An observation of nanotwin lamellae in Cd 0.6Mn 0.4Te crystal by atomic force microscopy

NASA Astrophysics Data System (ADS)

George, M. A.; Azoulay, M.; Collins, W. E.; Burger, A.; Silberman, E.

1993-05-01

Atomic force microscopy (AFM) is used to examine the structure of freshly cleaved Cd 0.6Mn 0.4Te surfaces. The present report complements previous results obtained with X-ray diffraction and optical microscopy which showed the existence of microtwins. The AFM analysis was performed under ambient conditions and yielded nanometer scale resolution images of single twin lamellae that ranged between 20 and 100 nm in width. This is a first observation using AFM of such a substructure, which we interpret as evidence for the presence of nonotwins.

Atomic species identification at the (101) anatase surface by simultaneous scanning tunnelling and atomic force microscopy

PubMed Central

Stetsovych, Oleksandr; Todorović, Milica; Shimizu, Tomoko K.; Moreno, César; Ryan, James William; León, Carmen Pérez; Sagisaka, Keisuke; Palomares, Emilio; Matolín, Vladimír; Fujita, Daisuke; Perez, Ruben; Custance, Oscar

2015-01-01

Anatase is a pivotal material in devices for energy-harvesting applications and catalysis. Methods for the accurate characterization of this reducible oxide at the atomic scale are critical in the exploration of outstanding properties for technological developments. Here we combine atomic force microscopy (AFM) and scanning tunnelling microscopy (STM), supported by first-principles calculations, for the simultaneous imaging and unambiguous identification of atomic species at the (101) anatase surface. We demonstrate that dynamic AFM-STM operation allows atomic resolution imaging within the material's band gap. Based on key distinguishing features extracted from calculations and experiments, we identify candidates for the most common surface defects. Our results pave the way for the understanding of surface processes, like adsorption of metal dopants and photoactive molecules, that are fundamental for the catalytic and photovoltaic applications of anatase, and demonstrate the potential of dynamic AFM-STM for the characterization of wide band gap materials. PMID:26118408

Real-space identification of intermolecular bonding with atomic force microscopy.

PubMed

Zhang, Jun; Chen, Pengcheng; Yuan, Bingkai; Ji, Wei; Cheng, Zhihai; Qiu, Xiaohui

2013-11-01

We report a real-space visualization of the formation of hydrogen bonding in 8-hydroxyquinoline (8-hq) molecular assemblies on a Cu(111) substrate, using noncontact atomic force microscopy (NC-AFM). The atomically resolved molecular structures enable a precise determination of the characteristics of hydrogen bonding networks, including the bonding sites, orientations, and lengths. The observation of bond contrast was interpreted by ab initio density functional calculations, which indicated the electron density contribution from the hybridized electronic state of the hydrogen bond. Intermolecular coordination between the dehydrogenated 8-hq and Cu adatoms was also revealed by the submolecular resolution AFM characterization. The direct identification of local bonding configurations by NC-AFM would facilitate detailed investigations of intermolecular interactions in complex molecules with multiple active sites.

Towards a unified description of the charge transport mechanisms in conductive atomic force microscopy studies of semiconducting polymers.

PubMed

Moerman, D; Sebaihi, N; Kaviyil, S E; Leclère, P; Lazzaroni, R; Douhéret, O

2014-09-21

In this work, conductive atomic force microscopy (C-AFM) is used to study the local electrical properties in thin films of self-organized fibrillate poly(3-hexylthiophene) (P3HT), as a reference polymer semiconductor. Depending on the geometrical confinement in the transport channel, the C-AFM current is shown to be governed either by the charge transport in the film or by the carrier injection at the tip-sample contact, leading to either bulk or local electrical characterization of the semiconducting polymer, respectively. Local I-V profiles allow discrimination of the different dominating electrical mechanisms, i.e., resistive in the transport regime and space charge limited current (SCLC) in the local regime. A modified Mott-Gurney law is analytically derived for the contact regime, taking into account the point-probe geometry of the contact and the radial injection of carriers. Within the SCLC regime, the probed depth is shown to remain below 12 nm with a lateral electrical resolution below 5 nm. This confirms that high resolution is reached in those C-AFM measurements, which therefore allows for the analysis of single organic semiconducting nanostructures. The carrier density and mobility in the volume probed under the tip under steady-state conditions are also determined in the SCLC regime.

Atomic Step Formation on Sapphire Surface in Ultra-precision Manufacturing

PubMed Central

Wang, Rongrong; Guo, Dan; Xie, Guoxin; Pan, Guoshun

2016-01-01

Surfaces with controlled atomic step structures as substrates are highly relevant to desirable performances of materials grown on them, such as light emitting diode (LED) epitaxial layers, nanotubes and nanoribbons. However, very limited attention has been paid to the step formation in manufacturing process. In the present work, investigations have been conducted into this step formation mechanism on the sapphire c (0001) surface by using both experiments and simulations. The step evolutions at different stages in the polishing process were investigated with atomic force microscopy (AFM) and high resolution transmission electron microscopy (HRTEM). The simulation of idealized steps was constructed theoretically on the basis of experimental results. It was found that (1) the subtle atomic structures (e.g., steps with different sawteeth, as well as steps with straight and zigzag edges), (2) the periodicity and (3) the degree of order of the steps were all dependent on surface composition and miscut direction (step edge direction). A comparison between experimental results and idealized step models of different surface compositions has been made. It has been found that the structure on the polished surface was in accordance with some surface compositions (the model of single-atom steps: Al steps or O steps). PMID:27444267

Atomic Step Formation on Sapphire Surface in Ultra-precision Manufacturing

NASA Astrophysics Data System (ADS)

Wang, Rongrong; Guo, Dan; Xie, Guoxin; Pan, Guoshun

2016-07-01

Surfaces with controlled atomic step structures as substrates are highly relevant to desirable performances of materials grown on them, such as light emitting diode (LED) epitaxial layers, nanotubes and nanoribbons. However, very limited attention has been paid to the step formation in manufacturing process. In the present work, investigations have been conducted into this step formation mechanism on the sapphire c (0001) surface by using both experiments and simulations. The step evolutions at different stages in the polishing process were investigated with atomic force microscopy (AFM) and high resolution transmission electron microscopy (HRTEM). The simulation of idealized steps was constructed theoretically on the basis of experimental results. It was found that (1) the subtle atomic structures (e.g., steps with different sawteeth, as well as steps with straight and zigzag edges), (2) the periodicity and (3) the degree of order of the steps were all dependent on surface composition and miscut direction (step edge direction). A comparison between experimental results and idealized step models of different surface compositions has been made. It has been found that the structure on the polished surface was in accordance with some surface compositions (the model of single-atom steps: Al steps or O steps).

Interplay between Mechanics, Electronics, and Energetics in Atomic-Scale Junctions

NASA Astrophysics Data System (ADS)

Aradhya, Sriharsha V.

The physical properties of materials at the nanoscale are controlled to a large extent by their interfaces. While much knowledge has been acquired about the properties of material in the bulk, there are many new and interesting phenomena at the interfaces that remain to be better understood. This is especially true at the scale of their constituent building blocks - atoms and molecules. Studying materials at this intricate level is a necessity at this point in time because electronic devices are rapidly approaching the limits of what was once thought possible, both in terms of their miniaturization as well as our ability to design their behavior. In this thesis I present our explorations of the interplay between mechanical properties, electronic transport and binding energetics of single atomic contacts and single-molecule junctions. Experimentally, we use a customized conducting atomic force microscope (AFM) that simultaneously measures the current and force across atomic-scale junctions. We use this instrument to study single atomic contacts of gold and silver and single-molecule junctions formed in the gap between two gold metallic point contacts, with molecules with a variety of backbones and chemical linker groups. Combined with density functional theory based simulations and analytical modeling, these experiments provide insight into the correlations between mechanics and electronic structure at the atomic level. In carrying out these experimental studies, we repeatedly form and pull apart nanoscale junctions between a metallized AFM cantilever tip and a metal-coated substrate. The force and conductance of the contact are simultaneously measured as each junction evolves through a series of atomic-scale rearrangements and bond rupture events, frequently resulting in single atomic contacts before rupturing completely. The AFM is particularly optimized to achieve high force resolution with stiff probes that are necessary to create and measure forces across atomic-size junctions that are otherwise difficult to fabricate using conventional lithographic techniques. In addition to the instrumentation, we have developed new algorithmic routines to perform statistical analyses of force data, with varying degrees of reliance on the conductance signatures. The key results presented in this thesis include our measurements with gold metallic contacts, through which we are able to rigorously characterize the stiffness and maximum forces sustained by gold single atomic contacts and many different gold-molecule-gold single-molecule junctions. In our experiments with silver metallic contacts we use statistical correlations in conductance to distinguish between pristine and oxygen-contaminated silver single atomic contacts. This allows us to separately obtain mechanical information for each of these structural motifs. The independently measured force data also provides new insights about atomic-scale junctions that are not possible to obtain through conductance measurements alone. Using a systematically designed set of molecules, we are able to demonstrate that quantum interference is not quenched in single-molecule junctions even at room temperature and ambient conditions. We have also been successful in conducting one of the first quantitative measurements of van der Waals forces at the metal-molecule interface at the single-molecule level. Finally, towards the end of this thesis, we present a general analytical framework to quantitatively reconstruct the binding energy curves of atomic-scale junctions directly from experiments, thereby unifying all of our mechanical measurements. I conclude with a summary of the work presented in this thesis, and an outlook for potential future studies that could be guided by this work.

Stabilization of Au Monatomic-High Islands on the (2 ×2 )-Nad Reconstructed Surface of Wurtzite AlN(0001)

NASA Astrophysics Data System (ADS)

Eydoux, Benoit; Baris, Bulent; Khoussa, Hassan; Guillermet, Olivier; Gauthier, Sébastien; Bouju, Xavier; Martrou, David

2017-10-01

Noncontact atomic force microscopy images show that gold grows on the (2 ×2 )-Nad reconstructed polar (0001) surface of AlN insulating films, in the form of large monatomic islands. High-resolution images and in situ reflection high-energy electron diffraction spectra reveal two moiré patterns from which an atomic model can be built. Density functional theory calculations confirm this model and give insight into the mechanisms that lead to the stabilization of the monolayer. Gold adsorption is accompanied, first, by a global vertical charge transfer from the AlN substrate that fulfills the electrostatic stability criterion for a polar material, and second, by lateral charge transfers that are driven by the local chemical properties of the (2 ×2 )-Nad reconstruction. These results present alternative strategies to grow metal electrodes onto nitride compounds with a better controlled interface, a crucial issue for applications.

Sub-diffraction nano manipulation using STED AFM.

PubMed

Chacko, Jenu Varghese; Canale, Claudio; Harke, Benjamin; Diaspro, Alberto

2013-01-01

In the last two decades, nano manipulation has been recognized as a potential tool of scientific interest especially in nanotechnology and nano-robotics. Contemporary optical microscopy (super resolution) techniques have also reached the nanometer scale resolution to visualize this and hence a combination of super resolution aided nano manipulation ineluctably gives a new perspective to the scenario. Here we demonstrate how specificity and rapid determination of structures provided by stimulated emission depletion (STED) microscope can aid another microscopic tool with capability of mechanical manoeuvring, like an atomic force microscope (AFM) to get topological information or to target nano scaled materials. We also give proof of principle on how high-resolution real time visualization can improve nano manipulation capability within a dense sample, and how STED-AFM is an optimal combination for this job. With these evidences, this article points to future precise nano dissections and maybe even to a nano-snooker game with an AFM tip and fluorospheres.

Modulating RNA Alignment Using Directional Dynamic Kinks: Application in Determining an Atomic-Resolution Ensemble for a Hairpin using NMR Residual Dipolar Couplings.

PubMed

Salmon, Loïc; Giambaşu, George M; Nikolova, Evgenia N; Petzold, Katja; Bhattacharya, Akash; Case, David A; Al-Hashimi, Hashim M

2015-10-14

Approaches that combine experimental data and computational molecular dynamics (MD) to determine atomic resolution ensembles of biomolecules require the measurement of abundant experimental data. NMR residual dipolar couplings (RDCs) carry rich dynamics information, however, difficulties in modulating overall alignment of nucleic acids have limited the ability to fully extract this information. We present a strategy for modulating RNA alignment that is based on introducing variable dynamic kinks in terminal helices. With this strategy, we measured seven sets of RDCs in a cUUCGg apical loop and used this rich data set to test the accuracy of an 0.8 μs MD simulation computed using the Amber ff10 force field as well as to determine an atomic resolution ensemble. The MD-generated ensemble quantitatively reproduces the measured RDCs, but selection of a sub-ensemble was required to satisfy the RDCs within error. The largest discrepancies between the RDC-selected and MD-generated ensembles are observed for the most flexible loop residues and backbone angles connecting the loop to the helix, with the RDC-selected ensemble resulting in more uniform dynamics. Comparison of the RDC-selected ensemble with NMR spin relaxation data suggests that the dynamics occurs on the ps-ns time scales as verified by measurements of R(1ρ) relaxation-dispersion data. The RDC-satisfying ensemble samples many conformations adopted by the hairpin in crystal structures indicating that intrinsic plasticity may play important roles in conformational adaptation. The approach presented here can be applied to test nucleic acid force fields and to characterize dynamics in diverse RNA motifs at atomic resolution.

Probing microbubble targeting with atomic force microscopy.

PubMed

Sboros, V; Glynos, E; Ross, J A; Moran, C M; Pye, S D; Butler, M; McDicken, W N; Brown, S B; Koutsos, V

2010-10-01

Microbubble science is expanding beyond ultrasound imaging applications to biological targeting and drug/gene delivery. The characteristics of molecular targeting should be tested by a measurement system that can assess targeting efficacy and strength. Atomic force microscopy (AFM) is capable of piconewton force resolution, and is reported to measure the strength of single hydrogen bonds. An in-house targeted microbubble modified using the biotin-avidin chemistry and the CD31 antibody was used to probe cultures of Sk-Hep1 hepatic endothelial cells. We report that the targeted microbubbles provide a single distribution of adhesion forces with a median of 93pN. This interaction is assigned to the CD31 antibody-antigen unbinding event. Information on the distances between the interaction forces was obtained and could be important for future microbubble fabrication. In conclusion, the capability of single microbubbles to target cell lines was shown to be feasible with AFM.

From surface to intracellular non-invasive nanoscale study of living cells impairments

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

Ewald, Dr. Maxime; Tetard, Laurene; Elie-Caille, Dr. Cecile

Among the enduring challenges in nanoscience, subsurface characterization of live cells holds major stakes. Developments in nanometrology for soft matter thriving on the sensitivity and high resolution benefits of atomic force microscopy have enabled detection of subsurface structures at the nanoscale (1,2,3). However, measurements in liquid environments remain complex (4,5,6,7), in particular in the subsurface domain. Here we introduce liquid-Mode Synthesizing Atomic Force Microscopy (l-MSAFM) to study both the inner structures and the chemically induced intracellular impairments of living cells. Specifically, we visualize the intracellular stress effects of glyphosate on living keratinocytes skin cells. This new approach for living cellmore » nanoscale imaging, l-MSAFM, in their physiological environment or in presence of a chemical stress agent confirmed the loss of inner structures induced by glyphosate. The ability to monitor the cell's inner response to external stimuli, non-destructively and in real time, has the potential to unveil critical nanoscale mechanisms of life science.« less

Immunoactive two-dimensional self-assembly of monoclonal antibodies in aqueous solution revealed by atomic force microscopy

NASA Astrophysics Data System (ADS)

Ido, Shinichiro; Kimiya, Hirokazu; Kobayashi, Kei; Kominami, Hiroaki; Matsushige, Kazumi; Yamada, Hirofumi

2014-03-01

The conformational flexibility of antibodies in solution directly affects their immune function. Namely, the flexible hinge regions of immunoglobulin G (IgG) antibodies are essential in epitope-specific antigen recognition and biological effector function. The antibody structure, which is strongly related to its functions, has been partially revealed by electron microscopy and X-ray crystallography, but only under non-physiological conditions. Here we observed monoclonal IgG antibodies in aqueous solution by high-resolution frequency modulation atomic force microscopy (FM-AFM). We found that monoclonal antibodies self-assemble into hexamers, which form two-dimensional crystals in aqueous solution. Furthermore, by directly observing antibody-antigen interactions using FM-AFM, we revealed that IgG molecules in the crystal retain immunoactivity. As the self-assembled monolayer crystal of antibodies retains immunoactivity at a neutral pH and is functionally stable at a wide range of pH and temperature, the antibody crystal is applicable to new biotechnological platforms for biosensors or bioassays.

From surface to intracellular non-invasive nanoscale study of living cells impairments

NASA Astrophysics Data System (ADS)

Ewald, M.; Tetard, L.; Elie-Caille, C.; Nicod, L.; Passian, A.; Bourillot, E.; Lesniewska, E.

2014-07-01

Among the enduring challenges in nanoscience, subsurface characterization of living cells holds major stakes. Developments in nanometrology for soft matter thriving on the sensitivity and high resolution benefits of atomic force microscopy have enabled detection of subsurface structures at the nanoscale. However, measurements in liquid environments remain complex, in particular in the subsurface domain. Here we introduce liquid-mode synthesizing atomic force microscopy (l-MSAFM) to study both the inner structures and the chemically induced intracellular impairments of living cells. Specifically, we visualize the intracellular stress effects of glyphosate on living keratinocytes skin cells. This new approach, l-MSAFM, for nanoscale imaging of living cell in their physiological environment or in presence of a chemical stress agent could resolve the loss of inner structures induced by glyphosate, the main component of a well-known pesticide (RoundUp™). This firsthand ability to monitor the cell’s inner response to external stimuli non-destructively and in liquid, has the potential to unveil critical nanoscale mechanisms of life science.

Structure of single-supported DMPC lipid bilayer membranes as a function of hydration level studied by neutron reflectivity and Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Miskowiec, A.; Schnase, P.; Bai, M.; Taub, H.; Hansen, F. Y.; Dubey, M.; Singh, S.; Majewski, J.

2012-02-01

We have recently been investigating the diffusion of water on single-supported DMPC lipid bilayer membranes at different levels of hydration, using high-resolution quasielastic neutron scattering (QNS). To aid in the interpretation of these QNS studies, we have conducted neutron reflectivity (NR) measurements on SPEAR at LANSCE to characterize the structure of similarly prepared samples. Protonated DMPC membranes were deposited onto SiO2-coated Si(100) substrates and characterized by Atomic Force Microscopy (AFM) at different levels of hydration. We find reasonable agreement between the membrane thickness determined by NR and AFM at room temperature. We also find consistency between the scattering length density (SLD) profile in the vicinity of the upper leaflet of the supported DMPC membrane and that found in a molecular dynamics simulation of a freestanding membrane at 303 K. However, the fit to the reflectivity curve can be improved by modifying the SLD profile near the leaflet closest to the SiO2 surface.

Development of first ever scanning probe microscopy capabilities for plutonium

NASA Astrophysics Data System (ADS)

Beaux, Miles F.; Cordoba, Miguel Santiago; Zocco, Adam T.; Vodnik, Douglas R.; Ramos, Michael; Richmond, Scott; Moore, David P.; Venhaus, Thomas J.; Joyce, Stephen A.; Usov, Igor O.

2017-04-01

Scanning probe microscopy capabilities have been developed for plutonium and its derivative compounds. Specifically, a scanning tunneling microscope and an atomic force microscope housed in an ultra-high vacuum system and an inert atmosphere glove box, respectively, were prepared for the introduction of small non-dispersible δ-Pu coupons. Experimental details, procedures, and preliminary imaging of δ-Pu coupons are presented to demonstrate the functionality of these new capabilities. These first of a kind capabilities for plutonium represent a significant step forward in the ability to characterize and understand plutonium surfaces with high spatial resolution.

Development of first ever scanning probe microscopy capabilities for plutonium

DOE PAGES

Beaux, Miles F.; Cordoba, Miguel Santiago; Zocco, Adam T.; ...

2017-04-01

Scanning probe microscopy capabilities have been developed for plutonium and its derivative compounds. Specifically, a scanning tunneling microscope and an atomic force microscope housed in an ultra-high vacuum system and an inert atmosphere glove box, respectively, were prepared for the introduction of small non-dispersible δ-Pu coupons. Experimental details, procedures, and preliminary imaging of δ-Pu coupons are presented to demonstrate the functionality of these new capabilities. In conclusion, these first of a kind capabilities for plutonium represent a significant step forward in the ability to characterize and understand plutonium surfaces with high spatial resolution.

PREFACE: NC-AFM 2003: Proceedings of the 6th International Conference on Non-contact Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Reichling, Michael

2004-02-01

Direct nanoscale and atomic resolution imaging is a key issue in nanoscience and nanotechnology. The invention of the dynamic force microscope in the early 1990s was an important step forward in this direction as this instrument provides a universal tool for measuring the topography and many other physical and chemical properties of surfaces at the nanoscale. Operation in the so-called non-contact mode now allows direct atomic resolution imaging of electrically insulating surfaces and nanostructures which has been an unsolved problem during the first decade of nanotechnology. Today, we face a most rapid development of the technique and an extension of its capabilities far beyond imaging; atomically resolved force spectroscopy provides information about local binding properties and researchers now develop sophisticated schemes of force controlled atomic manipulation with the tip of the force microscope. Progress in the field of non-contact force microscopy is discussed at the annually held NC-AFM conferences that are part of a series started in 1998 with a meeting in Osaka, Japan. The 6th International Conference on Non-contact Atomic Force Microscopy took place in Dingle, Ireland, from 31 August to 3 September 2003 and this special issue is a compilation of the original publications of work presented at this meeting. The papers published here well reflect recent achievements, current trends and some of the challenging new directions in non-contact force microscopy that have been discussed during the most stimulating conference days in Dingle. Fundamental aspects of forces and dissipation relevant in imaging and spectroscopy have been covered by experimental and theoretical contributions yielding a more detailed understanding of tip--surface interaction in force microscopy. Novel and improved imaging and spectroscopy techniques have been introduced that either improve the performance of force microscopy or pave the way towards new functionalities and applications. With regard to studies on the specific systems investigated, there was a strong emphasis on oxides and ionics, as well as on organic systems. Following previous pioneering work in uncovering the atomic structure of insulating oxides with force microscopy, it was shown in the meeting that this important class of materials is now accessible for a quantitative atomic scale surface characterization. Single organic molecules and ordered organic layers are building blocks for functional nanostructures currently developed in many laboratories for applications in molecular electronics and sensor technologies. The Dingle conference impressively demonstrated that dynamic force microscopy is ready for its application as an analytical tool for these promising future nanotechnologies. The meeting was a great success scientifically and participants enjoyed the beauty of the conference site. I would like to thank all members of the international steering committee, the programme committee and the co-chairs, J Pethica, A Shluger and G Thornton, for their efforts in preparing the meeting. The members of the local organising committee, J Ballentine-Armstrong, G Cross, S Dunne, S Jarvis and Ö Özer, kept the meeting running smoothly and created a very pleasant atmosphere. The generous financial support from Science Foundation Ireland (SFI), is greatly appreciated; SFI is dramatically raising the profile of Irish science. I would also like to express my sincere gratitude to N Couzin and the journal team from Institute of Physics Publishing for their editorial management and perfect co-operation in the preparation of this special issue.

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.

Mechanically adjustable single-molecule transistors and stencil mask nanofabrication of high-resolution scanning probes

NASA Astrophysics Data System (ADS)

Champagne, Alexandre

This dissertation presents the development of two original experimental techniques to probe nanoscale objects. The first one studies electronic transport in single organic molecule transistors in which the source-drain electrode spacing is mechanically adjustable. The second involves the fabrication of high-resolution scanning probe microscopy sensors using a stencil mask lithography technique. We describe the fabrication of transistors in which a single organic molecule can be incorporated. The source and drain leads of these transistors are freely suspended above a flexible substrate, and their spacing can be adjusted by bending the substrate. We detail the technology developed to carry out measurements on these samples. We study electronic transport in single C60 molecules at low temperature. We observe Coulomb blockaded transport and can resolve the discrete energy spectrum of the molecule. We are able to mechanically tune the spacing between the electrodes (over a range of 5 A) to modulate the lead-molecule coupling, and can electrostatically tune the energy levels on the molecule by up to 160 meV using a gate electrode. Initial progress in studying different transport regimes in other molecules is also discussed. We present a lithographic process that allows the deposition of metal nanostructures with a resolution down to 10 nm directly onto atomic force microscope (AFM) tips. We show that multiple layers of lithography can be deposited and aligned. We fabricate high-resolution magnetic force microscopy (MFM) probes using this method and discuss progress to fabricate other scanning probe microscopy (SPM) sensors.

InSe monolayer: synthesis, structure and ultra-high second-harmonic generation

NASA Astrophysics Data System (ADS)

Zhou, Jiadong; Shi, Jia; Zeng, Qingsheng; Chen, Yu; Niu, Lin; Liu, Fucai; Yu, Ting; Suenaga, Kazu; Liu, Xinfeng; Lin, Junhao; Liu, Zheng

2018-04-01

III–IV layered materials such as indium selenide have excellent photoelectronic properties. However, synthesis of materials in such group, especially with a controlled thickness down to monolayer, still remains challenging. Herein, we demonstrate the successful synthesis of monolayer InSe by physical vapor deposition (PVD) method. The high quality of the sample was confirmed by complementary characterization techniques such as Raman spectroscopy, atomic force microscopy (AFM) and high resolution annular dark field scanning transmission electron microscopy (ADF-STEM). We found the co-existence of different stacking sequence (β- and γ-InSe) in the same flake with a sharp grain boundary in few-layered InSe. Edge reconstruction is also observed in monolayer InSe, which has a distinct atomic structure from the bulk lattice. Moreover, we discovered that the second-harmonic generation (SHG) signal from monolayer InSe shows large optical second-order susceptibility that is 1–2 orders of magnitude higher than MoS2, and even 3 times of the largest value reported in monolayer GaSe. These results make atom-thin InSe a promising candidate for optoelectronic and photosensitive device applications.

Investigating biomolecular recognition at the cell surface using atomic force microscopy.

PubMed

Wang, Congzhou; Yadavalli, Vamsi K

2014-05-01

Probing the interaction forces that drive biomolecular recognition on cell surfaces is essential for understanding diverse biological processes. Force spectroscopy has been a widely used dynamic analytical technique, allowing measurement of such interactions at the molecular and cellular level. The capabilities of working under near physiological environments, combined with excellent force and lateral resolution make atomic force microscopy (AFM)-based force spectroscopy a powerful approach to measure biomolecular interaction forces not only on non-biological substrates, but also on soft, dynamic cell surfaces. Over the last few years, AFM-based force spectroscopy has provided biophysical insight into how biomolecules on cell surfaces interact with each other and induce relevant biological processes. In this review, we focus on describing the technique of force spectroscopy using the AFM, specifically in the context of probing cell surfaces. We summarize recent progress in understanding the recognition and interactions between macromolecules that may be found at cell surfaces from a force spectroscopy perspective. We further discuss the challenges and future prospects of the application of this versatile technique. Copyright © 2014 Elsevier Ltd. All rights reserved.

Combining Coarse-Grained Protein Models with Replica-Exchange All-Atom Molecular Dynamics

PubMed Central

Wabik, Jacek; Kmiecik, Sebastian; Gront, Dominik; Kouza, Maksim; Koliński, Andrzej

2013-01-01

We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a model system of protein folding. After reconstructing atomistic details, conformations derived from the CABS simulation were subjected to replica-exchange molecular dynamics simulations with OPLS-AA and AMBER99sb force fields in explicit solvent. Such a combination accelerates system convergence several times in comparison with all-atom simulations starting from the extended chain conformation, demonstrated by the analysis of melting curves, the number of native-like conformations as a function of time and secondary structure propagation. The results strongly suggest that the proposed multiscale method could be an efficient and accurate tool for high-resolution studies of protein folding dynamics in larger systems. PMID:23665897

Protein crystals as scanned probes for recognition atomic force microscopy.

PubMed

Wickremasinghe, Nissanka S; Hafner, Jason H

2005-12-01

Lysozyme crystal growth has been localized at the tip of a conventional silicon nitride cantilever through seeded nucleation. After cross-linking with glutaraldehyde, lysozyme protein crystal tips image gold nanoparticles and grating standards with a resolution comparable to that of conventional tips. Force spectra between the lysozyme crystal tips and surfaces covered with antilysozyme reveal an adhesion force that drops significantly upon blocking with free lysozyme, thus confirming that lysozyme crystal tips can detect molecular recognition interactions.

Close encounters with DNA

PubMed Central

Maffeo, C.; Yoo, J.; Comer, J.; Wells, D. B.; Luan, B.; Aksimentiev, A.

2014-01-01

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena and we review the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field. PMID:25238560

Close encounters with DNA.

PubMed

Maffeo, C; Yoo, J; Comer, J; Wells, D B; Luan, B; Aksimentiev, A

2014-10-15

Over the past ten years, the all-atom molecular dynamics method has grown in the scale of both systems and processes amenable to it and in its ability to make quantitative predictions about the behavior of experimental systems. The field of computational DNA research is no exception, witnessing a dramatic increase in the size of systems simulated with atomic resolution, the duration of individual simulations and the realism of the simulation outcomes. In this topical review, we describe the hallmark physical properties of DNA from the perspective of all-atom simulations. We demonstrate the amazing ability of such simulations to reveal the microscopic physical origins of experimentally observed phenomena. We also discuss the frustrating limitations associated with imperfections of present atomic force fields and inadequate sampling. The review is focused on the following four physical properties of DNA: effective electric charge, response to an external mechanical force, interaction with other DNA molecules and behavior in an external electric field.

Computational simulation of subatomic-resolution AFM and STM images for graphene/hexagonal boron nitride heterostructures with intercalated defects

NASA Astrophysics Data System (ADS)

Lee, Junsu; Kim, Minjung; Chelikowsky, James R.; Kim, Gunn

2016-07-01

Using ab initio density functional calculations, we predict subatomic-resolution atomic force microscopy (AFM) and scanning tunneling microscopy (STM) images of vertical heterostructures of graphene/hexagonal boron nitride (h-BN) with an intercalated metal atom (Li, K, Cr, Mn, Co, or Cu), and study the effects of the extrinsic metal defect on the interfacial coupling. We find that the structural deformation of the graphene/h-BN layer caused by the metal defect strongly affects the AFM images, whereas orbital hybridization between the metal defect and the graphene/h-BN layer characterizes the STM images.

Force Spectroscopy with 9-μs Resolution and Sub-pN Stability by Tailoring AFM Cantilever Geometry.

PubMed

Edwards, Devin T; Faulk, Jaevyn K; LeBlanc, Marc-André; Perkins, Thomas T

2017-12-19

Atomic force microscopy (AFM)-based single-molecule force spectroscopy (SMFS) is a powerful yet accessible means to characterize the unfolding/refolding dynamics of individual molecules and resolve closely spaced, transiently occupied folding intermediates. On a modern commercial AFM, these applications and others are now limited by the mechanical properties of the cantilever. Specifically, AFM-based SMFS data quality is degraded by a commercial cantilever's limited combination of temporal resolution, force precision, and force stability. Recently, we modified commercial cantilevers with a focused ion beam to optimize their properties for SMFS. Here, we extend this capability by modifying a 40 × 18 μm 2 cantilever into one terminated with a gold-coated, 4 × 4 μm 2 reflective region connected to an uncoated 2-μm-wide central shaft. This "Warhammer" geometry achieved 8.5-μs resolution coupled with improved force precision and sub-pN stability over 100 s when measured on a commercial AFM. We highlighted this cantilever's biological utility by first resolving a calmodulin unfolding intermediate previously undetected by AFM and then measuring the stabilization of calmodulin by myosin light chain kinase at dramatically higher unfolding velocities than in previous AFM studies. More generally, enhancing data quality via an improved combination of time resolution, force precision, and force stability will broadly benefit biological applications of AFM. Published by Elsevier Inc.

DMD-based LED-illumination super-resolution and optical sectioning microscopy.

PubMed

Dan, Dan; Lei, Ming; Yao, Baoli; Wang, Wen; Winterhalder, Martin; Zumbusch, Andreas; Qi, Yujiao; Xia, Liang; Yan, Shaohui; Yang, Yanlong; Gao, Peng; Ye, Tong; Zhao, Wei

2013-01-01

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×10(7) pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens.

DMD-based LED-illumination Super-resolution and optical sectioning microscopy

PubMed Central

Dan, Dan; Lei, Ming; Yao, Baoli; Wang, Wen; Winterhalder, Martin; Zumbusch, Andreas; Qi, Yujiao; Xia, Liang; Yan, Shaohui; Yang, Yanlong; Gao, Peng; Ye, Tong; Zhao, Wei

2013-01-01

Super-resolution three-dimensional (3D) optical microscopy has incomparable advantages over other high-resolution microscopic technologies, such as electron microscopy and atomic force microscopy, in the study of biological molecules, pathways and events in live cells and tissues. We present a novel approach of structured illumination microscopy (SIM) by using a digital micromirror device (DMD) for fringe projection and a low-coherence LED light for illumination. The lateral resolution of 90 nm and the optical sectioning depth of 120 μm were achieved. The maximum acquisition speed for 3D imaging in the optical sectioning mode was 1.6×107 pixels/second, which was mainly limited by the sensitivity and speed of the CCD camera. In contrast to other SIM techniques, the DMD-based LED-illumination SIM is cost-effective, ease of multi-wavelength switchable and speckle-noise-free. The 2D super-resolution and 3D optical sectioning modalities can be easily switched and applied to either fluorescent or non-fluorescent specimens. PMID:23346373

Refractive index profiles of Ge-doped optical fibers with nanometer spatial resolution using atomic force microscopy.

PubMed

Pace, P; Huntington, Shane; Lyytikäinen, K; Roberts, A; Love, J

2004-04-05

We show a quantitative connection between Refractive Index Profiles (RIP) and measurements made by an Atomic Force Microscope (AFM). Germanium doped fibers were chemically etched in hydrofluoric acid solution (HF) and the wet etching characteristics of germanium were studied using an AFM. The AFM profiles were compared to both a concentration profile of the preform determined using a Scanning Electron Microscope (SEM) and a RIP of the fiber measured using a commercial profiling instrument, and were found to be in excellent agreement. It is now possible to calculate the RIP of a germanium doped fiber directly from an AFM profile.

Large-Scale Fabrication of Carbon Nanotube Probe Tips For Atomic Force Microscopy Critical Dimension Imaging Applications

NASA Technical Reports Server (NTRS)

Ye, Qi Laura; Cassell, Alan M.; Stevens, Ramsey M.; Meyyappan, Meyya; Li, Jun; Han, Jie; Liu, Hongbing; Chao, Gordon

2004-01-01

Carbon nanotube (CNT) probe tips for atomic force microscopy (AFM) offer several advantages over Si/Si3N4 probe tips, including improved resolution, shape, and mechanical properties. This viewgraph presentation discusses these advantages, and the drawbacks of existing methods for fabricating CNT probe tips for AFM. The presentation introduces a bottom up wafer scale fabrication method for CNT probe tips which integrates catalyst nanopatterning and nanomaterials synthesis with traditional silicon cantilever microfabrication technology. This method makes mass production of CNT AFM probe tips feasible, and can be applied to the fabrication of other nanodevices with CNT elements.

Glyphosate-induced stiffening of HaCaT keratinocytes, a Peak Force Tapping study on living cells.

PubMed

Heu, Celine; Berquand, Alexandre; Elie-Caille, Celine; Nicod, Laurence

2012-04-01

The skin is the first physiological barrier, with a complex constitution, that provides defensive functions against multiple physical and chemical aggressions. Glyphosate is an extensively used herbicide that has been shown to increase the risk of cancer. Moreover there is increasing evidence suggesting that the mechanical phenotype plays an important role in malignant transformation. Atomic force microscopy (AFM) has emerged within the last decade as a powerful tool for providing a nanometer-scale resolution imaging of biological samples. Peak Force Tapping (PFT) is a newly released AFM-based investigation technique allowing extraction of chemical and mechanical properties from a wide range of samples at a relatively high speed and a high resolution. The present work uses the PFT technology to investigate HaCaT keratinocytes, a human epidermal cell line, and offers an original approach to study chemically-induced changes in the cellular mechanical properties under near-physiological conditions. These experiments indicate glyphosate induces cell membrane stiffening, and the appearance of cytoskeleton structures at a subcellular level, for low cytotoxic concentrations whereas cells exposed to IC50 (inhibitory concentration 50%) treatment exhibit control-like mechanical behavior despite obvious membrane damages. Quercetin, a well-known antioxidant, reverses the glyphosate-induced mechanical phenotype. Copyright © 2012 Elsevier Inc. All rights reserved.

Toward correlating structure and mechanics of platelets.

PubMed

Sorrentino, Simona; Studt, Jan-Dirk; Horev, Melanie Bokstad; Medalia, Ohad; Sapra, K Tanuj

2016-09-02

The primary physiological function of blood platelets is to seal vascular lesions after injury and form hemostatic thrombi in order to prevent blood loss. This task relies on the formation of strong cellular-extracellular matrix interactions in the subendothelial lesions. The cytoskeleton of a platelet is key to all of its functions: its ability to spread, adhere and contract. Despite the medical significance of platelets, there is still no high-resolution structural information of their cytoskeleton. Here, we discuss and present 3-dimensional (3D) structural analysis of intact platelets by using cryo-electron tomography (cryo-ET) and atomic force microscopy (AFM). Cryo-ET provides in situ structural analysis and AFM gives stiffness maps of the platelets. In the future, combining high-resolution structural and mechanical techniques will bring new understanding of how structural changes modulate platelet stiffness during activation and adhesion.

Preparation of superhydrophobic and transparent micro-nano hybrid coatings from polymethylhydroxysiloxane and silica ormosil aerogels

NASA Astrophysics Data System (ADS)

Nagappan, Saravanan; Park, Jin Joo; Park, Sung Soo; Ha, Chang-Sik

2014-12-01

Superhydrophobic and transparent polymethylhydroxysiloxane (PMHOS)/silica ormosil aerogel hybrids were prepared successfully by mixing of PMHOS with various weight percentages of silica ormosil aerogels (as synthesized from methyltriethoxysilane (MTES) and methyltrimethoxysilane (MTMS) precursors) in separate seal perfume glass vials. The hybrids were spin coated on glass substrate at 1000 rpm for 60 seconds and used for further analysis. The surface morphology and chemical compositions of the hybrids were analyzed by high resolution scanning electron microscopy, high resolution transmission electron microscopy, atomic force spectroscopy, adsorption and desorption isotherm, and X-ray photoelectron spectroscopy. The transparency, thermal decomposition and static contact angle (SCA) of each sample were measured by UV-Visible spectrophotometer, TGA and drop shape analysis system, respectively. The spin coated substrates showed good superhydrophobic properties, thermal stability as well as transparency on the glass substrates.

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.

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy.

PubMed

Banerjee, T; Banerjee, S; Sett, S; Ghosh, S; Rakshit, T; Mukhopadhyay, R

2016-01-01

DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA-the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA-the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time.

Discriminating Intercalative Effects of Threading Intercalator Nogalamycin, from Classical Intercalator Daunomycin, Using Single Molecule Atomic Force Spectroscopy

PubMed Central

Sett, S.; Ghosh, S.; Rakshit, T.; Mukhopadhyay, R.

2016-01-01

DNA threading intercalators are a unique class of intercalating agents, albeit little biophysical information is available on their intercalative actions. Herein, the intercalative effects of nogalamycin, which is a naturally-occurring DNA threading intercalator, have been investigated by high-resolution atomic force microscopy (AFM) and spectroscopy (AFS). The results have been compared with those of the well-known chemotherapeutic drug daunomycin, which is a non-threading classical intercalator bearing structural similarity to nogalamycin. A comparative AFM assessment revealed a greater increase in DNA contour length over the entire incubation period of 48 h for nogalamycin treatment, whereas the contour length increase manifested faster in case of daunomycin. The elastic response of single DNA molecules to an externally applied force was investigated by the single molecule AFS approach. Characteristic mechanical fingerprints in the overstretching behaviour clearly distinguished the nogalamycin/daunomycin-treated dsDNA from untreated dsDNA—the former appearing less elastic than the latter, and the nogalamycin-treated DNA distinguished from the daunomycin-treated DNA—the classically intercalated dsDNA appearing the least elastic. A single molecule AFS-based discrimination of threading intercalation from the classical type is being reported for the first time. PMID:27183010

Nanomechanics of Cells and Biomaterials Studied by Atomic Force Microscopy.

PubMed

Kilpatrick, Jason I; Revenko, Irène; Rodriguez, Brian J

2015-11-18

The behavior and mechanical properties of cells are strongly dependent on the biochemical and biomechanical properties of their microenvironment. Thus, understanding the mechanical properties of cells, extracellular matrices, and biomaterials is key to understanding cell function and to develop new materials with tailored mechanical properties for tissue engineering and regenerative medicine applications. Atomic force microscopy (AFM) has emerged as an indispensable technique for measuring the mechanical properties of biomaterials and cells with high spatial resolution and force sensitivity within physiologically relevant environments and timescales in the kPa to GPa elastic modulus range. The growing interest in this field of bionanomechanics has been accompanied by an expanding array of models to describe the complexity of indentation of hierarchical biological samples. Furthermore, the integration of AFM with optical microscopy techniques has further opened the door to a wide range of mechanotransduction studies. In recent years, new multidimensional and multiharmonic AFM approaches for mapping mechanical properties have been developed, which allow the rapid determination of, for example, cell elasticity. This Progress Report provides an introduction and practical guide to making AFM-based nanomechanical measurements of cells and surfaces for tissue engineering applications. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Optimizing qPlus sensor assemblies for simultaneous scanning tunneling and noncontact atomic force microscopy operation based on finite element method analysis

DOE PAGES

Dagdeviren, Omur E.; Schwarz, Udo D.

2017-03-20

Quartz tuning forks that have a probe tip attached to the end of one of its prongs while the other prong is arrested to a holder (“qPlus” configuration) have gained considerable popularity in recent years for high-resolution atomic force microscopy imaging. The small size of the tuning forks and the complexity of the sensor architecture, however, often impede predictions on how variations in the execution of the individual assembly steps affect the performance of the completed sensor. Extending an earlier study that provided numerical analysis of qPlus-style setups without tips, this work quantifies the influence of tip attachment on themore » operational characteristics of the sensor. The results using finite element modeling show in particular that for setups that include a metallic tip that is connected via a separate wire to enable the simultaneous collection of local forces and tunneling currents, the exact realization of this wire connection has a major effect on sensor properties such as spring constant, quality factor, resonance frequency, and its deviation from an ideal vertical oscillation.« less

Optimizing qPlus sensor assemblies for simultaneous scanning tunneling and noncontact atomic force microscopy operation based on finite element method analysis

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

Dagdeviren, Omur E.; Schwarz, Udo D.

Quartz tuning forks that have a probe tip attached to the end of one of its prongs while the other prong is arrested to a holder (“qPlus” configuration) have gained considerable popularity in recent years for high-resolution atomic force microscopy imaging. The small size of the tuning forks and the complexity of the sensor architecture, however, often impede predictions on how variations in the execution of the individual assembly steps affect the performance of the completed sensor. Extending an earlier study that provided numerical analysis of qPlus-style setups without tips, this work quantifies the influence of tip attachment on themore » operational characteristics of the sensor. The results using finite element modeling show in particular that for setups that include a metallic tip that is connected via a separate wire to enable the simultaneous collection of local forces and tunneling currents, the exact realization of this wire connection has a major effect on sensor properties such as spring constant, quality factor, resonance frequency, and its deviation from an ideal vertical oscillation.« less

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.

System analysis of force feedback microscopy

NASA Astrophysics Data System (ADS)

Rodrigues, Mario S.; Costa, Luca; Chevrier, Joël; Comin, Fabio

2014-02-01

It was shown recently that the Force Feedback Microscope (FFM) can avoid the jump-to-contact in Atomic force Microscopy even when the cantilevers used are very soft, thus increasing force resolution. In this letter, we explore theoretical aspects of the associated real time control of the tip position. We take into account lever parameters such as the lever characteristics in its environment, spring constant, mass, dissipation coefficient, and the operating conditions such as controller gains and interaction force. We show how the controller parameters are determined so that the FFM functions at its best and estimate the bandwidth of the system under these conditions.

The influence of spatially and temporally high-resolution wind forcing on the power input to near-inertial waves in the ocean

NASA Astrophysics Data System (ADS)

Rimac, Antonija; von Storch, Jin-Song; Eden, Carsten

2013-04-01

The estimated power required to sustain global general circulation in the ocean is about 2 TW. This power is supplied with wind stress and tides. Energy spectrum shows pronounced maxima at near-inertial frequency. Near-inertial waves excited by high-frequency winds represent an important source for deep ocean mixing since they can propagate into the deep ocean and dissipate far away from the generation sites. The energy input by winds to near-inertial waves has been studied mostly using slab ocean models and wind stress forcing with coarse temporal resolution (e.g. 6-hourly). Slab ocean models lack the ability to reproduce fundamental aspects of kinetic energy balance and systematically overestimate the wind work. Also, slab ocean models do not account the energy used for the mixed layer deepening or the energy radiating downward into the deep ocean. Coarse temporal resolution of the wind forcing strongly underestimates the near-inertial energy. To overcome this difficulty we use an eddy permitting ocean model with high-frequency wind forcing. We establish the following model setup: We use the Max Planck Institute Ocean Model (MPIOM) on a tripolar grid with 45 km horizontal resolution and 40 vertical levels. We run the model with wind forcings that vary in horizontal and temporal resolution. We use high-resolution (1-hourly with 35 km horizontal resolution) and low-resolution winds (6-hourly with 250 km horizontal resolution). We address the following questions: Is the kinetic energy of near-inertial waves enhanced when high-resolution wind forcings are used? If so, is this due to higher level of overall wind variability or higher spatial or temporal resolution of wind forcing? How large is the power of near-inertial waves generated by winds? Our results show that near-inertial waves are enhanced and the near-inertial kinetic energy is two times higher (in the storm track regions 3.5 times higher) when high-resolution winds are used. Filtering high-resolution winds in space and time, the near-inertial kinetic energy reduces. The reduction is faster when a temporal filter is used suggesting that the high-frequency wind forcing is more efficient in generating near-inertial wave energy than the small-scale wind forcing. Using low-resolution wind forcing the wind generated power to near-inertial waves is 0.55 TW. When we use high-resolution wind forcing the result is 1.6 TW meaning that the result increases by 300%.

Restoration of high-resolution AFM images captured with broken probes

NASA Astrophysics Data System (ADS)

Wang, Y. F.; Corrigan, D.; Forman, C.; Jarvis, S.; Kokaram, A.

2012-03-01

A type of artefact is induced by damage of the scanning probe when the Atomic Force Microscope (AFM) captures a material surface structure with nanoscale resolution. This artefact has a dramatic form of distortion rather than the traditional blurring artefacts. Practically, it is not easy to prevent the damage of the scanning probe. However, by using natural image deblurring techniques in image processing domain, a comparatively reliable estimation of the real sample surface structure can be generated. This paper introduces a novel Hough Transform technique as well as a Bayesian deblurring algorithm to remove this type of artefact. The deblurring result is successful at removing blur artefacts in the AFM artefact images. And the details of the fibril surface topography are well preserved.

Dual Optical Levers for Atomic Force Microscopy

NASA Astrophysics Data System (ADS)

Kawakatsu, Hideki; Bleuler, Hannes; Saito, Takashi; Hiroshi, Kougami

1995-06-01

Development of micro machined cantilever and optical lever detection system has greatly facilitated the operation of atomic force microscopy. However, since the detection system measures only the deflection of the cantilever at one set point where the laser beam is focused, care must be taken in implementing force control or in interpreting the acquired data. In this paper, a dual optical lever detection system is introduced, which has the potential to resolve the deformation of the cantilever with multidegree of freedom and thus detect the position of the tip end point with resolution in the 10 pm order. The detection system proved to be effective in real-time monitoring of the behavior of the tip end point while scanning, and in explaining the scanning direction dependence of the acquired images.

Relaxometry imaging of superparamagnetic magnetite nanoparticles at ambient conditions

NASA Astrophysics Data System (ADS)

Finkler, Amit; Schmid-Lorch, Dominik; Häberle, Thomas; Reinhard, Friedemann; Zappe, Andrea; Slota, Michael; Bogani, Lapo; Wrachtrup, Jörg

We present a novel technique to image superparamagnetic iron oxide nanoparticles via their fluctuating magnetic fields. The detection is based on the nitrogen-vacancy (NV) color center in diamond, which allows optically detected magnetic resonance (ODMR) measurements on its electron spin structure. In combination with an atomic-force-microscope, this atomic-sized color center maps ambient magnetic fields in a wide frequency range from DC up to several GHz, while retaining a high spatial resolution in the sub-nanometer range. We demonstrate imaging of single 10 nm sized magnetite nanoparticles using this spin noise detection technique. By fitting simulations (Ornstein-Uhlenbeck process) to the data, we are able to infer additional information on such a particle and its dynamics, like the attempt frequency and the anisotropy constant. This is of high interest to the proposed application of magnetite nanoparticles as an alternative MRI contrast agent or to the field of particle-aided tumor hyperthermia.

Delaminated graphene at silicon carbide facets: atomic scale imaging and spectroscopy.

PubMed

Nicotra, Giuseppe; Ramasse, Quentin M; Deretzis, Ioannis; La Magna, Antonino; Spinella, Corrado; Giannazzo, Filippo

2013-04-23

Atomic-resolution structural and spectroscopic characterization techniques (scanning transmission electron microscopy and electron energy loss spectroscopy) are combined with nanoscale electrical measurements (conductive atomic force microscopy) to study at the atomic scale the properties of graphene grown epitaxially through the controlled graphitization of a hexagonal SiC(0001) substrate by high temperature annealing. This growth technique is known to result in a pronounced electron-doping (∼10(13) cm(-2)) of graphene, which is thought to originate from an interface carbon buffer layer strongly bound to the substrate. The scanning transmission electron microscopy analysis, carried out at an energy below the knock-on threshold for carbon to ensure no damage is imparted to the film by the electron beam, demonstrates that the buffer layer present on the planar SiC(0001) face delaminates from it on the (112n) facets of SiC surface steps. In addition, electron energy loss spectroscopy reveals that the delaminated layer has a similar electronic configuration to purely sp2-hybridized graphene. These observations are used to explain the local increase of the graphene sheet resistance measured around the surface steps by conductive atomic force microscopy, which we suggest is due to significantly lower substrate-induced doping and a resonant scattering mechanism at the step regions. A first-principles-calibrated theoretical model is proposed to explain the structural instability of the buffer layer on the SiC facets and the resulting delamination.

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.

Nanoscale visualization and characterization of Myxococcus xanthus cells with atomic force microscopy

PubMed Central

Pelling, Andrew E.; Li, Yinuo; Shi, Wenyuan; Gimzewski, James K.

2005-01-01

Multicellular microbial communities are the predominant form of existence for microorganisms in nature. As one of the most primitive social organisms, Myxococcus xanthus has been an ideal model bacterium for studying intercellular interaction and multicellular organization. Through previous genetic and EM studies, various extracellular appendages and matrix components have been found to be involved in the social behavior of M. xanthus, but none of them was directly visualized and analyzed under native conditions. Here, we used atomic force microscopy (AFM) imaging and in vivo force spectroscopy to characterize these cellular structures under native conditions. AFM imaging revealed morphological details on the extracellular ultrastructures at an unprecedented resolution, and in vivo force spectroscopy of live cells in fluid allowed us to nanomechanically characterize extracellular polymeric substances. The findings provide the basis for AFM as a useful tool for investigating microbial-surface ultrastructures and nanomechanical properties under native conditions. PMID:15840722

MIDAS: Lessons learned from the first spaceborne atomic force microscope

NASA Astrophysics Data System (ADS)

Bentley, Mark Stephen; Arends, Herman; Butler, Bart; Gavira, Jose; Jeszenszky, Harald; Mannel, Thurid; Romstedt, Jens; Schmied, Roland; Torkar, Klaus

2016-08-01

The Micro-Imaging Dust Analysis System (MIDAS) atomic force microscope (AFM) onboard the Rosetta orbiter was the first such instrument launched into space in 2004. Designed only a few years after the technique was invented, MIDAS is currently orbiting comet 67P Churyumov-Gerasimenko and producing the highest resolution 3D images of cometary dust ever made in situ. After more than a year of continuous operation much experience has been gained with this novel instrument. Coupled with operations of the Flight Spare and advances in terrestrial AFM a set of "lessons learned" has been produced, cumulating in recommendations for future spaceborne atomic force microscopes. The majority of the design could be reused as-is, or with incremental upgrades to include more modern components (e.g. the processor). Key additional recommendations are to incorporate an optical microscope to aid the search for particles and image registration, to include a variety of cantilevers (with different spring constants) and a variety of tip geometries.

Torsional tapping atomic force microscopy for molecular resolution imaging of soft matter

NASA Astrophysics Data System (ADS)

Hobbs, Jamie; Mullin, Nic

2012-02-01

Despite considerable advances in image resolution on challenging, soft systems, a method for obtaining molecular resolution on `real' samples with significant surface roughness has remained elusive. Here we will show that a relatively new technique, torsional tapping AFM (TTAFM), is capable of imaging with resolution down to 3.7 Angrstrom on the surface of `bulk' polymer films [1]. In TTAFM T-shaped cantilevers are driven into torsional oscillation. As the tip is offset from the rotation axis this provides a tapping motion. Due to the high frequency and Q of the oscillation and relatively small increase in spring constant, improved cantilever dynamics and force sensitivity are obtained. As the tip offset from the torsional axis is relatively small (typically 25 microns), the optical lever sensitivity is considerably improved compared to flexural oscillation. Combined these give a reduction in noise floor by a factor of 12 just by changing the cantilever geometry. The ensuing low noise allows the use of ultra-sharp `whisker' tips with minimal blunting. As the cantilevers remain soft in the flexural axis, the force when imaging with error is also reduced, further protecting the tip. We will show that this combination allows routine imaging of the molecular structure of semicrystalline polymer films, including chain folds, loose loops and tie-chains in polyethylene, and the helical conformation of polypropylene within the crystal, using a standard, commercial AFM. [4pt] [1] N Mullin, JK Hobbs, PRL 107, 197801 (2011)

Atomic force microscopy capable of vibration isolation with low-stiffness Z-axis actuation.

PubMed

Ito, Shingo; Schitter, Georg

2018-03-01

For high-resolution imaging without bulky external vibration isolation, this paper presents an atomic force microscope (AFM) capable of vibration isolation with its internal Z-axis (vertical) actuators moving the AFM probe. Lorentz actuators (voice coil actuators) are used for the Z-axis actuation, and flexures guiding the motion are designed to have a low stiffness between the mover and the base. The low stiffness enables a large Z-axis actuation of more than 700 µm and mechanically isolates the probe from floor vibrations at high frequencies. To reject the residual vibrations, the probe tracks the sample by using a displacement sensor for feedback control. Unlike conventional AFMs, the Z-axis actuation attains a closed-loop control bandwidth that is 35 times higher than the first mechanical resonant frequency. The closed-loop AFM system has robustness against the flexures' nonlinearity and uses the first resonance for better sample tracking. For further improvement, feedforward control with a vibration sensor is combined, and the resulting system rejects 98.4% of vibrations by turning on the controllers. The AFM system is demonstrated by successful AFM imaging in a vibrational environment. Copyright © 2017 Elsevier B.V. All rights reserved.

Advances in research on structural characterisation of agricultural products using atomic force microscopy.

PubMed

Liu, Dongli; Cheng, Fang

2011-03-30

Atomic force microscopy (AFM) has many unique features compared with other conventional microscopies, such as high magnification with high resolution, minimal sample preparation, acquiring 2D and 3D images at the same time, observing ongoing processes directly, the possibility of manipulating macromolecules, etc. As a nanotechnology tool, AFM has been used to investigate the nanostructure of materials in many fields. This mini-review focuses mainly on its latest application to characterise the macromolecular nanostructure and surface topography of agricultural products. First the fundamentals of AFM are briefly explained. Then the macromolecular nanostructure information on agricultural products from AFM images is introduced by exploring the structure-function relationship in three aspects: agricultural product processing, agricultural product ripening and storage, and genetic and environmental factors. The surface topography characterisation of agricultural products using AFM is also discussed. The results reveal that AFM could be a powerful nanotechnology tool to acquire a deeper understanding of the mechanisms of structure and quality variations of agricultural products, which could be instructive in improving processing and storage technologies, and AFM is also helpful to reveal the essential nature of a product at nanoscale. Copyright © 2011 Society of Chemical Industry.

AtomicJ: An open source software for analysis of force curves

NASA Astrophysics Data System (ADS)

Hermanowicz, Paweł; Sarna, Michał; Burda, Kvetoslava; Gabryś, Halina

2014-06-01

We present an open source Java application for analysis of force curves and images recorded with the Atomic Force Microscope. AtomicJ supports a wide range of contact mechanics models and implements procedures that reduce the influence of deviations from the contact model. It generates maps of mechanical properties, including maps of Young's modulus, adhesion force, and sample height. It can also calculate stacks, which reveal how sample's response to deformation changes with indentation depth. AtomicJ analyzes force curves concurrently on multiple threads, which allows for high speed of analysis. It runs on all popular operating systems, including Windows, Linux, and Macintosh.

Reconciling Structural and Thermodynamic Predictions Using All-Atom and Coarse-Grain Force Fields: The Case of Charged Oligo-Arginine Translocation into DMPC Bilayers

PubMed Central

2015-01-01

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide–water and peptide–membrane interactions allow prediction of free energy minima at the bilayer–water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are −2.51, −4.28, and −5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are −0.83, −3.33, and −3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations. PMID:25290376

Reconciling structural and thermodynamic predictions using all-atom and coarse-grain force fields: the case of charged oligo-arginine translocation into DMPC bilayers.

PubMed

Hu, Yuan; Sinha, Sudipta Kumar; Patel, Sandeep

2014-10-16

Using the translocation of short, charged cationic oligo-arginine peptides (mono-, di-, and triarginine) from bulk aqueous solution into model DMPC bilayers, we explore the question of the similarity of thermodynamic and structural predictions obtained from molecular dynamics simulations using all-atom and Martini coarse-grain force fields. Specifically, we estimate potentials of mean force associated with translocation using standard all-atom (CHARMM36 lipid) and polarizable and nonpolarizable Martini force fields, as well as a series of modified Martini-based parameter sets. We find that we are able to reproduce qualitative features of potentials of mean force of single amino acid side chain analogues into model bilayers. In particular, modifications of peptide-water and peptide-membrane interactions allow prediction of free energy minima at the bilayer-water interface as obtained with all-atom force fields. In the case of oligo-arginine peptides, the modified parameter sets predict interfacial free energy minima as well as free energy barriers in almost quantitative agreement with all-atom force field based simulations. Interfacial free energy minima predicted by a modified coarse-grained parameter set are -2.51, -4.28, and -5.42 for mono-, di-, and triarginine; corresponding values from all-atom simulations are -0.83, -3.33, and -3.29, respectively, all in units of kcal/mol. We found that a stronger interaction between oligo-arginine and the membrane components and a weaker interaction between oligo-arginine and water are crucial for producing such minima in PMFs using the polarizable CG model. The difference between bulk aqueous and bilayer center states predicted by the modified coarse-grain force field are 11.71, 14.14, and 16.53 kcal/mol, and those by the all-atom model are 6.94, 8.64, and 12.80 kcal/mol; those are of almost the same order of magnitude. Our simulations also demonstrate a remarkable similarity in the structural aspects of the ensemble of configurations generated using the all-atom and coarse-grain force fields. Both resolutions show that oligo-arginine peptides adopt preferential orientations as they translocate into the bilayer. The guiding theme centers on charged groups maintaining coordination with polar and charged bilayer components as well as local water. We also observe similar behaviors related with membrane deformations.

Efficiency calibration of the first multilayer-coated holographic ion-etched flight grating for a sounding rocket high-resolution spectrometer.

PubMed

Kowalski, M P; Barbee, T W; Heidemann, K F; Gursky, H; Rife, J C; Hunter, W R; Fritz, G G; Cruddace, R G

1999-11-01

We have fabricated the four flight gratings for a sounding rocket high-resolution spectrometer using a holographic ion-etching technique. The gratings are spherical (4000-mm radius of curvature), large (160 mm x 90 mm), and have a laminar groove profile of high density (3600 grooves/mm). They have been coated with a high-reflectance multilayer of Mo/Si. Using an atomic force microscope, we examined the surface characteristics of the first grating before and after multilayer coating. The average roughness is approximately 3 A rms after coating. Using synchrotron radiation, we completed an efficiency calibration map over the wavelength range 225-245 A. At an angle of incidence of 5 degrees and a wavelength of 234 A, the average efficiency in the first inside order is 10.4 +/- 0.5%, and the derived groove efficiency is 34.8 +/- 1.6%. These values exceed all previously published results for a high-density grating.

Cellular Force Microscopy for in Vivo Measurements of Plant Tissue Mechanics1[W][OA

PubMed Central

Routier-Kierzkowska, Anne-Lise; Weber, Alain; Kochova, Petra; Felekis, Dimitris; Nelson, Bradley J.; Kuhlemeier, Cris; Smith, Richard S.

2012-01-01

Although growth and morphogenesis are controlled by genetics, physical shape change in plant tissue results from a balance between cell wall loosening and intracellular pressure. Despite recent work demonstrating a role for mechanical signals in morphogenesis, precise measurement of mechanical properties at the individual cell level remains a technical challenge. To address this challenge, we have developed cellular force microscopy (CFM), which combines the versatility of classical microindentation techniques with the high automation and resolution approaching that of atomic force microscopy. CFM’s large range of forces provides the possibility to map the apparent stiffness of both plasmolyzed and turgid tissue as well as to perform micropuncture of cells using very high stresses. CFM experiments reveal that, within a tissue, local stiffness measurements can vary with the level of turgor pressure in an unexpected way. Altogether, our results highlight the importance of detailed physically based simulations for the interpretation of microindentation results. CFM’s ability to be used both to assess and manipulate tissue mechanics makes it a method of choice to unravel the feedbacks between mechanics, genetics, and morphogenesis. PMID:22353572

Micromachined Chip Scale Thermal Sensor for Thermal Imaging.

PubMed

Shekhawat, Gajendra S; Ramachandran, Srinivasan; Jiryaei Sharahi, Hossein; Sarkar, Souravi; Hujsak, Karl; Li, Yuan; Hagglund, Karl; Kim, Seonghwan; Aden, Gary; Chand, Ami; Dravid, Vinayak P

2018-02-27

The lateral resolution of scanning thermal microscopy (SThM) has hitherto never approached that of mainstream atomic force microscopy, mainly due to poor performance of the thermal sensor. Herein, we report a nanomechanical system-based thermal sensor (thermocouple) that enables high lateral resolution that is often required in nanoscale thermal characterization in a wide range of applications. This thermocouple-based probe technology delivers excellent lateral resolution (∼20 nm), extended high-temperature measurements >700 °C without cantilever bending, and thermal sensitivity (∼0.04 °C). The origin of significantly improved figures-of-merit lies in the probe design that consists of a hollow silicon tip integrated with a vertically oriented thermocouple sensor at the apex (low thermal mass) which interacts with the sample through a metallic nanowire (50 nm diameter), thereby achieving high lateral resolution. The efficacy of this approach to SThM is demonstrated by imaging embedded metallic nanostructures in silica core-shell, metal nanostructures coated with polymer films, and metal-polymer interconnect structures. The nanoscale pitch and extremely small thermal mass of the probe promise significant improvements over existing methods and wide range of applications in several fields including semiconductor industry, biomedical imaging, and data storage.

Preparation and performance of broadband antireflective sub-wavelength structures on Ge substrate

NASA Astrophysics Data System (ADS)

Shen, Xiang-Wei; Liu, Zheng-Tang; Li, Yang-Ping; Lu, Hong-Cheng; Xu, Qi-Yuan; Liu, Wen-Ting

2009-01-01

Sub-wavelength structures (SWS) were prepared on Ge substrates through photolithography and reactive ion etching (RIE) technology for broadband antireflective purposes in the long wave infrared (LWIR) waveband of 8-12 μm. Topography of the etched patterns was observed using high resolution optical microscope and atomic force microscope (AFM). Infrared transmission performance of the SWS was investigated by Fourier transform infrared (FTIR) spectrometer. Results show that the etched patterns were of high uniformity and fidelity, the SWS exhibited a good broadband antireflective performance with the increment of the average transmittance which is over 8-12 μm up to 8%.

Error mapping of high-speed AFM systems

NASA Astrophysics Data System (ADS)

Klapetek, Petr; Picco, Loren; Payton, Oliver; Yacoot, Andrew; Miles, Mervyn

2013-02-01

In recent years, there have been several advances in the development of high-speed atomic force microscopes (HSAFMs) to obtain images with nanometre vertical and lateral resolution at frame rates in excess of 1 fps. To date, these instruments are lacking in metrology for their lateral scan axes; however, by imaging a series of two-dimensional lateral calibration standards, it has been possible to obtain information about the errors associated with these HSAFM scan axes. Results from initial measurements are presented in this paper and show that the scan speed needs to be taken into account when performing a calibration as it can lead to positioning errors of up to 3%.

Rewritable ghost floating gates by tunnelling triboelectrification for two-dimensional electronics

PubMed Central

Kim, Seongsu; Kim, Tae Yun; Lee, Kang Hyuck; Kim, Tae-Ho; Cimini, Francesco Arturo; Kim, Sung Kyun; Hinchet, Ronan; Kim, Sang-Woo; Falconi, Christian

2017-01-01

Gates can electrostatically control charges inside two-dimensional materials. However, integrating independent gates typically requires depositing and patterning suitable insulators and conductors. Moreover, after manufacturing, gates are unchangeable. Here we introduce tunnelling triboelectrification for localizing electric charges in very close proximity of two-dimensional materials. As representative materials, we use chemical vapour deposition graphene deposited on a SiO2/Si substrate. The triboelectric charges, generated by friction with a Pt-coated atomic force microscope tip and injected through defects, are trapped at the air–SiO2 interface underneath graphene and act as ghost floating gates. Tunnelling triboelectrification uniquely permits to create, modify and destroy p and n regions at will with the spatial resolution of atomic force microscopes. As a proof of concept, we draw rewritable p/n+ and p/p+ junctions with resolutions as small as 200 nm. Our results open the way to time-variant two-dimensional electronics where conductors, p and n regions can be defined on demand. PMID:28649986

Rewritable ghost floating gates by tunnelling triboelectrification for two-dimensional electronics

NASA Astrophysics Data System (ADS)

Kim, Seongsu; Kim, Tae Yun; Lee, Kang Hyuck; Kim, Tae-Ho; Cimini, Francesco Arturo; Kim, Sung Kyun; Hinchet, Ronan; Kim, Sang-Woo; Falconi, Christian

2017-06-01

Gates can electrostatically control charges inside two-dimensional materials. However, integrating independent gates typically requires depositing and patterning suitable insulators and conductors. Moreover, after manufacturing, gates are unchangeable. Here we introduce tunnelling triboelectrification for localizing electric charges in very close proximity of two-dimensional materials. As representative materials, we use chemical vapour deposition graphene deposited on a SiO2/Si substrate. The triboelectric charges, generated by friction with a Pt-coated atomic force microscope tip and injected through defects, are trapped at the air-SiO2 interface underneath graphene and act as ghost floating gates. Tunnelling triboelectrification uniquely permits to create, modify and destroy p and n regions at will with the spatial resolution of atomic force microscopes. As a proof of concept, we draw rewritable p/n+ and p/p+ junctions with resolutions as small as 200 nm. Our results open the way to time-variant two-dimensional electronics where conductors, p and n regions can be defined on demand.

Study of the influence of strained superlattices introduced into a metamorphic buffer on the electrophysical properties and the atomic structure of InAlAs/InGaAs MHEMT heterostructures

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

Galiev, G. B.; Pushkarev, S. S., E-mail: s_s_e_r_p@mail.ru; Vasil'evskii, I. S.

The results of studying the influence of strained superlattices introduced into a metamorphic buffer on the electrophysical properties and atomic crystal structure of In{sub 0.70}Al{sub 0.30}As/In{sub 0.76}Ga{sub 0.24}As/In{sub 0.70}Al{sub 0.30}As metamorphic high-electron-mobility transistor (MHEMT) nanoheterostructures on GaAs substrates are presented. Two types of MHEMT structures are grown by molecular beam epitaxy, namely, one with a linear increase in x in the In{sub x}Al{sub 1-x}As metamorphic buffer, and the second with two mismatched superlattices introduced inside the metamorphic buffer. The electrophysical and structural parameters of the grown samples are studied by the van der Pauw method, transmission electron microscopy (including scanningmore » and high-resolution microscopy), atomic-force microscopy, and energy dispersive X-ray analysis. It is revealed that the introduction of superlattices into a metamorphic buffer substantially improves the electrophysical and structural characteristics of MHEMT structures.« less

Atomic force microscopic study of the effects of ethanol on yeast cell surface morphology.

PubMed

Canetta, Elisabetta; Adya, Ashok K; Walker, Graeme M

2006-02-01

The detrimental effects of ethanol toxicity on the cell surface morphology of Saccharomyces cerevisiae (strain NCYC 1681) and Schizosaccharomyces pombe (strain DVPB 1354) were investigated using an atomic force microscope (AFM). In combination with culture viability and mean cell volume measurements AFM studies allowed us to relate the cell surface morphological changes, observed on nanometer lateral resolution, with the cellular stress physiology. Exposing yeasts to increasing stressful concentrations of ethanol led to decreased cell viabilities and mean cell volumes. Together with the roughness and bearing volume analyses of the AFM images, the results provided novel insight into the relative ethanol tolerance of S. cerevisiae and Sc. pombe.

Lysenin Toxin Membrane Insertion Is pH-Dependent but Independent of Neighboring Lysenins.

PubMed

Munguira, Ignacio L B; Takahashi, Hirohide; Casuso, Ignacio; Scheuring, Simon

2017-11-07

Pore-forming toxins form a family of proteins that act as virulence factors of pathogenic bacteria, but similar proteins are found in all kingdoms of life, including the vertebrate immune system. They are secreted as soluble monomers that oligomerize on target membranes in the so-called prepore state; after activation, they insert into the membrane and adopt the pore state. Lysenin is a pore-forming toxin from the earthworm Eisenida foetida, of which both the soluble and membrane-inserted structures are solved. However, the activation and membrane-insertion mechanisms have remained elusive. Here, we used high-speed atomic force microscopy to directly visualize the membrane-insertion mechanism. Changing the environmental pH from pH 7.5 to below pH 6.0 favored membrane insertion. We detected a short α-helix in the soluble structure that comprised three glutamic acids (Glu92, Glu94, and Glu97) that we hypothesized may represent a pH-sensor (as in similar toxins, e.g., Listeriolysin). Mutant lysenin still can form pores, but mutating these glutamic acids to glutamines rendered the toxin pH-insensitive. On the other hand, toxins in the pore state did not favor insertion of neighboring prepores; indeed, pore insertion breaks the hexagonal ordered domains of prepores and separates from neighboring molecules in the membrane. pH-dependent activation of toxins may represent a common feature of pore-forming toxins. High-speed atomic force microscopy with single-molecule resolution at high temporal resolution and the possibility of exchanging buffers during the experiments presents itself as a unique tool for the study of toxin-state conversion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Local conductance: A means to extract polarization and depolarizing fields near domain walls in ferroelectrics

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

Douglas, A. M.; Kumar, A.; Gregg, J. M.

Conducting atomic force microscopy images of bulk semiconducting BaTiO{sub 3} surfaces show clear stripe domain contrast. High local conductance correlates with strong out-of-plane polarization (mapped independently using piezoresponse force microscopy), and current-voltage characteristics are consistent with dipole-induced alterations in Schottky barriers at the metallic tip-ferroelectric interface. Indeed, analyzing current-voltage data in terms of established Schottky barrier models allows relative variations in the surface polarization, and hence the local domain structure, to be determined. Fitting also reveals the signature of surface-related depolarizing fields concentrated near domain walls. Domain information obtained from mapping local conductance appears to be more surface-sensitive than thatmore » from piezoresponse force microscopy. In the right materials systems, local current mapping could therefore represent a useful complementary technique for evaluating polarization and local electric fields with nanoscale resolution.« less

Imaging and Quantitation of a Succession of Transient Intermediates Reveal the Reversible Self-Assembly Pathway of a Simple Icosahedral Virus Capsid.

PubMed

Medrano, María; Fuertes, Miguel Ángel; Valbuena, Alejandro; Carrillo, Pablo J P; Rodríguez-Huete, Alicia; Mateu, Mauricio G

2016-11-30

Understanding the fundamental principles underlying supramolecular self-assembly may facilitate many developments, from novel antivirals to self-organized nanodevices. Icosahedral virus particles constitute paradigms to study self-assembly using a combination of theory and experiment. Unfortunately, assembly pathways of the structurally simplest virus capsids, those more accessible to detailed theoretical studies, have been difficult to study experimentally. We have enabled the in vitro self-assembly under close to physiological conditions of one of the simplest virus particles known, the minute virus of mice (MVM) capsid, and experimentally analyzed its pathways of assembly and disassembly. A combination of electron microscopy and high-resolution atomic force microscopy was used to structurally characterize and quantify a succession of transient assembly and disassembly intermediates. The results provided an experiment-based model for the reversible self-assembly pathway of a most simple (T = 1) icosahedral protein shell. During assembly, trimeric capsid building blocks are sequentially added to the growing capsid, with pentamers of building blocks and incomplete capsids missing one building block as conspicuous intermediates. This study provided experimental verification of many features of self-assembly of a simple T = 1 capsid predicted by molecular dynamics simulations. It also demonstrated atomic force microscopy imaging and automated analysis, in combination with electron microscopy, as a powerful single-particle approach to characterize at high resolution and quantify transient intermediates during supramolecular self-assembly/disassembly reactions. Finally, the efficient in vitro self-assembly achieved for the oncotropic, cell nucleus-targeted MVM capsid may facilitate its development as a drug-encapsidating nanoparticle for anticancer targeted drug delivery.

Characterization of single α-tracks by photoresist detection and AFM analysis-focus on biomedical science and technology

NASA Astrophysics Data System (ADS)

Falzone, Nadia; Myhra, Sverre; Chakalova, Radka; Hill, Mark A.; Thomson, James; Vallis, Katherine A.

2013-11-01

The interactions between energetic ions and biological and/or organic target materials have recently attracted theoretical and experimental attention, due to their implications for detector and device technologies, and for therapeutic applications. Most of the attention has focused on detection of the primary ionization tracks, and their effects, while recoil target atom tracks remain largely unexplored. Detection of tracks by a negative tone photoresist (SU-8), followed by standard development, in combination with analysis by atomic force microscopy, shows that both primary and recoil tracks are revealed as conical spikes, and can be characterized at high spatial resolution. The methodology has the potential to provide detailed information about single impact events, which may lead to more effective and informative detector technologies and advanced therapeutic procedures. In comparison with current characterization methods the advantageous features include: greater spatial resolution by an order of magnitude (20 nm) detection of single primary and associated recoil tracks; increased range of fluence (to 2.5 × 109 cm-2) sensitivity to impacts at grazing angle incidence; and better definition of the lateral interaction volume in target materials.

Focal depth measurement of scanning helium ion microscope

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

Guo, Hongxuan, E-mail: Guo.hongxuan@nims.go.jp; Itoh, Hiroshi; Wang, Chunmei

2014-07-14

When facing the challenges of critical dimension measurement of complicated nanostructures, such as of the three dimension integrated circuit, characterization of the focal depth of microscopes is important. In this Letter, we developed a method for characterizing the focal depth of a scanning helium ion microscope (HIM) by using an atomic force microscope tip characterizer (ATC). The ATC was tilted in a sample chamber at an angle to the scanning plan. Secondary electron images (SEIs) were obtained at different positions of the ATC. The edge resolution of the SEIs shows the nominal diameters of the helium ion beam at differentmore » focal levels. With this method, the nominal shapes of the helium ion beams were obtained with different apertures. Our results show that a small aperture is necessary to get a high spatial resolution and high depth of field images with HIM. This work provides a method for characterizing and improving the performance of HIM.« less

Two-dimensional dopant profiling of gallium nitride p-n junctions by scanning capacitance microscopy

NASA Astrophysics Data System (ADS)

Lamhamdi, M.; Cayrel, F.; Frayssinet, E.; Bazin, A. E.; Yvon, A.; Collard, E.; Cordier, Y.; Alquier, D.

2016-04-01

Two-dimensional imaging of dopant profiles for n and p-type regions are relevant for the development of new power semiconductors, especially for gallium nitride (GaN) for which classical profiling techniques are not adapted. This is a challenging task since it needs a technique with simultaneously good sensitivity, high spatial resolution and high dopant gradient resolution. To face these challenges, scanning capacitance microscopy combined with Atomic Force Microscopy is a good candidate, presenting reproducible results, as demonstrated in literature. In this work, we attempt to distinguish reliably and qualitatively the various doping concentrations and type at p-n and unipolar junctions. For both p-n and unipolar junctions three kinds of samples were prepared and measured separately. The space-charge region of the p-n metallurgical junction, giving rise to different contrasts under SCM imaging, is clearly observed, enlightening the interest of the SCM technique.

Focal depth measurement of scanning helium ion microscope

NASA Astrophysics Data System (ADS)

Guo, Hongxuan; Itoh, Hiroshi; Wang, Chunmei; Zhang, Han; Fujita, Daisuke

2014-07-01

When facing the challenges of critical dimension measurement of complicated nanostructures, such as of the three dimension integrated circuit, characterization of the focal depth of microscopes is important. In this Letter, we developed a method for characterizing the focal depth of a scanning helium ion microscope (HIM) by using an atomic force microscope tip characterizer (ATC). The ATC was tilted in a sample chamber at an angle to the scanning plan. Secondary electron images (SEIs) were obtained at different positions of the ATC. The edge resolution of the SEIs shows the nominal diameters of the helium ion beam at different focal levels. With this method, the nominal shapes of the helium ion beams were obtained with different apertures. Our results show that a small aperture is necessary to get a high spatial resolution and high depth of field images with HIM. This work provides a method for characterizing and improving the performance of HIM.

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.

Cross-Sectional Investigations on Epitaxial Silicon Solar Cells by Kelvin and Conducting Probe Atomic Force Microscopy: Effect of Illumination.

PubMed

Narchi, Paul; Alvarez, Jose; Chrétien, Pascal; Picardi, Gennaro; Cariou, Romain; Foldyna, Martin; Prod'homme, Patricia; Kleider, Jean-Paul; I Cabarrocas, Pere Roca

2016-12-01

Both surface photovoltage and photocurrent enable to assess the effect of visible light illumination on the electrical behavior of a solar cell. We report on photovoltage and photocurrent measurements with nanometer scale resolution performed on the cross section of an epitaxial crystalline silicon solar cell, using respectively Kelvin probe force microscopy and conducting probe atomic force microscopy. Even though two different setups are used, the scans were performed on locations within 100-μm distance in order to compare data from the same area and provide a consistent interpretation. In both measurements, modifications under illumination are observed in accordance with the theory of PIN junctions. Moreover, an unintentional doping during the deposition of the epitaxial silicon intrinsic layer in the solar cell is suggested from the comparison between photovoltage and photocurrent measurements.

Ultraflat Au nanoplates as a new building block for molecular electronics.

PubMed

Jeong, Wooseok; Lee, Miyeon; Lee, Hyunsoo; Lee, Hyoban; Kim, Bongsoo; Park, Jeong Young

2016-05-27

We demonstrate the charge transport properties of a self-assembled organic monolayer on Au nanoplates with conductive probe atomic force microscopy (CP-AFM). Atomically flat Au nanoplates, a few hundred micrometers on each side, that have only (111) surfaces, were synthesized using the chemical vapor transport method; these nanoplates were employed as the substrates for hexadecanethiol (HDT) self-assembled monolayers (SAMs). Atomic-scale high-resolution images show (√3 x √3) R30° molecular periodicity, indicating a well-ordered structure of the HDT on the Au nanoplates. We observed reduced friction and adhesion forces on the HDT SAMs on Au nanoplates, compared with Si substrates, which is consistent with the lubricating nature of HDT SAMs. The electrical properties, such as I-V characteristics and current as a function of load, were measured using CP-AFM. We obtained a tunneling decay constant (β) of 0.57 Å(-1), including through-bond (βtb = 0.99 Å(-1)) and through-space (βts = 1.36 Å(-1)) decay constants for the two-pathway model. This indicates that the charge transport properties of HDT SAMs on Au nanoplates are consistent with those on a Au (111) film, suggesting that SAMs on nanoplates can provide a new building block for molecular electronics.

Investigating bioconjugation by atomic force microscopy

PubMed Central

2013-01-01

Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures. PMID:23855448

Investigating bioconjugation by atomic force microscopy.

PubMed

Tessmer, Ingrid; Kaur, Parminder; Lin, Jiangguo; Wang, Hong

2013-07-15

Nanotechnological applications increasingly exploit the selectivity and processivity of biological molecules. Integration of biomolecules such as proteins or DNA into nano-systems typically requires their conjugation to surfaces, for example of carbon-nanotubes or fluorescent quantum dots. The bioconjugated nanostructures exploit the unique strengths of both their biological and nanoparticle components and are used in diverse, future oriented research areas ranging from nanoelectronics to biosensing and nanomedicine. Atomic force microscopy imaging provides valuable, direct insight for the evaluation of different conjugation approaches at the level of the individual molecules. Recent technical advances have enabled high speed imaging by AFM supporting time resolutions sufficient to follow conformational changes of intricately assembled nanostructures in solution. In addition, integration of AFM with different spectroscopic and imaging approaches provides an enhanced level of information on the investigated sample. Furthermore, the AFM itself can serve as an active tool for the assembly of nanostructures based on bioconjugation. AFM is hence a major workhorse in nanotechnology; it is a powerful tool for the structural investigation of bioconjugation and bioconjugation-induced effects as well as the simultaneous active assembly and analysis of bioconjugation-based nanostructures.

Exchange spring in A1/L1{sub 0} FePt composite and its application in magnetic force microscope

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

Li, Guoqing, E-mail: gqli@swu.edu.cn; Zhu, Yanyan, E-mail: zhubai@swu.edu.cn; Zhang, Yong

2015-02-23

This paper reported fabrication of Fe{sub x}Pt{sub 100-x} films with (001) epitaxy on MgO(100) substrates. The atomic percentage of Fe was changed within the range of x = 10–85 in order to search the optimal atomic ratio for achieving both high and isotropic-like coercivity. It was found that the Fe{sub 60}Pt{sub 40} film exhibited large coercivities exceeding 5 kOe along both in-plane and out-of-plane directions due to the formation of A1/L1{sub 0} FePt composite. A penta-domain model for hard/soft/hard exchange spring system was proposed to interpret the anomalous magnetization behaviors observed in Fe{sub 60}Pt{sub 40} sample. By using Fe{sub 60}Pt{sub 40} asmore » the magnetic coating layer on a probe of magnetic force microscope, the flux changes at a linear density of 1000 kfci could be readily observed at a resolution of ∼13 nm.« less

Unravelling the biodiversity of nanoscale signatures of spider silk fibres

NASA Astrophysics Data System (ADS)

Silva, Luciano P.; Rech, Elibio L.

2013-12-01

Living organisms are masters at designing outstanding self-assembled nanostructures through a hierarchical organization of modular proteins. Protein-based biopolymers improved and selected by the driving forces of molecular evolution are among the most impressive archetypes of nanomaterials. One of these biomacromolecules is the myriad of compound fibroins of spider silks, which combine surprisingly high tensile strength with great elasticity. However, no consensus on the nano-organization of spider silk fibres has been reached. Here we explore the biodiversity of spider silk fibres, focusing on nanoscale characterization with high-resolution atomic force microscopy. Our results reveal an evolution of the nanoroughness, nanostiffness, nanoviscoelastic, nanotribological and nanoelectric organization of microfibres, even when they share similar sizes and shapes. These features are related to unique aspects of their molecular structures. The results show that combined nanoscale analyses of spider silks may enable the screening of appropriate motifs for bioengineering synthetic fibres from recombinant proteins.

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

Fast time-resolved electrostatic force microscopy: Achieving sub-cycle time resolution

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

Karatay, Durmus U.; Harrison, Jeffrey S.; Glaz, Micah S.

The ability to measure microsecond- and nanosecond-scale local dynamics below the diffraction limit with widely available atomic force microscopy hardware would enable new scientific studies in fields ranging from biology to semiconductor physics. However, commercially available scanning-probe instruments typically offer the ability to measure dynamics only on time scales of milliseconds to seconds. Here, we describe in detail the implementation of fast time-resolved electrostatic force microscopy using an oscillating cantilever as a means to measure fast local dynamics following a perturbation to a sample. We show how the phase of the oscillating cantilever relative to the perturbation event is criticalmore » to achieving reliable sub-cycle time resolution. We explore how noise affects the achievable time resolution and present empirical guidelines for reducing noise and optimizing experimental parameters. Specifically, we show that reducing the noise on the cantilever by using photothermal excitation instead of piezoacoustic excitation further improves time resolution. We demonstrate the discrimination of signal rise times with time constants as fast as 10 ns, and simultaneous data acquisition and analysis for dramatically improved image acquisition times.« less

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.

An in vivo study of electrical charge distribution on the bacterial cell wall by atomic force microscopy in vibrating force mode

NASA Astrophysics Data System (ADS)

Marlière, Christian; Dhahri, Samia

2015-05-01

We report an in vivo electromechanical atomic force microscopy (AFM) study of charge distribution on the cell wall of Gram+ Rhodococcus wratislaviensis bacteria, naturally adherent to a glass substrate, under physiological conditions. The method presented in this paper relies on a detailed study of AFM approach/retract curves giving the variation of the interaction force versus distance between the tip and the sample. In addition to classical height and mechanical (as stiffness) data, mapping of local electrical properties, such as bacterial surface charge, was proved to be feasible at a spatial resolution better than a few tens of nanometers. This innovative method relies on the measurement of the cantilever's surface stress through its deflection far from (>10 nm) the repulsive contact zone: the variations of surface stress come from the modification of electrical surface charge of the cantilever (as in classical electrocapillary measurements) likely stemming from its charging during contact of both the tip and the sample electrical double layers. This method offers an important improvement in local electrical and electrochemical measurements at the solid/liquid interface, particularly in high-molarity electrolytes when compared to techniques focused on the direct use of electrostatic force. It thus opens a new way to directly investigate in situ biological electrical surface processes involved in numerous practical applications and fundamental problems such as bacterial adhesion, biofilm formation, microbial fuel cells, etc.We report an in vivo electromechanical atomic force microscopy (AFM) study of charge distribution on the cell wall of Gram+ Rhodococcus wratislaviensis bacteria, naturally adherent to a glass substrate, under physiological conditions. The method presented in this paper relies on a detailed study of AFM approach/retract curves giving the variation of the interaction force versus distance between the tip and the sample. In addition to classical height and mechanical (as stiffness) data, mapping of local electrical properties, such as bacterial surface charge, was proved to be feasible at a spatial resolution better than a few tens of nanometers. This innovative method relies on the measurement of the cantilever's surface stress through its deflection far from (>10 nm) the repulsive contact zone: the variations of surface stress come from the modification of electrical surface charge of the cantilever (as in classical electrocapillary measurements) likely stemming from its charging during contact of both the tip and the sample electrical double layers. This method offers an important improvement in local electrical and electrochemical measurements at the solid/liquid interface, particularly in high-molarity electrolytes when compared to techniques focused on the direct use of electrostatic force. It thus opens a new way to directly investigate in situ biological electrical surface processes involved in numerous practical applications and fundamental problems such as bacterial adhesion, biofilm formation, microbial fuel cells, etc. Electronic supplementary information (ESI) available. See DOI: 10.1039/c5nr00968e

Harnessing the damping properties of materials for high-speed atomic force microscopy.

PubMed

Adams, Jonathan D; Erickson, Blake W; Grossenbacher, Jonas; Brugger, Juergen; Nievergelt, Adrian; Fantner, Georg E

2016-02-01

The success of high-speed atomic force microscopy in imaging molecular motors, enzymes and microbes in liquid environments suggests that the technique could be of significant value in a variety of areas of nanotechnology. However, the majority of atomic force microscopy experiments are performed in air, and the tapping-mode detection speed of current high-speed cantilevers is an order of magnitude lower in air than in liquids. Traditional approaches to increasing the imaging rate of atomic force microscopy have involved reducing the size of the cantilever, but further reductions in size will require a fundamental change in the detection method of the microscope. Here, we show that high-speed imaging in air can instead be achieved by changing the cantilever material. We use cantilevers fabricated from polymers, which can mimic the high damping environment of liquids. With this approach, SU-8 polymer cantilevers are developed that have an imaging-in-air detection bandwidth that is 19 times faster than those of conventional cantilevers of similar size, resonance frequency and spring constant.

Near-Field Acoustical Imaging using Lateral Bending Mode of Atomic Force Microscope Cantilevers

NASA Astrophysics Data System (ADS)

Caron, A.; Rabe, U.; Rödel, J.; Arnold, W.

Scanning probe microscopy techniques enable one to investigate surface properties such as contact stiffness and friction between the probe tip and a sample with nm resolution. So far the bending and the torsional eigenmodes of an atomic force microscope cantilever have been used to image variations of elasticity and shear elasticity, respectively. Such images are near-field images with the resolution given by the contact radius typically between 10 nm and 50 nm. We show that the flexural modes of a cantilever oscillating in the width direction and parallel to the sample surface can also be used for imaging. Additional to the dominant in-plane component of the oscillation, the lateral modes exhibit a vertical component as well, provided there is an asymmetry in the cross-section of the cantilever or in its suspension. The out-of-plane deflection renders the lateral modes detectable by the optical position sensors used in atomic force microscopes. We studied cracks which were generated by Vickers indents, in submicro- and nanocrystalline ZrO2. Images of the lateral contact stiffness were obtained by vibrating the cantilever close to a contact-resonance frequency. A change in contact stiffness causes a shift of the resonant frequency and hence a change of the cantilever vibration amplitude. The lateral contact-stiffness images close to the crack faces display a contrast that we attribute to altered elastic properties indicating a process zone. This could be caused by a stress-induced phase transformation during crack propagation. Using the contact mode of an atomic force microscope, we measured the crack-opening displacement as a function of distance from the crack tip, and we determined the crack-tip toughness Ktip. Furthermore, K1c was inferred from the length of radial cracks of Vickers indents that were measured using classical scanning acoustic microscopy

Fundamental edge broadening effects during focused electron beam induced nanosynthesis

DOE PAGES

Schmied, Roland; Fowlkes, Jason Davidson; Winkler, Robert; ...

2015-02-16

In this study, we explore lateral broadening effects of 3D structures fabricated through focused electron beam induced deposition using MeCpPt(IV)Me 3 precursor. In particular, the scaling behavior of proximity effects as a function of the primary electron energy and the deposit height is investigated through experiments and validated through simulations. Correlated Kelvin force microscopy and conductive atomic force microscopy measurements identified conductive and non-conductive proximity regions. It was determined that the highest primary electron energies enable the highest edge sharpness while lower energies contain a complex convolution of broadening effects. In addition, it is demonstrated that intermediate energies lead tomore » even more complex proximity effects that significantly reduce lateral edge sharpness and thus should be avoided if desiring high lateral resolution.« less

Asymmetric Flow-Field Flow Fractionation (AF4) of Aqueous C60 Aggregates with Dynamic Light Scattering Size and LC-MS

EPA Science Inventory

Current methods for the size determination of nanomaterials in aqueous suspension include dynamic or static light scattering and electron or atomic force microscopy techniques. Light scattering techniques are limited by poor resolution and the scattering intensity dependence on p...

3-Dimensional atomic scale structure of the ionic liquid-graphite interface elucidated by AM-AFM and quantum chemical simulations

NASA Astrophysics Data System (ADS)

Page, Alister J.; Elbourne, Aaron; Stefanovic, Ryan; Addicoat, Matthew A.; Warr, Gregory G.; Voïtchovsky, Kislon; Atkin, Rob

2014-06-01

In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition.In situ amplitude modulated atomic force microscopy (AM-AFM) and quantum chemical simulations are used to resolve the structure of the highly ordered pyrolytic graphite (HOPG)-bulk propylammonium nitrate (PAN) interface with resolution comparable with that achieved for frozen ionic liquid (IL) monolayers using STM. This is the first time that (a) molecular resolution images of bulk IL-solid interfaces have been achieved, (b) the lateral structure of the IL graphite interface has been imaged for any IL, (c) AM-AFM has elucidated molecular level structure immersed in a viscous liquid and (d) it has been demonstrated that the IL structure at solid surfaces is a consequence of both thermodynamic and kinetic effects. The lateral structure of the PAN-graphite interface is highly ordered and consists of remarkably well-defined domains of a rhomboidal superstructure composed of propylammonium cations preferentially aligned along two of the three directions in the underlying graphite lattice. The nanostructure is primarily determined by the cation. Van der Waals interactions between the propylammonium chains and the surface mean that the cation is enriched in the surface layer, and is much less mobile than the anion. The presence of a heterogeneous lateral structure at an ionic liquid-solid interface has wide ranging ramifications for ionic liquid applications, including lubrication, capacitive charge storage and electrodeposition. Electronic supplementary information (ESI) available. See DOI: 10.1039/c4nr01219d

Effects of growth rate on structural property and adatom migration behaviors for growth of GaInNAs/GaAs (001) by molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Li, Jingling; Gao, Peng; Zhang, Shuguang; Wen, Lei; Gao, Fangliang; Li, Guoqiang

2018-03-01

We have investigated the structural properties and the growth mode of GaInNAs films prepared at different growth rates (Rg) by molecular beam epitaxy. The crystalline structure is studied by high resolution X-ray diffraction, and the evolution of GaInNAs film surface morphologies is studied by atomic force microscopy. It is found that both the crystallinity and the surface roughness are improved by increasing Rg, and the change in the growth mode is attributed to the adatom migration behaviors particularly for In atoms, which is verified by elemental analysis. In addition, we have presented some theoretical calculation results related to the N adsorption energy to show the unique N migration behavior, which is instructive to interpret the growth mechanism of GaInNAs films.

Brain tissue stiffness is a sensitive marker for acidosis.

PubMed

Holtzmann, Kathrin; Gautier, Hélène O B; Christ, Andreas F; Guck, Jochen; Káradóttir, Ragnhildur Thóra; Franze, Kristian

2016-09-15

Carbon dioxide overdose is frequently used to cull rodents for tissue harvesting. However, this treatment may lead to respiratory acidosis, which potentially could change the properties of the investigated tissue. Mechanical tissue properties often change in pathological conditions and may thus offer a sensitive generic readout for changes in biological tissues with clinical relevance. In this study, we performed force-indentation measurements with an atomic force microscope on acute cerebellar slices from adult rats to test if brain tissue undergoes changes following overexposure to CO2 compared to other methods of euthanasia. The pH significantly decreased in brain tissue of animals exposed to CO2. Concomitant with the drop in pH, cerebellar grey matter significantly stiffened. Tissue stiffening was reproduced by incubation of acute cerebellar slices in acidic medium. Tissue stiffness provides an early, generic indicator for pathophysiological changes in the CNS. Atomic force microscopy offers unprecedented high spatial resolution to detect such changes. Our results indicate that the stiffness particularly of grey matter strongly correlates with changes of the pH in the cerebellum. Furthermore, the method of tissue harvesting and preparation may not only change tissue stiffness but very likely also other physiologically relevant parameters, highlighting the importance of appropriate sample preparation. Copyright © 2016 The Authors. Published by Elsevier B.V. All rights reserved.

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.

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

Viscoelastic Properties of Confluent MDCK II Cells Obtained from Force Cycle Experiments.

PubMed

Brückner, Bastian Rouven; Nöding, Helen; Janshoff, Andreas

2017-02-28

The local mechanical properties of cells are frequently probed by force indentation experiments carried out with an atomic force microscope. Application of common contact models provides a single parameter, the Young's modulus, to describe the elastic properties of cells. The viscoelastic response of cells, however, is generally measured in separate microrheological experiments that provide complex shear moduli as a function of time or frequency. Here, we present a straightforward way to obtain rheological properties of cells from regular force distance curves collected in typical force indentation measurements. The method allows us to record the stress-strain relationship as well as changes in the weak power law of the viscoelastic moduli. We derive an analytical function based on the elastic-viscoelastic correspondence principle applied to Hertzian contact mechanics to model both indentation and retraction curves. Rheological properties are described by standard viscoelastic models and the paradigmatic weak power law found to interpret the viscoelastic properties of living cells best. We compare our method with atomic force microscopy-based active oscillatory microrheology and show that the method to determine the power law coefficient is robust against drift and largely independent of the indentation depth and indenter geometry. Cells were subject to Cytochalasin D treatment to provoke a drastic change in the power law coefficient and to demonstrate the feasibility of the approach to capture rheological changes extremely fast and precisely. The method is easily adaptable to different indenter geometries and acquires viscoelastic data with high spatiotemporal resolution. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Diatom Valve Three-Dimensional Representation: A New Imaging Method Based on Combined Microscopies

PubMed Central

Ferrara, Maria Antonietta; De Tommasi, Edoardo; Coppola, Giuseppe; De Stefano, Luca; Rea, Ilaria; Dardano, Principia

2016-01-01

The frustule of diatoms, unicellular microalgae, shows very interesting photonic features, generally related to its complicated and quasi-periodic micro- and nano-structure. In order to simulate light propagation inside and through this natural structure, it is important to develop three-dimensional (3D) models for synthetic replica with high spatial resolution. In this paper, we present a new method that generates images of microscopic diatoms with high definition, by merging scanning electron microscopy and digital holography microscopy or atomic force microscopy data. Starting from two digital images, both acquired separately with standard characterization procedures, a high spatial resolution (Δz = λ/20, Δx = Δy ≅ 100 nm, at least) 3D model of the object has been generated. Then, the two sets of data have been processed by matrix formalism, using an original mathematical algorithm implemented on a commercially available software. The developed methodology could be also of broad interest in the design and fabrication of micro-opto-electro-mechanical systems. PMID:27690008

Characterization of virus-like particles by atomic force microscopy in ambient conditions

NASA Astrophysics Data System (ADS)

Oropesa, Reinier; Ramos, Jorge R.; Falcón, Viviana; Felipe, Ariel

2013-06-01

Recombinant virus-like particles (VLPs) are attractive candidates for vaccine design since they resemble native viroids in size and morphology, but they are non-infectious due to the absence of a viral genome. The visualization of surface morphologies and structures can be used to deepen the understanding of physical, chemical, and biological phenomena. Atomic force microscopy (AFM) is a useful tool for the visualization of soft biological samples in a nanoscale resolution. In this work we have investigated the morphology of recombinant surface antigens of hepatitis B (rHBsAg) VLPs from Cuban vaccine against hepatitis B. The rHBsAg VLPs sizes estimated by AFM between 15 and 30 nm are similar to those reported on previous transmission electron microscopy (TEM) studies.

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

High-resolution analysis of the mechanical behavior of tissue

NASA Astrophysics Data System (ADS)

Hudnut, Alexa W.; Armani, Andrea M.

2017-06-01

The mechanical behavior and properties of biomaterials, such as tissue, have been directly and indirectly connected to numerous malignant physiological states. For example, an increase in the Young's Modulus of tissue can be indicative of cancer. Due to the heterogeneity of biomaterials, it is extremely important to perform these measurements using whole or unprocessed tissue because the tissue matrix contains important information about the intercellular interactions and the structure. Thus, developing high-resolution approaches that can accurately measure the elasticity of unprocessed tissue samples is of great interest. Unfortunately, conventional elastography methods such as atomic force microscopy, compression testing, and ultrasound elastography either require sample processing or have poor resolution. In the present work, we demonstrate the characterization of unprocessed salmon muscle using an optical polarimetric elastography system. We compare the results of compression testing within different samples of salmon skeletal muscle with different numbers of collagen membranes to characterize differences in heterogeneity. Using the intrinsic collagen membranes as markers, we determine the resolution of the system when testing biomaterials. The device reproducibly measures the stiffness of the tissues at variable strains. By analyzing the amount of energy lost by the sample during compression, collagen membranes that are 500 μm in size are detected.

A thermal microprobe fabricated with wafer-stage processing

NASA Astrophysics Data System (ADS)

Zhang, Yongxia; Zhang, Yanwei; Blaser, Juliana; Sriram, T. S.; Enver, Ahsan; Marcus, R. B.

1998-05-01

A thermal microprobe has been designed and built for high resolution temperature sensing. The thermal sensor is a thin-film thermocouple junction at the tip of an atomic force microprobe (AFM) silicon probe needle. Only wafer-stage processing steps are used for the fabrication. For high resolution temperature sensing it is essential that the junction be confined to a short distance at the AFM tip. This confinement is achieved by a controlled photoresist coating process. Experiment prototypes have been made with an Au/Pd junction confined to within 0.5 μm of the tip, with the two metals separated elsewhere by a thin insulating oxide layer. Processing begins with double-polished, n-type, 4 in. diameter, 300-μm-thick silicon wafers. Atomically sharp probe tips are formed by a combination of dry and wet chemical etching, and oxidation sharpening. The metal layers are sputtering deposited and the cantilevers are released by a combination of KOH and dry etching. A resistively heated calibration device was made for temperature calibration of the thermal microprobe over the temperature range 25-110 °C. Over this range the thermal outputs of two microprobes are 4.5 and 5.6 μV/K and is linear. Thermal and topographical images are also obtained from a heated tungsten thin film fuse.

Evaluation of the electrical contact area in contact-mode scanning probe microscopy

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

Celano, Umberto, E-mail: celano@imec.be, E-mail: u.celano@gmail.com; Chintala, Ravi Chandra; Vandervorst, Wilfried

The tunneling current through an atomic force microscopy (AFM) tip is used to evaluate the effective electrical contact area, which exists between tip and sample in contact-AFM electrical measurements. A simple procedure for the evaluation of the effective electrical contact area is described using conductive atomic force microscopy (C-AFM) in combination with a thin dielectric. We characterize the electrical contact area for coated metal and doped-diamond tips operated at low force (<200 nN) in contact mode. In both cases, we observe that only a small fraction (<10 nm{sup 2}) of the physical contact (∼100 nm{sup 2}) is effectively contributing to the transportmore » phenomena. Assuming this reduced area is confined to the central area of the physical contact, these results explain the sub-10 nm electrical resolution observed in C-AFM measurements.« less

Recent advances in micromechanical characterization of polymer, biomaterial, and cell surfaces with atomic force microscopy

NASA Astrophysics Data System (ADS)

Chyasnavichyus, Marius; Young, Seth L.; Tsukruk, Vladimir V.

2015-08-01

Probing of micro- and nanoscale mechanical properties of soft materials with atomic force microscopy (AFM) gives essential information about the performance of the nanostructured polymer systems, natural nanocomposites, ultrathin coatings, and cell functioning. AFM provides efficient and is some cases the exclusive way to study these properties nondestructively in controlled environment. Precise force control in AFM methods allows its application to variety of soft materials and can be used to go beyond elastic properties and examine temperature and rate dependent materials response. In this review, we discuss experimental AFM methods currently used in the field of soft nanostructured composites and biomaterials. We discuss advantages and disadvantages of common AFM probing techniques, which allow for both qualitative and quantitative mappings of the elastic modulus of soft materials with nanosacle resolution. We also discuss several advanced techniques for more elaborate measurements of viscoelastic properties of soft materials and experiments on single cells.

Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains.

PubMed

Sabater, Carlos; Untiedt, Carlos; van Ruitenbeek, Jan M

2015-01-01

This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a 'Berry force'. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose.

Nanoscale live cell optical imaging of the dynamics of intracellular microvesicles in neural cells.

PubMed

Lee, Sohee; Heo, Chaejeong; Suh, Minah; Lee, Young Hee

2013-11-01

Recent advances in biotechnology and imaging technology have provided great opportunities to investigate cellular dynamics. Conventional imaging methods such as transmission electron microscopy, scanning electron microscopy, and atomic force microscopy are powerful techniques for cellular imaging, even at the nanoscale level. However, these techniques have limitations applications in live cell imaging because of the experimental preparation required, namely cell fixation, and the innately small field of view. In this study, we developed a nanoscale optical imaging (NOI) system that combines a conventional optical microscope with a high resolution dark-field condenser (Cytoviva, Inc.) and halogen illuminator. The NOI system's maximum resolution for live cell imaging is around 100 nm. We utilized NOI to investigate the dynamics of intracellular microvesicles of neural cells without immunocytological analysis. In particular, we studied direct, active random, and moderate random dynamic motions of intracellular microvesicles and visualized lysosomal vesicle changes after treatment of cells with a lysosomal inhibitor (NH4Cl). Our results indicate that the NOI system is a feasible, high-resolution optical imaging system for live small organelles that does not require complicated optics or immunocytological staining processes.

Large area scanning probe microscope in ultra-high vacuum demonstrated for electrostatic force measurements on high-voltage devices.

PubMed

Gysin, Urs; Glatzel, Thilo; Schmölzer, Thomas; Schöner, Adolf; Reshanov, Sergey; Bartolf, Holger; Meyer, Ernst

2015-01-01

The resolution in electrostatic force microscopy (EFM), a descendant of atomic force microscopy (AFM), has reached nanometre dimensions, necessary to investigate integrated circuits in modern electronic devices. However, the characterization of conducting or semiconducting power devices with EFM methods requires an accurate and reliable technique from the nanometre up to the micrometre scale. For high force sensitivity it is indispensable to operate the microscope under high to ultra-high vacuum (UHV) conditions to suppress viscous damping of the sensor. Furthermore, UHV environment allows for the analysis of clean surfaces under controlled environmental conditions. Because of these requirements we built a large area scanning probe microscope operating under UHV conditions at room temperature allowing to perform various electrical measurements, such as Kelvin probe force microscopy, scanning capacitance force microscopy, scanning spreading resistance microscopy, and also electrostatic force microscopy at higher harmonics. The instrument incorporates beside a standard beam deflection detection system a closed loop scanner with a scan range of 100 μm in lateral and 25 μm in vertical direction as well as an additional fibre optics. This enables the illumination of the tip-sample interface for optically excited measurements such as local surface photo voltage detection. We present Kelvin probe force microscopy (KPFM) measurements before and after sputtering of a copper alloy with chromium grains used as electrical contact surface in ultra-high power switches. In addition, we discuss KPFM measurements on cross sections of cleaved silicon carbide structures: a calibration layer sample and a power rectifier. To demonstrate the benefit of surface photo voltage measurements, we analysed the contact potential difference of a silicon carbide p/n-junction under illumination.

Nanophotonic Atomic Force Microscope Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale [Nanophotonic AFM Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale

DOE PAGES

Chae, Jungseok; An, Sangmin; Ramer, Georg; ...

2017-08-03

The atomic force microscope (AFM) offers a rich observation window on the nanoscale, yet many dynamic phenomena are too fast and too weak for direct AFM detection. Integrated cavity-optomechanics is revolutionizing micromechanical sensing; however, it has not yet impacted AFM. Here, we make a groundbreaking advance by fabricating picogram-scale probes integrated with photonic resonators to realize functional AFM detection that achieve high temporal resolution (<10 ns) and picometer vertical displacement uncertainty simultaneously. The ability to capture fast events with high precision is leveraged to measure the thermal conductivity (η), for the first time, concurrently with chemical composition at the nanoscalemore » in photothermal induced resonance experiments. The intrinsic η of metal–organic-framework individual microcrystals, not measurable by macroscale techniques, is obtained with a small measurement uncertainty (8%). The improved sensitivity (50×) increases the measurement throughput 2500-fold and enables chemical composition measurement of molecular monolayer-thin samples. In conclusion, our paradigm-shifting photonic readout for small probes breaks the common trade-off between AFM measurement precision and ability to capture transient events, thus transforming the ability to observe nanoscale dynamics in materials.« less

Optimizing purification process of MIM-I-BAR domain by introducing atomic force microscope and dynamics simulations.

PubMed

Zhang, Yue; Lou, Zhichao; Lin, Xubo; Wang, Qiwei; Cao, Meng; Gu, Ning

2017-09-01

MIM (missing in metastasis) is a member of I-BAR (inverse BAR) domain protein family, which functions as a putative metastasis suppressor. However, methods of gaining high purity MIM-I-BAR protein are barely reported. Here, by optimizing the purification process including changing the conditions of cell lysate and protein elution, we successfully purified MIM protein. The purity of the obtained protein was up to ∼90%. High-resolution atomic force microscope (AFM) provides more visual images, ensuring that we can observe the microenvironment around the target protein, as well as the conformations of the purification products following each purification process. MIM protein with two different sizes were observed on mica surface with AFM. Combining with molecular dynamics simulations, these molecules were revealed as MIM monomer and dimer. Furthermore, our study attaches importance to the usage of imidazole with suitable concentrations during the affinity chromatography process, as well as the removal of excessive imidazole after the affinity chromatography process. All these results indicate that the method described here was successful in purifying MIM protein and maintaining their natural properties, and is supposed to be used to purify other proteins with low solubility. Copyright © 2017. Published by Elsevier B.V.

Nanophotonic Atomic Force Microscope Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale [Nanophotonic AFM Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale

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

Chae, Jungseok; An, Sangmin; Ramer, Georg

The atomic force microscope (AFM) offers a rich observation window on the nanoscale, yet many dynamic phenomena are too fast and too weak for direct AFM detection. Integrated cavity-optomechanics is revolutionizing micromechanical sensing; however, it has not yet impacted AFM. Here, we make a groundbreaking advance by fabricating picogram-scale probes integrated with photonic resonators to realize functional AFM detection that achieve high temporal resolution (<10 ns) and picometer vertical displacement uncertainty simultaneously. The ability to capture fast events with high precision is leveraged to measure the thermal conductivity (η), for the first time, concurrently with chemical composition at the nanoscalemore » in photothermal induced resonance experiments. The intrinsic η of metal–organic-framework individual microcrystals, not measurable by macroscale techniques, is obtained with a small measurement uncertainty (8%). The improved sensitivity (50×) increases the measurement throughput 2500-fold and enables chemical composition measurement of molecular monolayer-thin samples. In conclusion, our paradigm-shifting photonic readout for small probes breaks the common trade-off between AFM measurement precision and ability to capture transient events, thus transforming the ability to observe nanoscale dynamics in materials.« less

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants

PubMed Central

Ewen, James P.; Gattinoni, Chiara; Thakkar, Foram M.; Morgan, Neal; Spikes, Hugh A.; Dini, Daniele

2016-01-01

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n-hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n-hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n-hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed. PMID:28773773

A Comparison of Classical Force-Fields for Molecular Dynamics Simulations of Lubricants.

PubMed

Ewen, James P; Gattinoni, Chiara; Thakkar, Foram M; Morgan, Neal; Spikes, Hugh A; Dini, Daniele

2016-08-02

For the successful development and application of lubricants, a full understanding of their complex nanoscale behavior under a wide range of external conditions is required, but this is difficult to obtain experimentally. Nonequilibrium molecular dynamics (NEMD) simulations can be used to yield unique insights into the atomic-scale structure and friction of lubricants and additives; however, the accuracy of the results depend on the chosen force-field. In this study, we demonstrate that the use of an accurate, all-atom force-field is critical in order to; (i) accurately predict important properties of long-chain, linear molecules; and (ii) reproduce experimental friction behavior of multi-component tribological systems. In particular, we focus on n -hexadecane, an important model lubricant with a wide range of industrial applications. Moreover, simulating conditions common in tribological systems, i.e., high temperatures and pressures (HTHP), allows the limits of the selected force-fields to be tested. In the first section, a large number of united-atom and all-atom force-fields are benchmarked in terms of their density and viscosity prediction accuracy of n -hexadecane using equilibrium molecular dynamics (EMD) simulations at ambient and HTHP conditions. Whilst united-atom force-fields accurately reproduce experimental density, the viscosity is significantly under-predicted compared to all-atom force-fields and experiments. Moreover, some all-atom force-fields yield elevated melting points, leading to significant overestimation of both the density and viscosity. In the second section, the most accurate united-atom and all-atom force-field are compared in confined NEMD simulations which probe the structure and friction of stearic acid adsorbed on iron oxide and separated by a thin layer of n -hexadecane. The united-atom force-field provides an accurate representation of the structure of the confined stearic acid film; however, friction coefficients are consistently under-predicted and the friction-coverage and friction-velocity behavior deviates from that observed using all-atom force-fields and experimentally. This has important implications regarding force-field selection for NEMD simulations of systems containing long-chain, linear molecules; specifically, it is recommended that accurate all-atom potentials, such as L-OPLS-AA, are employed.

Characterizing the effect of polymyxin B antibiotics to lipopolysaccharide on Escherichia coli surface using atomic force microscopy.

PubMed

Oh, Yoo Jin; Plochberger, Birgit; Rechberger, Markus; Hinterdorfer, Peter

2017-06-01

Lipopolysaccharide (LPS) on gram-negative bacterial outer membranes is the first target for antimicrobial agents, due to their spatial proximity to outer environments of microorganisms. To develop antibacterial compounds with high specificity for LPS binding, the understanding of the molecular nature and their mode of recognition is of key importance. In this study, atomic force microscopy (AFM) and single molecular force spectroscopy were used to characterize the effects of antibiotic polymyxin B (PMB) to the bacterial membrane at the nanoscale. Isolated LPS layer and the intact bacterial membrane were examined with respect to morphological changes at different concentrations of PMB. Our results revealed that 3 hours of 10 μg/mL of PMB exposure caused the highest roughness changes on intact bacterial surfaces, arising from the direct binding of PMB to LPS on the bacterial membrane. Single molecular force spectroscopy was used to probe specific interaction forces between the isolated LPS layer and PMB coupled to the AFM tip. A short range interaction regime mediated by electrostatic forces was visible. Unbinding forces between isolated LPS and PMB were about 30 pN at a retraction velocity of 500 nm/s. We further investigated the effects of the polycationic peptide PMB on bacterial outer membranes and monitored its influences on the deterioration of the bacterial membrane structure. Polymyxin B binding led to rougher appearances and wrinkles on the outer membranes surface, which may finally lead to lethal membrane damage of bacteria. Our studies indicate the potential of AFM for applications in pathogen recognition and nano-resolution approaches in microbiology. Copyright © 2017 John Wiley & Sons, Ltd.

Atomic force microscopy imaging of macromolecular complexes.

PubMed

Santos, Sergio; Billingsley, Daniel; Thomson, Neil

2013-01-01

This chapter reviews amplitude modulation (AM) AFM in air and its applications to high-resolution imaging and interpretation of macromolecular complexes. We discuss single DNA molecular imaging and DNA-protein interactions, such as those with topoisomerases and RNA polymerase. We show how relative humidity can have a major influence on resolution and contrast and how it can also affect conformational switching of supercoiled DNA. Four regimes of AFM tip-sample interaction in air are defined and described, and relate to water perturbation and/or intermittent mechanical contact of the tip with either the molecular sample or the surface. Precise control and understanding of the AFM operational parameters is shown to allow the user to switch between these different regimes: an interpretation of the origins of topographical contrast is given for each regime. Perpetual water contact is shown to lead to a high-resolution mode of operation, which we term SASS (small amplitude small set-point) imaging, and which maximizes resolution while greatly decreasing tip and sample wear and any noise due to perturbation of the surface water. Thus, this chapter provides sufficient information to reliably control the AFM in the AM AFM mode of operation in order to image both heterogeneous samples and single macromolecules including complexes, with high resolution and with reproducibility. A brief introduction to AFM, its versatility and applications to biology is also given while providing references to key work and general reviews in the field.

Defect mediated van der Waals epitaxy of hexagonal boron nitride on graphene

NASA Astrophysics Data System (ADS)

Heilmann, M.; Bashouti, M.; Riechert, H.; Lopes, J. M. J.

2018-04-01

Van der Waals heterostructures comprising of hexagonal boron nitride and graphene are promising building blocks for novel two-dimensional devices such as atomically thin transistors or capacitors. However, demonstrators of those devices have been so far mostly fabricated by mechanical assembly, a non-scalable and time-consuming method, where transfer processes can contaminate the surfaces. Here, we investigate a direct growth process for the fabrication of insulating hexagonal boron nitride on high quality epitaxial graphene using plasma assisted molecular beam epitaxy. Samples were grown at varying temperatures and times and studied using atomic force microscopy, revealing a growth process limited by desorption at high temperatures. Nucleation was mostly commencing from morphological defects in epitaxial graphene, such as step edges or wrinkles. Raman spectroscopy combined with x-ray photoelectron measurements confirm the formation of hexagonal boron nitride and prove the resilience of graphene against the nitrogen plasma used during the growth process. The electrical properties and defects in the heterostructures were studied with high lateral resolution by tunneling current and Kelvin probe force measurements. This correlated approach revealed a nucleation apart from morphological defects in epitaxial graphene, which is mediated by point defects. The presented results help understanding the nucleation and growth behavior during van der Waals epitaxy of 2D materials, and point out a route for a scalable production of van der Waals heterostructures.

A microelectromechanical systems (MEMS) force-displacement transducer for sub-5 nm nanoindentation and adhesion measurements

NASA Astrophysics Data System (ADS)

Zhang, Youfeng; Oh, Yunje; Stauffer, Douglas; Polycarpou, Andreas A.

2018-04-01

We present a highly sensitive force-displacement transducer capable of performing ultra-shallow nanoindentation and adhesion measurements. The transducer utilizes electrostatic actuation and capacitive sensing combined with microelectromechanical fabrication technologies. Air indentation experiments report a root-mean-square (RMS) force resolution of 1.8 nN and an RMS displacement resolution of 0.019 nm. Nanoindentation experiments on a standard fused quartz sample report a practical RMS force resolution of 5 nN and an RMS displacement resolution of 0.05 nm at sub-10 nm indentation depths, indicating that the system has a very low system noise for indentation experiments. The high sensitivity and low noise enables the transducer to obtain high-resolution nanoindentation data at sub-5 nm contact depths. The sensitive force transducer is used to successfully perform nanoindentation measurements on a 14 nm thin film. Adhesion measurements were also performed, clearly capturing the pull-on and pull-off forces during approach and separation of two contacting surfaces.

Nanoscale Infrared Spectroscopy of Biopolymeric Materials

Treesearch

Curtis Marcott; Michael Lo; Kevin Kjoller; Craig Prater; Roshan Shetty; Joseph Jakes; Isao Noda

2012-01-01

Atomic Force Microscopy (AFM) and infrared (IR) spectroscopy have been combined in a single instrument capable of producing 100 nm spatial resolution IR spectra and images. This new capability enables the spectroscopic characterization of biomaterial domains at levels not previously possible. A tunable IR laser source generating pulses on the order of 10 ns was used...

Development and applications of optical interferometric micrometrology in the Angstrom and subangstrom range

NASA Technical Reports Server (NTRS)

Lauer, James L.; Abel, Phillip B.

1988-01-01

The characteristics of the scanning tunneling microscope and atomic force microscope (AFM) are briefly reviewed, and optical methods, mainly interferometry, of sufficient resolution to measure AFM deflections are discussed. The methods include optical resonators, laser interferometry, multiple-beam interferometry, and evanescent wave detection. Experimental results using AFM are reviewed.

Convergent Inquiry in Science & Engineering: The Use of Atomic Force Microscopy in a Biology Class

ERIC Educational Resources Information Center

Lee, Il-Sun; Byeon, Jung-Ho; Kwon, Yong-Ju

2013-01-01

The purpose of this study was to design a teaching method suitable for science high school students using atomic force microscopy. During their scientific inquiry procedure, high school students observed a micro-nanostructure of a biological sample, which is unobservable via an optical microscope. The developed teaching method enhanced students'…

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.

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

Atomic-scale imaging of DNA using scanning tunnelling microscopy.

PubMed

Driscoll, R J; Youngquist, M G; Baldeschwieler, J D

1990-07-19

The scanning tunnelling microscope (STM) has been used to visualize DNA under water, under oil and in air. Images of single-stranded DNA have shown that submolecular resolution is possible. Here we describe atomic-resolution imaging of duplex DNA. Topographic STM images of uncoated duplex DNA on a graphite substrate obtained in ultra-high vacuum are presented that show double-helical structure, base pairs, and atomic-scale substructure. Experimental STM profiles show excellent correlation with atomic contours of the van der Waals surface of A-form DNA derived from X-ray crystallography. A comparison of variations in the barrier to quantum mechanical tunnelling (barrier-height) with atomic-scale topography shows correlation over the phosphate-sugar backbone but anticorrelation over the base pairs. This relationship may be due to the different chemical characteristics of parts of the molecule. Further investigation of this phenomenon should lead to a better understanding of the physics of imaging adsorbates with the STM and may prove useful in sequencing DNA. The improved resolution compared with previously published STM images of DNA may be attributable to ultra-high vacuum, high data-pixel density, slow scan rate, a fortuitously clean and sharp tip and/or a relatively dilute and extremely clean sample solution. This work demonstrates the potential of the STM for characterization of large biomolecular structures, but additional development will be required to make such high resolution imaging of DNA and other large molecules routine.

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

Detecting molecules and cells labeled with magnetic particles using an atomic magnetometer

NASA Astrophysics Data System (ADS)

Yu, Dindi; Ruangchaithaweesuk, Songtham; Yao, Li; Xu, Shoujun

2012-09-01

The detection of magnetically labeled molecules and cells involves three essential parameters: sensitivity, spatial resolution, and molecular specificity. We report on the use of atomic magnetometry and its derivative techniques to achieve high performance in terms of all these parameters. With a sensitivity of 80 fT/√Hz for dc magnetic fields, we show that 7,000 streptavidin-conjugated magnetic microparticles magnetized by a permanent magnet produce a magnetic field of 650 pT; this result predicts that a single such particle can be detected during one second of signal averaging. Spatial information is obtained using a scanning magnetic imaging scheme. The spatial resolution is 20 μm with a detection distance of more than 1 cm; this distance is much longer than that in previous reports. The molecular specificity is achieved using force-induced remnant magnetization spectroscopy, which currently uses an atomic magnetometer for detection. As an example, we perform measurement of magnetically labeled human CD4+ T cells, whose count in the blood is the diagnostic criterion for human immunodeficiency virus infection. Magnetic particles that are specifically bound to the cells are resolved from nonspecifically bound particles and quantitatively correlate with the number of cells. The magnetic particles have an overall size of 2.8 μm, with a magnetic core in nanometer regime. The combination of our techniques is predicted to be useful in molecular and cellular imaging.

Note: Production of stable colloidal probes for high-temperature atomic force microscopy applications

NASA Astrophysics Data System (ADS)

Ditscherlein, L.; Peuker, U. A.

2017-04-01

For the application of colloidal probe atomic force microscopy at high temperatures (>500 K), stable colloidal probe cantilevers are essential. In this study, two new methods for gluing alumina particles onto temperature stable cantilevers are presented and compared with an existing method for borosilicate particles at elevated temperatures as well as with cp-cantilevers prepared with epoxy resin at room temperature. The durability of the fixing of the particle is quantified with a test method applying high shear forces. The force is calculated with a mechanical model considering both the bending as well as the torsion on the colloidal probe.

High harmonic interferometry of the Lorentz force in strong mid-infrared laser fields

NASA Astrophysics Data System (ADS)

Pisanty, Emilio; Hickstein, Daniel D.; Galloway, Benjamin R.; Durfee, Charles G.; Kapteyn, Henry C.; Murnane, Margaret M.; Ivanov, Misha

2018-05-01

The interaction of intense mid-infrared laser fields with atoms and molecules leads to a range of new opportunities, from the production of bright, coherent radiation in the soft x-ray range, to imaging molecular structures and dynamics with attosecond temporal and sub-angstrom spatial resolution. However, all these effects, which rely on laser-driven recollision of an electron removed by the strong laser field and its parent ion, suffer from the rapidly increasing role of the magnetic field component of the driving pulse: the associated Lorentz force pushes the electrons off course in their excursion and suppresses all recollision-based processes, including high harmonic generation as well as elastic and inelastic scattering. Here we show how the use of two non-collinear beams with opposite circular polarizations produces a forwards ellipticity which can be used to monitor, control, and cancel the effect of the Lorentz force. This arrangement can thus be used to re-enable recollision-based phenomena in regimes beyond the long-wavelength breakdown of the dipole approximation, and it can be used to observe this breakdown in high harmonic generation using currently available light sources.

Imaging thermal conductivity with nanoscale resolution using a scanning spin probe

DOE PAGES

Laraoui, Abdelghani; Aycock-Rizzo, Halley; Gao, Yang; ...

2015-11-20

The ability to probe nanoscale heat flow in a material is often limited by lack of spatial resolution. Here, we use a diamond-nanocrystal-hosted nitrogen-vacancy centre attached to the apex of a silicon thermal tip as a local temperature sensor. We apply an electrical current to heat up the tip and rely on the nitrogen vacancy to monitor the thermal changes the tip experiences as it is brought into contact with surfaces of varying thermal conductivity. By combining atomic force and confocal microscopy, we image phantom microstructures with nanoscale resolution, and attain excellent agreement between the thermal conductivity and topographic maps.more » The small mass and high thermal conductivity of the diamond host make the time response of our technique short, which we demonstrate by monitoring the tip temperature upon application of a heat pulse. Our approach promises multiple applications, from the investigation of phonon dynamics in nanostructures to the characterization of heterogeneous phase transitions and chemical reactions in various solid-state systems.« less

Metalorganic chemical vapor deposition growth of InAs/GaSb type II superlattices with controllable AsxSb1-x interfaces

PubMed Central

2012-01-01

InAs/GaSb type II superlattices were grown on (100) GaSb substrates by metalorganic chemical vapor deposition (MOCVD). A plane of mixed As and Sb atoms connecting the InAs and GaSb layers was introduced to compensate the tensile strain created by the InAs layer in the SL. Characterizations of the samples by atomic force microscopy and high-resolution X-ray diffraction demonstrate flat surface morphology and good crystalline quality. The lattice mismatch of approximately 0.18% between the SL and GaSb substrate is small compared to the MOCVD-grown supperlattice samples reported to date in the literature. Considerable optical absorption in 2- to 8-μm infrared region has been realized. PACS: 78.67.Pt; 81.15.Gh; 63.22.Np; 81.05.Ea PMID:22373387

Structural and mechanical characterization of hybrid metallic-inorganic nanosprings

NASA Astrophysics Data System (ADS)

Habtoun, Sabrina; Houmadi, Said; Reig, Benjamin; Pouget, Emilie; Dedovets, Dmytro; Delville, Marie-Hélène; Oda, Reiko; Cristiano, Fuccio; Bergaud, Christian

2017-10-01

Silica nanosprings (NS) are fabricated by a sol-gel deposition of silica precursors onto a template made of self-assembled organic chiral nanostructures. They are deposited and assembled on microstructured silicon substrates, and then metallized and clamped in a single lithography-free step using a focused ion beam (FIB). The resulting suspended hybrid metallic/inorganic NS are then characterized with high-resolution transmission electron microscopy (HRTEM) and scanning TEM/energy-dispersive X-ray spectroscopy (STEM/EDX), showing the atomic structure of the metallic layer. Three-point bending tests are also carried out using an atomic force microscope (AFM) and supported by finite element method (FEM) simulation with COMSOL Multiphysics allowing the characterization of the mechanical behavior and the estimation of the stiffness of the resulting NS. The information obtained on the structural and mechanical properties of the NS is discussed for future nano-electro-mechanical system (NEMS) applications.

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

Atomic force microscopy of biological samples

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

Doktycz, Mitchel John

2010-01-01

The ability to evaluate structural-functional relationships in real time has allowed scanning probe microscopy (SPM) to assume a prominent role in post genomic biological research. In this mini-review, we highlight the development of imaging and ancillary techniques that have allowed SPM to permeate many key areas of contemporary research. We begin by examining the invention of the scanning tunneling microscope (STM) by Binnig and Rohrer in 1982 and discuss how it served to team biologists with physicists to integrate high-resolution microscopy into biological science. We point to the problems of imaging nonconductive biological samples with the STM and relate howmore » this led to the evolution of the atomic force microscope (AFM) developed by Binnig, Quate, and Gerber, in 1986. Commercialization in the late 1980s established SPM as a powerful research tool in the biological research community. Contact mode AFM imaging was soon complemented by the development of non-contact imaging modes. These non-contact modes eventually became the primary focus for further new applications including the development of fast scanning methods. The extreme sensitivity of the AFM cantilever was recognized and has been developed into applications for measuring forces required for indenting biological surfaces and breaking bonds between biomolecules. Further functional augmentation to the cantilever tip allowed development of new and emerging techniques including scanning ion-conductance microscopy (SICM), scanning electrochemical microscope (SECM), Kelvin force microscopy (KFM) and scanning near field ultrasonic holography (SNFUH).« less

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.

Silver nanowires for highly reproducible cantilever based AFM-TERS microscopy: towards a universal TERS probe.

PubMed

Walke, Peter; Fujita, Yasuhiko; Peeters, Wannes; Toyouchi, Shuichi; Frederickx, Wout; De Feyter, Steven; Uji-I, Hiroshi

2018-04-26

Tip-enhanced Raman scattering (TERS) microscopy is a unique analytical tool to provide complementary chemical and topographic information of surfaces with nanometric resolution. However, difficulties in reliably producing the necessary metallized scanning probe tips has limited its widespread utilisation, particularly in the case of cantilever-based atomic force microscopy. Attempts to alleviate tip related issues using colloidal or bottom-up engineered tips have so far not reported consistent probes for both Raman and topographic imaging. Here we demonstrate the reproducible fabrication of cantilever-based high-performance TERS probes for both topographic and Raman measurements, based on an approach that utilises noble metal nanowires as the active TERS probe. The tips show 10 times higher TERS contrasts than the most typically used electrochemically-etched tips, and show a reproducibility for TERS greater than 90%, far greater than found with standard methods. We show that TERS can be performed in tapping as well as contact AFM mode, with optical resolutions around or below 15 nm, and with a maximum resolution achieved in tapping-mode of 6 nm. Our work illustrates that superior TERS probes can be produced in a fast and cost-effective manner using simple wet-chemistry methods, leading to reliable and reproducible high-resolution and high-sensitivity TERS, and thus renders the technique applicable for a broad community.

Single Molecule Science for Personalized Nanomedicine: Atomic Force Microscopy of Biopolymer-Protein Interactions

NASA Astrophysics Data System (ADS)

Hsueh, Carlin

Nanotechnology has a unique and relatively untapped utility in the fields of medicine and dentistry at the level of single-biopolymer and -molecule diagnostics. In recent years atomic force microscopy (AFM) has garnered much interest due to its ability to obtain atomic-resolution of molecular structures and probe biophysical behaviors of biopolymers and proteins in a variety of biologically significant environments. The work presented in this thesis focuses on the nanoscale manipulation and observation of biopolymers to develop an innovative technology for personalized medicine while understanding complex biological systems. These studies described here primarily use AFM to observe biopolymer interactions with proteins and its surroundings with unprecedented resolution, providing a better understanding of these systems and interactions at the nanoscale. Transcriptional profiling, the measure of messenger RNA (mRNA) abundance in a single cell, is a powerful technique that detects "behavior" or "symptoms" at the tissue and cellular level. We have sought to develop an alternative approach, using our expertise in AFM and single molecule nanotechnology, to achieve a cost-effective high throughput method for sensitive detection and profiling of subtle changes in transcript abundance. The technique does not require amplification of the mRNA sample because the AFM provides three-dimensional views of molecules with unprecedented resolution, requires minimal sample preparation, and utilizes a simple tagging chemistry on cDNA molecules. AFM images showed collagen polymers in teeth and of Drebrin-A remodeling of filamentous actin structure and mechanics. AFM was used to image collagen on exposed dentine tubules and confirmed tubule occlusion with a desensitizing prophylaxis paste by Colgate-Palmolive. The AFM also superseded other microscopy tools in resolving F-actin helix remodeling and possible cooperative binding by a neuronal actin binding protein---Drebrin-A, an interaction that can provide scientists with a better understanding of debilitating neurological diseases, such as Alzheimer's and Down Syndrome at the molecular level. These observations provide extraordinary access to the subtle signs and behavior indicating early onset of disease in cells and tissues and to the dynamics of disease development and treatment.

Electrical Measurements and Nanomechanics Using Scanning Probe Microscopy

NASA Astrophysics Data System (ADS)

Chang, Yong

2002-10-01

In the early 1980s, G. Binnig et al. invented the Scanning Tunneling Microscopy (STM) [1], making it possible to obtain atomic resolution images of conducting surfaces. After that, many different types of Scanning Probe Microscopy (SPM) were invented and some of the most useful representatives are Atomic Force Microscopy (AFM) [2], Electrostatic Force Microscopy (EFM) [3] and Kelvin Probe Force Microscopy (KPFM) [4,5]. In 1985, G. Binnig et al. [2] invented the AFM, which now is used as a fundamental tool in many fields of research. Developed from AFM, Y. Martin et al. [3] invented EFM in 1987. The development of AC mode AFM allows the detection of weak long-range forces. EFM has also been used to study other systems and phenomena, such as thin liquid films on solid surfaces [6], electrically stressed gold nanowires [7], and spatial charge distribution in quantum wires [8]. In 1991, M. Nonnenmacher et al. [5] invented Kelvin Probe Force Microscopy. KPFM is used to study any property that affects the tip-surface Contact Potential Difference (CPD), such as voltage signals in integrated circuits (IC) [9], charged grain boundaries in polycrystalline silicon [10] and surface potential variations in multilayer semiconductor devices [11]. The aim of this poster is to discuss the application of SPM to electrical measurements. The theory of SPM was presented. The AFM was firstly introduced as it was developed before the other two. The design and theory were discussed. The force-distance curve was introduced. After this EFM was presented. EFM was developed from AC mode AFM. The technique was achieved by applying a DC voltage between the tip and the sample. The design, theory and features of it were surveyed. KPFM was also discussed. KPFM was developed from EFM. The central part of this technique is to measure the CPD. Experimental measurements of SPM were described after theory part. Research work using AFM was presented. The newest technique of AFM, UHV-AFM has been used in investigating the nano-mechanical properties of different materials. Normally common AFM has shortcomings as it has either strict limit resolution or difficulties in interpreting the data from the measurements. In order to solve these problems, Ultra High Vacuum (UHV) conditions were applied to acquire quantitative results. A typical UHV-AFM uses a cantilever whose spring constant is relatively high (>100 N/m) to obtain high-resolution image. Experimental measurements using KPFM was presented after AFM. Researchers are using KPFM to acquire the topography and measuring the CPD of semiconductor or metal surfaces. Similarly as in AFM, KPFM works best in UHV environment. A typical UHV-KPFM also uses a cantilever whose spring constant is relatively high. A UHV-KPFM may be able to achieve a high resolution in CPD images. In the past 20 years many different kinds of SPM were invented and used. AFM, EFM, and KPFM are representatives of them. Researchers are still developing new techniques. However, in recent years, they pay more attention in improving the measurement accuracy instead of trying to invent new SPM. These three SPM continue to be frequently used. The current capabilities of SPM do not satisfy us completely. We still cant measure the Electrical field directly. We actually measure the capacitance gradient. There are also some other questions. This is because the electrostatic force depends very strongly on the geometry of the probe at all length scales, so any model is subject to two big problems. First, the geometry is not known with complete accuracy; and second, the tip shape can change during an experiment due to wear. In the future, maybe the problems could be overcome by using a tip with a very well defined shape, such as a carbon nanotube, for which a realistic geometrical model could be more easily constructed, and the wear could be avoided or reduced.

Large area high-speed metrology SPM system.

PubMed

Klapetek, P; Valtr, M; Picco, L; Payton, O D; Martinek, J; Yacoot, A; Miles, M

2015-02-13

We present a large area high-speed measuring system capable of rapidly generating nanometre resolution scanning probe microscopy data over mm(2) regions. The system combines a slow moving but accurate large area XYZ scanner with a very fast but less accurate small area XY scanner. This arrangement enables very large areas to be scanned by stitching together the small, rapidly acquired, images from the fast XY scanner while simultaneously moving the slow XYZ scanner across the region of interest. In order to successfully merge the image sequences together two software approaches for calibrating the data from the fast scanner are described. The first utilizes the low uncertainty interferometric sensors of the XYZ scanner while the second implements a genetic algorithm with multiple parameter fitting during the data merging step of the image stitching process. The basic uncertainty components related to these high-speed measurements are also discussed. Both techniques are shown to successfully enable high-resolution, large area images to be generated at least an order of magnitude faster than with a conventional atomic force microscope.

Large area high-speed metrology SPM system

NASA Astrophysics Data System (ADS)

Klapetek, P.; Valtr, M.; Picco, L.; Payton, O. D.; Martinek, J.; Yacoot, A.; Miles, M.

2015-02-01

We present a large area high-speed measuring system capable of rapidly generating nanometre resolution scanning probe microscopy data over mm2 regions. The system combines a slow moving but accurate large area XYZ scanner with a very fast but less accurate small area XY scanner. This arrangement enables very large areas to be scanned by stitching together the small, rapidly acquired, images from the fast XY scanner while simultaneously moving the slow XYZ scanner across the region of interest. In order to successfully merge the image sequences together two software approaches for calibrating the data from the fast scanner are described. The first utilizes the low uncertainty interferometric sensors of the XYZ scanner while the second implements a genetic algorithm with multiple parameter fitting during the data merging step of the image stitching process. The basic uncertainty components related to these high-speed measurements are also discussed. Both techniques are shown to successfully enable high-resolution, large area images to be generated at least an order of magnitude faster than with a conventional atomic force microscope.

Atomic force microscopic imaging of Acanthamoeba castellanii and Balamuthia mandrillaris trophozoites and cysts.

PubMed

Aqeel, Yousuf; Siddiqui, Ruqaiyyah; Ateeq, Muhammad; Raza Shah, Muhammad; Kulsoom, Huma; Khan, Naveed Ahmed

2015-01-01

Light microscopy and electron microscopy have been successfully used in the study of microbes, as well as free-living protists. Unlike light microscopy, which enables us to observe living organisms or the electron microscope which provides a two-dimensional image, atomic force microscopy provides a three-dimensional surface profile. Here, we observed two free-living amoebae, Acanthamoeba castellanii and Balamuthia mandrillaris under the phase contrast inverted microscope, transmission electron microscope and atomic force microscope. Although light microscopy was of lower magnification, it revealed functional biology of live amoebae such as motility and osmoregulation using contractile vacuoles of the trophozoite stage, but it is of limited value in defining the cyst stage. In contrast, transmission electron microscopy showed significantly greater magnification and resolution to reveal the ultra-structural features of trophozoites and cysts including intracellular organelles and cyst wall characteristics but it only produced a snapshot in time of a dead amoeba cell. Atomic force microscopy produced three-dimensional images providing detailed topographic description of shape and surface, phase imaging measuring boundary stiffness, and amplitude measurements including width, height and length of A. castellanii and B. mandrillaris trophozoites and cysts. These results demonstrate the importance of the application of various microscopic methods in the biological and structural characterization of the whole cell, ultra-structural features, as well as surface components and cytoskeleton of protist pathogens. © 2014 The Author(s) Journal of Eukaryotic Microbiology © 2014 International Society of Protistologists.

Noncontact atomic force microscopy in liquid environment with quartz tuning fork and carbon nanotube probe

NASA Astrophysics Data System (ADS)

Kageshima, Masami; Jensenius, Henriette; Dienwiebel, Martin; Nakayama, Yoshikazu; Tokumoto, Hiroshi; Jarvis, Suzanne P.; Oosterkamp, Tjerk H.

2002-03-01

A force sensor for noncontact atomic force microscopy in liquid environment was developed by combining a multiwalled carbon nanotube (MWNT) probe with a quartz tuning fork. Solvation shells of octamethylcyclotetrasiloxane on a graphite surface were detected both in the frequency shift and dissipation. Due to the high aspect ratio of the CNT probe, the long-range background force was barely detectable in the solvation region.

Characterization of fiber-forming peptides and proteins by means of atomic force microscopy.

PubMed

Creasey, Rhiannon G; Gibson, Christopher T; Voelcker, Nicolas H

2012-05-01

The atomic force microscope (AFM) is widely used in biological sciences due to its ability to perform imaging experiments at high resolution in a physiological environment, without special sample preparation such as fixation or staining. AFM is unique, in that it allows single molecule information of mechanical properties and molecular recognition to be gathered. This review sets out to identify methodological applications of AFM for characterization of fiber-forming proteins and peptides. The basics of AFM operation are detailed, with in-depth information for any life scientist to get a grasp on AFM capabilities. It also briefly describes antibody recognition imaging and mapping of nanomechanical properties on biological samples. Subsequently, examples of AFM application to fiber-forming natural proteins, and fiber-forming synthetic peptides are given. Here, AFM is used primarily for structural characterization of fibers in combination with other techniques, such as circular dichroism and fluorescence spectroscopy. More recent developments in antibody recognition imaging to identify constituents of protein fibers formed in human disease are explored. This review, as a whole, seeks to encourage the life scientists dealing with protein aggregation phenomena to consider AFM as a part of their research toolkit, by highlighting the manifold capabilities of this technique.

Interfacial Shear Strength of Multilayer Graphene Oxide Films.

PubMed

Daly, Matthew; Cao, Changhong; Sun, Hao; Sun, Yu; Filleter, Tobin; Singh, Chandra Veer

2016-02-23

Graphene oxide (GO) is considered as one of the most promising layered materials with tunable physical properties and applicability in many important engineering applications. In this work, the interfacial behavior of multilayer GO films was directly investigated via GO-to-GO friction force microscopy, and the interfacial shear strength (ISS) was measured to be 5.3 ± 3.2 MPa. Based on high resolution atomic force microscopy images and the available chemical data, targeted molecular dynamics simulations were performed to evaluate the influence of functional structure, topological defects, and interlayer registry on the shear response of the GO films. Theoretical values for shear strength ranging from 17 to 132 MPa were predicted for the different structures studied, providing upper bounds for the ISS. Computational results also revealed the atomic origins of the stochastic nature of friction measurements. Specifically, the wide scatter in experimental measurements was attributed to variations in functional structure and topological defects within the sliding volume. The findings of this study provide important insight for understanding the significant differences in strength between monolayer and bulk graphene oxide materials and can be useful for engineering topological structures with tunable mechanical properties.

Correlative STED and Atomic Force Microscopy on Live Astrocytes Reveals Plasticity of Cytoskeletal Structure and Membrane Physical Properties during Polarized Migration

PubMed Central

Curry, Nathan; Ghézali, Grégory; Kaminski Schierle, Gabriele S.; Rouach, Nathalie; Kaminski, Clemens F.

2017-01-01

The plasticity of the cytoskeleton architecture and membrane properties is important for the establishment of cell polarity, adhesion and migration. Here, we present a method which combines stimulated emission depletion (STED) super-resolution imaging and atomic force microscopy (AFM) to correlate cytoskeletal structural information with membrane physical properties in live astrocytes. Using STED compatible dyes for live cell imaging of the cytoskeleton, and simultaneously mapping the cell surface topology with AFM, we obtain unprecedented detail of highly organized networks of actin and microtubules in astrocytes. Combining mechanical data from AFM with optical imaging of actin and tubulin further reveals links between cytoskeleton organization and membrane properties. Using this methodology we illustrate that scratch-induced migration induces cytoskeleton remodeling. The latter is caused by a polarization of actin and microtubule elements within astroglial cell processes, which correlates strongly with changes in cell stiffness. The method opens new avenues for the dynamic probing of the membrane structural and functional plasticity of living brain cells. It is a powerful tool for providing new insights into mechanisms of cell structural remodeling during physiological or pathological processes, such as brain development or tumorigenesis. PMID:28469559

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.

Simulation of Mean Flow and Turbulence over a 2D Building Array Using High-Resolution CFD and a Distributed Drag Force Approach

DTIC Science & Technology

2016-06-16

procedure. The predictive capabilities of the high-resolution computational fluid dynamics ( CFD ) simulations of urban flow are validated against a very...turbulence over a 2D building array using high-resolution CFD and a distributed drag force approach a Department of Mechanical Engineering, University

In situ detection of porosity initiation during aluminum thin film anodizing

NASA Astrophysics Data System (ADS)

Van Overmeere, Quentin; Nysten, Bernard; Proost, Joris

2009-02-01

High-resolution curvature measurements have been performed in situ during aluminum thin film anodizing in sulfuric acid. A well-defined transition in the rate of internal stress-induced curvature change is shown to allow for the accurate, real-time detection of porosity initiation. The validity of this in situ diagnostic tool was confirmed by a quantitative analysis of the spectral density distributions of the anodized surfaces. These were obtained by analyzing ex situ atomic force microscopy images of surfaces anodized for different times, and allowed to correlate the in situ detected transition in the rate of curvature change with the appearance of porosity.

On-Surface Synthesis and Characterization of 9-Atom Wide Armchair Graphene Nanoribbons

DOE PAGES

Talirz, Leopold; Söde, Hajo; Dumslaff, Tim; ...

2017-01-27

The bottom-up approach to synthesize graphene nanoribbons strives not only to introduce a band gap into the electronic structure of graphene but also to accurately tune its value by designing both the width and edge structure of the ribbons with atomic precision. Within this paper, we report the synthesis of an armchair graphene nanoribbon with a width of nine carbon atoms on Au(111) through surface-assisted aryl–aryl coupling and subsequent cyclodehydrogenation of a properly chosen molecular precursor. By combining high-resolution atomic force microscopy, scanning tunneling microscopy, and Raman spectroscopy, we demonstrate that the atomic structure of the fabricated ribbons is exactlymore » as designed. Angle-resolved photoemission spectroscopy and Fourier-transformed scanning tunneling spectroscopy reveal an electronic band gap of 1.4 eV and effective masses of ≈0.1 m e for both electrons and holes, constituting a substantial improvement over previous efforts toward the development of transistor applications. We use ab initio calculations to gain insight into the dependence of the Raman spectra on excitation wavelength as well as to rationalize the symmetry-dependent contribution of the ribbons’ electronic states to the tunneling current. Lastly, we propose a simple rule for the visibility of frontier electronic bands of armchair graphene nanoribbons in scanning tunneling spectroscopy.« less

A micromachined membrane-based active probe for biomolecular mechanics measurement

NASA Astrophysics Data System (ADS)

Torun, H.; Sutanto, J.; Sarangapani, K. K.; Joseph, P.; Degertekin, F. L.; Zhu, C.

2007-04-01

A novel micromachined, membrane-based probe has been developed and fabricated as assays to enable parallel measurements. Each probe in the array can be individually actuated, and the membrane displacement can be measured with high resolution using an integrated diffraction-based optical interferometer. To illustrate its application in single-molecule mechanics experiments, this membrane probe was used to measure unbinding forces between L-selectin reconstituted in a polymer-cushioned lipid bilayer on the probe membrane and an antibody adsorbed on an atomic force microscope cantilever. Piconewton range forces between single pairs of interacting molecules were measured from the cantilever bending while using the membrane probe as an actuator. The integrated diffraction-based optical interferometer of the probe was demonstrated to have <10 fm Hz-1/2 noise floor for frequencies as low as 3 Hz with a differential readout scheme. With soft probe membranes, this low noise level would be suitable for direct force measurements without the need for a cantilever. Furthermore, the probe membranes were shown to have 0.5 µm actuation range with a flat response up to 100 kHz, enabling measurements at fast speeds.

Transmission/Scanning Transmission Electron Microscopy | Materials Science

Science.gov Websites

imaging such as high resolution TEM. Transmission electron diffraction patterns help to determine the microstructure of a material and its defects. Phase-contrast imaging or high-resolution (HR) TEM imaging gives high scattering angle can be collected to form high-resolution, chemically sensitive, atomic number (Z

Force-detected nuclear magnetic resonance: recent advances and future challenges.

PubMed

Poggio, M; Degen, C L

2010-08-27

We review recent efforts to detect small numbers of nuclear spins using magnetic resonance force microscopy. Magnetic resonance force microscopy (MRFM) is a scanning probe technique that relies on the mechanical measurement of the weak magnetic force between a microscopic magnet and the magnetic moments in a sample. Spurred by the recent progress in fabricating ultrasensitive force detectors, MRFM has rapidly improved its capability over the last decade. Today it boasts a spin sensitivity that surpasses conventional, inductive nuclear magnetic resonance detectors by about eight orders of magnitude. In this review we touch on the origins of this technique and focus on its recent application to nanoscale nuclear spin ensembles, in particular on the imaging of nanoscale objects with a three-dimensional (3D) spatial resolution better than 10 nm. We consider the experimental advances driving this work and highlight the underlying physical principles and limitations of the method. Finally, we discuss the challenges that must be met in order to advance the technique towards single nuclear spin sensitivity-and perhaps-to 3D microscopy of molecules with atomic resolution.

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

Confocal Raman spectroscopy and AFM for evaluation of sidewalls in type II superlattice FPAs

NASA Astrophysics Data System (ADS)

Rotter, T. J.; Busani, T.; Rathi, P.; Jaeckel, F.; Reyes, P. A.; Malloy, K. J.; Ukhanov, A. A.; Plis, E.; Krishna, S.; Jaime-Vasquez, M.; Baril, N. F.; Benson, J. D.; Tenne, D. A.

2015-06-01

We propose to utilize confocal Raman spectroscopy combined with high resolution atomic force microscopy (AFM) for nondestructive characterisation of the sidewalls of etched and passivated small pixel (24 μm×24 μm) focal plane arrays (FPA) fabricated using LW/LWIR InAs/GaSb type-II strained layer superlattice (T2SL) detector material. Special high aspect ratio Si and GaAs AFM probes, with tip length of 13 μm and tip aperture less than 7°, allow characterisation of the sidewall morphology. Confocal microscopy enables imaging of the sidewall profile through optical sectioning. Raman spectra measured on etched T2SL FPA single pixels enable us to quantify the non-uniformity of the mesa delineation process.

Subdaily growth patterns and organo-mineral nanostructure of the growth layers in the calcitic prisms of the shell of Concholepas concholepas Bruguière, 1789 (Gastropoda, Muricidae).

PubMed

Guzman, Nury; Ball, Alexander D; Cuif, Jean-Pierre; Dauphin, Yannicke; Denis, Alain; Ortlieb, Luc

2007-10-01

Fluorochrome marking of the gastropod Concholepas concholepas has shown that the prismatic units of the shell are built by superimposition of isochronic growth layers of about 2 mum. Fluorescent growth marks make it possible to establish the high periodicity of the cyclic biomineralization process at a standard growth rhythm of about 45 layers a day. Sulphated polysaccharides have been identified within the growth layers by using synchrotron radiation, whereas high resolution mapping enables the banding pattern of the mineral phase to be correlated with the layered distribution of polysaccharides. Atomic force microscopy has shown that the layers are made of nanograins densely packed in an organic component.

Evidence for non-conservative current-induced forces in the breaking of Au and Pt atomic chains

PubMed Central

Sabater, Carlos; Untiedt, Carlos

2015-01-01

Summary This experimental work aims at probing current-induced forces at the atomic scale. Specifically it addresses predictions in recent work regarding the appearance of run-away modes as a result of a combined effect of the non-conservative wind force and a ‘Berry force’. The systems we consider here are atomic chains of Au and Pt atoms, for which we investigate the distribution of break down voltage values. We observe two distinct modes of breaking for Au atomic chains. The breaking at high voltage appears to behave as expected for regular break down by thermal excitation due to Joule heating. However, there is a low-voltage breaking mode that has characteristics expected for the mechanism of current-induced forces. Although a full comparison would require more detailed information on the individual atomic configurations, the systems we consider are very similar to those considered in recent model calculations and the comparison between experiment and theory is very encouraging for the interpretation we propose. PMID:26734525

Hierarchical Coarse-Graining Via a Generalized Yvon-Born Green Framework: Many-Body Correlations, Mappings, and Structural Accuracy

NASA Astrophysics Data System (ADS)

Rudzinski, Joseph F.

Atomically-detailed molecular dynamics simulations have emerged as one of the most powerful theoretic tools for studying complex, condensed-phase systems. Despite their ability to provide incredible molecular insight, these simulations are insufficient for investigating complex biological processes, e.g., protein folding or molecular aggregation, on relevant length and time scales. The increasing scope and sophistication of atomically-detailed models has motivated the development of "hierarchical" approaches, which parameterize a low resolution, coarse-grained (CG) model based on simulations of an atomically-detailed model. The utility of hierarchical CG models depends on their ability to accurately incorporate the correct physics of the underlying model. One approach for ensuring this "consistency" between the models is to parameterize the CG model to reproduce the structural ensemble generated by the high resolution model. The many-body potential of mean force is the proper CG energy function for reproducing all structural distributions of the atomically-detailed model, at the CG level of resolution. However, this CG potential is a configuration-dependent free energy function that is generally too complicated to represent or simulate. The multiscale coarse-graining (MS-CG) method employs a generalized Yvon-Born-Green (g-YBG) relation to directly determine a variationally optimal approximation to the many-body potential of mean force. The MS-CG/g-YBG method provides a convenient and transparent framework for investigating the equilibrium structure of the system, at the CG level of resolution. In this work, we investigate the fundamental limitations and approximations of the MS-CG/g-YBG method. Throughout the work, we propose several theoretic constructs to directly relate the MS-CG/g-YBG method to other popular structure-based CG approaches. We investigate the physical interpretation of the MS-CG/g-YBG correlation matrix, the quantity responsible for disentangling the various contributions to the average force on a CG site. We then employ an iterative extension of the MS-CG/g-YBG method that improves the accuracy of a particular set of low order correlation functions relative to the original MS-CG/g-YBG model. We demonstrate that this method provides a powerful framework for identifying the precise source of error in an MS-CG/g-YBG model. We then propose a method for identifying an optimal CG representation, prior to the development of the CG model. We employ these techniques together to demonstrate that in the cases where the MS-CG/g-YBG method fails to determine an accurate model, a fundamental problem likely exists with the chosen CG representation or interaction set. Additionally, we explicitly demonstrate that while the iterative model successfully improves the accuracy of the low order structure, it does so by distorting the higher order structural correlations relative to the underlying model. Finally, we apply these methods to investigate the utility of the MS-CG/g- YBG method for developing models for systems with complex intramolecular structure. Overall, our results demonstrate the power of the g-YBG framework for developing accurate CG models and for investigating the driving forces of equilibrium structures for complex condensed-phase systems. This work also explicitly motivates future development of bottom-up CG methods and highlights some outstanding problems in the field. iii.

Optimized Model Surfaces for Advanced Atomic Force Microscopy Studies of Surface Nanobubbles.

PubMed

Song, Bo; Zhou, Yi; Schönherr, Holger

2016-11-01

The formation of self-assembled monolayers (SAMs) of binary mixtures of 16-mercaptohexadecanoic acid (MHDA) and 1-octadecanethiol (ODT) on ultraflat template-stripped gold (TSG) surfaces was systematically investigated to clarify the assembly behavior, composition, and degree of possible phase segregation in light of atomic force microscopy (AFM) studies of surface nanobubbles on these substrates. The data for SAMs on TSG were compared to those obtained by adsorption on rough evaporated gold, as reported in a previous study. Quartz crystal microbalance and surface plasmon resonance data acquired in situ on TSG indicate that similar to SAM formation on conventional evaporated gold substrates ODT and MHDA form monolayers and bilayers, respectively. The second layer on MHDA, whose formation is attributed to hydrogen bonding, can be easily removed by adequate rinsing with water. The favorable agreement of the grazing incidence reflection Fourier transform infrared (GIR FTIR) spectroscopy and contact angle data analyzed with the Israelachvili-Gee model suggests that the binary SAMs do not segregate laterally. This conclusion is fully validated by high-resolution friction force AFM observations down to a length scale of 8-10 nm, which is much smaller than the typical observed surface nanobubble radii. Finally, correspondingly functionalized TSG substrates are shown to be valuable supports for studying surface nanobubbles by AFM in water and for addressing the relation between surface functionality and nanobubble formation and properties.

Clean Transfer of Large Graphene Single Crystals for High-Intactness Suspended Membranes and Liquid Cells.

PubMed

Zhang, Jincan; Lin, Li; Sun, Luzhao; Huang, Yucheng; Koh, Ai Leen; Dang, Wenhui; Yin, Jianbo; Wang, Mingzhan; Tan, Congwei; Li, Tianran; Tan, Zhenjun; Liu, Zhongfan; Peng, Hailin

2017-07-01

The atomically thin 2D nature of suspended graphene membranes holds promising in numerous technological applications. In particular, the outstanding transparency to electron beam endows graphene membranes great potential as a candidate for specimen support of transmission electron microscopy (TEM). However, major hurdles remain to be addressed to acquire an ultraclean, high-intactness, and defect-free suspended graphene membrane. Here, a polymer-free clean transfer of sub-centimeter-sized graphene single crystals onto TEM grids to fabricate large-area and high-quality suspended graphene membranes has been achieved. Through the control of interfacial force during the transfer, the intactness of large-area graphene membranes can be as high as 95%, prominently larger than reported values in previous works. Graphene liquid cells are readily prepared by π-π stacking two clean single-crystal graphene TEM grids, in which atomic-scale resolution imaging and temporal evolution of colloid Au nanoparticles are recorded. This facile and scalable production of clean and high-quality suspended graphene membrane is promising toward their wide applications for electron and optical microscopy. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Submicrometer fiber-optic chemical sensors: Measuring pH inside single cells

NASA Astrophysics Data System (ADS)

Kopelman, R.

Starting from scratch, we went in two and a half years to 0.04 micron optical microscopy resolution. We have demonstrated the application of near-field scanning optical microscopy to DNA samples and opened the new fields of near-field scanning spectroscopy and submicron opto-chemical sensors. All of these developments have been important steps towards in-situ DNA imaging and characterization on the nanoscale. Our first goal was to make NSOM (near-field scanning optical microscopy) a working enterprise, capable of 'zooming-in' towards a sample and imaging with a resolution exceeding that of traditional microscopy by a factor of ten. This has been achieved. Not only do we have a resolution of about 40 nm but we can image a 1 x 1 micron object in less than 10 seconds. Furthermore, the NSOM is a practical instrument. The tips survive for days or weeks of scanning and new methods of force feedback will soon protect the most fragile samples. Reproducible images of metal gratings, gold particles, dye balls (for calibration) and of several DNA samples have been made, proving the practicality of our approach. We also give highly resolved Force/NSOM images of human blood cells. Our second goal has been to form molecular optics (e.g., exciton donor) tips with a resolution of 2-10 nm for molecular excitation microscopy (MEM). We have produced such tips, and scanned with them, but only with a resolution comparable to that of our standard NSOM tips. However, we have demonstrated their potential for high resolution imaging capabilities: (1) An energy transfer (tip to sample) based feedback capability. (2) A Kasha (external heavy atom) effect based feedback. In addition, a novel and practical opto-chemical sensor that is a billion times smaller than the best ones available has been developed as well. Finally, we have also performed spatially resolved fluorescence spectroscopy.

Ultrahigh resolution optical coherence elastography combined with a rigid micro-endoscope (Conference Presentation)

NASA Astrophysics Data System (ADS)

Fang, Qi; Curatolo, Andrea; Wijesinghe, Philip; Hamzah, Juliana; Ganss, Ruth; Noble, Peter B.; Karnowski, Karol; Sampson, David D.; Kim, Jun Ki; Lee, Wei M.; Kennedy, Brendan F.

2017-02-01

The mechanical forces that living cells experience represent an important framework in the determination of a range of intricate cellular functions and processes. Current insight into cell mechanics is typically provided by in vitro measurement systems; for example, atomic force microscopy (AFM) measurements are performed on cells in culture or, at best, on freshly excised tissue. Optical techniques, such as Brillouin microscopy and optical elastography, have been used for ex vivo and in situ imaging, recently achieving cellular-scale resolution. The utility of these techniques in cell mechanics lies in quick, three-dimensional and label-free mechanical imaging. Translation of these techniques toward minimally invasive in vivo imaging would provide unprecedented capabilities in tissue characterization. Here, we take the first steps along this path by incorporating a gradient-index micro-endoscope into an ultrahigh resolution optical elastography system. Using this endoscope, a lateral resolution of 2 µm is preserved over an extended depth-of-field of 80 µm, achieved by Bessel beam illumination. We demonstrate this combined system by imaging stiffness of a silicone phantom containing stiff inclusions and a freshly excised murine liver tissue. Additionally, we test this system on murine ribs in situ. We show that our approach can provide high quality extended depth-of-field images through an endoscope and has the potential to measure cell mechanics deep in tissue. Eventually, we believe this tool will be capable of studying biological processes and disease progression in vivo.

Study on deposition of Al2O3 films by plasma-assisted atomic layer with different plasma sources

NASA Astrophysics Data System (ADS)

Haiying, WEI; Hongge, GUO; Lijun, SANG; Xingcun, LI; Qiang, CHEN

2018-04-01

In this paper, Al2O3 thin films are deposited on a hydrogen-terminated Si substrate by using two home-built electron cyclotron resonance (ECR) and magnetic field enhanced radio frequency plasma-assisted atomic layer deposition (PA-ALD) devices with Al(CH3)3 (trimethylaluminum, TMA) and oxygen plasma used as precursor and oxidant, respectively. The thickness, chemical composition, surface morphology and group reactions are characterized by in situ spectroscopic ellipsometer, x-ray photoelectric spectroscopy, atomic force microscopy, scanning electron microscopy, a high-resolution transmission electron microscope and in situ mass spectrometry (MS), respectively. We obtain that both ECR PA-ALD and the magnetic field enhanced PA-ALD can deposit thin films with high density, high purity, and uniformity at a high deposition rate. MS analysis reveals that the Al2O3 deposition reactions are not simple reactions between TMA and oxygen plasma to produce alumina, water and carbon dioxide. In fact, acetylene, carbon monoxide and some other by-products also appear in the exhaustion gas. In addition, the presence of bias voltage has a certain effect on the deposition rate and surface morphology of films, which may be attributed to the presence of bias voltage controlling the plasma energy and density. We conclude that both plasma sources have a different deposition mechanism, which is much more complicated than expected.

Tip-enhanced Raman mapping with top-illumination AFM.

PubMed

Chan, K L Andrew; Kazarian, Sergei G

2011-04-29

Tip-enhanced Raman mapping is a powerful, emerging technique that offers rich chemical information and high spatial resolution. Currently, most of the successes in tip-enhanced Raman scattering (TERS) measurements are based on the inverted configuration where tips and laser are approaching the sample from opposite sides. This results in the limitation of measurement for transparent samples only. Several approaches have been developed to obtain tip-enhanced Raman mapping in reflection mode, many of which involve certain customisations of the system. We have demonstrated in this work that it is also possible to obtain TERS nano-images using an upright microscope (top-illumination) with a gold-coated Si atomic force microscope (AFM) cantilever without significant modification to the existing integrated AFM/Raman system. A TERS image of a single-walled carbon nanotube has been achieved with a spatial resolution of ∼ 20-50 nm, demonstrating the potential of this technique for studying non-transparent nanoscale materials.

Fabrication of cobalt magnetic nanostructures using atomic force microscope lithography.

PubMed

Chu, Haena; Yun, Seonghun; Lee, Haiwon

2013-12-01

Cobalt nanopatterns are promising assemblies for patterned magnetic storage applications. The fabrication of cobalt magnetic nanostructures on n-tridecylamine x hydrochloride (TDA x HCl) self-assembled monolayer (SAM) modified silicon surfaces using direct writing atomic force microscope (AFM) lithography for localized electrochemical reduction of cobalt ions was demonstrated. The ions were reduced to form metal nanowires along the direction of the electricfield between the AFM tip and the substrate. In this lithography process, TDA x HCI SAMs play an important role in the lithography process for improving the resolution of cobalt nanopatterns by preventing nonspecific reduction of cobalt ions on the unwritten background. Cobalt nanowires and nanodots with width of 225 +/- 26 nm and diameter of 208 +/- 28 nm were successfully fabricated. Platinium-coated polydimethylsiloxane (PDMS) stamp was used fabricating bulk cobalt structures which can be detected by energy dispersive X-ray spectroscopy for element analysis and the physical and magnetic properties of these cobalt nanopatterns were characterized using AFM and magnetic force microscope.

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

Fabrication of electron beam deposited tip for atomic-scale atomic force microscopy in liquid.

PubMed

Miyazawa, K; Izumi, H; Watanabe-Nakayama, T; Asakawa, H; Fukuma, T

2015-03-13

Recently, possibilities of improving operation speed and force sensitivity in atomic-scale atomic force microscopy (AFM) in liquid using a small cantilever with an electron beam deposited (EBD) tip have been intensively explored. However, the structure and properties of an EBD tip suitable for such an application have not been well-understood and hence its fabrication process has not been established. In this study, we perform atomic-scale AFM measurements with a small cantilever and clarify two major problems: contaminations from a cantilever and tip surface, and insufficient mechanical strength of an EBD tip having a high aspect ratio. To solve these problems, here we propose a fabrication process of an EBD tip, where we attach a 2 μm silica bead at the cantilever end and fabricate a 500-700 nm EBD tip on the bead. The bead height ensures sufficient cantilever-sample distance and enables to suppress long-range interaction between them even with a short EBD tip having high mechanical strength. After the tip fabrication, we coat the whole cantilever and tip surface with Si (30 nm) to prevent the generation of contamination. We perform atomic-scale AFM imaging and hydration force measurements at a mica-water interface using the fabricated tip and demonstrate its applicability to such an atomic-scale application. With a repeated use of the proposed process, we can reuse a small cantilever for atomic-scale measurements for several times. Therefore, the proposed method solves the two major problems and enables the practical use of a small cantilever in atomic-scale studies on various solid-liquid interfacial phenomena.

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

Roles of curli, cellulose and BapA in Salmonella biofilm morphology studied by atomic force microscopy.

PubMed

Jonas, Kristina; Tomenius, Henrik; Kader, Abdul; Normark, Staffan; Römling, Ute; Belova, Lyubov M; Melefors, Ojar

2007-07-24

Curli, cellulose and the cell surface protein BapA are matrix components in Salmonella biofilms. In this study we have investigated the roles of these components for the morphology of bacteria grown as colonies on agar plates and within a biofilm on submerged mica surfaces by applying atomic force microscopy (AFM) and light microscopy. AFM imaging was performed on colonies of Salmonella Typhimurium grown on agar plates for 24 h and on biofilms grown for 4, 8, 16 or 24 h on mica slides submerged in standing cultures. Our data show that in the wild type curli were visible as extracellular material on and between the cells and as fimbrial structures at the edges of biofilms grown for 16 h and 24 h. In contrast to the wild type, which formed a three-dimensional biofilm within 24 h, a curli mutant and a strain mutated in the global regulator CsgD were severely impaired in biofilm formation. A mutant in cellulose production retained some capability to form cell aggregates, but not a confluent biofilm. Extracellular matrix was observed in this mutant to almost the same extent as in the wild type. Overexpression of CsgD led to a much thicker and a more rapidly growing biofilm. Disruption of BapA altered neither colony and biofilm morphology nor the ability to form a biofilm within 24 h on the submerged surfaces. Besides curli, the expression of flagella and pili as well as changes in cell shape and cell size could be monitored in the growing biofilms. Our work demonstrates that atomic force microscopy can efficiently be used as a tool to monitor the morphology of bacteria grown as colonies on agar plates or within biofilms formed in a liquid at high resolution.

Combined use of atomic force microscopy, X-ray photoelectron spectroscopy, and secondary ion mass spectrometry for cell surface analysis.

PubMed

Dague, Etienne; Delcorte, Arnaud; Latgé, Jean-Paul; Dufrêne, Yves F

2008-04-01

Understanding the surface properties of microbial cells is a major challenge of current microbiological research and a key to efficiently exploit them in biotechnology. Here, we used three advanced surface analysis techniques with different sensitivity, probing depth, and lateral resolution, that is, in situ atomic force microscopy, X-ray photoelectron spectroscopy, and secondary ion mass spectrometry, to gain insight into the surface properties of the conidia of the human fungal pathogen Aspergillus fumigatus. We show that the native ultrastructure, surface protein and polysaccharide concentrations, and amino acid composition of three mutants affected in hydrophobin production are markedly different from those of the wild-type, thereby providing novel insight into the cell wall architecture of A. fumigatus. The results demonstrate the power of using multiple complementary techniques for probing microbial cell surfaces.

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.

Toward tunable doping in graphene FETs by molecular self-assembled monolayers

NASA Astrophysics Data System (ADS)

Li, Bing; Klekachev, Alexander V.; Cantoro, Mirco; Huyghebaert, Cedric; Stesmans, André; Asselberghs, Inge; de Gendt, Stefan; de Feyter, Steven

2013-09-01

In this paper, we report the formation of self-assembled monolayers (SAMs) of oleylamine (OA) on highly oriented pyrolytic graphite (HOPG) and graphene surfaces and demonstrate the potential of using such organic SAMs to tailor the electronic properties of graphene. Molecular resolution Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) images reveal the detailed molecular ordering. The electrical measurements show that OA strongly interacts with graphene leading to n-doping effects in graphene devices. The doping levels are tunable by varying the OA deposition conditions. Importantly, neither hole nor electron mobilities are decreased by the OA modification. As a benefit from this noncovalent modification strategy, the pristine characteristics of the device are recoverable upon OA removal. From this study, one can envision the possibility to correlate the graphene-based device performance with the molecular structure and supramolecular ordering of the organic dopant.In this paper, we report the formation of self-assembled monolayers (SAMs) of oleylamine (OA) on highly oriented pyrolytic graphite (HOPG) and graphene surfaces and demonstrate the potential of using such organic SAMs to tailor the electronic properties of graphene. Molecular resolution Atomic Force Microscopy (AFM) and Scanning Tunneling Microscopy (STM) images reveal the detailed molecular ordering. The electrical measurements show that OA strongly interacts with graphene leading to n-doping effects in graphene devices. The doping levels are tunable by varying the OA deposition conditions. Importantly, neither hole nor electron mobilities are decreased by the OA modification. As a benefit from this noncovalent modification strategy, the pristine characteristics of the device are recoverable upon OA removal. From this study, one can envision the possibility to correlate the graphene-based device performance with the molecular structure and supramolecular ordering of the organic dopant. Electronic supplementary information (ESI) available: AFM images of self-assembled monolayers of OA on HOPG; AFM height image of the graphene surface on a SiC substrate; high resolution STM image of a self-assembled monolayer of OA on HOPG; transfer curves of a graphene FET with and without baking steps; transfer curves of a graphene FET under high vacuum conditions; transfer curves of a graphene FET and its Raman response before and after OA treatment; transfer curves of a graphene FET before and after rinsing with n-hexane. See DOI: 10.1039/c3nr01255g

Atomic force microscopy of red-light photoreceptors using peakforce quantitative nanomechanical property mapping.

PubMed

Kroeger, Marie E; Sorenson, Blaire A; Thomas, J Santoro; Stojković, Emina A; Tsonchev, Stefan; Nicholson, Kenneth T

2014-10-24

Atomic force microscopy (AFM) uses a pyramidal tip attached to a cantilever to probe the force response of a surface. The deflections of the tip can be measured to ~10 pN by a laser and sectored detector, which can be converted to image topography. Amplitude modulation or "tapping mode" AFM involves the probe making intermittent contact with the surface while oscillating at its resonant frequency to produce an image. Used in conjunction with a fluid cell, tapping-mode AFM enables the imaging of biological macromolecules such as proteins in physiologically relevant conditions. Tapping-mode AFM requires manual tuning of the probe and frequent adjustments of a multitude of scanning parameters which can be challenging for inexperienced users. To obtain high-quality images, these adjustments are the most time consuming. PeakForce Quantitative Nanomechanical Property Mapping (PF-QNM) produces an image by measuring a force response curve for every point of contact with the sample. With ScanAsyst software, PF-QNM can be automated. This software adjusts the set-point, drive frequency, scan rate, gains, and other important scanning parameters automatically for a given sample. Not only does this process protect both fragile probes and samples, it significantly reduces the time required to obtain high resolution images. PF-QNM is compatible for AFM imaging in fluid; therefore, it has extensive application for imaging biologically relevant materials. The method presented in this paper describes the application of PF-QNM to obtain images of a bacterial red-light photoreceptor, RpBphP3 (P3), from photosynthetic R. palustris in its light-adapted state. Using this method, individual protein dimers of P3 and aggregates of dimers have been observed on a mica surface in the presence of an imaging buffer. With appropriate adjustments to surface and/or solution concentration, this method may be generally applied to other biologically relevant macromolecules and soft materials.

Imaging surface nanobubbles at graphite-water interfaces with different atomic force microscopy modes.

PubMed

Yang, Chih-Wen; Lu, Yi-Hsien; Hwang, Ing-Shouh

2013-05-08

We have imaged nanobubbles on highly ordered pyrolytic graphite (HOPG) surfaces in pure water with different atomic force microscopy (AFM) modes, including the frequency-modulation, the tapping, and the PeakForce techniques. We have compared the performance of these modes in obtaining the surface profiles of nanobubbles. The frequency-modulation mode yields a larger height value than the other two modes and can provide more accurate measurement of the surface profiles of nanobubbles. Imaging with PeakForce mode shows that a nanobubble appears smaller and shorter with increasing peak force and disappears above a certain peak force, but the size returns to the original value when the peak force is reduced. This indicates that imaging with high peak forces does not cause gas removal from the nanobubbles. Based on the presented findings and previous AFM observations, the existing models for nanobubbles are reviewed and discussed. The model of gas aggregate inside nanobubbles provides a better explanation for the puzzles of the high stability and the contact angle of surface nanobubbles.

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy

PubMed Central

Rottler, Jörg; Plotkin, Steven S.

2016-01-01

Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered. PMID:27898663

As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy.

PubMed

Habibi, Mona; Rottler, Jörg; Plotkin, Steven S

2016-11-01

Mechanical unfolding of a single domain of loop-truncated superoxide dismutase protein has been simulated via force spectroscopy techniques with both all-atom (AA) models and several coarse-grained models having different levels of resolution: A Gō model containing all heavy atoms in the protein (HA-Gō), the associative memory, water mediated, structure and energy model (AWSEM) which has 3 interaction sites per amino acid, and a Gō model containing only one interaction site per amino acid at the Cα position (Cα-Gō). To systematically compare results across models, the scales of time, energy, and force had to be suitably renormalized in each model. Surprisingly, the HA-Gō model gives the softest protein, exhibiting much smaller force peaks than all other models after the above renormalization. Clustering to render a structural taxonomy as the protein unfolds showed that the AA, HA-Gō, and Cα-Gō models exhibit a single pathway for early unfolding, which eventually bifurcates repeatedly to multiple branches only after the protein is about half-unfolded. The AWSEM model shows a single dominant unfolding pathway over the whole range of unfolding, in contrast to all other models. TM alignment, clustering analysis, and native contact maps show that the AWSEM pathway has however the most structural similarity to the AA model at high nativeness, but the least structural similarity to the AA model at low nativeness. In comparison to the AA model, the sequence of native contact breakage is best predicted by the HA-Gō model. All models consistently predict a similar unfolding mechanism for early force-induced unfolding events, but diverge in their predictions for late stage unfolding events when the protein is more significantly disordered.

Single-Molecule Microscopy and Force Spectroscopy of Membrane Proteins

NASA Astrophysics Data System (ADS)

Engel, Andreas; Janovjak, Harald; Fotiadis, Dimtrios; Kedrov, Alexej; Cisneros, David; Müller, Daniel J.

Single-molecule atomic force microscopy (AFM) provides novel ways to characterize the structure-function relationship of native membrane proteins. High-resolution AFM topographs allow observing the structure of single proteins at sub-nanometer resolution as well as their conformational changes, oligomeric state, molecular dynamics and assembly. We will review these feasibilities illustrating examples of membrane proteins in native and reconstituted membranes. Classification of individual topographs of single proteins allows understanding the principles of motions of their extrinsic domains, to learn about their local structural flexibilities and to find the entropy minima of certain conformations. Combined with the visualization of functionally related conformational changes these insights allow understanding why certain flexibilities are required for the protein to function and how structurally flexible regions allow certain conformational changes. Complementary to AFM imaging, single-molecule force spectroscopy (SMFS) experiments detect molecular interactions established within and between membrane proteins. The sensitivity of this method makes it possible to measure interactions that stabilize secondary structures such as transmembrane α-helices, polypeptide loops and segments within. Changes in temperature or protein-protein assembly do not change the locations of stable structural segments, but influence their stability established by collective molecular interactions. Such changes alter the probability of proteins to choose a certain unfolding pathway. Recent examples have elucidated unfolding and refolding pathways of membrane proteins as well as their energy landscapes.

High Atom Number in Microsized Atom Traps

DTIC Science & Technology

2015-12-14

forces on the order of (hbar)(k) (Omega), where Omega is the laser Rabi frequency. We have observed behavior compatible with bichromatic slowing and... Rabi frequency. We have observed behavior compatible with bichromatic slowing and cooling of some atoms in atomic beam. Results were presented at the

Chelant Enhanced Solution Processing for Wafer Scale Synthesis of Transition Metal Dichalcogenide Thin Films.

PubMed

Ionescu, Robert; Campbell, Brennan; Wu, Ryan; Aytan, Ece; Patalano, Andrew; Ruiz, Isaac; Howell, Stephen W; McDonald, Anthony E; Beechem, Thomas E; Mkhoyan, K Andre; Ozkan, Mihrimah; Ozkan, Cengiz S

2017-07-25

It is of paramount importance to improve the control over large area growth of high quality molybdenum disulfide (MoS 2 ) and other types of 2D dichalcogenides. Such atomically thin materials have great potential for use in electronics, and are thought to make possible the first real applications of spintronics. Here in, a facile and reproducible method of producing wafer scale atomically thin MoS 2 layers has been developed using the incorporation of a chelating agent in a common organic solvent, dimethyl sulfoxide (DMSO). Previously, solution processing of a MoS 2 precursor, ammonium tetrathiomolybdate ((NH 4 ) 2 MoS 4 ), and subsequent thermolysis was used to produce large area MoS 2 layers. Our work here shows that the use of ethylenediaminetetraacetic acid (EDTA) in DMSO exerts superior control over wafer coverage and film thickness, and the results demonstrate that the chelating action and dispersing effect of EDTA is critical in growing uniform films. Raman spectroscopy, photoluminescence (PL), x-ray photoelectron spectroscopy (XPS), Fourier transform infrared spectroscopy (FTIR), atomic force microscopy (AFM) and high-resolution scanning transmission electron microscopy (HR-STEM) indicate the formation of homogenous few layer MoS 2 films at the wafer scale, resulting from the novel chelant-in-solution method.

The 2DX robot: a membrane protein 2D crystallization Swiss Army knife.

PubMed

Iacovache, Ioan; Biasini, Marco; Kowal, Julia; Kukulski, Wanda; Chami, Mohamed; van der Goot, F Gisou; Engel, Andreas; Rémigy, Hervé-W

2010-03-01

Among the state-of-the-art techniques that provide experimental information at atomic scale for membrane proteins, electron crystallography, atomic force microscopy and solid state NMR make use of two-dimensional crystals. We present a cyclodextrin-driven method for detergent removal implemented in a fully automated robot. The kinetics of the reconstitution processes is precisely controlled, because the detergent complexation by cyclodextrin is of stoichiometric nature. The method requires smaller volumes and lower protein concentrations than established 2D crystallization methods, making it possible to explore more conditions with the same amount of protein. The method yielded highly ordered 2D crystals diffracting to high resolution from the pore-forming toxin Aeromonas hydrophila aerolysin (2.9A), the plant aquaporin SoPIP2;1 (3.1A) and the human aquaporin-8 (hAQP8; 3.3A). This new method outperforms traditional 2D crystallization approaches in terms of accuracy, flexibility, throughput, and allows the usage of detergents having low critical micelle concentration (CMC), which stabilize the structure of membrane proteins in solution. (c) 2009 Elsevier Inc. All rights reserved.

Solidification of a liquid crystal: Morphologies and transitions. Ph.D. thesis, Simon Fraser University (Canada)

NASA Astrophysics Data System (ADS)

Hutter, Jeffrey Lee

When a material freezes, the form it takes depends on the solidification conditions. For instance, as the undercooling is increased, one typically sees solidification into less-ordered forms. The resulting growth modes appear to be generic, with qualitative similarities between systems whose microscopic details are quite dissimilar. I have used both optical and atomic-force microscopy to study the transitions between different growth morphologies during the solidification of a particular liquid crystal, 10 OCB. We have observed six different solidification modes, each with a distinct micro and meso structure. The front-velocity-vs.-undercooling curve has a discontinuity in its slope and, in some cases, in the curve itself at mode transitions, suggesting that these transitions are analogous to phase transitions. Such transitions have been seen in other systems, but no general rule has been found that can predict which morphology will be selected. We show that, contrary to intuition and widespread speculation, the fastest-growing mode is not always the one selected. One of the growth modes exhibited by 10 OCB is known as banded spherulitic growth. Spherulites have been seen in a wide variety of materials including minerals, pure elements, polymers, biomolecules, and metal alloys. However, despite a century of study, there is no generally accepted theory of spherulitic growth. In particular, the cause of the concentric banding seen in many spherulites remains a mystery. Our studies of banded spherulites in 10 OCB using both optical and atomic-force microscopy show that the bands are associated with a density modulation and thus are not merely the result of a birefringent effect, as is commonly believed. As the atomic-force microscope (AFM) is a relatively new tool, some time was spent studying its capabilities. We found that because the AFM resolution is largely determined by attractive forces between the tip of the probe and the sample, resolution can be improved by imaging in a suitable liquid medium. We also developed a simple method for calibrating AFM cantilevers--a crucial step in using the AFM to obtain quantitative force data. This work is presented in an appendix.

Deviatoric stresses promoted metallization in rhenium disulfide

NASA Astrophysics Data System (ADS)

Zhuang, Yukai; Dai, Lidong; Li, Heping; Hu, Haiying; Liu, Kaixiang; Yang, Linfei; Pu, Chang; Hong, Meiling; Liu, Pengfei

2018-04-01

The structural, vibrational and electronic properties of ReS2 were investigated up to ~34 GPa by Raman spectroscopy, AC impedance spectroscopy, atomic force microscopy and high-resolution transmission electron microscopy, combining with first-principle calculations under two different pressure environments. The experimental results showed that ReS2 endured a structural transition at ~2.5 GPa both under non-hydrostatic and hydrostatic conditions. We found that a metallization occurred at ~27.5 GPa under non-hydrostatic conditions and at ~35.4 GPa under hydrostatic conditions. The occurrence of distinct metallization point attributed to the influence of deviatoric stresses, which significantly affected the layered structure and the weak van der Waals interaction for ReS2.

Electrical conduction at domain walls in multiferroic BiFeO3

NASA Astrophysics Data System (ADS)

Seidel, Jan; Martin, Lane; He, Qing; Zhan, Qian; Chu, Ying-Hao; Rother, Axel; Hawkridge, Michael; Maksymovych, Peter; Yu, Pu; Gajek, Martin; Balke, Nina; Kalinin, Sergei; Gemming, Sybille; Wang, Feng; Catalán, Gustau; Scott, James; Spaldin, Nicola; Orenstein, Joseph; Ramesh, Ramamoorthy

2009-03-01

We report the observation of room temperature electronic conductivity at ferroelectric domain walls in BiFeO3. The origin and nature of the observed conductivity is probed using a combination of conductive atomic force microscopy, high resolution transmission electron microscopy and first-principles density functional computations. We show that a structurally driven change in both the electrostatic potential and local electronic structure (i.e., a decrease in band gap) at the domain wall leads to the observed electrical conductivity. We estimate the conductivity in the wall to be several orders of magnitude higher than for the bulk material. Additionally we demonstrate the potential for device applications of such conducting nanoscale features.

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

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.

The Effect of Growth Environment on the Morphological and Extended Defect Evolution in GaN Grown by Metalorganic Chemical Vapor Deposition

NASA Astrophysics Data System (ADS)

Fini, P.; Wu, X.; Tarsa, E.; Golan, Y.; Srikant, V.; Keller, S.; Denbaars, S.; Speck, J.

1998-08-01

The evolution of morphology and associated extended defects in GaN thin films grown on sapphire by metalorganic chemical vapor deposition (MOCVD) are shown to depend strongly on the growth environment. For the commonly used two-step growth process, a change in growth parameter such as reactor pressure influences the initial high temperature (HT) GaN growth mechanism. By means of transmission electron microscopy (TEM), atomic force microscopy (AFM), and high resolution X-ray diffraction (HRXRD) measurements, it is shown that the initial density of HT islands on the nucleation layer (NL) and subsequently the threading dislocation density in the HT GaN film may be directly controlled by tailoring the initial HT GaN growth conditions.

Reactive molecular beam epitaxial growth and in situ photoemission spectroscopy study of iridate superlattices

NASA Astrophysics Data System (ADS)

Fan, C. C.; Liu, Z. T.; Cai, S. H.; Wang, Z.; Xiang, P.; Zhang, K. L.; Liu, W. L.; Liu, J. S.; Wang, P.; Zheng, Y.; Shen, D. W.; You, L. X.

2017-08-01

High-quality (001)-oriented perovskite [(SrIrO3)m/(SrTiO3)] superlattices (m=1/2, 1, 2, 3 and ∞ ) films have been grown on SrTiO3(001) epitaxially using reactive molecular beam epitaxy. Compared to previously reported superlattices synthesized by pulsed laser deposition, our superlattices exhibit superior crystalline, interface and surface structure, which have been confirmed by high-resolution X-ray diffraction, scanning transmission electron microscopy and atomic force microscopy, respectively. The transport measurements confirm a novel insulator-metal transition with the change of dimensionality in these superlattices, and our first systematic in situ photoemission spectroscopy study indicates that the increasing strength of effective correlations induced by reducing dimensionality would be the dominating origin of this transition.

Spatial Imaging of Strongly Interacting Rydberg Atoms

NASA Astrophysics Data System (ADS)

Thaicharoen, Nithiwadee

The strong interactions between Rydberg excitations can result in spatial correlations between the excitations. The ability to control the interaction strength and the correlations between Rydberg atoms is applicable in future technological implementations of quantum computation. In this thesis, I investigates how both the character of the Rydberg-Rydberg interactions and the details of the excitation process affect the nature of the spatial correlations and the evolution of those correlations in time. I first describes the experimental apparatus and methods used to perform high-magnification Rydberg-atom imaging, as well as three experiments in which these methods play an important role. The obtained Rydberg-atom positions reveal the correlations in the many-body Rydberg-atom system and their time dependence with sub-micron spatial resolution. In the first experiment, atoms are excited to a Rydberg state that experiences a repulsive van der Waals interaction. The Rydberg excitations are prepared with a well-defined initial separation, and the effect of van der Waals forces is observed by tracking the interatomic distance between the Rydberg atoms. The atom trajectories and thereby the interaction coefficient C6 are extracted from the pair correlation functions of the Rydberg atom positions. In the second experiment, the Rydberg atoms are prepared in a highly dipolar state by using adiabatic state transformation. The atom-pair kinetics that follow from the strong dipole-dipole interactions are observed. The pair correlation results provide the first direct visualization of the electric-dipole interaction and clearly exhibit its anisotropic nature. In both the first and the second experiment, results of semi-classical simulations of the atom-pair trajectories agree well with the experimental data. In the analysis, I use energy conservation and measurements of the initial positions and the terminal velocities of the atom pairs to extract the C6 and C 3 interaction coefficients. The final experiment demonstrates the ability to enhance or suppress the degree of spatial correlation in a system of Rydberg excitations, using a rotary-echo excitation process in concert with particular excitation laser detunings. The work in this thesis demonstrates an ability to control long-range interactions between Rydberg atoms, which paves the way towards preparing and studying increasingly complex many-body systems.

A universal strategy for the creation of machine learning-based atomistic force fields

NASA Astrophysics Data System (ADS)

Huan, Tran Doan; Batra, Rohit; Chapman, James; Krishnan, Sridevi; Chen, Lihua; Ramprasad, Rampi

2017-09-01

Emerging machine learning (ML)-based approaches provide powerful and novel tools to study a variety of physical and chemical problems. In this contribution, we outline a universal strategy to create ML-based atomistic force fields, which can be used to perform high-fidelity molecular dynamics simulations. This scheme involves (1) preparing a big reference dataset of atomic environments and forces with sufficiently low noise, e.g., using density functional theory or higher-level methods, (2) utilizing a generalizable class of structural fingerprints for representing atomic environments, (3) optimally selecting diverse and non-redundant training datasets from the reference data, and (4) proposing various learning approaches to predict atomic forces directly (and rapidly) from atomic configurations. From the atomistic forces, accurate potential energies can then be obtained by appropriate integration along a reaction coordinate or along a molecular dynamics trajectory. Based on this strategy, we have created model ML force fields for six elemental bulk solids, including Al, Cu, Ti, W, Si, and C, and show that all of them can reach chemical accuracy. The proposed procedure is general and universal, in that it can potentially be used to generate ML force fields for any material using the same unified workflow with little human intervention. Moreover, the force fields can be systematically improved by adding new training data progressively to represent atomic environments not encountered previously.

All-Atom Internal Coordinate Mechanics (ICM) Force Field for Hexopyranoses and Glycoproteins.

PubMed

Arnautova, Yelena A; Abagyan, Ruben; Totrov, Maxim

2015-05-12

We present an extension of the all-atom internal-coordinate force field, ICMFF, that allows for simulation of heterogeneous systems including hexopyranose saccharides and glycan chains in addition to proteins. A library of standard glycan geometries containing α- and β-anomers of the most common hexapyranoses, i.e., d-galactose, d-glucose, d-mannose, d-xylose, l-fucose, N -acetylglucosamine, N -acetylgalactosamine, sialic, and glucuronic acids, is created based on the analysis of the saccharide structures reported in the Cambridge Structural Database. The new force field parameters include molecular electrostatic potential-derived partial atomic charges and the torsional parameters derived from quantum mechanical data for a collection of minimal molecular fragments and related molecules. The ϕ/ψ torsional parameters for different types of glycosidic linkages are developed using model compounds containing the key atoms in the full carbohydrates, i.e., glycosidic-linked tetrahydropyran-cyclohexane dimers. Target data for parameter optimization include two-dimensional energy surfaces corresponding to the ϕ/ψ glycosidic dihedral angles in the disaccharide analogues, as determined by quantum mechanical MP2/6-31G** single-point energies on HF/6-31G** optimized structures. To achieve better agreement with the observed geometries of glycosidic linkages, the bond angles at the O-linkage atoms are added to the internal variable set and the corresponding bond bending energy term is parametrized using quantum mechanical data. The resulting force field is validated on glycan chains of 1-12 residues from a set of high-resolution X-ray glycoprotein structures based on heavy atom root-mean-square deviations of the lowest-energy glycan conformations generated by the biased probability Monte Carlo (BPMC) molecular mechanics simulations from the native structures. The appropriate BPMC distributions for monosaccharide-monosaccharide and protein-glycan linkages are derived from the extensive analysis of conformational properties of glycoprotein structures reported in the Protein Data Bank. Use of the BPMC search leads to significant improvements in sampling efficiency for glycan simulations. Moreover, good agreement with the X-ray glycoprotein structures is achieved for all glycan chain lengths. Thus, average/median RMSDs are 0.81/0.68 Å for one-residue glycans and 1.32/1.47 Å for three-residue glycans. RMSD from the native structure for the lowest-energy conformation of the 12-residue glycan chain (PDB ID 3og2) is 1.53 Å. Additionally, results obtained for free short oligosaccharides using the new force field are in line with the available experimental data, i.e., the most populated conformations in solution are predicted to be the lowest energy ones. The newly developed parameters allow for the accurate modeling of linear and branched hexopyranose glycosides in heterogeneous systems.

A review of demodulation techniques for amplitude-modulation atomic force microscopy

PubMed Central

Harcombe, David M; Ragazzon, Michael R P; Moheimani, S O Reza; Fleming, Andrew J

2017-01-01

In this review paper, traditional and novel demodulation methods applicable to amplitude-modulation atomic force microscopy are implemented on a widely used digital processing system. As a crucial bandwidth-limiting component in the z-axis feedback loop of an atomic force microscope, the purpose of the demodulator is to obtain estimates of amplitude and phase of the cantilever deflection signal in the presence of sensor noise or additional distinct frequency components. Specifically for modern multifrequency techniques, where higher harmonic and/or higher eigenmode contributions are present in the oscillation signal, the fidelity of the estimates obtained from some demodulation techniques is not guaranteed. To enable a rigorous comparison, the performance metrics tracking bandwidth, implementation complexity and sensitivity to other frequency components are experimentally evaluated for each method. Finally, the significance of an adequate demodulator bandwidth is highlighted during high-speed tapping-mode atomic force microscopy experiments in constant-height mode. PMID:28900596

Frequency modulation atomic force microscopy: a dynamic measurement technique for biological systems

NASA Astrophysics Data System (ADS)

Higgins, Michael J.; Riener, Christian K.; Uchihashi, Takayuki; Sader, John E.; McKendry, Rachel; Jarvis, Suzanne P.

2005-03-01

Frequency modulation atomic force microscopy (FM-AFM) has been modified to operate in a liquid environment within an atomic force microscope specifically designed for investigating biological samples. We demonstrate the applicability of FM-AFM to biological samples using the spectroscopy mode to measure the unbinding forces of a single receptor-ligand (biotin-avidin) interaction. We show that quantitative adhesion force measurements can only be obtained provided certain modifications are made to the existing theory, which is used to convert the detected frequency shifts to an interaction force. Quantitative force measurements revealed that the unbinding forces for the biotin-avidin interaction were greater than those reported in previous studies. This finding was due to the use of high average tip velocities, which were calculated to be two orders of magnitude greater than those typically used in unbinding receptor-ligand experiments. This study therefore highlights the potential use of FM-AFM to study a range of biological systems, including living cells and/or single biomolecule interactions.

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.

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.

Nanomechanical force transducers for biomolecular and intracellular measurements: is there room to shrink and why do it?

PubMed

Sirbuly, Donald J; Friddle, Raymond W; Villanueva, Joshua; Huang, Qian

2015-02-01

Over the past couple of decades there has been a tremendous amount of progress on the development of ultrasensitive nanomechanical instruments, which has enabled scientists to peer for the first time into the mechanical world of biomolecular systems. Currently, work-horse instruments such as the atomic force microscope and optical/magnetic tweezers have provided the resolution necessary to extract quantitative force data from various molecular systems down to the femtonewton range, but it remains difficult to access the intracellular environment with these analytical tools as they have fairly large sizes and complicated feedback systems. This review is focused on highlighting some of the major milestones and discoveries in the field of biomolecular mechanics that have been made possible by the development of advanced atomic force microscope and tweezer techniques as well as on introducing emerging state-of-the-art nanomechanical force transducers that are addressing the size limitations presented by these standard tools. We will first briefly cover the basic setup and operation of these instruments, and then focus heavily on summarizing advances in in vitro force studies at both the molecular and cellular level. The last part of this review will include strategies for shrinking down the size of force transducers and provide insight into why this may be important for gaining a more complete understanding of cellular activity and function.

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

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

Helium cluster isolation spectroscopy

NASA Astrophysics Data System (ADS)

Higgins, John Paul

Clusters of helium, each containing ~103- 104 atoms, are produced in a molecular beam and are doped with alkali metal atoms (Li, Na, and K) and large organic molecules. Electronic spectroscopy in the visible and UV regions of the spectrum is carried out on the dopant species. Since large helium clusters are liquid and attain an equilibrium internal temperature of 0.4 K, they interact weakly with atoms or molecules absorbed on their surface or resident inside the cluster. The spectra that are obtained are characterized by small frequency shifts from the positions of the gas phase transitions, narrow lines, and cold vibrational temperatures. Alkali atoms aggregate on the helium cluster surface to form dimers and trimers. The spectra of singlet alkali dimers exhibit the presence of elementary excitations in the superfluid helium cluster matrix. It is found that preparation of the alkali molecules on the surface of helium clusters leads to the preferential formation of high-spin, van der Waals bound, triplet dimers and quartet trimers. Four bound-bound and two bound-free transitions are observed in the triplet manifold of the alkali dimers. The quartet trimers serve as an ideal system for the study of a simple unimolecular reaction in the cold helium cluster environment. Analysis of the lowest quartet state provides valuable insight into three-body forces in a van der Waals trimer. The wide range of atomic and molecular systems studied in this thesis constitutes a preliminary step in the development of helium cluster isolation spectroscopy, a hybrid technique combining the advantages of high resolution spectroscopy with the synthetic, low temperature environment of matrices.

Atomistic Interrogation of B–N Co-dopant Structures and Their Electronic Effects in Graphene

DOE PAGES

Schiros, Theanne; Nordlund, Dennis; Palova, Lucia; ...

2016-06-21

Chemical doping has been demonstrated to be an effective method for producing high-quality, large-area graphene with controlled carrier concentrations and an atomically tailored work function. Furthermore, the emergent optoelectronic properties and surface reactivity of carbon nanostructures are dictated by the microstructure of atomic dopants. Co-doping of graphene with boron and nitrogen offers the possibility to further tune the electronic properties of graphene at the atomic level, potentially creating p- and n-type domains in a single carbon sheet, opening a gap between valence and conduction bands in the 2-D semimetal. When using a suite of high-resolution synchrotron-based X-ray techniques, scanning tunnelingmore » microscopy, and density functional theory based computation we visualize and characterize B–N dopant bond structures and their electronic effects at the atomic level in single-layer graphene grown on a copper substrate. We find there is a thermodynamic driving force for B and N atoms to cluster into BNC structures in graphene, rather than randomly distribute into isolated B and N graphitic dopants, although under the present growth conditions, kinetics limit segregation of large B–N domains. We also observe that the doping effect of these BNC structures, which open a small band gap in graphene, follows the B:N ratio (B > N, p-type; B < N, n-type; B=N, neutral). We attribute this to the comparable electron-withdrawing and -donating effects, respectively, of individual graphitic B and N dopants, although local electrostatics also play a role in the work function change.« less

Origin of colossal dielectric response in (In + Nb) co-doped TiO2 rutile ceramics: a potential electrothermal material.

PubMed

Ke, Shanming; Li, Tao; Ye, Mao; Lin, Peng; Yuan, Wenxiang; Zeng, Xierong; Chen, Lang; Huang, Haitao

2017-08-31

(In + Nb) co-doped TiO 2 (TINO) rutile is an emerging material with a colossal dielectric permittivity (CP) and a low dielectric loss over wide temperature and frequency ranges. The electrical inhomogeneous nature of TINO ceramics is demonstrated by direct local current probing with high-resolution conductive atomic force microscopy (cAFM). The CP response in TINO is found to originate from the electron-pinned defect dipole induced conductive cluster effect and the electrode effect. Two types of dielectric relaxations are simultaneously observed due to these two effects. With the given synthesis condition, we found TINO shows a highly leaky feature that impairs its application as a dielectric material. However, the fast-temperature-rising phenomenon found in this work may open a new door for TINO to be applied as a potential electrothermal material with high efficiency, oxidation-proof, high temperature stability, and energy saving.

3D Structural Model of High-Performance Non-Fullerene Polymer Solar Cells as Revealed by High-Resolution AFM.

PubMed

Shi, Shaowei; Chen, Xiaofeng; Liu, Xubo; Wu, Xuefei; Liu, Feng; Zhang, Zhi-Guo; Li, Yongfang; Russell, Thomas P; Wang, Dong

2017-07-26

Rapid improvements in nonfullerene polymer solar cells (PSCs) have brought power conversion efficiencies to greater than 12%. To further improve device performance, a fundamental understanding of the correlations between structure and performance is essential. In this paper, based on a typical high-performance system consisting of J61(one donor-acceptor (D-A) copolymer of benzodithiophene and fluorine substituted benzotriazole) and ITIC (3,9-bis(2-methylene-(3-(1,1-dicyanomethylene)-indanone)-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3-d:2',3'-d']-s-indaceno[1,2-b:5,6-b']-dithiophene), a 3D structural model is directly imaged by employing high-resolution atomic force microscopy (AFM). Hierarchical morphologies ranging from fiberlike crystallites, several nanometers in size, to a bicontinuous morphology, having domains tens of nanometers in size, are observed. A fibrillar interpenetrating networks of J61-rich domains embedded in a matrix comprised of a J61/ITIC is seen, reflecting the partial miscibility of J61 with ITIC. These hierarchical nanostructural characteristics are coupled to significantly enhanced exciton dissociation, and further contribute to photocurrent and final device performance.

Enhanced resolution imaging of ultrathin ZnO layers on Ag(111) by multiple hydrogen molecules in a scanning tunneling microscope junction

NASA Astrophysics Data System (ADS)

Liu, Shuyi; Shiotari, Akitoshi; Baugh, Delroy; Wolf, Martin; Kumagai, Takashi

2018-05-01

Molecular hydrogen in a scanning tunneling microscope (STM) junction has been found to enhance the lateral spatial resolution of the STM imaging, referred to as scanning tunneling hydrogen microscopy (STHM). Here we report atomic resolution imaging of 2- and 3-monolayer (ML) thick ZnO layers epitaxially grown on Ag(111) using STHM. The enhanced resolution can be obtained at a relatively large tip to surface distance and resolves a more defective structure exhibiting dislocation defects for 3-ML-thick ZnO than for 2 ML. In order to elucidate the enhanced imaging mechanism, the electric and mechanical properties of the hydrogen molecular junction (HMJ) are investigated by a combination of STM and atomic force microscopy. It is found that the HMJ shows multiple kinklike features in the tip to surface distance dependence of the conductance and frequency shift curves, which are absent in a hydrogen-free junction. Based on a simple modeling, we propose that the junction contains several hydrogen molecules and sequential squeezing of the molecules out of the junction results in the kinklike features in the conductance and frequency shift curves. The model also qualitatively reproduces the enhanced resolution image of the ZnO films.

Determining the Molecular Growth Mechanisms of Protein Crystal Faces by Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

Nadarajah, Arunan; Li, Huayu; Pusey, Marc L.

1999-01-01

A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height. Theoretical analyses of the packing also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces as they were being incorporated into the lattice. Images of individual growth events on the (110) face of tetragonal lysozyme crystals were observed, shown by jump discontinuities in the growth step in the linescan images as shown in the figure. The growth unit dimension in the scanned direction was obtained from these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme growth unit sizes were obtained. A variety of unit sizes corresponding to 43 helices, were shown to participate in the growth process, with the 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

Nanoscale characterization of effect of L-arginine on Streptococcus mutans biofilm adhesion by atomic force microscopy.

PubMed

Sharma, Shivani; Lavender, Stacey; Woo, JungReem; Guo, Lihong; Shi, Wenyuan; Kilpatrick-Liverman, LaTonya; Gimzewski, James K

2014-07-01

A major aetiological factor of dental caries is the pathology of the dental plaque biofilms. The amino acid L-arginine (Arg) is found naturally in saliva as a free molecule or as a part of salivary peptides and proteins. Plaque bacteria metabolize Arg to produce alkali and neutralize glycolytic acids, promoting a less cariogenous oral microbiome. Here, we explored an alternative and complementary mechanism of action of Arg using atomic force microscopy. The nanomechanical properties of Streptococcus mutans biofilm extracellular matrix were characterized under physiological buffer conditions. We report the effect of Arg on the adhesive behaviour and structural properties of extracellular polysaccharides in S. mutans biofilms. High-resolution imaging of biofilm surfaces can reveal additional structural information on bacterial cells embedded within the surrounding extracellular matrix. A dense extracellular matrix was observed in biofilms without Arg compared to those grown in the presence of Arg. S. mutans biofilms grown in the presence of Arg could influence the production and/or composition of extracellular membrane glucans and thereby affect their adhesion properties. Our results suggest that the presence of Arg in the oral cavity could influence the adhesion properties of S. mutans to the tooth surface. © 2014 The Authors.

Development of a Hybrid Atomic Force Microscopic Measurement System Combined with White Light Scanning Interferometry

PubMed Central

Guo, Tong; Wang, Siming; Dorantes-Gonzalez, Dante J.; Chen, Jinping; Fu, Xing; Hu, Xiaotang

2012-01-01

A hybrid atomic force microscopic (AFM) measurement system combined with white light scanning interferometry for micro/nanometer dimensional measurement is developed. The system is based on a high precision large-range positioning platform with nanometer accuracy on which a white light scanning interferometric module and an AFM head are built. A compact AFM head is developed using a self-sensing tuning fork probe. The head need no external optical sensors to detect the deflection of the cantilever, which saves room on the head, and it can be directly fixed under an optical microscopic interferometric system. To enhance the system’s dynamic response, the frequency modulation (FM) mode is adopted for the AFM head. The measuring data can be traceable through three laser interferometers in the system. The lateral scanning range can reach 25 mm × 25 mm by using a large-range positioning platform. A hybrid method combining AFM and white light scanning interferometry is proposed to improve the AFM measurement efficiency. In this method, the sample is measured firstly by white light scanning interferometry to get an overall coarse morphology, and then, further measured with higher resolution by AFM. Several measuring experiments on standard samples demonstrate the system’s good measurement performance and feasibility of the hybrid measurement method. PMID:22368463

Development of a hybrid atomic force microscopic measurement system combined with white light scanning interferometry.

PubMed

Guo, Tong; Wang, Siming; Dorantes-Gonzalez, Dante J; Chen, Jinping; Fu, Xing; Hu, Xiaotang

2012-01-01

A hybrid atomic force microscopic (AFM) measurement system combined with white light scanning interferometry for micro/nanometer dimensional measurement is developed. The system is based on a high precision large-range positioning platform with nanometer accuracy on which a white light scanning interferometric module and an AFM head are built. A compact AFM head is developed using a self-sensing tuning fork probe. The head need no external optical sensors to detect the deflection of the cantilever, which saves room on the head, and it can be directly fixed under an optical microscopic interferometric system. To enhance the system's dynamic response, the frequency modulation (FM) mode is adopted for the AFM head. The measuring data can be traceable through three laser interferometers in the system. The lateral scanning range can reach 25 mm × 25 mm by using a large-range positioning platform. A hybrid method combining AFM and white light scanning interferometry is proposed to improve the AFM measurement efficiency. In this method, the sample is measured firstly by white light scanning interferometry to get an overall coarse morphology, and then, further measured with higher resolution by AFM. Several measuring experiments on standard samples demonstrate the system's good measurement performance and feasibility of the hybrid measurement method.

Elastic modulus measurements at variable temperature: Validation of atomic force microscopy techniques

NASA Astrophysics Data System (ADS)

Natali, Marco; Reggente, Melania; Passeri, Daniele; Rossi, Marco

2016-06-01

The development of polymer-based nanocomposites to be used in critical thermal environments requires the characterization of their mechanical properties, which are related to their chemical composition, size, morphology and operating temperature. Atomic force microscopy (AFM) has been proven to be a useful tool to develop techniques for the mechanical characterization of these materials, thanks to its nanometer lateral resolution and to the capability of exerting ultra-low loads, down to the piconewton range. In this work, we demonstrate two techniques, one quasi-static, i.e., AFM-based indentation (I-AFM), and one dynamic, i.e., contact resonance AFM (CR-AFM), for the mechanical characterization of compliant materials at variable temperature. A cross-validation of I-AFM and CR-AFM has been performed by comparing the results obtained on two reference materials, i.e., low-density polyethylene (LDPE) and polycarbonate (PC), which demonstrated the accuracy of the techniques.

Nanomechanical DNA origami 'single-molecule beacons' directly imaged by atomic force microscopy

PubMed Central

Kuzuya, Akinori; Sakai, Yusuke; Yamazaki, Takahiro; Xu, Yan; Komiyama, Makoto

2011-01-01

DNA origami involves the folding of long single-stranded DNA into designed structures with the aid of short staple strands; such structures may enable the development of useful nanomechanical DNA devices. Here we develop versatile sensing systems for a variety of chemical and biological targets at molecular resolution. We have designed functional nanomechanical DNA origami devices that can be used as 'single-molecule beacons', and function as pinching devices. Using 'DNA origami pliers' and 'DNA origami forceps', which consist of two levers ~170 nm long connected at a fulcrum, various single-molecule inorganic and organic targets ranging from metal ions to proteins can be visually detected using atomic force microscopy by a shape transition of the origami devices. Any detection mechanism suitable for the target of interest, pinching, zipping or unzipping, can be chosen and used orthogonally with differently shaped origami devices in the same mixture using a single platform. PMID:21863016

Atomic force microscopy – looking at mechanosensors on the cell surface

PubMed Central

Heinisch, Jürgen J.; Lipke, Peter N.; Beaussart, Audrey; El Kirat Chatel, Sofiane; Dupres, Vincent; Alsteens, David; Dufrêne, Yves F.

2012-01-01

Summary Living cells use cell surface proteins, such as mechanosensors, to constantly sense and respond to their environment. However, the way in which these proteins respond to mechanical stimuli and assemble into large complexes remains poorly understood at the molecular level. In the past years, atomic force microscopy (AFM) has revolutionized the way in which biologists analyze cell surface proteins to molecular resolution. In this Commentary, we discuss how the powerful set of advanced AFM techniques (e.g. live-cell imaging and single-molecule manipulation) can be integrated with the modern tools of molecular genetics (i.e. protein design) to study the localization and molecular elasticity of individual mechanosensors on the surface of living cells. Although we emphasize recent studies on cell surface proteins from yeasts, the techniques described are applicable to surface proteins from virtually all organisms, from bacteria to human cells. PMID:23077172

Role of small oligomers on the amyloidogenic aggregation free-energy landscape.

PubMed

He, Xianglan; Giurleo, Jason T; Talaga, David S

2010-01-08

We combine atomic-force-microscopy particle-size-distribution measurements with earlier measurements on 1-anilino-8-naphthalene sulfonate, thioflavin T, and dynamic light scattering to develop a quantitative kinetic model for the aggregation of beta-lactoglobulin into amyloid. We directly compare our simulations to the population distributions provided by dynamic light scattering and atomic force microscopy. We combine species in the simulation according to structural type for comparison with fluorescence fingerprint results. The kinetic model of amyloidogenesis leads to an aggregation free-energy landscape. We define the roles of and propose a classification scheme for different oligomeric species based on their location in the aggregation free-energy landscape. We relate the different types of oligomers to the amyloid cascade hypothesis and the toxic oligomer hypothesis for amyloid-related diseases. We discuss existing kinetic mechanisms in terms of the different types of oligomers. We provide a possible resolution to the toxic oligomer-amyloid coincidence.

Progress in the Correlative Atomic Force Microscopy and Optical Microscopy

PubMed Central

Zhou, Lulu; Cai, Mingjun; Tong, Ti; Wang, Hongda

2017-01-01

Atomic force microscopy (AFM) has evolved from the originally morphological imaging technique to a powerful and multifunctional technique for manipulating and detecting the interactions between molecules at nanometer resolution. However, AFM cannot provide the precise information of synchronized molecular groups and has many shortcomings in the aspects of determining the mechanism of the interactions and the elaborate structure due to the limitations of the technology, itself, such as non-specificity and low imaging speed. To overcome the technical limitations, it is necessary to combine AFM with other complementary techniques, such as fluorescence microscopy. The combination of several complementary techniques in one instrument has increasingly become a vital approach to investigate the details of the interactions among molecules and molecular dynamics. In this review, we reported the principles of AFM and optical microscopy, such as confocal microscopy and single-molecule localization microscopy, and focused on the development and use of correlative AFM and optical microscopy. PMID:28441775

Nanoscale monitoring of drug actions on cell membrane using atomic force microscopy

PubMed Central

Li, Mi; Liu, Lian-qing; Xi, Ning; Wang, Yue-chao

2015-01-01

Knowledge of the nanoscale changes that take place in individual cells in response to a drug is useful for understanding the drug action. However, due to the lack of adequate techniques, such knowledge was scarce until the advent of atomic force microscopy (AFM), which is a multifunctional tool for investigating cellular behavior with nanometer resolution under near-physiological conditions. In the past decade, researchers have applied AFM to monitor the morphological and mechanical dynamics of individual cells following drug stimulation, yielding considerable novel insight into how the drug molecules affect an individual cell at the nanoscale. In this article we summarize the representative applications of AFM in characterization of drug actions on cell membrane, including topographic imaging, elasticity measurements, molecular interaction quantification, native membrane protein imaging and manipulation, etc. The challenges that are hampering the further development of AFM for studies of cellular activities are aslo discussed. PMID:26027658

Submolecular resolution in scanning probe images of Sn-phthalocyanines on Cu(1 0 0) using metal tips

NASA Astrophysics Data System (ADS)

Buchmann, Kristof; Hauptmann, Nadine; Foster, Adam S.; Berndt, Richard

2017-10-01

Single Sn-phthalocyanine (SnPc) molecules adsorb on Cu(1 0 0) with the Sn ion above (Sn-up) or below (Sn-down) the molecular plane. Here we use a combination of atomic force microscopy (AFM), scanning tunnelling microscopy (STM) and first principles calculations to understand the adsorption configuration and origin of observed contrast of molecules in the Sn-down state. AFM with metallic tips images the pyrrole nitrogen atoms in these molecules as attractive features while STM reveals a chirality of the electronic structure of the molecules close to the Fermi level E_F, which is not observed in AFM. Using density functional theory calculations, the origin of the submolecular contrast is analysed and, while the electrostatic forces turn out to be negligible, the van der Waals interaction between the phenyl rings of SnPc and the substrate deform the molecule, push the pyrrole nitrogen atoms away from the substrate and thus induce the observed submolecular contrast. Simulated STM images reproduce the chirality of the electronic structure near E_F.

Use of scanning near-field optical microscope with an aperture probe for detection of luminescent nanodiamonds

NASA Astrophysics Data System (ADS)

Shershulin, V. A.; Samoylenko, S. R.; Shenderova, O. A.; Konov, V. I.; Vlasov, I. I.

2017-02-01

The suitability of scanning near-field optical microscopy (SNOM) to image photoluminescent diamond nanoparticles with nanoscale resolution is demonstrated. Isolated diamond nanocrystals with an average size of 100 nm, containing negatively charged nitrogen-vacancy (NV-) centers, were chosen as tested material. The NV- luminescence was stimulated by continuous 532 nm laser light. Sizes of analyzed crystallites were monitored by an atomic force microscope. The lateral resolution of the order of 100 nm was reached in SNOM imaging of diamond nanoparticles using 150 nm square aperture of the probe.

Asymmetric-detection time-stretch optical microscopy (ATOM) for ultrafast high-contrast cellular imaging in flow

PubMed Central

Wong, Terence T. W.; Lau, Andy K. S.; Ho, Kenneth K. Y.; Tang, Matthew Y. H.; Robles, Joseph D. F.; Wei, Xiaoming; Chan, Antony C. S.; Tang, Anson H. L.; Lam, Edmund Y.; Wong, Kenneth K. Y.; Chan, Godfrey C. F.; Shum, Ho Cheung; Tsia, Kevin K.

2014-01-01

Accelerating imaging speed in optical microscopy is often realized at the expense of image contrast, image resolution, and detection sensitivity – a common predicament for advancing high-speed and high-throughput cellular imaging. We here demonstrate a new imaging approach, called asymmetric-detection time-stretch optical microscopy (ATOM), which can deliver ultrafast label-free high-contrast flow imaging with well delineated cellular morphological resolution and in-line optical image amplification to overcome the compromised imaging sensitivity at high speed. We show that ATOM can separately reveal the enhanced phase-gradient and absorption contrast in microfluidic live-cell imaging at a flow speed as high as ~10 m/s, corresponding to an imaging throughput of ~100,000 cells/sec. ATOM could thus be the enabling platform to meet the pressing need for intercalating optical microscopy in cellular assay, e.g. imaging flow cytometry – permitting high-throughput access to the morphological information of the individual cells simultaneously with a multitude of parameters obtained in the standard assay. PMID:24413677

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.

Non-thermalization in trapped atomic ion spin chains

NASA Astrophysics Data System (ADS)

Hess, P. W.; Becker, P.; Kaplan, H. B.; Kyprianidis, A.; Lee, A. C.; Neyenhuis, B.; Pagano, G.; Richerme, P.; Senko, C.; Smith, J.; Tan, W. L.; Zhang, J.; Monroe, C.

2017-10-01

Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state. This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'.

Non-thermalization in trapped atomic ion spin chains.

PubMed

Hess, P W; Becker, P; Kaplan, H B; Kyprianidis, A; Lee, A C; Neyenhuis, B; Pagano, G; Richerme, P; Senko, C; Smith, J; Tan, W L; Zhang, J; Monroe, C

2017-12-13

Linear arrays of trapped and laser-cooled atomic ions are a versatile platform for studying strongly interacting many-body quantum systems. Effective spins are encoded in long-lived electronic levels of each ion and made to interact through laser-mediated optical dipole forces. The advantages of experiments with cold trapped ions, including high spatio-temporal resolution, decoupling from the external environment and control over the system Hamiltonian, are used to measure quantum effects not always accessible in natural condensed matter samples. In this review, we highlight recent work using trapped ions to explore a variety of non-ergodic phenomena in long-range interacting spin models, effects that are heralded by the memory of out-of-equilibrium initial conditions. We observe long-lived memory in static magnetizations for quenched many-body localization and prethermalization, while memory is preserved in the periodic oscillations of a driven discrete time crystal state.This article is part of the themed issue 'Breakdown of ergodicity in quantum systems: from solids to synthetic matter'. © 2017 The Author(s).

Charge density wave order in 1D mirror twin boundaries of single-layer MoSe 2

DOE PAGES

Barja, Sara; Wickenburg, Sebastian; Liu, Zhen-Fei; ...

2016-04-18

Here, We provide direct evidence for the existence of isolated, one-dimensional charge density waves at mirror twin boundaries (MTBs) of single-layer semiconducting MoSe 2. Such MTBs have been previously observed by transmission electron microscopy and have been predicted to be metallic in MoSe 2 and MoS 2. Our low-temperature scanning tunnelling microscopy/spectroscopy measurements revealed a substantial bandgap of 100 meV opening at the Fermi energy in the otherwise metallic one-dimensional structures. We found a periodic modulation in the density of states along the MTB, with a wavelength of approximately three lattice constants. In addition to mapping the energy-dependent densitymore » of states, we determined the atomic structure and bonding of the MTB through simultaneous high-resolution non-contact atomic force microscopy. Density functional theory calculations based on the observed structure reproduced both the gap opening and the spatially resolved density of states.« less

Microscale analysis of in vitro anaerobic degradation of lignocellulosic wastes by rumen microorganisms.

PubMed

Hu, Zhen-Hu; Liu, Shao-Yang; Yue, Zheng-Bo; Yan, Li-Feng; Yang, Ming-Tao; Yu, Han-Qing

2008-01-01

Anaerobic degradation of lignin in waste straw by ruminal microbes was directly observed using atomic force microscope (AFM). A series of high-resolution AFM images of the straw surface in the biodegradation show that the wax flakelets and lignin granules covering the straw surface were removed by the rumen microorganisms. Such degradation resulted in an exposure of cellulose fibers located inside the straw. The appearance of holes and microfibers in fermentation reveals that tunneling might be one of the ways for rumen microorganisms to attack the straw. Increases in the atomic ratio of oxygen to carbon (O/C) and the ratio C2/C3 in C1s spectra of X-ray photoelectron spectroscopy confirm that more cellulose was exposed on the surface after the anaerobic fermentation of straw. Gas chromatography/mass spectrometry analytical results demonstrate the decomposition of lignin by rumen microorganisms. Fourier transform infrared spectroscopy spectra and the measurement of degradation efficiency of the main straw components further verify these microscaled observations.

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.

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.

Assembly of live micro-organisms on microstructured PDMS stamps by convective/capillary deposition for AFM bio-experiments

NASA Astrophysics Data System (ADS)

Dague, E.; Jauvert, E.; Laplatine, L.; Viallet, B.; Thibault, C.; Ressier, L.

2011-09-01

Immobilization of live micro-organisms on solid substrates is an important prerequisite for atomic force microscopy (AFM) bio-experiments. The method employed must immobilize the cells firmly enough to enable them to withstand the lateral friction forces exerted by the tip during scanning but without denaturing the cell interface. In this work, a generic method for the assembly of living cells on specific areas of substrates is proposed. It consists in assembling the living cells within the patterns of microstructured, functionalized poly-dimethylsiloxane (PDMS) stamps using convective/capillary deposition. This versatile approach is validated by applying it to two systems of foremost importance in biotechnology and medicine: Saccharomyces cerevisiae yeasts and Aspergillus fumigatus fungal spores. We show that this method allows multiplexing AFM nanomechanical measurements by force spectroscopy on S. cerevisiae yeasts and high-resolution AFM imaging of germinated Aspergillus conidia in buffer medium. These two examples clearly demonstrate the immense potential of micro-organism assembly on functionalized, microstructured PDMS stamps by convective/capillary deposition for performing rigorous AFM bio-experiments on living cells.

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.

Atomic Force Microscope (AFM) measurements and analysis on Sagem 05R0025 secondary substrate

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

Soufli, R; Baker, S L; Robinson, J C

2006-02-22

The summary of Atomic Force Microscope (AFM) on Sagem 05R0025 secondary substrate: (1) 2 x 2 {micro}m{sup 2} and 10 x 10 {micro}m{sup 2} AFM measurements and analysis on Sagem 05R0025 secondary substrate at LLNL indicate rather uniform and extremely isotropic finish across the surface, with high-spatial frequency roughness {sigma} in the range 5.1-5.5 {angstrom} rms; (2) the marked absence of pronounced long-range polishing marks in any direction, combined with increased roughness in the very high spatial frequencies, are consistent with ion-beam polishing treatment on the surface. These observations are consistent with all earlier mirrors they measured from the samemore » vendor; and (3) all data were obtained with a Digital Instruments Dimension 5000{trademark} atomic force microscope.« less

Rotary-Atomizer Electric Power Generator

NASA Astrophysics Data System (ADS)

Nguyen, Trieu; Tran, Tuan; de Boer, Hans; van den Berg, Albert; Eijkel, Jan C. T.

2015-03-01

We report experimental and theoretical results on a ballistic energy-conversion method based on a rotary atomizer working with a droplet acceleration-deceleration cycle. In a rotary atomizer, liquid is fed onto the center of a rotating flat surface, where it spreads out under the action of the centrifugal force and creates "atomized" droplets at its edge. The advantage of using a rotary atomizer is that the centrifugal force exerted on the fluid on a smooth, large surface is not only a robust form of acceleration, as it avoids clogging, but also easily allows high throughput, and produces high electrical power. We successfully demonstrate an output power of 4.9 mW and a high voltage up to 3120 V. At present, the efficiency of the system is still low (0.14%). However, the conversion mechanism of the system is fully interpreted in this paper, permitting a conceptual understanding of system operation and providing a roadmap for system optimization. This observation will open up a road for building power-generation systems in the near future.

The influence of spatially and temporally high-resolution wind forcing on the power input to near-inertial waves in the ocean

NASA Astrophysics Data System (ADS)

Rimac, A.; Eden, C.; von Storch, J.

2012-12-01

Coexistence of stable stratification, the meridional overturning circulation and meso-scale eddies and their influence on the ocean's circulation still raise complex questions concerning the ocean energetics. Oceanic general circulation is mainly forced by the wind field and deep water tides. Its essential energetics are the conversion of kinetic energy of the winds and tides into oceanic potential and kinetic energy. Energy needed for the circulation is bound to internal wave fields. Direct internal wave generation by the wind at the sea surface is one of the sources of this energy. Previous studies using mixed-layer type of models and low frequency wind forcings (six-hourly and daily) left room for improvement. Using mixed-layer models it is not possible to assess the distribution of near-inertial energy into the deep ocean. Also, coarse temporal resolution of wind forcing strongly underestimates the near-inertial wave energy. To overcome this difficulty we use a high resolution ocean model with high frequency wind forcings. We establish the following model setup: We use the Max Planck Institute Ocean Model (MPIOM) on a tripolar grid with 45km horizontal resolution and 40 vertical levels. We run the model with wind forcings that vary in horizontal (250km versus 40km) and temporal resolution (six versus one-hourly). In our study we answer the following questions: How big is the wind kinetic energy input to the near-inertial waves? Is the kinetic energy of the near-inertial waves enhanced when high-frequency wind forcings are used? If so, by how much and why, due to higher level of temporal wind variability or due to better spatial representation of the near-inertial waves? How big is the total power of near-inertial waves generated by the wind at the surface of the ocean? We run the model for one year. Our model results show that the near-inertial waves are excited both using wind forcings of high and low horizontal and temporal resolution. Near-inertial energy is almost two times higher when we force the model with high frequency wind forcings. The influence on the energy mostly depends on the time difference between two forcing fields while the spatial difference has little influence.

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.

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.

Nanomechanical properties of α-synuclein amyloid fibrils: a comparative study by nanoindentation, harmonic force microscopy, and Peakforce QNM

PubMed Central

2011-01-01

We report on the use of three different atomic force spectroscopy modalities to determine the nanomechanical properties of amyloid fibrils of the human α-synuclein protein. α-Synuclein forms fibrillar nanostructures of approximately 10 nm diameter and lengths ranging from 100 nm to several microns, which have been associated with Parkinson's disease. Atomic force microscopy (AFM) has been used to image the morphology of these protein fibrils deposited on a flat surface. For nanomechanical measurements, we used single-point nanoindentation, in which the AFM tip as the indenter is moved vertically to the fibril surface and back while the force is being recorded. We also used two recently developed AFM surface property mapping techniques: Harmonic force microscopy (HarmoniX) and Peakforce QNM. These modalities allow extraction of mechanical parameters of the surface with a lateral resolution and speed comparable to tapping-mode AFM imaging. Based on this phenomenological study, the elastic moduli of the α-synuclein fibrils determined using these three different modalities are within the range 1.3-2.1 GPa. We discuss the relative merits of these three methods for the determination of the elastic properties of protein fibrils, particularly considering the differences and difficulties of each method. PMID:21711775

Quantitative measurement of solvation shells using frequency modulated atomic force microscopy

NASA Astrophysics Data System (ADS)

Uchihashi, T.; Higgins, M.; Nakayama, Y.; Sader, J. E.; Jarvis, S. P.

2005-03-01

The nanoscale specificity of interaction measurements and additional imaging capability of the atomic force microscope make it an ideal technique for measuring solvation shells in a variety of liquids next to a range of materials. Unfortunately, the widespread use of atomic force microscopy for the measurement of solvation shells has been limited by uncertainties over the dimensions, composition and durability of the tip during the measurements, and problems associated with quantitative force calibration of the most sensitive dynamic measurement techniques. We address both these issues by the combined use of carbon nanotube high aspect ratio probes and quantifying the highly sensitive frequency modulation (FM) detection technique using a recently developed analytical method. Due to the excellent reproducibility of the measurement technique, additional information regarding solvation shell size as a function of proximity to the surface has been obtained for two very different liquids. Further, it has been possible to identify differences between chemical and geometrical effects in the chosen systems.

Structural and waveguiding characteristics of Er3+:Yb3Al5-yGayO12 films grown by the liquid phase epitaxy

NASA Astrophysics Data System (ADS)

Hlásek, T.; Rubešová, K.; Jakeš, V.; Nekvindová, P.; Kučera, M.; Daniš, S.; Veis, M.; Havránek, V.

2015-11-01

Erbium (Er3+) doped ytterbium garnet (Er:Yb3Al5-yGayO12; y = 0, 0.55 and 1.1) single crystalline thick films have been grown by the low-temperature liquid phase epitaxy method (LPE). The composition of the films was determined using the high resolution XRD, the particle-induced X-ray emission spectroscopy (PIXE) and the particle-induced gamma-ray emission spectroscopy (PIGE). The lattice mismatch between films and substrates was investigated by the high-resolution X-ray diffraction. The surface analysis was carried out by the atomic force microscopy (AFM). Pure infrared emission of Er3+ ions was observed in all films containing gallium. The characteristics such as refractive index, thickness and light propagation were studied by the m-line spectroscopy (MLS) using several wavelengths (633, 964, 1311 and 1552 nm). All samples, where y = 1.1, were multimode waveguides. For these reasons, the Er:Yb3Al3.9Ga1.1O12 seems to be a promising material for light amplifiers in the IR region.

Fast photodynamics of azobenzene probed by scanning excited-state potential energy surfaces using slow spectroscopy

NASA Astrophysics Data System (ADS)

Tan, Eric M. M.; Amirjalayer, Saeed; Smolarek, Szymon; Vdovin, Alexander; Zerbetto, Francesco; Buma, Wybren Jan

2015-01-01

Azobenzene, a versatile and polymorphic molecule, has been extensively and successfully used for photoswitching applications. The debate over its photoisomerization mechanism leveraged on the computational scrutiny with ever-increasing levels of theory. However, the most resolved absorption spectrum for the transition to S1(nπ*) has not followed the computational advances and is more than half a century old. Here, using jet-cooled molecular beam and multiphoton ionization techniques we report the first high-resolution spectra of S1(nπ*) and S2(ππ*). The photophysical characterization reveals directly the structural changes upon excitation and the timescales of dynamical processes. For S1(nπ*), we find that changes in the hybridization of the nitrogen atoms are the driving force that triggers isomerization. In combination with quantum chemical calculations we conclude that photoisomerization occurs along an inversion-assisted torsional pathway with a barrier of ~2 kcal mol-1. This methodology can be extended to photoresponsive molecular systems so far deemed non-accessible to high-resolution spectroscopy.

Effect of defects on reaction of NiO surface with Pb-contained solution

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

Kim, Jongjin; Hou, Binyang; Park, Changyong

In order to understand the role of defects in chemical reactions, we used two types of samples, which are molecular beam epitaxy (MBE) grown NiO(001) film on Mg(001) substrate as the defect free NiO prototype and NiO grown on Ni(110) single crystal as the one with defects. In-situ observations for oxide-liquid interfacial structure and surface morphology were performed for both samples in water and Pb-contained solution using high-resolution X-ray reflectivity and atomic force microscopy. For the MBE grown NiO, no significant changes were detected in the high-resolution X-ray reflectivity data with monotonic increase in roughness. Meanwhile, in the case ofmore » native grown NiO on Ni(110), significant changes in both the morphology and atomistic structure at the interface were observed when immersed in water and Pb-contained solution. Our results provide simple and direct experimental evidence of the role of the defects in chemical reaction of oxide surfaces with both water and Pb-contained solution.« less

A Novel Method to Reconstruct the Force Curve by Higher Harmonics of the First Two Flexural Modes in Frequency Modulation Atomic Force Microscope (FM-AFM).

PubMed

Zhang, Suoxin; Qian, Jianqiang; Li, Yingzi; Zhang, Yingxu; Wang, Zhenyu

2018-06-04

Atomic force microscope (AFM) is an idealized tool to measure the physical and chemical properties of the sample surfaces by reconstructing the force curve, which is of great significance to materials science, biology, and medicine science. Frequency modulation atomic force microscope (FM-AFM) collects the frequency shift as feedback thus having high force sensitivity and it accomplishes a true noncontact mode, which means great potential in biological sample detection field. However, it is a challenge to establish the relationship between the cantilever properties observed in practice and the tip-sample interaction theoretically. Moreover, there is no existing method to reconstruct the force curve in FM-AFM combining the higher harmonics and the higher flexural modes. This paper proposes a novel method that a full force curve can be reconstructed by any order higher harmonics of the first two flexural modes under any vibration amplitude in FM-AFM. Moreover, in the small amplitude regime, short range forces are reconstructed more accurately by higher harmonics analysis compared with fundamental harmonics using the Sader-Jarvis formula.

Beyond experimental noise: Analyzing single-molecule data of heterogeneous systems. Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb and S.K. Sarkar

NASA Astrophysics Data System (ADS)

Meroz, Yasmine

2015-06-01

In the 1980s the world witnessed the advent of single-molecule experiments. The first atomic resolution characterization of a surface was reported by scanning tunneling microscope (STM) in 1982 [1], followed by atomic force microscope (AFM) in 1986 [2]. The first optical detection and spectroscopy of a single molecule in a solid took place in 1989 [3,4], in a time where essentially all chemical experiments were made on bulk, i.e. averaging over millions of copies of the same molecule.

Ensemble modeling of very small ZnO nanoparticles.

PubMed

Niederdraenk, Franziska; Seufert, Knud; Stahl, Andreas; Bhalerao-Panajkar, Rohini S; Marathe, Sonali; Kulkarni, Sulabha K; Neder, Reinhard B; Kumpf, Christian

2011-01-14

The detailed structural characterization of nanoparticles is a very important issue since it enables a precise understanding of their electronic, optical and magnetic properties. Here we introduce a new method for modeling the structure of very small particles by means of powder X-ray diffraction. Using thioglycerol-capped ZnO nanoparticles with a diameter of less than 3 nm as an example we demonstrate that our ensemble modeling method is superior to standard XRD methods like, e.g., Rietveld refinement. Besides fundamental properties (size, anisotropic shape and atomic structure) more sophisticated properties like imperfections in the lattice, a size distribution as well as strain and relaxation effects in the particles and-in particular-at their surface (surface relaxation effects) can be obtained. Ensemble properties, i.e., distributions of the particle size and other properties, can also be investigated which makes this method superior to imaging techniques like (high resolution) transmission electron microscopy or atomic force microscopy, in particular for very small nanoparticles. For the particles under study an excellent agreement of calculated and experimental X-ray diffraction patterns could be obtained with an ensemble of anisotropic polyhedral particles of three dominant sizes, wurtzite structure and a significant relaxation of Zn atoms close to the surface.

Increased imaging speed and force sensitivity for bio-applications with small cantilevers using a conventional AFM setup

PubMed Central

Leitner, Michael; Fantner, Georg E.; Fantner, Ernest J.; Ivanova, Katerina; Ivanov, Tzvetan; Rangelow, Ivo; Ebner, Andreas; Rangl, Martina; Tang, Jilin; Hinterdorfer, Peter

2012-01-01

In this study, we demonstrate the increased performance in speed and sensitivity achieved by the use of small AFM cantilevers on a standard AFM system. For this, small rectangular silicon oxynitride cantilevers were utilized to arrive at faster atomic force microscopy (AFM) imaging times and more sensitive molecular recognition force spectroscopy (MRFS) experiments. The cantilevers we used had lengths between 13 and 46 μm, a width of about 11 μm, and a thickness between 150 and 600 nm. They were coated with chromium and gold on the backside for a better laser reflection. We characterized these small cantilevers through their frequency spectrum and with electron microscopy. Due to their small size and high resonance frequency we were able to increase the imaging speed by a factor of 10 without any loss in resolution for images from several μm scansize down to the nanometer scale. This was shown on bacterial surface layers (s-layer) with tapping mode under aqueous, near physiological conditions and on nuclear membranes in contact mode in ambient environment. In addition, we showed that single molecular forces can be measured with an up to 5 times higher force sensitivity in comparison to conventional cantilevers with similar spring constants. PMID:22721963

Ultra-sensitive magnetic microscopy with an atomic magnetometer and flux guides

NASA Astrophysics Data System (ADS)

Kim, Young Jin; Savukov, Igor

Many applications in neuroscience, biomedical research, and material science require high-sensitivity, high-resolution magnetometry. In order to meet this need we recently combined a cm-size spin-exchange relaxation-free Atomic Magnetometer (AM) with a flux guide (FG) to produce ultra-sensitive FG-AM magnetic microscopy. The FG serves to transmit the target magnetic flux to the AM thus enhancing both the sensitivity and resolution to tiny magnetic objects. In this talk, we will describe existing and next generation FG-AM devices and present experimental and numerical tests of its sensitivity and resolution. We demonstrate that an optimized FG-AM has sufficient resolution and sensitivity for the detection of a small number of neurons, which would be an important milestone in neuroscience. In addition, as a demonstration of one possible application of the FG-AM device, we conducted high-resolution magnetic imaging of micron-size magnetic particles. We will show that the device can produce clear microscopic magnetic image of 10 μm-size magnetic particles.

VEDA: a web-based virtual environment for dynamic atomic force microscopy.

PubMed

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Invited Article: VEDA: A web-based virtual environment for dynamic atomic force microscopy

NASA Astrophysics Data System (ADS)

Melcher, John; Hu, Shuiqing; Raman, Arvind

2008-06-01

We describe here the theory and applications of virtual environment dynamic atomic force microscopy (VEDA), a suite of state-of-the-art simulation tools deployed on nanoHUB (www.nanohub.org) for the accurate simulation of tip motion in dynamic atomic force microscopy (dAFM) over organic and inorganic samples. VEDA takes advantage of nanoHUB's cyberinfrastructure to run high-fidelity dAFM tip dynamics computations on local clusters and the teragrid. Consequently, these tools are freely accessible and the dAFM simulations are run using standard web-based browsers without requiring additional software. A wide range of issues in dAFM ranging from optimal probe choice, probe stability, and tip-sample interaction forces, power dissipation, to material property extraction and scanning dynamics over hetereogeneous samples can be addressed.

Imaging contrast and tip-sample interaction of non-contact amplitude modulation atomic force microscopy with Q-control

NASA Astrophysics Data System (ADS)

Shi, Shuai; Guo, Dan; Luo, Jianbin

2017-10-01

Active quality factor (Q) exhibits many promising properties in dynamic atomic force microscopy. Energy dissipation and image contrasts are investigated in the non-contact amplitude modulation atomic force microscopy (AM-AFM) with an active Q-control circuit in the ambient air environment. Dissipated power and virial were calculated to compare the highly nonlinear interaction of tip-sample and image contrasts with different Q gain values. Greater free amplitudes and lower effective Q values show better contrasts for the same setpoint ratio. Active quality factor also can be employed to change tip-sample interaction force in non-contact regime. It is meaningful that non-destructive and better contrast images can be realized in non-contact AM-AFM by applying an active Q-control to the dynamic system.

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

Behavior of P85 and P188 Poloxamer Molecules: Computer Simulations Using United Atom Force Field.

DOE PAGES

Goliaei, Ardeshir; Lau, Edmond Y.; Adhikari, Upendra; ...

2016-05-27

To study the interaction between poloxamer molecules and lipid bilayers using molecular dynamics simulation technique with the united atom resolution, we augmented the GROMOS force field to include poloxamers. We validated the force field by calculating the radii of gyration of two poloxamers, P85 and P188, solvated in water and by considering the poloxamer density distributions at the air/water interface. The emphasis of our simulations was on the study of the interaction between poloxamers and lipid bilayer. At the water/lipid bilayer interface, we observed that both poloxamers studied, P85 and P188, behaved like surfactants: the hydrophilic blocks of poloxamers becamemore » adsorbed at the polar interface, while their hydrophobic block penetrated the interface into the aliphatic tail region of the lipid bilayer. We also observed that when P85 and P188 poloxamers interacted with damaged membranes that contained pores, the hydrophobic blocks of copolymers penetrated into the membrane in the vicinity of the pore and compressed the membrane. Lastly, due to this compression, water molecules were evacuated from the pore.« less

The role of cell body density in ruminant retina mechanics assessed by atomic force and Brillouin microscopy

NASA Astrophysics Data System (ADS)

Weber, Isabell P.; Yun, Seok Hyun; Scarcelli, Giuliano; Franze, Kristian

2017-12-01

Cells in the central nervous system (CNS) respond to the stiffness of their environment. CNS tissue is mechanically highly heterogeneous, thus providing motile cells with region-specific mechanical signals. While CNS mechanics has been measured with a variety of techniques, reported values of tissue stiffness vary greatly, and the morphological structures underlying spatial changes in tissue stiffness remain poorly understood. We here exploited two complementary techniques, contact-based atomic force microscopy and contact-free Brillouin microscopy, to determine the mechanical properties of ruminant retinae, which are built up by different tissue layers. As in all vertebrate retinae, layers of high cell body densities (‘nuclear layers’) alternate with layers of low cell body densities (‘plexiform layers’). Different tissue layers varied significantly in their mechanical properties, with the photoreceptor layer being the stiffest region of the retina, and the inner plexiform layer belonging to the softest regions. As both techniques yielded similar results, our measurements allowed us to calibrate the Brillouin microscopy measurements and convert the Brillouin shift into a quantitative assessment of elastic tissue stiffness with optical resolution. Similar as in the mouse spinal cord and the developing Xenopus brain, we found a strong correlation between nuclear densities and tissue stiffness. Hence, the cellular composition of retinae appears to strongly contribute to local tissue stiffness, and Brillouin microscopy shows a great potential for the application in vivo to measure the mechanical properties of transparent tissues.

In situ observation of fluoride-ion-induced hydroxyapatite collagen detachment on bone fracture surfaces by atomic force microscopy

NASA Astrophysics Data System (ADS)

Kindt, J. H.; Thurner, P. J.; Lauer, M. E.; Bosma, B. L.; Schitter, G.; Fantner, G. E.; Izumi, M.; Weaver, J. C.; Morse, D. E.; Hansma, P. K.

2007-04-01

The topography of freshly fractured bovine and human bone surfaces was determined by the use of atomic force microscopy (AFM). Fracture surfaces from both kinds of samples exhibited complex landscapes formed by hydroxyapatite mineral platelets with lateral dimensions ranging from ~90 nm × 60 nm to ~20 nm × 20 nm. Novel AFM techniques were used to study these fracture surfaces during various chemical treatments. Significant topographical changes were observed following exposure to aqueous solutions of ethylenediaminetetraacetic acid (EDTA) or highly concentrated sodium fluoride (NaF). Both treatments resulted in the apparent loss of the hydroxyapatite mineral platelets on a timescale of a few seconds. Collagen fibrils situated beneath the overlying mineral platelets were clearly exposed and could be resolved with high spatial resolution in the acquired AFM images. Time-dependent mass loss experiments revealed that the applied agents (NaF or EDTA) had very different resulting effects. Despite the fact that the two treatments exhibited nearly identical results following examination by AFM, bulk bone samples treated with EDTA exhibited a ~70% mass loss after 72 h, whereas for the NaF-treated samples, the mass loss was only of the order of ~10%. These results support those obtained from previous mechanical testing experiments, suggesting that enhanced formation of superficial fluoroapatite dramatically weakens the protein-hydroxyapatite interfaces. Additionally, we discovered that treatment with aqueous solutions of NaF resulted in the effective extraction of noncollagenous proteins from bone powder.

From Graphite to Graphene via Scanning Tunneling Microscopy

NASA Astrophysics Data System (ADS)

Qi, Dejun

The primary objective of this dissertation is to study both graphene on graphite and pristine freestanding grapheme using scanning tunneling microscopy (STM) and density functional theory (DFT) simulation technique. In the experiment part, good quality tungsten metalic tips for experiment were fabricated using our newly developed tip making setup. Then a series of measurements using a technique called electrostatic-manipulation scanning tunneling microscopy (EM-STM) of our own development were performed on a highly oriented pyrolytic graphite (HOPG) surface. The electrostatic interaction between the STM tip and the sample can be tuned to produce both reversible and irreversible large-scale movement of the graphite surface. Under this influence, atomic-resolution STM images reveal that a continuous electronic transition between two distinct patterns can be systematically controlled. DFT calculations reveal that this transition can be related to vertical displacements of the top layer of graphite relative to the bulk. Evidence for horizontal shifts in the top layer of graphite is also presented. Excellent agreement is found between experimental STM images and those simulated using DFT. In addition, the EM-STM technique was also used to controllably and reversibly pull freestanding graphene membranes up to 35 nm from their equilibrium height. Atomic-scale corrugation amplitudes 20 times larger than the STM electronic corrugation for graphene on a substrate were observed. The freestanding graphene membrane responds to a local attractive force created at the STM tip as a highly conductive yet flexible grounding plane with an elastic restoring force.

Temperature-Controlled High-Speed AFM: Real-Time Observation of Ripple Phase Transitions.

PubMed

Takahashi, Hirohide; Miyagi, Atsushi; Redondo-Morata, Lorena; Scheuring, Simon

2016-11-01

With nanometer lateral and Angstrom vertical resolution, atomic force microscopy (AFM) has contributed unique data improving the understanding of lipid bilayers. Lipid bilayers are found in several different temperature-dependent states, termed phases; the main phases are solid and fluid phases. The transition temperature between solid and fluid phases is lipid composition specific. Under certain conditions some lipid bilayers adopt a so-called ripple phase, a structure where solid and fluid phase domains alternate with constant periodicity. Because of its narrow regime of existence and heterogeneity ripple phase and its transition dynamics remain poorly understood. Here, a temperature control device to high-speed atomic force microscopy (HS-AFM) to observe dynamics of phase transition from ripple phase to fluid phase reversibly in real time is developed and integrated. Based on HS-AFM imaging, the phase transition processes from ripple phase to fluid phase and from ripple phase to metastable ripple phase to fluid phase could be reversibly, phenomenologically, and quantitatively studied. The results here show phase transition hysteresis in fast cooling and heating processes, while both melting and condensation occur at 24.15 °C in quasi-steady state situation. A second metastable ripple phase with larger periodicity is formed at the ripple phase to fluid phase transition when the buffer contains Ca 2+ . The presented temperature-controlled HS-AFM is a new unique experimental system to observe dynamics of temperature-sensitive processes at the nanoscopic level. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Line-edge quality optimization of electron beam resist for high-throughput character projection exposure utilizing atomic force microscope analysis

NASA Astrophysics Data System (ADS)

Ikeno, Rimon; Mita, Yoshio; Asada, Kunihiro

2017-04-01

High-throughput electron-beam lithography (EBL) by character projection (CP) and variable-shaped beam (VSB) methods is a promising technique for low-to-medium volume device fabrication with regularly arranged layouts, such as standard-cell logics and memory arrays. However, non-VLSI applications like MEMS and MOEMS may not fully utilize the benefits of CP method due to their wide variety of layout figures including curved and oblique edges. In addition, the stepwise shapes that appear on such irregular edges by VSB exposure often result in intolerable edge roughness, which may degrade performances of the fabricated devices. In our former study, we proposed a general EBL methodology for such applications utilizing a combination of CP and VSB methods, and demonstrated its capabilities in electron beam (EB) shot reduction and edge-quality improvement by using a leading-edge EB exposure tool, ADVANTEST F7000S-VD02, and high-resolution Hydrogen Silsesquioxane resist. Both scanning electron microscope and atomic force microscope observations were used to analyze quality of the resist edge profiles to determine the influence of the control parameters used in the exposure-data preparation process. In this study, we carried out detailed analysis of the captured edge profiles utilizing Fourier analysis, and successfully distinguish the systematic undulation by the exposed CP character profiles from random roughness components. Such capability of precise edge-roughness analysis is useful to our EBL methodology to maintain both the line-edge quality and the exposure throughput by optimizing the control parameters in the layout data conversion.

High-spatial-resolution mapping of catalytic reactions on single particles

DOE PAGES

Wu, Chung-Yeh; Wolf, William J.; Levartovsky, Yehonatan; ...

2017-01-26

We report the critical role in surface reactions and heterogeneous catalysis of metal atoms with low coordination numbers, such as found at atomic steps and surface defects, is firmly established. But despite the growing availability of tools that enable detailed in situ characterization, so far it has not been possible to document this role directly. Surface properties can be mapped with high spatial resolution, and catalytic conversion can be tracked with a clear chemical signature; however, the combination of the two, which would enable high-spatial-resolution detection of reactions on catalytic surfaces, has rarely been achieved. Single-molecule fluorescence spectroscopy has beenmore » used to image and characterize single turnover sites at catalytic surfaces, but is restricted to reactions that generate highly fluorescing product molecules. Herein the chemical conversion of N-heterocyclic carbene molecules attached to catalytic particles is mapped using synchrotron-radiation-based infrared nanospectroscopy with a spatial resolution of 25 nanometres, which enabled particle regions that differ in reactivity to be distinguished. Lastly, these observations demonstrate that, compared to the flat regions on top of the particles, the peripheries of the particles-which contain metal atoms with low coordination numbers-are more active in catalysing oxidation and reduction of chemically active groups in surface-anchored N-heterocyclic carbene molecules.« less

Characterization of an Atomic Hydrogen Source for Charge Exchange Experiments

NASA Technical Reports Server (NTRS)

Leutenegger, M. A.; Beierdorfer, P.; Betancourt-Martinez, G. L.; Brown, G. V.; Hell, N; Kelley, R. L.; Kilbourne, C. A.; Magee, E. W.; Porter, F. S.

2016-01-01

We characterized the dissociation fraction of a thermal dissociation atomic hydrogen source byinjecting the mixed atomic and molecular output of the source into an electron beam ion trapcontaining highly charged ions and recording the x-ray spectrum generated by charge exchangeusing a high-resolution x-ray calorimeter spectrometer. We exploit the fact that the charge exchangestate-selective capture cross sections are very different for atomic and molecular hydrogen incidenton the same ions, enabling a clear spectroscopic diagnostic of the neutral species.

Three phase crystallography and solute distribution analysis during residual austenite decomposition in tempered nanocrystalline bainitic steels

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

Caballero, F.G.; Yen, Hung-Wei; Australian Centre for Microscopy and Microanalysis, The University of Sydney, NSW 2006

2014-02-15

Interphase carbide precipitation due to austenite decomposition was investigated by high resolution transmission electron microscopy and atom probe tomography in tempered nanostructured bainitic steels. Results showed that cementite (θ) forms by a paraequilibrium transformation mechanism at the bainitic ferrite–austenite interface with a simultaneous three phase crystallographic orientation relationship. - Highlights: • Interphase carbide precipitation due to austenite decomposition • Tempered nanostructured bainitic steels • High resolution transmission electron microscopy and atom probe tomography • Paraequilibrium θ with three phase crystallographic orientation relationship.

Applications of atomic force microscopy to the studies of biomaterials in biomolecular systems

NASA Astrophysics Data System (ADS)

Ma, Xiang

Atomic force microscopy (AFM) is a unique tool for the studies of nanoscale structures and interactions. In this dissertation, I applied AFM to study transitions among multiple states of biomaterials in three different microscopic biomolecular systems: MukB-dependent DNA condensation, holdfast adhesion, and virus elasticity. To elucidate the mechanism of MukB-dependent DNA condensation, I have studied the conformational changes of MukB proteins as indicators for the strength of interactions between MukB, DNA and other molecular factors, such as magnesium and ParC proteins, using high-resolution AFM imaging. To determine the physical origins of holdfast adhesion, I have investigated the dynamics of adhesive force development of the holdfast, employing AFM force spectroscopy. By measuring rupture forces between the holdfast and the substrate, I showed that the holdfast adhesion is strongly time-dependent and involves transformations at multiple time scales. Understanding the mechanisms of adhesion force development of the holdfast will be critical for future engineering of holdfasts properties for various applications. Finally, I have examined the elasticity of self-assembled hepatitis B virus-like particles (HBV VLPs) and brome mosaic virus (BMV) in response to changes of pH and salinity, using AFM nanoindentation. The distributions of elasticity were mapped on a single particle level and compared between empty, RNA- and gold-filled HBV VLPs. I found that a single HBV VLP showed heterogeneous distribution of elasticity and a two-step buckling transition, suggesting a discrete property of HBV capsids. For BMV, I have showed that viruses containing different RNA molecules can be distinguished by mechanical measurements, while they are indistinguishable by morphology. I also studied the effect of pH on the elastic behaviors of three-particle BMV and R3/4 BMV. This study can yield insights into RNA presentation/release mechanisms, and could help us to design novel drug delivery vehicles.

The nature of (sub-)micrometre cometary dust particles detected with MIDAS

NASA Astrophysics Data System (ADS)

Mannel, T.; Bentley, M. S.; Torkar, K.; Jeszenszky, H.; Romstedt, J.; Schmied, R.

2015-10-01

The MIDAS Atomic Force Microscope (AFM) onboard Rosetta collects dust particles and produces three-dimensional images with nano- to micrometre resolution. To date, several tens of particles have been detected, allowing determination of their properties at the smallest scale. The key features will be presented, including the particle size, their fragile character, and their morphology. These findings will be compared with the results of other Rosetta dust experiments.

Atomic scale structure and chemistry of interfaces by Z-contrast imaging and electron energy loss spectroscopy in the stem

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

McGibbon, M.M.; Browning, N.D.; Chisholm, M.F.

The macroscopic properties of many materials are controlled by the structure and chemistry at grain boundaries. A basic understanding of the structure-property relationship requires a technique which probes both composition and chemical bonding on an atomic scale. High-resolution Z-contrast imaging in the scanning transmission electron microscope (STEM) forms an incoherent image in which changes in atomic structure and composition across an interface can be interpreted directly without the need for preconceived atomic structure models. Since the Z-contrast image is formed by electrons scattered through high angles, parallel detection electron energy loss spectroscopy (PEELS) can be used simultaneously to provide complementarymore » chemical information on an atomic scale. The fine structure in the PEEL spectra can be used to investigate the local electronic structure and the nature of the bonding across the interface. In this paper we use the complimentary techniques of high resolution Z-contrast imaging and PEELS to investigate the atomic structure and chemistry of a 25{degree} symmetric tilt boundary in a bicrystal of the electroceramic SrTiO{sub 3}.« less

Quantum crystallographic charge density of urea

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

Wall, Michael E.

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

Quantum crystallographic charge density of urea

DOE PAGES

Wall, Michael E.

2016-06-08

Standard X-ray crystallography methods use free-atom models to calculate mean unit-cell charge densities. Real molecules, however, have shared charge that is not captured accurately using free-atom models. To address this limitation, a charge density model of crystalline urea was calculated using high-level quantum theory and was refined against publicly available ultra-high-resolution experimental Bragg data, including the effects of atomic displacement parameters. The resulting quantum crystallographic model was compared with models obtained using spherical atom or multipole methods. Despite using only the same number of free parameters as the spherical atom model, the agreement of the quantum model with the datamore » is comparable to the multipole model. The static, theoretical crystalline charge density of the quantum model is distinct from the multipole model, indicating the quantum model provides substantially new information. Hydrogen thermal ellipsoids in the quantum model were very similar to those obtained using neutron crystallography, indicating that quantum crystallography can increase the accuracy of the X-ray crystallographic atomic displacement parameters. Lastly, the results demonstrate the feasibility and benefits of integrating fully periodic quantum charge density calculations into ultra-high-resolution X-ray crystallographic model building and refinement.« less

AFM Structural Characterization of Drinking Water Biofilm ...

EPA Pesticide Factsheets

Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodology will allow future in situ investigations to temporally monitor mixed culture drinking water biofilm structural changes during disinfection treatments. Due to the complexity of mixed culture drinking water biofilm, direct visual observation under in situ conditions has been challenging. In this study, atomic force microscopy (AFM) revealed the three dimensional morphology and arrangement of drinking water relevant biofilm in air and aqueous solution. Operating parameters were optimized to improve imaging of structural details for a mature biofilm in liquid. By using a soft cantilever (0.03 N/m) and slow scan rate (0.5 Hz), biofilm and individual bacterial cell’s structural topography were resolved and continuously imaged in liquid without loss of spatial resolution or sample damage. The developed methodo

High efficiency and enhanced ESD properties of UV LEDs by inserting p-GaN/p-AlGaN superlattice

NASA Astrophysics Data System (ADS)

Huang, Yong; Li, PeiXian; Yang, Zhuo; Hao, Yue; Wang, XiaoBo

2014-05-01

Significantly improved electrostatic discharge (ESD) properties of InGaN/GaN-based UV light-emitting diode (LED) with inserting p-GaN/p-AlGaN superlattice (p-SLs) layers (instead of p-AlGaN single layer) between multiple quantum wells and Mg-doped GaN layer are reported. The pass yield of the LEDs increased from 73.53% to 93.81% under negative 2000 V ESD pulses. In addition, the light output power (LOP) and efficiency droop at high injection current were also improved. The mechanism of the enhanced ESD properties was then investigated. After excluding the effect of capacitance modulation, high-resolution X-ray diffraction (XRD) and atomic force microscope (AFM) measurements demonstrated that the dominant mechanism of the enhanced ESD properties is the material quality improved by p-SLs, which indicated less leakage paths, rather than the current spreading improved by p-SLs.

Breaking the Time Barrier in Kelvin Probe Force Microscopy: Fast Free Force Reconstruction Using the G-Mode Platform

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

Collins, Liam; Ahmadi, Mahshid; Wu, Ting

The atomic force microscope (AFM) offers unparalleled insight into structure and material functionality across nanometer length scales. However, the spatial resolution afforded by the AFM tip is counterpoised by slow detection speeds compared to other common microscopy techniques (e.g. optical, scanning electron microscopy etc.). In this work, we develop an AFM imaging approach allowing ultrafast reconstruction of the tip-sample forces having ~2 orders of magnitude higher time resolution than standard detection methods. Fast free force recovery (F3R) overcomes the widely-viewed temporal bottleneck in AFM, i.e. the mechanical bandwidth of the cantilever, enabling time-resolved imaging at sub-bandwidth speeds. We demonstrate quantitativemore » recovery of electrostatic forces with ~10 µs temporal resolution, free from cantilever ring-down effects. We further apply the F3R method to Kelvin probe force microscopy (KPFM) measurements. F3R-KPFM is an open loop imaging approach (i.e. no bias feedback), allowing ultrafast surface potential measurements (e.g. < 20 µs) to be performed at regular KPFM scan speeds. F3R-KPFM is demonstrated for exploration of ion migration in organometallic halide perovskites materials and shown to allow spatio-temporal imaging of positively charged ion migration under applied electric field, as well as subsequent formation of accumulated charges at the perovskite/electrode interface. In this work we demonstrate quantitative F3R-KPFM measurements – however, we fully expect the F3R approach to be valid for all modes of non-contact AFM operation, including non-invasive probing of ultrafast electrical and magnetic dynamics.« less

Breaking the Time Barrier in Kelvin Probe Force Microscopy: Fast Free Force Reconstruction Using the G-Mode Platform

DOE PAGES

Collins, Liam; Ahmadi, Mahshid; Wu, Ting; ...

2017-08-06

The atomic force microscope (AFM) offers unparalleled insight into structure and material functionality across nanometer length scales. However, the spatial resolution afforded by the AFM tip is counterpoised by slow detection speeds compared to other common microscopy techniques (e.g. optical, scanning electron microscopy etc.). In this work, we develop an AFM imaging approach allowing ultrafast reconstruction of the tip-sample forces having ~2 orders of magnitude higher time resolution than standard detection methods. Fast free force recovery (F3R) overcomes the widely-viewed temporal bottleneck in AFM, i.e. the mechanical bandwidth of the cantilever, enabling time-resolved imaging at sub-bandwidth speeds. We demonstrate quantitativemore » recovery of electrostatic forces with ~10 µs temporal resolution, free from cantilever ring-down effects. We further apply the F3R method to Kelvin probe force microscopy (KPFM) measurements. F3R-KPFM is an open loop imaging approach (i.e. no bias feedback), allowing ultrafast surface potential measurements (e.g. < 20 µs) to be performed at regular KPFM scan speeds. F3R-KPFM is demonstrated for exploration of ion migration in organometallic halide perovskites materials and shown to allow spatio-temporal imaging of positively charged ion migration under applied electric field, as well as subsequent formation of accumulated charges at the perovskite/electrode interface. In this work we demonstrate quantitative F3R-KPFM measurements – however, we fully expect the F3R approach to be valid for all modes of non-contact AFM operation, including non-invasive probing of ultrafast electrical and magnetic dynamics.« less

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

DOE PAGES

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

2017-12-21

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

New Angles on Standard Force Fields: Toward a General Approach for Treating Atomic-Level Anisotropy

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

Van Vleet, Mary J.; Misquitta, Alston J.; Schmidt, J. R.

Nearly all standard force fields employ the “sum-of-spheres” approximation, which models intermolecular interactions purely in terms of interatomic distances. Nonetheless, atoms in molecules can have significantly nonspherical shapes, leading to interatomic interaction energies with strong orientation dependencies. Neglecting this “atomic-level anisotropy” can lead to significant errors in predicting interaction energies. Herein, we propose a simple, transferable, and computationally efficient model (MASTIFF) whereby atomic-level orientation dependence can be incorporated into ab initio intermolecular force fields. MASTIFF includes anisotropic exchange-repulsion, charge penetration, and dispersion effects, in conjunction with a standard treatment of anisotropic long-range (multipolar) electrostatics. To validate our approach, we benchmarkmore » MASTIFF against various sum-of-spheres models over a large library of intermolecular interactions between small organic molecules. MASTIFF achieves quantitative accuracy, with respect to both high-level electronic structure theory and experiment, thus showing promise as a basis for “next-generation” force field development.« less

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Energy shift and Casimir-Polder force for an atom out of thermal equilibrium near a dielectric substrate

NASA Astrophysics Data System (ADS)

Zhou, Wenting; Yu, Hongwei

2014-09-01

We study the energy shift and the Casimir-Polder force of an atom out of thermal equilibrium near the surface of a dielectric substrate. We first generalize, adopting the local source hypothesis, the formalism proposed by Dalibard, Dupont-Roc, and Cohen-Tannoudji [J. Phys. (Paris) 43, 1617 (1982), 10.1051/jphys:0198200430110161700; J. Phys. (Paris) 45, 637 (1984), 10.1051/jphys:01984004504063700], which separates the contributions of thermal fluctuations and radiation reaction to the energy shift and allows a distinct treatment of atoms in the ground and excited states, to the case out of thermal equilibrium, and then we use the generalized formalism to calculate the energy shift and the Casimir-Polder force of an isotropically polarizable neutral atom. We identify the effects of the thermal fluctuations that originate from the substrate and the environment and discuss in detail how the Casimir-Polder force out of thermal equilibrium behaves in three different distance regions in both the low-temperature limit and the high-temperature limit for both the ground-state and excited-state atoms, with special attention devoted to the distinctive features as opposed to thermal equilibrium. In particular, we recover the distinctive behavior of the atom-wall force out of thermal equilibrium at large distances in the low-temperature limit recently found in a different theoretical framework, and furthermore we give a concrete region where this behavior holds.

A combined averaging and frequency mixing approach for force identification in weakly nonlinear high-Q oscillators: Atomic force microscope

NASA Astrophysics Data System (ADS)

Sah, Si Mohamed; Forchheimer, Daniel; Borgani, Riccardo; Haviland, David

2018-02-01

We present a polynomial force reconstruction of the tip-sample interaction force in Atomic Force Microscopy. The method uses analytical expressions for the slow-time amplitude and phase evolution, obtained from time-averaging over the rapidly oscillating part of the cantilever dynamics. The slow-time behavior can be easily obtained in either the numerical simulations or the experiment in which a high-Q resonator is perturbed by a weak nonlinearity and a periodic driving force. A direct fit of the theoretical expressions to the simulated and experimental data gives the best-fit parameters for the force model. The method combines and complements previous works (Platz et al., 2013; Forchheimer et al., 2012 [2]) and it allows for computationally more efficient parameter mapping with AFM. Results for the simulated asymmetric piecewise linear force and VdW-DMT force models are compared with the reconstructed polynomial force and show a good agreement. It is also shown that the analytical amplitude and phase modulation equations fit well with the experimental data.

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

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

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

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

NASA Astrophysics Data System (ADS)

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-04-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ~10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level.

DNA origami-based shape IDs for single-molecule nanomechanical genotyping

PubMed Central

Zhang, Honglu; Chao, Jie; Pan, Dun; Liu, Huajie; Qiang, Yu; Liu, Ke; Cui, Chengjun; Chen, Jianhua; Huang, Qing; Hu, Jun; Wang, Lianhui; Huang, Wei; Shi, Yongyong; Fan, Chunhai

2017-01-01

Variations on DNA sequences profoundly affect how we develop diseases and respond to pathogens and drugs. Atomic force microscopy (AFM) provides a nanomechanical imaging approach for genetic analysis with nanometre resolution. However, unlike fluorescence imaging that has wavelength-specific fluorophores, the lack of shape-specific labels largely hampers widespread applications of AFM imaging. Here we report the development of a set of differentially shaped, highly hybridizable self-assembled DNA origami nanostructures serving as shape IDs for magnified nanomechanical imaging of single-nucleotide polymorphisms. Using these origami shape IDs, we directly genotype single molecules of human genomic DNA with an ultrahigh resolution of ∼10 nm and the multiplexing ability. Further, we determine three types of disease-associated, long-range haplotypes in samples from the Han Chinese population. Single-molecule analysis allows robust haplotyping even for samples with low labelling efficiency. We expect this generic shape ID-based nanomechanical approach to hold great potential in genetic analysis at the single-molecule level. PMID:28382928

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

Conduction at domain walls in oxide multiferroics

NASA Astrophysics Data System (ADS)

Seidel, J.; Martin, L. W.; He, Q.; Zhan, Q.; Chu, Y.-H.; Rother, A.; Hawkridge, M. E.; Maksymovych, P.; Yu, P.; Gajek, M.; Balke, N.; Kalinin, S. V.; Gemming, S.; Wang, F.; Catalan, G.; Scott, J. F.; Spaldin, N. A.; Orenstein, J.; Ramesh, R.

2009-03-01

Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO3. The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

Conduction at domain walls in oxide multiferroics.

PubMed

Seidel, J; Martin, L W; He, Q; Zhan, Q; Chu, Y-H; Rother, A; Hawkridge, M E; Maksymovych, P; Yu, P; Gajek, M; Balke, N; Kalinin, S V; Gemming, S; Wang, F; Catalan, G; Scott, J F; Spaldin, N A; Orenstein, J; Ramesh, R

2009-03-01

Domain walls may play an important role in future electronic devices, given their small size as well as the fact that their location can be controlled. Here, we report the observation of room-temperature electronic conductivity at ferroelectric domain walls in the insulating multiferroic BiFeO(3). The origin and nature of the observed conductivity are probed using a combination of conductive atomic force microscopy, high-resolution transmission electron microscopy and first-principles density functional computations. Our analyses indicate that the conductivity correlates with structurally driven changes in both the electrostatic potential and the local electronic structure, which shows a decrease in the bandgap at the domain wall. Additionally, we demonstrate the potential for device applications of such conducting nanoscale features.

The Micro Imaging and Dust Analysis System - New Possibilities for Space Sciences

NASA Astrophysics Data System (ADS)

Schmied, R.; Torkar, K..; Jeszenszky, H.; Romstedt, J.; Mannel, T.; Bentley, M. S.

2015-10-01

The Rosetta mission addresses a range of fundamental questions in Solar System and cometary science and the MIDAS instrument on-board the orbiter is one of the dust analysis systems. While GIADA analyses the dust flux and spatial distribution as a function of time and space and COSIMA investigates the elemental composition of cometary grains, MIDAS is a unique high resolution Atomic Force Microscope (AFM) combined with a dust collection and handling system designed to reveal the three-dimensional topographical structure of nanoand micrometer sized dust particles [1]. In this work we concentrate on the instrumental functionality and limitations coming from the constcution and operation dealing with an AFM fabricated nearly 20 years ago and operating in a harsh environment.

DHS Internship Summary-Crystal Assembly at Different Length Scales

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

Mishchenko, L

2009-08-06

I was part of a project in which in situ atomic force microscopy (AFM) was used to monitor growth and dissolution of atomic and colloidal crystals. At both length scales, the chemical environment of the system greatly altered crystal growth and dissolution. Calcium phosphate was used as a model system for atomic crystals. A dissolution-reprecipitation reaction was observed in this first system, involving the conversion of brushite (DCPD) to octacalcium phosphate (OCP). In the second system, polymeric colloidal crystals were dissolved in an ionic solvent, revealing the underlying structure of the crystal. The dissolved crystal was then regrown through anmore » evaporative step method. Recently, we have also found that colloids can be reversibly deposited in situ onto an ITO (indium tin oxide) substrate via an electrochemistry setup. The overall goal of this project was to develop an understanding of the mechanisms that control crystallization and order, so that these might be controlled during material synthesis. Controlled assembly of materials over a range of length scales from molecules to nanoparticles to colloids is critical for designing new materials. In particular, developing materials for sensor applications with tailorable properties and long range order is important. In this work, we examine two of these length scales: small molecule crystallization of calcium phosphate (whose crystal phases include DCPD, OCP, and HAP) and colloidal crystallization of Poly(methyl methacrylate) beads. Atomic Force Microscopy is ideal for this line of work because it allows for the possibility of observing non-conducting samples in fluid during growth with high resolution ({approx} 10 nm). In fact, during atomic crystal growth one can observe changes in atomic steps, and with colloidal crystals, one can monitor the individual building blocks of the crystal. Colloids and atoms crystallize under the influence of different forces acting at different length scales as seen in Table 1. In particular, molecular crystals, which are typically dominated by ionic and covalent bonding, are an order of magnitude more strongly bonded than colloidal crystals. In molecular crystals, ordering is driven by the interaction potentials between molecules. By contrast, colloidal assembly is a competition between the repulsive electrostatic forces that prevent aggregation in solution (due to surface charge), and short-range van der Waals and entropic forces that leads to ordering. Understanding atomic crystallization is fundamentally important for fabrication of tailorable crystalline materials, for example for biological or chemical sensors. The transformation of brushite to OCP not only serves as a model system for atomic crystal growth (applicable to many other crystal growth processes), but is also important in bone cements. Colloidal crystals have unique optical properties which respond to chemical and mechanical stimuli, making them very important for sensing applications. The mechanism of colloidal crystal assembly is thus fundamentally important. Our in situ dissolution and regrowth experiments are one good method of analyzing how these crystals pack under different conditions and how defect sites are formed and filled. In these experiments, a silica additive was used to strengthen the colloidal crystal during initial assembly (ex situ) and to increase domain size and long range order. Reversible electrodeposition of colloids onto a conductive substrate (ITO in our case) is another system which can further our knowledge of colloidal assembly. This experiment holds promise of allowing in situ observation of colloidal crystal growth and the influence of certain additives on crystal order. The ultimate goal would be to achieve long range order in these crystals by changing the surface charge or the growth environment.« less

Oxidized crystalline (3 × 1)-O surface phases of InAs and InSb studied by high-resolution photoelectron spectroscopy

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

Tuominen, M., E-mail: tmleir@utu.fi, E-mail: pekka.laukkanen@utu.fi; Lång, J.; Dahl, J.

2015-01-05

The pre-oxidized crystalline (3×1)-O structure of InAs(100) has been recently found to significantly improve insulator/InAs junctions for devices, but the atomic structure and formation of this useful oxide layer are not well understood. We report high-resolution photoelectron spectroscopy analysis of (3×1)-O on InAs(100) and InSb(100). The findings reveal that the atomic structure of (3×1)-O consists of In atoms with unexpected negative (between −0.64 and −0.47 eV) and only moderate positive (In{sub 2}O type) core-level shifts; highly oxidized group-V sites; and four different oxygen sites. These fingerprint shifts are compared to those of previously studied oxides of III-V to elucidate oxidation processes.

Novel combination of near-field s-SNOM microscopy with peak-force tapping for nano-chemical and nano-mechanical material characterization with sub-20 nm spatial resolution

NASA Astrophysics Data System (ADS)

Wagner, Martin; Carneiro, Karina; Habelitz, Stefan; Mueller, Thomas; BNS Team; UCSF Team

Heterogeneity in material systems requires methods for nanoscale chemical identification. Scattering scanning near-field microscopy (s-SNOM) is chemically sensitive in the infrared fingerprint region while providing down to 10 nm spatial resolution. This technique detects material specific tip-scattering in an atomic force microscope. Here, we present the first combination of s-SNOM with peak-force tapping (PFT), a valuable AFM technique that allows precise force control between tip and sample down to 10s of pN. The latter is essential for imaging fragile samples, but allows also quantitative extraction of nano-mechanical properties, e.g. the modulus. PFT can further be complemented by KPFM or conductive AFM for nano-electrical mapping, allowing access to nanoscale optical, mechanical and electrical information in a single instrument. We will address several questions ranging from graphene plasmonics to material distributions in polymers. We highlight a biological application where dental amelogenin protein was studied via s-SNOM to learn about its self-assembly into nanoribbons. At the same time PFT allows to track crystallization to distinguish protein from apatite crystals for which amelogenin is supposed to act as a template.

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

p{sup +}-doping analysis of laser fired contacts for silicon solar cells by Kelvin probe force microscopy

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

Ebser, J., E-mail: Jan.Ebser@uni-konstanz.de; Sommer, D.; Fritz, S.

Local rear contacts for silicon passivated emitter and rear contact solar cells can be established by point-wise treating an Al layer with laser radiation and thereby establishing an electrical contact between Al and Si bulk through the dielectric passivation layer. In this laser fired contacts (LFC) process, Al can establish a few μm thick p{sup +}-doped Si region below the metal/Si interface and forms in this way a local back surface field which reduces carrier recombination at the contacts. In this work, the applicability of Kelvin probe force microscopy (KPFM) to the investigation of LFCs considering the p{sup +}-doping distributionmore » is demonstrated. The method is based on atomic force microscopy and enables the evaluation of the lateral 2D Fermi-level characteristics at sub-micrometer resolution. The distribution of the electrical potential and therefore the local hole concentration in and around the laser fired region can be measured. KPFM is performed on mechanically polished cross-sections of p{sup +}-doped Si regions formed by the LFC process. The sample preparation is of great importance because the KPFM signal is very surface sensitive. Furthermore, the measurement is responsive to sample illumination and the height of the applied voltage between tip and sample. With other measurement techniques like micro-Raman spectroscopy, electrochemical capacitance-voltage, and energy dispersive X-ray analysis, a high local hole concentration in the range of 10{sup 19 }cm{sup −3} is demonstrated in the laser fired region. This provides, in combination with the high spatial resolution of the doping distribution measured by KPFM, a promising approach for microscopic understanding and further optimization of the LFC process.« less

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.

EDITORIAL: Three decades of scanning tunnelling microscopy that changed the course of surface science Three decades of scanning tunnelling microscopy that changed the course of surface science

NASA Astrophysics Data System (ADS)

Ramachandra Rao, M. S.; Margaritondo, Giorgio

2011-11-01

Three decades ago, with a tiny tip of platinum, the scientific world saw the real space imaging of single atoms with unprecedented spatial resolution. This signalled the birth of one of the most versatile surface probes, based on the physics of quantum mechanical tunnelling: the scanning tunnelling microscope (STM). Invented in 1981 by Gerd Binnig and Heinrich Rohrer of IBM, Zurich, it led to their award of the 1986 Nobel Prize. Atoms, once speculated to be abstract entities used by theoreticians for mere calculations, can be seen to exist for real with the nano-eye of an STM tip that also gives real-space images of molecules and adsorbed complexes on surfaces. From a very fundamental perspective, the STM changed the course of surface science and engineering. STM also emerged as a powerful tool to study various fundamental phenomena relevant to the properties of surfaces in technological applications such as tribology, medical implants, catalysis, sensors and biology—besides elucidating the importance of local bonding geometries and defects, non-periodic structures and the co-existence of nano-scale phases. Atom-level probing, once considered a dream, has seen the light with the evolution of STM. An important off-shoot of STM was the atomic force microscope (AFM) for surface mapping of insulating samples. Then followed the development of a flurry of techniques under the general name of scanning probe microscopy (SPM). These techniques (STM, AFM, MFM, PFM etc) designed for atomic-scale-resolution imaging and spectroscopy, have led to brand new developments in surface analysis. All of these novel methods enabled researchers in recent years to image and analyse complex surfaces on microscopic and nanoscopic scales. All of them utilize a small probe for sensing the surface. The invention of AFM by Gerd Binnig, Calvin Quate and Christopher Gerber opened up new opportunities for characterization of a variety of materials, and various industrial applications could be envisaged. AFM observations of thin-film surfaces give us a picture of surface topography and morphology and any visible defects. The growing importance of ultra-thin films for magnetic recording in hard disk drive systems requires an in-depth understanding of the fundamental mechanisms occurring during growth. This special issue of Journal of Physics D: Applied Physics covers all of the different aspects of SPM that illustrate the achievements of this methodology: nanoscale imaging and mapping (Chiang, and Douillard and Charra), piezoresponse force microscopy (Soergel) and STM engineering (Okuyama and Hamada, and Huang et al). Chiang takes the reader on a journey along the STM imaging of atoms and molecules on surfaces. Jesse and Kalinin explore the band excitations that occur during the corresponding processes. Jia et al propose STM and molecular beam epitaxy as a winning experimental combination at the interface of science and technology. Douillard and Charra describe the high-resolution mapping of plasmonic modes using photoemission and scanning tunnelling microscopy. Cricenti et al demonstrate the importance of SPM in material science and biology. Wiebe et al have probed atomic scale magnetism, revealed by spin polarized scanning tunnelling microscopy. In addition, Simon et al present Fourier transform scanning tunnelling spectroscopy and the possibility to obtain constant energy maps and band dispersion using local measurements. Lackinger and Heckl give a perspective of the use of STM to study covalent intermolecular coupling reactions on surfaces. Okuyama and Hamada investigated hydrogen bond imaging and engineering with STM. Soergel describes the study of substrate-dependent self-assembled CuPc molecules using piezo force microscope (PFM). We are very grateful to the authors and reviewers for the papers in this special issue of Journal of Physics D: Applied Physics. Their contributions have provided a comprehensive picture of the evolution, status and potential of scanning probe microscopy, conveying to the readers the full excitement of this forefront domain of physics.

Non-contact quantification of laser micro-impulse in water by atomic force microscopy and its application for biomechanics

NASA Astrophysics Data System (ADS)

Hosokawa, Yoichiroh

2011-12-01

We developed a local force measurement system of a femtosecond laser-induced impulsive force, which is due to shock and stress waves generated by focusing an intense femtosecond laser into water with a highly numerical aperture objective lens. In this system, the force localized in micron-sized region was detected by bending movement of a cantilever of atomic force microscope (AFM). Here we calculated the bending movement of the AFM cantilever when the femtosecond laser is focused in water at the vicinity of the cantilever and the impulsive force is loaded on the cantilever. From the result, a method to estimate the total of the impulsive force at the laser focal point was suggested and applied to estimate intercellular adhesion strength.

Characterization of atomic-layer MoS2 synthesized using a hot filament chemical vapor deposition method

NASA Astrophysics Data System (ADS)

Ying-Zi, Peng; Yang, Song; Xiao-Qiang, Xie; Yuan, Li; Zheng-Hong, Qian; Ru, Bai

2016-05-01

Atomic-layer MoS2 ultrathin films are synthesized using a hot filament chemical vapor deposition method. A combination of atomic force microscopy (AFM), x-ray diffraction (XRD), high-resolution transition electron microscopy (HRTEM), photoluminescence (PL), and x-ray photoelectron spectroscopy (XPS) characterization methods is applied to investigate the crystal structures, valence states, and compositions of the ultrathin film areas. The nucleation particles show irregular morphology, while for a larger size somewhere, the films are granular and the grains have a triangle shape. The films grow in a preferred orientation (002). The HRTEM images present the graphene-like structure of stacked layers with low density of stacking fault, and the interlayer distance of plane is measured to be about 0.63 nm. It shows a clear quasi-honeycomb-like structure and 6-fold coordination symmetry. Room-temperature PL spectra for the atomic layer MoS2 under the condition of right and left circular light show that for both cases, the A1 and B1 direct excitonic transitions can be observed. In the meantime, valley polarization resolved PL spectra are obtained. XPS measurements provide high-purity samples aside from some contaminations from the air, and confirm the presence of pure MoS2. The stoichiometric mole ratio of S/Mo is about 2.0-2.1, suggesting that sulfur is abundant rather than deficient in the atomic layer MoS2 under our experimental conditions. Project supported by the Natural Science Foundation of Zhejiang Province, China (Grant Nos. LY16F040003 and LY16A040007) and the National Natural Science Foundation of China (Grant Nos. 51401069 and 11574067).

Atomic Force Microscopy Studies of Functional and Dysfunctional Pulmonary Surfactant Films. I. Micro- and Nanostructures of Functional Pulmonary Surfactant Films and the Effect of SP-A

PubMed Central

Zuo, Yi Y.; Keating, Eleonora; Zhao, Lin; Tadayyon, Seyed M.; Veldhuizen, Ruud A. W.; Petersen, Nils O.; Possmayer, Fred

2008-01-01

Monolayers of a functional pulmonary surfactant (PS) can reach very low surface tensions well below their equilibrium value. The mechanism by which PS monolayers reach such low surface tensions and maintain film stability remains unknown. As shown previously by fluorescence microscopy, phospholipid phase transition and separation seem to be important for the normal biophysical properties of PS. This work studied phospholipid phase transitions and separations in monolayers of bovine lipid extract surfactant using atomic force microscopy. Atomic force microscopy showed phospholipid phase separation on film compression and a monolayer-to-multilayer transition at surface pressure 40–50 mN/m. The tilted-condensed phase consisted of domains not only on the micrometer scale, as detected previously by fluorescence microscopy, but also on the nanometer scale, which is below the resolution limits of conventional optical methods. The nanodomains were embedded uniformly within the liquid-expanded phase. On compression, the microdomains broke up into nanodomains, thereby appearing to contribute to tilted-condensed and liquid-expanded phase remixing. Addition of surfactant protein A altered primarily the nanodomains and promoted the formation of multilayers. We conclude that the nanodomains play a predominant role in affecting the biophysical properties of PS monolayers and the monolayer-to-multilayer transition. PMID:18212010

Impact of Short-Range Forces on Defect Production from High-Energy Collisions

DOE PAGES

Stoller, R. E.; Tamm, A.; Béland, L. K.; ...

2016-04-25

Primary radiation damage formation in solid materials typically involves collisions between atoms that have up to a few hundred keV of kinetic energy. The distance between two colliding atoms can approach 0.05 nm during these collisions. At such small atomic separations, force fields fitted to equilibrium properties tend to significantly underestimate the potential energy of the colliding dimer. To enable molecular dynamics simulations of high-energy collisions, it is common practice to use a screened Coulomb force field to describe the interactions and to smoothly join this to the equilibrium force field at a suitable interatomic spacing. But, there is nomore » accepted standard method for choosing the parameters used in the joining process, and our results prove that defect production is sensitive to how the force fields are linked. A new procedure is presented that involves the use of ab initio calculations to determine the magnitude and spatial dependence of the pair interactions at intermediate distances, along with systematic criteria for choosing the joining parameters. Results are presented for the case of nickel, which demonstrate the use and validity of the procedure.« less

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.

Atomistic simulations of materials: Methods for accurate potentials and realistic time scales

NASA Astrophysics Data System (ADS)

Tiwary, Pratyush

This thesis deals with achieving more realistic atomistic simulations of materials, by developing accurate and robust force-fields, and algorithms for practical time scales. I develop a formalism for generating interatomic potentials for simulating atomistic phenomena occurring at energy scales ranging from lattice vibrations to crystal defects to high-energy collisions. This is done by fitting against an extensive database of ab initio results, as well as to experimental measurements for mixed oxide nuclear fuels. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We expect these to be reliable potentials for carrying out damage simulations (and molecular dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies. A hybrid stochastic and deterministic algorithm is proposed that while maintaining fully atomistic resolution, allows one to achieve milliseconds and longer time scales for several thousands of atoms. The method exploits the rare event nature of the dynamics like other such methods, but goes beyond them by (i) not having to pick a scheme for biasing the energy landscape, (ii) providing control on the accuracy of the boosted time scale, (iii) not assuming any harmonic transition state theory (HTST), and (iv) not having to identify collective coordinates or interesting degrees of freedom. The method is validated by calculating diffusion constants for vacancy-mediated diffusion in iron metal at low temperatures, and comparing against brute-force high temperature molecular dynamics. We also calculate diffusion constants for vacancy diffusion in tantalum metal, where we compare against low-temperature HTST as well. The robustness of the algorithm with respect to the only free parameter it involves is ascertained. The method is then applied to perform tensile tests on gold nanopillars on strain rates as low as 100/s, bringing out the perils of high strain-rate molecular dynamics calculations. We also calculate temperature and stress dependence of activation free energy for surface nucleation of dislocations in pristine gold nanopillars under realistic loads. While maintaining fully atomistic resolution, we reach the fraction-of-a-second time scale regime. It is found that the activation free energy depends significantly and nonlinearly on the driving force (stress or strain) and temperature, leading to very high activation entropies for surface dislocation nucleation.

Reorganization energy upon charging a single molecule on an insulator measured by atomic force microscopy

NASA Astrophysics Data System (ADS)

Fatayer, Shadi; Schuler, Bruno; Steurer, Wolfram; Scivetti, Ivan; Repp, Jascha; Gross, Leo; Persson, Mats; Meyer, Gerhard

2018-05-01

Intermolecular single-electron transfer on electrically insulating films is a key process in molecular electronics1-4 and an important example of a redox reaction5,6. Electron-transfer rates in molecular systems depend on a few fundamental parameters, such as interadsorbate distance, temperature and, in particular, the Marcus reorganization energy7. This crucial parameter is the energy gain that results from the distortion of the equilibrium nuclear geometry in the molecule and its environment on charging8,9. The substrate, especially ionic films10, can have an important influence on the reorganization energy11,12. Reorganization energies are measured in electrochemistry13 as well as with optical14,15 and photoemission spectroscopies16,17, but not at the single-molecule limit and nor on insulating surfaces. Atomic force microscopy (AFM), with single-charge sensitivity18-22, atomic-scale spatial resolution20 and operable on insulating films, overcomes these challenges. Here, we investigate redox reactions of single naphthalocyanine (NPc) molecules on multilayered NaCl films. Employing the atomic force microscope as an ultralow current meter allows us to measure the differential conductance related to transitions between two charge states in both directions. Thereby, the reorganization energy of NPc on NaCl is determined as (0.8 ± 0.2) eV, and density functional theory (DFT) calculations provide the atomistic picture of the nuclear relaxations on charging. Our approach presents a route to perform tunnelling spectroscopy of single adsorbates on insulating substrates and provides insight into single-electron intermolecular transport.

Thickness-controlled direct growth of nanographene and nanographite film on non-catalytic substrates

NASA Astrophysics Data System (ADS)

Du, Lei; Yang, Liu; Hu, Zhiting; Zhang, Jiazhen; Huang, Chunlai; Sun, Liaoxin; Wang, Lin; Wei, Dacheng; Chen, Gang; Lu, Wei

2018-05-01

Metal-catalyzed chemical vapor deposition (CVD) has been broadly employed for large-scale production of high-quality graphene. However, a following transfer process to targeted substrates is needed, which is incompatible with current silicon technology. We here report a new CVD approach to form nanographene and nanographite films with accurate thickness control directly on non-catalytic substrates such as silicon dioxide and quartz at 800 °C. The growth time is as short as a few seconds. The approach includes using 9-bis(diethylamino)silylanthracene as the carbon source and an atomic layer deposition (ALD) controlling system. The structure of the formed nanographene and nanographite films were characterized using atomic force microscopy, high resolution transmission electron microscopy, Raman scattering, and x-ray photoemission spectroscopy. The nanographite film exhibits a transmittance higher than 80% at 550 nm and a sheet electrical resistance of 2000 ohms per square at room temperature. A negative temperature-dependence of the resistance of the nanographite film is also observed. Moreover, the thickness of the films can be precisely controlled via the deposition cycles using an ALD system, which promotes great application potential for optoelectronic and thermoelectronic-devices.

Thickness-controlled direct growth of nanographene and nanographite film on non-catalytic substrates.

PubMed

Du, Lei; Yang, Liu; Hu, Zhiting; Zhang, Jiazhen; Huang, Chunlai; Sun, Liaoxin; Wang, Lin; Wei, Dacheng; Chen, Gang; Lu, Wei

2018-05-25

Metal-catalyzed chemical vapor deposition (CVD) has been broadly employed for large-scale production of high-quality graphene. However, a following transfer process to targeted substrates is needed, which is incompatible with current silicon technology. We here report a new CVD approach to form nanographene and nanographite films with accurate thickness control directly on non-catalytic substrates such as silicon dioxide and quartz at 800 °C. The growth time is as short as a few seconds. The approach includes using 9-bis(diethylamino)silylanthracene as the carbon source and an atomic layer deposition (ALD) controlling system. The structure of the formed nanographene and nanographite films were characterized using atomic force microscopy, high resolution transmission electron microscopy, Raman scattering, and x-ray photoemission spectroscopy. The nanographite film exhibits a transmittance higher than 80% at 550 nm and a sheet electrical resistance of 2000 ohms per square at room temperature. A negative temperature-dependence of the resistance of the nanographite film is also observed. Moreover, the thickness of the films can be precisely controlled via the deposition cycles using an ALD system, which promotes great application potential for optoelectronic and thermoelectronic-devices.

A Fifth Force: Generalized through Superconductors

NASA Technical Reports Server (NTRS)

Robertson, Glen A.

1999-01-01

The connection between the Biefield-Brown Effect, the recent repeat of the 1902 Trouton-Noble (TN) experiments, and the gravity shielding experiments was explored. This connection is visualized through high capacitive electron concentrations. From this connection, a theory is proposed that connects mass energy to gravity and a fifth force. The theory called the Gravi-Atomic Energy theory presents two new terms: Gravi-atomic energy and quantum vacuum pressure (QVP). Gravi-atomic energy is defined as the radiated mass energy, which acts on vacuum energy to create a QVP about a mass, resulting in gravity and the fifth force. The QVP emission from a superconductor was discussed followed by the description of a test for QVP from a superconductor using a Cavendish balance.

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.

Structural and mechanical heterogeneity of the erythrocyte membrane reveals hallmarks of membrane stability.

PubMed

Picas, Laura; Rico, Félix; Deforet, Maxime; Scheuring, Simon

2013-02-26

The erythrocyte membrane, a metabolically regulated active structure that comprises lipid molecules, junctional complexes, and the spectrin network, enables the cell to undergo large passive deformations when passing through the microvascular system. Here we use atomic force microscopy (AFM) imaging and quantitative mechanical mapping at nanometer resolution to correlate structure and mechanics of key components of the erythrocyte membrane, crucial for cell integrity and function. Our data reveal structural and mechanical heterogeneity modulated by the metabolic state at unprecedented nanometer resolution. ATP-depletion, reducing skeletal junction phosphorylation in RBC cells, leads to membrane stiffening. Analysis of ghosts and shear-force opened erythrocytes show that, in the absence of cytosolic kinases, spectrin phosphorylation results in membrane stiffening at the extracellular face and a reduced junction remodeling in response to loading forces. Topography and mechanical mapping of single components at the cytoplasmic face reveal that, surprisingly, spectrin phosphorylation by ATP softens individual filaments. Our findings suggest that, besides the mechanical signature of each component, the RBC membrane mechanics is regulated by the metabolic state and the assembly of its structural elements.

Observation of Switchable Photoresponse of a Monolayer WSe2-MoS2 Lateral Heterostructure via Photocurrent Spectral Atomic Force Microscopic Imaging.

PubMed

Son, Youngwoo; Li, Ming-Yang; Cheng, Chia-Chin; Wei, Kung-Hwa; Liu, Pingwei; Wang, Qing Hua; Li, Lain-Jong; Strano, Michael S

2016-06-08

In the pursuit of two-dimensional (2D) materials beyond graphene, enormous advances have been made in exploring the exciting and useful properties of transition metal dichalcogenides (TMDCs), such as a permanent band gap in the visible range and the transition from indirect to direct band gap due to 2D quantum confinement, and their potential for a wide range of device applications. In particular, recent success in the synthesis of seamless monolayer lateral heterostructures of different TMDCs via chemical vapor deposition methods has provided an effective solution to producing an in-plane p-n junction, which is a critical component in electronic and optoelectronic device applications. However, spatial variation of the electronic and optoelectonic properties of the synthesized heterojunction crystals throughout the homogeneous as well as the lateral junction region and the charge carrier transport behavior at their nanoscale junctions with metals remain unaddressed. In this work, we use photocurrent spectral atomic force microscopy to image the current and photocurrent generated between a biased PtIr tip and a monolayer WSe2-MoS2 lateral heterostructure. Current measurements in the dark in both forward and reverse bias reveal an opposite characteristic diode behavior for WSe2 and MoS2, owing to the formation of a Schottky barrier of dissimilar properties. Notably, by changing the polarity and magnitude of the tip voltage applied, pixels that show the photoresponse of the heterostructure are observed to be selectively switched on and off, allowing for the realization of a hyper-resolution array of the switchable photodiode pixels. This experimental approach has significant implications toward the development of novel optoelectronic technologies for regioselective photodetection and imaging at nanoscale resolutions. Comparative 2D Fourier analysis of physical height and current images shows high spatial frequency variations in substrate/MoS2 (or WSe2) contact that exceed the frequencies imposed by the underlying substrates. These results should provide important insights in the design and understanding of electronic and optoelectronic devices based on quantum confined atomically thin 2D lateral heterostructures.

Characterization of an atomic hydrogen source for charge exchange experiments

DOE PAGES

Leutenegger, M. A.; Beiersdorfer, P.; Betancourt-Martinez, G. L.; ...

2016-07-02

Here, we characterized the dissociation fraction of a thermal dissociation atomic hydrogen source by injecting the mixed atomic and molecular output of the source into an electron beam ion trap containing highly charged ions and recording the x-ray spectrum generated by charge exchange using a high-resolution x-ray calorimeter spectrometer. We exploit the fact that the charge exchange state-selective capture cross sections are very different for atomic and molecular hydrogen incident on the same ions, enabling a clear spectroscopic diagnostic of the neutral species.

The Ehrenfest force field: Topology and consequences for the definition of an atom in a molecule.

PubMed

Martín Pendás, A; Hernández-Trujillo, J

2012-10-07

The Ehrenfest force is the force acting on the electrons in a molecule due to the presence of the other electrons and the nuclei. There is an associated force field in three-dimensional space that is obtained by the integration of the corresponding Hermitian quantum force operator over the spin coordinates of all of the electrons and the space coordinates of all of the electrons but one. This paper analyzes the topology induced by this vector field and its consequences for the definition of molecular structure and of an atom in a molecule. Its phase portrait reveals: that the nuclei are attractors of the Ehrenfest force, the existence of separatrices yielding a dense partitioning of three-dimensional space into disjoint regions, and field lines connecting the attractors through these separatrices. From the numerical point of view, when the Ehrenfest force field is obtained as minus the divergence of the kinetic stress tensor, the induced topology was found to be highly sensitive to choice of gaussian basis sets at long range. Even the use of large split valence and highly uncontracted basis sets can yield spurious critical points that may alter the number of attraction basins. Nevertheless, at short distances from the nuclei, in general, the partitioning of three-dimensional space with the Ehrenfest force field coincides with that induced by the gradient field of the electron density. However, exceptions are found in molecules where the electron density yields results in conflict with chemical intuition. In these cases, the molecular graphs of the Ehrenfest force field reveal the expected atomic connectivities. This discrepancy between the definition of an atom in a molecule between the two vector fields casts some doubts on the physical meaning of the integration of Ehrenfest forces over the basins of the electron density.

Roles of curli, cellulose and BapA in Salmonella biofilm morphology studied by atomic force microscopy

PubMed Central

Jonas, Kristina; Tomenius, Henrik; Kader, Abdul; Normark, Staffan; Römling, Ute; Belova, Lyubov M; Melefors, Öjar

2007-01-01

Background Curli, cellulose and the cell surface protein BapA are matrix components in Salmonella biofilms. In this study we have investigated the roles of these components for the morphology of bacteria grown as colonies on agar plates and within a biofilm on submerged mica surfaces by applying atomic force microscopy (AFM) and light microscopy. Results AFM imaging was performed on colonies of Salmonella Typhimurium grown on agar plates for 24 h and on biofilms grown for 4, 8, 16 or 24 h on mica slides submerged in standing cultures. Our data show that in the wild type curli were visible as extracellular material on and between the cells and as fimbrial structures at the edges of biofilms grown for 16 h and 24 h. In contrast to the wild type, which formed a three-dimensional biofilm within 24 h, a curli mutant and a strain mutated in the global regulator CsgD were severely impaired in biofilm formation. A mutant in cellulose production retained some capability to form cell aggregates, but not a confluent biofilm. Extracellular matrix was observed in this mutant to almost the same extent as in the wild type. Overexpression of CsgD led to a much thicker and a more rapidly growing biofilm. Disruption of BapA altered neither colony and biofilm morphology nor the ability to form a biofilm within 24 h on the submerged surfaces. Besides curli, the expression of flagella and pili as well as changes in cell shape and cell size could be monitored in the growing biofilms. Conclusion Our work demonstrates that atomic force microscopy can efficiently be used as a tool to monitor the morphology of bacteria grown as colonies on agar plates or within biofilms formed in a liquid at high resolution. PMID:17650335

Imaging viscoelastic properties of live cells by AFM: power-law rheology on the nanoscale.

PubMed

Hecht, Fabian M; Rheinlaender, Johannes; Schierbaum, Nicolas; Goldmann, Wolfgang H; Fabry, Ben; Schäffer, Tilman E

2015-06-21

We developed force clamp force mapping (FCFM), an atomic force microscopy (AFM) technique for measuring the viscoelastic creep behavior of live cells with sub-micrometer spatial resolution. FCFM combines force-distance curves with an added force clamp phase during tip-sample contact. From the creep behavior measured during the force clamp phase, quantitative viscoelastic sample properties are extracted. We validate FCFM on soft polyacrylamide gels. We find that the creep behavior of living cells conforms to a power-law material model. By recording short (50-60 ms) force clamp measurements in rapid succession, we generate, for the first time, two-dimensional maps of power-law exponent and modulus scaling parameter. Although these maps reveal large spatial variations of both parameters across the cell surface, we obtain robust mean values from the several hundreds of measurements performed on each cell. Measurements on mouse embryonic fibroblasts show that the mean power-law exponents and the mean modulus scaling parameters differ greatly among individual cells, but both parameters are highly correlated: stiffer cells consistently show a smaller power-law exponent. This correlation allows us to distinguish between wild-type cells and cells that lack vinculin, a dominant protein of the focal adhesion complex, even though the mean values of viscoelastic properties between wildtype and knockout cells did not differ significantly. Therefore, FCFM spatially resolves viscoelastic sample properties and can uncover subtle mechanical signatures of proteins in living cells.

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.

Interplay between Switching Driven by the Tunneling Current and Atomic Force of a Bistable Four-Atom Si Quantum Dot.

PubMed

Yamazaki, Shiro; Maeda, Keisuke; Sugimoto, Yoshiaki; Abe, Masayuki; Zobač, Vladimír; Pou, Pablo; Rodrigo, Lucia; Mutombo, Pingo; Pérez, Ruben; Jelínek, Pavel; Morita, Seizo

2015-07-08

We assemble bistable silicon quantum dots consisting of four buckled atoms (Si4-QD) using atom manipulation. We demonstrate two competing atom switching mechanisms, downward switching induced by tunneling current of scanning tunneling microscopy (STM) and opposite upward switching induced by atomic force of atomic force microscopy (AFM). Simultaneous application of competing current and force allows us to tune switching direction continuously. Assembly of the few-atom Si-QDs and controlling their states using versatile combined AFM/STM will contribute to further miniaturization of nanodevices.

Determining the Molecular Growth Mechanisms of Protein Crystal faces by Atomic Force Microscopy

NASA Technical Reports Server (NTRS)

Li, Huayu; Nadarajah, Arunan; Pusey, Marc L.

1998-01-01

A high resolution atomic force microscopy (AFM) study had shown that the molecular packing on the tetragonal lysozyme (110) face corresponded to only one of two possible packing arrangements, suggesting that growth layers on this face were of bimolecular height (Li et al., 1998). Theoretical analyses of the packing had also indicated that growth of this face should proceed by the addition of growth units of at least tetramer size corresponding to the 43 helices in the crystal. In this study an AFM linescan technique was devised to measure the dimensions of individual growth units on protein crystal faces. The growth process of tetragonal lysozyme crystals was slowed down by employing very low supersaturations. As a result images of individual growth events on the (110) face were observed, shown by jump discontinuities in the growth step in the linescan images. The growth unit dimension in the scanned direction was obtained by suitably averaging these images. A large number of scans in two directions on the (110) face were performed and the distribution of lysozyme aggregate sizes were obtained. A variety of growth units, all of which were 43 helical lysozyme aggregates, were shown to participate in the growth process with a 43 tetramer being the minimum observed size. This technique represents a new application for AFM allowing time resolved studies of molecular process to be carried out.

Measuring the Autocorrelation Function of Nanoscale Three-Dimensional Density Distribution in Individual Cells Using Scanning Transmission Electron Microscopy, Atomic Force Microscopy, and a New Deconvolution Algorithm.

PubMed

Li, Yue; Zhang, Di; Capoglu, Ilker; Hujsak, Karl A; Damania, Dhwanil; Cherkezyan, Lusik; Roth, Eric; Bleher, Reiner; Wu, Jinsong S; Subramanian, Hariharan; Dravid, Vinayak P; Backman, Vadim

2017-06-01

Essentially all biological processes are highly dependent on the nanoscale architecture of the cellular components where these processes take place. Statistical measures, such as the autocorrelation function (ACF) of the three-dimensional (3D) mass-density distribution, are widely used to characterize cellular nanostructure. However, conventional methods of reconstruction of the deterministic 3D mass-density distribution, from which these statistical measures can be calculated, have been inadequate for thick biological structures, such as whole cells, due to the conflict between the need for nanoscale resolution and its inverse relationship with thickness after conventional tomographic reconstruction. To tackle the problem, we have developed a robust method to calculate the ACF of the 3D mass-density distribution without tomography. Assuming the biological mass distribution is isotropic, our method allows for accurate statistical characterization of the 3D mass-density distribution by ACF with two data sets: a single projection image by scanning transmission electron microscopy and a thickness map by atomic force microscopy. Here we present validation of the ACF reconstruction algorithm, as well as its application to calculate the statistics of the 3D distribution of mass-density in a region containing the nucleus of an entire mammalian cell. This method may provide important insights into architectural changes that accompany cellular processes.

Transmembrane myosin chitin synthase involved in mollusc shell formation produced in Dictyostelium is active

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

Schoenitzer, Veronika; Universitaet Regensburg, Biochemie I, Universitaetsstrasse 31, D-93053 Regensburg; Eichner, Norbert

Highlights: Black-Right-Pointing-Pointer Dictyostelium produces the 264 kDa myosin chitin synthase of bivalve mollusc Atrina. Black-Right-Pointing-Pointer Chitin synthase activity releases chitin, partly associated with the cell surface. Black-Right-Pointing-Pointer Membrane extracts of transgenic slime molds produce radiolabeled chitin in vitro. Black-Right-Pointing-Pointer Chitin producing Dictyostelium cells can be characterized by atomic force microscopy. Black-Right-Pointing-Pointer This model system enables us to study initial processes of chitin biomineralization. -- Abstract: Several mollusc shells contain chitin, which is formed by a transmembrane myosin motor enzyme. This protein could be involved in sensing mechanical and structural changes of the forming, mineralizing extracellular matrix. Here we report themore » heterologous expression of the transmembrane myosin chitin synthase Ar-CS1 of the bivalve mollusc Atrina rigida (2286 amino acid residues, M.W. 264 kDa/monomer) in Dictyostelium discoideum, a model organism for myosin motor proteins. Confocal laser scanning immunofluorescence microscopy (CLSM), chitin binding GFP detection of chitin on cells and released to the cell culture medium, and a radiochemical activity assay of membrane extracts revealed expression and enzymatic activity of the mollusc chitin synthase in transgenic slime mold cells. First high-resolution atomic force microscopy (AFM) images of Ar-CS1 transformed cellulose synthase deficient D. discoideumdcsA{sup -} cell lines are shown.« less