Mode Atomic Force Microscopy Imaging Research Articles

DNA structure and dynamics: an atomic force microscopy study.

This review primarily outlines the most recent atomic force microscopy (AFM) studies of DNA structure and dynamics. Sample preparation techniques allowing reliable and reproducible imaging of various DNA topologies are reviewed. Such important issues as imaging of supercoiled DNA conformations at different ionic conditions and detection of local alternative structures that are stabilized by negative DNA supercoiling are discussed in length in the article. The possibility of imaging DNA structural dynamics at different levels is another major focus of the article. Using time-lapse AFM imaging mode of nondried samples, such extensive DNA dynamic processes as transition of one local structure into another (H-DNA to B-form transition), the conformational transitions of DNA Holliday junctions and their branch migration were observed. Potential future applications of this single-molecule dynamics mode of AFM to analyses of various biochemical processes involving DNA are discussed.

Nanobubble Trouble on Gold Surfaces

When analyzing surfaces related to biosensors with in situ atomic force microscopy (AFM), the existence of nanobubbles called for our attention. The bubbles seem to form spontaneously when gold surfaces are immersed in clean water and are probably a general phenomenon at water−solid interfaces. Besides from giving rise to undesired effects in, for example, biosensors, nanobubbles can also cause artifacts in AFM imaging. We have observed nanobubbles on unmodified gold surfaces, immersed in clean water, using standard silicon AFM probes. Nanobubbles can be made to disappear from contact mode AFM images and then to reappear by changing the scanning force. By combining contact mode AFM imaging and local force measurements, the interaction between the nanobubbles and the probe can be analyzed and give information about the characteristics of nanobubbles. A model of the forces between the AFM probe tip and the nanobubble indicates that a small tip cone angle and a relatively hydrophilic tip surface makes it possible to image nanobubbles with contact mode AFM even though the tip has penetrated the surface of the bubble.

Combined scanning electrochemical atomic force microscopy for tapping mode imaging

With the integration of submicro- and nanoelectrodes into atomic force microscopy (AFM) tips using microfabrication techniques, an elegant approach combining scanning electrochemical microscopy (SECM) with atomic force microscopy has recently been demonstrated. Simultaneous imaging of topography and electrochemistry at a sample surface in AFM tapping mode with integrated SECM–AFM cantilevers oscillated at or near their resonance frequency is shown. In contrast to contact mode AFM imaging frictional forces at the sample surface are minimized. Hence, topographical and electrochemical information of soft surfaces (e.g., biological species) can be obtained.

Surface characterization, microstructure, and wetting of networks from ,-dihydroxy(polydimethylsiloxane) and 1,1,2,2-tetrahydrotridecafluoro octyltriethoxysilane

Surface-modified siloxane networks were prepared using the dibutyltin diacetate catalyzed reaction of α,ω-dihydroxy(polydimethylsiloxane), HO(Me2SiO)nH, with tridecafluoro-1,1,2,2-tetrahydrooctyl triethoxysilane, [CF3(CF2)5(CH2)2Si(OC2H5)3, FTEOS]. Surface characterization of these elastomers was carried out using electron spectroscopy for chemical analysis (ESCA) and atomic force microscopy (AFM). Surface phase separation occurs as a function of increasing ratio of FTEOS to HO(Me2SiO)nH. Dynamic contact angle (DCA) analysis with water as the interrogating fluid showed that water contamination affects DCA data in the compositional range 4x–8x, where “x” is the ratio of ethoxy groups from FTEOS to OH groups in HO(Me2SiO)nH. Diffusion of polydimethylsiloxane oil species from the coatings is blocked in compositions of 10x or greater. Chemical stability is also enhanced for 10x and 12x compositions. (A) Tapping mode AFM images. Image area 30 × 30 × 1 μm. (B) DCA data with arrows showing collapse due to water surface contamination, 4x-0.8 cycle before collapse, 6x-1 cycle, 8x-1.6 cycles, 10x and 12x-stable. Stage speed 100 μm · s−1 and dwell times between sample immersion and withdrawal 10 s.

The Location and Effects of Coke Deposition in Fluid Cracking Catalysts during Gas Oil Cracking at Microactivity Test Conditions

Nitrogen porosimetry, atomic force microscopy (AFM), and microcalorimetry together with microactivity testing have been used to characterize some of the effects of coke deposition on a fluid cracking catalyst (FCC) during gas oil cracking. Contact mode AFM images have revealed that coke forms raised surface features consisting of molecules and chain of molecules; evidence of pore blockage by coke deposits could not be obtained in the images generated. Nitrogen porosimetry results indicate that during gas oil cracking, coke is deposited inside (68%) as well as outside (32%) the catalyst porous structure. About 60% of the total coke in the porous structure is uniformly deposited within its microspace, decreasing the micropore volume and causing a shift of its pore size distribution profile toward smaller pore width values. The rest of the coke (40%) is located in mesopores without closing any part of the internal porosity to nitrogen sorption and therefore to catalysis. There is a moderate decrease in acid site strength and acid site density in the coked FCC. Both BET and Langmuir methods grossly underestimate the FCC surface area and only the density functional theory method yields reliable surface area and pore volume measurements over the entire micro–meso porosity range.

Adhesion imaging of carbon‐fibre‐reinforced materials in the pulsed force mode of the atomic force microscope

AbstractThe microstructure and microscopic mechanical and adhesive properties of carbon‐fibre bundles infiltrated with pyrolytic carbon were investigated using a combination of different scanning force techniques. Contact mode atomic force microscopy imaging was combined with lateral force imaging and adhesion force and local stiffness imaging in the pulsed force mode of the atomic force microscope. A clear material contrast was obtained between carbon fibre and pyrocarbon matrix in the adhesion and stiffness images, as well as in the friction force images, which gives valuable information about the different microscopic properties of the fibre and matrix. The significantly higher adhesive forces determined on the fibres compared with the carbon matrix may be attributed to a higher concentration of polar groups on the fibre cross‐sections due to the high degree of orientation of the graphene layers along the fibre axis. In addition, a much higher degree of spatial variation of adhesive and frictional forces is observed within the fibre compared with the matrix, indicating a higher degree of homogeneity within the pyrocarbon matrix. The data derived from the experiments give microscopic information that is essential for a more detailed understanding of the resulting macroscopic properties of these materials. Copyright © 2002 John Wiley & Sons, Ltd.

NANOSTRUCTURE OF THE DIATOM FRUSTULE AS REVEALED BY ATOMIC FORCE AND SCANNING ELECTRON MICROSCOPY

The cell wall (frustule) of the freshwater diatom Pinnularia viridis (Nitzsch) Ehrenberg is composed of an assembly of highly silicified components and associated organic layers. We used atomic force microscopy (AFM) to investigate the nanostructure and relationship between the outermost surface organics and the siliceous frustule components of live diatoms under natural hydrated conditions. Contact mode AFM imaging revealed that the walls were coated in a thick mucilaginous material that was interrupted only in the vicinity of the raphe fissure. Analysis of this mucilage by force mode AFM demonstrated it to be a nonadhesive, soft, and compressible material. Application of greater force to the sample during repeated scanning enabled the mucilage to be swept from the hard underlying siliceous components and piled into columns on either side of the scan area by the scanning action of the tip. The mucilage columns remained intact for several hours without dissolving or settling back onto the cleaned valve surface, thereby revealing a cohesiveness that suggested a degree of cross‐linking. The hard silicified surfaces of the diatom frustule appeared to be relatively smooth when living cells were imaged by AFM or when field‐emission SEM was used to image chemically cleaned walls. AFM analysis of P. viridis frustules cleaved in cross‐section revealed the nanostructure of the valve silica to be composed of a conglomerate of packed silica spheres that were 44.8 ± 0.7 nm in diameter. The silica spheres that comprised the girdle band biosilica were 40.3 ± 0.8 nm in diameter. Analysis of another heavily silicified diatom, Hantzschia amphioxys (Ehrenberg) Grunow, showed that the valve biosilica was composed of packed silica spheres that were 37.1 ± 1.4 nm and that silica particles from the girdle bands were 38.1 ± 0.5 nm. These results showed little variation in the size range of the silica particles within a particular frustule component (valve or girdle band), but there may be differences in particle size between these components within a diatom frustule and significant differences are found between species.

Ge Layer Transfer To Si For Photovoltaic Applications

ABSTRACTWe have successfully used hydrophobic direct wafer bonding along with hydrogen-induced layer splitting of germanium to transfer 700 nm thick, single-crystal germanium (100) films to silicon (100) substrates without using a metallic bonding layer. The metal-free nature of the bond makes the bonded wafers suitable for subsequent epitaxial growth of layered solar cells at high temperatures without concern about metal contamination of the device active region. Contact mode atomic force microscopy images of the transferred germanium surface generated by the formation of micro-bubbles and micro-cracks along the hydrogen-induced layer-splitting interface reveals minimum rms surface roughness of between 10 nm and 23 nm. Electrical measurements indicated ohmic I-V characteristics for germanium layers bonded to silicon substrates with ∼400 Ω cm−2 resistance at the interface. Triple-junction solar cell structures grown on these Ge/Si heterostructure templates by metal-organic chemical vapor deposition show comparable photoluminescence intensity and minority carrier lifetime to a control structure grown on bulk Ge. The use of a molecular beam epitaxy Ge buffer layer to smooth the cleaved surface of the Ge heterostructure has been shown to smooth the rms surface roughness from ∼11 nm to as low as 1.5 nm with a mesa-like morphology that has a top surface roughness of under 1.0 nm giving a promising surface for improved solar cell growth on solar cell structures.

Effect of an Oxidized Gold Substrate on Alkanethiol Self-Assembly

UV-cleaned gold substrates incubated in solutions of alkanethiol show islands on the monolayer surface when imaged with noncontact atomic force microscopy (AFM). The height of the islands above the monolayer is approximately twice the height of the alkanethiol monolayer, and the diameter of the islands is 20-200 nm. These islands are easily pushed aside during contact mode AFM imaging without damaging the underlying monolayer. Islands are observed on gold substrates exposed to solutions of octadecane-, hexadecane-, and dodecanethiol and 1′-thiahexa(ethylene oxide)-1-octadecane at 0.01-1.0 mM concentrations in ethanol and hexadecane. AFM on samples with submonolayer coverage shows that the islands are not observed until the late stages of monolayer formation. Islands are not observed on freshly deposited gold substrates or on UV-cleaned gold substrates that are exposed to ethanol for longer than 10 min prior to incubation in alkanethiol solutions. We conclude that the island formation is associated with oxidation of the gold surface and that the islands are primarily composed of alkanethiol. We hypothesize that the stability of these structures may be due to the formation of multimolecular complexes of alkanethiols.

Friction Coefficients Derived from Apparent Height Variations in Contact Mode Atomic Force Microscopy Images

Self-organized monolayer domains of liquid crystal (LC) on mica surface were investigated by contact mode atomic force microscopy (AFM) and friction force microscopy (FFM). By analyzing contributions of friction to the apparent height in AFM height images, we calculated the friction forces and the relevant friction coefficients. It is observed that the difference between the magnitude of the friction force on LC monolayers and mica was proportional to the normal load. The friction coefficients of the LC monolayers and bare mica were obtained as 0.076 and 0.094, respectively. In addition, frictional asymmetry of LC monolayers was observed in our study, which was attributed to the molecular tilt, and a possible explanation was proposed in terms of the stick−slip motion of the tip apex on the molecular scale.

Non-contact atomic force microscopy imaging of TiO 2(100) surfaces

Atomically resolved non-contact fm mode atomic force microscopy images have been obtained from TiO 2(100) surfaces. The 1×1 surface is observed, as well as the 1×3 phase previously imaged with STM. The morphology of the latter reconstruction consists of (110) microfacets. An additional reconstruction with 1×3 symmetry is observed, which is assigned to a phase intermediate between the 1×1 and 1×3-microfacet terminations.

Minority carrier diffusion length and lifetime in GaN

Electron beam induced current measurements on planar Schottky diodes on undoped GaN grown by metalorganic chemical vapor deposition are reported. The minority carrier diffusion length of 0.28 μm has been measured, indicating minority carrier lifetime of 6.5 ns. The tapping mode atomic force microscopy imaging of the surfaces and scanning electron microscopy of the cross sections have been used to characterize the linear dislocations and columnar structure of the GaN. The possible influence of recombination on the extended defects in GaN on the minority carrier diffusion length and lifetime is discussed, and contrasted to other recombination mechanisms.

Substructure and responses of cholinergic synaptic vesicles in the atomic force microscope

The substructure and responses of individual 100-nm synaptic vesicles to osmotic stress have been probed with an atomic force microscope (AFM) operating in tapping mode. Cholinergic synaptic vesicles from the electric organ of Torpedo californicawere imaged continuously as the osmolarity of the buffer was decreased.Vesicles in hyposmotic buffer lysed to form flat circular structures on the mica surface with a diameter about two times that of intact vesicles and a thickness of 7.2 ± 1.7 nm, which can accommodate the lipid bilayer plus the internal proteoglycan. Images of intact vesicles in air reveal creases in the membrane surface. Phase mode AFM images of lysed vesicles in air show the presence of a material not seen on intact vesicles that might be intravesicular proteoglycan released from the membrane at very low osmotic and ionic strength. J. Neurosci. Res. 52:350–355, 1998. © 1998 Wiley-Liss, Inc.

Nanomechanical basis for imaging soft materials with tapping mode atomic force microscopy

The surfaces of virgin and chemically etched poly(tetrafluoroethylene) (PTFE) have been studied using scanning electron microscopy (SEM), and atomic force microscopy (AFM) in both contact and tapping modes. Contact mode AFM images of this relatively soft polymeric material are dominated by tip-induced imaging artifacts. When subsequent, AFM imaging was performed in tapping mode these artifacts were eliminated, and comparable tapping mode AFM and SEM images were obtained for even the highly porous, unstable surface that results from sodium naphthalenide etching. Interfacial force microscopy force versus displacement, and creep experiments were performed to determine the nanomechanical nature of virgin PTFE. These experiments show that virgin PTFE is a viscoelastic material which is capable of supporting large forces on the millisecond time scale but creeps dramatically at longer times. Clearly, with scanning probe techniques which utilize constant probe force feedback, one should expect image distortions, as we observe, with soft materials such as virgin or etched PTFE. Conversely, with tapping mode AFM, rational images require contact times (μs) that are much shorter than creep times (ms). Thus, viscoelastic material characteristics determine the need for tapping mode AFM over contact mode AFM. By comparing tapping mode AFM images of virgin and etched PTFE surfaces, we can understand the three-dimensional character of the etched surface necessary for mechanical interlocking and resultant strong metal adhesion.

5535668 Corrugated pallet: Besaw Larry G; Farley Timothy R, Jasper, IN, United States assigned to The Servants Inc

Through force spectroscopy, we use an atomic force microscope (AFM) to compare the forces between two extra heavy crude oil (EHCO) droplets. This is done in various aqueous environments in order to compare said forces in the presence of a variety of surfactants and ionic species. A crude oil droplet is attached to the AFM cantilever and pressed against other droplets placed on a substrate. Differences in the behavior of the forces as a function of surfactant chemistry, concentration and the velocity of the approach and retract of the droplets are observed for droplets with a range of diameters 10<Ø (µm)<70. The surfactant H4 (dodecyl-polyglucoside, designed at the Instituto Mexicano del Petroleo) is found to cause the highest forces between the droplets and greatest reduction of drop deformation when pressed together. Qualitative agreement is observed with previous theoretical works with regards to the addition of ionic compounds such as sea-water – the droplets approach more closely and coalescence may be favored in some cases. It is possible to observe structure on the surface of other oil drops by tapping mode AFM imaging. It is believed that this is the first time this has been done on extra heavy crude oil droplets.

Use of a repositionable substrate to acquire and compare distinct atomic force microscope images of a field of microtubules

Many scanning probe microscope (SPM) experiments of interest require removing the sample from the scanning head of the SPM for processing or examination by other techniques and then replacing it in the SPM head and relocating the original sample area. For feature sizes below 1 μm this is often a tedious, if not impossible, task. To resolve this problem we have designed a patterned substrate which can be used with any SPM to relocate sub-micrometer features even after removal, and subsequent replacement of the sample in the scanning head. The use of this device with an atomic force microscope (AFM) is demonstrated by imaging a field of chicken brain microtubules with several different AFM probes and scan modes. Contact, Tapping™, and error-signal mode AFM images were acquired using normal pyramidal tips and Park Scientific Ultralevers. Images of individual tubules were obtained with all three imaging modes, allowing direct comparison with respect to height, width and feature resolution.