Insights and guidelines to interpret forces and deformations at the nanoscale by using a tapping mode AFM simulator: dForce 2.0

Gisbert, Victor G.; García, Ricardo García

doi:10.1039/d3sm00334e

Cited by 6 publications

(6 citation statements)

References 102 publications

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“…Fig. 5a shows a comparison of the values of the virial of the first mode obtained in the experiment with the values obtained by using dForce 2.0 57 as a function of the amplitude ratio A 1 / A 01 . The simulations are performed by using the Hamaker constant value for a multilayer MoS 2 flake obtained in the bimodal AM–FM experiments ( H MoS 2 ≈ 0.85 eV).…”

Section: Resultsmentioning

confidence: 95%

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Fast and high-resolution mapping of van der Waals forces of 2D materials interfaces with bimodal AFM

Gisbert,

Garcia

2023

Nanoscale

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Section: Resultsmentioning

confidence: 95%

“…For example, by reducing A 1 we reduce d min , which in turn increases the strength of the van der Waals forces. In parallel, we use a numerical simulation platform, dForce, 57,58 to simulate the bimodal AM-FM observables under the experimental conditions. Fig.…”

Section: Validation Of Bimodal Am-fm To Characterize Van Der Waals Fo...mentioning

confidence: 99%

Fast and high-resolution mapping of van der Waals forces of 2D materials interfaces with bimodal AFM

Gisbert,

Garcia

2023

Nanoscale

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“…36 They were determined by using a dynamic AFM simulator (dForce 2.0). 40 The height of the collagen nanostructures is determined from tapping mode AFM topographic images. Figure 1d shows a collagen system with the presence of three different nanostructures: collagen molecules, nanofibrils, and nanoribbons.…”

Section: Resultsmentioning

confidence: 99%

“…In the simulations, the collagen-mimetic molecules interact via screened electrostatic interactions as well as via generic nonspecific attractive interactions (Figure c). Depending on the interaction strengths, such rods might form either clusters or collagen-like nanoribbons and nanobundles . We model the electrostatic interactions using a Debye–Hueckel potential and Lennard-Jones potential for nonspecific interactions.…”

Section: Resultsmentioning

confidence: 99%

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In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures

Garcia-Sacristan,

Gisbert,

Klein

et al. 2024

ACS Nano

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Collagen is the most abundant protein in tissue scaffolds in live organisms. Collagen can self-assemble in vitro, which has led to a number of biotechnological and biomedical applications. To understand the dominant factors that participate in the formation of collagen nanostructures, here we study in real time and with nanoscale resolution the disassembly and reassembly of collagens. We implement a high-speed force microscope, which provides in situ high spatiotemporal resolution images of collagen nanostructures under changing pH conditions. The disassembly and reassembly are dominated by the electrostatic interactions among amino-acid residues of different molecules. Acidic conditions favor disassembly by neutralizing negatively charged residues. The process sets a net repulsive force between collagen molecules. A neutral pH favors the presence of negative and positively charged residues along the collagen molecules, which promotes their electrostatic attraction. Molecular dynamics simulations reproduce the experimental behavior and validate the electrostatic-based model of the disassembly and reassembly processes.

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NanoLocz: Image Analysis Platform for AFM, High‐Speed AFM, and Localization AFM

Heath,

Micklethwaite,

Storer

2024

Small Methods

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Atomic Force Microscopy (AFM), High‐Speed AFM (HS‐AFM) simulation AFM, and Localization AFM (LAFM) enable the study of molecules and surfaces with increasingly higher spatiotemporal resolution. However, effective and rapid analysis of the images and movies produced by these techniques can be challenging, often requiring the use of multiple image processing software applications and scripts. Here, NanoLocz, an open‐source solution that offers advanced analysis capabilities for the AFM community, is presented. Integration and continued development of AFM analysis tools is essential to improve access to data, increase throughput, and open new analysis opportunities. NanoLocz efficiently leverages the rich data AFM has to offer by incorporating and combining existing and newly developed analysis methods for AFM, HS‐AFM, simulation AFM, and LAFM seamlessly. It facilitates and streamlines AFM analysis workflows from import of raw data, through to various analysis workflows. Here, the study demonstrates the capabilities of NanoLocz and the new methods it enables including single‐molecule LAFM, time‐resolved LAFM, and simulation LAFM.

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Insights and guidelines to interpret forces and deformations at the nanoscale by using a tapping mode AFM simulator: dForce 2.0

Abstract: dForce 2.0 simulates tapping and bimodal AFM observables and properties. The code incorporates 26 interaction force models. It might be freely downloaded from the article. It might be run from a personal computer.

Cited by 6 publications

References 102 publications

Fast and high-resolution mapping of van der Waals forces of 2D materials interfaces with bimodal AFM

Fast and high-resolution mapping of van der Waals forces of 2D materials interfaces with bimodal AFM

In Operando Imaging Electrostatic-Driven Disassembly and Reassembly of Collagen Nanostructures

NanoLocz: Image Analysis Platform for AFM, High‐Speed AFM, and Localization AFM

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