scholarly journals TopoStats – a program for automated tracing of biomolecules from AFM images

2020 ◽  
Author(s):  
Joseph G. Beton ◽  
Robert Moorehead ◽  
Luzie Helfmann ◽  
Robert Gray ◽  
Bart W. Hoogenboom ◽  
...  
Keyword(s):  
Dna Origami ◽  
Contour Length ◽  
Wide Field ◽  
User Input ◽  
Force Microscopy ◽  
Atomic Force ◽  
Wide Field Of View ◽  
Pore Forming Proteins ◽  
Automated Tracing ◽  
Microscopy Images

AbstractWe present TopoStats, a Python toolkit for automated editing and analysis of Atomic Force Microscopy images. The program automates identification and tracing of individual molecules in circular and linear conformations without user input. TopoStats was able to identify and trace a range of molecules within AFM images, finding, on average, 90% of all individual molecules and molecular assemblies within a wide field of view, and without the need for prior processing. DNA minicircles of varying size, DNA origami rings and pore forming proteins were identified and accurately traced with contour lengths of traces typically within 10 nm of the predicted contour length. TopoStats was also able to reliably identify and trace linear and enclosed circular molecules within a mixed population. The program is freely available via GitHub (https://github.com/afm-spm/TopoStats) and is intended to be modified and adapted for use if required.

scholarly journals Atomic Force Microscopy Investigation of the Interactions between the MCM Helicase and DNA

Materials ◽  
2021 ◽  
Vol 14 (3) ◽  
pp. 687
Author(s):  
Amna Abdalla Mohammed Khalid ◽  
Pietro Parisse ◽  
Barbara Medagli ◽  
Silvia Onesti ◽  
Loredana Casalis
Keyword(s):  
Atomic Force Microscopy ◽  
Nucleic Acid ◽  
Single Molecule ◽  
Protein Complex ◽  
The Other ◽  
Contour Length ◽  
Force Microscopy ◽  
Atomic Force ◽  
Mcm Complex ◽  
Dna Double Helix

The MCM (minichromosome maintenance) protein complex forms an hexameric ring and has a key role in the replication machinery of Eukaryotes and Archaea, where it functions as the replicative helicase opening up the DNA double helix ahead of the polymerases. Here, we present a study of the interaction between DNA and the archaeal MCM complex from Methanothermobacter thermautotrophicus by means of atomic force microscopy (AFM) single molecule imaging. We first optimized the protocol (surface treatment and buffer conditions) to obtain AFM images of surface-equilibrated DNA molecules before and after the interaction with the protein complex. We discriminated between two modes of interaction, one in which the protein induces a sharp bend in the DNA, and one where there is no bending. We found that the presence of the MCM complex also affects the DNA contour length. A possible interpretation of the observed behavior is that in one case the hexameric ring encircles the dsDNA, while in the other the nucleic acid wraps on the outside of the ring, undergoing a change of direction. We confirmed this topographical assignment by testing two mutants, one affecting the N-terminal β-hairpins projecting towards the central channel, and thus preventing DNA loading, the other lacking an external subdomain and thus preventing wrapping. The statistical analysis of the distribution of the protein complexes between the two modes, together with the dissection of the changes of DNA contour length and binding angle upon interaction, for the wild type and the two mutants, is consistent with the hypothesis. We discuss the results in view of the various modes of nucleic acid interactions that have been proposed for both archaeal and eukaryotic MCM complexes.

scholarly journals Simulating noncontact atomic force microscopy images

2019 ◽  
Vol 3 (11) ◽  
Author(s):  
James R. Chelikowsky ◽  
Dingxin Fan ◽  
Alex J. Lee ◽  
Yuki Sakai
Keyword(s):  
Atomic Force Microscopy ◽  
Force Microscopy ◽  
Atomic Force ◽  
Microscopy Images

scholarly journals Corrosion Behavior and Mechanical Properties of a Nanocomposite Superhydrophobic Coating

Coatings ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 652
Author(s):  
Divine Sebastian ◽  
Chun-Wei Yao ◽  
Lutfun Nipa ◽  
Ian Lian ◽  
Gary Twu
Keyword(s):  
Electron Microscopy ◽  
Mechanical Properties ◽  
Scanning Electron Microscopy ◽  
Atomic Force Microscopy ◽  
Nanocomposite Coating ◽  
Superhydrophobic Coating ◽  
Force Microscopy ◽  
Atomic Force ◽  
Microscopy Images ◽  
Scanning Electron

In this work, a mechanically durable anticorrosion superhydrophobic coating is developed using a nanocomposite coating solution composed of silica nanoparticles and epoxy resin. The nanocomposite coating developed was tested for its superhydrophobic behavior using goniometry; surface morphology using scanning electron microscopy and atomic force microscopy; elemental composition using energy dispersive X-ray spectroscopy; corrosion resistance using atomic force microscopy; and potentiodynamic polarization measurements. The nanocomposite coating possesses hierarchical micro/nanostructures, according to the scanning electron microscopy images, and the presence of such structures was further confirmed by the atomic force microscopy images. The developed nanocomposite coating was found to be highly superhydrophobic as well as corrosion resistant, according to the results from static contact angle measurement and potentiodynamic polarization measurement, respectively. The abrasion resistance and mechanical durability of the nanocomposite coating were studied by abrasion tests, and the mechanical properties such as reduced modulus and Berkovich hardness were evaluated with the aid of nanoindentation tests.

scholarly journals Influence of Growth Temperature of the Nucleation Layer on the Growth of InP on Si (001)

Coatings ◽  
2019 ◽  
Vol 9 (12) ◽  
pp. 823
Author(s):  
Shizheng Yang ◽  
Hongliang Lv ◽  
Likun Ai ◽  
Fangkun Tian ◽  
Silu Yan ◽  
...  
Keyword(s):  
Growth Temperature ◽  
Wafer Level ◽  
X Ray Diffraction ◽  
Nucleation Layer ◽  
Force Microscopy ◽  
Gas Source ◽  
Atomic Force ◽  
Growth Method ◽  
Step Growth ◽  
Microscopy Images

InP layers grown on Si (001) were achieved by the two-step growth method using gas source molecular beam epitaxy. The effects of growth temperature of nucleation layer on InP/Si epitaxial growth were investigated systematically. Cross-section morphology, surface morphology and crystal quality were characterized by scanning electron microscope images, atomic force microscopy images, high-resolution X-ray diffraction (XRD), rocking curves and reciprocal space maps. The InP/Si interface and surface became smoother and the XRD peak intensity was stronger with the nucleation layer grown at 350 °C. The Results show that the growth temperature of InP nucleation layer can significantly affect the growth process of InP film, and the optimal temperature of InP nucleation layer is required to realize a high-quality wafer-level InP layers on Si (001).

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