka, John W

2011-09-01

We have used new kinetic fitting procedures to obtain infrared (IR) absolute spectra for intermediates of the main bacteriorhodopsin (bR) photocycle(s). The linear-algebra-based procedures of Hendler et al. (J. Phys. Chem. B, 105, 3319-3228 (2001)) for obtaining clean absolute visible spectra of bR photocycle intermediates were adapted for use with IR data. This led to isolation, for the first time, of corresponding clean absolute IR spectra, including the separation of the M intermediate into its M(F) and M(S) components from parallel photocycles. This in turn permitted the computation of clean IR difference spectra between pairs of successive intermediates, allowing for the most rigorous analysis to date of changes occurring at each step of the photocycle. The statistical accuracy of the spectral calculation methods allows us to identify, with great confidence, new spectral features. One of these is a very strong differential IR band at 1650 cm(-1) for the L intermediate at room temperature that is not present in analogous L spectra measured at cryogenic temperatures. This band, in one of the noisiest spectral regions, has not been identified in any previous time-resolved IR papers, although retrospectively it is apparent as one of the strongest L absorbance changes in their raw data, considered collectively. Additionally, our results are most consistent with Arg82 as the primary proton-release group (PRG), rather than a protonated water cluster or H-bonded grouping of carboxylic residues. Notably, the Arg82 deprotonation occurs exclusively in the M(F) pathway of the parallel cycles model of the photocycle. © 2011 Society for Applied Spectroscopy

Structural and electronic properties for atomic clusters

NASA Astrophysics Data System (ADS)

Sun, Yan

We have studied the structural and electronic properties for different groups of atomic clusters by doing a global search on the potential energy surface using the Taboo Search in Descriptors Space (TSDS) method and calculating the energies with Kohn-Sham Density Functional Theory (KS-DFT). Our goal was to find the structural and electronic principles for predicting the structure and stability of clusters. For Ben (n = 3--20), we have found that the evolution of geometric and electronic properties with size reflects a change in the nature of the bonding from van der Waals to metallic and then bulk-like. The cluster sizes with extra stability agree well with the predictions of the jellium model. In the 4d series of transition metal (TM) clusters, as the d-type bonding becomes more important, the preferred geometric structure changes from icosahedral (Y, Zr), to distorted compact structures (Nb, Mo), and FCC or simple cubic crystal fragments (Tc, Ru, Rh) due to the localized nature of the d-type orbital. Analysis of relative isomer energies and their electronic density of states suggest that these clusters tend to follow a maximum hardness principle (MHP). For A4B12 clusters (A is divalent, B is monovalent), we found unusually large (on average 1.95 eV) HOMO-LUMO gap values. This shows the extra stability at an electronic closed shell (20 electrons) predicted by the jellium model. The importance of symmetry, closed electronic and ionic shells in stability is shown by the relative stability of homotops of Mg4Ag12 which also provides support for the hypothesis that clusters that satisfy more than one stability criterion ("double magic") should be particularly stable.

Halorhodopsin pumps Cl– and bacteriorhodopsin pumps protons by a common mechanism that uses conserved electrostatic interactions

PubMed Central

Gunner, M. R.

2014-01-01

Key mutations differentiate the functions of homologous proteins. One example compares the inward ion pump halorhodopsin (HR) and the outward proton pump bacteriorhodopsin (BR). Of the nine essential buried ionizable residues in BR, six are conserved in HR. However, HR changes three BR acids, D85 in a central cluster of ionizable residues, D96, nearer the intracellular, and E204, nearer the extracellular side of the membrane to the small, neutral amino acids T111, V122, and T230, respectively. In BR, acidic amino acids are stationary anions whose proton affinity is modulated by conformational changes, establishing a sequence of directed binding and release of protons. Multiconformation continuum electrostatics calculations of chloride affinity and residue protonation show that, in reaction intermediates where an acid is ionized in BR, a Cl– is bound to HR in a position near the deleted acid. In the HR ground state, Cl– binds tightly to the central cluster T111 site and weakly to the extracellular T230 site, recovering the charges on ionized BR-D85 and neutral E204 in BR. Imposing key conformational changes from the BR M intermediate into the HR structure results in the loss of Cl– from the central T111 site and the tight binding of Cl– to the extracellular T230 site, mirroring the changes that protonate BR-D85 and ionize E204 in BR. The use of a mobile chloride in place of D85 and E204 makes HR more susceptible to the environmental pH and salt concentrations than BR. These studies shed light on how ion transfer mechanisms are controlled through the interplay of protein and ion electrostatics. PMID:25362051

Structure and Dynamics with Ultrafast Electron Microscopes

NASA Astrophysics Data System (ADS)

Siwick, Bradley

In this talk I will describe how combining ultrafast lasers and electron microscopes in novel ways makes it possible to directly `watch' the time-evolving structure of condensed matter, both at the level of atomic-scale structural rearrangements in the unit cell and at the level of a material's nano- microstructure. First, I will briefly describe my group's efforts to develop ultrafast electron diffraction using radio- frequency compressed electron pulses in the 100keV range, a system that rivals the capabilities of xray free electron lasers for diffraction experiments. I will give several examples of the new kinds of information that can be gleaned from such experiments. In vanadium dioxide we have mapped the detailed reorganization of the unit cell during the much debated insulator-metal transition. In particular, we have been able to identify and separate lattice structural changes from valence charge density redistribution in the material on the ultrafast timescale. In doing so we uncovered a previously unreported optically accessible phase/state of vanadium dioxide that has monoclinic crystallography like the insulator, but electronic structure and properties that are more like the rutile metal. We have also combined these dynamic structural measurements with broadband ultrafast spectroscopy to make detailed connections between structure and properties for the photoinduced insulator to metal transition. Second, I will show how dynamic transmission electron microscopy (DTEM) can be used to make direct, real space images of nano-microstructural evolution during laser-induced crystallization of amorphous semiconductors at unprecedented spatio-temporal resolution. This is a remarkably complex process that involves several distinct modes of crystal growth and the development of intricate microstructural patterns on the nanosecond to ten microsecond timescales all of which can be imaged directly with DTEM.

Anomalous Electron Spectrum and Its Relation to Peak Structure of Electron Scattering Rate in Cuprate Superconductors

NASA Astrophysics Data System (ADS)

Gao, Deheng; Mou, Yingping; Feng, Shiping

2018-02-01

The recent discovery of a direct link between the sharp peak in the electron quasiparticle scattering rate of cuprate superconductors and the well-known peak-dip-hump structure in the electron quasiparticle excitation spectrum is calling for an explanation. Within the framework of the kinetic-energy-driven superconducting mechanism, the complicated line-shape in the electron quasiparticle excitation spectrum of cuprate superconductors is investigated. It is shown that the interaction between electrons by the exchange of spin excitations generates a notable peak structure in the electron quasiparticle scattering rate around the antinodal and nodal regions. However, this peak structure disappears at the hot spots, which leads to that the striking peak-dip-hump structure is developed around the antinodal and nodal regions, and vanishes at the hot spots. The theory also confirms that the sharp peak observed in the electron quasiparticle scattering rate is directly responsible for the remarkable peak-dip-hump structure in the electron quasiparticle excitation spectrum of cuprate superconductors.

Electron acoustic nonlinear structures in planetary magnetospheres

NASA Astrophysics Data System (ADS)

Shah, K. H.; Qureshi, M. N. S.; Masood, W.; Shah, H. A.

2018-04-01

In this paper, we have studied linear and nonlinear propagation of electron acoustic waves (EAWs) comprising cold and hot populations in which the ions form the neutralizing background. The hot electrons have been assumed to follow the generalized ( r , q ) distribution which has the advantage that it mimics most of the distribution functions observed in space plasmas. Interestingly, it has been found that unlike Maxwellian and kappa distributions, the electron acoustic waves admit not only rarefactive structures but also allow the formation of compressive solitary structures for generalized ( r , q ) distribution. It has been found that the flatness parameter r , tail parameter q , and the nonlinear propagation velocity u affect the propagation characteristics of nonlinear EAWs. Using the plasmas parameters, typically found in Saturn's magnetosphere and the Earth's auroral region, where two populations of electrons and electron acoustic solitary waves (EASWs) have been observed, we have given an estimate of the scale lengths over which these nonlinear waves are expected to form and how the size of these structures would vary with the change in the shape of the distribution function and with the change of the plasma parameters.

Electronic Structure of Actinides under Pressure

NASA Astrophysics Data System (ADS)

Johansson, Borje

2006-03-01

The series of heavy radioactive elements known as the actinides all have similar elemental properties. However, when the volume per atom in the condensed phase is illustrated as a function of atomic number, perhaps the most dramatic anomaly in the periodic table becomes apparent. The atomic volume of americium is almost 50% larger than it is for the preceding element plutonium. For the element after americium, curium, the atomic volume is very close to that of americium. The same holds also for the next elements berkelium and californium. Accordingly from americium and onwards the actinides behave very similar to the corresponding rare-earth elements - a second lanthanide series of metallic elements can be identified. This view is strongly supported by the fact that all these elements adopt the dhcp structure, a structure typical for the lanthanides. The reason for this behavior is found in the behavior of the 5f electrons. For the earlier actinides, up to and including plutonium, the 5f electrons form metallic states and contribute most significantly to the bonding. In Np and Pu they even dominate the bonding, while all of a sudden they become localized in Am, very much like the 4f electrons in the lanthanide series, and contribute no longer to the cohesion. This withdrawal of 5f bonding gives rise to the large volume expansion between plutonium and americium. This difference between the light and heavy actinide suggests that it would be most worthwhile to strongly compress the transplutonium elements, thereby forcing the individual 5f electron wave functions into strong contact with each other (overlap). Recently high pressure experiments have been performed for americium and curium and dramatic crystal structure changes have been observed. These results and other high pressure data will be discussed in relation to the basic electronic structure of these elements.

The electronic structure of lithium metagallate.

PubMed

Johnson, N W; McLeod, J A; Moewes, A

2011-11-09

Herein we present a study of the electronic structure of lithium metagallate (LiGaO(2)), a material of interest in the field of optoelectronics. We use soft x-ray spectroscopy to probe the electronic structure of both the valence and conduction bands and compare our measurements to ab initio density functional theory calculations. We use several different exchange-correlation functionals, but find that no single theoretical approach used herein accurately quantifies both the band gap and the Ga 3d(10) states in LiGaO(2). We derive a band gap of 5.6 eV, and characterize electron hybridization in both the valence and conduction bands. Our study of the x-ray spectra may prove useful in analysing spectra from more complicated LiGaO(2) heterostructures. © 2011 IOP Publishing Ltd

Proton storage site in bacteriorhodopsin: new insights from QM/MM simulations of microscopic pKa and infrared spectra

PubMed Central

Goyal, Puja; Ghosh, Nilanjan; Phatak, Prasad; Clemens, Maike; Gaus, Michael; Elstner, Marcus; Cui, Qiang

2011-01-01

Identifying the group that acts as the proton storage/loading site is a challenging but important problem for understanding the mechanism of proton pumping in biomolecular proton pumps, such as bacteriorhodopsin (bR) and cytochrome c oxidase. Recent experimental studies of bR propelled the idea that the proton storage/release group (PRG) in bR is not an amino acid but a water cluster embedded in the protein. We argue that this idea is at odds with our knowledge of protein electrostatics, since invoking the water cluster as PRG would require the protein to raise the pKa of a hydronium by almost 11 pKa units, which is difficult considering known cases of pKa shifts in proteins. Our recent QM/MM simulations suggested an alternative “intermolecular proton bond” model in which the stored proton is shared between two conserved Glu residues (194 and 204). Here we show that this model leads to microscopic pKa values consistent with available experimental data and the functional requirement of a PRG. Extensive QM/MM simulations also show that, independent of a number of technical issues, such as the influence of QM region size, starting x-ray structure and nuclear quantum effects, the “intermolecular proton bond” model is qualitatively consistent with available spectroscopic data. Potential of mean force calculations show explicitly that the stored proton strongly prefers the pair of Glu residues over the water cluster. The results and analyses help highlight the importance of considering protein electrostatics and provide arguments for why the “intermolecular proton bond” model is likely applicable to PRG in biomolecular proton pumps in general. PMID:21761868

Electronic structure of lanthanide scandates

NASA Astrophysics Data System (ADS)

Mizzi, Christopher A.; Koirala, Pratik; Marks, Laurence D.

2018-02-01

X-ray photoelectron spectroscopy, ultraviolet photoelectron spectroscopy, and density functional theory calculations were used to study the electronic structure of three lanthanide scandates: GdSc O3,TbSc O3 , and DySc O3 . X-ray photoelectron spectra simulated from first-principles calculations using a combination of on-site hybrid and GGA +U methods were found to be in good agreement with experimental x-ray photoelectron spectra. The hybrid method was used to model the ground state electronic structure and the GGA +U method accounted for the shift of valence state energies due to photoelectron emission via a Slater-Janak transition state approach. From these results, the lanthanide scandate valence bands were determined to be composed of Ln 4 f ,O 2 p , and Sc 3 d states, in agreement with previous work. However, contrary to previous work the minority Ln 4 f states were found to be located closer to, and in some cases at, the valence band maximum. This suggests that minority Ln 4 f electrons may play a larger role in lanthanide scandate properties than previously thought.

The Key Ingredients of the Electronic Structure of FeSe

NASA Astrophysics Data System (ADS)

Coldea, Amalia I.; Watson, Matthew D.

2018-03-01

FeSe is a fascinating superconducting material at the frontier of research in condensed matter physics. Here, we provide an overview of the current understanding of the electronic structure of FeSe, focusing in particular on its low-energy electronic structure as determined from angle-resolved photoemission spectroscopy, quantum oscillations, and magnetotransport measurements of single-crystal samples. We discuss the unique place of FeSe among iron-based superconductors, as it is a multiband system exhibiting strong orbitally dependent electronic correlations and unusually small Fermi surfaces and is prone to different electronic instabilities. We pay particular attention to the evolution of the electronic structure that accompanies the tetragonal-orthorhombic structural distortion of the lattice around 90 K, which stabilizes a unique nematic electronic state. Finally, we discuss how the multiband multiorbital nematic electronic structure impacts our understanding of the superconductivity, and show that the tunability of the nematic state with chemical and physical pressure helps to disentangle the role of different competing interactions relevant for enhancing superconductivity.

Electronic structure of germanium selenide investigated using ultra-violet photo-electron spectroscopy

NASA Astrophysics Data System (ADS)

Mishra, P.; Lohani, H.; Kundu, A. K.; Patel, R.; Solanki, G. K.; Menon, Krishnakumar S. R.; Sekhar, B. R.

2015-07-01

The valence band electronic structure of GeSe single crystals has been investigated using angle resolved photoemission spectroscopy (ARPES) and x-ray photoelectron spectroscopy. The experimentally observed bands from ARPES, match qualitatively with our LDA-based band structure calculations along the Γ-Z, Γ-Y and Γ-T symmetry directions. The valence band maximum occurs nearly midway along the Γ-Z direction, at a binding energy of -0.5 eV, substantiating the indirect band gap of GeSe. Non-dispersive features associated with surface states and indirect transitions have been observed. The difference in hybridization of Se and Ge 4p orbitals leads to the variation of dispersion along the three symmetry directions. The predominance of the Se 4pz orbitals, evidenced from theoretical calculations, may be the cause for highly dispersive bands along the Γ-T direction. Detailed electronic structure analysis reveals the significance of the cation-anion 4p orbitals hybridization in the valence band dispersion of IV-VI semiconductors. This is the first comprehensive report of the electronic structure of a GeSe single crystal using ARPES in conjugation with theoretical band structure analysis.

The molecular mechanism of excitation in visual transduction and bacteriorhodopsin

PubMed Central

Lewis, Aaron

1978-01-01

An electronic theory of excitation is proposed and described in terms of a three-dimensional excited/ground-state energy surface which elucidates the photochemical and excited-state dynamics of rhodopsins. In this theory the primary action of light is to produce significant electron redistribution in the retinal, thereby generating new interactions that vibrationally excite and perturb the ground-state protein conformation. Thus, light energy causes charge redistribution in the retinal and induces transient charge-density assisted bond rearrangements (such as proton translocation) in the protein structure which is stabilized by subsequent retinal structural alteration. In this theory the isoprenoid chain of the retinal is considered a structurally pliable molecular entity that can generate charge redistributions and can be subsequently achieve intermediate conformations or various isomeric states to minimize the energy of the new protein structure generated by light. Thus, the 11-cis to all trans isomerization of the retinylidene chromophore is not considered a primary mechanism of excitation. An alternate biological role for this molecular process (which is eventually completed in all photoreceptors but not in bacterial rhodopsins) is to provide the irreversibility needed for effective quantum detection on the time scale of a neural response. Finally, it will be demonstrated that this mechanism, which readily accounts for the photophysical and photochemical data, can also be restated in terms of the Monod, Wyman, and Changeux terminology suggesting that aggregates of these pigments may function allosterically. PMID:273216

Electronic Structure and Thermoelectric Properties of Transition Metal Monosilicides

NASA Astrophysics Data System (ADS)

Pshenay-Severin, D. A.; Ivanov, Yu. V.; Burkov, A. T.; Novikov, S. V.; Zaitsev, V. K.; Reith, H.

2018-06-01

We present theoretical and experimental results on electronic structure and thermoelectric properties of cobalt monosilicide (CoSi) and of Co1- x M x Si diluted alloys (M = Fe and Ni) at temperatures from 2 K to 800 K. CoSi crystallizes into a non-centrosymmetric cubic B20 structure, which suggests the possibility of a topologically non-trivial electronic structure. We show that the electronic structure of CoSi exhibits linear band crossings in close vicinity to Fermi energy, confirming the possibility of non-trivial topology. The proximity of the linear-dispersion bands to Fermi energy implies their important contribution to the electronic transport. Calculation of thermopower of CoSi, using ab initio band structure and the constant relaxation time approximation, is carried out. It reveals that many body corrections to the electronic spectrum are important in order to obtain qualitative agreement of theoretical and experimental temperature dependences of thermopower. Phonon dispersion and lattice thermal conductivity are calculated. The phonons give a major contribution to the thermal conductivity of the compound below room temperature.

Chemical modulation of electronic structure at the excited state

NASA Astrophysics Data System (ADS)

Li, F.; Song, C.; Gu, Y. D.; Saleem, M. S.; Pan, F.

2017-12-01

Spin-polarized electronic structures are the cornerstone of spintronics, and have thus attracted a significant amount of interest; in particular, researchers are looking into how to modulate the electronic structure to enable multifunctional spintronics applications, especially in half-metallic systems. However, the control of the spin polarization has only been predicted in limited two-dimensional systems with spin-polarized Dirac structures and is difficult to achieve experimentally. Here, we report the modulation of the electronic structure in the light-induced excited state in a typical half-metal, L a1 /2S r1 /2Mn O3 -δ . According to the spin-transport measurements, there appears a light-induced increase in magnetoresistance due to the enhanced spin scattering, which is closely associated with the excited spin polarization. Strikingly, the light-induced variation can be enhanced via alcohol processing and reduced by oxygen annealing. X-ray photoelectron spectroscopy measurements show that in the chemical process, a redox reaction occurs with a change in the valence of Mn. Furthermore, first-principles calculations reveal that the change in the valence of Mn alters the electronic structure and consequently modulates the spin polarization in the excited state. Our findings thus report a chemically tunable electronic structure, demonstrating interesting physics and the potential for multifunctional applications and ultrafast spintronics.

Electronic structure and electron-phonon coupling in TiH$$_2$$

DOE PAGES

Shanavas, Kavungal Veedu; Lindsay, Lucas R.; Parker, David S.

2016-06-15

Calculations using first principles methods and strong coupling theory are carried out to understand the electronic structure and superconductivity in cubic and tetragonal TiHmore » $$_2$$. A large electronic density of states at the Fermi level in the cubic phase arises from Ti-$$t_{2g}$$ states and leads to a structural instability against tetragonal distortion at low temperatures. However, constraining the in-plane lattice constants diminishes the energy gain associated with the tetragonal distortion, allowing the cubic phase to be stable at low temperatures. Furthermore, calculated phonon dispersions show decoupled acoustic and optic modes arising from Ti and H vibrations, respectively and frequencies of optic modes to be rather high. The cubic phase has a large electron-phonon coupling parameter $$\\lambda$$ and critical temperature of several K. Contribution of the hydrogen sublattice to $$\\lambda$$ is found to be small in this material, which we understand from strong coupling theory to be due to the small H-$s$ DOS at the Fermi level and high energy of hydrogen modes at the tetrahedral sites.« less

Peculiar properties of photoinduced hydroxylaminolysis in different bacteriorhodopsin-based media using O-substituted hydroxylamines.

PubMed

Dyukova, Tatyana V; Druzhko, Anna B

2010-01-01

The process of photoinduced hydroxylaminolysis has been re-examined in different bacteriorhodopsin (BR)-based media using O-substituted hydroxylamines, in particular, O-(4-nitrobenzyl) hydroxylamine hydrochloride (NBHA), O-(2,3,4,5,6-pentafluorobenzyl) hydroxylamine hydrochloride (FBHA) and O-(t-butyl) hydroxylamine hydrochloride (BHA). Both wild type (WT) and D96N BR-based gelatine films and gels were studied. The expected increase in the bleaching rate of BR in gelatin films by using O-substituted hydroxylamines in place of HA was not achieved. On the other hand, it was shown that in gels HA derivatives NBHA and FBHA (as against HA itself) do provide about three- to four-fold higher bleaching rate. By contrast to that in films, D96N BR in gels demonstrates more effective bleaching as compared to WT BR. The plausible interpretation for the results is discussed in frames of reduced mobilities of large-sized molecules of O-substituted hydroxylamines in dehydrated media. FBHA- or NBHA-modified gels possess higher photosensitivity both with D96N and WT BR (as compared with that for HA-modified gels) and offer a potentiality for application as an irreversible-recording medium. As anticipated, it is specifically D96N BR gel modified with FBHA that may present a promising medium suitable for write-once recording thus extending the range of recording materials in the optical processing field. © 2010 The Authors. Journal Compilation. The American Society of Photobiology.

Wavelets in electronic structure calculations

NASA Astrophysics Data System (ADS)

Modisette, Jason Perry

1997-09-01

Ab initio calculations of the electronic structure of bulk materials and large clusters are not possible on today's computers using current techniques. The storage and diagonalization of the Hamiltonian matrix are the limiting factors in both memory and execution time. The scaling of both quantities with problem size can be reduced by using approximate diagonalization or direct minimization of the total energy with respect to the density matrix in conjunction with a localized basis. Wavelet basis members are much more localized than conventional bases such as Gaussians or numerical atomic orbitals. This localization leads to sparse matrices of the operators that arise in SCF multi-electron calculations. We have investigated the construction of the one-electron Hamiltonian, and also the effective one- electron Hamiltonians that appear in density-functional and Hartree-Fock theories. We develop efficient methods for the generation of the kinetic energy and potential matrices, the Hartree and exchange potentials, and the local exchange-correlation potential of the LDA. Test calculations are performed on one-electron problems with a variety of potentials in one and three dimensions.

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

Electronic structure and electron energy-loss spectroscopy of ZrO2 zirconia

NASA Astrophysics Data System (ADS)

Dash, L. K.; Vast, Nathalie; Baranek, Philippe; Cheynet, Marie-Claude; Reining, Lucia

2004-12-01

The atomic and electronic structures of zirconia are calculated within density functional theory, and their evolution is analyzed as the crystal-field symmetry changes from tetrahedral [cubic (c-ZrO2) and tetragonal (t-ZrO2) phases] to octahedral (hypothetical rutile ZrO2 ), to a mixing of these symmetries (monoclinic phase, m-ZrO2 ). We find that the theoretical bulk modulus in c-ZrO2 is 30% larger than the experimental value, showing that the introduction of yttria in zirconia has a significant effect. Electronic structure fingerprints which characterize each phase from their electronic spectra are identified. We have carried out electron energy-loss spectroscopy experiments at low momentum transfer and compared these results to the theoretical spectra calculated within the random phase approximation. We show a dependence of the valence and 4p ( N2,3 edge) plasmons on the crystal structure, the dependence of the latter being brought into the spectra by local-field effects. Last, we attribute low energy excitations observed in EELS of m-ZrO2 to defect states 2eV above the top of the intrinsic valence band, and the EELS fundamental band gap value is reconciled with the 5.2 or 5.8eV gaps determined by vacuum ultraviolet spectroscopy.

Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization

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

Lin, Qisheng; Miller, Gordon J.

Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e –/atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Furthermore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate.

Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization

DOE PAGES

Lin, Qisheng; Miller, Gordon J.

2017-12-18

Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e –/atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Furthermore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate.

Electronic structure of multi-walled carbon fullerenes

NASA Astrophysics Data System (ADS)

Doore, Keith; Cook, Matthew; Clausen, Eric; Lukashev, Pavel V.; Kidd, Tim E.; Stollenwerk, Andrew J.

2017-02-01

Despite an enormous amount of research on carbon based nanostructures, relatively little is known about the electronic structure of multi-walled carbon fullerenes, also known as carbon onions. In part, this is due to the very high computational expense involved in estimating electronic structure of large molecules. At the same time, experimentally, the exact crystal structure of the carbon onion is usually unknown, and therefore one relies on qualitative arguments only. In this work we present the results of a computational study on a series of multi-walled fullerenes and compare their electronic structures to experimental data. Experimentally, the carbon onions were fabricated using ultrasonic agitation of isopropanol alcohol and deposited onto the surface of highly ordered pyrolytic graphite using a drop cast method. Scanning tunneling microscopy images indicate that the carbon onions produced using this technique are ellipsoidal with dimensions on the order of 10 nm. The majority of differential tunneling spectra acquired on individual carbon onions are similar to that of graphite with the addition of molecular-like peaks, indicating that these particles span the transition between molecules and bulk crystals. A smaller, yet sizable number exhibited a semiconducting gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) levels. These results are compared with the electronic structure of different carbon onion configurations calculated using first-principles. Similar to the experimental results, the majority of these configurations are metallic with a minority behaving as semiconductors. Analysis of the configurations investigated here reveals that each carbon onion exhibiting an energy band gap consisted only of non-metallic fullerene layers, indicating that the interlayer interaction is not significant enough to affect the total density of states in these structures.

The stabilities and electron structures of Al-Mg clusters with 18 and 20 valence electrons

NASA Astrophysics Data System (ADS)

Yang, Huihui; Chen, Hongshan

2017-07-01

The spherical jellium model predicts that metal clusters having 18 and 20 valence electrons correspond to the magic numbers and will show specific stabilities. We explore in detail the geometric structures, stabilities and electronic structures of Al-Mg clusters containing 18 and 20 valence electrons by using genetic algorithm combined with density functional theories. The stabilities of the clusters are governed by the electronic configurations and Mg/Al ratios. The clusters with lower Mg/Al ratios are more stable. The molecular orbitals accord with the shell structures predicted by the jellium model but the 2S level interweaves with the 1D levels and the 2S and 1D orbitals form a subgroup. The clusters having 20 valence electrons form closed 1S21P61D102S2 shells and show enhanced stability. The Al-Mg clusters with a valence electron count of 18 do not form closed shells because one 1D orbital is unoccupied. The ionization potential and electron affinity are closely related to the electronic configurations; their values are determined by the subgroups the HOMO or LUMO belong to. Supplementary material in the form of one pdf file available from the Journal web page at http://https://doi.org/10.1140/epjd/e2017-80042-9

Solvent-free MALDI-MS for the analysis of a membrane protein via the mini ball mill approach: case study of bacteriorhodopsin.

PubMed

Trimpin, Sarah; Deinzer, Max L

2007-01-01

A mini ball mill (MBM) solvent-free matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) method allows for the analysis of bacteriorhodopsin (BR), an integral membrane protein that previously presented special analytical problems. For well-defined signals in the molecular ion region of the analytes, a desalting procedure of the MBM sample directly on the MALDI target plate was used to reduce adduction by sodium and other cations that are normally attendant with hydrophobic peptides and proteins as a result of the sample preparation procedure. Mass analysis of the intact hydrophobic protein and the few hydrophobic and hydrophilic tryptic peptides available in the digest is demonstrated with this robust new approach. MS and MS/MS spectra of BR tryptic peptides and intact protein were generally superior to the traditional solvent-based method using the desalted "dry" MALDI preparation procedure. The solvent-free method expands the range of peptides that can be effectively analyzed by MALDI-MS to those that are hydrophobic and solubility-limited.

Electronic structure of binuclear acetylacetonates of boron difluoride

NASA Astrophysics Data System (ADS)

Tikhonov, Sergey A.; Svistunova, Irina V.; Samoilov, Ilya S.; Osmushko, Ivan S.; Borisenko, Aleksandr V.; Vovna, Vitaliy I.

2018-05-01

The electronic structure of boron difluoride acetylacetonate and its three derivatives was studied using photoelectron and absorption spectroscopy, as well as the density functional theory. In a series of binuclear acetylacetonate complexes containing bridge-moieties of sulfur and selenium atoms, it was found an appreciable mixing of the π3-orbital of the chelate cycle with atomic orbitals S 3p and Se 4p resulting in destabilization of the HOMO levels by 0.4-0.6 eV, in comparison with the monomer. The positively charged fragment C(CH3)-CX-C(CH3) causes the field effect, which leads to stabilization of the LUMO levels by 0.3-0.4 eV and C 1s-levels by 0.5-1.2 eV. An analysis of the research results on the electronic structure made it possible to determine the effect of substituents in the γ position on the absorption spectra, which is mainly determined by the electron density transfer from the chalcogen atoms to the chelate cycles. It is shown that the calculated energy intervals between electron levels correlate well with the structure of the photoelectron spectra of valence and core electrons.

Electronic structure of the benzene dimer cation

NASA Astrophysics Data System (ADS)

Pieniazek, Piotr A.; Krylov, Anna I.; Bradforth, Stephen E.

2007-07-01

The benzene and benzene dimer cations are studied using the equation-of-motion coupled-cluster model with single and double substitutions for ionized systems. The ten lowest electronic states of the dimer at t-shaped, sandwich, and displaced sandwich configurations are described and cataloged based on the character of the constituent fragment molecular orbitals. The character of the states, bonding patterns, and important features of the electronic spectrum are explained using qualitative dimer molecular orbital linear combination of fragment molecular orbital framework. Relaxed ground state geometries are obtained for all isomers. Calculations reveal that the lowest energy structure of the cation has a displaced sandwich structure and a binding energy of 20kcal/mol, while the t-shaped isomer is 6kcal/mol higher. The calculated electronic spectra agree well with experimental gas phase action spectra and femtosecond transient absorption in liquid benzene. Both sandwich and t-shaped structures feature intense charge resonance bands, whose location is very sensitive to the interfragment distance. Change in the electronic state ordering was observed between σ and πu states, which correlate to the B˜ and C˜ bands of the monomer, suggesting a reassignment of the local excitation peaks in the gas phase experimental spectrum.

Electronic structure of the high-temperature oxide superconductors

NASA Astrophysics Data System (ADS)

Pickett, Warren E.

1989-04-01

Since the discovery of superconductivity above 30 K by Bednorz and Müller in the La copper oxide system, the critical temperature has been raised to 90 K in YBa2Cu3O7 and to 110 and 125 K in Bi-based and Tl-based copper oxides, respectively. In the two years since this Nobel-prize-winning discovery, a large number of electronic structure calculations have been carried out as a first step in understanding the electronic properties of these materials. In this paper these calculations (mostly of the density-functional type) are gathered and reviewed, and their results are compared with the relevant experimental data. The picture that emerges is one in which the important electronic states are dominated by the copper d and oxygen p orbitals, with strong hybridization between them. Photon, electron, and positron spectroscopies provide important information about the electronic states, and comparison with electronic structure calculations indicates that, while many features can be interpreted in terms of existing calculations, self-energy corrections ("correlations") are important for a more detailed understanding. The antiferromagnetism that occurs in some regions of the phase diagram poses a particularly challenging problem for any detailed theory. The study of structural stability, lattice dynamics, and electron-phonon coupling in the copper oxides is also discussed. Finally, a brief review is given of the attempts so far to identify interaction constants appropriate for a model Hamiltonian treatment of many-body interactions in these materials.

Electronic Structure Principles and Aromaticity

ERIC Educational Resources Information Center

Chattaraj, P. K.; Sarkar, U.; Roy, D. R.

2007-01-01

The relationship between aromaticity and stability in molecules on the basis of quantities such as hardness and electrophilicity is explored. The findings reveal that aromatic molecules are less energetic, harder, less polarizable, and less electrophilic as compared to antiaromatic molecules, as expected from the electronic structure principles.

Probing specific molecular processes and intermediates by time-resolved Fourier transform infrared spectroscopy: application to the bacteriorhodopsin photocycle.

PubMed

Lórenz-Fonfría, Víctor A; Kandori, Hideki; Padrós, Esteve

2011-06-23

We present a general approach for probing the kinetics of specific molecular processes in proteins by time-resolved Fourier transform infrared (IR) spectroscopy. Using bacteriorhodopsin (bR) as a model we demonstrate that by appropriately monitoring some selected IR bands it is possible obtaining the kinetics of the most important events occurring in the photocycle, namely changes in the chromophore and the protein backbone conformation, and changes in the protonation state of the key residues implicated in the proton transfers. Besides confirming widely accepted views of the bR photocycle, our analysis also sheds light into some disputed issues: the degree of retinal torsion in the L intermediate to respect the ground state; the possibility of a proton transfer from Asp85 to Asp212; the relationship between the protonation/deprotonation of Asp85 and the proton release complex; and the timing of the protein backbone dynamics. By providing a direct way to estimate the kinetics of photocycle intermediates the present approach opens new prospects for a robust quantitative kinetic analysis of the bR photocycle, which could also benefit the study of other proteins involved in photosynthesis, in phototaxis, or in respiratory chains.

Writing Electron Dot Structures: Abstract of Issue 9905M

NASA Astrophysics Data System (ADS)

Magnell, Kenneth R.

1999-10-01

Writing Electron Dot Structures is a computer program for Mac OS that provides drill with feedback for students learning to write electron dot structures. While designed for students in the first year of college general chemistry it may also be used by high school chemistry students. A systematic method similar to that found in many general chemistry texts is employed:

1. determine the number of valence shell electrons,
2. select the central atom,
3. construct a skeleton,
4. add electrons to complete octets,
5. examine the structure for resonance forms.

NASA Astrophysics Data System (ADS)

Moutenet, Alice; Georges, Antoine; Ferrero, Michel

2018-04-01

We present a theoretical investigation of the effects of correlations on the electronic structure of the Mott insulator Sr2IrO4 upon electron doping. A rapid collapse of the Mott gap upon doping is found, and the electronic structure displays a strong momentum-space differentiation at low doping level: The Fermi surface consists of pockets centered around (π /2 ,π /2 ) , while a pseudogap opens near (π ,0 ) . Its physical origin is shown to be related to short-range spin correlations. The pseudogap closes upon increasing doping, but a differentiated regime characterized by a modulation of the spectral intensity along the Fermi surface persists to higher doping levels. These results, obtained within the cellular dynamical mean-field-theory framework, are discussed in comparison to recent photoemission experiments and an overall good agreement is found.

Electronic Structure of Small Lanthanide Containing Molecules

NASA Astrophysics Data System (ADS)

Kafader, Jared O.; Ray, Manisha; Topolski, Josey E.; Chick Jarrold, Caroline

2016-06-01

Lanthanide-based materials have unusual electronic properties because of the high number of electronic degrees of freedom arising from partial occupation of 4f orbitals, which make these materials optimal for their utilization in many applications including electronics and catalysis. Electronic spectroscopy of small lanthanide molecules helps us understand the role of these 4f electrons, which are generally considered core-like because of orbital contraction, but are energetically similar to valence electrons. The spectroscopy of small lanthanide-containing molecules is relatively unexplored and to broaden this understanding we have completed the characterization of small cerium, praseodymium, and europium molecules using photoelectron spectroscopy coupled with DFT calculations. The characterization of PrO, EuH, EuO/EuOH, and CexOy molecules have allowed for the determination of their electron affinity, the assignment of numerous anion to neutral state transitions, modeling of anion/neutral structures and electron orbital occupation.

Robert Hofstadter, Electron Scattering, the Structure of the Nucleons, and

Science.gov Websites

, Electron Scattering, the Structure of the Nucleons, and Scintillation Counters Resources with Additional -point particles and therefore possessed structure. For this work Hofstadter was awarded the Nobel Prize structure of the nucleons, and scintillation counters is available in electronic documents and on the Web

Structural and electronic properties of monolayer group III monochalcogenides

NASA Astrophysics Data System (ADS)

Demirci, S.; Avazlı, N.; Durgun, E.; Cahangirov, S.

2017-03-01

We investigate the structural, mechanical, and electronic properties of the two-dimensional hexagonal structure of group III-VI binary monolayers, M X (M =B , Al, Ga, In and X =O , S, Se, Te) using first-principles calculations based on the density functional theory. The structural optimization calculations and phonon spectrum analysis indicate that all of the 16 possible binary compounds are thermally stable. In-plane stiffness values cover a range depending on the element types and can be as high as that of graphene, while the calculated bending rigidity is found to be an order of magnitude higher than that of graphene. The obtained electronic band structures show that M X monolayers are indirect band-gap semiconductors. The calculated band gaps span a wide optical spectrum from deep ultraviolet to near infrared. The electronic structure of oxides (M O ) is different from the rest because of the high electronegativity of oxygen atoms. The dispersions of the electronic band edges and the nature of bonding between atoms can also be correlated with electronegativities of constituent elements. The unique characteristics of group III-VI binary monolayers can be suitable for high-performance device applications in nanoelectronics and optics.

Electron-Poor Polar Intermetallics: Complex Structures, Novel Clusters, and Intriguing Bonding with Pronounced Electron Delocalization.

PubMed

Lin, Qisheng; Miller, Gordon J

2018-01-16

Intermetallic compounds represent an extensive pool of candidates for energy related applications stemming from magnetic, electric, optic, caloric, and catalytic properties. The discovery of novel intermetallic compounds can enhance understanding of the chemical principles that govern structural stability and chemical bonding as well as finding new applications. Valence electron-poor polar intermetallics with valence electron concentrations (VECs) between 2.0 and 3.0 e - /atom show a plethora of unprecedented and fascinating structural motifs and bonding features. Therefore, establishing simple structure-bonding-property relationships is especially challenging for this compound class because commonly accepted valence electron counting rules are inappropriate. During our efforts to find quasicrystals and crystalline approximants by valence electron tuning near 2.0 e - /atom, we observed that compositions close to those of quasicrystals are exceptional sources for unprecedented valence electron-poor polar intermetallics, e.g., Ca 4 Au 10 In 3 containing (Au 10 In 3 ) wavy layers, Li 14.7 Mg 36.8 Cu 21.5 Ga 66 adopting a type IV clathrate framework, and Sc 4 Mg x Cu 15-x Ga 7.5 that is incommensurately modulated. In particular, exploratory syntheses of AAu 3 T (A = Ca, Sr, Ba and T = Ge, Sn) phases led to interesting bonding features for Au, such as columns, layers, and lonsdaleite-type tetrahedral frameworks. Overall, the breadth of Au-rich polar intermetallics originates, in part, from significant relativistics effect on the valence electrons of Au, effects which result in greater 6s/5d orbital mixing, a small effective metallic radius, and an enhanced Mulliken electronegativity, all leading to ultimate enhanced binding with nearly all metals including itself. Two other successful strategies to mine electron-poor polar intermetallics include lithiation and "cation-rich" phases. Along these lines, we have studied lithiated Zn-rich compounds in which structural

The energetics of the primary proton transfer in bacteriorhodopsin revisited: it is a sequential light-induced charge separation after all.

PubMed

Braun-Sand, Sonja; Sharma, Pankaz K; Chu, Zhen T; Pisliakov, Andrei V; Warshel, Arieh

2008-05-01

The light-induced proton transport in bacteriorhodopsin has been considered as a model for other light-induced proton pumps. However, the exact nature of this process is still unclear. For example, it is not entirely clear what the driving force of the initial proton transfer is and, in particular, whether it reflects electrostatic forces or other effects. The present work simulates the primary proton transfer (PT) by a specialized combination of the EVB and the QCFF/PI methods. This combination allows us to obtain sufficient sampling and a quantitative free energy profile for the PT at different protein configurations. The calculated profiles provide new insight about energetics of the primary PT and its coupling to the protein conformational changes. Our finding confirms the tentative analysis of an earlier work (A. Warshel, Conversion of light energy to electrostatic energy in the proton pump of Halobacterium halobium, Photochem. Photobiol. 30 (1979) 285-290) and determines that the overall PT process is driven by the energetics of the charge separation between the Schiff base and its counterion Asp85. Apparently, the light-induced relaxation of the steric energy of the chromophore leads to an increase in the ion-pair distance, and this drives the PT process. Our use of the linear response approximation allows us to estimate the change in the protein conformational energy and provides the first computational description of the coupling between the protein structural changes and the PT process. It is also found that the PT is not driven by twist-modulated changes of the Schiff base's pKa, changes in the hydrogen bond directionality, or other non-electrostatic effects. Overall, based on a consistent use of structural information as the starting point for converging free energy calculations, we conclude that the primary event should be described as a light-induced formation of an unstable ground state, whose relaxation leads to charge separation and to the

Structural Dynamics of Electronic Systems

NASA Astrophysics Data System (ADS)

Suhir, E.

2013-03-01

The published work on analytical ("mathematical") and computer-aided, primarily finite-element-analysis (FEA) based, predictive modeling of the dynamic response of electronic systems to shocks and vibrations is reviewed. While understanding the physics of and the ability to predict the response of an electronic structure to dynamic loading has been always of significant importance in military, avionic, aeronautic, automotive and maritime electronics, during the last decade this problem has become especially important also in commercial, and, particularly, in portable electronics in connection with accelerated testing of various surface mount technology (SMT) systems on the board level. The emphasis of the review is on the nonlinear shock-excited vibrations of flexible printed circuit boards (PCBs) experiencing shock loading applied to their support contours during drop tests. At the end of the review we provide, as a suitable and useful illustration, the exact solution to a highly nonlinear problem of the dynamic response of a "flexible-and-heavy" PCB to an impact load applied to its support contour during drop testing.

Nature-Inspired Structural Materials for Flexible Electronic Devices.

PubMed

Liu, Yaqing; He, Ke; Chen, Geng; Leow, Wan Ru; Chen, Xiaodong

2017-10-25

Exciting advancements have been made in the field of flexible electronic devices in the last two decades and will certainly lead to a revolution in peoples' lives in the future. However, because of the poor sustainability of the active materials in complex stress environments, new requirements have been adopted for the construction of flexible devices. Thus, hierarchical architectures in natural materials, which have developed various environment-adapted structures and materials through natural selection, can serve as guides to solve the limitations of materials and engineering techniques. This review covers the smart designs of structural materials inspired by natural materials and their utility in the construction of flexible devices. First, we summarize structural materials that accommodate mechanical deformations, which is the fundamental requirement for flexible devices to work properly in complex environments. Second, we discuss the functionalities of flexible devices induced by nature-inspired structural materials, including mechanical sensing, energy harvesting, physically interacting, and so on. Finally, we provide a perspective on newly developed structural materials and their potential applications in future flexible devices, as well as frontier strategies for biomimetic functions. These analyses and summaries are valuable for a systematic understanding of structural materials in electronic devices and will serve as inspirations for smart designs in flexible electronics.

Theoretical Study of tip apex electronic structure in Scanning Tunneling Microscope

NASA Astrophysics Data System (ADS)

Choi, Heesung; Huang, Min; Randall, John; Cho, Kyeongjae

2011-03-01

Scanning Tunneling Microscope (STM) has been widely used to explore diverse surface properties with an atomic resolution, and STM tip has played a critical role in controlling surface structures. However, detailed information of atomic and electronic structure of STM tip and the fundamental understanding of STM images are still incomplete. Therefore, it is important to develop a comprehensive understanding of the electronic structure of STM tip. We have studied the atomic and electronic structures of STM tip with various transition metals (TMs) by DFT method. The d-electrons of TM tip apex atoms show different orbital states near the Fermi level. We will present comprehensive data of STM tips from our DFT calculation. Verified quantification of the tip electronic structures will lead to fundamental understanding of STM tip structure-property relationship. This work is supported by the DARPA TBN Program and the Texas ETF. DARPA Tip Based Nanofabrication Program and the Emerging Technology Fund of the State of Texas.

Structural stability and electronic structure of transition metal compound: HfN

NASA Astrophysics Data System (ADS)

Sarwan, Madhu; Shukoor, V. Abdul; Singh, Sadhna

2018-05-01

The structural stability of transition metal nitride (HfN) has been investigated using density functional theory (DFT) with the help of Quantum-espresso codes. Our calculations confirm that the hafnium nitride (HfN) is stable in zinc-blende (B3) and rock-salt (B1) type structure. We have also reported the structural and electronic properties of HfN compound. These structural properties have been compared with experimental and theoretical data available on this compound.

Electronic structure of scandium-doped MgB2

NASA Astrophysics Data System (ADS)

de La Peña, Omar; Agrestini, Stefano

2005-03-01

Recently has been reported the synthesis of a new superconducting alloy based on MgB2, where Mg is partially substituted with Sc. In order to analyze the effect of Sc doping on the structural and superconducting properties of Mg1-xScxB2, we have performed a detailed study of the electronic structure for this new diboride. The calculations have been done using the first-principles LAPW method, within the supercell approach for modeling the doping. In this work we report results for the electronic band structure, Fermi surface, and density of states. The effect of the Sc-d orbitals on the structural and electronic properties of Mg1-xScxB2 is analyzed. Increasing the Sc concentration (x) the σ-band is gradually filled, because Sc have one valence electron more than Mg. Interestingly, the analysis of the band structure shows that even for ScB2 the top of the σ-band remain above the Fermi level, nevertheless the σ-band presents high dispersion and has an important contribution of d states. In this way, in addition to the band filling effect, Sc doping gradually reduces the two-dimensional character of the σ- band in Mg1-xScxB2 as a result of increasing the sp(B)-d(Sc) hybridization. This research was partially supported by Consejo Nacional de Ciencia y Tecnolog'ia (CONACYT, M'exico) under Grant. No. 43830-F

First-principle simulations of electronic structure in semicrystalline polyethylene

NASA Astrophysics Data System (ADS)

Moyassari, A.; Unge, M.; Hedenqvist, M. S.; Gedde, U. W.; Nilsson, F.

2017-05-01

In order to increase our fundamental knowledge about high-voltage cable insulation materials, realistic polyethylene (PE) structures, generated with a novel molecular modeling strategy, have been analyzed using first principle electronic structure simulations. The PE structures were constructed by first generating atomistic PE configurations with an off-lattice Monte Carlo method and then equilibrating the structures at the desired temperature and pressure using molecular dynamics simulations. Semicrystalline, fully crystalline and fully amorphous PE, in some cases including crosslinks and short-chain branches, were analyzed. The modeled PE had a structure in agreement with established experimental data. Linear-scaling density functional theory (LS-DFT) was used to examine the electronic structure (e.g., spatial distribution of molecular orbitals, bandgaps and mobility edges) on all the materials, whereas conventional DFT was used to validate the LS-DFT results on small systems. When hybrid functionals were used, the simulated bandgaps were close to the experimental values. The localization of valence and conduction band states was demonstrated. The localized states in the conduction band were primarily found in the free volume (result of gauche conformations) present in the amorphous regions. For branched and crosslinked structures, the localized electronic states closest to the valence band edge were positioned at branches and crosslinks, respectively. At 0 K, the activation energy for transport was lower for holes than for electrons. However, at room temperature, the effective activation energy was very low (˜0.1 eV) for both holes and electrons, which indicates that the mobility will be relatively high even below the mobility edges and suggests that charge carriers can be hot carriers above the mobility edges in the presence of a high electrical field.

Theoretical investigation of the electronic structure of a substituted nickel phthalocyanine

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

Kaur, Prabhjot, E-mail: prabhphysics@gmail.com; Sachdeva, Ritika; Singh, Sukhwinder

2016-05-23

The optimized geometry and electronic structure of an organic compound nickel phthalocyanine tetrasulfonic acid tetra sodium salt have been investigated using density functional theory. We have also optimized the structure of nickel phthalocyanine tetrasulfonic acid tetra sodium salt in dimethyl sulfoxide to study effects of solvent on the electronic structure and transitions. Experimentally, the electronic transitions have been studied using UV-VIS spectroscopic technique. It is observed that the electronic transitions obtained from the theoretical studies generally agree with the experiment.

Atomic and electronic structure of exfoliated black phosphorus

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

Wu, Ryan J.; Topsakal, Mehmet; Jeong, Jong Seok

2015-11-15

Black phosphorus, a layered two-dimensional crystal with tunable electronic properties and high hole mobility, is quickly emerging as a promising candidate for future electronic and photonic devices. Although theoretical studies using ab initio calculations have tried to predict its atomic and electronic structure, uncertainty in its fundamental properties due to a lack of clear experimental evidence continues to stymie our full understanding and application of this novel material. In this work, aberration-corrected scanning transmission electron microscopy and ab initio calculations are used to study the crystal structure of few-layer black phosphorus. Directly interpretable annular dark-field images provide a three-dimensional atomic-resolutionmore » view of this layered material in which its stacking order and all three lattice parameters can be unambiguously identified. In addition, electron energy-loss spectroscopy (EELS) is used to measure the conduction band density of states of black phosphorus, which agrees well with the results of density functional theory calculations performed for the experimentally determined crystal. Furthermore, experimental EELS measurements of interband transitions and surface plasmon excitations are also consistent with simulated results. Finally, the effects of oxidation on both the atomic and electronic structure of black phosphorus are analyzed to explain observed device degradation. The transformation of black phosphorus into amorphous PO{sub 3} or H{sub 3}PO{sub 3} during oxidation may ultimately be responsible for the degradation of devices exposed to atmosphere over time.« less

Structure and Electronic Properties of Interface-Confined Oxide Nanostructures

DOE PAGES

Liu, Yun; Ning, Yanxiao; Yu, Liang; ...

2017-09-16

The controlled fabrication of nanostructures has often made use of a substrate template to mediate and control the growth kinetics. Electronic substrate-mediated interactions have been demonstrated to guide the assembly of organic molecules or the nucleation of metal atoms but usually at cryogenic temperatures, where the diffusion has been limited. Combining STM, STS, and DFT studies, we report that the strong electronic interaction between transition metals and oxides could indeed govern the growth of low-dimensional oxide nanostructures. As a demonstration, a series of FeO triangles, which are of the same structure and electronic properties but with different sizes (side lengthmore » >3 nm), are synthesized on Pt(111). The strong interfacial interaction confines the growth of FeO nanostructures, leading to a discrete size distribution and a uniform step structure. Given the same interfacial configuration, as-grown FeO nanostructures not only expose identical edge/surface structure but also exhibit the same electronic properties, as manifested by the local density of states and local work functions. We expect the interfacial confinement effect can be generally applied to control the growth of oxide nanostructures on transition metal surfaces. These oxide nanostructures of the same structure and electronic properties are excellent models for studies of nanoscale effects and applications.« less

Structure and Electronic Properties of Interface-Confined Oxide Nanostructures

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

Liu, Yun; Ning, Yanxiao; Yu, Liang

The controlled fabrication of nanostructures has often made use of a substrate template to mediate and control the growth kinetics. Electronic substrate-mediated interactions have been demonstrated to guide the assembly of organic molecules or the nucleation of metal atoms but usually at cryogenic temperatures, where the diffusion has been limited. Combining STM, STS, and DFT studies, we report that the strong electronic interaction between transition metals and oxides could indeed govern the growth of low-dimensional oxide nanostructures. As a demonstration, a series of FeO triangles, which are of the same structure and electronic properties but with different sizes (side lengthmore » >3 nm), are synthesized on Pt(111). The strong interfacial interaction confines the growth of FeO nanostructures, leading to a discrete size distribution and a uniform step structure. Given the same interfacial configuration, as-grown FeO nanostructures not only expose identical edge/surface structure but also exhibit the same electronic properties, as manifested by the local density of states and local work functions. We expect the interfacial confinement effect can be generally applied to control the growth of oxide nanostructures on transition metal surfaces. These oxide nanostructures of the same structure and electronic properties are excellent models for studies of nanoscale effects and applications.« less

Structural and electronic properties of L-amino acids

NASA Astrophysics Data System (ADS)

Tulip, P. R.; Clark, S. J.

2005-05-01

The structural and electronic properties of four L-amino acids alanine, leucine, isoleucine, and valine have been investigated using density functional theory (DFT) and the generalized gradient approximation. Within the crystals, it is found that the constituent molecules adopt zwitterionic configurations, in agreement with experimental work. Lattice constants are found to be in good agreement with experimentally determined values, although certain discrepancies do exist due to the description of van der Waals interactions. We find that these materials possess wide DFT band gaps in the region of 5 eV, with electrons highly localized to the constituent molecules. It is found that the main mechanisms behind crystal formation are dipolar interactions and hydrogen bonding of a primarily electrostatic character, in agreement with current biochemical understanding of these systems. The electronic structure suggests that the amine and carboxy functional groups are dominant in determining band structure.

Engineering the electronic structure of graphene superlattices via Fermi velocity modulation

NASA Astrophysics Data System (ADS)

Lima, Jonas R. F.

2017-01-01

Graphene superlattices have attracted much research interest in the last years, since it is possible to manipulate the electronic properties of graphene in these structures. It has been verified that extra Dirac points appear in the electronic structure of the system. The electronic structure in the vicinity of these points has been studied for a gapless and gapped graphene superlattice and for a graphene superlattice with a spatially modulated energy gap. In each case a different behavior was obtained. In this work we show that via Fermi velocity engineering it is possible to tune the electronic properties of a graphene superlattice to match all the previous cases studied. We also obtained new features of the system never observed before, reveling that the electronic structure of graphene is very sensitive to the modulation of the Fermi velocity. The results obtained here are relevant for the development of novel graphene-based electronic devices.

Electronic Structure of GdCuGe Intermetallic Compound

NASA Astrophysics Data System (ADS)

Lukoyanov, A. V.; Knyazev, Yu. V.; Kuz'min, Yu. I.

2018-04-01

The electronic structure of GdCuGe intermetallic compound has been studied. Spin-polarized energy spectrum calculations have been performed by the band method with allowance for strong electron correlations in the 4 f-shell of gadolinium ions. Antiferromagnetic ordering of GdCuGe at low temperatures has been obtained in a theoretical calculation, with the value of the effective magnetic moment of gadolinium ions reproduced in fair agreement with experimental data. The electronic density of states has been analyzed. An optical conductivity spectrum has been calculated for GdCuGe; it reveals specific features that are analogous to the ones discovered previously in the GdCuSi compound with a similar hexagonal structure.

Boron difluoride dibenzoylmethane derivatives: Electronic structure and luminescence

NASA Astrophysics Data System (ADS)

Tikhonov, Sergey A.; Vovna, Vitaliy I.; Osmushko, Ivan S.; Fedorenko, Elena V.; Mirochnik, Anatoliy G.

2018-01-01

Electronic structure and optical properties of boron difluoride dibenzoylmethanate and four of its derivatives have been studied by X-ray photoelectron spectroscopy, absorption and luminescence spectroscopy and quantum chemistry (DFT, TDDFT). The relative quantum luminescence yields have been revealed to correlate with charge transfers of HOMO-LUMO transitions, energy barriers of aromatic substituents rotation and the lifetime of excited states in the investigated complexes. The bathochromic shift of intensive bands in the optical spectra has been observed to occur when the functional groups are introduced into p-positions of phenyl cycles due to destabilizing HOMO levels. Calculated energy intervals between electronic levels correlate well with XPS spectra structure of valence and core electrons.

Electronic and structural properties of Lu under pressure: Relation to structural phases of the rare-earth metals

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

Min, B.I.; Oguchi, T.; Jansen, H.J.F.

1986-07-15

Ground-state electronic and structural properties of Lu under pressure are investigated with use of the self-consistent all-electron total-energy linear muffin-tin orbital band-structure method within a local-density-functional approximation. Pressure-induced structural transitions are found to occur in the following sequence: hcp--(Sm-type)--dhcp--fcc, which is the same as that observed in the crystal structures of the trivalent rare-earth metals with decreasing atomic number. This structural transition is correlated with the increase in the number of d-italic electrons under pressure.

Free electron laser-driven ultrafast rearrangement of the electronic structure in Ti

PubMed Central

Principi, E.; Giangrisostomi, E.; Cucini, R.; Bencivenga, F.; Battistoni, A.; Gessini, A.; Mincigrucci, R.; Saito, M.; Di Fonzo, S.; D'Amico, F.; Di Cicco, A.; Gunnella, R.; Filipponi, A.; Giglia, A.; Nannarone, S.; Masciovecchio, C.

2015-01-01

High-energy density extreme ultraviolet radiation delivered by the FERMI seeded free-electron laser has been used to create an exotic nonequilibrium state of matter in a titanium sample characterized by a highly excited electron subsystem at temperatures in excess of 10 eV and a cold solid-density ion lattice. The obtained transient state has been investigated through ultrafast absorption spectroscopy across the Ti M2,3-edge revealing a drastic rearrangement of the sample electronic structure around the Fermi level occurring on a time scale of about 100 fs. PMID:26798835

Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool

PubMed Central

Zhang, Jian; Frerman, Frank E.; Kim, Jung-Ja P.

2006-01-01

Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a 4Fe4S flavoprotein located in the inner mitochondrial membrane. It catalyzes ubiquinone (UQ) reduction by ETF, linking oxidation of fatty acids and some amino acids to the mitochondrial respiratory chain. Deficiencies in ETF or ETF-QO result in multiple acyl-CoA dehydrogenase deficiency, a human metabolic disease. Crystal structures of ETF-QO with and without bound UQ were determined, and they are essentially identical. The molecule forms a single structural domain. Three functional regions bind FAD, the 4Fe4S cluster, and UQ and are closely packed and share structural elements, resulting in no discrete structural domains. The UQ-binding pocket consists mainly of hydrophobic residues, and UQ binding differs from that of other UQ-binding proteins. ETF-QO is a monotopic integral membrane protein. The putative membrane-binding surface contains an α-helix and a β-hairpin, forming a hydrophobic plateau. The UQ—flavin distance (8.5 Å) is shorter than the UQ—cluster distance (18.8 Å), and the very similar redox potentials of FAD and the cluster strongly suggest that the flavin, not the cluster, transfers electrons to UQ. Two possible electron transfer paths can be envisioned. First, electrons from the ETF flavin semiquinone may enter the ETF-QO flavin one by one, followed by rapid equilibration with the cluster. Alternatively, electrons may enter via the cluster, followed by equilibration between centers. In both cases, when ETF-QO is reduced to a two-electron reduced state (one electron at each redox center), the enzyme is primed to reduce UQ to ubiquinol via FAD. PMID:17050691

Structure of electron transfer flavoprotein-ubiquinone oxidoreductase and electron transfer to the mitochondrial ubiquinone pool.

PubMed

Zhang, Jian; Frerman, Frank E; Kim, Jung-Ja P

2006-10-31

Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) is a 4Fe4S flavoprotein located in the inner mitochondrial membrane. It catalyzes ubiquinone (UQ) reduction by ETF, linking oxidation of fatty acids and some amino acids to the mitochondrial respiratory chain. Deficiencies in ETF or ETF-QO result in multiple acyl-CoA dehydrogenase deficiency, a human metabolic disease. Crystal structures of ETF-QO with and without bound UQ were determined, and they are essentially identical. The molecule forms a single structural domain. Three functional regions bind FAD, the 4Fe4S cluster, and UQ and are closely packed and share structural elements, resulting in no discrete structural domains. The UQ-binding pocket consists mainly of hydrophobic residues, and UQ binding differs from that of other UQ-binding proteins. ETF-QO is a monotopic integral membrane protein. The putative membrane-binding surface contains an alpha-helix and a beta-hairpin, forming a hydrophobic plateau. The UQ-flavin distance (8.5 A) is shorter than the UQ-cluster distance (18.8 A), and the very similar redox potentials of FAD and the cluster strongly suggest that the flavin, not the cluster, transfers electrons to UQ. Two possible electron transfer paths can be envisioned. First, electrons from the ETF flavin semiquinone may enter the ETF-QO flavin one by one, followed by rapid equilibration with the cluster. Alternatively, electrons may enter via the cluster, followed by equilibration between centers. In both cases, when ETF-QO is reduced to a two-electron reduced state (one electron at each redox center), the enzyme is primed to reduce UQ to ubiquinol via FAD.

Bulk and surface electronic structures of MgO

NASA Astrophysics Data System (ADS)

Schönberger, U.; Aryasetiawan, F.

1995-09-01

The bulk electronic structure of MgO is calculated from first principles including correlation effects within the GW approximation. The band gap, the position of the 2s O band, and the valence band width are in good agreement with experiment. From the quasiparticle band structure, optical transitions corresponding to the main optical absorption peaks are identified. The energy-loss spectrum is also calculated and compared with experiment. The surface electronic structure of MgO(100) is calculated self-consistently within the local-density approximation. It is found that states observed in a recent photoemission experiment outside the bulk allowed states are close to surface states.

The structural, electronic and optical properties of Au-ZnO interface structure from the first-principles calculation

NASA Astrophysics Data System (ADS)

Huo, Jin-Rong; Li, Lu; Cheng, Hai-Xia; Wang, Xiao-Xu; Zhang, Guo-Hua; Qian, Ping

2018-03-01

The interface structure, electronic and optical properties of Au-ZnO are studied using the first-principles calculation based on density functional theory (DFT). Given the interfacial distance, bonding configurations and terminated surface, we built the optimal interface structure and calculated the electronic and optical properties of the interface. The total density of states, partial electronic density of states, electric charge density and atomic populations (Mulliken) are also displayed. The results show that the electrons converge at O atoms at the interface, leading to a stronger binding of interfaces and thereby affecting the optical properties of interface structures. In addition, we present the binding energies of different interface structures. When the interface structure of Au-ZnO gets changed, furthermore, varying optical properties are exhibited.

Electronic structure of PPP@ZnO from all-electron quasiarticle calculations

NASA Astrophysics Data System (ADS)

Höffling, Benjamin; Nabok, Dimitri; Draxl, Claudia; Condensed Matter Theory Group, Humboldt University Berlin Team

We investigate the electronic properties of poly(para-phenylene) (PPP) adsorbed on the non-polar (001) surface of rocksalt (rs) ZnO using all-electron density functional theory (DFT) as well as quasiparticle (QP) calculations within the GW approach. A particular focus is put on the electronic band discontinuities at the interface, where we investigate the impact of quantum confinement, molecular polarization, and charge rearrangement. For our prototypical system, PPP@ZnO, we find a type-I heterostructure. Comparison of the band offsets derived from a QP-treatment of the hybrid system with predictions based on mesoscopic methods, like the Shockley-Anderson model or alignment via the electrostatic potential, reveals the inadequacy of these simple approaches for the prediction of the electronic structure of such inorganic/organic heterosystems. Finally, we explore the optical excitations of the interface compared to the features of the pristine components and discuss the methodological implications for the ab-initio treatment of interface electronics.

Advanced understanding on electronic structure of molecular semiconductors and their interfaces

NASA Astrophysics Data System (ADS)

Akaike, Kouki

2018-03-01

Understanding the electronic structure of organic semiconductors and their interfaces is critical to optimizing functionalities for electronics applications, by rational chemical design and appropriate combination of device constituents. The unique electronic structure of a molecular solid is characterized as (i) anisotropic electrostatic fields that originate from molecular quadrupoles, (ii) interfacial energy-level lineup governed by simple electrostatics, and (iii) weak intermolecular interactions that make not only structural order but also energy distributions of the frontier orbitals sensitive to atmosphere and interface growth. This article shows an overview on these features with reference to the improved understanding of the orientation-dependent electronic structure, comprehensive mechanisms of molecular doping, and energy-level alignment. Furthermore, the engineering of ionization energy by the control of the electrostatic fields and work function of practical electrodes by contact-induced doping is briefly described for the purpose of highlighting how the electronic structure impacts the performance of organic devices.

Electronic structures and magnetic/optical properties of metal phthalocyanine complexes

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

Baba, Shintaro; Suzuki, Atsushi, E-mail: suzuki@mat.usp.ac.jp; Oku, Takeo

2016-02-01

Electronic structures and magnetic / optical properties of metal phthalocyanine complexes were studied by quantum calculations using density functional theory. Effects of central metal and expansion of π orbital on aromatic ring as conjugation system on the electronic structures, magnetic, optical properties and vibration modes of infrared and Raman spectra of metal phthalocyanines were investigated. Electron and charge density distribution and energy levels near frontier orbital and excited states were influenced by the deformed structures varied with central metal and charge. The magnetic parameters of chemical shifts in {sup 13}C-nuclear magnetic resonance ({sup 13}C-NMR), principle g-tensor, A-tensor, V-tensor of electricmore » field gradient and asymmetry parameters derived from the deformed structures with magnetic interaction of nuclear quadruple interaction based on electron and charge density distribution with a bias of charge near ligand under crystal field.« less

Water channel structures analysed by electron crystallography.

PubMed

Tani, Kazutoshi; Fujiyoshi, Yoshinori

2014-05-01

The mechanisms underlying water transport through aquaporin (AQP) have been debated for two decades. The water permeation phenomenon of AQP seems inexplicable because the Grotthuss mechanism does not allow for simultaneous fast water permeability and inhibition of proton transfer through the hydrogen bonds of water molecules. The AQP1 structure determined by electron crystallography provided the first insights into the proton exclusion mechanism despite fast water permeation. Although several studies have provided clues about the mechanism based on the AQP structure, each proposed mechanism remains incomplete. The present review is focused on AQP function and structure solved by electron crystallography in an attempt to fill the gaps between the findings in the absence and presence of lipids. Many AQP structures can be superimposed regardless of the determination method. The AQP fold is preserved even under conditions lacking lipids, but the water arrangement in the channel pore differs. The differences might be explained by dipole moments formed by the two short helices in the lipid bilayer. In addition, structure analyses of double-layered two-dimensional crystals of AQP suggest an array formation and cell adhesive function. Electron crystallography findings not only have contributed to resolve some of the water permeation mechanisms, but have also elucidated the multiple functions of AQPs in the membrane. The roles of AQPs in the brain remain obscure, but their multiple activities might be important in the regulation of brain and other biological functions. This article is part of a Special Issue entitled Aquaporins. © 2013.

Modification of electronic structure, magnetic structure, and topological phase of bismuthene by point defects

NASA Astrophysics Data System (ADS)

Kadioglu, Yelda; Kilic, Sevket Berkay; Demirci, Salih; Aktürk, O. Üzengi; Aktürk, Ethem; Ciraci, Salim

2017-12-01

This paper reveals how the electronic structure, magnetic structure, and topological phase of two-dimensional (2D), single-layer structures of bismuth are modified by point defects. We first showed that a free-standing, single-layer, hexagonal structure of bismuth, named h-bismuthene, exhibits nontrivial band topology. We then investigated interactions between single foreign adatoms and bismuthene structures, which comprise stability, bonding, electronic structure, and magnetic structures. Localized states in diverse locations of the band gap and resonant states in band continua of bismuthene are induced upon the adsorption of different adatoms, which modify electronic and magnetic properties. Specific adatoms result in reconstruction around the adsorption site. Single vacancies and divacancies can form readily in bismuthene structures and remain stable at high temperatures. Through rebondings, Stone-Whales-type defects are constructed by divacancies, which transform into a large hole at high temperature. Like adsorbed adatoms, vacancies induce also localized gap states, which can be eliminated through rebondings in divacancies. We also showed that not only the optical and magnetic properties, but also the topological features of pristine h-bismuthene can be modified by point defects. The modification of the topological features depends on the energies of localized states and also on the strength of coupling between point defects.

Electronic structure of nitrides PuN and UN

NASA Astrophysics Data System (ADS)

Lukoyanov, A. V.; Anisimov, V. I.

2016-11-01

The electronic structure of uranium and plutonium nitrides in ambient conditions and under pressure is investigated using the LDA + U + SO band method taking into account the spin-orbit coupling and the strong correlations of 5 f electrons of actinoid ions. The parameters of these interactions for the equilibrium cubic structure are calculated additionally. The application of pressure reduces the magnetic moment in PuN due to predominance of the f 6 configuration and the jj-type coupling. An increase in the occupancy of the 5 f state in UN leads to a decrease in the magnetic moment, which is also detected in the trigonal structure of the UN x β phase (La2O3-type structure). The theoretical results are in good agreement with the available experimental data.

Electronic Structure Contributions to Reactivity in Xanthine Oxidase Family Enzymes

PubMed Central

Stein, Benjamin W.; Kirk, Martin L.

2016-01-01

We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the 2-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function. PMID:25425163

Electronic structure contributions to reactivity in xanthine oxidase family enzymes.

PubMed

Stein, Benjamin W; Kirk, Martin L

2015-03-01

We review the xanthine oxidase (XO) family of pyranopterin molybdenum enzymes with a specific emphasis on electronic structure contributions to reactivity. In addition to xanthine and aldehyde oxidoreductases, which catalyze the two-electron oxidation of aromatic heterocycles and aldehyde substrates, this mini-review highlights recent work on the closely related carbon monoxide dehydrogenase (CODH) that catalyzes the oxidation of CO using a unique Mo-Cu heterobimetallic active site. A primary focus of this mini-review relates to how spectroscopy and computational methods have been used to develop an understanding of critical relationships between geometric structure, electronic structure, and catalytic function.

Geometric and electronic structures of potassium-adsorbed rubrene complexes

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

Li, Tsung-Lung, E-mail: quantum@mail.ncyu.edu.tw; Lu, Wen-Cai, E-mail: wencailu@jlu.edu.cn; State Key Laboratory of Theoretical and Computational Chemistry, Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin 130021

2015-06-28

The geometric and electronic structures of potassium-adsorbed rubrene complexes are studied in this article. It is found that the potassium-rubrene (K{sub 1}RUB) complexes inherit the main symmetry characteristics from their pristine counterparts and are thus classified into D{sub 2}- and C{sub 2h}-like complexes according to the relative orientations of the four phenyl side groups. The geometric structures of K{sub 1}RUB are governed by two general effects on the total energy: Deformation of the carbon frame of the pristine rubrene increases the total energy, while proximity of the potassium ion to the phenyl ligands decreases the energy. Under these general rules,more » the structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB, however, exhibit their respective peculiarities. These peculiarities can be illustrated by their energy profiles of equilibrium structures. For the potassium adsorption-sites, the D{sub 2}-like complexes show minimum-energy basins, whereas the C{sub 2h}-like ones have single-point minimum-energies. If the potassium atom ever has the energy to diffuse from the minimum-energy site, the potassium diffusion path on the D{sub 2}-like complexes is most likely along the backbone in contrast to the C{sub 2h}-like ones. Although the electronic structures of the minimum-energy structures of D{sub 2}- and C{sub 2h}-like K{sub 1}RUB are very alike, decompositions of their total spectra reveal insights into the electronic structures. First, the spectral shapes are mainly determined by the facts that, in comparison with the backbone carbons, the phenyl carbons have more uniform chemical environments and far less contributions to the electronic structures around the valence-band edge. Second, the electron dissociated from the potassium atom mainly remains on the backbone and has little effects on the electronic structures of the phenyl groups. Third, the two phenyls on the same side of the backbone as the potassium atom have more similar chemical

A Structural Model of a P450-Ferredoxin Complex from Orientation-Selective Double Electron-Electron Resonance Spectroscopy.

PubMed

Bowen, Alice M; Johnson, Eachan O D; Mercuri, Francesco; Hoskins, Nicola J; Qiao, Ruihong; McCullagh, James S O; Lovett, Janet E; Bell, Stephen G; Zhou, Weihong; Timmel, Christiane R; Wong, Luet Lok; Harmer, Jeffrey R

2018-02-21

Cytochrome P450 (CYP) monooxygenases catalyze the oxidation of chemically inert carbon-hydrogen bonds in diverse endogenous and exogenous organic compounds by atmospheric oxygen. This C-H bond oxy-functionalization activity has huge potential in biotechnological applications. Class I CYPs receive the two electrons required for oxygen activation from NAD(P)H via a ferredoxin reductase and ferredoxin. The interaction of Class I CYPs with their cognate ferredoxin is specific. In order to reconstitute the activity of diverse CYPs, structural characterization of CYP-ferredoxin complexes is necessary, but little structural information is available. Here we report a structural model of such a complex (CYP199A2-HaPux) in frozen solution derived from distance and orientation restraints gathered by the EPR technique of orientation-selective double electron-electron resonance (os-DEER). The long-lived oscillations in the os-DEER spectra were well modeled by a single orientation of the CYP199A2-HaPux complex. The structure is different from the two known Class I CYP-Fdx structures: CYP11A1-Adx and CYP101A1-Pdx. At the protein interface, HaPux residues in the [Fe 2 S 2 ] cluster-binding loop and the α3 helix and the C-terminus residue interact with CYP199A2 residues in the proximal loop and the C helix. These residue contacts are consistent with biochemical data on CYP199A2-ferredoxin binding and electron transfer. Electron-tunneling calculations indicate an efficient electron-transfer pathway from the [Fe 2 S 2 ] cluster to the heme. This new structural model of a CYP-Fdx complex provides the basis for tailoring CYP enzymes for which the cognate ferredoxin is not known, to accept electrons from HaPux and display monooxygenase activity.

Modifying the photoelectric behavior of bacteriorhodopsin by site-directed mutagenesis: electrochemical and genetic engineering approaches to molecular devices

NASA Astrophysics Data System (ADS)

Hong, F. T.; Hong, F. H.; Needleman, R. B.; Ni, B.; Chang, M.

1992-07-01

Bacteriorhodopsins (bR's) modified by substitution of the chromophore with synthetic vitamin A analogues or by spontaneous mutation have been reported as successful examples of using biomaterials to construct molecular optoelectronic devices. The operation of these devices depends on desirable optical properties derived from molecular engineering. This report examines the effect of site-directed mutagenesis on the photoelectric behavior of bR thin films with an emphasis on their application to the construction of molecular devices based on their unique photoelectric behavior. We examine the photoelectric signals induced by a microsecond light pulse in thin films which contain reconstituted oriented purple membrane sheets isolated from several mutant strains of Halobacterium halobium. A recently developed expression system is used to synthesize mutant bR's in their natural host, H. halobium. We then use a unique analytical method (tunable voltage clamp method) to investigate the effect of pH on the relaxation of two components of the photoelectric signals, B1 and B2. We found that for the four mutant bR's examined, the pH dependence of the B2 component varies significantly. Our results suggest that genetic engineering approaches can produce mutant bR's with altered photoelectric characteristics that can be exploited in the construction of devices.

The reaction of hydroxylamine with bacteriorhodopsin studied with mutants that have altered photocycles: selective reactivity of different photointermediates.

PubMed Central

Subramaniam, S; Marti, T; Rösselet, S J; Rothschild, K J; Khorana, H G

1991-01-01

The reaction of the retinylidene Schiff base in bacteriorhodopsin (bR) to the water-soluble reagent hydroxylamine is enhanced by greater than 2 orders of magnitude under illumination. We have used this reaction as a probe for changes in Schiff base reactivity during the photocycle of wild-type bR and mutants defective in proton transport. We report here that under illumination at pH 6, the D85N mutant has a 20-fold lower rate and the D212N mutant has a greater than 4-fold higher rate for the light-dependent reaction with hydroxylamine compared with wild-type bR. In contrast, the reactivities of wild-type bR and the D96N and T46V mutants are similar. It has been previously shown that the D96N and T46V replacements have no significant effect on the kinetics of "M" formation but have dramatic effects on rate of the decay of M. We therefore conclude that the hydroxylamine reaction occurs before formation of the M intermediate. Most likely it occurs at the "L" stage of the cycle and reflects increased water accessibility to the Schiff base due to a light-driven change in protein conformation. PMID:2006195

Electronic Structure Approach to Tunable Electronic Properties of Hybrid Organic-Inorganic Perovskites

NASA Astrophysics Data System (ADS)

Liu, Garnett; Huhn, William; Mitzi, David B.; Kanai, Yosuke; Blum, Volker

We present a study of the electronic structure of layered hybrid organic-inorganic perovskite (HOIP) materials using all-electron density-functional theory. Varying the nature of the organic and inorganic layers should enable systematically fine-tuning the carrier properties of each component. Using the HSE06 hybrid density functional including spin-orbit coupling (SOC), we validate the principle of tuning subsystem-specific parts of the electron band structures and densities of states in CH3NH3PbX3 (X=Cl, Br, I) compared to a modified organic component in layered (C6H5C2H4NH3) 2PbX4 (X=Cl, Br, I) and C20H22S4N2PbX4 (X=Cl, Br, I). We show that tunable shifts of electronic levels indeed arise by varying Cl, Br, I as the inorganic components, and CH3NH3+ , C6H5C2H4NH3+ , C20H22S4N22 + as the organic components. SOC is found to play an important role in splitting the conduction bands of the HOIP compounds investigated here. The frontier orbitals of the halide shift, increasing the gap, when Cl is substituted for Br and I.

Growth Behavior and Electronic Structure of Noble Metal-Doped Germanium Clusters.

PubMed

Mahtout, Sofiane; Siouani, Chaouki; Rabilloud, Franck

2018-01-18

Structures, energetics, and electronic properties of noble metal-doped germanium (MGe n with M = Cu, Ag, Au; n = 1-19) clusters are systematically investigated by using the density functional theory (DFT) approach. The endohedral structures in which the metal atom is encapsulated inside of a germanium cage appear at n = 10 when the dopant is Cu and n = 12 for M = Ag and Au. While Cu doping enhances the stability of the corresponding germanium frame, the binding energies of AgGe n and AuGe n are always lower than those of pure germanium clusters. Our results highlight the great stability of the CuGe 10 cluster in a D 4d structure and, to a lesser extent, that of AgGe 15 and AuGe 15 , which exhibits a hollow cage-like geometry. The sphere-type geometries obtained for n = 10-15 present a peculiar electronic structure in which the valence electrons of the noble metal and Ge atoms are delocalized and exhibit a shell structure associated with the quasi-spherical geometry. It is found that the coinage metal is able to give both s- and d-type electrons to be reorganized together with the valence electrons of Ge atoms through a pooling of electrons. The cluster size dependence of the stability, the frontier orbital energy gap, the vertical ionization potentials, and electron affinities are given.

Writing silica structures in liquid with scanning transmission electron microscopy.

PubMed

van de Put, Marcel W P; Carcouët, Camille C M C; Bomans, Paul H H; Friedrich, Heiner; de Jonge, Niels; Sommerdijk, Nico A J M

2015-02-04

Silica nanoparticles are imaged in solution with scanning transmission electron microscopy (STEM) using a liquid cell with silicon nitride (SiN) membrane windows. The STEM images reveal that silica structures are deposited in well-defined patches on the upper SiN membranes upon electron beam irradiation. The thickness of the deposits is linear with the applied electron dose. Scanning electron microscopy (SEM) and atomic force microscopy (AFM) demonstrate that the deposited patches are a result of the merging of the original 20 nm-diameter nanoparticles, and that the related surface roughness depends on the electron dose rate used. Using this approach, sub-micrometer scale structures are written on the SiN in liquid by controlling the electron exposure as function of the lateral position. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Computational Chemistry Using Modern Electronic Structure Methods

ERIC Educational Resources Information Center

Bell, Stephen; Dines, Trevor J.; Chowdhry, Babur Z.; Withnall, Robert

2007-01-01

Various modern electronic structure methods are now days used to teach computational chemistry to undergraduate students. Such quantum calculations can now be easily used even for large size molecules.

Electronic structures of Al-Si clusters and the magic number structure Al8Si4

NASA Astrophysics Data System (ADS)

Du, Ning; Su, Mingzhi; Chen, Hongshan

2018-02-01

The low-energy structures of Al8Sim (m = 1-6) have been determined by using the genetic algorithm combined with density functional theory and the Second-order Moller-Plesset perturbation theory (MP2) models. The results show that the close-packed structures are preferable in energy for Al-Si clusters and in most cases there exist a few isomers with close energies. The valence molecular orbitals, the orbital level structures and the electron localisation function (ELF) consistently demonstrate that the electronic structures of Al-Si clusters can be described by the jellium model. Al8Si4 corresponds to a magic number structure with pronounced stability and large energy gap; the 40 valence electrons form closed 1S21P61D102S21F142P6 shells. The ELF attractors also suggest weak covalent Si-Si, Si-Al and Al-Al bonding, and doping Si in aluminium clusters promotes the covalent interaction between Al atoms.

The structural and electronic properties of metal atoms adsorbed on graphene

NASA Astrophysics Data System (ADS)

Liu, Wenjiang; Zhang, Cheng; Deng, Mingsen; Cai, Shaohong

2017-09-01

Based on density functional theory (DFT), we studied the structural and electronic properties of seven different metal atoms adsorbed on graphene (M + graphene). The geometries, adsorption energies, density of states (DOS), band structures, electronic dipole moment, magnetic moment and work function (WF) of M + graphene were calculated. The adsorption energies ΔE indicated that Li, Na, K, Ca and Fe adsorbed on graphene were tending to form stable structures. However, diffusion would occur on Cu and Ag adsorbed on graphene. In addition, the electronic structure near the Fermi level of graphene was significantly affected by Fe (Cu and Ag), compared with Li (Na, K and Ca). The electronic dipole moment and magnetic moment of M + graphene were sensitive to the adsorbed metal atoms. Moreover, we found electropositive (electronegative) adsorption can decrease (increase) the WF of the surface. Specially, the WF of Ag + graphene and Fe + graphene would increase because surface dipole moment make a contribution to electron.

Site-specific electronic structure analysis by channeling EELS and first-principles calculations.

PubMed

Tatsumi, Kazuyoshi; Muto, Shunsuke; Yamamoto, Yu; Ikeno, Hirokazu; Yoshioka, Satoru; Tanaka, Isao

2006-01-01

Site-specific electronic structures were investigated by electron energy loss spectroscopy (EELS) under electron channeling conditions. The Al-K and Mn-L(2,3) electron energy loss near-edge structure (ELNES) of, respectively, NiAl2O4 and Mn3O4 were measured. Deconvolution of the raw spectra with the instrumental resolution function restored the blunt and hidden fine features, which allowed us to interpret the experimental spectral features by comparing with theoretical spectra obtained by first-principles calculations. The present method successfully revealed the electronic structures specific to the differently coordinated cationic sites.

Electron Heat Flux in Pressure Balance Structures at Ulysses

NASA Technical Reports Server (NTRS)

Yamauchi, Yohei; Suess, Steven T.; Sakurai, Takashi; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Pressure balance structures (PBSs) are a common feature in the high-latitude solar wind near solar minimum. Rom previous studies, PBSs are believed to be remnants of coronal plumes and be related to network activity such as magnetic reconnection in the photosphere. We investigated the magnetic structures of the PBSs, applying a minimum variance analysis to Ulysses/Magnetometer data. At 2001 AGU Spring meeting, we reported that PBSs have structures like current sheets or plasmoids, and suggested that they are associated with network activity at the base of polar plumes. In this paper, we have analyzed high-energy electron data at Ulysses/SWOOPS to see whether bi-directional electron flow exists and confirm the conclusions more precisely. As a result, although most events show a typical flux directed away from the Sun, we have obtained evidence that some PBSs show bi-directional electron flux and others show an isotropic distribution of electron pitch angles. The evidence shows that plasmoids are flowing away from the Sun, changing their flow direction dynamically in a way not caused by Alfven waves. From this, we have concluded that PBSs are generated due to network activity at the base of polar plumes and their magnetic structures axe current sheets or plasmoids.

Fine Structure in the Secondary Electron Emission Peak for Diamond Crystal with (100) Negative Electron Affinity Surface

NASA Technical Reports Server (NTRS)

Asnin, V. M.; Krainsky, I. L.

1998-01-01

A fine structure was discovered in the low-energy peak of the secondary electron emission spectra of the diamond surface with negative electron affinity. We studied this structure for the (100) surface of the natural type-IIb diamond crystal. We have found that the low-energy peak consists of a total of four maxima. The relative energy positions of three of them could be related to the electron energy minima near the bottom of the conduction band. The fourth peak, having the lowest energy, was attributed to the breakup of the bulk exciton at the surface during the process of secondary electron emission.

β-armchair antimony nanotube: Structure, stability and electronic properties

NASA Astrophysics Data System (ADS)

Singh, Shilpa; Gupta, Sanjeev K.; Sonvane, Yogesh; Gajjar, P. N.

2018-05-01

In the present work, we have used density functional theory (DFT) to investigate the structure, stability and electronic properties of β-armchair antimony nanotube (ASbNT). We have calculated formation energy and found that β-armchair antimony nanotube (ASbNT) is energetically less stable than β-antimonene. The result shows that β-ASbNT of higher diameter are more stable than nanotubes of lower diameter while electronic band structure shows semiconducting nature of these nanotubes.

Test report: Shock test of the electron/proton spectrometer structural test unit

NASA Technical Reports Server (NTRS)

Vincent, D. L.

1972-01-01

A shock test of the electron-proton spectrometer structural test unit was conducted. The purpose of the shock test was to verify the structural integrity of the electron-spectrometer design and to obtain data on the shock response of the electronics and electronic housing. The test equipment is described and typical shock response data are provided.

Structural complexities in the active layers of organic electronics.

PubMed

Lee, Stephanie S; Loo, Yueh-Lin

2010-01-01

The field of organic electronics has progressed rapidly in recent years. However, understanding the direct structure-function relationships between the morphology in electrically active layers and the performance of devices composed of these materials has proven difficult. The morphology of active layers in organic electronics is inherently complex, with heterogeneities existing across multiple length scales, from subnanometer to micron and millimeter range. A major challenge still facing the organic electronics community is understanding how the morphology across all of the length scales in active layers collectively determines the device performance of organic electronics. In this review we highlight experiments that have contributed to the elucidation of structure-function relationships in organic electronics and also point to areas in which knowledge of such relationships is still lacking. Such knowledge will lead to the ability to select active materials on the basis of their inherent properties for the fabrication of devices with prespecified characteristics.

Advances in structural and functional analysis of membrane proteins by electron crystallography

PubMed Central

Wisedchaisri, Goragot; Reichow, Steve L.; Gonen, Tamir

2011-01-01

Summary Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography. PMID:22000511

Electronic Structure Calculation of Permanent Magnets using the KKR Green's Function Method

NASA Astrophysics Data System (ADS)

Doi, Shotaro; Akai, Hisazumi

2014-03-01

Electronic structure and magnetic properties of permanent magnetic materials, especially Nd2Fe14B, are investigated theoretically using the KKR Green's function method. Important physical quantities in magnetism, such as magnetic moment, Curie temperature, and anisotropy constant, which are obtained from electronics structure calculations in both cases of atomic-sphere-approximation and full-potential treatment, are compared with past band structure calculations and experiments. The site preference of heavy rare-earth impurities are also evaluated through the calculation of formation energy with the use of coherent potential approximations. Further, the development of electronic structure calculation code using the screened KKR for large super-cells, which is aimed at studying the electronic structure of realistic microstructures (e.g. grain boundary phase), is introduced with some test calculations.

Actinide electronic structure and atomic forces

NASA Astrophysics Data System (ADS)

Albers, R. C.; Rudin, Sven P.; Trinkle, Dallas R.; Jones, M. D.

2000-07-01

We have developed a new method[1] of fitting tight-binding parameterizations based on functional forms developed at the Naval Research Laboratory.[2] We have applied these methods to actinide metals and report our success using them (see below). The fitting procedure uses first-principles local-density-approximation (LDA) linear augmented plane-wave (LAPW) band structure techniques[3] to first calculate an electronic-structure band structure and total energy for fcc, bcc, and simple cubic crystal structures for the actinide of interest. The tight-binding parameterization is then chosen to fit the detailed energy eigenvalues of the bands along symmetry directions, and the symmetry of the parameterization is constrained to agree with the correct symmetry of the LDA band structure at each eigenvalue and k-vector that is fit to. By fitting to a range of different volumes and the three different crystal structures, we find that the resulting parameterization is robust and appears to accurately calculate other crystal structures and properties of interest.

Electron spin relaxation in two polymorphic structures of GaN

NASA Astrophysics Data System (ADS)

Kang, Nam Lyong

2015-03-01

The relaxation process of electron spin in systems of electrons interacting with piezoelectric deformation phonons that are mediated through spin-orbit interactions was interpreted from a microscopic point of view using the formula for the electron spin relaxation times derived by a projection-reduction method. The electron spin relaxation times in two polymorphic structures of GaN were calculated. The piezoelectric material constant for the wurtzite structure obtained by a comparison with a previously reported experimental result was {{P}pe}=1.5 × {{10}29} eV {{m}-1}. The temperature and magnetic field dependence of the relaxation times for both wurtzite and zinc-blende structures were similar, but the relaxation times in zinc-blende GaN were smaller and decreased more rapidly with increasing temperature and magnetic field than that in wurtzite GaN. This study also showed that the electron spin relaxation for wurtzite GaN at low density could be explained by the Elliot-Yafet process but not for zinc-blende GaN in the metallic regime.

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

PubMed

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

2012-02-08

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

Instructional Approach to Molecular Electronic Structure Theory

ERIC Educational Resources Information Center

Dykstra, Clifford E.; Schaefer, Henry F.

1977-01-01

Describes a graduate quantum mechanics projects in which students write a computer program that performs ab initio calculations on the electronic structure of a simple molecule. Theoretical potential energy curves are produced. (MLH)

Configuration-specific electronic structure of strongly interacting interfaces: TiOPc on Cu(110)

NASA Astrophysics Data System (ADS)

Maughan, Bret; Zahl, Percy; Sutter, Peter; Monti, Oliver L. A.

2017-12-01

We use low-temperature scanning tunneling microscopy in combination with angle-resolved ultraviolet and two-photon photoemission spectroscopy to investigate the interfacial electronic structure of titanyl phthalocyanine (TiOPc) on Cu(110). We show that the presence of two unique molecular adsorption configurations is crucial for a molecular-level analysis of the hybridized interfacial electronic structure. Specifically, thermally induced self-assembly exposes marked adsorbate-configuration-specific contributions to the interfacial electronic structure. The results of this work demonstrate an avenue towards understanding and controlling interfacial electronic structure in chemisorbed films even for the case of complex film structure.

Present and future of membrane protein structure determination by electron crystallography.

PubMed

Ubarretxena-Belandia, Iban; Stokes, David L

2010-01-01

Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. Copyright © 2010 Elsevier Inc. All rights reserved.

Present and future of membrane protein structure determination by electron crystallography

PubMed Central

Ubarretxena-Belandia, Iban; Stokes, David L.

2011-01-01

Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This review describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. PMID:21115172

Structure of Wet Specimens in Electron Microscopy

ERIC Educational Resources Information Center

Parsons, D. F.

1974-01-01

Discussed are past work and recent advances in the use of electron microscopes for viewing structures immersed in gas and liquid. Improved environmental chambers make it possible to examine wet specimens easily. (Author/RH)

Real-space visualization of conformation-independent oligothiophene electronic structure

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

Taber, Benjamen N.; Kislitsyn, Dmitry A.; Gervasi, Christian F.

2016-05-21

We present scanning tunneling microscopy and spectroscopy (STM/STS) investigations of the electronic structures of different alkyl-substituted oligothiophenes on the Au(111) surface. STM imaging showed that on Au(111), oligothiophenes adopted distinct straight and bent conformations. By combining STS maps with STM images, we visualize, in real space, particle-in-a-box-like oligothiophene molecular orbitals. We demonstrate that different planar conformers with significant geometrical distortions of oligothiophene backbones surprisingly exhibit very similar electronic structures, indicating a low degree of conformation-induced electronic disorder. The agreement of these results with gas-phase density functional theory calculations implies that the oligothiophene interaction with the Au(111) surface is generally insensitivemore » to molecular conformation.« less

Advances in structural and functional analysis of membrane proteins by electron crystallography.

PubMed

Wisedchaisri, Goragot; Reichow, Steve L; Gonen, Tamir

2011-10-12

Electron crystallography is a powerful technique for the study of membrane protein structure and function in the lipid environment. When well-ordered two-dimensional crystals are obtained the structure of both protein and lipid can be determined and lipid-protein interactions analyzed. Protons and ionic charges can be visualized by electron crystallography and the protein of interest can be captured for structural analysis in a variety of physiologically distinct states. This review highlights the strengths of electron crystallography and the momentum that is building up in automation and the development of high throughput tools and methods for structural and functional analysis of membrane proteins by electron crystallography. Copyright © 2011 Elsevier Ltd. All rights reserved.

Electronic and structural properties of B i2S e3:Cu

NASA Astrophysics Data System (ADS)

Sobczak, Kamil; Strak, Pawel; Kempisty, Pawel; Wolos, Agnieszka; Hruban, Andrzej; Materna, Andrzej; Borysiuk, Jolanta

2018-04-01

Electronic and structural properties of B i2S e3 and its extension to copper doped B i2S e3:Cu were studied using combined ab initio simulations and transmission electron microscopy based techniques, including electron energy loss spectroscopy, energy filtered transmission electron microscopy, and energy dispersive x-ray spectroscopy. The stability of the mixed phases was investigated for substitutional and intercalation changes of basic B i2S e3 structure. Four systems were compared: B i2S e3 , structures obtaining by Cu intercalation of the van der Waals gap, by substitution of Bi by Cu in quintuple layers, and C u2Se . The structures were identified and their electronic properties were obtained. Transmission electron microscopy measurements of B i2S e3 and the B i2S e3:Cu system identified the first structure as uniform and the second as composite, consisting of a nonuniform lower-Cu-content matrix and randomly distributed high-Cu-concentration precipitates. Critical comparison of the ab initio and experimental data identified the matrix as having a B i2S e3 dominant part with randomly distributed Cu-intercalated regions having 1Cu-B i2S e3 structure. The precipitates were determined to have 3Cu-B i2S e3 structure.

Crystal structure and electronic properties of a thiolate-protected Au24 nanocluster

NASA Astrophysics Data System (ADS)

Das, Anindita; Li, Tao; Li, Gao; Nobusada, Katsuyuki; Zeng, Chenjie; Rosi, Nathaniel L.; Jin, Rongchao

2014-05-01

Solving the total structures of gold nanoclusters is of critical importance for understanding their electronic, optical and catalytic properties. Herein, we report the X-ray structure of a charge-neutral Au24(SCH2Ph-tBu)20 nanocluster. This structure features a bi-tetrahedral Au8 kernel protected by four tetrameric staple-like motifs. Electronic structure analysis is further carried out and the optical absorption spectrum is interpreted. The Au24(SCH2Ph-tBu)20, Au23(S-c-C6H11)16 and Au25(SCH2CH2Ph)18 nanoclusters constitute the first crystallographically characterized ``trio''.Solving the total structures of gold nanoclusters is of critical importance for understanding their electronic, optical and catalytic properties. Herein, we report the X-ray structure of a charge-neutral Au24(SCH2Ph-tBu)20 nanocluster. This structure features a bi-tetrahedral Au8 kernel protected by four tetrameric staple-like motifs. Electronic structure analysis is further carried out and the optical absorption spectrum is interpreted. The Au24(SCH2Ph-tBu)20, Au23(S-c-C6H11)16 and Au25(SCH2CH2Ph)18 nanoclusters constitute the first crystallographically characterized ``trio''. Electronic supplementary information (ESI) available: Experimental and supporting Fig. S1-S3. CCDC NUMBER(1000102). For ESI and crystallographic data in CIF or other electronic format see DOI: 10.1039/c4nr01350f

Electronic structure of free and doped actinides: N and Z dependences of energy levels and electronic structure parameters

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

Kulagin, N.

2005-02-15

Theoretical study of electronic structure of antinide ions and its dependence on N and Z are presented in this paper. The main 5f{sup N} and excited 5f{sup N}n'l'{sup N'} configurations of actinides have been studied using Hartree-Fock-Pauli approximation. Results of calculations of radial integrals and the energy of X-ray lines for all 5f ions with electronic state AC{sup +1}-AC{sup +4} show approximate dependence on N and Z. A square of N and cubic of Z are ewalized for the primary electronic parameters of the actinides. Theoretical values of radial integrals for free actinides and for ions in a cluster AC{supmore » +n}:[L]{sub k} are compared, too.« less

Electronic structure and magneto-optical effects in CeSb

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

Liechtenstein, A.I.; Antropov, V.P.; Harmon, B.N.

1994-04-15

The electronic structure and magneto-optical spectra of CeSb have been calculated using the self-consistent local-density approximation with explicit on-site Coulomb parameters for the correlated [ital f] state of cerium. The essential electronic structure of cerium antimonide consists of one occupied [ital f] band, predominantly with orbital [ital m]=[minus]3 character and spin [sigma]=1 located 2 eV below the Fermi level and interacting with broad Sb [ital p] bands crossing [ital E][sub [ital F

Electronic structure of polycrystalline CVD-graphene revealed by Nano-ARPES

NASA Astrophysics Data System (ADS)

Chen, Chaoyu; Avila, José; Asensio, Maria C.

2017-06-01

The ability to explore electronic structure and their role in determining material’s macroscopic behaviour is essential to explain and engineer functions of material and device. Since its debut in 2004, graphene has attracted global research interest due to its unique properties. Chemical vapor deposition (CVD) has emerged as an important method for the massive preparation and production of graphene for various applications. Here by employing angle-resolved photoemission spectroscopy with nanoscale spatial resolution ˜ 100 nm (Nano-ARPES), we describe the approach to measure the electronic structure of polycrystalline graphene on copper foils, demonstrating the power of Nano-ARPES to detect the electronic structure of microscopic single crystalline domains, being fully compatible with conventional ARPES. Similar analysis could be employed to other microscopic materials

Three-dimensionality of the bulk electronic structure in WTe 2

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

Wu, Yun; Jo, Na Hyun; Mou, Daixiang

Inmore » this paper, we use temperature- and field-dependent resistivity measurements (Shubnikov–de Haas quantum oscillations) and ultrahigh-resolution, tunable, vacuum ultraviolet laser-based angle-resolved photoemission spectroscopy (ARPES) to study the three-dimensionality (3D) of the bulk electronic structure in WTe 2 , a type II Weyl semimetal. The bulk Fermi surface (FS) consists of two pairs of electron pockets and two pairs of hole pockets along the Χ–Γ–Χ direction as detected by using an incident photon energy of 6.7 eV, which is consistent with the previously reported data. However, if using an incident photon energy of 6.36 eV, another pair of tiny electron pockets is detected on both sides of the Γ point, which is in agreement with the small quantum oscillation frequency peak observed in the magnetoresistance. Therefore, the bulk, 3D FS consists of three pairs of electron pockets and two pairs of hole pockets in total. With the ability of fine tuning the incident photon energy, we demonstrate the strong three-dimensionality of the bulk electronic structure in WTe 2 . Finally, the combination of resistivity and ARPES measurements reveals the complete, and consistent, picture of the bulk electronic structure of this material.« less

Three-dimensionality of the bulk electronic structure in WTe 2

DOE PAGES

Wu, Yun; Jo, Na Hyun; Mou, Daixiang; ...

2017-05-18

Inmore » this paper, we use temperature- and field-dependent resistivity measurements (Shubnikov–de Haas quantum oscillations) and ultrahigh-resolution, tunable, vacuum ultraviolet laser-based angle-resolved photoemission spectroscopy (ARPES) to study the three-dimensionality (3D) of the bulk electronic structure in WTe 2 , a type II Weyl semimetal. The bulk Fermi surface (FS) consists of two pairs of electron pockets and two pairs of hole pockets along the Χ–Γ–Χ direction as detected by using an incident photon energy of 6.7 eV, which is consistent with the previously reported data. However, if using an incident photon energy of 6.36 eV, another pair of tiny electron pockets is detected on both sides of the Γ point, which is in agreement with the small quantum oscillation frequency peak observed in the magnetoresistance. Therefore, the bulk, 3D FS consists of three pairs of electron pockets and two pairs of hole pockets in total. With the ability of fine tuning the incident photon energy, we demonstrate the strong three-dimensionality of the bulk electronic structure in WTe 2 . Finally, the combination of resistivity and ARPES measurements reveals the complete, and consistent, picture of the bulk electronic structure of this material.« less

Bright-field electron tomography of individual inorganic fullerene-like structures

NASA Astrophysics Data System (ADS)

Bar Sadan, Maya; Wolf, Sharon G.; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS2 or MoS2 fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The

Electronic structure and properties of lanthanum

NASA Astrophysics Data System (ADS)

Nixon, Lane; Papaconstantopoulos, Dimitrios

2008-03-01

The total energy and electronic structure of lanthanum have been calculated in the bcc, fcc, hcp and dhcp structures for pressures up to 50 GPa. The full potential linearized-augmented-planewave method was used with both the local-density and general-gradient approximations. The correct phase ordering has been found, with lattice parameters and bulk moduli in good agreement with experimental data. The GGA method shows excellent agreement overall while the LDA results show larger discrepancies. The calculated strain energies for the fcc and bcc structures demonstrate the respective stable and unstable configurations at ambient conditions. The calculated superconductivity properties under pressure for the fcc structure are also found to agree well with measurements. Both LDA and GGA, with minor differences, reproduce well the experimental results for Tc.

Multi-band Electronic Structure of Ferromagnetic CeRuPO

NASA Astrophysics Data System (ADS)

Takahashi, Masaya; Ootsuki, Daiki; Horio, Masafumi; Arita, Masashi; Namatame, Hirofumi; Taniguchi, Masaki; Saini, Naurang L.; Sugawara, Hitoshi; Mizokawa, Takashi

2018-04-01

We have studied the multi-band electronic structure of ferromagnetic CeRuPO (TC = 15 K) by means of angle-resolved photoemission spectroscopy (ARPES). The ARPES results show that three hole bands exist around the zone center and two of them cross the Fermi level (EF). Around the zone corner, two electron bands are observed and cross EF. These hole and electron bands, which can be assigned to the Ru 4d bands, are basically consistent with the band-structure calculation including their orbital characters. However, one of the electron bands with Ru 4d 3z2 - r2 character is strongly renormalized indicating correlation effect due to hybridization with the Ce 4f orbitals. The Ru 4d 3z2 - r2 band changes across TC suggesting that the out-of-plane 3z2 - r2 orbital channel plays essential roles in the ferromagnetism.

Effect of strain on the electronic structure of graphene

NASA Astrophysics Data System (ADS)

Martinez, Edgar; Cifuentes, Eduardo; de Coss, Romeo

2008-03-01

Graphene has been attracting interest due to its remarkable physical properties resulting from an electron spectrum resembling relativistic dynamics (Dirac fermions). Thus, is desirable to know methods for controling the charge carriers in graphene. In this work, we propose that the electronic properties of graphene can be modulated via isotropic and uniaxial strain. We have studied the electronic structure of graphene under mechanical deformation by means of first principles calculations. We present results for the charge distribution, electronic density of states, and band structure. We focus the analysis on the behavior of the Dirac cones and the number of the charge carriers as a function of strain. We find that an isotropic tensile strain increases the effective mass of carriers and an isotropic compression strain decrease it. Uniaxial tensile strain induce a similar behavior, as strain increase effective mass increase. Thus, our results show that strain allows controllable tuning of the graphene electronic properties. This research was supported by Consejo Nacional de Ciencia y Tecnolog'ia (Conacyt) under Grant No. 43830-F.

False-color representation of electron-density structures of the polar ionosphere

NASA Astrophysics Data System (ADS)

Schlegel, K.

The use of false-color displays to represent EISCAT electron-density measurements for the polar E and F regions is described and demonstrated. Consideration is given to images of a spring sunrise, wavelike structures, the total-electron-content trough, E-region structures, and midnight-sun phenomena. It is suggested that examination of false-color images can facilitate the selection of structures for more detailed analysis.

Connections between Concepts Revealed by the Electronic Structure of Carbon Monoxide

ERIC Educational Resources Information Center

Liu, Ying; Liu, Bihui; Liu, Yue; Drew, Michael G. B.

2012-01-01

Different models for the electronic structure of carbon monoxide are suggested in influential textbooks. Therefore, this electronic structure offers an interesting subject in teaching because it can be used as an example to relate seemingly conflicting concepts. Understanding the connections between ostensibly different methods and between…

Surface electronic structure of the topological Kondo-insulator candidate correlated electron system SmB6.

PubMed

Neupane, M; Alidoust, N; Xu, S-Y; Kondo, T; Ishida, Y; Kim, D J; Liu, Chang; Belopolski, I; Jo, Y J; Chang, T-R; Jeng, H-T; Durakiewicz, T; Balicas, L; Lin, H; Bansil, A; Shin, S; Fisk, Z; Hasan, M Z

2013-01-01

The Kondo insulator SmB6 has long been known to exhibit low-temperature transport anomalies whose origin is of great interest. Here we uniquely access the surface electronic structure of the anomalous transport regime by combining state-of-the-art laser and synchrotron-based angle-resolved photoemission techniques. We observe clear in-gap states (up to ~4 meV), whose temperature dependence is contingent on the Kondo gap formation. In addition, our observed in-gap Fermi surface oddness tied with the Kramers' point topology, their coexistence with the two-dimensional transport anomaly in the Kondo hybridization regime, as well as their robustness against thermal recycling, taken together, collectively provide strong evidence for protected surface metallicity with a Fermi surface whose topology is consistent with the theoretically predicted topological Fermi surface. Our observations of systematic surface electronic structure provide the fundamental electronic parameters for the anomalous Kondo ground state of correlated electron material SmB6.

Features of the electronic structure of FeTe compounds

NASA Astrophysics Data System (ADS)

Grechnev, G. E.; Lyogenkaya, A. A.; Panfilov, A. S.; Logosha, A. V.; Kotlyar, O. V.; Gnezdilov, V. P.; Makarova, I. P.; Chareev, D. A.; Mitrofanova, E. S.

2015-12-01

A theoretical and experimental study of the electronic structure and nature of the chemical bonds in FeTe compounds in antiferromagnetic (AFM) and paramagnetic phases was carried out. It is established that the nature of the chemical bonds is mainly metallic, and the presence of covalent bonds Fe-Te and Te-Te helps to stabilize the structural distortions of the tetragonal phase of FeTe in the low-temperature region. It is found that the bicollinear AFM structure corresponds to the ground state of the FeTe compound and the calculated value of the magnetic moment MFe = -2.4μB is in good agreement with the data from neutron diffraction measurements. At the same time, the Fermi surface (FS) of the low-temperature AFM phase is radically different from the FS of the paramagnetic FeTe. Reconstructing the FS can lead to a sign change of the Hall coefficient observed in FeTe. The calculation results serve as evidence of the fact that the electronic structures and magnetic properties of FeTe are well-described by the model of itinerant d-electrons and the density functional theory (DFT-GGA).

Electronic band structure effects in the stopping of protons in copper [Electronic band structure non-linear effects in the stopping of protons in copper

DOE PAGES

Quashie, Edwin E.; Saha, Bidhan C.; Correa, Alfredo A.

2016-10-05

Here, we present an ab initio study of the electronic stopping power of protons in copper over a wide range of proton velocities v = 0.02–10a.u. where we take into account nonlinear effects. Time-dependent density functional theory coupled with molecular dynamics is used to study electronic excitations produced by energetic protons. A plane-wave pseudopotential scheme is employed to solve the time-dependent Kohn-Sham equations for a moving ion in a periodic crystal. The electronic excitations and the band structure determine the stopping power of the material and alter the interatomic forces for both channeling and off-channeling trajectories. Our off-channeling results aremore » in quantitative agreement with experiments, and at low velocity they unveil a crossover region of superlinear velocity dependence (with a power of ~1.5) in the velocity range v = 0.07–0.3a.u., which we associate to the copper crystalline electronic band structure. The results are rationalized by simple band models connecting two separate regimes. We find that the limit of electronic stopping v → 0 is not as simple as phenomenological models suggest and it is plagued by band-structure effects.« less

Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent

PubMed Central

Nakane, Takanori; Hanashima, Shinya; Suzuki, Mamoru; Saiki, Haruka; Hayashi, Taichi; Kakinouchi, Keisuke; Sugiyama, Shigeru; Kawatake, Satoshi; Matsuoka, Shigeru; Matsumori, Nobuaki; Nango, Eriko; Kobayashi, Jun; Shimamura, Tatsuro; Kimura, Kanako; Mori, Chihiro; Kunishima, Naoki; Sugahara, Michihiro; Takakyu, Yoko; Inoue, Shigeyuki; Masuda, Tetsuya; Hosaka, Toshiaki; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Inoue, Tsuyoshi; Nureki, Osamu; Iwata, So; Murata, Michio; Mizohata, Eiichi

2016-01-01

The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams. PMID:27799539

Membrane protein structure determination by SAD, SIR, or SIRAS phasing in serial femtosecond crystallography using an iododetergent.

PubMed

Nakane, Takanori; Hanashima, Shinya; Suzuki, Mamoru; Saiki, Haruka; Hayashi, Taichi; Kakinouchi, Keisuke; Sugiyama, Shigeru; Kawatake, Satoshi; Matsuoka, Shigeru; Matsumori, Nobuaki; Nango, Eriko; Kobayashi, Jun; Shimamura, Tatsuro; Kimura, Kanako; Mori, Chihiro; Kunishima, Naoki; Sugahara, Michihiro; Takakyu, Yoko; Inoue, Shigeyuki; Masuda, Tetsuya; Hosaka, Toshiaki; Tono, Kensuke; Joti, Yasumasa; Kameshima, Takashi; Hatsui, Takaki; Yabashi, Makina; Inoue, Tsuyoshi; Nureki, Osamu; Iwata, So; Murata, Michio; Mizohata, Eiichi

2016-11-15

The 3D structure determination of biological macromolecules by X-ray crystallography suffers from a phase problem: to perform Fourier transformation to calculate real space density maps, both intensities and phases of structure factors are necessary; however, measured diffraction patterns give only intensities. Although serial femtosecond crystallography (SFX) using X-ray free electron lasers (XFELs) has been steadily developed since 2009, experimental phasing still remains challenging. Here, using 7.0-keV (1.771 Å) X-ray pulses from the SPring-8 Angstrom Compact Free Electron Laser (SACLA), iodine single-wavelength anomalous diffraction (SAD), single isomorphous replacement (SIR), and single isomorphous replacement with anomalous scattering (SIRAS) phasing were performed in an SFX regime for a model membrane protein bacteriorhodopsin (bR). The crystals grown in bicelles were derivatized with an iodine-labeled detergent heavy-atom additive 13a (HAD13a), which contains the magic triangle, I3C head group with three iodine atoms. The alkyl tail was essential for binding of the detergent to the surface of bR. Strong anomalous and isomorphous difference signals from HAD13a enabled successful phasing using reflections up to 2.1-Å resolution from only 3,000 and 4,000 indexed images from native and derivative crystals, respectively. When more images were merged, structure solution was possible with data truncated at 3.3-Å resolution, which is the lowest resolution among the reported cases of SFX phasing. Moreover, preliminary SFX experiment showed that HAD13a successfully derivatized the G protein-coupled A2a adenosine receptor crystallized in lipidic cubic phases. These results pave the way for de novo structure determination of membrane proteins, which often diffract poorly, even with the brightest XFEL beams.

Electron Scale Structures and Magnetic Reconnection Signatures in the Turbulent Magnetosheath

NASA Technical Reports Server (NTRS)

Yordanova, E.; Voros, Z.; Varsani, A.; Graham, D. B.; Norgren, C.; Khotyaintsev, Yu. V.; Vaivads, A.; Eriksson, E.; Nakamura, R.; Lindqvist, P.-A.;

Electronic structure and optical properties of metal doped tetraphenylporphyrins

NASA Astrophysics Data System (ADS)

Shah, Esha V.; Roy, Debesh R.

2018-05-01

A density functional scrutiny on the structure, electronic and optical properties of metal doped tetraphenylporphyrins MTPP (M=Fe, Co, Ni) is performed. The structural stability of the molecules is evaluated based on the electronic parameters like HOMO-LUMO gap (HLG), chemical hardness (η) and binding energy of the central metal atom to the molecular frame etc. The computed UltraViolet-Visible (UV-Vis) optical absorption spectra for all the compounds are also compared. The molecular structures reported are the lowest energy configurations. The entire calculations are carried out with a widely reliable functional, viz. B3LYP with a popular basis set which includes a scaler relativistic effect, viz. LANL2DZ.

Atomic electron tomography: 3D structures without crystals

DOE PAGES

Miao, Jianwei; Ercius, Peter; Billinge, S. J. L.

2016-09-23

Crystallography has been fundamental to the development of many fields of science over the last century. However, much of our modern science and technology relies on materials with defects and disorders, and their three-dimensional (3D) atomic structures are not accessible to crystallography. One method capable of addressing this major challenge is atomic electron tomography. By combining advanced electron microscopes and detectors with powerful data analysis and tomographic reconstruction algorithms, it is now possible to determine the 3D atomic structure of crystal defects such as grain boundaries, stacking faults, dislocations, and point defects, as well as to precisely localize the 3Dmore » coordinates of individual atoms in materials without assuming crystallinity. In this work, we review the recent advances and the interdisciplinary science enabled by this methodology. We also outline further research needed for atomic electron tomography to address long-standing unresolved problems in the physical sciences.« less

Electronic structure and chemical bonding of the electron-poor II-V semiconductors ZnSb and ZnAs

NASA Astrophysics Data System (ADS)

Benson, Daryn; Sankey, Otto F.; Häussermann, Ulrich

2011-09-01

The binary compounds ZnSb and ZnAs with the CdSb structure are semiconductors (II-V), although the average electron concentration (3.5 per atom) is lower than that of the tetrahedrally bonded III-V and II-VI archetype systems (four per atom). We report a detailed electronic structure and chemical bonding analysis for ZnSb and ZnAs based on first-principles calculations. ZnSb and ZnAs are compared to the zinc blende-type semiconductors GaSb, ZnTe, GaAs, and ZnSe, as well as the more ionic, hypothetical, II-V systems MgSb and MgAs. We establish a clearly covalent bonding scenario for ZnSb and ZnAs where multicenter bonded structural entities (rhomboid rings Zn2Sb2 and Zn2As2) are connected to each other by classical two-center, two-electron bonds. This bonding scenario is only compatible with a weak ionicity in II-V semiconductor systems, and weak ionicity appears as a necessary condition for the stability of the CdSb structure type. It is argued that a chemical bonding scenario with mixed multicenter and two-center bonding resembles that of boron and boron-rich compounds and is typical of electron-poor sp-bonded semiconductors with average valence electron concentrations below four per atom.

Electron Energization and Structure of the Diffusion Region During Asymmetric Reconnection

NASA Technical Reports Server (NTRS)

Chen, Li-Jen; Hesse, Michael; Wang, Shan; Bessho, Naoki; Daughton, William

2016-01-01

Results from particle-in-cell simulations of reconnection with asymmetric upstream conditions are reported to elucidate electron energization and structure of the electron diffusion region (EDR). Acceleration of unmagnetized electrons results in discrete structures in the distribution functions and supports the intense current and perpendicular heating in the EDR. The accelerated electrons are cyclotron turned by the reconnected magnetic field to produce the outflow jets, and as such, the acceleration by the reconnection electric field is limited, leading to resistivity without particle-particle or particle-wave collisions. A map of electron distributions is constructed, and its spatial evolution is compared with quantities previously proposed to be EDR identifiers to enable effective identifications of the EDR in terrestrial magnetopause reconnection.

The Electrical Structure of Discharges Modified by Electron Beams

NASA Astrophysics Data System (ADS)

Haas, F. A.; Braithwaite, N. St. J.

1997-10-01

Injection of an electron beam into a low pressure plasma modifies both the electrical structure and the distributions of charged particle energies. The electrical structure is investigated here in a one-dimensional model by representing the discharge as two collisionless sheaths with a monenergetic electron beam, linked by a quasi-neutral collisional region. The latter is modelled by fluid equations in which the beam current decreases with position. Since the electrodes are connected by an external conductor this implies through Kirchoff's laws that the thermal electron current must correspondingly increase with position. Given the boundary conditions and beam input at the first electrode then the rest of the system is uniquely described. The model reveals the dependence of the sheath potentials at the emitting and absorbing surfaces on the beam current. The model is relevant to externally injected beams and to electron beams originating from secondary processes on surfaces exposed to the plasma.

Electronic structure of antibiotic erythromycin

NASA Astrophysics Data System (ADS)

Novak, Igor; Kovač, Branka

2015-03-01

The electronic structure of erythromycin A (ERYMA) molecule has been studied by UV photoelectron spectroscopy and assigned (in the low ionization energy region only) by empirical arguments. The two orbitals with highest energy (lowest ionization energy) are localized on the nitrogen of the desosamine sugar functional group and on the ester group of macrolide (lactone) ring. We discuss how these orbital energies can help to rationalize the known mode of binding of ERYMA to their biological receptors.

Structural, magnetic and electronic structure properties of Co doped ZnO nanoparticles

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

Kumar, Shalendra, E-mail: shailuphy@gmail.com; School of Materials Science and Engineering, Changwon National University, Changwon, Gyeongnam 641-773; Song, T.K., E-mail: tksong@changwon.ac.kr

Highlights: • XRD and HR-TEM results show the single phase nature of Co doped ZnO nanoparticles. • XMCD and dc magnetization results indicate the RT-FM in Co doped ZnO nanoparticles. • Co L{sub 3,2} NEXAFS spectra infer that Co ions are in 2+ valence state. • O K edge NEXAFS spectra show that O vacancy increases with Co doping in ZnO. - Abstract: We reported structural, magnetic and electronic structure studies of Co doped ZnO nanoparticles. Doping of Co ions in ZnO host matrix has been studied and confirmed using various methods; such as X-ray diffraction (XRD), field emission scanningmore » electron microscopy (FE-SEM), energy dispersed X-ray (EDX), high resolution transmission electron microscopy (HR-TEM), Fourier transform infrared spectroscopy (FT-IR), near edge X-ray absorption fine structure (NEXAFS) spectroscopy, magnetic hysteresis loop measurements and X-ray magnetic circular dichroism (XMCD). From the XRD and HR-TEM results, it is observed that Co doped ZnO nanoparticles have single phase nature with wurtzite structure and exclude the possibility of secondary phase formation. FE-SEM and TEM micrographs show that pure and Co doped nanoparticles are nearly spherical in shape. O K edge NEXAFS spectra indicate that O vacancies increase with Co doping. The Co L{sub 3,2} edge NEXAFS spectra revealed that Co ions are in 2+ valence state. DC magnetization hysteresis loops and XMCD results clearly showed the intrinsic origin of temperature ferromagnetism in Co doped ZnO nanoparticles.« less

Multi-million atom electronic structure calculations for quantum dots

NASA Astrophysics Data System (ADS)

Usman, Muhammad

Quantum dots grown by self-assembly process are typically constructed by 50,000 to 5,000,000 structural atoms which confine a small, countable number of extra electrons or holes in a space that is comparable in size to the electron wavelength. Under such conditions quantum dots can be interpreted as artificial atoms with the potential to be custom tailored to new functionality. In the past decade or so, these nanostructures have attracted significant experimental and theoretical attention in the field of nanoscience. The new and tunable optical and electrical properties of these artificial atoms have been proposed in a variety of different fields, for example in communication and computing systems, medical and quantum computing applications. Predictive and quantitative modeling and simulation of these structures can help to narrow down the vast design space to a range that is experimentally affordable and move this part of nanoscience to nano-Technology. Modeling of such quantum dots pose a formidable challenge to theoretical physicists because: (1) Strain originating from the lattice mismatch of the materials penetrates deep inside the buffer surrounding the quantum dots and require large scale (multi-million atom) simulations to correctly capture its effect on the electronic structure, (2) The interface roughness, the alloy randomness, and the atomistic granularity require the calculation of electronic structure at the atomistic scale. Most of the current or past theoretical calculations are based on continuum approach such as effective mass approximation or k.p modeling capturing either no or one of the above mentioned effects, thus missing some of the essential physics. The Objectives of this thesis are: (1) to model and simulate the experimental quantum dot topologies at the atomistic scale; (2) to theoretically explore the essential physics i.e. long range strain, linear and quadratic piezoelectricity, interband optical transition strengths, quantum confined

Interdependence of spin structure, anion height and electronic structure of BaFe{sub 2}As{sub 2}

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

Sen, Smritijit, E-mail: smritijit.sen@gmail.com; Ghosh, Haranath, E-mail: hng@rrcat.gov.in; Homi Bhabha National Institute, Anushaktinagar, Mumbai, 400094

2016-05-06

Superconducting as well as other electronic properties of Fe-based superconductors are quite sensitive to the structural parameters specially, on anion height which is intimately related to z{sub As}, the fractional z co-ordinate of As atom. Due to presence of strong magnetic fluctuation in these Fe-based superconductors, optimized structural parameters (lattice parameters a, b, c) including z{sub As} using density functional theory (DFT) under generalized gradient approximation (GGA) does not match experimental values accurately. In this work, we show that the optimized value of z{sub As} is strongly influenced by the spin structures in the orthorhombic phase of BaFe{sub 2}As{sub 2}more » system. We take all possible spin structures for the orthorhombic BaFe{sub 2}As{sub 2} system and then optimize z{sub As}. Using these optimized structures we calculate electronic structures like density of states, band structures etc., for each spin configurations. From these studies we show that the electronic structure, orbital order which is responsible for structural as well as related to nematic transition, are significantly influenced by the spin structures.« less

Band structure and unconventional electronic topology of CoSi

NASA Astrophysics Data System (ADS)

Pshenay-Severin, D. A.; Ivanov, Y. V.; Burkov, A. A.; Burkov, A. T.

2018-04-01

Semimetals with certain crystal symmetries may possess unusual electronic structure topology, distinct from that of the conventional Weyl and Dirac semimetals. Characteristic property of these materials is the existence of band-touching points with multiple (higher than two-fold) degeneracy and nonzero Chern number. CoSi is a representative of this group of materials exhibiting the so-called ‘new fermions’. We report on an ab initio calculation of the electronic structure of CoSi using density functional methods, taking into account the spin-orbit interactions. The linearized \

Electronic structure of BaNi2As2

NASA Astrophysics Data System (ADS)

Zhou, Bo; Xu, Min; Zhang, Yan; Xu, Gang; He, Cheng; Yang, L. X.; Chen, Fei; Xie, B. P.; Cui, Xiao-Yu; Arita, Masashi; Shimada, Kenya; Namatame, Hirofumi; Taniguchi, Masaki; Dai, X.; Feng, D. L.

2011-01-01

BaNi2As2, with a first-order phase transition around 131 K, is studied by the angle-resolved photoemission spectroscopy. The measured electronic structure is compared to the local-density approximation calculations, revealing similar large electronlike bands around M¯ and differences along Γ¯-X¯. We further show that the electronic structure of BaNi2As2 is distinct from that of the sibling iron pnictides. Particularly, there is no signature of band folding, indicating no collinear spin-density-wave-related magnetic ordering. Moreover, across the strong first-order phase transition, the band shift exhibits a hysteresis, which is directly related to the significant lattice distortion in BaNi2As2.

Toward Single Electron Nanoelectronics Using Self-Assembled DNA Structure.

PubMed

Tapio, Kosti; Leppiniemi, Jenni; Shen, Boxuan; Hytönen, Vesa P; Fritzsche, Wolfgang; Toppari, J Jussi

2016-11-09

DNA based structures offer an adaptable and robust way to develop customized nanostructures for various purposes in bionanotechnology. One main aim in this field is to develop a DNA nanobreadboard for a controllable attachment of nanoparticles or biomolecules to form specific nanoelectronic devices. Here we conjugate three gold nanoparticles on a defined size TX-tile assembly into a linear pattern to form nanometer scale isolated islands that could be utilized in a room temperature single electron transistor. To demonstrate this, conjugated structures were trapped using dielectrophoresis for current-voltage characterization. After trapping only high resistance behavior was observed. However, after extending the islands by chemical growth of gold, several structures exhibited Coulomb blockade behavior from 4.2 K up to room temperature, which gives a good indication that self-assembled DNA structures could be used for nanoelectronic patterning and single electron devices.

Structural, electronic structure and antibacterial properties of graphene-oxide nano-sheets

NASA Astrophysics Data System (ADS)

Sharma, Aditya; Varshney, Mayora; Nanda, Sitansu Sekhar; Shin, Hyun Joon; Kim, Namdong; Yi, Dong Kee; Chae, Keun-Hwa; Ok Won, Sung

2018-04-01

Correlation between the structural/electronic structure properties and bio-activity of graphene-based materials need to be thoroughly evaluated before their commercial implementation in the health and environment precincts. To better investigate the local hybridization of sp2/sp3 orbitals of the functional groups of graphene-oxide (GO) and their execution in the antimicrobial mechanism, we exemplify the antibacterial activity of GO sheets towards the Escherichia coli bacteria (E. coli) by applying the field-emission scanning electron microscopy (FESEM), near edge X-ray absorption fine structure (NEXAFS) and scanning transmission X-ray microscope (STXM) techniques. C K-edge and O K-edge NEXAFS spectra have revealed lesser sp2 carbon atoms in the aromatic ring and attachment of functional oxygen groups at GO sheets. Entrapment of E. coli bacteria by GO sheets is evidenced by FESEM investigations and has also been corroborated by nano-scale imaging of bacteria using the STXM. Spectroscopy evidence of functional oxygen moieties with GO sheets and physiochemical entrapment of E. coli bacteria have assisted us to elaborate the mechanism of cellular oxidative stress-induced disruption of bacterial membrane.

ESTEST: A Framework for the Verification and Validation of Electronic Structure Codes

NASA Astrophysics Data System (ADS)

Yuan, Gary; Gygi, Francois

2011-03-01

ESTEST is a verification and validation (V& V) framework for electronic structure codes that supports Qbox, Quantum Espresso, ABINIT, the Exciting Code and plans support for many more. We discuss various approaches to the electronic structure V& V problem implemented in ESTEST, that are related to parsing, formats, data management, search, comparison and analyses. Additionally, an early experiment in the distribution of V& V ESTEST servers among the electronic structure community will be presented. Supported by NSF-OCI 0749217 and DOE FC02-06ER25777.

Electronic and structural reconstruction in titanate heterostructures from first principles

NASA Astrophysics Data System (ADS)

Mulder, Andrew T.; Fennie, Craig J.

2014-03-01

Recent advances in transition metal oxide heterostructures have opened new routes to create materials with novel functionalities and properties. One direction has been to combine a Mott insulating perovskite with an electronic d1 configuration, such as LaTiO3, with a band insulating d0 perovskite, such as SrTiO3. An exciting recent development is the demonstration of interfacial conductivity in GdTiO3/SrTiO3 heterostructures that display a complex structural motif of octahedral rotations and ferromagnetic properties similar to bulk GdTiO3. In this talk we present our first principles investigation of the interplay of structural, electronic, magnetic, and orbital degrees of freedom for a wide range of d1/d0 titanate heterostructures. We find evidence for both rotation driven ferroelectricity and a symmetry breaking electronic reconstruction with a concomitant structural distortion at the interface. We argue that these materials represent an ideal platform to realize novel functionalities such as the electric field control of electronic and magnetic properties.

On the versatility of electronic structures in polymethine dyes

NASA Astrophysics Data System (ADS)

Pascal, Simon; Haefele, Alexandre; Monnereau, Cyrille; Charaf-Eddin, Azzam; Jacquemin, Denis; Le Guennic, Boris; Maury, Olivier; Andraud, Chantal

2014-10-01

This article provides an overview of the photophysical behavior diversity of polymethine chromophores which are ubiquitous in biological imaging and material sciences. One major challenge in this class of chromophore is to correlate the chemical structure to the observed optical properties, especially when symmetry-breaking phenomena occur. With the constant concern for rationalization of their spectroscopy, we propose an extended classification of polymethine dyes based on their ground state electronic configuration using three limit forms namely: cyanine, dipole and bis-dipole. The chemical modifications of the dye and the influence of exogenous parameters can promote dramatic spectroscopic changes that can be correlated to significant electronic reorganization between the three-abovementioned forms. The deep understanding of such phenomena should allow to identify, predict and take advantage of the versatile electronic structure of polymethines.

Unravelling the structural-electronic impact of arylamine electron-donating antennas on the performances of efficient ruthenium sensitizers for dye-sensitized solar cells

NASA Astrophysics Data System (ADS)

Chen, Wang-Chao; Kong, Fan-Tai; Ghadari, Rahim; Li, Zhao-Qian; Guo, Fu-Ling; Liu, Xue-Peng; Huang, Yang; Yu, Ting; Hayat, Tasawar; Dai, Song-Yuan

2017-04-01

We report a systematic research to understand the structural-electronic impact of the arylamine electron-donating antennas on the performances of the ruthenium complexes for dye-sensitized solar cells. Three ruthenium complexes functionalized with different arylamine electron-donating antennas (N,N-diethyl-aniline in RC-31, julolidine in RC-32 and N,N-dibenzyl-aniline in RC-36) are designed and synthesized. The photoelectric properties of RC dyes exhibit apparent discrepancy, which are ascribed to different structural nature and electronic delocalization ability of these arylamine electron-donating system. In conjunction with TiO2 microspheres photoanode and a typical coadsorbent DPA, the devices sensitized by RC-36 achieve the best conversion efficiency of 10.23%. The UV-Vis absorption, electrochemical measurement, incident photon-to-current conversion efficiency and transient absorption spectra confirm that the excellent performance of RC-36 is induced by synergistically structural-electronic impacts from enhanced absorption capacity and well-tuned electronic characteristics. These observations provide valuable insights into the molecular engineering methodology based on fine tuning structural-electronic impact of electron-donating antenna in efficient ruthenium sensitizers.

Electronic and structural transitions in dense liquid sodium.

PubMed

Raty, Jean-Yves; Schwegler, Eric; Bonev, Stanimir A

2007-09-27

At ambient conditions, the light alkali metals are free-electron-like crystals with a highly symmetric structure. However, they were found recently to exhibit unexpected complexity under pressure. It was predicted from theory--and later confirmed by experiment--that lithium and sodium undergo a sequence of symmetry-breaking transitions, driven by a Peierls mechanism, at high pressures. Measurements of the sodium melting curve have subsequently revealed an unprecedented (and still unexplained) pressure-induced drop in melting temperature from 1,000 K at 30 GPa down to room temperature at 120 GPa. Here we report results from ab initio calculations that explain the unusual melting behaviour in dense sodium. We show that molten sodium undergoes a series of pressure-induced structural and electronic transitions, analogous to those observed in solid sodium but commencing at much lower pressure in the presence of liquid disorder. As pressure is increased, liquid sodium initially evolves by assuming a more compact local structure. However, a transition to a lower-coordinated liquid takes place at a pressure of around 65 GPa, accompanied by a threefold drop in electrical conductivity. This transition is driven by the opening of a pseudogap, at the Fermi level, in the electronic density of states--an effect that has not hitherto been observed in a liquid metal. The lower-coordinated liquid emerges at high temperatures and above the stability region of a close-packed free-electron-like metal. We predict that similar exotic behaviour is possible in other materials as well.

Electronic correlation in magnetic contributions to structural energies

NASA Astrophysics Data System (ADS)

Haydock, Roger

For interacting electrons the density of transitions [see http://arxiv.org/abs/1405.2288] replaces the density of states in calculations of structural energies. Extending previous work on paramagnetic metals, this approach is applied to correlation effects on the structural stability of magnetic transition metals. Supported by the H. V. Snyder Gift to the University of Oregon.

Electron beam enhanced surface modification for making highly resolved structures

DOEpatents

Pitts, John R.

1986-01-01

A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

Electron beam enhanced surface modification for making highly resolved structures

DOEpatents

Pitts, J.R.

1984-10-10

A method for forming high resolution submicron structures on a substrate is provided by direct writing with a submicron electron beam in a partial pressure of a selected gas phase characterized by the ability to dissociate under the beam into a stable gaseous leaving group and a reactant fragment that combines with the substrate material under beam energy to form at least a surface compound. Variations of the method provide semiconductor device regions on doped silicon substrates, interconnect lines between active sites, three dimensional electronic chip structures, electron beam and optical read mass storage devices that may include color differentiated data areas, and resist areas for use with selective etching techniques.

Electronic structure properties of UO2 as a Mott insulator

NASA Astrophysics Data System (ADS)

Sheykhi, Samira; Payami, Mahmoud

2018-06-01

In this work using the density functional theory (DFT), we have studied the structural, electronic and magnetic properties of uranium dioxide with antiferromagnetic 1k-, 2k-, and 3k-order structures. Ordinary approximations in DFT, such as the local density approximation (LDA) or generalized gradient approximation (GGA), usually predict incorrect metallic behaviors for this strongly correlated electron system. Using Hubbard term correction for f-electrons, LDA+U method, as well as using the screened Heyd-Scuseria-Ernzerhof (HSE) hybrid functional for the exchange-correlation (XC), we have obtained the correct ground-state behavior as an insulator, with band gaps in good agreement with experiment.

Electronic structure of hydrogenated diamond: Microscopical insight into surface conductivity

NASA Astrophysics Data System (ADS)

Iacobucci, S.; Alippi, Paola; Calvani, P.; Girolami, M.; Offi, F.; Petaccia, L.; Trucchi, D. M.

2016-07-01

We have correlated the surface conductivity of hydrogen-terminated diamond to the electronic structure in the Fermi region. Significant density of electronic states (DOS) in proximity of the Fermi edge has been measured by photoelectron spectroscopy (PES) on surfaces exposed to air, corresponding to a p -type electric conductive regime, while upon annealing a depletion of the DOS has been achieved, resembling the diamond insulating state. The surface and subsurface electronic structure has been determined, exploiting the different probing depths of PES applied in a photon energy range between 7 and 31 eV. Ab initio density functional calculations including surface charge depletion and band-bending effects favorably compare with electronic states measured by angular-resolved photoelectron spectroscopy. Such states are organized in the energy-momentum space in a twofold structure: one, bulk-derived, band disperses in the Γ -X direction with an average hole effective mass of (0.43 ±0.02 ) m0 , where m0 is the bare electron mass; a second flatter band, with an effective mass of (2.2 ±0.9 ) m0 , proves that a hole gas confined in the topmost layers is responsible for the conductivity of the (2 ×1 ) hydrogen-terminated diamond (100 ) surface.

Three dimensional electron microscopy and in silico tools for macromolecular structure determination

PubMed Central

Borkotoky, Subhomoi; Meena, Chetan Kumar; Khan, Mohammad Wahab; Murali, Ayaluru

2013-01-01

Recently, structural biology witnessed a major tool - electron microscopy - in solving the structures of macromolecules in addition to the conventional techniques, X-ray crystallography and nuclear magnetic resonance (NMR). Three dimensional transmission electron microscopy (3DTEM) is one of the most sophisticated techniques for structure determination of molecular machines. Known to give the 3-dimensional structures in its native form with literally no upper limit on size of the macromolecule, this tool does not need the crystallization of the protein. Combining the 3DTEM data with in silico tools, one can have better refined structure of a desired complex. In this review we are discussing about the recent advancements in three dimensional electron microscopy and tools associated with it. PMID:27092033

Photoinduced electron transfer pathways in hydrogen-evolving reduced graphene oxide-boosted hybrid nano-bio catalyst.

PubMed

Wang, Peng; Dimitrijevic, Nada M; Chang, Angela Y; Schaller, Richard D; Liu, Yuzi; Rajh, Tijana; Rozhkova, Elena A

2014-08-26

Photocatalytic production of clean hydrogen fuels using water and sunlight has attracted remarkable attention due to the increasing global energy demand. Natural and synthetic dyes can be utilized to sensitize semiconductors for solar energy transformation using visible light. In this study, reduced graphene oxide (rGO) and a membrane protein bacteriorhodopsin (bR) were employed as building modules to harness visible light by a Pt/TiO2 nanocatalyst. Introduction of the rGO boosts the nano-bio catalyst performance that results in hydrogen production rates of approximately 11.24 mmol of H2 (μmol protein)(-1) h(-1). Photoelectrochemical measurements show a 9-fold increase in photocurrent density when TiO2 electrodes were modified with rGO and bR. Electron paramagnetic resonance and transient absorption spectroscopy demonstrate an interfacial charge transfer from the photoexcited rGO to the semiconductor under visible light.

Electron-hole liquid in semiconductors and low-dimensional structures

NASA Astrophysics Data System (ADS)

Sibeldin, N. N.

2017-11-01

The condensation of excitons into an electron-hole liquid (EHL) and the main EHL properties in bulk semiconductors and low-dimensional structures are considered. The EHL properties in bulk materials are discussed primarily in qualitative terms based on the experimental results obtained for germanium and silicon. Some of the experiments in which the main EHL thermodynamic parameters (density and binding energy) have been obtained are described and the basic factors that determine these parameters are considered. Topics covered include the effect of external perturbations (uniaxial strain and magnetic field) on EHL stability; phase diagrams for a nonequilibrium exciton-gas-EHL system; information on the size and concentration of electron-hole drops (EHDs) under various experimental conditions; the kinetics of exciton condensation and of recombination in the exciton-gas-EHD system; dynamic EHD properties and the motion of EHDs under the action of external forces; the properties of giant EHDs that form in potential wells produced by applying an inhomogeneous strain to the crystal; and effects associated with the drag of EHDs by nonequilibrium phonons (phonon wind), including the dynamics and formation of an anisotropic spatial structure of the EHD cloud. In discussing EHLs in low-dimensional structures, a number of studies are reviewed on the observation and experimental investigation of phenomena such as spatially indirect (dipolar) electron-hole and exciton (dielectric) liquids in GaAs/AlGaAs structures with double quantum wells (QWs), EHDs containing only a few electron-hole pairs (dropletons), EHLs in type-I silicon QWs, and spatially direct and dipolar EHLs in type-II silicon-germanium heterostructures.

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

Characterization of electronic structure of periodically strained graphene

DOE PAGES

Aslani, Marjan; Garner, C. Michael; Kumar, Suhas; ...

2015-11-03

We induced periodic biaxial tensile strain in polycrystalline graphene by wrapping it over a substrate with repeating pillar-like structures with a periodicity of 600 nm. Using Raman spectroscopy, we determined to have introduced biaxial strains in graphene in the range of 0.4% to 0.7%. Its band structure was characterized using photoemission from valance bands, shifts in the secondary electron emission, and x-ray absorption from the carbon 1s levels to the unoccupied graphene conduction bands. It was observed that relative to unstrained graphene, strained graphene had a higher work function and higher density of states in the valence and conduction bands.more » Furthermore, we measured the conductivity of the strained and unstrained graphene in response to a gate voltage and correlated the changes in their behavior to the changes in the electronic structure. From these sets of data, we propose a simple band diagram representing graphene with periodic biaxial strain.« less

Electronic Structure of Ytterbium-Doped Strontium Fluoroapatite: Photoemission and Photoabsorption Investigation

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

Nelson, Art J.; Van Buuren, Tony W.; Bostedt, C

X-ray photoemission and x-ray photoabsorption were used to study the composition and the electronic structure of ytterbium-doped strontium fluoroapatite (Yb:S-FAP). High resolution photoemission measurements on the valence band electronic structure and Sr 3d, P 2p and 2s, Yb 4d and 4p, F 1s and O 1s core lines were used to evaluate the surface and near surface chemistry of this fluoroapatite. Element specific density of unoccupied electronic states in Yb:S-FAP were probed by x-ray absorption spectroscopy (XAS) at the Yb 4d (N4,5-edge), Sr 3d (M4,5-edge), P 2p (L2,3-edge), F 1s and O 1s (K-edges) absorption edges. These results provide themore » first measurements of the electronic structure and surface chemistry of this material.« less

Extraordinary electronic properties in uncommon structure types

NASA Astrophysics Data System (ADS)

Ali, Mazhar Nawaz

In this thesis I present the results of explorations into several uncommon structure types. In Chapter 1 I go through the underlying idea of how we search for new compounds with exotic properties in solid state chemistry. The ideas of exploring uncommon structure types, building up from the simple to the complex, using chemical intuition and thinking by analogy are discussed. Also, the history and basic concepts of superconductivity, Dirac semimetals, and magnetoresistance are briefly reviewed. In chapter 2, the 1s-InTaS2 structural family is introduced along with the discovery of a new member of the family, Ag0:79VS2; the synthesis, structure, and physical properties of two different polymorphs of the material are detailed. Also in this chapter, we report the observation of superconductivity in another 1s structure, PbTaSe2. This material is especially interesting due to it being very heavy (resulting in very strong spin orbit coulping (SOC)), layered, and noncentrosymmetric. Electronic structure calculations reveal the presence of a bulk 3D Dirac cone (very similar to graphene) that is gapped by SOC originating from the hexagonal Pb layer. In Chapter 3 we show the re-investigation of the crystal structure of the 3D Dirac semimetal, Cd3As2. It is found to be centrosymmetric, rather than noncentrosymmetric, and as such all bands are spin degenerate and there is a 4-fold degenerate bulk Dirac point at the Fermi level, making Cd3As2 a 3D electronic analog to graphene. Also, for the first time, scanning tunneling microscopy experiments identify a 2x2 surface reconstruction in what we identify as the (112) cleavage plane of single crystals; needle crystals grow with a [110] long axis direction. Lastly, in chapter 4 we report the discovery of "titanic" (sadly dubbed ⪉rge, nonsaturating" by Nature editors and given the acronym XMR) magnetoresistance (MR) in the non-magnetic, noncentrosymmetric, layered transition metal dichalcogenide WTe2; over 13 million% at 0.53 K in

Chemical and Structural Stability of Lithium-Ion Battery Electrode Materials under Electron Beam

DOE PAGES

Lin, Feng; Markus, Isaac M.; Doeff, Marca M.; ...

2014-07-16

Our investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. But, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiation, the surface and bulk of battery materials undergo chemical and structural evolution equivalent to that observed during charge-discharge cycling. In a lithiated NiO nanosheet, a Li2CO3-containing surface reaction layer (SRL) was gradually decomposed during electron energy loss spectroscopy (EELS) acquisition. For cycled LiNi 0.4Mn 0.4Co 0.18Ti 0.02O 2 particles, repeated electron beam irradiation induced a phase transition from an Rmore » $$\\bar{3}$$m layered structure to an rock-salt structure, which is attributed to the stoichiometric lithium and oxygen removal from R$$\\bar{3}$$m 3a and 6c sites, respectively. Nevertheless, it is still feasible to preserve pristine chemical environments by minimizing electron beam damage, for example, in using fast electron imaging and spectroscopy. Finally, the present study provides examples of electron beam damage on lithium-ion battery materials and suggests that special attention is necessary to prevent misinterpretation of experimental results.« less

Gapped electronic structure of epitaxial stanene on InSb(111)

DOE PAGES

Xu, Cai-Zhi; Chan, Yang-Hao; Chen, Peng; ...

2018-01-11

We report that stanene (single-layer gray tin), with an electronic structure akin to that of graphene but exhibiting a much larger spin-orbit gap, offers a promising platform for room-temperature electronics based on the quantum spin Hall (QSH) effect. This material has received much theoretical attention, but a suitable substrate for stanene growth that results in an overall gapped electronic structure has been elusive; a sizable gap is necessary for room-temperature applications. Here, we report a study of stanene, epitaxially grown on the (111)B-face of indium antimonide (InSb). Angle-resolved photoemission spectroscopy measurements reveal a gap of 0.44 eV, in agreement withmore » our first-principles calculations. Lastly, the results indicate that stanene on InSb(111) is a strong contender for electronic QSH applications.« less

Gapped electronic structure of epitaxial stanene on InSb(111)

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

Xu, Cai-Zhi; Chan, Yang-Hao; Chen, Peng

We report that stanene (single-layer gray tin), with an electronic structure akin to that of graphene but exhibiting a much larger spin-orbit gap, offers a promising platform for room-temperature electronics based on the quantum spin Hall (QSH) effect. This material has received much theoretical attention, but a suitable substrate for stanene growth that results in an overall gapped electronic structure has been elusive; a sizable gap is necessary for room-temperature applications. Here, we report a study of stanene, epitaxially grown on the (111)B-face of indium antimonide (InSb). Angle-resolved photoemission spectroscopy measurements reveal a gap of 0.44 eV, in agreement withmore » our first-principles calculations. Lastly, the results indicate that stanene on InSb(111) is a strong contender for electronic QSH applications.« less

Positive semidefinite tensor factorizations of the two-electron integral matrix for low-scaling ab initio electronic structure.

PubMed

Hoy, Erik P; Mazziotti, David A

2015-08-14

Tensor factorization of the 2-electron integral matrix is a well-known technique for reducing the computational scaling of ab initio electronic structure methods toward that of Hartree-Fock and density functional theories. The simplest factorization that maintains the positive semidefinite character of the 2-electron integral matrix is the Cholesky factorization. In this paper, we introduce a family of positive semidefinite factorizations that generalize the Cholesky factorization. Using an implementation of the factorization within the parametric 2-RDM method [D. A. Mazziotti, Phys. Rev. Lett. 101, 253002 (2008)], we study several inorganic molecules, alkane chains, and potential energy curves and find that this generalized factorization retains the accuracy and size extensivity of the Cholesky factorization, even in the presence of multi-reference correlation. The generalized family of positive semidefinite factorizations has potential applications to low-scaling ab initio electronic structure methods that treat electron correlation with a computational cost approaching that of the Hartree-Fock method or density functional theory.

Slow electron acoustic double layer (SEADL) structures in bi-ion plasma with trapped electrons

NASA Astrophysics Data System (ADS)

Shan, Shaukat Ali; Imtiaz, Nadia

2018-05-01

The properties of ion acoustic double layer (IADL) structures in bi-ion plasma with electron trapping are investigated by using the quasi-potential analysis. The κ-distributed trapped electrons number density expression is truncated to some finite order of the electrostatic potential. By utilizing the reductive perturbation method, a modified Schamel equation which describes the evolution of the slow electron acoustic double layer (SEADL) with the modified speed due to the presence of bi-ion species is investigated. The Sagdeev-like potential has been derived which accounts for the effect of the electron trapping and superthermality in a bi-ion plasma. It is found that the superthermality index, the trapping efficiency of electrons, and ion to electron temperature ratio are the inhibiting parameters for the amplitude of the slow electron acoustic double layers (SEADLs). However, the enhanced population of the cold ions is found to play a supportive role for the low frequency DLs in bi-ion plasmas. The illustrations have been presented with the help of the bi-ion plasma parameters in the Earth's ionosphere F-region.

Structural phase transition, electronic structure and optical properties of half Heusler alloys LiBeZ (Z = As, Sb)

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

Amudhavalli, A.; Rajeswarapalanichamy, R., E-mail: rajeswarapalanichamy@gmail.com

2016-05-23

Ab initio calculations are performed to investigate the structural stability, electronic structure, mechanical properties and optical properties of half Heusler alloys (LiBeAs and LiBeSb) for three different phases of zinc blende crystal structure. Among the considered phases, α- phase is found to be the most stable phase for these alloys at normal pressure. A pressure induced structural phase transition from α-phase to β- phase is observed for LiBeAs. The electronic structure reveals that these alloys are semiconductors. The optical properties confirm that these alloys are semiconductor in nature.

Electronic origin of structural transition in 122 Fe based superconductors

NASA Astrophysics Data System (ADS)

Ghosh, Haranath; Sen, Smritijit; Ghosh, Abyay

2017-03-01

Direct quantitative correlations between the orbital order and orthorhombicity is achieved in a number of Fe-based superconductors of 122 family. The former (orbital order) is calculated from first principles simulations using experimentally determined doping and temperature dependent structural parameters while the latter (the orthorhombicity) is taken from already established experimental studies; when normalized, both the above quantities quantitatively corresponds to each other in terms of their doping as well as temperature variations. This proves that the structural transition in Fe-based materials is electronic in nature due to orbital ordering. An universal correlations among various structural parameters and electronic structure are also obtained. Most remarkable among them is the mapping of two Fe-Fe distances in the low temperature orthorhombic phase, with the band energies Edxz, Edyz of Fe at the high symmetry points of the Brillouin zone. The fractional co-ordinate zAs of As which essentially determines anion height is inversely (directly) proportional to Fe-As bond distances (with exceptions of K doped BaFe2As2) for hole (electron) doped materials as a function of doping. On the other hand, Fe-As bond-distance is found to be inversely (directly) proportional to the density of states at the Fermi level for hole (electron) doped systems. Implications of these results to current issues of Fe based superconductivity are discussed.

Structural and electronic properties of the alkali metal incommensurate phases

NASA Astrophysics Data System (ADS)

Woolman, Gavin; Naden Robinson, Victor; Marqués, Miriam; Loa, Ingo; Ackland, Graeme J.; Hermann, Andreas

2018-05-01

Under pressure, the alkali elements sodium, potassium, and rubidium adopt nonperiodic structures based on two incommensurate interpenetrating lattices. While all elements form the same "host" lattice, their "guest" lattices are all distinct. The physical mechanism that stabilizes these phases is not known, and detailed calculations are challenging due to the incommensurability of the lattices. Using a series of commensurate approximant structures, we tackle this issue using density functional theory calculations. In Na and K, the calculations prove accurate enough to reproduce not only the stability of the host-guest phases, but also the complicated pressure dependence of the host-guest ratio and the two guest-lattice transitions. We find Rb-IV to be metastable at all pressures, and suggest it is a high-temperature phase. The electronic structure of these materials is unique: they exhibit two distinct, coexisting types of electride behavior, with both fully localized pseudoanions and electrons localized in 1D wells in the host lattice, leading to low conductivity. While all phases feature pseudogaps in the electronic density of states, the perturbative free-electron picture applies to Na, but not to K and Rb, due to significant d -orbital population in the latter.

Structure-function insights of membrane and soluble proteins revealed by electron crystallography.

PubMed

Dreaden, Tina M; Devarajan, Bharanidharan; Barry, Bridgette A; Schmidt-Krey, Ingeborg

2013-01-01

Electron crystallography is emerging as an important method in solving protein structures. While it has found extensive applications in the understanding of membrane protein structure and function at a wide range of resolutions, from revealing oligomeric arrangements to atomic models, electron crystallography has also provided invaluable information on the soluble α/β-tubulin which could not be obtained by any other method to date. Examples of critical insights from selected structures of membrane proteins as well as α/β-tubulin are described here, demonstrating the vast potential of electron crystallography that is first beginning to unfold.

Electronic structure and electron-phonon interaction in hexagonal yttrium by density functional calculations

NASA Astrophysics Data System (ADS)

Singh, Prabhakar P.

2007-03-01

To understand the pressure-induced changes in the electronic structure and the electron-phonon interaction in yttrium, we have studied hexagonal-close-packed (hcp) yttrium, stable at ambient pressure, and double hexagonal-close-packed (dhcp) yttrium, stable up to around 44GPa , using density-functional-based methods. Our results show that as one goes from hcp yttrium to dhcp yttrium, there are (i) a substantial charge transfer from s→d with extensive modifications of the d band and a sizable reduction in the density of states at the Fermi energy, (ii) a substantial stiffening of phonon modes with the electron-phonon coupling covering the entire frequency range, and (iii) an increase in the electron-phonon coupling constant λ from 0.55 to 1.24, leading to a change in the superconducting transition temperature Tc from 0.3to15.3K for μ*=0.2 .

Electronic structure and superconductivity of FeSe-related superconductors.

PubMed

Liu, Xu; Zhao, Lin; He, Shaolong; He, Junfeng; Liu, Defa; Mou, Daixiang; Shen, Bing; Hu, Yong; Huang, Jianwei; Zhou, X J

2015-05-13

FeSe superconductors and their related systems have attracted much attention in the study of iron-based superconductors owing to their simple crystal structure and peculiar electronic and physical properties. The bulk FeSe superconductor has a superconducting transition temperature (Tc) of ~8 K and it can be dramatically enhanced to 37 K at high pressure. On the other hand, its cousin system, FeTe, possesses a unique antiferromagnetic ground state but is non-superconducting. Substitution of Se with Te in the FeSe superconductor results in an enhancement of Tc up to 14.5 K and superconductivity can persist over a large composition range in the Fe(Se,Te) system. Intercalation of the FeSe superconductor leads to the discovery of the AxFe2-ySe2 (A = K, Cs and Tl) system that exhibits a Tc higher than 30 K and a unique electronic structure of the superconducting phase. A recent report of possible high temperature superconductivity in single-layer FeSe/SrTiO3 films with a Tc above 65 K has generated much excitement in the community. This pioneering work opens a door for interface superconductivity to explore for high Tc superconductors. The distinct electronic structure and superconducting gap, layer-dependent behavior and insulator-superconductor transition of the FeSe/SrTiO3 films provide critical information in understanding the superconductivity mechanism of iron-based superconductors. In this paper, we present a brief review of the investigation of the electronic structure and superconductivity of the FeSe superconductor and related systems, with a particular focus on the FeSe films.

Disentangling the surface and bulk electronic structures of LaOFeAs

DOE PAGES

Zhang, P.; Ma, J.; Qian, T.; ...

2016-09-20

We performed a comprehensive angle-resolved photoemission spectroscopy study of the electronic band structure of LaOFeAs single crystals. We found that samples cleaved at low temperature show an unstable and very complicated band structure, whereas samples cleaved at high temperature exhibit a stable and clearer electronic structure. Using in situ surface doping with K and supported by first-principles calculations, we identify both surface and bulk bands. Our assignments are confirmed by the difference in the temperature dependence of the bulk and surface states.

Electronic structure and optical properties of GdNi2Mnx compounds

NASA Astrophysics Data System (ADS)

Knyazev, Yu. V.; Lukoyanov, A. V.; Kuz'min, Yu. I.; Gaviko, V. S.

2018-02-01

The electronic structure and optical properties of GdNi2Mnx compounds (x = 0, 0.4, 0.6) were investigated. Spin-polarized electronic structure calculations were performed in the approximation of local electron spin density corrected for strong electron correlations using the LSDA+U method. The changes in the magnetic moments and exchange interactions in GdNi2Mnx (x = 0, 0.4, 0.6) governing the increase in the Curie temperature with manganese concentration were determined. The optical constants of the compounds were measured by the ellipsometric method in the wide spectral range of 0.22-15 μm. The peculiarities of the evolution of the frequency dependences of optical conductivity with a change in the manganese content were revealed. Based on the calculated densities of electron states, the behavior of these dispersion curves in the region of interband absorption of light was discussed. The concentration dependences of several electronic characteristics were determined.

Electronic structure of the organic semiconductor copper phthalocyanine: experiment and theory.

PubMed

Aristov, V Yu; Molodtsova, O V; Maslyuk, V V; Vyalikh, D V; Zhilin, V M; Ossipyan, Yu A; Bredow, T; Mertig, I; Knupfer, M

2008-01-21

The electronic structure of the organic semiconductor copper-phthalocyanine (CuPc) has been determined by a combination of conventional and resonant photoemission, near-edge x-ray absorption, as well as by the first-principles calculations. The experimentally obtained electronic valence band structure of CuPc is in very good agreement with the calculated density of states results, allowing the derivation of detailed site specific information.

Electronic structure imperfections and chemical bonding at graphene interfaces

NASA Astrophysics Data System (ADS)

Schultz, Brian Joseph

nanomaterial with lateral dimensions in the hundreds of microns if not larger, with a corresponding atomic vertical thickness poses significant difficulties. Graphene's unique structure is dominated by surface area or potentially hybridized interfaces; consequently, the true realization of this remarkable nanomaterial in device constructs relies on engineering graphene interfaces at the surface in order to controllably mold the electronic structure. Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy and the transmission mode analogue scanning transmission X-ray microscopy (STXM) are particularly useful tools to study the unoccupied states of graphene and graphene interfaces. In addition, polarized NEXAFS and STXM studies provide information on surface orientation, bond sterics, and the extent of substrate alignment before and after interfacial hybridization. The work presented in this dissertation is fundamentally informed by NEXAFS and STXM measurements on graphene/metal, graphene/dielectric, and graphene/organic interfaces. We start with a general review of the electronic structure of freestanding graphene and graphene interfaces in Chapter 1. In Chapter 2, we investigate freestanding single-layer graphene via STXM and NEXAFS demonstrating that electronic structure heterogeneities from synthesis and processing are ubiquitous in 2-dimensional graphene. We show the mapping of discrete charge transfer regions as a result of doped impurities that decorate the surfaces of graphene and that transfer processing imparts local electronic corrugations or ripples. In corroboration with density functional theory, definitive assignments to the spectral features, global steric orientations of the localized domains, and quantitative charge transfer schemes are evidenced. In the following chapters, we deliberately (Chapter 3) incorporate substitutional nitrogen into reduced graphene oxide to induce C--N charge redistribution and improve global conductivity, (Chapter 4

Steering Charge Kinetics of Tin Niobate Photocatalysts: Key Roles of Phase Structure and Electronic Structure

NASA Astrophysics Data System (ADS)

Huang, Shushu; Wang, Chunyan; Sun, Hao; Wang, Xiaojing; Su, Yiguo

2018-05-01

Tin niobate photocatalysts with the phase structures of froodite (SnNb2O6) and pyrochlore (Sn2Nb2O7) were obtained by a facile solvothermal method in order to explore the impact of phase structure and electronic structure on the charge kinetics and photocatalytic performance. By employing tin niobate as a model compound, the effects of phase structure over electronic structure, photocatalytic activity toward methyl orange solution and hydrogen evolution were systematically investigated. It is found that the variation of phase structure from SnNb2O6 to Sn2Nb2O7 accompanied with modulation of particle size and band edge potentials that has great consequences on photocatalytic performance. In combination with the electrochemical impedance spectroscopy (EIS), transient photocurrent responses, transient absorption spectroscopy (TAS), and the analysis of the charge-carrier dynamics suggested that variation of electronic structure has great impacts on the charge separation and transfer rate of tin niobate photocatalysts and the subsequent photocatalytic performance. Moreover, the results of the X-ray photoelectron spectroscopy (XPS) indicated that the existent of Sn4+ species in Sn2Nb2O7 could result in a decrease in photocatalytic activity. Photocatalytic test demonstrated that the SnNb2O6 (froodite) catalyst possesses a higher photocatalytic activity toward MO degradation and H2 evolution compared with the sample of Sn2Nb2O7 (pyrochlore). On the basis of spin resonance measurement and trapping experiment, it is expected that photogenerated holes, O2 -•, and OH• active species dominate the photodegradation of methyl orange.

Steering Charge Kinetics of Tin Niobate Photocatalysts: Key Roles of Phase Structure and Electronic Structure.

PubMed

Huang, Shushu; Wang, Chunyan; Sun, Hao; Wang, Xiaojing; Su, Yiguo

2018-05-23

Tin niobate photocatalysts with the phase structures of froodite (SnNb 2 O 6 ) and pyrochlore (Sn 2 Nb 2 O 7 ) were obtained by a facile solvothermal method in order to explore the impact of phase structure and electronic structure on the charge kinetics and photocatalytic performance. By employing tin niobate as a model compound, the effects of phase structure over electronic structure, photocatalytic activity toward methyl orange solution and hydrogen evolution were systematically investigated. It is found that the variation of phase structure from SnNb 2 O 6 to Sn 2 Nb 2 O 7 accompanied with modulation of particle size and band edge potentials that has great consequences on photocatalytic performance. In combination with the electrochemical impedance spectroscopy (EIS), transient photocurrent responses, transient absorption spectroscopy (TAS), and the analysis of the charge-carrier dynamics suggested that variation of electronic structure has great impacts on the charge separation and transfer rate of tin niobate photocatalysts and the subsequent photocatalytic performance. Moreover, the results of the X-ray photoelectron spectroscopy (XPS) indicated that the existent of Sn 4+ species in Sn 2 Nb 2 O 7 could result in a decrease in photocatalytic activity. Photocatalytic test demonstrated that the SnNb 2 O 6 (froodite) catalyst possesses a higher photocatalytic activity toward MO degradation and H 2 evolution compared with the sample of Sn 2 Nb 2 O 7 (pyrochlore). On the basis of spin resonance measurement and trapping experiment, it is expected that photogenerated holes, O 2 -• , and OH • active species dominate the photodegradation of methyl orange.

Understanding the Electronic Structure of the a-B5C:Hx-to-Metal Interface

DTIC Science & Technology

2016-06-01

investigating electronic structure is optical absorption spectroscopy, where the absorbance spectrum represents a superposition of optical transitions...6201 Fort Belvoir, VA 22060-6201 T E C H N IC A L R E P O R T DTRA-TR-16-63 Understanding the Electronic Structure of the a-B5C:Hx-to...42 4.4. Electronic Structure and Charge Transport Models

Electronic and structural ground state of heavy alkali metals at high pressure

DOE PAGES

Fabbris, G.; Lim, J.; Veiga, L. S. I.; ...

2015-02-17

Here, alkali metals display unexpected properties at high pressure, including emergence of low symmetry crystal structures, that appear to occur due to enhanced electronic correlations among the otherwise nearly-free conduction electrons. We investigate the high pressure electronic and structural ground state of K, Rb, and Cs using x-ray absorption spectroscopy and x-ray diffraction measurements together with ab initio theoretical calculations. The sequence of phase transitions under pressure observed at low temperature is similar in all three heavy alkalis except for the absence of the oC84 phase in Cs. Both the experimental and theoretical results point to pressure-enhanced localization of themore » valence electrons characterized by pseudo-gap formation near the Fermi level and strong spd hybridization. Although the crystal structures predicted to host magnetic order in K are not observed, the localization process appears to drive these alkalis closer to a strongly correlated electron state.« less

Electronic and structural ground state of heavy alkali metals at high pressure

NASA Astrophysics Data System (ADS)

Fabbris, G.; Lim, J.; Veiga, L. S. I.; Haskel, D.; Schilling, J. S.

2015-02-01

Alkali metals display unexpected properties at high pressure, including emergence of low-symmetry crystal structures, which appear to occur due to enhanced electronic correlations among the otherwise nearly free conduction electrons. We investigate the high-pressure electronic and structural ground state of K, Rb, and Cs using x-ray absorption spectroscopy and x-ray diffraction measurements together with a b i n i t i o theoretical calculations. The sequence of phase transitions under pressure observed at low temperature is similar in all three heavy alkalis except for the absence of the o C 84 phase in Cs. Both the experimental and theoretical results point to pressure-enhanced localization of the valence electrons characterized by pseudogap formation near the Fermi level and strong s p d hybridization. Although the crystal structures predicted to host magnetic order in K are not observed, the localization process appears to drive these alkalis closer to a strongly correlated electron state.

Reconfiguring crystal and electronic structures of MoS 2 by substitutional doping

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

Suh, Joonki; Tan, Teck Leong; Zhao, Weijie

Doping of traditional semiconductors has enabled technological applications in modern electronics by tailoring their chemical, optical and electronic properties. However, substitutional doping in two-dimensional semiconductors is at a comparatively early stage, and the resultant effects are less explored. In this work, we report unusual effects of degenerate doping with Nb on structural, electronic and optical characteristics of MoS 2 crystals. The doping readily induces a structural transformation from naturally occurring 2H stacking to 3R stacking. Electronically, a strong interaction of the Nb impurity states with the host valence bands drastically and nonlinearly modifies the electronic band structure with the valencemore » band maximum of multilayer MoS 2 at the Γ point pushed upward by hybridization with the Nb states. Finally, when thinned down to monolayers, in stark contrast, such significant nonlinear effect vanishes, instead resulting in strong and broadband photoluminescence via the formation of exciton complexes tightly bound to neutral acceptors.« less

Reconfiguring crystal and electronic structures of MoS 2 by substitutional doping

DOE PAGES

Suh, Joonki; Tan, Teck Leong; Zhao, Weijie; ...

2018-01-15

Doping of traditional semiconductors has enabled technological applications in modern electronics by tailoring their chemical, optical and electronic properties. However, substitutional doping in two-dimensional semiconductors is at a comparatively early stage, and the resultant effects are less explored. In this work, we report unusual effects of degenerate doping with Nb on structural, electronic and optical characteristics of MoS 2 crystals. The doping readily induces a structural transformation from naturally occurring 2H stacking to 3R stacking. Electronically, a strong interaction of the Nb impurity states with the host valence bands drastically and nonlinearly modifies the electronic band structure with the valencemore » band maximum of multilayer MoS 2 at the Γ point pushed upward by hybridization with the Nb states. Finally, when thinned down to monolayers, in stark contrast, such significant nonlinear effect vanishes, instead resulting in strong and broadband photoluminescence via the formation of exciton complexes tightly bound to neutral acceptors.« less

Advancing Efficient All-Electron Electronic Structure Methods Based on Numeric Atom-Centered Orbitals for Energy Related Materials

NASA Astrophysics Data System (ADS)

Blum, Volker

This talk describes recent advances of a general, efficient, accurate all-electron electronic theory approach based on numeric atom-centered orbitals; emphasis is placed on developments related to materials for energy conversion and their discovery. For total energies and electron band structures, we show that the overall accuracy is on par with the best benchmark quality codes for materials, but scalable to large system sizes (1,000s of atoms) and amenable to both periodic and non-periodic simulations. A recent localized resolution-of-identity approach for the Coulomb operator enables O (N) hybrid functional based descriptions of the electronic structure of non-periodic and periodic systems, shown for supercell sizes up to 1,000 atoms; the same approach yields accurate results for many-body perturbation theory as well. For molecular systems, we also show how many-body perturbation theory for charged and neutral quasiparticle excitation energies can be efficiently yet accurately applied using basis sets of computationally manageable size. Finally, the talk highlights applications to the electronic structure of hybrid organic-inorganic perovskite materials, as well as to graphene-based substrates for possible future transition metal compound based electrocatalyst materials. All methods described here are part of the FHI-aims code. VB gratefully acknowledges contributions by numerous collaborators at Duke University, Fritz Haber Institute Berlin, TU Munich, USTC Hefei, Aalto University, and many others around the globe.

Point Mutations in Membrane Proteins Reshape Energy Landscape and Populate Different Unfolding Pathways

PubMed Central

Sapra, K. Tanuj; Balasubramanian, G. Prakash; Labudde, Dirk; Bowie, James U.; Muller, Daniel J.

2009-01-01

Using single-molecule force spectroscopy, we investigated the effect of single point mutations on the energy landscape and unfolding pathways of the transmembrane protein bacteriorhodopsin. We show that the unfolding energy barriers in the energy landscape of the membrane protein followed a simple two-state behavior and represent a manifestation of many converging unfolding pathways. Although the unfolding pathways of wild-type and mutant bacteriorhodopsin did not change, indicating the presence of same ensemble of structural unfolding intermediates, the free energies of the rate-limiting transition states of the bacteriorhodopsin mutants decreased as the distance of those transition states to the folded intermediate states decreased. Thus, all mutants exhibited Hammond behavior and a change in the free energies of the intermediates along the unfolding reaction coordinate and, consequently, their relative occupancies. This is the first experimental proof showing that point mutations can reshape the free energy landscape of a membrane protein and force single proteins to populate certain unfolding pathways over others. PMID:18191146

Soluble fullerene derivatives: The effect of electronic structure on transistor performance and air stability

NASA Astrophysics Data System (ADS)

Ball, James M.; Bouwer, Ricardo K. M.; Kooistra, Floris B.; Frost, Jarvist M.; Qi, Yabing; Domingo, Ester Buchaca; Smith, Jeremy; de Leeuw, Dago M.; Hummelen, Jan C.; Nelson, Jenny; Kahn, Antoine; Stingelin, Natalie; Bradley, Donal D. C.; Anthopoulos, Thomas D.

2011-07-01

The family of soluble fullerene derivatives comprises a widely studied group of electron transporting molecules for use in organic electronic and optoelectronic devices. For electronic applications, electron transporting (n-channel) materials are required for implementation into organic complementary logic circuit architectures. To date, few soluble candidate materials have been studied that fulfill the stringent requirements of high carrier mobility and air stability. Here we present a study of three soluble fullerenes with varying electron affinity to assess the impact of electronic structure on device performance and air stability. Through theoretical and experimental analysis of the electronic structure, characterization of thin-film structure, and characterization of transistor device properties we find that the air stability of the present series of fullerenes not only depends on the absolute electron affinity of the semiconductor but also on the disorder within the thin-film.

Structural, Optical, and Electronic Characterization of Fe-Doped Alumina Nanoparticles

NASA Astrophysics Data System (ADS)

Heiba, Zein K.; Mohamed, Mohamed Bakr; Wahba, Adel Maher; Imam, N. G.

2018-01-01

The effects of iron doping on the structural, optical, and electronic properties of doped alumina have been studied. Single-phase iron-doped alumina Al2- x Fe x O3 ( x = 0.00 to 0.30) nanoparticles were synthesized via citrate-precursor method. Formation of single-phase hexagonal corundum structure with no other separate phases was demonstrated by x-ray diffraction (XRD) analysis and Fourier-transform infrared spectroscopy. The effects of iron doping on the α-Al2O3 structural parameters, viz. atomic coordinates, lattice parameters, crystallite size, and microstrain, were estimated from XRD data by applying the Rietveld profile fitting method. Transmission electron microscopy further confirmed the nanosize nature of the prepared samples with size ranging from 12 nm to 83 nm. The electronic band structure was investigated using density functional theory calculations to explain the decrease in the energy gap of Al2- x Fe x O3 as the amount of Fe was increased. The colored emission peaks in the visible region (blue, red, violet) of the electromagnetic spectrum obtained for the Fe-doped α-Al2O3 nanoparticles suggest their potential application as ceramic nanopigments.

Multigrid Methods in Electronic Structure Calculations

NASA Astrophysics Data System (ADS)

Briggs, Emil

1996-03-01

Multigrid techniques have become the method of choice for a broad range of computational problems. Their use in electronic structure calculations introduces a new set of issues when compared to traditional plane wave approaches. We have developed a set of techniques that address these issues and permit multigrid algorithms to be applied to the electronic structure problem in an efficient manner. In our approach the Kohn-Sham equations are discretized on a real-space mesh using a compact representation of the Hamiltonian. The resulting equations are solved directly on the mesh using multigrid iterations. This produces rapid convergence rates even for ill-conditioned systems with large length and/or energy scales. The method has been applied to both periodic and non-periodic systems containing over 400 atoms and the results are in very good agreement with both theory and experiment. Example applications include a vacancy in diamond, an isolated C60 molecule, and a 64-atom cell of GaN with the Ga d-electrons in valence which required a 250 Ry cutoff. A particular strength of a real-space multigrid approach is its ready adaptability to massively parallel computer architectures. The compact representation of the Hamiltonian is especially well suited to such machines. Tests on the Cray-T3D have shown nearly linear scaling of the execution time up to the maximum number of processors (512). The MPP implementation has been used for studies of a large Amyloid Beta Peptide (C_146O_45N_42H_210) found in the brains of Alzheimers disease patients. Further applications of the multigrid method will also be described. (in collaboration D. J. Sullivan and J. Bernholc)

DFT investigation on the electronic structure of Faujasite

NASA Astrophysics Data System (ADS)

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian; Buimaga-Iarinca, Luiza

2013-11-01

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed for describing atomic charge distribution in the chosen systems.

Second moment scaling and the relationship of geometric and electronic structure

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

Hoistad, L.M.

1993-01-01

Extended Hueckel band calculations were used to show the ditellurides in the CdI[sub 2] structure type with more than 16 valence electrons/MTe[sub 2] unit should have an instability due to their electronic structure. Single crystal X-ray diffraction studies of the electron rich Ta[sub 1[minus]x]Ti[sub x]Te[sub 2] (x = 0.2, 0.3, 0.4 and 0.5) show that a statistical distortion of the CdI[sub 2] structure type has indeed occurred for these compounds confirming the theoretical calculations. Second Moment Scaled Hueckel theory was used to examine the basis of the Hume-Rothery phases are face centered cubic, hexagonal closest packed ([zeta], [epsilon] and [eta]-hcp),more » body centered cubic, [beta]-Mn and [gamma]-brass structures. Good agreement between the experimental and theoretically predicted electron concentration ranges was achieved when an s, p and contracted d orbital model was used. The results presented in this thesis were the first theoretical calculations that corroborate the entire set of Hume-Rothery electron concentration rules. Second Moment Scaled Hueckel energies were used for constructing structure maps for intermetallic compounds with stoichiometry ZA[sub 2], ZA[sub 3] and ZA[sub 6]. Calculations were performed only on the covalent network of the A atoms. The structure types considered were SmSb[sub 2], ZrSi[sub 2], Cu[sub 2]Sb, AuCu[sub 3], TiNi[sub 3], TiCu[sub 3], BiF[sub 3], SnNi[sub 3], NdTe[sub 3], TiS[sub 3], SmAu[sub 6], CeCu[sub 6] and PuGa[sub 6]. The bond distance variation found for closo-borohydrides B[sub 8]H[sub 8][sup 2[minus

Stable holey two-dimensional C2N structures with tunable electronic structure

NASA Astrophysics Data System (ADS)

Longuinhos, R.; Ribeiro-Soares, J.

2018-05-01

C2N holey two-dimensional crystals, or C2N -h2D, a recently synthesized carbon nitride layered material, show promising properties for electronic devices, highly selective molecular filters, and supercapacitors. Few studies have investigated the stacking order in C2N -h2D, which is fundamental to determine its optical activity and plays an important role in its band gap and in the diffusion barrier for ions and molecules through its structure. In this work, we investigate the phonon stability of several bulk C2N -h2D polytypes by using first-principles calculations. Among the polytypes addressed, only one does not display phonon instabilities and is expected to be observed in equilibrium. The electronic structure evolution of dynamically stable C2N -h2D from monolayer to bilayer and to bulk is unveiled. The direct band gap at Γ can be decreased by 34% from monolayer to bulk, offering opportunities for tuning it in optoelectronics. In addition, the effective masses of both carriers become smaller as the number of layers increases, and their anisotropy along in-plane directions displayed in the monolayer is reduced, which suggest that the carrier mobility may be tuned as well. These effects are then explained according to the interaction of the orbitals in neighboring layers. The results presented here shed light on the geometry and electronic structure of an emerging layered material due to its specific stacking and increasing number of layers and suggest new perspectives for applications in optoelectronics.

Energetics and electronic structures of chemically decorated C60 chains

NASA Astrophysics Data System (ADS)

Furutani, Sho; Okada, Susumu

2018-06-01

We studied the energetics and electronic structures of one-dimensional molecular chains of [6,6]-phenyl-C61-butyric acid methyl ester (PCBM) using the density functional theory (DFT). Our DFT calculations show that the binding energies of PCBM range from 90 to 300 meV, depending on not only the intermolecular spacing but also the intermolecular arrangements owing to the interaction between functional groups and C60. The electronic structure of PCBM chains are also sensitive to the mutual arrangements of PCBM in their chain structure. The calculated effective masses of the conduction band range from 0.58 to 634.97m e, giving rise to anisotropic transport properties in their condensed phase.

Electronic structure of shandite Co3Sn2S2

NASA Astrophysics Data System (ADS)

Dedkov, Y. S.; Holder, M.; Molodtsov, S. L.; Rosner, H.

2008-03-01

The electronic structure of shandite Co3Sn2S2 was determined by photoelectron spectroscopy and compared with ab initio band structure calculations. Presented results give evidence that this compound has half-metallic ferromagnetic properties.

Structural and electronic properties of copper-doped chalcogenide glasses

NASA Astrophysics Data System (ADS)

Guzman, David M.; Strachan, Alejandro

2017-10-01

Using ab initio molecular dynamics based on density functional theory, we study the atomic and electronic structure, and transport properties of copper-doped germanium-based chalcogenide glasses. These mixed ionic-electronic conductor materials exhibit resistance or threshold switching under external electric field depending on slight variations of chemical composition. Understanding the origin of the transport character is essential for the functionalization of glassy chalcogenides for nanoelectronics applications. To this end, we generated atomic structures for GeX3 and GeX6 (X = S, Se, Te) at different copper concentrations and characterized the atomic origin of electronic states responsible for transport and the tendency of copper clustering as a function of metal concentration. Our results show that copper dissolution energies explain the tendency of copper to agglomerate in telluride glasses, consistent with filamentary conduction. In contrast, copper is less prone to cluster in sulfides and selenides leading to hysteresisless threshold switching where the nature of transport is dominated by electronic midgap defects derived from polar chalcogen bonds and copper atoms. Simulated I -V curves show that at least 35% by weight of copper is required to achieve the current demands of threshold-based devices for memory applications.

The Electronic Structure of Transition Metal Coated Fullerenes

NASA Astrophysics Data System (ADS)

Patton, David C.; Pederson, Mark R.; Kaxiras, Efthimios

1998-03-01

Clusters composed of fullerene molecules with an outer shell of transition metal atoms in the composition C_60M_62 (M being a transition metal) have been produced with laser vaporisation techniques(F. Tast, N. Malinowski, S. Frank, M. Heinebrodt, I.M.L. Billas, and T. P. Martin, Z. Phys D 40), 351 (1997).. We have studied several of these very large systems with a parallel version of the all-electron NRLMOL cluster code. Optimized geometries of the metal encased fullerenes C_60Ti_62 and C_60V_62 are presented along with their HOMO-LUMO gaps, electron affinities, ionization energies, and cohesive energies. We compare the stability of these clusters to relaxed met-car structures (e.g. Ti_8C_12) and to relaxed rocksalt metal-carbide fragments (TiC)n with n=8 and 32. In addition to metal-coated fullerenes we consider the possibility of a trilayered structure consisting of a small shell of metal atoms enclosed by a metal coated fullerene. The nature of bonding in these systems is analyzed by studying the electronic charge distributions.

Structural Fingerprinting of Nanocrystals in the Transmission Electron Microscope

NASA Astrophysics Data System (ADS)

Rouvimov, Sergei; Plachinda, Pavel; Moeck, Peter

2010-03-01

Three novel strategies for the structurally identification of nanocrystals in a transmission electron microscope are presented. Either a single high-resolution transmission electron microscopy image [1] or a single precession electron diffractogram (PED) [2] may be employed. PEDs from fine-grained crystal powders may also be utilized. Automation of the former two strategies is in progress and shall lead to statistically significant results on ensembles of nanocrystals. Open-access databases such as the Crystallography Open Database which provides more than 81,500 crystal structure data sets [3] or its mainly inorganic and educational subsets [4] may be utilized. [1] http://www.scientificjournals.org/journals 2007/j/of/dissertation.htm [2] P. Moeck and S. Rouvimov, in: {Drugs and the Pharmaceutical Sciences}, Vol. 191, 2009, 270-313 [3] http://cod.ibt.lt, http://www.crystallography.net, http://cod.ensicaen.fr, http://nanocrystallography.org, http://nanocrystallography.net, http://journals.iucr.org/j/issues/2009/04/00/kk5039/kk5039.pdf [4] http://nanocrystallography.research.pdx.edu/CIF-searchable

Effects of Electronic Reading Environments' Structure on L2 Reading Comprehension

ERIC Educational Resources Information Center

Al-Seghayer, Khalid

2017-01-01

This study examines the effects of an electronic reading environment's structure on second language (L2) reading comprehension. In particular, this study explores whether clarifying the underlying structure of an electronic text, along with the ways in which its units or nodes are organized and interrelated results in better comprehension as well…

A photovoltaic device structure based on internal electron emission.

PubMed

McFarland, Eric W; Tang, Jing

2003-02-06

There has been an active search for cost-effective photovoltaic devices since the development of the first solar cells in the 1950s (refs 1-3). In conventional solid-state solar cells, electron-hole pairs are created by light absorption in a semiconductor, with charge separation and collection accomplished under the influence of electric fields within the semiconductor. Here we report a multilayer photovoltaic device structure in which photon absorption instead occurs in photoreceptors deposited on the surface of an ultrathin metal-semiconductor junction Schottky diode. Photoexcited electrons are transferred to the metal and travel ballistically to--and over--the Schottky barrier, so providing the photocurrent output. Low-energy (approximately 1 eV) electrons have surprisingly long ballistic path lengths in noble metals, allowing a large fraction of the electrons to be collected. Unlike conventional cells, the semiconductor in this device serves only for majority charge transport and separation. Devices fabricated using a fluorescein photoreceptor on an Au/TiO2/Ti multilayer structure had typical open-circuit photovoltages of 600-800 mV and short-circuit photocurrents of 10-18 micro A cm(-2) under 100 mW cm(-2) visible band illumination: the internal quantum efficiency (electrons measured per photon absorbed) was 10 per cent. This alternative approach to photovoltaic energy conversion might provide the basis for durable low-cost solar cells using a variety of materials.

Structural evolution and electronic properties of n-type doped hydrogenated amorphous silicon thin films

NASA Astrophysics Data System (ADS)

He, Jian; Li, Wei; Xu, Rui; Qi, Kang-Cheng; Jiang, Ya-Dong

2011-12-01

The relationship between structure and electronic properties of n-type doped hydrogenated amorphous silicon (a-Si:H) thin films was investigated. Samples with different features were prepared by plasma enhanced chemical vapor deposition (PECVD) at various substrate temperatures. Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy were used to evaluate the structural evolution, meanwhile, electronic-spin resonance (ESR) and optical measurement were applied to explore the electronic properties of P-doped a-Si:H thin films. Results reveal that the changes in materials structure affect directly the electronic properties and the doping efficiency of dopant.

Photoemission and Photoabsorption Investigation of the Electronic Structure of Ytterbium Doped Strontium Fluoroapatite

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

Nelson, A J; van Buuren, T; Bostedt, C

X-ray photoemission and x-ray photoabsorption were used to study the composition and the electronic structure of ytterbium doped strontium fluoroapatite (Yb:S-FAP). High resolution photoemission measurements on the valence band electronic structure was used to evaluate the density of occupied states of this fluoroapatite. Element specific density of unoccupied electronic states in Yb:S-FAP were probed by x-ray absorption spectroscopy (XAS) at the Yb 4d (N{sub 4,5}-edge), Sr 3d (M{sub 4,5}-edge), P 2p (L{sub 2,3}-edge), F 1s and O 1s (K-edges) absorption edges. These results provide the first measurements of the electronic structure and surface chemistry of this material.

Spectroscopic investigation of the electronic structure of yttria-stabilized zirconia

NASA Astrophysics Data System (ADS)

Götsch, Thomas; Bertel, Erminald; Menzel, Alexander; Stöger-Pollach, Michael; Penner, Simon

2018-03-01

The electronic structure and optical properties of yttria-stabilized zirconia are investigated as a function of the yttria content using multiple experimental and theoretical methods, including electron energy-loss spectroscopy, Kramers-Kronig analysis to obtain the optical parameters, photoelectron spectroscopy, and density functional theory. It is shown that many properties, including the band gaps, the crystal field splitting, the so-called defect gap between acceptor (YZr') and donor (VO••) states, as well as the index of refraction in the visible range exhibit the same "zig-zag-like" trend as the unit cell height does, showing the influence of an increased yttria content as well as of the tetragonal-cubic phase transition between 8 mol % and 20 mol %Y2O3 . Also, with Čerenkov spectroscopy (CS), a new technique is presented, providing information complementary to electron energy-loss spectroscopy. In CS, the Čerenkov radiation emitted inside the TEM is used to measure the onset of optical absorption. The apparent absorption edges in the Čerenkov spectra correspond to the energetic difference between the disorder states close to the valence band and the oxygen-vacancy-related electronic states within the band gap. Theoretical computations corroborate this assignment: they find both, the acceptor states and the donor states, at the expected energies in the band structures for diverse yttria concentrations. In the end, a schematic electronic structure diagram of the area around the band gap is constructed, including the chemical potential of the electrons obtained from photoelectron spectroscopy. The latter reveal that tetragonal YSZ corresponds to a p -type semiconductor, whereas the cubic samples exhibit n -type semiconductor properties.

Electronic structure of HxVO2 probed with in-situ spectroscopic ellipsometry

NASA Astrophysics Data System (ADS)

Kim, So Yeun; Sandilands, Luke J.; Kang, Taedong; Son, Jaeseok; Sohn, C. H.; Yoon, Hyojin; Son, Junwoo; Moon, S. J.; Noh, T. W.

Vanadium dioxide (VO2) undergoes a metal-to-insulator transition (MIT) near 340K. Despite extensive studies on this material, the role of electron-electron correlation and electron-lattice interactions in driving this MIT is still under debate. Recently, it was demonstrated that hydrogen can be reversibly absorbed into VO2 thin film without destroying the lattice framework. This H-doping allows systematic control of the electron density and lattice structure which in turn leads to a insulator (VO2) - metal (HxVO2) - insulator (HVO2) phase modulation. To better understand the phase modulation of HxVO2, we used in-situ spectroscopic ellipsometry to monitor the electronic structure during the hydrogenization process, i.e. we measured the optical conductivity of HxVO2 while varying x. Starting in the high temperature rutile metallic phase of VO2, we observed a large change in the electronic structure upon annealing in H gas at 370K: the low energy conductivity is continuously suppressed, consistent with reported DC resistivity data, while the conductivity peaks at high energy show strong changes in energy and spectral weight. The implications of our results for the MIT in HxVO2 will be discussed.

Electronic Structure of Energetic Molecules and Crystals Under Compression

NASA Astrophysics Data System (ADS)

Kay, Jeffrey

Understanding how the electronic structure of energetic materials change under compression is important to elucidating mechanisms of shock-induced reactions and detonation. In this presentation, the electronic structure of prototypical energetic crystals are examined under high degrees of compression using ab initio quantum chemical calculations. The effects of compression on and interactions between the constituent molecules are examined in particular. The insights these results provide into previous experimental observations and theoretical predictions of energetic materials under high pressure are discussed. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. DOE's National Nuclear Security Administration under contract DE-AC04-94AL85000.

Valence electronic structure of cobalt phthalocyanine from an optimally tuned range-separated hybrid functional.

PubMed

Brumboiu, Iulia Emilia; Prokopiou, Georgia; Kronik, Leeor; Brena, Barbara

2017-07-28

We analyse the valence electronic structure of cobalt phthalocyanine (CoPc) by means of optimally tuning a range-separated hybrid functional. The tuning is performed by modifying both the amount of short-range exact exchange (α) included in the hybrid functional and the range-separation parameter (γ), with two strategies employed for finding the optimal γ for each α. The influence of these two parameters on the structural, electronic, and magnetic properties of CoPc is thoroughly investigated. The electronic structure is found to be very sensitive to the amount and range in which the exact exchange is included. The electronic structure obtained using the optimal parameters is compared to gas-phase photo-electron data and GW calculations, with the unoccupied states additionally compared with inverse photo-electron spectroscopy measurements. The calculated spectrum with tuned γ, determined for the optimal value of α = 0.1, yields a very good agreement with both experimental results and with GW calculations that well-reproduce the experimental data.

Structures and electronic states of halogen-terminated graphene nano-flakes

NASA Astrophysics Data System (ADS)

Tachikawa, Hiroto; Iyama, Tetsuji

2015-12-01

Halogen-functionalized graphenes are utilized as electronic devices and energy materials. In the present paper, the effects of halogen-termination of graphene edge on the structures and electronic states of graphene flakes have been investigated by means of density functional theory (DFT) method. It was found that the ionization potential (Ip) and electron affinity of graphene (EA) are blue-shifted by the halogen termination, while the excitation energy is red-shifted. The drastic change showed a possibility as electronic devices such as field-effect transistors. The change of electronic states caused by the halogen termination of graphene edge was discussed on the basis of the theoretical results.

Structural and electronic properties of double-walled boron nitride nanocones

NASA Astrophysics Data System (ADS)

Brito, E.; Silva, T. S.; Guerra, T.; Leite, L.; Azevedo, S.; Freitas, A.; Kaschny, J. R.

2018-01-01

First principles calculations were applied to study the structural and electronic properties of different configurations of double-walled boron nitride nanocones with a disclination angle of 60°. The analysis includes different rotation angles, distance between apexes, as well as distinct types of antiphase boundaries. The calculations indicate that the non-rotated configuration of double-walled nanocone with a defective line composed by C and N atoms, forming C-N bonds, is the most stable configuration. It was found that the yam angle, apexes distance and defective line composition present significant influence on the electronic properties of such structures. Moreover, analyzing the spin charge density, for the electronic states near the Fermi level, it was also found that the configuration with a defective line containing C atoms presents a net magnetic moment.

3D structure of eukaryotic flagella/cilia by cryo-electron tomography.

PubMed

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex.

Atomic and electronic structures of an extremely fragile liquid.

PubMed

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-12-18

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia-Thornton number-number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr-O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr-O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid.

Atomic and electronic structures of an extremely fragile liquid

PubMed Central

Kohara, Shinji; Akola, Jaakko; Patrikeev, Leonid; Ropo, Matti; Ohara, Koji; Itou, Masayoshi; Fujiwara, Akihiko; Yahiro, Jumpei; Okada, Junpei T.; Ishikawa, Takehiko; Mizuno, Akitoshi; Masuno, Atsunobu; Watanabe, Yasuhiro; Usuki, Takeshi

2014-01-01

The structure of high-temperature liquids is an important topic for understanding the fragility of liquids. Here we report the structure of a high-temperature non-glass-forming oxide liquid, ZrO2, at an atomistic and electronic level. The Bhatia–Thornton number–number structure factor of ZrO2 does not show a first sharp diffraction peak. The atomic structure comprises ZrO5, ZrO6 and ZrO7 polyhedra with a significant contribution of edge sharing of oxygen in addition to corner sharing. The variety of large oxygen coordination and polyhedral connections with short Zr–O bond lifetimes, induced by the relatively large ionic radius of zirconium, disturbs the evolution of intermediate-range ordering, which leads to a reduced electronic band gap and increased delocalization in the ionic Zr–O bonding. The details of the chemical bonding explain the extremely low viscosity of the liquid and the absence of a first sharp diffraction peak, and indicate that liquid ZrO2 is an extremely fragile liquid. PMID:25520236

Probing Structural and Electronic Dynamics with Ultrafast Electron Microscopy

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

Plemmons, DA; Suri, PK; Flannigan, DJ

In this Perspective, we provide an overview,of the field of ultrafast electron microscopy (UEM). We begin by briefly discussing the emergence of methods for probing ultrafast structural dynamics and the information that can be obtained. Distinctions are drawn between the two main types a probes for femtosecond (fs) dynamics fast electrons and X-ray photons and emphasis is placed on hour the nature of charged particles is exploited in ultrafast electron-based' experiments:. Following this, we describe the versatility enabled by the ease with which electron trajectories and velocities can be manipulated with transmission electron microscopy (TEM): hardware configurations, and we emphasizemore » how this is translated to the ability to measure scattering intensities in real, reciprocal, and energy space from presurveyed and selected rianoscale volumes. Owing to decades of ongoing research and development into TEM instrumentation combined with advances in specimen holder technology, comprehensive experiments can be conducted on a wide range of materials in various phases via in situ methods. Next, we describe the basic operating concepts, of UEM, and we emphasize that its development has led to extension of several of the formidable capabilities of TEM into the fs domain, dins increasing the accessible temporal parameter spade by several orders of magnitude. We then divide UEM studies into those conducted in real (imaging), reciprocal (diffraction), and energy (spectroscopy) spate. We begin each of these sections by providing a brief description of the basic operating principles and the types of information that can be gathered followed by descriptions of how these approaches are applied in UM, the type of specimen parameter space that can be probed, and an example of the types of dynamics that can be resolved. We conclude with an Outlook section, wherein we share our perspective on some future directions of the field pertaining to continued instrument development

Electronic structures of Plutonium compounds with the NaCl-type monochalcogenides structure

NASA Astrophysics Data System (ADS)

Maehira, Takahiro; Tatetsu, Yasutomi

2012-12-01

We calculate the energy band structure and the Fermi surface of PuS, PuSe and PuTe by using a self-consistent relativistic linear augmented-plane-wave method with the exchange and correlation potential in a local density approximation. It is found in common that the energy bands in the vicinity of the Fermi level are mainly due to the hybridization between Pu 5/ and monochalcogenide p electrons. The obtained main Fermi surfaces are composed of two hole sheets and one electron sheet, all of which are constructed from the band having the Pu 5/ state and the monochalcogenide p state.

The electronic structure of Au25 clusters: between discrete and continuous

NASA Astrophysics Data System (ADS)

Katsiev, Khabiboulakh; Lozova, Nataliya; Wang, Lu; Sai Krishna, Katla; Li, Ruipeng; Mei, Wai-Ning; Skrabalak, Sara E.; Kumar, Challa S. S. R.; Losovyj, Yaroslav

2016-08-01

Here, an approach based on synchrotron resonant photoemission is employed to explore the transition between quantization and hybridization of the electronic structure in atomically precise ligand-stabilized nanoparticles. While the presence of ligands maintains quantization in Au25 clusters, their removal renders increased hybridization of the electronic states in the vicinity of the Fermi level. These observations are supported by DFT studies.Here, an approach based on synchrotron resonant photoemission is employed to explore the transition between quantization and hybridization of the electronic structure in atomically precise ligand-stabilized nanoparticles. While the presence of ligands maintains quantization in Au25 clusters, their removal renders increased hybridization of the electronic states in the vicinity of the Fermi level. These observations are supported by DFT studies. Electronic supplementary information (ESI) available: Experimental details including chemicals, sample preparation, and characterization methods. Computation techniques, SV-AUC, GIWAXS, XPS, UPS, MALDI-TOF, ESI data of Au25 clusters. See DOI: 10.1039/c6nr02374f

DFT investigation on the electronic structure of Faujasite

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

Popeneciu, Horea; Calborean, Adrian; Tudoran, Cristian

2013-11-13

We report here first-principle pseudopotential DFT calculations to investigate relevant aspects of the electronic structure of zeolites based FAU. Fundamental molecular issues of the band-gap and electronic population analysis were reviewed under GGA/RPBE level of theory, corroborated with a DZP basis set and Troullier-Martins norm conserving pseudo-potentials. The atom-projected density of states and the analysis of HOMO-LUMO frontier orbitals at Gamma point were performed. Their electronic transfers are discussed through the alignment and relative positions of orbitals in order to determine the way that the molecule interacts with adsorbed molecules and other practical applications. Mulliken population analysis was employed formore » describing atomic charge distribution in the chosen systems.« less

Structural dynamics of lipid bilayers using ultrafast electron crystallography

NASA Astrophysics Data System (ADS)

Chen, Songye; Seidel, Marco; Zewail, Ahmed

2007-03-01

The structures and dynamics of bilayers of crystalline fatty acids and phospholipids were studied using ultrafast electron crystallography (UEC). The systems investigated are arachidic (eicosanoic) acid and dimyristoyl phosphatidic acid (DMPA), deposited on a substrate by the Langmuir-Blodgett technique. The atomic structures under different preparation conditions were determined. The structural dynamics following a temperature jump induced by femtosecond laser on the substrates were obtained and compared to the equilibrium temperature dependence.

Design and analysis of multifunctional structures for embedded electronics in unmanned aerial vehicles

NASA Astrophysics Data System (ADS)

Kothari, Rushabh M.

Multifunctional structures are a new trend in the aerospace industry for the next generation structural design. Many future structures are expected to be something in addition to a load bearing structure. The design and analysis of multifunctional structures combining structural, electrical and thermal functionalities are presented here. The sandwich beam is considered as a starting point for the load bearing structure and then it is modified with a cavity to embed avionics and thermal controls. The embedded avionics inside the load bearing structure would allow weight reduction of the aerospace vehicle due to elimination of separate electronics housing, interconnects, cables etc. The cavity reduces strength of the structure so various reinforcements methods are evaluated. The result of various reinforcements and their effectiveness are presented. The current generation of electronics produce massive amount of heat. In the case of embedded electronics, the excessive heat presents a major challenge to the structural and heat transfer engineers. The embedded nature of electronics prevents the use of the classical heat dissipative methods such as fans and high velocity air flows, etc. The integrated thermal control of the electronics has been designed using passive heat transfer device and highly optimized particulate composite thermal interface material (TIM). The TIMs are used to fill the air gaps and reduce contact resistance between two surfaces, such as electronics and heat dissipators. The efficiency of TIM directly affects the overall heat transfer ability of the integrated thermal control system. The effect of the particles at micron and nano scales are studied for the particulate composite TIM. The thermal boundary resistance study for the particulate composite TIM with nano silica particles is presented in this thesis. The FEA analysis is used to model thermal boundary resistance and compared with the theoretical micromechanics model. The heat pipes are

Electronic structure and insulating gap in epitaxial VO 2 polymorphs

DOE PAGES

Lee, Shinbuhm; Meyer, Tricia L.; Sohn, Changhee; ...

2015-12-24

Here, determining the origin of the insulating gap in the monoclinic VO 2(M1) is a long-standing issue. The difficulty of this study arises from the simultaneous occurrence of structural and electronic transitions upon thermal cycling. Here, we compare the electronic structure of the M1 phase with that of single crystalline insulating VO 2(A) and VO 2(B) thin films to better understand the insulating phase of VO 2. As these A and B phases do not undergo a structural transition upon thermal cycling, we comparatively study the origin of the gap opening in the insulating VO 2 phases. By x-ray absorptionmore » and optical spectroscopy, we find that the shift of unoccupied t 2g orbitals away from the Fermi level is a common feature, which plays an important role for the insulating behavior in VO 2 polymorphs. The distinct splitting of the half-filled t 2g orbital is observed only in the M1 phase, widening the bandgap up to ~0.6 eV. Our approach of comparing all three insulating VO 2 phases provides insight into a better understanding of the electronic structure and the origin of the insulating gap in VO 2.« less

The structure of the electron diffusion region during asymmetric anti-parallel magnetic reconnection

NASA Astrophysics Data System (ADS)

Swisdak, M.; Drake, J. F.; Price, L.; Burch, J. L.; Cassak, P.

2017-12-01

The structure of the electron diffusion region during asymmetric magnetic reconnection is ex- plored with high-resolution particle-in-cell simulations that focus on an magnetopause event ob- served by the Magnetospheric Multiscale Mission (MMS). A major surprise is the development of a standing, oblique whistler-like structure with regions of intense positive and negative dissipation. This structure arises from high-speed electrons that flow along the magnetosheath magnetic sepa- ratrices, converge in the dissipation region and jet across the x-line into the magnetosphere. The jet produces a region of negative charge and generates intense parallel electric fields that eject the electrons downstream along the magnetospheric separatrices. The ejected electrons produce the parallel velocity-space crescents documented by MMS.

Electronic Structure and Properties of Berkelium Iodates.

PubMed

Silver, Mark A; Cary, Samantha K; Garza, Alejandro J; Baumbach, Ryan E; Arico, Alexandra A; Galmin, Gregory A; Chen, Kuan-Wen; Johnson, Jason A; Wang, Jamie C; Clark, Ronald J; Chemey, Alexander; Eaton, Teresa M; Marsh, Matthew L; Seidler, Kevin; Galley, Shane S; van de Burgt, Lambertus; Gray, Ashley L; Hobart, David E; Hanson, Kenneth; Van Cleve, Shelley M; Gendron, Frédéric; Autschbach, Jochen; Scuseria, Gustavo E; Maron, Laurent; Speldrich, Manfred; Kögerler, Paul; Celis-Barros, Cristian; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro; Ruf, Michael; Albrecht-Schmitt, Thomas E

2017-09-27

The reaction of 249 Bk(OH) 4 with iodate under hydrothermal conditions results in the formation of Bk(IO 3 ) 3 as the major product with trace amounts of Bk(IO 3 ) 4 also crystallizing from the reaction mixture. The structure of Bk(IO 3 ) 3 consists of nine-coordinate Bk III cations that are bridged by iodate anions to yield layers that are isomorphous with those found for Am III , Cf III , and with lanthanides that possess similar ionic radii. Bk(IO 3 ) 4 was expected to adopt the same structure as M(IO 3 ) 4 (M = Ce, Np, Pu), but instead parallels the structural chemistry of the smaller Zr IV cation. Bk III -O and Bk IV -O bond lengths are shorter than anticipated and provide further support for a postcurium break in the actinide series. Photoluminescence and absorption spectra collected from single crystals of Bk(IO 3 ) 4 show evidence for doping with Bk III in these crystals. In addition to luminescence from Bk III in the Bk(IO 3 ) 4 crystals, a broad-band absorption feature is initially present that is similar to features observed in systems with intervalence charge transfer. However, the high-specific activity of 249 Bk (t 1/2 = 320 d) causes oxidation of Bk III and only Bk IV is present after a few days with concomitant loss of both the Bk III luminescence and the broadband feature. The electronic structure of Bk(IO 3 ) 3 and Bk(IO 3 ) 4 were examined using a range of computational methods that include density functional theory both on clusters and on periodic structures, relativistic ab initio wave function calculations that incorporate spin-orbit coupling (CASSCF), and by a full-model Hamiltonian with spin-orbit coupling and Slater-Condon parameters (CONDON). Some of these methods provide evidence for an asymmetric ground state present in Bk IV that does not strictly adhere to Russel-Saunders coupling and Hund's Rule even though it possesses a half-filled 5f 7 shell. Multiple factors contribute to the asymmetry that include 5f electrons being present in

Electronic Structure and Transport in Solids from First Principles

NASA Astrophysics Data System (ADS)

Mustafa, Jamal Ibrahim

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

Bright-field electron tomography of individual inorganic fullerene-like structures.

PubMed

Bar Sadan, Maya; Wolf, Sharon G; Houben, Lothar

2010-03-01

Nanotubes and fullerene-like nanoparticles of various inorganic layered compounds have been studied extensively in recent years. Their characterisation on the atomic scale has proven essential for progress in synthesis as well as for the theoretical modelling of their physical properties. We show that with electron tomography it is possible to achieve a reliable reconstruction of the 3D structure of nested WS(2) or MoS(2) fullerene-like and nanotube structures with sub-nanometre resolution using electron microscopes that are not aberration-corrected. Model-based simulations were used to identify imaging parameters, under which structural features such as the shell structure can be retained in the tomogram reconstructed from bright-field micrographs. The isolation of a particle out of an agglomerate for the analysis of a single structure and its interconnection with other particles is facilitated through the tomograms. The internal structure of the layers within the particle alongside the shape and content of its internal void are reconstructed. The tomographic reconstruction yields insights regarding the growth process as well as structural defects, such as non-continuous layers, which relate to the lubrication properties.

Structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na)

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

Santhosh, M.; Rajeswarapalanichamy, R., E-mail: rrpalanichamy@gmail.com; Manikandan, M.

2016-05-06

Ab initio calculations are performed to investigate the structural stability, electronic structure and mechanical properties of alkali gallium hydrides AGaH{sub 4} (A = Li, Na) for three different crystal structures, namely tetragonal (P42{sub 1}c), tetragonal (P4{sub 2}/nmc) and monoclinic (P2{sub 1}/c). Among the considered structures, tetragonal (P42{sub 1}c) phase is found to be the most stable phase for these hydrides at normal pressure. A pressure induced structural phase transition from tetragonal (P42{sub 1}c) to tetragonal (P4{sub 2}/nmc) is observed. The electronic structure reveals that these hydrides are insulators. The calculated elastic constants indicate that these ternary imides are mechanically stablemore » at normal pressure.« less

Polymeric Thin Films for Organic Electronics: Properties and Adaptive Structures

PubMed Central

Cataldo, Sebastiano; Pignataro, Bruno

2013-01-01

This review deals with the correlation between morphology, structure and performance of organic electronic devices including thin film transistors and solar cells. In particular, we report on solution processed devices going into the role of the 3D supramolecular organization in determining their electronic properties. A selection of case studies from recent literature are reviewed, relying on solution methods for organic thin-film deposition which allow fine control of the supramolecular aggregation of polymers confined at surfaces in nanoscopic layers. A special focus is given to issues exploiting morphological structures stemming from the intrinsic polymeric dynamic adaptation under non-equilibrium conditions. PMID:28809362

Variability of Protein Structure Models from Electron Microscopy.

PubMed

Monroe, Lyman; Terashi, Genki; Kihara, Daisuke

2017-04-04

An increasing number of biomolecular structures are solved by electron microscopy (EM). However, the quality of structure models determined from EM maps vary substantially. To understand to what extent structure models are supported by information embedded in EM maps, we used two computational structure refinement methods to examine how much structures can be refined using a dataset of 49 maps with accompanying structure models. The extent of structure modification as well as the disagreement between refinement models produced by the two computational methods scaled inversely with the global and the local map resolutions. A general quantitative estimation of deviations of structures for particular map resolutions are provided. Our results indicate that the observed discrepancy between the deposited map and the refined models is due to the lack of structural information present in EM maps and thus these annotations must be used with caution for further applications. Copyright © 2017 Elsevier Ltd. All rights reserved.

Optical and electronic structure description of metal-doped phthalocyanines.

PubMed

Leal, Luciano Almeida; da Cunha, Wiliam Ferreira; Ribeiro Junior, Luiz Antonio; Pereira, Tamires Lima; Blawid, Stefan Michael; de Sousa Junior, Rafael Timóteo; da Silva Filho, Demétrio Antonio

2017-05-01

Phthalocyanines represent a crucial class of organic compounds with high technological appeal. By doping the center of these systems with metals, one obtains the so-called metal-phthalocyanines, whose property of being an effective electron donor allows for potentially interesting uses in organic electronics. In this sense, investigating optical and electronic structure changes in the phthalocyanine profiles in the presence of different metals is of fundamental importance for evaluating the appropriateness of the resulting system as far as these uses are concerned. In the present work, we carry out this kind of effort for phthalocyanines doped with different metals, namely, copper, nickel, and magnesium. Density functional theory was applied to obtain the absorption spectra, and electronic and structural properties of the complexes. Our results suggest that depending on the dopant, a different level of change is achieved. Moreover, electrostatic potential energy mapping shows how the charge distribution can be affected by solar radiation. Our contribution is crucial in describing the best possible candidates for use in different organic photovoltaic applications. Graphical Abstract Representation of meta-phthalocyanine systems. All calculations of this work are based on varying metal position along z axis, considering the z-axis has its zero point matching with the center of phthalocyanine cavityconsidering.

Electronic Structure and Properties of Deformed Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Yang, Liu; Arnold, Jim (Technical Monitor)

2001-01-01

A theoretical framework based on Huckel tight-binding model has been formulated to analyze the electronic structure of carbon nanotubes under uniform deformation. The model successfully quantifies the dispersion relation, density of states and bandgap change of nanotubes under uniform stretching, compression, torsion and bending. Our analysis shows that the shifting of the Fermi point away from the Brillouin zone vertices is the key reason for these changes. As a result of this shifting, the electronic structure of deformed carbon nanotubes varies dramatically depending on their chirality and deformation mode. Treating the Fermi point as a function of strain and tube chirality, the analytical solution preserves the concise form of undeformed carbon nanotubes. It predicts the shifting, merging and splitting of the Van Hove singularities in the density of states and the zigzag pattern of bandgap change under strains. Four orbital tight-binding simulations of carbon nanotubes under uniform stretching, compression, torsion and bending have been performed to verify the analytical solution. Extension to more complex systems are being performed to relate this analytical solution to the spectroscopic characterization, device performance and proposed quantum structures induced by the deformation. The limitations of this model will also be discussed.

Structure and navigation for electronic publishing

NASA Astrophysics Data System (ADS)

Tillinghast, John; Beretta, Giordano B.

1998-01-01

The sudden explosion of the World Wide Web as a new publication medium has given a dramatic boost to the electronic publishing industry, which previously was a limited market centered around CD-ROMs and on-line databases. While the phenomenon has parallels to the advent of the tabloid press in the middle of last century, the electronic nature of the medium brings with it the typical characteristic of 4th wave media, namely the acceleration in its propagation speed and the volume of information. Consequently, e-publications are even flatter than print media; Shakespeare's Romeo and Juliet share the same computer screen with a home-made plagiarized copy of Deep Throat. The most touted tool for locating useful information on the World Wide Web is the search engine. However, due to the medium's flatness, sought information is drowned in a sea of useless information. A better solution is to build tools that allow authors to structure information so that it can easily be navigated. We experimented with the use of ontologies as a tool to formulate structures for information about a specific topic, so that related concepts are placed in adjacent locations and can easily be navigated using simple and ergonomic user models. We describe our effort in building a World Wide Web based photo album that is shared among a small network of people.

Electronic structures of GaAs/AlxGa1-xAs quantum double rings

PubMed Central

Xia, Jian-Bai

2006-01-01

In the framework of effective mass envelope function theory, the electronic structures of GaAs/AlxGa1-xAs quantum double rings (QDRs) are studied. Our model can be used to calculate the electronic structures of quantum wells, wires, dots, and the single ring. In calculations, the effects due to the different effective masses of electrons and holes in GaAs and AlxGa1-xAs and the valence band mixing are considered. The energy levels of electrons and holes are calculated for different shapes of QDRs. The calculated results are useful in designing and fabricating the interrelated photoelectric devices. The single electron states presented here are useful for the study of the electron correlations and the effects of magnetic fields in QDRs.

Three-dimensional structural analysis of eukaryotic flagella/cilia by electron cryo-tomography

PubMed Central

Bui, Khanh Huy; Pigino, Gaia; Ishikawa, Takashi

2011-01-01

Electron cryo-tomography is a potential approach to analyzing the three-dimensional conformation of frozen hydrated biological macromolecules using electron microscopy. Since projections of each individual object illuminated from different orientations are merged, electron tomography is capable of structural analysis of such heterogeneous environments as in vivo or with polymorphism, although radiation damage and the missing wedge are severe problems. Here, recent results on the structure of eukaryotic flagella, which is an ATP-driven bending organelle, from green algae Chlamydomonas are presented. Tomographic analysis reveals asymmetric molecular arrangements, especially that of the dynein motor proteins, in flagella, giving insight into the mechanism of planar asymmetric bending motion. Methodological challenges to obtaining higher-resolution structures from this technique are also discussed. PMID:21169680

3D structure of eukaryotic flagella/cilia by cryo-electron tomography

PubMed Central

Ishikawa, Takashi

2013-01-01

Flagella/cilia are motile organelles with more than 400 proteins. To understand the mechanism of such complex systems, we need methods to describe molecular arrange-ments and conformations three-dimensionally in vivo. Cryo-electron tomography enabled us such a 3D structural analysis. Our group has been working on 3D structure of flagella/cilia using this method and revealed highly ordered and beautifully organized molecular arrangement. 3D structure gave us insights into the mechanism to gener-ate bending motion with well defined waveforms. In this review, I summarize our recent structural studies on fla-gella/cilia by cryo-electron tomography, mainly focusing on dynein microtubule-based ATPase motor proteins and the radial spoke, a regulatory protein complex. PMID:27493552

Growth and Electronic Structure of Heusler Compounds for Use in Electron Spin Based Devices

NASA Astrophysics Data System (ADS)

Patel, Sahil Jaykumar

Spintronic devices, where information is carried by the quantum spin state of the electron instead of purely its charge, have gained considerable interest for their use in future computing technologies. For optimal performance, a pure spin current, where all electrons have aligned spins, must be generated and transmitted across many interfaces and through many types of materials. While conventional spin sources have historically been elemental ferromagnets, like Fe or Co, these materials pro duce only partially spin polarized currents. To increase the spin polarization of the current, materials like half-metallic ferromagnets, where there is a gap in the minority spin density of states around the Fermi level, or topological insulators, where the current transport is dominated by spin-locked surface states, show promise. A class of materials called Heusler compounds, with electronic structures that range from normal metals, to half metallic ferromagnets, semiconductors, superconductors and even topological insulators, interfaces well with existing device technologies, and through the use of molecular beam epitaxy (MBE) high quality heterostructures and films can be grown. This dissertation examines the electronic structure of surfaces and interfaces of both topological insulator (PtLuSb-- and PtLuBi--) and half-metallic ferromagnet (Co2MnSi-- and Co2FeSi--) III-V semiconductor heterostructures. PtLuSb and PtLuBi growth by MBE was demonstrated on Alx In1--xSb (001) ternaries. PtLuSb (001) surfaces were observed to reconstruct with either (1x3) or c(2x2) unit cells depending on Sb overpressure and substrate temperature. viii The electronic structure of these films was studied by scanning tunneling microscopy/spectroscopy (STM/STS) and photoemission spectroscopy. STS measurements as well as angle resolved photoemission spectropscopy (ARPES) suggest that PtLuSb has a zero-gap or semimetallic band structure. Additionally, the observation of linearly dispersing surface

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

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

Indium antimonide quantum well structures for electronic device applications

NASA Astrophysics Data System (ADS)

Edirisooriya, Madhavie

The electron effective mass is smaller in InSb than in any other III-V semiconductor. Since the electron mobility depends inversely on the effective mass, InSb-based devices are attractive for field effect transistors, magnetic field sensors, ballistic transport devices, and other applications where the performance depends on a high mobility or a long mean free path. In addition, electrons in InSb have a large g-factor and strong spin orbit coupling, which makes them well suited for certain spin transport devices. The first n-channel InSb high electron mobility transistor (HEMT) was produced in 2005 with a power-delay product superior to HEMTs with a channel made from any other III-V semiconductor. The high electron mobility in the InSb quantum-well channel increases the switching speed and lowers the required supply voltage. This dissertation focuses on several materials challenges that can further increase the appeal of InSb quantum wells for transistors and other electronic device applications. First, the electron mobility in InSb quantum wells, which is the highest for any semiconductor quantum well, can be further increased by reducing scattering by crystal defects. InSb-based heteroepitaxy is usually performed on semi-insulating GaAs (001) substrates due to the lack of a lattice matched semi-insulating substrate. The 14.6% mismatch between the lattice parameters of GaAs and InSb results in the formation of structural defects such as threading dislocations and microtwins which degrade the electrical and optical properties of InSb-based devices. Chapter 1 reviews the methods and procedures for growing InSb-based heterostructures by molecular beam epitaxy. Chapters 2 and 3 introduce techniques for minimizing the crystalline defects in InSb-based structures grown on GaAs substrates. Chapter 2 discusses a method of reducing threading dislocations by incorporating AlyIn1-ySb interlayers in an AlxIn1-xSb buffer layer and the reduction of microtwin defects by growth

Electronic Structure of Buried Interfaces - Oral Presentation

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

Porter, Zachary

In the electronics behind computer memory storage, the speed and size are dictated by the performance of permanent magnets inside devices called read heads. Complicated magnets made of stacked layers of thin films can be engineered to have properties that yield more energy storage and faster switching times compared to conventional iron or cobalt magnets. The reason is that magnetism is a result of subtle interactions amongst electrons; just how neurons come together on large scales to make cat brains and dog brains, ensembles of electrons interact and become ferromagnets and paramagnets. These interactions make magnets too difficult to studymore » in their entirety, so I focus on the interfaces between layers, which are responsible for the coupling materials physicists hope to exploit to produce next-generation magnets. This project, I study a transition metal oxide material called LSCO, Lanthanum Cobaltite, which can be a paramagnet or a ferromagnet depending on how you tweak the electronic structure. It exhibits an exciting behavior: its sum is greater than the sum of its parts. When another similar material called a LSMO, Lanthanum Manganite, is grown on top of it, their interface has a different type of magnetism from the LSCO or the LSMO! I hope to explain this by demonstrating differently charged ions in the interface. The typical method for quantifying this is x-ray absorption, but all conventional techniques look at every layer simultaneously, averaging the interfaces and the LSCO layers that we want to characterize separately. Instead, I must use a new reflectivity technique, which tracks the intensity of reflected x-rays at different angles, at energies near the absorption peaks of certain elements, to track changes in the electronic structure of the material. The samples were grown by collaborators at the Takamura group at U.C. Davis and probed with this “resonant reflectivity” technique on Beamline 2-1 at the Stanford Synchrotron Radiation

Structural, electronic and vibrational properties of lanthanide monophosphide at high pressure

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

Panchal, J. M., E-mail: amitjignesh@yahoo.co.in; Department of Physics, University School of Sciences, Gujarat University, Ahmedabad 380009, Gujarat; Joshi, Mitesh

2016-05-06

A first-principles plane wave self-consistent method with the ultra-soft-pseudopotential scheme in the framework of the density functional theory (DFT) is performed to study structural, electronic and vibrational properties of LaP for Rock-salt (NaCl/Bl) and Cesium-chloride (CsCl/B2) phases. The instability of Rock-salt (NaCl/Bl) phases around the transition is discussed. Conclusions based on electronic energy band structure, density of state, phonon dispersion and phonon density of states in both phases are outlined. The calculated results are consistence and confirm the successful applicability of quasi-harmonic phonon theory for structural instability studies for the alloys.

Electronic structure and thermoelectric properties of half-Heusler compounds with eight electron valence count—KScX (X = C and Ge)

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

Ciftci, Yasemin O.; Mahanti, Subhendra D.

Electronic band structure and structural properties of two representative half-Heusler (HH) compounds with 8 electron valence count (VC), KScC and KScGe, have been studied using first principles methods within density functional theory and generalized gradient approximation. These systems differ from the well studied class of HH compounds like ZrNiSn and ZrCoSb which have VC = 18 because of the absence of d electrons of the transition metal atoms Ni and Co. Electronic transport properties such as Seebeck coefficient (S), electrical conductivity (σ), electronic thermal conductivity (κ{sub e}) (the latter two scaled by electronic relaxation time), and the power factor (S{sup 2}σ) havemore » been calculated using semi-classical Boltzmann transport theory within constant relaxation time approximation. Both the compounds are direct band gap semiconductors with band extrema at the X point. Their electronic structures show a mixture of heavy and light bands near the valance band maximum and highly anisotropic conduction and valence bands near the band extrema, desirable features of good thermoelectric. Optimal p- or n-type doping concentrations have been estimated based on thermopower and maximum power factors. The optimum room temperature values of S are ∼1.5 times larger than that of the best room temperature thermoelectric Bi{sub 2}Te{sub 3}. We also discuss the impact of the band structure on deviations from Weidemann-Franz law as one tunes the chemical potential across the band gap.« less

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin: mechanism and evidence for two M species

NASA Technical Reports Server (NTRS)

Druckmann, S.; Friedman, N.; Lanyi, J. K.; Needleman, R.; Ottolenghi, M.; Sheves, M.

1992-01-01

The back photoreaction of the M intermediate in the photocycle of bacteriorhodopsin is investigated both for the native pigment and its D96N mutant. The experimental setup is based on creating the M intermediate by a first pulse, followed by a (blue) laser pulse which drives the back photoreaction of M. Experiments are carried out varying the delay between the two pulses, as well as the temperature over the -25 degrees C-20 degrees C range. It is found that the kinetic patterns of the M back photoreaction change with time after the generation of this intermediate. The data provide independent evidence for the suggestion of a photocycle mechanism based on two distinct M intermediates. They are thus in keeping with the consecutive model of Varo and Lanyi (Biochemistry 30, 5016-5022; 1991), although they cannot exclude other models such as those based on branched or parallel cycles. More generally, we offer a "photochemical" approach to discriminating between intermediate stages in the photocycle which does not depend on spectroscopic and/or kinetic data. While markedly affecting the rate of the M --> N transition in the photocycle, the rate of the thermal step in back photoreaction of M, at both room and low temperatures, is not significantly affected by the D96N mutation. It is proposed that while Asp 96 is the Schiff-base protonating moiety in the M --> N transition, another residue (most probably Asp 85) reprotonates the Schiff base following light absorption by M.

Nanoscale Insight and Control of Structural and Electronic Properties of Organic Semiconductor / Metal Interfaces

NASA Astrophysics Data System (ADS)

Maughan, Bret

Organic semiconductor interfaces are promising materials for use in next-generation electronic and optoelectronic devices. Current models for metal-organic interfacial electronic structure and dynamics are inadequate for strongly hybridized systems. This work aims to address this issue by identifying the factors most important for understanding chemisorbed interfaces with an eye towards tuning the interfacial properties. Here, I present the results of my research on chemisorbed interfaces formed between thin-films of phthalocyanine molecules grown on monocrystalline Cu(110). Using atomically-resolved nanoscale imaging in combination with surface-sensitive photoemission techniques, I show that single-molecule level interactions control the structural and electronic properties of the interface. I then demonstrate that surface modifications aimed at controlling interfacial interactions are an effective way to tailor the physical and electronic structure of the interface. This dissertation details a systematic investigation of the effect of molecular and surface functionalization on interfacial interactions. To understand the role of molecular structure, two types of phthalocyanine (Pc) molecules are studied: non-planar, dipolar molecules (TiOPc), and planar, non-polar molecules (H2Pc and CuPc). Multiple adsorption configurations for TiOPc lead to configuration-dependent self-assembly, Kondo screening, and electronic energy-level alignment. To understand the role of surface structure, the Cu(110) surface is textured and passivated by oxygen chemisorption prior to molecular deposition, which gives control over thin-film growth and interfacial electronic structure in H2Pc and CuPc films. Overall, the work presented here demonstrates a method for understanding interfacial electronic structure of strongly hybridized interfaces, an important first step towards developing more robust models for metal-organic interfaces, and reliable, predictive tuning of interfacial

High Electron Mobility Transistor Structures on Sapphire Substrates Using CMOS Compatible Processing Techniques

NASA Technical Reports Server (NTRS)

Mueller, Carl; Alterovitz, Samuel; Croke, Edward; Ponchak, George

2004-01-01

System-on-a-chip (SOC) processes are under intense development for high-speed, high frequency transceiver circuitry. As frequencies, data rates, and circuit complexity increases, the need for substrates that enable high-speed analog operation, low-power digital circuitry, and excellent isolation between devices becomes increasingly critical. SiGe/Si modulation doped field effect transistors (MODFETs) with high carrier mobilities are currently under development to meet the active RF device needs. However, as the substrate normally used is Si, the low-to-modest substrate resistivity causes large losses in the passive elements required for a complete high frequency circuit. These losses are projected to become increasingly troublesome as device frequencies progress to the Ku-band (12 - 18 GHz) and beyond. Sapphire is an excellent substrate for high frequency SOC designs because it supports excellent both active and passive RF device performance, as well as low-power digital operations. We are developing high electron mobility SiGe/Si transistor structures on r-plane sapphire, using either in-situ grown n-MODFET structures or ion-implanted high electron mobility transistor (HEMT) structures. Advantages of the MODFET structures include high electron mobilities at all temperatures (relative to ion-implanted HEMT structures), with mobility continuously improving to cryogenic temperatures. We have measured electron mobilities over 1,200 and 13,000 sq cm/V-sec at room temperature and 0.25 K, respectively in MODFET structures. The electron carrier densities were 1.6 and 1.33 x 10(exp 12)/sq cm at room and liquid helium temperature, respectively, denoting excellent carrier confinement. Using this technique, we have observed electron mobilities as high as 900 sq cm/V-sec at room temperature at a carrier density of 1.3 x 10(exp 12)/sq cm. The temperature dependence of mobility for both the MODFET and HEMT structures provides insights into the mechanisms that allow for enhanced

Measurement of the electron structure function F2e at LEP energies

NASA Astrophysics Data System (ADS)

Abdallah, J.; Abreu, P.; Adam, W.; Adzic, P.; Albrecht, T.; Alemany-Fernandez, R.; Allmendinger, T.; Allport, P. P.; Amaldi, U.; Amapane, N.; Amato, S.; Anashkin, E.; Andreazza, A.; Andringa, S.; Anjos, N.; Antilogus, P.; Apel, W.-D.; Arnoud, Y.; Ask, S.; Asman, B.; Augustin, J. E.; Augustinus, A.; Baillon, P.; Ballestrero, A.; Bambade, P.; Barbier, R.; Bardin, D.; Barker, G. J.; Baroncelli, A.; Battaglia, M.; Baubillier, M.; Becks, K.-H.; Begalli, M.; Behrmann, A.; Belous, K.; Ben-Haim, E.; Benekos, N.; Benvenuti, A.; Berat, C.; Berggren, M.; Bertrand, D.; Besancon, M.; Besson, N.; Bloch, D.; Blom, M.; Bluj, M.; Bonesini, M.; Boonekamp, M.; Booth, P. S. L.; Borisov, G.; Botner, O.; Bouquet, B.; Bowcock, T. J. V.; Boyko, I.; Bracko, M.; Brenner, R.; Brodet, E.; Bruckman, P.; Brunet, J. M.; Buschbeck, B.; Buschmann, P.; Calvi, M.; Camporesi, T.; Canale, V.; Carena, F.; Castro, N.; Cavallo, F.; Chapkin, M.; Charpentier, Ph.; Checchia, P.; Chierici, R.; Chliapnikov, P.; Chudoba, J.; Chung, S. U.; Cieslik, K.; Collins, P.; Contri, R.; Cosme, G.; Cossutti, F.; Costa, M. J.; Crennell, D.; Cuevas, J.; D'Hondt, J.; da Silva, T.; da Silva, W.; Della Ricca, G.; de Angelis, A.; de Boer, W.; de Clercq, C.; de Lotto, B.; de Maria, N.; de Min, A.; de Paula, L.; di Ciaccio, L.; di Simone, A.; Doroba, K.; Drees, J.; Eigen, G.; Ekelof, T.; Ellert, M.; Elsing, M.; Espirito Santo, M. C.; Fanourakis, G.; Fassouliotis, D.; Feindt, M.; Fernandez, J.; Ferrer, A.; Ferro, F.; Flagmeyer, U.; Foeth, H.; Fokitis, E.; Fulda-Quenzer, F.; Fuster, J.; Gandelman, M.; Garcia, C.; Gavillet, Ph.; Gazis, E.; Gokieli, R.; Golob, B.; Gomez-Ceballos, G.; Gonçalves, P.; Graziani, E.; Grosdidier, G.; Grzelak, K.; Guy, J.; Haag, C.; Hallgren, A.; Hamacher, K.; Hamilton, K.; Haug, S.; Hauler, F.; Hedberg, V.; Hennecke, M.; Hoffman, J.; Holmgren, S.-O.; Holt, P. J.; Houlden, M. A.; Jackson, J. N.; Jarlskog, G.; Jarry, P.; Jeans, D.; Johansson, E. K.; Jonsson, P.; Joram, C.; Jungermann, L.; Kapusta, F.; Katsanevas, S.; Katsoufis, E.; Kernel, G.; Kersevan, B. P.; Kerzel, U.; King, B. T.; Kjaer, N. J.; Kluit, P.; Kokkinias, P.; Kourkoumelis, C.; Kouznetsov, O.; Krumstein, Z.; Kucharczyk, M.; Lamsa, J.; Leder, G.; Ledroit, F.; Leinonen, L.; Leitner, R.; Lemonne, J.; Lepeltier, V.; Lesiak, T.; Liebig, W.; Liko, D.; Lipniacka, A.; Lopes, J. H.; Lopez, J. M.; Loukas, D.; Lutz, P.; Lyons, L.; MacNaughton, J.; Malek, A.; Maltezos, S.; Mandl, F.; Marco, J.; Marco, R.; Marechal, B.; Margoni, M.; Marin, J.-C.; Mariotti, C.; Markou, A.; Martinez-Rivero, C.; Masik, J.; Mastroyiannopoulos, N.; Matorras, F.; Matteuzzi, C.; Mazzucato, F.; Mazzucato, M.; Mc Nulty, R.; Meroni, C.; Migliore, E.; Mitaroff, W.; Mjoernmark, U.; Moa, T.; Moch, M.; Moenig, K.; Monge, R.; Montenegro, J.; Moraes, D.; Moreno, S.; Morettini, P.; Mueller, U.; Muenich, K.; Mulders, M.; Mundim, L.; Murray, W.; Muryn, B.; Myatt, G.; Myklebust, T.; Nassiakou, M.; Navarria, F.; Nawrocki, K.; Nemecek, S.; Nicolaidou, R.; Nikolenko, M.; Oblakowska-Mucha, A.; Obraztsov, V.; Olshevski, A.; Onofre, A.; Orava, R.; Osterberg, K.; Ouraou, A.; Oyanguren, A.; Paganoni, M.; Paiano, S.; Palacios, J. P.; Palka, H.; Papadopoulou, Th. D.; Pape, L.; Parkes, C.; Parodi, F.; Parzefall, U.; Passeri, A.; Passon, O.; Peralta, L.; Perepelitsa, V.; Perrotta, A.; Petrolini, A.; Piedra, J.; Pieri, L.; Pierre, F.; Pimenta, M.; Piotto, E.; Podobnik, T.; Poireau, V.; Pol, M. E.; Polok, G.; Pozdniakov, V.; Pukhaeva, N.; Pullia, A.; Radojicic, D.; Rebecchi, P.; Rehn, J.; Reid, D.; Reinhardt, R.; Renton, P.; Richard, F.; Ridky, J.; Rivero, M.; Rodriguez, D.; Romero, A.; Ronchese, P.; Roudeau, P.; Rovelli, T.; Ruhlmann-Kleider, V.; Ryabtchikov, D.; Sadovsky, A.; Salmi, L.; Salt, J.; Sander, C.; Savoy-Navarro, A.; Schwickerath, U.; Sekulin, R.; Siebel, M.; Sisakian, A.; Slominski, W.; Smadja, G.; Smirnova, O.; Sokolov, A.; Sopczak, A.; Sosnowski, R.; Spassov, T.; Stanitzki, M.; Stocchi, A.; Strauss, J.; Stugu, B.; Szczekowski, M.; Szeptycka, M.; Szumlak, T.; Szwed, J.; Tabarelli, T.; Tegenfeldt, F.; Timmermans, J.; Tkatchev, L.; Tobin, M.; Todorovova, S.; Tomé, B.; Tonazzo, A.; Tortosa, P.; Travnicek, P.; Treille, D.; Tristram, G.; Trochimczuk, M.; Troncon, C.; Turluer, M.-L.; Tyapkin, I. A.; Tyapkin, P.; Tzamarias, S.; Uvarov, V.; Valenti, G.; van Dam, P.; van Eldik, J.; van Remortel, N.; van Vulpen, I.; Vegni, G.; Veloso, F.; Venus, W.; Verdier, P.; Verzi, V.; Vilanova, D.; Vitale, L.; Vrba, V.; Wahlen, H.; Washbrook, A. J.; Weiser, C.; Wicke, D.; Wickens, J.; Wilkinson, G.; Winter, M.; Witek, M.; Yushchenko, O.; Zalewska, A.; Zalewski, P.; Zavrtanik, D.; Zhuravlov, V.; Zimin, N. I.; Zintchenko, A.; Zupan, M.; Delphi Collaboration

2014-10-01

The hadronic part of the electron structure function F2e has been measured for the first time, using e+e- data collected by the DELPHI experiment at LEP, at centre-of-mass energies of √{ s} = 91.2- 209.5 GeV. The data analysis is simpler than that of the measurement of the photon structure function. The electron structure function F2e data are compared to predictions of phenomenological models based on the photon structure function. It is shown that the contribution of large target photon virtualities is significant. The data presented can serve as a cross-check of the photon structure function F2γ analyses and help in refining existing parameterisations.

Structural, electronic and photocatalytic properties of atomic defective BiI3 monolayers

NASA Astrophysics Data System (ADS)

Yan, Huang; Ziyu, Hu; Xu, Gong; Xiaohong, Shao

2018-01-01

The structural, electronic and photocatalytic properties of five vacancy-containing 2D BiI3 monolayers are investigated by the first-principle calculations. The electronic structures show that the five structures are stable and have comparable binding energies to that of the pristine BiI3 monolayer, and the defects can tune the band gaps. Optical spectra indicate that the five structures retain high absorption capacity for visible light. The spin-orbit coupling (SOC) effect is found to play an important role in the band edge of defective structures, and the VBi and VBi-I3 defective BiI3 monolayers can make absolute band edges straddle water redox potentials more easily.

High-Resolution Structural and Electronic Properties of Epitaxial Topological Crystalline Insulator Films

NASA Astrophysics Data System (ADS)

Dagdeviren, Omur; Zhou, Chao; Zou, Ke; Simon, Georg; Albright, Stephen; Mandal, Subhasish; Morales-Acosta, Mayra; Zhu, Xiaodong; Ismail-Beigi, Sohrab; Walker, Frederick; Ahn, Charles; Schwarz, Udo; Altman, Eric

Revealing the local electronic properties of surfaces and their link to structural properties is an important problem for topological crystalline insulators (TCI) in which metallic surface states are protected by crystal symmetry. The microstructure and electronic properties of TCI SnTe film surfaces grown by molecular beam epitaxy were characterized using scanning probe microscopy. These results reveal the influence of various defects on the electronic properties: tilt boundaries leading to dislocation arrays that serve as periodic nucleation sites for pit growth; screw dislocations, and point defects. These features have varying length scale and display variations in the electronic structure of the surface, which are mapped with scanning tunneling microscopy images as standing waves superimposed on atomic scale images of the surface topography that consequently shape the wave patterns. Since the growth process results in symmetry breaking defects that patterns the topological states, we propose that the scanning probe tip can pattern the surface and electronic structure and enable the fabrication of topological devices on the SnTe surface. Financial support from the National Science Foundation through the Yale Materials Research Science and Engineering Center (Grant No. MRSEC DMR-1119826) and FAME.

Basic electronic properties of iron selenide under variation of structural parameters

NASA Astrophysics Data System (ADS)

Guterding, Daniel; Jeschke, Harald O.; Valentí, Roser

2017-09-01

Since the discovery of high-temperature superconductivity in the thin-film FeSe /SrTiO3 system, iron selenide and its derivates have been intensively scrutinized. Using ab initio density functional theory calculations we review the electronic structures that could be realized in iron selenide if the structural parameters could be tuned at liberty. We calculate the momentum dependence of the susceptibility and investigate the symmetry of electron pairing within the random phase approximation. Both the susceptibility and the symmetry of electron pairing depend on the structural parameters in a nontrivial way. These results are consistent with the known experimental behavior of binary iron chalcogenides and, at the same time, reveal two promising ways of tuning superconducting transition temperatures in these materials: on one hand by expanding the iron lattice of FeSe at constant iron-selenium distance and, on the other hand, by increasing the iron-selenium distance with unchanged iron lattice.

Ultrafast structural and electronic dynamics of the metallic phase in a layered manganite

PubMed Central

Piazza, L.; Ma, C.; Yang, H. X.; Mann, A.; Zhu, Y.; Li, J. Q.; Carbone, F.

2013-01-01

The transition between different states in manganites can be driven by various external stimuli. Controlling these transitions with light opens the possibility to investigate the microscopic path through which they evolve. We performed femtosecond (fs) transmission electron microscopy on a bi-layered manganite to study its response to ultrafast photoexcitation. We show that a photoinduced temperature jump launches a pressure wave that provokes coherent oscillations of the lattice parameters, detected via ultrafast electron diffraction. Their impact on the electronic structure are monitored via ultrafast electron energy loss spectroscopy, revealing the dynamics of the different orbitals in response to specific structural distortions. PMID:26913564

Electronic structure engineering in silicene via atom substitution and a new two-dimensional Dirac structure Si3C

NASA Astrophysics Data System (ADS)

Yin, Na; Dai, Ying; Wei, Wei; Huang, Baibiao

2018-04-01

A lot of efforts have been made towards the band gap opening in two-dimensional silicene, the silicon version of graphene. In the present work, the electronic structures of single atom doped (B, N, Al and P) and codoped (B/N and Al/P) silicene monolayers are systematically examined on the base of density functional electronic calculations. Our results demonstrate that single atom doping can realize electron or hole doping in the silicene; while codoping, due to the syergistic effects, results in finite band gap in silicene at the Dirac point without significantly degrading the electronic properties. In addition, the characteristic of band gap shows dependence on the doping concentration. Importantly, we predict a new two-dimensional Dirac structure, the graphene-like Si3C, which also shows linear band dispersion relation around the Fermi level. Our results demonstrates an important perspective to engineer the electronic and optical properties of silicene.

Electron Pitch-Angle Distribution in Pressure Balance Structures Measured by Ulysses/SWOOPS

NASA Technical Reports Server (NTRS)

Yamauchi, Yohei; Suess, Steven T.; Sakurai, Takashi; Six, N. Frank (Technical Monitor)

2002-01-01

Pressure balance structures (PBSs) are a common feature in the high-latitude solar wind near solar minimum. From previous studies, PBSs are believed to be remnants of coronal plumes. Yamauchi et al [2002] investigated the magnetic structures of the PBSs, applying a minimum variance analysis to Ulysses/Magnetometer data. They found that PBSs contain structures like current sheets or plasmoids, and suggested that PBSs are associated with network activity such as magnetic reconnection in the photosphere at the base of polar plumes. We have investigated energetic electron data from Ulysses/SWOOPS to see whether bi-directional electron flow exists and we have found evidence supporting the earlier conclusions. We find that 45 ot of 53 PBSs show local bi-directional or isotopic electron flux or flux associated with current-sheet structure. Only five events show the pitch-angle distribution expected for Alfvenic fluctuations. We conclude that PBSs do contain magnetic structures such as current sheets or plasmoids that are expected as a result of network activity at the base of polar plumes.

Electronic structure probed with positronium: Theoretical viewpoint

NASA Astrophysics Data System (ADS)

Kuriplach, Jan; Barbiellini, Bernardo

2018-05-01

We inspect carefully how the positronium can be used to study the electronic structure of materials. Recent combined experimental and computational study [A.C.L. Jones et al., Phys. Rev. Lett. 117, 216402 (2016)] has shown that the positronium affinity can be used to benchmark the exchange-correlation approximations in copper. Here we investigate whether an improvement can be achieved by increasing the numerical precision of calculations and by employing the strongly constrained and appropriately normed (SCAN) scheme, and extend the study to other selected systems like aluminum and high entropy alloys. From the methodological viewpoint, the computations of the positronium affinity are further refined and an alternative way of determining the electron chemical potential using charged supercells is examined.

Transmission electron microscopy in molecular structural biology: A historical survey.

PubMed

Harris, J Robin

2015-09-01

In this personal, historic account of macromolecular transmission electron microscopy (TEM), published data from the 1940s through to recent times is surveyed, within the context of the remarkable progress that has been achieved during this time period. The evolution of present day molecular structural biology is described in relation to the associated biological disciplines. The contribution of numerous electron microscope pioneers to the development of the subject is discussed. The principal techniques for TEM specimen preparation, thin sectioning, metal shadowing, negative staining and plunge-freezing (vitrification) of thin aqueous samples are described, with a selection of published images to emphasise the virtues of each method. The development of digital image analysis and 3D reconstruction is described in detail as applied to electron crystallography and reconstructions from helical structures, 2D membrane crystals as well as single particle 3D reconstruction of icosahedral viruses and macromolecules. The on-going development of new software, algorithms and approaches is highlighted before specific examples of the historical progress of the structural biology of proteins and viruses are presented. Copyright © 2014 Elsevier Inc. All rights reserved.

Electronic structure and electric polarity of edge-functionalized graphene nanoribbons

NASA Astrophysics Data System (ADS)

Taira, Remi; Yamanaka, Ayaka; Okada, Susumu

2017-08-01

On the basis of the density functional theory combined with the effective screening medium method, we studied the electronic structure of graphene nanoribbons with zigzag edges, which are terminated by functional groups. The work function of the nanoribbons is sensitive to the functional groups. The edge state inherent in the zigzag edges is robust against edge functionalization. OH termination causes the injection of electrons into the nearly free electron states situated alongside the nanoribbons, resulting in the formation of free electron channels outside the nanoribbons. We also demonstrated that the polarity of zigzag graphene nanoribbons is controllable by the asymmetrical functionalization of their edges.

Bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}: New crystal structure type and electronic structure

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

Eliziario Nunes, Sayonara; Department of Materials Engineering, Federal University of São Carlos, 13565-905 São Carlos, SP; Wang, Chun-Hai

2015-02-15

We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}, known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn{sub 2}VO{sub 6} adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO{sub 4} tetrahedra, ZnO{sub 6} octahedra and VO{sub 4} tetrahedra, and Bi{sub 2}O{sub 12} dimers. It is the only known member of the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu;more » A=V, P, As) family which does not appear to be structurally closely related to others. The electronic structure of BiZn{sub 2}VO{sub 6}, calculated by DFT methods, shows that it is an indirect gap semiconductor with a calculated band gap of 1.6 eV, which compares favourably to the experimentally measured value of 2.4 eV. - Graphical abstract: The crystal structure of BiZn{sub 2}VO{sub 6}, a new structure type in the BiM{sub 2}AO{sub 6} (M=Mg, Ca, Cd, Cu, Pb, Mn, Zn; A=V, P, As) family. - Highlights: • Structure solution from PXRD data by repeated minimisations from random starting values. • New structure type in the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family. • Electronic structure calculation.« less

Accelerated Electron-Beam Formation with a High Capture Coefficient in a Parallel Coupled Accelerating Structure

NASA Astrophysics Data System (ADS)

Chernousov, Yu. D.; Shebolaev, I. V.; Ikryanov, I. M.

2018-01-01

An electron beam with a high (close to 100%) coefficient of electron capture into the regime of acceleration has been obtained in a linear electron accelerator based on a parallel coupled slow-wave structure, electron gun with microwave-controlled injection current, and permanent-magnet beam-focusing system. The high capture coefficient was due to the properties of the accelerating structure, beam-focusing system, and electron-injection system. Main characteristics of the proposed systems are presented.

Modeling and simulation of electronic structure, material interface and random doping in nano electronic devices

PubMed Central

Chen, Duan; Wei, Guo-Wei

2010-01-01

The miniaturization of nano-scale electronic devices, such as metal oxide semiconductor field effect transistors (MOSFETs), has given rise to a pressing demand in the new theoretical understanding and practical tactic for dealing with quantum mechanical effects in integrated circuits. Modeling and simulation of this class of problems have emerged as an important topic in applied and computational mathematics. This work presents mathematical models and computational algorithms for the simulation of nano-scale MOSFETs. We introduce a unified two-scale energy functional to describe the electrons and the continuum electrostatic potential of the nano-electronic device. This framework enables us to put microscopic and macroscopic descriptions in an equal footing at nano scale. By optimization of the energy functional, we derive consistently-coupled Poisson-Kohn-Sham equations. Additionally, layered structures are crucial to the electrostatic and transport properties of nano transistors. A material interface model is proposed for more accurate description of the electrostatics governed by the Poisson equation. Finally, a new individual dopant model that utilizes the Dirac delta function is proposed to understand the random doping effect in nano electronic devices. Two mathematical algorithms, the matched interface and boundary (MIB) method and the Dirichlet-to-Neumann mapping (DNM) technique, are introduced to improve the computational efficiency of nano-device simulations. Electronic structures are computed via subband decomposition and the transport properties, such as the I-V curves and electron density, are evaluated via the non-equilibrium Green's functions (NEGF) formalism. Two distinct device configurations, a double-gate MOSFET and a four-gate MOSFET, are considered in our three-dimensional numerical simulations. For these devices, the current fluctuation and voltage threshold lowering effect induced by the discrete dopant model are explored. Numerical convergence

Comparison of electronic structure between monolayer silicenes on Ag (111)

NASA Astrophysics Data System (ADS)

Chun-Liang, Lin; Ryuichi, Arafune; Maki, Kawai; Noriaki, Takagi

2015-08-01

The electronic structures of monolayer silicenes (4 × 4 and ) grown on Ag (111) surface are studied by scanning tunneling spectroscopy (STS) and density functional theory (DFT) calculations. While both phases have similar electronic structures around the Fermi level, significant differences are observed in the higher energy unoccupied states. The DFT calculations show that the contributions of Si 3pz orbitals to the unoccupied states are different because of their different buckled configurations. Project supported by the Ministry of Education, Culture, Sports, Science and Technology (MEXT) through Grants-in-Aid for Scientific Research (Grant Nos. 24241040 and 25110008) and the World Premier International Research Center Initiative (WPI), MEXT, Japan.

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 4-acetylpyridine

NASA Astrophysics Data System (ADS)

Atilgan, A.; Yurdakul, Ş.; Erdogdu, Y.; Güllüoğlu, M. T.

2018-06-01

The spectroscopic (UV-Vis and infrared), structural and some electronic property observations of the 4-acetylpyridine (4-AP) were reported, which are investigated by using some spectral methods and DFT calculations. FT-IR spectra were obtained for 4-AP at room temperature in the region 4000 cm-1- 400 cm-1. In the DFT calculations, the B3LYP functional with 6-311G++G(d,p) basis set was applied to carry out the quantum mechanical calculations. The Fourier Transform Infrared (FT-IR) and FT-Raman spectra were interpreted by using of normal coordinate analysis based on scaled quantum mechanical force field. The present work expands our understanding of the both the vibrational and structural properties as well as some electronic properties of the 4-AP by means of the theoretical and experimental methods.

3D structure of individual nanocrystals in solution by electron microscopy

DOE PAGES

Park, Jungwok; Elmlund, Hans; Ercius, Peter; ...

2015-07-17

Here, knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unorderedmore » nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.« less

3D structure of individual nanocrystals in solution by electron microscopy

NASA Astrophysics Data System (ADS)

Park, Jungwon; Elmlund, Hans; Ercius, Peter; Yuk, Jong Min; Limmer, David T.; Chen, Qian; Kim, Kwanpyo; Han, Sang Hoon; Weitz, David A.; Zettl, A.; Alivisatos, A. Paul

2015-07-01

Knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unordered nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.

3D structure of individual nanocrystals in solution by electron microscopy

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

Park, Jungwok; Elmlund, Hans; Ercius, Peter

Here, knowledge about the synthesis, growth mechanisms, and physical properties of colloidal nanoparticles has been limited by technical impediments. We introduce a method for determining three-dimensional (3D) structures of individual nanoparticles in solution. We combine a graphene liquid cell, high-resolution transmission electron microscopy, a direct electron detector, and an algorithm for single-particle 3D reconstruction originally developed for analysis of biological molecules. This method yielded two 3D structures of individual platinum nanocrystals at near-atomic resolution. Because our method derives the 3D structure from images of individual nanoparticles rotating freely in solution, it enables the analysis of heterogeneous populations of potentially unorderedmore » nanoparticles that are synthesized in solution, thereby providing a means to understand the structure and stability of defects at the nanoscale.« less

Structure and properties of parts produced by electron-beam additive manufacturing

NASA Astrophysics Data System (ADS)

Klimenov, Vasilii; Klopotov, Anatolii; Fedorov, Vasilii; Abzaev, Yurii; Batranin, Andrey; Kurgan, Kirill; Kairalapov, Daniyar

2017-12-01

The paper deals with the study of structure, microstructure, composition and microhardness of a tube processed by electron-beam additive manufacturing using optical and scanning electron microscopy. The structure and macrodefects of a tube made of Grade2 titanium alloy is studied using the X-ray computed tomography. The principles of layer-by-layer assembly and boundaries after powder sintering are set out in this paper. It is found that the titanium alloy has two phases. Future work will involve methods to improve properties of created parts.

Phase Diagram and Electronic Structure of Praseodymium and Plutonium

DOE PAGES

Lanatà, Nicola; Yao, Yongxin; Wang, Cai-Zhuang; ...

2015-01-29

We develop a new implementation of the Gutzwiller approximation in combination with the local density approximation, which enables us to study complex 4f and 5f systems beyond the reach of previous approaches. We calculate from first principles the zero-temperature phase diagram and electronic structure of Pr and Pu, finding good agreement with the experiments. Our study of Pr indicates that its pressure-induced volume-collapse transition would not occur without change of lattice structure—contrarily to Ce. Our study of Pu shows that the most important effect originating the differentiation between the equilibrium densities of its allotropes is the competition between the Peierlsmore » effect and the Madelung interaction and not the dependence of the electron correlations on the lattice structure.« less

Electronic Structure and Surface Physics of Two-dimensional Material Molybdenum Disulfide

NASA Astrophysics Data System (ADS)

Jin, Wencan

The interest in two-dimensional materials and materials physics has grown dramatically over the past decade. The family of two-dimensional materials, which includes graphene, transition metal dichalcogenides, phosphorene, hexagonal boron nitride, etc., can be fabricated into atomically thin films since the intralayer bonding arises from their strong covalent character, while the interlayer interaction is mediated by weak van der Waals forces. Among them, molybdenum disulfide (MoS2) has attracted much interest for its potential applications in opto-electronic and valleytronics devices. Previously, much of the experimental studies have concentrated on optical and transport measurements while neglecting direct experimental determination of the electronic structure of MoS2, which is crucial to the full understanding of its distinctive properties. In particular, like other atomically thin materials, the interactions with substrate impact the surface structure and morphology of MoS2, and as a result, its structural and physical properties can be affected. In this dissertation, the electronic structure and surface structure of MoS2 are directly investigated using angle-resolved photoemission spectroscopy and cathode lens microscopy. Local-probe angle-resolved photoemission spectroscopy measurements of monolayer, bilayer, trilayer, and bulk MoS 2 directly demonstrate the indirect-to-direct bandgap transition due to quantum confinement as the MoS2 thickness is decreased from multilayer to monolayer. The evolution of the interlayer coupling in this transition is also investigated using density functional theory calculations. Also, the thickness-dependent surface roughness is characterized using selected-area low energy electron diffraction (LEED) and the surface structural relaxation is investigated using LEED I-V measurements combined with dynamical LEED calculations. Finally, bandgap engineering is demonstrated via tuning of the interlayer interactions in van der Waals

Electronic and crystal structure of NiTi martensite

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

Sanati, M.; Albers, R.C.; Pinski, F.J.

1998-11-01

All of the first-principles electronic-structure calculations for the martensitic structure of NiTi have used the experimental atomic parameters reported by Michal and Sinclair [Acta Crystallogr., Sect. B: Struct. Crystallogr. Cryst. Chem. {bold B37}, 1803 (1981)]. We have used first-principles, full-potential, linear muffin-tin orbital calculations to examine the total energy of all the experimental martensitic structures reported in the literature. We find that another crystal structure, that of Kudoh {ital et al.} [Acta Metall. Mater. {bold 33}, 2049 (1985)], has the lowest total energy at zero temperature. Ground-state and formation energies were calculated for all of the experimental structures. Total andmore » local densities of states were calculated and compared with each other for the structures of both Kudoh {ital et al.} and Michal and Sinclair thinsp {copyright} {ital 1998} {ital The American Physical Society}« less

Computational Search for Strong Topological Insulators: An Exercise in Data Mining and Electronic Structure

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

Klintenberg, M.; Haraldsen, Jason T.; Balatsky, Alexander V.

In this paper, we report a data-mining investigation for the search of topological insulators by examining individual electronic structures for over 60,000 materials. Using a data-mining algorithm, we survey changes in band inversion with and without spin-orbit coupling by screening the calculated electronic band structure for a small gap and a change concavity at high-symmetry points. Overall, we were able to identify a number of topological candidates with varying structures and composition. Lastly, our overall goal is expand the realm of predictive theory into the determination of new and exotic complex materials through the data mining of electronic structure.

Computational Search for Strong Topological Insulators: An Exercise in Data Mining and Electronic Structure

DOE PAGES

Klintenberg, M.; Haraldsen, Jason T.; Balatsky, Alexander V.

2014-06-19

In this paper, we report a data-mining investigation for the search of topological insulators by examining individual electronic structures for over 60,000 materials. Using a data-mining algorithm, we survey changes in band inversion with and without spin-orbit coupling by screening the calculated electronic band structure for a small gap and a change concavity at high-symmetry points. Overall, we were able to identify a number of topological candidates with varying structures and composition. Lastly, our overall goal is expand the realm of predictive theory into the determination of new and exotic complex materials through the data mining of electronic structure.

Effect of solute atoms on dislocation motion in Mg: An electronic structure perspective

PubMed Central

Tsuru, T.; Chrzan, D. C.

2015-01-01

Solution strengthening is a well-known approach to tailoring the mechanical properties of structural alloys. Ultimately, the properties of the dislocation/solute interaction are rooted in the electronic structure of the alloy. Accordingly, we compute the electronic structure associated with, and the energy barriers to dislocation cross-slip. The energy barriers so obtained can be used in the development of multiscale models for dislocation mediated plasticity. The computed electronic structure can be used to identify substitutional solutes likely to interact strongly with the dislocation. Using the example of a-type screw dislocations in Mg, we compute accurately the Peierls barrier to prismatic plane slip and argue that Y, Ca, Ti, and Zr should interact strongly with the studied dislocation, and thereby decrease the dislocation slip anisotropy in the alloy. PMID:25740411

Symmetry and electronic structure of noble-metal nanoparticles and the role of relativity.

PubMed

Häkkinen, Hannu; Moseler, Michael; Kostko, Oleg; Morgner, Nina; Hoffmann, Margarita Astruc; von Issendorff, Bernd

2004-08-27

We present high resolution UV-photoelectron spectra of cold mass selected Cun-, Agn-, and Aun- with n=53-58. The observed electron density of states is not the expected simple electron shell structure, but is strongly influenced by electron-lattice interactions. Only Cu55- and Ag55- exhibit highly degenerate states. This is a direct consequence of their icosahedral symmetry, as is confirmed by density functional theory calculations. Neighboring sizes exhibit perturbed electronic structures, as they are formed by removal or addition of atoms to the icosahedron and therefore have lower symmetries. Gold clusters in the same size range show completely different spectra with almost no degeneracy, which indicates that they have structures of much lower symmetry. This behavior is related to strong relativistic bonding effects in gold, as demonstrated by ab initio calculations for Au55-.

Coherent Terahertz Radiation from Multiple Electron Beams Excitation within a Plasmonic Crystal-like structure.

PubMed

Zhang, Yaxin; Zhou, Yucong; Gang, Yin; Jiang, Guili; Yang, Ziqiang

2017-01-23

Coherent terahertz radiation from multiple electron beams excitation within a plasmonic crystal-like structure (a three-dimensional holes array) which is composed of multiple stacked layers with 3 × 3 subwavelength holes array has been proposed in this paper. It has been found that in the structure the electromagnetic fields in each hole can be coupled with one another to construct a composite mode with strong field intensity. Therefore, the multiple electron beams injection can excite and efficiently interact with such mode. Meanwhile, the coupling among the electron beams is taken place during the interaction so that a very strong coherent terahertz radiation with high electron conversion efficiency can be generated. Furthermore, due to the coupling, the starting current density of this mechanism is much lower than that of traditional electron beam-driven terahertz sources. This multi-beam radiation system may provide a favorable way to combine photonics structure with electronics excitation to generate middle, high power terahertz radiation.

Coherent Terahertz Radiation from Multiple Electron Beams Excitation within a Plasmonic Crystal-like structure

PubMed Central

Zhang, Yaxin; Zhou, Yucong; Gang, Yin; Jiang, Guili; Yang, Ziqiang

2017-01-01

Coherent terahertz radiation from multiple electron beams excitation within a plasmonic crystal-like structure (a three-dimensional holes array) which is composed of multiple stacked layers with 3 × 3 subwavelength holes array has been proposed in this paper. It has been found that in the structure the electromagnetic fields in each hole can be coupled with one another to construct a composite mode with strong field intensity. Therefore, the multiple electron beams injection can excite and efficiently interact with such mode. Meanwhile, the coupling among the electron beams is taken place during the interaction so that a very strong coherent terahertz radiation with high electron conversion efficiency can be generated. Furthermore, due to the coupling, the starting current density of this mechanism is much lower than that of traditional electron beam-driven terahertz sources. This multi-beam radiation system may provide a favorable way to combine photonics structure with electronics excitation to generate middle, high power terahertz radiation. PMID:28112234

Effect of substitutions and defects in half-Heusler FeVSb studied by electron transport measurements and KKR-CPA electronic structure calculations

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

Jodin, L.; Tobola, J.; Pecheur, P.

2004-11-01

The structural and electron transport properties of the pure and Co-, Ti-, and Zr-substituted FeVSb half-Heusler phases have been investigated using x-ray diffraction, Moessbauer spectroscopy, and Electron Probe Microscopy Analysis as well as resistivity, thermopower, and Hall effect measurements in the 80-900 K temperature range. In a parallel study, the electronic structures of FeVSb and the aforementioned alloys were calculated using the Korringa-Kohn-Rostoker method with the coherent potential approximation (KKR-CPA) in the LDA framework. The electronic densities of states and dispersion curves were obtained. The crystal structure stability and site preference analysis were addressed using total energy computations. Most ofmore » these experimental results correspond to electronic structure computations only if they take into account extra crystal defects such as antisite defects or vacancies present to various extents in the samples. Indeed a remarkable variation of KKR-CPA density of states occurring both in FeVSb and FeV{sub 1-x}Zr{sub x}Sb including defects may explain why FeVSb is not fully semiconducting as well as why there is a change of the thermopower sign in the FeV{sub 1-x}Zr{sub x}Sb versus x content.« less

Structural Ordering of Semiconducting Polymers and Small-Molecules for Organic Electronics

NASA Astrophysics Data System (ADS)

O'Hara, Kathryn Allison

Semiconducting polymers and small-molecules can be readily incorporated into electronic devices such as organic photovoltaics (OPVs), thermoelectrics (OTEs), organic light emitting diodes (OLEDs), and organic thin film transistors (OTFTs). Organic materials offer the advantage of being processable from solution to form flexible and lightweight thin films. The molecular design, processing, and resulting thin film morphology of semiconducting polymers drastically affect the optical and electronic properties. Charge transport within films of semiconducting polymers relies on the nanoscale organization to ensure electronic coupling through overlap of molecular orbitals and to provide continuous transport pathways. While the angstrom-scale packing details can be studied using X-ray scattering methods, an understanding of the mesoscale, or the length scale over which smaller ordered regions connect, is much harder to achieve. Grain boundaries play an important role in semiconducting polymer thin films where the average grain size is much smaller than the total distance which charges must traverse in order to reach the electrodes in a device. The majority of semiconducting polymers adopt a lamellar packing structure in which the conjugated backbones align in parallel pi-stacks separated by the alkyl side-chains. Only two directions of transport are possible--along the conjugated backbone and in the pi-stacking direction. Currently, the discussion of transport between crystallites is centered around the idea of tie-chains, or "bridging" polymer chains connecting two ordered regions. However, as molecular structures become increasingly complex with the development of new donor-acceptor copolymers, additional forms of connectivity between ordered domains should be considered. High resolution transmission electron microscopy (HRTEM) is a powerful tool for directly imaging the crystalline grain boundaries in polymer and small-molecule thin films. Recently, structures

First principles study of structural stability, electronic structure and mechanical properties of ReN and TcN

NASA Astrophysics Data System (ADS)

Rajeswarapalanichamy, R.; Kavitha, M.; Sudha Priyanga, G.; Iyakutti, K.

2015-03-01

The crystal structure, structural stability, electronic and mechanical properties of ReN and TcN are investigated using first principles calculations. We have considered five different crystal structures: NaCl, zinc blende (ZB), NiAs, tungsten carbide (WC) and wurtzite (WZ). Among these ZB phase is found to be the lowest energy phase for ReN and TcN at normal pressure. Pressure induced structural phase transitions from ZB to WZ phase at 214 GPa in ReN and ZB to NiAs phase at 171 GPa in TcN are predicted. The electronic structure reveals that both ReN and TcN are metallic in nature. The computed elastic constants indicate that both the nitrides are mechanically stable. As ReN in NiAs phase has high bulk and shear moduli and low Poisson's ratio, it is found to be a potential ultra incompressible super hard material.

Electronic structure, magnetic and structural properties of Ni doped ZnO nanoparticles

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

Kumar, Shalendra, E-mail: shailuphy@gmail.com; Vats, Prashant; Gautam, S.

Highlights: • XRD, and HR-TEM results show the single phase nature of Ni doped ZnO nanoparticles. • dc magnetization results indicate the RT-FM in Ni doped ZnO nanoparticles. • Ni L{sub 3,2} edge NEXAFS spectra infer that Ni ions are in +2 valence state. • O K edge NEXAFS spectra show that O vacancy increases with Ni doping in ZnO. - Abstract: We report structural, magnetic and electronic structural properties of Ni doped ZnO nanoparticles prepared by auto-combustion method. The prepared nanoparticles were characterized by using X-ray diffraction (XRD), high resolution transmission electron microscopy (HR-TEM), near edge X-ray absorption finemore » structure (NEXAFS) spectroscopy, and dc magnetization measurements. The XRD and HR-TEM results indicate that Ni doped ZnO nanoparticles have single phase nature with wurtzite lattice and exclude the presence of secondary phase. NEXAFS measurements performed at Ni L{sub 3,2}-edges indicates that Ni ions are in +2 valence state and exclude the presence of Ni metal clusters. O K-edge NEXAFS spectra indicate an increase in oxygen vacancies with Ni-doping, while Zn L{sub 3,2}-edge show the absence of Zn-vacancies. The magnetization measurements performed at room temperature shows that pure and Ni doped ZnO exhibits ferromagnetic behavior.« less

Electronic structure of some complex thermoelectrics - role of dimensional confinement and nanostructuring

NASA Astrophysics Data System (ADS)

Mahanti, Subhendra D.; Hoang, Khang

2016-12-01

Thermoelectric materials are of great current interest for a number of energy-related applications such as waste heat recovery, terrestrial cooling, and thermoelectric power generation. There have been several significant recent advances in improving the thermoelectric figure of merit ZT; in some instances, ZT > 2 at high temperatures. Concepts like electron-crystal phonon-glass, dimensional confinement, nanostructuring, energy filtering, and intrinsic lattice anharmonicity have not only acted as guiding principles in synthesizing new materials but also for electronic structure engineering using theoretical calculations. In this review paper, we discuss these concepts and present a few examples of theoretical studies of electronic structure and transport properties illustrating how some of these ideas work. The four types of systems we discuss are quaternary chalcogenides LAST-m, nanoscale mixtures of half-Heusler and Heusler compounds, ternary chalcogenide compounds of type ABX2 where the electronic structure near the band gap depends sensitively on the ordering of A and B atoms, and naturally occurring bulk superlattices formed out of alternating ionic and semiconducting bilayers as in SrFAgTe.

Lipidic cubic phase serial millisecond crystallography using synchrotron radiation

PubMed Central

Nogly, Przemyslaw; James, Daniel; Wang, Dingjie; White, Thomas A.; Zatsepin, Nadia; Shilova, Anastasya; Nelson, Garrett; Liu, Haiguang; Johansson, Linda; Heymann, Michael; Jaeger, Kathrin; Metz, Markus; Wickstrand, Cecilia; Wu, Wenting; Båth, Petra; Berntsen, Peter; Oberthuer, Dominik; Panneels, Valerie; Cherezov, Vadim; Chapman, Henry; Schertler, Gebhard; Neutze, Richard; Spence, John; Moraes, Isabel; Burghammer, Manfred; Standfuss, Joerg; Weierstall, Uwe

2015-01-01

Lipidic cubic phases (LCPs) have emerged as successful matrixes for the crystallization of membrane proteins. Moreover, the viscous LCP also provides a highly effective delivery medium for serial femtosecond crystallography (SFX) at X-ray free-electron lasers (XFELs). Here, the adaptation of this technology to perform serial millisecond crystallography (SMX) at more widely available synchrotron microfocus beamlines is described. Compared with conventional microcrystallography, LCP-SMX eliminates the need for difficult handling of individual crystals and allows for data collection at room temperature. The technology is demonstrated by solving a structure of the light-driven proton-pump bacteriorhodopsin (bR) at a resolution of 2.4 Å. The room-temperature structure of bR is very similar to previous cryogenic structures but shows small yet distinct differences in the retinal ligand and proton-transfer pathway. PMID:25866654

Density functional studies of the defect-induced electronic structure modifications in bilayer boronitrene

NASA Astrophysics Data System (ADS)

Ukpong, A. M.; Chetty, N.

2012-05-01

The van der Waals interaction-corrected density functional theory is used in this study to investigate the formation, energetic stability, and inter-layer cohesion in bilayer hexagonal boronitrene. The effect of inter-layer separation on the electronic structure is systematically investigated. The formation and energetic stability of intrinsic defects are also investigated at the equilibrium inter-layer separation. It is found that nonstoichiometric defects, and their complexes, that induce excess nitrogen or excess boron, in each case, are relatively more stable in the atmosphere that corresponds to the excess atomic species. The modifications of the electronic structure due to formation of complexes are also investigated. It is shown that van der Waals density functional theory gives an improved description of the cohesive properties but not the electronic structure in bilayer boronitrene compared to other functionals. We identify energetically favourable topological defects that retain the energy gap in the electronic structure, and discuss their implications for band gap engineering in low-n layer boronitrene insulators. The relative strengths and weaknesses of the functionals in predicting the properties of bilayer boronitrene are also discussed.

Electronic Structure and Morphology of Graphene Layers on SiC

NASA Astrophysics Data System (ADS)

Ohta, Taisuke

2008-03-01

Recent years have witnessed the discovery and the unique electronic properties of graphene, a sheet of carbon atoms arranged in a honeycomb lattice. The unique linear dispersion relation of charge carriers near the Fermi level (``Dirac Fermions'') lead to exciting transport properties, such as an unusual quantum Hall effect, and have aroused scientific and technological interests. On the way towards graphene-based electronics, a knowledge of the electronic band structure and the morphology of epitaxial graphene films on silicon carbide substrates is imperative. We have studied the evolution of the occupied band structure and the morphology of graphene layers on silicon carbide by systematically increasing the layer thickness. Using angle-resolved photoemission spectroscopy (ARPES), we examine this unique 2D system in its development from single layer to multilayers, by characteristic changes in the π band, the highest occupied state, and the dispersion relation in the out-of-plane electron wave vector in particular. The evolution of the film morphology is evaluated by the combination of low-energy electron microscopy and ARPES. By exploiting the sensitivity of graphene's electronic states to the charge carrier concentration, changes in the on-site Coulomb potential leading to a change of π and π* bands can be examined using ARPES. We demonstrate that, in a graphene bilayer, the gap between π and π* bands can be controlled by selectively adjusting relative carrier concentrations, which suggests a possible application of the graphene bilayer for switching functions in electronic devices. This work was done in collaboration with A. Bostwick, J. L. McChesney, and E. Rotenberg at Advanced Light Source, Lawrence Berkeley National Laboratory, K. Horn at Fritz-Haber-Institut, K. V. Emtsev and Th. Seyller at Lehrstuhl für Technische Physik, Universität Erlangen-Nürnberg, and F. El Gabaly and A. K. Schmid at National Center for Electron Microscopy, Lawrence Berkeley

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

Designing Semiconductor Heterostructures Using Digitally Accessible Electronic-Structure Data

NASA Astrophysics Data System (ADS)

Shapera, Ethan; Schleife, Andre

Semiconductor sandwich structures, so-called heterojunctions, are at the heart of modern applications with tremendous societal impact: Light-emitting diodes shape the future of lighting and solar cells are promising for renewable energy. However, their computer-based design is hampered by the high cost of electronic structure techniques used to select materials based on alignment of valence and conduction bands and to evaluate excited state properties. We describe, validate, and demonstrate an open source Python framework which rapidly screens existing online databases and user-provided data to find combinations of suitable, previously fabricated materials for optoelectronic applications. The branch point energy aligns valence and conduction bands of different materials, requiring only the bulk density functional theory band structure. We train machine learning algorithms to predict the dielectric constant, electron mobility, and hole mobility with material descriptors available in online databases. Using CdSe and InP as emitting layers for LEDs and CH3NH3PbI3 and nanoparticle PbS as absorbers for solar cells, we demonstrate our broadly applicable, automated method.

Band structure of an electron in a kind of periodic potentials with singularities

NASA Astrophysics Data System (ADS)

Hai, Kuo; Yu, Ning; Jia, Jiangping

2018-06-01

Noninteracting electrons in some crystals may experience periodic potentials with singularities and the governing Schrödinger equation cannot be defined at the singular points. The band structure of a single electron in such a one-dimensional crystal has been calculated by using an equivalent integral form of the Schrödinger equation. Both the perturbed and exact solutions are constructed respectively for the cases of a general singular weak-periodic system and its an exactly solvable version, Kronig-Penney model. Any one of them leads to a special band structure of the energy-dependent parameter, which results in an effective correction to the previous energy-band structure and gives a new explanation for forming the band structure. The used method and obtained results could be a valuable aid in the study of energy bands in solid-state physics, and the new explanation may trigger investigation to different physical mechanism of electron band structures.

Electronic structure of gadolinium complexes in ZnO in the GW approximation

NASA Astrophysics Data System (ADS)

Rosa, A. L.; Frauenheim, Th.

2018-04-01

The role of intrinsic defects has been investigated to determine binding energies and the electronic structure of Gd complexes in ZnO. We use density-functional theory and the GW method to show that the presence of vacancies and interstitials affect the electronic structure of Gd doped ZnO. However, the strong localization of the Gd-f and d states suggest that carrier mediated ferromagnetism in this material may be difficult to achieve.

The Electronic Structure Signature of the Spin Cross-Over Transition of [Co(dpzca)2

NASA Astrophysics Data System (ADS)

Zhang, Xin; Mu, Sai; Liu, Yang; Luo, Jian; Zhang, Jian; N'Diaye, Alpha T.; Enders, Axel; Dowben, Peter A.

2018-05-01

The unoccupied electronic structure of the spin crossover molecule cobalt (II) N-(2-pyrazylcarbonyl)-2-pyrazinecarboxamide, [Co(dpzca)2] was investigated, using X-ray absorption spectroscopy (XAS) and compared with magnetometry (SQUID) measurements. The temperature dependence of the XAS and molecular magnetic susceptibility χmT are in general agreement for [Co(dpzca)2], and consistent with density functional theory (DFT). This agreement of magnetic susceptibility and X-ray absorption spectroscopy provides strong evidence that the changes in magnetic moment can be ascribed to changes in electronic structure. Calculations show the choice of Coulomb correlation energy U has a profound effect on the electronic structure of the low spin state, but has little influence on the electronic structure of the high spin state. In the temperature dependence of the XAS, there is also evidence of an X-ray induced excited state trapping for [Co(dpzca)2] at 15 K.

Analysis of boron carbides' electronic structure

NASA Technical Reports Server (NTRS)

Howard, Iris A.; Beckel, Charles L.

1986-01-01

The electronic properties of boron-rich icosahedral clusters were studied as a means of understanding the electronic structure of the icosahedral borides such as boron carbide. A lower bound was estimated on bipolaron formation energies in B12 and B11C icosahedra, and the associated distortions. While the magnitude of the distortion associated with bipolaron formation is similar in both cases, the calculated formation energies differ greatly, formation being much more favorable on B11C icosahedra. The stable positions of a divalent atom relative to an icosahedral borane was also investigated, with the result that a stable energy minimum was found when the atom is at the center of the borane, internal to the B12 cage. If incorporation of dopant atoms into B12 cages in icosahedral boride solids is feasible, novel materials might result. In addition, the normal modes of a B12H12 cluster, of the C2B10 cage in para-carborane, and of a B12 icosahedron of reduced (D sub 3d) symmetry, such as is found in the icosahedral borides, were calculated. The nature of these vibrational modes will be important in determining, for instance, the character of the electron-lattice coupling in the borides, and in analyzing the lattice contribution to the thermal conductivity.

Electronic structure of ruthenium-doped iron chalcogenides

NASA Astrophysics Data System (ADS)

Winiarski, M. J.; Samsel-Czekała, M.; Ciechan, A.

2014-12-01

The structural and electronic properties of hypothetical RuxFe1-xSe and RuxFe1-xTe systems have been investigated from first principles within the density functional theory (DFT). Reasonable values of lattice parameters and chalcogen atomic positions in the tetragonal unit cell of iron chalcogenides have been obtained with the use of norm-conserving pseudopotentials. The well known discrepancies between experimental data and DFT-calculated results for structural parameters of iron chalcogenides are related to the semicore atomic states which were frozen in the used here approach. Such an approach yields valid results of the electronic structures of the investigated compounds. The Ru-based chalcogenides exhibit the same topology of the Fermi surface (FS) as that of FeSe, differing only in subtle FS nesting features. Our calculations predict that the ground states of RuSe and RuTe are nonmagnetic, whereas those of the solid solutions RuxFe1-xSe and RuxFe1-xTe become the single- and double-stripe antiferromagnetic, respectively. However, the calculated stabilization energy values are comparable for each system. The phase transitions between these magnetic arrangements may be induced by slight changes of the chalcogen atom positions and the lattice parameters a in the unit cell of iron selenides and tellurides. Since the superconductivity in iron chalcogenides is believed to be mediated by the spin fluctuations in single-stripe magnetic phase, the RuxFe1-xSe and RuxFe1-xTe systems are good candidates for new superconducting iron-based materials.

New determination of the fine structure constant from the electron value and QED.

PubMed

Gabrielse, G; Hanneke, D; Kinoshita, T; Nio, M; Odom, B

2006-07-21

Quantum electrodynamics (QED) predicts a relationship between the dimensionless magnetic moment of the electron (g) and the fine structure constant (alpha). A new measurement of g using a one-electron quantum cyclotron, together with a QED calculation involving 891 eighth-order Feynman diagrams, determine alpha(-1)=137.035 999 710 (96) [0.70 ppb]. The uncertainties are 10 times smaller than those of nearest rival methods that include atom-recoil measurements. Comparisons of measured and calculated g test QED most stringently, and set a limit on internal electron structure.

Visualizing spatial correlation: structural and electronic orders in iron-based superconductors on atomic scale

NASA Astrophysics Data System (ADS)

Maksov, Artem; Ziatdinov, Maxim; Li, Li; Sefat, Athena; Maksymovych, Petro; Kalinin, Sergei

Crystalline matter on the nanoscale level often exhibits strongly inhomogeneous structural and electronic orders, which have a profound effect on macroscopic properties. This may be caused by subtle interplay between chemical disorder, strain, magnetic, and structural order parameters. We present a novel approach based on combination of high resolution scanning tunneling microscopy/spectroscopy (STM/S) and deep data style analysis for automatic separation, extraction, and correlation of structural and electronic behavior which might lead us to uncovering the underlying sources of inhomogeneity in in iron-based family of superconductors (FeSe, BaFe2As2) . We identify STS spectral features using physically robust Bayesian linear unmixing, and show their direct relevance to the fundamental physical properties of the system, including electronic states associated with individual defects and impurities. We collect structural data from individual unit cells on the crystalline lattice, and calculate both global and local indicators of spatial correlation with electronic features, demonstrating, for the first time, a direct quantifiable connection between observed structural order parameters extracted from the STM data and electronic order parameters identified within the STS data. This research was sponsored by the Division of Materials Sciences and Engineering, Office of Science, Basic Energy Sciences, US DOE.

Stacking the Deck: Leveraging Surface Interactions to Tune Interfacial Electronic Structure

NASA Astrophysics Data System (ADS)

Maughan, Bret; Eads, Calley; Zahl, Percy; Sutter, Peter; Monti, Oliver

We present results from a series of experiments aimed at understanding and controlling molecular interactions in phthalocyanine (Pc) thin-films on Cu(110) to tailor the interfacial electronic structure. Using low-temperature scanning tunneling microscopy (LT-STM), we identify interactions that drive surface-molecule coupling, molecular self-assembly and thin-film order. We provide evidence that interactions with native Cu adatoms play a pivotal role in self-assembly of Pc systems, along with anisotropic nanoribbon growth dynamics, supported by an agent-based kinetic Monte Carlo (AB-KMC) simulation. We show further that self-assembled nanoribbon length can be controlled using surface diffusion barriers and that ordered 2D thin-film growth is promoted by diminishing surface-molecule interactions that otherwise dominate native Cu(110) interfaces. Altogether, this detailed structural understanding allows us to interpret interfacial electronic structure and dynamics, uncovered through ultraviolet (UPS) and two-photon photoemission (2PPE) spectroscopy experiments, in molecular configuration-specific detail. In all, our understanding of interfacial processes guides strategic modifications to both surface and molecule to harness interfacial interactions and thereby modify the collective electronic structure of the interface. NSF No. CHE-1213243 and No. CHE-1565497, Arizona TRIF, DOE/BNL Cntrct No. DE-SC0012704, and DOE No. DE-SC0016343.

Electric field effect on the electronic structure of 2D Y2C electride

NASA Astrophysics Data System (ADS)

Oh, Youngtek; Lee, Junsu; Park, Jongho; Kwon, Hyeokshin; Jeon, Insu; Wng Kim, Sung; Kim, Gunn; Park, Seongjun; Hwang, Sung Woo

2018-07-01

Electrides are ionic compounds in which electrons confined in the interstitial spaces serve as anions and are attractive owing to their exotic physical and chemical properties in terms of their low work function and efficient charge-transfer characteristics. Depending on the topology of the anionic electrons, the surface electronic structures of electrides can be significantly altered. In particular, the electronic structures of two-dimensional (2D) electride surfaces are of interest because the localized anionic electrons at the interlayer space can be naturally exposed to cleaved surfaces. In this paper, we report the electronic structure of 2D Y2C electride surface using scanning tunneling microscopy (STM) and first-principles calculations, which reveals that anionic electrons at a cleaved surface are absorbed by the surface and subsequently resurged onto the surface due to an applied electric field. We highlight that the estranged anionic electrons caused by the electric field occupy the slightly shifted crystallographic site compared with a bulk Y2C electride. We also measure the work function of the Y2C single crystal, and it shows a slightly lower value than the calculated one, which appears to be due to the electric field from the STM junction.

Third-order polynomial model for analyzing stickup state laminated structure in flexible electronics

NASA Astrophysics Data System (ADS)

Meng, Xianhong; Wang, Zihao; Liu, Boya; Wang, Shuodao

2018-02-01

Laminated hard-soft integrated structures play a significant role in the fabrication and development of flexible electronics devices. Flexible electronics have advantageous characteristics such as soft and light-weight, can be folded, twisted, flipped inside-out, or be pasted onto other surfaces of arbitrary shapes. In this paper, an analytical model is presented to study the mechanics of laminated hard-soft structures in flexible electronics under a stickup state. Third-order polynomials are used to describe the displacement field, and the principle of virtual work is adopted to derive the governing equations and boundary conditions. The normal strain and the shear stress along the thickness direction in the bi-material region are obtained analytically, which agree well with the results from finite element analysis. The analytical model can be used to analyze stickup state laminated structures, and can serve as a valuable reference for the failure prediction and optimal design of flexible electronics in the future.

Origin of the 20-electron structure of Mg3 MnH7 : Density functional calculations

NASA Astrophysics Data System (ADS)

Gupta, M.; Singh, D. J.; Gupta, R.

2005-03-01

The electronic structure and stability of the 20-electron complex hydride, Mg3MnH7 is studied using density functional calculations. The heat of formation is larger in magnitude than that of MgH2 . The deviation from the 18-electron rule is explained by the predominantly ionic character of the band structure and a large crystal-field splitting of the Mn d bands. In particular, each H provides one deep band accomodating two electrons, while the Mn t2g bands hold an additional six electrons per formula unit.

Structural and electronic properties of GaAs and GaP semiconductors

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

Rani, Anita; Kumar, Ranjan

2015-05-15

The Structural and Electronic properties of Zinc Blende phase of GaAs and GaP compounds are studied using self consistent SIESTA-code, pseudopotentials and Density Functional Theory (DFT) in Local Density Approximation (LDA). The Lattice Constant, Equillibrium Volume, Cohesive Energy per pair, Compressibility and Band Gap are calculated. The band gaps calcultated with DFT using LDA is smaller than the experimental values. The P-V data fitted to third order Birch Murnaghan equation of state provide the Bulk Modulus and its pressure derivatives. Our Structural and Electronic properties estimations are in agreement with available experimental and theoretical data.

A novel Gaussian-Sinc mixed basis set for electronic structure calculations

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

Jerke, Jonathan L.; Lee, Young; Tymczak, C. J.

2015-08-14

A Gaussian-Sinc basis set methodology is presented for the calculation of the electronic structure of atoms and molecules at the Hartree–Fock level of theory. This methodology has several advantages over previous methods. The all-electron electronic structure in a Gaussian-Sinc mixed basis spans both the “localized” and “delocalized” regions. A basis set for each region is combined to make a new basis methodology—a lattice of orthonormal sinc functions is used to represent the “delocalized” regions and the atom-centered Gaussian functions are used to represent the “localized” regions to any desired accuracy. For this mixed basis, all the Coulomb integrals are definablemore » and can be computed in a dimensional separated methodology. Additionally, the Sinc basis is translationally invariant, which allows for the Coulomb singularity to be placed anywhere including on lattice sites. Finally, boundary conditions are always satisfied with this basis. To demonstrate the utility of this method, we calculated the ground state Hartree–Fock energies for atoms up to neon, the diatomic systems H{sub 2}, O{sub 2}, and N{sub 2}, and the multi-atom system benzene. Together, it is shown that the Gaussian-Sinc mixed basis set is a flexible and accurate method for solving the electronic structure of atomic and molecular species.« less

Projected quasiparticle theory for molecular electronic structure

NASA Astrophysics Data System (ADS)

Scuseria, Gustavo E.; Jiménez-Hoyos, Carlos A.; Henderson, Thomas M.; Samanta, Kousik; Ellis, Jason K.

2011-09-01

We derive and implement symmetry-projected Hartree-Fock-Bogoliubov (HFB) equations and apply them to the molecular electronic structure problem. All symmetries (particle number, spin, spatial, and complex conjugation) are deliberately broken and restored in a self-consistent variation-after-projection approach. We show that the resulting method yields a comprehensive black-box treatment of static correlations with effective one-electron (mean-field) computational cost. The ensuing wave function is of multireference character and permeates the entire Hilbert space of the problem. The energy expression is different from regular HFB theory but remains a functional of an independent quasiparticle density matrix. All reduced density matrices are expressible as an integration of transition density matrices over a gauge grid. We present several proof-of-principle examples demonstrating the compelling power of projected quasiparticle theory for quantum chemistry.

Effect of potassium doping on electronic structure and thermoelectric properties of topological crystalline insulator

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

Roychowdhury, Subhajit; Biswas, Kanishka, E-mail: kanishka@jncasr.ac.in; Sandhya Shenoy, U.

2016-05-09

Topological crystalline insulator (TCI), Pb{sub 0.6}Sn{sub 0.4}Te, exhibits metallic surface states protected by crystal mirror symmetry with negligibly small band gap. Enhancement of its thermoelectric performances needs tuning of its electronic structure particularly through engineering of its band gap. While physical perturbations tune the electronic structure of TCI by breaking of the crystal mirror symmetry, chemical means such as doping have been more attractive recently as they result in better thermoelectric performance in TCIs. Here, we demonstrate that K doping in TCI, Pb{sub 0.6}Sn{sub 0.4}Te, breaks the crystal mirror symmetry locally and widens electronic band gap, which is confirmed bymore » direct electronic absorption spectroscopy and electronic structure calculations. K doping in Pb{sub 0.6}Sn{sub 0.4}Te increases p-type carrier concentration and suppresses the bipolar conduction via widening a band gap, which collectively boosts the thermoelectric figure of merit (ZT) to 1 at 708 K.« less

Effects of moiré lattice structure on electronic properties of graphene

NASA Astrophysics Data System (ADS)

Huang, Lunan; Wu, Yun; Hershberger, M. T.; Mou, Daixiang; Schrunk, Benjamin; Tringides, Michael C.; Hupalo, Myron; Kaminski, Adam

2017-07-01

We study structural and electronic properties of graphene grown on silicone carbide (SiC) substrate using a scanning tunneling microscope, spot-profile-analysis low-energy electron diffraction, and angle-resolved photoemission spectroscopy. We find several new replicas of Dirac cones in the Brillouin zone. Their locations can be understood in terms of a combination of basis vectors linked to SiC 6 × 6 and graphene 6 √{3 }×6 √{3 } reconstruction. Therefore, these new features originate from the moiré caused by the lattice mismatch between SiC and graphene. More specifically, Dirac cone replicas are caused by underlying weak modulation of the ionic potential by the substrate that is then experienced by the electrons in the graphene. We also demonstrate that this effect is equally strong in single- and trilayer graphene; therefore, the additional Dirac cones are intrinsic features rather than the result of photoelectron diffraction. These new features in the electronic structure are very important for the interpretation of recent transport measurements and can assist in tuning the properties of graphene for practical applications.

Nonlinear electron transport mobility in asymmetric wide quantum well structure

NASA Astrophysics Data System (ADS)

Nayak, Rasmita K.; Das, Sudhakar; Panda, Ajit K.; Sahu, Trinath

2018-05-01

The nonlinearity of multisubband electron mobility µ in a GaAs/AlxGa1-xAs wide quantum well structure is studied by varying the well width w and doping concentration Nd b (Nd t ) lying in the bottom (top) barrier. The electrons diffuse into the well and accumulate near the interfaces forming two sheets of coupled two dimensional electron gases equivalent to a double quantum well structure. We show that interchange of doping concentrations N db and N dt lead to the enhancement of µ as a function of w as long as N dt > N db , even though the surface electron density remains unaltered. Further, keeping Nd b unchanged, variation of Nd t leads to nonlinearity in µ near the resonance of subband states at Nd t = Nd b at which the subband energy levels exhibit anticrossing. The variation of µ becomes prominent by increasing the well width and resonant doping concentration. The nonlinearity in µ is mostly because of the change in the interface roughness scattering potential through intersubband effects due to the substantial changes in the distributions of the subband wave functions around resonance. Our results of nonmonotonic variation of µ can be utilized for low temperature coupled quantum well devices.

Synthesis, extraction and electronic structure of Ce@C2n

NASA Astrophysics Data System (ADS)

Liu, Bing-Bing; Zou, Guang-Tian; Yang, Hai-Bin; Yu, San; Lu, Jin-Shan; Liu, Zi-Yang; Liu, Shu-Ying; Xu, Wen-Guo

1997-11-01

In view of the growing interest in endohedral lanthanide fullerenes, Ce, as a typical+ 4 oxidation state lanthanide element, has been systematically studied. The synthesis, extraction and electronic structure of Ce @ C2n are investigated. Soot containing Ce@C2n was synthesized in high yield by carbonizing CeO2-containing graphite rods and are back-burning the CeC2-enriched cathode deposit in a DC arc plasma apparatus. Ce@C2n dominated by Ce@C82, can be efficiently extracted from the insoluble part of the soot after toluene Soxhlet extraction by pyridine at high temperature and high pressure in a closed vessel. About 60% Ce@C2n(2n = 82, 80, 78, 76) and 35% Ce@C82 can be enriched in the pyridine extract. This fact is identified by desorption electron impact mass spectrometry (DEI MS). The electronic structure of Ce@C2n is analyzed by using X-ray photoemission spectroscopy (XPS) of pyridine-free film. It is suggested that the encapsulated Ce atom is in a charge state close to+ 3 and was effectively protected from reaction with water and oxygen by the enclosing fullerene cage. Unlike theoretical expectation, the electronic state of Ce@C82 is formally described as Ce+3@C3-82.

Electronic and structural properties of vacancies and hydrogen adsorbates on trilayer graphene

NASA Astrophysics Data System (ADS)

Menezes, Marcos G.; Capaz, Rodrigo B.

2015-08-01

Using ab initio calculations, we study the electronic and structural properties of vacancies and hydrogen adsorbates on trilayer graphene. Those defects are found to share similar low-energy electronic features, since they both remove a pz electron from the honeycomb lattice and induce a defect level near the Fermi energy. However, a vacancy also leaves unpaired σ electrons on the lattice, which lead to important structural differences and also contribute to magnetism. We explore both ABA and ABC stackings and compare properties such as formation energies, magnetic moments, spin density and the local density of states (LDOS) of the defect levels. These properties show a strong sensitivity to the layer in which the defect is placed and smaller sensitivities to sublattice placing and stacking type. Finally, for the ABC trilayer, we also study how these states behave in the presence of an external field, which opens a tunable gap in the band structure of the non-defective system. The pz defect states show a strong hybridization with band states as the field increases, with reduction and eventually loss of magnetization, and a non-magnetic, midgap-like state is found when the defect is at the middle layer.

Electronic and Structural Properties of Vacancies and Hydrogen Adsorbates on Trilayer Graphene

NASA Astrophysics Data System (ADS)

Menezes, Marcos; Capaz, Rodrigo

2015-03-01

Using ab initio calculations, we study the electronic and structural properties of vacancies and hydrogen adsorbates on trilayer graphene. Those defects are found to share similar low-energy electronic features, since they both remove a pz electron from the honeycomb lattice and induce a defect level near the Fermi energy. However, a vacancy also leaves unpaired σ electrons on the lattice, which lead to important structural differences and also contribute to magnetism. We explore both ABA and ABC stackings and compare properties such as formation energies, magnetic moments, spin density and the local density of states (LDOS) of the defect levels. These properties show a strong sensitivity to the layer in which the defect is placed and smaller sensitivities to sublattice placing and stacking type. Finally, for the ABC trilayer, we also study how these states behave in the presence of an external electrical field, which opens a tunable gap in the band structure of the non-defective system. The pz defect states show a strong hybridization with band states as the field increases, with reduction and eventually loss of magnetization, and a non-magnetic, midgap-like state is found when the defect is at the middle layer.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal.

PubMed

Clabbers, M T B; van Genderen, E; Wan, W; Wiegers, E L; Gruene, T; Abrahams, J P

2017-09-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm 3 , i.e. no more than 6 × 10 5 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures.

Protein structure determination by electron diffraction using a single three-dimensional nanocrystal

PubMed Central

Clabbers, M. T. B.; van Genderen, E.; Wiegers, E. L.; Gruene, T.; Abrahams, J. P.

2017-01-01

Three-dimensional nanometre-sized crystals of macromolecules currently resist structure elucidation by single-crystal X-ray crystallography. Here, a single nanocrystal with a diffracting volume of only 0.14 µm3, i.e. no more than 6 × 105 unit cells, provided sufficient information to determine the structure of a rare dimeric polymorph of hen egg-white lysozyme by electron crystallography. This is at least an order of magnitude smaller than was previously possible. The molecular-replacement solution, based on a monomeric polyalanine model, provided sufficient phasing power to show side-chain density, and automated model building was used to reconstruct the side chains. Diffraction data were acquired using the rotation method with parallel beam diffraction on a Titan Krios transmission electron microscope equipped with a novel in-house-designed 1024 × 1024 pixel Timepix hybrid pixel detector for low-dose diffraction data collection. Favourable detector characteristics include the ability to accurately discriminate single high-energy electrons from X-rays and count them, fast readout to finely sample reciprocal space and a high dynamic range. This work, together with other recent milestones, suggests that electron crystallography can provide an attractive alternative in determining biological structures. PMID:28876237

Deep learning and the electronic structure problem

NASA Astrophysics Data System (ADS)

Mills, Kyle; Spanner, Michael; Tamblyn, Isaac

In the past decade, the fields of artificial intelligence and computer vision have progressed remarkably. Supported by the enthusiasm of large tech companies, as well as significant hardware advances and the utilization of graphical processing units to accelerate computations, deep neural networks (DNN) are gaining momentum as a robust choice for many diverse machine learning applications. We have demonstrated the ability of a DNN to solve a quantum mechanical eigenvalue equation directly, without the need to compute a wavefunction, and without knowledge of the underlying physics. We have trained a convolutional neural network to predict the total energy of an electron in a confining, 2-dimensional electrostatic potential. We numerically solved the one-electron Schrödinger equation for millions of electrostatic potentials, and used this as training data for our neural network. Four classes of potentials were assessed: the canonical cases of the harmonic oscillator and infinite well, and two types of randomly generated potentials for which no analytic solution is known. We compare the performance of the neural network and consider how these results could lead to future advances in electronic structure theory.

Direct Visualization of Local Electromagnetic Field Structures by Scanning Transmission Electron Microscopy.

PubMed

Shibata, Naoya; Findlay, Scott D; Matsumoto, Takao; Kohno, Yuji; Seki, Takehito; Sánchez-Santolino, Gabriel; Ikuhara, Yuichi

2017-07-18

The functional properties of materials and devices are critically determined by the electromagnetic field structures formed inside them, especially at nanointerface and surface regions, because such structures are strongly associated with the dynamics of electrons, holes and ions. To understand the fundamental origin of many exotic properties in modern materials and devices, it is essential to directly characterize local electromagnetic field structures at such defect regions, even down to atomic dimensions. In recent years, rapid progress in the development of high-speed area detectors for aberration-corrected scanning transmission electron microscopy (STEM) with sub-angstrom spatial resolution has opened new possibilities to directly image such electromagnetic field structures at very high-resolution. In this Account, we give an overview of our recent development of differential phase contrast (DPC) microscopy for aberration-corrected STEM and its application to many materials problems. In recent years, we have developed segmented-type STEM detectors which divide the detector plane into 16 segments and enable simultaneous imaging of 16 STEM images which are sensitive to the positions and angles of transmitted/scattered electrons on the detector plane. These detectors also have atomic-resolution imaging capability. Using these segmented-type STEM detectors, we show DPC STEM imaging to be a very powerful tool for directly imaging local electromagnetic field structures in materials and devices in real space. For example, DPC STEM can clearly visualize the local electric field variation due to the abrupt potential change across a p-n junction in a GaAs semiconductor, which cannot be observed by normal in-focus bright-field or annular type dark-field STEM imaging modes. DPC STEM is also very effective for imaging magnetic field structures in magnetic materials, such as magnetic domains and skyrmions. Moreover, real-time imaging of electromagnetic field structures can

Lithium halide monolayers: Structural, electronic and optical properties by first principles study

NASA Astrophysics Data System (ADS)

Safari, Mandana; Maskaneh, Pegah; Moghadam, Atousa Dashti; Jalilian, Jaafar

2016-09-01

Using first principle study, we investigate the structural, electronic and optical properties of lithium halide monolayers (LiF, LiCl, LiBr). In contrast to graphene and other graphene-like structures that form hexagonal rings in plane, these compounds can form and stabilize in cubic shape interestingly. The type of band structure in these insulators is identified as indirect type and ionic nature of their bonds are illustrated as well. The optical properties demonstrate extremely transparent feature for them as a result of wide band gap in the visible range; also their electron transitions are indicated for achieving a better vision on the absorption mechanism in these kinds of monolayers.

Electronic structure of the Cu + impurity center in sodium chloride

NASA Astrophysics Data System (ADS)

Chermette, H.; Pedrini, C.

1981-08-01

The multiple-scattering Xα method is used to describe the electronic structure of Cu+ in sodium chloride. Several improvements are brought to the conventional Xα calculation. In particular, the cluster approximation is used by taking into account external lattice potential. The ''transition state'' procedure is applied in order to get the various multiplet levels. The fine electronic structure of the impurity centers is obtained after a calculation of the spin-orbit interactions. These results are compared with those given by a modified charge-consistent extended Hückel method (Fenske-type calculation) and the merit of each method is discussed. The present calculation produces good quantitative agreement with experiment concerning mainly the optical excitations and the emission mechanism of the Cu+ luminescent centers in NaCl.

Antiferroic electronic structure in the nonmagnetic superconducting state of the iron-based superconductors

PubMed Central

Shimojima, Takahiro; Malaeb, Walid; Nakamura, Asuka; Kondo, Takeshi; Kihou, Kunihiro; Lee, Chul-Ho; Iyo, Akira; Eisaki, Hiroshi; Ishida, Shigeyuki; Nakajima, Masamichi; Uchida, Shin-ichi; Ohgushi, Kenya; Ishizaka, Kyoko; Shin, Shik

2017-01-01

A major problem in the field of high-transition temperature (Tc) superconductivity is the identification of the electronic instabilities near superconductivity. It is known that the iron-based superconductors exhibit antiferromagnetic order, which competes with the superconductivity. However, in the nonmagnetic state, there are many aspects of the electronic instabilities that remain unclarified, as represented by the orbital instability and several in-plane anisotropic physical properties. We report a new aspect of the electronic state of the optimally doped iron-based superconductors by using high–energy resolution angle-resolved photoemission spectroscopy. We find spectral evidence for the folded electronic structure suggestive of an antiferroic electronic instability, coexisting with the superconductivity in the nonmagnetic state of Ba1−xKxFe2As2. We further establish a phase diagram showing that the antiferroic electronic structure persists in a large portion of the nonmagnetic phase covering the superconducting dome. These results motivate consideration of a key unknown electronic instability, which is necessary for the achievement of high-Tc superconductivity in the iron-based superconductors. PMID:28875162

Antiferroic electronic structure in the nonmagnetic superconducting state of the iron-based superconductors.

PubMed

Shimojima, Takahiro; Malaeb, Walid; Nakamura, Asuka; Kondo, Takeshi; Kihou, Kunihiro; Lee, Chul-Ho; Iyo, Akira; Eisaki, Hiroshi; Ishida, Shigeyuki; Nakajima, Masamichi; Uchida, Shin-Ichi; Ohgushi, Kenya; Ishizaka, Kyoko; Shin, Shik

2017-08-01

A major problem in the field of high-transition temperature ( T c ) superconductivity is the identification of the electronic instabilities near superconductivity. It is known that the iron-based superconductors exhibit antiferromagnetic order, which competes with the superconductivity. However, in the nonmagnetic state, there are many aspects of the electronic instabilities that remain unclarified, as represented by the orbital instability and several in-plane anisotropic physical properties. We report a new aspect of the electronic state of the optimally doped iron-based superconductors by using high-energy resolution angle-resolved photoemission spectroscopy. We find spectral evidence for the folded electronic structure suggestive of an antiferroic electronic instability, coexisting with the superconductivity in the nonmagnetic state of Ba 1- x K x Fe 2 As 2 . We further establish a phase diagram showing that the antiferroic electronic structure persists in a large portion of the nonmagnetic phase covering the superconducting dome. These results motivate consideration of a key unknown electronic instability, which is necessary for the achievement of high- T c superconductivity in the iron-based superconductors.

Electronic structure and nature of the color centers in MgF2

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

Freidman, S.P.; Golota, A.F.; Galakhov, V.R.

1986-09-01

The electronic structure and spectroscopic properties of samples of magnesium fluoride with different numbers of defects have been investigated with the use of the methods of x-ray photoelectron, x-ray emission, ESR, and optical spectroscopy. Nonempirical self-consistent calculations of the electronic structure of clusters which simulate stoichiometric and defective MgF2 have been carried out. The color centers in the approx. 5-eV energy range are attributed to the presence of vacancies in the anionic sublattice.

Statistical Fine Structure in the Inhomogeneously Broadened Electronic Origin of Pentacene in p-Terphenyl.

DTIC Science & Technology

1988-01-29

Electronic Origin of Pentacene in p-Terphenyl by T. P. Carter, M. Manavi, and W. E. Moerner Prepared for Publication inDTIC Journal of Chemical Physics...Classification) Statistical Fine Structure in the Inhomogeneously Broadened Electronic Origin of Pentacene in p-Terphenyl 12. PERSONAL AUTHOR(S) T. P...of pentacene in p-terphenyl using laser FM spectroscopy. Statistical fine structure is time-independent structure on the inhomogeneous line caused by

HREELS to identify electronic structures of organic thin films.

PubMed

Oeter, D; Ziegler, C; Göpel, W

1995-10-01

The electronic structure of alpha-oligothiophene (alphanT) thin films has been investigated for increasing chain lengths of n= 4-8 thiophene units with high resolution electron energy loss spectroscopy (HREELS) in the specular reflection geometry at a primary energy of 15 eV. The great advantage of this technique in contrast to UV/VIS absorption spectroscopy results from the fact, that the impact scattering mechanism of HREELS makes it possible to also detect optically forbidden electronic transitions. On the other hand, the electrons used as probes in HREELS have a wavelength which is two orders of magnitudes smaller if compared to those of photons used in UV/VIS absorption spectroscopy. Therefore individual molecules are excited by HREELS independent from each other and hence the excitation of collective excitons is not possible. As a result, information about the orientation of the molecules cannot be achieved with HREELS, which, however, is possible in polarization-dependent UV/VIS spectroscopy.

Spin structure of electron subbands in (110)-grown quantum wells

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

Nestoklon, M. O.; Tarasenko, S. A.; Jancu, J.-M.

We present the theory of fine structure of electron states in symmetric and asymmetric zinc-blende-type quantum wells with the (110) crystallographic orientation. By combining the symmetry analysis, sp{sup 3}d{sup 5}s* tight-binding method, and envelope-function approach we obtain quantitative description of in-plane wave vector, well width and applied electric field dependencies of the zero-magnetic-field spin splitting of electron subbands and extract spin-orbit-coupling parameters.

8 MeV electron beam induced modifications in the thermal, structural and electrical properties of nanophase CeO2 for potential electronics applications

NASA Astrophysics Data System (ADS)

Babitha, K. K.; Sreedevi, A.; Priyanka, K. P.; Ganesh, S.; Varghese, Thomas

2018-06-01

The effect of 8 MeV electron beam irradiation on the thermal, structural and electrical properties of CeO2 nanoparticles synthesized by chemical precipitation route was investigated. The dose dependent effect of electron irradiation was studied using various characterization techniques such as, thermogravimetric and differential thermal analyses, X-ray diffraction, Fourier transformed infrared spectroscopy and impedance spectroscopy. Systematic investigation based on the results of structural studies confirm that electron beam irradiation induces defects and particle size variation on CeO2 nanoparticles, which in turn results improvements in AC conductivity, dielectric constant and loss tangent. Structural modifications and high value of dielectric constant for CeO2 nanoparticles due to electron beam irradiation make it as a promising material for the fabrication of gate dielectric in metal oxide semiconductor devices.

Ab initio structure determination of nanocrystals of organic pharmaceutical compounds by electron diffraction at room temperature using a Timepix quantum area direct electron detector

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