Simultaneous small- and wide-angle scattering at high X-ray energies.

PubMed

Daniels, J E; Pontoni, D; Hoo, Rui Ping; Honkimäki, V

2010-07-01

Combined small- and wide-angle X-ray scattering (SAXS/WAXS) is a powerful technique for the study of materials at length scales ranging from atomic/molecular sizes (a few angstroms) to the mesoscopic regime ( approximately 1 nm to approximately 1 microm). A set-up to apply this technique at high X-ray energies (E > 50 keV) has been developed. Hard X-rays permit the execution of at least three classes of investigations that are significantly more difficult to perform at standard X-ray energies (8-20 keV): (i) in situ strain analysis revealing anisotropic strain behaviour both at the atomic (WAXS) as well as at the mesoscopic (SAXS) length scales, (ii) acquisition of WAXS patterns to very large q (>20 A(-1)) thus allowing atomic pair distribution function analysis (SAXS/PDF) of micro- and nano-structured materials, and (iii) utilization of complex sample environments involving thick X-ray windows and/or samples that can be penetrated only by high-energy X-rays. Using the reported set-up a time resolution of approximately two seconds was demonstrated. It is planned to further improve this time resolution in the near future.

Near-atomic resolution visualization of human transcription promoter opening

PubMed Central

He, Yuan; Yan, Chunli; Fang, Jie; Inouye, Carla; Tjian, Robert; Ivanov, Ivaylo; Nogales, Eva

2016-01-01

In eukaryotic transcription initiation, a large multi-subunit pre-initiation complex (PIC) that assembles at the core promoter is required for the opening of the duplex DNA and identification of the start site for transcription by RNA polymerase II. Here we use cryo-electron microscropy (cryo-EM) to determine near-atomic resolution structures of the human PIC in a closed state (engaged with duplex DNA), an open state (engaged with a transcription bubble), and an initially transcribing complex (containing six base pairs of DNA–RNA hybrid). Our studies provide structures for previously uncharacterized components of the PIC, such as TFIIE and TFIIH, and segments of TFIIA, TFIIB and TFIIF. Comparison of the different structures reveals the sequential conformational changes that accompany the transition from each state to the next throughout the transcription initiation process. This analysis illustrates the key role of TFIIB in transcription bubble stabilization and provides strong structural support for a translocase activity of XPB. PMID:27193682

Charge-density analysis of a protein structure at subatomic resolution: the human aldose reductase case.

PubMed

Guillot, Benoît; Jelsch, Christian; Podjarny, Alberto; Lecomte, Claude

2008-05-01

The valence electron density of the protein human aldose reductase was analyzed at 0.66 angstroms resolution. The methodological developments in the software MoPro to adapt standard charge-density techniques from small molecules to macromolecular structures are described. The deformation electron density visible in initial residual Fourier difference maps was significantly enhanced after high-order refinement. The protein structure was refined after transfer of the experimental library multipolar atom model (ELMAM). The effects on the crystallographic statistics, on the atomic thermal displacement parameters and on the structure stereochemistry are analyzed. Constrained refinements of the transferred valence populations Pval and multipoles Plm were performed against the X-ray diffraction data on a selected substructure of the protein with low thermal motion. The resulting charge densities are of good quality, especially for chemical groups with many copies present in the polypeptide chain. To check the effect of the starting point on the result of the constrained multipolar refinement, the same charge-density refinement strategy was applied but using an initial neutral spherical atom model, i.e. without transfer from the ELMAM library. The best starting point for a protein multipolar refinement is the structure with the electron density transferred from the database. This can be assessed by the crystallographic statistical indices, including Rfree, and the quality of the static deformation electron-density maps, notably on the oxygen electron lone pairs. The analysis of the main-chain bond lengths suggests that stereochemical dictionaries would benefit from a revision based on recently determined unrestrained atomic resolution protein structures.

Dictionary learning based noisy image super-resolution via distance penalty weight model

PubMed Central

Han, Yulan; Zhao, Yongping; Wang, Qisong

2017-01-01

In this study, we address the problem of noisy image super-resolution. Noisy low resolution (LR) image is always obtained in applications, while most of the existing algorithms assume that the LR image is noise-free. As to this situation, we present an algorithm for noisy image super-resolution which can achieve simultaneously image super-resolution and denoising. And in the training stage of our method, LR example images are noise-free. For different input LR images, even if the noise variance varies, the dictionary pair does not need to be retrained. For the input LR image patch, the corresponding high resolution (HR) image patch is reconstructed through weighted average of similar HR example patches. To reduce computational cost, we use the atoms of learned sparse dictionary as the examples instead of original example patches. We proposed a distance penalty model for calculating the weight, which can complete a second selection on similar atoms at the same time. Moreover, LR example patches removed mean pixel value are also used to learn dictionary rather than just their gradient features. Based on this, we can reconstruct initial estimated HR image and denoised LR image. Combined with iterative back projection, the two reconstructed images are applied to obtain final estimated HR image. We validate our algorithm on natural images and compared with the previously reported algorithms. Experimental results show that our proposed method performs better noise robustness. PMID:28759633

Mn doped InSb studied at the atomic scale by cross-sectional scanning tunneling microscopy

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

Mauger, S. J. C.; Bocquel, J.; Koenraad, P. M., E-mail: p.m.koenraad@tue.nl

2015-11-30

We present an atomically resolved study of metal-organic vapor epitaxy grown Mn doped InSb. Both topographic and spectroscopic measurements have been performed by cross-sectional scanning tunneling microscopy (STM). The measurements on the Mn doped InSb samples show a perfect crystal structure without any precipitates and reveal that Mn acts as a shallow acceptor. The Mn concentration of the order of ∼10{sup 20 }cm{sup −3} obtained from the cross-sectional STM data compare well with the intended doping concentration. While the pair correlation function of the Mn atoms showed that their local distribution is uncorrelated beyond the STM resolution for observing individual dopants,more » disorder in the Mn ion location giving rise to percolation pathways is clearly noted. The amount of clustering that we see is thus as expected for a fully randomly disordered distribution of the Mn atoms and no enhanced clustering or second phase material was observed.« less

Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies.

PubMed

Petkov, Valeri; Prasai, Binay; Shan, Shiyao; Ren, Yang; Wu, Jinfang; Cronk, Hannah; Luo, Jin; Zhong, Chuan-Jian

2016-05-19

Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum.

Two-photon Direct Frequency Comb Spectroscopy of Alkali Atoms

NASA Astrophysics Data System (ADS)

Nguyen, Khoa; Pradhananga, Trinity; Palm, Christopher; Stalnaker, Jason; Kimball, Derek Jackson

2012-06-01

We are using direct frequency comb spectroscopy to study transition frequencies and excited state hyperfine structure in potassium and rubidium using 2-photon transitions excited directly with the frequency-doubled output of a erbium fiber optical frequency comb. The frequency comb output is directed in two counterpropagating directions through a vapor cell containing the atomic vapor of interest. A pair of optical filters is used to select teeth of the comb in order to identify the transition wavelengths. A photomultiplier tube (PMT) measures fluorescence from a decay channel wavelength selected with another optical filter. Using different combinations of filters enables a wide range of transitions to be investigated. By scanning the repetition rate, a Doppler-free spectrum can be obtained enabling kHz-resolution spectral measurements. The thermal motion of the atoms in the vapor cell actually eliminates the need to fine-tune the offset frequency and repetition rate, alleviating a somewhat challenging requirement for spectroscopy of cold atoms. Our investigations are laying the groundwork for a long-term research program to use direct frequency comb spectroscopy to understand the complex spectra of rare-earth atoms.

Direct Frequency Comb Spectroscopy of Alkali Atoms

NASA Astrophysics Data System (ADS)

Pradhananga, Trinity; Palm, Christopher; Nguyen, Khoa; Guttikonda, Srikanth; Kimball, Derek Jackson

2011-11-01

We are using direct frequency comb spectroscopy to study transition frequencies and excited state hyperfine structure in potassium and rubidium using 2-photon transitions excited directly with the frequency-doubled output of a erbium fiber optical frequency comb. The frequency comb output is directed in two counterpropagating directions through a vapor cell containing the atomic vapor of interest. A pair of optical filters is used to select teeth of the comb in order to identify the transition wavelengths. A photomultiplier tube (PMT) measures fluorescence from a decay channel wavelength selected with another optical filter. Using different combinations of filters enables a wide range of transitions to be investigated. By scanning the repetition rate, a Doppler-free spectrum can be obtained enabling kHz-resolution spectral measurements. The thermal motion of the atoms in the vapor cell actually eliminates the need to fine-tune the offset frequency and repetition rate, alleviating a somewhat challenging requirement for spectroscopy of cold atoms. Our investigations are laying the groundwork for a long-term research program to use direct frequency comb spectroscopy to understand the complex spectra of rare-earth atoms.

In situ synthesis of twelve dialkyltartrate-boric acid complexes and two polyols-boric acid complexes and their applications as chiral ion-pair selectors in nonaqueous capillary electrophoresis.

PubMed

Wang, Li-Juan; Yang, Juan; Yang, Geng-Liang; Chen, Xing-Guo

2012-07-27

In this paper, twelve dialkyltartrate-boric acid complexes and two polyols-boric acid complexes were in situ synthesized by the reaction of different dialkyltartrates or polyols with boric acid in methanol containing triethylamine. All of the twelve dialkyltartrate-boric acid complexes were found to have relatively good chiral separation performance in nonaqueous capillary electrophoresis (NACE). Their chiral recognition effects in terms of both enantioselectivity (α) and resolution (R(s)) were similar when the number of carbon atoms was below six in the alkyl group of alcohol moiety. The dialkyltartrates containing alkyl groups of different structures but the same number of carbon atoms, i.e. one of straight chain and one of branched chain, also provided similar chiral recognition effects. Furthermore, it was demonstrated for the first time that two methanol insoluble polyols, D-mannitol and D-sorbitol, could react with boric acid to prepare chiral ion-pair selectors using methanol as the solvent medium. Copyright © 2012 Elsevier B.V. All rights reserved.

Resonance of an unshared electron pair between two atoms connected by a single bond

PubMed Central

Pauling, Linus

1983-01-01

The reported structure of the dimer of a compound of bicovalent tin indicates that the tin-tin bond is of a new type. It can be described as involving resonance between two structures in which there is transfer of an electron pair from one tin atom to the other. The tin atoms are connected by a single covalent bond (each also forms two covalent bonds with carbon atoms), and an unshared electron pair resonates between the fourth sp3 orbitals of the two atoms. Similar structures probably occur in digermene and distannene. PMID:16593329

Stereoselective virtual screening of the ZINC database using atom pair 3D-fingerprints.

PubMed

Awale, Mahendra; Jin, Xian; Reymond, Jean-Louis

2015-01-01

Tools to explore large compound databases in search for analogs of query molecules provide a strategically important support in drug discovery to help identify available analogs of any given reference or hit compound by ligand based virtual screening (LBVS). We recently showed that large databases can be formatted for very fast searching with various 2D-fingerprints using the city-block distance as similarity measure, in particular a 2D-atom pair fingerprint (APfp) and the related category extended atom pair fingerprint (Xfp) which efficiently encode molecular shape and pharmacophores, but do not perceive stereochemistry. Here we investigated related 3D-atom pair fingerprints to enable rapid stereoselective searches in the ZINC database (23.2 million 3D structures). Molecular fingerprints counting atom pairs at increasing through-space distance intervals were designed using either all atoms (16-bit 3DAPfp) or different atom categories (80-bit 3DXfp). These 3D-fingerprints retrieved molecular shape and pharmacophore analogs (defined by OpenEye ROCS scoring functions) of 110,000 compounds from the Cambridge Structural Database with equal or better accuracy than the 2D-fingerprints APfp and Xfp, and showed comparable performance in recovering actives from decoys in the DUD database. LBVS by 3DXfp or 3DAPfp similarity was stereoselective and gave very different analogs when starting from different diastereomers of the same chiral drug. Results were also different from LBVS with the parent 2D-fingerprints Xfp or APfp. 3D- and 2D-fingerprints also gave very different results in LBVS of folded molecules where through-space distances between atom pairs are much shorter than topological distances. 3DAPfp and 3DXfp are suitable for stereoselective searches for shape and pharmacophore analogs of query molecules in large databases. Web-browsers for searching ZINC by 3DAPfp and 3DXfp similarity are accessible at www.gdb.unibe.ch and should provide useful assistance to drug discovery projects. Graphical abstractAtom pair fingerprints based on through-space distances (3DAPfp) provide better shape encoding than atom pair fingerprints based on topological distances (APfp) as measured by the recovery of ROCS shape analogs by fp similarity.

An Electron Density Source-Function Study of DNA Base Pairs in Their Neutral and Ionized Ground States†.

PubMed

Gatti, Carlo; Macetti, Giovanni; Boyd, Russell J; Matta, Chérif F

2018-07-05

The source function (SF) decomposes the electron density at any point into contributions from all other points in the molecule, complex, or crystal. The SF "illuminates" those regions in a molecule that most contribute to the electron density at a point of reference. When this point of reference is the bond critical point (BCP), a commonly used surrogate of chemical bonding, then the SF analysis at an atomic resolution within the framework of Bader's Quantum Theory of Atoms in Molecules returns the contribution of each atom in the system to the electron density at that BCP. The SF is used to locate the important regions that control the hydrogen bonds in both Watson-Crick (WC) DNA dimers (adenine:thymine (AT) and guanine:cytosine (GC)) which are studied in their neutral and their singly ionized (radical cationic and anionic) ground states. The atomic contributions to the electron density at the BCPs of the hydrogen bonds in the two dimers are found to be delocalized to various extents. Surprisingly, gaining or loosing an electron has similar net effects on some hydrogen bonds concealing subtle compensations traced to atomic sources contributions. Coarser levels of resolutions (groups, rings, and/or monomers-in-dimers) reveal that distant groups and rings often have non-negligible effects especially on the weaker hydrogen bonds such as the third weak CH⋅⋅⋅O hydrogen bond in AT. Interestingly, neither the purine nor the pyrimidine in the neutral or ionized forms dominate any given hydrogen bond despite that the former has more atoms that can act as source or sink for the density at its BCP. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

Ex situ investigation of the step bunching on crystal surfaces by atomic force microscopy

NASA Astrophysics Data System (ADS)

Krasinski, Mariusz J.

1997-07-01

We are describing ex situ observation of step bunching on the surfaces of solution grown potassium dihydrogen phosphate (KDP) and sodium chlorate monocrystals. The measurements have been done with the use of atomic force microscope. The use of this equipment allowed us to see directly the structure of macrosteps. Observation confirmed the existence of step pinning which is one of the proposed mechanisms of step bunching. Despite the very high resolution of AFM it was not possible to determine the nature of pinning point. The monatomic steps on KDP and sodium chlorate crystal surfaces are mainly one unit cell high what seems to be the result of the steps pairing. The origin of observed step pattern is discussed in frames of existing theories.

Blind prediction of noncanonical RNA structure at atomic accuracy.

PubMed

Watkins, Andrew M; Geniesse, Caleb; Kladwang, Wipapat; Zakrevsky, Paul; Jaeger, Luc; Das, Rhiju

2018-05-01

Prediction of RNA structure from nucleotide sequence remains an unsolved grand challenge of biochemistry and requires distinct concepts from protein structure prediction. Despite extensive algorithmic development in recent years, modeling of noncanonical base pairs of new RNA structural motifs has not been achieved in blind challenges. We report a stepwise Monte Carlo (SWM) method with a unique add-and-delete move set that enables predictions of noncanonical base pairs of complex RNA structures. A benchmark of 82 diverse motifs establishes the method's general ability to recover noncanonical pairs ab initio, including multistrand motifs that have been refractory to prior approaches. In a blind challenge, SWM models predicted nucleotide-resolution chemical mapping and compensatory mutagenesis experiments for three in vitro selected tetraloop/receptors with previously unsolved structures (C7.2, C7.10, and R1). As a final test, SWM blindly and correctly predicted all noncanonical pairs of a Zika virus double pseudoknot during a recent community-wide RNA-Puzzle. Stepwise structure formation, as encoded in the SWM method, enables modeling of noncanonical RNA structure in a variety of previously intractable problems.

Learning surface molecular structures via machine vision

NASA Astrophysics Data System (ADS)

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-01

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (`read out') all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds and thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. The method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

DOE PAGES

Zhang, Yan; Inouye, Hideyo; Crowley, Michael; ...

2016-10-14

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. As a result, this algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

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

Zhang, Yan; Inouye, Hideyo; Crowley, Michael

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. This algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Diffraction pattern simulation of cellulose fibrils using distributed and quantized pair distances

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

Zhang, Yan; Inouye, Hideyo; Crowley, Michael

Intensity simulation of X-ray scattering from large twisted cellulose molecular fibrils is important in understanding the impact of chemical or physical treatments on structural properties such as twisting or coiling. This paper describes a highly efficient method for the simulation of X-ray diffraction patterns from complex fibrils using atom-type-specific pair-distance quantization. Pair distances are sorted into arrays which are labelled by atom type. Histograms of pair distances in each array are computed and binned and the resulting population distributions are used to represent the whole pair-distance data set. These quantized pair-distance arrays are used with a modified and vectorized Debyemore » formula to simulate diffraction patterns. This approach utilizes fewer pair distances in each iteration, and atomic scattering factors are moved outside the iteration since the arrays are labelled by atom type. As a result, this algorithm significantly reduces the computation time while maintaining the accuracy of diffraction pattern simulation, making possible the simulation of diffraction patterns from large twisted fibrils in a relatively short period of time, as is required for model testing and refinement.« less

Atom-Pair Kinetics with Strong Electric-Dipole Interactions.

PubMed

Thaicharoen, N; Gonçalves, L F; Raithel, G

2016-05-27

Rydberg-atom ensembles are switched from a weakly to a strongly interacting regime via adiabatic transformation of the atoms from an approximately nonpolar into a highly dipolar quantum state. The resultant electric dipole-dipole forces are probed using a device akin to a field ion microscope. Ion imaging and pair-correlation analysis reveal the kinetics of the interacting atoms. Dumbbell-shaped pair-correlation images demonstrate the anisotropy of the binary dipolar force. The dipolar C_{3} coefficient, derived from the time dependence of the images, agrees with the value calculated from the permanent electric-dipole moment of the atoms. The results indicate many-body dynamics akin to disorder-induced heating in strongly coupled particle systems.

Effect of Destined High-Pressure Torsion on the Structure and Mechanical Properties of Rare Earth-Based Metallic Glasses

NASA Astrophysics Data System (ADS)

Zhao, W.; Cheng, H.; Jiang, X.; Wu, M. L.; Li, G.

2018-03-01

Changes in the atomic structure and mechanical properties of rare earth-based metallic glasses caused by destined high-pressure torsion (HPT) were studied by X-ray diffraction synchrotron radiation and nanoindentation. Results showed that destined HPT improved nanohardness and wear resistance, which indicated the significant contributions of this technique. The diffraction patterns showed that the contents of pairs between solvent and solute atoms with a large negative mixing enthalpy increased, whereas those of pairs between solvent atoms and between solute atoms decreased after destined HPT. Thus, the process was improved by increasing the proportion of high-intensity pairs between solvent and solute atoms.

Anharmonic Normal Mode Analysis of Elastic Network Model Improves the Modeling of Atomic Fluctuations in Protein Crystal Structures

PubMed Central

Zheng, Wenjun

2010-01-01

Abstract Protein conformational dynamics, despite its significant anharmonicity, has been widely explored by normal mode analysis (NMA) based on atomic or coarse-grained potential functions. To account for the anharmonic aspects of protein dynamics, this study proposes, and has performed, an anharmonic NMA (ANMA) based on the Cα-only elastic network models, which assume elastic interactions between pairs of residues whose Cα atoms or heavy atoms are within a cutoff distance. The key step of ANMA is to sample an anharmonic potential function along the directions of eigenvectors of the lowest normal modes to determine the mean-squared fluctuations along these directions. ANMA was evaluated based on the modeling of anisotropic displacement parameters (ADPs) from a list of 83 high-resolution protein crystal structures. Significant improvement was found in the modeling of ADPs by ANMA compared with standard NMA. Further improvement in the modeling of ADPs is attained if the interactions between a protein and its crystalline environment are taken into account. In addition, this study has determined the optimal cutoff distances for ADP modeling based on elastic network models, and these agree well with the peaks of the statistical distributions of distances between Cα atoms or heavy atoms derived from a large set of protein crystal structures. PMID:20550915

Spatial, Temporal and Spectral Satellite Image Fusion via Sparse Representation

NASA Astrophysics Data System (ADS)

Song, Huihui

Remote sensing provides good measurements for monitoring and further analyzing the climate change, dynamics of ecosystem, and human activities in global or regional scales. Over the past two decades, the number of launched satellite sensors has been increasing with the development of aerospace technologies and the growing requirements on remote sensing data in a vast amount of application fields. However, a key technological challenge confronting these sensors is that they tradeoff between spatial resolution and other properties, including temporal resolution, spectral resolution, swath width, etc., due to the limitations of hardware technology and budget constraints. To increase the spatial resolution of data with other good properties, one possible cost-effective solution is to explore data integration methods that can fuse multi-resolution data from multiple sensors, thereby enhancing the application capabilities of available remote sensing data. In this thesis, we propose to fuse the spatial resolution with temporal resolution and spectral resolution, respectively, based on sparse representation theory. Taking the study case of Landsat ETM+ (with spatial resolution of 30m and temporal resolution of 16 days) and MODIS (with spatial resolution of 250m ~ 1km and daily temporal resolution) reflectance, we propose two spatial-temporal fusion methods to combine the fine spatial information of Landsat image and the daily temporal resolution of MODIS image. Motivated by that the images from these two sensors are comparable on corresponding bands, we propose to link their spatial information on available Landsat- MODIS image pair (captured on prior date) and then predict the Landsat image from the MODIS counterpart on prediction date. To well-learn the spatial details from the prior images, we use a redundant dictionary to extract the basic representation atoms for both Landsat and MODIS images based on sparse representation. Under the scenario of two prior Landsat-MODIS image pairs, we build the corresponding relationship between the difference images of MODIS and ETM+ by training a low- and high-resolution dictionary pair from the given prior image pairs. In the second scenario, i.e., only one Landsat- MODIS image pair being available, we directly correlate MODIS and ETM+ data through an image degradation model. Then, the fusion stage is achieved by super-resolving the MODIS image combining the high-pass modulation in a two-layer fusion framework. Remarkably, the proposed spatial-temporal fusion methods form a unified framework for blending remote sensing images with phenology change or land-cover-type change. Based on the proposed spatial-temporal fusion models, we propose to monitor the land use/land cover changes in Shenzhen, China. As a fast-growing city, Shenzhen faces the problem of detecting the rapid changes for both rational city planning and sustainable development. However, the cloudy and rainy weather in region Shenzhen located makes the capturing circle of high-quality satellite images longer than their normal revisit periods. Spatial-temporal fusion methods are capable to tackle this problem by improving the spatial resolution of images with coarse spatial resolution but frequent temporal coverage, thereby making the detection of rapid changes possible. On two Landsat-MODIS datasets with annual and monthly changes, respectively, we apply the proposed spatial-temporal fusion methods to the task of multiple change detection. Afterward, we propose a novel spatial and spectral fusion method for satellite multispectral and hyperspectral (or high-spectral) images based on dictionary-pair learning and sparse non-negative matrix factorization. By combining the spectral information from hyperspectral image, which is characterized by low spatial resolution but high spectral resolution and abbreviated as LSHS, and the spatial information from multispectral image, which is featured by high spatial resolution but low spectral resolution and abbreviated as HSLS, this method aims to generate the fused data with both high spatial and high spectral resolutions. Motivated by the observation that each hyperspectral pixel can be represented by a linear combination of a few endmembers, this method first extracts the spectral bases of LSHS and HSLS images by making full use of the rich spectral information in LSHS data. The spectral bases of these two categories data then formulate a dictionary-pair due to their correspondence in representing each pixel spectra of LSHS data and HSLS data, respectively. Subsequently, the LSHS image is spatially unmixed by representing the HSLS image with respect to the corresponding learned dictionary to derive its representation coefficients. Combining the spectral bases of LSHS data and the representation coefficients of HSLS data, we finally derive the fused data characterized by the spectral resolution of LSHS data and the spatial resolution of HSLS data.

Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry

DOE PAGES

Mooers, Blaine H. M.

2016-03-24

Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 Å) and the computer program SIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by the lMiller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides,more » 580 non-H RNA atoms) without TPS. Lastly, more sensitive methods are needed for the automated detection of partial TPS.« less

Direct-methods structure determination of a trypanosome RNA-editing substrate fragment with translational pseudosymmetry

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

Mooers, Blaine H. M.

Using direct methods starting from random phases, the crystal structure of a 32-base-pair RNA (675 non-H RNA atoms in the asymmetric unit) was determined using only the native diffraction data (resolution limit 1.05 Å) and the computer program SIR2014. The almost three helical turns of the RNA in the asymmetric unit introduced partial or imperfect translational pseudosymmetry (TPS) that modulated the intensities when averaged by the lMiller indices but still escaped automated detection. Almost six times as many random phase sets had to be tested on average to reach a correct structure compared with a similar-sized RNA hairpin (27 nucleotides,more » 580 non-H RNA atoms) without TPS. Lastly, more sensitive methods are needed for the automated detection of partial TPS.« less

Light-induced picosecond rotational disordering of the inorganic sublattice in hybrid perovskites.

PubMed

Wu, Xiaoxi; Tan, Liang Z; Shen, Xiaozhe; Hu, Te; Miyata, Kiyoshi; Trinh, M Tuan; Li, Renkai; Coffee, Ryan; Liu, Shi; Egger, David A; Makasyuk, Igor; Zheng, Qiang; Fry, Alan; Robinson, Joseph S; Smith, Matthew D; Guzelturk, Burak; Karunadasa, Hemamala I; Wang, Xijie; Zhu, Xiaoyang; Kronik, Leeor; Rappe, Andrew M; Lindenberg, Aaron M

2017-07-01

Femtosecond resolution electron scattering techniques are applied to resolve the first atomic-scale steps following absorption of a photon in the prototypical hybrid perovskite methylammonium lead iodide. Following above-gap photoexcitation, we directly resolve the transfer of energy from hot carriers to the lattice by recording changes in the mean square atomic displacements on 10-ps time scales. Measurements of the time-dependent pair distribution function show an unexpected broadening of the iodine-iodine correlation function while preserving the Pb-I distance. This indicates the formation of a rotationally disordered halide octahedral structure developing on picosecond time scales. This work shows the important role of light-induced structural deformations within the inorganic sublattice in elucidating the unique optoelectronic functionality exhibited by hybrid perovskites and provides new understanding of hot carrier-lattice interactions, which fundamentally determine solar cell efficiencies.

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

Wu, Xiaoxi; Tan, Liang Z.; Shen, Xiaozhe

Femtosecond resolution electron scattering techniques are applied to resolve the first atomic-scale steps following absorption of a photon in the prototypical hybrid perovskite methylammonium lead iodide. Following above-gap photoexcitation, we directly resolve the transfer of energy from hot carriers to the lattice by recording changes in the mean square atomic displacements on 10-ps time scales. Measurements of the time-dependent pair distribution function show an unexpected broadening of the iodine-iodine correlation function while preserving the Pb-I distance. This indicates the formation of a rotationally disordered halide octahedral structure developing on picosecond time scales. Here, this work shows the important role ofmore » light-induced structural deformations within the inorganic sublattice in elucidating the unique optoelectronic functionality exhibited by hybrid perovskites and provides new understanding of hot carrier-lattice interactions, which fundamentally determine solar cell efficiencies.« less

Direct pair production in heavy-ion--atom collisions

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

Anholt, R.; Jakubassa-Amundsen, D.H.; Amundsen, P.A.

1983-02-01

Direct pair production in approx.5-MeV/amu heavy-ion--atom collisions with uranium target atoms is calculated with the plane-wave Born approximation and the semiclassical approximation. Briggs's approximation is used to obtain the electron and positron wave functions. Since pair production involves high momentum transfer q from the moving projectile to the vacuum, use is made of a high-q approximation to greatly simplify the numerical computations. Coulomb deflection of the projectile, the effect of finite nuclear size on the elec- tronic wave functions, and the energy loss by the projectile exciting the pair are all taken into account in these calculations.

Local structure of NiPd solid solution alloys and its response to ion irradiation

DOE PAGES

Zhang, Fuxiang; Ullah, Mohammad Wali; Zhao, Shijun; ...

2018-04-27

The local structure of Ni$-$Pd solid solution alloys with compositions of Ni 80Pd 20 and Ni 50Pd 50 was investigated with anomalous X-ray diffraction, X-ray absorption and theoretical calculation/simulation. The fcc lattice is distorted for both alloys, and the Pd$-$Pd atomic pair distance is +4.4% and +1.4% larger than ideal values in Ni 80Pd 20 and Ni 50Pd 50 alloys, respectively. The corresponding atomic pair distance of Ni$-$Ni is -1.8% and -3.0% less than the ideal values. Different short-range orders in the alloys were quantitatively identified at the atomic level. In Ni 80Pd 20, Pd atoms are likely to formmore » Pd$-$Pd pairs, while Pd atoms are connected with Pd atoms in the second shell in the equiatomic solid solution alloy. Upon ion irradiation, little change of interatomic distance, but modification of chemical short-range order was observed. The number of Pd$-$Pd pairs decreases to the lowest value at 0.1 dpa, and further irradiation make it increase.« less

Local structure of NiPd solid solution alloys and its response to ion irradiation

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

Zhang, Fuxiang; Ullah, Mohammad Wali; Zhao, Shijun

The local structure of Ni$-$Pd solid solution alloys with compositions of Ni 80Pd 20 and Ni 50Pd 50 was investigated with anomalous X-ray diffraction, X-ray absorption and theoretical calculation/simulation. The fcc lattice is distorted for both alloys, and the Pd$-$Pd atomic pair distance is +4.4% and +1.4% larger than ideal values in Ni 80Pd 20 and Ni 50Pd 50 alloys, respectively. The corresponding atomic pair distance of Ni$-$Ni is -1.8% and -3.0% less than the ideal values. Different short-range orders in the alloys were quantitatively identified at the atomic level. In Ni 80Pd 20, Pd atoms are likely to formmore » Pd$-$Pd pairs, while Pd atoms are connected with Pd atoms in the second shell in the equiatomic solid solution alloy. Upon ion irradiation, little change of interatomic distance, but modification of chemical short-range order was observed. The number of Pd$-$Pd pairs decreases to the lowest value at 0.1 dpa, and further irradiation make it increase.« less

Learning surface molecular structures via machine vision

DOE PAGES

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

2017-08-10

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

Learning surface molecular structures via machine vision

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

Ziatdinov, Maxim; Maksov, Artem; Kalinin, Sergei V.

Recent advances in high resolution scanning transmission electron and scanning probe microscopies have allowed researchers to perform measurements of materials structural parameters and functional properties in real space with a picometre precision. In many technologically relevant atomic and/or molecular systems, however, the information of interest is distributed spatially in a non-uniform manner and may have a complex multi-dimensional nature. One of the critical issues, therefore, lies in being able to accurately identify (‘read out’) all the individual building blocks in different atomic/molecular architectures, as well as more complex patterns that these blocks may form, on a scale of hundreds andmore » thousands of individual atomic/molecular units. Here we employ machine vision to read and recognize complex molecular assemblies on surfaces. Specifically, we combine Markov random field model and convolutional neural networks to classify structural and rotational states of all individual building blocks in molecular assembly on the metallic surface visualized in high-resolution scanning tunneling microscopy measurements. We show how the obtained full decoding of the system allows us to directly construct a pair density function—a centerpiece in analysis of disorder-property relationship paradigm—as well as to analyze spatial correlations between multiple order parameters at the nanoscale, and elucidate reaction pathway involving molecular conformation changes. Here, the method represents a significant shift in our way of analyzing atomic and/or molecular resolved microscopic images and can be applied to variety of other microscopic measurements of structural, electronic, and magnetic orders in different condensed matter systems.« less

The Crystal Structure of Non-Modified and Bipyridine-Modified PNA Duplexes

PubMed Central

Yeh, Joanne I.; Pohl, Ehmke; Truan, Daphne; He, Wei; Sheldrick, George M.; Du, Shoucheng; Achim, Catalina

2011-01-01

Peptide nucleic acid (PNA) is a synthetic analogue of DNA that commonly has an N-aminoethlyl-glycine backbone. The crystal structure of two PNA duplexes, one containing eight standard nucleobase pairs (GGCATCGG)2 (pdb: 3MBS), and the other containing the same nucleobase pairs and a central pair of bipyridine ligands (pdb: 3MBU), has been solved with a resolution of 1.2 Å and 1.05 Å, respectively. The non-modified PNA duplex adopts a P-type helical structure s i m i l a r t o that of previously characterized PNAs. The atomic-level resolution of the structures allowed us to observe for the first time specific modes of interaction between the terminal lysines of the PNA and the backbone and nucleobases situated in the vicinity of the lysines, which are considered an important factor in the induction of a preferred handedness in PNA duplexes. These results support the notion that while PNA typically adopts a P-type helical structure, its flexibility is relatively high. For example, the base pair rise in the bipyridine-containing PNA is the largest measured to date in a PNA homoduplex. The two bipyridines are bulged out of the duplex and are aligned parallel to the minor groove of the PNA. In the case of the bipyridine-containing PNA, two bipyridines from adjacent PNA duplexes form a π-stacked pair that relates the duplexes within the crystal. The bulging out of the bipyridines causes bending of the PNA duplex, which is in contrast to the structure previously reported for biphenyl-modified DNA duplexes in solution, where the biphenyls are π-stacking with adjacent nucleobase pairs and adopt an intrahelical geometry [Johar et al., Chem. Eur. J., 2008, 14, 2080]. This difference shows that relatively small perturbations can significantly impact the relative position of nucleobase analogues in nucleic acid duplexes. PMID:20859960

Resolution Quality and Atom Positions in Sub-?ngstr?m Electron Microscopy

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

O'Keefe, Michael A.; Allard Jr, Lawrence Frederick; Blom, Douglas Allen

2005-01-01

John Cowley pioneered use of transmission electron microscopy (TEM) for high-resolution imaging and helped spur improvements in resolution that enabled researchers to pinpoint the positions of all but the lightest atoms within a crystal structure. Sub-{angstrom} capabilities allow imaging of even the lightest atoms. Initially achieved with software aberration correction (focal-series reconstruction of the specimen exit-surface wave), sub-{angstrom} imaging will become commonplace for next-generation electron microscopes with hardware-corrected lenses and monochromated electron beams. Currently, advanced HR-TEMs can image columns of light atoms (carbon, oxygen, nitrogen) in complex structures, including the lithium atoms present in battery materials. The ability to determinemore » whether an image peak represents one single atom (or atom column) instead of several depends on the resolution of the HR-(S)TEM. Rayleigh's resolution criterion, an accepted standard in optics, was derived as a means for judging when two image intensity peaks from two sources of light (stars) are distinguishable from a single source. Atom spacings closer than the Rayleigh limit have been resolved in HR-TEM, suggesting that it may be useful to consider other limits, such as the Sparrow resolution criterion. From the viewpoint of the materials scientist, it is important to be able to use the image to determine whether an image feature represents one or more atoms (resolution), and where the atoms (or atom columns) are positioned relative to one another (resolution quality). When atoms and the corresponding image peaks are separated by more than the Rayleigh limit of the HR-(S)TEM, it is possible to adjust imaging parameters so that relative peak positions in the image correspond to relative atom positions in the specimen. When atoms are closer than the Rayleigh limit, we must find the relationship of the peak position to the atom position by peak fitting or, if we have a suitable model, by image simulation.« less

On the temperature dependence of H-U{sub iso} in the riding hydrogen model

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

Lübben, Jens; Volkmann, Christian; Grabowsky, Simon

The temperature dependence of hydrogen U{sub iso} and parent U{sub eq} in the riding hydrogen model is investigated by neutron diffraction, aspherical-atom refinements and QM/MM and MO/MO cluster calculations. Fixed values of 1.2 or 1.5 appear to be underestimated, especially at temperatures below 100 K. The temperature dependence of H-U{sub iso} in N-acetyl-l-4-hydroxyproline monohydrate is investigated. Imposing a constant temperature-independent multiplier of 1.2 or 1.5 for the riding hydrogen model is found to be inaccurate, and severely underestimates H-U{sub iso} below 100 K. Neutron diffraction data at temperatures of 9, 150, 200 and 250 K provide benchmark results for thismore » study. X-ray diffraction data to high resolution, collected at temperatures of 9, 30, 50, 75, 100, 150, 200 and 250 K (synchrotron and home source), reproduce neutron results only when evaluated by aspherical-atom refinement models, since these take into account bonding and lone-pair electron density; both invariom and Hirshfeld-atom refinement models enable a more precise determination of the magnitude of H-atom displacements than independent-atom model refinements. Experimental efforts are complemented by computing displacement parameters following the TLS+ONIOM approach. A satisfactory agreement between all approaches is found.« less

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix.

PubMed

Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy; He, Jing

2017-01-01

Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4-7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map-model pairs.

Comparing an Atomic Model or Structure to a Corresponding Cryo-electron Microscopy Image at the Central Axis of a Helix

PubMed Central

Zeil, Stephanie; Kovacs, Julio; Wriggers, Willy

2017-01-01

Abstract Three-dimensional density maps of biological specimens from cryo-electron microscopy (cryo-EM) can be interpreted in the form of atomic models that are modeled into the density, or they can be compared to known atomic structures. When the central axis of a helix is detectable in a cryo-EM density map, it is possible to quantify the agreement between this central axis and a central axis calculated from the atomic model or structure. We propose a novel arc-length association method to compare the two axes reliably. This method was applied to 79 helices in simulated density maps and six case studies using cryo-EM maps at 6.4–7.7 Å resolution. The arc-length association method is then compared to three existing measures that evaluate the separation of two helical axes: a two-way distance between point sets, the length difference between two axes, and the individual amino acid detection accuracy. The results show that our proposed method sensitively distinguishes lateral and longitudinal discrepancies between the two axes, which makes the method particularly suitable for the systematic investigation of cryo-EM map–model pairs. PMID:27936925

Ambient atomic resolution atomic force microscopy with qPlus sensors: Part 1.

PubMed

Wastl, Daniel S

2017-01-01

Atomic force microscopy (AFM) is an enormous tool to observe nature in highest resolution and understand fundamental processes like friction and tribology on the nanoscale. Atomic resolution in highest quality was possible only in well-controlled environments like ultrahigh vacuum (UHV) or controlled buffer environments (liquid conditions) and more specified for long-term high-resolution analysis at low temperatures (∼4 K) in UHV where drift is nearly completely absent. Atomic resolution in these environments is possible and is widely used. However, in uncontrolled environments like air, with all its pollutants and aerosols, unspecified thin liquid films as thin as a single molecular water-layer of 200 pm or thicker condensation films with thicknesses up to hundred nanometer, have been a problem for highest resolution since the invention of the AFM. The goal of true atomic resolution on hydrophilic as well as hydrophobic samples was reached recently. In this manuscript we want to review the concept of ambient AFM with atomic resolution. The reader will be introduced to the phenomenology in ambient conditions and the problems will be explained and analyzed while a method for scan parameter optimization will be explained. Recently developed concepts and techniques how to reach atomic resolution in air and ultra-thin liquid films will be shown and explained in detail, using several examples. Microsc. Res. Tech. 80:50-65, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Correlation in photon pairs generated using four-wave mixing in a cold atomic ensemble

NASA Astrophysics Data System (ADS)

Ferdinand, Andrew Richard; Manjavacas, Alejandro; Becerra, Francisco Elohim

2017-04-01

Spontaneous four-wave mixing (FWM) in atomic ensembles can be used to generate narrowband entangled photon pairs at or near atomic resonances. While extensive research has been done to investigate the quantum correlations in the time and polarization of such photon pairs, the study and control of high dimensional quantum correlations contained in their spatial degrees of freedom has not been fully explored. In our work we experimentally investigate the generation of correlated light from FWM in a cold ensemble of cesium atoms as a function of the frequencies of the pump fields in the FWM process. In addition, we theoretically study the spatial correlations of the photon pairs generated in the FWM process, specifically the joint distribution of their orbital angular momentum (OAM). We investigate the width of the distribution of the OAM modes, known as the spiral bandwidth, and the purity of OAM correlations as a function of the properties of the pump fields, collected photons, and the atomic ensemble. These studies will guide experiments involving high dimensional entanglement of photons generated from this FWM process and OAM-based quantum communication with atomic ensembles. This work is supported by AFORS Grant FA9550-14-1-0300.

Resolution Quality and Atom Positions in Sub-Angstrom Electron Microscopy

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

O'Keefe, Michael A.; Allard, Lawrence F.; Blom, Douglas A.

2005-02-15

Ability to determine whether an image peak represents one single atom or several depends on resolution of the HR-(S)TEM. Rayleigh's resolution criterion, an accepted standard in optics, was derived as a means for judging when two image intensity peaks from two sources of light (stars) are distinguishable from a single source. Atom spacings closer than the Rayleigh limit have been resolved in HR-TEM, suggesting that it may be useful to consider other limits, such as the Sparrow resolution criterion. From the viewpoint of the materials scientist, it is important to be able to use the image to determine whether anmore » image feature represents one or more atoms (resolution), and where the atoms (or atom columns) are positioned relative to one another (resolution quality). When atoms and the corresponding image peaks are separated by more than the Rayleigh limit of the HR-(S)TEM, it is possible to adjust imaging parameters so that relative peak positions in the image correspond to relative atom positions in the specimen. When atoms are closer than the Rayleigh limit, we must find the relationship of the peak position to the atom position by peak fitting or, if we have a suitable model, by image simulation. Our Rayleigh-Sparrow parameter QRS reveals the ''resolution quality'' of a microscope image. QRS values greater than 1 indicate a clearly resolved twin peak, while values between 1 and 0 mean a lower-quality resolution and an image with peaks displaced from the relative atom positions. The depth of the twin-peak minimum can be used to determine the value of QRS and the true separation of the atom peaks that sum to produce the twin peak in the image. The Rayleigh-Sparrow parameter can be used to refine relative atom positions in defect images where atoms are closer than the Rayleigh limit of the HR-(S)TEM, reducing the necessity for full image simulations from large defect models.« less

Light-induced picosecond rotational disordering of the inorganic sublattice in hybrid perovskites

DOE PAGES

Wu, Xiaoxi; Tan, Liang Z.; Shen, Xiaozhe; ...

2017-07-26

Femtosecond resolution electron scattering techniques are applied to resolve the first atomic-scale steps following absorption of a photon in the prototypical hybrid perovskite methylammonium lead iodide. Following above-gap photoexcitation, we directly resolve the transfer of energy from hot carriers to the lattice by recording changes in the mean square atomic displacements on 10-ps time scales. Measurements of the time-dependent pair distribution function show an unexpected broadening of the iodine-iodine correlation function while preserving the Pb-I distance. This indicates the formation of a rotationally disordered halide octahedral structure developing on picosecond time scales. Here, this work shows the important role ofmore » light-induced structural deformations within the inorganic sublattice in elucidating the unique optoelectronic functionality exhibited by hybrid perovskites and provides new understanding of hot carrier-lattice interactions, which fundamentally determine solar cell efficiencies.« less

The pair-production channel in atomic processes

NASA Astrophysics Data System (ADS)

Belkacem, Ali; Sørensen, Allan H.

2006-06-01

Assisted by the creation of electron-positron pairs, new channels for ionization, excitation, and charge transfer open in atomic collisions when the energy is raised to relativistic values. At extreme energies these pair-production channels usually dominate the "traditional" contributions to cross sections that involve only "positive-energy" electrons. An extensive body of theoretical and experimental work has been performed over the last two decades to investigate charge-changing processes catalyzed by pair production in relativistic heavy ion collisions. We review some of these studies.

Nitrogen vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in B 1 TiN studied by ab initio and classical molecular dynamics with optimized potentials

NASA Astrophysics Data System (ADS)

Sangiovanni, D. G.; Alling, B.; Steneteg, P.; Hultman, L.; Abrikosov, I. A.

2015-02-01

We use ab initio and classical molecular dynamics (AIMD and CMD) based on the modified embedded-atom method (MEAM) potential to simulate diffusion of N vacancy and N self-interstitial point defects in B 1 TiN. TiN MEAM parameters are optimized to obtain CMD nitrogen point-defect jump rates in agreement with AIMD predictions, as well as an excellent description of Ti Nx(˜0.7

Matter-wave entanglement and teleportation by molecular dissociation and collisions.

PubMed

Opatrný, T; Kurizki, G

2001-04-02

We propose dissociation of cold diatomic molecules as a source of atom pairs with highly correlated (entangled) positions and momenta, approximating the original quantum state introduced by Einstein, Podolsky, and Rosen (EPR) [Phys. Rev. 47, 777 (1935)]. Wave packet teleportation is shown to be achievable by its collision with one of the EPR correlated atoms and manipulation of the other atom in the pair.

Matter-Wave Entanglement and Teleportation by Molecular Dissociation and Collisions

NASA Astrophysics Data System (ADS)

Opatrný, T.; Kurizki, G.

2001-04-01

We propose dissociation of cold diatomic molecules as a source of atom pairs with highly correlated (entangled) positions and momenta, approximating the original quantum state introduced by Einstein, Podolsky, and Rosen (EPR) [Phys. Rev. 47, 777 (1935)]. Wave packet teleportation is shown to be achievable by its collision with one of the EPR correlated atoms and manipulation of the other atom in the pair.

Visualising reacting single atoms under controlled conditions: Advances in atomic resolution in situ Environmental (Scanning) Transmission Electron Microscopy (E(S)TEM)

NASA Astrophysics Data System (ADS)

Boyes, Edward D.; Gai, Pratibha L.

2014-02-01

Advances in atomic resolution Environmental (Scanning) Transmission Electron Microscopy (E(S)TEM) for probing gas-solid catalyst reactions in situ at the atomic level under controlled reaction conditions of gas environment and temperature are described. The recent development of the ESTEM extends the capability of the ETEM by providing the direct visualisation of single atoms and the atomic structure of selected solid state heterogeneous catalysts in their working states in real-time. Atomic resolution E(S)TEM provides a deeper understanding of the dynamic atomic processes at the surface of solids and their mechanisms of operation. The benefits of atomic resolution-E(S)TEM to science and technology include new knowledge leading to improved technological processes with substantial economic benefits, improved healthcare, reductions in energy needs and the management of environmental waste generation. xml:lang="fr"

Protein-protein interaction specificity is captured by contact preferences and interface composition.

PubMed

Nadalin, Francesca; Carbone, Alessandra

2018-02-01

Large-scale computational docking will be increasingly used in future years to discriminate protein-protein interactions at the residue resolution. Complete cross-docking experiments make in silico reconstruction of protein-protein interaction networks a feasible goal. They ask for efficient and accurate screening of the millions structural conformations issued by the calculations. We propose CIPS (Combined Interface Propensity for decoy Scoring), a new pair potential combining interface composition with residue-residue contact preference. CIPS outperforms several other methods on screening docking solutions obtained either with all-atom or with coarse-grain rigid docking. Further testing on 28 CAPRI targets corroborates CIPS predictive power over existing methods. By combining CIPS with atomic potentials, discrimination of correct conformations in all-atom structures reaches optimal accuracy. The drastic reduction of candidate solutions produced by thousands of proteins docked against each other makes large-scale docking accessible to analysis. CIPS source code is freely available at http://www.lcqb.upmc.fr/CIPS. alessandra.carbone@lip6.fr. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Partitioned key-value store with atomic memory operations

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

Bent, John M.; Faibish, Sorin; Grider, Gary

A partitioned key-value store is provided that supports atomic memory operations. A server performs a memory operation in a partitioned key-value store by receiving a request from an application for at least one atomic memory operation, the atomic memory operation comprising a memory address identifier; and, in response to the atomic memory operation, performing one or more of (i) reading a client-side memory location identified by the memory address identifier and storing one or more key-value pairs from the client-side memory location in a local key-value store of the server; and (ii) obtaining one or more key-value pairs from themore » local key-value store of the server and writing the obtained one or more key-value pairs into the client-side memory location identified by the memory address identifier. The server can perform functions obtained from a client-side memory location and return a result to the client using one or more of the atomic memory operations.« less

On the effect of irradiation-induced resolution in modelling fission gas release in UO2 LWR fuel

NASA Astrophysics Data System (ADS)

Lösönen, Pekka

2017-12-01

Irradiation resolution of gas atoms and vacancies from intra- and intergranular bubbles in sintered UO2 fuel was studied by comparing macroscopic models with a more mechanistic approach. The applied macroscopic models imply the resolution rate of gas atoms to be proportional to gas concentration in intragranular bubbles and at grain boundary (including intergranular bubbles). A relation was established between the macroscopic models and a single encounter of an energetic fission fragment with a bubble. The effect of bubble size on resolution was quantified. The number of resoluted gas atoms per encounter of a fission fragment per bubble was of the same order of magnitude for intra- and intergranular bubbles. However, the resulting macroscopic resolution rate of gas atoms was about two orders of magnitude larger from intragranular bubbles. The number of vacancies resoluted from a grain face bubble by a passing fission fragment was calculated. The obtained correlations for resolution of gas atoms from intragranular bubbles and grain boundaries and for resolution of vacancies from grain face bubbles were used to demonstrate the effect of irradiation resolution on fission gas release.

Evaluation of interatomic potentials for rainbow scattering under axial channeling at KCl(0 0 1) surface by three-dimensional computer simulations based on binary collision approximation

NASA Astrophysics Data System (ADS)

Takeuchi, Wataru

2017-05-01

The rainbow angles corresponding to prominent peaks in the angular distributions of scattered projectiles with small angle, attributed to rainbow scattering (RS), under axial surface channeling conditions are strongly influenced by the interatomic potentials between projectiles and target atoms. The dependence of rainbow angles on normal energy of projectile energy to the target surface, being experimentally obtained by Specht et al. for RS of He, N, Ne and Ar atoms under <1 0 0> and <1 1 0> axial channeling conditions at a KCl(0 0 1) surface with projectile energies of 1-60 keV, was evaluated by the three-dimensional computer simulations using the ACOCT code based on the binary collision approximation with interatomic pair potentials. Good agreement between the ACOCT results using the ZBL pair potential and the individual pair potentials calculated from Hartree-Fock (HF) wave functions and the experimental ones was found for RS of He, N and Ne atoms from the atomic rows along <1 0 0> direction. For <1 1 0> direction, the ACOCT results employing the Moliere pair potential with adjustable screening length of O'Connor-Biersack (OB) formula, the ZBL pair potential and the individual HF pair potentials except for Ar → KCl using the OB pair potential are nearly in agreement with the experimental ones.

Transfer of a weakly bound electron in collisions of Rydberg atoms with neutral particles. II. Ion-pair formation and resonant quenching of the Rb(nl) and Ne(nl) States by Ca, Sr, and Ba atoms

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

Narits, A. A.; Mironchuk, E. S.; Lebedev, V. S., E-mail: vlebedev@sci.lebedev.ru

2013-10-15

Electron-transfer processes are studied in thermal collisions of Rydberg atoms with alkaline-earth Ca(4s{sup 2}), Sr(5s{sup 2}), and Ba(6s{sup 2}) atoms capable of forming negative ions with a weakly bound outermost p-electron. We consider the ion-pair formation and resonant quenching of highly excited atomic states caused by transitions between Rydberg covalent and ionic terms of a quasi-molecule produced in collisions of particles. The contributions of these reaction channels to the total depopulation cross section of Rydberg states of Rb(nl) and Ne(nl) atoms as functions of the principal quantum number n are compared for selectively excited nl-levels with l Much-Less-Than n andmore » for states with large orbital quantum numbers l = n - 1, n - 2. It is shown that the contribution from resonant quenching dominates at small values of n, and the ion-pair formation process begins to dominate with increasing n. The values and positions of the maxima of cross sections for both processes strongly depend on the electron affinity of an alkaline-earth atom and on the orbital angular momentum l of a highly excited atom. It is shown that in the case of Rydberg atoms in states with large l {approx} n - 1, the rate constants of ion-pair formation and collisional quenching are considerably lower than those for nl-levels with l Much-Less-Than n.« less

Majorana edge States in atomic wires coupled by pair hopping.

PubMed

Kraus, Christina V; Dalmonte, Marcello; Baranov, Mikhail A; Läuchli, Andreas M; Zoller, P

2013-10-25

We present evidence for Majorana edge states in a number conserving theory describing a system of spinless fermions on two wires that are coupled by pair hopping. Our analysis is based on a combination of a qualitative low energy approach and numerical techniques using the density matrix renormalization group. In addition, we discuss an experimental realization of pair-hopping interactions in cold atom gases confined in optical lattices.

Principle and Reconstruction Algorithm for Atomic-Resolution Holography

NASA Astrophysics Data System (ADS)

Matsushita, Tomohiro; Muro, Takayuki; Matsui, Fumihiko; Happo, Naohisa; Hosokawa, Shinya; Ohoyama, Kenji; Sato-Tomita, Ayana; Sasaki, Yuji C.; Hayashi, Kouichi

2018-06-01

Atomic-resolution holography makes it possible to obtain the three-dimensional (3D) structure around a target atomic site. Translational symmetry of the atomic arrangement of the sample is not necessary, and the 3D atomic image can be measured when the local structure of the target atomic site is oriented. Therefore, 3D local atomic structures such as dopants and adsorbates are observable. Here, the atomic-resolution holography comprising photoelectron holography, X-ray fluorescence holography, neutron holography, and their inverse modes are treated. Although the measurement methods are different, they can be handled with a unified theory. The algorithm for reconstructing 3D atomic images from holograms plays an important role. Although Fourier transform-based methods have been proposed, they require the multiple-energy holograms. In addition, they cannot be directly applied to photoelectron holography because of the phase shift problem. We have developed methods based on the fitting method for reconstructing from single-energy and photoelectron holograms. The developed methods are applicable to all types of atomic-resolution holography.

Sparse maps—A systematic infrastructure for reduced-scaling electronic structure methods. II. Linear scaling domain based pair natural orbital coupled cluster theory

NASA Astrophysics Data System (ADS)

Riplinger, Christoph; Pinski, Peter; Becker, Ute; Valeev, Edward F.; Neese, Frank

2016-01-01

Domain based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)) is a highly efficient local correlation method. It is known to be accurate and robust and can be used in a black box fashion in order to obtain coupled cluster quality total energies for large molecules with several hundred atoms. While previous implementations showed near linear scaling up to a few hundred atoms, several nonlinear scaling steps limited the applicability of the method for very large systems. In this work, these limitations are overcome and a linear scaling DLPNO-CCSD(T) method for closed shell systems is reported. The new implementation is based on the concept of sparse maps that was introduced in Part I of this series [P. Pinski, C. Riplinger, E. F. Valeev, and F. Neese, J. Chem. Phys. 143, 034108 (2015)]. Using the sparse map infrastructure, all essential computational steps (integral transformation and storage, initial guess, pair natural orbital construction, amplitude iterations, triples correction) are achieved in a linear scaling fashion. In addition, a number of additional algorithmic improvements are reported that lead to significant speedups of the method. The new, linear-scaling DLPNO-CCSD(T) implementation typically is 7 times faster than the previous implementation and consumes 4 times less disk space for large three-dimensional systems. For linear systems, the performance gains and memory savings are substantially larger. Calculations with more than 20 000 basis functions and 1000 atoms are reported in this work. In all cases, the time required for the coupled cluster step is comparable to or lower than for the preceding Hartree-Fock calculation, even if this is carried out with the efficient resolution-of-the-identity and chain-of-spheres approximations. The new implementation even reduces the error in absolute correlation energies by about a factor of two, compared to the already accurate previous implementation.

Constructing simple yet accurate potentials for describing the solvation of HCl/water clusters in bulk helium and nanodroplets.

PubMed

Boese, A Daniel; Forbert, Harald; Masia, Marco; Tekin, Adem; Marx, Dominik; Jansen, Georg

2011-08-28

The infrared spectroscopy of molecules, complexes, and molecular aggregates dissolved in superfluid helium clusters, commonly called HElium NanoDroplet Isolation (HENDI) spectroscopy, is an established, powerful experimental technique for extracting high resolution ro-vibrational spectra at ultra-low temperatures. Realistic quantum simulations of such systems, in particular in cases where the solute is undergoing a chemical reaction, require accurate solute-helium potentials which are also simple enough to be efficiently evaluated over the vast number of steps required in typical Monte Carlo or molecular dynamics sampling. This precludes using global potential energy surfaces as often parameterized for small complexes in the realm of high-resolution spectroscopic investigations that, in view of the computational effort imposed, are focused on the intermolecular interaction of rigid molecules with helium. Simple Lennard-Jones-like pair potentials, on the other hand, fall short in providing the required flexibility and accuracy in order to account for chemical reactions of the solute molecule. Here, a general scheme of constructing sufficiently accurate site-site potentials for use in typical quantum simulations is presented. This scheme employs atom-based grids, accounts for local and global minima, and is applied to the special case of a HCl(H(2)O)(4) cluster solvated by helium. As a first step, accurate interaction energies of a helium atom with a set of representative configurations sampled from a trajectory following the dissociation of the HCl(H(2)O)(4) cluster were computed using an efficient combination of density functional theory and symmetry-adapted perturbation theory, i.e. the DFT-SAPT approach. For each of the sampled cluster configurations, a helium atom was placed at several hundred positions distributed in space, leading to an overall number of about 400,000 such quantum chemical calculations. The resulting total interaction energies, decomposed into several energetic contributions, served to fit a site-site potential, where the sites are located at the atomic positions and, additionally, pseudo-sites are distributed along the lines joining pairs of atom sites within the molecular cluster. This approach ensures that this solute-helium potential is able to describe both undissociated molecular and dissociated (zwitter-) ionic configurations, as well as the interconnecting reaction pathway without re-adjusting partial charges or other parameters depending on the particular configuration. Test calculations of the larger HCl(H(2)O)(5) cluster interacting with helium demonstrate the transferability of the derived site-site potential. This specific potential can be readily used in quantum simulations of such HCl/water clusters in bulk helium or helium nanodroplets, whereas the underlying construction procedure can be generalized to other molecular solutes in other atomic solvents such as those encountered in rare gas matrix isolation spectroscopy.

Competing bosonic condensates in optical lattice with a mixture of single and pair hoppings

NASA Astrophysics Data System (ADS)

Travin, V. M.; Kopeć, T. K.

2017-01-01

A system of ultra-cold atoms with single boson and pair tunneling of bosonic atoms is considered in an optical lattice at arbitrary temperature. A mean-field theory was applied to the extended Bose-Hubbard Hamiltonian describing the system in order to investigate the competition between superfluid and pair superfluid as a function of the chemical potential and the temperature. To this end we have applied a method based on the Laplace transform method for the efficient calculation of the statistical sum for the quantum Hamiltonian. These results may be of interest for experiments on cold atom systems in optical lattices.

Thermal motion in proteins: Large effects on the time-averaged interaction energies

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

Goethe, Martin, E-mail: martingoethe@ub.edu; Rubi, J. Miguel; Fita, Ignacio

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothingmore » effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.« less

Thermal motion in proteins: Large effects on the time-averaged interaction energies

NASA Astrophysics Data System (ADS)

Goethe, Martin; Fita, Ignacio; Rubi, J. Miguel

2016-03-01

As a consequence of thermal motion, inter-atomic distances in proteins fluctuate strongly around their average values, and hence, also interaction energies (i.e. the pair-potentials evaluated at the fluctuating distances) are not constant in time but exhibit pronounced fluctuations. These fluctuations cause that time-averaged interaction energies do generally not coincide with the energy values obtained by evaluating the pair-potentials at the average distances. More precisely, time-averaged interaction energies behave typically smoother in terms of the average distance than the corresponding pair-potentials. This averaging effect is referred to as the thermal smoothing effect. Here, we estimate the strength of the thermal smoothing effect on the Lennard-Jones pair-potential for globular proteins at ambient conditions using x-ray diffraction and simulation data of a representative set of proteins. For specific atom species, we find a significant smoothing effect where the time-averaged interaction energy of a single atom pair can differ by various tens of cal/mol from the Lennard-Jones potential at the average distance. Importantly, we observe a dependency of the effect on the local environment of the involved atoms. The effect is typically weaker for bulky backbone atoms in beta sheets than for side-chain atoms belonging to other secondary structure on the surface of the protein. The results of this work have important practical implications for protein software relying on free energy expressions. We show that the accuracy of free energy expressions can largely be increased by introducing environment specific Lennard-Jones parameters accounting for the fact that the typical thermal motion of protein atoms depends strongly on their local environment.

High-resolution imaging of silicene on an Ag(111) surface by atomic force microscopy

NASA Astrophysics Data System (ADS)

Onoda, Jo; Yabuoshi, Keisuke; Miyazaki, Hiroki; Sugimoto, Yoshiaki

2017-12-01

Silicene, a two-dimensional (2D) honeycomb arrangement of Si atoms, is expected to have better electronic properties than graphene and has been mostly synthesized on Ag surfaces. Although scanning tunneling microscopy (STM) has been used for visualizing its atomic structure in real space, the interpretation of STM contrast is not straightforward and only the topmost Si atoms were observed on the (4 ×4 ) silicene/Ag(111) surface. Here, we demonstrate that high-resolution atomic force microscopy (AFM) can resolve all constituent Si atoms in the buckled honeycomb arrangement of the (4 ×4 ) silicene. Site-specific force spectroscopy attributes the origin of the high-resolution AFM images to chemical bonds between the AFM probe apex and the individual Si atoms on the (4 ×4 ) silicene. A detailed analysis of the geometric parameters suggests that the pulling up of lower-buckled Si atoms by the AFM tip could be a key for high-resolution AFM, implying a weakening of the Si-Ag interactions at the interface. We expect that high-resolution AFM will also unveil atomic structures of edges and defects of silicene, or other emerging 2D materials.

Quantum Computation by Optically Coupled Steady Atoms/Quantum-Dots Inside a Quantum Cavity

NASA Technical Reports Server (NTRS)

Pradhan, P.; Wang, K. L.; Roychowdhury, V. P.; Anantram, M. P.; Mor, T.; Saini, Subhash (Technical Monitor)

1999-01-01

We present a model for quantum computation using $n$ steady 3-level atoms kept inside a quantum cavity, or using $n$ quantum-dots (QDs) kept inside a quantum cavity. In this model one external laser is pointed towards all the atoms/QDs, and $n$ pairs of electrodes are addressing the atoms/QDs, so that each atom is addressed by one pair. The energy levels of each atom/QD are controlled by an external Stark field given to the atom/QD by its external pair of electrodes. Transition between two energy levels of an individual atom/ QD are controlled by the voltage on its electrodes, and by the external laser. Interactions between two atoms/ QDs are performed with the additional help of the cavity mode (using on-resonance condition). Laser frequency, cavity frequency, and energy levels are far off-resonance most of the time, and they are brought to the resonance (using the Stark effect) only at the time of operations. Steps for a controlled-NOT gate between any two atoms/QDs have been described for this model. Our model demands some challenging technological efforts, such as manufacturing single-electron QDs inside a cavity. However, it promises big advantages over other existing models which are currently implemented, and might enable a much easier scale-up, to compute with many more qubits.

Quasi-planar elemental clusters in pair interactions approximation

NASA Astrophysics Data System (ADS)

Chkhartishvili, Levan

2016-01-01

The pair-interactions approximation, when applied to describe elemental clusters, only takes into account bonding between neighboring atoms. According to this approach, isomers of wrapped forms of 2D clusters - nanotubular and fullerene-like structures - and truly 3D clusters, are generally expected to be more stable than their quasi-planar counterparts. This is because quasi-planar clusters contain more peripheral atoms with dangling bonds and, correspondingly, fewer atoms with saturated bonds. However, the differences in coordination numbers between central and peripheral atoms lead to the polarization of bonds. The related corrections to the molar binding energy can make small, quasi-planar clusters more stable than their 2D wrapped allotropes and 3D isomers. The present work provides a general theoretical frame for studying the relative stability of small elemental clusters within the pair interactions approximation.

Stabilizing Rabi oscillation of a charge qubit via the atomic clock technique

NASA Astrophysics Data System (ADS)

Yu, Deshui; Landra, Alessandro; Kwek, Leong Chuan; Amico, Luigi; Dumke, Rainer

2018-02-01

We propose a superconducting circuit-atom hybrid, where the Rabi oscillation of single excess Cooper pair in the island is stabilized via the common atomic clock technique. The noise in the superconducting circuit is mapped onto the voltage source which biases the Cooper-pair box via an inductor and a gate capacitor. The fast fluctuations of the gate charge are significantly suppressed by an inductor-capacitor resonator, leading to a long-relaxation-time Rabi oscillation. More importantly, the residual low-frequency fluctuations are further reduced by using the general feedback-control method, in which the voltage bias is stabilized via continuously measuring the dc-Stark-shift-induced atomic Ramsey signal. The stability and coherence time of the resulting charge-qubit Rabi oscillation are both enhanced. The principal structure of this Cooper-pair-box oscillator is studied in detail.

Atomic-batched tensor decomposed two-electron repulsion integrals

NASA Astrophysics Data System (ADS)

Schmitz, Gunnar; Madsen, Niels Kristian; Christiansen, Ove

2017-04-01

We present a new integral format for 4-index electron repulsion integrals, in which several strategies like the Resolution-of-the-Identity (RI) approximation and other more general tensor-decomposition techniques are combined with an atomic batching scheme. The 3-index RI integral tensor is divided into sub-tensors defined by atom pairs on which we perform an accelerated decomposition to the canonical product (CP) format. In a first step, the RI integrals are decomposed to a high-rank CP-like format by repeated singular value decompositions followed by a rank reduction, which uses a Tucker decomposition as an intermediate step to lower the prefactor of the algorithm. After decomposing the RI sub-tensors (within the Coulomb metric), they can be reassembled to the full decomposed tensor (RC approach) or the atomic batched format can be maintained (ABC approach). In the first case, the integrals are very similar to the well-known tensor hypercontraction integral format, which gained some attraction in recent years since it allows for quartic scaling implementations of MP2 and some coupled cluster methods. On the MP2 level, the RC and ABC approaches are compared concerning efficiency and storage requirements. Furthermore, the overall accuracy of this approach is assessed. Initial test calculations show a good accuracy and that it is not limited to small systems.

Deuterium supersaturation in low-energy plasma-loaded tungsten surfaces

NASA Astrophysics Data System (ADS)

Gao, L.; Jacob, W.; von Toussaint, U.; Manhard, A.; Balden, M.; Schmid, K.; Schwarz-Selinger, T.

2017-01-01

Fundamental understanding of hydrogen-metal interactions is challenging due to a lack of knowledge on defect production and/or evolution upon hydrogen ingression, especially for metals undergoing hydrogen irradiation with ion energy below the displacement thresholds reported in literature. Here, applying a novel low-energy argon-sputter depth profiling method with significantly improved depth resolution for tungsten (W) surfaces exposed to deuterium (D) plasma at 300 K, we show the existence of a 10 nm thick D-supersaturated surface layer (DSSL) with an unexpectedly high D concentration of ~10 at.% after irradiation with ion energy of 215 eV. Electron back-scatter diffraction reveals that the W lattice within this DSSL is highly distorted, thus strongly blurring the Kikuchi pattern. We explain this strong damage by the synergistic interaction of energetic D ions and solute D atoms with the W lattice. Solute D atoms prevent the recombination of vacancies with interstitial W atoms, which are produced by collisions of energetic D ions with W lattice atoms (Frenkel pairs). This proposed damaging mechanism could also be active on other hydrogen-irradiated metal surfaces. The present work provides deep insight into hydrogen-induced lattice distortion at plasma-metal interfaces and sheds light on its modelling work.

Stereo-selective binding of chlorobenzene on Si(111)-7×7

NASA Astrophysics Data System (ADS)

Cao, Y.; Deng, J. F.; Xu, G. Q.

2000-03-01

The adsorption and binding of chlorobenzene (C6H5Cl) on clean and D-modified Si(111)-7×7 surfaces have been investigated using high resolution electron energy loss spectroscopy (HREELS) and thermal desorption spectroscopy (TDS). On a clean surface, both chemisorbed and physisorbed C6H5Cl are observed at an adsorption temperature of 110 K. The HREEL spectra show direct evidence for the presence of both sp2 and sp3 carbon atoms in chemisorbed C6H5Cl molecules on Si(111)-7×7. Upon D-modification, the chemisorption of C6H5Cl decreases rapidly with increasing D-coverage (θD). At θD=1/3 ML, only physisorbed chlorobenzene is detected, which strongly suggests the involvement of rest-atoms in the chemisorption of C6H5Cl. Combined with the scanning tunneling microscopy (STM) results by Chen et al. [Surf. Sci. 340, 224 (1995)] showing the participation of adatoms in the binding, we propose that the 2,5-carbon atoms in C6H5Cl are stereo-selectively di-σ bonded to a pair of adjacent adatom and rest-atom on the Si(111)-7×7 surface, yielding a 2,5-chlorocyclohexadienelike surface adduct.

Atomic-batched tensor decomposed two-electron repulsion integrals.

PubMed

Schmitz, Gunnar; Madsen, Niels Kristian; Christiansen, Ove

2017-04-07

We present a new integral format for 4-index electron repulsion integrals, in which several strategies like the Resolution-of-the-Identity (RI) approximation and other more general tensor-decomposition techniques are combined with an atomic batching scheme. The 3-index RI integral tensor is divided into sub-tensors defined by atom pairs on which we perform an accelerated decomposition to the canonical product (CP) format. In a first step, the RI integrals are decomposed to a high-rank CP-like format by repeated singular value decompositions followed by a rank reduction, which uses a Tucker decomposition as an intermediate step to lower the prefactor of the algorithm. After decomposing the RI sub-tensors (within the Coulomb metric), they can be reassembled to the full decomposed tensor (RC approach) or the atomic batched format can be maintained (ABC approach). In the first case, the integrals are very similar to the well-known tensor hypercontraction integral format, which gained some attraction in recent years since it allows for quartic scaling implementations of MP2 and some coupled cluster methods. On the MP2 level, the RC and ABC approaches are compared concerning efficiency and storage requirements. Furthermore, the overall accuracy of this approach is assessed. Initial test calculations show a good accuracy and that it is not limited to small systems.

Probing the effect of electron channelling on atomic resolution energy dispersive X-ray quantification.

PubMed

MacArthur, Katherine E; Brown, Hamish G; Findlay, Scott D; Allen, Leslie J

2017-11-01

Advances in microscope stability, aberration correction and detector design now make it readily possible to achieve atomic resolution energy dispersive X-ray mapping for dose resilient samples. These maps show impressive atomic-scale qualitative detail as to where the elements reside within a given sample. Unfortunately, while electron channelling is exploited to provide atomic resolution data, this very process makes the images rather more complex to interpret quantitatively than if no electron channelling occurred. Here we propose small sample tilt as a means for suppressing channelling and improving quantification of composition, whilst maintaining atomic-scale resolution. Only by knowing composition and thickness of the sample is it possible to determine the atomic configuration within each column. The effects of neighbouring atomic columns with differing composition and of residual channelling on our ability to extract exact column-by-column composition are also discussed. Copyright © 2017 Elsevier B.V. All rights reserved.

Electric field imaging of single atoms

PubMed Central

Shibata, Naoya; Seki, Takehito; Sánchez-Santolino, Gabriel; Findlay, Scott D.; Kohno, Yuji; Matsumoto, Takao; Ishikawa, Ryo; Ikuhara, Yuichi

2017-01-01

In scanning transmission electron microscopy (STEM), single atoms can be imaged by detecting electrons scattered through high angles using post-specimen, annular-type detectors. Recently, it has been shown that the atomic-scale electric field of both the positive atomic nuclei and the surrounding negative electrons within crystalline materials can be probed by atomic-resolution differential phase contrast STEM. Here we demonstrate the real-space imaging of the (projected) atomic electric field distribution inside single Au atoms, using sub-Å spatial resolution STEM combined with a high-speed segmented detector. We directly visualize that the electric field distribution (blurred by the sub-Å size electron probe) drastically changes within the single Au atom in a shape that relates to the spatial variation of total charge density within the atom. Atomic-resolution electric field mapping with single-atom sensitivity enables us to examine their detailed internal and boundary structures. PMID:28555629

Re-evaluation of low-resolution crystal structures via interactive molecular-dynamics flexible fitting (iMDFF): a case study in complement C4.

PubMed

Croll, Tristan Ian; Andersen, Gregers Rom

2016-09-01

While the rapid proliferation of high-resolution structures in the Protein Data Bank provides a rich set of templates for starting models, it remains the case that a great many structures both past and present are built at least in part by hand-threading through low-resolution and/or weak electron density. With current model-building tools this task can be challenging, and the de facto standard for acceptable error rates (in the form of atomic clashes and unfavourable backbone and side-chain conformations) in structures based on data with dmax not exceeding 3.5 Å reflects this. When combined with other factors such as model bias, these residual errors can conspire to make more serious errors in the protein fold difficult or impossible to detect. The three recently published 3.6-4.2 Å resolution structures of complement C4 (PDB entries 4fxg, 4fxk and 4xam) rank in the top quartile of structures of comparable resolution both in terms of Rfree and MolProbity score, yet, as shown here, contain register errors in six β-strands. By applying a molecular-dynamics force field that explicitly models interatomic forces and hence excludes most physically impossible conformations, the recently developed interactive molecular-dynamics flexible fitting (iMDFF) approach significantly reduces the complexity of the conformational space to be searched during manual rebuilding. This substantially improves the rate of detection and correction of register errors, and allows user-guided model building in maps with a resolution lower than 3.5 Å to converge to solutions with a stereochemical quality comparable to atomic resolution structures. Here, iMDFF has been used to individually correct and re-refine these three structures to MolProbity scores of <1.7, and strategies for working with such challenging data sets are suggested. Notably, the improved model allowed the resolution for complement C4b to be extended from 4.2 to 3.5 Å as demonstrated by paired refinement.

Atomic charges of sulfur in ionic liquids: experiments and calculations.

PubMed

Fogarty, Richard M; Rowe, Rebecca; Matthews, Richard P; Clough, Matthew T; Ashworth, Claire R; Brandt, Agnieszka; Corbett, Paul J; Palgrave, Robert G; Smith, Emily F; Bourne, Richard A; Chamberlain, Thomas W; Thompson, Paul B J; Hunt, Patricia A; Lovelock, Kevin R J

2017-12-14

Experimental near edge X-ray absorption fine structure (NEXAFS) spectra, X-ray photoelectron (XP) spectra and Auger electron spectra are reported for sulfur in ionic liquids (ILs) with a range of chemical structures. These values provide experimental measures of the atomic charge in each IL and enable the evaluation of the suitability of NEXAFS spectroscopy and XPS for probing the relative atomic charge of sulfur. In addition, we use Auger electron spectroscopy to show that when XPS binding energies differ by less than 0.5 eV, conclusions on atomic charge should be treated with caution. Our experimental data provides a benchmark for calculations of the atomic charge of sulfur obtained using different methods. Atomic charges were computed for lone ions and ion pairs, both in the gas phase (GP) and in a solvation model (SMD), with a wide range of ion pair conformers considered. Three methods were used to compute the atomic charges: charges from the electrostatic potential using a grid based method (ChelpG), natural bond orbital (NBO) population analysis and Bader's atoms in molecules (AIM) approach. By comparing the experimental and calculated measures of the atomic charge of sulfur, we provide an order for the sulfur atoms, ranging from the most negative to the most positive atomic charge. Furthermore, we show that both ChelpG and NBO are reasonable methods for calculating the atomic charge of sulfur in ILs, based on the agreement with both the XPS and NEXAFS spectroscopy results. However, the atomic charges of sulfur derived from ChelpG are found to display significant, non-physical conformational dependence. Only small differences in individual atomic charge of sulfur were observed between lone ion (GP) and ion pair IL(SMD) model systems, indicating that ion-ion interactions do not strongly influence individual atomic charges.

Detection of a Cooper-pair density wave in Bi 2Sr 2CaCu 2O 8+x

DOE PAGES

Hamidian, M. H.; Edkins, S. D.; Joo, Sang Hyun; ...

2016-04-13

The quantum condensate of Cooper pairs forming a superconductor was originally conceived as being translationally invariant. In theory, however, pairs can exist with finite momentum Q, thus generating a state with a spatially modulated Cooper-pair density. Such a state has been created in ultracold 6Li gas but never observed directly in any superconductor. It is now widely hypothesized that the pseudogap phase of the copper oxide superconductors contains such a ‘pair density wave’ state. In this paper we report the use of nanometre-resolution scanned Josephson tunnelling microscopy to image Cooper pair tunnelling from a d-wave superconducting microscope tip to themore » condensate of the superconductor Bi 2Sr 2CaCu 2O 8+x. We demonstrate condensate visualization capabilities directly by using the Cooper-pair density variations surrounding zinc impurity atoms and at the Bi 2Sr 2CaCu 2O 8+x crystal supermodulation. Then, by using Fourier analysis of scanned Josephson tunnelling images, we discover the direct signature of a Cooper-pair density modulation at wavevectors Q P ≈ (0.25, 0)2π/a 0 and (0, 0.25)2π/a 0 in Bi 2Sr 2CaCu 2O 8+x. The amplitude of these modulations is about five per cent of the background condensate density and their form factor exhibits primarily s or s' symmetry. Finally, this phenomenology is consistent with Ginzburg–Landau theory when a charge density wave with d-symmetry form factor and wavevector Q C = Q P coexists with a d-symmetry superconductor; it is also predicted by several contemporary microscopic theories for the pseudogap phase.« less

Entanglement of two individual neutral atoms using Rydberg blockade.

PubMed

Wilk, T; Gaëtan, A; Evellin, C; Wolters, J; Miroshnychenko, Y; Grangier, P; Browaeys, A

2010-01-08

We report the generation of entanglement between two individual 87Rb atoms in hyperfine ground states |F=1,M=1> and |F=2,M=2> which are held in two optical tweezers separated by 4 microm. Our scheme relies on the Rydberg blockade effect which prevents the simultaneous excitation of the two atoms to a Rydberg state. The entangled state is generated in about 200 ns using pulsed two-photon excitation. We quantify the entanglement by applying global Raman rotations on both atoms. We measure that 61% of the initial pairs of atoms are still present at the end of the entangling sequence. These pairs are in the target entangled state with a fidelity of 0.75.

Determination of atomic-scale chemical composition at semiconductor heteroepitaxial interfaces by high-resolution transmission electron microscopy.

PubMed

Wen, C; Ma, Y J

2018-03-01

The determination of atomic structures and further quantitative information such as chemical compositions at atomic scale for semiconductor defects or heteroepitaxial interfaces can provide direct evidence to understand their formation, modification, and/or effects on the properties of semiconductor films. The commonly used method, high-resolution transmission electron microscopy (HRTEM), suffers from difficulty in acquiring images that correctly show the crystal structure at atomic resolution, because of the limitation in microscope resolution or deviation from the Scherzer-defocus conditions. In this study, an image processing method, image deconvolution, was used to achieve atomic-resolution (∼1.0 Å) structure images of small lattice-mismatch (∼1.0%) AlN/6H-SiC (0001) and large lattice-mismatch (∼8.5%) AlSb/GaAs (001) heteroepitaxial interfaces using simulated HRTEM images of a conventional 300-kV field-emission-gun transmission electron microscope under non-Scherzer-defocus conditions. Then, atomic-scale chemical compositions at the interface were determined for the atomic intermixing and Lomer dislocation with an atomic step by analyzing the deconvoluted image contrast. Furthermore, the effect of dynamical scattering on contrast analysis was also evaluated for differently weighted atomic columns in the compositions. Copyright © 2018 Elsevier Ltd. All rights reserved.

DFT investigation of the vibrational properties of GC Watson-Crick and Hoogsteen base pairs in the presence of Mg²⁺, Ca²⁺, and Cu²⁺ ions.

PubMed

Morari, Cristian; Muntean, Cristina M; Tripon, Carmen; Buimaga-Iarinca, Luiza; Calborean, Adrian

2014-04-01

The binding effects of Mg²⁺, Ca²⁺, and Cu²⁺ ions on the vibrational properties of guanine-cytosine base pairs have been performed using density functional theory investigations. Both Watson-Crick and Hoogsteen configurations of the base pairs were investigated. In Watson-Crick configuration, the metal was coordinated at N7 atom of guanine, while in the case of Hoogsteen configuration, the coordination is at N3 atom of guanine. We have pointed out the geometric properties of the metal-GC base pairs structure, as well as the vibrational bands that can be used to detect the presence of metallic ions in the Watson-Crick and Hoogsteen GC structures. For the geometric models used by us, the vibrational amplitudes of metallic atoms were stronger for wavenumbers lower than 500 cm⁻¹. This suggests that in the experimental studies on DNA the presence of the three metallic atoms (Mg, Ca, and Cu) can be explicitly detected at low frequencies.

Rattler behavior in As skutterudites and oxy-skutterudites

NASA Astrophysics Data System (ADS)

Bridges, Frank; Car, Brad; Hoffman-Stapleton, Mikaela; Keiber, Trevor; Sutton, Logan; Maple, M. Brian

2014-03-01

We report EXAFS measurements for the series CeX4As12 (X = Fe, Ru, Os) and NdCu3Ru4O12 as a function of temperature for most elements in the structure. In each case the rare earth atom is a ``rattler'' atom, with a low Einstein temperature while the skutterudite cage structure is relatively stiff. From temperature dependencies of the correlated Debye model for the cage atoms, one can estimate the effective spring constant for various atom pairs. We also find for the oxy-skutterudites that the planar CuO4 sub-structure is very stiff, and likely vibrates as a rigid unit. We compare the behavior of the As-skutterudites with other skutterudites and with the oxy-skutterudites, and discuss in terms of the rigid cage model. The second neighbor pair Ce-X for the As-skutterudites is softer than expected while for the oxy-skutterudites the second neighbor Nd-Ru pair is stiffer than the nearest neighbor Nd-O pair. Models are need to explore this behavior. Support: NSF DMR1005568.

Evaluation of variability in high-resolution protein structures by global distance scoring.

PubMed

Anzai, Risa; Asami, Yoshiki; Inoue, Waka; Ueno, Hina; Yamada, Koya; Okada, Tetsuji

2018-01-01

Systematic analysis of the statistical and dynamical properties of proteins is critical to understanding cellular events. Extraction of biologically relevant information from a set of high-resolution structures is important because it can provide mechanistic details behind the functional properties of protein families, enabling rational comparison between families. Most of the current structural comparisons are pairwise-based, which hampers the global analysis of increasing contents in the Protein Data Bank. Additionally, pairing of protein structures introduces uncertainty with respect to reproducibility because it frequently accompanies other settings for superimposition. This study introduces intramolecular distance scoring for the global analysis of proteins, for each of which at least several high-resolution structures are available. As a pilot study, we have tested 300 human proteins and showed that the method is comprehensively used to overview advances in each protein and protein family at the atomic level. This method, together with the interpretation of the model calculations, provide new criteria for understanding specific structural variation in a protein, enabling global comparison of the variability in proteins from different species.

Observation of dynamic atom-atom correlation in liquid helium in real space.

PubMed

Dmowski, W; Diallo, S O; Lokshin, K; Ehlers, G; Ferré, G; Boronat, J; Egami, T

2017-05-04

Liquid 4 He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom-atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4 He atoms in the Bose-Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDF peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom-atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.

Unambiguous determination of H-atom positions: comparing results from neutron and high-resolution X-ray crystallography.

PubMed

Gardberg, Anna S; Del Castillo, Alexis Rae; Weiss, Kevin L; Meilleur, Flora; Blakeley, Matthew P; Myles, Dean A A

2010-05-01

The locations of H atoms in biological structures can be difficult to determine using X-ray diffraction methods. Neutron diffraction offers a relatively greater scattering magnitude from H and D atoms. Here, 1.65 A resolution neutron diffraction studies of fully perdeuterated and selectively CH(3)-protonated perdeuterated crystals of Pyrococcus furiosus rubredoxin (D-rubredoxin and HD-rubredoxin, respectively) at room temperature (RT) are described, as well as 1.1 A resolution X-ray diffraction studies of the same protein at both RT and 100 K. The two techniques are quantitatively compared in terms of their power to directly provide atomic positions for D atoms and analyze the role played by atomic thermal motion by computing the sigma level at the D-atom coordinate in simulated-annealing composite D-OMIT maps. It is shown that 1.65 A resolution RT neutron data for perdeuterated rubredoxin are approximately 8 times more likely overall to provide high-confidence positions for D atoms than 1.1 A resolution X-ray data at 100 K or RT. At or above the 1.0sigma level, the joint X-ray/neutron (XN) structures define 342/378 (90%) and 291/365 (80%) of the D-atom positions for D-rubredoxin and HD-rubredoxin, respectively. The X-ray-only 1.1 A resolution 100 K structures determine only 19/388 (5%) and 8/388 (2%) of the D-atom positions above the 1.0sigma level for D-rubredoxin and HD-rubredoxin, respectively. Furthermore, the improved model obtained from joint XN refinement yielded improved electron-density maps, permitting the location of more D atoms than electron-density maps from models refined against X-ray data only.

N vacancy, self-interstitial diffusion, and Frenkel-pair formation/dissociation in TiN studied by ab-initio and classical molecular dynamics

NASA Astrophysics Data System (ADS)

Sangiovanni, Davide G.; Alling, Björn; Hultman, Lars; Abrikosov, Igor A.

2015-03-01

We use ab-initio and classical molecular dynamics (AIMD, CMD) to simulate diffusion of N vacancy and N self-interstitial point-defects in B1 TiN. The physical properties of TiN, important material system for thin film and coatings applications, are largely dictated by concentration and mobility of point defects. We determine N dilute-point-defect diffusion pathways, activation energies, attempt frequencies, and diffusion coefficients as a function of temperature. In addition, MD simulations reveal an unanticipated atomistic process, which controls the spontaneous formation of N-self-interstitial/N-vacancy pairs (Frenkel pairs) in defect-free TiN. This entails that a N lattice atom leaves its bulk position and bonds to a neighboring N lattice atom. In most cases, Frenkel-pair NI and NV recombine within a fraction of ns; 50% of these processes result in the exchange of two nitrogen lattice atoms. Occasionally, however, Frenkel-pair N-interstitial atoms permanently escape from the anion vacancy site, thus producing unpaired NI and NV point defects. The Knut and Alice Wallenberg foundation (Isotope Project, 2011.0094), the Swedish Research Council (VR) Linköping Linnaeus Initiative LiLi-NFM (Grant 2008-6572), and the Swedish Government Strategic Research (Grant MatLiU 2009-00971).

Anisotropy of stress correlation in two-dimensional liquids and a pseudospin model

DOE PAGES

Wu, Bin; Iwashita, Takuya; Egami, Takeshi

2015-11-04

Liquids are condensed matter in which atoms are strongly correlated in position and momentum. The atomic pair density function (PDF) is used often in describing such correlation. However, elucidation of many properties requires higher degrees of correlation than the pair correlation. For instance, viscosity depends upon the stress correlations in space and time. We examine the cross correlation between the stress correlation at the atomic level and the PDF for two-dimensional liquids. We introduce the concept of the stress-resolved pair distribution function (SRPDF) that uses the sign of atomic-level stress as a selection rule to include particles from density correlations.more » The connection between SRPDFs and stress correlation function is explained through an approximation in which the shear stress is replaced by a pseudospin. Lastly, we further assess the possibility of interpreting the long-range stress correlation as a consequence of short-range Ising-like pseudospin interactions.« less

Nonlinear Sensing With Collective States of Ultracold Atoms in Optical Lattices

DTIC Science & Technology

2015-04-02

20) E. Tiesinga, “Particle-hole Pair Coherence in Mott insulator quench dynamics” at the June 2014, Division of atomic, molecular, and optical...Jian, Philip R. Johnson, Eite Tiesinga. Particle-Hole Pair Coherence in Mott Insulator Quench Dynamics, P H Y S I C A L R E V I EW L E T T E R S (01...lattices. We focused on techniques that make use of the coherent superposition states in atom number. These state are not unlike the photon number

Human Tau Isoforms Assemble into Ribbon-like Fibrils That Display Polymorphic Structure and Stability*

PubMed Central

Wegmann, Susanne; Jung, Yu Jin; Chinnathambi, Subashchandrabose; Mandelkow, Eva-Maria; Mandelkow, Eckhard; Muller, Daniel J.

2010-01-01

Fibrous aggregates of Tau protein are characteristic features of Alzheimer disease. We applied high resolution atomic force and EM microscopy to study fibrils assembled from different human Tau isoforms and domains. All fibrils reveal structural polymorphism; the “thin twisted” and “thin smooth” fibrils resemble flat ribbons (cross-section ∼10 × 15 nm) with diverse twist periodicities. “Thick fibrils” show periodicities of ∼65–70 nm and thicknesses of ∼9–18 nm such as routinely reported for “paired helical filaments” but structurally resemble heavily twisted ribbons. Therefore, thin and thick fibrils assembled from different human Tau isoforms challenge current structural models of paired helical filaments. Furthermore, all Tau fibrils reveal axial subperiodicities of ∼17–19 nm and, upon exposure to mechanical stress or hydrophobic surfaces, disassemble into uniform fragments that remain connected by thin thread-like structures (∼2 nm). This hydrophobically induced disassembly is inhibited at enhanced electrolyte concentrations, indicating that the fragments resemble structural building blocks and the fibril integrity depends largely on hydrophobic and electrostatic interactions. Because full-length Tau and repeat domain constructs assemble into fibrils of similar thickness, the “fuzzy coat” of Tau protein termini surrounding the fibril axis is nearly invisible for atomic force microscopy and EM, presumably because of its high flexibility. PMID:20566652

Superconductivity in an electron band just above the Fermi level: possible route to BCS-BEC superconductivity.

PubMed

Okazaki, K; Ito, Y; Ota, Y; Kotani, Y; Shimojima, T; Kiss, T; Watanabe, S; Chen, C-T; Niitaka, S; Hanaguri, T; Takagi, H; Chainani, A; Shin, S

2014-02-28

Conventional superconductivity follows Bardeen-Cooper-Schrieffer(BCS) theory of electrons-pairing in momentum-space, while superfluidity is the Bose-Einstein condensation(BEC) of atoms paired in real-space. These properties of solid metals and ultra-cold gases, respectively, are connected by the BCS-BEC crossover. Here we investigate the band dispersions in FeTe(0.6)Se(0.4)(Tc = 14.5 K ~ 1.2 meV) in an accessible range below and above the Fermi level(EF) using ultra-high resolution laser angle-resolved photoemission spectroscopy. We uncover an electron band lying just 0.7 meV (~8 K) above EF at the Γ-point, which shows a sharp superconducting coherence peak with gap formation below Tc. The estimated superconducting gap Δ and Fermi energy [Symbol: see text]F indicate composite superconductivity in an iron-based superconductor, consisting of strong-coupling BEC in the electron band and weak-coupling BCS-like superconductivity in the hole band. The study identifies the possible route to BCS-BEC superconductivity.

Fast resolution change in neutral helium atom microscopy

NASA Astrophysics Data System (ADS)

Flatabø, R.; Eder, S. D.; Ravn, A. K.; Samelin, B.; Greve, M. M.; Reisinger, T.; Holst, B.

2018-05-01

In neutral helium atom microscopy, a beam of atoms is scanned across a surface. Though still in its infancy, neutral helium microscopy has seen a rapid development over the last few years. The inertness and low energy of the helium atoms (less than 0.1 eV) combined with a very large depth of field and the fact that the helium atoms do not penetrate any solid material at low energies open the possibility for a non-destructive instrument that can measure topology on the nanoscale even on fragile and insulating surfaces. The resolution is determined by the beam spot size on the sample. Fast resolution change is an attractive property of a microscope because it allows different aspects of a sample to be investigated and makes it easier to identify specific features. However up till now it has not been possible to change the resolution of a helium microscope without breaking the vacuum and changing parts of the atom source. Here we present a modified source design, which allows fast, step wise resolution change. The basic design idea is to insert a moveable holder with a series of collimating apertures in front of the source, thus changing the effective source size of the beam and thereby the spot size on the surface and thus the microscope resolution. We demonstrate a design with 3 resolution steps. The number of resolution steps can easily be extended.

What transmission electron microscopes can visualize now and in the future.

PubMed

Müller, Shirley A; Aebi, Ueli; Engel, Andreas

2008-09-01

Our review concentrates on the progress made in high-resolution transmission electron microscopy (TEM) in the past decade. This includes significant improvements in sample preparation by quick-freezing aimed at preserving the specimen in a close-to-native state in the high vacuum of the microscope. Following advances in cold stage and TEM vacuum technology systems, the observation of native, frozen hydrated specimens has become a widely used approach. It fostered the development of computer guided, fully automated low-dose data acquisition systems allowing matched pairs of images and diffraction patterns to be recorded for electron crystallography, and the collection of entire tilt-series for electron tomography. To achieve optimal information transfer to atomic resolution, field emission electron guns combined with acceleration voltages of 200-300 kV are now routinely used. The outcome of these advances is illustrated by the atomic structure of mammalian aquaporin-O and by the pore-forming bacterial cytotoxin ClyA resolved to 12 A. Further, the Yersinia injectisome needle, a bacterial pseudopilus and the binding of phalloidin to muscle actin filaments were chosen to document the advantage of the high contrast offered by dedicated scanning transmission electron microscopy (STEM) and/or the STEM's ability to measure the mass of protein complexes and directly link this to their shape. Continued progress emerging from leading research laboratories and microscope manufacturers will eventually enable us to determine the proteome of a single cell by electron tomography, and to more routinely solve the atomic structure of membrane proteins by electron crystallography.

Two-photon direct frequency comb spectroscopy of alkali atoms

NASA Astrophysics Data System (ADS)

Palm, Christopher; Pradhananga, Trinity; Nguyen, Khoa; Montcrieffe, Caitlin; Kimball, Derek

2012-11-01

We have studied transition frequencies and excited state hyperfine structure in rubidium using 2-photon transitions excited directly with the frequency-doubled output of a erbium fiber optical frequency comb. The frequency comb output is directed in two counterpropagating directions through a vapor cell containing the rubidium vapor. A pair of optical filters is used to select teeth of the comb in order to identify the transition wavelengths. A photomultiplier tube (PMT) measures fluorescence from a decay channel wavelength selected with another optical filter. Using different combinations of filters enables a wide range of transitions to be investigated. By scanning the repetition rate, a Doppler-free spectrum can be obtained enabling kHz-resolution spectral measurements. An interesting dependence of the 2-photon spectrum on the energy of the intermediate state of the 2-photon transition is discussed. Our investigations are laying the groundwork for a long-term research program to use direct frequency comb spectroscopy to understand the complex spectra of rare-earth atoms.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

PubMed Central

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-01-01

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed. PMID:28117741

Relationship between ion pair geometries and electrostatic strengths in proteins.

PubMed Central

Kumar, Sandeep; Nussinov, Ruth

2002-01-01

The electrostatic free energy contribution of an ion pair in a protein depends on two factors, geometrical orientation of the side-chain charged groups with respect to each other and the structural context of the ion pair in the protein. Conformers in NMR ensembles enable studies of the relationship between geometry and electrostatic strengths of ion pairs, because the protein structural contexts are highly similar across different conformers. We have studied this relationship using a dataset of 22 unique ion pairs in 14 NMR conformer ensembles for 11 nonhomologous proteins. In different NMR conformers, the ion pairs are classified as salt bridges, nitrogen-oxygen (N-O) bridges and longer-range ion pairs on the basis of geometrical criteria. In salt bridges, centroids of the side-chain charged groups and at least a pair of side-chain nitrogen and oxygen atoms of the ion-pairing residues are within a 4 A distance. In N-O bridges, at least a pair of the side-chain nitrogen and oxygen atoms of the ion-pairing residues are within 4 A distance, but the distance between the side-chain charged group centroids is greater than 4 A. In the longer-range ion pairs, the side-chain charged group centroids as well as the side-chain nitrogen and oxygen atoms are more than 4 A apart. Continuum electrostatic calculations indicate that most of the ion pairs have stabilizing electrostatic contributions when their side-chain charged group centroids are within 5 A distance. Hence, most (approximately 92%) of the salt bridges and a majority (68%) of the N-O bridges are stabilizing. Most (approximately 89%) of the destabilizing ion pairs are the longer-range ion pairs. In the NMR conformer ensembles, the electrostatic interaction between side-chain charged groups of the ion-pairing residues is the strongest for salt bridges, considerably weaker for N-O bridges, and the weakest for longer-range ion pairs. These results suggest empirical rules for stabilizing electrostatic interactions in proteins. PMID:12202384

Exotic superfluidity and pairing phenomena in atomic Fermi gases in mixed dimensions.

PubMed

Zhang, Leifeng; Che, Yanming; Wang, Jibiao; Chen, Qijin

2017-10-11

Atomic Fermi gases have been an ideal platform for simulating conventional and engineering exotic physical systems owing to their multiple tunable control parameters. Here we investigate the effects of mixed dimensionality on the superfluid and pairing phenomena of a two-component ultracold atomic Fermi gas with a short-range pairing interaction, while one component is confined on a one-dimensional (1D) optical lattice whereas the other is in a homogeneous 3D continuum. We study the phase diagram and the pseudogap phenomena throughout the entire BCS-BEC crossover, using a pairing fluctuation theory. We find that the effective dimensionality of the non-interacting lattice component can evolve from quasi-3D to quasi-1D, leading to strong Fermi surface mismatch. Upon pairing, the system becomes effectively quasi-two dimensional in the BEC regime. The behavior of T c bears similarity to that of a regular 3D population imbalanced Fermi gas, but with a more drastic departure from the regular 3D balanced case, featuring both intermediate temperature superfluidity and possible pair density wave ground state. Unlike a simple 1D optical lattice case, T c in the mixed dimensions has a constant BEC asymptote.

Geometrical analysis of Cys-Cys bridges in proteins and their prediction from incomplete structural information

NASA Technical Reports Server (NTRS)

Goldblum, A.; Rein, R.

1987-01-01

Analysis of C-alpha atom positions from cysteines involved in disulphide bridges in protein crystals shows that their geometric characteristics are unique with respect to other Cys-Cys, non-bridging pairs. They may be used for predicting disulphide connections in incompletely determined protein structures, such as low resolution crystallography or theoretical folding experiments. The basic unit for analysis and prediction is the 3 x 3 distance matrix for Cx positions of residues (i - 1), Cys(i), (i +1) with (j - 1), Cys(j), (j + 1). In each of its columns, row and diagonal vector--outer distances are larger than the central distance. This analysis is compared with some analytical models.

High-temperature atomic superfluidity in lattice Bose-Fermi mixtures.

PubMed

Illuminati, Fabrizio; Albus, Alexander

2004-08-27

We consider atomic Bose-Fermi mixtures in optical lattices and study the superfluidity of fermionic atoms due to s-wave pairing induced by boson-fermion interactions. We prove that the induced fermion-fermion coupling is always attractive if the boson-boson on-site interaction is repulsive, and predict the existence of an enhanced BEC-BCS crossover as the strength of the lattice potential is varied. We show that for direct on-site fermion-fermion repulsion, the induced attraction can give rise to superfluidity via s-wave pairing at striking variance with the case of pure systems of fermionic atoms with direct repulsive interactions.

Location of Framework Al Atoms in the Channels of ZSM-5: Effect of the (Hydrothermal) Synthesis.

PubMed

Pashkova, Veronika; Sklenak, Stepan; Klein, Petr; Urbanova, Martina; Dědeček, Jiří

2016-03-14

(27) Al 3Q MAS NMR and UV/Vis spectroscopy with bare Co(II) ions as probes of Al pairs in the zeolite framework were employed to analyze the location of framework Al atoms in the channel system of zeolite ZSM-5. Furthermore, the effect of Na(+) ions together with tetrapropylammonium cation (TPA(+)) in the ZSM-5 synthesis gel on the location of Al in the channel system was investigated. Zeolites prepared using exclusively TPA(+) as a structure-directing agent (i.e., in the absence of Na(+) ions) led to 55-90% of Al atoms located at the channel intersection, regardless the presence or absence of Al pairs [Al-O-(Si-O)2 -Al sequences in one ring] in the zeolite framework. The presence of Na(+) ions in the synthesis gel did not modify the Al location at the channel intersection (55-95% of Al atoms) and led only to changes in i) the distribution of framework Al atoms between Al pairs (decrease) and single isolated Al atoms (increase), and ii) the siting of Al in distinguishable framework tetrahedral sites. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic modeling of cryo-electron microscopy reconstructions--joint refinement of model and imaging parameters.

PubMed

Chapman, Michael S; Trzynka, Andrew; Chapman, Brynmor K

2013-04-01

When refining the fit of component atomic structures into electron microscopic reconstructions, use of a resolution-dependent atomic density function makes it possible to jointly optimize the atomic model and imaging parameters of the microscope. Atomic density is calculated by one-dimensional Fourier transform of atomic form factors convoluted with a microscope envelope correction and a low-pass filter, allowing refinement of imaging parameters such as resolution, by optimizing the agreement of calculated and experimental maps. A similar approach allows refinement of atomic displacement parameters, providing indications of molecular flexibility even at low resolution. A modest improvement in atomic coordinates is possible following optimization of these additional parameters. Methods have been implemented in a Python program that can be used in stand-alone mode for rigid-group refinement, or embedded in other optimizers for flexible refinement with stereochemical restraints. The approach is demonstrated with refinements of virus and chaperonin structures at resolutions of 9 through 4.5 Å, representing regimes where rigid-group and fully flexible parameterizations are appropriate. Through comparisons to known crystal structures, flexible fitting by RSRef is shown to be an improvement relative to other methods and to generate models with all-atom rms accuracies of 1.5-2.5 Å at resolutions of 4.5-6 Å. Copyright © 2013 Elsevier Inc. All rights reserved.

Controlled dipole-dipole interactions between K Rydberg atoms in a laser-chopped effusive beam

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

Kutteruf, M. R.; Jones, R. R.

2010-12-15

We explore pulsed-field control of resonant dipole-dipole interactions between K Rydberg atoms. A laser-based atomic beam chopper is used to reduce the relative velocities of Rydberg atoms excited from an effusive thermal source. Resonant energy transfer (RET) between pairs of atoms is controlled via Stark tuning of the relevant Rydberg energy levels. Resonance line shapes in the electric field dependence of the RET probability are used to determine the effective temperature of the sample. We demonstrate that the relative atom velocities can be reduced to the point where the duration of the electric-field tuning pulses, and not the motion ofmore » neighboring atoms, defines the interaction time for each pair within the ensemble. Coherent, transform-limited broadening of the resonance line shape is observed as the tuning pulse duration is reduced below the natural time scale for collisions.« less

First-principles study of the solid solution of hydrogen in lanthanum

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

Schoellhammer, Gunther; Herzig, Peter; Wolf, Walter

2011-09-01

Results from first-principles investigations of the energetical, structural, electronic, and vibrational properties of model structures probing the metal-rich region of the lanthanum-hydrogen system, i.e., the region of the solid solution of hydrogen in lanthanum, are presented. We have studied the site preference and the ordering tendency of hydrogen atoms interstitially bonded in close-packed lanthanum. Spatially separated hydrogen atoms have turned out to exhibit an energetical preference for the occupation of octahedral interstitial sites at low temperature. Indications for a reversal of the site preference in favor of the occupation of tetrahedral interstitial sites at elevated temperature have been found. Linearmore » arrangements consisting of pairs of octahedrally and/or tetrahedrally coordinated hydrogen atoms collinearly bonded to a central lanthanum atom have turned out to be energetically favorable structure elements. Further stabilization is achieved if such hydrogen pairs are in turn linked together so that extended chains of La-H bonds are formed. Pair formation and chain linking counteract the energetical preference for octahedral coordination observed for separated hydrogen atoms.« less

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

PubMed Central

Chen, F.-R.; Van Dyck, D.; Kisielowski, C.

2016-01-01

Resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we report a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose rate electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. We apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances. PMID:26887849

Atomic resolution images of graphite in air

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

Grigg, D.A.; Shedd, G.M.; Griffis, D.

One sample used for proof of operation for atomic resolution in STM is highly oriented pyrolytic graphite (HOPG). This sample has been imaged with many different STM`s obtaining similar results. Atomic resolution images of HOPG have now been obtained using an STM designed and built at the Precision Engineering Center. This paper discusses the theoretical predictions and experimental results obtained in imaging of HOPG.

Dielectric constant of atomic fluids with variable polarizability

PubMed Central

Alder, B. J.; Beers, J. C.; Strauss, H. L.; Weis, J. J.

1980-01-01

The Clausius-Mossotti function for the dielectric constant is expanded in terms of single atom and pair polarizabilities, leading to contributions that depend on both the trace and the anisotropy of the pair-polarizability tensor. The short-range contribution of the anisotropic part to the pair polarizabilities has previously been obtained empirically from light scattering experiments, whereas the trace contribution is now empirically determined by comparison to dielectric experiments. For helium, the short-range trace part agrees well with electronic structure calculations, whereas for argon qualitative agreement is achieved. PMID:16592830

Dielectric constant of atomic fluids with variable polarizability.

PubMed

Alder, B J; Beers, J C; Strauss, H L; Weis, J J

1980-06-01

The Clausius-Mossotti function for the dielectric constant is expanded in terms of single atom and pair polarizabilities, leading to contributions that depend on both the trace and the anisotropy of the pair-polarizability tensor. The short-range contribution of the anisotropic part to the pair polarizabilities has previously been obtained empirically from light scattering experiments, whereas the trace contribution is now empirically determined by comparison to dielectric experiments. For helium, the short-range trace part agrees well with electronic structure calculations, whereas for argon qualitative agreement is achieved.

Two-Particle Four-Mode Interferometer for Atoms

NASA Astrophysics Data System (ADS)

Dussarrat, Pierre; Perrier, Maxime; Imanaliev, Almazbek; Lopes, Raphael; Aspect, Alain; Cheneau, Marc; Boiron, Denis; Westbrook, Christoph I.

2017-10-01

We present a free-space interferometer to observe two-particle interference of a pair of atoms with entangled momenta. The source of atom pairs is a Bose-Einstein condensate subject to a dynamical instability, and the interferometer is realized using Bragg diffraction on optical lattices, in the spirit of our recent Hong-Ou-Mandel experiment. We report on an observation ruling out the possibility of a purely mixed state at the input of the interferometer. We explain how our current setup can be extended to enable a test of a Bell inequality on momentum observables.

Scanning transmission electron microscopy: Albert Crewe's vision and beyond.

PubMed

Krivanek, Ondrej L; Chisholm, Matthew F; Murfitt, Matthew F; Dellby, Niklas

2012-12-01

Some four decades were needed to catch up with the vision that Albert Crewe and his group had for the scanning transmission electron microscope (STEM) in the nineteen sixties and seventies: attaining 0.5Å resolution, and identifying single atoms spectroscopically. With these goals now attained, STEM developments are turning toward new directions, such as rapid atomic resolution imaging and exploring atomic bonding and electronic properties of samples at atomic resolution. The accomplishments and the future challenges are reviewed and illustrated with practical examples. Copyright © 2012 Elsevier B.V. All rights reserved.

Observation of dynamic atom-atom correlation in liquid helium in real space

DOE PAGES

Dmowski, W.; Diallo, S. O.; Lokshin, K.; ...

2017-05-04

Liquid 4He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom–atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4He atoms in the Bose–Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDFmore » peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom–atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.« less

Observation of dynamic atom-atom correlation in liquid helium in real space

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

Dmowski, W.; Diallo, S. O.; Lokshin, K.

Liquid 4He becomes superfluid and flows without resistance below temperature 2.17 K. Superfluidity has been a subject of intense studies and notable advances were made in elucidating the phenomenon by experiment and theory. Nevertheless, details of the microscopic state, including dynamic atom–atom correlations in the superfluid state, are not fully understood. Here using a technique of neutron dynamic pair-density function (DPDF) analysis we show that 4He atoms in the Bose–Einstein condensate have environment significantly different from uncondensed atoms, with the interatomic distance larger than the average by about 10%, whereas the average structure changes little through the superfluid transition. DPDFmore » peak not seen in the snap-shot pair-density function is found at 2.3 Å, and is interpreted in terms of atomic tunnelling. The real space picture of dynamic atom–atom correlations presented here reveal characteristics of atomic dynamics not recognized so far, compelling yet another look at the phenomenon.« less

Autocorrelation descriptor improvements for QSAR: 2DA_Sign and 3DA_Sign

NASA Astrophysics Data System (ADS)

Sliwoski, Gregory; Mendenhall, Jeffrey; Meiler, Jens

2016-03-01

Quantitative structure-activity relationship (QSAR) is a branch of computer aided drug discovery that relates chemical structures to biological activity. Two well established and related QSAR descriptors are two- and three-dimensional autocorrelation (2DA and 3DA). These descriptors encode the relative position of atoms or atom properties by calculating the separation between atom pairs in terms of number of bonds (2DA) or Euclidean distance (3DA). The sums of all values computed for a given small molecule are collected in a histogram. Atom properties can be added with a coefficient that is the product of atom properties for each pair. This procedure can lead to information loss when signed atom properties are considered such as partial charge. For example, the product of two positive charges is indistinguishable from the product of two equivalent negative charges. In this paper, we present variations of 2DA and 3DA called 2DA_Sign and 3DA_Sign that avoid information loss by splitting unique sign pairs into individual histograms. We evaluate these variations with models trained on nine datasets spanning a range of drug target classes. Both 2DA_Sign and 3DA_Sign significantly increase model performance across all datasets when compared with traditional 2DA and 3DA. Lastly, we find that limiting 3DA_Sign to maximum atom pair distances of 6 Å instead of 12 Å further increases model performance, suggesting that conformational flexibility may hinder performance with longer 3DA descriptors. Consistent with this finding, limiting the number of bonds in 2DA_Sign from 11 to 5 fails to improve performance.

Atomic-Resolution Spectrum Imaging of Semiconductor Nanowires.

PubMed

Zamani, Reza R; Hage, Fredrik S; Lehmann, Sebastian; Ramasse, Quentin M; Dick, Kimberly A

2018-03-14

Over the past decade, III-V heterostructure nanowires have attracted a surge of attention for their application in novel semiconductor devices such as tunneling field-effect transistors (TFETs). The functionality of such devices critically depends on the specific atomic arrangement at the semiconductor heterointerfaces. However, most of the currently available characterization techniques lack sufficient spatial resolution to provide local information on the atomic structure and composition of these interfaces. Atomic-resolution spectrum imaging by means of electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope (STEM) is a powerful technique with the potential to resolve structure and chemical composition with sub-angstrom spatial resolution and to provide localized information about the physical properties of the material at the atomic scale. Here, we demonstrate the use of atomic-resolution EELS to understand the interface atomic arrangement in three-dimensional heterostructures in semiconductor nanowires. We observed that the radial interfaces of GaSb-InAs heterostructure nanowires are atomically abrupt, while the axial interface in contrast consists of an interfacial region where intermixing of the two compounds occurs over an extended spatial region. The local atomic configuration affects the band alignment at the interface and, hence, the charge transport properties of devices such as GaSb-InAs nanowire TFETs. STEM-EELS thus represents a very promising technique for understanding nanowire physical properties, such as differing electrical behavior across the radial and axial heterointerfaces of GaSb-InAs nanowires for TFET applications.

Experimental purification of two-atom entanglement.

PubMed

Reichle, R; Leibfried, D; Knill, E; Britton, J; Blakestad, R B; Jost, J D; Langer, C; Ozeri, R; Seidelin, S; Wineland, D J

2006-10-19

Entanglement is a necessary resource for quantum applications--entanglement established between quantum systems at different locations enables private communication and quantum teleportation, and facilitates quantum information processing. Distributed entanglement is established by preparing an entangled pair of quantum particles in one location, and transporting one member of the pair to another location. However, decoherence during transport reduces the quality (fidelity) of the entanglement. A protocol to achieve entanglement 'purification' has been proposed to improve the fidelity after transport. This protocol uses separate quantum operations at each location and classical communication to distil high-fidelity entangled pairs from lower-fidelity pairs. Proof-of-principle experiments distilling entangled photon pairs have been carried out. However, these experiments obtained distilled pairs with a low probability of success and required destruction of the entangled pairs, rendering them unavailable for further processing. Here we report efficient and non-destructive entanglement purification with atomic quantum bits. Two noisy entangled pairs were created and distilled into one higher-fidelity pair available for further use. Success probabilities were above 35 per cent. The many applications of entanglement purification make it one of the most important techniques in quantum information processing.

Beyond-Born-Oppenheimer effects in sub-kHz-precision photoassociation spectroscopy of ytterbium atoms

NASA Astrophysics Data System (ADS)

Borkowski, Mateusz; Buchachenko, Alexei A.; Ciuryło, Roman; Julienne, Paul S.; Yamada, Hirotaka; Kikuchi, Yuu; Takahashi, Kakeru; Takasu, Yosuke; Takahashi, Yoshiro

2017-12-01

We present high-resolution two-color photoassociation spectroscopy of Bose-Einstein condensates of ytterbium atoms. The use of narrow Raman resonances and careful examination of systematic shifts enabled us to measure 13 bound-state energies for three isotopologues of the ground-state ytterbium molecule with standard uncertainties of the order of 500 Hz. The atomic interactions are modeled using an ab initio based mass-scaled Born-Oppenheimer potential whose long-range van der Waals parameters and total WKB phase are fitted to experimental data. We find that the quality of the fit of this model, of about 112.9 kHz (rms) can be significantly improved by adding the recently calculated beyond-Born-Oppenheimer (BBO) adiabatic corrections [J. J. Lutz and J. M. Hutson, J. Mol. Spectrosc. 330, 43 (2016), 10.1016/j.jms.2016.08.007] and by partially treating the nonadiabatic effects using distance-dependent reduced masses. Our BBO interaction model represents the experimental data to within about 30.2 kHz on average, which is 3.7 times better than the "reference" Born-Oppenheimer model. We calculate the s -wave scattering lengths for bosonic isotopic pairs of ytterbium atoms with error bars over two orders of magnitude smaller than previous determinations. For example, the s -wave scattering length for 174Yb is +5.55812 (50 ) nm.

Probing Long-Range Neutrino-Mediated Forces with Atomic and Nuclear Spectroscopy.

PubMed

Stadnik, Yevgeny V

2018-06-01

The exchange of a pair of low-mass neutrinos between electrons, protons, and neutrons produces a "long-range" 1/r^{5} potential, which can be sought for in phenomena originating on the atomic and subatomic length scales. We calculate the effects of neutrino-pair exchange on transition and binding energies in atoms and nuclei. In the case of atomic s-wave states, there is a large enhancement of the induced energy shifts due to the lack of a centrifugal barrier and the highly singular nature of the neutrino-mediated potential. We derive limits on neutrino-mediated forces from measurements of the deuteron binding energy and transition energies in positronium, muonium, hydrogen, and deuterium, as well as isotope-shift measurements in calcium ions. Our limits improve on existing constraints on neutrino-mediated forces from experiments that search for new macroscopic forces by 18 orders of magnitude. Future spectroscopy experiments have the potential to probe long-range forces mediated by the exchange of pairs of standard-model neutrinos and other weakly charged particles.

Probing Long-Range Neutrino-Mediated Forces with Atomic and Nuclear Spectroscopy

NASA Astrophysics Data System (ADS)

Stadnik, Yevgeny V.

2018-06-01

The exchange of a pair of low-mass neutrinos between electrons, protons, and neutrons produces a "long-range" 1 /r5 potential, which can be sought for in phenomena originating on the atomic and subatomic length scales. We calculate the effects of neutrino-pair exchange on transition and binding energies in atoms and nuclei. In the case of atomic s -wave states, there is a large enhancement of the induced energy shifts due to the lack of a centrifugal barrier and the highly singular nature of the neutrino-mediated potential. We derive limits on neutrino-mediated forces from measurements of the deuteron binding energy and transition energies in positronium, muonium, hydrogen, and deuterium, as well as isotope-shift measurements in calcium ions. Our limits improve on existing constraints on neutrino-mediated forces from experiments that search for new macroscopic forces by 18 orders of magnitude. Future spectroscopy experiments have the potential to probe long-range forces mediated by the exchange of pairs of standard-model neutrinos and other weakly charged particles.

Creation of economical and robust large area MCPs by ALD method for photodetectors

NASA Astrophysics Data System (ADS)

Mane, Anil U.; Elam, Jeffrey W.; Wagner, Robert G.; Siegmund, Oswald H. W.; Minot, Michael J.

2016-09-01

We report a cost-effective and production achievable path to fabricate robust large-area microchannel plates (MCPs), which offers the new prospect for larger area MCP-based detector technologies. We used atomic Layer Deposition (ALD), a thin film growth technique, to independently adjust the desired electrical resistance and secondary electron emission (SEE) properties of low cost borosilicate glass micro-capillary arrays (MCAs). These capabilities allow a separation of the substrate material properties from the signal amplification properties. This methodology enables the functionalization of microporous, highly insulating MCA substrates to produce sturdy, large format MCPs with unique properties such as high gain (<107/MCP pair), low background noise, 10ps time resolution, sub-micron spatial resolution and excellent stability after only a short (2-3days) scrubbing time. The ALD self-limiting growth mechanism allows atomic level control over the thickness and composition of resistive and secondary electron emission (SEE) layers that can be deposited conformally on high aspect ratio ( 100) capillary glass arrays. We have developed several robust and consistent production doable ALD processes for the resistive coatings and SEE layers to give us precise control over the MCP parameters. Further, the adjustment of MCPs resistance by tailoring the ALD material composition permits the use of these MCPs at high or low temperature detector applications. Here we discuss ALD method for MCP functionalization and a variety of MCP testing results.

The First Row Anomaly and Recoupled Pair Bonding in the Halides of the Late p-Block Elements

PubMed Central

2012-01-01

The dramatic differences between the properties of molecules formed from the late p-block elements of the first row of the periodic table (N–F) and those of the corresponding elements in subsequent rows is well recognized as the first row anomaly. Certain properties of the atoms, such as the relative energies and spatial extents of the ns and np orbitals, can explain some of these differences, but not others. In this Account, we summarize the results of our recent computational studies of the halides of the late p-block elements. Our studies point to a single underlying cause for many of these differences: the ability of the late p-block elements in the second and subsequent rows of the periodic table to form recoupled pair bonds and recoupled pair bond dyads with very electronegative ligands. Recoupled pair bonds form when an electron in a singly occupied ligand orbital recouples the pair of electrons in a doubly occupied lone pair orbital on the central atom, leading to a central atom-ligand bond. Recoupled pair bond dyads occur when a second ligand forms a bond with the orbital left over from the initial recoupled pair bond. Recoupled pair bonds and recoupled pair bond dyads enable the late p-block elements to form remarkably stable hypervalent compounds such as PF5 and SF6 and lead to unexpected excited states in smaller halides of the late p-block elements such as SF and SF2. Recoupled pair bonding also causes the Fn–1X–F bond energies to oscillate dramatically once the normal valences of the central atoms have been satisfied. In addition, recoupled pair bonding provides a lower-energy pathway for inversion in heavily fluorinated compounds (PF3 and PF2H, but not PH2F and PH3) and leads to unusual intermediates and products in reactions involving halogens and late p-block element compounds, such as (CH3)2S + F2. Although this Account focuses on the halides of the second row, late p-block elements, recoupled pair bonds and recoupled pair bond dyads are important in the chemistry of p-block elements beyond the second row (As, Se, and Br) and for compounds of these elements with other very electronegative ligands, such as OH and O. Knowledge of recoupled pair bonding is thus critical to understanding the properties and reactivity of molecules containing the late p-block elements beyond the first row. PMID:23151313

The first row anomaly and recoupled pair bonding in the halides of the late p-block elements.

PubMed

Dunning, Thom H; Woon, David E; Leiding, Jeff; Chen, Lina

2013-02-19

The dramatic differences between the properties of molecules formed from the late p-block elements of the first row of the periodic table (N-F) and those of the corresponding elements in subsequent rows is well recognized as the first row anomaly. Certain properties of the atoms, such as the relative energies and spatial extents of the ns and np orbitals, can explain some of these differences, but not others. In this Account, we summarize the results of our recent computational studies of the halides of the late p-block elements. Our studies point to a single underlying cause for many of these differences: the ability of the late p-block elements in the second and subsequent rows of the periodic table to form recoupled pair bonds and recoupled pair bond dyads with very electronegative ligands. Recoupled pair bonds form when an electron in a singly occupied ligand orbital recouples the pair of electrons in a doubly occupied lone pair orbital on the central atom, leading to a central atom-ligand bond. Recoupled pair bond dyads occur when a second ligand forms a bond with the orbital left over from the initial recoupled pair bond. Recoupled pair bonds and recoupled pair bond dyads enable the late p-block elements to form remarkably stable hypervalent compounds such as PF(5) and SF(6) and lead to unexpected excited states in smaller halides of the late p-block elements such as SF and SF(2). Recoupled pair bonding also causes the F(n-1)X-F bond energies to oscillate dramatically once the normal valences of the central atoms have been satisfied. In addition, recoupled pair bonding provides a lower-energy pathway for inversion in heavily fluorinated compounds (PF(3) and PF(2)H, but not PH(2)F and PH(3)) and leads to unusual intermediates and products in reactions involving halogens and late p-block element compounds, such as (CH(3))(2)S + F(2). Although this Account focuses on the halides of the second row, late p-block elements, recoupled pair bonds and recoupled pair bond dyads are important in the chemistry of p-block elements beyond the second row (As, Se, and Br) and for compounds of these elements with other very electronegative ligands, such as OH and O. Knowledge of recoupled pair bonding is thus critical to understanding the properties and reactivity of molecules containing the late p-block elements beyond the first row.

In-line three-dimensional holography of nanocrystalline objects at atomic resolution

DOE PAGES

Chen, F. -R.; Van Dyck, D.; Kisielowski, C.

2016-02-18

We report that resolution and sensitivity of the latest generation aberration-corrected transmission electron microscopes allow the vast majority of single atoms to be imaged with sub-Ångstrom resolution and their locations determined in an image plane with a precision that exceeds the 1.9-pm wavelength of 300 kV electrons. Such unprecedented performance allows expansion of electron microscopic investigations with atomic resolution into the third dimension. Here we show a general tomographic method to recover the three-dimensional shape of a crystalline particle from high-resolution images of a single projection without the need for sample rotation. The method is compatible with low dose ratemore » electron microscopy, which improves on signal quality, while minimizing electron beam-induced structure modifications even for small particles or surfaces. Lastly, we apply it to germanium, gold and magnesium oxide particles, and achieve a depth resolution of 1–2 Å, which is smaller than inter-atomic distances.« less

xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.

PubMed

McGreevy, Ryan; Singharoy, Abhishek; Li, Qufei; Zhang, Jingfen; Xu, Dong; Perozo, Eduardo; Schulten, Klaus

2014-09-01

X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7 Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.

Attractive electron-electron interactions within robust local fitting approximations.

PubMed

Merlot, Patrick; Kjærgaard, Thomas; Helgaker, Trygve; Lindh, Roland; Aquilante, Francesco; Reine, Simen; Pedersen, Thomas Bondo

2013-06-30

An analysis of Dunlap's robust fitting approach reveals that the resulting two-electron integral matrix is not manifestly positive semidefinite when local fitting domains or non-Coulomb fitting metrics are used. We present a highly local approximate method for evaluating four-center two-electron integrals based on the resolution-of-the-identity (RI) approximation and apply it to the construction of the Coulomb and exchange contributions to the Fock matrix. In this pair-atomic resolution-of-the-identity (PARI) approach, atomic-orbital (AO) products are expanded in auxiliary functions centered on the two atoms associated with each product. Numerical tests indicate that in 1% or less of all Hartree-Fock and Kohn-Sham calculations, the indefinite integral matrix causes nonconvergence in the self-consistent-field iterations. In these cases, the two-electron contribution to the total energy becomes negative, meaning that the electronic interaction is effectively attractive, and the total energy is dramatically lower than that obtained with exact integrals. In the vast majority of our test cases, however, the indefiniteness does not interfere with convergence. The total energy accuracy is comparable to that of the standard Coulomb-metric RI method. The speed-up compared with conventional algorithms is similar to the RI method for Coulomb contributions; exchange contributions are accelerated by a factor of up to eight with a triple-zeta quality basis set. A positive semidefinite integral matrix is recovered within PARI by introducing local auxiliary basis functions spanning the full AO product space, as may be achieved by using Cholesky-decomposition techniques. Local completion, however, slows down the algorithm to a level comparable with or below conventional calculations. Copyright © 2013 Wiley Periodicals, Inc.

Properties of atomic pairs produced in the collision of Bose-Einstein condensates

NASA Astrophysics Data System (ADS)

Ziń, Paweł; Wasak, Tomasz

2018-04-01

During a collision of Bose-Einstein condensates correlated pairs of atoms are emitted. The scattered massive particles, in analogy to photon pairs in quantum optics, might be used in the violation of Bell's inequalities, demonstration of Einstein-Podolsky-Rosen correlations, or sub-shot-noise atomic interferometry. Usually, a theoretical description of the collision relies either on stochastic numerical methods or on analytical treatments involving various approximations. Here, we investigate elastic scattering of atoms from colliding elongated Bose-Einstein condensates within the Bogoliubov method, carefully controlling performed approximations at every stage of the analysis. We derive expressions for the one- and two-particle correlation functions. The obtained formulas, which relate the correlation functions to the condensate wave function, are convenient for numerical calculations. We employ the variational approach for condensate wave functions to obtain analytical expressions for the correlation functions, whose properties we analyze in detail. We also present a useful semiclassical model of the process and compare its results with the quantum one. The results are relevant for recent experiments with excited helium atoms, as well as for planned experiments aimed at investigating the nonclassicality of the system.

Full Counting Statistics for Interacting Fermions with Determinantal Quantum Monte Carlo Simulations.

PubMed

Humeniuk, Stephan; Büchler, Hans Peter

2017-12-08

We present a method for computing the full probability distribution function of quadratic observables such as particle number or magnetization for the Fermi-Hubbard model within the framework of determinantal quantum Monte Carlo calculations. Especially in cold atom experiments with single-site resolution, such a full counting statistics can be obtained from repeated projective measurements. We demonstrate that the full counting statistics can provide important information on the size of preformed pairs. Furthermore, we compute the full counting statistics of the staggered magnetization in the repulsive Hubbard model at half filling and find excellent agreement with recent experimental results. We show that current experiments are capable of probing the difference between the Hubbard model and the limiting Heisenberg model.

Systematics of ground state multiplets of atomic nuclei in the delta-interaction approach

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

Imasheva, L. T.; Ishkhanov, B. S.; Stepanov, M. E., E-mail: stepanov@depni.sinp.msu.ru

2015-12-15

Pairing forces between nucleons in an atomic nucleus strongly influence its structure. One of the manifestations of pair interaction is the ground state multiplet (GSM) formation in the spectrum of low-lying excited states of even–even nuclei. The value of GSM splitting is determined by the value of pair interaction of nucleons; for each isotope, it can be estimated on the basis of experimental nuclear masses. The quality of this estimate is characterized by the degree of reproduction of GSM levels in the nucleus. The GSM systematics in even–even nuclei with a pair of identical nucleons in addition to the filledmore » nuclear core is considered on the basis of delta interaction.« less

Ultrabright, narrow-band photon-pair source for atomic quantum memories

NASA Astrophysics Data System (ADS)

Tsai, Pin-Ju; Chen, Ying-Cheng

2018-06-01

We demonstrate an ultrabright, narrow-band and frequency-tunable photon-pair source based on cavity-enhanced spontaneous parametric down conversion (SPDC) which is compatible with atomic transition of rubidium D 2-line (780 nm) or cesium D 2-line (852 nm). With the pump beam alternating between a high and a low power phase, the output is switching between the optical parametric oscillator (OPO) and photon-pair generation mode. We utilize the OPO output light to lock the cavity length to maintain the double resonances of signal and idler, as well as to lock the signal frequency to cesium atomic transition. With a type-II phase matching and a double-passed pump scheme such that the cluster frequency spacing is larger than the SPDC bandwidth, the photon-pair output is in a nearly single-mode operation as confirmed by a scanning Fabry–Perot interferometer with its output detected by a photomultiplier. The achieved generation and detection rates are 7.24× {10}5 and 6142 s‑1 mW‑1, respectively. The correlation time of the photon pair is 21.6(2.2) ns, corresponding to a bandwidth of 2π × 6.6(6) MHz. The spectral brightness is 1.06× {10}5 s‑1 mW‑1 MHz‑1. This is a relatively high value under a single-mode operation with the cavity-SPDC scheme. The generated single photons can be readily used in experiments related to atomic quantum memories.

Very strong Rydberg atom scattering in K(12p)-CH3NO2 collisions: Role of transient ion pair formation

NASA Astrophysics Data System (ADS)

Kelley, M.; Buathong, S.; Dunning, F. B.

2017-05-01

Collisions between K(12p) Rydberg atoms and CH3NO2 target molecules are studied. Whereas CH3NO2 can form long-lived valence-bound CH3NO2-ions, the data provide no evidence for production of long-lived K+⋯ CH3NO2 - ion pair states. Rather, the data show that collisions result in unusually strong Rydberg atom scattering. This behavior is attributed to ion-ion scattering resulting from formation of transient ion pair states through transitions between the covalent K(12p) + CH3NO2 and ionic K+ + (dipole bound) CH3NO2-terms in the quasimolecule formed during collisions. The ion-pair states are destroyed through rapid dissociation of the CH3NO2 - ions induced by the field of the K+ core ion, the detached electron remaining bound to the K+ ion in a Rydberg state. Analysis of the experimental data shows that ion pair lifetimes ≳10 ps are sufficient to account for the present observations. The present results are consistent with recent theoretical predictions that Rydberg collisions with CH3NO2 will result in strong collisional quenching. The work highlights a new mechanism for Rydberg atom scattering that could be important for collisions with other polar targets. For purposes of comparison, results obtained following K(12p)-SF6 collisions are also included.

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

Rodriguez, Jose A.; Ivanova, Magdalena I.; Sawaya, Michael R.

We report that the protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates thatmore » this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. Finally, the NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.« less

Simulation of atomic diffusion in the Fcc NiAl system: A kinetic Monte Carlo study

DOE PAGES

Alfonso, Dominic R.; Tafen, De Nyago

2015-04-28

The atomic diffusion in fcc NiAl binary alloys was studied by kinetic Monte Carlo simulation. The environment dependent hopping barriers were computed using a pair interaction model whose parameters were fitted to relevant data derived from electronic structure calculations. Long time diffusivities were calculated and the effect of composition change on the tracer diffusion coefficients was analyzed. These results indicate that this variation has noticeable impact on the atomic diffusivities. A reduction in the mobility of both Ni and Al is demonstrated with increasing Al content. As a result, examination of the pair interaction between atoms was carried out formore » the purpose of understanding the predicted trends.« less

Image super-resolution via sparse representation.

PubMed

Yang, Jianchao; Wright, John; Huang, Thomas S; Ma, Yi

2010-11-01

This paper presents a new approach to single-image super-resolution, based on sparse signal representation. Research on image statistics suggests that image patches can be well-represented as a sparse linear combination of elements from an appropriately chosen over-complete dictionary. Inspired by this observation, we seek a sparse representation for each patch of the low-resolution input, and then use the coefficients of this representation to generate the high-resolution output. Theoretical results from compressed sensing suggest that under mild conditions, the sparse representation can be correctly recovered from the downsampled signals. By jointly training two dictionaries for the low- and high-resolution image patches, we can enforce the similarity of sparse representations between the low resolution and high resolution image patch pair with respect to their own dictionaries. Therefore, the sparse representation of a low resolution image patch can be applied with the high resolution image patch dictionary to generate a high resolution image patch. The learned dictionary pair is a more compact representation of the patch pairs, compared to previous approaches, which simply sample a large amount of image patch pairs, reducing the computational cost substantially. The effectiveness of such a sparsity prior is demonstrated for both general image super-resolution and the special case of face hallucination. In both cases, our algorithm generates high-resolution images that are competitive or even superior in quality to images produced by other similar SR methods. In addition, the local sparse modeling of our approach is naturally robust to noise, and therefore the proposed algorithm can handle super-resolution with noisy inputs in a more unified framework.

Mapping atomic motions with ultrabright electrons: towards fundamental limits in space-time resolution.

PubMed

Manz, Stephanie; Casandruc, Albert; Zhang, Dongfang; Zhong, Yinpeng; Loch, Rolf A; Marx, Alexander; Hasegawa, Taisuke; Liu, Lai Chung; Bayesteh, Shima; Delsim-Hashemi, Hossein; Hoffmann, Matthias; Felber, Matthias; Hachmann, Max; Mayet, Frank; Hirscht, Julian; Keskin, Sercan; Hada, Masaki; Epp, Sascha W; Flöttmann, Klaus; Miller, R J Dwayne

2015-01-01

The long held objective of directly observing atomic motions during the defining moments of chemistry has been achieved based on ultrabright electron sources that have given rise to a new field of atomically resolved structural dynamics. This class of experiments requires not only simultaneous sub-atomic spatial resolution with temporal resolution on the 100 femtosecond time scale but also has brightness requirements approaching single shot atomic resolution conditions. The brightness condition is in recognition that chemistry leads generally to irreversible changes in structure during the experimental conditions and that the nanoscale thin samples needed for electron structural probes pose upper limits to the available sample or "film" for atomic movies. Even in the case of reversible systems, the degree of excitation and thermal effects require the brightest sources possible for a given space-time resolution to observe the structural changes above background. Further progress in the field, particularly to the study of biological systems and solution reaction chemistry, requires increased brightness and spatial coherence, as well as an ability to tune the electron scattering cross-section to meet sample constraints. The electron bunch density or intensity depends directly on the magnitude of the extraction field for photoemitted electron sources and electron energy distribution in the transverse and longitudinal planes of electron propagation. This work examines the fundamental limits to optimizing these parameters based on relativistic electron sources using re-bunching cavity concepts that are now capable of achieving 10 femtosecond time scale resolution to capture the fastest nuclear motions. This analysis is given for both diffraction and real space imaging of structural dynamics in which there are several orders of magnitude higher space-time resolution with diffraction methods. The first experimental results from the Relativistic Electron Gun for Atomic Exploration (REGAE) are given that show the significantly reduced multiple electron scattering problem in this regime, which opens up micron scale systems, notably solution phase chemistry, to atomically resolved structural dynamics.

Conductive Atomic Force Microscopy | Materials Science | NREL

Science.gov Websites

electrical measurement techniques is the high spatial resolution. For example, C-AFM measurements on : High-resolution image of a sample semiconductor device; the image shows white puff-like clusters on a dark background and was obtained using atomic force microscopy. Bottom: High-resolution image of the

Mapping the geographic distribution of canopy species communities in lowland Amazon rainforest with CAO-AToMS (Invited)

NASA Astrophysics Data System (ADS)

Feret, J.; Asner, G. P.

2013-12-01

Mapping regional canopy diversity will greatly advance our understanding as well as the conservation of tropical rainforests. Changes in species composition across space and time are particularly important to understand the influence of climate, human activity and environmental factors on these ecosystems, but to date such monitoring is extremely challenging and is facing a scale gap between small-scale, highly detailed field studies and large-scale, low-resolution satellite observations. Advances were recently made in the field of spectroscopic imagery for the estimation of canopy alpha-diversity, and an original approach based on the segmentation of the spectral space proved its ability to estimate Shannon diversity index with unprecedented accuracy. We adapted this method in order to estimate spectral dissimilarity across landscape as a proxy for changes in species composition. We applied this approach and mapped species composition over four sites located in lowland rainforest of Peruvian Amazon. This study was based on spectroscopic imagery acquired using the Carnegie Airborne Observatory (CAO) Airborne Taxonomic Mapping System (AToMS), operating a unique sensor combining the fine spectral and spatial resolution required for such task. We obtained accurate estimation of Bray-Curtis distance between pairs of plots, which is the most commonly used metric to estimate dissimilarity in species composition (n=497 pairs, r=0.63). The maps of species composition were then compared to topo-hydrographic properties. Our results indicated a strong shift in species composition and community diversity between floodplain and terra firme terrain conditions as well as a significantly higher diversity of species communities within Amazonian floodplains. These results pave the way for global mapping of tropical canopy diversity at fine geographic resolution.

Pilot Production of Large Area Microchannel Plates and Picosecond Photodetectors

NASA Astrophysics Data System (ADS)

Minot, M.; Adams, B.; Abiles, M.; Bond, J.; Craven, C.; Cremer, T.; Foley, M.; Lyashenko, A.; Popecki, M.; Stochaj, M.; Worstell, W.; Elam, J.; Mane, A.; Siegmund, O.; Ertley, C.

2016-09-01

Pilot production performance is reported for large area atomic layer deposition (ALD) coated microchannel plates (ALD-GCA-MCPs) and for Large Area Picosecond Photodetectors (LAPPD™) which incorporate them. "Hollowcore" glass capillary array (GCA) substrates are coated with ALD resistive and emissive layers to form the ALDGCA- MCPs, an approach that facilitates independent selection of glass substrates that are mechanically stronger and that have lower levels of radioactive alkali elements compared to conventional MCP lead glass, reducing background noise[1,2,3,4]. ALD-GCA-MCPs have competitive gain ( 104 each or 107 for a chevron pair ), enhanced lifetime and gain stability (7 C cm-2 of charge extraction), reduced background levels (0.028 events cm-2 sec-1) and low gamma-ray detection efficiency. They can be fabricated in large area (20cm X 20 cm) planar and curved formats suitable for use in high radiation environment applications, including astronomy, space instrumentation, and remote night time sensing. The LAPPD™ photodetector incorporates these ALD-GCA-MCPs in an all-glass hermetic package with top and bottom plates and sidewalls made of borosilicate float glass. Signals are generated by a bi-alkali Na2KSb photocathode, amplified with a stacked chevron pair of ALD-GCA-MCPs. Signals are collected on RF strip-line anodes integrated into to the bottom plates which exit the detector via pin-free hermetic seals under the side walls [5]. Tests show that LAPPDTMs have electron gains greater than 107, submillimeter spatial resolution for large (multiphoton) pulses and several mm for single photons, time resolution less than 50 picoseconds for single photons, predicted resolution less than 5 picoseconds for large pulses, high stability versus charge extraction[6], and good uniformity for applications including astrophysics, neutron detection, high energy physics Cherenkov light detection, and quantum-optical photon-correlation experiments.

Determination of atomic positions from time resolved high resolution transmission electron microscopy images.

PubMed

Hussaini, Zahra; Lin, Pin Ann; Natarajan, Bharath; Zhu, Wenhui; Sharma, Renu

2018-03-01

For many reaction processes, such as catalysis, phase transformations, nanomaterial synthesis etc., nanoscale observations at high spatial (sub-nanometer) and temporal (millisecond) resolution are required to characterize and comprehend the underlying factors that favor one reaction over another. The combination of such spatial and temporal resolution (up to 600 µs), while rich in information, produces a large number of snapshots, each of which must be analyzed to obtain the structural (and thereby chemical) information. Here we present a methodology for automated quantitative measurement of real-time atomic position fluctuations in a nanoparticle. We leverage a combination of several image processing algorithms to precisely identify the positions of the atomic columns in each image. A geometric model is then used to measure the time-evolution of distances and angles between neighboring atomic columns to identify different phases and quantify local structural fluctuations. We apply this technique to determine the atomic-level fluctuations in the relative fractions of metal and metal-carbide phases in a cobalt catalyst nanoparticle during single-walled carbon nanotube (SWCNT) growth. These measurements provided a means to obtain the number of carbon atoms incorporated into and released from the catalyst particle, thereby helping resolve carbon reaction pathways during SWCNT growth. Further we demonstrate the use of this technique to measure the reaction kinetics of iron oxide reduction. Apart from reducing the data analysis time, the statistical approach allows us to measure atomic distances with sub-pixel resolution. We show that this method can be applied universally to measure atomic positions with a precision of 0.01 nm from any set of atomic-resolution video images. With the advent of high time-resolution direct detection cameras, we anticipate such methods will be essential in addressing the metrology problem of quantifying large datasets of time-resolved images in future. Published by Elsevier B.V.

Effects of ligand electronegativity on recoupled pair bonds with application to sulfurane precursors.

PubMed

Lindquist, Beth A; Woon, David E; Dunning, Thom H

2014-07-31

Recoupled pair bonds (RPBs) are conditional bonds-they only form for selected central atoms and ligands. A complete theoretical description of RPBs requires an understanding of the properties of the central atom and ligands that enable such bonds to be formed. In this work, we show that ligand electronegativity is positively correlated with recoupled pair bond strength for a variety of ligands interacting with the 3p(2) pair of sulfur. We also describe substituent (X) effects on the SF(a(4)Σ(-)) state by investigating X2SF species. These effects generally mirror those observed for covalently bound analogues, but we found that recoupled pair bonding can lead to breakdowns in the expected relationships among bond length, strength, and force constant for some of these species. Finally, we compare the properties of two molecules of practical interest that are bound by recoupled pair bonds: the dimethyl sulfur fluoride and hydroxide radicals (DMS-F and DMS-OH).

Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures.

PubMed

Kirillova, Svetlana; Carugo, Oliviero

2011-10-19

Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs.

Hydration sites of unpaired RNA bases: a statistical analysis of the PDB structures

PubMed Central

2011-01-01

Background Hydration is crucial for RNA structure and function. X-ray crystallography is the most commonly used method to determine RNA structures and hydration and, therefore, statistical surveys are based on crystallographic results, the number of which is quickly increasing. Results A statistical analysis of the water molecule distribution in high-resolution X-ray structures of unpaired RNA nucleotides showed that: different bases have the same penchant to be surrounded by water molecules; clusters of water molecules indicate possible hydration sites, which, in some cases, match those of the major and minor grooves of RNA and DNA double helices; complex hydrogen bond networks characterize the solvation of the nucleotides, resulting in a significant rigidity of the base and its surrounding water molecules. Interestingly, the hydration sites around unpaired RNA bases do not match, in general, the positions that are occupied by the second nucleotide when the base-pair is formed. Conclusions The hydration sites around unpaired RNA bases were found. They do not replicate the atom positions of complementary bases in the Watson-Crick pairs. PMID:22011380

Ab initio calculation of atomic interactions on Al(110): implications for epitaxial growth

NASA Astrophysics Data System (ADS)

Fichthorn, Kristen; Tiwary, Yogesh

2007-03-01

Using first-principles calculations based on density-functional theory, we resolved atomic interactions between adsorbed Al atoms on Al(110). Relevant pair and trio interactions were quantified. We find that pair interactions extend to the third in-channel and second cross-channel neighbor on the anisotropic (110) surface. Beyond these distances, pair interactions are negligible. The nearest-neighbor interaction in the in-channel direction is attractive, but nearest-neighbor cross-channel interaction is repulsive. While nearest-neighbor, cross-channel repulsion does not support the experimental observation of 3D hut formation in Al/Al(110) homoepitaxial growth [1], we find that trio interactions can be significant and attractive and they support cross-channel bonding. The pair and trio interactions have direct and indirect components. We have quantified the electronic and elastic components of the indirect, substrate-mediated interactions. We also probe the influence of these interactions on the energy barriers for adatom hopping. [1] F. Buatier de Mongeot, W. Zhu, A. Molle, R. Buzio, C. Boragno, U. Valbusa, E. Wang, and Z. Zhang, Phys. Rev. Lett. 91, 016102 (2003).

Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible (3)He/10 T cryostat.

PubMed

von Allwörden, H; Ruschmeier, K; Köhler, A; Eelbo, T; Schwarz, A; Wiesendanger, R

2016-07-01

The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped (3)He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambers are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).

Length-extension resonator as a force sensor for high-resolution frequency-modulation atomic force microscopy in air.

PubMed

Beyer, Hannes; Wagner, Tino; Stemmer, Andreas

2016-01-01

Frequency-modulation atomic force microscopy has turned into a well-established method to obtain atomic resolution on flat surfaces, but is often limited to ultra-high vacuum conditions and cryogenic temperatures. Measurements under ambient conditions are influenced by variations of the dew point and thin water layers present on practically every surface, complicating stable imaging with high resolution. We demonstrate high-resolution imaging in air using a length-extension resonator operating at small amplitudes. An additional slow feedback compensates for changes in the free resonance frequency, allowing stable imaging over a long period of time with changing environmental conditions.

Reduction of Solvent Effect in Reverse Phase Gradient Elution LC-ICP-MS

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

Sullivan, Patrick Allen

2005-12-17

Quantification in liquid chromatography (LC) is becoming very important as more researchers are using LC, not as an analytical tool itself, but as a sample introduction system for other analytical instruments. The ability of LC instrumentation to quickly separate a wide variety of compounds makes it ideal for analysis of complex mixtures. For elemental speciation, LC is joined with inductively coupled plasma mass spectrometry (ICP-MS) to separate and detect metal-containing, organic compounds in complex mixtures, such as biological samples. Often, the solvent gradients required to perform complex separations will cause matrix effects within the plasma. This limits the sensitivity ofmore » the ICP-MS and the quantification methods available for use in such analyses. Traditionally, isotope dilution has been the method of choice for LC-ICP-MS quantification. The use of naturally abundant isotopes of a single element in quantification corrects for most of the effects that LC solvent gradients produce within the plasma. However, not all elements of interest in speciation studies have multiple naturally occurring isotopes; and polyatomic interferences for a given isotope can develop within the plasma, depending on the solvent matrix. This is the case for reverse phase LC separations, where increasing amounts of organic solvent are required. For such separations, an alternative to isotope dilution for quantification would be is needed. To this end, a new method was developed using the Apex-Q desolvation system (ESI, Omaha, NE) to couple LC instrumentation with an ICP-MS device. The desolvation power of the system allowed greater concentrations of methanol to be introduced to the plasma prior to destabilization than with direct methanol injection into the plasma. Studies were performed, using simulated and actual linear methanol gradients, to find analyte-internal standard (AIS) pairs whose ratio remains consistent (deviations {+-} 10%) over methanol concentration ranges of 5%-35% (simulated) and 8%-32% (actual). Quadrupole (low resolution) and sector field (high resolution) ICP-MS instrumentation were utilized in these studies. Once an AIS pair is determined, quantification studies can be performed. First, an analysis is performed by adding both elements of the AIS pair post-column while performing the gradient elution without sample injection. A comparison of the ratio of the measured intensities to the atomic ratio of the two standards is used to determine a correction factor that can be used to account for the matrix effects caused by the mobile phase. Then, organic and/or biological molecules containing one of the two elements in the AIS pair are injected into the LC column. A gradient method is used to vary the methanol-water mixture in the mobile phase and to separate out the compounds in a given sample. A standard solution of the second ion in the AIS pair is added continuously post-column. By comparing the ratio of the measured intensities to the atomic ratio of the eluting compound and internal standard, the concentration of the injected compound can be determined.« less

Cluster adsorption on amorphous and crystalline surfaces - A molecular dynamics study of model Pt on Cu and model Pd on Pt

NASA Technical Reports Server (NTRS)

Garofalini, S. H.; Halicioglu, T.; Pound, G. M.

1981-01-01

Molecular dynamics was used to study the structure, dispersion and short-time behavior of ten-atom clusters adsorbed onto amorphous and crystalline substrates, in which the cluster atoms differed from the substrate atoms. Two adatom-substrate model systems were chosen; one, in which the interaction energy between adatom pairs was greater than that between substrate pairs, and the other, in which the reverse was true. At relatively low temperature ranges, increased dispersion of cluster atoms occurred: (a) on the amorphous substrate as compared to the FCC(100) surface, (b) with increasing reduced temperature, and (c) with adatom-substrate interaction energy stronger than adatom-adatom interaction. Two-dimensional clusters (rafts) on the FCC(100) surface displayed migration of edge atoms only, indicating a mechanism for the cluster rotation and shape changes found in experimental studies.

GIRAF: a method for fast search and flexible alignment of ligand binding interfaces in proteins at atomic resolution

PubMed Central

Kinjo, Akira R.; Nakamura, Haruki

2012-01-01

Comparison and classification of protein structures are fundamental means to understand protein functions. Due to the computational difficulty and the ever-increasing amount of structural data, however, it is in general not feasible to perform exhaustive all-against-all structure comparisons necessary for comprehensive classifications. To efficiently handle such situations, we have previously proposed a method, now called GIRAF. We herein describe further improvements in the GIRAF protein structure search and alignment method. The GIRAF method achieves extremely efficient search of similar structures of ligand binding sites of proteins by exploiting database indexing of structural features of local coordinate frames. In addition, it produces refined atom-wise alignments by iterative applications of the Hungarian method to the bipartite graph defined for a pair of superimposed structures. By combining the refined alignments based on different local coordinate frames, it is made possible to align structures involving domain movements. We provide detailed accounts for the database design, the search and alignment algorithms as well as some benchmark results. PMID:27493524

Flow Property Measurement Using Laser-Induced Fluorescence in the NASA Ames Interaction Heating Facility

NASA Technical Reports Server (NTRS)

Grinstead, Jay Henderson; Porter, Barry J.; Carballo, Julio Enrique

2011-01-01

The spectroscopic diagnostic technique of two photon absorption laser-induced fluorescence (TALIF) of atomic species has been applied to single-point measurements of velocity and static temperature in the NASA Ames Interaction Heating Facility (IHF) arc jet. Excitation spectra of atomic oxygen and nitrogen were recorded while scanning a tunable dye laser over the absorption feature. Thirty excitation spectra were acquired during 8 arc jet runs at two facility operating conditions; the number of scans per run varied between 2 and 6. Curve fits to the spectra were analyzed to recover their Doppler shifts and widths, from which the flow velocities and static temperatures, respectively, were determined. An increase in the number of independent flow property pairs from each as-measured scan was obtained by extracting multiple lower-resolution scans. The larger population sample size enabled the mean property values and their uncertainties for each run to be characterized with greater confidence. The average plus or minus 2 sigma uncertainties in the mean velocities and temperatures for all 8 runs were plus or minus 1.4% and plus or minus 11%, respectively.

Probing localized strain in solution-derived YB a2C u3O7 -δ nanocomposite thin films

NASA Astrophysics Data System (ADS)

Guzman, Roger; Gazquez, Jaume; Mundet, Bernat; Coll, Mariona; Obradors, Xavier; Puig, Teresa

2017-07-01

Enhanced pinning due to nanoscale strain is unique to the high-Tc cuprates, where pairing may be modified with lattice distortion. Therefore a comprehensive understanding of the defect landscape is required for a broad range of applications. However, determining the type and distribution of defects and their associated strain constitutes a critical task, and for this aim, real-space techniques for atomic resolution characterization are necessary. Here, we use scanning transmission electron microscopy (STEM) to study the atomic structure of individual defects of solution-derived YB a2C u3O7 (YBCO) nanocomposites, where the inclusion of incoherent secondary phase nanoparticles within the YBCO matrix dramatically increases the density of Y1B a2C u4O8 (Y124) intergrowths, the commonest defect in YBCO thin films. The formation of the Y124 is found to trigger a concatenation of strain-derived interactions with other defects and the concomitant nucleation of intrinsic defects, which weave a web of randomly distributed nanostrained regions that profoundly transform the vortex-pinning landscape of the YBCO nanocomposite thin films.

Scalable quantum computer architecture with coupled donor-quantum dot qubits

DOEpatents

Schenkel, Thomas; Lo, Cheuk Chi; Weis, Christoph; Lyon, Stephen; Tyryshkin, Alexei; Bokor, Jeffrey

2014-08-26

A quantum bit computing architecture includes a plurality of single spin memory donor atoms embedded in a semiconductor layer, a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, wherein a first voltage applied across at least one pair of the aligned quantum dot and donor atom controls a donor-quantum dot coupling. A method of performing quantum computing in a scalable architecture quantum computing apparatus includes arranging a pattern of single spin memory donor atoms in a semiconductor layer, forming a plurality of quantum dots arranged with the semiconductor layer and aligned with the donor atoms, applying a first voltage across at least one aligned pair of a quantum dot and donor atom to control a donor-quantum dot coupling, and applying a second voltage between one or more quantum dots to control a Heisenberg exchange J coupling between quantum dots and to cause transport of a single spin polarized electron between quantum dots.

Quantum nonlinear optics without photons

NASA Astrophysics Data System (ADS)

Stassi, Roberto; Macrı, Vincenzo; Kockum, Anton Frisk; Di Stefano, Omar; Miranowicz, Adam; Savasta, Salvatore; Nori, Franco

2017-08-01

Spontaneous parametric down-conversion is a well-known process in quantum nonlinear optics in which a photon incident on a nonlinear crystal spontaneously splits into two photons. Here we propose an analogous physical process where one excited atom directly transfers its excitation to a pair of spatially separated atoms with probability approaching 1. The interaction is mediated by the exchange of virtual rather than real photons. This nonlinear atomic process is coherent and reversible, so the pair of excited atoms can transfer the excitation back to the first one: the atomic analog of sum-frequency generation of light. The parameters used to investigate this process correspond to experimentally demonstrated values in ultrastrong circuit quantum electrodynamics. This approach can be extended to realize other nonlinear interatomic processes, such as four-atom mixing, and is an attractive architecture for the realization of quantum devices on a chip. We show that four-qubit mixing can efficiently implement quantum repetition codes and, thus, can be used for error-correction codes.

Interlayer electron-hole pair multiplication by hot carriers in atomic layer semiconductor heterostructures

NASA Astrophysics Data System (ADS)

Barati, Fatemeh; Grossnickle, Max; Su, Shanshan; Lake, Roger; Aji, Vivek; Gabor, Nathaniel

Two-dimensional heterostructures composed of atomically thin transition metal dichalcogenides provide the opportunity to design novel devices for the study of electron-hole pair multiplication. We report on highly efficient multiplication of interlayer electron-hole pairs at the interface of a tungsten diselenide / molybdenum diselenide heterostructure. Electronic transport measurements of the interlayer current-voltage characteristics indicate that layer-indirect electron-hole pairs are generated by hot electron impact excitation. Our findings, which demonstrate an efficient energy relaxation pathway that competes with electron thermalization losses, make 2D semiconductor heterostructures viable for a new class of hot-carrier energy harvesting devices that exploit layer-indirect electron-hole excitations. SHINES, an Energy Frontier Research Center funded by the U.S. Department of Energy, Air Force Office of Scientific Research.

Polymeric spatial resolution test patterns for mass spectrometry imaging using nano-thermal analysis with atomic force microscopy

DOE PAGES

Tai, Tamin; Kertesz, Vilmos; Lin, Ming -Wei; ...

2017-05-11

As the spatial resolution of mass spectrometry imaging technologies has begun to reach into the nanometer regime, finding readily available or easily made resolution reference materials has become particularly challenging for molecular imaging purposes. This study describes the fabrication, characterization and use of vertical line array polymeric spatial resolution test patterns for nano-thermal analysis/atomic force microscopy/mass spectrometry chemical imaging.

Polymeric spatial resolution test patterns for mass spectrometry imaging using nano-thermal analysis with atomic force microscopy

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

Tai, Tamin; Kertesz, Vilmos; Lin, Ming -Wei

As the spatial resolution of mass spectrometry imaging technologies has begun to reach into the nanometer regime, finding readily available or easily made resolution reference materials has become particularly challenging for molecular imaging purposes. This study describes the fabrication, characterization and use of vertical line array polymeric spatial resolution test patterns for nano-thermal analysis/atomic force microscopy/mass spectrometry chemical imaging.

High viscosity environments: an unexpected route to obtain true atomic resolution with atomic force microscopy.

PubMed

Weber, Stefan A L; Kilpatrick, Jason I; Brosnan, Timothy M; Jarvis, Suzanne P; Rodriguez, Brian J

2014-05-02

Atomic force microscopy (AFM) is widely used in liquid environments, where true atomic resolution at the solid-liquid interface can now be routinely achieved. It is generally expected that AFM operation in more viscous environments results in an increased noise contribution from the thermal motion of the cantilever, thereby reducing the signal-to-noise ratio (SNR). Thus, viscous fluids such as ionic and organic liquids have been generally avoided for high-resolution AFM studies despite their relevance to, e.g. energy applications. Here, we investigate the thermal noise limitations of dynamic AFM operation in both low and high viscosity environments theoretically, deriving expressions for the amplitude, phase and frequency noise resulting from the thermal motion of the cantilever, thereby defining the performance limits of amplitude modulation, phase modulation and frequency modulation AFM. We show that the assumption of a reduced SNR in viscous environments is not inherent to the technique and demonstrate that SNR values comparable to ultra-high vacuum systems can be obtained in high viscosity environments under certain conditions. Finally, we have obtained true atomic resolution images of highly ordered pyrolytic graphite and mica surfaces, thus revealing the potential of high-resolution imaging in high viscosity environments.

High viscosity environments: an unexpected route to obtain true atomic resolution with atomic force microscopy

NASA Astrophysics Data System (ADS)

Weber, Stefan A. L.; Kilpatrick, Jason I.; Brosnan, Timothy M.; Jarvis, Suzanne P.; Rodriguez, Brian J.

2014-05-01

Atomic force microscopy (AFM) is widely used in liquid environments, where true atomic resolution at the solid-liquid interface can now be routinely achieved. It is generally expected that AFM operation in more viscous environments results in an increased noise contribution from the thermal motion of the cantilever, thereby reducing the signal-to-noise ratio (SNR). Thus, viscous fluids such as ionic and organic liquids have been generally avoided for high-resolution AFM studies despite their relevance to, e.g. energy applications. Here, we investigate the thermal noise limitations of dynamic AFM operation in both low and high viscosity environments theoretically, deriving expressions for the amplitude, phase and frequency noise resulting from the thermal motion of the cantilever, thereby defining the performance limits of amplitude modulation, phase modulation and frequency modulation AFM. We show that the assumption of a reduced SNR in viscous environments is not inherent to the technique and demonstrate that SNR values comparable to ultra-high vacuum systems can be obtained in high viscosity environments under certain conditions. Finally, we have obtained true atomic resolution images of highly ordered pyrolytic graphite and mica surfaces, thus revealing the potential of high-resolution imaging in high viscosity environments.

Super-resolution imaging and tracking of protein-protein interactions in sub-diffraction cellular space

NASA Astrophysics Data System (ADS)

Liu, Zhen; Xing, Dong; Su, Qian Peter; Zhu, Yun; Zhang, Jiamei; Kong, Xinyu; Xue, Boxin; Wang, Sheng; Sun, Hao; Tao, Yile; Sun, Yujie

2014-07-01

Imaging the location and dynamics of individual interacting protein pairs is essential but often difficult because of the fluorescent background from other paired and non-paired molecules, particularly in the sub-diffraction cellular space. Here we develop a new method combining bimolecular fluorescence complementation and photoactivated localization microscopy for super-resolution imaging and single-molecule tracking of specific protein-protein interactions. The method is used to study the interaction of two abundant proteins, MreB and EF-Tu, in Escherichia coli cells. The super-resolution imaging shows interesting distribution and domain sizes of interacting MreB-EF-Tu pairs as a subpopulation of total EF-Tu. The single-molecule tracking of MreB, EF-Tu and MreB-EF-Tu pairs reveals intriguing localization-dependent heterogonous dynamics and provides valuable insights to understanding the roles of MreB-EF-Tu interactions.

Super-resolution imaging and tracking of protein–protein interactions in sub-diffraction cellular space

PubMed Central

Liu, Zhen; Xing, Dong; Su, Qian Peter; Zhu, Yun; Zhang, Jiamei; Kong, Xinyu; Xue, Boxin; Wang, Sheng; Sun, Hao; Tao, Yile; Sun, Yujie

2014-01-01

Imaging the location and dynamics of individual interacting protein pairs is essential but often difficult because of the fluorescent background from other paired and non-paired molecules, particularly in the sub-diffraction cellular space. Here we develop a new method combining bimolecular fluorescence complementation and photoactivated localization microscopy for super-resolution imaging and single-molecule tracking of specific protein–protein interactions. The method is used to study the interaction of two abundant proteins, MreB and EF-Tu, in Escherichia coli cells. The super-resolution imaging shows interesting distribution and domain sizes of interacting MreB–EF-Tu pairs as a subpopulation of total EF-Tu. The single-molecule tracking of MreB, EF-Tu and MreB–EF-Tu pairs reveals intriguing localization-dependent heterogonous dynamics and provides valuable insights to understanding the roles of MreB–EF-Tu interactions. PMID:25030837

Concept for room temperature single-spin tunneling force microscopy with atomic spatial resolution

NASA Astrophysics Data System (ADS)

Payne, Adam

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy (AFM) system noise. The results show that the approach could provide single-spin measurement of electrically isolated defect states with atomic spatial resolution at room temperature.

Atomic-resolution single-spin magnetic resonance detection concept based on tunneling force microscopy

NASA Astrophysics Data System (ADS)

Payne, A.; Ambal, K.; Boehme, C.; Williams, C. C.

2015-05-01

A study of a force detected single-spin magnetic resonance measurement concept with atomic spatial resolution is presented. The method is based upon electrostatic force detection of spin-selection rule controlled single-electron tunneling between two electrically isolated paramagnetic states. Single-spin magnetic resonance detection is possible by measuring the force detected tunneling charge noise on and off spin resonance. Simulation results of this charge noise, based upon physical models of the tunneling and spin physics, are directly compared to measured atomic force microscopy system noise. The results show that the approach could provide single-spin measurement of electrically isolated qubit states with atomic spatial resolution at room temperature.

Virtual interface substructure synthesis method for normal mode analysis of super-large molecular complexes at atomic resolution.

PubMed

Chen, Xuehui; Sun, Yunxiang; An, Xiongbo; Ming, Dengming

2011-10-14

Normal mode analysis of large biomolecular complexes at atomic resolution remains challenging in computational structure biology due to the requirement of large amount of memory space and central processing unit time. In this paper, we present a method called virtual interface substructure synthesis method or VISSM to calculate approximate normal modes of large biomolecular complexes at atomic resolution. VISSM introduces the subunit interfaces as independent substructures that join contacting molecules so as to keep the integrity of the system. Compared with other approximate methods, VISSM delivers atomic modes with no need of a coarse-graining-then-projection procedure. The method was examined for 54 protein-complexes with the conventional all-atom normal mode analysis using CHARMM simulation program and the overlap of the first 100 low-frequency modes is greater than 0.7 for 49 complexes, indicating its accuracy and reliability. We then applied VISSM to the satellite panicum mosaic virus (SPMV, 78,300 atoms) and to F-actin filament structures of up to 39-mer, 228,813 atoms and found that VISSM calculations capture functionally important conformational changes accessible to these structures at atomic resolution. Our results support the idea that the dynamics of a large biomolecular complex might be understood based on the motions of its component subunits and the way in which subunits bind one another. © 2011 American Institute of Physics

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

NASA Astrophysics Data System (ADS)

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

2015-08-01

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in irradiated materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1.0a0 to 3.3a0 have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomic level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a0 by taking the average of the recombination distances from 80 simulation cases. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.

Alloy solution hardening with solute pairs

DOEpatents

Mitchell, John W.

1976-08-24

Solution hardened alloys are formed by using at least two solutes which form associated solute pairs in the solvent metal lattice. Copper containing equal atomic percentages of aluminum and palladium is an example.

Analysis of spatial correlations in a model two-dimensional liquid through eigenvalues and eigenvectors of atomic-level stress matrices.

PubMed

Levashov, V A; Stepanov, M G

2016-01-01

Considerations of local atomic-level stresses associated with each atom represent a particular approach to address structures of disordered materials at the atomic level. We studied structural correlations in a two-dimensional model liquid using molecular dynamics simulations in the following way. We diagonalized the atomic-level stress tensor of every atom and investigated correlations between the eigenvalues and orientations of the eigenvectors of different atoms as a function of distance between them. It is demonstrated that the suggested approach can be used to characterize structural correlations in disordered materials. In particular, we found that changes in the stress correlation functions on decrease of temperature are the most pronounced for the pairs of atoms with separation distance that corresponds to the first minimum in the pair density function. We also show that the angular dependencies of the stress correlation functions previously reported by Wu et al. [Phys. Rev. E 91, 032301 (2015)10.1103/PhysRevE.91.032301] do not represent the anisotropic Eshelby's stress fields, as it is suggested, but originate in the rotational properties of the stress tensors.

Ultrafast Scavenging of the Precursor of H(•) Atom, (e(-), H3O(+)), in Aqueous Solutions.

PubMed

Balcerzyk, Anna; Schmidhammer, Uli; Wang, Furong; de la Lande, Aurélien; Mostafavi, Mehran

2016-09-01

Picosecond pulse radiolysis measurements have been performed in several highly concentrated HClO4 and H3PO4 aqueous solutions containing silver ions at different concentrations. Silver ion reduction is used to unravel the ultrafast reduction reactions observed at the end of a 7 ps electron pulse. Solvated electrons and silver atoms are observed by the pulse (electron beam)-probe (supercontinuum light) method. In highly acidic solutions, ultrafast reduction of silver ions is observed, a finding that is not compatible with a reaction between the H(•) atom and silver ions, which is known to be thermally activated. In addition, silver ion reduction is found to be even more efficient in phosphoric acid solution than that in neutral solution. In the acidic solutions investigated here, the species responsible for the reduction of silver atoms is considered to be the precursor of the H(•) atom. This precursor, denoted (e(-), H3O(+)), is a pair constituting an electron (not fully solvated) and H3O(+). Its structure differs from that of the pair of a solvated electron and a hydronium ion (es(-), H3O(+)), which absorbs in the visible region. The (e(-), H3O(+)) pair , called the pre-H(•) atom here, undergoes ultrafast electron transfer and can, like the presolvated electron, reduce silver ions much faster than the H(•) atom. Moreover, it is found that with the same concentration of H3O(+) the reduction reaction is favored in the phosphoric acid solution compared to that in the perchloric acid solution because of the less-efficient electron solvation process. The kinetics show that among the three reducing species, (e(-), H3O(+)), (es(-), H3O(+)), and H(•) atom, the first one is the most efficient.

The Atomic Dating Game.

ERIC Educational Resources Information Center

Cummo, Evelyn; Matthews, Catherine E.

2002-01-01

Presents an activity designed to provide students with opportunities to practice drawing atomic models and discover the logical pairings of whole families on the periodic table. Follows the format of a television game show. (DDR)

4D Flexible Atom-Pairs: An efficient probabilistic conformational space comparison for ligand-based virtual screening

PubMed Central

2011-01-01

Background The performance of 3D-based virtual screening similarity functions is affected by the applied conformations of compounds. Therefore, the results of 3D approaches are often less robust than 2D approaches. The application of 3D methods on multiple conformer data sets normally reduces this weakness, but entails a significant computational overhead. Therefore, we developed a special conformational space encoding by means of Gaussian mixture models and a similarity function that operates on these models. The application of a model-based encoding allows an efficient comparison of the conformational space of compounds. Results Comparisons of our 4D flexible atom-pair approach with over 15 state-of-the-art 2D- and 3D-based virtual screening similarity functions on the 40 data sets of the Directory of Useful Decoys show a robust performance of our approach. Even 3D-based approaches that operate on multiple conformers yield inferior results. The 4D flexible atom-pair method achieves an averaged AUC value of 0.78 on the filtered Directory of Useful Decoys data sets. The best 2D- and 3D-based approaches of this study yield an AUC value of 0.74 and 0.72, respectively. As a result, the 4D flexible atom-pair approach achieves an average rank of 1.25 with respect to 15 other state-of-the-art similarity functions and four different evaluation metrics. Conclusions Our 4D method yields a robust performance on 40 pharmaceutically relevant targets. The conformational space encoding enables an efficient comparison of the conformational space. Therefore, the weakness of the 3D-based approaches on single conformations is circumvented. With over 100,000 similarity calculations on a single desktop CPU, the utilization of the 4D flexible atom-pair in real-world applications is feasible. PMID:21733172

Solitonic excitations in collisions of superfluid nuclei a qualitatively new phenomenon distinct from the Josephson effect

NASA Astrophysics Data System (ADS)

Sekizawa, Kazuyuki; Wlazłowski, Gabriel; Magierski, Piotr

2017-11-01

Recently, we have reported a novel role of pairing in low-energy heavy ion reactions at energies above the Coulomb barrier, which may have a detectable impact on reaction outcomes, such as the kinetic energy of fragments and the fusion cross section [arXiv:1611.10261, arXiv:1702.00069]. The phenomenon mimics the one studied experimentally with ultracold atomic gases, where two clouds of fermionic superfluids with different phases of the pairing fields are forced to merge, inducing various excitation modes of the pairing field. Although it originates from the phase difference of the pairing fields, the physics behind it is markedly different from the so-called Josephson effect. In this short contribution, we will briefly outline the results discussed in our recent papers and explain relations with the field of ultracold atomic gases.

[Mass spectrometric and quantum chemical study of dimeric associates of nucleosides].

PubMed

Sukhodub, L F; Aksenov, S A; Boldeskul, A I

1995-01-01

Deoxyribonucleosides H-bonded pairs were investigated using fast atom bombardment mass spectrometry and MNDO/H quantum chemistry method. It was shown that "rare" (enol or imin) forms of the nitrogen bases could form pairs with energy comparable with "canonical" base pair energy. It was shown that pair stability rows, which are measured using different experimental techniques, were in conformity each with other.

Quantum Atomic Clock Synchronization: An Entangled Concept of Nonlocal Simultaneity

NASA Technical Reports Server (NTRS)

Abrams, D.; Dowling, J.; Williams, C.; Jozsa, R.

2000-01-01

We demonstrate that two spatially separated parties (Alice and Bob) can utilize shared prior quantum entanglement, as well as a classical information channel, to establish a synchronized pair of atomic clocks.

Modelling the atomic structure of Al92U8 metallic glass.

PubMed

Michalik, S; Bednarcik, J; Jóvári, P; Honkimäki, V; Webb, A; Franz, H; Fazakas, E; Varga, L K

2010-10-13

The local atomic structure of the glassy Al(92)U(8) alloy was modelled by the reverse Monte Carlo (RMC) method, fitting x-ray diffraction (XRD) and extended x-ray absorption fine structure (EXAFS) signals. The final structural model was analysed by means of partial pair correlation functions, coordination number distributions and Voronoi tessellation. In our study we found that the most probable atomic separations between Al-Al and U-Al pairs in the glassy Al(92)U(8) alloy are 2.7 Å and 3.1 Å with coordination numbers 11.7 and 17.1, respectively. The Voronoi analysis did not support evidence of the existence of well-defined building blocks directly embedded in the amorphous matrix. The dense-random-packing model seems to be adequate for describing the connection between solvent and solute atoms.

Intensity and amplitude correlations in the fluorescence from atoms with interacting Rydberg states

NASA Astrophysics Data System (ADS)

Xu, Qing; Mølmer, Klaus

2015-09-01

We explore the fluorescence signals from a pair of atoms driven towards Rydberg states on a three-level ladder transition. The dipole-dipole interactions between Rydberg excited atoms significantly distort the dark state and electromagnetically induced transparency behavior observed with independent atoms and, thus, their steady-state light emission. We calculate and analyze the temporal correlations between intensities and amplitudes of the signals emitted by the atoms and explain their origin in the atomic Rydberg state interactions.

Topological lattice using multi-frequency radiation

NASA Astrophysics Data System (ADS)

Andrijauskas, Tomas; Spielman, I. B.; Juzeliūnas, Gediminas

2018-05-01

We describe a novel technique for creating an artificial magnetic field for ultracold atoms using a periodically pulsed pair of counter propagating Raman lasers that drive transitions between a pair of internal atomic spin states: a multi-frequency coupling term. In conjunction with a magnetic field gradient, this dynamically generates a rectangular lattice with a non-staggered magnetic flux. For a wide range of parameters, the resulting Bloch bands have non-trivial topology, reminiscent of Landau levels, as quantified by their Chern numbers.

Watching Silica's Dance: Imaging the Structure and Dynamics of the Atomic (Re-) Arrangements in 2D Glass

NASA Astrophysics Data System (ADS)

Muller, David

2014-03-01

Even though glasses are almost ubiquitous--in our windows, on our iPhones, even on our faces--they are also mysterious. Because glasses are notoriously difficult to study, basic questions like: ``How are the atoms arranged? Where and how do glasses break?'' are still under contention. We use aberration corrected transmission electron microscopy (TEM) to image the atoms in a new two-dimensional phase of silica glass - freestanding it becomes the world's thinnest pane of glass at only 3-atoms thick, and take a unique look into these questions. Using atom-by-atom imaging and spectroscopy, we are able to reconstruct the full structure and bonding of this 2D glass and identify it as a bi-tetrahedral layer of SiO2. Our images also strikingly resemble Zachariasen's original cartoon models of glasses, drawn in 1932. As such, our work realizes an 80-year-old vision for easily understandable glassy systems and introduces promising methods to test theoretical predictions against experimental data. We image atoms in the disordered solid and track their motions in response to local strain. We directly obtain ring statistics and pair distribution functions that span short-, medium-, and long-range order, and test these against long-standing theoretical predictions of glass structure and dynamics. We use the electron beam to excite atomic rearrangements, producing surprisingly rich and beautiful videos of how a glass bends and breaks, as well as the exchange of atoms at a solid/liquid interface. Detailed analyses of these videos reveal a complex dance of elastic and plastic deformations, phase transitions, and their interplay. These examples illustrate the wide-ranging and fundamental materials physics that can now be studied at atomic-resolution via transmission electron microscopy of two-dimensional glasses. Work in collaboration with: S. Kurasch, U. Kaiser, R. Hovden, Q. Mao, J. Kotakoski, J. S. Alden, A. Shekhawat, A. A. Alemi, J. P. Sethna, P. L. McEuen, A.V. Krasheninnikov, A. Srivastava, V. Skakalova, J. C. Meyer, and J.H. Smet. This work was supported by the NSF through the Cornell Center for Materials Research (NSF DMR-1120296).

MicroED Structure of Au146(p-MBA)57 at Subatomic Resolution Reveals a Twinned FCC Cluster.

PubMed

Vergara, Sandra; Lukes, Dylan A; Martynowycz, Michael W; Santiago, Ulises; Plascencia-Villa, Germán; Weiss, Simon C; de la Cruz, M Jason; Black, David M; Alvarez, Marcos M; López-Lozano, Xochitl; Barnes, Christopher O; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L; Gonen, Tamir; Yacaman, Miguel Jose; Calero, Guillermo

2017-11-16

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au 146 (p-MBA) 57 (p-MBA: para-mercaptobenzoic acid), solved by electron micro-diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure, whereas the surface gold atoms follow a C 2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au 146 (p-MBA) 57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault.

MicroED structure of Au146(p-MBA)57 at subatomic resolution reveals a twinned FCC cluster

PubMed Central

Vergara, Sandra; Lukes, Dylan A.; Martynowycz, Michael W.; Santiago, Ulises; Plascencia-Villa, German; Weiss, Simon C.; de la Cruz, M. Jason; Black, David M.; Alvarez, Marcos M.; Lopez-Lozano, Xochitl; Barnes, Christopher O.; Lin, Guowu; Weissker, Hans-Christian; Whetten, Robert L.; Gonen, Tamir; Jose-Yacaman, Miguel; Calero, Guillermo

2018-01-01

Solving the atomic structure of metallic clusters is fundamental to understanding their optical, electronic, and chemical properties. Herein we present the structure of the largest aqueous gold cluster, Au146(p-MBA)57 (p-MBA: para-mercaptobenzoic acid), solved by electron diffraction (MicroED) to subatomic resolution (0.85 Å) and by X-ray diffraction at atomic resolution (1.3 Å). The 146 gold atoms may be decomposed into two constituent sets consisting of 119 core and 27 peripheral atoms. The core atoms are organized in a twinned FCC structure whereas the surface gold atoms follow a C2 rotational symmetry about an axis bisecting the twinning plane. The protective layer of 57 p-MBAs fully encloses the cluster and comprises bridging, monomeric, and dimeric staple motifs. Au146(p-MBA)57 is the largest cluster observed exhibiting a bulk-like FCC structure as well as the smallest gold particle exhibiting a stacking fault. PMID:29072840

Set-up of a high-resolution 300 mK atomic force microscope in an ultra-high vacuum compatible {sup 3}He/10 T cryostat

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

Allwörden, H. von; Ruschmeier, K.; Köhler, A.

The design of an atomic force microscope with an all-fiber interferometric detection scheme capable of atomic resolution at about 500 mK is presented. The microscope body is connected to a small pumped {sup 3}He reservoir with a base temperature of about 300 mK. The bakeable insert with the cooling stage can be moved from its measurement position inside the bore of a superconducting 10 T magnet into an ultra-high vacuum chamber, where the tip and sample can be exchanged in situ. Moreover, single atoms or molecules can be evaporated onto a cold substrate located inside the microscope. Two side chambersmore » are equipped with standard surface preparation and surface analysis tools. The performance of the microscope at low temperatures is demonstrated by resolving single Co atoms on Mn/W(110) and by showing atomic resolution on NaCl(001).« less

Linear-scaling explicitly correlated treatment of solids: periodic local MP2-F12 method.

PubMed

Usvyat, Denis

2013-11-21

Theory and implementation of the periodic local MP2-F12 method in the 3*A fixed-amplitude ansatz is presented. The method is formulated in the direct space, employing local representation for the occupied, virtual, and auxiliary orbitals in the form of Wannier functions (WFs), projected atomic orbitals (PAOs), and atom-centered Gaussian-type orbitals, respectively. Local approximations are introduced, restricting the list of the explicitly correlated pairs, as well as occupied, virtual, and auxiliary spaces in the strong orthogonality projector to the pair-specific domains on the basis of spatial proximity of respective orbitals. The 4-index two-electron integrals appearing in the formalism are approximated via the direct-space density fitting technique. In this procedure, the fitting orbital spaces are also restricted to local fit-domains surrounding the fitted densities. The formulation of the method and its implementation exploits the translational symmetry and the site-group symmetries of the WFs. Test calculations are performed on LiH crystal. The results show that the periodic LMP2-F12 method substantially accelerates basis set convergence of the total correlation energy, and even more so the correlation energy differences. The resulting energies are quite insensitive to the resolution-of-the-identity domain sizes and the quality of the auxiliary basis sets. The convergence with the orbital domain size is somewhat slower, but still acceptable. Moreover, inclusion of slightly more diffuse functions, than those usually used in the periodic calculations, improves the convergence of the LMP2-F12 correlation energy with respect to both the size of the PAO-domains and the quality of the orbital basis set. At the same time, the essentially diffuse atomic orbitals from standard molecular basis sets, commonly utilized in molecular MP2-F12 calculations, but problematic in the periodic context, are not necessary for LMP2-F12 treatment of crystals.

Massively parallel sensing of trace molecules and their isotopologues with broadband subharmonic mid-infrared frequency combs

NASA Astrophysics Data System (ADS)

Muraviev, A. V.; Smolski, V. O.; Loparo, Z. E.; Vodopyanov, K. L.

2018-04-01

Mid-infrared spectroscopy offers supreme sensitivity for the detection of trace gases, solids and liquids based on tell-tale vibrational bands specific to this spectral region. Here, we present a new platform for mid-infrared dual-comb Fourier-transform spectroscopy based on a pair of ultra-broadband subharmonic optical parametric oscillators pumped by two phase-locked thulium-fibre combs. Our system provides fast (7 ms for a single interferogram), moving-parts-free, simultaneous acquisition of 350,000 spectral data points, spaced by a 115 MHz intermodal interval over the 3.1-5.5 µm spectral range. Parallel detection of 22 trace molecular species in a gas mixture, including isotopologues containing isotopes such as 13C, 18O, 17O, 15N, 34S, 33S and deuterium, with part-per-billion sensitivity and sub-Doppler resolution is demonstrated. The technique also features absolute optical frequency referencing to an atomic clock, a high degree of mutual coherence between the two mid-infrared combs with a relative comb-tooth linewidth of 25 mHz, coherent averaging and feasibility for kilohertz-scale spectral resolution.

Nanofibre optic force transducers with sub-piconewton resolution via near-field plasmon–dielectric interactions

PubMed Central

Huang, Qian; Lee, Joon; Arce, Fernando Teran; Yoon, Ilsun; Angsantikul, Pavimol; Liu, Justin; Shi, Yuesong; Villanueva, Josh; Thamphiwatana, Soracha; Ma, Xuanyi; Zhang, Liangfang; Chen, Shaochen; Lal, Ratnesh; Sirbuly, Donald J.

2018-01-01

Ultrasensitive nanomechanical instruments, including the atomic force microscope (AFM)1–4 and optical and magnetic tweezers5–8, have helped shed new light on the complex mechanical environments of biological processes. However, it is difficult to scale down the size of these instruments due to their feedback mechanisms9, which, if overcome, would enable high-density nanomechanical probing inside materials. A variety of molecular force probes including mechanophores10, quantum dots11, fluorescent pairs12,13 and molecular rotors14–16 have been designed to measure intracellular stresses; however, fluorescence-based techniques can have short operating times due to photo-instability and it is still challenging to quantify the forces with high spatial and mechanical resolution. Here, we develop a compact nanofibre optic force transducer (NOFT) that utilizes strong near-field plasmon–dielectric interactions to measure local forces with a sensitivity of <200 fN. The NOFT system is tested by monitoring bacterial motion and heart-cell beating as well as detecting infrasound power in solution. PMID:29576804

Local Chemical Ordering and Negative Thermal Expansion in PtNi Alloy Nanoparticles.

PubMed

Li, Qiang; Zhu, He; Zheng, Lirong; Fan, Longlong; Wang, Na; Rong, Yangchun; Ren, Yang; Chen, Jun; Deng, Jinxia; Xing, Xianran

2017-12-13

An atomic insight into the local chemical ordering and lattice strain is particular interesting to recent emerging bimetallic nanocatalysts such as PtNi alloys. Here, we reported the atomic distribution, chemical environment, and lattice thermal evolution in full-scale structural description of PtNi alloy nanoparticles (NPs). The different segregation of elements in the well-faceted PtNi nanoparticles is convinced by extended X-ray absorption fine structure (EXAFS). Atomic pair distribution function (PDF) study evidences the coexistence of the face-centered cubic and tetragonal ordering parts in the local environment of PtNi nanoparticles. Further reverse Monte Carlo (RMC) simulation with PDF data obviously exposed the segregation as Ni and Pt in the centers of {111} and {001} facets, respectively. Layer-by-layer statistical analysis up to 6 nm for the local atomic pairs revealed the distribution of local tetragonal ordering on the surface. This local coordination environment facilitates the distribution of heteroatomic Pt-Ni pairs, which plays an important role in the negative thermal expansion of Pt 41 Ni 59 NPs. The present study on PtNi alloy NPs from local short-range coordination to long-range average lattice provides a new perspective on tailoring physical properties in nanomaterials.

Pairing preferences of the model mono-valence mono-atomic ions investigated by molecular simulation

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

Zhang, Qiang; Department of Chemistry, Bohai University, Jinzhou 121000; Zhang, Ruiting

2014-05-14

We carried out a series of potential of mean force calculations to study the pairing preferences of a series of model mono-atomic 1:1 ions with evenly varied sizes. The probabilities of forming the contact ion pair (CIP) and the single water separate ion pair (SIP) were presented in the two-dimensional plots with respect to the ion sizes. The pairing preferences reflected in these plots largely agree with the empirical rule of matching ion sizes in the small and big size regions. In the region that the ion sizes are close to the size of the water molecule; however, a significantmore » deviation from this conventional rule is observed. Our further analysis indicated that this deviation originates from the competition between CIP and the water bridging SIP state. The competition is mainly an enthalpy modulated phenomenon in which the existing of the water bridging plays a significant role.« less

Formation of bimetallic clusters in superfluid helium nanodroplets analysed by atomic resolution electron tomography

PubMed Central

Haberfehlner, Georg; Thaler, Philipp; Knez, Daniel; Volk, Alexander; Hofer, Ferdinand; Ernst, Wolfgang E.; Kothleitner, Gerald

2015-01-01

Structure, shape and composition are the basic parameters responsible for properties of nanoscale materials, distinguishing them from their bulk counterparts. To reveal these in three dimensions at the nanoscale, electron tomography is a powerful tool. Advancing electron tomography to atomic resolution in an aberration-corrected transmission electron microscope remains challenging and has been demonstrated only a few times using strong constraints or extensive filtering. Here we demonstrate atomic resolution electron tomography on silver/gold core/shell nanoclusters grown in superfluid helium nanodroplets. We reveal morphology and composition of a cluster identifying gold- and silver-rich regions in three dimensions and we estimate atomic positions without using any prior information and with minimal filtering. The ability to get full three-dimensional information down to the atomic scale allows understanding the growth and deposition process of the nanoclusters and demonstrates an approach that may be generally applicable to all types of nanoscale materials. PMID:26508471

Scattered electrons in microscopy and microanalysis

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

Ottensmeyer, F.P.

The use of scattered electrons alone for direct imaging of biological specimens makes it possible to obtain structural information at atomic and near-atomic spatial resolutions of 0.3 to 0.5 nanometer. While this is not as good as the resolution possible with x-ray crystallography, such an approach provides structural information rapidly on individual macromolecules that have not been, and possibly cannot be, crystallized. Analysis of the spectrum of energies of scattered electrons and imaging of the latter with characteristic energy bands within the spectrum produces a powerful new technique of atomic microanalysis. This technique, which has a spatial resolution of aboutmore » 0.5 nanometer and a minimum detection sensitivity of about 50 atoms of phosphorus, is especially useful for light atom analysis and appears to have applications in molecular biology, cell biology, histology, pathology, botany, and many other fields.« less

Scattered electrons in microscopy and microanalysis

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

Ottensmeyer, F.P.

The use of scattered electrons alone for direct imaging of biological specimens makes it possible to obtain structural information at atomic and near-atomic spatial resolutions of 0.3 to 0.5 nanometer. While this is not as good as the resolution possible with x-ray crystallography, such an approach provides structural information rapidly on individual macromolecules that have not been, and possibly cannot be, crystallized. Analysis of the spectrum of energies of scattered electrons and imaging of the latter with characteristic energy bands within the spectrum produce a powerful new technique of atomic microanalysis. This technique, which has a spatial resolution of aboutmore » 0.5 nanometer and a minimum detection sensitivity of about 50 atoms of phosphorus, is especially useful for light atom analysis and appears to have applications in molecular biology, cell biology, histology, pathology, botany, and many other fields.« less

High resolution time interval counter

DOEpatents

Condreva, Kenneth J.

1994-01-01

A high resolution counter circuit measures the time interval between the occurrence of an initial and a subsequent electrical pulse to two nanoseconds resolution using an eight megahertz clock. The circuit includes a main counter for receiving electrical pulses and generating a binary word--a measure of the number of eight megahertz clock pulses occurring between the signals. A pair of first and second pulse stretchers receive the signal and generate a pair of output signals whose widths are approximately sixty-four times the time between the receipt of the signals by the respective pulse stretchers and the receipt by the respective pulse stretchers of a second subsequent clock pulse. Output signals are thereafter supplied to a pair of start and stop counters operable to generate a pair of binary output words representative of the measure of the width of the pulses to a resolution of two nanoseconds. Errors associated with the pulse stretchers are corrected by providing calibration data to both stretcher circuits, and recording start and stop counter values. Stretched initial and subsequent signals are combined with autocalibration data and supplied to an arithmetic logic unit to determine the time interval in nanoseconds between the pair of electrical pulses being measured.

High resolution time interval counter

DOEpatents

Condreva, K.J.

1994-07-26

A high resolution counter circuit measures the time interval between the occurrence of an initial and a subsequent electrical pulse to two nanoseconds resolution using an eight megahertz clock. The circuit includes a main counter for receiving electrical pulses and generating a binary word--a measure of the number of eight megahertz clock pulses occurring between the signals. A pair of first and second pulse stretchers receive the signal and generate a pair of output signals whose widths are approximately sixty-four times the time between the receipt of the signals by the respective pulse stretchers and the receipt by the respective pulse stretchers of a second subsequent clock pulse. Output signals are thereafter supplied to a pair of start and stop counters operable to generate a pair of binary output words representative of the measure of the width of the pulses to a resolution of two nanoseconds. Errors associated with the pulse stretchers are corrected by providing calibration data to both stretcher circuits, and recording start and stop counter values. Stretched initial and subsequent signals are combined with autocalibration data and supplied to an arithmetic logic unit to determine the time interval in nanoseconds between the pair of electrical pulses being measured. 3 figs.

Marvels of enzyme catalysis at true atomic resolution: distortions, bond elongations, hidden flips, protonation states and atom identities.

PubMed

Neumann, Piotr; Tittmann, Kai

2014-12-01

Although general principles of enzyme catalysis are fairly well understood nowadays, many important details of how exactly the substrate is bound and processed in an enzyme remain often invisible and as such elusive. In fortunate cases, structural analysis of enzymes can be accomplished at true atomic resolution thus making possible to shed light on otherwise concealed fine-structural traits of bound substrates, intermediates, cofactors and protein groups. We highlight recent structural studies of enzymes using ultrahigh-resolution X-ray protein crystallography showcasing its enormous potential as a tool in the elucidation of enzymatic mechanisms and in unveiling fundamental principles of enzyme catalysis. We discuss the observation of seemingly hyper-reactive, physically distorted cofactors and intermediates with elongated scissile substrate bonds, the detection of 'hidden' conformational and chemical equilibria and the analysis of protonation states with surprising findings. In delicate cases, atomic resolution is required to unambiguously disclose the identity of atoms as demonstrated for the metal cluster in nitrogenase. In addition to the pivotal structural findings and the implications for our understanding of enzyme catalysis, we further provide a practical framework for resolution enhancement through optimized data acquisition and processing. Copyright © 2014 Elsevier Ltd. All rights reserved.

ATOMIC RESOLUTION CRYO ELECTRON MICROSCOPY OF MACROMOLECULAR COMPLEXES

PubMed Central

ZHOU, Z. HONG

2013-01-01

Single-particle cryo electron microscopy (cryoEM) is a technique for determining three-dimensional (3D) structures from projection images of molecular complexes preserved in their “native,” noncrystalline state. Recently, atomic or near-atomic resolution structures of several viruses and protein assemblies have been determined by single-particle cryoEM, allowing ab initio atomic model building by following the amino acid side chains or nucleic acid bases identifiable in their cryoEM density maps. In particular, these cryoEM structures have revealed extended arms contributing to molecular interactions that are otherwise not resolved by the conventional structural method of X-ray crystallography at similar resolutions. High-resolution cryoEM requires careful consideration of a number of factors, including proper sample preparation to ensure structural homogeneity, optimal configuration of electron imaging conditions to record high-resolution cryoEM images, accurate determination of image parameters to correct image distortions, efficient refinement and computation to reconstruct a 3D density map, and finally appropriate choice of modeling tools to construct atomic models for functional interpretation. This progress illustrates the power of cryoEM and ushers it into the arsenal of structural biology, alongside conventional techniques of X-ray crystallography and NMR, as a major tool (and sometimes the preferred one) for the studies of molecular interactions in supramolecular assemblies or machines. PMID:21501817

Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method

NASA Astrophysics Data System (ADS)

Neese, Frank; Wennmohs, Frank; Hansen, Andreas

2009-03-01

Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Møller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol-1. Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500 times faster. The method performs best in conjunction with large and flexible basis sets. These results open the way for large-scale chemical applications.

Efficient and accurate local approximations to coupled-electron pair approaches: An attempt to revive the pair natural orbital method.

PubMed

Neese, Frank; Wennmohs, Frank; Hansen, Andreas

2009-03-21

Coupled-electron pair approximations (CEPAs) and coupled-pair functionals (CPFs) have been popular in the 1970s and 1980s and have yielded excellent results for small molecules. Recently, interest in CEPA and CPF methods has been renewed. It has been shown that these methods lead to competitive thermochemical, kinetic, and structural predictions. They greatly surpass second order Moller-Plesset and popular density functional theory based approaches in accuracy and are intermediate in quality between CCSD and CCSD(T) in extended benchmark studies. In this work an efficient production level implementation of the closed shell CEPA and CPF methods is reported that can be applied to medium sized molecules in the range of 50-100 atoms and up to about 2000 basis functions. The internal space is spanned by localized internal orbitals. The external space is greatly compressed through the method of pair natural orbitals (PNOs) that was also introduced by the pioneers of the CEPA approaches. Our implementation also makes extended use of density fitting (or resolution of the identity) techniques in order to speed up the laborious integral transformations. The method is called local pair natural orbital CEPA (LPNO-CEPA) (LPNO-CPF). The implementation is centered around the concepts of electron pairs and matrix operations. Altogether three cutoff parameters are introduced that control the size of the significant pair list, the average number of PNOs per electron pair, and the number of contributing basis functions per PNO. With the conservatively chosen default values of these thresholds, the method recovers about 99.8% of the canonical correlation energy. This translates to absolute deviations from the canonical result of only a few kcal mol(-1). Extended numerical test calculations demonstrate that LPNO-CEPA (LPNO-CPF) has essentially the same accuracy as parent CEPA (CPF) methods for thermochemistry, kinetics, weak interactions, and potential energy surfaces but is up to 500 times faster. The method performs best in conjunction with large and flexible basis sets. These results open the way for large-scale chemical applications.

Binding effects of Mn²⁺ and Zn²⁺ ions on the vibrational properties of guanine-cytosine base pairs in the Watson-Crick and Hoogsteen configurations.

PubMed

Morari, Cristian; Bogdan, Diana; Muntean, Cristina M

2012-11-01

The binding effects of Mn²⁺ and Zn²⁺ ions on the vibrational properties of guanine-cytosine base pairs have been performed using density functional theory investigations. The calculations were carried out on Watson-Crick and Hoogsteen configurations of the base pairs. We have found, that in Watson-Crick configuration, the metal is coordinated to N7 atom of guanine while, in the case of Hoogsteen configuration, the coordination is at N3 atom of guanine. We have pointed out the vibrational bands that can be used to detect the presence of metallic ions in the Watson-Crick and Hoogsteen structures. Our results show that the vibrational amplitudes of metallic atoms are strong for wavenumbers lower than 600 cm⁻¹. Also, we predict that the distinction between Watson-Crick and Hoogsteen configurations can be seen around 85, 170 and 310 cm⁻¹.

Entangled photons from single atoms and molecules

NASA Astrophysics Data System (ADS)

Nordén, Bengt

2018-05-01

The first two-photon entanglement experiment performed 50 years ago by Kocher and Commins (KC) provided isolated pairs of entangled photons from an atomic three-state fluorescence cascade. In view of questioning of Bell's theorem, data from these experiments are re-analyzed and shown sufficiently precise to confirm quantum mechanical and dismiss semi-classical theory without need for Bell's inequalities. Polarization photon correlation anisotropy (A) is useful: A is near unity as predicted quantum mechanically and well above the semi-classic range, 0 ⩽ A ⩽ 1 / 2 . Although yet to be found, one may envisage a three-state molecule emitting entangled photon pairs, in analogy with the KC atomic system. Antibunching in fluorescence from single molecules in matrix and entangled photons from quantum dots promise it be possible. Molecules can have advantages to parametric down-conversion as the latter photon distribution is Poissonian and unsuitable for producing isolated pairs of entangled photons. Analytical molecular applications of entangled light are also envisaged.

Superfluidity and BCS-BEC crossover of ultracold atomic Fermi gases in mixed dimensions

NASA Astrophysics Data System (ADS)

Zhang, Leifeng; Chen, Qijin

Atomic Fermi gases have been under active investigation in the past decade. Here we study the superfluid and pairing phenomena of a two-component ultracold atomic Fermi gas in the presence of mixed dimensionality, in which one component is confined on a 1D optical lattice whereas the other is free in the 3D continuum. We assume a short-range pairing interaction and determine the superfluid transition temperature Tc and the phase diagram for the entire BCS-BEC crossover, using a pairing fluctuation theory which includes self-consistently the contributions of finite momentum pairs. We find that, as the lattice depth increases and the lattice spacing decreases, the behavior of Tc becomes very similar to that of a population imbalance Fermi gas in a simple 3D continuum. There is no superfluidity even at T = 0 below certain threshold of pairing strength in the BCS regime. Nonmonotonic Tc behavior and intermediate temperature superfluidity emerge, and for deep enough lattice, the Tc curve will split into two parts. Implications for experiment will be discussed. References: 1. Q.J. Chen, Ioan Kosztin, B. Janko, and K. Levin, Phys. Rev. B 59, 7083 (1999). 2. Chih-Chun Chien, Qijin Chen, Yan He, and K. Levin, Phys. Rev. Lett. 97, 090402(2006). Work supported by NSF of China and the National Basic Research Program of China.

Neutrino Photoproduction on the Electron of a Hydrogen-Like Atom

NASA Astrophysics Data System (ADS)

Skobelev, V. V.

2017-10-01

The process of interaction of a photon with the bound electron of a hydrogen-like atom with creation of a neutrino pair γ +{(Ze)}^{\\ast \\ast}\\to \\overline{νν}+{(Ze)}^{\\ast } is considered here for the first time. This process can take place with and without a change in the energy of the pair relative to the energy of the "initial" photon due to atomic transitions. It is shown that in the case when the system of atoms is located in an equilibrium radiation field with temperature T << m e this process can be neglected in comparison with spontaneous emission of the hydrogen-like atom {(Ze)}^{\\ast}\\to (Ze)+ν\\overline{ν} , despite the smaller power of the expansion parameter ( Zα) < < 1, α = e 2/ ℏc ≈ 1/137 in the expressions for the cross sections and probabilities. Calculations have been performed for the first time using the density matrix, introduced in the previous paper, of the electron in the field of the nucleus in the leading approximation in (Zα).

Spatial Multiplexing of Atom-Photon Entanglement Sources using Feedforward Control and Switching Networks.

PubMed

Tian, Long; Xu, Zhongxiao; Chen, Lirong; Ge, Wei; Yuan, Haoxiang; Wen, Yafei; Wang, Shengzhi; Li, Shujing; Wang, Hai

2017-09-29

The light-matter quantum interface that can create quantum correlations or entanglement between a photon and one atomic collective excitation is a fundamental building block for a quantum repeater. The intrinsic limit is that the probability of preparing such nonclassical atom-photon correlations has to be kept low in order to suppress multiexcitation. To enhance this probability without introducing multiexcitation errors, a promising scheme is to apply multimode memories to the interface. Significant progress has been made in temporal, spectral, and spatial multiplexing memories, but the enhanced probability for generating the entangled atom-photon pair has not been experimentally realized. Here, by using six spin-wave-photon entanglement sources, a switching network, and feedforward control, we build a multiplexed light-matter interface and then demonstrate a ∼sixfold (∼fourfold) probability increase in generating entangled atom-photon (photon-photon) pairs. The measured compositive Bell parameter for the multiplexed interface is 2.49±0.03 combined with a memory lifetime of up to ∼51  μs.

Structure of the toxic core of α-synuclein from invisible crystals

DOE PAGES

Rodriguez, Jose A.; Ivanova, Magdalena I.; Sawaya, Michael R.; ...

2015-09-09

We report that the protein α-synuclein is the main component of Lewy bodies, the neuron-associated aggregates seen in Parkinson disease and other neurodegenerative pathologies. An 11-residue segment, which we term NACore, appears to be responsible for amyloid formation and cytotoxicity of human α-synuclein. Here we describe crystals of NACore that have dimensions smaller than the wavelength of visible light and thus are invisible by optical microscopy. As the crystals are thousands of times too small for structure determination by synchrotron X-ray diffraction, we use micro-electron diffraction to determine the structure at atomic resolution. The 1.4 Å resolution structure demonstrates thatmore » this method can determine previously unknown protein structures and here yields, to our knowledge, the highest resolution achieved by any cryo-electron microscopy method to date. The structure exhibits protofibrils built of pairs of face-to-face β-sheets. X-ray fibre diffraction patterns show the similarity of NACore to toxic fibrils of full-length α-synuclein. Finally, the NACore structure, together with that of a second segment, inspires a model for most of the ordered portion of the toxic, full-length α-synuclein fibril, presenting opportunities for the design of inhibitors of α-synuclein fibrils.« less

Dual wavelength imaging of a scrape-off layer in an advanced beam-driven field-reversed configuration

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

Osin, D.; Schindler, T., E-mail: dosin@trialphaenergy.com

2016-11-15

A dual wavelength imaging system has been developed and installed on C-2U to capture 2D images of a He jet in the Scrape-Off Layer (SOL) of an advanced beam-driven Field-Reversed Configuration (FRC) plasma. The system was designed to optically split two identical images and pass them through 1 nm FWHM filters. Dual wavelength images are focused adjacent on a large format CCD chip and recorded simultaneously with a time resolution down to 10 μs using a gated micro-channel plate. The relatively compact optical system images a 10 cm plasma region with a spatial resolution of 0.2 cm and can bemore » used in a harsh environment with high electro-magnetic noise and high magnetic field. The dual wavelength imaging system provides 2D images of either electron density or temperature by observing spectral line pairs emitted by He jet atoms in the SOL. A large field of view, combined with good space and time resolution of the imaging system, allows visualization of macro-flows in the SOL. First 2D images of the electron density and temperature observed in the SOL of the C-2U FRC are presented.« less

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions.

PubMed

West, Aaron C; Schmidt, Michael W; Gordon, Mark S; Ruedenberg, Klaus

2017-02-09

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the juxtaposed nonbonded quasi-atoms and a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions, and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. The theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.

Native flexibility of structurally homologous proteins: insights from anisotropic network model.

PubMed

Sarkar, Ranja

2017-01-01

Single-molecule microscopic experiments can measure the mechanical response of proteins to pulling forces applied externally along different directions (inducing different residue pairs in the proteins by uniaxial tension). This response to external forces away from equilibrium should in principle, correlate with the flexibility or stiffness of proteins in their folded states. Here, a simple topology-based atomistic anisotropic network model (ANM) is shown which captures the protein flexibility as a fundamental property that determines the collective dynamics and hence, the protein conformations in native state. An all-atom ANM is used to define two measures of protein flexibility in the native state. One measure quantifies overall stiffness of the protein and the other one quantifies protein stiffness along a particular direction which is effectively the mechanical resistance of the protein towards external pulling force exerted along that direction. These measures are sensitive to the protein sequence and yields reliable values through computations of normal modes of the protein. ANM at an atomistic level (heavy atoms) explains the experimental (atomic force microscopy) observations viz., different mechanical stability of structurally similar but sequentially distinct proteins which, otherwise were implied to possess similar mechanical properties from analytical/theoretical coarse-grained (backbone only) models. The results are exclusively demonstrated for human fibronectin (FN) protein domains. The topology of interatomic contacts in the folded states of proteins essentially determines the native flexibility. The mechanical differences of topologically similar proteins are captured from a high-resolution (atomic level) ANM at a low computational cost. The relative trend in flexibility of such proteins is reflected in their stability differences that they exhibit while unfolding in atomic force microscopic (AFM) experiments.

Atomic scale simulations of pyrochlore oxides with a tight-binding variable-charge model: implications for radiation tolerance.

PubMed

Sattonnay, G; Tétot, R

2014-02-05

Atomistic simulations with new interatomic potentials derived from a tight-binding variable-charge model were performed in order to investigate the lattice properties and the defect formation energies in Gd2Ti2O7 and Gd2Zr2O7 pyrochlores. The main objective was to determine the role played by the defect stability on the radiation tolerance of these compounds. Calculations show that the titanate has a more covalent character than the zirconate. Moreover, the properties of oxygen Frenkel pairs, cation antisite defects and cation Frenkel pairs were studied. In Gd2Ti2O7 the cation antisite defect and the Ti-Frenkel pair are not stable: they evolve towards more stable defect configurations during the atomic relaxation process. This phenomenon is driven by a decrease of the Ti coordination number down to five which leads to a local atomic reorganization and strong structural distortions around the defects. These kinds of atomic rearrangements are not observed around defects in Gd2Zr2O7. Therefore, the defect stability in A2B2O7 depends on the ability of B atoms to accommodate high coordination number (higher than six seems impossible for Ti). The accumulation of structural distortions around Ti-defects due to this phenomenon could drive the Gd2Ti2O7 amorphization induced by irradiation.

HI properties and star formation history of a fly-by pair of blue compact dwarf galaxies

NASA Astrophysics Data System (ADS)

Kim, Jinhyub; Chung, Aeree; Wong, O. Ivy; Lee, Bumhyun; Sung, Eon-Chang; Staveley-Smith, Lister

2017-09-01

A fly-by interaction has been suggested to be one of the major explanations for enhanced star formation in blue compact dwarf (BCD) galaxies, yet no direct evidence for this scenario has been found to date. In the Hi Parkes all-sky survey (HIPASS), ESO 435-IG 020 and ESO 435-G 016, a BCD pair were found in a common, extended gas envelope of atomic hydrogen, providing an ideal case to test the hypothesis that the starburst in BCDs can be indeed triggered by a fly-by interaction. Using high-resolution data from the Australia Telescope Compact Array (ATCA), we investigated Hi properties and the spectral energy distribution (SED) of the BCD pair to study their interaction and star formation histories. The high-resolution Hi data of both BCDs reveal a number of peculiarities, which are suggestive of tidal perturbation. Meanwhile, 40% of the HIPASS flux is not accounted for in the ATCA observations with no Hi gas bridge found between the two BCDs. Intriguingly, in the residual of the HIPASS and the ATCA data, 10% of the missing flux appears to be located between the two BCDs. While the SED-based age of the most dominant young stellar population is old enough to have originated from the interaction with any neighbors (including the other of the two BCDs), the most recent star formation activity traced by strong Hα emission in ESO 435-IG 020 and the shear motion of gas in ESO 435-G 016, suggest a more recent or current tidal interaction. Based on these and the residual emission between the HIPASS and the ATCA data, we propose an interaction between the two BCDs as the origin of their recently enhanced star formation activity. The shear motion on the gas disk, potentially with re-accretion of the stripped gas, could be responsible for the active star formation in this BCD pair. The reduced datacube (FITS file) is only available at the CDS via anonymous ftp to http://cdsarc.u-strasbg.fr (http://130.79.128.5) or via http://cdsarc.u-strasbg.fr/viz-bin/qcat?J/A+A/605/A54

Sequence-dependent base pair stepping dynamics in XPD helicase unwinding

PubMed Central

Qi, Zhi; Pugh, Robert A; Spies, Maria; Chemla, Yann R

2013-01-01

Helicases couple the chemical energy of ATP hydrolysis to directional translocation along nucleic acids and transient duplex separation. Understanding helicase mechanism requires that the basic physicochemical process of base pair separation be understood. This necessitates monitoring helicase activity directly, at high spatio-temporal resolution. Using optical tweezers with single base pair (bp) resolution, we analyzed DNA unwinding by XPD helicase, a Superfamily 2 (SF2) DNA helicase involved in DNA repair and transcription initiation. We show that monomeric XPD unwinds duplex DNA in 1-bp steps, yet exhibits frequent backsteps and undergoes conformational transitions manifested in 5-bp backward and forward steps. Quantifying the sequence dependence of XPD stepping dynamics with near base pair resolution, we provide the strongest and most direct evidence thus far that forward, single-base pair stepping of a helicase utilizes the spontaneous opening of the duplex. The proposed unwinding mechanism may be a universal feature of DNA helicases that move along DNA phosphodiester backbones. DOI: http://dx.doi.org/10.7554/eLife.00334.001 PMID:23741615

A Mapping of the Electron Localization Function for Earth Materials

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

Gibbs, Gerald V.; Cox, David F.; Ross, Nancy

2005-06-01

The electron localization function, ELF, generated for a number of geometry-optimized earth materials, provides a graphical representation of the spatial localization of the probability electron density distribution as embodied in domains ascribed to localized bond and lone pair electrons. The lone pair domains, displayed by the silica polymorphs quartz, coesite and cristobalite, are typically banana-shaped and oriented perpendicular to the plane of the SiOSi angle at ~0.60 Å from the O atom on the reflex side of the angle. With decreasing angle, the domains increase in magnitude, indicating an increase in the nucleophilic character of the O atom, rendering itmore » more susceptible to potential electrophilic attack. The Laplacian isosurface maps of the experimental and theoretical electron density distribution for coesite substantiates the increase in the size of the domain with decreasing angle. Bond pair domains are displayed along each of the SiO bond vectors as discrete concave hemispherically-shaped domains at ~0.70 Å from the O atom. For more closed-shell ionic bonded interactions, the bond and lone pair domains are often coalesced, resulting in concave hemispherical toroidal-shaped domains with local maxima centered along the bond vectors. As the shared covalent character of the bonded interactions increases, the bond and lone pair domains are better developed as discrete domains. ELF isosurface maps generated for the earth materials tremolite, diopside, talc and dickite display banana-shaped lone pair domains associated with the bridging O atoms of SiOSi angles and concave hemispherical toroidal bond pair domains associated with the nonbridging ones. The lone pair domains in dickite and talc provide a basis for understanding the bonded interactions between the adjacent neutral layers. Maps were also generated for beryl, cordierite, quartz, low albite, forsterite, wadeite, åkermanite, pectolite, periclase, hurlbutite, thortveitite and vanthoffite. Strategies are reviewed for finding potential H docking sites in the silica polymorphs and related materials. As observed in an earlier study, the ELF is capable of generating bond and lone pair domains that are similar in number and arrangement to those provided by Laplacian and deformation electron density distributions. The formation of the bond and lone pair domains in the silica polymorphs and the progressive decrease in the SiO length as the value of the electron density at the bond critical point increases indicates that the SiO bonded interaction has a substantial component of covalent character.« less

Evidence of Antiblockade in an Ultracold Rydberg Gas

NASA Astrophysics Data System (ADS)

Amthor, Thomas; Giese, Christian; Hofmann, Christoph S.; Weidemüller, Matthias

2010-01-01

We present the experimental observation of the antiblockade in an ultracold Rydberg gas recently proposed by Ates et al. [Phys. Rev. Lett. 98, 023002 (2007)PRLTAO0031-900710.1103/PhysRevLett.98.023002]. Our approach allows the control of the pair distribution in the gas and is based on a strong coupling of one transition in an atomic three-level system, while introducing specific detunings of the other transition. When the coupling energy matches the interaction energy of the Rydberg long-range interactions, the otherwise blocked excitation of close pairs becomes possible. A time-resolved spectroscopic measurement of the Penning ionization signal is used to identify slight variations in the Rydberg pair distribution of a random arrangement of atoms. A model based on a pair interaction Hamiltonian is presented which well reproduces our experimental observations and allows one to deduce the distribution of nearest-neighbor distances.

An atomistic geometrical model of the B-DNA configuration for DNA-radiation interaction simulations

NASA Astrophysics Data System (ADS)

Bernal, M. A.; Sikansi, D.; Cavalcante, F.; Incerti, S.; Champion, C.; Ivanchenko, V.; Francis, Z.

2013-12-01

In this paper, an atomistic geometrical model for the B-DNA configuration is explained. This model accounts for five organization levels of the DNA, up to the 30 nm chromatin fiber. However, fragments of this fiber can be used to construct the whole genome. The algorithm developed in this work is capable to determine which is the closest atom with respect to an arbitrary point in space. It can be used in any application in which a DNA geometrical model is needed, for instance, in investigations related to the effects of ionizing radiations on the human genetic material. Successful consistency checks were carried out to test the proposed model. Catalogue identifier: AEPZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEPZ_v1_0.html Program obtainable from: CPC Program Library, Queen’s University, Belfast, N. Ireland Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 1245 No. of bytes in distributed program, including test data, etc.: 6574 Distribution format: tar.gz Programming language: FORTRAN. Computer: Any. Operating system: Multi-platform. RAM: 2 Gb Classification: 3. Nature of problem: The Monte Carlo method is used to simulate the interaction of ionizing radiation with the human genetic material in order to determine DNA damage yields per unit absorbed dose. To accomplish this task, an algorithm to determine if a given energy deposition lies within a given target is needed. This target can be an atom or any other structure of the genetic material. Solution method: This is a stand-alone subroutine describing an atomic-resolution geometrical model of the B-DNA configuration. It is able to determine the closest atom to an arbitrary point in space. This model accounts for five organization levels of the human genetic material, from the nucleotide pair up to the 30 nm chromatin fiber. This subroutine carries out a series of coordinate transformations to find which is the closest atom containing an arbitrary point in space. Atom sizes are according to the corresponding van der Waals radii. Restrictions: The geometrical model presented here does not include the chromosome organization level but it could be easily build up by using fragments of the 30 nm chromatin fiber. Unusual features: To our knowledge, this is the first open source atomic-resolution DNA geometrical model developed for DNA-radiation interaction Monte Carlo simulations. In our tests, the current model took into account the explicit position of about 56×106 atoms, although the user may enhance this amount according to the necessities. Running time: This subroutine can process about 2 million points within a few minutes in a typical current computer.

Teaching Valence Shell Electron Pair Repulsion (VSEPR) Theory

ERIC Educational Resources Information Center

Talbot, Christopher; Neo, Choo Tong

2013-01-01

This "Science Note" looks at the way that the shapes of simple molecules can be explained in terms of the number of electron pairs in the valence shell of the central atom. This theory is formally known as valence shell electron pair repulsion (VSEPR) theory. The article explains the preferred shape of chlorine trifluoride (ClF3),…

Sparsity of the normal matrix in the refinement of macromolecules at atomic and subatomic resolution.

PubMed

Jelsch, C

2001-09-01

The normal matrix in the least-squares refinement of macromolecules is very sparse when the resolution reaches atomic and subatomic levels. The elements of the normal matrix, related to coordinates, thermal motion and charge-density parameters, have a global tendency to decrease rapidly with the interatomic distance between the atoms concerned. For instance, in the case of the protein crambin at 0.54 A resolution, the elements are reduced by two orders of magnitude for distances above 1.5 A. The neglect a priori of most of the normal-matrix elements according to a distance criterion represents an approximation in the refinement of macromolecules, which is particularly valid at very high resolution. The analytical expressions of the normal-matrix elements, which have been derived for the coordinates and the thermal parameters, show that the degree of matrix sparsity increases with the diffraction resolution and the size of the asymmetric unit.

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

Cable, J.W.

The diffuse scattering of neutrons from magnetic materials provides unique and important information regarding the spatial correlations of the atoms and the spins. Such measurements have been extensively applied to magnetically ordered systems, such as the ferromagnetic binary alloys, for which the observed correlations describe the magnetic moment fluctuations associated with local environment effects. With the advent of polarization analysis, these techniques are increasingly being applied to study disordered paramagnetic systems such as the spin-glasses and the diluted magnetic semiconductors. The spin-pair correlations obtained are essential in understanding the exchange interactions of such systems. In this paper, we describe recentmore » neutron diffuse scattering results on the atom-pair and spin-pair correlations in some of these disordered magnetic systems. 56 refs.« less

Instability of Fulde-Ferrell-Larkin-Ovchinnikov states in atomic Fermi gases in three and two dimensions

NASA Astrophysics Data System (ADS)

Wang, Jibiao; Che, Yanming; Zhang, Leifeng; Chen, Qijin

2018-04-01

The exotic Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) states have been actively searched for experimentally since the mean-field based FFLO theories were put forward half a century ago. Here, we investigate the stability of FFLO states in the presence of pairing fluctuations. We conclude that FFLO superfluids cannot exist in continuum in three and two dimensions, due to their intrinsic instability, associated with infinite quantum degeneracy of the pairs. These results address the absence of convincing experimental observations of FFLO phases in both condensed matter and in ultracold atomic Fermi gases with a population imbalance. We predict that the true ground state has a pair momentum distribution highly peaked on an entire constant energy surface.

Is there a Stobbs factor in atomic-resolution STEM-EELS mapping?

PubMed

Xin, Huolin L; Dwyer, Christian; Muller, David A

2014-04-01

Recent work has convincingly argued that the Stobbs factor-disagreement in contrast between simulated and experimental atomic-resolution images-in ADF-STEM imaging can be accounted for by including the incoherent source size in simulation. However, less progress has been made for atomic-resolution STEM-EELS mapping. Here we have performed carefully calibrated EELS mapping experiments of a [101] DyScO3 single-crystal specimen, allowing atomic-resolution EELS signals to be extracted on an absolute scale for a large range of thicknesses. By simultaneously recording the elastic signal, also on an absolute scale, and using it to characterize the source size, sample thickness and inelastic mean free path, we eliminate all free parameters in the simulation of the core-loss signals. Coupled with double channeling simulations that incorporate both core-loss inelastic scattering and dynamical elastic and thermal diffuse scattering, the present work enables a close scrutiny of the scattering physics in the inelastic channel. We found that by taking into account the effective source distribution determined from the ADF images, both the absolute signal and the contrast in atomic-resolution Dy-M5 maps can be closely reproduced by the double-channeling simulations. At lower energy losses, discrepancies are present in the Sc-L2,3 and Dy-N4,5 maps due to the energy-dependent spatial distribution of the background spectrum, core-hole effects, and omitted complexities in the final states. This work has demonstrated the possibility of using quantitative STEM-EELS for element-specific column-by-column atom counting at higher energy losses and for atomic-like final states, and has elucidated several possible improvements for future theoretical work. Copyright © 2014 Elsevier B.V. All rights reserved.

Impact of Pb content on the physical parameters of Se-Te-Pb system

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

Anjali,; Sharma, Raman; Thakur, Nagesh

2015-05-15

In the present study, we have investigated the impact of Pb content on the physical parameters in Se-Te-Pb system via average coordination number, constraints, the fraction of floppy modes, cross-linking density, lone pairs electrons, heat of atomization, mean bond energy, cohesive energy and electronegativity. The bulk samples have been prepared by using melt quenching technique. X-ray diffraction pattern of various samples indicates the amorphous nature of investigated glassy alloys. It is observed that average coordination number, average number of constraints and cross-linking density increase with Pb content. However, lone-pair electrons, floppy modes, average heat of atomization, cohesive energy and meanmore » bond energy are found to decrease with Pb atomic percentage.« less

Four-dimensional ultrafast electron microscopy of phase transitions

PubMed Central

Grinolds, Michael S.; Lobastov, Vladimir A.; Weissenrieder, Jonas; Zewail, Ahmed H.

2006-01-01

Reported here is direct imaging (and diffraction) by using 4D ultrafast electron microscopy (UEM) with combined spatial and temporal resolutions. In the first phase of UEM, it was possible to obtain snapshot images by using timed, single-electron packets; each packet is free of space–charge effects. Here, we demonstrate the ability to obtain sequences of snapshots (“movies”) with atomic-scale spatial resolution and ultrashort temporal resolution. Specifically, it is shown that ultrafast metal–insulator phase transitions can be studied with these achieved spatial and temporal resolutions. The diffraction (atomic scale) and images (nanometer scale) we obtained manifest the structural phase transition with its characteristic hysteresis, and the time scale involved (100 fs) is now studied by directly monitoring coordinates of the atoms themselves. PMID:17130445

Aberrated electron probes for magnetic spectroscopy with atomic resolution: Theory and practical aspects

DOE PAGES

Rusz, Ján; Idrobo, Juan Carlos

2016-03-24

It was recently proposed that electron magnetic circular dichroism (EMCD) can be measured in scanning transmission electron microscopy (STEM) with atomic resolution by tuning the phase distribution of a electron beam. Here, we describe the theoretical and practical aspects for the detection of out-of-plane and in-plane magnetization utilizing atomic size electron probes. Here we present the calculated optimized astigmatic probes and discuss how to achieve them experimentally.

Quantum memory with optically trapped atoms.

PubMed

Chuu, Chih-Sung; Strassel, Thorsten; Zhao, Bo; Koch, Markus; Chen, Yu-Ao; Chen, Shuai; Yuan, Zhen-Sheng; Schmiedmayer, Jörg; Pan, Jian-Wei

2008-09-19

We report the experimental demonstration of quantum memory for collective atomic states in a far-detuned optical dipole trap. Generation of the collective atomic state is heralded by the detection of a Raman scattered photon and accompanied by storage in the ensemble of atoms. The optical dipole trap provides confinement for the atoms during the quantum storage while retaining the atomic coherence. We probe the quantum storage by cross correlation of the photon pair arising from the Raman scattering and the retrieval of the atomic state stored in the memory. Nonclassical correlations are observed for storage times up to 60 mus.

From average to local structure: a Rietveld and an atomic pair distribution function (PDF) study of selenium clusters in zeolite-NdY.

PubMed

Abeykoon, A M Milinda; Donner, Wolfgang; Brunelli, Michela; Castro-Colin, Miguel; Jacobson, Allan J; Moss, Simon C

2009-09-23

The structure of Se particles in the approximately 13 A diameter alpha-cages of zeolite NdY has been determined by Rietveld refinement and pair distribution function (PDF) analysis of X-ray data. With the diffuse scattering subtracted an average structure comprised of an undistorted framework containing nanoclusters of 20 Se atoms is observed. The intracluster correlations and the cluster-framework correlations which give rise to diffuse scattering were modeled by using PDF analysis.

Tuning the electronic structure of graphene through alkali metal and halogen atom intercalation

NASA Astrophysics Data System (ADS)

Ahmad, Sohail; Miró, Pere; Audiffred, Martha; Heine, Thomas

2018-04-01

The deposition, intercalation and co-intercalation of heavy alkali metals and light halogens atoms in graphene mono- and bilayers have been studied using first principles density-functional calculations. Both the deposition and the intercalation of alkali metals gives rise to n-type doping due to the formation of M+-C- pairs. The co-intercalation of a 1:1 ratio of alkali metals and halogens derives into the formation of ionic pairs among the intercalated species, unaltering the electronic structure of the layered material.

Sub-Terrahertz Spectroscopy of E.COLI Dna: Experiment, Statistical Model, and MD Simulations

NASA Astrophysics Data System (ADS)

Sizov, I.; Dorofeeva, T.; Khromova, T.; Gelmont, B.; Globus, T.

2012-06-01

We will present result of combined experimental and computational study of sub-THz absorption spectra from Escherichia coli (E.coli) DNA. Measurements were conducted using a Bruker FTIR spectrometer with a liquid helium cooled bolometer and a recently developed frequency domain sensor operating at room temperature, with spectral resolution of 0.25 cm-1 and 0.03 cm-1, correspondingly. We have earlier demonstrated that molecular dynamics (MD) simulation can be effectively applied for characterizing relatively small biological molecules, such as transfer RNA or small protein thioredoxin from E. coli , and help to understand and predict their absorption spectra. Large size of DNA macromolecules ( 5 million base pairs for E. coli DNA) prevents, however, direct application of MD simulation at the current level of computational capabilities. Therefore, by applying a second order Markov chain approach and Monte-Carlo technique, we have developed a new statistical model to construct DNA sequences from biological cells. These short representative sequences (20-60 base pairs) are built upon the most frequently repeated fragments (2-10 base pairs) in the original DNA. Using this new approach, we constructed DNA sequences for several non-pathogenic strains of E.coli, including a well-known strain BL21, uro-pathogenic strain, CFT073, and deadly EDL933 strain (O157:H7), and used MD simulations to calculate vibrational absorption spectra of these strains. Significant differences are clearly present in spectra of strains in averaged spectra and in all components for particular orientations. The mechanism of interaction of THz radiation with a biological molecule is studied by analyzing dynamics of atoms and correlation of local vibrations in the modeled molecule. Simulated THz vibrational spectra of DNA are compared with experimental results. With the spectral resolution of 0.1 cm-1 or better, which is now available in experiments, the very easy discrimination between different strains of the same bacteria becomes possible.

Radical Chemistry and Charge Manipulation with an Atomic Force Microscope

NASA Astrophysics Data System (ADS)

Gross, Leo

The fuctionalization of tips by atomic manipulation dramatically increased the resolution of atomic force microscopy (AFM). The combination of high-resolution AFM with atomic manipulation now offers the unprecedented possibility to custom-design individual molecules by making and breaking bonds with the tip of the microscope and directly characterizing the products on the atomic scale. We recently applied this technique to generate and study reaction intermediates and to investigate chemical reactions trigged by atomic manipulation. We formed diradicals by dissociating halogen atoms and then reversibly triggered ring-opening and -closing reactions via atomic manipulation, allowing us to switch and control the molecule's reactivity, magnetic and optical properties. Additional information about charge states and charge distributions can be obtained by Kelvin probe force spectroscopy. On multilayer insulating films we investigated single-electron attachment, detachment and transfer between individual molecules. EU ERC AMSEL (682144), EU project PAMS (610446).

Elemental and lattice-parameter mapping of binary oxide superlattices of (LaNiO 3 ) 4 /(LaMnO 3 ) 2 at atomic resolution

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

Kwon, Ji-Hwan; Lu, Ping; Hoffman, Jason

2016-12-19

We construct the elemental distribution and lattice strain maps from the measured atomic column positions in a (LaNiO3)(4)/(LaMnO3)(2) superlattice over a large field of view. The correlation between the distribution of B-cations and the lattice parameter in the form of Vegard's law is validated using atomic resolution energy dispersive x-ray spectroscopy (EDS). The maps show negligible Mn intermixing in the LaNiO3 layer, while Ni intermixing in the LaMnO3 layer improves away from the substrate interface to 9.5 atomic% from the 8th period onwards, indicating that the superlattice interfacial sharpness is established as the distance from the substrate increases. The mapsmore » allow an observation of the compositional defects of the B-sites, which is not possible by Z-contrast alone. Thus, this study demonstrates a promising approach for atomic scale correlative study of lattice strain and composition, and a method for the calibration of atomic resolution EDS maps.« less

Hybrid-denovo: a de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags.

PubMed

Chen, Xianfeng; Johnson, Stephen; Jeraldo, Patricio; Wang, Junwen; Chia, Nicholas; Kocher, Jean-Pierre A; Chen, Jun

2018-03-01

Illumina paired-end sequencing has been increasingly popular for 16S rRNA gene-based microbiota profiling. It provides higher phylogenetic resolution than single-end reads due to a longer read length. However, the reverse read (R2) often has significant low base quality, and a large proportion of R2s will be discarded after quality control, resulting in a mixture of paired-end and single-end reads. A typical 16S analysis pipeline usually processes either paired-end or single-end reads but not a mixture. Thus, the quantification accuracy and statistical power will be reduced due to the loss of a large amount of reads. As a result, rare taxa may not be detectable with the paired-end approach, or low taxonomic resolution will result in a single-end approach. To have both the higher phylogenetic resolution provided by paired-end reads and the higher sequence coverage by single-end reads, we propose a novel OTU-picking pipeline, hybrid-denovo, that can process a hybrid of single-end and paired-end reads. Using high-quality paired-end reads as a gold standard, we show that hybrid-denovo achieved the highest correlation with the gold standard and performed better than the approaches based on paired-end or single-end reads in terms of quantifying the microbial diversity and taxonomic abundances. By applying our method to a rheumatoid arthritis (RA) data set, we demonstrated that hybrid-denovo captured more microbial diversity and identified more RA-associated taxa than a paired-end or single-end approach. Hybrid-denovo utilizes both paired-end and single-end 16S sequencing reads and is recommended for 16S rRNA gene targeted paired-end sequencing data.

Reducing Earth Topography Resolution for SMAP Mission Ground Tracks Using K-Means Clustering

NASA Technical Reports Server (NTRS)

Rizvi, Farheen

2013-01-01

The K-means clustering algorithm is used to reduce Earth topography resolution for the SMAP mission ground tracks. As SMAP propagates in orbit, knowledge of the radar antenna footprints on Earth is required for the antenna misalignment calibration. Each antenna footprint contains a latitude and longitude location pair on the Earth surface. There are 400 pairs in one data set for the calibration model. It is computationally expensive to calculate corresponding Earth elevation for these data pairs. Thus, the antenna footprint resolution is reduced. Similar topographical data pairs are grouped together with the K-means clustering algorithm. The resolution is reduced to the mean of each topographical cluster called the cluster centroid. The corresponding Earth elevation for each cluster centroid is assigned to the entire group. Results show that 400 data points are reduced to 60 while still maintaining algorithm performance and computational efficiency. In this work, sensitivity analysis is also performed to show a trade-off between algorithm performance versus computational efficiency as the number of cluster centroids and algorithm iterations are increased.

Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2;#8242;-deoxyadenosine:dT Base Pairing in DNA

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

Kowal, Ewa A.; Ganguly, Manjori; Pallan, Pradeep S.

As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2'-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson-Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C-H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 {angstrom} resolution in the presence of Mg{sup 2+}. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry andmore » the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA.« less

Altering the Electrostatic Potential in the Major Groove: Thermodynamic and Structural Characterization of 7-Deaza-2′-deoxyadenosine:dT Base Pairing in DNA

PubMed Central

2011-01-01

As part of an ongoing effort to explore the effect of major groove electrostatics on the thermodynamic stability and structure of DNA, a 7-deaza-2′-deoxyadenosine:dT (7-deaza-dA:dT) base pair in the Dickerson–Drew dodecamer (DDD) was studied. The removal of the electronegative N7 atom on dA and the replacement with an electropositive C–H in the major groove was expected to have a significant effect on major groove electrostatics. The structure of the 7-deaza-dA:dT base pair was determined at 1.1 Å resolution in the presence of Mg2+. The 7-deaza-dA, which is isosteric for dA, had minimal effect on the base pairing geometry and the conformation of the DDD in the crystalline state. There was no major groove cation association with the 7-deaza-dA heterocycle. In solution, circular dichroism showed a positive Cotton effect centered at 280 nm and a negative Cotton effect centered at 250 nm that were characteristic of a right-handed helix in the B-conformation. However, temperature-dependent NMR studies showed increased exchange between the thymine N3 imino proton of the 7-deaza-dA:dT base pair and water, suggesting reduced stacking interactions and an increased rate of base pair opening. This correlated with the observed thermodynamic destabilization of the 7-deaza-dA modified duplex relative to the DDD. A combination of UV melting and differential scanning calorimetry experiments were conducted to evaluate the relative contributions of enthalpy and entropy in the thermodynamic destabilization of the DDD. The most significant contribution arose from an unfavorable enthalpy term, which probably results from less favorable stacking interactions in the modified duplex, which was accompanied by a significant reduction in the release of water and cations from the 7-deaza-dA modified DNA. PMID:22059929

Note: A rigid piezo motor with large output force and an effective method to reduce sliding friction force.

PubMed

Guo, Ying; Hou, Yubin; Lu, Qingyou

2014-05-01

We present a completely practical TunaDrive piezo motor. It consists of a central piezo stack sandwiched by two arm piezo stacks and two leg piezo stacks, respectively, which is then sandwiched and spring-clamped by a pair of parallel polished sapphire rods. It works by alternatively fast expanding and contracting the arm/leg stacks while slowly expanding/contracting the central stack simultaneously. The key point is that sufficiently fast expanding and contracting a limb stack can make its two sliding friction forces well cancel, resulting in the total sliding friction force is <10% of the total static friction force, which can help increase output force greatly. The piezo motor's high compactness, precision, and output force make it perfect in building a high-quality harsh-condition (vibration resistant) atomic resolution scanning probe microscope.

Multichordal charge exchange recombination spectroscopy on Doublet III (abstract)

NASA Astrophysics Data System (ADS)

Seraydarian, R. P.; Burrell, K. H.; Kahn, C.

1985-05-01

Single shot, multipoint ion temperature and plasma rotation profiles have been routinely obtained on the Doublet III tokamak for 32 consecutive time slices with 20-ms resolution. A six-chord tangentially viewing spectroscopic diagnostic has been built to look at radiation emitted by fully stripped low-Z impurity ions (He, C, O) that have undergone charge exchange recombination with hydrogen atoms from a 3-MW heating beam. The main components of the instrument are a single monochromator for wavelength dispersion, a single image intensifier tube for photon gain, and a pair of 1024-element linear photodiode arrays for detection. A special arrangement of fiber optics allows simultaneous data acquisition from all chords without the use of scanning mirrors or other moving parts. Ion temperature profiles taken under a variety of plasma conditions will be presented.

Local Structures of High-Entropy Alloys (HEAs) on Atomic Scales: An Overview

DOE PAGES

Diao, Haoyan; Santodonato, Louis J.; Tang, Zhi; ...

2015-08-29

The high-entropy alloys (HEAs), containing several elements mixed in equimolar or near-equimolar ratios, have shown exceptional engineering properties. Local structures on atomic level are essential to understand the mechanical behaviors and related mechanisms. In this paper, the local structure and stress on the atomic level are reviewed by the pair-distribution function (PDF) of neutron-diffraction data, ab-initio-molecular-dynamics (AIMD) simulations, and atomic-probe microscopy (APT).

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions

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

West, Aaron C.; Schmidt, Michael W.; Gordon, Mark S.

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the non-bonded juxtaposed quasi-atoms andmore » a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. Lastly, the theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.« less

Intrinsic Resolution of Molecular Electronic Wave Functions and Energies in Terms of Quasi-atoms and Their Interactions

DOE PAGES

West, Aaron C.; Schmidt, Michael W.; Gordon, Mark S.; ...

2017-01-30

A general intrinsic energy resolution has been formulated for strongly correlated wave functions in the full molecular valence space and its subspaces. The information regarding the quasi-atomic organization of the molecular electronic structure is extracted from the molecular wave function without introducing any additional postulated model state wave functions. To this end, the molecular wave function is expressed in terms of quasi-atomic molecular orbitals, which maximize the overlap between subspaces of the molecular orbital space and the free-atom orbital spaces. As a result, the molecular wave function becomes the superposition of a wave function representing the non-bonded juxtaposed quasi-atoms andmore » a wave function describing the interatomic electron migrations that create bonds through electron sharing. The juxtaposed nonbonded quasi-atoms are shown to consist of entangled quasi-atomic states from different atoms. The binding energy is resolved as a sum of contributions that are due to quasi-atom formation, quasiclassical electrostatic interactions and interatomic interferences caused by electron sharing. The contributions are further resolved according to orbital interactions. The various transformations that generate the analysis are determined by criteria that are independent of the working orbital basis used for calculating the molecular wave function. Lastly, the theoretical formulation of the resolution is quantitatively validated by an application to the C 2 molecule.« less

A re-evaluation of thermal expansion measurements of metallic liquids and glasses from x-ray scattering experiments

NASA Astrophysics Data System (ADS)

Gangopadhyay, A. K.; Kelton, K. F.

2018-05-01

Previous studies reported a number of anomalies when estimates of linear thermal expansion coefficients of metallic liquids and glasses from x-ray scattering experiments were compared with direct measurements of volume/length changes with temperature. In most cases, the first peak of the pair correlation function showed a contraction, while the structure factor showed an expansion, but both at rates much different from those expected from the direct volume measurements. In addition, the relationship between atomic volume and the characteristic lengths obtained from the structure factor from scattering experiments was found to have a fractional exponent instead of one equal to three, as expected from the Ehrenfest relation. This has led to the speculation that the atomic packing in liquids and glasses follow a fractal behavior. These issues are revisited in this study using more in-depth analysis of recent higher resolution data and some new ideas suggested in the literature. The main conclusion is that for metallic alloys, at least to a large extent, most of these anomalies arise from complicated interplays of the temperature dependences of the various partial structure factors, which contribute to the total intensities of the scattering peaks.

Multilevel Summation of Electrostatic Potentials Using Graphics Processing Units*

PubMed Central

Hardy, David J.; Stone, John E.; Schulten, Klaus

2009-01-01

Physical and engineering practicalities involved in microprocessor design have resulted in flat performance growth for traditional single-core microprocessors. The urgent need for continuing increases in the performance of scientific applications requires the use of many-core processors and accelerators such as graphics processing units (GPUs). This paper discusses GPU acceleration of the multilevel summation method for computing electrostatic potentials and forces for a system of charged atoms, which is a problem of paramount importance in biomolecular modeling applications. We present and test a new GPU algorithm for the long-range part of the potentials that computes a cutoff pair potential between lattice points, essentially convolving a fixed 3-D lattice of “weights” over all sub-cubes of a much larger lattice. The implementation exploits the different memory subsystems provided on the GPU to stream optimally sized data sets through the multiprocessors. We demonstrate for the full multilevel summation calculation speedups of up to 26 using a single GPU and 46 using multiple GPUs, enabling the computation of a high-resolution map of the electrostatic potential for a system of 1.5 million atoms in under 12 seconds. PMID:20161132

On local pairs vs. BCS: Quo vadis high-T c superconductivity

DOE PAGES

Pavuna, D.; Dubuis, G.; Bollinger, A. T.; ...

2016-07-28

Since the discovery of high-temperature superconductivity in cuprates, proposals have been made that pairing may be local, in particular in underdoped samples. Furthermore, we briefly review evidence for local pairs from our experiments on thin films of La 2–xSr xCuO 4, synthesized by atomic layer-by-layer molecular beam epitaxy (ALL-MBE).

Structural mechanism of enoyl-CoA hydratase: three atoms from a single water are added in either an E1cb stepwise or concerted fashion.

PubMed

Bahnson, Brian J; Anderson, Vernon E; Petsko, Gregory A

2002-02-26

We have determined the crystal structure of the enzyme enoyl-CoA hydratase (ECH) from rat liver with the bound substrate 4-(N,N-dimethylamino)cinnamoyl-CoA using X-ray diffraction data to a resolution of 2.3 A. In addition to the thiolester substrate, the catalytic water, which is added in the hydration reaction, has been modeled into well-defined electron density in each of the six active sites of the physiological hexamer within the crystallographic asymmetric unit. The catalytic water bridges Glu(144) and Glu(164) of the enzyme and has a lone pair of electrons poised to react with C(3) of the enzyme-bound alpha,beta-unsaturated thiolester. The water molecule, which bridges two glutamate residues, is reminiscent of the enolase active site. However, unlike enolase, which has a lysine available to donate a proton, there are no other sources of protons available from other active site residues in ECH. Furthermore, an analysis of the hydrogen-bonding network of the active site suggests that both Glu(144) and Glu(164) are ionized and carry a negative charge with no reasonable place to have a protonated carboxylate. This lack of hydrogen-bonding acceptors that could accommodate a source of a proton, other than from the water molecule, leads to a hypothesis that the three atoms from a single water molecule are added across the double bond to form the hydrated product. The structural results are discussed in connection with details of the mechanism, which have been elucidated from kinetics, site-directed mutagenesis, and spectroscopy of enzyme-substrate species, in presenting an atomic-resolution mechanism of the reaction. Contrary to the previous interpretation, the structure of the E-S complex together with previously determined kinetic isotope effects is consistent with either a concerted mechanism or an E1cb stepwise mechanism.

Note: High-speed Z tip scanner with screw cantilever holding mechanism for atomic-resolution atomic force microscopy in liquid

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

Reza Akrami, Seyed Mohammad; Miyata, Kazuki; Asakawa, Hitoshi

High-speed atomic force microscopy has attracted much attention due to its unique capability of visualizing nanoscale dynamic processes at a solid/liquid interface. However, its usability and resolution have yet to be improved. As one of the solutions for this issue, here we present a design of a high-speed Z-tip scanner with screw holding mechanism. We perform detailed comparison between designs with different actuator size and screw arrangement by finite element analysis. Based on the design giving the best performance, we have developed a Z tip scanner and measured its performance. The measured frequency response of the scanner shows a flatmore » response up to ∼10 kHz. This high frequency response allows us to achieve wideband tip-sample distance regulation. We demonstrate the applicability of the scanner to high-speed atomic-resolution imaging by visualizing atomic-scale calcite crystal dissolution process in water at 2 s/frame.« less

An atomic model of brome mosaic virus using direct electron detection and real-space optimization.

PubMed

Wang, Zhao; Hryc, Corey F; Bammes, Benjamin; Afonine, Pavel V; Jakana, Joanita; Chen, Dong-Hua; Liu, Xiangan; Baker, Matthew L; Kao, Cheng; Ludtke, Steven J; Schmid, Michael F; Adams, Paul D; Chiu, Wah

2014-09-04

Advances in electron cryo-microscopy have enabled structure determination of macromolecules at near-atomic resolution. However, structure determination, even using de novo methods, remains susceptible to model bias and overfitting. Here we describe a complete workflow for data acquisition, image processing, all-atom modelling and validation of brome mosaic virus, an RNA virus. Data were collected with a direct electron detector in integrating mode and an exposure beyond the traditional radiation damage limit. The final density map has a resolution of 3.8 Å as assessed by two independent data sets and maps. We used the map to derive an all-atom model with a newly implemented real-space optimization protocol. The validity of the model was verified by its match with the density map and a previous model from X-ray crystallography, as well as the internal consistency of models from independent maps. This study demonstrates a practical approach to obtain a rigorously validated atomic resolution electron cryo-microscopy structure.

Automated structure refinement of macromolecular assemblies from cryo-EM maps using Rosetta.

PubMed

Wang, Ray Yu-Ruei; Song, Yifan; Barad, Benjamin A; Cheng, Yifan; Fraser, James S; DiMaio, Frank

2016-09-26

Cryo-EM has revealed the structures of many challenging yet exciting macromolecular assemblies at near-atomic resolution (3-4.5Å), providing biological phenomena with molecular descriptions. However, at these resolutions, accurately positioning individual atoms remains challenging and error-prone. Manually refining thousands of amino acids - typical in a macromolecular assembly - is tedious and time-consuming. We present an automated method that can improve the atomic details in models that are manually built in near-atomic-resolution cryo-EM maps. Applying the method to three systems recently solved by cryo-EM, we are able to improve model geometry while maintaining the fit-to-density. Backbone placement errors are automatically detected and corrected, and the refinement shows a large radius of convergence. The results demonstrate that the method is amenable to structures with symmetry, of very large size, and containing RNA as well as covalently bound ligands. The method should streamline the cryo-EM structure determination process, providing accurate and unbiased atomic structure interpretation of such maps.

Atomic-scale properties of Ni-based FCC ternary, and quaternary alloys

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

Tamm, Artur; Aabloo, Alvo; Klintenberg, Mattias

2015-08-26

The aim of our study is to characterize some atomic-scale properties of Ni-based FCC multicomponent alloys. For this purpose, we use Monte Carlo method combined with density functional theory calculations to study short-range order (SRO), atomic displacements, electronic density of states, and magnetic moments in equimolar ternary NiCrCo, and quaternary NiCrCoFe alloys. The salient features for the ternary alloy are a negative SRO parameter between Ni Cr and a positive between Cr Cr pairs as well as a weakly magnetic state. For the quaternary alloy we predict negative SRO parameter for Ni Cr and Ni Fe pairs and positive formore » Cr Cr and Fe Fe pairs. Atomic displacements for both ternary and quaternary alloys are negligible. In contrast to the ternary, the quaternary alloy shows a complex magnetic structure. The electronic structure of the ternary and quaternary alloys shows differences near the Fermi energy between a random solid solution and the predicted structure with SRO. Despite that, the calculated EXAFS spectra does not show enough contrast to discriminate between random and ordered structures. Finally, the predicted SRO has an impact on point-defect energetics, electron phonon coupling and thermodynamic functions and thus, SRO should not be neglected when studying properties of these two alloys.« less

Application of Internal Standard Method for Several 3d-Transition Metallic Elements in Flame Atomic Absorption Spectrometry Using a Multi-wavelength High-resolution Spectrometer.

PubMed

Toya, Yusuke; Itagaki, Toshiko; Wagatsuma, Kazuaki

2017-01-01

We investigated a simultaneous internal standard method in flame atomic absorption spectrometry (FAAS), in order to better the analytical precision of 3d-transition metals contained in steel materials. For this purpose, a new spectrometer system for FAAS, comprising a bright xenon lamp as the primary radiation source and a high-resolution Echelle monochromator, was employed to measure several absorption lines at a wavelength width of ca. 0.3 nm at the same time, which enables the absorbances of an analytical line and also an internal standard line to be estimated. In considering several criteria for selecting an internal standard element and the absorption line, it could be suggested that platinum-group elements: ruthenium, rhodium, or palladium, were suitable for an internal standard element to determine the 3d-transition metal elements, such as titanium, iron, and nickel, by measuring an appropriate pair of these absorption lines simultaneously. Several variances of the absorption signal, such as a variation in aspirated amounts of sample solution and a short-period drift of the primary light source, would be corrected and thus reduced, when the absorbance ratio of the analytical line to the internal standard line was measured. In Ti-Pd, Ni-Rh, and Fe-Ru systems chosen as typical test samples, the repeatability of the signal respnses was investigated with/without the internal standard method, resulting in better precision when the internal standard method was applied in the FAAS with a nitrous oxide-acetylene flame rather than an air-acetylene flame.

Selective excitation enables assignment of proton resonances and (1)H-(1)H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy.

PubMed

Zhang, Rongchun; Ramamoorthy, Ayyalusamy

2015-07-21

Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of (1)H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as (13)C or (15)N. In this method, after the initial preparation of proton magnetization and cross-polarization to (13)C nuclei, transverse magnetization of desired (13)C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferred to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific (13)C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of (1)H-(1)H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.

Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson-Crick DNA Base Pairs in Solution.

PubMed

Röttger, Katharina; Marroux, Hugo J B; Grubb, Michael P; Coulter, Philip M; Böhnke, Hendrik; Henderson, Alexander S; Galan, M Carmen; Temps, Friedrich; Orr-Ewing, Andrew J; Roberts, Gareth M

2015-12-01

Ultrafast deactivation pathways bestow photostability on nucleobases and hence preserve the structural integrity of DNA following absorption of ultraviolet (UV) radiation. One controversial recovery mechanism proposed to account for this photostability involves electron-driven proton transfer (EDPT) in Watson-Crick base pairs. The first direct observation is reported of the EDPT process after UV excitation of individual guanine-cytosine (G⋅C) Watson-Crick base pairs by ultrafast time-resolved UV/visible and mid-infrared spectroscopy. The formation of an intermediate biradical species (G[-H]⋅C[+H]) with a lifetime of 2.9 ps was tracked. The majority of these biradicals return to the original G⋅C Watson-Crick pairs, but up to 10% of the initially excited molecules instead form a stable photoproduct G*⋅C* that has undergone double hydrogen-atom transfer. The observation of these sequential EDPT mechanisms across intermolecular hydrogen bonds confirms an important and long debated pathway for the deactivation of photoexcited base pairs, with possible implications for the UV photochemistry of DNA. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Constructing Molecular Models with Low-Cost Toy Beads

ERIC Educational Resources Information Center

Ng, Pun-hon; Wong, Siu-ling; Mak, Se-yuen

2012-01-01

In teaching the science of the nano world, ball-and-stick molecular models are frequently used as 3D representations of molecules. Unlike a chemical formula, a molecular model allows us to visualise the 3D shape of the molecule and the relative positions of its atoms, the bonds between atoms and why a pair of mirror isomers with the same atoms,…

Metal atomization spray nozzle

DOEpatents

Huxford, Theodore J.

1993-01-01

A spray nozzle for a magnetohydrodynamic atomization apparatus has a feed passage for molten metal and a pair of spray electrodes mounted in the feed passage. The electrodes, diverging surfaces which define a nozzle throat and diverge at an acute angle from the throat. Current passes through molten metal when fed through the throat which creates the Lorentz force necessary to provide atomization of the molten metal.

Effects of helium concentration and radiation temperature on interaction of helium atoms with displacement cascades in bcc iron

NASA Astrophysics Data System (ADS)

Gao, Chan; Tian, Dongfeng; Li, Maosheng; Qian, Dazhi

2018-03-01

In fusion applications, helium, implanted or created by transmutation, plays an important role in the response of reduced-activation ferritic/martensitic steels to neutron radiation damage. The effects of helium concentration and radiation temperature on interaction of interstitial helium atoms with displacement cascades have been studied in Fe-He system using molecular dynamics with recently developed Fe-He potential. Results indicate that interstitial helium atoms produce no additional defects at peak time and promote recombination of Frenkel pairs at lower helium concentrations, but suppress recombination of Frenkel pairs at larger helium concentrations. Moreover, large helium concentrations promote the production of defects at the end of cascades. The number of substitutional helium atoms increases with helium concentration at peak time and the end of cascades, but the number of substitutional helium atoms at peak time is smaller than that at the end of displacement cascades. High radiation temperatures promote the production at peak time and the recombination of defects at the end of cascades. The number of substitutional helium atoms increases with radiation temperature, but that at peak time is smaller than that at the end of cascades.

Automatic Traffic Advisory and Resolution Service (ATARS) Algorithms Including Resolution-Advisory-Register Logic. Volume 2. Sections 12 through 19. Appendices,

DTIC Science & Technology

1981-06-01

pairwise conflict or an indication of BCAS control . A Pair Record is also created when an aircraft receives a resolution advisory from BCAS or from a non ...replying site: Update track numbers: ILS!I’ (pair record shows a non -connected site in control ) T"_N CALL AI!CPAFTPAIRriwTIFICRTaOI: ( both aircraft...Springfield, Virginia 22161 a>- U S Department of Transportain Systems Research & Development Service LWashington, D.C. 20590 94 This document is

Effect of post-implantation annealing on Al-N isoelectronic trap formation in silicon: Al-N pair formation and defect recovery mechanisms

NASA Astrophysics Data System (ADS)

Mori, Takahiro; Morita, Yukinori; Matsukawa, Takashi

2018-05-01

The effect of post-implantation annealing (PIA) on Al-N isoelectronic trap (IET) formation in silicon has been experimentally investigated to discuss the Al-N IET formation and implantation-induced defect recovery mechanisms. We performed a photoluminescence study, which indicated that self-interstitial clusters and accompanying vacancies are generated in the ion implantation process. It is supposed that Al and N atoms move to the vacancy sites and form stable Al-N pairs in the PIA process. Furthermore, the PIA process recovers self-interstitial clusters while transforming their atomic configuration. The critical temperature for the formation/dissociation of Al-N pairs was found to be 450 °C, with which we describe the process integration for devices utilizing Al-N IET technology.

Simulation of defects in fusion plasma first wall materials

NASA Astrophysics Data System (ADS)

T, Troev; N, Nankov; T, Yoshiie

2014-06-01

Numerical calculations of radiation damages in beryllium, alpha-iron and tungsten irradiated by fusion neutrons were performed using molecular dynamics (MD) simulations. The displacement cascades efficiency has been calculated using the Norgett-Robinson-Torrens (NRT) formula, the universal pair-potential of Ziegler-Biersack-Littmark (ZBL) and the EAM inter-atomic potential. The pair potential overestimates the defects production by a factor of 2. The ZBL pair potential results and the EAM are comparable at higher primary knock-on atom (PKA) energies (E > 100 keV). We found that the most common types of defects are single vacancies, di-vacancies, interstitials and small number of interstitial clusters. On the bases of calculated results, the behavior of vacancies, empty nano-voids and nano-voids with hydrogen and helium were discussed.

Atomic-resolution transmission electron microscopy of electron beam–sensitive crystalline materials

NASA Astrophysics Data System (ADS)

Zhang, Daliang; Zhu, Yihan; Liu, Lingmei; Ying, Xiangrong; Hsiung, Chia-En; Sougrat, Rachid; Li, Kun; Han, Yu

2018-02-01

High-resolution imaging of electron beam–sensitive materials is one of the most difficult applications of transmission electron microscopy (TEM). The challenges are manifold, including the acquisition of images with extremely low beam doses, the time-constrained search for crystal zone axes, the precise image alignment, and the accurate determination of the defocus value. We develop a suite of methods to fulfill these requirements and acquire atomic-resolution TEM images of several metal organic frameworks that are generally recognized as highly sensitive to electron beams. The high image resolution allows us to identify individual metal atomic columns, various types of surface termination, and benzene rings in the organic linkers. We also apply our methods to other electron beam–sensitive materials, including the organic-inorganic hybrid perovskite CH3NH3PbBr3.

2-Amino-5-chloro-pyrimidin-1-ium hydrogen maleate.

PubMed

Fun, Hoong-Kun; Hemamalini, Madhukar; Rajakannan, Venkatachalam

2012-01-01

In the title salt, C(4)H(5)ClN(3) (+)·C(4)H(3)O(4) (-), the 2-amino-5-chloro-pyrimidinium cation is protonated at one of its pyrimidine N atoms. In the roughly planar (r.m.s. deviation = 0.026 Å) hydrogen malate anion, an intra-molecular O-H⋯O hydrogen bond generates an S(7) ring. In the crystal, the protonated N atom and the 2-amino group of the cation are hydrogen bonded to the carboxyl-ate O atoms of the anion via a pair of N-H⋯O hydrogen bonds, forming an R(2) (2)(8) ring motif. The ion pairs are connected via further N-H⋯O hydrogen bonds and a short C-H⋯O inter-action, forming layers lying parallel to the bc plane.

Phase contrast scanning transmission electron microscopy imaging of light and heavy atoms at the limit of contrast and resolution.

PubMed

Yücelen, Emrah; Lazić, Ivan; Bosch, Eric G T

2018-02-08

Using state of the art scanning transmission electron microscopy (STEM) it is nowadays possible to directly image single atomic columns at sub-Å resolution. In standard (high angle) annular dark field STEM ((HA)ADF-STEM), however, light elements are usually invisible when imaged together with heavier elements in one image. Here we demonstrate the capability of the recently introduced Integrated Differential Phase Contrast STEM (iDPC-STEM) technique to image both light and heavy atoms in a thin sample at sub-Å resolution. We use the technique to resolve both the Gallium and Nitrogen dumbbells in a GaN crystal in [[Formula: see text

Image quality improvement in cone-beam CT using the super-resolution technique.

PubMed

Oyama, Asuka; Kumagai, Shinobu; Arai, Norikazu; Takata, Takeshi; Saikawa, Yusuke; Shiraishi, Kenshiro; Kobayashi, Takenori; Kotoku, Jun'ichi

2018-04-05

This study was conducted to improve cone-beam computed tomography (CBCT) image quality using the super-resolution technique, a method of inferring a high-resolution image from a low-resolution image. This technique is used with two matrices, so-called dictionaries, constructed respectively from high-resolution and low-resolution image bases. For this study, a CBCT image, as a low-resolution image, is represented as a linear combination of atoms, the image bases in the low-resolution dictionary. The corresponding super-resolution image was inferred by multiplying the coefficients and the high-resolution dictionary atoms extracted from planning CT images. To evaluate the proposed method, we computed the root mean square error (RMSE) and structural similarity (SSIM). The resulting RMSE and SSIM between the super-resolution images and the planning CT images were, respectively, as much as 0.81 and 1.29 times better than those obtained without using the super-resolution technique. We used super-resolution technique to improve the CBCT image quality.

Prediction of the electron redundant SinNn fullerenes

NASA Astrophysics Data System (ADS)

Yang, Huihui; Song, Yan; Zhang, Yan; Chen, Hongshan

2018-05-01

The stabilities and electronic structures of SimAln-mNn and SinNn (n = 16, 20, m = 12 and n = 24, m = 16) fullerene-like cages have been investigated using density functional method B3LYP and the second-order perturbation theory MP2. The results show that the SimAln-mNn and SinNn fullerenes are more stable than the AlN counterparts. Comparing with the corresponding AlnNn cages, one silicon atom in each Si2N2 square protrudes and the excess electrons reside as lone pair electrons at the outside of the protrudent Si atoms. Analyses on the electronic structures suggest that the Sisbnd N bonds are covalent bonding with strong polarity. The ELF (electron localization function) shows large electron pair probability between Si and N atoms. The orbital interactions between Si and N are stronger than that between Al and N atoms; the overlap integral is 0.40 per Sisbnd N bond in SinNn and 0.34 per Alsbnd N bond in AlnNn. The AIM (atoms in molecule) charges on the Al atoms in AlnNn and SimAln-mNn are 2.37 and 2.40. The charges on the in-plane and protrudent Si atoms are about 2.88 and 1.50 respectively. Considering the large local dipole moments around the protrudent Si atoms, the electrostatic interactions are also favorable to the SiN cages.

Detecting and locating light atoms from high-resolution STEM images: The quest for a single optimal design.

PubMed

Gonnissen, J; De Backer, A; den Dekker, A J; Sijbers, J; Van Aert, S

2016-11-01

In the present paper, the optimal detector design is investigated for both detecting and locating light atoms from high resolution scanning transmission electron microscopy (HR STEM) images. The principles of detection theory are used to quantify the probability of error for the detection of light atoms from HR STEM images. To determine the optimal experiment design for locating light atoms, use is made of the so-called Cramér-Rao Lower Bound (CRLB). It is investigated if a single optimal design can be found for both the detection and location problem of light atoms. Furthermore, the incoming electron dose is optimised for both research goals and it is shown that picometre range precision is feasible for the estimation of the atom positions when using an appropriate incoming electron dose under the optimal detector settings to detect light atoms. Copyright © 2016 Elsevier B.V. All rights reserved.

Polymerization of a divalent/tetravalent metal-storing atom-mimicking dendrimer.

PubMed

Albrecht, Ken; Hirabayashi, Yuki; Otake, Masaya; Mendori, Shin; Tobari, Yuta; Azuma, Yasuo; Majima, Yutaka; Yamamoto, Kimihisa

2016-12-01

The phenylazomethine dendrimer (DPA) has a layer-by-layer electron density gradient that is an analog of the Bohr atom (atom mimicry). In combination with electron pair mimicry, the polymerization of this atom-mimicking dendrimer was achieved. The valency of the mimicked atom was controlled by changing the chemical structure of the dendrimer. By mimicking a divalent atom, a one-dimensional (1D) polymer was obtained, and by using a planar tetravalent atom mimic, a 2D polymer was obtained. These poly(dendrimer) polymers could store Lewis acids (SnCl 2 ) in their unoccupied orbitals, thus indicating that these poly(dendrimer) polymers consist of a series of nanocontainers.

Entropic Comparison of Atomic-Resolution Electron Tomography of Crystals and Amorphous Materials.

PubMed

Collins, S M; Leary, R K; Midgley, P A; Tovey, R; Benning, M; Schönlieb, C-B; Rez, P; Treacy, M M J

2017-10-20

Electron tomography bears promise for widespread determination of the three-dimensional arrangement of atoms in solids. However, it remains unclear whether methods successful for crystals are optimal for amorphous solids. Here, we explore the relative difficulty encountered in atomic-resolution tomography of crystalline and amorphous nanoparticles. We define an informational entropy to reveal the inherent importance of low-entropy zone-axis projections in the reconstruction of crystals. In turn, we propose considerations for optimal sampling for tomography of ordered and disordered materials.

Chromatic Aberration Correction for Atomic Resolution TEM Imaging from 20 to 80 kV.

PubMed

Linck, Martin; Hartel, Peter; Uhlemann, Stephan; Kahl, Frank; Müller, Heiko; Zach, Joachim; Haider, Max; Niestadt, Marcel; Bischoff, Maarten; Biskupek, Johannes; Lee, Zhongbo; Lehnert, Tibor; Börrnert, Felix; Rose, Harald; Kaiser, Ute

2016-08-12

Atomic resolution in transmission electron microscopy of thin and light-atom materials requires a rigorous reduction of the beam energy to reduce knockon damage. However, at the same time, the chromatic aberration deteriorates the resolution of the TEM image dramatically. Within the framework of the SALVE project, we introduce a newly developed C_{c}/C_{s} corrector that is capable of correcting both the chromatic and the spherical aberration in the range of accelerating voltages from 20 to 80 kV. The corrector allows correcting axial aberrations up to fifth order as well as the dominating off-axial aberrations. Over the entire voltage range, optimum phase-contrast imaging conditions for weak signals from light atoms can be adjusted for an optical aperture of at least 55 mrad. The information transfer within this aperture is no longer limited by chromatic aberrations. We demonstrate the performance of the microscope using the examples of 30 kV phase-contrast TEM images of graphene and molybdenum disulfide, showing unprecedented contrast and resolution that matches image calculations.

Modeling protein structure at near atomic resolutions with Gorgon.

PubMed

Baker, Matthew L; Abeysinghe, Sasakthi S; Schuh, Stephen; Coleman, Ross A; Abrams, Austin; Marsh, Michael P; Hryc, Corey F; Ruths, Troy; Chiu, Wah; Ju, Tao

2011-05-01

Electron cryo-microscopy (cryo-EM) has played an increasingly important role in elucidating the structure and function of macromolecular assemblies in near native solution conditions. Typically, however, only non-atomic resolution reconstructions have been obtained for these large complexes, necessitating computational tools for integrating and extracting structural details. With recent advances in cryo-EM, maps at near-atomic resolutions have been achieved for several macromolecular assemblies from which models have been manually constructed. In this work, we describe a new interactive modeling toolkit called Gorgon targeted at intermediate to near-atomic resolution density maps (10-3.5 Å), particularly from cryo-EM. Gorgon's de novo modeling procedure couples sequence-based secondary structure prediction with feature detection and geometric modeling techniques to generate initial protein backbone models. Beyond model building, Gorgon is an extensible interactive visualization platform with a variety of computational tools for annotating a wide variety of 3D volumes. Examples from cryo-EM maps of Rotavirus and Rice Dwarf Virus are used to demonstrate its applicability to modeling protein structure. Copyright © 2011 Elsevier Inc. All rights reserved.

The role of gas in determining image quality and resolution during in situ scanning transmission electron microscopy experiments

DOE PAGES

Zhu, Yuanyuan; Browning, Nigel D.

2017-05-24

As gas-solid heterogeneous catalytic reactions are molecular in nature, a full mechanistic understanding of the process requires atomic scale characterization under realistic operating conditions. While atomic resolution imaging has become a routine in modern high-vacuum (scanning) transmission electron microscopy ((S)TEM), both image quality and resolution nominally degrade when reaction gases are introduced. In this work, we systematically assess the effects of different gases at various pressures on the quality and resolution of images obtained at room temperature in the annular dark field STEM imaging mode using a differentially pumped (DP) gas cell. This imaging mode is largely free from inelasticmore » scattering effects induced by the presence of gases and retains good imaging properties over a wide range of gas mass/pressures. Furthermore, we demonstrate the application of the ESTEM with atomic resolution images of a complex oxide alkane oxidation catalyst MoVNbTeOx (M1) immersed in light and heavy gas environments.« less

Atomic-Resolution X-ray Energy-Dispersive Spectroscopy Chemical Mapping of Substitutional Dy Atoms in a High-Coercivity Neodymium Magnet

NASA Astrophysics Data System (ADS)

Itakura, Masaru; Watanabe, Natsuki; Nishida, Minoru; Daio, Takeshi; Matsumura, Syo

2013-05-01

We have investigated local element distributions in a Dy-doped Nd2Fe14B hot-deformed magnet by atomic-column resolution chemical mapping using an X-ray energy-dispersive spectrometer (XEDS) attached to an aberration-corrected scanning transmission electron microscope (Cs-corrected STEM). The positions of the Nd and Dy atomic columns were visualized in the XEDS maps. The substitution of Dy was limited to a surface layer 2-3 unit cells thick in the Nd2Fe14B grains, and the Dy atoms preferentially occupied the 4f-Nd sites of Nd2Fe14B. These results provide further insights into the principal mechanism governing the coercivity enhancement due to Dy doping.

Sub-atomic resolution X-ray crystallography and neutron crystallography: promise, challenges and potential.

PubMed

Blakeley, Matthew P; Hasnain, Samar S; Antonyuk, Svetlana V

2015-07-01

The International Year of Crystallography saw the number of macromolecular structures deposited in the Protein Data Bank cross the 100000 mark, with more than 90000 of these provided by X-ray crystallography. The number of X-ray structures determined to sub-atomic resolution (i.e. ≤1 Å) has passed 600 and this is likely to continue to grow rapidly with diffraction-limited synchrotron radiation sources such as MAX-IV (Sweden) and Sirius (Brazil) under construction. A dozen X-ray structures have been deposited to ultra-high resolution (i.e. ≤0.7 Å), for which precise electron density can be exploited to obtain charge density and provide information on the bonding character of catalytic or electron transfer sites. Although the development of neutron macromolecular crystallography over the years has been far less pronounced, and its application much less widespread, the availability of new and improved instrumentation, combined with dedicated deuteration facilities, are beginning to transform the field. Of the 83 macromolecular structures deposited with neutron diffraction data, more than half (49/83, 59%) were released since 2010. Sub-mm(3) crystals are now regularly being used for data collection, structures have been determined to atomic resolution for a few small proteins, and much larger unit-cell systems (cell edges >100 Å) are being successfully studied. While some details relating to H-atom positions are tractable with X-ray crystallography at sub-atomic resolution, the mobility of certain H atoms precludes them from being located. In addition, highly polarized H atoms and protons (H(+)) remain invisible with X-rays. Moreover, the majority of X-ray structures are determined from cryo-cooled crystals at 100 K, and, although radiation damage can be strongly controlled, especially since the advent of shutterless fast detectors, and by using limited doses and crystal translation at micro-focus beams, radiation damage can still take place. Neutron crystallography therefore remains the only approach where diffraction data can be collected at room temperature without radiation damage issues and the only approach to locate mobile or highly polarized H atoms and protons. Here a review of the current status of sub-atomic X-ray and neutron macromolecular crystallography is given and future prospects for combined approaches are outlined. New results from two metalloproteins, copper nitrite reductase and cytochrome c', are also included, which illustrate the type of information that can be obtained from sub-atomic-resolution (∼0.8 Å) X-ray structures, while also highlighting the need for complementary neutron studies that can provide details of H atoms not provided by X-ray crystallography.

Investigation on nanoscale processes on the BaF{sub 2}(111) surface in various solutions by frequency modulation atomic force microscopy

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

Kobayashi, Naritaka, E-mail: naritaka@mail.saitama-u.ac.jp; Kawamura, Ryuzo; Yoshikawa, Hiroshi Y.

2016-06-07

In this study, we have directly observed nanoscale processes that occur on BaF{sub 2}(111) surfaces in various solutions using liquid-environment frequency modulation atomic force microscopy (FM-AFM) with a true atomic resolution. In addition, to investigate atomic-scale mechanisms of crystal growth process of BaF{sub 2}, we determined a suitable solution for atomic-resolution FM-AFM imaging of the BaF{sub 2}(111) surface. For undersaturated solutions, the surface is roughened by barium hydroxo complexes in the case of high pH, whereas by dissolution and proton or water molecule adsorption throughout the surface in the case of low pH. On the other hand, for supersaturated solutions,more » the surface shows two-dimensional nucleation and growth (σ = 0.1) and three-dimensional crystal growth with tetrahedral structures (σ = 1), where σ is the degree of supersaturation. The atomic-resolution imaging of the BaF{sub 2}(111) surface has been demonstrated in potassium fluoride (KF) and the supersaturated (σ = 0.1 and 1) solutions, wherein atomically flat terraces are shown at least for about 30 min.« less

Complex vibrations in arsenide skutterudites and oxyskutterudites

NASA Astrophysics Data System (ADS)

Bridges, F.; Car, B.; Sutton, L.; Hoffman-Stapleton, M.; Keiber, T.; Baumbach, R. E.; Maple, M. B.; Henkie, Z.; Wawryk, R.

2015-01-01

The local structure of two skutterudite families—Ce M4As12 (M =Fe , Ru, Os) and L n Cu3Ru4O12 (L n =La , Pr, and Nd)—have been studied using the extended x-ray absorption fine structure (EXAFS) technique with a focus on the lattice vibrations about the rare-earth "rattler atoms" and the extent to which these vibrations can be considered local modes, with the rattler vibrating inside a nearly rigid cage. X-ray absorption data at all the metal edges were collected over a temperature range of 4 to 300 K and analyzed using standard procedures. The pair distances from EXAFS results agree quite well with the average structure obtained from diffraction. The cage structure is formed by the M and As atoms in Ce M4As12 and by Cu, O, and Ru atoms in L n Cu3Ru4O12 . Although some of the bonds within the cage are quite stiff (correlated Debye temperatures, θcD, are ˜500 K for Ce M4As12 and above 800 K for L n Cu3Ru4O12 ), we show that the structure is not completely rigid. For the rattler atom the nearest-neighbor pairs have a relatively low Einstein temperature, θE:˜100 - 120 K for Ce-As and ˜130 K for L n -O . Surprisingly, the behaviors of the second-neighbor pairs are quite different: for Ce M4As12 the second-neighbor pairs (Ce -M ) have a weaker bond while for L n Cu3Ru4O12 the L n -Ru second-neighbor pair has a stiffer effective spring constant than the first-neighbor pair. In addition, we show that the As4 or CuO4 rings are relatively rigid units and that their vibrations are anisotropic within these cubic structures, with stiff restoring forces perpendicular to the rings and much weaker restoring forces in directions parallel to the rings. Consequently vibrations of the rings may also act as "rattlers" and help suppress thermal conductivity. In general neither the rigid-cage approximation nor the simple reduced-mass approximation are sufficient for describing rattler behavior.

Spectroscopic signatures of different symmetries of the superconducting order parameter in metal-decorated graphene

NASA Astrophysics Data System (ADS)

Saari, Timo; Nieminen, Jouko; Bansil, Arun

2017-06-01

Motivated by the recent experiments indicating superconductivity in metal-decorated graphene sheets, we investigate their quasi-particle structure within the framework of an effective tight-binding Hamiltonian augmented by appropriate BCS-like pairing terms for p-type order parameter. The normal state band structure of graphene is modified not only through interaction with adsorbed metal atoms, but also due to the folding of bands at Brillouin zone boundaries resulting from a \\sqrt{3}× \\sqrt{3}R{{30}\\circ} reconstruction. Several different types of pairing symmetries are analyzed utilizing Nambu-Gorkov Green’s function techniques to show that p+\\text{i}p -symmetric nearest-neighbor pairing yields the most enhanced superconducting gap. The character of the order parameter depends on the nature of the atomic orbitals involved in the pairing process and exhibits interesting angular and radial asymmetries. Finally, we suggest a method to distinguish between singlet and triplet type superconductivity in the presence of magnetic substitutional impurities using scanning tunneling spectroscopy.

Bonding in Heavier Group 14 Zero-Valent Complexes-A Combined Maximum Probability Domain and Valence Bond Theory Approach.

PubMed

Turek, Jan; Braïda, Benoît; De Proft, Frank

2017-10-17

The bonding in heavier Group 14 zero-valent complexes of a general formula L 2 E (E=Si-Pb; L=phosphine, N-heterocyclic and acyclic carbene, cyclic tetrylene and carbon monoxide) is probed by combining valence bond (VB) theory and maximum probability domain (MPD) approaches. All studied complexes are initially evaluated on the basis of the structural parameters and the shape of frontier orbitals revealing a bent structural motif and the presence of two lone pairs at the central E atom. For the VB calculations three resonance structures are suggested, representing the "ylidone", "ylidene" and "bent allene" structures, respectively. The influence of both ligands and central atoms on the bonding situation is clearly expressed in different weights of the resonance structures for the particular complexes. In general, the bonding in the studied E 0 compounds, the tetrylones, is best described as a resonating combination of "ylidone" and "ylidene" structures with a minor contribution of the "bent allene" structure. Moreover, the VB calculations allow for a straightforward assessment of the π-backbonding (E→L) stabilization energy. The validity of the suggested resonance model is further confirmed by the complementary MPD calculations focusing on the E lone pair region as well as the E-L bonding region. Likewise, the MPD method reveals a strong influence of the σ-donating and π-accepting properties of the ligand. In particular, either one single domain or two symmetrical domains are found in the lone pair region of the central atom, supporting the predominance of either the "ylidene" or "ylidone" structures having one or two lone pairs at the central atom, respectively. Furthermore, the calculated average populations in the lone pair MPDs correlate very well with the natural bond orbital (NBO) populations, and can be related to the average number of electrons that is backdonated to the ligands. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic-scale analysis of cation ordering in reduced calcium titanate.

PubMed

Li, Luying; Hu, Xiaokang; Jiang, Fan; Jing, Wenkui; Guo, Cong; Jia, Shuangfeng; Gao, Yihua; Wang, Jianbo

2017-11-03

The phenomenon of cation ordering is closely related to certain physical properties of complex oxides, which necessitates the search of underlying structure-property relationship at atomic resolution. Here we study the superlattices within reduced calcium titanate single crystal micro-pillars, which are unexpected from the originally proposed atomic model. Bright and dark contrasts at alternating Ti double layers perpendicular to b axis are clearly observed, but show no signs in corresponding image simulations based on the proposed atomic model. The multi-dimensional chemical analyses at atomic resolution reveal periodic lower Ti concentrations at alternating Ti double layers perpendicular to b axis. The following in-situ heating experiment shows no phase transition at the reported T c and temperature independence of the superlattices. The dimerization of the Ti-Ti bonds at neighboring double rutile-type chains within Ti puckered sheets are directly observed, which is found to be not disturbed by the cation ordering at alternating Ti double layers. The characterization of cation ordering of complex oxides from chemical and structural point of view at atomic resolution, and its reaction to temperature variations are important for further understanding their basic physical properties and exploiting potential applications.

Metal atomization spray nozzle

DOEpatents

Huxford, T.J.

1993-11-16

A spray nozzle for a magnetohydrodynamic atomization apparatus has a feed passage for molten metal and a pair of spray electrodes mounted in the feed passage. The electrodes, diverging surfaces which define a nozzle throat and diverge at an acute angle from the throat. Current passes through molten metal when fed through the throat which creates the Lorentz force necessary to provide atomization of the molten metal. 6 figures.

High-Resolution Crystal Structure of a Silver(I)-RNA Hybrid Duplex Containing Watson-Crick-like C-Silver(I)-C Metallo-Base Pairs.

PubMed

Kondo, Jiro; Tada, Yoshinari; Dairaku, Takenori; Saneyoshi, Hisao; Okamoto, Itaru; Tanaka, Yoshiyuki; Ono, Akira

2015-11-02

Metallo-base pairs have been extensively studied for applications in nucleic acid-based nanodevices and genetic code expansion. Metallo-base pairs composed of natural nucleobases are attractive because nanodevices containing natural metallo-base pairs can be easily prepared from commercially available sources. Previously, we have reported a crystal structure of a DNA duplex containing T-Hg(II)-T base pairs. Herein, we have determined a high-resolution crystal structure of the second natural metallo-base pair between pyrimidine bases C-Ag(I)-C formed in an RNA duplex. One Ag(I) occupies the center between two cytosines and forms a C-Ag(I)-C base pair through N3-Ag(I)-N3 linear coordination. The C-Ag(I)-C base pair formation does not disturb the standard A-form conformation of RNA. Since the C-Ag(I)-C base pair is structurally similar to the canonical Watson-Crick base pairs, it can be a useful building block for structure-based design and fabrication of nucleic acid-based nanodevices. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Generation, storage, and retrieval of nonclassical states of light using atomic ensembles

NASA Astrophysics Data System (ADS)

Eisaman, Matthew D.

This thesis presents the experimental demonstration of several novel methods for generating, storing, and retrieving nonclassical states of light using atomic ensembles, and describes applications of these methods to frequency-tunable single-photon generation, single-photon memory, quantum networks, and long-distance quantum communication. We first demonstrate emission of quantum-mechanically correlated pulses of light with a time delay between the pulses that is coherently controlled by utilizing 87Rb atoms. The experiment is based on Raman scattering, which produces correlated pairs of excited atoms and photons, followed by coherent conversion of the atomic states into a different photon field after a controllable delay. We then describe experiments demonstrating a novel approach for conditionally generating nonclassical pulses of light with controllable photon numbers, propagation direction, timing, and pulse shapes. We observe nonclassical correlations in relative photon number between correlated pairs of photons, and create few-photon light pulses with sub-Poissonian photon-number statistics via conditional detection on one field of the pair. Spatio-temporal control over the pulses is obtained by exploiting long-lived coherent memory for photon states and electromagnetically induced transparency (EIT) in an optically dense atomic medium. Finally, we demonstrate the use of EIT for the controllable generation, transmission, and storage of single photons with tunable frequency, timing, and bandwidth. To this end, we study the interaction of single photons produced in a "source" ensemble of 87Rb atoms at room temperature with another "target" ensemble. This allows us to simultaneously probe the spectral and quantum statistical properties of narrow-bandwidth single-photon pulses, revealing that their quantum nature is preserved under EIT propagation and storage. We measure the time delay associated with the reduced group velocity of the single-photon pulses and report observations of their storage and retrieval. Together these experiments utilize atomic ensembles to realize a narrow-bandwidth single-photon source, single-photon memory that preserves the quantum nature of the single photons, and a primitive quantum network comprised of two atomic-ensemble quantum memories connected by a single photon in an optical fiber. Each of these experimental demonstrations represents an essential element for the realization of long-distance quantum communication.

Molecular Dynamics Simulations of Simple Liquids

ERIC Educational Resources Information Center

Speer, Owner F.; Wengerter, Brian C.; Taylor, Ramona S.

2004-01-01

An experiment, in which students were given the opportunity to perform molecular dynamics simulations on a series of molecular liquids using the Amber suite of programs, is presented. They were introduced to both physical theories underlying classical mechanics simulations and to the atom-atom pair distribution function.

Multi-technology Investigation of the Atomic Structure of Calcium Silicate Hydrates

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

Geng, Guoqing; Kilcoyne, David A.; Benmore, Chris J.

2015-01-01

In this study, synthetic C-S-H samples were investigated to reveal the feature at atomic scale. Rietveld refinement was applied to high resolution X-ray scattering data, yielding the lattice constants of the pseudocrystal structure, as well as the crystallinity along three axes. Near Edge X-ray Absorption Fine Structure (NEXAFS) spectra was collected at calcium L3,2-edge. Evolution of calcium coordination symmetry were studied by investigating spectra characteristics. Pair Distribution Function (PDF) study yields the statistics of atom pair distribution. Coordination number of Ca and Si were obtained by integrating Radial distribution function. Atomic model based on dimeric structure were discussed and comparedmore » with experimental data. Synthetic C-S-H samples with increasing Ca/Si ratio exhibit pseudo-crystal structure, resembling Dreierketten configuration similar to natural tobermorite structure. Along c-axis, the repeated structure could not survives two layers in case of low Ca/Si ratio (0.70, 1.05). But in high Ca/Si ratio (1.42) case, the crystallinity along c-axis is much bigger. The coordination number of Ca decreases with increasing Ca/Si ratio. Octahedrally coordinated Ca are observed in sample with Ca/Si ratio of 1.42. Various dimeric models are compared with experimental data. In case of Ca/Si ratio of 1.42, SiO4 tetrahedron chain needs to be shortened in linkage, most probably by substituting bridging SiO4 tetrahedron with CaO6 octahedron. These octahedrons in interlayer space act like pins to join two adjacent layer structures together. The crystallinity is thus increased along c-axis, and average coordination number is therefore reduced. In case of Ca/Si 1.05, crystallinity is low along c-axis since, indicating that not too many Ca ions exist in interlayer space to hold two layers together. Instead, negative charge of end oxygen could be balanced by proton. Ca/Si 0.70 has long tetrahedron chain linkage within layer while the linkage between adjacent layers are not strong, resulting in low crystallinity along c-axis. Neither Ca/Si ratio 0.70 nor 1.42 sample contains any Ca in octahedral symmetry, as indicated by the weak crystal field splitting of NEXAFS spectra.« less

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

Zhu, Yuanyuan; Browning, Nigel D.

As gas-solid heterogeneous catalytic reactions are molecular in nature, a full mechanistic understanding of the process requires atomic scale characterization under realistic operating conditions. While atomic resolution imaging has become a routine in modern high-vacuum (scanning) transmission electron microscopy ((S)TEM), both image quality and resolution nominally degrade when reaction gases are introduced. In this work, we systematically assess the effects of different gases at various pressures on the quality and resolution of images obtained at room temperature in the annular dark field STEM imaging mode using a differentially pumped (DP) gas cell. This imaging mode is largely free from inelasticmore » scattering effects induced by the presence of gases and retains good imaging properties over a wide range of gas mass/pressures. We demonstrate the application of the ESTEM with atomic resolution images of a complex oxide alkane oxidation catalyst MoVNbTeOx (M1) immersed in light and heavy gas environments.« less

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

Zhu, Yuanyuan; Browning, Nigel D.

As gas-solid heterogeneous catalytic reactions are molecular in nature, a full mechanistic understanding of the process requires atomic scale characterization under realistic operating conditions. While atomic resolution imaging has become a routine in modern high-vacuum (scanning) transmission electron microscopy ((S)TEM), both image quality and resolution nominally degrade when reaction gases are introduced. In this work, we systematically assess the effects of different gases at various pressures on the quality and resolution of images obtained at room temperature in the annular dark field STEM imaging mode using a differentially pumped (DP) gas cell. This imaging mode is largely free from inelasticmore » scattering effects induced by the presence of gases and retains good imaging properties over a wide range of gas mass/pressures. Furthermore, we demonstrate the application of the ESTEM with atomic resolution images of a complex oxide alkane oxidation catalyst MoVNbTeOx (M1) immersed in light and heavy gas environments.« less

Effects of Concentration on Like-Charge Pairing of Guanidinium Ions and on the Structure of Water: An All-Atom Molecular Dynamics Simulation Study.

PubMed

Bandyopadhyay, Dibyendu; Bhanja, K; Mohan, Sadhana; Ghosh, Swapan K; Choudhury, Niharendu

2015-08-27

Like-charge ion-pair formation in an aqueous solution of guanidinium chloride (GdmCl) has two important facets. On one hand, it describes the role of the arginine (ARG) side chain in aggregation and dimer formation in proteins, and on the other hand, it lends support for the direct mechanism of protein denaturation by GdmCl. We employ all-atom molecular dynamics simulations to investigate the effect of GdmCl concentration on the like-charge ion-pair formation of guanidinium ions (Gdm(+)). From analyses of the radial distribution function (RDF) between the carbon atoms of two guanidinium moieties, the existence of both contact pairs and solvent-separated pairs has been observed. Although the peak height corresponding to the contact-pair state decreases, the number of Gdm(+) ions in the contact-pair state actually increases with increasing GdmCl concentration. We have also investigated the effect of the concentration of Gdm(+) on the structure of water. The effect of GdmCl concentration on the radial and tetrahedral structures of water is found to be negligibly small; however, GdmCl concentration has a considerable effect on the hydrogen-bonding structure of water. It is demonstrated that the presence of chloride ions, not Gdm(+), in the first solvation shell of water causes the distortion in the hydrogen-bonding network of water. In order to establish that Gdm(+) not only stacks against another Gdm(+) but also directly attacks the ARG residue of a protein or peptide, simulation of an ARG-rich peptide in 6 M aqueous solution of GdmCl has been performed. The analyses of RDFs and orientation distributions reveal that the Gdm(+) moiety of the GdmCl attacks the same moiety in the ARG side chain with a parallel stacking orientation.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: an ab initio study.

PubMed

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF3X-B that involve one trifluorohalomethane CF3X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH3 and PH3), two n-pairs (H2O and H2S), two n-pairs with an unsaturated bond (H2CO and H2CS), and a single π-pair (C2H4) and two π-pairs (C2H2). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C-X bond lengths shorten, while the C-X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.

Evolution in time of an N-atom system. II. Calculation of the eigenstates

NASA Astrophysics Data System (ADS)

Rudolph, Terry; Yavin, Itay; Freedhoff, Helen

2004-01-01

We calculate the energy eigenvalues and eigenstates corresponding to coherent single and multiple excitations of a number of different arrays of N identical two-level atoms (TLA’s) or qubits, including polygons, “diamond” structures, polygon multilayers, icosahedra, and dodecahedra. We assume only that the coupling occurs via an exchange interaction which depends on the separation between the atoms. We include the interactions between all pairs of atoms, and our results are valid for arbitrary separations relative to the radiation wavelength.

γ-ray telescopes using conversions to e+e- pairs: event generators, angular resolution and polarimetry

NASA Astrophysics Data System (ADS)

Gros, P.; Bernard, D.

2017-02-01

We benchmark various available event generators in Geant4 and EGS5 in the light of ongoing projects for high angular-resolution pair-conversion telescopes at low energy. We compare the distributions of key kinematic variables extracted from the geometry of the three final state particles. We validate and use as reference an exact generator using the full 5D differential cross-section of the conversion process. We focus in particular on the effect of the unmeasured recoiling nucleus on the angular resolution. We show that for high resolution trackers, the choice of the generator affects the estimated resolution of the telescope. We also show that the current available generator are unable to describe accurately a linearly polarised photon source.

Super resolution reconstruction of infrared images based on classified dictionary learning

NASA Astrophysics Data System (ADS)

Liu, Fei; Han, Pingli; Wang, Yi; Li, Xuan; Bai, Lu; Shao, Xiaopeng

2018-05-01

Infrared images always suffer from low-resolution problems resulting from limitations of imaging devices. An economical approach to combat this problem involves reconstructing high-resolution images by reasonable methods without updating devices. Inspired by compressed sensing theory, this study presents and demonstrates a Classified Dictionary Learning method to reconstruct high-resolution infrared images. It classifies features of the samples into several reasonable clusters and trained a dictionary pair for each cluster. The optimal pair of dictionaries is chosen for each image reconstruction and therefore, more satisfactory results is achieved without the increase in computational complexity and time cost. Experiments and results demonstrated that it is a viable method for infrared images reconstruction since it improves image resolution and recovers detailed information of targets.

Atomic-resolution 3D structure of amyloid β fibrils: The Osaka mutation

DOE PAGES

Schutz, Anne K.; Wall, Joseph; Vagt, Toni; ...

2014-11-13

Despite its central importance for understanding the molecular basis of Alzheimer's disease (AD), high-resolution structural information on amyloid β-peptide (Aβ) fibrils, which are intimately linked with AD, is scarce. We report an atomic-resolution fibril structure of the Aβ 1-40 peptide with the Osaka mutation (E22Δ), associated with early-onset AD. The structure, which differs substantially from all previously proposed models, is based on a large number of unambiguous intra- and intermolecular solid-state NMR distance restraints

Achieving atomic resolution magnetic dichroism by controlling the phase symmetry of an electron probe

DOE PAGES

Rusz, Jan; Idrobo, Juan -Carlos; Bhowmick, Somnath

2014-09-30

The calculations presented here reveal that an electron probe carrying orbital angular momentum is just a particular case of a wider class of electron beams that can be used to measure electron magnetic circular dichroism (EMCD) with atomic resolution. It is possible to obtain an EMCD signal with atomic resolution by simply breaking the symmetry of the electron probe phase front using the aberration-corrected optics of a scanning transmission electron microscope. The probe’s required phase distribution depends on the sample’s magnetic symmetry and crystal structure. The calculations indicate that EMCD signals that use the electron probe’s phase are as strongmore » as those obtained by nanodiffraction methods.« less

Effective theory of exotic superconductivity in LaAlO3/SrTiO3 interfaces

NASA Astrophysics Data System (ADS)

Esmailzadeh, Haniyeh; Moghaddam, Ali G.

2018-05-01

Motivated by experimental and theoretical works about superconductivity at the oxide interfaces, we provide a simple model for possible unconventional pairings inside the exotic two-dimensional electron gas formed in heterostructures of SrTiO3 and LaAlO3. At the low energy limit, the electron gas at the interfaces is usually modeled with an effective three band model considering of 3d t2g orbitals which are slightly coupled by atomic spin-orbit couplings (SOC). Considering direct superconducting pairing in two higher delocalized bands and by exploiting a perturbative scheme based on canonical transformation, we derive the effective pairing amplitudes with possibly exotic nature inside the localized dxy band as well as various inter-band pairing components. In particular we show that equal-spin triplet pairings are possible between the band dxy and any of other dxz and dyz bands. In addition weaker effective pairings take place inside the localized band itself and between delocalized dxz and dyz bands with singlet and opposite-spin triplet characters. These unconventional effective pairings are indeed mediated by SOC-induced higher order virtual transitions between the bands and particularly into the localized band. Our model suggest that unconventional effective superconductivity is possible at oxide interfaces, simply, due to the special band structure and important role of atomic SOC and perhaps other magnetic effects present at these heterostructures.

Measuring strain and rotation fields at the dislocation core in graphene

NASA Astrophysics Data System (ADS)

Bonilla, L. L.; Carpio, A.; Gong, C.; Warner, J. H.

2015-10-01

Strain fields, dislocations, and defects may be used to control electronic properties of graphene. By using advanced imaging techniques with high-resolution transmission electron microscopes, we have measured the strain and rotation fields about dislocations in monolayer graphene with single-atom sensitivity. These fields differ qualitatively from those given by conventional linear elasticity. However, atom positions calculated from two-dimensional (2D) discrete elasticity and three-dimensional discrete periodized Föppl-von Kármán equations (dpFvKEs) yield fields close to experiments when determined by geometric phase analysis. 2D theories produce symmetric fields whereas those from experiments exhibit asymmetries. Numerical solutions of dpFvKEs provide strain and rotation fields of dislocation dipoles and pairs that also exhibit asymmetries and, compared with experiments, may yield information on out-of-plane displacements of atoms. While discrete theories need to be solved numerically, analytical formulas for strains and rotation about dislocations can be obtained from 2D Mindlin's hyperstress theory. These formulas are very useful for fitting experimental data and provide a template to ascertain the importance of nonlinear and nonplanar effects. Measuring the parameters of this theory, we find two characteristic lengths between three and four times the lattice spacings that control dilatation and rotation about a dislocation. At larger distances from the dislocation core, the elastic fields decay to those of conventional elasticity. Our results may be relevant for strain engineering in graphene and other 2D materials of current interest.

Constrained-pairing mean-field theory. IV. Inclusion of corresponding pair constraints and connection to unrestricted Hartree-Fock theory.

PubMed

Tsuchimochi, Takashi; Henderson, Thomas M; Scuseria, Gustavo E; Savin, Andreas

2010-10-07

Our previously developed constrained-pairing mean-field theory (CPMFT) is shown to map onto an unrestricted Hartree-Fock (UHF) type method if one imposes a corresponding pair constraint to the correlation problem that forces occupation numbers to occur in pairs adding to one. In this new version, CPMFT has all the advantages of standard independent particle models (orbitals and orbital energies, to mention a few), yet unlike UHF, it can dissociate polyatomic molecules to the correct ground-state restricted open-shell Hartree-Fock atoms or fragments.

Nucleon Isovector Pairing in Nuclei: Microscopic Approach, Boson Representation, and Collective Model

NASA Astrophysics Data System (ADS)

Jolos, R. V.; Kartavenko, V. G.; Kolganova, E. A.

2018-03-01

Nucleon pair correlations in atomic nuclei are analyzed within a nuclear microscopic model with residual isovector pairing forces. These are formulated in the boson representation of fermion operators whereby the collective mode of pair excitations can be isolated without restricting the size of the one-particle basis. This method allows one to analyze the fluctuations in the nonsuperfluid phase of nuclear matter, its phase transition to the superfluid phase, and strong pair correlations. The performance of the method is exemplified by numerical results for the nuclei in the vicinity of the doubly magic 56Ni nucleus.

Study of Pair and many-body interactions in rare-gas halide atom clusters using negative ion zero electron kinetic energy (ZEKE) and threshold photodetachment spectroscopy

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

Yourshaw, Ivan

1998-07-09

The diatomic halogen atom-rare gas diatomic complexes KrBr -, XeBr -, and KrCl - are studied in this work by zero electron kinetic energy (ZEKE) spectroscopy in order to characterize the weak intermolecular diatomic potentials of these species. Also, the ZEKE and threshold photodetachment spectra of the polyatomic clusters Ar nBr - (n = 2-9) and Ar nI - (n = 2-19) are studied to obtain information about the non-additive effects on the interactions among the atoms. This work is part of an ongoing effort to characterize the pair and many-body potentials of the complete series of rare gas halidemore » clusters. In these studies we obtain information about both the anionic and neutral clusters.« less

Study on the structural transition of CoNi nanoclusters using molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Xia, J. H.; Gao, Xue-Mei

2018-04-01

In this work, the segregation and structural transitions of CoNi clusters, between 1500 and 300 K, have been investigated using molecular dynamics simulations with the embedded atom method potential. The radial distribution function was used to analyze the segregation during the cooling processes. It is found that Co atoms segregate to the inside and Ni atoms preferably to the surface during the cooling processes, the Co147Ni414 cluster becomes a core-shell structure. We discuss the structural transition according to the pair-correction function and pair-analysis technique, and finally the liquid Co147Ni414 crystallizes into the coexistence of hcp and fcc structure at 300 K. At the same time, it is found that the frozen structure of CoNi cluster is strongly related to the Co concentration.

Drying-induced atomic structural rearrangements in sodium-based calcium-alumino-silicate-hydrate gel and the mitigating effects of ZrO 2 nanoparticles

DOE PAGES

Yang, Kengran; Özçelik, V. Ongun; Garg, Nishant; ...

2018-01-01

Drying-induced nanoscopic alterations to the local atomic structure of silicate-activated slag and the mitigated effects of nano-ZrO2 are elucidated using in situ X-ray pair distribution function analysis.

Drying-induced atomic structural rearrangements in sodium-based calcium-alumino-silicate-hydrate gel and the mitigating effects of ZrO 2 nanoparticles

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

Yang, Kengran; Özçelik, V. Ongun; Garg, Nishant

Drying-induced nanoscopic alterations to the local atomic structure of silicate-activated slag and the mitigated effects of nano-ZrO2 are elucidated using in situ X-ray pair distribution function analysis.

Unraveling cellulose microfibrils: a twisted tale.

PubMed

Hadden, Jodi A; French, Alfred D; Woods, Robert J

2013-10-01

Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface. Copyright © 2013 Wiley Periodicals, Inc.

Unraveling Cellulose Microfibrils: A Twisted Tale

PubMed Central

Hadden, Jodi A.; French, Alfred D.; Woods, Robert J.

2014-01-01

Molecular dynamics (MD) simulations of cellulose microfibrils are pertinent to the paper, textile, and biofuels industries for their unique capacity to characterize dynamic behavior and atomic-level interactions with solvent molecules and cellulase enzymes. While high-resolution crystallographic data have established a solid basis for computational analysis of cellulose, previous work has demonstrated a tendency for modeled microfibrils to diverge from the linear experimental structure and adopt a twisted conformation. Here, we investigate the dependence of this twisting behavior on computational approximations and establish the theoretical basis for its occurrence. We examine the role of solvent, the effect of nonbonded force field parameters [partial charges and van der Waals (vdW) contributions], and the use of explicitly modeled oxygen lone pairs in both the solute and solvent. Findings suggest that microfibril twisting is favored by vdW interactions, and counteracted by both intrachain hydrogen bonds and solvent effects at the microfibril surface. PMID:23681971

Note: A rigid piezo motor with large output force and an effective method to reduce sliding friction force

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

Guo, Ying; Lu, Qingyou, E-mail: qxl@ustc.edu.cn; Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, Hefei, Anhui 230026

2014-05-15

We present a completely practical TunaDrive piezo motor. It consists of a central piezo stack sandwiched by two arm piezo stacks and two leg piezo stacks, respectively, which is then sandwiched and spring-clamped by a pair of parallel polished sapphire rods. It works by alternatively fast expanding and contracting the arm/leg stacks while slowly expanding/contracting the central stack simultaneously. The key point is that sufficiently fast expanding and contracting a limb stack can make its two sliding friction forces well cancel, resulting in the total sliding friction force is <10% of the total static friction force, which can help increasemore » output force greatly. The piezo motor's high compactness, precision, and output force make it perfect in building a high-quality harsh-condition (vibration resistant) atomic resolution scanning probe microscope.« less

Local structural and chemical ordering of nanosized Pt3±δCo probed by multiple-scattering x-ray absorption spectroscopy

NASA Astrophysics Data System (ADS)

Greco, Giorgia; Witkowska, Agnieszka; Principi, Emiliano; Minicucci, Marco; di Cicco, Andrea

2011-04-01

This work reports a detailed investigation of the local structure and chemical disorder of a Pt3±δCo thin film and Pt3±δCo nanoparticles. We have used a combination of techniques including x-ray absorption spectroscopy (XAS), x-ray diffraction (XRD), and high-resolution transmission electron microscopy (TEM). High-quality XAS spectra at the Co K edge and Pt L3 edge have been analyzed using double-edge multiple-scattering data analysis. Structural extended x-ray absorption fine structure (EXAFS) refinements have been performed accounting for the reduction of the coordination numbers and degeneracy of three-atom configurations, resulting from the measured size distribution and stoichiometry. The important effect of chemical ordering on pair and three-atom configurations has been studied using computer simulations based on a simple model accounting for substitutional disorder, defined by an order parameter s. It has been found that individual EXAFS signals related to the minority species (Co) are extremely sensitive to substitutional disorder so their intensities, especially those of the collinear three-atom configurations, can be used as a measure of the ordering level. The thin film has been found to be chemically disordered (s⩽0.4), in agreement with previous estimates. The Pt3±δCo nanoalloy has been found to be partially ordered (s=0.6±0.1) while the local structure around Co atoms is characterized by a higher level of structural disorder as compared to the bulk-like thin film. The robust approach for nanomaterial characterization used in this work combining different techniques can, in principle, be applied for structural refinements of any binary nanocrystalline functional system.

Lineshapes of Dipole-Dipole Resonances in a Cold Rydberg Gas

NASA Astrophysics Data System (ADS)

Richards, B. G.; Jones, R. R.

2015-05-01

We have examined the lineshapes associated with Stark tuned, dipole-dipole resonances involving Rydberg atoms in a cold gas. Rb atoms in a MOT are laser excited from the 5 p level to 32p3 / 2 in the presence of a weak electric field. A fast rising electric field pulse Stark tunes the total energy of two 32 p atom pairs so it is (nearly) degenerate with that of the 32s1 / 2+33s1 / 2 states. Because of the dipole-dipole coupling, atom pairs separated by a distance R, develop 32s1 / 2+33s1 / 2 character. The maximum probability for finding atoms in s-states depends on the detuning from degeneracy and on the dipole-dipole coupling. We obtain the ``resonance'' lineshape by measuring, via state-selective field ionization, the s-state population as a function of the tuning field. The resonance width decreases with density due to R-3 dependence of the dipole-dipole coupling. In principle, the lineshape provides information about the distribution of Rydberg atom spacings in the sample. For equally spaced atoms, the lineshape should be Lorentzian while for a random nearest neighbor distribution it appears as a cusp. At low densities nearly Gaussian lineshapes are observed with widths that are too large to be the result of inhomogeneous electric or magnetic fields. Supported by the NSF.

An Introduction to Atomic Layer Deposition with Thermal Applications

NASA Technical Reports Server (NTRS)

Dwivedi, Vivek H.

2015-01-01

Atomic Layer Deposition (ALD) is a cost effective nano-manufacturing technique that allows for the conformal coating of substrates with atomic control in a benign temperature and pressure environment. Through the introduction of paired precursor gases thin films can be deposited on a myriad of substrates ranging from glass, polymers, aerogels, and metals to high aspect ratio geometries. This talk will focus on the utilization of ALD for engineering applications.

Absenteeism among survivors of the atomic bombing of Hiroshima.

PubMed Central

Meigs, J W; Blot, W J; Inoue, S; Meigs, C R

1975-01-01

Atomic bomb survivors who worked at the Atomic Bomb Casualty Commission in Hiroshima during the years 1968-71 and held handbooks identifying them as survivors took significantly more days of both annual leave and sick leave than did matched and paired control subjects. These differences in leave-taking patterns are considered to be due to behavioural causes as they could not be attributed to radiation dose-response effects. PMID:1156567

An atomic gravitational wave interferometric sensor in low earth orbit (AGIS-LEO)

NASA Astrophysics Data System (ADS)

Hogan, Jason M.; Johnson, David M. S.; Dickerson, Susannah; Kovachy, Tim; Sugarbaker, Alex; Chiow, Sheng-Wey; Graham, Peter W.; Kasevich, Mark A.; Saif, Babak; Rajendran, Surjeet; Bouyer, Philippe; Seery, Bernard D.; Feinberg, Lee; Keski-Kuha, Ritva

2011-07-01

We propose an atom interferometer gravitational wave detector in low Earth orbit (AGIS-LEO). Gravitational waves can be observed by comparing a pair of atom interferometers separated by a 30 km baseline. In the proposed configuration, one or three of these interferometer pairs are simultaneously operated through the use of two or three satellites in formation flight. The three satellite configuration allows for the increased suppression of multiple noise sources and for the detection of stochastic gravitational wave signals. The mission will offer a strain sensitivity of {<10^{-18}/sqrt{Hz}} in the 50mHz-10Hz frequency range, providing access to a rich scientific region with substantial discovery potential. This band is not currently addressed with the LIGO, VIRGO, or LISA instruments. We analyze systematic backgrounds that are relevant to the mission and discuss how they can be mitigated at the required levels. Some of these effects do not appear to have been considered previously in the context of atom interferometry, and we therefore expect that our analysis will be broadly relevant to atom interferometric precision measurements. Finally, we present a brief conceptual overview of shorter-baseline ({lesssim100 m}) atom interferometer configurations that could be deployed as proof-of-principle instruments on the International Space Station (AGIS-ISS) or an independent satellite.

The origin of the superstructure in Bi2Sr2CaCu2O(8+delta) as revealed by scanning tunneling microscopy

NASA Astrophysics Data System (ADS)

Kirk, M. D.; Nogami, J.; Baski, A. A.; Mitzi, D. B.; Kapitulnik, A.

1988-12-01

Real-space images with atomic resolution of the BiO plane of Bi2Sr2CaCu2O(8+delta) were obtained with a scanning tunneling microscope. Single-crystal samples were cleaved and imaged under ultrahigh vacuum conditions at room temperature. The images clearly show the one-dimensional incommensurate superstructure along the b-axis that is common to this phase. High-resolution images show the position of the Bi atoms, revelaing the structural nature of the superlattice. A missing row of Bi atoms occurs either every nine or ten atomic sites in both 110-line directions, accounting for the measured incommensurate periodicity of the superstructure. A model is proposed that includes missing rows of atoms, as well as displacements of the atomic positions along both the a- and c-axis directions.

The Origin of the Superstructure in Bi2Sr2CaCu2O8+dgr as Revealed by Scanning Tunneling Microscopy.

PubMed

Kirk, M D; Nogami, J; Baski, A A; Mitzi, D B; Kapitulnik, A; Geballe, T H; Quate, C F

1988-12-23

Real-space images with atomic resolution of the BiO plane of Bi(2)Sr(2)CaCu(2)O(8+delta) were obtained with a scanning tunneling microscope. Single-crystal samples were cleaved and imaged under ultrahigh vacuum conditions at room temperature. The images clearly show the one-dimensional incommensurate superstructure along the b-axis that is common to this phase. High-resolution images show the position of the Bi atoms, revealing the structural nature of the superlattice. A missing row of Bi atoms occurs either every nine or ten atomic sites in both (110) directions, accounting for the measured incommensurate periodicity of the superstructure. A model is proposed that includes missing rows of atoms, as well as displacements of the atomic positions along both the a- and c-axis directions.

Atomic Structure and Properties of Extended Defects in Silicon

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

Buczko, R.; Chisholm, M.F.; Kaplan, T.

1998-10-15

The Z-contrast technique represents a new approach to high-resolution electron microscopy allowing for the first time incoherent imaging of materials on the atomic scale. The key advantages of the technique, an intrinsically higher resolution limit and directly interpretable, compositionally sensitive imaging, allow a new level of insight into the atomic configurations of extended defects in silicon. This experimental technique has been combined with theoretical calculations (a combination of first principles, tight binding, and classical methods) to extend this level of insight by obtaining the energetic and electronic structure of the defects.

Midinfrared absorption measured at a lambda/400 resolution with an atomic force microscope.

PubMed

Houel, Julien; Homeyer, Estelle; Sauvage, Sébastien; Boucaud, Philippe; Dazzi, Alexandre; Prazeres, Rui; Ortéga, Jean-Michel

2009-06-22

Midinfrared absorption can be locally measured using a detection combining an atomic force microscope and a pulsed excitation. This is illustrated for the midinfrared bulk GaAs phonon absorption and for the midinfrared absorption of thin SiO(2) microdisks. We show that the signal given by the cantilever oscillation amplitude of the atomic force microscope follows the spectral dependence of the bulk material absorption. The absorption spatial resolution achieved with microdisks is around 50 nanometer for an optical excitation around 22 micrometer wavelength.

Measurement of O and Ti atom displacements in TiO 2 during flash sintering experiments

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

Yoon, Bola; Yadav, Devinder; Raj, Rishi

In-situ flash experiments on rutile TiO 2 were performed at the synchrotron at the Brookhaven National Laboratory. Pair distribution function analysis of total X-ray scattering measurements yielded mean-square atomic displacements of oxygen and titanium atoms during the progression of the 3 stages of flash. The displacements are measured to be far greater for oxygen atoms than for titanium atoms. Thus, these large displacements may signal an “elastic softening” of the lattice, which, recently, has been predicted as a precursor to the onset of flash.

Measurement of O and Ti atom displacements in TiO 2 during flash sintering experiments

DOE PAGES

Yoon, Bola; Yadav, Devinder; Raj, Rishi; ...

2017-12-29

In-situ flash experiments on rutile TiO 2 were performed at the synchrotron at the Brookhaven National Laboratory. Pair distribution function analysis of total X-ray scattering measurements yielded mean-square atomic displacements of oxygen and titanium atoms during the progression of the 3 stages of flash. The displacements are measured to be far greater for oxygen atoms than for titanium atoms. Thus, these large displacements may signal an “elastic softening” of the lattice, which, recently, has been predicted as a precursor to the onset of flash.

Observation of entanglement of a single photon with a trapped atom.

PubMed

Volz, Jürgen; Weber, Markus; Schlenk, Daniel; Rosenfeld, Wenjamin; Vrana, Johannes; Saucke, Karen; Kurtsiefer, Christian; Weinfurter, Harald

2006-01-27

We report the observation of entanglement between a single trapped atom and a single photon at a wavelength suitable for low-loss communication over large distances, thereby achieving a crucial step towards long range quantum networks. To verify the entanglement, we introduce a single atom state analysis. This technique is used for full state tomography of the atom-photon qubit pair. The detection efficiency and the entanglement fidelity are high enough to allow in a next step the generation of entangled atoms at large distances, ready for a final loophole-free Bell experiment.

Structural and electronic properties of isovalent boron atoms in GaAs

NASA Astrophysics Data System (ADS)

Krammel, C. M.; Nattermann, L.; Sterzer, E.; Volz, K.; Koenraad, P. M.

2018-04-01

Boron containing GaAs, which is grown by metal organic vapour phase epitaxy, is studied at the atomic level by cross-sectional scanning tunneling microscopy (X-STM) and spectroscopy (STS). In topographic X-STM images, three classes of B related features are identified, which are attributed to individual B atoms on substitutional Ga sites down to the second layer below the natural {110} cleavage planes. The X-STM contrast of B atoms below the surface reflects primarily the structural modification of the GaAs matrix by the small B atoms. However, B atoms in the cleavage plane have in contrast to conventional isovalent impurities, such as Al and In, a strong influence on the local electronic structure similar to donors or acceptors. STS measurements show that B in the GaAs {110} surfaces gives rise to a localized state short below the conduction band (CB) edge while in bulk GaAs, the B impurity state is resonant with the CB. The analysis of BxGa1-xAs/GaAs quantum wells reveals a good crystal quality and shows that the incorporation of B atoms in GaAs can be controlled along the [001] growth direction at the atomic level. Surprisingly, the formation of the first and fourth nearest neighbor B pairs, which are oriented along the <110 > directions, is strongly suppressed at a B concentration of 1% while the third nearest neighbor B pairs are found more than twice as often than expected for a completely spatially random pattern.

The mystery of perpendicular fivefold axes and the fourth dimension in intermetallic structures.

PubMed

Berger, Robert F; Lee, Stephen; Johnson, Jeffreys; Nebgen, Ben; Sha, Fernando; Xu, Jiaqi

2008-01-01

The structures of eight related known intermetallic structure types are the impetus to this paper: Li21Si5, Mg44Rh7, Zn13(Fe,Ni)2, Mg6Pd, Na6Tl, Zn91Ir11, Li13Na29Ba19, and Al69Ta39. All belong to the F43m space group, have roughly 400 atoms in their cubic unit cells, are built up at least partially from the gamma-brass structure, and exhibit pseudo-tenfold symmetric diffraction patterns. These pseudo-tenfold axes lie in the {110} directions, and thus present a paradox. The {110} set is comprised of three pairs of perpendicular directions. Yet no 3D point group contains a single pair of perpendicular fivefold axes (by Friedel's Law, a fivefold axis leads to a tenfold diffraction pattern). The current work seeks to resolve this paradox. Its resolution is based on the largest of all 4D Platonic solids, the 600-cell. We first review the 600-cell, building an intuition discussing 4D polyhedroids (4D polytopes). We then show that the positions of common atoms in the F43m structures lie close to the positions of vertices in a 3D projection of the 600-cell. For this purpose, we develop a projection method that we call intermediate projection. The introduction of the 600-cell resolves the above paradox. This 4D Platonic solid contains numerous orthogonal fivefold rotations. The six fivefold directions that are best preserved after projection prove to lie along the {110} directions of the F43m structures. Finally, this paper shows that at certain ideal projected cluster sizes related to one another by the golden mean (tau=(1+ radical 5)/2), constructive interference leading to tenfold diffraction patterns is optimized. It is these optimal values that predominate in actual F43m structures. Explicit comparison of experimental cluster sizes and theoretically derived cluster sizes shows a clear correspondence, both for isolated and crystalline pairs of projected 600-cells.

An overview of heavy-atom derivatization of protein crystals

PubMed Central

Pike, Ashley C. W.; Garman, Elspeth F.; Krojer, Tobias; von Delft, Frank; Carpenter, Elisabeth P.

2016-01-01

Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative. PMID:26960118

Effects of the local structure dependence of evaporation fields on field evaporation behavior

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

Yao, Lan; Marquis, Emmanuelle A., E-mail: emarq@umich.edu; Withrow, Travis

2015-12-14

Accurate three dimensional reconstructions of atomic positions and full quantification of the information contained in atom probe microscopy data rely on understanding the physical processes taking place during field evaporation of atoms from needle-shaped specimens. However, the modeling framework for atom probe microscopy has only limited quantitative justification. Building on the continuum field models previously developed, we introduce a more physical approach with the selection of evaporation events based on density functional theory calculations. This model reproduces key features observed experimentally in terms of sequence of evaporation, evaporation maps, and depth resolution, and provides insights into the physical limit formore » spatial resolution.« less

Toward atomic-scale bright-field electron tomography for the study of fullerene-like nanostructures.

PubMed

Bar Sadan, Maya; Houben, Lothar; Wolf, Sharon G; Enyashin, Andrey; Seifert, Gotthard; Tenne, Reshef; Urban, Knut

2008-03-01

We present the advancement of electron tomography for three-dimensional structure reconstruction of fullerene-like particles toward atomic-scale resolution. The three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is achieved by the combination of low voltage operation of the electron microscope with aberration-corrected phase contrast imaging. The method enables the study of defects and irregularities in the three-dimensional structure of individual fullerene-like particles on the scale of 2-3 A. Control over shape, size, and atomic architecture is a key issue in synthesis and design of functional nanoparticles. Transmission electron microscopy (TEM) is the primary technique to characterize materials down to the atomic level, albeit the images are two-dimensional projections of the studied objects. Recent advancements in aberration-corrected TEM have demonstrated single atom sensitivity for light elements at subångström resolution. Yet, the resolution of tomographic schemes for three-dimensional structure reconstruction has not surpassed 1 nm3, preventing it from becoming a powerful tool for characterization in the physical sciences on the atomic scale. Here we demonstrate that negative spherical aberration imaging at low acceleration voltage enables tomography down to the atomic scale at reduced radiation damage. First experimental data on the three-dimensional reconstruction of nested molybdenum disulfide nanooctahedra is presented. The method is applicable to the analysis of the atomic architecture of a wide range of nanostructures where strong electron channeling is absent, in particular to carbon fullerenes and inorganic fullerenes.

Solvation and Spectral Line Shifts of Chromium Atoms in Helium Droplets Based on a Density Functional Theory Approach

PubMed Central

2014-01-01

The interaction of an electronically excited, single chromium (Cr) atom with superfluid helium nanodroplets of various size (10 to 2000 helium (He) atoms) is studied with helium density functional theory. Solvation energies and pseudo-diatomic potential energy surfaces are determined for Cr in its ground state as well as in the y7P, a5S, and y5P excited states. The necessary Cr–He pair potentials are calculated by standard methods of molecular orbital-based electronic structure theory. In its electronic ground state the Cr atom is found to be fully submerged in the droplet. A solvation shell structure is derived from fluctuations in the radial helium density. Electronic excitations of an embedded Cr atom are simulated by confronting the relaxed helium density (ρHe), obtained for Cr in the ground state, with interaction pair potentials of excited states. The resulting energy shifts for the transitions z7P ← a7S, y7P ← a7S, z5P ← a5S, and y5P ← a5S are compared to recent fluorescence and photoionization experiments. PMID:24906160

Solvation and spectral line shifts of chromium atoms in helium droplets based on a density functional theory approach.

PubMed

Ratschek, Martin; Pototschnig, Johann V; Hauser, Andreas W; Ernst, Wolfgang E

2014-08-21

The interaction of an electronically excited, single chromium (Cr) atom with superfluid helium nanodroplets of various size (10 to 2000 helium (He) atoms) is studied with helium density functional theory. Solvation energies and pseudo-diatomic potential energy surfaces are determined for Cr in its ground state as well as in the y(7)P, a(5)S, and y(5)P excited states. The necessary Cr-He pair potentials are calculated by standard methods of molecular orbital-based electronic structure theory. In its electronic ground state the Cr atom is found to be fully submerged in the droplet. A solvation shell structure is derived from fluctuations in the radial helium density. Electronic excitations of an embedded Cr atom are simulated by confronting the relaxed helium density (ρHe), obtained for Cr in the ground state, with interaction pair potentials of excited states. The resulting energy shifts for the transitions z(7)P ← a(7)S, y(7)P ← a(7)S, z(5)P ← a(5)S, and y(5)P ← a(5)S are compared to recent fluorescence and photoionization experiments.

Overview of Three-Dimensional Atomic-Resolution Holography and Imaging Techniques: Recent Advances in Local-Structure Science

NASA Astrophysics Data System (ADS)

Daimon, Hiroshi

2018-06-01

Local three-dimensional (3D) atomic arrangements without periodicity have not been able to be studied until recently. Recently, several holographies and related techniques have been developed to reveal the 3D atomic arrangement around specific atoms with no translational symmetry. This review gives an overview of these new local 3D atomic imaging techniques.

Coarse-grained protein-protein stiffnesses and dynamics from all-atom simulations

NASA Astrophysics Data System (ADS)

Hicks, Stephen D.; Henley, C. L.

2010-03-01

Large protein assemblies, such as virus capsids, may be coarse-grained as a set of rigid units linked by generalized (rotational and stretching) harmonic springs. We present an ab initio method to obtain the elastic parameters and overdamped dynamics for these springs from all-atom molecular-dynamics simulations of one pair of units at a time. The computed relaxation times of this pair give a consistency check for the simulation, and we can also find the corrective force needed to null systematic drifts. As a first application we predict the stiffness of an HIV capsid layer and the relaxation time for its breathing mode.

Facile Modulation of FLP Properties: A Phosphinylvinyl Grignard Reagent and Ga/P- and In/P2 -Based Frustrated Lewis Pairs.

PubMed

Backs, Jana; Lange, Merten; Possart, Josephine; Wollschläger, Agnes; Mück-Lichtenfeld, Christian; Uhl, Werner

2017-03-06

An Al/P-based frustrated Lewis pair (FLP) reacted with PhMgCl by an unexpected transmetalation and formation of a phosphinylvinyl Grignard reagent. This compound is well suited for the transfer of the basic FLP component to other Lewis acidic metal atoms and allowed the generation of a Ga/P and an In/P 2 FLP. The Ga FLP showed a behavior different to that of the corresponding Al FLP, the In FLP allowed the chelating coordination of an Au atom by Au-Cl bond activation. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Sb content on the physical properties of Ge-Se-Te chalcogenide glasses

NASA Astrophysics Data System (ADS)

Vashist, Priyanka; Anjali, Patial, Balbir Singh; Thakur, Nagesh

2018-05-01

In the present study, the bulk as-(Se80Te20)94-xGe6Sbx (x = 0, 1, 2, 4, 6, 8) glasses were synthesized using melt quenching technique. The physical properties viz coordination number, lone pair of electrons, number of constraints, glass transition temperature, mean bond energy, cohesive energy, electro-negativity and average heat of atomization of the investigated composition are reported and discussed. It is inferred that on increasing Sb content; average coordination number, average number of constraints, mean bond energy, cohesive energy and glass transition temperature increases but lone pair of electrons, average heat of atomization and deviation of stoichiometry decreases.

Photoionization and photofragmentation of the C 60 + molecular ion

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

Baral, K. K.; Aryal, N. B.; Esteves-Macaluso, D. A.

2016-03-01

Cross-section measurements are reported for single and double photoionization of Cmore » $$+\\atop{60}$$ ions in the photon energy range 18-150 eV accompanied by the loss of zero to seven pairs of carbon atoms, as well as for fragmentation without ionization resulting in loss of two to eight pairs of C atoms in the photon energy range 18-65 eV. Absolute measurements were performed by merging a beam of C$$+\\atop{60}$$ molecular ions with a beam of monochromatized synchrotron radiation. Product channels involving dissociation yielding smaller fullerene fragment ions account for nearly half of the total measured oscillator strength in this energy range. The sum of cross sections for the measured product channels is compared to a published calculation of the total photoabsorption cross section of neutral C 60 based on time-dependent density-functional theory. Lastly, this comparison and an accounting of oscillator strengths indicate that with the exception of C$$+\\atop{58}$$, the most important product channels resulting from photoabsorption were accounted for in the experiment. Threshold energies for the successive removal of carbon atom pairs accompanying photoionization are also determined from the measurements.« less

Atomic resolution holography.

PubMed

Hayashi, Kouichi

2014-11-01

Atomic resolution holography, such as X-ray fluorescence holography (XFH)[1] and photoelectron holography (PH), has the attention of researcher as an informative local structure analysis, because it provides three dimensional atomic images around specific elements within a range of a few nanometers. It can determine atomic arrangements around a specific element without any prior knowledge of structures. It is considered that the atomic resolution holographic is a third method of structural analysis at the atomic level after X-ray diffraction (XRD) and X-ray absorption fine structure (XAFS). As known by many researchers, XRD and XAFS are established methods that are widespread use in various fields. XRD and XAFS provide information on long-range translational periodicities and very local environments, respectively, whereas the atomic resolution holography gives 3D information on the local order and can visualize surrounding atoms with a large range of coordination shells. We call this feature "3D medium-range local structure observation".In addition to this feature, the atomic resolution holography is very sensitive to the displacement of atoms from their ideal positions, and one can obtain quantitative information about local lattice distortions by analyzing reconstructed atomic images[2] When dopants with different atomic radii from the matrix elements are present, the lattices around the dopants are distorted. However, using the conventional methods of structural analysis, one cannot determine the extent to which the local lattice distortions are preserved from the dopants. XFH is a good tool for solving this problem.Figure 1 shows a recent achievement on a relaxor ferroelectric of Pb(Mg1/3Nb2/3)O3 (PMN) using XFH. The structural studies of relaxor ferroelectrics have been carried out by X-ray or neutron diffractions, which suggested rhombohedral distortions of their lattices. However, their true pictures have not been obtained, yet. The Nb Kα holograms showed four separate Pb images, as shown in Fig.1. Using these images, we could obtain acute and obtuse rhombohedral structures of the crystal unit cells. Moreover, the Pb-Pb correlated images reconstructed from Pb Lα holograms showed a local structure of body center-like 2a0 ×2a0 × 2a0 superlattice, proving a rigid 3D network structural model combining the two kinds of rhombohedrons. This superstructure are believed to play an important role in the relaxor behaviour of PMN at atomic level[3].jmicro;63/suppl_1/i13/DFU047F1F1DFU047F1Fig. 1.3D images of the nearest Pb and O atoms around Nb in Pb(Mg1/3Nb2/3)O3. The cube represents 1/8 of the unit cell. © The Author 2014. Published by Oxford University Press on behalf of The Japanese Society of Microscopy. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Compact Single Site Resolution Cold Atom Experiment for Adiabatic Quantum Computing

DTIC Science & Technology

2016-02-03

goal of our scientific investigation is to demonstrate high fidelity and fast atom-atom entanglement between physically 1. REPORT DATE (DD-MM-YYYY) 4...of our scientific investigation is to demonstrate high fidelity and fast atom-atom entanglement between physically separated and optically addressed...Specifically, we will design and construct a set of compact single atom traps with integrated optics, suitable for heralded entanglement and loophole

Precisely detecting atomic position of atomic intensity images.

PubMed

Wang, Zhijun; Guo, Yaolin; Tang, Sai; Li, Junjie; Wang, Jincheng; Zhou, Yaohe

2015-03-01

We proposed a quantitative method to detect atomic position in atomic intensity images from experiments such as high-resolution transmission electron microscopy, atomic force microscopy, and simulation such as phase field crystal modeling. The evaluation of detection accuracy proves the excellent performance of the method. This method provides a chance to precisely determine atomic interactions based on the detected atomic positions from the atomic intensity image, and hence to investigate the related physical, chemical and electrical properties. Copyright © 2014 Elsevier B.V. All rights reserved.

Ion optical design of a collinear laser-negative ion beam apparatus.

PubMed

Diehl, C; Wendt, K; Lindahl, A O; Andersson, P; Hanstorp, D

2011-05-01

An apparatus for photodetachment studies on atomic and molecular negative ions of medium up to heavy mass (M ≃ 500) has been designed and constructed. Laser and ion beams are merged in the apparatus in a collinear geometry and atoms, neutral molecules and negative ions are detected in the forward direction. The ion optical design and the components used to optimize the mass resolution and the transmission through the extended field-free interaction region are described. A 90° sector field magnet with 50 cm bending radius in combination with two slits is used for mass dispersion providing a resolution of M∕ΔM≅800 for molecular ions and M∕ΔM≅400 for atomic ions. The difference in mass resolution for atomic and molecular ions is attributed to different energy distributions of the sputtered ions. With 1 mm slits, transmission from the source through the interaction region to the final ion detector was determined to be about 0.14%.

Selective excitation enables assignment of proton resonances and {sup 1}H-{sup 1}H distance measurement in ultrafast magic angle spinning solid state NMR spectroscopy

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

Zhang, Rongchun; Ramamoorthy, Ayyalusamy, E-mail: ramamoor@umich.edu

2015-07-21

Remarkable developments in ultrafast magic angle spinning (MAS) solid-state NMR spectroscopy enabled proton-based high-resolution multidimensional experiments on solids. To fully utilize the benefits rendered by proton-based ultrafast MAS experiments, assignment of {sup 1}H resonances becomes absolutely necessary. Herein, we propose an approach to identify different proton peaks by using dipolar-coupled heteronuclei such as {sup 13}C or {sup 15}N. In this method, after the initial preparation of proton magnetization and cross-polarization to {sup 13}C nuclei, transverse magnetization of desired {sup 13}C nuclei is selectively prepared by using DANTE (Delays Alternating with Nutations for Tailored Excitation) sequence and then, it is transferredmore » to bonded protons with a short-contact-time cross polarization. Our experimental results demonstrate that protons bonded to specific {sup 13}C atoms can be identified and overlapping proton peaks can also be assigned. In contrast to the regular 2D HETCOR experiment, only a few 1D experiments are required for the complete assignment of peaks in the proton spectrum. Furthermore, the finite-pulse radio frequency driven recoupling sequence could be incorporated right after the selection of specific proton signals to monitor the intensity buildup for other proton signals. This enables the extraction of {sup 1}H-{sup 1}H distances between different pairs of protons. Therefore, we believe that the proposed method will greatly aid in fast assignment of peaks in proton spectra and will be useful in the development of proton-based multi-dimensional solid-state NMR experiments to study atomic-level resolution structure and dynamics of solids.« less

Atomic-resolution structure of the CAP-Gly domain of dynactin on polymeric microtubules determined by magic angle spinning NMR spectroscopy.

PubMed

Yan, Si; Guo, Changmiao; Hou, Guangjin; Zhang, Huilan; Lu, Xingyu; Williams, John Charles; Polenova, Tatyana

2015-11-24

Microtubules and their associated proteins perform a broad array of essential physiological functions, including mitosis, polarization and differentiation, cell migration, and vesicle and organelle transport. As such, they have been extensively studied at multiple levels of resolution (e.g., from structural biology to cell biology). Despite these efforts, there remain significant gaps in our knowledge concerning how microtubule-binding proteins bind to microtubules, how dynamics connect different conformational states, and how these interactions and dynamics affect cellular processes. Structures of microtubule-associated proteins assembled on polymeric microtubules are not known at atomic resolution. Here, we report a structure of the cytoskeleton-associated protein glycine-rich (CAP-Gly) domain of dynactin motor on polymeric microtubules, solved by magic angle spinning NMR spectroscopy. We present the intermolecular interface of CAP-Gly with microtubules, derived by recording direct dipolar contacts between CAP-Gly and tubulin using double rotational echo double resonance (dREDOR)-filtered experiments. Our results indicate that the structure adopted by CAP-Gly varies, particularly around its loop regions, permitting its interaction with multiple binding partners and with the microtubules. To our knowledge, this study reports the first atomic-resolution structure of a microtubule-associated protein on polymeric microtubules. Our approach lays the foundation for atomic-resolution structural analysis of other microtubule-associated motors.

An Example-Based Super-Resolution Algorithm for Selfie Images

PubMed Central

William, Jino Hans; Venkateswaran, N.; Narayanan, Srinath; Ramachandran, Sandeep

2016-01-01

A selfie is typically a self-portrait captured using the front camera of a smartphone. Most state-of-the-art smartphones are equipped with a high-resolution (HR) rear camera and a low-resolution (LR) front camera. As selfies are captured by front camera with limited pixel resolution, the fine details in it are explicitly missed. This paper aims to improve the resolution of selfies by exploiting the fine details in HR images captured by rear camera using an example-based super-resolution (SR) algorithm. HR images captured by rear camera carry significant fine details and are used as an exemplar to train an optimal matrix-value regression (MVR) operator. The MVR operator serves as an image-pair priori which learns the correspondence between the LR-HR patch-pairs and is effectively used to super-resolve LR selfie images. The proposed MVR algorithm avoids vectorization of image patch-pairs and preserves image-level information during both learning and recovering process. The proposed algorithm is evaluated for its efficiency and effectiveness both qualitatively and quantitatively with other state-of-the-art SR algorithms. The results validate that the proposed algorithm is efficient as it requires less than 3 seconds to super-resolve LR selfie and is effective as it preserves sharp details without introducing any counterfeit fine details. PMID:27064500

Local structure and lattice dynamics study of low dimensional materials using atomic pair distribution function and high energy resolution inelastic x-ray scattering

NASA Astrophysics Data System (ADS)

Shi, Chenyang

Structure and dynamics lie at the heart of the materials science. A detailed knowledge of both subjects would be foundational in understanding the materials' properties and predicting their potential applications. However, the task becomes increasingly dicult as the particle size is reduced to the nanometer scale. For nanostructured materials their laboratory x-ray scattering patterns are overlapped and broadened, making structure determination impossible. Atomic pair distribution function technique based on either synchrotron x-ray or neutron scattering data is known as the tool of choice for probing local structures. However, to solve the "structure problem" in low-dimensional materials with PDF is still challenging. For example for 2D materials of interest in this thesis the crystallographic modeling approach often yields unphysical thermal factors along stacking direction where new chemical intuitions about their actual structures and new modeling methodology/program are needed. Beyond this, lattice dynamical investigations on nanosized particles are extremely dicult. Laboratory tools such as Raman and infra-red only probe phonons at Brillouin zone center. Although in literature there are a great number of theoretical studies of their vibrational properties based on either empirical force elds or density functional theory, various approximations made in theories make the theoretical predictions less reliable. Also, there lacks the direct experiment result to validate the theory against. In this thesis, we studied the structure and dynamics of a wide variety of technologically relevant low-dimensional materials through synchrotron based x-ray PDF and high energy resolution inelastic x-ray scattering (HERIX) techniques. By collecting PDF data and employing advanced modeling program such as DiPy-CMI, we successfully determined the atomic structures of (i) emerging Ti3C2, Nb4C3 MXenes (transition metal carbides and/or nitrides) that are promising for energy storage applications, and of (ii) zirconium phenylphosphonate ion exchange materials that are proposed to separate lanthanide ions from actinide ions in nuclear waste. Both material systems have two-dimensional layered nanocrystalline structure where we observed that the stacking of layers are not in good registry, also known as turbostratic" disorder. Consequently the signals from a single layer of atoms dominate the experimental PDF{thus building up a single slab model and simulating PDF using Debye function analysis was sucient to capture the main structural features in the measured PDF data. The information on correlation length of layers along the stacking direction, however, is contained in low-Q diraction peaks in either laboratory x-ray or synchrotron x-ray scattering patterns. On the lattice dynamics side, we rst investigated the trend of atomic bonding strength in size dependent platinum nanoparticles based on temperature dependent PDF data and measured Debye temperatures. An anomalous bond softening was observed at a particle size less than 2 nm. Since Debye model gives a simple quadratic phonon density of states (PDOS) curve, which is a simplified version of real lattice dynamics, we are motivated to measure full PDOS curves on three CdSe nanoclusters by using non-resonant inelastic x-ray scattering technique. We observed an overall blue-shift of PDOS curves with decreased sizes. Our current exemplary studies will open the door to a large number of future structural and lattice dynamical studies on a much broader range of low-dimensional material systems.

Position and Momentum Entanglement of Dipole-Dipole Interacting Atoms in Optical Lattices

NASA Astrophysics Data System (ADS)

Opatrný, T.; Kolář, M.; Kurizki, G.

We consider a possible realization of the position- and momentum-correlated atomic pairs that are confined to adjacent sites of two mutually shifted optical lattices and are entangled via laser-induced dipole-dipole interactions. The Einstein-Podolsky-Rosen (EPR) "paradox" [Einstein 1935] with translational variables is then modified by lattice-diffraction effects. We study a possible mechanism of creating such diatom entangled states by varying the effective mass of the atoms.

Subpicosecond X rotations of atomic clock states

NASA Astrophysics Data System (ADS)

Song, Yunheung; Lee, Han-gyeol; Kim, Hyosub; Jo, Hanlae; Ahn, Jaewook

2018-05-01

We demonstrate subpicosecond-timescale population transfer between the pair of hyperfine ground states of atomic rubidium using a single laser-pulse. Our scheme utilizes the geometric and dynamic phases induced during Rabi oscillation through the fine-structure excited state to construct an X rotation gate for the hyperfine-state qubit system. The experiment performed with a femtosecond laser and cold rubidium atoms, in a magnetooptical trap, shows over 98% maximal population transfer between the clock states.

Creating high-purity angular-momentum-state Rydberg atoms by a pair of unipolar laser pulses

NASA Astrophysics Data System (ADS)

Xin, PeiPei; Cheng, Hong; Zhang, ShanShan; Wang, HanMu; Xu, ZiShan; Liu, HongPing

2018-04-01

We propose a method of producing high-purity angular-momentum-state Rydberg atoms by a pair of unipolar laser pulses. The first positive-polarity optical half-cycle pulse is used to prepare an excited-state wave packet while the second one is less intense, but with opposite polarity and time delayed, and is employed to drag back the escaping free electron and clip the shape of the bound Rydberg wave packet, selectively increasing or decreasing a fraction of the angular-momentum components. An intelligent choice of laser parameters such as phase and amplitude helps us to control the orbital-angular-momentum composition of an electron wave packet with more facility; thus, a specified angular-momentum state with high purity can be achieved. This scheme of producing high-purity angular-momentum-state Rydberg atoms has significant application in quantum-information processing.

2,3-Diamino-pyridinium sorbate-sorbic acid (1/1).

PubMed

Hemamalini, Madhukar; Goh, Jia Hao; Fun, Hoong-Kun

2012-01-01

In the title mol-ecular salt-adduct, C(5)H(8)N(3) (+)·C(6)H(7)O(2) (-)·C(6)H(8)O(2), the 2,3-diamino-pyridinium cation is essentially planar, with a maximum deviation of 0.013 (2) Å, and is protanated at its pyridine N atom. The sorbate anion and sorbic acid mol-ecules exist in extended conformations. In the crystal, the protonated N atom and one of the two amino-group H atoms are hydrogen bonded to the sorbate anion through a pair of N-H⋯O hydrogen bonds, forming an R(1) (2)(6) ring motif. The carboxyl groups of the sorbic acid mol-ecules and the carboxyl-ate groups of the sorbate anions are connected via O-H⋯O hydrogen bonds. Furthermore, the ion pairs and neutral mol-ecules are connected via inter-molecular N-H⋯O hydrogen bonds, forming sheets lying parallel to (100).

Relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian: Relativistic pair correlation energies of the Xe atom

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

Eliav, E.; Kaldor, U.; Ishikawa, Y.

1994-12-31

Relativistic pair correlation energies of Xe were computed by employing a recently developed relativistic coupled cluster theory based on the no-pair Dirac-Coulomb-Breit Hamiltonian. The matrix Dirac-Fock-Breit SCF and relativistic coupled cluster calculations were performed by means of expansion in basis sets of well-tempered Gaussian spinors. A detailed study of the pair correlation energies in Xe is performed, in order to investigate the effects of the low-frequency Breit interaction on the correlation energies of Xe. Nonadditivity of correlation and relativistic (particularly Breit) effects is discussed.

Deposition-temperature dependence of structural anisotropy in amorphous Tb-Fe films

NASA Astrophysics Data System (ADS)

Harris, V. G.; Elam, W. T.; Koon, N. C.; Hellman, F.

1994-02-01

The anisotropic local structure in a series of amorphous Tb26Fe74 films deposited at different deposition temperatures and having different magnetic anisotropy energies have been investigated using polarization-dependent extended x-ray-absorption fine-structure measurements. Samples deposited at temperatures >=300 K exhibit anisotropic pair correlations where like atomic pairs are favored in plane and unlike pairs are favored out of plane. Both the anisotropic pair correlations and the perpendicular magnetic anisotropy increase with increasing deposition temperature. In contrast, a sample deposited at 77 K was found to have isotropic pair correlations, low perpendicular magnetic anisotropy, and a large (~=1%) in-plane compression.

Experiments with bosonic atoms for quantum gas assembly

NASA Astrophysics Data System (ADS)

Brown, Mark; Lin, Yiheng; Lester, Brian; Kaufman, Adam; Ball, Randall; Brossard, Ludovic; Isaev, Leonid; Thiele, Tobias; Lewis-Swan, Robert; Schymik, Kai-Niklas; Rey, Ana Maria; Regal, Cindy

2017-04-01

Quantum gas assembly is a promising platform for preparing and observing neutral atom systems on the single-atom level. We have developed a toolbox that includes ground-state laser cooling, high-fidelity loading techniques, addressable spin control, and dynamic spatial control and coupling of atoms. Already, this platform has enabled us to pursue a number of experiments studying entanglement and interference of pairs of bosonic atoms. We discuss our recent work in probabilistically entangling neutral atoms via interference, measurement, and post-selection as well as our future pursuits of interesting spin-motion dynamics of larger arrays of atoms. This work was supported by the David and Lucile Packard Foundation, National Science Foundation Physics Frontier Centers, and the National Defense Science and Engineering Graduate Fellowships program.

The Advanced Pair Telescope (APT) Mission Concept

NASA Technical Reports Server (NTRS)

Hunter, Stanley; Buckley, James H.

2008-01-01

We present a mission concept for the Advanced Pair Telescope (APT), a high-energy gamma-ray instrument with an order of magnitude improvement in sensitivity, 6 sr field of view, and angular resolution a factor of 3-10 times that of GLAST. With its very wide instantaneous field-of-view and large effective area, this instrument would be capable of detecting GRBs at very large redshifts, would enable a very high resolution study of SNRs and PWN, and could provide hour-scale temporal resolution of transients from many AGN and galactic sources. The APT instrument will consist of a Xe time-projection-chamber tracker that bridges the energy regime between Compton scattering and pair production and will provide an unprecedented improvement in angular resolution; a thick scintillating-fiber trackerlcalorimeter that will provide sensitivity and energy resolution to higher energies and will possess a factor of 10 improvement in geometric factor over GLAST; and an anticoincidence detector using scintillator-tiles to reject charged particles. After the anticipated 10-years of GLAST operation , the APT instrument would provide continued coverage of the critial high-energy gamma-ray band (between 30 MeV to 100 GeV), providing an essential component of broad-band multiwavelength studies of the high-energy universe.

MCORES: a system for noun phrase coreference resolution for clinical records.

PubMed

Bodnari, Andreea; Szolovits, Peter; Uzuner, Özlem

2012-01-01

Narratives of electronic medical records contain information that can be useful for clinical practice and multi-purpose research. This information needs to be put into a structured form before it can be used by automated systems. Coreference resolution is a step in the transformation of narratives into a structured form. This study presents a medical coreference resolution system (MCORES) for noun phrases in four frequently used clinical semantic categories: persons, problems, treatments, and tests. MCORES treats coreference resolution as a binary classification task. Given a pair of concepts from a semantic category, it determines coreferent pairs and clusters them into chains. MCORES uses an enhanced set of lexical, syntactic, and semantic features. Some MCORES features measure the distance between various representations of the concepts in a pair and can be asymmetric. MCORES was compared with an in-house baseline that uses only single-perspective 'token overlap' and 'number agreement' features. MCORES was shown to outperform the baseline; its enhanced features contribute significantly to performance. In addition to the baseline, MCORES was compared against two available third-party, open-domain systems, RECONCILE(ACL09) and the Beautiful Anaphora Resolution Toolkit (BART). MCORES was shown to outperform both of these systems on clinical records.

Electrical Conductivity through a Single Atomic Step Measured with the Proximity-Induced Superconducting Pair Correlation

DOE PAGES

Kim, Howon; Lin, Shi -Zeng; Graf, Matthias J.; ...

2016-09-08

Local disordered nanostructures in an atomically thick metallic layer on a semiconducting substrate play significant and decisive roles in transport properties of two-dimensional (2D) conductive systems. We measured the electrical conductivity through a step of monoatomic height in a truly microscopic manner by using as a signal the superconducting pair correlation induced by the proximity effect. The transport property across a step of a one-monolayer Pb surface metallic phase, formed on a Si(111) substrate, was evaluated by inducing the pair correlation around the local defect and measuring its response, i.e., the reduced density of states at the Fermi energy usingmore » scanning tunneling microscopy. We found that the step resistance has a significant contribution to the total resistance on a nominally flat surface. Our study also revealed that steps in the 2D metallic layer terminate the propagation of the pair correlation. Furthermore, superconductivity is enhanced between the first surface step and the superconductor–normal-metal interface by reflectionless tunneling when the step is located within a coherence length.« less

Electrical Conductivity through a Single Atomic Step Measured with the Proximity-Induced Superconducting Pair Correlation.

PubMed

Kim, Howon; Lin, Shi-Zeng; Graf, Matthias J; Miyata, Yoshinori; Nagai, Yuki; Kato, Takeo; Hasegawa, Yukio

2016-09-09

Local disordered nanostructures in an atomically thick metallic layer on a semiconducting substrate play significant and decisive roles in transport properties of two-dimensional (2D) conductive systems. We measured the electrical conductivity through a step of monoatomic height in a truly microscopic manner by using as a signal the superconducting pair correlation induced by the proximity effect. The transport property across a step of a one-monolayer Pb surface metallic phase, formed on a Si(111) substrate, was evaluated by inducing the pair correlation around the local defect and measuring its response, i.e., the reduced density of states at the Fermi energy using scanning tunneling microscopy. We found that the step resistance has a significant contribution to the total resistance on a nominally flat surface. Our study also revealed that steps in the 2D metallic layer terminate the propagation of the pair correlation. Superconductivity is enhanced between the first surface step and the superconductor-normal-metal interface by reflectionless tunneling when the step is located within a coherence length.

AlphaSpace: Fragment-Centric Topographical Mapping To Target Protein–Protein Interaction Interfaces

PubMed Central

2016-01-01

Inhibition of protein–protein interactions (PPIs) is emerging as a promising therapeutic strategy despite the difficulty in targeting such interfaces with drug-like small molecules. PPIs generally feature large and flat binding surfaces as compared to typical drug targets. These features pose a challenge for structural characterization of the surface using geometry-based pocket-detection methods. An attractive mapping strategy—that builds on the principles of fragment-based drug discovery (FBDD)—is to detect the fragment-centric modularity at the protein surface and then characterize the large PPI interface as a set of localized, fragment-targetable interaction regions. Here, we introduce AlphaSpace, a computational analysis tool designed for fragment-centric topographical mapping (FCTM) of PPI interfaces. Our approach uses the alpha sphere construct, a geometric feature of a protein’s Voronoi diagram, to map out concave interaction space at the protein surface. We introduce two new features—alpha-atom and alpha-space—and the concept of the alpha-atom/alpha-space pair to rank pockets for fragment-targetability and to facilitate the evaluation of pocket/fragment complementarity. The resulting high-resolution interfacial map of targetable pocket space can be used to guide the rational design and optimization of small molecule or biomimetic PPI inhibitors. PMID:26225450

Crystallographic and Molecular Dynamics Simulation Analysis of Escherichia Coli Dihydroneopterin Aldolase

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

Blaszczyk, Jaroslaw; Lu, Zhenwei; Li, Yue

2014-09-01

To understand the structural basis for the biochemical differences and further investigate the catalytic mechanism of DHNA, we have determined the structure of EcDHNA complexed with NP at 1.07-Å resolution [PDB:2O90], built an atomic model of EcDHNA complexed with the substrate DHNP, and performed molecular dynamics (MD) simulation analysis of the substrate complex. EcDHNA has the same fold as SaDHNA and also forms an octamer that consists of two tetramers, but the packing of one tetramer with the other is significantly different between the two enzymes. Furthermore, the structures reveal significant differences in the vicinity of the active site, particularlymore » in the loop that connects strands β3 and β4, mainly due to the substitution of nearby residues. The building of an atomic model of the complex of EcDHNA and the substrate DHNP and the MD simulation of the complex show that some of the hydrogen bonds between the substrate and the enzyme are persistent, whereas others are transient. The substrate binding model and MD simulation provide the molecular basis for the biochemical behaviors of the enzyme, including noncooperative substrate binding, indiscrimination of a pair of epimers as the substrates, proton wire switching during catalysis, and formation of epimerization product.« less

A cryogen-free low temperature scanning tunneling microscope capable of inelastic electron tunneling spectroscopy.

PubMed

Zhang, Shuai; Huang, Di; Wu, Shiwei

2016-06-01

The design and performance of a cryogen-free low temperature scanning tunneling microscope (STM) housed in ultrahigh vacuum (UHV) are reported. The cryogen-free design was done by directly integrating a Gifford-McMahon cycle cryocooler to a Besocke-type STM, and the vibration isolation was achieved by using a two-stage rubber bellow between the cryocooler and a UHV-STM interface with helium exchange gas cooling. A base temperature of 15 K at the STM was achieved, with a possibility to further decrease by using a cryocooler with higher cooling power and adding additional low temperature stage under the exchange gas interface. Atomically sharp STM images and high resolution dI/dV spectra on various samples were demonstrated. Furthermore, we reported the inelastic tunneling spectroscopy on a single carbon monoxide molecule adsorbed on Ag(110) surface with a cryogen-free STM for the first time. Being totally cryogen-free, the system not only saves the running cost significantly but also enables uninterrupted data acquisitions and variable temperature measurements with much ease. In addition, the system is capable of coupling light to the STM junction by a pair of lens inside the UHV chamber. We expect that these enhanced capabilities could further broaden our views to the atomic-scale world.

A cryogen-free low temperature scanning tunneling microscope capable of inelastic electron tunneling spectroscopy

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

Zhang, Shuai; Huang, Di; Wu, Shiwei, E-mail: swwu@fudan.edu.cn

The design and performance of a cryogen-free low temperature scanning tunneling microscope (STM) housed in ultrahigh vacuum (UHV) are reported. The cryogen-free design was done by directly integrating a Gifford-McMahon cycle cryocooler to a Besocke-type STM, and the vibration isolation was achieved by using a two-stage rubber bellow between the cryocooler and a UHV-STM interface with helium exchange gas cooling. A base temperature of 15 K at the STM was achieved, with a possibility to further decrease by using a cryocooler with higher cooling power and adding additional low temperature stage under the exchange gas interface. Atomically sharp STM imagesmore » and high resolution dI/dV spectra on various samples were demonstrated. Furthermore, we reported the inelastic tunneling spectroscopy on a single carbon monoxide molecule adsorbed on Ag(110) surface with a cryogen-free STM for the first time. Being totally cryogen-free, the system not only saves the running cost significantly but also enables uninterrupted data acquisitions and variable temperature measurements with much ease. In addition, the system is capable of coupling light to the STM junction by a pair of lens inside the UHV chamber. We expect that these enhanced capabilities could further broaden our views to the atomic-scale world.« less

Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111).

PubMed

Kroes, Geert-Jan; Pavanello, Michele; Blanco-Rey, María; Alducin, Maite; Auerbach, Daniel J

2014-08-07

Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of the incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction ("EF") model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated "post" ("p") the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the range 0.2-0.3 eV due to ehp excitation, which should be possible to observe. The average non-adiabatic energy losses for non-penetrative scattering exceed the adiabatic losses to phonons by 0.9-1.0 eV. This suggests that for scattering of hyperthermal H-atoms from coinage metals the dominant energy dissipation channel should be to ehp excitation. These predictions can be tested by experiments that combine techniques for generating H-atom beams that are well resolved in translational energy and for detecting the scattered atoms with high energy-resolution.

Energy correlations of photon pairs generated by a silicon microring resonator probed by Stimulated Four Wave Mixing.

PubMed

Grassani, Davide; Simbula, Angelica; Pirotta, Stefano; Galli, Matteo; Menotti, Matteo; Harris, Nicholas C; Baehr-Jones, Tom; Hochberg, Michael; Galland, Christophe; Liscidini, Marco; Bajoni, Daniele

2016-04-01

Compact silicon integrated devices, such as micro-ring resonators, have recently been demonstrated as efficient sources of quantum correlated photon pairs. The mass production of integrated devices demands the implementation of fast and reliable techniques to monitor the device performances. In the case of time-energy correlations, this is particularly challenging, as it requires high spectral resolution that is not currently achievable in coincidence measurements. Here we reconstruct the joint spectral density of photons pairs generated by spontaneous four-wave mixing in a silicon ring resonator by studying the corresponding stimulated process, namely stimulated four wave mixing. We show that this approach, featuring high spectral resolution and short measurement times, allows one to discriminate between nearly-uncorrelated and highly-correlated photon pairs.

Vacancy Transport and Interactions on Metal Surfaces

DTIC Science & Technology

2014-03-06

prevent obtaining systematical pictures with atomic scale resolution. Thus the experiments on adatom and mono -vacancy surface diffusion on Ag(110) were...vacuum conditions with atomic scale resolution with Scanning Tunneling Microscope (STM) and Field Ion Microscope (FIM). For each investigated material...experimental conditions for creation of surface vacancies on Au(100) has been determined and observations of surface diffusion of mono vacancies has been

Column ratio mapping: a processing technique for atomic resolution high-angle annular dark-field (HAADF) images.

PubMed

Robb, Paul D; Craven, Alan J

2008-12-01

An image processing technique is presented for atomic resolution high-angle annular dark-field (HAADF) images that have been acquired using scanning transmission electron microscopy (STEM). This technique is termed column ratio mapping and involves the automated process of measuring atomic column intensity ratios in high-resolution HAADF images. This technique was developed to provide a fuller analysis of HAADF images than the usual method of drawing single intensity line profiles across a few areas of interest. For instance, column ratio mapping reveals the compositional distribution across the whole HAADF image and allows a statistical analysis and an estimation of errors. This has proven to be a very valuable technique as it can provide a more detailed assessment of the sharpness of interfacial structures from HAADF images. The technique of column ratio mapping is described in terms of a [110]-oriented zinc-blende structured AlAs/GaAs superlattice using the 1 angstroms-scale resolution capability of the aberration-corrected SuperSTEM 1 instrument.

The First Non-Dispersive High-Resolution Spectroscopy of an X-ray-bright Galaxy Cluster

NASA Astrophysics Data System (ADS)

Yamaguchi, Hiroya; Hitomi Collaboration

2018-06-01

The Hitomi X-ray Observatory was equipped with the Soft X-ray Spectrometer (SXS), an X-ray microcalorimeter that achieved an energy resolution of 5 eV (@0.5-10 keV) for extended objects. This offered an unprecedented benchmark of atomic modeling and database for hot collisional plasmas, revealing both successes and challenges in the current atomic codes that are widely used by the X-ray astronomy community. I will review the Hitomi observations of the brightest part of the Perseus Cluster, whose X-ray spectrum is dominated by thermal emission from the intra-cluster medium (ICM). The SXS successfully measured the turbulent velocities and metal abundances of the ICM, which radically altered our understanding of the dynamics and chemical enrichment in this object. At the same time, the high-resolution X-ray data led to significant improvement in the atomic models, such as AtomDB and SPEX -- I will briefly overview how this improvement was made. Nevertheless, there are still significant discrepancies among the public atomic models, causing systematic uncertainties in measurements of the temperature, abundance, and degree of the resonance scattering. Requirements for future improvements will be summarized in this context.

Generation of Werner states via collective decay of coherently driven atoms

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

Agarwal, Girish S.; Kapale, Kishore T.

2006-02-15

We show deterministic generation of Werner states as a steady state of the collective decay dynamics of a pair of neutral atoms coupled to a leaky cavity and strong coherent drive. We also show how the scheme can be extended to generate a 2N-particle analogue of the bipartite Werner states.

Combining density functional theory (DFT) and pair distribution function (PDF) analysis to solve the structure of metastable materials: the case of metakaolin.

PubMed

White, Claire E; Provis, John L; Proffen, Thomas; Riley, Daniel P; van Deventer, Jannie S J

2010-04-07

Understanding the atomic structure of complex metastable (including glassy) materials is of great importance in research and industry, however, such materials resist solution by most standard techniques. Here, a novel technique combining thermodynamics and local structure is presented to solve the structure of the metastable aluminosilicate material metakaolin (calcined kaolinite) without the use of chemical constraints. The structure is elucidated by iterating between least-squares real-space refinement using neutron pair distribution function data, and geometry optimisation using density functional modelling. The resulting structural representation is both energetically feasible and in excellent agreement with experimental data. This accurate structural representation of metakaolin provides new insight into the local environment of the aluminium atoms, with evidence of the existence of tri-coordinated aluminium. By the availability of this detailed chemically feasible atomic description, without the need to artificially impose constraints during the refinement process, there exists the opportunity to tailor chemical and mechanical processes involving metakaolin and other complex metastable materials at the atomic level to obtain optimal performance at the macro-scale.

Toward resolving the catalytic mechanism of dihydrofolate reductase using neutron and ultrahigh-resolution X-ray crystallography [Neutron and ultrahigh resolution X-ray crystallography reveals water as the proton donor in the catalytic mechanism of dihydrofolate reductase

DOE PAGES

Wan, Qun; Bennett, Brad C.; Wilson, Mark A.; ...

2014-12-01

Dihydrofolate reductase (DHFR) catalyzes the NADPH-dependent reduction of dihydrofolate (DHF) to tetrahydrofolate (THF). An important step in the mechanism involves proton donation to the N5 atom of DHF. The inability to determine the protonation states of active site residues and substrate has led to the lack of consensus on a catalytic mechanism. To resolve this ambiguity, we conducted neutron and ultrahigh resolution X-ray crystallographic studies of the pseudo-Michaelis ternary complex of DHFR with folate and NADP + from E. coli. The neutron data were collected to 2.0 Å resolution using a 3.6 mm 3 crystal with the quasi-Laue technique, andmore » the structure reveals that the N3 atom of folate is protonated while Asp27 is negatively charged. Previous mechanisms have proposed a keto-to-enol tautomerization of the substrate to facilitate protonation of the N5 atom. The structure supports the existence of the keto tautomer due to protonation of the N3 atom, suggesting tautomerization is unnecessary for catalysis. In the 1.05 Å resolution X-ray structure of the ternary complex, conformational disorder of the Met20 side chain is coupled to electron density for a partially occupied water within hydrogen-bonding distance of the N5 atom of folate; this suggests direct protonation of substrate by solvent. We propose a catalytic mechanism for DHFR that involves stabilization of the keto tautomer of the substrate, elevation of the pK a of the N5 atom of DHF by Asp27, and protonation of N5 by water whose access to the active site is gated by fluctuation of the Met20 side chain even though the Met-20 loop is closed.« less

Atomic-scale sensing of the magnetic dipolar field from single atoms

NASA Astrophysics Data System (ADS)

Choi, Taeyoung; Paul, William; Rolf-Pissarczyk, Steffen; MacDonald, Andrew J.; Natterer, Fabian D.; Yang, Kai; Willke, Philip; Lutz, Christopher P.; Heinrich, Andreas J.

2017-05-01

Spin resonance provides the high-energy resolution needed to determine biological and material structures by sensing weak magnetic interactions. In recent years, there have been notable achievements in detecting and coherently controlling individual atomic-scale spin centres for sensitive local magnetometry. However, positioning the spin sensor and characterizing spin-spin interactions with sub-nanometre precision have remained outstanding challenges. Here, we use individual Fe atoms as an electron spin resonance (ESR) sensor in a scanning tunnelling microscope to measure the magnetic field emanating from nearby spins with atomic-scale precision. On artificially built assemblies of magnetic atoms (Fe and Co) on a magnesium oxide surface, we measure that the interaction energy between the ESR sensor and an adatom shows an inverse-cube distance dependence (r-3.01±0.04). This demonstrates that the atoms are predominantly coupled by the magnetic dipole-dipole interaction, which, according to our observations, dominates for atom separations greater than 1 nm. This dipolar sensor can determine the magnetic moments of individual adatoms with high accuracy. The achieved atomic-scale spatial resolution in remote sensing of spins may ultimately allow the structural imaging of individual magnetic molecules, nanostructures and spin-labelled biomolecules.

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

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

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in neutron irradiated nuclear materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1:0a₀ to 3:3a₀ have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomicmore » level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a₀ by taking the average of the recombination distances from 80 simulation cases. This value agrees well with the experimental estimate. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.« less

Recombination radius of a Frenkel pair and capture radius of a self-interstitial atom by vacancy clusters in bcc Fe

DOE PAGES

Nakashima, Kenichi; Stoller, Roger E.; Xu, Haixuan

2015-08-04

The recombination radius of a Frenkel pair is a fundamental parameter for the object kinetic Monte Carlo (OKMC) and mean field rate theory (RT) methods that are used to investigate irradiation damage accumulation in neutron irradiated nuclear materials. The recombination radius in bcc Fe has been studied both experimentally and numerically, however there is no general consensus about its value. The detailed atomistic processes of recombination also remain uncertain. Values from 1:0a₀ to 3:3a₀ have been employed as a recombination radius in previous studies using OKMC and RT. The recombination process of a Frenkel pair is investigated at the atomicmore » level using the self-evolved atomistic kinetic Monte Carlo (SEAKMC) method in this paper. SEAKMC calculations reveal that a self-interstitial atom recombines with a vacancy in a spontaneous reaction from several nearby sites following characteristic pathways. The recombination radius of a Frenkel pair is estimated to be 2.26a₀ by taking the average of the recombination distances from 80 simulation cases. This value agrees well with the experimental estimate. In addition, we apply these procedures to the capture radius of a self-interstitial atom by a vacancy cluster. The capture radius is found to gradually increase with the size of the vacancy cluster. The fitting curve for the capture radius is obtained as a function of the number of vacancies in the cluster.« less

Computational conformational antimicrobial analysis developing mechanomolecular theory for polymer biomaterials in materials science and engineering

NASA Astrophysics Data System (ADS)

Petersen, Richard C.

2014-03-01

Single-bond rotations or pyramidal inversions tend to either hide or expose relative energies that exist for atoms with nonbonding lone-pair electrons. Availability of lone-pair electrons depends on overall molecular electron distributions and differences in the immediate polarity of the surrounding pico/nanoenvironment. Stereochemistry three-dimensional aspects of molecules provide insight into conformations through single-bond rotations with associated lone-pair electrons on oxygen atoms in addition to pyramidal inversions with nitrogen atoms. When electrons are protected, potential energy is sheltered toward an energy minimum value to compatibilize molecularly with nonpolar environments. When electrons are exposed, maximum energy is available toward polar environment interactions. Computational conformational analysis software calculated energy profiles that exist during specific oxygen ether single-bond rotations with easy-to-visualize three-dimensional models for the trichlorinated bisaromatic ether triclosan antimicrobial polymer additive. As shown, fluctuating alternating bond rotations can produce complex interactions between molecules to provide entanglement strength for polymer toughness or alternatively disrupt weak secondary bonds of attraction to lower resin viscosity for new additive properties with nonpolar triclosan as a hydrophobic toughening/wetting agent. Further, bond rotations involving lone-pair electrons by a molecule at a nonpolar-hydrocarbon-membrane/polar-biologic-fluid interface might become sufficiently unstable to provide free mechanomolecular energies to disrupt weaker microbial membranes, for membrane transport of molecules into cells, provide cell signaling/recognition/defense and also generate enzyme mixing to speed reactions.

Probing and Manipulating Ultracold Fermi Superfluids

NASA Astrophysics Data System (ADS)

Jiang, Lei

Ultracold Fermi gas is an exciting field benefiting from atomic physics, optical physics and condensed matter physics. It covers many aspects of quantum mechanics. Here I introduce some of my work during my graduate study. We proposed an optical spectroscopic method based on electromagnetically-induced transparency (EIT) as a generic probing tool that provides valuable insights into the nature of Fermi paring in ultracold Fermi gases of two hyperfine states. This technique has the capability of allowing spectroscopic response to be determined in a nearly non-destructive manner and the whole spectrum may be obtained by scanning the probe laser frequency faster than the lifetime of the sample without re-preparing the atomic sample repeatedly. Both quasiparticle picture and pseudogap picture are constructed to facilitate the physical explanation of the pairing signature in the EIT spectra. Motivated by the prospect of realizing a Fermi gas of 40K atoms with a synthetic non-Abelian gauge field, we investigated theoretically BEC-HCS crossover physics in the presence of a Rashba spin-orbit coupling in a system of two-component Fermi gas with and without a Zeeman field that breaks the population balance. A new bound state (Rashba pair) emerges because of the spin-orbit interaction. We studied the properties of Rashba pairs using a standard pair fluctuation theory. As the two-fold spin degeneracy is lifted by spin-orbit interaction, bound pairs with mixed singlet and triplet pairings (referred to as rashbons) emerge, leading to an anisotropic superfluid. We discussed in detail the experimental signatures for observing the condensation of Rashba pairs by calculating various physical observables which characterize the properties of the system and can be measured in experiment. The role of impurities as experimental probes in the detection of quantum material properties is well appreciated. Here we studied the effect of a single classical impurity in trapped ultracold Fermi superfluids. Although a non-magnetic impurity does not change macroscopic properties of s-wave Fermi superfluids, depending on its shape and strength, a magnetic impurity can induce single or multiple mid-gap bound states. The multiple mid-gap states could coincide with the development of a Fulde-Ferrell-Larkin-Ovchinnikov (FFLO) phase within the superfluid. As an analog of the Scanning Tunneling Microscope, we proposed a modified radio frequency spectroscopic method to measure the focal density of states which can be employed to detect these states and other quantum phases of cold atoms. A key result of our self consistent Bogoliubov-de Gennes calculations is that a magnetic impurity can controllably induce an FFLO state at currently accessible experimental parameters.

Intermolecular interactions of trifluorohalomethanes with Lewis bases in the gas phase: An ab initio study

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

Wang, Yi-Siang; Yin, Chih-Chien; Chao, Sheng D., E-mail: sdchao@spring.iam.ntu.edu.tw

2014-10-07

We perform an ab initio computational study of molecular complexes with the general formula CF{sub 3}X—B that involve one trifluorohalomethane CF{sub 3}X (X = Cl or Br) and one of a series of Lewis bases B in the gas phase. The Lewis bases are so chosen that they provide a range of electron-donating abilities for comparison. Based on the characteristics of their electron pairs, we consider the Lewis bases with a single n-pair (NH{sub 3} and PH{sub 3}), two n-pairs (H{sub 2}O and H{sub 2}S), two n-pairs with an unsaturated bond (H{sub 2}CO and H{sub 2}CS), and a single π-pairmore » (C{sub 2}H{sub 4}) and two π-pairs (C{sub 2}H{sub 2}). The aim is to systematically investigate the influence of the electron pair characteristics and the central atom substitution effects on the geometries and energetics of the formed complexes. The counterpoise-corrected supermolecule MP2 and coupled-cluster single double with perturbative triple [CCSD(T)] levels of theory have been employed, together with a series of basis sets up to aug-cc-pVTZ. The angular and radial configurations, the binding energies, and the electrostatic potentials of the stable complexes have been compared and discussed as the Lewis base varies. For those complexes where halogen bonding plays a significant role, the calculated geometries and energetics are consistent with the σ-hole model. Upon formation of stable complexes, the C–X bond lengths shorten, while the C–X vibrational frequencies increase, thus rendering blueshifting halogen bonds. The central atom substitution usually enlarges the intermolecular bond distances while it reduces the net charge transfers, thus weakening the bond strengths. The analysis based on the σ-hole model is grossly reliable but requires suitable modifications incorporating the central atom substitution effects, in particular, when interaction components other than electrostatic contributions are involved.« less

Predicting protein complex geometries with a neural network.

PubMed

Chae, Myong-Ho; Krull, Florian; Lorenzen, Stephan; Knapp, Ernst-Walter

2010-03-01

A major challenge of the protein docking problem is to define scoring functions that can distinguish near-native protein complex geometries from a large number of non-native geometries (decoys) generated with noncomplexed protein structures (unbound docking). In this study, we have constructed a neural network that employs the information from atom-pair distance distributions of a large number of decoys to predict protein complex geometries. We found that docking prediction can be significantly improved using two different types of polar hydrogen atoms. To train the neural network, 2000 near-native decoys of even distance distribution were used for each of the 185 considered protein complexes. The neural network normalizes the information from different protein complexes using an additional protein complex identity input neuron for each complex. The parameters of the neural network were determined such that they mimic a scoring funnel in the neighborhood of the native complex structure. The neural network approach avoids the reference state problem, which occurs in deriving knowledge-based energy functions for scoring. We show that a distance-dependent atom pair potential performs much better than a simple atom-pair contact potential. We have compared the performance of our scoring function with other empirical and knowledge-based scoring functions such as ZDOCK 3.0, ZRANK, ITScore-PP, EMPIRE, and RosettaDock. In spite of the simplicity of the method and its functional form, our neural network-based scoring function achieves a reasonable performance in rigid-body unbound docking of proteins. Proteins 2010. (c) 2009 Wiley-Liss, Inc.

Multiscale registration algorithm for alignment of meshes

NASA Astrophysics Data System (ADS)

Vadde, Srikanth; Kamarthi, Sagar V.; Gupta, Surendra M.

2004-03-01

Taking a multi-resolution approach, this research work proposes an effective algorithm for aligning a pair of scans obtained by scanning an object's surface from two adjacent views. This algorithm first encases each scan in the pair with an array of cubes of equal and fixed size. For each scan in the pair a surrogate scan is created by the centroids of the cubes that encase the scan. The Gaussian curvatures of points across the surrogate scan pair are compared to find the surrogate corresponding points. If the difference between the Gaussian curvatures of any two points on the surrogate scan pair is less than a predetermined threshold, then those two points are accepted as a pair of surrogate corresponding points. The rotation and translation values between the surrogate scan pair are determined by using a set of surrogate corresponding points. Using the same rotation and translation values the original scan pairs are aligned. The resulting registration (or alignment) error is computed to check the accuracy of the scan alignment. When the registration error becomes acceptably small, the algorithm is terminated. Otherwise the above process is continued with cubes of smaller and smaller sizes until the algorithm is terminated. However at each finer resolution the search space for finding the surrogate corresponding points is restricted to the regions in the neighborhood of the surrogate points that were at found at the preceding coarser level. The surrogate corresponding points, as the resolution becomes finer and finer, converge to the true corresponding points on the original scans. This approach offers three main benefits: it improves the chances of finding the true corresponding points on the scans, minimize the adverse effects of noise in the scans, and reduce the computational load for finding the corresponding points.

Insights into the crystal chemistry of Earth materials rendered by electron density distributions: Pauling's rules revisited

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

Gibbs, Gerald V.; Ross, Nancy L.; Cox, David F.

2014-05-20

Pauling's first two rules are examined in terms of the accumulation of the electron density between bonded pairs of atoms for a relatively large number of oxide and silicate crystals and siloxane molecules. The distribution of the electron density shows that the radius of the oxygen atom is not fixed, but that it actually decreases systematically from ~1.40 Å to ~ 0.65 Å as the polarizing power and the electronegativity of the bonded metal atoms increase and the distribution of the O atom is progressively polarized and contracted along the bond vectors by the impact of the bonded interactions. Themore » contractions result in an aspherical oxygen atom that displays as many different bonded “radii” as it has bonded interactions. The bonded radii for the metal atoms match the Shannon and Prewitt ionic radii for the more electropositive atoms like potassium and sodium, but they are systematically larger for the more electronegative atoms like aluminum, silicon and phosphorous. Pauling's first rule is based on the assumption that the radius of the oxide anion is fixed and that the radii of the cations are such that radius sum of the spherical oxide anion and a cation necessarily equals the separation between the cation-anion bonded pair with the coordination number of the cation being determined by the ratio of the radii of the cation and anion. In the case of the bonded radii, the sum of the bonded radii for the metal atoms and the oxide anion necessarily equals the bond lengths by virtue of the way that the bonded radii were determined in the partitioning of the electron density along the bond path into metal and O atom parts. But, the radius ratio for the O and M atoms is an unsatisfactory rule for determining the coordination number of the metal atom inasmuch as a bonded O atom is not, in general, spherical, and its size varies substantially along its bonded directions. But by counting the number of bond paths that radiate from a bonded atom, the coordination number of the atom is determined uniquely independent of the asphericity and sizes of the atom. A power law connection established between the bond lengths and bond strengths for crystals and molecules is mirrored by a comparable power law connection between bond length and the accumulation of the electron density between bonded pairs of atoms, a connection that is consistent with Pauling's electroneutrality postulate that the charges of the atoms in an oxide are negligibly small. The connection indicates that a one-to-one correspondence exists between the accumulation between a pair of bonded atoms and the Pauling bond strength for M-O bonded interaction for all atoms of the periodic table. The connection provides a common basis for understanding the success of the manifold applications that have been made with the bond valence theory model together with the modeling of crystal structures, chemical zoning, leaching and cation transport in batteries and the like. We believe that the wide spread applications of the model in mineralogy and material science owes much of its success to the direct connection between bond strength and the quantum mechanical observable, the electron density distribution. Comparable power law expressions established for the bonded interactions for both crystals and molecules support Pauling's assertion that his second rule has significance for molecules as well as for crystals. A simple expression is found that provides a one to one connection between the accumulation of the electron density between bonded M and O atoms and the Pauling bond strength for all M atoms of the periodic table with ~ 95 % of the variation of the bond strength being explained in terms of a linear dependence on the accumulated electron density. Compelling evidence is presented that supports the argument that the Si-O bonded interactions for tiny siloxane molecules and silicate crystals are chemically equivalent.« less

Trapped atoms along nanophotonic resonators

NASA Astrophysics Data System (ADS)

Fields, Brian; Kim, May; Chang, Tzu-Han; Hung, Chen-Lung

2017-04-01

Many-body systems subject to long-range interactions have remained a very challenging topic experimentally. Ultracold atoms trapped in extreme proximity to the surface of nanophotonic structures provides a dynamic system combining the strong atom-atom interactions mediated by guided mode photons with the exquisite control implemented with trapped atom systems. The hybrid system promises pair-wise tunability of long-range interactions between atomic pseudo spins, allowing studies of quantum magnetism extending far beyond nearest neighbor interactions. In this talk, we will discuss our current status developing high quality nanophotonic ring resonators, engineered on CMOS compatible optical chips with integrated nanostructures that, in combination with a side illuminating beam, can realize stable atom traps approximately 100nm above the surface. We will report on our progress towards loading arrays of cold atoms near the surface of these structures and studying atom-atom interaction mediated by photons with high cooperativity.

Composition measurement in substitutionally disordered materials by atomic resolution energy dispersive X-ray spectroscopy in scanning transmission electron microscopy.

PubMed

Chen, Z; Taplin, D J; Weyland, M; Allen, L J; Findlay, S D

2017-05-01

The increasing use of energy dispersive X-ray spectroscopy in atomic resolution scanning transmission electron microscopy invites the question of whether its success in precision composition determination at lower magnifications can be replicated in the atomic resolution regime. In this paper, we explore, through simulation, the prospects for composition measurement via the model system of Al x Ga 1-x As, discussing the approximations used in the modelling, the variability in the signal due to changes in configuration at constant composition, and the ability to distinguish between different compositions. Results are presented in such a way that the number of X-ray counts, and thus the expected variation due to counting statistics, can be gauged for a range of operating conditions. Copyright © 2016 Elsevier B.V. All rights reserved.

Combinatorial effects on clumped isotopes and their significance in biogeochemistry

NASA Astrophysics Data System (ADS)

Yeung, Laurence Y.

2016-01-01

The arrangement of isotopes within a collection of molecules records their physical and chemical histories. Clumped-isotope analysis interrogates these arrangements, i.e., how often rare isotopes are bound together, which in many cases can be explained by equilibrium and/or kinetic isotope fractionation. However, purely combinatorial effects, rooted in the statistics of pairing atoms in a closed system, are also relevant, and not well understood. Here, I show that combinatorial isotope effects are most important when two identical atoms are neighbors on the same molecule (e.g., O2, N2, and D-D clumping in CH4). When the two halves of an atom pair are either assembled with different isotopic preferences or drawn from different reservoirs, combinatorial effects cause depletions in clumped-isotope abundance that are most likely between zero and -1‰, although they could potentially be -10‰ or larger for D-D pairs. These depletions are of similar magnitude, but of opposite sign, to low-temperature equilibrium clumped-isotope effects for many small molecules. Enzymatic isotope-pairing reactions, which can have site-specific isotopic fractionation factors and atom reservoirs, should express this class of combinatorial isotope effect, although it is not limited to biological reactions. Chemical-kinetic isotope effects, which are related to a bond-forming transition state, arise independently and express second-order combinatorial effects related to the abundance of the rare isotope. Heteronuclear moeties (e.g., Csbnd O and Csbnd H), are insensitive to direct combinatorial influences, but secondary combinatorial influences are evident. In general, both combinatorial and chemical-kinetic factors are important for calculating and interpreting clumped-isotope signatures of kinetically controlled reactions. I apply this analytical framework to isotope-pairing reactions relevant to geochemical oxygen, carbon, and nitrogen cycling that may be influenced by combinatorial clumped-isotope effects. These isotopic signatures, manifest as either directly bound isotope ;clumps; or as features of a molecule's isotopic anatomy, are linked to molecular mechanisms and may eventually provide additional information about biogeochemical cycling on environmentally relevant spatial scales.

Atomic scale imaging of magnetic circular dichroism by achromatic electron microscopy.

PubMed

Wang, Zechao; Tavabi, Amir H; Jin, Lei; Rusz, Ján; Tyutyunnikov, Dmitry; Jiang, Hanbo; Moritomo, Yutaka; Mayer, Joachim; Dunin-Borkowski, Rafal E; Yu, Rong; Zhu, Jing; Zhong, Xiaoyan

2018-03-01

In order to obtain a fundamental understanding of the interplay between charge, spin, orbital and lattice degrees of freedom in magnetic materials and to predict and control their physical properties 1-3 , experimental techniques are required that are capable of accessing local magnetic information with atomic-scale spatial resolution. Here, we show that a combination of electron energy-loss magnetic chiral dichroism 4 and chromatic-aberration-corrected transmission electron microscopy, which reduces the focal spread of inelastically scattered electrons by orders of magnitude when compared with the use of spherical aberration correction alone, can achieve atomic-scale imaging of magnetic circular dichroism and provide element-selective orbital and spin magnetic moments atomic plane by atomic plane. This unique capability, which we demonstrate for Sr 2 FeMoO 6 , opens the door to local atomic-level studies of spin configurations in a multitude of materials that exhibit different types of magnetic coupling, thereby contributing to a detailed understanding of the physical origins of magnetic properties of materials at the highest spatial resolution.

Atomic characterization of Si nanoclusters embedded in SiO2 by atom probe tomography

PubMed Central

2011-01-01

Silicon nanoclusters are of prime interest for new generation of optoelectronic and microelectronics components. Physical properties (light emission, carrier storage...) of systems using such nanoclusters are strongly dependent on nanostructural characteristics. These characteristics (size, composition, distribution, and interface nature) are until now obtained using conventional high-resolution analytic methods, such as high-resolution transmission electron microscopy, EFTEM, or EELS. In this article, a complementary technique, the atom probe tomography, was used for studying a multilayer (ML) system containing silicon clusters. Such a technique and its analysis give information on the structure at the atomic level and allow obtaining complementary information with respect to other techniques. A description of the different steps for such analysis: sample preparation, atom probe analysis, and data treatment are detailed. An atomic scale description of the Si nanoclusters/SiO2 ML will be fully described. This system is composed of 3.8-nm-thick SiO layers and 4-nm-thick SiO2 layers annealed 1 h at 900°C. PMID:21711666

Hydrogen atoms in protein structures: high-resolution X-ray diffraction structure of the DFPase

PubMed Central

2013-01-01

Background Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. Results A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. Conclusions A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism. PMID:23915572

Phase modulation atomic force microscope with true atomic resolution

NASA Astrophysics Data System (ADS)

Fukuma, Takeshi; Kilpatrick, Jason I.; Jarvis, Suzanne P.

2006-12-01

We have developed a dynamic force microscope (DFM) working in a novel operation mode which is referred to as phase modulation atomic force microscopy (PM-AFM). PM-AFM utilizes a fixed-frequency excitation signal to drive a cantilever, which ensures stable imaging even with occasional tip crash and adhesion to the surface. The tip-sample interaction force is detected as a change of the phase difference between the cantilever deflection and excitation signals and hence the time response is not influenced by the Q factor of the cantilever. These features make PM-AFM more suitable for high-speed imaging than existing DFM techniques such as amplitude modulation and frequency modulation atomic force microscopies. Here we present the basic principle of PM-AFM and the theoretical limit of its performance. The design of the developed PM-AFM is described and its theoretically limited noise performance is demonstrated. Finally, we demonstrate the true atomic resolution imaging capability of the developed PM-AFM by imaging atomic-scale features of mica in water.

Isotope analysis in the transmission electron microscope.

PubMed

Susi, Toma; Hofer, Christoph; Argentero, Giacomo; Leuthner, Gregor T; Pennycook, Timothy J; Mangler, Clemens; Meyer, Jannik C; Kotakoski, Jani

2016-10-10

The Ångström-sized probe of the scanning transmission electron microscope can visualize and collect spectra from single atoms. This can unambiguously resolve the chemical structure of materials, but not their isotopic composition. Here we differentiate between two isotopes of the same element by quantifying how likely the energetic imaging electrons are to eject atoms. First, we measure the displacement probability in graphene grown from either 12 C or 13 C and describe the process using a quantum mechanical model of lattice vibrations coupled with density functional theory simulations. We then test our spatial resolution in a mixed sample by ejecting individual atoms from nanoscale areas spanning an interface region that is far from atomically sharp, mapping the isotope concentration with a precision better than 20%. Although we use a scanning instrument, our method may be applicable to any atomic resolution transmission electron microscope and to other low-dimensional materials.

Photoionization Rate of Atomic Oxygen

NASA Astrophysics Data System (ADS)

Meier, R. R.; McLaughlin, B. M.; Warren, H. P.; Bishop, J.

2006-05-01

Accurate knowledge of the photoionization rate of atomic oxygen is important for the study and understanding of the ionospheres and emission processes of terrestrial, planetary, and cometary atmospheres. Past calculations of the photoionization rate have been carried out at various spectral resolutions, but none were at sufficiently high resolution to accommodate accidental resonances between solar emission lines and highly structured auto-ionization features in the photoionization cross section. A new version of the NRLEUV solar spectral irradiance model (at solar minimum) and a new model of the O photoionization cross section enable calculations at very high spectral resolution. We find unattenuated photoionization rates computed at 0.001 nm resolution are larger than those at moderate resolution (0.1 nm) by amounts approaching 20%. Allowing for attenuation in the terrestrial atmosphere, we find differences in photoionization rates computed at high and moderate resolution to vary with altitude, especially below 200 km where deviations of plus or minus 20% occur between the two cases.

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

Sato, Toyoto; Tomiyasu, Dr. Keisuke; Ikeda, Kazutaka

Local atomic structural investigations of LiAlD4, which is composed of Li+ and [AlD4], at 40 300 K were studied by total neutron scattering combined with pair distribution function (PDF) analysis for understanding of hydrogen release from LiAlD4. The results showed that the Al D pair distribution almost unchanged, while the Li D pair distribution clearly started to broaden and shrink above 200 250 K. The shrinking of the Li D pair distribution might lead to the local generation of LiD, which was speculated as the precursory phenomenon for the hydrogen release from LiAlD4.

High Resolution Numerical Simulations of Primary Atomization in Diesel Sprays with Single Component Reference Fuels

DTIC Science & Technology

2015-09-01

NC. 14. ABSTRACT A high-resolution numerical simulation of jet breakup and spray formation from a complex diesel fuel injector at diesel engine... diesel fuel injector at diesel engine type conditions has been performed. A full understanding of the primary atomization process in diesel fuel... diesel liquid sprays the complexity is further compounded by the physical attributes present including nozzle turbulence, large density ratios

Generation of non-classical correlated photon pairs via a ladder-type atomic configuration: theory and experiment.

PubMed

Ding, Dong-Sheng; Zhou, Zhi-Yuan; Shi, Bao-Sen; Zou, Xu-Bo; Guo, Guang-Can

2012-05-07

We experimentally generate a non-classical correlated two-color photon pair at 780 and 1529.4 nm in a ladder-type configuration using a hot 85Rb atomic vapor with the production rate of ~10(7)/s. The non-classical correlation between these two photons is demonstrated by strong violation of Cauchy-Schwarz inequality by the factor R = 48 ± 12. Besides, we experimentally investigate the relations between the correlation and some important experimental parameters such as the single-photon detuning, the powers of pumps. We also make a theoretical analysis in detail and the theoretical predictions are in reasonable agreement with our experimental results.

Relative Stabilities and Reactivities of Isolated Versus Conjugated Alkenes: Reconciliation Via a Molecular Orbital Approach

NASA Astrophysics Data System (ADS)

Sotiriou-Leventis, Chariklia; Hanna, Samir B.; Leventis, Nicholas

1996-04-01

The well-accepted practice of generating a pair of molecular orbitals, one of lower energy and another of higher energy than the original pair of overlapping atomic orbitals, and the concept of a particle in a one-dimensional box are implemented in a simplified, nonmathematical method that explains the relative stabilities and reactivities of alkenes with conjugated versus isolated double bonds. In this method, Huckel-type MO's of higher polyenes are constructed by energy rules of linear combination of atomic orbitals. One additional rule is obeyed: bonding molecular orbitals overlap only with bonding molecular orbitals, and antibonding molecular orbitals overlap only with antibonding molecular orbitals.

Atomic force microscopy as a tool for the investigation of living cells.

PubMed

Morkvėnaitė-Vilkončienė, Inga; Ramanavičienė, Almira; Ramanavičius, Arūnas

2013-01-01

Atomic force microscopy is a valuable and useful tool for the imaging and investigation of living cells in their natural environment at high resolution. Procedures applied to living cell preparation before measurements should be adapted individually for different kinds of cells and for the desired measurement technique. Different ways of cell immobilization, such as chemical fixation on the surface, entrapment in the pores of a membrane, or growing them directly on glass cover slips or on plastic substrates, result in the distortion or appearance of artifacts in atomic force microscopy images. Cell fixation allows the multiple use of samples and storage for a prolonged period; it also increases the resolution of imaging. Different atomic force microscopy modes are used for the imaging and analysis of living cells. The contact mode is the best for cell imaging because of high resolution, but it is usually based on the following: (i) image formation at low interaction force, (ii) low scanning speed, and (iii) usage of "soft," low resolution cantilevers. The tapping mode allows a cell to behave like a very solid material, and destructive shear forces are minimized, but imaging in liquid is difficult. The force spectroscopy mode is used for measuring the mechanical properties of cells; however, obtained results strongly depend on the cell fixation method. In this paper, the application of 3 atomic force microscopy modes including (i) contact, (ii) tapping, and (iii) force spectroscopy for the investigation of cells is described. The possibilities of cell preparation for the measurements, imaging, and determination of mechanical properties of cells are provided. The applicability of atomic force microscopy to diagnostics and other biomedical purposes is discussed.

Atomic-Scale Nuclear Spin Imaging Using Quantum-Assisted Sensors in Diamond

NASA Astrophysics Data System (ADS)

Ajoy, A.; Bissbort, U.; Lukin, M. D.; Walsworth, R. L.; Cappellaro, P.

2015-01-01

Nuclear spin imaging at the atomic level is essential for the understanding of fundamental biological phenomena and for applications such as drug discovery. The advent of novel nanoscale sensors promises to achieve the long-standing goal of single-protein, high spatial-resolution structure determination under ambient conditions. In particular, quantum sensors based on the spin-dependent photoluminescence of nitrogen-vacancy (NV) centers in diamond have recently been used to detect nanoscale ensembles of external nuclear spins. While NV sensitivity is approaching single-spin levels, extracting relevant information from a very complex structure is a further challenge since it requires not only the ability to sense the magnetic field of an isolated nuclear spin but also to achieve atomic-scale spatial resolution. Here, we propose a method that, by exploiting the coupling of the NV center to an intrinsic quantum memory associated with the nitrogen nuclear spin, can reach a tenfold improvement in spatial resolution, down to atomic scales. The spatial resolution enhancement is achieved through coherent control of the sensor spin, which creates a dynamic frequency filter selecting only a few nuclear spins at a time. We propose and analyze a protocol that would allow not only sensing individual spins in a complex biomolecule, but also unraveling couplings among them, thus elucidating local characteristics of the molecule structure.

Elemental Identification by Combining Atomic Force Microscopy and Kelvin Probe Force Microscopy.

PubMed

Schulz, Fabian; Ritala, Juha; Krejčí, Ondrej; Seitsonen, Ari Paavo; Foster, Adam S; Liljeroth, Peter

2018-06-01

There are currently no experimental techniques that combine atomic-resolution imaging with elemental sensitivity and chemical fingerprinting on single molecules. The advent of using molecular-modified tips in noncontact atomic force microscopy (nc-AFM) has made it possible to image (planar) molecules with atomic resolution. However, the mechanisms responsible for elemental contrast with passivated tips are not fully understood. Here, we investigate elemental contrast by carrying out both nc-AFM and Kelvin probe force microscopy (KPFM) experiments on epitaxial monolayer hexagonal boron nitride (hBN) on Ir(111). The hBN overlayer is inert, and the in-plane bonds connecting nearest-neighbor boron and nitrogen atoms possess strong covalent character and a bond length of only ∼1.45 Å. Nevertheless, constant-height maps of both the frequency shift Δ f and the local contact potential difference exhibit striking sublattice asymmetry. We match the different atomic sites with the observed contrast by comparison with nc-AFM image simulations based on the density functional theory optimized hBN/Ir(111) geometry, which yields detailed information on the origin of the atomic-scale contrast.

Hydrogen ADPs with Cu Kα data? Invariom and Hirshfeld atom modelling of fluconazole.

PubMed

Orben, Claudia M; Dittrich, Birger

2014-06-01

For the structure of fluconazole [systematic name: 2-(2,4-difluorophenyl)-1,3-bis(1H-1,2,4-triazol-1-yl)propan-2-ol] monohydrate, C13H12F2N6O·H2O, a case study on different model refinements is reported, based on single-crystal X-ray diffraction data measured at 100 K with Cu Kα radiation to a resolution of sin θ/λ of 0.6 Å(-1). The structure, anisotropic displacement parameters (ADPs) and figures of merit from the independent atom model are compared to `invariom' and `Hirshfeld atom' refinements. Changing from a spherical to an aspherical atom model lowers the figures of merit and improves both the accuracy and the precision of the geometrical parameters. Differences between results from the two aspherical-atom refinements are small. However, a refinement of ADPs for H atoms is only possible with the Hirshfeld atom density model. It gives meaningful results even at a resolution of 0.6 Å(-1), but requires good low-order data.

Scanning Transmission Electron Microscopy at High Resolution

PubMed Central

Wall, J.; Langmore, J.; Isaacson, M.; Crewe, A. V.

1974-01-01

We have shown that a scanning transmission electron microscope with a high brightness field emission source is capable of obtaining better than 3 Å resolution using 30 to 40 keV electrons. Elastic dark field images of single atoms of uranium and mercury are shown which demonstrate this fact as determined by a modified Rayleigh criterion. Point-to-point micrograph resolution between 2.5 and 3.0 Å is found in dark field images of micro-crystallites of uranium and thorium compounds. Furthermore, adequate contrast is available to observe single atoms as light as silver. Images PMID:4521050

Challenge of representing entropy at different levels of resolution in molecular simulation.

PubMed

Huang, Wei; van Gunsteren, Wilfred F

2015-01-22

The role of entropic contributions in processes involving biomolecules is illustrated using the process of vaporization or condensation of the solvents water and methanol and the process of polypeptide folding in solution using molecular models at different levels of resolution: subatomic, atomic, supra-atomic, and supramolecular. For the folding process, a β-hexapeptide that adopts, as inferred from NMR experiments, both a right-handed 2.710/12-helical fold and a left-handed 314-helical fold in methanol, is used to illustrate the challenge of modeling thermodynamically driven processes at different levels of resolution.

Low-temperature field ion microscopy of carbon nanotubes

NASA Astrophysics Data System (ADS)

Ksenofontov, V. A.; Gurin, V. A.; Gurin, I. V.; Kolosenko, V. V.; Mikhailovskij, I. M.; Sadanov, E. V.; Mazilova, T. I.; Velikodnaya, O. A.

2007-10-01

The methods of high-resolution field ion microscopy with sample cooling to liquid helium temperature are used in a study of the products of gas-phase catalytic pyrolysis of hydrocarbons in the form of graphitized fibers containing carbon nanotubes. Full atomic resolution of the end cap of closed carbon nanotubes is achieved for the first time. It is found that the atomic structure of the tops of the caps of subnanometer carbon tubes consists predominantly of hexagonal rings. A possible reason for the improvement of the resolution of field ion images of nanotubes upon deep cooling is discussed.

Analytical SuperSTEM for extraterrestrial materials research

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

Bradley, J P; Dai, Z R

2009-09-08

Electron-beam studies of extraterrestrial materials with significantly improved spatial resolution, energy resolution and sensitivity are enabled using a 300 keV SuperSTEM scanning transmission electron microscope with a monochromator and two spherical aberration correctors. The improved technical capabilities enable analyses previously not possible. Mineral structures can be directly imaged and analyzed with single-atomic-column resolution, liquids and implanted gases can be detected, and UV-VIS optical properties can be measured. Detection limits for minor/trace elements in thin (<100 nm thick) specimens are improved such that quantitative measurements of some extend to the sub-500 ppm level. Electron energy-loss spectroscopy (EELS) can be carried outmore » with 0.10-0.20 eV energy resolution and atomic-scale spatial resolution such that variations in oxidation state from one atomic column to another can be detected. Petrographic mapping is extended down to the atomic scale using energy-dispersive x-ray spectroscopy (EDS) and energy-filtered transmission electron microscopy (EFTEM) imaging. Technical capabilities and examples of the applications of SuperSTEM to extraterrestrial materials are presented, including the UV spectral properties and organic carbon K-edge fine structure of carbonaceous matter in interplanetary dust particles (IDPs), x-ray elemental maps showing the nanometer-scale distribution of carbon within GEMS (glass with embedded metal and sulfides), the first detection and quantification of trace Ti in GEMS using EDS, and detection of molecular H{sub 2}O in vesicles and implanted H{sub 2} and He in irradiated mineral and glass grains.« less

Atom-bond electronegativity equalization method fused into molecular mechanics. I. A seven-site fluctuating charge and flexible body water potential function for water clusters.

PubMed

Yang, Zhong-Zhi; Wu, Yang; Zhao, Dong-Xia

2004-02-08

Recently, experimental and theoretical studies on the water system are very active and noticeable. A transferable intermolecular potential seven points approach including fluctuation charges and flexible body (ABEEM-7P) based on a combination of the atom-bond electronegativity equalization and molecular mechanics (ABEEM/MM), and its application to small water clusters are explored and tested in this paper. The consistent combination of ABEEM and molecular mechanics (MM) is to take the ABEEM charges of atoms, bonds, and lone-pair electrons into the intermolecular electrostatic interaction term in molecular mechanics. To examine the charge transfer we have used two models coming from the charge constraint types: one is a charge neutrality constraint on whole water system and the other is on each water molecule. Compared with previous water force fields, the ABEEM-7P model has two characters: (1) the ABEEM-7P model not only presents the electrostatic interaction of atoms, bonds and lone-pair electrons and their changing in respond to different ambient environment but also introduces "the hydrogen bond interaction region" in which a new parameter k(lp,H)(R(lp,H)) is used to describe the electrostatic interaction of the lone-pair electron and the hydrogen atom which can form the hydrogen bond; (2) nonrigid but flexible water body permitting the vibration of the bond length and angle is allowed due to the combination of ABEEM and molecular mechanics, and for van der Waals interaction the ABEEM-7P model takes an all atom-atom interaction, i.e., oxygen-oxygen, hydrogen-hydrogen, oxygen-hydrogen interaction into account. The ABEEM-7P model based on ABEEM/MM gives quite accurate predictions for gas-phase state properties of the small water clusters (H(2)O)(n) (n=2-6), such as optimized geometries, monomer dipole moments, vibrational frequencies, and cluster interaction energies. Due to its explicit description of charges and the hydrogen bond, the ABEEM-7P model will be applied to discuss properties of liquid water, ice, aqueous solutions, and biological systems.

SIRIUS. An automated method for the analysis of the preferred packing arrangements between protein groups.

PubMed

Singh, J; Thornton, J M

1990-02-05

Automated methods have been developed to determine the preferred packing arrangement between interacting protein groups. A suite of FORTRAN programs, SIRIUS, is described for calculating and analysing the geometries of interacting protein groups using crystallographically derived atomic co-ordinates. The programs involved in calculating the geometries search for interacting pairs of protein groups using a distance criterion, and then calculate the spatial disposition and orientation of the pair. The second set of programs is devoted to analysis. This involves calculating the observed and expected distributions of the angles and assessing the statistical significance of the difference between the two. A database of the geometries of the 400 combinations of side-chain to side-chain interaction has been created. The approach used in analysing the geometrical information is illustrated here with specific examples of interactions between side-chains, peptide groups and particular types of atom. At the side-chain level, an analysis of aromatic-amino interactions, and the interactions of peptide carbonyl groups with arginine residues is presented. At the atomic level the analyses include the spatial disposition of oxygen atoms around tyrosine residues, and the frequency and type of contact between carbon, nitrogen and oxygen atoms. This information is currently being applied to the modelling of protein interactions.

Investigating the importance of Delaunay-based definition of atomic interactions in scoring of protein-protein docking results.

PubMed

Jafari, Rahim; Sadeghi, Mehdi; Mirzaie, Mehdi

2016-05-01

The approaches taken to represent and describe structural features of the macromolecules are of major importance when developing computational methods for studying and predicting their structures and interactions. This study attempts to explore the significance of Delaunay tessellation for the definition of atomic interactions by evaluating its impact on the performance of scoring protein-protein docking prediction. Two sets of knowledge-based scoring potentials are extracted from a training dataset of native protein-protein complexes. The potential of the first set is derived using atomic interactions extracted from Delaunay tessellated structures. The potential of the second set is calculated conventionally, that is, using atom pairs whose interactions were determined by their separation distances. The scoring potentials were tested against two different docking decoy sets and their performances were compared. The results show that, if properly optimized, the Delaunay-based scoring potentials can achieve higher success rate than the usual scoring potentials. These results and the results of a previous study on the use of Delaunay-based potentials in protein fold recognition, all point to the fact that Delaunay tessellation of protein structure can provide a more realistic definition of atomic interaction, and therefore, if appropriately utilized, may be able to improve the accuracy of pair potentials. Copyright © 2016 Elsevier Inc. All rights reserved.

The architecture of amyloid-like peptide fibrils revealed by X-ray scattering, diffraction and electron microscopy

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

Langkilde, Annette E., E-mail: annette.langkilde@sund.ku.dk; Morris, Kyle L.; Serpell, Louise C.

The aggregation process and the fibril state of an amyloidogenic peptide suggest monomer addition to be the prevailing mechanism of elongation and a model of the peptide packing in the fibrils has been obtained. Structural analysis of protein fibrillation is inherently challenging. Given the crucial role of fibrils in amyloid diseases, method advancement is urgently needed. A hybrid modelling approach is presented enabling detailed analysis of a highly ordered and hierarchically organized fibril of the GNNQQNY peptide fragment of a yeast prion protein. Data from small-angle X-ray solution scattering, fibre diffraction and electron microscopy are combined with existing high-resolution X-raymore » crystallographic structures to investigate the fibrillation process and the hierarchical fibril structure of the peptide fragment. The elongation of these fibrils proceeds without the accumulation of any detectable amount of intermediate oligomeric species, as is otherwise reported for, for example, glucagon, insulin and α-synuclein. Ribbons constituted of linearly arranged protofilaments are formed. An additional hierarchical layer is generated via the pairing of ribbons during fibril maturation. Based on the complementary data, a quasi-atomic resolution model of the protofilament peptide arrangement is suggested. The peptide structure appears in a β-sheet arrangement reminiscent of the β-zipper structures evident from high-resolution crystal structures, with specific differences in the relative peptide orientation. The complexity of protein fibrillation and structure emphasizes the need to use multiple complementary methods.« less

Design and evaluation of precise current integrator for scanning probe microscopy

NASA Astrophysics Data System (ADS)

Raczkowski, Kamil; Piasecki, Tomasz; Rudek, Maciej; Gotszalk, Teodor

2017-03-01

Several of the scanning probe microscopy (SPM) techniques, such as the scanning tunnelling microscopy (STM) or conductive atomic force microscopy (C-AFM), rely on precise measurements of current flowing between the investigated sample and the conductive nanoprobe. The parameters of current-to-voltage converter (CVC), which should detect current in the picompere range, are of utmost importance to those systems as they determine the microscopes’ measuring capabilities. That was the motivation for research on the precise current integrator (PCI), described in this paper, which could be used as the CVC in the C-AFM systems. The main design goal of the PCI was to provide a small and versatile device with the sub-picoampere level resolution with high dynamic range in the order of nanoamperes. The PCI was based on the integrating amplifier (Texas Instruments DDC112) paired with a STM32F4 microcontroller unit (MCU).The gain and bandwidth of the PCI might be easily changed by varying the integration time and the feedback capacitance. Depending on these parameters it was possible to obtain for example the 2.15 pA resolution at 688 nA range with 1 kHz bandwidth or 7.4 fA resolution at 0.98 nA range with 10 Hz bandwidth. The measurement of sinusoidal current with 28 fA amplitude was also presented. The PCI was integrated with the C-AFM system and used in the highly ordered pyrolytic graphite (HOPG) and graphene samples imaging.

Knowledge-Based Elastic Potentials for Docking Drugs or Proteins with Nucleic Acids

PubMed Central

Ge, Wei; Schneider, Bohdan; Olson, Wilma K.

2005-01-01

Elastic ellipsoidal functions defined by the observed hydration patterns around the DNA bases provide a new basis for measuring the recognition of ligands in the grooves of double-helical structures. Here a set of knowledge-based potentials suitable for quantitative description of such behavior is extracted from the observed positions of water molecules and amino acid atoms that form hydrogen bonds with the nitrogenous bases in high resolution crystal structures. Energies based on the displacement of hydrogen-bonding sites on drugs in DNA-crystal complexes relative to the preferred locations of water binding around the heterocyclic bases are low, pointing to the reliability of the potentials and the apparent displacement of water molecules by drug atoms in these structures. The validity of the energy functions has been further examined in a series of sequence substitution studies based on the structures of DNA bound to polyamides that have been designed to recognize the minor-groove edges of Watson-Crick basepairs. The higher energies of binding to incorrect sequences superimposed (without conformational adjustment or displacement of polyamide ligands) on observed high resolution structures confirm the hypothesis that the drug subunits associate with specific DNA bases. The knowledge-based functions also account satisfactorily for the measured free energies of DNA-polyamide association in solution and the observed sites of polyamide binding on nucleosomal DNA. The computations are generally consistent with mechanisms by which minor-groove binding ligands are thought to recognize DNA basepairs. The calculations suggest that the asymmetric distributions of hydrogen-bond-forming atoms on the minor-groove edge of the basepairs may underlie ligand discrimination of G·C from C·G pairs, in addition to the commonly believed role of steric hindrance. The analysis of polyamide-bound nucleosomal structures reveals other discrepancies in the expected chemical design, including unexpected contacts to DNA and modified basepair targets of some ligands. The ellipsoidal potentials thus appear promising as a mathematical tool for the study of drug- and protein-DNA interactions and for gaining new insights into DNA-binding mechanisms. PMID:15501936

Average and local atomic-scale structure in BaZrxTi(1-x)O3 (x = 0. 10, 0.20, 0.40) ceramics by high-energy x-ray diffraction and Raman spectroscopy.

PubMed

Buscaglia, Vincenzo; Tripathi, Saurabh; Petkov, Valeri; Dapiaggi, Monica; Deluca, Marco; Gajović, Andreja; Ren, Yang

2014-02-12

High-resolution x-ray diffraction (XRD), Raman spectroscopy and total scattering XRD coupled to atomic pair distribution function (PDF) analysis studies of the atomic-scale structure of archetypal BaZrxTi(1-x)O3 (x = 0.10, 0.20, 0.40) ceramics are presented over a wide temperature range (100-450 K). For x = 0.1 and 0.2 the results reveal, well above the Curie temperature, the presence of Ti-rich polar clusters which are precursors of a long-range ferroelectric order observed below TC. Polar nanoregions (PNRs) and relaxor behaviour are observed over the whole temperature range for x = 0.4. Irrespective of ceramic composition, the polar clusters are due to locally correlated off-centre displacement of Zr/Ti cations compatible with local rhombohedral symmetry. Formation of Zr-rich clusters is indicated by Raman spectroscopy for all compositions. Considering the isovalent substitution of Ti with Zr in BaZrxTi1-xO3, the mechanism of formation and growth of the PNRs is not due to charge ordering and random fields, but rather to a reduction of the local strain promoted by the large difference in ion size between Zr(4+) and Ti(4+). As a result, non-polar or weakly polar Zr-rich clusters and polar Ti-rich clusters are randomly distributed in a paraelectric lattice and the long-range ferroelectric order is disrupted with increasing Zr concentration.

Facet Dependent Disorder in the Pristine High Voltage Lithium-Manganese-Rich Cathode Material

DOE PAGES

Dixit, Hemant M.; Zhou, Wu; Idrobo Tapia, Juan Carlos; ...

2014-11-21

Defects and surface reconstructions are thought to be crucial for the long term stability of high-voltage lithium-manganese-rich cathodes. Unfortunately, many of these defects arise only after electrochemical cycling which occur under harsh conditions making it difficult to fully comprehend the role they play in degrading material performance. Recently, it has been observed that defects are present even in the pristine material. This study, therefore, focuses on examining the nature of the disorder observed in pristine Limore » $$_{1.2}$$Ni$$_{0.175}$$Mn$$_{0.525}$$Co$$_{0.1}$$O$$_2$$ (LNMCO) particles. Using atomic resolution Z-contrast imaging and electron energy-loss spectroscopy measurements we show that there are indeed a significant amount of anti-site defects present in this material; with transition metals substituting on Li metal sites. Furthermore, we find a strong tendency of segregation of these types of defects towards open facets (surfaces perpendicular to the layered arrangement of atoms), rather than closed facets (surfaces parallel to the layered arrangement of atoms). First principles calculations identify anti-site defect pairs of Ni swapping with Li ions as the predominant defect in the material. Furthermore, energetically favorable swapping of Ni on the Mn sites were observed to lead to Mn depletion at open facets. Relatively, low Ni migration barriers also support the notion that Ni are the predominant cause of disorder. These insights suggests that certain facets of the LNMCO particles may be more useful for inhibiting surface reconstruction and improving the stability of these materials through careful consideration of the exposed surface.« less

Structure of liquid tricalcium aluminate

NASA Astrophysics Data System (ADS)

Drewitt, James W. E.; Barnes, Adrian C.; Jahn, Sandro; Kohn, Simon C.; Walter, Michael J.; Novikov, Alexey N.; Neuville, Daniel R.; Fischer, Henry E.; Hennet, Louis

2017-02-01

The atomic-scale structure of aerodynamically levitated and laser-heated liquid tricalcium aluminate (Ca3Al2O6 ) was measured at 2073(30) K by using the method of neutron diffraction with Ca isotope substitution (NDIS). The results enable the detailed resolution of the local coordination environment around calcium and aluminum atoms, including the direct determination of the liquid partial structure factor, SCaCa(Q ) , and partial pair distribution function, gCaCa(r ) . Molecular dynamics (MD) simulation and reverse Monte Carlo (RMC) refinement methods were employed to obtain a detailed atomistic model of the liquid structure. The composition Ca3Al2O6 lies at the CaO-rich limit of the CaO:Al2O3 glass-forming system. Our results show that, although significantly depolymerized, liquid Ca3Al2O6 is largely composed of AlO4 tetrahedra forming an infinite network with a slightly higher fraction of bridging oxygen atoms than expected for the composition. Calcium-centered polyhedra exhibit a wide distribution of four- to sevenfold coordinated sites, with higher coordinated calcium preferentially bonding to bridging oxygens. Analysis of the MD configuration reveals the presence of ˜10 % unconnected AlO4 monomers and Al2O7 dimers in the liquid. As the CaO concentration increases, the number of these isolated units increases, such that the upper value for the glass-forming composition of CaO:Al2O3 liquids could be described in terms of a percolation threshold at which the glass can no longer support the formation of an infinitely connected AlO4 network.

Statistical analysis of dimer formation in supersaturated metal vapor based on molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Korenchenko, Anna E.; Vorontsov, Alexander G.; Gelchinski, Boris R.; Sannikov, Grigorii P.

2018-04-01

We discuss the problem of dimer formation during the homogeneous nucleation of atomic metal vapor in an inert gas environment. We simulated nucleation with molecular dynamics and carried out the statistical analysis of double- and triple-atomic collisions as the two ways of long-lived diatomic complex formation. Close pair of atoms with lifetime greater than the mean time interval between atom-atom collisions is called a long-lived diatomic complex. We found that double- and triple-atomic collisions gave approximately the same probabilities of long-lived diatomic complex formation, but internal energy of the resulted state was essentially lower in the second case. Some diatomic complexes formed in three-particle collisions are stable enough to be a critical nucleus.

Microcavities coupled to multilevel atoms

NASA Astrophysics Data System (ADS)

Schmid, Sandra Isabelle; Evers, Jörg

2011-11-01

A three-level atom in the Λ configuration coupled to a microcavity is studied. The two transitions of the atom are assumed to couple to different counterpropagating mode pairs in the cavity. We analyze the dynamics both in the strong-coupling and the bad-cavity limits. We find that, compared to a two-level setup, the third atomic state and the additional control field modes crucially modify the system dynamics and enable more advanced control schemes. All results are explained using appropriate dressed-state and eigenmode representations. As potential applications, we discuss optical switching and turnstile operations and detection of particles close to the resonator surface.

Instrumental requirements for the detection of electron beam-induced object excitations at the single atom level in high-resolution transmission electron microscopy.

PubMed

Kisielowski, C; Specht, P; Gygax, S M; Barton, B; Calderon, H A; Kang, J H; Cieslinski, R

2015-01-01

This contribution touches on essential requirements for instrument stability and resolution that allows operating advanced electron microscopes at the edge to technological capabilities. They enable the detection of single atoms and their dynamic behavior on a length scale of picometers in real time. It is understood that the observed atom dynamic is intimately linked to the relaxation and thermalization of electron beam-induced sample excitation. Resulting contrast fluctuations are beam current dependent and largely contribute to a contrast mismatch between experiments and theory if not considered. If explored, they open the possibility to study functional behavior of nanocrystals and single molecules at the atomic level in real time. Copyright © 2014 Elsevier Ltd. All rights reserved.

Tools for Model Building and Optimization into Near-Atomic Resolution Electron Cryo-Microscopy Density Maps.

PubMed

DiMaio, F; Chiu, W

2016-01-01

Electron cryo-microscopy (cryoEM) has advanced dramatically to become a viable tool for high-resolution structural biology research. The ultimate outcome of a cryoEM study is an atomic model of a macromolecule or its complex with interacting partners. This chapter describes a variety of algorithms and software to build a de novo model based on the cryoEM 3D density map, to optimize the model with the best stereochemistry restraints and finally to validate the model with proper protocols. The full process of atomic structure determination from a cryoEM map is described. The tools outlined in this chapter should prove extremely valuable in revealing atomic interactions guided by cryoEM data. © 2016 Elsevier Inc. All rights reserved.

Theory of a Quantum Scanning Microscope for Cold Atoms

NASA Astrophysics Data System (ADS)

Yang, D.; Laflamme, C.; Vasilyev, D. V.; Baranov, M. A.; Zoller, P.

2018-03-01

We propose and analyze a scanning microscope to monitor "live" the quantum dynamics of cold atoms in a cavity QED setup. The microscope measures the atomic density with subwavelength resolution via dispersive couplings to a cavity and homodyne detection within the framework of continuous measurement theory. We analyze two modes of operation. First, for a fixed focal point the microscope records the wave packet dynamics of atoms with time resolution set by the cavity lifetime. Second, a spatial scan of the microscope acts to map out the spatial density of stationary quantum states. Remarkably, in the latter case, for a good cavity limit, the microscope becomes an effective quantum nondemolition device, such that the spatial distribution of motional eigenstates can be measured backaction free in single scans, as an emergent quantum nondemolition measurement.

Theory of a Quantum Scanning Microscope for Cold Atoms.

PubMed

Yang, D; Laflamme, C; Vasilyev, D V; Baranov, M A; Zoller, P

2018-03-30

We propose and analyze a scanning microscope to monitor "live" the quantum dynamics of cold atoms in a cavity QED setup. The microscope measures the atomic density with subwavelength resolution via dispersive couplings to a cavity and homodyne detection within the framework of continuous measurement theory. We analyze two modes of operation. First, for a fixed focal point the microscope records the wave packet dynamics of atoms with time resolution set by the cavity lifetime. Second, a spatial scan of the microscope acts to map out the spatial density of stationary quantum states. Remarkably, in the latter case, for a good cavity limit, the microscope becomes an effective quantum nondemolition device, such that the spatial distribution of motional eigenstates can be measured backaction free in single scans, as an emergent quantum nondemolition measurement.

Ethene adsorption and dehydrogenation on clean and oxygen precovered Ni(111) studied by high resolution x-ray photoelectron spectroscopy

NASA Astrophysics Data System (ADS)

Lorenz, M. P. A.; Fuhrmann, T.; Streber, R.; Bayer, A.; Bebensee, F.; Gotterbarm, K.; Kinne, M.; Tränkenschuh, B.; Zhu, J. F.; Papp, C.; Denecke, R.; Steinrück, H.-P.

2010-07-01

The adsorption and thermal evolution of ethene (ethylene) on clean and oxygen precovered Ni(111) was investigated with high resolution x-ray photoelectron spectroscopy using synchrotron radiation at BESSY II. The high resolution spectra allow to unequivocally identify the local environment of individual carbon atoms. Upon adsorption at 110 K, ethene adsorbs in a geometry, where the two carbon atoms within the intact ethene molecule occupy nonequivalent sites, most likely hollow and on top; this new result unambiguously solves an old puzzle concerning the adsorption geometry of ethene on Ni(111). On the oxygen precovered surface a different adsorption geometry is found with both carbon atoms occupying equivalent hollow sites. Upon heating ethene on the clean surface, we can confirm the dehydrogenation to ethine (acetylene), which adsorbs in a geometry, where both carbon atoms occupy equivalent sites. On the oxygen precovered surface dehydrogenation of ethene is completely suppressed. For the identification of the adsorbed species and the quantitative analysis the vibrational fine structure of the x-ray photoelectron spectra was analyzed in detail.

Defects in oxide surfaces studied by atomic force and scanning tunneling microscopy

PubMed Central

König, Thomas; Simon, Georg H; Heinke, Lars; Lichtenstein, Leonid

2011-01-01

Summary Surfaces of thin oxide films were investigated by means of a dual mode NC-AFM/STM. Apart from imaging the surface termination by NC-AFM with atomic resolution, point defects in magnesium oxide on Ag(001) and line defects in aluminum oxide on NiAl(110), respectively, were thoroughly studied. The contact potential was determined by Kelvin probe force microscopy (KPFM) and the electronic structure by scanning tunneling spectroscopy (STS). On magnesium oxide, different color centers, i.e., F0, F+, F2+ and divacancies, have different effects on the contact potential. These differences enabled classification and unambiguous differentiation by KPFM. True atomic resolution shows the topography at line defects in aluminum oxide. At these domain boundaries, STS and KPFM verify F2+-like centers, which have been predicted by density functional theory calculations. Thus, by determining the contact potential and the electronic structure with a spatial resolution in the nanometer range, NC-AFM and STM can be successfully applied on thin oxide films beyond imaging the topography of the surface atoms. PMID:21977410

Reflections on the value of electron microscopy in the study of heterogeneous catalysts

PubMed Central

2017-01-01

Electron microscopy (EM) is arguably the single most powerful method of characterizing heterogeneous catalysts. Irrespective of whether they are bulk and multiphasic, or monophasic and monocrystalline, or nanocluster and even single-atom and on a support, their structures in atomic detail can be visualized in two or three dimensions, thanks to high-resolution instruments, with sub-Ångstrom spatial resolutions. Their topography, tomography, phase-purity, composition, as well as the bonding, and valence-states of their constituent atoms and ions and, in favourable circumstances, the short-range and long-range atomic order and dynamics of the catalytically active sites, can all be retrieved by the panoply of variants of modern EM. The latter embrace electron crystallography, rotation and precession electron diffraction, X-ray emission and high-resolution electron energy-loss spectra (EELS). Aberration-corrected (AC) transmission (TEM) and scanning transmission electron microscopy (STEM) have led to a revolution in structure determination. Environmental EM is already playing an increasing role in catalyst characterization, and new advances, involving special cells for the study of solid catalysts in contact with liquid reactants, have recently been deployed. PMID:28265196

A resolution measure for three-dimensional microscopy

PubMed Central

Chao, Jerry; Ram, Sripad; Abraham, Anish V.; Ward, E. Sally; Ober, Raimund J.

2009-01-01

A three-dimensional (3D) resolution measure for the conventional optical microscope is introduced which overcomes the drawbacks of the classical 3D (axial) resolution limit. Formulated within the context of a parameter estimation problem and based on the Cramer-Rao lower bound, this 3D resolution measure indicates the accuracy with which a given distance between two objects in 3D space can be determined from the acquired image. It predicts that, given enough photons from the objects of interest, arbitrarily small distances of separation can be estimated with prespecified accuracy. Using simulated images of point source pairs, we show that the maximum likelihood estimator is capable of attaining the accuracy predicted by the resolution measure. We also demonstrate how different factors, such as extraneous noise sources and the spatial orientation of the imaged object pair, can affect the accuracy with which a given distance of separation can be determined. PMID:20161040

Symmetric Resonance Charge Exchange Cross Section Based on Impact Parameter Treatment

NASA Technical Reports Server (NTRS)

Omidvar, Kazem; Murphy, Kendrah; Atlas, Robert (Technical Monitor)

2002-01-01

Using a two-state impact parameter approximation, a calculation has been carried out to obtain symmetric resonance charge transfer cross sections between nine ions and their parent atoms or molecules. Calculation is based on a two-dimensional numerical integration. The method is mostly suited for hydrogenic and some closed shell atoms. Good agreement has been obtained with the results of laboratory measurements for the ion-atom pairs H+-H, He+-He, and Ar+-Ar. Several approximations in a similar published calculation have been eliminated.

Controlling ferromagnetism of (In,Fe)As semiconductors by electron doping

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

Dang Vu, Nguyen; Fukushima, Tetsuya; Katayama-Yoshida, Hiroshi

2014-02-21

Based on experimental results, using the Korringa-Kohn-Rostoker coherent potential approximation (KKR-CPA) method and Monte Carlo simulation, we study the mechanism of ferromagnetic behavior of (In,Fe)As. We show that with doped Be atoms occupying in interstitial sites, chemical pair interactions between atoms and magnetic exchange interactions between Fe atoms change due to electron concentration. Therefore, by controlling the doping process, magnetic behavior of (In,Fe)As is controlled and ferromagnetism is observed in this semiconductor.

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

Zhou, Dan, E-mail: danzhou@is.mpg.de; Sigle, Wilfried; Wang, Yi

We studied ZrO{sub 2} − La{sub 2/3}Sr{sub 1/3}MnO{sub 3} pillar–matrix thin films which were found to show anomalous magnetic and electron transport properties. With the application of an aberration-corrected transmission electron microscope, interfacial chemistry, and atomic-arrangement of the system, especially of the pillar–matrix interface were revealed at atomic resolution. Minor amounts of Zr were found to occupy Mn positions within the matrix. The Zr concentration reaches a minimum near the pillar–matrix interface accompanied by oxygen vacancies. La and Mn diffusion into the pillar was revealed at atomic resolution and a concomitant change of the Mn valence state was observed.

Dual Resolution Images from Paired Fingerprint Cards

National Institute of Standards and Technology Data Gateway

NIST Dual Resolution Images from Paired Fingerprint Cards (Web, free access)   NIST Special Database 30 is being distributed for use in development and testing of fingerprint compression and fingerprint matching systems. The database allows the user to develop and evaluate data compression algorithms for fingerprint images scanned at both 19.7 ppmm (500 dpi) and 39.4 ppmm (1000 dpi). The data consist of 36 ten-print paired cards with both the rolled and plain images scanned at 19.7 and 39.4 pixels per mm. A newer version of the compression/decompression software on the CDROM can be found at the website http://www.nist.gov/itl/iad/ig/nigos.cfm as part of the NBIS package.

Molecular Dynamics Simulations of Grain Boundary and Bulk Diffusion in Metals.

NASA Astrophysics Data System (ADS)

Plimpton, Steven James

Diffusion is a microscopic mass transport mechanism that underlies many important macroscopic phenomena affecting the structural, electrical, and mechanical properties of metals. This thesis presents results from atomistic simulation studies of diffusion both in bulk and in the fast diffusion paths known as grain boundaries. Using the principles of molecular dynamics single boundaries are studied and their structure and dynamic properties characterized. In particular, tilt boundary bicrystal and bulk models of fcc Al and bcc alpha-Fe are simulated. Diffusion coefficients and activation energies for atomic motion are calculated for both models and compared to experimental data. The influence of the interatomic pair potential on the diffusion is studied in detail. A universal relation between the melting temperature that a pair potential induces in a simulated bulk model and the potential energy barrier height for atomic hopping is derived and used to correlate results for a wide variety of pair potentials. Using these techniques grain boundary and bulk diffusion coefficients for any fcc material can be estimated from simple static calculations without the need to perform more time-consuming dynamic simulations. The influences of two other factors on grain boundary diffusion are also studied because of the interest of the microelectronics industry in the diffusion related reliability problem known as electromigration. The first factor, known to affect the self diffusion rate of Al, is the presence of Cu impurity atoms in Al tilt boundaries. The bicrystal model for Al is seeded randomly with Cu atoms and a simple hybrid Morse potential used to model the Al-Cu interaction. While some effect due to the Cu is noted, it is concluded that pair potentials are likely an inadequate approximation for the alloy system. The second factor studied is the effect of the boundary orientation angle on the diffusion rate. Symmetric bcc Fe boundaries are relaxed to find optimal structures and their diffusion coefficients calculated. Good agreement is found with the dislocation pipe model for tilt boundary diffusion.

Atomic resolution ADF-STEM imaging of organic molecular crystal of halogenated copper phthalocyanine.

PubMed

Haruta, Mitsutaka; Yoshida, Kaname; Kurata, Hiroki; Isoda, Seiji

2008-05-01

Annular dark-field (ADF) scanning transmission electron microscopy (STEM) measurements are demonstrated for the first time to be applicable for acquiring Z-contrast images of organic molecules at atomic resolution. High-angle ADF imaging by STEM is a new technique that provides incoherent high-resolution Z-contrast images for organic molecules. In the present study, low-angle ADF-STEM is successfully employed to image the molecular crystal structure of hexadecachloro-Cu-phthalocyanine (Cl16-CuPc), an organic molecule. The structures of CuPc derivatives (polyhalogenated CuPc with Br and Cl) are determined quantitatively using the same technique to determine the occupancy of halogens at each chemical site. By comparing the image contrasts of atomic columns, the occupancy of Br is found to be ca. 56% at the inner position, slightly higher than that for random substitution and in good agreement with previous TEM results.

Evaluation of stacking faults and associated partial dislocations in AlSb/GaAs (001) interface by aberration-corrected high-resolution transmission electron microscopy

NASA Astrophysics Data System (ADS)

Wen, C.; Ge, B. H.; Cui, Y. X.; Li, F. H.; Zhu, J.; Yu, R.; Cheng, Z. Y.

2014-11-01

The stacking faults (SFs) in an AlSb/GaAs (001) interface were investigated using a 300 kV spherical aberration-corrected high-resolution transmission electron microscope (HRTEM). The structure and strain distribution of the single and intersecting (V-shaped) SFs associated with partial dislocations (PDs) were characterized by the [110] HRTEM images and geometric phase analysis, respectively. In the biaxial strain maps ɛxx and ɛyy, a SF can be divided into several sections under different strain states (positive or negative strain values). Furthermore, the strain state for the same section of a SF is in contrast to each other in ɛxx and ɛyy strain maps. The modification in the strain states was attributed to the variation in the local atomic displacements for the SF in the AlSb film on the GaAs substrate recorded in the lattice image. Finally, the single SF was found to be bounded by two 30° PDs. A pair of 30° PDs near the heteroepitaxial interface reacted to form a Lomer-Cottrell sessile dislocation located at the vertices of V-shaped SFs with opposite screw components. The roles of misfit dislocations, such as the PDs, in strain relaxation were also discussed.

High-resolution optical polarimetric elastography for measuring the mechanical properties of tissue

NASA Astrophysics Data System (ADS)

Hudnut, Alexa W.; Armani, Andrea M.

2018-02-01

Traditionally, chemical and molecular markers have been the predominate method in diagnostics. Recently, alternate methods of determining tissue and disease characteristics have been proposed based on testing the mechanical behavior of biomaterials. Existing methods for performing elastography measurements, such as atomic force microscopy, compression testing, and ultrasound elastography, require either extensive sample processing or have poor resolution. In the present work, we demonstrate an optical polarimetric elastography device to characterize the mechanical properties of salmon skeletal muscle. A fiber-coupled 1550nm laser paired with an optical polarizer is used to create a fiber optic sensing region. By measuring the change in polarization from the initial state to the final state within the fiber sensing region with a polarimeter, the loading-unloading curves can be determined for the biomaterial. The device is used to characterize the difference between samples with a range of collagen membranes. The loading-unloading curves are used to determine the change in polarization phase and energy loss of the samples at 10%, 20% and 30% strain. As expected, the energy loss is a better metric for measuring the mechanical properties of the tissues because it incorporates the entire loading-unloading curve rather than a single point. Using this metric, it is demonstrated the device can repeatedly differentiate between the different membrane configurations.

Trapping ultracold gases near cryogenic materials with rapid reconfigurability

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

Naides, Matthew A.; Turner, Richard W.; Lai, Ruby A.

We demonstrate an atom chip trapping system that allows the placement and high-resolution imaging of ultracold atoms within microns from any ≲100 μm-thin, UHV-compatible material, while also allowing sample exchange with minimal experimental downtime. The sample is not connected to the atom chip, allowing rapid exchange without perturbing the atom chip or laser cooling apparatus. Exchange of the sample and retrapping of atoms has been performed within a week turnaround, limited only by chamber baking. Moreover, the decoupling of sample and atom chip provides the ability to independently tune the sample temperature and its position with respect to the trapped ultracoldmore » gas, which itself may remain in the focus of a high-resolution imaging system. As a first demonstration of this system, we have confined a 700-nK cloud of 8 × 10{sup 4} {sup 87}Rb atoms within 100 μm of a gold-mirrored 100-μm-thick silicon substrate. The substrate was cooled to 35 K without use of a heat shield, while the atom chip, 120 μm away, remained at room temperature. Atoms may be imaged and retrapped every 16 s, allowing rapid data collection.« less

Scheme for generating the singlet state of three atoms trapped in distant cavities coupled by optical fibers

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

Wang, Dong-Yang; Wen, Jing-Ji; Bai, Cheng-Hua

2015-09-15

An effective scheme is proposed to generate the singlet state with three four-level atoms trapped in three distant cavities connected with each other by three optical fibers, respectively. After a series of appropriate atom–cavity interactions, which can be arbitrarily controlled via the selective pairing of Raman transitions and corresponding optical switches, a three-atom singlet state can be successfully generated. The influence of atomic spontaneous decay, photon leakage of cavities and optical fibers on the fidelity of the state is numerically simulated showing that the three-atom singlet state can be generated with high fidelity by choosing the experimental parameters appropriately.

Fast computation of high energy elastic collision scattering angle for electric propulsion plume simulation

NASA Astrophysics Data System (ADS)

Araki, Samuel J.

2016-11-01

In the plumes of Hall thrusters and ion thrusters, high energy ions experience elastic collisions with slow neutral atoms. These collisions involve a process of momentum exchange, altering the initial velocity vectors of the collision pair. In addition to the momentum exchange process, ions and atoms can exchange electrons, resulting in slow charge-exchange ions and fast atoms. In these simulations, it is particularly important to accurately perform computations of ion-atom elastic collisions in determining the plume current profile and assessing the integration of spacecraft components. The existing models are currently capable of accurate calculation but are not fast enough such that the calculation can be a bottleneck of plume simulations. This study investigates methods to accelerate an ion-atom elastic collision calculation that includes both momentum- and charge-exchange processes. The scattering angles are pre-computed through a classical approach with ab initio spin-orbit free potential and are stored in a two-dimensional array as functions of impact parameter and energy. When performing a collision calculation for an ion-atom pair, the scattering angle is computed by a table lookup and multiple linear interpolations, given the relative energy and randomly determined impact parameter. In order to further accelerate the calculations, the number of collision calculations is reduced by properly defining two cut-off cross-sections for the elastic scattering. In the MCC method, the target atom needs to be sampled; however, it is confirmed that initial target atom velocity does not play a significant role in typical electric propulsion plume simulations such that the sampling process is unnecessary. With these implementations, the computational run-time to perform a collision calculation is reduced significantly compared to previous methods, while retaining the accuracy of the high fidelity models.

An accurate full-dimensional potential energy surface for H-Au(111): Importance of nonadiabatic electronic excitation in energy transfer and adsorption.

PubMed

Janke, Svenja M; Auerbach, Daniel J; Wodtke, Alec M; Kandratsenka, Alexander

2015-09-28

We have constructed a potential energy surface (PES) for H-atoms interacting with fcc Au(111) based on fitting the analytic form of the energy from Effective Medium Theory (EMT) to ab initio energy values calculated with density functional theory. The fit used input from configurations of the H-Au system with Au atoms at their lattice positions as well as configurations with the Au atoms displaced from their lattice positions. It reproduces the energy, in full dimension, not only for the configurations used as input but also for a large number of additional configurations derived from ab initio molecular dynamics (AIMD) trajectories at finite temperature. Adiabatic molecular dynamics simulations on this PES reproduce the energy loss behavior of AIMD. EMT also provides expressions for the embedding electron density, which enabled us to develop a self-consistent approach to simulate nonadiabatic electron-hole pair excitation and their effect on the motion of the incident H-atoms. For H atoms with an energy of 2.7 eV colliding with Au, electron-hole pair excitation is by far the most important energy loss pathway, giving an average energy loss ≈3 times that of the adiabatic case. This increased energy loss enhances the probability of the H-atom remaining on or in the Au slab by a factor of 2. The most likely outcome for H-atoms that are not scattered also depends prodigiously on the energy transfer mechanism; for the nonadiabatic case, more than 50% of the H-atoms which do not scatter are adsorbed on the surface, while for the adiabatic case more than 50% pass entirely through the 4 layer simulation slab.

A Biochemical Magic Frequency

NASA Technical Reports Server (NTRS)

Weber, Arthur L.

1993-01-01

Life is composed principally of four classes of biomolecules - protein, nucleic acid, polysaccharide and lipid. Using 1) estimates of the reducing equivalents (electron pairs) needed to synthesize these biomolecules from carbon dioxide, and 2) measurements of the molecular composition of different organisms, we calculated the average number of electron pairs required for the reduction of carbon dioxide to biological carbon (electron pairs/carbon atom). These calculations showed that the carbon of the Earths biosphere is at the reduction level of formaldehyde that requires 2 electron pairs/carbon atom to be synthesized from carbon dioxide. This was also the reduction level of carbon of individual organisms, except for those that stored large amounts of fuel as lipid. Since this chemical property of life is easily discovered and probably universal, it's most likely known by other intelligent life in the universe. It could be the one thing we know about other carbon-based life in the universe, and the one thing that other intelligent life knows about us. We believe this common knowledge that formaldehyde represents the reduction level of life's carbon could lead to the selection of the 72.83814 GHz line of the 0,0,0,1,0,1 ground-state rotational transition of formaldehyde as a frequency for interstellar communication.

Atomic and electronic structure transformations of silver nanoparticles under rapid cooling conditions.

PubMed

Lobato, I; Rojas, J; Landauro, C V; Torres, J

2009-02-04

The structural evolution and dynamics of silver nanodrops Ag(2869) (4.4 nm in diameter) under rapid cooling conditions have been studied by means of molecular dynamics simulations and electronic density of state calculations. The interaction of silver atoms is modelled by a tight-binding semiempirical interatomic potential proposed by Cleri and Rosato. The pair correlation functions and the pair analysis technique are used to reveal the structural transition in the process of solidification. It is shown that Ag nanoparticles evolve into different nanostructures under different cooling processes. At a cooling rate of 1.5625 × 10(13) K s(-1) the nanoparticles preserve an amorphous-like structure containing a large amount of 1551 and 1541 pairs which correspond to icosahedral symmetry. For a lower cooling rate (1.5625 × 10(12) K s(-1)), the nanoparticles transform into a crystal-like structure consisting mainly of 1421 and 1422 pairs which correspond to the face centred cubic and hexagonal close packed structures, respectively. The variations of the electronic density of states for the differently cooled nanoparticles are small, but in correspondence with the structural changes.

Matrix isolation sublimation: An apparatus for producing cryogenic beams of atoms and molecules

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

Sacramento, R. L.; Alves, B. X.; Silva, B. A.

2015-07-15

We describe the apparatus to generate cryogenic beams of atoms and molecules based on matrix isolation sublimation. Isolation matrices of Ne and H{sub 2} are hosts for atomic and molecular species which are sublimated into vacuum at cryogenic temperatures. The resulting cryogenic beams are used for high-resolution laser spectroscopy. The technique also aims at loading atomic and molecular traps.

A dark-line two-dimensional magneto-optical trap of 85Rb atoms with high optical depth.

PubMed

Zhang, Shanchao; Chen, J F; Liu, Chang; Zhou, Shuyu; Loy, M M T; Wong, G K L; Du, Shengwang

2012-07-01

We describe the apparatus of a dark-line two-dimensional (2D) magneto-optical trap (MOT) of (85)Rb cold atoms with high optical depth (OD). Different from the conventional configuration, two (of three) pairs of trapping laser beams in our 2D MOT setup do not follow the symmetry axes of the quadrupole magnetic field: they are aligned with 45° angles to the longitudinal axis. Two orthogonal repumping laser beams have a dark-line volume in the longitudinal axis at their cross over. With a total trapping laser power of 40 mW and repumping laser power of 18 mW, we obtain an atomic OD up to 160 in an electromagnetically induced transparency (EIT) scheme, which corresponds to an atomic-density-length product NL = 2.05 × 10(15) m(-2). In a closed two-state system, the OD can become as large as more than 600. Our 2D MOT configuration allows full optical access of the atoms in its longitudinal direction without interfering with the trapping and repumping laser beams spatially. Moreover, the zero magnetic field along the longitudinal axis allows the cold atoms maintain a long ground-state coherence time without switching off the MOT magnetic field, which makes it possible to operate the MOT at a high repetition rate and a high duty cycle. Our 2D MOT is ideal for atomic-ensemble-based quantum optics applications, such as EIT, entangled photon pair generation, optical quantum memory, and quantum information processing.

Improved protein surface comparison and application to low-resolution protein structure data.

PubMed

Sael, Lee; Kihara, Daisuke

2010-12-14

Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy.

Frictional Behavior of Micro/nanotextured Surfaces Investigated by Atomic Force Microscope: a Review

NASA Astrophysics Data System (ADS)

Zhang, Xiaoliang; Jia, Junhong

2015-08-01

Tribological issues between friction pair are fundamental problems for minimized devices because of their higher surface-to-volume ratio. Micro/nanotexturing is an effective technique to reduce actual contact area between contact pair at the nanoscale. Micro/nanotexture made a great impact on the frictional behavior of textured surfaces. This paper summarizes the recent advancements in the field of frictional behavior of micro/nanotextured surfaces, which are based on solid surface contact in atmosphere environment, especially focusing on the factors influencing the frictional behavior: Surface property, texturing density, texturing height, texturing structure and size of contact pair (atomic force microscope (AFM) tip) and texturing structures. Summarizing the effects of these factors on the frictional behavior is helpful for the understanding and designing of the surfaces in sliding micro/nanoelectromechanical systems (MEMS/NEMS). Controlling and reducing the friction force in moving mechanical systems is very important for the performance and reliability of nanosystems, which contribute to a sustainable future.

Substrate temperature effect on the structural anisotropy in amorphous Tb-Fe films

NASA Astrophysics Data System (ADS)

Harris, V. G.; Hellman, F.; Elam, W. T.; Koon, N. C.

1993-05-01

Using extended x-ray absorption fine structures (EXAFS) measurements we have investigated the atomic environment around the Fe atom in a series of amorphous Tb0.26Fe0.74 films having different magnetic anisotropy energies owing to different deposition temperatures. The polarization properties of synchrotron radiation allowed the separate study of structure parallel and perpendicular to the sample plane. An anisotropy between these two structures was observed. Modeling results indicate this anisotropy is due to anisotropic pair correlations where the Fe-Fe pairs are statistically preferred in-plane and the Fe-Tb pairs out-of-plane. The amplitude of this anisotropy scales with both the substrate temperature and the magnetic anisotropy energy. A ≊1% in-plane compression of the Fe-Fe distance was measured between the in-plane and out-of-plane structure of the sample grown at 77 K. This sample had no detectable local chemical anisotropy suggesting that intrinsic stress plays an important role in determining its magnetic anisotropy.

Contact pair dynamics during folding of two small proteins: Chicken villin head piece and the Alzheimer protein β-amyloid

NASA Astrophysics Data System (ADS)

Mukherjee, Arnab; Bagchi, Biman

2004-01-01

The folding of an extended protein to its unique native state requires establishment of specific, predetermined, often distant, contacts between amino acid residue pairs. The dynamics of contact pair formation between various hydrophobic residues during folding of two different small proteins, the chicken villin head piece (HP-36) and the Alzheimer protein β-amyloid (βA-40), are investigated by Brownian dynamics (BD) simulations. These two proteins represent two very different classes—HP-36 being globular while βA-40 is nonglobular, stringlike. Hydropathy scale and nonlocal helix propensity of amino acids are used to model the complex interaction potential among the various amino acid residues. The minimalistic model we use here employs a connected backbone chain of atoms of equal size while an amino acid is attached to each backbone atom as an additional atom of differing sizes and interaction parameters, determined by the characteristics of each amino acid. Even for such simple models, we find that the low-energy structures obtained by BD simulations of both the model proteins mimic the native state of the real protein rather well, with a best root-mean-square deviation of 4.5 Å for HP-36. For βA-40 (where a single well-defined structure is not available), the simulated structures resemble the reported ensemble rather well, with the well-known β-bend correctly reproduced. We introduce and calculate a contact pair distance time correlation function, CPij(t), to quantify the dynamical evolution of the pair contact formation between the amino acid residue pairs i and j. The contact pair time correlation function exhibits multistage dynamics, including a two stage fast collapse, followed by a slow (microsecond long) late stage dynamics for several specific pairs. The slow late stage dynamics is in accordance with the findings of Sali et al. [A. Sali, E. Shakhnovich, and M. Karplus, Nature 369, 248 (1994)]. Analysis of the individual trajectories shows that the slow decay is due to the attempt of the protein to form energetically more favorable pair contacts to replace the less favorable ones. This late stage contact formation is a highly cooperative process, involving participation of several pairs and thus entropically unfavorable and expected to face a large free energy barrier. This is because any new pair contact formation among hydrophobic pairs will require breaking of several contacts, before the favorable ones can be formed. This aspect of protein folding dynamics is similar to relaxation in glassy liquids, where also α relaxation requires highly cooperative process of hopping. The present analysis suggests that waiting time for the necessary pair contact formation may obey the Poissonian distribution. We also study the dynamics of Förster energy transfer during folding between two tagged amino acid pairs. This dynamics can be studied by fluorescence resonance energy transfer (FRET). It is found that suitably placed donor-acceptor pairs can capture the slow dynamics during folding. The dynamics probed by FRET is predicted to be nonexponential.

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 now be realized through very fast data acquisition, processing, and reconstruction algorithms. If we use DPC STEM for atomic-resolution imaging using a sub-angstrom size electron probe, it has been shown that we can directly observe the atomic electric field inside atoms within crystals and even inside single atoms, the field between the atomic nucleus and the surrounding electron cloud, which possesses information about the atomic species, local chemical bonding and charge redistribution between bonded atoms. This possibility may open an alternative way for directly visualizing atoms and nanostructures, that is, seeing atoms as an entity of electromagnetic fields that reflect the intra- and interatomic electronic structures. In this Account, the current status of aberration-corrected DPC STEM is highlighted, along with some applications in real material and device studies.

Image-receptor performance: a comparison of Trophy RVG UI sensor and Kodak Ektaspeed Plus film.

PubMed

Ludlow, J; Mol, A

2001-01-01

Objective. This study compares the physical characteristics of the RVG UI sensor (RVG) with Ektaspeed Plus film. Dose-response curves were generated for film and for each of 6 available RVG modes. An aluminum step-wedge was used to evaluate exposure latitude. Spatial resolution was assessed by using a line-pair test tool. Latitude and resolution were assessed by observers for both modalities. The RVG was further characterized by its modulation transfer function. Exposure latitude was equal for film and RVG in the periodontal mode. Other gray scale modes demonstrated much lower latitude. The average maximum resolution was 15.3 line-pairs per millimeter (lp/mm) for RVG in high-resolution mode, 10.5 lp/mm for RVG in low-resolution mode, and 20 lp/mm for film (P <.0001). Modulation transfer function measurements supported the subjective assessments. In periodontal mode, the RVG UI sensor demonstrates exposure latitude similar to that of Ektaspeed Plus film. Film images exhibit significantly higher spatial resolution than the RVG images acquired in high-resolution mode.

Improved Apparatus to Study Matter-Wave Quantum Optics in a Sodium Spinor Bose-Einstein Condensate

NASA Astrophysics Data System (ADS)

Zhong, Shan; Bhagat, Anita; Zhang, Qimin; Schwettmann, Arne

2017-04-01

We present and characterize our recently improved experimental apparatus for studying matter-wave quantum optics in spin space in ultracold sodium gases. Improvements include our recent addition of a 3D-printed Helmholtz coil frame for field stabilization and a crossed optical dipole trap. Spin-exchange collisions in the F = 1 spinor Bose-Einstein condensate can be precisely controlled by microwave dressing, and generate pairs of entangled atoms with magnetic quantum numbers mF = + 1 and mF = - 1 from pairs of mF = 0 atoms. Spin squeezing generated by the collisions can reduce the noise of population measurements below the shot noise limit. Versatile microwave pulse sequences will be used to implement an interferometer, a phase-sensitive amplifier and other devices with sub-shot noise performance. With an added ion detector to detect Rydberg atoms via pulse-field ionization, we later plan to study the effect of Rydberg excitations on the spin evolution of the ultracold gas.

Stabilization of Polar Nanoregions in Pb-free Ferroelectrics

NASA Astrophysics Data System (ADS)

Pramanick, A.; Dmowski, W.; Egami, T.; Budisuharto, A. Setiadi; Weyland, F.; Novak, N.; Christianson, A. D.; Borreguero, J. M.; Abernathy, D. L.; Jørgensen, M. R. V.

2018-05-01

The formation of polar nanoregions through solid-solution additions is known to enhance significantly the functional properties of ferroelectric materials. Despite considerable progress in characterizing the microscopic behavior of polar nanoregions (PNR), understanding their real-space atomic structure and dynamics of their formation remains a considerable challenge. Here, using the method of dynamic pair distribution function, we provide direct insights into the role of solid-solution additions towards the stabilization of polar nanoregions in the Pb-free ferroelectric of Ba (Zr ,Ti )O3 . It is shown that for an optimum level of substitution of Ti by larger Zr ions, the dynamics of atomic displacements for ferroelectric polarization are slowed sufficiently below THz frequencies, which leads to increased local correlation among dipoles within PNRs. The dynamic pair distribution function technique demonstrates a unique capability to obtain insights into locally correlated atomic dynamics in disordered materials, including new Pb-free ferroelectrics, which is necessary to understand and control their functional properties.

Atomic and electronic properties of quasi-one-dimensional MOS2 nanowires

PubMed Central

Seivane, Lucas Fernandez; Barron, Hector; Botti, Silvana; Marques, Miguel Alexandre Lopes; Rubio, Ángel; López-Lozano, Xóchitl

2013-01-01

The structural, electronic and magnetic properties of quasi-one-dimensional MoS2 nanowires, passivated by extra sulfur, have been determined using ab initio density-functional theory. The nanostructures were simulated using several different models based on experimental electron microscopy images. It is found that independently of the geometrical details and the coverage of extra sulfur at the Mo-edge, quasi-one-dimensional metallic states are predominant in all the low-energy model structures despite their reduced dimensionality. These metallic states are localized mainly at the edges. However, the electronic and magnetic character of the NWs does not depend only on the S saturation but also on the symmetry configuration of the S edge atoms. Our results show that for the same S saturation the magnetization can be decreased by increasing the pairing of the S and Mo edge atoms. In spite of the observed pairing of S dimers at the Mo-edge, the nanowires do not experience a Peierls-like metal-insulator transition PMID:25429189

Programming of a Mn-coordinated 4-4‧-biphenyl dicarboxylic acid nanosystem on Au(1 1 1) and investigation of the non-covalent binding of C60 molecules

NASA Astrophysics Data System (ADS)

Zhang, Yan-Feng; Zhu, Na; Komeda, T.

The fabrication of Mn-based coordination networks on a Au(1 1 1) substrate with 4-4 '-biphenyl dicarboxylic acid (BDA) as the linker molecule was investigated by scanning tunneling microscopy. Intriguing structures of ladder and rectangular-shaped networks were obtained by controlling the ratios of deposited amount of BDA molecules and Mn atoms. These structures are well explained by models in which BDA molecules occupy the perimeter of the rectangles and a pair of two Mn atoms are placed at the lattice points. For the rectangular structure, further two phases of a rectangular and a square networks were identified in which the paired Mn atoms were directing an identical direction and 90° rotated in an alternate manner, respectively. In addition, it was revealed that the open space surrounded by rectangle BDA molecules could capture a dimer of C60 molecules which were deposited on the Mn-based BDA networks.

Diffusion and viscosity of liquid tin: Green-Kubo relationship-based calculations from molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Mouas, Mohamed; Gasser, Jean-Georges; Hellal, Slimane; Grosdidier, Benoît; Makradi, Ahmed; Belouettar, Salim

2012-03-01

Molecular dynamics (MD) simulations of liquid tin between its melting point and 1600 °C have been performed in order to interpret and discuss the ionic structure. The interactions between ions are described by a new accurate pair potential built within the pseudopotential formalism and the linear response theory. The calculated structure factor that reflects the main information on the local atomic order in liquids is compared to diffraction measurements. Having some confidence in the ability of this pair potential to give a good representation of the atomic structure, we then focused our attention on the investigation of the atomic transport properties through the MD computations of the velocity autocorrelation function and stress autocorrelation function. Using the Green-Kubo formula (for the first time to our knowledge for liquid tin) we determine the macroscopic transport properties from the corresponding microscopic time autocorrelation functions. The selfdiffusion coefficient and the shear viscosity as functions of temperature are found to be in good agreement with the experimental data.

Controlling the delocalization-localization transition of light via electromagnetically induced transparency

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

Cheng Jing; Huang Guoxiang; State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062

2011-05-15

We propose a scheme to realize a transition from delocalization to localization of light waves via electromagnetically induced transparency. The system we suggested is a resonant cold atomic ensemble having N configuration, with a control field consisting of two pairs of laser beams with different cross angles, which produce an electromagnetically induced quasiperiodic waveguide (EIQPW) for the propagation of a signal field. By appropriately tuning the incommensurate rate or relative modulation strength between the two pairs of control-field components, the signal field can exhibit the delocalization-localization transition as it transports inside the atomic ensemble. The delocalization-localization transition point is determinedmore » and the propagation property of the signal field is studied in detail. Our work provides a way of realizing wave localization via atomic coherence, which is quite different from the conventional, off-resonant mechanism-based Aubry-Andre model, and the great controllability of the EIQPW also allows an easy manipulation of the delocalization-localization transition.« less

Sub-nanometer Resolution Imaging with Amplitude-modulation Atomic Force Microscopy in Liquid

PubMed Central

Farokh Payam, Amir; Piantanida, Luca; Cafolla, Clodomiro; Voïtchovsky, Kislon

2016-01-01

Atomic force microscopy (AFM) has become a well-established technique for nanoscale imaging of samples in air and in liquid. Recent studies have shown that when operated in amplitude-modulation (tapping) mode, atomic or molecular-level resolution images can be achieved over a wide range of soft and hard samples in liquid. In these situations, small oscillation amplitudes (SAM-AFM) enhance the resolution by exploiting the solvated liquid at the surface of the sample. Although the technique has been successfully applied across fields as diverse as materials science, biology and biophysics and surface chemistry, obtaining high-resolution images in liquid can still remain challenging for novice users. This is partly due to the large number of variables to control and optimize such as the choice of cantilever, the sample preparation, and the correct manipulation of the imaging parameters. Here, we present a protocol for achieving high-resolution images of hard and soft samples in fluid using SAM-AFM on a commercial instrument. Our goal is to provide a step-by-step practical guide to achieving high-resolution images, including the cleaning and preparation of the apparatus and the sample, the choice of cantilever and optimization of the imaging parameters. For each step, we explain the scientific rationale behind our choices to facilitate the adaptation of the methodology to every user's specific system. PMID:28060262

Super-resolution atomic force photoactivated microscopy of biological samples (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Seunghyun; Kim, Hyemin; Shin, Seungjun; Doh, Junsang; Kim, Chulhong

2017-03-01

Optical microscopy (OM) and photoacoustic microscopy (PAM) have previously been used to image the optical absorption of intercellular features of biological cells. However, the optical diffraction limit ( 200 nm) makes it difficult for these modalities to image nanoscale inner cell structures and the distribution of internal cell components. Although super-resolution fluorescence microscopy, such as stimulated emission depletion microscopy (STED) and stochastic optical reconstruction microscopy (STORM), has successfully performed nanoscale biological imaging, these modalities require the use of exogenous fluorescence agents, which are unfavorable for biological samples. Our newly developed atomic force photoactivated microscopy (AFPM) can provide optical absorption images with nanoscale lateral resolution without any exogenous contrast agents. AFPM combines conventional atomic force microscopy (AFM) and an optical excitation system, and simultaneously provides multiple contrasts, such as the topography and magnitude of optical absorption. AFPM can detect the intrinsic optical absorption of samples with 8 nm lateral resolution, easily overcoming the diffraction limit. Using the label-free AFPM system, we have successfully imaged the optical absorption properties of a single melanoma cell (B16F10) and a rosette leaf epidermal cell of Arabidopsis (ecotype Columbia (Col-0)) with nanoscale lateral resolution. The remarkable images show the melanosome distribution of a melanoma cell and the biological structures of a plant cell. AFPM provides superior imaging of optical absorption with a nanoscale lateral resolution, and it promises to become widely used in biological and chemical research.

Structural Dynamics and Activity of Nanocatalysts Inside Fuel Cells by in-operando Atomic Pair Distribution Studies

NASA Astrophysics Data System (ADS)

Prasai, Binay

We present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). Using in-operando high-energy X-ray diffraction we tracked the evolution of the atomic structure and activity of noble metal-transition metal(NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Data were analyzed in terms of atomic pair distribution functions and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore, we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation.

Efficient simultaneous reverse Monte Carlo modeling of pair-distribution functions and extended x-ray-absorption fine structure spectra of crystalline disordered materials.

PubMed

Németh, Károly; Chapman, Karena W; Balasubramanian, Mahalingam; Shyam, Badri; Chupas, Peter J; Heald, Steve M; Newville, Matt; Klingler, Robert J; Winans, Randall E; Almer, Jonathan D; Sandi, Giselle; Srajer, George

2012-02-21

An efficient implementation of simultaneous reverse Monte Carlo (RMC) modeling of pair distribution function (PDF) and EXAFS spectra is reported. This implementation is an extension of the technique established by Krayzman et al. [J. Appl. Cryst. 42, 867 (2009)] in the sense that it enables simultaneous real-space fitting of x-ray PDF with accurate treatment of Q-dependence of the scattering cross-sections and EXAFS with multiple photoelectron scattering included. The extension also allows for atom swaps during EXAFS fits thereby enabling modeling the effects of chemical disorder, such as migrating atoms and vacancies. Significant acceleration of EXAFS computation is achieved via discretization of effective path lengths and subsequent reduction of operation counts. The validity and accuracy of the approach is illustrated on small atomic clusters and on 5500-9000 atom models of bcc-Fe and α-Fe(2)O(3). The accuracy gains of combined simultaneous EXAFS and PDF fits are pointed out against PDF-only and EXAFS-only RMC fits. Our modeling approach may be widely used in PDF and EXAFS based investigations of disordered materials. © 2012 American Institute of Physics

CO tip functionalization in subatomic resolution atomic force microscopy

NASA Astrophysics Data System (ADS)

Kim, Minjung; Chelikowsky, James R.

2015-10-01

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

CO tip functionalization in subatomic resolution atomic force microscopy

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

Kim, Minjung; Chelikowsky, James R.

2015-10-19

Noncontact atomic force microscopy (nc-AFM) employing a CO-functionalized tip displays dramatically enhanced resolution wherein covalent bonds of polycyclic aromatic hydrocarbon can be imaged. Employing real-space pseudopotential first-principles calculations, we examine the role of CO in functionalizing the nc-AFM tip. Our calculations allow us to simulate full AFM images and ascertain the enhancement mechanism of the CO molecule. We consider two approaches: one with an explicit inclusion of the CO molecule and one without. By comparing our simulations to existing experimental images, we ascribe the enhanced resolution of the CO functionalized tip to the special orbital characteristics of the CO molecule.

Designing and building a permanent magnet Zeeman slower for calcium atoms using a 3D printer

NASA Astrophysics Data System (ADS)

Parsagian, Alexandria; Kleinert, Michaela

2015-10-01

We present the design of a Zeeman slower for calcium atoms using permanent magnets instead of more traditional electromagnets and the novel technique of 3D printing to create a very robust and flexible structure for these magnets. Zeeman slowers are ideal tools to slow atoms from several hundreds of meters per second to just a few tens of meters per second. These slower atoms can then easily be trapped in a magneto-optical trap, making Zeeman slowers a very valuable tool in many cold atom labs. The use of permanent magnets and 3D printing results in a highly stable and robust slower that is suitable for undergraduate laboratories. In our design, we arranged 28 magnet pairs, 2.0 cm apart along the axis of the slower and at varying radial distances from the axis. We determined the radial position of the magnets by simulating the combined field of all magnet pairs using Mathematica and comparing it to the ideal theoretical field for a Zeeman slower. Finally, we designed a stable, robust, compact, and easy-to-align mounting structure for the magnets in Google Sketchup, which we then printed using a commercially available 3D printer by Solidoodle. The resulting magnetic field is well suited to slow calcium atoms from the 770 m/s rms velocity at a temperature of 950 K, down to the capture velocity of the magneto-optical trap.

Einstein-Podolsky-Rosen Entanglement of Narrow-Band Photons from Cold Atoms.

PubMed

Lee, Jong-Chan; Park, Kwang-Kyoon; Zhao, Tian-Ming; Kim, Yoon-Ho

2016-12-16

Einstein-Podolsky-Rosen (EPR) entanglement introduced in 1935 deals with two particles that are entangled in their positions and momenta. Here we report the first experimental demonstration of EPR position-momentum entanglement of narrow-band photon pairs generated from cold atoms. By using two-photon quantum ghost imaging and ghost interference, we demonstrate explicitly that the narrow-band photon pairs violate the separability criterion, confirming EPR entanglement. We further demonstrate continuous variable EPR steering for positions and momenta of the two photons. Our new source of EPR-entangled narrow-band photons is expected to play an essential role in spatially multiplexed quantum information processing, such as, storage of quantum correlated images, quantum interface involving hyperentangled photons, etc.

Einstein-Podolsky-Rosen Entanglement of Narrow-Band Photons from Cold Atoms

NASA Astrophysics Data System (ADS)

Lee, Jong-Chan; Park, Kwang-Kyoon; Zhao, Tian-Ming; Kim, Yoon-Ho

2016-12-01

Einstein-Podolsky-Rosen (EPR) entanglement introduced in 1935 deals with two particles that are entangled in their positions and momenta. Here we report the first experimental demonstration of EPR position-momentum entanglement of narrow-band photon pairs generated from cold atoms. By using two-photon quantum ghost imaging and ghost interference, we demonstrate explicitly that the narrow-band photon pairs violate the separability criterion, confirming EPR entanglement. We further demonstrate continuous variable EPR steering for positions and momenta of the two photons. Our new source of EPR-entangled narrow-band photons is expected to play an essential role in spatially multiplexed quantum information processing, such as, storage of quantum correlated images, quantum interface involving hyperentangled photons, etc.

Atomic pair distribution function at the Brazilian Synchrotron Light Laboratory: application to the Pb 1–x La xZr 0.40Ti 0.60O 3 ferroelectric system

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

Saleta, M. E.; Eleotério, M.; Mesquita, A.

2017-07-29

This work reports the setting up of the X-ray diffraction and spectroscopy beamline at the Brazilian Synchrotron Light Laboratory for performing total scattering experiments to be analyzed by atomic pair distribution function (PDF) studies. The results of a PDF refinement for Al 2O 3 standard are presented and compared with data acquired at a beamline of the Advanced Photon Source, where it is common to perform this type of experiment. A preliminary characterization of the Pb 1–xLa xZr 0.40Ti 0.60O 3 ferroelectric system, withx= 0.11, 0.12 and 0.15, is also shown.

Design and construction of a high-energy photon polarimeter

NASA Astrophysics Data System (ADS)

Dugger, M.; Ritchie, B. G.; Sparks, N.; Moriya, K.; Tucker, R. J.; Lee, R. J.; Thorpe, B. N.; Hodges, T.; Barbosa, F. J.; Sandoval, N.; Jones, R. T.

2017-09-01

We report on the design and construction of a high-energy photon polarimeter for measuring the degree of polarization of a linearly-polarized photon beam. The photon polarimeter uses the process of pair production on an atomic electron (triplet production). The azimuthal distribution of scattered atomic electrons following triplet production yields information regarding the degree of linear polarization of the incident photon beam. The polarimeter, operated in conjunction with a pair spectrometer, uses a silicon strip detector to measure the recoil electron distribution resulting from triplet photoproduction in a beryllium target foil. The analyzing power ΣA for the device using a 75 μm beryllium converter foil is about 0.2, with a relative systematic uncertainty in ΣA of 1.5%.

High-Resolution Crystal Structures of Protein Helices Reconciled with Three-Centered Hydrogen Bonds and Multipole Electrostatics

PubMed Central

Kuster, Daniel J.; Liu, Chengyu; Fang, Zheng; Ponder, Jay W.; Marshall, Garland R.

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.613 α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.613/10-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding. PMID:25894612

High-resolution crystal structures of protein helices reconciled with three-centered hydrogen bonds and multipole electrostatics.

PubMed

Kuster, Daniel J; Liu, Chengyu; Fang, Zheng; Ponder, Jay W; Marshall, Garland R

2015-01-01

Theoretical and experimental evidence for non-linear hydrogen bonds in protein helices is ubiquitous. In particular, amide three-centered hydrogen bonds are common features of helices in high-resolution crystal structures of proteins. These high-resolution structures (1.0 to 1.5 Å nominal crystallographic resolution) position backbone atoms without significant bias from modeling constraints and identify Φ = -62°, ψ = -43 as the consensus backbone torsional angles of protein helices. These torsional angles preserve the atomic positions of α-β carbons of the classic Pauling α-helix while allowing the amide carbonyls to form bifurcated hydrogen bonds as first suggested by Némethy et al. in 1967. Molecular dynamics simulations of a capped 12-residue oligoalanine in water with AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications), a second-generation force field that includes multipole electrostatics and polarizability, reproduces the experimentally observed high-resolution helical conformation and correctly reorients the amide-bond carbonyls into bifurcated hydrogen bonds. This simple modification of backbone torsional angles reconciles experimental and theoretical views to provide a unified view of amide three-centered hydrogen bonds as crucial components of protein helices. The reason why they have been overlooked by structural biologists depends on the small crankshaft-like changes in orientation of the amide bond that allows maintenance of the overall helical parameters (helix pitch (p) and residues per turn (n)). The Pauling 3.6(13) α-helix fits the high-resolution experimental data with the minor exception of the amide-carbonyl electron density, but the previously associated backbone torsional angles (Φ, Ψ) needed slight modification to be reconciled with three-atom centered H-bonds and multipole electrostatics. Thus, a new standard helix, the 3.6(13/10)-, Némethy- or N-helix, is proposed. Due to the use of constraints from monopole force fields and assumed secondary structures used in low-resolution refinement of electron density of proteins, such structures in the PDB often show linear hydrogen bonding.

Detecting magnetic ordering with atomic size electron probes

DOE PAGES

Idrobo, Juan Carlos; Rusz, Ján; Spiegelberg, Jakob; ...

2016-05-27

While magnetism originates at the atomic scale, the existing spectroscopic techniques sensitive to magnetic signals only produce spectra with spatial resolution on a larger scale. However, recently, it has been theoretically argued that atomic size electron probes with customized phase distributions can detect magnetic circular dichroism. Here, we report a direct experimental real-space detection of magnetic circular dichroism in aberration-corrected scanning transmission electron microscopy (STEM). Using an atomic size-aberrated electron probe with a customized phase distribution, we reveal the checkerboard antiferromagnetic ordering of Mn moments in LaMnAsO by observing a dichroic signal in the Mn L-edge. The novel experimental setupmore » presented here, which can easily be implemented in aberration-corrected STEM, opens new paths for probing dichroic signals in materials with unprecedented spatial resolution.« less

Atomic resolution study of the interfacial bonding at Si3N4/CeO2-δ grain boundaries

NASA Astrophysics Data System (ADS)

Walkosz, W.; Klie, R. F.; Öǧüt, S.; Borisevich, A.; Becher, P. F.; Pennycook, S. J.; Idrobo, J. C.

2008-08-01

Using a combination of atomic-resolution Z-contrast imaging and electron energy-loss spectroscopy (EELS) in the scanning transmission electron microscope, we examine the atomic and electronic structures at the interface between Si3N4 (101¯0) and CeO2-d intergranular film (IGF). Ce atoms are observed to segregate to the interface in a two-layer periodic arrangement, which is significantly different from the structure observed in a previous study. Our EELS experiments show (i) oxygen in direct contact with the terminating Si3N4 open-ring structures, (ii) a change in the Ce valence from a nominal oxidation state of +3 to almost +4 moving from the interface into the IGF, and (iii) a uniform concentration of Si in the film.

Atomic resolution characterization of a SrTiO{sub 3} grain boundary in the STEM

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

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

This paper uses the complementary techniques of high resolution Z-contrast imaging and PEELS (parallel detection electron energy loss spectroscopy) to investigate the atomic structure and chemistry of a 25 degree symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}. The gain boundary is composed of two different boundary structural units which occur in about equal numbers: one which contains Ti-O columns and the other without.

Atomic Force Microscope for Imaging and Spectroscopy

NASA Technical Reports Server (NTRS)

Pike, W. T.; Hecht, M. H.; Anderson, M. S.; Akiyama, T.; Gautsch, S.; deRooij, N. F.; Staufer, U.; Niedermann, Ph.; Howald, L.; Mueller, D.

2000-01-01

We have developed, built, and tested an atomic force microscope (AFM) for extraterrestrial applications incorporating a micromachined tip array to allow for probe replacement. It is part of a microscopy station originally intended for NASA's 2001 Mars lander to identify the size, distribution, and shape of Martian dust and soil particles. As well as imaging topographically down to nanometer resolution, this instrument can be used to reveal chemical information and perform infrared and Raman spectroscopy at unprecedented resolution.

Low-loss electron energy loss spectroscopy: An atomic-resolution complement to optical spectroscopies and application to graphene

DOE PAGES

Kapetanakis, Myron; Zhou, Wu; Oxley, Mark P.; ...

2015-09-25

Photon-based spectroscopies have played a central role in exploring the electronic properties of crystalline solids and thin films. They are a powerful tool for probing the electronic properties of nanostructures, but they are limited by lack of spatial resolution. On the other hand, electron-based spectroscopies, e.g., electron energy loss spectroscopy (EELS), are now capable of subangstrom spatial resolution. Core-loss EELS, a spatially resolved analog of x-ray absorption, has been used extensively in the study of inhomogeneous complex systems. In this paper, we demonstrate that low-loss EELS in an aberration-corrected scanning transmission electron microscope, which probes low-energy excitations, combined with amore » theoretical framework for simulating and analyzing the spectra, is a powerful tool to probe low-energy electron excitations with atomic-scale resolution. The theoretical component of the method combines density functional theory–based calculations of the excitations with dynamical scattering theory for the electron beam. We apply the method to monolayer graphene in order to demonstrate that atomic-scale contrast is inherent in low-loss EELS even in a perfectly periodic structure. The method is a complement to optical spectroscopy as it probes transitions entailing momentum transfer. The theoretical analysis identifies the spatial and orbital origins of excitations, holding the promise of ultimately becoming a powerful probe of the structure and electronic properties of individual point and extended defects in both crystals and inhomogeneous complex nanostructures. The method can be extended to probe magnetic and vibrational properties with atomic resolution.« less

Ultra-high resolution electron microscopy

DOE PAGES

Oxley, Mark P.; Lupini, Andrew R.; Pennycook, Stephen J.

2016-12-23

The last two decades have seen dramatic advances in the resolution of the electron microscope brought about by the successful correction of lens aberrations that previously limited resolution for most of its history. Here we briefly review these advances, the achievement of sub-Ångstrom resolution and the ability to identify individual atoms, their bonding configurations and even their dynamics and diffusion pathways. We then present a review of the basic physics of electron scattering, lens aberrations and their correction, and an approximate imaging theory for thin crystals which provides physical insight into the various different imaging modes. Then we proceed tomore » describe a more exact imaging theory starting from Yoshioka’s formulation and covering full image simulation methods using Bloch waves, the multislice formulation and the frozen phonon/quantum excitation of phonons models. Delocalization of inelastic scattering has become an important limiting factor at atomic resolution. We therefore discuss this issue extensively, showing how the full-width-half-maximum is the appropriate measure for predicting image contrast, but the diameter containing 50% of the excitation is an important measure of the range of the interaction. These two measures can differ by a factor of 5, are not a simple function of binding energy, and full image simulations are required to match to experiment. The Z-dependence of annular dark field images is also discussed extensively, both for single atoms and for crystals, and we show that temporal incoherence must be included accurately if atomic species are to be identified through matching experimental intensities to simulations. Finally we mention a few promising directions for future investigation.« less

Development of the Advanced Energetic Pair Telescope (AdEPT) for Medium-Energy Gamma-Ray Astronomy

NASA Technical Reports Server (NTRS)

Hunter, Stanley D.; Bloser, Peter F.; Dion, Michael P.; McConnell, Mark L.; deNolfo, Georgia A.; Son, Seunghee; Ryan, James M.; Stecker, Floyd W.

2011-01-01

Progress in high-energy gamma-ray science has been dramatic since the launch of INTEGRAL, AGILE and FERMI. These instruments, however, are not optimized for observations in the medium-energy (approx.0.3< E(sub gamma)< approx.200 MeV) regime where many astrophysical objects exhibit unique, transitory behavior, such as spectral breaks, bursts, and flares. We outline some of the major science goals of a medium-energy mission. These science goals are best achieved with a combination of two telescopes, a Compton telescope and a pair telescope, optimized to provide significant improvements in angular resolution and sensitivity. In this paper we describe the design of the Advanced Energetic Pair Telescope (AdEPT) based on the Three-Dimensional Track Imager (3-DTI) detector. This technology achieves excellent, medium-energy sensitivity, angular resolution near the kinematic limit, and gamma-ray polarization sensitivity, by high resolution 3-D electron tracking. We describe the performance of a 30x30x30 cm3 prototype of the AdEPT instrument.

Quantum Gas Microscope for Fermionic Atoms

NASA Astrophysics Data System (ADS)

Okan, Melih; Cheuk, Lawrence; Nichols, Matthew; Lawrence, Katherine; Zhang, Hao; Zwierlein, Martin

2016-05-01

Strongly interacting fermions define the properties of complex matter throughout nature, from atomic nuclei and modern solid state materials to neutron stars. Ultracold atomic Fermi gases have emerged as a pristine platform for the study of many-fermion systems. In this poster we demonstrate the realization of a quantum gas microscope for fermionic 40 K atoms trapped in an optical lattice and the recent experiments which allows one to probe strongly correlated fermions at the single atom level. We combine 3D Raman sideband cooling with high- resolution optics to simultaneously cool and image individual atoms with single lattice site resolution at a detection fidelity above 95%. The imaging process leaves the atoms predominantly in the 3D motional ground state of their respective lattice sites, inviting the implementation of a Maxwell's demon to assemble low-entropy many-body states. Single-site resolved imaging of fermions enables the direct observation of magnetic order, time resolved measurements of the spread of particle correlations, and the detection of many-fermion entanglement. NSF, AFOSR-PECASE, AFOSR-MURI on Exotic Phases of Matter, ARO-MURI on Atomtronics, ONR, a Grant from the Army Research Office with funding from the DARPA OLE program, and the David and Lucile Packard Foundation.

Computer Simulation of Global Profiles of Carbon Dioxide Using a Pulsed, 2-Micron, Coherent-Detection, Column-Content DIAL System

NASA Technical Reports Server (NTRS)

Kavaya, Michael J.; Singh, Upendra N.; Koch, Grady J.; Yu, Jirong; Frehlich, Rod G.

2009-01-01

We present preliminary results of computer simulations of the error in measuring carbon dioxide mixing ratio profiles from earth orbit. The simulated sensor is a pulsed, 2-micron, coherent-detection lidar alternately operating on at least two wavelengths. The simulated geometry is a nadir viewing lidar measuring the column content signal. Atmospheric absorption is modeled using FASCODE3P software with the HITRAN 2004 absorption line data base. Lidar shot accumulation is employed up to the horizontal resolution limit. Horizontal resolutions of 50, 100, and 200 km are shown. Assuming a 400 km spacecraft orbit, the horizontal resolutions correspond to measurement times of about 7, 14, and 28 s. We simulate laser pulse-pair repetition frequencies from 1 Hz to 100 kHz. The range of shot accumulation is 7 to 2.8 million pulse-pairs. The resultant error is shown as a function of horizontal resolution, laser pulse-pair repetition frequency, and laser pulse energy. The effect of different on and off pulse energies is explored. The results are compared to simulation results of others and to demonstrated 2-micron operating points at NASA Langley.

Atom optics in the time domain

NASA Astrophysics Data System (ADS)

Arndt, M.; Szriftgiser, P.; Dalibard, J.; Steane, A. M.

1996-05-01

Atom-optics experiments are presented using a time-modulated evanescent light wave as an atomic mirror in the trampoline configuration, i.e., perpendicular to the direction of the atomic free fall. This modulated mirror is used to accelerate cesium atoms, to focus their trajectories, and to apply a ``multiple lens'' to separately focus different velocity classes of atoms originating from a point source. We form images of a simple two-slit object to show the resolution of the device. The experiments are modelled by a general treatment analogous to classical ray optics.

Optical ferris wheel for ultracold atoms

NASA Astrophysics Data System (ADS)

Franke-Arnold, S.; Leach, J.; Padgett, M. J.; Lembessis, V. E.; Ellinas, D.; Wright, A. J.; Girkin, J. M.; Ohberg, P.; Arnold, A. S.

2007-07-01

We propose a versatile optical ring lattice suitable for trapping cold and quantum degenerate atomic samples. We demonstrate the realisation of intensity patterns from pairs of Laguerre-Gauss (exp(iℓө) modes with different ℓ indices. These patterns can be rotated by introducing a frequency shift between the modes. We can generate bright ring lattices for trapping atoms in red-detuned light, and dark ring lattices suitable for trapping atoms with minimal heating in the optical vortices of blue-detuned light. The lattice sites can be joined to form a uniform ring trap, making it ideal for studying persistent currents and the Mott insulator transition in a ring geometry.

Atomic Structure of Au 329(SR) 84 Faradaurate Plasmonic Nanomolecules

DOE PAGES

Kumara, Chanaka; Zuo, Xiaobing; Ilavsky, Jan; ...

2015-04-03

To design novel nanomaterials, it is important to precisely control the composition, determine the atomic structure, and manipulate the structure to tune the materials property. Here we present a comprehensive characterization of the material whose composition is Au 329(SR) 84 precisely, therefore referred to as a nanomolecule. The size homogeneity was shown by electron microscopy, solution X-ray scattering, and mass spectrometry. We proposed its atomic structure to contain the Au 260 core using experiments and modeling of a total-scattering-based atomic-pair distribution functional analysis. HAADF-STEM images shows fcc-like 2.0 ± 0.1 nm diameter nanomolecules.

Surface determination through atomically resolved secondary-electron imaging

PubMed Central

Ciston, J.; Brown, H. G.; D'Alfonso, A. J.; Koirala, P.; Ophus, C.; Lin, Y.; Suzuki, Y.; Inada, H.; Zhu, Y.; Allen, L. J.; Marks, L. D.

2015-01-01

Unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we report a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 × 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our work reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO5 units. Dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals. PMID:26082275

Chemical mapping and quantification at the atomic scale by scanning transmission electron microscopy.

PubMed

Chu, Ming-Wen; Chen, Cheng Hsuan

2013-06-25

With innovative modern material-growth methods, a broad spectrum of fascinating materials with reduced dimensions-ranging from single-atom catalysts, nanoplasmonic and nanophotonic materials to two-dimensional heterostructural interfaces-is continually emerging and extending the new frontiers of materials research. A persistent central challenge in this grand scientific context has been the detailed characterization of the individual objects in these materials with the highest spatial resolution, a problem prompting the need for experimental techniques that integrate both microscopic and spectroscopic capabilities. To date, several representative microscopy-spectroscopy combinations have become available, such as scanning tunneling microscopy, tip-enhanced scanning optical microscopy, atom probe tomography, scanning transmission X-ray microscopy, and scanning transmission electron microscopy (STEM). Among these tools, STEM boasts unique chemical and electronic sensitivity at unparalleled resolution. In this Perspective, we elucidate the advances in STEM and chemical mapping applications at the atomic scale by energy-dispersive X-ray spectroscopy and electron energy loss spectroscopy with a focus on the ultimate challenge of chemical quantification with atomic accuracy.

Surface determination through atomically resolved secondary-electron imaging

DOE PAGES

Ciston, J.; Brown, H. G.; D’Alfonso, A. J.; ...

2015-06-17

We report that unique determination of the atomic structure of technologically relevant surfaces is often limited by both a need for homogeneous crystals and ambiguity of registration between the surface and bulk. Atomically resolved secondary-electron imaging is extremely sensitive to this registration and is compatible with faceted nanomaterials, but has not been previously utilized for surface structure determination. Here we show a detailed experimental atomic-resolution secondary-electron microscopy analysis of the c(6 x 2) reconstruction on strontium titanate (001) coupled with careful simulation of secondary-electron images, density functional theory calculations and surface monolayer-sensitive aberration-corrected plan-view high-resolution transmission electron microscopy. Our workmore » reveals several unexpected findings, including an amended registry of the surface on the bulk and strontium atoms with unusual seven-fold coordination within a typically high surface coverage of square pyramidal TiO 5 units. Lastly, dielectric screening is found to play a critical role in attenuating secondary-electron generation processes from valence orbitals.« less

Frequency-Comb Based Double-Quantum Two-Dimensional Spectrum Identifies Collective Hyperfine Resonances in Atomic Vapor Induced by Dipole-Dipole Interactions

NASA Astrophysics Data System (ADS)

Lomsadze, Bachana; Cundiff, Steven T.

2018-06-01

Frequency-comb based multidimensional coherent spectroscopy is a novel optical method that enables high-resolution measurement in a short acquisition time. The method's resolution makes multidimensional coherent spectroscopy relevant for atomic systems that have narrow resonances. We use double-quantum multidimensional coherent spectroscopy to reveal collective hyperfine resonances in rubidium vapor at 100 °C induced by dipole-dipole interactions. We observe tilted and elongated line shapes in the double-quantum 2D spectra, which have never been reported for Doppler-broadened systems. The elongated line shapes suggest that the signal is predominately from the interacting atoms that have a near zero relative velocity.

Atomic force microscopy captures length phenotypes in single proteins

PubMed Central

Carrion-Vazquez, Mariano; Marszalek, Piotr E.; Oberhauser, Andres F.; Fernandez, Julio M.

1999-01-01

We use single-protein atomic force microscopy techniques to detect length phenotypes in an Ig module. To gain amino acid resolution, we amplify the mechanical features of a single module by engineering polyproteins composed of up to 12 identical repeats. We show that on mechanical unfolding, mutant polyproteins containing five extra glycine residues added to the folded core of the module extend 20 Å per module farther than the wild-type polyproteins. By contrast, similar insertions near the N or C termini have no effect. Hence, our atomic force microscopy measurements readily discriminate the location of the insert and measure its size with a resolution similar to that of NMR and x-ray crystallography. PMID:10500169

Proton conduction in electrolyte made of manganese dioxide for hydrogen gas sensor

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

Koyanaka, Hideki; Ueda, Yoshikatsu; Takeuchi, K

2012-01-01

We propose a network model of oxygen-pairs to store and conduct protons on the surface of manganese dioxide with a weak covalent bond like protons stored in pressured ice. The atomic distances of oxygen-pairs were estimated between 2.57 and 2.60 angstroms in crystal structures of ramsdellite-type and lambda-type manganese dioxides by using protonated samples and inelastic neutron scattering measurements. Good properties for a hydrogen gas sensor using electrolytes made of manganese dioxides that contain such oxygen-pairs were confirmed experimentally.

Imaging of radiation damage using complementary field ion microscopy and atom probe tomography.

PubMed

Dagan, Michal; Hanna, Luke R; Xu, Alan; Roberts, Steve G; Smith, George D W; Gault, Baptiste; Edmondson, Philip D; Bagot, Paul A J; Moody, Michael P

2015-12-01

Radiation damage in tungsten and a tungsten-tantalum alloy, both of relevance to nuclear fusion research, has been characterized using a combination of field ion microscopy (FIM) imaging and atom probe tomography (APT). While APT provides 3D analytical imaging with sub-nanometer resolution, FIM is capable of imaging the arrangements of single atoms on a crystal lattice and has the potential to provide insights into radiation induced crystal damage, all the way down to its smallest manifestation--a single vacancy. This paper demonstrates the strength of combining these characterization techniques. In ion implanted tungsten, it was found that atomic scale lattice damage is best imaged using FIM. In certain cases, APT reveals an identifiable imprint in the data via the segregation of solute and impurities and trajectory aberrations. In a W-5at%Ta alloy, a combined APT-FIM study was able to determine the atomic distribution of tantalum inside the tungsten matrix. An indirect method was implemented to identify tantalum atoms inside the tungsten matrix in FIM images. By tracing irregularities in the evaporation sequence of atoms imaged with FIM, this method enables the benefit of FIM's atomic resolution in chemical distinction between the two species. Copyright © 2015 Elsevier B.V. All rights reserved.

X-ray structure, symmetry and mechanism of an AMPA-subtype glutamate receptor

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

Sobolevsky, Alexander I.; Rosconi, Michael P.; Gouaux, Eric

2010-02-02

Ionotropic glutamate receptors mediate most excitatory neurotransmission in the central nervous system and function by opening a transmembrane ion channel upon binding of glutamate. Despite their crucial role in neurobiology, the architecture and atomic structure of an intact ionotropic glutamate receptor are unknown. Here we report the crystal structure of the {alpha}-amino-3-hydroxy-5-methyl-4-isoxazole propionic acid (AMPA)-sensitive, homotetrameric, rat GluA2 receptor at 3.6 {angstrom} resolution in complex with a competitive antagonist. The receptor harbours an overall axis of two-fold symmetry with the extracellular domains organized as pairs of local dimers and with the ion channel domain exhibiting four-fold symmetry. A symmetry mismatchmore » between the extracellular and ion channel domains is mediated by two pairs of conformationally distinct subunits, A/C and B/D. Therefore, the stereochemical manner in which the A/C subunits are coupled to the ion channel gate is different from the B/D subunits. Guided by the GluA2 structure and site-directed cysteine mutagenesis, we suggest that GluN1 and GluN2A NMDA (N-methyl-D-aspartate) receptors have a similar architecture, with subunits arranged in a 1-2-1-2 pattern. We exploit the GluA2 structure to develop mechanisms of ion channel activation, desensitization and inhibition by non-competitive antagonists and pore blockers.« less

Ab initio molecular dynamics calculations on scattering of hyperthermal H atoms from Cu(111) and Au(111)

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

Kroes, Geert-Jan, E-mail: g.j.kroes@chem.leidenuniv.nl; Pavanello, Michele; Blanco-Rey, María

2014-08-07

Energy loss from the translational motion of an atom or molecule impinging on a metal surface to the surface may determine whether the incident particle can trap on the surface, and whether it has enough energy left to react with another molecule present at the surface. Although this is relevant to heterogeneous catalysis, the relative extent to which energy loss of hot atoms takes place to phonons or electron-hole pair (ehp) excitation, and its dependence on the system's parameters, remain largely unknown. We address these questions for two systems that present an extreme case of the mass ratio of themore » incident atom to the surface atom, i.e., H + Cu(111) and H + Au(111), by presenting adiabatic ab initio molecular dynamics (AIMD) predictions of the energy loss and angular distributions for an incidence energy of 5 eV. The results are compared to the results of AIMDEFp calculations modeling energy loss to ehp excitation using an electronic friction (“EF”) model applied to the AIMD trajectories, so that the energy loss to the electrons is calculated “post” (“p”) the computation of the AIMD trajectory. The AIMD calculations predict average energy losses of 0.38 eV for Cu(111) and 0.13-0.14 eV for Au(111) for H-atoms that scatter from these surfaces without penetrating the surface. These energies closely correspond with energy losses predicted with Baule models, which is suggestive of structure scattering. The predicted adiabatic integral energy loss spectra (integrated over all final scattering angles) all display a lowest energy peak at an energy corresponding to approximately 80% of the average adiabatic energy loss for non-penetrative scattering. In the adiabatic limit, this suggests a way of determining the approximate average energy loss of non-penetratively scattered H-atoms from the integral energy loss spectrum of all scattered H-atoms. The AIMDEFp calculations predict that in each case the lowest energy loss peak should show additional energy loss in the range 0.2-0.3 eV due to ehp excitation, which should be possible to observe. The average non-adiabatic energy losses for non-penetrative scattering exceed the adiabatic losses to phonons by 0.9-1.0 eV. This suggests that for scattering of hyperthermal H-atoms from coinage metals the dominant energy dissipation channel should be to ehp excitation. These predictions can be tested by experiments that combine techniques for generating H-atom beams that are well resolved in translational energy and for detecting the scattered atoms with high energy-resolution.« less

Imaging active topological defects in carbon nanotubes

NASA Astrophysics Data System (ADS)

Suenaga, Kazu; Wakabayashi, Hideaki; Koshino, Masanori; Sato, Yuta; Urita, Koki; Iijima, Sumio

2007-06-01

A single-walled carbon nanotube (SWNT) is a wrapped single graphene layer, and its plastic deformation should require active topological defects-non-hexagonal carbon rings that can migrate along the nanotube wall. Although in situ transmission electron microscopy (TEM) has been used to examine the deformation of SWNTs, these studies deal only with diameter changes and no atomistic mechanism has been elucidated experimentally. Theory predicts that some topological defects can form through the Stone-Wales transformation in SWNTs under tension at 2,000 K, and could act as a dislocation core. We demonstrate here, by means of high-resolution (HR)-TEM with atomic sensitivity, the first direct imaging of pentagon-heptagon pair defects found in an SWNT that was heated at 2,273 K. Moreover, our in situ HR-TEM observation reveals an accumulation of topological defects near the kink of a deformed nanotube. This result suggests that dislocation motions or active topological defects are indeed responsible for the plastic deformation of SWNTs.

Crystallographic observation of nonenzymatic RNA primer extension.

PubMed

Zhang, Wen; Walton, Travis; Li, Li; Szostak, Jack W

2018-05-31

The importance of genome replication has inspired detailed crystallographic studies of enzymatic DNA/RNA polymerization. In contrast, the mechanism of nonenzymatic polymerization is less well understood, despite its critical role in the origin of life. Here we report the direct observation of nonenzymatic RNA primer extension through time-resolved crystallography. We soaked crystals of an RNA primer-template-dGMP complex with guanosine-5'-phosphoro-2-aminoimidazolide for increasing times. At early times we see the activated ribonucleotides bound to the template, followed by formation of the imidazolium-bridged dinucleotide intermediate. At later times, we see a new phosphodiester bond forming between the primer and the incoming nucleotide. The intermediate is pre-organized because of the constraints of base-pairing with the template and hydrogen bonding between the imidazole amino group and both flanking phosphates. Our results provide atomic-resolution insight into the mechanism of nonenzymatic primer extension, and set the stage for further structural dissection and optimization of the RNA copying process. © 2018, Zhang et al.

A single-chip event sequencer and related microcontroller instrumentation for atomic physics research.

PubMed

Eyler, E E

2011-01-01

A 16-bit digital event sequencer with 50 ns resolution and 50 ns trigger jitter is implemented by using an internal 32-bit timer on a dsPIC30F4013 microcontroller, controlled by an easily modified program written in standard C. It can accommodate hundreds of output events, and adjacent events can be spaced as closely as 1.5 μs. The microcontroller has robust 5 V inputs and outputs, allowing a direct interface to common laboratory equipment and other electronics. A USB computer interface and a pair of analog ramp outputs can be added with just two additional chips. An optional display/keypad unit allows direct interaction with the sequencer without requiring an external computer. Minor additions also allow simple realizations of other complex instruments, including a precision high-voltage ramp generator for driving spectrum analyzers or piezoelectric positioners, and a low-cost proportional integral differential controller and lock-in amplifier for laser frequency stabilization with about 100 kHz bandwidth.

Structural Characterization of the Boca/Mesd Maturation Factors for LDL-Receptor-Type beta Propeller Domains

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

M Collins; W Hendrickson

2011-12-31

Folding and trafficking of low-density lipoprotein receptor (LDLR) family members, which play essential roles in development and homeostasis, are mediated by specific chaperones. The Boca/Mesd chaperone family specifically promotes folding and trafficking of the YWTD {beta} propeller-EGF domain pair found in the ectodomain of all LDLR members. Limited proteolysis, NMR spectroscopy, analytical ultracentrifugation, and X-ray crystallography were used to define a conserved core composed of a structured domain that is preceded by a disordered N-terminal region. High-resolution structures of the ordered domain were determined for homologous proteins from three metazoans. Seven independent protomers reveal a novel ferrodoxin-like superfamily fold withmore » two distinct {beta} sheet topologies. A conserved hydrophobic surface forms a dimer interface in each crystal, but these differ substantially at the atomic level, indicative of nonspecific hydrophobic interactions that may play a role in the chaperone activity of the Boca/Mesd family.« less

Nanomechanical DNA origami pH sensors.

PubMed

Kuzuya, Akinori; Watanabe, Ryosuke; Yamanaka, Yusei; Tamaki, Takuya; Kaino, Masafumi; Ohya, Yuichi

2014-10-16

Single-molecule pH sensors have been developed by utilizing molecular imaging of pH-responsive shape transition of nanomechanical DNA origami devices with atomic force microscopy (AFM). Short DNA fragments that can form i-motifs were introduced to nanomechanical DNA origami devices with pliers-like shape (DNA Origami Pliers), which consist of two levers of 170-nm long and 20-nm wide connected at a Holliday-junction fulcrum. DNA Origami Pliers can be observed as in three distinct forms; cross, antiparallel and parallel forms, and cross form is the dominant species when no additional interaction is introduced to DNA Origami Pliers. Introduction of nine pairs of 12-mer sequence (5'-AACCCCAACCCC-3'), which dimerize into i-motif quadruplexes upon protonation of cytosine, drives transition of DNA Origami Pliers from open cross form into closed parallel form under acidic conditions. Such pH-dependent transition was clearly imaged on mica in molecular resolution by AFM, showing potential application of the system to single-molecular pH sensors.

Fermion Superfluidity

NASA Technical Reports Server (NTRS)

Strecker, Kevin; Truscott, Andrew; Partridge, Guthrie; Chen, Ying-Cheng

2003-01-01

Dual evaporation gives 50 million fermions at T = 0.1 T(sub F). Demonstrated suppression of interactions by coherent superposition - applicable to atomic clocks. Looking for evidence of Cooper pairing and superfluidity.

Generalized valence bond description of the ground states (X(1)Σg(+)) of homonuclear pnictogen diatomic molecules: N2, P2, and As2.

PubMed

Xu, Lu T; Dunning, Thom H

2015-06-09

The ground state, X1Σg+, of N2 is a textbook example of a molecule with a triple bond consisting of one σ and two π bonds. This assignment, which is usually rationalized using molecular orbital (MO) theory, implicitly assumes that the spins of the three pairs of electrons involved in the bonds are singlet-coupled (perfect pairing). However, for a six-electron singlet state, there are five distinct ways to couple the electron spins. The generalized valence bond (GVB) wave function lifts this restriction, including all of the five spin functions for the six electrons involved in the bond. For N2, we find that the perfect pairing spin function is indeed dominant at Re but that it becomes progressively less so from N2 to P2 and As2. Although the perfect pairing spin function is still the most important spin function in P2, the importance of a quasi-atomic spin function, which singlet couples the spins of the electrons in the σ orbitals while high spin coupling those of the electrons in the π orbitals on each center, has significantly increased relative to N2 and, in As2, the perfect pairing and quasi-atomic spin couplings are on essentially the same footing. This change in the spin coupling of the electrons in the bonding orbitals down the periodic table may contribute to the rather dramatic decrease in the strengths of the Pn2 bonds from N2 to As2 as well as in the increase in their chemical reactivity and should be taken into account in more detailed analyses of the bond energies in these species. We also compare the spin coupling in N2 with that in C2, where the quasi-atomic spin coupling dominants around Re.

Unraveling DNA dynamics using atomic force microscopy.

PubMed

Suzuki, Yuki; Yoshikawa, Yuko; Yoshimura, Shige H; Yoshikawa, Kenichi; Takeyasu, Kunio

2011-01-01

The elucidation of structure-function relationships of biological samples has become important issue in post-genomic researches. In order to unveil the molecular mechanisms controlling gene regulations, it is essential to understand the interplay between fundamental DNA properties and the dynamics of the entire molecule. The wide range of applicability of atomic force microscopy (AFM) has allowed us to extract physicochemical properties of DNA and DNA-protein complexes, as well as to determine their topographical information. Here, we review how AFM techniques have been utilized to study DNA and DNA-protein complexes and what types of analyses have accelerated the understanding of the DNA dynamics. We begin by illustrating the application of AFM to investigate the fundamental feature of DNA molecules; topological transition of DNA, length dependent properties of DNA molecules, flexibility of double-stranded DNA, and capability of the formation of non-Watson-Crick base pairing. These properties of DNA are critical for the DNA folding and enzymatic reactions. The technical advancement in the time-resolution of AFM and sample preparation methods enabled visual analysis of DNA-protein interactions at sub-second time region. DNA tension-dependent enzymatic reaction and DNA looping dynamics by restriction enzymes were examined at a nanoscale in physiological environments. Contribution of physical properties of DNA to dynamics of nucleosomes and transition of the higher-order structure of reconstituted chromatin are also reviewed. Copyright © 2011 John Wiley & Sons, Inc.

Atomic resolution chemical bond analysis of oxygen in La2CuO4

NASA Astrophysics Data System (ADS)

Haruta, M.; Nagai, T.; Lugg, N. R.; Neish, M. J.; Nagao, M.; Kurashima, K.; Allen, L. J.; Mizoguchi, T.; Kimoto, K.

2013-08-01

The distorted CuO6 octahedron in La2CuO4 was studied using aberration-corrected scanning transmission electron microscopy at atomic resolution. The near-edge structure in the oxygen K-edge electron energy-loss spectrum was recorded as a function of the position of the electron probe. After background subtraction, the measured spectrum image was processed using a recently developed inversion process to remove the mixing of signals on the atomic columns due to elastic and thermal scattering. The spectra were then compared with first-principles band structure calculations based on the local-density approximation plus on-site Coulomb repulsion (LDA + U) approach. In this article, we describe in detail not only anisotropic chemical bonding of the oxygen 2p state with the Cu 3d state but also with the Cu 4p and La 5d/4f states. Furthermore, it was found that buckling of the CuO2 plane was also detectable at the atomic resolution oxygen K-edge. Lastly, it was found that the effects of core-hole in the O K-edge were strongly dependent on the nature of the local chemical bonding, in particular, whether it is ionic or covalent.

High-resolution studies of the Majorana atomic chain platform

NASA Astrophysics Data System (ADS)

Feldman, Benjamin E.; Randeria, Mallika T.; Li, Jian; Jeon, Sangjun; Xie, Yonglong; Wang, Zhijun; Drozdov, Ilya K.; Andrei Bernevig, B.; Yazdani, Ali

2017-03-01

Ordered assemblies of magnetic atoms on the surface of conventional superconductors can be used to engineer topological superconducting phases and realize Majorana fermion quasiparticles (MQPs) in a condensed matter setting. Recent experiments have shown that chains of Fe atoms on Pb generically have the required electronic characteristics to form a one-dimensional topological superconductor and have revealed spatially resolved signatures of localized MQPs at the ends of such chains. Here we report higher-resolution measurements of the same atomic chain system performed using a dilution refrigerator scanning tunnelling microscope (STM). With significantly better energy resolution than previous studies, we show that the zero-bias peak (ZBP) in Fe chains has no detectable splitting from hybridization with other states. The measurements also reveal that the ZBP exhibits a distinctive `double eye’ spatial pattern on nanometre length scales. Theoretically we show that this is a general consequence of STM measurements of MQPs with substantial spectral weight in the superconducting substrate, a conclusion further supported by measurements of Pb overlayers deposited on top of the Fe chains. Finally, we report experiments performed with superconducting tips in search of the particle-hole symmetric MQP signature expected in such measurements.

Infrared absorption nano-spectroscopy using sample photoexpansion induced by tunable quantum cascade lasers.

PubMed

Lu, Feng; Belkin, Mikhail A

2011-10-10

We report a simple technique that allows obtaining mid-infrared absorption spectra with nanoscale spatial resolution under low-power illumination from tunable quantum cascade lasers. Light absorption is detected by measuring associated sample thermal expansion with an atomic force microscope. To detect minute thermal expansion we tune the repetition frequency of laser pulses in resonance with the mechanical frequency of the atomic force microscope cantilever. Spatial resolution of better than 50 nm is experimentally demonstrated.

Variable Entry Biased Paracentric Hemispherical Deflector: Experimental results on energy resolution for different entry positions

NASA Astrophysics Data System (ADS)

Dogan, Mevlut; Ulu, Melike; Gennerakis, Giannis; Zouros, Theo J. M.

2014-04-01

A new hemispherical deflector analyzer (HDA) which is designed for electron energy analysis in atomic collisions has been constructed and tested. Using the crossed beam technique at the electron spectrometer, test measurements were performed for electron beam (200 eV) - Helium atoms interactions. These first experimental results show that the paracentric entries give almost twice as good resolution as that for the conventional entry. Supporting simulations of the entire lens+HDA spectrometer are found in relatively good agreement with experiment.

Insights into the Electronic Structure of Ozone and Sulfur Dioxide from Generalized Valence Bond Theory: Addition of Hydrogen Atoms.

PubMed

Lindquist, Beth A; Takeshita, Tyler Y; Dunning, Thom H

2016-05-05

Ozone (O3) and sulfur dioxide (SO2) are valence isoelectronic species, yet their properties and reactivities differ dramatically. In particular, O3 is highly reactive, whereas SO2 is chemically relatively stable. In this paper, we investigate serial addition of hydrogen atoms to both the terminal atoms of O3 and SO2 and to the central atom of these species. It is well-known that the terminal atoms of O3 are much more amenable to bond formation than those of SO2. We show that the differences in the electronic structure of the π systems in the parent triatomic species account for the differences in the addition of hydrogen atoms to the terminal atoms of O3 and SO2. Further, we find that the π system in SO2, which is a recoupled pair bond dyad, facilitates the addition of hydrogen atoms to the sulfur atom, resulting in stable HSO2 and H2SO2 species.

Magnetic trapping of cold bromine atoms.

PubMed

Rennick, C J; Lam, J; Doherty, W G; Softley, T P

2014-01-17

Magnetic trapping of bromine atoms at temperatures in the millikelvin regime is demonstrated for the first time. The atoms are produced by photodissociation of Br2 molecules in a molecular beam. The lab-frame velocity of Br atoms is controlled by the wavelength and polarization of the photodissociation laser. Careful selection of the wavelength results in one of the pair of atoms having sufficient velocity to exactly cancel that of the parent molecule, and it remains stationary in the lab frame. A trap is formed at the null point between two opposing neodymium permanent magnets. Dissociation of molecules at the field minimum results in the slowest fraction of photofragments remaining trapped. After the ballistic escape of the fastest atoms, the trapped slow atoms are lost only by elastic collisions with the chamber background gas. The measured loss rate is consistent with estimates of the total cross section for only those collisions transferring sufficient kinetic energy to overcome the trapping potential.

Quantum State Transmission in a Superconducting Charge Qubit-Atom Hybrid

PubMed Central

Yu, Deshui; Valado, María Martínez; Hufnagel, Christoph; Kwek, Leong Chuan; Amico, Luigi; Dumke, Rainer

2016-01-01

Hybrids consisting of macroscopic superconducting circuits and microscopic components, such as atoms and spins, have the potential of transmitting an arbitrary state between different quantum species, leading to the prospective of high-speed operation and long-time storage of quantum information. Here we propose a novel hybrid structure, where a neutral-atom qubit directly interfaces with a superconducting charge qubit, to implement the qubit-state transmission. The highly-excited Rydberg atom located inside the gate capacitor strongly affects the behavior of Cooper pairs in the box while the atom in the ground state hardly interferes with the superconducting device. In addition, the DC Stark shift of the atomic states significantly depends on the charge-qubit states. By means of the standard spectroscopic techniques and sweeping the gate voltage bias, we show how to transfer an arbitrary quantum state from the superconducting device to the atom and vice versa. PMID:27922087

Improving the accuracy of walking piezo motors.

PubMed

den Heijer, M; Fokkema, V; Saedi, A; Schakel, P; Rost, M J

2014-05-01

Many application areas require ultraprecise, stiff, and compact actuator systems with a high positioning resolution in combination with a large range as well as a high holding and pushing force. One promising solution to meet these conflicting requirements is a walking piezo motor that works with two pairs of piezo elements such that the movement is taken over by one pair, once the other pair reaches its maximum travel distance. A resolution in the pm-range can be achieved, if operating the motor within the travel range of one piezo pair. However, applying the typical walking drive signals, we measure jumps in the displacement up to 2.4 μm, when the movement is given over from one piezo pair to the other. We analyze the reason for these large jumps and propose improved drive signals. The implementation of our new drive signals reduces the jumps to less than 42 nm and makes the motor ideally suitable to operate as a coarse approach motor in an ultra-high vacuum scanning tunneling microscope. The rigidity of the motor is reflected in its high pushing force of 6.4 N.

Improved protein surface comparison and application to low-resolution protein structure data

PubMed Central

2010-01-01

Background Recent advancements of experimental techniques for determining protein tertiary structures raise significant challenges for protein bioinformatics. With the number of known structures of unknown function expanding at a rapid pace, an urgent task is to provide reliable clues to their biological function on a large scale. Conventional approaches for structure comparison are not suitable for a real-time database search due to their slow speed. Moreover, a new challenge has arisen from recent techniques such as electron microscopy (EM), which provide low-resolution structure data. Previously, we have introduced a method for protein surface shape representation using the 3D Zernike descriptors (3DZDs). The 3DZD enables fast structure database searches, taking advantage of its rotation invariance and compact representation. The search results of protein surface represented with the 3DZD has showngood agreement with the existing structure classifications, but some discrepancies were also observed. Results The three new surface representations of backbone atoms, originally devised all-atom-surface representation, and the combination of all-atom surface with the backbone representation are examined. All representations are encoded with the 3DZD. Also, we have investigated the applicability of the 3DZD for searching protein EM density maps of varying resolutions. The surface representations are evaluated on structure retrieval using two existing classifications, SCOP and the CE-based classification. Conclusions Overall, the 3DZDs representing backbone atoms show better retrieval performance than the original all-atom surface representation. The performance further improved when the two representations are combined. Moreover, we observed that the 3DZD is also powerful in comparing low-resolution structures obtained by electron microscopy. PMID:21172052

Measuring Roughnesses Of Optical Surfaces

NASA Technical Reports Server (NTRS)

Coulter, Daniel R.; Al-Jumaily, Gahnim A.; Raouf, Nasrat A.; Anderson, Mark S.

1994-01-01

Report discusses use of scanning tunneling microscopy and atomic force microscopy to measure roughnesses of optical surfaces. These techniques offer greater spatial resolution than other techniques. Report notes scanning tunneling microscopes and atomic force microscopes resolve down to 1 nm.

Surface structure. Subatomic resolution force microscopy reveals internal structure and adsorption sites of small iron clusters.

PubMed

Emmrich, Matthias; Huber, Ferdinand; Pielmeier, Florian; Welker, Joachim; Hofmann, Thomas; Schneiderbauer, Maximilian; Meuer, Daniel; Polesya, Svitlana; Mankovsky, Sergiy; Ködderitzsch, Diemo; Ebert, Hubert; Giessibl, Franz J

2015-04-17

Clusters built from individual iron atoms adsorbed on surfaces (adatoms) were investigated by atomic force microscopy (AFM) with subatomic resolution. Single copper and iron adatoms appeared as toroidal structures and multiatom clusters as connected structures, showing each individual atom as a torus. For single adatoms, the toroidal shape of the AFM image depends on the bonding symmetry of the adatom to the underlying structure [twofold for copper on copper(110) and threefold for iron on copper(111)]. Density functional theory calculations support the experimental data. The findings correct our previous work, in which multiple minima in the AFM signal were interpreted as a reflection of the orientation of a single front atom, and suggest that dual and triple minima in the force signal are caused by dimer and trimer tips, respectively. Copyright © 2015, American Association for the Advancement of Science.

Chemical bond imaging using higher eigenmodes of tuning fork sensors in atomic force microscopy

NASA Astrophysics Data System (ADS)

Ebeling, Daniel; Zhong, Qigang; Ahles, Sebastian; Chi, Lifeng; Wegner, Hermann A.; Schirmeisen, André

2017-05-01

We demonstrate the ability of resolving the chemical structure of single organic molecules using non-contact atomic force microscopy with higher normal eigenmodes of quartz tuning fork sensors. In order to achieve submolecular resolution, CO-functionalized tips at low temperatures are used. The tuning fork sensors are operated in ultrahigh vacuum in the frequency modulation mode by exciting either their first or second eigenmode. Despite the high effective spring constant of the second eigenmode (on the order of several tens of kN/m), the force sensitivity is sufficiently high to achieve atomic resolution above the organic molecules. This is observed for two different tuning fork sensors with different tip geometries (small tip vs. large tip). These results represent an important step towards resolving the chemical structure of single molecules with multifrequency atomic force microscopy techniques where two or more eigenmodes are driven simultaneously.

The linac coherent light source single particle imaging road map

PubMed Central

Aquila, A.; Barty, A.; Bostedt, C.; Boutet, S.; Carini, G.; dePonte, D.; Drell, P.; Doniach, S.; Downing, K. H.; Earnest, T.; Elmlund, H.; Elser, V.; Gühr, M.; Hajdu, J.; Hastings, J.; Hau-Riege, S. P.; Huang, Z.; Lattman, E. E.; Maia, F. R. N. C.; Marchesini, S.; Ourmazd, A.; Pellegrini, C.; Santra, R.; Schlichting, I.; Schroer, C.; Spence, J. C. H.; Vartanyants, I. A.; Wakatsuki, S.; Weis, W. I.; Williams, G. J.

2015-01-01

Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electron laser sources. PMID:26798801

The linac coherent light source single particle imaging road map

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

Aquila, A.; Barty, A.; Bostedt, C.

Intense femtosecond x-ray pulses from free-electron laser sources allow the imaging of individual particles in a single shot. Early experiments at the Linac Coherent Light Source (LCLS) have led to rapid progress in the field and, so far, coherent diffractive images have been recorded from biological specimens, aerosols, and quantum systems with a few-tens-of-nanometers resolution. In March 2014, LCLS held a workshop to discuss the scientific and technical challenges for reaching the ultimate goal of atomic resolution with single-shot coherent diffractive imaging. This paper summarizes the workshop findings and presents the roadmap toward reaching atomic resolution, 3D imaging at free-electronmore » laser sources.« less

Aberration corrected 1.2-MV cold field-emission transmission electron microscope with a sub-50-pm resolution

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

Akashi, Tetsuya; Takahashi, Yoshio; Tanigaki, Toshiaki, E-mail: toshiaki.tanigaki.mv@hitachi.com

2015-02-16

Atomic-resolution electromagnetic field observation is critical to the development of advanced materials and to the unveiling of their fundamental physics. For this purpose, a spherical-aberration corrected 1.2-MV cold field-emission transmission electron microscope has been developed. The microscope has the following superior properties: stabilized accelerating voltage, minimized electrical and mechanical fluctuation, and coherent electron emission. These properties have enabled to obtain 43-pm information transfer. On the bases of these performances, a 43-pm resolution has been obtained by correcting lens aberrations up to the third order. Observations of GaN [411] thin crystal showed a projected atomic locations with a separation of 44 pm.

Super resolution reconstruction of μ-CT image of rock sample using neighbour embedding algorithm

NASA Astrophysics Data System (ADS)

Wang, Yuzhu; Rahman, Sheik S.; Arns, Christoph H.

2018-03-01

X-ray computed tomography (μ-CT) is considered to be the most effective way to obtain the inner structure of rock sample without destructions. However, its limited resolution hampers its ability to probe sub-micro structures which is critical for flow transportation of rock sample. In this study, we propose an innovative methodology to improve the resolution of μ-CT image using neighbour embedding algorithm where low frequency information is provided by μ-CT image itself while high frequency information is supplemented by high resolution scanning electron microscopy (SEM) image. In order to obtain prior for reconstruction, a large number of image patch pairs contain high- and low- image patches are extracted from the Gaussian image pyramid generated by SEM image. These image patch pairs contain abundant information about tomographic evolution of local porous structures under different resolution spaces. Relying on the assumption of self-similarity of porous structure, this prior information can be used to supervise the reconstruction of high resolution μ-CT image effectively. The experimental results show that the proposed method is able to achieve the state-of-the-art performance.

Design considerations for ultra-precision magnetic bearing supported slides

NASA Technical Reports Server (NTRS)

Slocum, Alexander H.; Eisenhaure, David B.

1993-01-01

Development plans for a prototype servocontrolled machine with 1 angstrom resolution of linear motion and 50 mm range of travel are described. Two such devices could then be combined to produce a two dimensional machine for probing large planar objects with atomic resolution, the Angstrom Resolution Measuring Machine (ARMM).

Modeling DNA bubble formation at the atomic scale

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

Beleva, V; Rasmussen, K. O.; Garcia, A. E.

We describe the fluctuations of double stranded DNA molecules using a minimalist Go model over a wide range of temperatures. Minimalist models allow us to describe, at the atomic level, the opening and formation of bubbles in DNA double helices. This model includes all the geometrical constraints in helix melting imposed by the 3D structure of the molecule. The DNA forms melted bubbles within double helices. These bubbles form and break as a function of time. The equilibrium average number of broken base pairs shows a sharp change as a function of T. We observe a temperature profile of sequencemore » dependent bubble formation similar to those measured by Zeng et al. Long nuclei acid molecules melt partially through the formations of bubbles. It is known that CG rich sequences melt at higher temperatures than AT rich sequences. The melting temperature, however, is not solely determined by the CG content, but by the sequence through base stacking and solvent interactions. Recently, models that incorporate the sequence and nonlinear dynamics of DNA double strands have shown that DNA exhibits a very rich dynamics. Recent extensions of the Bishop-Peyrard model show that fluctuations in the DNA structure lead to opening in localized regions, and that these regions in the DNA are associated with transcription initiation sites. 1D and 2D models of DNA may contain enough information about stacking and base pairing interactions, but lack the coupling between twisting, bending and base pair opening imposed by the double helical structure of DNA that all atom models easily describe. However, the complexity of the energy function used in all atom simulations (including solvent, ions, etc) does not allow for the description of DNA folding/unfolding events that occur in the microsecond time scale.« less

Vernier-like super resolution with guided correlated photon pairs.

PubMed

Nespoli, Matteo; Goan, Hsi-Sheng; Shih, Min-Hsiung

2016-01-11

We describe a dispersion-enabled, ultra-low power realization of super-resolution in an integrated Mach-Zehnder interferometer. Our scheme is based on a Vernier-like effect in the coincident detection of frequency correlated, non-degenerate photon pairs at the sensor output in the presence of group index dispersion. We design and simulate a realistic integrated refractive index sensor in a silicon nitride on silica platform and characterize its performance in the proposed scheme. We present numerical results showing a sensitivity improvement upward of 40 times over a traditional sensing scheme. The device we design is well within the reach of modern semiconductor fabrication technology. We believe this is the first metrology scheme that uses waveguide group index dispersion as a resource to attain super-resolution.

Formation routes and structural details of the CaF1 layer on Si(111) from high-resolution noncontact atomic force microscopy data

NASA Astrophysics Data System (ADS)

Rahe, Philipp; Smith, Emily F.; Wollschläger, Joachim; Moriarty, Philip J.

2018-03-01

We investigate the CaF1/Si (111 ) interface using a combination of high-resolution scanning tunneling and noncontact atomic force microscopy operated at cryogenic temperature as well as x-ray photoelectron spectroscopy. Submonolayer CaF1 films grown at substrate temperatures between 550 and 600 ∘C on Si (111 ) surfaces reveal the existence of two island types that are distinguished by their edge topology, nucleation position, measured height, and inner defect structure. Our data suggest a growth model where the two island types are the result of two reaction pathways during CaF1 interface formation. A key difference between these two pathways is identified to arise from the excess species during the growth process, which can be either fluorine or silicon. Structural details as a result of this difference are identified by means of high-resolution noncontact atomic force microscopy and add insights into the growth mode of this heteroepitaxial insulator-on-semiconductor system.

Design and construction of a high-energy photon polarimeter

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

Dugger, M.; Ritchie, B. G.; Sparks, N.

Here, we report on the design and construction of a high-energy photon polarimeter for measuring the degree of polarization of a linearly-polarized photon beam. The photon polarimeter uses the process of pair production on an atomic electron (triplet production). The azimuthal distribution of scattered atomic electrons following triplet production yields information regarding the degree of linear polarization of the incident photon beam. Furthermore, the polarimeter, operated in conjunction with a pair spectrometer, uses a silicon strip detector to measure the recoil electron distribution resulting from triplet photoproduction in a beryllium target foil. The analyzing power Σ A for the devicemore » using a 75 μm beryllium converter foil is about 0.2, with a relative systematic uncertainty in Σ A of 1.5%.« less

Reverse Monte Carlo simulation of Se{sub 80}Te{sub 20} and Se{sub 80}Te{sub 15}Sb{sub 5} glasses

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

Abdel-Baset, A. M.; Rashad, M.; Moharram, A. H.

2013-12-16

Two-dimensional Monte Carlo of the total pair distribution functions g(r) is determined for Se{sub 80}Te{sub 20} and Se{sub 80}Te{sub 15}Sb{sub 5} alloys, and then it used to assemble the three-dimensional atomic configurations using the reverse Monte Carlo simulation. The partial pair distribution functions g{sub ij}(r) indicate that the basic structure unit in the Se{sub 80}Te{sub 15}Sb{sub 5} glass is di-antimony tri-selenide units connected together through Se-Se and Se-Te chain. The structure of Se{sub 80}Te{sub 20} alloys is a chain of Se-Te and Se-Se in addition to some rings of Se atoms.

Design and construction of a high-energy photon polarimeter

DOE PAGES

Dugger, M.; Ritchie, B. G.; Sparks, N.; ...

2017-06-12

Here, we report on the design and construction of a high-energy photon polarimeter for measuring the degree of polarization of a linearly-polarized photon beam. The photon polarimeter uses the process of pair production on an atomic electron (triplet production). The azimuthal distribution of scattered atomic electrons following triplet production yields information regarding the degree of linear polarization of the incident photon beam. Furthermore, the polarimeter, operated in conjunction with a pair spectrometer, uses a silicon strip detector to measure the recoil electron distribution resulting from triplet photoproduction in a beryllium target foil. The analyzing power Σ A for the devicemore » using a 75 μm beryllium converter foil is about 0.2, with a relative systematic uncertainty in Σ A of 1.5%.« less

Finding Semirigid Domains in Biomolecules by Clustering Pair-Distance Variations

PubMed Central

Schreiner, Wolfgang

2014-01-01

Dynamic variations in the distances between pairs of atoms are used for clustering subdomains of biomolecules. We draw on a well-known target function for clustering and first show mathematically that the assignment of atoms to clusters has to be crisp, not fuzzy, as hitherto assumed. This reduces the computational load of clustering drastically, and we demonstrate results for several biomolecules relevant in immunoinformatics. Results are evaluated regarding the number of clusters, cluster size, cluster stability, and the evolution of clusters over time. Crisp clustering lends itself as an efficient tool to locate semirigid domains in the simulation of biomolecules. Such domains seem crucial for an optimum performance of subsequent statistical analyses, aiming at detecting minute motional patterns related to antigen recognition and signal transduction. PMID:24959586

Combination of the pair density approximation and the Takahashi–Imada approximation for path integral Monte Carlo simulations

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

Zillich, Robert E., E-mail: robert.zillich@jku.at

2015-11-15

We construct an accurate imaginary time propagator for path integral Monte Carlo simulations for heterogeneous systems consisting of a mixture of atoms and molecules. We combine the pair density approximation, which is highly accurate but feasible only for the isotropic interactions between atoms, with the Takahashi–Imada approximation for general interactions. We present finite temperature simulations results for energy and structure of molecules–helium clusters X{sup 4}He{sub 20} (X=HCCH and LiH) which show a marked improvement over the Trotter approximation which has a 2nd-order time step bias. We show that the 4th-order corrections of the Takahashi–Imada approximation can also be applied perturbativelymore » to a 2nd-order simulation.« less

Ultracold Atoms in a Square Lattice with Spin-Orbit Coupling: Charge Order, Superfluidity, and Topological Signatures

NASA Astrophysics Data System (ADS)

Rosenberg, Peter; Shi, Hao; Zhang, Shiwei

2017-12-01

We present an ab initio, numerically exact study of attractive fermions in square lattices with Rashba spin-orbit coupling. The ground state of this system is a supersolid, with coexisting charge and superfluid order. The superfluid is composed of both singlet and triplet pairs induced by spin-orbit coupling. We perform large-scale calculations using the auxiliary-field quantum Monte Carlo method to provide the first full, quantitative description of the charge, spin, and pairing properties of the system. In addition to characterizing the exotic physics, our results will serve as essential high-accuracy benchmarks for the intense theoretical and especially experimental efforts in ultracold atoms to realize and understand an expanding variety of quantum Hall and topological superconductor systems.

Syntheses, Raman spectra, and X-ray crystal structures of [XeF(5)][mu-F(OsO(3)F(2))(2)] and [M][OsO(3)F(3)] (M = XeF(5)(+), Xe(2)F(11)(+)).

PubMed

Hughes, Michael J; Mercier, Hélène P A; Schrobilgen, Gary J

2010-04-05

Stoichiometric amounts of XeF(6) and (OsO(3)F(2))(infinity) react at 25-50 degrees C to form salts of the known XeF(5)(+) and Xe(2)F(11)(+) cations, namely, [XeF(5)][mu-F(OsO(3)F(2))(2)], [XeF(5)][OsO(3)F(3)], and [Xe(2)F(11)][OsO(3)F(3)]. Although XeF(6) is oxophilic toward a number of transition metal and main-group oxides and oxide fluorides, fluoride/oxide metathesis was not observed. The series provides the first examples of noble-gas cations that are stabilized by metal oxide fluoride anions and the first example of a mu-F(OsO(3)F(2))(2)(-) salt. Both [XeF(5)][mu-F(OsO(3)F(2))(2)] and [Xe(2)F(11)][OsO(3)F(3)] are orange solids at room temperature. The [XeF(5)][OsO(3)F(3)] salt is an orange liquid at room temperature that solidifies at 5-0 degrees C. When the salts are heated at 50 degrees C under 1 atm of N(2) for more than 2 h, significant XeF(6) loss occurs. The X-ray crystal structures (-173 degrees C) show that the salts exist as discrete ion pairs and that the osmium coordination spheres in OsO(3)F(3)(-) and mu-F(OsO(3)F(2))(2)(-) are pseudo-octahedral OsO(3)F(3)-units having facial arrangements of oxygen and fluorine atoms. The mu-F(OsO(3)F(2))(2)(-) anion is comprised of two symmetry-related OsO(3)F(2)-groups that are fluorine-bridged to one another. Ion pairing results from secondary bonding interactions between the fluorine/oxygen atoms of the anions and the xenon atom of the cation, with the Xe...F/O contacts occurring opposite the axial fluorine and from beneath the equatorial XeF(4)-planes of the XeF(5)(+) and Xe(2)F(11)(+) cations so as to avoid the free valence electron lone pairs of the xenon atoms. The xenon atoms of [XeF(5)][mu-F(OsO(3)F(2))(2)] and [Xe(2)F(11)][OsO(3)F(3)] are nine-coordinate and the xenon atom of [XeF(5)][OsO(3)F(3)] is eight-coordinate. Quantum-chemical calculations at SVWN and B3LYP levels of theory were used to obtain the gas-phase geometries, vibrational frequencies, and NBO bond orders, valencies, and NPA charges of the ion pairs, [Xe(2)F(11)][OsO(3)F(3)], [XeF(5)][OsO(3)F(3)], and [XeF(5)][mu-F(OsO(3)F(2))(2)], as well as those of the free ions, Xe(2)F(11)(+), XeF(5)(+), OsO(3)F(3)(-), and mu-F(OsO(3)F(2))(2)(-). The Raman spectra (-150 degrees C) of the salts have been assigned based on the ion pairs observed in the crystal structures and the calculated vibrational frequencies and intensities of the gas-phase ion pairs.

Module for multiphoton high-resolution hyperspectral imaging and spectroscopy

NASA Astrophysics Data System (ADS)

Zeytunyan, Aram; Baldacchini, Tommaso; Zadoyan, Ruben

2018-02-01

We developed a module for dual-output, dual-wavelength lasers that facilitates multiphoton imaging and spectroscopy experiments and enables hyperspectral imaging with spectral resolution up to 5 cm-1. High spectral resolution is achieved by employing spectral focusing. Specifically, two sets of grating pairs are used to control the chirps in each laser beam. In contrast with the approach that uses fixed-length glass rods, grating pairs allow matching the spectral resolution and the linewidths of the Raman lines of interest. To demonstrate the performance of the module, we report the results of spectral focusing CARS and SRS microscopy experiments for various test samples and Raman shifts. The developed module can be used for a variety of multimodal imaging and spectroscopy applications, such as single- and multi-color two-photon fluorescence, second harmonic generation, third harmonic generation, pump-probe, transient absorption, and others.