Multiscale materials modelling at the mesoscale

Yip, Sidney; Short, Michael P.

doi:10.1038/nmat3746

Cited by 109 publications

(81 citation statements)

References 26 publications

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“…protein folding | proton NMR | energy landscape | hydration water A n intriguing problem of statistical physics concerns the evolutionary pathways that molecular systems follow as they form mesoscale structures and exhibit new functional behaviors (1). An example of this problem is the self-organization of biosystems that evolve from basic molecules.…”

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confidence: 99%

“…This challenging subject is studied by using a variety of theoretical methods (2)(3)(4). The free-energy landscape model is nowadays the most used to describe such phenomena and especially the aging of the protein folding mechanism (1,5,6), i.e., the way in which proteins fold to their native state and then unfold (protein denaturation) (6,7). The model is based on the idea that in complex materials and systems there are many thermodynamical configurations in which the free-energy surface exhibits a number of local minima separated by barriers, i.e., as the system explores its phase space the trajectory of its evolution is an alternating sequence of local energy minima and saddle points (transition states), which are associated with the positions of all of the system particles.…”

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confidence: 99%

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Energy landscape in protein folding and unfolding

Mallamace

Corsaro

Mallamace

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

105

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We use 1 H NMR to probe the energy landscape in the protein folding and unfolding process. Using the scheme ⇄ reversible unfolded (intermediate) → irreversible unfolded (denatured) state, we study the thermal denaturation of hydrated lysozyme that occurs when the temperature is increased. Using thermal cycles in the range 295 < T < 365 K and following different trajectories along the protein energy surface, we observe that the hydrophilic (the amide NH) and hydrophobic (methyl CH 3 and methine CH) peptide groups evolve and exhibit different behaviors. We also discuss the role of water and hydrogen bonding in the protein configurational stability.protein folding | proton NMR | energy landscape | hydration water A n intriguing problem of statistical physics concerns the evolutionary pathways that molecular systems follow as they form mesoscale structures and exhibit new functional behaviors (1). An example of this problem is the self-organization of biosystems that evolve from basic molecules. This challenging subject is studied by using a variety of theoretical methods (2-4). The free-energy landscape model is nowadays the most used to describe such phenomena and especially the aging of the protein folding mechanism (1, 5, 6), i.e., the way in which proteins fold to their native state and then unfold (protein denaturation) (6, 7). The model is based on the idea that in complex materials and systems there are many thermodynamical configurations in which the free-energy surface exhibits a number of local minima separated by barriers, i.e., as the system explores its phase space the trajectory of its evolution is an alternating sequence of local energy minima and saddle points (transition states), which are associated with the positions of all of the system particles. A trajectory thus specifies the path of the system as it evolves by moving across its energy landscape.A peptide is a linear chain of amino acids, and globular proteins are polypeptide chains that fold into their native conformation. During the folding process a polypeptide undergoes many conformational changes and there is a significant decrease in the system configurational entropy as the native state is approached. To understand folding we focus on how proteins search conformational space. The process is accompanied by many microscopic reactions, the nature of which is determined by the specifics of the energy surface. Thus, the characteristics of the energy surface of a polypeptide chain are the key to a quantitative understanding of folding. Although the degrees of freedom of a polypeptide chain allow an enormously large number of possible configurations, "constraints" on the energy decrease these configurations visited in the folding reaction to a limited number (8). Understanding the free-energy surface ("landscape") enables us to understand the folding process. A balance between the potential energy and the configurational entropy leads to a freeenergy barrier that generates the two-state folding behavior usually observed in small proteins. The...

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confidence: 99%

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confidence: 99%

Energy landscape in protein folding and unfolding

Mallamace

Corsaro

Mallamace

et al. 2016

Proc. Natl. Acad. Sci. U.S.A.

105

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“…We believe not only that our findings will provide major steps toward precise control of the dopant-dopant and the dopant-host matrix interactions on the mesoscale but also that the results offer exciting opportunities for the construction of next-generation composite and fibers, which are urgently needed in high-capacity telecommunication, remote sensing and defense applications. [31][32][33] Furthermore, the understanding of and manipulation on the mesoscale could lead to new material functionalities, which could potentially be applied in engineering a variety of materials, such as ceramics, 34 cements, 35 organic dyes 36 and other composites, 37 where the mesoscale architecture becomes the typical microstructure of the applied system.…”

Section: Discussionmentioning

confidence: 99%

Mesoscale engineering of photonic glass for tunable luminescence

Fang

et al. 2016

NPG Asia Mater

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Control of the optical behavior of active materials through manipulation of their microstructure has led to the development of high-performance photonic devices with enhanced integration density, improved quantum efficiencies and controllable color output. However, the achievement of robust light-harvesting materials with tunable, broadband and flattened emission remains a long-standing goal owing to the limited inhomogeneous broadening in ordinary hosts. Here, we describe an effective strategy for the management of photon emission by manipulating the mesoscale heterogeneities in optically active materials. Importantly, this unique approach enables control of dopant-dopant and dopant-host interactions on the extended mesoscale. This allows the generation of intriguing optical phenomena such as a high activation ratio of the dopant (close to 100%), dramatically inhomogeneous broadening (up to 480 nm), notable emission enhancement and, moreover, simultaneously extension of the emission bandwidth and flattening of the spectral shape in glass and fiber. Our results highlight that the findings connect the understanding of and manipulation in the mesoscale realm to functional behavior on the macroscale, and the approach to manage the dopants based on mesoscale engineering may provide new opportunities for the construction of a robust fiber light source.

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“…In the past two years a frontier for materials research at an intermediate regime between microscopic and macroscopic scales has emerged with the prospect of scientific advances coupled with technological impact [1][2] [3]. Many types of materials are known for their functional behavior on the macro-scale.…”

Section: The Mesoscale Science Frontiermentioning

confidence: 99%