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30 results for “Atomic Force Microscopy”
Real-space imaging of an anisotropic atomic charge of σ-hole by means of Kelvin probe force microscopy
<p>Data set for the publication with the title 'Real-space imaging of an anisotropic atomic charge of σ-hole by means of Kelvin probe force microscopy'.</p> <p>An anisotropic charge distribution on individual atoms, such as σ-holes, may strongly affect the material and structural properties of systems. However, the spatial resolution of such anisotropic charge distributions on an atom represents a long-standing experimental challenge. In particular, the existence of the σ-hole on halogen atoms has been demonstrated only indirectly through the determination of the crystal structures of organic molecules containing halogens or via theoretical calculations, but its direct experimental visualization has not yet been reported . Here we demonstrate that Kelvin probe force microscopy with a properly functionalized probe can image the anisotropic charge of the σ-hole and of a quadrupolar charge of a carbon monoxide molecule. This achievement opens a new way to characterize biological and chemical systems where anisotropic atomic charges play a decisive role.</p>
Asperity level characterisation of abrasive wear using atomic force microscopy
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Data from: Adhesion force mapping on wood by atomic force microscopy: influence of surface roughness and tip geometry
This study attempts to address the interpretation of atomic force microscopy (AFM) adhesion force measurements conducted on the heterogeneous rough surface of wood and natural fibre materials. The influences of wood surface roughness, tip geometry and wear on the adhesion force distribution are examined by cyclic measurements conducted on wood surface under dry inert conditions. It was found that both the variation of tip and surface roughness of wood can widen the distribution of adhesion forces, which are essential for data interpretation. When a common Si AFM tip with nanometre size is used, the influence of tip wear can be significant. Therefore, control experiments should take the sequence of measurements into consideration, e.g. repeated experiments with used tip. In comparison, colloidal tips provide highly reproducible results. Similar average values but different distributions are shown for the adhesion measured on two major components of wood surface (cell wall and lumen). Evidence supports the hypothesis that the difference of the adhesion force distribution on these two locations was mainly induced by their surface roughness.
Atomic Force Microscopy data of Poly-3-hydroxybutarate and Poly-3-hydroxyvalerate films
<p>This dataset consists of atomic force microscopy (AFM) scans of <em><strong>Polyhydroxyalkanoate</strong></em> films in text (.txt) format as well as their corresponding previews in (.png) format. </p> <p>The surfaces of <strong><em>Poly-3-hydroxybutarate (P3HB [100%])</em></strong> and <em><strong>Poly-3-hydroxyvalerate (P3HB-co-P3HV) [90% :10%]) </strong></em>of six film thicknesses, three scan sizes (5µm, 10µm and 30µm) and three unique scan areas have been scanned with AFM equipment from NT-MDT spectrum instruments.</p> <p>This dataset has been used in the work <a href="../doi/10.5281/zenodo.10621269" target="_blank" rel="noopener">10.5281/zenodo.10621269</a> within which the scan data has been divided into multiple sub-pools for experimentation. Details on the structure of the dataset are as follows: </p> <ul> <li>The (.txt) format of the scanned images can be opened using Gwyddion (<a href="http://gwyddion.net/">gwyddion.net</a>)</li> </ul> <pre><code>FOLDER INDEX ITMO_PHA-AFM-SCAN-Data/ ├── Set.1_P3HB.(Homopolymer) │ ├── Size_5um │ │ ├── TXT │ │ │ └── 17(.txt)s │ │ └── IMG │ │ │ └── 17(.png)s │ ├── Size_10um │ │ ├── TXT │ │ │ └── 17(.txt)s │ │ └── IMG │ │ │ └── 17(.png)s │ └── Size_30um │ ├── TXT │ │ └── 18(.txt)s │ └── IMG │ └── 18(.png)s ├── Set.2_P3HB-co-P3HV.(Heteropolymer) │ ├── Size_5um │ │ ├── TXT │ │ │ └── 18(.txt)s │ │ └── IMG │ │ │ └── 18(.png)s │ ├── Size_10um │ │ ├── TXT │ │ │ └── 18(.txt)s │ │ └── IMG │ │ │ └── 18(.png)s │ └── Size_30um │ ├── TXT │ │ └── 17(.txt)s │ └── IMG │ └── 17(.png)s │ └── Read_me.txt</code></pre> <p><br>For convenience, we show an example of referencing data pools using the <em><strong>Folder Index</strong></em></p> <p>E.g. </p> <ul> <li>With reference to the article(<a href="https://doi.org/10.1021/acsomega.4c02502">https://doi.org/10.1021/acsomega.4c02502</a>), Case 1(a) is a data pool consisting only of scan data from P3HB polymer with all three sizes of data, in this case the reference is written as: <strong><em>(P1,L2) </em></strong></li> <li>Similarly, in case of Case 2(b), which is a data pool consisting of scan data from P3HB and P3HB-co-P3HV polymers with exclusively 30µm scan sizes, the reference is written as: <strong><em>(P1, L2[30]) + (P2, L2[30])</em></strong></li> </ul> <p>The .txt and .png files have been named using the following nomenculatrue: </p> <h3><strong> P_Thickness.N_Area.A_Size.S.txt</strong></h3> <p> <strong>P </strong>– Polymer (P3HB or P3HBV)<br><strong>Thickness.N</strong> – Film thickness of the scanned sample (1-6)<br><strong> Area.A</strong> – Scanned area within the film (1-3)<br><strong> Size.S</strong> – Size of the scanned area (5µm,10µm,30µm)</p> <p>e.g. (P3HB_Thickness.1_Area.1_Size.5.txt)</p> <p><strong>Please cite this dataset when used in applications as:</strong><br><em>Ireddy, A. T. S., & Ghorabe, F. D. E. (2024). Atomic Force Microscopy data of Poly-3-hydroxybutarate and Poly-3-hydroxyvalerate films [Data set]. Zenodo. https://doi.org/10.5281/zenodo.10649355</em></p> <p><br>For additonal details, please contact: <a href="mailto:ireddy@itmo.ru">ireddy@itmo.ru</a></p>
Machine Learning for Analyzing Atomic Force Microscopy (AFM) Images Generated from Polymer Blends
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Code and Data for Transfer Learning for Multi-material Classification of Transition Metal Dichalcogenides with Atomic Force Microscopy
<p>The data consists of atomic force microscopy (AFM) images of metal organic chemical deposition (MOCVD) grown transition metal dichalcogenides (TMDs), MoS2, WS2, WSe2, MoSe2, and Mo-WSe2, used for the results reported in the manuscript "Transfer Learning for Multi-material Classification of Transition Metal Dichalcogenides with Atomic Force Microscopy". The TMDs are grown at the Penn State's 2D crystal consortium (2DCC). The raw data is also available on the LiST (https://data.<br>2dccmip.org/Rut1mMC8u25M). The file names have the format: imageSNo_TMD_sampleLabel_sampleId_set.tif, where SNo, TMD, sampleLabel, sampleId, and set are serial numbers (1, 2, 3, ...), class of TMD (e.g. MoS2, WS2, ...), sample label, sample id, and train or test set, as used in the manuscript. There could be multiple images from the same samples (taken from the center, edges, etc, of wafer). Images from the same sample have the same sample label and sample id. In using the data, it is recommended that the same sample is not present in more than one data set to avoid data leakage. Additionally, github_static consists of the codes used to generate the results reported in the manuscript.</p>
Data from: Simulation assisted analysis of the intrinsic stiffness for short DNA molecules imaged with scanning atomic force microscopy
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Data from: Adhesion force mapping on wood by atomic force microscopy: influence of surface roughness and tip geometry
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Effects of 32 Days Aboard the ISS on Gastrocnemius Tendon Nanomechanics (Gastrocnemius tendon, RR-1 and Atomic Force Microscopy)
Collagen is an essential component of connective tissue and plays a crucial role in elasticity, stability, and force distribution. While the adaptations of tendon to internal stimuli have been extensively researched, the impact of environmental factors (such as microgravity) on its structure and function at the nanoscopic scale (i.e., fibril level) remains largely unexplored. The purpose of this study was to determine the effects of 32 days (d) aboard the International Space Station (ISS) on murine tendon collagen fibril morphology and nanomechanics (Young’s Modulus, YM). Gastronemius tendon samples from 16wk old female C57BL/6J mice aboard NASA Rodent Research-1 underwent chemical processing and mechanical isolation. Subsequently, collagen fibrils (n equals 17) were studied via atomic force microscopy (AFM, JPK NanoWizard 4a) to compare the morphology (diameter, height) and nanomechanics (average YM) between spaceflight (SF) and ground control (GC) mouse tendon samples. The qp-BioAC-CB1 cantilever (spring constant: 0.3 N/m, tip radius: 10µm) was used under quantitative imaging mode (Qi) for all force and morphological measurements. The data from 17 micrographs (SF n equals 5; GC n equals 12) was processed via the JPK Data Processing Software (Version 6.4.5.), and finally analyzed via Gwyddion (Version 2.62). To our knowledge, this is the first investigation to use AFM QI-mode on tendon collagen fibrils after spaceflight. Mean fibril size and YM were similar between Space Flight (SF) and Ground Control (GC) mouse tendon fibrils after 32 days of space flight; these results suggest that collagen fibrils may require more time to adapt to changes in their environment, and/or more rapid changes may take place at different levels of the collagen hierarchy. This data provides valuable insights into mammalian tissue adaptations during spaceflight, and future research should continue these investigations with longer-duration missions to build a time-course of tendon adaptations to microgravity. This dataset includes results from atomic force microscopy using gastronemius tendon tissue.
Effects of 32 Days Aboard the ISS on Quadricep Tendon Nanomechanics (Quadricep femoris tendon, RR-1 and Atomic Force Microscopy)
Collagen is an essential component of connective tissue and plays a crucial role in elasticity, stability, and force distribution. While the adaptations of tendon to internal stimuli have been extensively researched, the impact of environmental factors (such as microgravity) on its structure and function at the nanoscopic scale (i.e., fibril level) remains largely unexplored. The purpose of this study was to determine the effects of 32 days (d) aboard the International Space Station (ISS) on murine tendon collagen fibril morphology and nanomechanics (Young’s Modulus, YM). Quadriceps tendon samples from 16wk old female C57BL/6J mice aboard NASA Rodent Research-1 underwent chemical processing and mechanical isolation. Subsequently, collagen fibrils (n equals 38) were studied via atomic force microscopy (AFM, JPK NanoWizard 4a) to compare the morphology (diameter, height) and nanomechanics (average YM) between spaceflight (SF) and ground control (GC) mouse tendon samples. The qp-BioAC-CB1 cantilever (spring constant: 0.3 N/m, tip radius: 10µm) was used under quantitative imaging mode (Qi) for all force and morphological measurements. The data from 17 micrographs (SF n equals 23; GC n equals 15) was processed via the JPK Data Processing Software (Version 6.4.5.), and finally analyzed via Gwyddion (Version 2.62). To our knowledge, this is the first investigation to use AFM QI-mode on tendon collagen fibrils after spaceflight. Mean fibril size and YM were similar between SF and GC mouse tendon fibrils after 32 days of space flight; these results suggest that collagen fibrils may require more time to adapt to changes in their environment, and/or more rapid changes may take place at different levels of the collagen hierarchy. This data provides valuable insights into mammalian tissue adaptations during spaceflight, and future research should continue these investigations with longer-duration missions to build a time-course of tendon adaptations to microgravity. All results derived are from atomic force microscopy using quadriceps femoris tendon tissue.
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