Phenomenological models of Bombyx mori silk fibroin and their mechanical behavior using molecular dynamics simulations

Patel, Mrinal; Dubey, Devendra K.; Singh, Shveta

doi:10.1016/j.msec.2019.110414

Cited by 39 publications

(43 citation statements)

References 77 publications

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“… VESTA 44 visualization of most (a) and least (b) favorable water molecule positions in the (Ala–Gly) 16 SF crystal model (experimental data for SF crystal model from the literature 1 , 17 , 19 , 20 , 22 , 27 , 28 ). The brown ball and sticks depict the carbon atoms; light gray, the hydrogen atoms; red, the oxygen atoms; and pale blue, the nitrogen atoms.…”

Section: Resultsmentioning

confidence: 99%

“…Construction of the (Ala–Gly) n SF unit cell followed the methodology described by Yamane et al 1 The initial unit cell was created by arranging four Ala–Gly chains with repeated β-turns according to information from the experiment and simulation on SF. 1 , 17 , 19 , 20 , 22 , 27 , 28 To simulate the bulk system of the repeated polymer chains, a periodic boundary condition was implemented, where nitrogen and carbon-terminals were connected to mirror images of themselves, and the resulting structure is illustrated in Figure 7 .…”

Section: Methodsmentioning

confidence: 99%

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Atomistic Simulation of Water Incorporation and Mobility inBombyx moriSilk Fibroin

et al. 2021

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Bombyx mori silk fibroin (SF) is a biopolymer that can be processed into materials with attractive properties (e.g., biocompatibility and degradability) for use in a multitude of technical and medical applications (including textiles, sutures, drug delivery devices, tissue scaffolds, etc.). Utilizing the information from experimental and computational SF studies, a simplified SF model has been produced (alanine–glycine [Ala–Gly] n crystal structure), enabling the application of both molecular dynamic and density functional theory techniques to offer a unique insight into SF-based materials. The secondary structure of the computational model has been evaluated using Ramachandran plots under different environments (e.g., different temperatures and ensembles). In addition, the mean square displacement of water incorporated into the SF model was investigated: the diffusion coefficients, activation energies, most and least favorable positions of water, and trajectory of water diffusion through the SF model are obtained. With further computational study and in combination with experimental data, the behavior/degradation of SF (and similar biomaterials) can be elucidated. Consequently, greater control of the aforementioned technologies may be achieved and positively affect their potential applications.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Atomistic Simulation of Water Incorporation and Mobility inBombyx moriSilk Fibroin

et al. 2021

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“…In this review, the author showed how solid-state NMR coupled with stable isotope labeling of the silks and the related silk peptides, and combination of solid-state NMR and MD simulation have contributed to a better understanding the structure and dynamics of the spider dragline silks in the dry and hydrated states. Recently, the excellent mechanical properties of spider silk fiber have been challenged to predict on the basis of the atomic resolution structure of the crystalline region embedded in a softer-amorphous region using MD simulations [73][74][75][76][77][78][79][80][81][82][83][84][85]. In the future, such a prediction of the mechanical properties of natural and recombinant spider silks [11,57,59,61] is expected to increase more and more for molecular design of new materials with excellent mechanical properties.…”

Section: Conclusion and Future Aspectsmentioning

confidence: 99%

“…MD simulation can play a critical role in connecting experimental restraints with potentially plausible molecular structures. Therefore, it has been also used to understand the structure and structural changes of silk fibroins including silk fiber formation mechanism and the chain dynamics [73][74][75][76][77][78][79][80][81][82][83][84][85]. Especially, combination of solid-state NMR and MD simulations was very strong analytical tools to understand the local conformation and dynamics of the spider dragline silk in atomic resolution [56,58,62,63,65].…”

Section: Introductionmentioning

confidence: 99%

Structure and Dynamics of Spider Silk Studied with Solid-State Nuclear Magnetic Resonance and Molecular Dynamics Simulation

Asakura¹

2020

Molecules

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This review will introduce very recent studies using solid-state nuclear magnetic resonance (NMR) and molecular dynamics (MD) simulation on the structure and dynamics of spider dragline silks conducted by the author’s research group. Spider dragline silks possess extraordinary mechanical properties by combining high tensile strength with outstanding elongation before breaking, and therefore continue to attract attention of researchers in biology, biochemistry, biophysics, analytical chemistry, polymer technology, textile technology, and tissue engineering. However, the inherently non-crystalline structure means that X-ray diffraction and electron diffraction methods provide only limited information because it is difficult to study the molecular structure of the amorphous region. The most detailed picture of the structure and dynamics of the silks in the solid state experimentally have come from solid-state NMR measurements coupled with stable isotope labeling of the silks and the related silk peptides. In addition, combination of solid-state NMR and MD simulation was very powerful analytical tools to understand the local conformation and dynamics of the spider dragline silk in atomic resolution. In this review, the author will emphasize how solid-state NMR and MD simulation have contributed to a better understanding of the structure and dynamics in the spider dragline silks.

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“…On the other side, this paradigm can preserve the quality of primary raw materials for the textile industry that will directly be reflected on the quality of textile products. [11,12].…”

Section: Methodsmentioning

confidence: 99%

The modelling and introductions of new type ribs of lattice of the two cylinder of gin

et al. 2021

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Using the above data on the manufacture of grates and taking into consideration the bending vibrations of the saw cylinders and displacement of the grates under dynamic load. Taking into account the primary factors of sectional and individual grates ribs also in order to prevent cross-displacement of grates ribs. We modeled and introduced a new type of grates ribs for a single- chamber and two-cylinder gin, which is comprised of the top and bottom, grates ribs aligned with three brackets and tightening laths with a new type of fastening respectively. In the article, consider the simulated static load experimental model of a new grate ribs lattice, which allows eliminating lateral. Displacement of ribs at dynamic loading.

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Phenomenological models of Bombyx mori silk fibroin and their mechanical behavior using molecular dynamics simulations

Cited by 39 publications

References 77 publications

Atomistic Simulation of Water Incorporation and Mobility inBombyx moriSilk Fibroin

Atomistic Simulation of Water Incorporation and Mobility inBombyx moriSilk Fibroin

Structure and Dynamics of Spider Silk Studied with Solid-State Nuclear Magnetic Resonance and Molecular Dynamics Simulation

The modelling and introductions of new type ribs of lattice of the two cylinder of gin

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