Science method

Atomic Force Microscopy - Science method

Atomic Force Microscopy are aFM is a very high-resolution type of scanning probe microscopy, with demonstrated resolution on the order of fractions of a nanometer, more than 1000 times better than the optical diffraction limit.
Questions related to Atomic Force Microscopy
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Hello! I am new to AFM and am trying to analyze a DNA origami structure created by my colleagues. I am currently using a FlexAFM in air, dynamic mode, with a Tap150Al-G cantilever to visualize our DNA origami sample, but I'm facing some challenges. The sample is a hexagon made of six equilateral triangles, each with a side length of 40 nm, resulting in an 80 nm diagonal. The protocol I'm following for fixing the sample on mica is as follows: I apply 10 µL of the sample (origami in buffer) to freshly cleaved mica, let it sit for 7 minutes, then wash it with ultrapure water to remove excess salts, and finally let it dry in the air for 10-20 minutes.
However, the images I obtained (attached) are not what I expected. Could I have damaged the origami during the sample preparation process? I’m unsure if it’s relevant to mention, but we used only half of the scaffold to create the hexagon, with the other half potentially appearing in the background.
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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.
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I am evaluating to buy a nanosurf coreAFM or a Oxford WITEC AFM.
Does anyone have experience with both AFMs, especially with Oxford Witec?
From my perspective, the Oxford, in this case coupled with a Raman, is an accessory coupled to the Raman microscope, while the Nanocore is a standalone AFM.
I would expect better performance with the dedicated one.
My I have your suggestions and inputs?
Thanks for your comments!
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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
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I'm planning to characterize my liposome vesicles using Atomic Force Microscopy (AFM). Most research papers recommend using freshly cleaved mica discs due to their atomically flat and clean surfaces, which seem ideal for imaging soft nanoscale structures like liposomes.
However, in my lab we currently have only glass discs available. What are the key differences between mica and glass discs in terms of AFM imaging performance? Could using glass significantly affect the resolution or stability of liposome observation?
If anyone has experience using glass substrates for liposome imaging in AFM, I’d really appreciate your insights or suggestions.
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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
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Hi all. Apparently all hardware is fine (several green LEDs everywhere, on controller, back of acquisition card, etc.), yet there is no DSP recognized by the PC. Drivers are probably requested for the Sheldon Instruments card C6713. Anyone ever had same issue and solved that? Please help.
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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?
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I have developed an AFM, and I want to capture an impressive image with it. So far, I have only scanned calibration samples. The resolution power and sharpness of the images are quite good. I thought I could image a virus with the AFM. However, I am a physicist. Where can I obtain a non-hazardous virus sample that I can find locally and prepare with my limited knowledge? How can I prepare it?
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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.
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Hello! I'm new to using AFM to analyze nanoparticles in a solution, and I have a question. I see a "line fit 2.79 nm" bar on the right side of my image. Does this refer to the height of the features in the image? For example, does the white area correspond to an approximate height of 2.79 nm? I noticed in another sample, which doesn't have nanoparticles, that it shows "line fit 700 pm." From this, I’m guessing that this value might represent the maximum height. Could you confirm this? Thank you!
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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.
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I am particularly interested in understanding the best techniques and approaches for accurately determining roughness parameters at each layer interface.
I have another question about X-ray reflectivity (XRR) and atomic force microscopy (AFM). However, I am unsure how to interpret multilayer roughness data from XRR fitting or how to correlate it with AFM measurements.
Any advice, recommended tools, or references to relevant literature would be greatly appreciated.
Thank you in advance for your insights!
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Thank you, Dr
Chaitanya Kumar
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I am working on characterizing thin films and would like to measure their thickness using the Hitachi AFM5100N model. Could someone provide a step-by-step guide or tips on the best approach to accurately measure film thickness with this AFM model?
  • The choice of cantilever/probe for such measurements.
  • Recommended settings or modes (e.g., contact, non-contact, or tapping).
  • Any challenges or precautions to keep in mind during the process.
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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.
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Hi There,
I fabricated hydrogel microparticles. Now I am trying to measure its stiffness using AFM contact mode.
Issue I am facing is, when i put those beads onto a glass slide, they swim around in that tiny droplet hence it makes it difficult to strike using cantilever. Anyone who has done AFM with their sample immersed in water?
Kind Regards
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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.
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I made microbeads (40-70um) using a hydrogel. Now I am trying to measure its stiffness using AFM contact mode. I am having difficulty in targeting the particle using the cantilever as particles keeps swimming around in that tiny droplet on a glass slide. I tried to coat the glass side using gelatin but it didn't do any good.
Anyone expert in dealing with immersed sample for AFM contact mode? Especially biological samples
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There are several papers used Bind-Silane product to attach acrylamide beads. Please check here:
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.
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Is there any explanation for the strange curve feature at the beginning of the AFM tip contacting the sample membrane? Is it that there is some dust attaching the AFM tip or any other reason? How to avoid it?
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This is quite common when the tip adhere to cell membrane. See the reference:
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I am using Nanoscope IV multimode AFM. The laser is clearly reaching the quad photodetector window after reflecting from the cantilever and mirror. But there is no change in the VERT (9.99) and HORZ (9.99) signals, and the SUM is always ZERO.
If anyone has any idea to solve this issue, I will be very grateful.
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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.
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Hi everyone!
For our coursework we need to create a test pattern for atomic force microscope calibration using colloidal spherical particles. I think that across the board this structure is the most suitable in all directions. To create this structure, what is the best way for us to do it? I thought we could use a PDMS stamp or are there any other methods you could share?
Thank you so much
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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.
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I'm trying to cleave mica with a blade, but it breaks (it's brittle) before I can cleave it. Is there a specific way to achieve a clean cut with mica?
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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!
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Can I use a glass substrate rather than mica to characterize liposomes in AFM?
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Yes, any flat-parallel surfaces will be ok. Mica, glass, silicon wafer, and so on.
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Hello everyone,
I am currently working with PS-b-P2VP block copolymers dissolved in toluene at a concentration of 5 mg/ml, aiming to create surface coatings with hexagonally packed nanostructures. However, I am facing several challenges and would greatly appreciate any guidance or suggestions from those with experience in this area.
Here are the specific issues I am encountering:
  1. Surface Coating on Glass: The toluene solution does not spread evenly across the surface despite thoroughly cleaning the glass substrate. Are there specific cleaning protocols or surface treatments that could improve the wetting properties of the glass?
  2. Nanostructure Formation: When examining the coated glass with atomic force microscopy (AFM), the nanostructures appear sparse and not fully packed. In contrast, other studies report achieving complete hexagonal packing. What additional factors should I consider to improve the packing density of the nanostructures?
  3. Drying Process: Currently, I am drying the coated glass substrates in air. Could a more effective drying method enhance the formation and stability of the nanostructures?
Any insights, protocols, or references to relevant literature would be incredibly helpful. Thank you in advance for your assistance.
Best regards,
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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:
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I'm studying magnetic domains in 2D ferromagnetic materials and magnetoplasmonic structures using MFM, but electrostatic interactions are making it difficult. I've tried grounding the sample. Recently, I learned about combining EFM and MFM. Can anyone guide me on performing this hybrid mode or suggest other methods?
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I want to quantify some roughness parameters using AFM data. I tried to quantify some of them by Gwyddion software but its HHCF doesn’t have a fitting function contemplating all parameters I need.
Fit function that I found in my Gwyddion version:
y = 2sigma^2 * ( 1 - exp ( - ( r/E )^2 ))
, where, sigma is the interface width and E is the lateral correlation lenght.
Fit funtion that I was looking for:
y = 2sigma^2 * ( 1 - exp ( - ( r/E )^(2a) ))
, where a is the Hurst exponent.
I also tried to export data to origin and tried to set a new fitting function, but I got stuck on how to build it. Something went wrong since my limit bounds aren't being followed.
If anyone could help me with some insights I will be really grateful.
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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.
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I am trying to do Roughness Measurement for Alumina templates . I am getting streaks when playing around with I-Gain & P-Gain but not a good image of publication quality.
Could someone suggest an approach to this ?
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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.
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I am studying the surface topography of bacteria-degraded cellulose and lignin using the non-contact mode of Atomic Force Microscopy (AFM), which requires a solvent to make a dispersion of the powdered material. Can we use water as a good solvent for this analysis?
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Kurt Haunreiter Thank you
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Hello,
Can anyone advise on methods to investigate a polymer on a surface?
I have tried XPS, tapping AFM, ellipsometry, contact angle and CV and EIS. I know something is on the surface but the question is what does it look like and how is it binding and I don't know how to determine that. the polymer is mostly benzene rings with one anchoring unit to bind to surfaces.
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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
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I recently conducted an AFM of metal oxides to get information about the size, shape, and arrangement of the grain. However, I couldn't find any grains in the obtained result (procedure for AFM image done by using Gwyddion software). This result brought me confusion, which could be due to analysis issues or possibly my incorrect interpretation. However, I have received the correct results of XRD, FTIR, and FE-SEM of the same material, which suggests that there is no issue with the synthesis method. Anyone who has experience with AFM will help me solve this issue. Thank you so much for the time.
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Jürgen Weippert thank you for giving me an informative response.
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I recently conducted an AFM of metal oxides to get information about the size, shape, and arrangement of the grain. However, I couldn't find any grains in the obtained result (procedure for AFM image done by using Gwyddion software). This result brought me confusion, which could be due to analysis issues or possibly my incorrect interpretation. However, I have received the correct results of XRD, FTIR, and FE-SEM of the same material, which suggests that there is no issue with the synthesis method. Anyone who has experience with AFM will help me solve this issue. Thank you so much for the time.
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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.)
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When scanning a 1-micron area at 0.5 Hz using the Dimension Icon in QNM mode, I observed wave-like artifacts in the topography channel. Even after attempting various order flattening methods, the artifacts persisted. However, reducing the scan rate to below 0.3 Hz eliminated these artifacts. What might be the cause of these wave-like artifacts in AFM topography
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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!
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I have AFM scans of a uniformly textured surface of 16x16um size. I would like to obtain the slope distribution of the surface using Nanoscope, as I plan on trying to relate this parameter to the growth of layers on this textured surface.
I am aware that this can be done by using the Gwyddion software in a fairly simple manner. However, I have been using Nanoscope already for quite some time for my image processing and would like to carry out this additional step of processing in the same software.
Thank you, in advance!!
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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!
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The effect of film thickness on the optical properties of tin oxide films What are your opinions? I would like to obtain results and data on this subject, as well as the structural properties of this membrane, examined by FESEM, AFM, and XRD. Thank you very much.
📷
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Interesting...
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The landing process of the AFM (NT-MDT) we use does not work. Although the computer program appears to be running, but it does not come close to your fingertips. We cannot observe any mechanical movement. Be more than happy to help with this.
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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?
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Dear colleagues,
I defended my Ph.D. thesis in October 2016 and now I am looking for a postdoctoral position in microscopy (AFM, TEM, SEM) and biophysics of microorganisms (especially, viruses, I like them :)).
My CV is attached. If there is an open position in your lab, please, write me.
Best regards,
Denis  
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That sounds like an exciting field! Here are some steps you can take to find a postdoctoral position in microscopy and physics of microorganisms:
  1. Identify Research Groups: Look for research groups or labs that specialize in microscopy and physics of microorganisms. Search university websites, scientific journals, and research databases for relevant publications and projects.
  2. Networking: Attend scientific conferences, workshops, and seminars related to microscopy, microbiology, and physics. Network with researchers in the field and express your interest in potential postdoctoral opportunities. You can also reach out to professors or researchers whose work you admire to inquire about available positions.
  3. Online Resources: Explore online platforms and job boards dedicated to academic and research positions. Websites like Nature Careers, Science Careers, and ResearchGate often list postdoctoral positions in various scientific disciplines.
  4. Collaborations: Consider collaborating with researchers who are conducting interdisciplinary work at the intersection of microscopy and microbiology. Collaborative projects can provide valuable insights and connections within the scientific community.
  5. Tailored Applications: Customize your application materials, including your CV, cover letter, and research statement, to highlight your expertise in microscopy and physics of microorganisms. Emphasize relevant skills, research experience, and achievements that align with the requirements of the position.
  6. Funding Opportunities: Look for postdoctoral fellowship programs or research grants that support projects in your area of interest. Many funding agencies offer fellowships specifically for early-career researchers pursuing research in microscopy, microbiology, or physics.
  7. Stay Informed: Stay updated on the latest developments and advancements in microscopy techniques, microbiology, and physics research. Familiarize yourself with emerging trends and technologies that could enhance your research interests and expertise.
  8. Persistence and Patience: Finding the right postdoctoral position can take time and persistence. Be proactive in your search, maintain a positive attitude, and keep refining your skills and qualifications to increase your competitiveness as a candidate.
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.
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I have created a FE model including:
1. Bead (Green),
2.Cell (Red)
3.Components inside the Cell, beams, truss, and nucleus.
Constraint:
Embedmentt, all components embed in cell.
Boundary condition:
1. Bottom of cell are fixed
2. Bead compress along the Z direction with 500nm
I have finish the calculation through Implicit Dynamic, however, actually i don't have densities of each material (those used in Implicit Dynamic are assumptions).
So, can i solve this question just with E and v with Abaqus/standard?
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You can, however the simulation will be too slow in term of convergence.
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I'm trying to perform the CAFM of exfoliated graphene flake on gold substrate but the results aren't reseaonable.
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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.
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Dear all,
I got particle size from AFM , it is more than 140nm but for same sample i got large surface more than 170 m2 /g with pore volume 0.06 ml/g by use BET surface area.
Is it possible?
Best regards
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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!
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I have encountered some technical problems during AFM analysis. The surface and scale bar do not match well when I run the collected data through Nanoscope analysis. For AFM scanning, I use tapping mode. There may be issues such as (1) cantilever model, (2) tapping mode, and (3) contact mode, etc
Thanks in advance
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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.
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please do you know: How to adjust NX10 Atomic Force Microscopy to mode butterfly loop?
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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!
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how d i interpret or determine with the mesure distance the pitchand compare characteristic freature szeand density among three media with statistical data things like total projected area, mean grain areaand mean grain size
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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.
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in analyzing AFM image how can one explain the mean differences in the AFM images
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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...
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Hello! What is the easiest way to calibrate the lateral force in AFM? I am using JPK Nano wizard AFM instrument. There are several methods in the literature. Can anyone suggest the easiest way to do it?
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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.
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Can anyone suggest something to resolve the issue of distorted friction images on the AFM? We tried several things: switching off the system and computer, reconnecting wires, changing tip, scan rate, scan angles, gain values, vibration table, and sample. The scans are taken in contact mode at a very low normal load. The topography images are still better but friction images are just noise. We are using the 5500 Agilent Technologies AFM (pretty old). Thank you.
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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
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I used dispersion sample preperation for the AFM test but I just can't seem to acquire clear pictures of the particles sticking together!
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Seniha Simale Su Uygan
Thank you so much.
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I wanna study a multiferroic material which is ferroelectric and antiferromagnetic using CASTEP. I need your guidance regarding study of AFM material and also i wanna know how spin polarization box work ?
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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?
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Hello everybody.
I'm trying to study HPHT synthetic diamond plates with low (first nm roughness). When i taking 100×100 μm photo by AFM, you can see a lot of flakes/dirt on them.
The question is how can i remove this dirt? I already tryed ultrasonic cleaning in ethanol, but it doesn't remove dirt at all.
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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.
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What could be the reason for this situation in the AFM image? Is what is marked a DEFECT? and why. This is an image (AFM) for ZnO prepared by Sputtering method with -200 V as bias voltage and after annealing at 450 °C.
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Thank you so much Dr. Whipper
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Hello all! I would like to know about the force spectroscopy whether a Bruker ScanAsyst system with Nanoscope Analysis user interface can provide single-molecule force measurements data. Any special modules needed to perform the single-molecule force (SMF) measurements ? I am able to get only indentation force curves (Force-distance curves) which might not be the same as SMF curves.
A clarity in the discussion is highly appreciated.
Thanks in advance!
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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?
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Can AFM measures the roughness of the sample? How? What are the largest area dim.s?
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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.
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How to analyze an AFM image?
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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.
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Generally height height correlation function is computed in one dimension along fast scaning axis (x direction). My query is " how to compute hhch in polar coordinates fron afm measurement".
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A step by step instruction will be very helpful.
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We are using Shimadzu SPM-9700HT AFM in the lab. It uses a 650nm laser for cantilever detection. I want to replace the laser to a longer wavelength to avoid excitation of fluorescent samples. If you have experience of replacing the laser unit, would you please be able to share the experience here?
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Normally laser in AFM system is focused on cantilever (only) and does no affect sample surface.
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hello everyone could anyone knows intrenship programm on AFM and STM ? I can use only 2 modes of it, if is there any commertial intrenship programm I wanted to take in part it
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Mr. Thank you for your help
I understand you, and I'll check this link
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about type of josephson junction is called step edge ,considering that the created step edge is in micro-nanometer scale, how can you determine the area to be measured in AFM analysis ؟How to determine the border of the covered area from the etched area under the microscope (AFM or SEM)?
Is there a need to mark the back of the sample?
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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.
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Hello,
I am a Master's student of Mechanical Engineering at Gwangju Institute of Science and Technology, South Korea. What can be a good thesis topic for mechanical students on AFM research?
I am working on AFM for the last six months. I have gained sufficient knowledge about the components of AFM, and their effect on the speed of AFM.
For my thesis, I want to work on the side of Signal Processing (to improve the resolution of the acquired images), I am more familiar with the control work and if the control doesn't take a long time I will be happy to work on the control side.
I have searched a lot about research trends on AFM and get to know we have two trends
1. High-Speed AFM
2. High-Resolution AFM
For High Resolution I didn't find any publication and ideas, almost every author say they use FFT and Gwyddion software for making images better. Please suggest me some topics for my MS thesis. I have AFM Device and my lab has almost all the necessary tools and components to work with it.
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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.
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It is an old AFM system with no technical support available anymore. I would like to start a discussion thread for the researchers still using it and discuss the issues faced while using the equipment. Currently, I am facing issues with the friction images.
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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.
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Welcome
I use NaioAFM from Nanosurf company. please how I can get a solution for the background noise (electronic noise) during measurement.
PID parameters are
I 1000
P 1000
D 0
Scan rate 1 sec/line
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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.
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Hello,
I typically use sharp AFM probes to do friction measurements on silica. I blunt the tips somewhat and convert the apex to thick silica by annealing in air at very high temps, which produces a very smooth apex. Unfortunately, in recent experiments, the wear rate rapidly converts the tip to a punch which creates all sorts of problems for me.
I was hoping to work around this problem by moving to sililca colloidal probes, which are very common of course. My question is what is/are good supplier(s) to obtain colloids in an appropriate size range (10-50um I guess) for gluing to AFM cantilevers, and critically, with very low roughness values (<1 nm at least) to make the contact mechanics comprehensible, and ideally though perhaps not critically, without the the substantial fraction of Na that is inherent to the synthesis of many colloidal silicas.
Porosity is not a major concern unless it affects the roughness. I am having trouble locating appropriate suppliers for such colloids. Any tips would be greatly appreciated.
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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.
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In a few articles, I have come across images that are similar to SEM cross-sectional images but taken with AFM, but the article does not mention the details. Can you help me to measure in this way?
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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.
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Anybody has run into similar problema, recently we our research, we've runnning through this issue in the AFM images. They're distorted, elongated in the side, but the center seems to be ok.
We've tried to change the tip, the sample, faster scanning, let ir "rest" or use for longer times. But nothing seems to resolve.
Someone knows how to help, please.
We tested in 0º and 90º
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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.
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Why do we conduct AFM analysis?
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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.
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Nanaoparticles size & morphology by AFM
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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.
(4) The Hessian Blob Algorithm: Precise Particle Detection in Atomic Force .... https://www.nature.com/articles/s41598-018-19379-x.
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I want to investigate the formation of microcavities on a surface before and after some experiment. Is AFM capable of performing that ? or what should i use ?
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Yeah, it's subjected to a good characterization technique and AFM has three major abilities: force measurement, topographic imaging, and manipulation.
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I've been looking for methods for immobilizing 5'-Thiol modified dsDNA on gold slides. Most of what I've come across suggests using DTT followed by a desalting step or using TCEP. However, I haven't had any luck reducing and then conjugating the DNA onto the gold slides. I've seen some methods use DTT1,2, and some use TCEP3, and some include an incubation step with MCH2,3 after the thiol reducing step. It's been difficult finding a complete and satisfactorily detailed method online.
The DNA I am using is a 1 kb long double-stranded molecule with a 5'-Thio modification at one end and a 5'6-FAM modification at the other end. I need to synthesize the strands myself via PCR using two modified primers and a template strand rather than ordering the fully modified 1 kb strand, so my working concentrations are usually fairly low (~70-100 ng/uL after PCR and spin-column purification).
Can anyone provide a detailed method that has worked for them for reducing thiol modified DNA and immobilizing it onto gold surfaces or gold monolayers?
  1. Hegner, M., Wagner, P. & Semenza, G. Immobilizing DNA on gold via thiol modification for atomic force microscopy imaging in buffer solutions. FEBS Letters 336, 452–456 (1993).
  2. Ladik, A. V., Geiger, F. M. & Walter, S. R. Immobilization of DNA onto Gold and Dehybridization of Surface-Bound DNA on Glass. 5.
  3. Das, J. et al. Reagentless biomolecular analysis using a molecular pendulum. Nat. Chem. 13, 428–434 (2021).
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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
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Hi scientific community!
I was hoping to get some input on a problem I am currently having deciding how to fix my samples for AFM. I am using AFM to detect stiffness of the ECM in fibrotic areas, and have the option to leave my samples unfixed (we have tested that this works), or go for PFA, NBF or a solvent method like methanol.
Since we know methanol will dehydrate the ECM and PFA or NBF will cross-link it, we were intending to go straight for measuring the unfixed tissue, since this would be most "correct". However, whilst the main structural proteins like collagen will be fine for the time period of the AFM experiment if kept cool, it has come to my attention that other smaller, less stable ECM proteins could degrade if unfixed, which could affect the integrity of the fibrosis and therefore the resulting stiffness measurement.
Most previous literature either uses unfixed tissue or PFA.
What seems the best method to you - to fix the ECM, or to go ahead unfixed?
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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
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We are trying to compare these two systems in the process of purchasing one of them. Our applications revolve around surface roughness quantification, mineral wettability evaluation, and surface force measurements on rock samples. I would appreciate your expert views.
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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
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Dear All, can anyone explain to me how to measure the elastic modulus of a material through force-volume AFM curves? I am using Nanoscope Analysis software but the results seem not to be accurate.
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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
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Hi! I'm doing scans using an atomic force microscopy (Brucker). The problem is when the scan ends, a message appears and I can't do another scan. The message says: " File captured, tip withdrawn, high voltage turned off".
Please, ¿someboday can help me?
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In Nanoscope, there are the options "capture" and "capture withdraw". If "capture withdraw" is chosen, it does what you describe.
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Nanoindentation is a attachment with AFM or it is a separate testing procedure? Nanoindentation gives property at nanolevel? Young's modulus, Hardness, Stiffness, Load vs Depth, Load Vs Hardness properties alone cane be obtained using nanoindentation or any other properties can also be known using nanoindentation? Where I can get all these things done in India? Please share your suggestions. Many of the prestigious institutions saying machine under maintenance, machine not working or operator not available.
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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.
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Is there any method to calculate the thickness of the films by AFM analysis.
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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
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I want to calculate Skewness parameter. The data obtained from AFM is consist of Ra, Rq, Rp, and Rv. It does not measure Rsk. How can I calculate Rsk from Rq numerically?
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Dear Jürgen Weippert rt thanks alot for your help.
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I am trying to perform covalent immobilization of streptavidin protein on glass surface. This is done by first coating the glass with 2% APTES-toluene and then with 2.5% glutaraldehyde-water solution. Then I add the streptavidin which is in PBS (pH 7.4) on the glass coverslip. This doesn't seem to work. Please let me know the right pH, salt and temperature conditions that are appropriate for the reaction between glutaraldehyde and amine groups created by APTES coating on glass.
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Specially with "HRTEM" it'is quite difficult get high resolution morphology in real sense!! Or the require knowledge, expertise is lacking off? Let produce a significant and directional concluding discussions here!!! This is my earnest appeal to all
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How can I get AFM images of bare FTO? I can't fix the difference between Backward and Forward due to the conductivity of the FTO. (PARKSYTEM XE-07)
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Dear Jürgen Weippert thanks for reply. I solved the problem.
Best regards.
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The tip will be used for scalpel AFM technique but its contaminated with Si. I have tried with low conc. of HF and sulfuric acid in ultrasonication, but the cantilever itself blew away. Normal water or acetone with ultrasound also didn't work.
Is there any easy option for the cleaning, either wet or dry?
Describing some easy option rather than sharing some scientific article, will be greatly cheered :)
Thanks
Swarnendu
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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!
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I have this issue with drying short DNA fragments on mica for AFM experiment.
As you can see DNA in this AFM image DNA has a preference to face in a certain direction.
I think it was caused by solution drying with nitrogen gas gun. Nitrogen gas perhaps pushes away the solution in a direction along with DNA.
How can I avoid this orientation skewness?
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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!
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Hi,
Can anyone suggest a formula/method/technique to calculate the spring constant and also resonance frequency of an AFM cantilever after metal deposition?
Thanks in advance,
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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 ( ).
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I've interested in being able to conduct TEM analysis on my AFM probes after use. I'm currently struggling to find a way to mount the AFM probes into a TEM sample holder that normally accepts TEM grids. Has anyone had success doing this? Thank you.
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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!
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We have a new AFM with a capability to achive high resolution images (up to 50nm). The AFM tips can scan the surface of the object and as well, can penetrate into the object. We also have the capability to use the tip for scanning planktonic bacterial cells inside a medium.
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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
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During AFM imaging, the tip does the raster scanning in xy-axes and deflects in z-axis due to the topographical changes on the surface being imaged. The height adjustments made by the piezo at every point on the surface during the scanning is recorded to reconstruct a 3D topographical image. How does the laser beam remain on the tip while the tip moves all over the surface? Isn't the optics static inside the scanner that is responsible for directing the laser beam onto the cantilever or does it move in sync with the tip? How is it that only the z-signal is affected due to the topography but the xy-signal of the QPD not affected by the movement of the tip?
or in other words, why is the QPD signal affected only due to the bending and twisting of the cantilever and not due to its translation?
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Indeed, in the case of a tip-scanning AFM the incident laser beam should follow the tip scanning motion, to record throughout the deflection signal for the same spot on the cantilever backside. This can be achieved by integrating the laser diode with a kind of tube (with its long axis parallel to the z-axis) that carries the cantilever holder at its lower end and is kind of hinged at its upper end. The scan piezos would act on the entire tube, incl the laser diode, in a plane between the tube's upper and lower ends. Whether or not your AFM system works exactly the same way I cannot tell for sure though.
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I have got the FM and AFM1 configurations and able to optimize by giving MAGMOM. But how to get AFM 2 and AFM 3 ? and how the MAGMOMS are to be provided? I need step by step procedure. Thank you.
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after the interaction of drug the enhancement in the SPR band was observed the intewraction was proved by FTIR and AFM the AFM resiults shows aggregation of NPs the of NPS increases from 40nm to 200 studied bty AFM i also study time depedent interaction of drug and nanoparticles the DLS spectra showing abrupt results how to interpret the results.
DLS result attached plz guide
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Check out this website:
Get your results analyzed by an expert quickly! The service is not free but it's very affordable and definitely worth it.
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I have grown Ge on glass with in-situ annealing. firstly the rms roughness and height decreases then increases with temperature while grain size increases for all temperature.
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Also compressive strain follows same trend i.e first increases then decreases
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FFT image of AFM
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Yes you can , read these papers , i hope its help you .
Sincerely
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I am quite new to AFM imaging and I'm having struggles in getting accurate topography images to measure surface roughness. My issue is that even though I it seems that the trace and retrace profiles match I am unsure if I accurately traced the surface or the image is an artifact. I'd like to ask for any tips or suggestions?
The afm machine is bruker multimode afm.
The mode I normally use is air tapping mode.
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You make sure that
1. Tip is sharp enough
2. Tip is landed properly on the surface through f-d curve
3. sample is firmly fixed on holder
4. feedback parameters are set appropriately
you may attach a topography image for further comments
Good luck for better images
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I've been trying to do this for years. The recommended way of using curved tweezers to grab it near the back gets me way less than 50% success. Cantilever tweezers dont work because the probe is too recessed. I've tried grabbing from the front with self-locking and normal sharp tweezers. I have somewhat unsteady hands, but they aren't that bad. I am 95% successful on the Asylum MFP3D, as long as I remove the metal tongue contraption completely first.
Any tips aside from the ones above that don't work for me?
I often need to use the same tip more than once lately for technical, not financial, reasons, so the current situation is untenable.
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I like using a tweezer that looks like this (not exactly this model, it's just the first image I found):
I dare to say that my "success rate" with that model should be in the 90% range.
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I would like to perform surface roughness of natural fibers by either using AFM or Laser micrsocpy, what are the main sample preparation steps involved for better results and accurate measurement?
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Hello
I would suggest that you measure your natural fibers using a microscope with calibrated scale bars, so you could have roughly ideas how big features of your fibers are. If the feature is small enough i.e. less than 10nm. You can try to use AFM.
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I am working on Casimir and Double layer force in liquid(water) by AFM, but many bubbles appear after injection of water into the AFM tip holder, I am not able to remove air bubbles from the water. Is there any way I can remove bubbles from water?
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Some ultrasonic cleaning devices support special degassing modes for liquid solutions (by pulse frequency variation) . Maybe degassing water by ultrasonic could help you?.
Also the creation of a rough vacuum with the help of a pump and a suitable container would extract air from water...
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tapping mode tips are too stiff to measure extracellular matrix roughness. I am looking to find the right cantilever type with a stiffness (k-value) that is able to do so in solution.
Thank you in advance
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For ExtraCellular Matrix samples I would use PeakForce QNM (Hybride Mode or similar) with contact mode cantilever (e.g. soft Ultra-Short Cantilevers from Nanoworld are good candidates)
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Anybody working with elasticity measurements with a Keysight 9500 AFM? Trying to use PicoView plugins but it seems they are not compatible. Any information would help!
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Hi Catalina, I have used Keysight 5500 with Picoscan software. Could you be more specific on the issue you are facing? Are you unable to obtain the Fx curves?
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I need to open and elaborate a force-distance curve measurement file with Gwyddion.
How can I normalize the raw data, apply a model (e.g. Hertz) and get mechanical info of the material behavior (elastic modulus and adhesion force)?
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Good day! I just wanted to recommend you NanoPlot, designed by Piotr Mariusz Pieczywek Here is the link: https://github.com/ppieczywek/NanoPlot
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How do I prepare my sample for AFM characterization of NPs?
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Similar to what Yuri have suggested. Depending on your nanoparticles, it is probably best to centrifuge your sample to get more of the NPs when put it on a clean substrate. You can use silicon wafer, coverslip, or any clean substrate to hold your NPs. Here's what I would try:
1. suspend the NPs in ethanol. then centrifuge.
2. discard most of the liquid after centrifuge.
3. take 5 uL of the NPs and put it on Si wafer.
4. left to dry and should be ready for AFM.
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Which software i can use as well? Any link of video will be helpfull. Thanks
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Dear Jürgen Weippert . Thank you so much for asking . Yes I can, but sometimes the answer can be from different angles (articles). The reader usually concentrate on the first answer ( article ) and ignore the rest . So if each answer alone, you can guarantee that all answers (articles) from different angles are read. Thank you so much. Wish you the best always.
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I am getting different roughness values ​​for same sample surface by Taylor Hobson surface profilometer and AFM. Approximately half the roughness value coming in case of AFM as compared to surface profilometer. Why is this happening, please answer about it, I have to put a specific reason in my journal.
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If you are taking a surface (area) roughness by AFM and a profile (line) roughness by profilometer, then they are not directly comparable. You could try extracting a profile from the AFM surface and analysing that for comparison (making sure you account for the difference in tip radius), but I think you will probably find 3 issues;
- Firstly, you should take several measurements and compare the average. >10 samples from each surface would be appropriate.
- Your surface could have directionality - therefore, the direction of your profile sample across the surface is of importance.
- Also, your surface could have features which are not consistent with scale. Your profile scan is 400 times longer than the longest feature you might have seen with the AFM.
Overall, I would say that the most likely reason for the difference is that there are features with a wavelength which cannot be captured by such a small area of investigation under the AFM.
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Has anybody run into similar issues with regards to the Nanoscope III where, when scanning, the image is seemingly elongated as seen in the image below? Having run through the manual and other forums we have restarted the AFM many times, let the laser heat up, left it off over the weekend, and have still run into this issue. Since the Nanoscope will start working sporadically from time to time, the tip is likely not the problem. Does anyone have any recommendations or thoughts as to what the issue could be?
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Such stubborn deformations could also result from a kind of obstruction of the scanner motion. Friction forces could be at play, possibly caused by debris or other particles that got stuck in the (narrow) gap between the sample holder and the surrounding area of the stage. If accessible, it could also be worthwhile taking a thorough look at the scanner.
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- Diamond suspension 1 um
- Colloidal SiO2 suspension (a few nm)
- Cleant in acetone ethanol and water by ultrasound bath
- Finally wiped with water with lens tissue and last dipped in ethyl ether
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We Can Analyse Different Materials by AFM, Such As Polymers, Metals, Fibers and elc., Then for Each of Category of Materials we Need a Different Method for Clean Pollishing.
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I was trying to image PDMS gels with AFM. I was not able to get any proper picture of the substrate, there was false engagement and noise. The substrate is plasma treated and coated with collagen. Any suggestions?
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There are many, many possibilities... It is quite rare, but you might have static charges on the PDMS and on the tip. They can exert very high repulsive forces.
Another problem could be a very thick and extremely soft collagen layer, almost liquid - not likely, is it?
Assuming you worked in noncontact/oscillation/tapping, I would mount an old (i.e. cheap) tip, switch to contact mode, and approach at very high setpoint force. The tip might well penetrate the collagen, but not the SiO2 layer (the plasma-treated top surface of your PDMS), and you should obtain some (poor) image. Maybe a starting point for troubleshooting.
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In AFM analysis under hybrid parameters there is a term called average profile wavelength which involves both amplitude and space parameters.
I am unable to understand the physical significance of the same. Can someone please explain the term in simple words ? In its equation La = 2pie Ra/delta a what is denominator term ?
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The denominator term (delta_a) is the arithmetic mean of the slope of the surface profile. i.e. it is the arithmetic average of dZ/dX for each point of the profile. For more detail how the average wavelength is defined and calculated, it is probably best to refer to ISO 4287 and 4288.
The average wavelength parameter was developed by Spragg and Whitehouse (https://doi.org/10.1177/002029407200500301). It is a kind of simplification of the autocorrelation analysis to assess the repeatability and dominant wavelengths of a surface. This is of importance for functional surface, but it is dependent on the “function” that the surface is trying to provide. More can be found on this topic in the paper from Spragg and Whitehouse (above) and in the Modern Tribology Handbook - Chapter 2 Surface Roughness Analysis and Measurement Techniques from Bhushan.
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Hi everyone,
I'm trying to get a monolayer and far a part of 100 nm polystyrene beads on mica, I diluted the beads with MilliQ Water, and I tried different concentration but I ended up with multilayers in the most areas of the mica.
My experiment should be done in liquid and an ambient conditions and it requires the polystyrene beads on mica like the image attached.
Any suggestions?
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Use the Langmuir-Blodget method. Create a "gaseous" layer of balls on the surface of the water. Then press it until a dense monolayer with ball contacts appears. Lower the mica plate and then slowly raise it up. It may be necessary to select a solvent for the dispersion.
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Hello. Is there any way we can find the surface area of a roughened surface? Is there a certain constant that we can multiply by the surface roughness to get a measurement of the surface area?
Any non-AFM ideas?
Thank you for your time,
Bill
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Measurement of the specific surface area of disperse materials by low-temperature gas adsorption: Workshop
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Hi everyone, Can Atomic Force Microscopy be used in place of scanning electron microscope for characterization of nanoparticles?
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Nanoparticles Characterization Techniques used are as follows:
  • Spectroscopic Analysis (UV-Visible Spectroscopy)
  • Transmission Electron Microscopy (TEM)
  • Dynamic Light Scattering (DLS)
  • Zeta Potential.
  • Inductively Coupled Plasma Mass Spectrometry (ICP-MS)
  • Dark Field Microscopy.
  • Aerodynamic Particle Sizer (APS
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If I want to do surface characterization of a material which characterization technique is better SEM or AFM and why? All relevant answers are appreciated!
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Regarding material characterization, “better” depends on the sample under analysis. I would rather say that the best characterization can be obtained by combining SEM and AFM. For instance, if you are analyzing a nanocorrugated surface, SEM can give you the lateral dimensions of your nanofeatures, but you don’t have quantitative information in the vertical direction. On the other hand, AFM images are the result of the convolution of the real morphology with the shape of the AFM tip, so the lateral dimensions are always overestimated, but you can get the real quantitative value of the height of such nanotopographic motifs.
In SEM, besides using the standard secondary electrons detection, you can also take images with back-scattered electrons detection. The signal collected in those images formed with back-scattered electrons depends on the atomic number Z of the elements: higher Z produces a bigger number of back-scattered electrons detected. Consequently, if you are analyzing a composite material with metallic nanoparticles in it, such particles can be clearly distinguished with brighter contrast than the ceramic or the organic compound in the matrix. If the matrix is also metallic, they can also be distinguished if their atomic number is different enough. Moreover, by performing Energy Dispersive X-Ray analysis you can get the composition of the sample.
In AFM, an experienced user can get chemical contrast at the surface of a nanocomposite using the lateral force in contact mode or the phase signal in non-contact mode, which are related to friction and dissipative forces (adhesion, viscoelasticity, etc.), respectively. Furthermore, AFM allows for measuring some mechanical properties, characterizing electric transport (Conductive atomic force microscopy, C-AFM), and modifying the surface of the sample (indentation and even atom manipulation). Finally, advanced modes and special tips give access to other properties, and actually new microscopies are developed from the AFM: Kelvin probe force microscopy (KPFM) to obtain a map of the work function, Magnetic force microscopy (MFM) to characterize the magnetic domain structure of the sample, or Piezo-response Force Microscopy (PFM) to image the piezoelectric domains, to name a few.
I hope it helps, good luck with your research!
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I am trying to draw schematics of a droplet attached to the cantilever of an atomic force microscope (AFM). Can anyone please introduce a software for this purpose?
Thanks
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I tried Adobe Illustrator and it works really fine.
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I have certain metallic films treated via ion beam irradiation. I am analyzing the evaluation in topographical features. I have used NANOSURF FLEX AFM for the particular characterization. For analysis, I am using the recommended software which comes with the system. We are provided with different options (filters & signals) to present our micrographs. When we change these options, the area roughness changes significantly. For example, choosing the default setting of line fit shows normal roughness, however, changing the filter to derived data also changes area roughness decreases. Similarly, when we change the signal type from the z-axis to amplitude or phase, the roughness also changes.
I have consulted the literature and found that different approaches are used in different studies. I will definitely report the filters and signals I will be using for analysis. My question is which option is most viable for absolute area roughness.
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This answer may sound simplistic, but my natural propensity has always been to use the image format that best displays the data I want to show. If others want specific formats, one can include those as secondary or back-up data.