AFM indentation was conducted on a JPK NanoWizard-1 (JPK Instruments) operating in force spectroscopy mode, mounted on an inverted optical microscope (IX-81; Olympus). AFM pyramidal cantilevers (MLCT; Bruker) with a spring constant of 0.07 N/m were used with a 35 μm glass bead attached to the cantilever tip. Before measurements with the adapted cantilevers, their sensitivity was calculated by measuring the slope of the force–distance curve in the AFM software on an empty region of the Petri dish. For cell indentation tests, the cantilever was aligned over regions in the middle of the cells using an IX-81 inverted optical microscope. For each group, 30 individual cells were tested. Force–curve acquisition was performed with an approach speed of 5 μm/s and a maximum set force of 1.5 nN. Elastic moduli were calculated from the force–distance curves by fitting the contact region of the approach curve with the Hertz contact model using the AFM software (JPK Instruments).
Afm software
Manufactured by Bruker
Sourced in Germany, United States
The AFM software is a comprehensive suite of tools designed to operate and analyze data from Bruker's Atomic Force Microscopes. It provides a user-friendly interface for controlling the microscope, acquiring high-resolution images, and performing advanced data processing and analysis.
Automatically generated - may contain errors
Lab products found in correlation
Jpk nanowizard 1, by Bruker (1 mentions)
Afm pyramidal cantilevers mlct, by Bruker (1 mentions)
Zyla 5, by Oxford Instruments (1 mentions)
Nanowizard 4, by Bruker (1 mentions)
Dulbecco modified eagle medium (dmem), by Thermo Fisher Scientific (1 mentions)
Bl rc150vb, by Olympus (1 mentions)
Multimode scanning probe microscope, by Bruker (1 mentions)
Auriga compact, by Zeiss (1 mentions)
Dimension icon afm, by Bruker (1 mentions)
Scanasyst air, by Bruker (1 mentions)
6 protocols using afm software
1
AFM Indentation of Mammalian Cells
2
Extrinsic Compression of E5.5 Embryos
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All atomic force microscopy (AFM) experiments were carried out with NanoWizard 4 (JPK Instruments, Berlin, Germany) controlled by AFM software (JPK Instruments). The head unit and stage of the atomic force microscope were both mounted on an inverted microscope (IX73; Olympus, Tokyo, Japan) and laser alignment was achieved with a CCD camera (Zyla5.5; Andor Technology, Belfast, UK). For extrinsic compression experiments using AFM, tipless cantilevers (AIOAL-TL-10; BudgetSensors, Sophia, Bulgaria) glued with 30-mm diameter glass beads were used. A sustained force of 30 nN was applied to compress E5.5 living embryos in DMEM (Life Technologies) supplemented with 10% fetal bovine serum (Hyclone, Thermo Scientific) for 10 min after their RM were left intact, completely removed and pierced.
3
Atomic Force Microscopy Cantilever Calibration
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System calibrations were carried out as per manufacturing guidelines (JPK user's manual). Briefly, the cantilever's spring constant and resonance frequencies were determined prior to conducting the experiments. The nominal spring stiffness for cantilevers (BL-RC-150VB) of 0.005 N/m provided by the manufacturer (Olympus) was used to compare our experimentally derived spring constants that were determine for each experimental run. We experimentally determined the spring constant for each cantilever used using analysis of thermal noise during AFM system calibration. Soft cantilevers such as the ones used here are susceptible to thermal fluctuations. JPK's AFM software enables the user to calculate resonance frequency of each cantilever in EBS from the thermal noise spectrum recorded. The thermal resonance curve (dominant peak) can be fitted to Lorentz function, which allows calculation of the spring constant. The spring stiffness was experimentally calculated as 0.0049 ± 0.0005 N/m. The nominal resonance frequency of the cantilever was well above the frequency range of interest in this study.
4
Atomic Force Microscopy Visualization of NC:NA Complexes
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NC:NA complexes were assembled under conditions used for EMSA with 1 ng/ L of M13 ssDNA and in a binding solution containing 10 mM TrisAcetate pH 7.0, 50 mM sodium acetate, 2.5 to 5 mM magnesium diacetate, and 0.5 mM TCEP. A freshly cleaved muscovite mica surface was pre-treated for 2 min with a fresh dilution of spermidine (50 M), extensively rinsed with water and dried under a nitrogen flow [96 (link)]. A 5 L drop of the NP complexes was deposited on the surface and incubated for 3–5 min and dried with nitrogen gas. AFM images were carried out in air with a multimode scanning probe microscope (Bruker, USA) operating with a Nanoscope IIIa or V controller (Bruker, USA) and silicon AC160TS cantilevers (Olympus, Japan) using the tapping mode at their resonant frequency. The scan frequency was typically 1.0 Hz per line and the modulation amplitude was a few nanometers. A second-order polynomial function was used to remove the background with the AFM software (Bruker, USA).
5
Nanostructure Analysis of Sweet Cherry SSP
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The SSP fraction of sweet cherry flesh was separated and determined using a previously published method.15 (link) Carbazole colourimetry was used to determine the extracted SSP content. The nanostructure and quantitative parameters of SSP were measured using a Multimode NanoScope IIIa AFM (ZhuoLun MicroNano Equipment Co., Ltd Shanghai, China) in tapping mode at a scan rate of 0.5–2 Hz. The samples were treated according to the method of Xin et al.15 (link) Approximately 10 μL of diluted sample was distributed on a mica sheet and dried using an aurilave. Atomic force microscopy (AFM) images for samples from each treatment were analysed offline using the AFM software (Bruker Corp., Santa Barbara, CA). The reliable results were obtained from the analysis of at least 80 single chains for each sample.
6
Morphological Characterization of Substrates
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The morphology of all the produced substrates was characterized using a high‐resolution field emission scanning electron microscope (SEM) with focused ion beam (Auriga Compact, Zeiss, Germany). AFM (AFM Dimension Icon, Bruker, USA) was also used in PeakForce Tapping (ScanAsyst) mode in air. AFM cantilevers (ScanAsyst‐Air, Bruker), made of silicon nitride, were used with a spring constant of 0.4 N/m and frequency of 70 kHz. The images, with a scan size of 20 × 20 μm, were analyzed using a commercial AFM software (Bruker) and the surface roughness was measured as the root mean square (RMS) roughness. RMS was calculated using the Z‐sensor height signal. A total of 18 locations (six locations of three replicates) were analyzed per formulation.
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