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[Display omitted] • Hierarchical architected materials achieve enhanced mechanical properties. • A deep learning approach based on an attention-based diffusion model is capable of providing both, forward and inverse predictions. • We discover hierarchical microstructure candidates for a specified nonlinear mechanical response. • We demonstrate single-shot end-to-end performance in both forward/inverse directions across the entire deformation regime. • Biologically inspired materials design for high-throughput discovery specifically for diverse nonlinear constitutive relationships is provided. Inspired by natural materials, hierarchical architected materials can achieve enhanced properties including achieving tailored mechanical responses. However, the design space for such materials is often exceedingly large, and both predicting mechanical properties of complex hierarchically organized materials and designing such materials for specific target properties can be extremely difficult. In this paper we report a deep learning approach using an attention-based diffusion model, capable of providing both, forward predictions of nonlinear mechanical properties as a function of the hierarchical material structure as well as solving inverse design problems in order to discover hierarchical microstructure candidates for a specified nonlinear mechanical response. We exemplify the method for a system of compressively loaded four-hierarchy level materials derived from a family of honeycomb structures, where patterns of distributed buckling events are unitary deformation events that control small- and large-scale deformation behavior. Our model offers exquisite single-shot end-to-end performance in both forward and inverse directions across the entire range of deformation regime, and is capable of rapidly discovering multiple solutions that satisfy a design objective in accordance with the known physical behavior elucidated by, and validated with, coarse-grained simulations. The model provides an effective way towards biologically inspired materials design for high-throughput discovery in order to achieve diverse nonlinear constitutive relationships. [ABSTRACT FROM AUTHOR]

[Display omitted] Attention-based transformer neural networks have had significant impact in recent years. However, their applicability to model the behavior of physical systems has not yet been broadly explored. This is partly due to the high computational burden owing to the nonlinear scaling of very deep models, preventing application to a range of physical systems, in particular complex field data. Here we report the development of a general-purpose attention-based deep neural network model using a multi-headed self-attention approach, FieldPerceiver, that is capable of effectively predicting physical field data – such as stress, energy and displacement fields, as well as predicting overall material properties that characterize the statistics of stress distributions due to applied loading and crack defects, solely based on descriptive input that characterizes the material microstructure based on a set of interacting building blocks, all while capturing extreme short- and long-range relationships. Not using images as input, but rather realizing a neural olog description of materials where the categorization is learned by multi-headed attention, the model has no domain knowledge in its formulation, uses no convolutional layers, scales well to extremely large sizes and has no knowledge about specific properties of the material building blocks. Specifically, as applied to a fracture mechanics problem considered here, the model is capable of capturing size, orientation and geometry effects of crack problems for near- and far-field predictions, offering an alternative way to model materials failure based on language modeling without any convolutional layers commonly used in similar problems. We show that the FieldPerceiver can be used in a general framework, where the model can use insights learned during an initial, general training stage in order to fine-tune predictions for new scenarios, even when using only small additional datasets, revealing its broad generalization capacity. Once trained, the model can make predictions of thousands of scenarios within just a few minutes of compute time. It would take tens of hours, days or months to compute similar output using molecular dynamics simulation, for instance. [ABSTRACT FROM AUTHOR]

We propose a simple general framework to predict folding, native states, energy barriers, protein unfolding, as well as mutation induced diseases and other protein structural analyses. The model should not be considered as an alternative to classical approaches (Molecular Dynamics or Monte Carlo) because it neglects low scale details and rather focuses on global features of proteins and structural information. We aim at the description of phenomena that are out of the range of classical molecular modeling approaches due to the large computational cost: multimolecular interactions, cyclic behavior under variable external interactions, and similar. To demonstrate the effectiveness of the approach in a real case, we focus on the folding and unfolding behavior of tropoelastin and its mutations. Specifically, we derive a discrete mechanical model whose structure is deduced based on a coarse graining approach that allows us to group the amino acids sequence in a smaller number of 'equivalent' masses. Nearest neighbor energy terms are then introduced to reproduce the interaction of such amino acid groups. Nearest and non-nearest neighbor energy terms, inter and intra functional blocks are phenomenologically added in the form of Morse potentials. As we show, the resulting system reproduces important properties of the folding-unfolding mechanical response, including the monotonic and cyclic force-elongation behavior, representing a physiologically important information for elastin. The comparison with the experimental behavior of mutated tropoelastin confirms the predictivity of the model. Classical approaches to the study of phenomena at the molecular scale such as Molecular Dynamics (MD) represent an incredible tool to unveil mechanical and conformational properties of macromolecules, in particular for biological and medical applications. On the other hand, due to the computational cost, the time and spatial scales are limited. Focusing of the real case of tropoelastin, we propose a new approach based on a careful coarse graining of the system, able to describe the overall properties of the macromolecule and amenable of extension to larger scale effects (protein bundles, protein-protein interactions, cyclic loading). The comparison with tropoelastin behavior, also for mutations, is very promising. [Display omitted] [ABSTRACT FROM AUTHOR]

Understanding the properties and behavior of biomineralized protein-based materials at the organic-inorganic interface is critical to optimize the performance of such materials for biomedical applications. To that end, this work investigates biomineralized protein-based films with applications for bone regeneration. These films were generated using a chimeric protein fusing the consensus repeat derived from the spider Nephila clavipes major ampullate dragline silk with the silica-promoting peptide R5 derived from the Cylindrotheca fusiformis silaffin gene. The effect of pH on the size of silica nanoparticles during their biomineralization on silk films was investigated, as well as the potential impact of nanoparticle size on the differentiation of human mesenchymal stem cells (hMSCs) into osteoblasts. To that end, induction of the integrin αV subunit and the osteogenic markers Runx2 transcription factor and Bone Sialoprotein (BSP) was followed. The results indicated that pH values of 7-8 during biomineralization maximized the coverage of the film surface by silica nanoparticles yielding nanoparticles ranging 200-500 nm and showing enhanced osteoinduction in gene expression analysis. Lower (3-5) or high (10) pH values led to lower biomineralization and poor coverage of the protein surfaces, showing reduced osteoinduction. Molecular dynamics simulations confirmed the activation of the integrin αVβ3 in contact with silica nanoparticles, correlating with the experimental data on the induction of osteogenic markers. This work sheds light on the optimal conditions for the development of fit-for-purpose biomaterial designs for bone regeneration, while the agreement between experimental and computational results shows the potential of computational methods to predict the expression of osteogenic markers for biomaterials. The ability of biomineralized materials to induce hMSCs differentiation for bone tissue regeneration applications was analyzed. Biomaterials were created using a recombinant protein formed by the consensus repeat derived from the spider Nephila clavipes major ampullate dragline silk and the silica-promoting peptide R5 derived from the Cylindrotheca fusiformis silaffin gene. A combination of computational and experimental techniques revealed the optimal conditions for the synthesis of biomineralized silk-silica films with enhanced expression of markers related to bone regeneration. Image, graphical abstract [ABSTRACT FROM AUTHOR]

Creating materials with strength and toughness has been a long-sought goal. Conventional engineering materials often face a trade-off between strength and toughness, prompting researchers seeking to overcome these limitations to explore more sophisticated materials, such as composites. This paradigm shift in material design is spurred by nature, which exhibits a plethora of heterogeneous materials that offer outstanding material properties, and many natural materials are widely regarded as examples of high-performing hybrid materials. A classic example is nacre, also known as mother-of-pearl, which boasts a combination of high stiffness, strength, and fracture toughness. Various microstructural features contribute to the toughness of nacre, including mineral bridges (MBs), nano-asperities, and waviness of the constituent platelets. Recent research in biomimicry suggests that MBs contribute to the high strength and toughness observed in nacre and nacre-inspired materials. However, previous work in this area did not allow for complete control over the length scale of the bridges and had limitations on the volume fraction of mineral content. In this work, we present a systematic investigation elucidating the effects of structural parameters, such as volume fraction of mineral phase and density of MBs, on the mechanical response of nacre-inspired additive manufactured composites. Our results demonstrate that it is possible to tune the composite properties by tuning sizes and content of structural features (e.g. MBs and mineral content) in a heterogeneous material. Looking forward, this systematic approach enables materials-by-design of complex architectures to tackle demanding engineering challenges in the future. [ABSTRACT FROM AUTHOR]

Collagen is a ubiquitous protein with remarkable mechanical properties. It is highly elastic, shows large fracture strength and enables substantial energy dissipation during deformation. Most of the connective tissue in humans consists of collagen fibrils composed of a staggered array of tropocollagen molecules, which are connected by intermolecular cross-links. In this study, we report a three-dimensional coarse-grained model of collagen and analyze the influence of enzymatic cross-links on the mechanics of collagen fibrils. Two representatives immature and mature cross-links are implemented in the mesoscale model using a bottom-up approach. By varying the number, type and mechanical properties of cross-links in the fibrils and performing tensile test on the models, we systematically investigate the deformation mechanisms of cross-linked collagen fibrils. We find that cross-linked fibrils exhibit a three phase behavior, which agrees closer with experimental results than what was obtained using previous models. The fibril mechanical response is characterized by: (i) an initial elastic deformation corresponding to the collagen molecule uncoiling, (ii) a linear regime dominated by molecule sliding and (iii) the second stiffer elastic regime related to the stretching of the backbone of the tropocollagen molecules until the fibril ruptures. Our results suggest that both cross-link density and type dictate the stiffness of large deformation regime by increasing the number of interconnected molecules while cross-links mechanical properties determine the failure strain and strength of the fibril. These findings reveal that cross-links play an essential role in creating an interconnected fibrillar material of tunable toughness and strength. [ABSTRACT FROM AUTHOR]

Sewage sludge from wastewater treatment plants is a large source of organic waste with suboptimal disposal solutions available. Current common handling solutions include disposing of it as fertilizer on arable land, or direct discharge in the sea. This work investigates the valorization of sewage sludge into biocrude oils using hydrothermal liquefaction (HTL). Biocrude oils are bitumen-like materials with potential applications as green additives for asphalt binder, one of the most used materials in infrastructure. Here, we study the links for sewage sludge between feedstock (digested versus non-digested sludge), HTL conditions (temperature, biomass loading to the reactor and reaction time) and yields of biocrude oil. Our data suggests that non-digested sewage sludge leads to higher biocrude oil yields (30–40 wt%) at temperatures of 300–320 °C and biomass loadings of 20 wt%. Furthermore, we use density functional theory (DFT) calculations to study the reactivity and clustering mechanisms of asphaltenes – a key molecular component of asphalt binder, and largely responsible for its mechanical performance. Biobased asphaltenes are present in biocrude oil, and our aim was to understand their differences with fossil asphaltenes derived from petroleum. Our data suggests that biobased asphaltenes are similar to petroleum-based ones in terms of thermodynamic stability and π-π stacking, despite the higher content in polar chemical functionalities in biobased asphaltenes. Overall, the chemical features and intermolecular interactions indicate that biocrude oils produced from sewage sludge via HTL are promising candidates for application as asphalt additives. [Display omitted] • The production of asphalt additives from sewage sludge via HTL was investigated. • Non-digested sewage sludge led to higher biocrude oil yields than digested sludge. • DFT calculations provided an atomistic description of biobased and fossil asphaltenes. • Biobased asphaltenes have similar stability and π-π stacking than fossil asphaltenes. [ABSTRACT FROM AUTHOR]

Wood is a biological material with outstanding mechanical properties resulting from its hierarchical structure across different scales. Although earlier work has shown that the cellular structure of wood is a key factor that renders it excellent mechanical properties at light weight, the mechanical properties of the wood cell wall material itself still needs to be understood comprehensively. The wood cell wall material features a fiber reinforced composite structure, where cellulose fibrils act as stiff fibers, and hemicellulose and lignin molecules act as soft matrix. The angle between the fiber direction and the loading direction has been found to be the key factor controlling the mechanical properties. However, how the interactions between theses constitutive molecules contribute to the overall properties is still unclear, although the shearing between fibers has been proposed as a primary deformation mechanism. Here we report a molecular model of the wood cell wall material with atomistic resolution, used to assess the mechanical behavior under shear loading in order to understand the deformation mechanisms at the molecular level. The model includes an explicit description of cellulose crystals, hemicellulose, as well as lignin molecules arranged in a layered nanocomposite. The results obtained using this model show that the wood cell wall material under shear loading deforms in an elastic and then plastic manner. The plastic regime can be divided into two parts according to the different deformation mechanisms: yielding of the matrix and sliding of matrix along the cellulose surface. Our molecular dynamics study provides insights of the mechanical behavior of wood cell wall material at the molecular level, and paves a way for the multi-scale understanding of the mechanical properties of wood. [ABSTRACT FROM AUTHOR]

Thermal transport in monolayer graphene oxide (GO) with randomized surface epoxy and hydroxyl groups, at various degrees of oxidation (O:C ratio), is investigated using non-equilibrium molecular dynamics simulations. We find that the in-plane thermal conductivity of finite sized pristine graphene or GO (5-50nm in simulation) increases with length due to reduced phonon-boundary scattering. The intrinsic in-plane thermal conductivity and phonon mean free path of infinite pristine graphene or GO, are estimated based on the kinetic theory of phonon transport. We find that the thermal conductivity drops sharply to 17% of the pristine graphene value for a 1% O:C ratio, and to 1.5% for a typical GO with 20% O:C ratio, suggesting that typical GO is not a very good heat conductor compared to pristine graphene. Surface oxidation suppresses the density of state of the phonon mode due to C-C bonds (the G peak), reducing the phonon specific heat of this mode and hence, overall thermal conductivity. Phonon-defect scattering at the surface oxidized groups reduces the intrinsic mean free path of GO, also contributing to the reduction. Our results characterizes thermal transport in GO and offer insights into surface chemistry-mediated thermal transport in other 2D materials. [ABSTRACT FROM AUTHOR]

The scales of the arapaima (Arapaima gigas), one of the largest freshwater fish in the world, can serve as inspiration for the design of flexible dermal armor. Each scale is composed of two layers: a laminate composite of parallel collagen fibrils and a hard, highly mineralized surface layer. We review the structure of the arapaima scales and examine the functions of the different layers, focusing on the mechanical behavior, including tension and penetration of the scales, with and without the highly mineralized outer layer. We show that the fracture of the mineral and the stretching, rotation and delamination of collagen fibrils dissipate a significant amount of energy prior to catastrophic failure, providing high toughness and resistance to penetration by predator teeth. We show that the arapaima's scale has evolved to minimize damage from penetration by predator teeth through a Bouligand-like arrangement of successive layers, each consisting of parallel collagen fibrils with different orientations. This inhibits crack propagation and restricts damage to an area adjoining the penetration. The flexibility of the lamellae is instrumental to the redistribution of the compressive stresses in the underlying tissue, decreasing the severity of the concentrated load produced by the action of a tooth. The experimental results, combined with small-angle X-ray scattering characterization and molecular dynamics simulations, provide a complete picture of the mechanisms of deformation, delamination and rotation of the lamellae during tensile extension of the scale. [ABSTRACT FROM AUTHOR]

Abstract: Spider silks have been a focus of research for almost two decades due to their outstanding mechanical and biophysical properties. Recent advances in genetic engineering have led to the synthesis of recombinant spider silks, thus helping to unravel a fundamental understanding of structure–function–property relationships. The relationships between molecular composition, secondary structures and mechanical properties found in different types of spider silks are described, along with a discussion of artificial spinning of these proteins and their bioapplications, including the role of silks in biomineralization and fabrication of biomaterials with controlled properties. [Copyright &y& Elsevier]

Collagenous tissues, made of collagen molecules, such as tendon and bone, are intriguing materials that have the ability to respond to mechanical forces by altering their structures from the molecular level up, and convert them into biochemical signals that control many biological and pathological processes such as wound healing and tissue remodeling. It is clear that collagen synthesis and degradation are influenced by mechanical loading, and collagenous tissues have a remarkable built-in ability to alter the equilibrium between material formation and breakdown. However, how the mechanical force alters structures of collagen molecules and how the structural changes affect collagen degradation at molecular level is not well understood. The purpose of this article is to review the biomechanics of collagen, using a bottom-up approach that begins with the mechanics of collagen molecules. The current understanding of collagen degradation mechanisms is presented, followed by a discussion of recent studies on how mechanical force mediates collagen breakdown. Understanding the biomechanics of collagen molecules will provide the basis for understanding the mechanobiology of collagenous tissues. Addressing challenges in this field provides an opportunity for developing treatments, designing synthetic collagen materials for a variety of biomedical applications, and creating a new class of ‘smart’ structural materials that autonomously grow when needed, and break down when no longer required, with applications in nanotechnology, devices and civil engineering. [ABSTRACT FROM AUTHOR]

Abstract: Geometric confinement to the nanoscale, a concept that refers to the characteristic dimensions of structural features of materials at this length scale, has been shown to control the mechanical behavior of many biological materials or their building blocks, and such effects have also been suggested to play a crucial role in enhancing the strength and toughness of bone. Here we study the effect of geometric confinement on the fracture mechanism of hydroxyapatite (HAP) crystals that form the mineralized phase in bone. We report a series of molecular simulations of HAP crystals with an edge crack on the (001) plane under tensile loading, and we systematically vary the sample height whilst keeping the sample and the crack length constant. We find that by decreasing the sample height the stress concentration at the tip of the crack disappears for samples with a height smaller than 4.15nm, below which the material shows a different failure mode characterized by a more ductile mechanism with much larger failure strains, and the strength approaching that of a flaw-less crystal. This study directly confirms an earlier suggestion of a flaw-tolerant state that appears under geometric confinement and may explain the mechanical stability of the reinforcing HAP platelets in bone. [Copyright &y& Elsevier]

Abstract: Amyloid fibrils are most often associated with their pathological role in diseases like Alzheimer’s disease and Parkinson’s disease, but they are now increasingly being considered for uses in functional engineering materials. They are among the stiffest protein fibers known but they are also rather brittle, and it is unclear how this combination of properties affects the behavior of amyloid structures at larger length scales, such as in films, wires or plaques. Using a coarse-grained model for amyloid fibrils, we study the mechanical response of amyloid nanowires and examine fundamental mechanical properties, including mechanisms of deformation and failure under tensile loading. We also explore the effect of varying the breaking strain and adhesion strength of the constituent amyloid fibrils on the properties of the larger structure. We find that deformation in the nanowires is controlled by a combination of fibril sliding and fibril failure and that there exists a transition from brittle to ductile behavior by either increasing the fibril failure strain or decreasing the strength of adhesion between fibrils. Furthermore, our results reveal that the mechanical properties of the nanowires are quite sensitive to changes in the properties of the individual fibrils, and the larger scale structures are found to be more mechanically robust than the constituent fibrils, for all cases considered. More broadly, this work demonstrates the promise of utilizing self-assembled biological building blocks in the development of hierarchical nanomaterials. [Copyright &y& Elsevier]

Summary: Tailored materials with tunable properties are crucial for applications as biomaterials, for drug delivery, as functional coatings, or as lightweight composites. An emerging paradigm in designing such materials is the construction of hierarchical assemblies of simple building blocks into complex architectures with superior properties. We review this approach in a case study of silk, a genetically programmable and processable biomaterial, which, in its natural role serves as a versatile protein fiber with hierarchical organization to provide structural support, prey procurement or protection of eggs. Through an abstraction of knowledge from the physical system, silk, to a mathematical model using category theory, we describe how the mechanism of spinning fibers from proteins can be translated into music through a process that assigns a set of rules that governs the construction of the system. This technique allows one to express the structure, mechanisms and properties of the ‘material’ in a very different domain, ‘music’. The integration of science and art through categorization of structure–property relationships presents a novel paradigm to create new bioinspired materials, through the translation of structures and mechanisms from distinct hierarchical systems and in the context of the limited number of building blocks that universally governs these systems. [ABSTRACT FROM AUTHOR]

Abstract: Interfaces, defined as the surface of interactions between two parts of a system at a discontinuity, are very widely found in nature. While it is known that the specific structure of an interface plays an important role in defining its properties, it is less clear whether or not there exist universal scaling laws that govern the structural evolution of a very broad range of natural interfaces. Here we show that cooperativity of interacting elements, leading to great strength at low material use, is a key concept that governs the structural evolution of many natural interfaces. We demonstrate this concept for the cases of β-sheet proteins in spider silk, gecko feet, legs of caterpillars, and self-assembling of penguins into huddles, which range in scales from the submolecular to the macroscopic level. A general model is proposed that explains the size and structure of biological interfaces from a fundamental point of view. [Copyright &y& Elsevier]

Abstract: Spider silk is a self-assembling biopolymer that outperforms many known materials in terms of its mechanical performance despite being constructed from simple and inferior building blocks. While experimental studies have shown that the molecular structure of silk has a direct influence on the stiffness, toughness, and failure strength of silk, few molecular-level analyses of the nanostructure of silk assemblies in particular under variations of genetic sequences have been reported. Here we report atomistic-level structures of the MaSp1 protein from the Nephila Clavipes spider dragline silk sequence, obtained using an in silico approach based on replica exchange molecular dynamics (REMD) and explicit water molecular dynamics. We apply this method to study the effects of a systematic variation of the poly-alanine repeat lengths, a parameter controlled by the genetic makeup of silk, on the resulting molecular structure of silk at the nanoscale. Confirming earlier experimental and computational work, a structural analysis reveals that poly-alanine regions in silk predominantly form distinct and orderly -sheet crystal domains while disorderly regions are formed by glycine-rich repeats that consist of -helix type structures and -turns. Our predictions are directly validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots combined with an analysis of the secondary structure content. The key result of our study is our finding of a strong dependence of the resulting silk nanostructure depending on the poly-alanine length. We observe that the wildtype poly-alanine repeat length of six residues defines a critical minimum length that consistently results in clearly defined -sheet nanocrystals. For poly-alanine lengths below six, the -sheet nanocrystals are not well-defined or not visible at all, while for poly-alanine lengths at and above six, the characteristic nanocomposite structure of silk emerges with no significant improvement of the quality of the -sheet nanocrystal geometry. We present a simple biophysical model that explains these computational observations based on the mechanistic insight gained from the molecular simulations. Our findings set the stage for understanding how variations in the spidroin sequence can be used to engineer the structure and thereby functional properties of this biological superfiber, and present a design strategy for the genetic optimization of spidroins for enhanced mechanical properties. The approach used here may also find application in the design of other self-assembled molecular structures and fibers and in particular biologically inspired or completely synthetic systems. [Copyright &y& Elsevier]

Abstract: Disulfide bonds are important chemical cross-links that control the elasticity of fibrous protein materials such as hair, feather, wool and gluten in breadmaking dough. Here we present a novel computational approach using the first-principles-based ReaxFF reactive force field and demonstrate that this approach can be used to show that the fracture strength of disulfide bonds is decreased under the presence of reducing agents, due to a loss of cross-link stability controlled by the chemical microenvironment. Simulations in explicit solvents and dithiothreitol (DTT) indicate an intermediate step involving weakened elongated bonds, illustrating the tunability of the elasticity, rupture mechanism and strength of proteins. We provide a mechanistic insight into the fracture mechanism of protein disulfide bonds and illustrate the importance of the redox microenvironment, where factors such as accessibility, mechanical strain and local redox potential govern the dominating rupture mechanism and location. The method used here provides a general computational protocol for studying mechanochemical fracture of large-scale protein materials concurrently with experimental efforts. [Copyright &y& Elsevier]

Abstract: Carbon nanotubes and graphene have paved the way for the next step in the evolution of carbon materials. Among the novel forms of carbon allotropes is graphyne – a two-dimensional lattice of sp–sp2 -hybridized carbon atoms similar to graphene for which recent progress has been made in synthesizing dehydrobenzoannulene precursors that form subunits of graphyne. Here, we characterize the mechanical properties of single-atomic-layer graphyne sheets by full atomistic first-principles-based ReaxFF molecular dynamics. Atomistic modeling is carried out to determine its mechanical properties for both in-plane and bending deformation including material failure, as well as intersheet adhesion. Unlike graphene, the fracture strain and stress of graphyne depends strongly on the direction of the applied strain and the alignment with carbon triple-bond linkages, ranging from 48.2 to 107.5GPa with ultimate strains of 8.2–13.2%. The intersheet adhesion and out-of-plane bending stiffnesses are comparable to graphene, despite the density of graphyne being only one-half of that of graphene. Unlike graphene, the sparser carbon arrangement in graphyne combined with the directional dependence on the acetylenic groups results in internal stiffening dependent on the direction of applied loading, leading to a nonlinear stress–strain behavior. [Copyright &y& Elsevier]

Summary: It is popular stance that successful growth – be it structural, economic or biological – requires a stable foundation. The hierarchical structure of native biological materials and tissues introduces variations in form and function across a multitude of scales. Yet, many synthetic scaffolds and substrates in which such materials are assembled, the foundation, are designed at a single scale. The result is an uncertain or shaky foundation for material assembly and tissue growth, where changes in the scaffold properties and architecture result in unpredictable behaviors in tissue development, and proven, reliable scaffolds for one tissue type may be completely unsuitable for another. This is in contrast to the behavior of foundations for civil engineering structures, which provide a decoupling of the foundation from the building design since different foundations can support equivalent functional structures. Current advancements in the design of biologically active foundations shed light on proven scaffolds and substrates, but cannot be used to design and predict success from the bottom-up. This is because while the phenomenological coupling between materials and substrates has been well investigated and has yielded methodologies for biomaterial synthesis, the underlying mechanisms of self-assembly and growth are not fully understood. A potential solution lies in the utilization of hierarchical material foundations, with molecular, fibrillar and other interactions designed across all length- and time-scales with engineered, predictive, and repeatable outcomes. The potential to realize such hierarchical multiscale scaffolds can be found in the exploitation of responsive, or mutable, polymer systems that exhibit precise control and variegated chemical functionalities for applications in diverse areas such as regenerative medicine, cancer treatment or drug delivery. [ABSTRACT FROM AUTHOR]

Abstract: In this paper, the molecular dynamics (MD) simulation technique is described in the context of structural mechanics applications, providing a fundamental understanding of the atomistic approach, and demonstrating its applicability. Atomistic models provide a bottom-up description of material properties and processes, and MD simulation is capable of solving the dynamic evolution of equilibrium and non-equilibrium processes. The applicability of the technique to structural engineering problems is demonstrated through an interface debonding problem in a multi-layered material system usually encountered in composite structures. Interface debonding may lead to a possible premature failure of fiber reinforced polymer (FRP) bonded reinforced concrete (RC) structural elements subjected to moisture. Existing knowledge on meso-scale fracture mechanics may not fully explain the weakening of the interface between concrete and epoxy, when the interface is under moisture; there is a need to study the moisture affected debonding of the interface using a more fundamental approach that incorporates chemistry in the description of materials. The results of the atomistic modeling presented in this paper show that the adhesive strength (in terms of energy) between epoxy and silica is weakened in the presence of water through its interaction with epoxy. This is correlated with the existing meso-scale experimental data. This example demonstrates that MD simulation can be effectively used in studying the durability of the system through an understanding of how materials interact with the environment at the molecular level. In view of the limitation of MD simulation on both length- and time-scales, future research may focus on the development of a bridging technique between MD and finite element modeling (FEM) to be able to correlate the results from the nano- to the macro-scale. [Copyright &y& Elsevier]

Abstract: Amyloid fibrils and plaques are detected in the brain tissue of patients affected by Alzheimer’s disease, but have also been found as part of normal physiological processes such as bacterial adhesion. Due to their highly organized structures, amyloid proteins have also been used for the development of nanomaterials, for a variety of applications including biomaterials for tissue engineering, nanolectronics, or optical devices. Past research on amyloid fibrils resulted in advances in identifying their mechanical properties, revealing a remarkable stiffness. However, the failure mechanism under tensile loading has not been elucidated yet, despite its importance for the understanding of key mechanical properties of amyloid fibrils and plaques as well as the growth and aggregation of amyloids into long fibers and plaques. Here we report a molecular level analysis of failure of amyloids under uniaxial tensile loading. Our molecular modeling results demonstrate that amyloid fibrils are extremely stiff with a Young’s modulus in the range of 18–30 GPa, in good agreement with previous experimental and computational findings. The most important contribution of our study is our finding that amyloid fibrils fail at relatively small strains of 2.5%–4%, and at stress levels in the range of 1.02 to 0.64 GPa, in good agreement with experimental findings. Notably, we find that the strength properties of amyloid fibrils are extremely length dependent, and that longer amyloid fibrils show drastically smaller failure strains and failure stresses. As a result, longer fibrils in excess of hundreds of nanometers to micrometers have a greatly enhanced propensity towards spontaneous fragmentation and failure. We use a combination of simulation results and simple theoretical models to define critical fibril lengths where distinct failure mechanisms dominate. [Copyright &y& Elsevier]

Abstract: Collagen is a key constituent in structural materials found in biology, including bone, tendon, skin and blood vessels. Here we report a first molecular level model of an entire overlap region of a C-terminal cross-linked type I collagen assembly and carry out a nanomechanical characterization based on large-scale molecular dynamics simulation in explicit water solvent. Our results show that the deformation mechanism and strength of the structure are greatly affected by the presence of the cross-link, and by the specific loading condition of how the stretching is applied. We find that the presence of a cross-link results in greater strength during deformation as complete intermolecular slip is prevented, and thereby particularly affects larger deformation levels. Conversely, the lack of a cross-link results in the onset of intermolecular sliding during deformation and as a result an overall weaker structure is obtained. Through a detailed analysis of the distribution of deformation by calculating the molecular strain we show that the location of largest strains does not occur around the covalent bonding region, but is found in regions further away from this location. The insight developed from understanding collagenous materials from a fundamental molecular level upwards could play a role in advancing our understanding of physiological and disease states of connective tissues, and also enable the development of new scaffolding material for applications in regenerative medicine and biologically inspired materials. [ABSTRACT FROM AUTHOR]

Abstract: Biological systems contain highly functional and mutable materials ranging from inferior building blocks with weak chemical bonding (e.g. H-bonds in spider silk), to abundantly available materials (e.g. silica in some sea creatures), to structurally inferior materials (e.g. extremely brittle crystals in mineralized tissues like nacre or bone). Although wide and varying, biology commonly exhibits unlikely harmony within material structures and physiologic functionality. How can we exploit our knowledge of biological systems in designing synthetic materials, and can we extrapolate from this, a broad yet fundamental similarity between protein materials to a subject as classical and ancient as music? [ABSTRACT FROM AUTHOR]

Abstract: The cell’s cytoskeleton, providing cells with structure and shape, consists of different structural proteins, including microtubules, actin microfilaments and intermediate filaments. It has been suggested that intermediate filaments play a crucial role in providing mechanical stability to cells. By utilizing a simple coarse-grained computational model of the intermediate filament network in eukaryotic cells, we show here that intermediate filaments play a significant role in the cell mechanical behavior at large deformation, and reveal mechanistic insight into cell deformation under varying intermediate filament densities. We find that intermediate filament-deficient cells display an altered mechanical behavior, featuring a softer mechanical response at large deformation while the mechanical properties remain largely unchanged under small deformation. We compare the results with experimental studies in vimentin-deficient cells, showing good qualitative agreement. Our results suggest that intermediate filaments contribute to cell stiffness and deformation at large deformation, and thus play a significant role in maintaining cell structural integrity in response to applied stress and strain, in agreement with earlier hypotheses. The simulation results also suggest that changes in the filament density result in profound alterations of the deformation state of the cell nucleus, leading to greater stretch in the direction of loading and greater contraction in the orthogonal direction as the intermediate filament density is increased. Our model opens the door to future studies to investigate disease states, the effects of amino acid mutations and how structural changes at different levels in the cell’s structural makeup influence biomechanical properties. [Copyright &y& Elsevier]

Abstract: The animal cell cytoskeleton consists of three interconnected filament systems: actin microfilaments, microtubules and the lesser known intermediate filaments (IFs). All mature IF proteins share a common tripartite domain structure and the ability to assemble into 8–12nm wide filaments. At the time of their discovery in the 1980s, IFs were only considered as passive elements of the cytoskeleton mainly involved in maintaining the mechanical integrity of tissues. Since then, our knowledge of IFs structure, assembly plan and functions has improved dramatically. Especially, single IFs show a unique combination of extensibility, flexibility and toughness that is a direct consequence of their unique assembly plan. In this review we will first discuss the mechanical design of IFs by combining the experimental data with recent multi-scale modeling results. Then we will discuss how mechanical forces may interact with IFs in vivo both directly and through the activation of other proteins such as kinases. [Copyright &y& Elsevier]

Abstract: Collagen is an important structural protein in vertebrates and is responsible for the integrity of many tissues like bone, teeth, cartilage and tendon. The mechanical properties of these tissues are primarily determined by their hierarchical arrangement and the role of the collagen matrix in their structures. Here we report a series of Steered Molecular Dynamics (SMD) simulations in explicit solvent, used to elucidate the influence of the pulling rate on the Young’s modulus of individual tropocollagen molecules. We stretch a collagen peptide model sequence [(Gly-Pro-Hyp)10]3 with pulling rates ranging from 0.01 to 100 m/s, reaching much smaller deformation rates than reported in earlier SMD studies. Our results clearly demonstrate a strong influence of the loading velocity on the observed mechanical properties. Most notably, we find that Young’s modulus converges to a constant value of approximately 4 GPa tangent modulus at 8% tensile strain when the initially crimped molecule is straightened out, for pulling rates below 0.5 m/s. This enables us for the first time to predict the elastic properties of a single tropocollagen molecule at physiologically and experimentally relevant pulling rates, directly from atomistic-level calculations. At deformation rates larger than 0.5 m/s, Young’s modulus increases continuously and approaches values in excess of 15 GPa for deformation rates larger than 100 m/s. The analyses of the molecular deformation mechanisms show that the tropocollagen molecule unfolds in distinctly different ways, depending on the loading rate, which explains the observation of different values of Young’s modulus at different loading rates. For low pulling rates, the triple helix first uncoils completely at 10%–20% strain, then undergoes some recoiling in the opposite direction, and finally straightens for strains larger than 30%. At intermediate rates, the molecule uncoils linearly with increasing strain up to 35% strain. Finally, at higher velocities the triple helix does not uncoil during stretching. [Copyright &y& Elsevier]

Abstract: Proteins constitute the building blocks of biological materials such as tendon, bone, skin, spider silk or cells. An important trait of these materials is that they display highly characteristic hierarchical structures, across multiple scales, from nano to macro. Protein materials are intriguing examples of materials that balance multiple tasks, representing some of the most sustainable material solutions that integrate structure and function. Here we review progress in understanding the deformation and fracture mechanisms of hierarchical protein materials by using a materials science approach to develop structure-process-property relations, an effort defined as materiomics. Deformation processes begin with an erratic motion of individual atoms around flaws or defects that quickly evolve into formation of macroscopic fractures as chemical bonds rupture rapidly, eventually compromising the integrity of the structure or the biological system leading to failure. The combination of large-scale atomistic simulation, multi-scale modeling methods, theoretical analyses combined with experimental validation provides a powerful approach in studying deformation and failure phenomena in protein materials. Here we review studies focused on the molecular origin of deformation and fracture processes of three types of protein materials. The review includes studies of collagen – Nature’s super-glue; beta-sheet rich protein structures as found in spider silk – a natural fiber that can reach the strength of a steel cable; as well as intermediate filaments – a class of alpha-helix based structural proteins responsible for the mechanical integrity of eukaryotic cells. The article concludes with a discussion of the significance of universally found structural patterns such as the staggered collagen fibril architecture or the alpha-helical protein motif. [Copyright &y& Elsevier]

Proteins are the fundamental building blocks of a vast array of biological materials involved in critical functions of life, many of which are based on highly characteristic nanostructured arrangements of protein components that include collagen, alpha helices, or beta sheets. Bone, providing structure to our body, or spider silk, used for prey procurement, are examples of materials that have incredible elasticity, strength, and robustness unmatched by many synthetic materials. This is mainly attributed to their structural formation with molecular precision. We review recent advances in using large-scale atomistic and molecular modeling to elucidate the deformation and fracture mechanics of vimentin intermediate filaments (IFs), which are hierarchical self-assembled protein networks that provide structure and stability to eukaryotic cells. We compare the fracture and failure mechanisms of biological protein materials (BPMs) with those observed in brittle and ductile crystalline materials such as metals or ceramics. Our studies illustrate how atomistic-based multiscale modeling can be employed to provide a first principles based material description of deformation and fracture, linking nano- to macroscales. [Copyright &y& Elsevier]