1,007 research outputs found
Protein vibrational frequencies dataset: Rapid Prediction of Protein Natural Frequencies using Graph Neural Networks
No full textDataset for machine learning model, based on graph neural network, to predict protein natural frequencies using Graph Neural Networks.
Code: https://github.com/lamm-mit/ProteinMechanicsGNN
Paper:
Rapid Prediction of Protein Natural Frequencies using Graph Neural Networks
Kai Guo and Markus J. Buehler
Digital Discovery, 2022, DOI: 10.1039/D1DD00007
Advanced Structural Materials by Bioinspiration
No full textIn the quest of increasing safety and efficiency in structural applications, learning from natural materials can be a promising approach. Nature has evolved for billions of years to develop elaborate strategies, achieving optimal material solutions. A brief review of exemplar natural materials is provided here, with a focus on their multiscale structures. The design motifs, common to biological structural materials, are summarized, with a highlight on the structure-property relationship. A review of recent advancement in the manufacturing of bio-inspired composites is given, followed by recent and successful case studies. Finally, a critical discussion, highlighting the limitations of the current techniques, and prospecting the future challenges for the design of novel materials for engineering applications
Defining Nascent Bone by the Molecular Nanomechanics of Mineralized Collagen Fibrils
No full textHere we focus on recent advances in understanding the deformation and fracture behavior of collagen, Nature's most abundant protein material and the basis for many biological composites including bone, dentin or cornea. We show that it is due to the basis of the collagen structure that leads to its high strength and ability to sustain large deformation, as relevant to its physiological role in tissues such as bone and muscle. Experiment has shown that collagen isolated from different sources of tissues universally displays a design that consists of tropocollagen molecules with lengths of approximately 300 nanometers. Using a combination of theoretical analyses and multi-scale modeling, we have discovered that the characteristic structure and characteristic dimensions of the collagen nanostructure is the key to the ability to take advantage of the nanoscale properties of individual tropocollagen molecules at larger scales, leading to a tough material at the micro- and mesoscale. This is achieved by arranging tropocollagen molecules into a staggered assembly at a specific optimal molecular length scale. During bone formation, nanoscale mineral particles precipitate at highly specific locations in the collagen structure. These mineralized collagen fibrils are highly conserved, nanostructural primary building blocks of bone. By direct molecular simulation of the bone's nanostructure, we show that it is due to the characteristic nanostructure of mineralized collagen fibrils that leads to its high strength and ability to sustain large deformation, as relevant to its physiological role, creating a strong and tough material. We present a thorough analysis of the molecular mechanisms of protein and mineral phases in deformation, and report discovery of a new fibrillar toughening mechanism that has major implications on the fracture mechanics of bone. Our studies of collagen and bone illustrate how hierarchical multi-scale modeling linking quantum chemistry with continuum fracture mechanics approaches can be used to develop predictive models of hierarchical protein materials. We conclude with a discussion of the significance of hierarchical multi-scale structures for the material properties and illustrate how these structures enable one to overcome some of the limitations of conventional materials design, combining disparate material properties such as strength and robustness.National Science Foundation (U.S.)United States. Army Research Offic
Nanomaterials: Strenght in numbers
No full textSelf-assembly of proteins commonly associated with neurodegenerative diseases can be exploited to make well-ordered and strong functional macroscopic materials
Evidence of the Most Stretchable Egg Sac Silk Stalk, of the European Spider of the Year Meta menardi
No full textSpider silks display generally strong mechanical properties, even if differences between species and within the same species can be observed. While many different types of silks have been tested, the mechanical properties of stalks of silk taken from the egg sac of the cave spider Meta menardi have not yet been analyzed. Meta menardi has recently been chosen as the “European spider of the year 2012”, from the European Society of Arachnology. Here we report a study where silk stalks were collected directly from several caves in the north-west of Italy. Field emission scanning electron microscope (FESEM) images showed that stalks are made up of a large number of threads, each of them with diameter of 6.03±0.58 µm. The stalks were strained at the constant rate of 2 mm/min, using a tensile testing machine. The observed maximum stress, strain and toughness modulus, defined as the area under the stress-strain curve, are 0.64 GPa, 751% and 130.7 MJ/m[superscript 3], respectively. To the best of our knowledge, such an observed huge elongation has never been reported for egg sac silk stalks and suggests a huge unrolling microscopic mechanism of the macroscopic stalk that, as a continuation of the protective egg sac, is expected to be composed by fibres very densely and randomly packed. The Weibull statistics was used to analyze the results from mechanical testing, and an average value of Weibull modulus (m) is deduced to be in the range of 1.5–1.8 with a Weibull scale parameter (σ[subscript 0]) in the range of 0.33–0.41 GPa, showing a high coefficient of correlation (R[superscript 2] = 0.97).Presidential Early Career Award for Scientists and Engineers (award number N00014-10-1-0562
On The Role of Access Charges Under Network Competition
No full textWe aim to clarify the role of access charges under two-way network competition, employing a reduced-form approach. Retaining the key features of specific network competition models but imposing less structure, we analyze the impact of changes in access charges on linear and non-linear retail prices. We derive su.cient conditions for usage fees to be increasing (and subscriber charges to be decreasing) in access charges. These conditions are shown to be satisfied only under rather restrictive assumptions on the demand for calls, suggesting that implementing collusion by inflating access charges is likely to be nonfeasible.network competition, two-way access, collusion, nonlinear retail prices
Molecular and nanostructural mechanisms of deformation, strength and toughness of spider silk fibrils
No full textSpider silk is one of the strongest, most extensible and toughest biological materials known, exceeding the properties of many engineered materials including steel. Silks feature a hierarchical architecture where highly organized, densely H-bonded beta-sheet nanocrystals are arranged within a semi-amorphous protein matrix consisting of 31-helices and beta-turn protein structures. By using a bottom-up molecular-based mesoscale model that bridges the scales from Angstroms to hundreds of nanometers, here we show that the specific combination of a crystalline phase and a semi-amorphous matrix is crucial for the unique properties of silks. Specifically, our results reveal that the superior mechanical properties of spider silk can be explained solely by structural effects, where the geometric confinement of beta-sheet nanocrystals combined with highly extensible semi-amorphous domains with a large hidden length is the key to reach great strength and great toughness, despite the dominance of mechanically inferior chemical interactions such as H-bonding. Our model directly shows that semi-amorphous regions unravel first when silk is being stretched, leading to the large extensibility of silk. Conversely, the large-deformation mechanical properties and ultimate tensile strength of silk is controlled by the strength of beta-sheet nanocrystals, which is directly related to their size, where small beta-sheet nanocrystals are crucial to reach outstanding levels of strength and toughness. Our model agrees well with observations in recent experiments, where it was shown that a significant change in the strength and toughness can be achieved solely by tuning the size of beta-sheet nanocrystals. Our findings unveil the material design strategy that enables silks to achieve superior material performance despite simple and inferior constituents, resulting in a new paradigm in materials design where enhanced functionality is not achieved using complex building blocks, but rather through the utilization of simple repetitive constitutive elements arranged in hierarchical structures
Hierarchical Structure Controls Nanomechanical Properties of Vimentin Intermediate Filaments
No full textIntermediate filaments (IFs), in addition to microtubules and microfilaments, are one of the three major components of the cytoskeleton in eukaryotic cells, playing a vital role in mechanotransduction and in providing mechanical stability to cells (Figure 1) [1]. Despite the importance of IF mechanics for cell biology and cell mechanics, the structural basis for their mechanical properties remains unknown. Specifically, our understanding of fundamental filament properties, such as the basis for their great extensibility, stiffening properties, and their exceptional mechanical resilience remains limited. This has prevented us from answering fundamental structure-function relationship questions related to the biomechanical role of intermediate filaments, which is crucial to link structure and function in the protein material’s biological context
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