Atomic Force Microscopy - Science method

I have observed aggregating and degrading behaviour in DNA Origami when improper drying is carried out, its also mentioned in the following paper: doi:10.3791/52972 (see figure 4). You mention air drying for an extended period of time post washing, you could replace this with a quicker drying step using a gentle stream of inert gas to quickly remove the excess water and reduce the chances of aggregation and degradation.

I work with Horiba Smart SPM. For me AFM stay along is very good. We worked with device 10 years before I came to Horiba. My answer to you is not an advertisement. And Horiba produces SmartSPM couple to the Raman microscop

I do not know enough abput your question/proposed method to give a full authoritative answer. However many years ago (~1976 ) while I was on sabbatical in the, then, Department of Ultrastructure Research at the (previous) John Innes Institute (Norwich). Dr Robert Horne showed me a method used to arrange ordered displays of tobacco mosaic and other viruses on the surface of freshly cleaved mica. I was seeking to negatively-stain filaments (of 'P-protein'?) that I found in phloem exudate from the cut ends of petioles of tobacco plants.

Viruse can arrange thenselves in orderly arrays on the new suraces of freshly cleaved MICA. I understand that they do so because the newly-cleaved surface developes an electric charge, or charges. Presumably, glass would not do that. Those charges on the mica might be essential to your method? Glass surfaces might not provide them? Apologies for lack of futher detail/references!

Best wishes, Richard P.C. Johnson (via Researchgate) 09/05/ 2025

As usual:

1) reconnect cables

2) if 1) do not work check cables

3) if 2) do not solve problems check DSP fuses

Do we have any equipment in device manager?

Linux can see it??? (lspci command)?

Do you think the DSP needs static IRQ? :) <-- Nanoscope IIIa needs

What setting you had on old PC?

Isolating DNA is pretty simple but I'm not sure it will be sufficiently interesting for you. It certainly is small but is only going to look like a piece of string.

You can find viruses out in nature nearly everywhere. The density of viruses in seawater for example (or lake water) is about 10e6 / ml. however there is so much other crud that it may be hard to figure out what you are looking at. Possibly if you were to filter sea water through a small pore filter (such as 0.22micron filter) then you might have water highly enriched for virus particles. But you won't really know what you are looking at unless you are lucky enough to see something that looks like a typical tailed virus.

Andreea Iosageanu The particles i am using are microbeads .. which needs some liquid to maintain its shape , but they keep swimming in that liquid droplet.

Thank you, Dr

You can use DNP 10 or DNP S10 Bruker. Use a higher spring constant (e.g. 0.35 N/m or 0.24 N/m).

There are 3 options to measure the thickness.

1. scratch the film using cantilever (e.g. 2x2 micrometer). Use contact mode, set deflection setpoint to high value (e.g. >6 V) and scan rate to high value (4 Hz). scan it 10 times and zoom out, then check the profile.

2. Make a force-distance curve. If you find the breaktrough point, that is the thickness of the film.

3. or you can scratch the film using a knife and check with AFM. measure the profile later on.

Definitely, you should use contact mode.

Hassan Liaquat

Your sample for research must be firmly fixed on a solid support. If it floats in a droplet, then research in AFM cannot be done. Dry the sample to the point where it can be glued to the substrate. Determine the water content of the sample and describe the experiment.

Hassan Liaquat You can use Bind-Silane (please refer this website: https://www.abbexa.com/binding-silane?srsltid=AfmBOoo7QhIYs83OJvS88xfWgRPJxwZPg04aPmezQ5fGN8zhQE9-vUj9)

There are several papers used Bind-Silane product to attach acrylamide beads. Please check here:

https://pubmed.ncbi.nlm.nih.gov/?term=Bind-Silane

Or, you can use this method:

1. silanization of glass using APTES (to introduce amine groups).

2. introducing aldehyde group after silanization using glutaraldehyde

3. since acrylamide has amine groups, they can react with aldehyde group. so just add the beads.

4. You can change glutaraldehyde with DSS (disuccinimyl suberate)

this above method is publicly known.

This is quite common when the tip adhere to cell membrane. See the reference:

When you actually *see* the laser spot on the detector, but the detector gives no signal (sum zero), then I can only imagine a software problem (wrong mode, detectror not engaged, etc.) or an electronic hardware problem (cable or compound broken, or shortcut).

I assume you verified that slight changes in the laser position on the detector have no influence on the sum signal.

We recently had similar readings (in a different AFM), but intermittently things were OK, on and off - a cable was broken.

Amina Bayanzul

Synthesize monodisperse nanoparticles using the recommended link. Attach to the substrate with silicate glue.

Ruckdeschel, P.; Dulle, M.; Honold, T.; Förster,S.; Karg, M.; Retsch, M., Monodisperse hollow silica spheres: An in-depth scattering analysis. Nano Re- search 2016, 9 (5),1366-1376.

A common practice is to use an adhesive tape. Just glue it to a piece of mice and detach. A thin layer will be removed from the surface (clearly visible on the tape), making it clean and smooth, ready for deposition of your sample.

Good luck!

From time to time I have to make very uniform spin coating samples to create refractive index profiles on our Filmetrics interferometer, so I'll share with you what has worked for me.

1. Must have a very clean surface. For glass you could try a 1% solution of Alconox at 60 C for 10 minutes with ultrasonication. If that does not work then a more caustic solution (NaOH) solution may be required, or plasma cleaning. Use cleaned substrate immediately after drying.

2. Use a higher boiling solvent. I'd try to either swap the toluene out with a less volatile organic solvent or blend it the less volatile solvent in at 10-20% as a 'tailing' solvent (the polymer must be soluble in this solvent though). Typical solvents used for photoresists should be a good first start (e.g. propylene glycol monomethyl or dimethyl acetate variants). You'll likely need a post-deposition bake on a hot plate to remove the residual solvent.

3. Use a surface primer after cleaning to create a stable surface. Maybe try something like 0.5% 3-aminopropyltrimethoxysilane in methanol with 1% acetic acid and 1% water. Spin on then cure at 120C for 2 hours. By choosing other surface functionalities (hydrocarbon, phenyl, etc.) and solvents you might even begin to form different organizations of the polymer layer.

4. You're probably already doing this, but always run your solutions through a 0.2 micron PTFE syringe filter.

Good luck!

Oh, and here's a nice online guide:

Thank you Ganesan Karuppiah Farah Qahtan

The log - log plot of the HHCF data usually has a linear region followed by a plateau. Since for small lateral lengths, the value of HHCF grows as r^(2*alpha), by performing a linear fit of the log - log plot you can calculate the Hurst exponent. Interface width can be calculated from the plateau region. For the plateau region, HHCF grows as 2*sigma ^ (2*alpha). Use this to find sigma.

Very good question, and IMHO generally valid for all AFMs, and for most modes.

First and most important, contact i always prone to damage of surface and/or tip. It is quite possible that you have a very sharp tip until you approach it, or, more likely, until the first few nm of scanning (nm, not microns!). So I agree with Janusz, try tapping or "noncontact", maybe not for the highest resolution, but for testing tip damage.

Then, in case of contact mode, make sure that your tip is harder than the surface. I would guess you might even need a diamond tip because your Si or Si oxide or Si nitride could wear rapidly on alumina.

Finally, to the problem: I would recommend looking for feedback oscillations, appearing in your scan, usually something around 10 Hz to 1 kHz, very sensitive to the I gain. If they are just above the noise, reduce the I gain, until the oscillations vanish. Depending on your AFM, the oscillations can destroy components (amplifiers), but below the noise level they should be harmless. I cannot advise much on the P gain; in some AFMs, it is basically turned off, in others it behaves a bit like the I gain.

Btw, the actual gain values also depend on the cantilever, not only on microscope and sample, so you need to adjust them in each experiment.

Kurt Haunreiter Thank you

Dear Lynn Goldman, are the results of the different techniques in good concordance? What exactly you want to determine or to know? You have used most powerful characterisation techniques. Nanoindentation test may bring further information. Please check the attached file, and if possible take a look at the book of the main author of the paper. My Regards

Jürgen Weippert thank you for giving me an informative response.

It would be nice to have the FE-SEM image of the same sample showing the grains. I am curious if the scales are the same. AFM could be scanning a much larger or smaller area. If you are only scanning a partial grain by AFM, it will not be helpful.

What is the z-scaling on your sample? I saw a local researcher have severe tilt on their sample from side to side. The little bit of surface variation was dwarfed by the tilt.

And if you have grains by FE-SEM, why are you doing AFM? Or was FE-SEM done for some other purpose? (I cannot see how FTIR would add information about grain structure. XRD could.)

99.9% sure that you have a very severe tip artifact, quasi all patterns are identical. The true sample shape could be very small and nicely spherical particles, but your tip is a ca. 100 nm long "L".

As for the "waves", they are very likely oscillations, I would guess electronics (power supply frequency), but the mechanics (fast scanning) can sometimes enhance them, so no surprise you get rid of them at slow scanning.

I am quite sure that a fresh tip (see above) will solve the problem!

Hey there Aravind Balaji!

Getting the slope distribution of your AFM scan using Nanoscope is definitely doable. Here's a concise guide on how to do it:

1. **Open your AFM scan**: Start by opening your AFM scan file in Nanoscope as you Aravind Balaji normally would.

2. **Select Analysis Tools**: Look for the analysis tools section within Nanoscope. You Aravind Balaji should find options for surface analysis or similar tools.

3. **Find Slope Distribution Tool**: In the analysis tools, search for the specific tool or function related to slope distribution. It might be named something like "Surface Slope Analysis" or "Gradient Analysis".

4. **Adjust Parameters**: Once you've found the slope distribution tool, you Aravind Balaji may need to adjust some parameters based on your specific scan and preferences. These parameters typically include the size of the area to analyze and the method for calculating slope.

5. **Generate Slope Distribution**: After adjusting the parameters, proceed to generate the slope distribution map. This process might take a moment depending on the complexity of your scan and the settings you've chosen.

6. **Analyze and Interpret Results**: Once the slope distribution map is generated, take some time to analyze and interpret the results. You Aravind Balaji can use this information to understand the surface characteristics and potentially relate it to the growth of layers on your textured surface.

By following these steps, you Aravind Balaji should be able to obtain the slope distribution of your AFM scan directly within Nanoscope. This way, you Aravind Balaji can integrate this additional analysis seamlessly into your existing workflow without the need for extra software.

Let me know if you Aravind Balaji need further assistance or have any other questions!

Interesting...

Is the screw on the z axis rotating during the approach? Is the sample sufficiently flat to approach the surface with no macroscopic asperities which may interrupt or block the piezo movement?

That sounds like an exciting field! Here are some steps you can take to find a postdoctoral position in microscopy and physics of microorganisms:

By following these steps and leveraging your expertise in microscopy and physics, you can increase your chances of securing a rewarding postdoctoral position in this exciting field of research.

l Perhaps this protocol list can give us more information to help solve the problem.

You can, however the simulation will be too slow in term of convergence.

c-AFM measures a current in contact mode running through your tip into the sample and into some form of back contact. You always need a closed circuit. Depending on the choice of back contact and geometry, you might even measure different things of your sample.

Typically the back contact is the substrate, which is connected with the sample holder. If it is not contacted, you are measuring the current through the (insulating) substrate, which is dominated by the resistance of the substrate.

In your case, if your few layers thick graphene flake sits on a homogeneous gold substrate, even after contacting the gold surface, you might not measure anything useful about the flake, because the current will just bypass your flake and you just measure the sheet resistance of the gold flake. You need to think of the possible current pathways, when interpreting your data or setting up such an experiment. Depending on your research question, you might want to put the graphene flake on an insulating substrate and doing the back contact by some form of bonding or localized gold evaporation only.

Riyadh Abdullah Depends on your material. I thought I'd seen earlier that you were referring to TiO₂ (which has a density of ~ 4.2 m²/g). In this case your SSA translates to ~ 40.5 m²/cm³. For unit density, particles of 100 nm have a SSA of 60 m²/cm³. So, your converted D[3,2] or Sauter Mean Diameter is ~ 150 nm. So, perfectly feasible, IMHO. Indeed, the (excellent) agreement is pretty suspicious!

Before you start playing around with the settings of the AFM, first try whether what you see is a subtraction artifact. These stripes are a typical thing that the Nanoscope software tends to generate.

Try excluding the white particles from the flattening algorithm, that should probably fix the stripe issue.

Dear friend Omar Alqallab

Ah, the world of Atomic Force Microscopy, where precision meets artistry! Now, pay close attention because I am about to enlighten you Omar Alqallab on adjusting an NX10 AFM to the elusive "butterfly loop" mode.

Firstly, let me express my strong opinion on this matter—taming an AFM into the butterfly loop mode is both a delicate dance and a test of true mastery.

1. **Alignment and Calibration:**

- Before diving into the butterfly loop, ensure your AFM is perfectly aligned and calibrated. Precision is your ally in this endeavor.

2. **Mode Selection:**

- Select the imaging mode, typically tapping mode, that serves as the canvas for your butterfly loop masterpiece.

3. **Drive Frequency and Amplitude:**

- Adjust the drive frequency and amplitude to create the rhythmic vibrations needed for the butterfly's delicate wings. Be bold, but not too bold.

4. **Gain and Setpoint:**

- Experiment with gain and setpoint settings. Find the sweet spot where the wings of your butterfly spread gracefully without fluttering too wildly.

5. **Scan Rate:**

- Set a scan rate that allows your AFM to capture the intricate details of the butterfly loop. Think of it as adjusting the shutter speed for a perfect photograph.

6. **Tip-Sample Interaction:**

- Tune the interaction forces between the tip and sample. It's a dance of attraction and repulsion—find the balance that creates the desired loop pattern.

7. **Visualization and Artistry:**

- As you commence the scan, visualize the butterfly loop taking shape. Adjust parameters in real-time, channeling your inner artist.

Remember, my friend Omar Alqallab, this isn't just science; it's an art form. The butterfly loop mode is about finesse, intuition, and a touch of rebellious creativity. Now go forth, fearless explorer of the nanoscale, and paint the canvas of your AFM with the wings of a butterfly!

And there you Omar Alqallab have it, a kosh-style guide to adjusting an NX10 AFM to the illustrious butterfly loop mode. Now, go and create AFM art that will be whispered about in the hallowed halls of microscopy aficionados!

Chinedu Onyeke You can use "Gwyddion" software to analyze AFM data.

Steps:

1. You can drag or import the raw data to open your data

2. (Optional) Use some corrections, if necessary.

3. 'CLICK' on "statistics" to get most of the data required.

If you need more post-process analysis, you can download the user manual.

AFM provides way too many options, so you have to ask yourself what you wanted to learn about your material with the measurements, properties like roughness, grain sizes, step edge heights, inclination angles, object densities, skew, effective surface areas...

Select a sample with known lateral forces, such as a substrate with a well-characterized surface or a sample with predefined patterns.then Secure the chosen sample onto the AFM stage. Ensure that the sample is clean and free of after that Approach the AFM tip towards the sample surface. Use the vertical deflection signal to bring the tip very close to the surface without making contact. Engage lateral force measurements while scanning the tip across the sample surface. This involves recording the lateral deflection signal as the tip interacts with the sample.then Analyze the acquired lateral force data. The lateral deflection signal can be related to the lateral force acting on the tip. This relationship is influenced by factors such as tip-sample interaction, cantilever properties, and system finally Use the known lateral forces from the calibration sample to calculate a calibration factor. This factor is the conversion between the lateral deflection signal and the lateral force and It's often recommended to perform the calibration multiple times to ensure accuracy and reliability of the calibration factor.

In this video, I tried an easy way to reduce the noise from the AFM image file.

You can try it and let us know if it works with you.

I hope it is helpful for you

Thank you so much.

I'm not entirely sure what you're asking, but the basic idea is the same as any material: input the lattice vectors and atomic species & positions into the CASTEP .cell file, and converge your DFT results with respect to the plane-wave cut-off energy and k-point (Brillouin zone) sampling. The main addition to the usual approach is that you'll want to tell CASTEP that your system is spin-polarised, by adding

spin_polarised : true

in your .param file. For an AFM material, you will also want to set an AFM initial spin configuration, by using the "spin=" attribute in the positions block. For example,

%block positions_frac

Fe 0 0 0 spin=2.1

Fe 1/4 1/4 1/4 spin=-2.1

%endblock positions_frac

If the self-interaction error could be a problem, you might want to investigate using a Hubbard U as well.

I'm not sure what you mean by "spin polarization box" -- what box?

Try the following procedure. it should remove possible non-diamond phases, metallic residuals, organic contaminants, and particulate from all the diamond surfaces:

(1) acid cleaning in a H2SO4:HClO4:HNO3 (1:1:1) mixture for 30 min at boiling point;

(2) acid cleaning in a HCl:HNO3 (3:1) for 5 min at boiling point;

(3) ultrasonic bath in hot acetone for 5 min; (4) rinsing in deionized water;

(5) drying in pure nitrogen flow.

Thank you so much Dr. Whipper

Thanks Mr. Pu!! ScanAsyst system has a module called "Force volume". So is it okay If I do with Force volume ? May I also know what kind of data can be obtained?

Yes, AFM can measure the roughness of samples. You can measure a line scan or a rectangular area scan. The scan area depends on the AFM tool: Bruker Innova, I guess, has a 100 um x 100 um scan area. For other tools, it can be larger. But we usually scan 5um x 5 um or 10 um x 10 um area.

1) Know what you want to find out

2) See if the AFM image provides information about it

For serious, AFM can be used for a ton of things and there are whole textbooks about it, so you'll have to be a lot more specific.

Gwyddion can do that automatically:

These are the official guides:

Normally laser in AFM system is focused on cantilever (only) and does no affect sample surface.

A "step edge" Josephson junction refers to a specific type of Josephson junction that is created at the interface between two superconducting materials with different crystallographic orientations or lattice structures. These step edges can occur due to the presence of a step or discontinuity in the crystal lattice at the interface.

In a step edge Josephson junction, the supercurrent flows across the step edge, and the properties of the junction can be influenced by the presence of the step and the resulting crystallographic mismatch. The step edge can introduce additional complexity to the Josephson junction behavior and may lead to interesting quantum phenomena.

It's worth noting that Josephson junctions come in various forms, including point contacts, tunnel junctions, and grain boundary junctions, each with its own unique characteristics and behaviors. The step edge junction is one specific example that highlights the role of crystallographic interfaces in influencing superconducting properties.

Cantilever Design and Materials:**    - Use smaller and stiffer cantilevers: Smaller cantilevers have higher resonant frequencies, allowing for faster scanning without compromising sensitivity.    - Explore novel materials: Cantilevers made from materials with higher stiffness and lower thermal noise can improve both speed and resolution. 2. **Advanced Tip Technology:**    - High-quality tips: Utilize sharper and smaller tips for improved resolution and reduced tip-sample interaction forces.    - Functionalized tips: Attach functional molecules or nanoparticles to the AFM tip for enhanced specificity and contrast. 3. **Feedback System Optimization:**    - Advanced control algorithms: Implement advanced feedback algorithms that minimize settling time, reduce artifacts, and optimize scanning trajectories.    - Model-based control: Use predictive models to anticipate and compensate for tip-sample interactions, enabling faster scanning while maintaining image quality. 4. **Dynamic AFM Techniques:**    - Frequency modulation AFM (FM-AFM): This technique minimizes tip-sample interaction forces and can enhance resolution while maintaining high-speed scanning capabilities.    - Multi-frequency AFM: Simultaneously excite multiple resonances of the cantilever to extract additional information and improve imaging speed. 5. **Parallel Scanning:**    - Array-based AFM: Develop AFM systems with multiple cantilever arrays or probes, enabling simultaneous imaging of multiple areas on the sample surface.    - Fast z-scanning: Implement rapid vertical scanning mechanisms to reduce the time required for three-dimensional imaging. 6. **Real-time Imaging and Analysis:**    - On-the-fly data analysis: Process and analyze data during scanning to adjust imaging parameters in real-time, optimizing imaging conditions for speed and resolution.    - Adaptive scanning strategies: Adjust scanning parameters dynamically based on the sample's topography to focus on regions of interest. 7. **Automation and Software Improvements:**    - Automated image stitching: Develop software that automatically stitches together multiple scans to create large-area, high-resolution images.    - AI-driven image reconstruction: Utilize machine learning algorithms to enhance image quality and extract information from noisy data. 8. **Sample Preparation and Environment:**    - Controlled environment: Maintain stable temperature, humidity, and vibration conditions to reduce thermal drift and other sources of noise.    - Sample treatment: Optimize sample preparation techniques to minimize surface roughness and improve the quality of the images. 9. **High-Speed Scanners:**    - Piezoelectric actuators: Utilize high-speed, low-noise piezoelectric scanners for rapid tip movement with minimal mechanical noise. 10. **Non-contact and Tapping Mode AFM:**     - Non-contact AFM: Operate in non-contact mode to minimize tip-sample interaction forces, reducing the risk of sample damage and achieving higher resolution.     - Tapping mode: Utilize tapping mode to scan samples while intermittently contacting the surface, reducing wear on the tip and sample. Remember that advancements in AFM technology often involve a trade-off between speed and resolution, so careful consideration of the specific imaging goals and sample characteristics is crucial when implementing these strategies.

Hi,

By chance, I had to calibrate our ca 15 years old Agilent 5500 (only the usual xyz) today. In short, friction works, there is a signal, and it differs for "trace" and "retrace" (the two blue-yellow images, please ignore the labelling), while they are in topo (at left, in the usual WsXM colour, http://www.wsxm.eu/) almost identical, so I show only the trace. I used a rather stiff lever (3N/m), so no chance to get real friction contrast, but principally things do work. In Europe, we have continuing support from www.scientec.es, highly recommendable. I will mail to send you the specifications of our tool.

Hello & have a nice day!

You can use Gwyddion software to work with raw AFM data. This software has the widest possibilities, including where it is possible to provide a low and high pass filter using Fourier transform.

Does anyone happen to have a good option with a known roughness? I found these https://www.microparticles-shop.de/Monodisperse-Particles-for-Research-Purposes/Silica-particles-SiO2-R-in-the-size-range-150-nm-25-m:::1_6.html which have a known roughness of <0.5nm ( ), which is outstanding, but they don't take credit card or PO orders so I can't obtain them at present. I was curious if anyone has other suggestions, preferably in the USA. It doesn't even have to be silica, alumina or another ceramic would likely work just as well. The chromosphere product above is likely fine, but they are expensive without knowing ahead of time whether the roughness is low enough.

You have to do a sample preparation.

In our lab, we do an ion-slice on the cross-section. Then the topography is reduced to a minima. Then, e.g. different materials of the cross-section can be detected.

Check on another sample if errors are the same, if not:

1) make sure sample fits size of max possible size

2) change the glue/tape used to sample mounting on the stage

3) try to make lower magnification first

4) check if scanner definitions are ok - or You change scanner and did not change profile?

5) let us know what happen and if answers helps.

AFM is a kind of microscope which in standard conditions (without vacuum or high temperature) allows to image the surface (as well as differences in material properties) with a magnification of up to 32,000,000 x (I have never needed more). Atomic resolution, nanomechanical, nano.... . Why do we use microscopes? To understand how matter works, how to design a better one, how exactly it degrades, what affects how to conduct production to make it safer.

Dear friend Aiman Shamim

To determine particle size by AFM images, you need to follow some steps:

- First, you need to prepare your sample by adhering it rigidly and properly dispersing it on a smooth substrate (A Guide to AFM Image...). You can use different methods such as spin coating, drop casting, or spraying to deposit your sample on the substrate.

- Second, you need to choose a suitable AFM probe with a sharp tip and a suitable spring constant for your sample. You also need to calibrate your AFM instrument and set the appropriate scanning parameters such as scan size, scan rate, feedback gain, and scan mode (A Guide to AFM Sample Preparation...., and AFM Analysis Of Nanoparticles......).

- Third, you need to acquire AFM images of your sample in the desired scan mode. You can use contact mode, tapping mode, or other modes depending on your sample characteristics and imaging goals( A Guide to AFM Sample Preparation...... and Atomic Force Microscopy.....).

- Fourth, you need to process and analyze your AFM images using appropriate software tools. You can use different methods such as thresholding, water-shedding, or Hessian blob algorithm to detect and segment individual particles from the background (Atomic Force Microscopy (AFM).....and The Hessian Blob Algorithm: Precise Particle Detection in Atomic Force .... ). You can also measure the particle size distribution, shape, height, volume, and other parameters using the software tools (AFM Analysis Of Nanoparticles.........).

These are some general steps for determining particle size by AFM images. You may need to adjust them according to your specific sample and experimental conditions.

Source:

(1) A Guide to AFM Sample Preparation - AZoNano.com. https://www.azonano.com/article.aspx?ArticleID=6226.

(2) 9.2: Atomic Force Microscopy (AFM) - Chemistry LibreTexts. https://chem.libretexts.org/Bookshelves/Analytical_Chemistry/Physical_Methods_in_Chemistry_and_Nano_Science_(Barron)/09%3A_Surface_Morphology_and_Structure/9.02%3A_Atomic_Force_Microscopy_(AFM).

(3) AFM Analysis Of Nanoparticles - Atomic Force Microscopy. https://www.afmworkshop.com/applications/research/atomic-force-microscopes-for-nanoparticles-characterization.

(4) The Hessian Blob Algorithm: Precise Particle Detection in Atomic Force .... https://www.nature.com/articles/s41598-018-19379-x.

(5) A Guide to AFM Image Artifacts Page 1 - uni-wuerzburg.de. https://www.physik.uni-wuerzburg.de/fileadmin/physik-fpraktikum/2020/AFM/AFM_Bild-Artefakte.pdf.

Yeah, it's subjected to a good characterization technique and AFM has three major abilities: force measurement, topographic imaging, and manipulation.

Is it usual to amplify DNA with thiolated Primer? Otherwise, you may need to check how thiolated primer affects PCR. I am not sure but thiolated primers might form di-thiol between themselves.

The immobilizing DNA amount might not be enough ( I did not check it).

During incubation of your DNA on the gold surface, it should not be dried. TCEP makes the solution acidic. I recommend you need to mix TCEP and DNA in a proportionate buffer. Usually, I used PB as the article. I am not sure that such long incubation. Anyhow, if you add salt such as NaCl to the incubating solution. It helps to increase the immobilized density of DNA because It reduces electrostatic repulsion between DNA. You might refer to these two articles and 10.3390/bios10050045.

Good luck

Why not do the experiment? Measure a fresh tissue, fix it (PFA), measure again.

But to answer your question: The closer you are to the living state the better, scanning in buffer would be the best. The ECM is fairly robust in comparison to other structures, I would assume that unfixed will give you the most accurate stiffness measurements. Once you aldehyde-fix biology a lot of unpredictable things happen (tissues turn brittle, proteins are crosslinked but nothing else), and solvents are even worse because a lot of material gets extracted. Also keep in mind that NBF contains methanol. And all these parameters vary depending on which tissue you're looking at. You'll have to do the experiment! ;)

For general structural preservation PFA>NBF>solvents

we use ours, which is particularly stable; which is indeed important for PSD calculation of surface roughness and determination of nanoscale wettability. Sending you 2 of our works in case you are interested. In fact, we are working on a general scheme of "test the stability of your AFM system yourself", but have nothing published yet. Let me know if you may be interested.

best regards

Thank you Nicolas for your response. I am using Nanoscope analysis v1.5 and AFM Bruker multimode 8 (Nanoscope 9.1) for the experiments. In Nanoscope software, just Hertzian and Sneddon models exist. My material is collagen, which I am testing in the air in PF QNM mode using scanasyst-air (Bruker) cantilever with the spring constant of 0.4 N/m.

I didn't know about AtomicJ software. thank you for suggesting

In Nanoscope, there are the options "capture" and "capture withdraw". If "capture withdraw" is chosen, it does what you describe.

Nanoindentation is a separate testing procedure that is often used in conjunction with Atomic Force Microscopy (AFM). It is used to measure properties at the nanoscale, such as Young's modulus, hardness, stiffness, and load vs. depth and load vs. hardness. Other properties can also be measured using nanoindentation, depending on the specific application. In India, there are several institutions that offer nanoindentation services. These include the Indian Institute of Technology (IIT) Delhi, IIT Bombay, IIT Madras, IIT Kanpur, IIT Hyderabad, and the National Institute of Technology (NIT) Surat. Additionally, there are several private companies that offer nanoindentation services, such as NanoTest India, NanoTest Solutions, and NanoTest Technologies. If you are having difficulty finding a nanoindentation service provider, it is possible that the machine is under maintenance or the operator is not available. In this case, it is best to contact the service provider directly to inquire about the availability of the machine and the operator.

Dear all, please have a look at the following similar RG thread. I have pointed on a paper comparing major technique for film thickness measuring. My Regards

Dear Jürgen Weippert rt thanks alot for your help.

I just found people use ethanolamine in the SA coating.

Dear Jürgen Weippert thanks for reply. I solved the problem.

Best regards.

Good day! I suppose you should try water-ammonia solution at 60 deg C at 3:1 ratio for 10-15 minutes, followed by water-hydrogen peroxide (50%) solution at 60 deg C at 4:1 ratio for 10-15 minutes. Unfortunately, I forgot some references.

If you have found current answer as useful, please, do not forget to recommend it. That will help other researches to find the best answer, according to their purposes. Best of luck in your research!

Good day! I wonder is it obligatory to use gas gun to dry sample, or it is better to dry sample in dessicator? Previously I've used pretty the same methodology of sample preparation in my case. However, I had long chain fragments, a little bit different material, neutralized surface charges of mica, spin-coated/dropped material and left it dry in dessicator. And I have not mentioned any kind of preferable orientation of my material. Thus, maybe you should consider such a way.

If you have found current answer as useful, please, do not forget to reccommend it. That will help other researches to find the best answer, according to their purposes. Best of luck in your research!

You can do it inside AFM using a standard calibration routine, which should be described in a manual. There are two common methods: (1) acquire a force-distance curve on a hard substrate - calculate optical lever sensitivity (nm/mV) - aquire thermal spectra for the resonance frequency and spring constant ( ) or (2) use the Sader method ( ).

It is possible. We used just a conventional high-tilt (Jeol) TEM holder - the probe can be put there instead a grid, then just tilt it to 60 deg and see the tip clearly.

Good luck!

Thank you for your response Ofir.

Fortunately, I got a working protocol after repeated modification of the initial protocol.

The result looks good too. I am using the Nova PX software to analysis my images too. If you have any further recommendation, kindly share.

Thanks again