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Nanotribological Properties of Oxidized Diamond/Silica Interfaces: Insights into the Atomistic Mechanisms of Wear and Friction by Ab Initio Molecular Dynamics Simulations.

ABSTRACT: Controlling friction and wear at silica-diamond interfaces is crucial for their relevant applications in tribology such as micro-electromechanical systems and atomic force microscopes. However, the tribological performance on diamond surfaces is highly affected by the working environment where atmospheric gases are present. In this work, we investigate the effects of adsorbed oxygen on the friction and wear of diamond surfaces sliding against silica by massive ab initio molecular dynamics simulations. Different surface orientations, O-coverages, and tribological conditions are considered. The results suggest that diamond surfaces with full oxygen passivation are very effective in preventing surface adhesion, and as a result present extremely low friction and wear. At low oxygen coverage, Si-O-C bond formation was observed as well as atomistic wear initiated from C-C bond breaking at extreme pressure. The analysis of electronic structures of the configurations resulting from key tribochemical reactions clarifies the mechanisms of friction reduction and atomistic wear. Overall, our accurate in silico experiments shed light on the influence of adsorbed oxygen on the tribological properties and wear mechanisms of diamond against silica.

SUBMITTER: Ta HTT

PROVIDER: S-EPMC10520978 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature

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Nanotribological Properties of Oxidized Diamond/Silica Interfaces: Insights into the Atomistic Mechanisms of Wear and Friction by Ab Initio Molecular Dynamics Simulations.

Ta Huong Thi Thuy HTT Tran Nam Van NV Righi Maria Clelia MC

ACS applied nano materials 20230904 18

Controlling friction and wear at silica-diamond interfaces is crucial for their relevant applications in tribology such as micro-electromechanical systems and atomic force microscopes. However, the tribological performance on diamond surfaces is highly affected by the working environment where atmospheric gases are present. In this work, we investigate the effects of adsorbed oxygen on the friction and wear of diamond surfaces sliding against silica by massive ab initio molecular dynamics simula ...[more]

PMID: 37767208

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Project description:BackgroundPredicting 3-dimensional protein structures from amino-acid sequences is an important unsolved problem in computational structural biology. The problem becomes relatively easier if close homologous proteins have been solved, as high-resolution models can be built by aligning target sequences to the solved homologous structures. However, for sequences without similar folds in the Protein Data Bank (PDB) library, the models have to be predicted from scratch. Progress in the ab initio structure modeling is slow. The aim of this study was to extend the TASSER (threading/assembly/refinement) method for the ab initio modeling and examine systemically its ability to fold small single-domain proteins.ResultsWe developed I-TASSER by iteratively implementing the TASSER method, which is used in the folding test of three benchmarks of small proteins. First, data on 16 small proteins (< 90 residues) were used to generate I-TASSER models, which had an average Calpha-root mean square deviation (RMSD) of 3.8A, with 6 of them having a Calpha-RMSD < 2.5A. The overall result was comparable with the all-atomic ROSETTA simulation, but the central processing unit (CPU) time by I-TASSER was much shorter (150 CPU days vs. 5 CPU hours). Second, data on 20 small proteins (< 120 residues) were used. I-TASSER folded four of them with a Calpha-RMSD < 2.5A. The average Calpha-RMSD of the I-TASSER models was 3.9A, whereas it was 5.9A using TOUCHSTONE-II software. Finally, 20 non-homologous small proteins (< 120 residues) were taken from the PDB library. An average Calpha-RMSD of 3.9A was obtained for the third benchmark, with seven cases having a Calpha-RMSD < 2.5A.ConclusionOur simulation results show that I-TASSER can consistently predict the correct folds and sometimes high-resolution models for small single-domain proteins. Compared with other ab initio modeling methods such as ROSETTA and TOUCHSTONE II, the average performance of I-TASSER is either much better or is similar within a lower computational time. These data, together with the significant performance of automated I-TASSER server (the Zhang-Server) in the 'free modeling' section of the recent Critical Assessment of Structure Prediction (CASP)7 experiment, demonstrate new progresses in automated ab initio model generation. The I-TASSER server is freely available for academic users http://zhang.bioinformatics.ku.edu/I-TASSER.

Dataset Information

Nanotribological Properties of Oxidized Diamond/Silica Interfaces: Insights into the Atomistic Mechanisms of Wear and Friction by Ab Initio Molecular Dynamics Simulations.

Publications

Nanotribological Properties of Oxidized Diamond/Silica Interfaces: Insights into the Atomistic Mechanisms of Wear and Friction by Ab Initio Molecular Dynamics Simulations.

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