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Naturally occurring biomaterials often have amazing functions, such as mechanical, thermal, electromagnetic, biological, optical and acoustic. These superior performances are often due to their hierarchical organizations of natural materials, starting from the nanoscopic scale and extending all the way to the macroscopic level. This topical issue features articles dedicated to understanding, designing and characterizing complex de novo hierarchical materials for a variety of applications. This research area is quickly evolving, and we hope that future work will drive the rational designs of innovative functional materials and generate deep impacts to broad engineering fields that address major societal challenges and needs.

Protein folding poses unique challenges for large, disordered proteins due to the low resolution of structural data accessible in experiment and on the basis of short time scales and limited sampling attainable in computation. Such molecules are uniquely suited to accelerated-sampling molecular dynamics algorithms due to a flat-energy landscape. We apply these methods to report here the folded structure in water from a fully extended chain of tropoelastin, a 698-amino acid molecular precursor to elastic fibers that confer elasticity and recoil to tissues, finding good agreement with experimental data. We then study a series of artificial and disease-related mutations, yielding molecular mechanisms to explain structural differences and variation in hierarchical assembly observed in experiment. The present model builds a framework for studying assembly and disease and yields critical insight into molecular mechanisms behind these processes. These results suggest that proteins with disordered regions are suitable candidates for characterization by this approach., Competing Interests: The authors declare no conflict of interest.

Biomineralization at the organic-inorganic interface is critical to many biology material functions in vitro and in vivo . Recombinant silk-silica fusion peptides are organic-inorganic hybrid material systems that can be effectively used to study and control biologically-mediated mineralization due to the genetic basis of sequence control. However, to date, the mechanisms by which these functionalized silk-silica proteins trigger the differentiation of human mesenchymal stem cells (hMSCs) to osteoblasts remain unknown. To address this challenge, we analyzed silk-silica surfaces for silica-hMSC receptor binding and activation, and the intracellular pathways involved in the induction of osteogenesis on these bioengineered biomaterials. The induction of gene expression of αVβ3 integrin, all three Mitogen-activated Protein Kinsases (MAPKs) as well as c-Jun, Runt-related Transcription Factor 2 (Runx2) and osteoblast marker genes was demonstrated upon growth of the hMSCs on the silk-silica materials. This induction of key markers of osteogenesis correlated with the content of silica on the materials. Moreover, computational simulations were performed for silk/silica-integrin binding which showed activation of αVβ3 integrin in contact with silica. This integrated computational and experimental approach provides insight into interactions that regulate osteogenesis towards more efficient biomaterial designs.

Adaptive hydrogels tailor-made from silk-elastin-like proteins (SELPs) possess excellent biocompatibility and biodegradability with properties that are tunable and responsive to multiple simultaneous external stimuli. To unravel the molecular mechanisms of their physical response to external stimuli in tandem with experiments, here we predict and measure the variation in structural properties as a function of temperature through coarse-grained (CG) modeling of individual and crosslinked SE 8Y and S 4 E 8Y molecules, which have ratios of 1:8 and 4:8 of silk to elastin blocks respectively. Extensive structural reshuffling in single SE 8Y molecules led to the increased compactness of the structure, whereas S 4 E 8Y molecules did not experience any significant changes as they already adopted very compact structures at low temperatures. Crosslinking of SE 8Y molecules at high concentrations impeded their structural transition at high temperatures that drastically reduced the degree of deswelling through extensive suppression of the structural shuffling and the trapping of the molecules in high potential energy states due to inter-molecular constraints. This integrative experimental and computational understanding of the thermal response in single molecules of SELPs and their crosslinked networks should lead to further improvements in the properties of SELP hydrogels through predictive designs and their wider applications in biomaterials and tissue engineering., Competing Interests: Conflicts of interest There are no conflicts to declare.

Enzymatic collagen cross-linking has been shown to play an important role in the macroscopic elastic and plastic deformation of bone across ages. However, its direct contribution to collagen fibril deformation is unknown. The aim of this study is to determine how covalent intermolecular connections from enzymatic collagen cross-links contribute to collagen fibril elastic and plastic deformation of adults and children's bone matrix. We used ex vivo data previously obtained from biochemical analysis of children and adults bone samples (n = 14; n = 8, respectively) to create 22 sample-specific computational models of cross-linked collagen fibrils. By simulating a tensile test for each fibril, we computed the modulus of elasticity (E), ultimate tensile and yield stress (σ u and σ y ), and elastic, plastic and total work (W e , W p and W tot ) for each collagen fibril. We present a novel difference between children and adult bone in the deformation of the collagen phase and suggest a link between collagen fibril scale and macroscale for elastic behavior in children bone under the influence of immature enzymatic cross-links. We show a parametric linear correlation between W e and immature enzymatic collagen cross-links at the collagen fibril scale in the children population that is similar to the one we found at the macroscale in our previous study. Finally, we suggest the key role of covalent intermolecular connections to stiffness parameters (e.g. elastic modulus and W e ) in children's collagen fibril and to toughness parameters in adult's collagen fibril, respectively., (Copyright © 2018. Published by Elsevier Inc.)

In the 50 years that succeeded Richard Feynman's exposition of the idea that there is "plenty of room at the bottom" for manipulating individual atoms for the synthesis and manufacturing processing of materials, the materials-by-design paradigm is being developed gradually through synergistic integration of experimental material synthesis and characterization with predictive computational modeling and optimization. This paper reviews how this paradigm creates the possibility to develop materials according to specific, rational designs from the molecular to the macroscopic scale. We discuss promising techniques in experimental small-scale material synthesis and large-scale fabrication methods to manipulate atomistic or macroscale structures, which can be designed by computational modeling. These include recombinant protein technology to produce peptides and proteins with tailored sequences encoded by recombinant DNA, self-assembly processes induced by conformational transition of proteins, additive manufacturing for designing complex structures, and qualitative and quantitative characterization of materials at different length scales. We describe important material characterization techniques using numerous methods of spectroscopy and microscopy. We detail numerous multi-scale computational modeling techniques that complements these experimental techniques: DFT at the atomistic scale; fully atomistic and coarse-grain molecular dynamics at the molecular to mesoscale; continuum modeling at the macroscale. Additionally, we present case studies that utilize experimental and computational approaches in an integrated manner to broaden our understanding of the properties of two-dimensional materials and materials based on silk and silk-elastin-like proteins.

A molybdenum disulfide (MoS 2 ) layered system is a two-dimensional (2D) material, which is expected to provide the next generation of electronic devices together with graphene and other 2D materials. Due to its significance for future electronics applications, gaining a deep insight into the fundamental mechanisms upon MoS 2 fracture is crucial to prevent mechanical failure toward reliable applications. Here, we report direct experimental observation and atomic modeling of the complex failure behaviors of bilayer MoS 2 originating from highly variable interlayer frictions, elucidated with in situ transmission electron microscopy and large-scale reactive molecular dynamics simulations. Our results provide a systematic understanding of the effects that different stacking and loading conditions have on the failure mechanisms and crack-tip behaviors in the bilayer MoS 2 systems. Our findings unveil essential properties in fracture of this 2D material and provide mechanistic insight into its mechanical failure.

Nanofibrillar materials, such as cellulose, chitin and silk, are highly ordered architectures, formed through the self-assembly of repetitive building blocks into higher-order structures, which are stabilized by non-covalent interactions. This hierarchical building principle endows many biological materials with remarkable mechanical strength, anisotropy, flexibility and optical properties, such as structural colour. These features make nanofibrillar biopolymers interesting candidates for the development of strong, sustainable and biocompatible materials for environmental, energy, optical and biomedical applications. However, recreating their architecture is challenging from an engineering perspective. Rational design approaches, applying a combination of theoretical and experimental protocols, have enabled the design of biopolymer-based materials through mimicking nature's multiscale assembly approach. In this Review, we summarize hierarchical design strategies of cellulose, silk and chitin, focusing on nanoconfinement, fibrillar orientation and alignment in 2D and 3D structures. These multiscale architectures are discussed in the context of mechanical and optical properties, and different fabrication strategies for the manufacturing of biopolymer nanofibril-based materials are investigated. We highlight the contribution of rational material design strategies to the development of mechanically anisotropic and responsive materials and examine the future of the material-by-design paradigm., Competing Interests: Competing interests The authors declare no competing interests.

Scleroproteins are an important category of proteins within the human body that adopt filamentous, elongated conformations in contrast with typical globular proteins. These include keratin, collagen, and elastin, which often serve a common mechanical function in structural support of cells and tissues. Genetic mutations alter these proteins, disrupting their functions and causing diseases. Computational characterization of these mutations has proven to be extremely valuable in identifying the intricate structure-function relationships of scleroproteins from the molecular scale up, especially if combined with multiscale experimental analysis and the synthesis of model proteins to test specific structure-function relationships. In this work, we review numerous critical diseases that are related to keratin, collagen, and elastin, and through several case studies, we propose ways of extensively utilizing multiscale modeling, from atomistic to coarse-grained molecular dynamics simulations, to uncover the molecular origins for some of these diseases and to aid in the development of novel cures and therapies. As case studies, we examine the effects of the genetic disease Epidermolytic Hyperkeratosis (EHK) on the structure and aggregation of keratins 1 and 10; we propose models to understand the diseases of Osteogenesis Imperfecta (OI) and Alport syndrome (AS) that affect the mechanical and aggregation properties of collagen; and we develop atomistic molecular dynamics and elastic network models of elastin to determine the role of mutations in diseases such as Cutis Laxa and Supravalvular Aortic Stenosis on elastin's structure and molecular conformational motions and implications for assembly.

Hydrogels have been the focus of extensive research due to their potential use in fields including biomedical, pharmaceutical, biosensors, and cosmetics. However, the general weak mechanical properties of hydrogels limit their utility. Here, we generate pristine silk fibroin (SF) hydrogels with excellent mechanical properties via a binary solvent induced conformation transition (BSICT) strategy. In this method, the conformational transition of SF is regulated by moderate binary solvent diffusion and SF/solvent interactions. β-sheet formation serves as the physical crosslinks that connect disparate protein chains to form continuous 3D hydrogel networks, avoiding complex chemical and/or physical treatments. The Young's modulus of these new BSICT-silk fibroin hydrogels can reach up to 6.5±0.2 MPa, tens to hundreds of times higher than that of conventional hydrogels (0.01-0.1 MPa). These new materials filled the "empty soft materials space" in the elastic modulus/strain Ashby plot. More remarkably, the BSICT-SF hydrogels can be processed into different constructions through different polymer and/or metal based processing techniques, such as molding, laser cutting, and machining. Thus, these new hydrogel systems exhibit potential utility in many biomedical and engineering fields.

The production of structural and functional materials with enhanced mechanical properties through the integration of soft and hard components is a common approach to Nature's materials design. However, directly mimicking these optimized design routes in the lab for practical applications remains challenging. For example, graphene and silk are two materials with complementary mechanical properties that feature ultrahigh stiffness and toughness, respectively. Yet no simple and controllable approach has been developed to homogeneously integrate these two components into functional composites, mainly due to the hydrophobicity and chemical inertness of the graphene. In this study, well-dispersed and highly stable graphene/silk fibroin (SF) suspension systems were developed, which are suitable for processing to fabricate polymorphic materials, such as films, fibers, and coatings. The obtained graphene/SF nanocomposites maintain the electronic advantages of graphene, and they also allow tailorable mechanical performance to form including ultrahigh stretchable (with a strain to failure to 611±85%), or high strength (339 MPa) and high stiffness (7.4 GPa) material systems. More remarkably, the electrical resistances of these graphene/SF materials are sensitive to material deformation, body movement, as well as humidity and chemical environmental changes. These unique features promise their utility as wearable sensors, smart textiles, intelligent skins, and human-machine interfaces.

Two-dimensional (2D) materials are among the most promising candidates for next-generation electronics due to their atomic thinness, allowing for flexible transparent electronics and ultimate length scaling. Thus far, atomically thin p-n junctions, metal-semiconductor contacts, and metal-insulator barriers have been demonstrated. Although 2D materials achieve the thinnest possible devices, precise nanoscale control over the lateral dimensions is also necessary. Here, we report the direct synthesis of sub-nanometre-wide one-dimensional (1D) MoS 2 channels embedded within WSe 2 monolayers, using a dislocation-catalysed approach. The 1D channels have edges free of misfit dislocations and dangling bonds, forming a coherent interface with the embedding 2D matrix. Periodic dislocation arrays produce 2D superlattices of coherent MoS 2 1D channels in WSe 2 . Using molecular dynamics simulations, we have identified other combinations of 2D materials where 1D channels can also be formed. The electronic band structure of these 1D channels offers the promise of carrier confinement in a direct-gap material and the charge separation needed to access the ultimate length scales necessary for future electronic applications.

Developing fundamental tools and insight into biomaterial designs for predictive functional outcomes remains critical for the field. Silk is a promising candidate as a biomaterial for tissue engineering scaffolds, particularly where high mechanical loads or slow rates of degradation are desirable. Although bioinspired synthetic spider silks are feasible biomaterials for this purpose, insight into how well the degradation rate can be programmed by fine tuning the sequence remains to be determined. Here we integrated experimental approaches and computational modelling to investigate the degradation of two bioengineered spider silk block copolymers, H(AB) 2 and H(AB) 12 , which were designed based on the consensus domains of Nephila clavipes dragline silk. The effect of protein chain length and secondary structure on degradation was analysed in vivo. The degradation rate of H(AB) 12 , the silk with longer chain length/higher molecular weight, and higher crystallinity, was slower when compared to H(AB) 2 . Using full atomistic modelling, it was determined that the faster degradation of H(AB) 2 was due to the lower folded molecular structure of the silk and the greater accessibility to solvent. Comparison of the specific surface areas of proteins via modelling showed that higher exposure of random coil and lower exposure of ordered domains in H(AB) 2 led to the more reactive silk with a higher degradation rate when compared with H(AB) 12 , as validated by the experimental results. The study, based on two simple silk designs demonstrated that the control of sequence can lead to programmable degradation rates for these biomaterials, providing a suitable model system with which to study variables in protein polymer design to predict degradation rates in vivo. This approach should reduce the use of animal screening, while also accelerating translation of such biomaterials for repair and regenerative systems. Copyright © 2016 John Wiley & Sons, Ltd., (Copyright © 2016 John Wiley & Sons, Ltd.)

Bone and its substructures have recently been a source of inspiration for the design of novel composites, offering optimal strength-toughness and stiffness-density combinations, traits endowed by the abundance of complex biointerfaces. Bone-inspired design combined with engineering principles may offer a path toward reaching an optimal strength-toughness balance in new materials. On the one hand, with the advent of micro- and nanoreinforcements and novel manufacturing techniques, new possibilities for advanced materials have opened. On the other hand, the endeavor for novel materials with radically improved properties is spurring the research toward accurate and versatile numerical models to be used in the design phase. In this work, we present a 2D lattice spring model to predict the performance of previously tested 3D-printed bone-inspired composites, and their failure modes. The model has the capacity to correctly estimate the material performance and to reproduce the bonelike toughening mechanisms, occurring at different length scales in our composites. The numerical results show how the material properties, the interfaces, the reinforcement geometry, and the topological pattern affect the stress distribution and the propagation of defects, significantly decreasing the flaw sensitivity of the material. Our framework could be used for the design of new materials with improved fracture resistance and balance with stiffness and strength.

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., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

The integration of modeling and experimentation is an integral component of all engineering design. Developing the technologies to achieve this represents a critical challenge in biomaterials because of the hierarchical structures that comprise them and the spectra of timescales upon which they operate. Progress in integrating modeling and experiment in biomaterials represents progress towards harnessing them for engineering application. We present here a summary of the state of the art, and outlooks for the field as a whole.

Silk and elastin are exemplary protein materials that exhibit exceptional material properties. Silk is uniquely strong, surpassing engineering materials such as Kevlar and steel, while elastin has exquisite flexibility and can reversibly fold into a more structured form at high temperatures when many other proteins would unfold and denature. This phenomenon in elastin is termed the inverse temperature transition. It is a reversible, controllable process that motivates applications in drug delivery, shape change materials, and biomimetic devices. Silk-elastinlike protein polymers (SELPs), which combine repeating B. mori silk and elastin blocks, have been introduced as biologically inspired materials that combine the distinctive properties of the component parts to achieve strong and extensible, tunable biomaterials. Here, we considered a single SELP sequence to examine temperature transition effects at the molecular scale. SELP molecular models were created using Replica Exchange Molecular Dynamics, an accelerated sampling method, and confirmed in experiment by comparing secondary structure distributions. A molecular collapse of the SELP molecule was observed with increased temperature in both molecular simulation and experiment. Temperature-specific differences were observed in the mechanical properties and the unfolding pathways of the polypeptide. Using the Bell-Evans model, we analyzed the free energy landscape associated with molecular unfolding at temperatures below and above the transition temperature range ( T t ) of the polypeptide. We found that at physiological pulling rates, the energy barrier to unfold SELPs was counterintuitively higher above T t . Our findings offer a foundational perspective on the molecular scale mechanisms of temperature-induced phase transition in SELPs, and suggest a novel approach to combine simulation and experiment to study materials for multifunctional biomimetic applications.

Mineralized polymeric biomaterials provide useful options toward mechanically robust systems for some tissue repairs. Silks as a mechanically robust protein-based material provide a starting point for biomaterial options, particularly when combined with silica toward organic-inorganic hybrid systems. To further understand the interplay between silk proteins and silica related to material properties, we systematically study the role of three key domains in bioengineered spider silk fusion proteins with respect to β-sheet formation and mineralization: (i) a core silk domain for materials assembly, (ii) a histidine tag for purification, and (iii) a silicification domain for mineralization. Computational simulations are used to identify the effect of each domain on the protein folding and accessibility of positively charged amino acids for silicification and predictions are then compared with experimental data. The results show that the addition of the silica and histidine domains reduces β-sheet structure in the materials, and increases solvent-accessible surface area to the positive charged amino acids, leading to higher levels of silica precipitation. Moreover, the simulations show that the location of the charged biomineralization domain has small effect on the protein folding and consequently surface exposure of charged amino acids. Those surfaces display correlation with the amount of silicification in experiments. The results demonstrate that the exposure of the positively charged amino acids impacts protein function related to mineralization. In addition, processing parameters (solvating agent, the method of β-sheet induction and temperature) affect protein secondary structure, folding and function. This integrated modeling and experimental approach provides insight into sequence-structure-function relationships for control of mineralized protein biomaterial structures.

A variety of artificial spinning methods have been applied to produce regenerated silk fibers; however, how to spin regenerated silk fibers that retain the advantages of natural silks in terms of structural hierarchy and mechanical properties remains challenging. Here, we show a bioinspired approach to spin regenerated silk fibers. First, we develop a nematic silk microfibril solution, highly viscous and stable, by partially dissolving silk fibers into microfibrils. This solution maintains the hierarchical structures in natural silks and serves as spinning dope. It is then spun into regenerated silk fibers by direct extrusion in the air, offering a useful route to generate polymorphic and hierarchical regenerated silk fibers with physical properties beyond natural fiber construction. The materials maintain the structural hierarchy and mechanical properties of natural silks, including a modulus of 11 ± 4 GPa, even higher than natural spider silk. It can further be functionalized with a conductive silk/carbon nanotube coating, responsive to changes in humidity and temperature.

Spider dragline silk is a protein material that has evolved over millions of years to achieve finely tuned mechanical properties. A less known feature of some dragline silk fibers is that they shrink along the main axis by up to 50% when exposed to high humidity, a phenomenon called supercontraction. This contrasts the typical behavior of many other materials that swell when exposed to humidity. Molecular level details and mechanisms of the supercontraction effect are heavily debated. Here we report a molecular dynamics analysis of supercontraction in Nephila clavipes silk combined with in situ mechanical testing and Raman spectroscopy linking the reorganization of the nanostructure to the polar and charged amino acids in the sequence. We further show in our in silico approach that point mutations of these groups not only suppress the supercontraction effect, but even reverse it, while maintaining the exceptional mechanical properties of the silk material. This work has imminent impact on the design of biomimetic equivalents and recombinant silks for which supercontraction may or may not be a desirable feature. The approach applied is appropriate to explore the effect of point mutations on the overall physical properties of protein based materials.

Graphene and other two-dimensional materials have unique physical and chemical properties of broad relevance. It has been suggested that the transformation of these atomically planar materials to three-dimensional (3D) geometries by bending, wrinkling, or folding could significantly alter their properties and lead to novel structures and devices with compact form factors, but strategies to enable this shape change remain limited. We report a benign thermally responsive method to fold and unfold monolayer graphene into predesigned, ordered 3D structures. The methodology involves the surface functionalization of monolayer graphene using ultrathin noncovalently bonded mussel-inspired polydopamine and thermoresponsive poly( N -isopropylacrylamide) brushes. The functionalized graphene is micropatterned and self-folds into ordered 3D structures with reversible deformation under a full control by temperature. The structures are characterized using spectroscopy and microscopy, and self-folding is rationalized using a multiscale molecular dynamics model. Our work demonstrates the potential to design and fabricate ordered 3D graphene structures with predictable shape and dynamics. We highlight applicability by encapsulating live cells and creating nonlinear resistor and creased transistor devices.

Graphene has excellent mechanical, thermal and electrical properties. However, there are limitations in utilizing monolayers of graphene for mechanical engineering applications due to its atomic thickness and lack of bending rigidity. Synthesizing graphene aerogels or foams is one approach to utilize graphene in three-dimensional bulk forms. Recently, graphene with a gyroidal geometry has been proposed. A gyroid is a triply periodic minimal surface that allows graphene sheets to form a three-dimensional structure. Its light weight and high mechanical strength suggests that the graphene that constitutes this geometry can synergistically contribute to the mechanics of the bulk material. However, it is not clear whether gyroid graphene can preserve the high thermal conductivity of pristine graphene sheets. Here, we investigate the thermal conductivities of gyroid graphene with different porosities by using full-atom molecular dynamics simulations. In contrast to its excellent mechanical properties, we find that the thermal conductivity of gyroid graphene is more than 300 times lower than that of pristine graphene, with a bulk density of only about one-third of that of graphene. We derive a scaling law showing that the thermal conductivity does not vary much with different bulk densities, which contrasts the behavior of conventional porous materials. Our analysis shows that the poor thermal conductivity of gyroid graphene can be attributed to defects and curvatures of graphene, which increase with the density, resulting in the reduction of a phonon mean free path by phonon scattering. Our study shows that three-dimensional porous graphene has potential that may be utilized in designing new lightweight structural materials with low and density-insensitive thermal properties and superior mechanical strength.

Accurate prediction and validation of the assembly of bioinspired peptide sequences into fibers with defined mechanical characteristics would aid significantly in designing and creating materials with desired properties. This process may also be utilized to provide insight into how the molecular architecture of many natural protein fibers is assembled. In this work, computational modeling and experimentation are used in tandem to determine how peptide terminal modification affects a fiber-forming core domain. Modeling shows that increased terminal molecular weight and hydrophilicity improve peptide chain alignment under shearing conditions and promote consolidation of semicrystalline domains. Mechanical analysis shows acute improvements to strength and elasticity, but significantly reduced extensibility and overall toughness. These results highlight an important entropic function that terminal domains of fiber-forming peptides exhibit as chain alignment promoters, which ultimately has notable consequences on the mechanical behavior of the final fiber products., (© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

In this study, the pH-dependent friction of layer-by-layer assemblies of poly(allylamine hydrochloride) and poly(acrylic acid) (PAH/PAA) are quantified for microtube array structures via experimental and simulated lateral force microscopy (LFM). A novel coarse-grain tube model is developed, utilizing a molecular dynamics (MD) framework with a Hertzian soft contact potential (such that F ∼ δ 3/2 ) to allow the efficient dynamic simulation of 3D arrays consisting of hundreds of tubes at micrometer length scales. By quantitatively comparing experimental LFM and computational results, the coupling between geometry (tube spacing and swelling) and material properties (intrinsic stiffness) results in a transition from bending dominated deformation to bending combined with inter-tube contact, independent of material adhesion assumptions. Variation of tube spacing (and thus control of contact) can be used to exploit the normal and lateral resistance of the tube arrays as a function of pH (2.0/5.5), beyond the effect of areal tube density, with increased resistances (potential mutability) up to a factor of ∼60. This study provides a novel modeling platform to assess and design dynamic polyelectrolyte-based substrates/coatings with tailorable stimulus-responsive surface friction. Our results show that micro-geometry can be used alongside stimulus-responsive material changes to amplify and systematically tune mutability.

Silk is a promising material for biomedical applications, and much research is focused on how application-specific, mechanical properties of silk can be designed synthetically through proper amino acid sequences and processing parameters. This protocol describes an iterative process between research disciplines that combines simulation, genetic synthesis, and fiber analysis to better design silk fibers with specific mechanical properties. Computational methods are used to assess the protein polymer structure as it forms an interconnected fiber network through shearing and how this process affects fiber mechanical properties. Model outcomes are validated experimentally with the genetic design of protein polymers that match the simulation structures, fiber fabrication from these polymers, and mechanical testing of these fibers. Through iterative feedback between computation, genetic synthesis, and fiber mechanical testing, this protocol will enable a priori prediction capability of recombinant material mechanical properties via insights from the resulting molecular architecture of the fiber network based entirely on the initial protein monomer composition. This style of protocol may be applied to other fields where a research team seeks to design a biomaterial with biomedical application-specific properties. This protocol highlights when and how the three research groups (simulation, synthesis, and engineering) should be interacting to arrive at the most effective method for predictive design of their material., Competing Interests: Notes The authors declare no competing financial interest.

An order of magnitude tougher than nacre, conch shells are known for being one of the toughest body armors in nature. However, the complexity of the conch shell architecture creates a barrier to emulating its cross-lamellar structure in synthetic materials. Here, a 3D biomimetic conch shell prototype is presented, which can replicate the crack arresting mechanisms embedded in the natural architecture. Through an integrated approach combining simulation, additive manufacturing, and drop tower testing, the function of hierarchy in conch shell's multiscale microarchitectures is explicated. The results show that adding the second level of cross-lamellar hierarchy can boost impact performance by 70% and 85% compared to a single-level hierarchy and the stiff constituent, respectively. The overarching mechanism responsible for the impact resistance of conch shell is the generation of pathways for crack deviation, which can be generalized to the design of future protective apparatus such as helmets and body armor., (© 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Multiscale modeling of muscular-skeletal systems-the materials and structures that help organisms support themselves and move-is a rapidly growing field of study that has contributed key elements to the understanding of these systems, especially from a multiscale perspective. The systems, including materials such as bone and muscle, have hierarchical structures ranging from the nano- to the macroscale, and it is difficult to understand their macroscopic behaviors, both physiological and pathological, without knowledge of their hierarchical structures and properties. In this review, we discuss the methods of multiscale modeling. Through a series of case studies about key materials in muscular-skeletal systems, we describe how different methods can bridge the gap between hierarchical structures and their roles in the systems' mechanical properties. In particular, we emphasize the importance of the quality of minerals in bone. Finally, we discuss biomimetic material designs facilitated by additive manufacturing technology.

While individual carbon nanotubes (CNTs) are known as one of the strongest fibers ever known, even the strongest fabricated macroscale CNT yarns and fibers are still significantly weaker than individual nanotubes. The loss in mechanical properties is mainly because the deformation mechanism of CNT fibers is highly governed by the weak shear strength corresponding to sliding of nanotubes on each other. Adding polymer coating to the bundles, and twisting the CNT yarns to enhance the intertube interactions are both efficient methods to improve the mechanical properties of macroscale yarns. Here, we perform molecular dynamics (MD) simulations to unravel the unknown deformation mechanism in the intertube polymer chains and also local deformations of the CNTs at the atomistic scale. Our results show that the lateral pressure can have both beneficial and adverse effects on shear strength of polymer coated CNTs, depending on the local deformations at the atomistic scale. In this paper we also introduce a bottom-up bridging strategy between a full atomistic model and a coarse-grained (CG) model. Our trained CG model is capable of incorporating the atomistic scale local deformations of each CNT to the larger scale collect behavior of bundles, which enables the model to accurately predict the effect of lateral pressure on larger CNT bundles and yarns. The developed multiscale CG model is implemented to study the effect of lateral pressure on the shear strength of straight polymer coated CNT yarns, and also the effect of twisting on the pull-out force of bundles in spun CNT yarns.

Soluble elastin-like peptides (ELPs) can be engineered into a range of physical forms, from hydrogels and scaffolds to fibers and artificial tissues, finding numerous applications in medicine and engineering as "smart polymers". Elastin-like peptides are attractive candidates as a platform for novel biomaterial design because they exhibit a highly tunable response spectrum, with reversible phase transition capabilities. Here, we report the design of the first virtual library of elastin-like protein models using methods for enhanced sampling to study the effect of peptide chemistry, chain length, and salt concentration on the structural transitions of ELPs, exposing associated molecular mechanisms. We describe the behavior of the local molecular structure under increasing temperatures and the effect of peptide interactions with nearest hydration shell water molecules on peptide mobility and propensity to exhibit structural transitions. Shifts in the magnitude of structural transitions at the single-molecule scale are explained from the perspective of peptide-ion-water interactions in a library of four unique elastin-like peptide systems. Predictions of structural transitions are subsequently validated in experiment. This library is a valuable resource for recombinant protein design and synthesis as it elucidates mechanisms at the single-molecule level, paving a feedback path between simulation and experiment for smart material designs, with applications in biomedicine and diagnostic devices., (Copyright © 2017. Published by Elsevier Ltd.)

The nanometer-sized plate-like morphology of bone mineral is necessary for proper bone mechanics and physiology. However, mechanisms regulating the morphology of these mineral nanocrystals remain unclear. The dominant hypothesis attributes the size and shape regulation to organic-mineral interactions. Here, we present data supporting the hypothesis that physicochemical effects of carbonate integration within the apatite lattice control the morphology, size, and mechanics of bioapatite mineral crystals. Carbonated apatites synthesized in the absence of organic molecules presented plate-like morphologies and nanoscale crystallite dimensions. Experimentally-determined crystallite size, lattice spacing, solubility and atomic order were modified by carbonate concentration. Molecular dynamics (MD) simulations and density functional theory (DFT) calculations predicted changes in surface energy and elastic moduli with carbonate concentration. Combining these results with a scaling law predicted the experimentally observed scaling of size and energetics with carbonate concentration. The experiments and models describe a clear mechanism by which crystal dimensions are controlled by carbonate substitution. Furthermore, the results demonstrate that carbonate substitution is sufficient to drive the formation of bone-like crystallites. This new understanding points to pathways for biomimetic synthesis of novel, nanostructured biomaterials., (Copyright © 2017 Elsevier Ltd. All rights reserved.)

Tailored biomaterials with tunable functional properties are crucial for a variety of task-specific applications ranging from healthcare to sustainable, novel bio-nanodevices. To generate polymeric materials with predictive functional outcomes, exploiting designs from nature while morphing them toward non-natural systems offers an important strategy. Silks are Nature's building blocks and are produced by arthropods for a variety of uses that are essential for their survival. Due to the genetic control of encoded protein sequence, mechanical properties, biocompatibility, and biodegradability, silk proteins have been selected as prototype models to emulate for the tunable designs of biomaterial systems. The bottom up strategy of material design opens important opportunities to create predictive functional outcomes, following the exquisite polymeric templates inspired by silks. Recombinant DNA technology provides a systematic approach to recapitulate, vary, and evaluate the core structure peptide motifs in silks and then biosynthesize silk-based polymers by design. Post-biosynthesis processing allows for another dimension of material design by controlled or assisted assembly. Multiscale modeling, from the theoretical prospective, provides strategies to explore interactions at different length scales, leading to selective material properties. Synergy among experimental and modeling approaches can provide new and more rapid insights into the most appropriate structure-function relationships to pursue while also furthering our understanding in terms of the range of silk-based systems that can be generated. This approach utilizes nature as a blueprint for initial polymer designs with useful functions (e.g., silk fibers) but also employs modeling-guided experiments to expand the initial polymer designs into new domains of functional materials that do not exist in nature. The overall path to these new functional outcomes is greatly accelerated via the integration of modeling with experiment. In this Account, we summarize recent advances in understanding and functionalization of silk-based protein systems, with a focus on the integration of simulation and experiment for biopolymer design. Spider silk was selected as an exemplary protein to address the fundamental challenges in polymer designs, including specific insights into the role of molecular weight, hydrophobic/hydrophilic partitioning, and shear stress for silk fiber formation. To expand current silk designs toward biointerfaces and stimuli responsive materials, peptide modules from other natural proteins were added to silk designs to introduce new functions, exploiting the modular nature of silk proteins and fibrous proteins in general. The integrated approaches explored suggest that protein folding, silk volume fraction, and protein amino acid sequence changes (e.g., mutations) are critical factors for functional biomaterial designs. In summary, the integrated modeling-experimental approach described in this Account suggests a more rationally directed and more rapid method for the design of polymeric materials. It is expected that this combined use of experimental and computational approaches has a broad applicability not only for silk-based systems, but also for other polymer and composite materials.

Multilayer architectures in water purification membranes enable increased water throughput, high filter efficiency, and high molecular loading capacity. However, the preparation of membranes with well-organized multilayer structures, starting from the nanoscale to maximize filtration efficiency, remains a challenge. We report a complete strategy to fully realize a novel biomaterial-based multilayer nanoporous membrane via the integration of computational simulation and experimental fabrication. Our comparative computational simulations, based on coarse-grained models of protein nanofibrils and mineral plates, reveal that the multilayer structure can only form with weak interactions between nanofibrils and mineral plates. We demonstrate experimentally that silk nanofibril (SNF) and hydroxyapatite (HAP) can be used to fabricate highly ordered multilayer membranes with nanoporous features by combining protein self-assembly and in situ biomineralization. The production is optimized to be a simple and highly repeatable process that does not require sophisticated equipment and is suitable for scaled production of low-cost water purification membranes. These membranes not only show ultrafast water penetration but also exhibit broad utility and high efficiency of removal and even reuse (in some cases) of contaminants, including heavy metal ions, dyes, proteins, and other nanoparticles in water. Our biomimetic design and synthesis of these functional SNF/HAP materials have established a paradigm that could lead to the large-scale, low-cost production of multilayer materials with broad spectrum and efficiency for water purification, with applications in wastewater treatment, biomedicine, food industry, and the life sciences.

Mechanical injury to connective tissue causes changes in collagen structure and material behaviour, but the role and mechanisms of molecular damage have not been established. In the case of mechanical subfailure damage, no apparent macroscale damage can be detected, yet this damage initiates and potentiates in pathological processes. Here, we utilize collagen hybridizing peptide (CHP), which binds unfolded collagen by triple helix formation, to detect molecular level subfailure damage to collagen in mechanically stretched rat tail tendon fascicle. Our results directly reveal that collagen triple helix unfolding occurs during tensile loading of collagenous tissues and thus is an important damage mechanism. Steered molecular dynamics simulations suggest that a likely mechanism for triple helix unfolding is intermolecular shearing of collagen α-chains. Our results elucidate a probable molecular failure mechanism associated with subfailure injuries, and demonstrate the potential of CHP targeting for diagnosis, treatment and monitoring of tissue disease and injury.

Human type III collagen has been suggested to play vital roles in a series of pathophysiological conditions. Sequence analysis among major fibril-forming collagens (types I, II, and III) revealed that Gly-Gly pairs are a distinct sequence feature in type III collagen. This motif occurs more than five times as often in type III compared to type I and II collagens. We used an integrated computational modeling and biophysical approach to analyze the glycine pair motifs to understand how they govern the structure of type III collagen at the molecular level. Triple helical peptides to model the regions of type III collagen containing GG motifs were used to analyze structural and thermodynamic effects of GG incorporation into the collagen sequence. We found that when amino acids adjacent to a GG motif are charged, the collagen adopts a more flexible, random conformation. The GG motif led to altered hydrogen bond patterns and decreased global melting temperatures of the triple helical peptides. The local entropic destabilization effect of the glycine pair helps explain the difference in the flexibility between types I and III collagen fibrils. This finding reveals potential physiological roles of type III collagen in regulating the mechanical properties of collagen fibrils and may enable the design of future collagen-like materials with tunable mechanical properties.

The Nvjp-1 protein is a key component in the jaws of Nereis virens, a species of marine worm. It contains over 25 mol % of histidine, which is believed to play a key role in the metal-coordinated cross-linking responsible for the structural stability and exceptional mechanical performance of the worm jaw. Understanding the nanoscale mechanism behind this cross-linking and its pathway in affecting the macroscopic mechanical behavior of the material is crucial to develop bioinspired mechanomutable materials based on Nvjp-1. Here, we use a combination of multiscale modeling and experimental synthesis to understand the behavior of this heterologous-expressed protein from the nano- to the macroscale. We have built a bottom-up molecular-based model, which includes electronic-based density functional theory calculations, atomistic simulation of the nanoscale properties with replica exchange molecular dynamics, and an elastic network model for describing the macroscale behavior at different pHs. This multiscale modeling supports the experimental synthesis of a photo-cross-linked Nvjp-1 hydrogel by proving both the nanoscale mechanisms and mechanical behavior predictions. Our theoretical results agree well with the experimental observations, showing that Nvjp-1 forms a more compact structure in the presence of Zn 2+ ions with a suitable pH environment, leading to the formation of more stable intramolecular metal-coordinated cross-links. These metal-coordinated cross-links induce nanoscale aggregation of Nvjp-1, which is responsible for the hydrogel contraction observed in experiments and predicted by the model.

A set of computational methods that contains a brute-force algorithmic generation of chemical isomers, molecular dynamics (MD) simulations, and density functional theory (DFT) calculations is reported and applied to investigate nearly 3000 probable molecular structures of polydopamine (PDA) and eumelanin. All probable early-polymerized 5,6-dihydroxyindole (DHI) oligomers, ranging from dimers to tetramers, have been systematically analyzed to find the most stable geometry connections as well as to propose a set of molecular models that represents the chemically diverse nature of PDA and eumelanin. Our results indicate that more planar oligomers have a tendency to be more stable. This finding is in good agreement with recent experimental observations, which suggested that PDA and eumelanin are composed of nearly planar oligomers that appear to be stacked together via π-π interactions to form graphite-like layered aggregates. We also show that there is a group of tetramers notably more stable than the others, implying that even though there is an inherent chemical diversity in PDA and eumelanin, the molecular structures of the majority of the species are quite repetitive. Our results also suggest that larger oligomers are less likely to form. This observation is also consistent with experimental measurements, supporting the existence of small oligomers instead of large polymers as main components of PDA and eumelanin. In summary, this work brings an insight into the controversial structure of PDA and eumelanin, explaining some of the most important structural features, and providing a set of molecular models for more accurate modeling of eumelanin-like materials.

Recent advances in three-dimensional (3D) graphene assembly have shown how we can make solid porous materials that are lighter than air. It is plausible that these solid materials can be mechanically strong enough for applications under extreme conditions, such as being a substitute for helium in filling up an unpowered flight balloon. However, knowledge of the elastic modulus and strength of the porous graphene assembly as functions of its structure has not been available, preventing evaluation of its feasibility. We combine bottom-up computational modeling with experiments based on 3D-printed models to investigate the mechanics of porous 3D graphene materials, resulting in new designs of carbon materials. Our study reveals that although the 3D graphene assembly has an exceptionally high strength at relatively high density (given the fact that it has a density of 4.6% that of mild steel and is 10 times as strong as mild steel), its mechanical properties decrease with density much faster than those of polymer foams. Our results provide critical densities below which the 3D graphene assembly starts to lose its mechanical advantage over most polymeric cellular materials.

We combine in situ transmission electron microscopy and large-scale molecular dynamics simulations to investigate brittle fracture in 2D monolayer MoS 2 , revealing that cracks propagate with a tip of atomic sharpness through the preferential direction with least energy release. We find that sparse vacancy defects cause crack deflections, while increasing defect density shifts the fracture mechanism from brittle to ductile by the migration of vacancies in the strain fields into networks. The fracture toughness of defective MoS 2 is found to exceed that of graphene due to interactions between the atomically sharp crack tips and vacancy clusters during propagation. These results show that monolayer 2D materials are ideal for revealing fundamental aspects of fracture mechanics not previously possible with thicker materials, similar to studies of dislocation behavior in 2D materials.

Molecular alteration in type I collagen, i.e., substituting the α2 chain with α1 chain in tropocollagen molecule, can cause osteogenesis imperfecta (OI), a brittle bone disease, which can be represented by a mouse model (oim/oim). In this work, we use dual-frequency Atomic Force Microscopy (AFM) and incorporated with molecular modeling to quantify the ultrastructure and stiffness of the individual native collagen fibers from wildtype (+/+) and oim/oim diseased mice humeri. Our work presents direct experimental evidences that the +/+ fibers have highly organized and compact ultrastructure and corresponding ordered stiffness distribution. In contrast, oim/oim fibers have ordered but loosely packed ultrastructure with uncorrelated stiffness distribution, as well as local defects. The molecular model also demonstrates the structural and molecular packing differences between +/+ and oim/oim collagens. The molecular mutation significantly altered sub-fibril structure and mechanical property of collagen fibers. This study can give the new insight for the mechanisms and treatment of the brittle bone disease., (Copyright © 2016 Elsevier Ltd. All rights reserved.)

The increasing interest in developing nanodevices for biophysical and biomedical applications results in concerns about thermal management at interfaces between tissues and electronic devices. However, there is neither sufficient knowledge nor suitable tools for the characterization of thermal properties at interfaces between materials of contrasting mechanics, which are essential for design with reliability. Here we use computational simulations to quantify thermal transfer across the cell membrane-graphene interface. We find that the intercalated water displays a layered order below a critical value of ∼1 nm nanoconfinement, mediating the interfacial thermal coupling, and efficiently enhancing the thermal dissipation. We thereafter develop an analytical model to evaluate the critical value for power generation in graphene before significant heat is accumulated to disturb living tissues. These findings may provide a basis for the rational design of wearable and implantable nanodevices in biosensing and thermotherapic treatments where thermal dissipation and transport processes are crucial.

A method to directly extract silk nanofibrils from native silk fibers at the single nanofibrils scale is reported. The resulting silk nanofibrils, which retain structural features and physical properties of native silk fibers, show potential utility in optical and electronic devices., (© 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

Current trends in biomaterial designs require a detailed understanding of structure-function relationships to efficiently address specific utilities. As a prototype, spider silk has been widely studied with diversified characterization or simulation methods, exploiting the integration of experimental and modeling approaches to gain insight into structure-function relationships. However, the assembly mechanisms of spider silk in natural and non-natural environments remain incompletely understood. In the present study, experimental and simulation approaches were utilized to study assembly mechanisms of recombinant spider silks. Two spider silk constructs, H(AB) 12 and H(AB) 12 NtSp, were produced and studied. Deconvoluted Fourier transform infrared spectroscopy (FTIR) spectra and molecular dynamics simulations, before and after ethanol treatment, were analyzed to quantify secondary structures, and a higher helix content was observed in H(AB) 12 NtSp compared with that in H(AB) 12 . Time-resolved FTIR analysis was used to monitor conformation transitions. A higher rate of β-sheet formation was found in H(AB) 12 NtSp compared with that in H(AB) 12 . These results suggest that the N-terminal domain accelerates self-assembly of recombinant spidroins under ethanol treatment. The approaches used in this study provide insights into the function of the N-terminal domain in conformational transitions of spider silks under non-natural conditions as well as fiber formation. This approach should enable more efficient design, synthesis, and preparation of new recombinant spidroin materials with tunable mechanical properties.

Spider silk is a remarkable material that provides a template for upscaling molecular properties to the macroscale. In this article we review fundamental aspects of the mechanisms behind these behaviors, discuss the molecular makeup, chemical designs, and how these integrate in a complex arrangement to form webs, cocoons and other material architectures. Moreover, this review paper explores the unique ability of silk to tolerate various kinds of defects, in a way enabling this material platform to serve as one of the most resilient materials in nature. We conclude the discussion with a summary of key scaling laws, an attempt model and define hierarchical length-scales, and the translation to synthetic materials.

A major barrier to the systematic improvement of biomimetic peptide-mediated strategies for the controlled growth of inorganic nanomaterials in environmentally benign conditions lies in the lack of clear conceptual connections between the sequence of the peptide and its surface binding affinity, with binding being facilitated by noncovalent interactions. Peptide conformation, both in the adsorbed and in the nonadsorbed state, is the key relationship that connects peptide-materials binding with peptide sequence. Here, we combine experimental peptide-titania binding characterization with state-of-the-art conformational sampling via molecular simulations to elucidate these structure/binding relationships for two very different titania-binding peptide sequences. The two sequences (Ti-1, QPYLFATDSLIK; Ti-2, GHTHYHAVRTQT) differ in their overall hydropathy, yet via quartz-crystal microbalance measurements and predictions from molecular simulations, we show these sequences both support very similar, strong titania-binding affinities. Our molecular simulations reveal that the two sequences exhibit profoundly different modes of surface binding, with Ti-1 acting as an entropically driven binder while Ti-2 behaves as an enthalpically driven binder. The integrated approach presented here provides a rational basis for peptide sequence engineering to achieve the in situ growth and organization of titania nanostructures in aqueous media and for the design of sequences suitable for a range of technological applications that involve the interface between titania and biomolecules.

Quantifying the deformation of biological tissues under mechanical loading is crucial to understand its biomechanical response in physiological conditions and important for designing materials and treatments for biomedical applications. However, strain measurements for biological tissues subjected to large deformations and humid environments are challenging for conventional methods due to several limitations such as strain range, boundary conditions, surface bonding and biocompatibility. Here we propose the use of silk solutions and printing to synthesize prototype strain gauges for large strain measurements in biological tissues. The study shows that silk-based strain gauges can be stretched up to 1300% without failure, which is more than two orders of magnitude larger than conventional strain gauges, and the mechanics can be tuned by adjusting ion content. We demonstrate that the printing approach can accurately provide well bonded fluorescent features on the silk membranes using designs which can accurately measure strain in the membrane. The results show that these new strain gauges measure large deformations in the materials by eliminating the effects of sliding from the boundaries, making the measurements more accurate than direct outputs from tensile machines.

Elastomeric, robust, and biocompatible hydrogels are rare, while the need for these types of biomaterials in biomedical-related uses remains high. Here, a new family of genetically engineered silk-elastin copolymers (SELPs) with encoded enzymatic crosslinking sites is developed for a new generation of stimuli-responsive yet robust hydrogels. Input into the designs is guided by simulation, and realized via genetic engineering strategies. The avoidance of gamma irradiation or chemical crosslinking during gel fabrication, in lieu of an enzymatic process, expands the versatility of these new gels for the incorporation of labile proteins and cells. In the present study, the new SELP hydrogels offers sequence dependent, reversible stimuli-responsive features. Their stiffness covers almost the full range of the elasticity of soft tissues. Further, physical modification of the silk domains provided a secondary control point to fine-tune mechanical stiffness while preserving stimuli-responsive features, with implications for a variety of biomedical materials and device needs.

We report a new ultrathin filtration membrane prepared from silk nanofibrils (SNFs), directly exfoliated from natural Bombyx mori silk fibers to retain structure and physical properties. These membranes can be prepared with a thickness down to 40 nm with a narrow distribution of pore sizes ranging from 8 to 12 nm. Typically, 40 nm thick membranes prepared from SNFs have pure water fluxes of 13 000 L h(-1) m(-2) bar(-1), more than 1000 times higher than most commercial ultrathin filtration membranes and comparable with the highest water flux reported previously. The commercial membranes are commonly prepared from polysulfone, poly(ether sulfone), and polyamide. The SNF-based ultrathin membranes exhibit efficient separation for dyes, proteins, and colloids of nanoparticles with at least a 64% rejection of Rhodamine B. This broad-spectrum filtration membrane would have potential utility in applications such as wastewater treatment, nanotechnology, food industry, and life sciences in part due to the protein-based membrane polymer (silk), combined with the robust mechanical and separation performance features.

PDMPO (2-(4-pyridyl)-5-((4-(2-dimethylaminoethylaminocarbamoyl)methoxy)phenyl)oxazole), has unique silica specific fluorescence and is used in biology to understand biosilicification. This 'silicaphilic' fluorescence is not well understood nor is the response to local environmental variables like solvent and pH. We investigated PDMPO in a range of environments: using UV-vis and fluorescence spectroscopy supported by computational data, (SPARC, molecular dynamics simulations, density functional theory calculations), dynamic light scattering and zeta potential measurements to understand the PDMPO-silica interaction. From absorption data, PDMPO exhibited a pKa of 4.20 for PDMPOH2(2+) to PDMPOH(+). Fluorescence emission measurements revealed large shifts in excited state pKa* values with different behaviour when bound to silica (pKa* of 10.4). PDMPO bound to silica particles is located in the Stern layer with the dye exhibiting pH dependent depolarising motion. In aqueous solution, PDMPO showed strong chromaticity with correlation between the maximum emission wavelength for PDMPOH(+)* and dielectric constant (4.8-80). Additional chromatic effects were attributed to changes in solvent accessible surface area. Chromatic effects were also observed for silica bound dye which allow its use as a direct probe of bulk pH over a range far in excess of what is possible for the dye alone (3-5.2). The unique combination of chromaticity and excited state dynamics allows PDMPO to monitor pH from 3 to 13 while also reporting on surface environment opening a new frontier in the quantitative understanding of (bio)silicification.

Single-walled carbon nanotubes (SWCNTs) have great potential for cell-based therapies due to their unique intrinsic optical and physical characteristics. Consequently, broad classes of dispersants have been identified that individually suspend SWCNTs in water and cell media in addition to reducing nanotube toxicity to cells. Unambiguous control and verification of the localization and distribution of SWCNTs within cells, particularly to the nucleus, is needed to advance subcellular technologies utilizing nanotubes. Here we report delivery of SWCNTs to the nucleus by noncovalently attaching the tail domain of the nuclear protein lamin B1 (LB1), which we engineer from the full-length LMNB1 cDNA. More than half of this low molecular weight globular protein is intrinsically disordered but has an immunoglobulin-fold composed of a central hydrophobic core, which is highly suitable for associating with SWCNTs, stably suspending SWCNTs in water and cell media. In addition, LB1 has an exposed nuclear localization sequence to promote active nuclear import of SWCNTs. These SWCNTs-LB1 dispersions in water and cell media display near-infrared (NIR) absorption spectra with sharp van Hove peaks and an NIR fluorescence spectra, suggesting that LB1 individually disperses nanotubes. The dispersing capability of SWCNTs by LB1 is similar to that by albumin proteins. The SWCNTs-LB1 dispersions with concentrations ≥150 μg/mL (≥30 μg/mL) in water (cell media) remain stable for ≥75 days (≥3 days) at 4 °C (37 °C). Further, molecular dynamics modeling of association of LB1 with SWCNTs reveal that the exposure of the nuclear localization sequence is independent of LB1 binding conformation. Measurements from confocal Raman spectroscopy and microscopy, NIR fluorescence imaging of SWCNTs, and fluorescence lifetime imaging microscopy show that millions of these SWCNTs-LB1 complexes enter HeLa cells, localize to the nucleus of cells, and interact with DNA. We postulate that the modification of native cellular proteins as noncovalent dispersing agents to provide specific transport will open new possibilities to utilize both SWCNT and protein properties for multifunctional subcellular targeting applications. Specifically, nuclear targeting could allow delivery of anticancer therapies, genetic treatments, or DNA to the nucleus.