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1.  The Influence of Doping with Transition Metal Ions on the Structure and Magnetic Properties of Zinc Oxide Thin Films 
The Scientific World Journal  2014;2014:265969.
Zn1−xNixO (x = 0.03 ÷ 0.10) and Zn1−xFexO (x = 0.03 ÷ 0.15) thin films were synthesized by sol-gel method. The structure and the surface morphology of zinc oxide thin films doped with transition metal (TM) ions have been investigated by X-ray diffraction (XRD) and atomic force microscopy (AFM). The magnetic studies were done using vibrating sample magnetometer (VSM) at room temperature. Experimental results revealed that the substitution of Ni ions in ZnO wurtzite lattice for the contents x = 0.03 ÷ 0.10 (Ni2+) leads to weak ferromagnetism of thin films. For Zn1−xFexO with x = 0.03 ÷ 0.05, the Fe3+ ions are magnetic coupling by superexchange interaction via oxygen ions in wurtzite structure. For x = 0.10 ÷ 0.15 (Fe3+) one can observe the increasing of secondary phase of ZnFe2O4 spinel. The Zn0.9Fe0.1O film shows a superparamagnetic behavior due to small crystallite sizes and the net spin magnetic moments arisen from the interaction between the iron ions through an oxygen ion in the spinel structure.
doi:10.1155/2014/265969
PMCID: PMC3934575  PMID: 24683324
2.  Effect of the tip state during qPlus noncontact atomic force microscopy of Si(100) at 5 K: Probing the probe 
Summary
Background: Noncontact atomic force microscopy (NC-AFM) now regularly produces atomic-resolution images on a wide range of surfaces, and has demonstrated the capability for atomic manipulation solely using chemical forces. Nonetheless, the role of the tip apex in both imaging and manipulation remains poorly understood and is an active area of research both experimentally and theoretically. Recent work employing specially functionalised tips has provided additional impetus to elucidating the role of the tip apex in the observed contrast.
Results: We present an analysis of the influence of the tip apex during imaging of the Si(100) substrate in ultra-high vacuum (UHV) at 5 K using a qPlus sensor for noncontact atomic force microscopy (NC-AFM). Data demonstrating stable imaging with a range of tip apexes, each with a characteristic imaging signature, have been acquired. By imaging at close to zero applied bias we eliminate the influence of tunnel current on the force between tip and surface, and also the tunnel-current-induced excitation of silicon dimers, which is a key issue in scanning probe studies of Si(100).
Conclusion: A wide range of novel imaging mechanisms are demonstrated on the Si(100) surface, which can only be explained by variations in the precise structural configuration at the apex of the tip. Such images provide a valuable resource for theoreticians working on the development of realistic tip structures for NC-AFM simulations. Force spectroscopy measurements show that the tip termination critically affects both the short-range force and dissipated energy.
doi:10.3762/bjnano.3.3
PMCID: PMC3304327  PMID: 22428093
force spectroscopy; image contrast; noncontact AFM; qPlus; Si(001); Si(100); tip (apex) structure
3.  An NC-AFM and KPFM study of the adsorption of a triphenylene derivative on KBr(001) 
Summary
The adsorption on KBr(001) of a specially designed molecule, consisting of a flat aromatic triphenylene core equipped with six flexible propyl chains ending with polar cyano groups, is investigated by using atomic force microscopy in the noncontact mode (NC-AFM) coupled to Kelvin probe force microscopy (KPFM) in ultrahigh vacuum at room temperature. Two types of monolayers are identified, one in which the molecules lie flat on the surface (MLh) and another in which they stand approximately upright (MLv). The Kelvin voltage on these two structures is negatively shifted relative to that of the clean KBr surface, revealing the presence of surface dipoles with a component pointing along the normal to the surface. These findings are interpreted with the help of numerical simulations. It is shown that the surface–molecule interaction is dominated by the electrostatic interaction of the cyano groups with the K+ ions of the substrate. The molecule is strongly adsorbed in the MLh structure with an adsorption energy of 1.8 eV. In the MLv layer, the molecules form π-stacked rows aligned along the polar directions of the KBr surface. In these rows, the molecules are less strongly bound to the substrate, but the structure is stabilized by the strong intermolecular interaction due to π-stacking.
doi:10.3762/bjnano.3.25
PMCID: PMC3323911  PMID: 22496995
atomic force microscopy; insulating surfaces; Kelvin force probe microscopy; molecular adsorption
4.  (2n × 1) Reconstructions of TiO2(011) Revealed by Noncontact Atomic Force Microscopy and Scanning Tunneling Microscopy 
We have used noncontact atomic force microscopy (NC-AFM) and scanning tunneling microscopy (STM) to study the rutile TiO2(011) surface. A series of (2n × 1) reconstructions were observed, including two types of (4 × 1) reconstruction. High-resolution NC-AFM and STM images indicate that the (4 × 1)-α phase has the same structural elements as the more widely reported (2 × 1) reconstruction. An array of analogous higher-order (2n × 1) reconstructions were also observed where n = 3–5. On the other hand, the (4 × 1)-β reconstruction seems to be a unique structure without higher-order analogues. A model is proposed for this structure that is also based on the (2 × 1) reconstruction but with additional microfacets of {111} character.
doi:10.1021/jp507422s
PMCID: PMC4191060  PMID: 25309642
5.  Unique mechanical properties of nanostructured transparent MgAl2O4 ceramics 
Nanoscale Research Letters  2013;8(1):261.
Nanoindentation tests were performed on nanostructured transparent magnesium aluminate (MgAl2O4) ceramics to determine their mechanical properties. These tests were carried out on samples at different applied loads ranging from 300 to 9,000 μN. The elastic recovery for nanostructured transparent MgAl2O4 ceramics at different applied loads was derived from the force-depth data. The results reveal a remarkable enhancement in plastic deformation as the applied load increases from 300 to 9,000 μN. After the nanoindetation tests, scanning probe microscope images show no cracking in nanostructured transparent MgAl2O4 ceramics, which confirms the absence of any cracks and fractures around the indentation. Interestingly, the flow of the material along the edges of indent impressions is clearly presented, which is attributed to the dislocation introduced. High-resolution transmission electron microscopy observation indicates the presence of dislocations along the grain boundary, suggesting that the generation and interaction of dislocations play an important role in the plastic deformation of nanostructured transparent ceramics. Finally, the experimentally measured hardness and Young’s modulus, as derived from the load–displacement data, are as high as 31.7 and 314 GPa, respectively.
doi:10.1186/1556-276X-8-261
PMCID: PMC3672023  PMID: 23724845
Nanostructured transparent ceramic; Nanoindentation; Hardness; Elastic modulus
6.  Morphological and Structural Changes on Human Dental Enamel After Er:YAG Laser Irradiation: AFM, SEM, and EDS Evaluation 
Photomedicine and Laser Surgery  2011;29(7):493-500.
Abstract
Objective:
The purpose of this study was to evaluate, using atomic force microscopy (AFM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS), the morphological and structural changes of the enamel after irradiation with the Er:YAG laser.
Background data:
A previous study showed that subablative Er:YAG laser irradiation produced undesirable morphological changes on the enamel surface, such as craters and cracks; however, the enamel acid resistance was not increased.
Methods:
Fifty-two samples of human enamel were divided into four groups (n = 13): Group I was the control (no laser irradiation), whereas Groups II, III, and IV were irradiated with the Er:YAG 100 mJ (12.7 J/cm2), 100 mJ (7.5 J/cm2), and 150 mJ (11 J/cm2), respectively, at 10 Hz with water spray. The morphological changes were observed by AFM and SEM. The weight percentages (wt%) of calcium (Ca), phosphorus (P), oxygen (O) and chlorine (Cl) were determined in the resultant craters and their periphery using EDS. Kruskal–Wallis and Mann–Whitney U tests were performed (p ≤ 0.05) to distinguish significant differences among the groups.
Results:
The AFM images showed cracks with depths between 250 nm and 750 nm for Groups II and IV, respectively, and the widths of these cracks were 5.37 μm and 2.58 μm. The interior of the cracks showed a rough surface. The SEM micrographs revealed morphological changes. Significant differences were detected in Ca, P, and Cl in the crater and its periphery.
Conclusions:
AFM observations showed triangular-shaped cracks, whereas craters and cracks were evident by SEM in all irradiated samples. It was not possible to establish a characteristic chemical pattern in the craters.
doi:10.1089/pho.2010.2925
PMCID: PMC3128321  PMID: 21417912
7.  Local Electronic and Chemical Structure of Oligo-acetylene Derivatives Formed Through Radical Cyclizations at a Surface 
Nano Letters  2014;14(5):2251-2255.
Semiconducting π-conjugated polymers have attracted significant interest for applications in light-emitting diodes, field-effect transistors, photovoltaics, and nonlinear optoelectronic devices. Central to the success of these functional organic materials is the facile tunability of their electrical, optical, and magnetic properties along with easy processability and the outstanding mechanical properties associated with polymeric structures. In this work we characterize the chemical and electronic structure of individual chains of oligo-(E)-1,1′-bi(indenylidene), a polyacetylene derivative that we have obtained through cooperative C1–C5 thermal enediyne cyclizations on Au(111) surfaces followed by a step-growth polymerization of the (E)-1,1′-bi(indenylidene) diradical intermediates. We have determined the combined structural and electronic properties of this class of oligomers by characterizing the atomically precise chemical structure of individual monomer building blocks and oligomer chains (via noncontact atomic force microscopy (nc-AFM)), as well as by imaging their localized and extended molecular orbitals (via scanning tunneling microscopy and spectroscopy (STM/STS)). Our combined structural and electronic measurements reveal that the energy associated with extended π-conjugated states in these oligomers is significantly lower than the energy of the corresponding localized monomer orbitals, consistent with theoretical predictions.
doi:10.1021/nl403791q
PMCID: PMC4022646  PMID: 24387223
Conducting polymers; C1−C5 thermal enediyne cyclization; radical step-growth polymerization; noncontact atomic force microscopy (nc-AFM); scanning tunneling microscopy (STM); density functional theory (DFT)
8.  Isolation and Biophysical Study of Fruit Cuticles 
The cuticle, a hydrophobic protective layer on the aerial parts of terrestrial plants, functions as a versatile defensive barrier to various biotic and abiotic stresses and also regulates water flow from the external environment.1 A biopolyester (cutin) and long-chain fatty acids (waxes) form the principal structural framework of the cuticle; the functional integrity of the cuticular layer depends on the outer 'epicuticular' layer as well as the blend consisting of the cutin biopolymer and 'intracuticular' waxes.2 Herein, we describe a comprehensive protocol to extract waxes exhaustively from commercial tomato (Solanum lycopersicum) fruit cuticles or to remove epicuticular and intracuticular waxes sequentially and selectively from the cuticle composite. The method of Jetter and Schäffer (2001) was adapted for the stepwise extraction of epicuticular and intracuticular waxes from the fruit cuticle.3,4 To monitor the process of sequential wax removal, solid-state cross-polarization magic-angle-spinning (CPMAS) 13C NMR spectroscopy was used in parallel with atomic force microscopy (AFM), providing molecular-level structural profiles of the bulk materials complemented by information on the microscale topography and roughness of the cuticular surfaces. To evaluate the cross-linking capabilities of dewaxed cuticles from cultivated wild-type and single-gene mutant tomato fruits, MAS 13C NMR was used to compare the relative proportions of oxygenated aliphatic (CHO and CH2O) chemical moieties.
Exhaustive dewaxing by stepwise Soxhlet extraction with a panel of solvents of varying polarity provides an effective means to isolate wax moieties based on the hydrophobic characteristics of their aliphatic and aromatic constituents, while preserving the chemical structure of the cutin biopolyester. The mechanical extraction of epicuticular waxes and selective removal of intracuticular waxes, when monitored by complementary physical methodologies, provides an unprecedented means to investigate the cuticle assembly: this approach reveals the supramolecular organization and structural integration of various types of waxes, the architecture of the cutin-wax matrix, and the chemical composition of each constituent. In addition, solid-state 13C NMR reveals differences in the relative numbers of CHO and CH2O chemical moieties for wild-type and mutant red ripe tomato fruits. The NMR techniques offer exceptional tools to fingerprint the molecular structure of cuticular materials that are insoluble, amorphous, and chemically heterogeneous. As a noninvasive surface-selective imaging technique, AFM furnishes an effective and direct means to probe the structural organization of the cuticular assembly on the nm-μm length scale.
doi:10.3791/3529
PMCID: PMC3460570  PMID: 22490984
Biophysics;  Issue 61;  Plant Biology;  Tomato;  cuticle;  dewaxing;  cutin;  solid-state NMR;  contact mode AFM
9.  Atomic structure and composition of the yttria-stabilized zirconia (111) surface 
Surface Science  2013;612(100):69-76.
Anomalous and nonanomalous surface X-ray diffraction is used to investigate the atomic structure and composition of the yttria-stabilized zirconia (YSZ)(111) surface. By simulation it is shown that the method is sensitive to Y surface segregation, but that the data must contain high enough Fourier components in order to distinguish between different models describing Y/Zr disorder. Data were collected at room temperature after two different annealing procedures. First by applying oxidative conditions at 10− 5 mbar O2 and 700 K to the as-received samples, where we find that about 30% of the surface is covered by oxide islands, which are depleted in Y as compared with the bulk. After annealing in ultrahigh vacuum at 1270 K the island morphology of the surface remains unchanged but the islands and the first near surface layer get significantly enriched in Y. Furthermore, the observation of Zr and oxygen vacancies implies the formation of a porous surface region. Our findings have important implications for the use of YSZ as solid oxide fuel cell electrode material where yttrium atoms and zirconium vacancies can act as reactive centers, as well as for the use of YSZ as substrate material for thin film and nanoparticle growth where defects control the nucleation process.
Highlights
► Anomalous surface X-ray diffraction was used to investigate the YSZ(111) surface. ► The surface morphology exhibits a high number of small islands. ► After annealing in UHV the morphology persists and Y-segregation is observed. ► After annealing in UHV zirconium and oxygen vacancies are observed. ► The uncovered site occupancies and vacancies are important as reactive centers.
doi:10.1016/j.susc.2013.02.014
PMCID: PMC3626230  PMID: 23734067
Oxide surfaces; Surface structure; Solid-oxide fuel cell; SOFC; Cubic YSZ; Yttria stabilized zirconia
10.  Cage-Forming Compounds in the Ba–Rh–Ge System: From Thermoelectrics to Superconductivity 
Inorganic Chemistry  2013;52(2):931-943.
Phase relations and solidification behavior in the Ge-rich part of the phase diagram have been determined in two isothermal sections at 700 and 750 °C and in a liquidus projection. A reaction scheme has been derived in the form of a Schulz–Scheil diagram. Phase equilibria are characterized by three ternary compounds: τ1-BaRhGe3 (BaNiSn3-type) and two novel phases, τ2-Ba3Rh4Ge16 and τ3-Ba5Rh15Ge36-x, both forming in peritectic reactions. The crystal structures of τ2 and τ3 have been elucidated from single-crystal X-ray intensity data and were found to crystallize in unique structure types: Ba3Rh4Ge16 is tetragonal (I4/mmm, a = 0.65643(2) nm, c = 2.20367(8) nm, and RF = 0.0273), whereas atoms in Ba5Rh15Ge36–x (x = 0.25) arrange in a large orthorhombic unit cell (Fddd, a = 0.84570(2) nm, b = 1.4725(2) nm, c = 6.644(3) nm, and RF = 0.034). The body-centered-cubic superstructure of binary Ba8Ge43□3 was observed to extend at 800 °C to Ba8Rh0.6Ge43□2.4, while the clathrate type I phase, κI-Ba8RhxGe46–x–y□y, reveals a maximum solubility of x = 1.2 Rh atoms in the structure at a vacancy level of y = 2.0. The cubic lattice parameter increases with increasing Rh content. Clathrate I decomposes eutectoidally at 740 °C: κI ⇔ (Ge) + κIX + τ2. A very small solubility range is observed at 750 °C for the clathrate IX, κIX-Ba6RhxGe25–x (x ∼ 0.16). Density functional theory calculations have been performed to derive the enthalpies of formation and densities of states for various compositions Ba8RhxGe46–x (x = 0–6). The physical properties have been investigated for the phases κI, τ1, τ2, and τ3, documenting a change from thermoelectric (κI) to superconducting behavior (τ2). The electrical resistivity of κI-Ba8Rh1.2Ge42.8□2.0 increases almost linearly with the temperature from room temperature to 730 K, and the Seebeck coefficient is negative throughout the same temperature range. τ1-BaRhGe3 has a typical metallic electrical resistivity. A superconducting transition at TC = 6.5 K was observed for τ2-Ba3Rh4Ge16, whereas τ3-Ba5Rh15Ge35.75 showed metallic-like behavior down to 4 K.
Phase equilibria in the Ba−Rh−Ge system are characterized by three ternary cage compounds: τ 1-BaRhGe3 (BaNiSn3-type) and two novel phases with unique structures, τ 2-Ba3Rh4Ge16 and τ 3-Ba5Rh15Ge36−x, besides κI-Ba8RhxGe46−x−y□y (x ≤ 1.2 and y ≥ 2.0). Density functional theory calculations for the enthalpies of formation and density of states for various compositions Ba8RhxGe46−x (x = 0−6) demonstrate a strong stabilizing influence of Ge/Rh substitution. The physical properties have been investigated for κI, τ 1, τ 2, and τ 3, documenting a change from n-type thermoelectric (κI) to superconducting behavior (τ 2; TC = 6.5 K).
doi:10.1021/ic302139r
PMCID: PMC3557931  PMID: 23286379
11.  Effect of DNA Hairpin Loops on the Twist of Planar DNA Origami Tiles 
Langmuir  2011;28(4):1959-1965.
The development of scaffolded DNA origami, a technique in which a long single-stranded viral genome is folded into arbitrary shapes by hundreds of short synthetic oligonucleotides, represents an important milestone in DNA nanotechnology. Recent findings have revealed that two-dimensional (2D)DNA origami structures based on the original design parameters adopt a global twist with respect to the tile plane, which may be because the conformation of the constituent DNA (10.67 bp/turn) deviates from the natural B-type helical twist (10.4 bp/turn). Here we aim to characterize the effects of DNA hairpin loops on the overall curvature of the tile and explore their ability to control, and ultimately eliminate any unwanted curvature. A series of dumbbell-shaped DNA loops were selectively displayed on the surface of DNA origami tiles with the expectation that repulsive interactions among the neighboring dumbbell loops and between the loops and the DNA origami tile would influence the structural features of the underlying tiles. A systematic, atomic force microscopy (AFM) study of how the number and position of the DNA loops influenced the global twist of the structure was performed, and several structural models to explain the results were proposed. The observations unambiguously revealed that the first generation of rectangular shaped origami tiles adopt a conformation in which the upper right (corner 2) and bottom left (corner 4) corners bend upward out of the plane, causing linear superstructures attached by these corners to form twisted ribbons. Our experimental observations are consistent with the twist model predicted by the DNA mechanical property simulation software CanDo. Through the systematic design and organization of various numbers of dumbbell loops on both surfaces of the tile, a nearly planar rectangular origami tile was achieved.
doi:10.1021/la2037873
PMCID: PMC3319873  PMID: 22126326
12.  A measurement of the hysteresis loop in force-spectroscopy curves using a tuning-fork atomic force microscope 
Summary
Measurements of the frequency shift versus distance in noncontact atomic force microscopy (NC-AFM) allow measurements of the force gradient between the oscillating tip and a surface (force-spectroscopy measurements). When nonconservative forces act between the tip apex and the surface the oscillation amplitude is damped. The dissipation is caused by bistabilities in the potential energy surface of the tip–sample system, and the process can be understood as a hysteresis of forces between approach and retraction of the tip. In this paper, we present the direct measurement of the whole hysteresis loop in force-spectroscopy curves at 77 K on the PTCDA/Ag/Si(111) √3 × √3 surface by means of a tuning-fork-based NC-AFM with an oscillation amplitude smaller than the distance range of the hysteresis loop. The hysteresis effect is caused by the making and breaking of a bond between PTCDA molecules on the surface and a PTCDA molecule at the tip. The corresponding energy loss was determined to be 0.57 eV by evaluation of the force–distance curves upon approach and retraction. Furthermore, a second dissipation process was identified through the damping of the oscillation while the molecule on the tip is in contact with the surface. This dissipation process occurs mainly during the retraction of the tip. It reaches a maximum value of about 0.22 eV/cycle.
doi:10.3762/bjnano.3.23
PMCID: PMC3323909  PMID: 22496993
atomic force microscopy; energy dissipation; force spectroscopy; hysteresis loop; PTCDA/Ag/Si(111) √3 × √3
13.  Electronic structure and bandgap of γ-Al2O3 compound using mBJ exchange potential 
Nanoscale Research Letters  2012;7(1):488.
γ-Al2O3 is a porous metal oxide and described as a defective spinel with some cationic vacancies. In this work, we calculate the electronic density of states and band structure for the bulk of this material. The calculations are performed within the density functional theory using the full potential augmented plan waves plus local orbital method, as embodied in the WIEN2k code. We show that the modified Becke-Johnson exchange potential, as a semi-local method, can predict the bandgap in better agreement with the experiment even compared to the accurate but much more expensive green function method. Moreover, our electronic structure analysis indicates that the character of the valence band maximum mainly originates from the p orbital of those oxygen atoms that are close to the vacancy. The charge density results show that the polarization of the oxygen electron cloud is directed toward aluminum cations, which cause Al and O atoms to be tightly connected by a strong dipole bond.
doi:10.1186/1556-276X-7-488
PMCID: PMC3503660  PMID: 22937842
Bandgap; mBJ exchange potential; Density functional theory
14.  Atomic structure of titania nanosheet with vacancies 
Scientific Reports  2013;3:2801.
Titania nanosheets are two-dimensional single crystallites of titanium oxide with a thickness of one titanium or two oxygen atoms, and they show attractive material properties, such as photocatalytic reactions. Since a titania (Ti0.87O2) nanosheet is synthesized by the delamination of a parent layered K0.8Ti1.73Li0.27O4 crystal using a soft chemical procedure, substantial Ti vacancies are expected to be included and affect the material properties. The atomic arrangement of a titania nanosheet with vacancies has not been revealed owing to the difficulties of direct observation. Here, we have directly visualized the atomic arrangement and Ti vacancies of a titania nanosheet using advanced lower-voltage transmission electron microscopy (TEM). Analyses of the results of first-principles calculations and TEM image simulations for various Ti vacancy structure models indicate that two particular oxygen atoms around each Ti vacancy are desorbed, suggesting the sites where atomic reduction first occurs.
doi:10.1038/srep02801
PMCID: PMC3786289  PMID: 24077611
15.  Atomic Structures of Silicene Layers Grown on Ag(111): Scanning Tunneling Microscopy and Noncontact Atomic Force Microscopy Observations 
Scientific Reports  2013;3:2399.
Silicene, the considered equivalent of graphene for silicon, has been recently synthesized on Ag(111) surfaces. Following the tremendous success of graphene, silicene might further widen the horizon of two-dimensional materials with new allotropes artificially created. Due to stronger spin-orbit coupling, lower group symmetry and different chemistry compared to graphene, silicene presents many new interesting features. Here, we focus on very important aspects of silicene layers on Ag(111): First, we present scanning tunneling microscopy (STM) and non-contact Atomic Force Microscopy (nc-AFM) observations of the major structures of single layer and bi-layer silicene in epitaxy with Ag(111). For the (3 × 3) reconstructed first silicene layer nc-AFM represents the same lateral arrangement of silicene atoms as STM and therefore provides a timely experimental confirmation of the current picture of the atomic silicene structure. Furthermore, both nc-AFM and STM give a unifying interpretation of the second layer (√3 × √3)R ± 30° structure. Finally, we give support to the conjectured possible existence of less stable, ~2% stressed, (√7 × √7)R ± 19.1° rotated silicene domains in the first layer.
doi:10.1038/srep02399
PMCID: PMC3739010  PMID: 23928998
16.  Structural Studies of the Giant Mimivirus 
PLoS Biology  2009;7(4):e1000092.
Mimivirus is the largest known virus whose genome and physical size are comparable to some small bacteria, blurring the boundary between a virus and a cell. Structural studies of Mimivirus have been difficult because of its size and long surface fibers. Here we report the use of enzymatic digestions to remove the surface fibers of Mimivirus in order to expose the surface of the viral capsid. Cryo-electron microscopy (cryoEM) and atomic force microscopy were able to show that the 20 icosahedral faces of Mimivirus capsids have hexagonal arrays of depressions. Each depression is surrounded by six trimeric capsomers that are similar in structure to those in many other large, icosahedral double-stranded DNA viruses. Whereas in most viruses these capsomers are hexagonally close-packed with the same orientation in each face, in Mimivirus there are vacancies at the systematic depressions with neighboring capsomers differing in orientation by 60°. The previously observed starfish-shaped feature is well-resolved and found to be on each virus particle and is associated with a special pentameric vertex. The arms of the starfish fit into the gaps between the five faces surrounding the unique vertex, acting as a seal. Furthermore, the enveloped nucleocapsid is accurately positioned and oriented within the capsid with a concave surface facing the unique vertex. Thus, the starfish-shaped feature and the organization of the nucleocapsid might regulate the delivery of the genome to the host. The structure of Mimivirus, as well as the various fiber components observed in the virus, suggests that the Mimivirus genome includes genes derived from both eukaryotic and prokaryotic organisms. The three-dimensional cryoEM reconstruction reported here is of a virus with a volume that is one order of magnitude larger than any previously reported molecular assembly studied at a resolution of equal to or better than 65 Å.
Author Summary
Mimiviruses are larger than any other known virus, yet despite their size, the capsid has been shown to be a regular icosahedron. Using cryo-electron microscopy and atomic force microscopy, we show that the icosahedral symmetry is only approximate, in part because one of the 5-fold vertices has a unique “starfish-shaped” feature and because a better three-dimensional reconstruction was obtained by assuming only 5-fold symmetry. Contrary to expectations, the arrangement of the capsomers on the Mimivirus surface is not as that in many other large icosahedral dsDNA viruses. Instead, the faces of Mimivirus have systematic vacant sites that are surrounded by six capsomers with alternative orientations which differ by about 60°.
The structure of Mimivirus was examined with cryo-electron microscopy and atomic force microscopy. The quasi-icosahedral virus has a unique vertex decorated by a starfish-like feature. The capsomers form hexagonal arrays on each face.
doi:10.1371/journal.pbio.1000092
PMCID: PMC2671561  PMID: 19402750
17.  Polarity compensation in ultra-thin films of complex oxides: The case of a perovskite nickelate 
Scientific Reports  2014;4:6819.
We address the fundamental issue of growth of perovskite ultra-thin films under the condition of a strong polar mismatch at the heterointerface exemplified by the growth of a correlated metal LaNiO3 on the band insulator SrTiO3 along the pseudo cubic [111] direction. While in general the metallic LaNiO3 film can effectively screen this polarity mismatch, we establish that in the ultra-thin limit, films are insulating in nature and require additional chemical and structural reconstruction to compensate for such mismatch. A combination of in-situ reflection high-energy electron diffraction recorded during the growth, X-ray diffraction, and synchrotron based resonant X-ray spectroscopy reveal the formation of a chemical phase La2Ni2O5 (Ni2+) for a few unit-cell thick films. First-principles layer-resolved calculations of the potential energy across the nominal LaNiO3/SrTiO3 interface confirm that the oxygen vacancies can efficiently reduce the electric field at the interface.
doi:10.1038/srep06819
PMCID: PMC4212234  PMID: 25352069
18.  Dynamic Nanoparticles Assemblies 
Accounts of chemical research  2012;45(11):1916-1926.
CONSPECTUS
Importance
Although nanoparticle (NP) assemblies are at the beginning of their development, their unique geometrical shapes and media-responsive optical, electronic and magnetic properties have attracted significant interest. Nanoscale assembly bridges multiple sizes of materials: individual nanoparticles, discrete molecule-like or virus-like nanoscale agglomerates, microscale devices, and macroscale materials. The capacity to self-assemble can greatly facilitate the integration of nanotechnology with other technologies and, in particular, with microscale fabrication. In this Account, we describe developments in the emerging field of dynamic NP assemblies, which are spontaneously formed superstructures containing more than two inorganic nanoscale particles that display ability to change their geometrical, physical, chemical, and other attributes. In many ways, dynamic assemblies can represent a bottleneck in the ‘bottom-up’ fabrication of NP-based devices because they can produce a much greater variety of assemblies, but they also provide a convenient tool for variation of geometries and dimensions of nanoparticle assemblies.
Classification
Superstructures of NPs (and those held together by similar intrinsic forces) are classified into two groups: Class 1 where media and external fields can alter shape, conformation, and order of stable superstructures with a nearly constant number same. The future development of successful dynamic assemblies requires understanding the equilibrium in dynamic NP systems. The dynamic nature of Class 1 assemblies is associated with the equilibrium between different conformations of a superstructure and is comparable to the isomerization in classical chemistry. Class 2 assemblies involve the formation and/or breakage of linkages between the NPs, which is analogous to the classical chemical equilibrium for the formation of a molecule from atoms. Finer classification of NP assemblies in accord with established conventions in the field may include different size dimensionalities: discrete assemblies (artificial molecules), one-dimensional (spaced chains) and two-dimensional (sheets) and three-dimensional (superlattices, twisted structures) assemblies. Notably, these dimensional attributes must be regarded as primarily topological in nature because all of these superstructures can acquire complex three-dimensional shapes.
Preparation
We discuss three primary strategies used to prepare NP superstructures: (1) anisotropy-based assemblies utilizing either intrinsic force field anisotropy around NPs or external anisotropy associated with templates and/or applied fields; (2) assembly methods utilizing uniform NPs with isotropic interactions; and (3) methods based on mutual recognition of biomolecules, such as DNA and antigen-antibody interactions.
Applications
We consider optical, electronic, and magnetic properties of dynamic superstructures, focusing primarily on multiparticle effects in NP superstructures as represented by surface plasmon resonance, NP-NP charge transport, and multibody magnetization. Unique properties of NP superstructures are being applied to biosensing, drug delivery, and nanoelectronics. For both Class 1 and Class 2 dynamic assemblies, biosensing is the most dominant and well-developed area of dynamic nanostructures being successfully transitioned into practice. We can foresee the rapid development of dynamic NP assemblies toward applications in harvesting of dissipated energy, photonics, and electronics. The final part of the review is devoted to the fundamental questions facing dynamic assemblies of NPs in the future.
doi:10.1021/ar200305f
PMCID: PMC3479329  PMID: 22449243
19.  Dipole-driven self-organization of zwitterionic molecules on alkali halide surfaces 
Summary
We investigated the adsorption of 4-methoxy-4′-(3-sulfonatopropyl)stilbazolium (MSPS) on different ionic (001) crystal surfaces by means of noncontact atomic force microscopy. MSPS is a zwitterionic molecule with a strong electric dipole moment. When deposited onto the substrates at room temperature, MSPS diffuses to step edges and defect sites and forms disordered assemblies of molecules. Subsequent annealing induces two different processes: First, at high coverage, the molecules assemble into a well-organized quadratic lattice, which is perfectly aligned with the <110> directions of the substrate surface (i.e., rows of equal charges) and which produces a Moiré pattern due to coincidences with the substrate lattice constant. Second, at low coverage, we observe step edges decorated with MSPS molecules that run along the <110> direction. These polar steps most probably minimize the surface energy as they counterbalance the molecular dipole by presenting oppositely charged ions on the rearranged step edge.
doi:10.3762/bjnano.3.32
PMCID: PMC3323918  PMID: 22497002
alkali halide surface; noncontact atomic force microscopy; organic molecule; self-organization; zwitterion
20.  Field Dependence of the Spin Relaxation Within a Film of Iron Oxide Nanocrystals Formed via Electrophoretic Deposition 
Nanoscale Research Letters  2010;5(10):1540-1545.
The thermal relaxation of macrospins in a strongly interacting thin film of spinel-phase iron oxide nanocrystals (NCs) is probed by vibrating sample magnetometry (VSM). Thin films are fabricated by depositing FeO/Fe3O4 core–shell NCs by electrophoretic deposition (EPD), followed by sintering at 400°C. Sintering transforms the core–shell structure to a uniform spinel phase, which effectively increases the magnetic moment per NC. Atomic force microscopy (AFM) confirms a large packing density and a reduced inter-particle separation in comparison with colloidal assemblies. At an applied field of 25 Oe, the superparamagnetic blocking temperature is TBSP ≈ 348 K, which is much larger than the Néel-Brown approximation of TBSP ≈ 210 K. The enhanced value of TBSP is attributed to strong dipole–dipole interactions and local exchange coupling between NCs. The field dependence of the blocking temperature, TBSP(H), is characterized by a monotonically decreasing function, which is in agreement with recent theoretical models of interacting macrospins.
doi:10.1007/s11671-010-9674-2
PMCID: PMC2956047  PMID: 21076671
Electrophoretic deposition; Core–shell; Superparamagnetic; EPD; Iron oxide; Thin film
21.  Field Dependence of the Spin Relaxation Within a Film of Iron Oxide Nanocrystals Formed via Electrophoretic Deposition 
Nanoscale Research Letters  2010;5(10):1540-1545.
The thermal relaxation of macrospins in a strongly interacting thin film of spinel-phase iron oxide nanocrystals (NCs) is probed by vibrating sample magnetometry (VSM). Thin films are fabricated by depositing FeO/Fe3O4 core–shell NCs by electrophoretic deposition (EPD), followed by sintering at 400°C. Sintering transforms the core–shell structure to a uniform spinel phase, which effectively increases the magnetic moment per NC. Atomic force microscopy (AFM) confirms a large packing density and a reduced inter-particle separation in comparison with colloidal assemblies. At an applied field of 25 Oe, the superparamagnetic blocking temperature is TBSP ≈ 348 K, which is much larger than the Néel-Brown approximation of TBSP ≈ 210 K. The enhanced value of TBSP is attributed to strong dipole–dipole interactions and local exchange coupling between NCs. The field dependence of the blocking temperature, TBSP(H), is characterized by a monotonically decreasing function, which is in agreement with recent theoretical models of interacting macrospins.
doi:10.1007/s11671-010-9674-2
PMCID: PMC2956047  PMID: 21076671
Electrophoretic deposition; Core–shell; Superparamagnetic; EPD; Iron oxide; Thin film
22.  Origin of New Broad Raman D and G Peaks in Annealed Graphene 
Scientific Reports  2013;3:2700.
Since graphene, a single sheet of graphite, has all of its carbon atoms on the surface, its property is very sensitive to materials contacting the surface. Herein, we report novel Raman peaks observed in annealed graphene and elucidate their chemical origins by Raman spectroscopy and atomic force microscopy (AFM). Graphene annealed in oxygen-free atmosphere revealed very broad additional Raman peaks overlapping the D, G and 2D peaks of graphene itself. Based on the topographic confirmation by AFM, the new Raman peaks were attributed to amorphous carbon formed on the surface of graphene by carbonization of environmental hydrocarbons. While the carbonaceous layers were formed for a wide range of annealing temperature and time, they could be effectively removed by prolonged annealing in vacuum. This study underlines that spectral features of graphene and presumably other 2-dimensional materials are highly vulnerable to interference by foreign materials of molecular thickness.
doi:10.1038/srep02700
PMCID: PMC3776959  PMID: 24048447
23.  Electronic and magnetic phase diagram in KxFe2-ySe2 superconductors 
Scientific Reports  2012;2:212.
The correlation and competition between antiferromagnetism and superconductivity are one of the most fundamental issues in high temperature superconductors. Superconductivity in high temperature cuprate superconductors arises from suppressing an antiferromagnetic (AFM) Mott insulator1 while in iron-pnictide superconductors arises from AFM semimetals and can coexist with AFM orders23456789. This difference raises many intriguing debates on the relation between the two classes of high temperature superconductors. Recently, superconductivity at 32 K has been reported in iron-chalcogenide superconductors AxFe2−ySe2 (A = K, Rb, and Cs)101112. They have the same structure as that of iron-pnictide 122-system131415. Here, we report electronic and magnetic phase diagram of KxFe2−ySe2 system as a function of Fe valence. We find a superconducting phase sandwiched between two AFM insulating phases. The two insulating phases are characterized by two distinct superstructures caused by Fe vacancy orders with modulation wave vectors of q1 = (1/5, 3/5, 0) and q2 = (1/4, 3/4, 0), respectively.
doi:10.1038/srep00212
PMCID: PMC3252543  PMID: 22355726
24.  Multimode Resistive Switching in Single ZnO Nanoisland System 
Scientific Reports  2013;3:2405.
Resistive memory has attracted a great deal of attention as an alternative to contemporary flash memory. Here we demonstrate an interesting phenomenon that multimode resistive switching, i.e. threshold-like, self-rectifying and ordinary bipolar switching, can be observed in one self-assembled single-crystalline ZnO nanoisland with base diameter and height ranging around 30 and 40 nm on Si at different levels of current compliance. Current-voltage characteristics, conductive atomic force microscopy (C-AFM), and piezoresponse force microscopy results show that the threshold-like and self-rectifying types of switching are controlled by the movement of oxygen vacancies in ZnO nanoisland between the C-AFM tip and Si substrate while ordinary bipolar switching is controlled by formation and rupture of conducting nano-filaments. Threshold-like switching leads to a very small switching power density of 1 × 103 W/cm2.
doi:10.1038/srep02405
PMCID: PMC3740279  PMID: 23934276
25.  Probing three-dimensional surface force fields with atomic resolution: Measurement strategies, limitations, and artifact reduction 
Summary
Noncontact atomic force microscopy (NC-AFM) is being increasingly used to measure the interaction force between an atomically sharp probe tip and surfaces of interest, as a function of the three spatial dimensions, with picometer and piconewton accuracy. Since the results of such measurements may be affected by piezo nonlinearities, thermal and electronic drift, tip asymmetries, and elastic deformation of the tip apex, these effects need to be considered during image interpretation.
In this paper, we analyze their impact on the acquired data, compare different methods to record atomic-resolution surface force fields, and determine the approaches that suffer the least from the associated artifacts. The related discussion underscores the idea that since force fields recorded by using NC-AFM always reflect the properties of both the sample and the probe tip, efforts to reduce unwanted effects of the tip on recorded data are indispensable for the extraction of detailed information about the atomic-scale properties of the surface.
doi:10.3762/bjnano.3.73
PMCID: PMC3458610  PMID: 23019560
atomic force microscopy; force spectroscopy; NC-AFM; three-dimensional atomic force microscopy; tip asymmetry; tip elasticity

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