Scaling law to determine peak forces in tapping-mode AFM experiments on finite elastic soft matter systems

Guzman, Horacio V.

doi:10.3762/bjnano.8.98

Cited by 8 publications

(7 citation statements)

References 41 publications

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“…3) that helps to hold together the structure before the largest force of rupture of intermolecular interactions (F max = 250 ± 11 pN for CoV2 and F max = 200 ± 13 pN for CoV1). The observed difference of ≈50 pN is the equivalent of non-invasive AFM indentation of proteins 33,34 and it suggests that random mutations of the RBD have led to increased stability of the CoV2 RBD compared to the CoV1 RBD. Some deviation from the mean values of our result via Single Molecule Force Spectroscopy (SMFS) are expected, but the conclusive differential effect as this point is mostly due to the structural differences.…”

Section: Resultsmentioning

confidence: 94%

Quantitative determination of mechanical stability in the novel coronavirus spike protein

et al. 2020

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Section: Resultsmentioning

confidence: 94%

Quantitative determination of mechanical stability in the novel coronavirus spike protein

et al. 2020

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“…Typical length scales of biological fibrils are in the range from nanometers to micrometers. Hence, AFM that can be operated, for example, in static (contact) and dynamic modes, has been one of the main methods to study such systems [28–29]. On one hand, AFM in contact mode has been used to provoke the mechanical deformation of fibrils obtaining the Young’s modulus (here denoted as Y T ) [30–32].…”

Section: Introductionmentioning

confidence: 99%

Mechanical and thermodynamic properties of Aβ₄₂, Aβ₄₀, and α-synuclein fibrils: a coarse-grained method to complement experimental studies

Poma¹,

Guzman²,

Li³

et al. 2019

Beilstein J. Nanotechnol.

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We perform molecular dynamics simulation on several relevant biological fibrils associated with neurodegenerative diseases such as Aβ40, Aβ42, and α-synuclein systems to obtain a molecular understanding and interpretation of nanomechanical characterization experiments. The computational method is versatile and addresses a new subarea within the mechanical characterization of heterogeneous soft materials. We investigate both the elastic and thermodynamic properties of the biological fibrils in order to substantiate experimental nanomechanical characterization techniques that are quickly developing and reaching dynamic imaging with video rate capabilities. The computational method qualitatively reproduces results of experiments with biological fibrils, validating its use in extrapolation to macroscopic material properties. Our computational techniques can be used for the co-design of new experiments aiming to unveil nanomechanical properties of biological fibrils from a point of view of molecular understanding. Our approach allows a comparison of diverse elastic properties based on different deformations , i.e., tensile (Y L), shear (S), and indentation (Y T) deformation. From our analysis, we find a significant elastic anisotropy between axial and transverse directions (i.e., Y T > Y L) for all systems. Interestingly, our results indicate a higher mechanostability of Aβ42 fibrils compared to Aβ40, suggesting a significant correlation between mechanical stability and aggregation propensity (rate) in amyloid systems. That is, the higher the mechanical stability the faster the fibril formation. Finally, we find that α-synuclein fibrils are thermally less stable than β-amyloid fibrils. We anticipate that our molecular-level analysis of the mechanical response under different deformation conditions for the range of fibrils considered here will provide significant insights for the experimental observations.

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“…The AFM is widely used for mechanical properties mapping of matter [Gar20]. Hence, the first comparison of the four scenarios points out to the force response versus time according to a Hertzian interaction [Guz17]. In Figure 5, we see the humid air (RH = 60.1%) changes the measurement conditions by almost 10%.…”

Section: Resultsmentioning

confidence: 97%

pyDAMPF: a Python package for modeling mechanical properties of hygroscopic materials under interaction with a nanoprobe

Menacho¹,

Ramírez-Ávila²,

Guzman³

2022

Proceedings of the Python in Science Conference

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pyDAMPF is a tool oriented to the Atomic Force Microscopy (AFM) community, which allows the simulation of the physical properties of materials under variable relative humidity (RH). In particular, pyDAMPF is mainly focused on the mechanical properties of polymeric hygroscopic nanofibers that play an essential role in designing tissue scaffolds for implants and filtering devices. Those mechanical properties have been mostly studied from a very coarse perspective reaching a micrometer scale. However, at the nanoscale, the mechanical response of polymeric fibers becomes cumbersome due to both experimental and theoretical limitations. For example, the response of polymeric fibers to RH demands advanced models that consider sub-nanometric changes in the local structure of each single polymer chain. From an experimental viewpoint, choosing the optimal cantilevers to scan the fibers under variable RH is not trivial.In this article, we show how to use pyDAMPF to choose one optimal nanoprobe for planned experiments with a hygroscopic polymer. Along these lines, We show how to evaluate common and non-trivial operational parameters from an AFM cantilever of different manufacturers. Our results show in a stepwise approach the most relevant parameters to compare the cantilevers based on a non-invasive criterion of measurements. The computing engine is written in Fortran, and wrapped into Python. This aims to reuse physics code without losing interoperability with high-level packages. We have also introduced an in-house and transparent method for allowing multi-thread computations to the users of the pyDAMPF code, which we benchmarked for various computing architectures (PC, Google Colab and an HPC facility) and results in very favorable speed-up compared to former AFM simulators.

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Scaling law to determine peak forces in tapping-mode AFM experiments on finite elastic soft matter systems

Cited by 8 publications

References 41 publications

Quantitative determination of mechanical stability in the novel coronavirus spike protein

Quantitative determination of mechanical stability in the novel coronavirus spike protein

Mechanical and thermodynamic properties of Aβ₄₂, Aβ₄₀, and α-synuclein fibrils: a coarse-grained method to complement experimental studies

pyDAMPF: a Python package for modeling mechanical properties of hygroscopic materials under interaction with a nanoprobe

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Scaling law to determine peak forces in tapping-mode AFM experiments on finite elastic soft matter systems

Cited by 8 publications

References 41 publications

Quantitative determination of mechanical stability in the novel coronavirus spike protein

Quantitative determination of mechanical stability in the novel coronavirus spike protein

Mechanical and thermodynamic properties of Aβ42, Aβ40, and α-synuclein fibrils: a coarse-grained method to complement experimental studies

pyDAMPF: a Python package for modeling mechanical properties of hygroscopic materials under interaction with a nanoprobe

Contact Info

Product

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Mechanical and thermodynamic properties of Aβ₄₂, Aβ₄₀, and α-synuclein fibrils: a coarse-grained method to complement experimental studies