I May Not Have Symptoms, but COVID-19 Is a Huge Headache.

The COVID-19 pandemic was an unprecedented surprise, to say the least. Academia is rooted in group assemblies - from classroom to conferences - which were promptly cancelled and/or shifted to remote efforts. Here are some perspectives from Professors involved.

Mutable polyelectrolyte tube arrays: mesoscale modeling and lateral force microscopy.

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 ∼ δ3/2) 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.

Materiomics for Oral Disease Diagnostics and Personal Health Monitoring: Designer Biomaterials for the Next Generation Biomarkers.

We live in exciting times for a new generation of biomarkers being enabled by advances in the design and use of biomaterials for medical and clinical applications, from nano- to macro-materials, and protein to tissue. Key challenges arise, however, due to both scientific complexity and compatibility of the interface of biology and engineered materials. The linking of mechanisms across scales by using a materials science approach to provide structure-process-property relations characterizes the emerging field of 'materiomics,' which offers enormous promise to provide the hitherto missing tools for biomaterial development for clinical diagnostics and the next generation biomarker applications towards personal health monitoring. Put in other words, the emerging field of materiomics represents an essentially systematic approach to the investigation of biological material systems, integrating natural functions and processes with traditional materials science perspectives. Here we outline how materiomics provides a game-changing technology platform for disruptive innovation in biomaterial science to enable the design of tailored and functional biomaterials--particularly, the design and screening of DNA aptamers for targeting biomarkers related to oral diseases and oral health monitoring. Rigorous and complementary computational modeling and experimental techniques will provide an efficient means to develop new clinical technologies in silico, greatly accelerating the translation of materiomics-driven oral health diagnostics from concept to practice in the clinic.

Ranking of Molecular Biomarker Interaction with Targeted DNA Nucleobases via Full Atomistic Molecular Dynamics.

DNA-based sensors can detect disease biomarkers, including acetone and ethanol for diabetes and H2S for cardiovascular diseases. Before experimenting on thousands of potential DNA segments, we conduct full atomistic steered molecular dynamics (SMD) simulations to screen the interactions between different DNA sequences with targeted molecules to rank the nucleobase sensing performance. We study and rank the strength of interaction between four single DNA nucleotides (Adenine (A), Guanine (G), Cytosine (C), and Thymine (T)) on single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA) with acetone, ethanol, H2S and HCl. By sampling forward and reverse interaction paths, we compute the free-energy profiles of eight systems for the four targeted molecules. We find that dsDNA react differently than ssDNA to the targeted molecules, requiring more energy to move the molecule close to DNA as indicated by the potential of mean force (PMF). Comparing the PMF values of different systems, we obtain a relative ranking of DNA base for the detection of each molecule. Via the same procedure, we could generate a library of DNA sequences for the detection of a wide range of chemicals. A DNA sensor array built with selected sequences differentiating many disease biomarkers can be used in disease diagnosis and monitoring.

Mechanical properties and defect sensitivity of diamond nanothreads.

One of the newest carbon allotropes synthesized are diamond nanothreads. Using molecular dynamics, we determine the stiffness (850 GPa), strength (26.4 nN), extension (14.9%), and bending rigidity (5.35 × 10(-28) N·m(2)). The 1D nature of the nanothread results in a tenacity of 4.1 × 10(7) N·m/kg, exceeding nanotubes and graphene. As the thread consists of repeating Stone-Wales defects, through steered molecular dynamics (SMD), we explore the effect of defect density on the strength, stiffness, and extension of the system.

Confinement and controlling the effective compressive stiffness of carbyne.

Carbyne is a one-dimensional chain of carbon atoms, consisting of repeating sp-hybridized groups, thereby representing a minimalist molecular rod or chain. While exhibiting exemplary mechanical properties in tension (a 1D modulus on the order of 313 nN and a strength on the order of 11 nN), its use as a structural component at the molecular scale is limited due to its relative weakness in compression and the immediate onset of buckling under load. To circumvent this effect, here, we probe the effect of confinement to enhance the mechanical behavior of carbyne chains in compression. Through full atomistic molecular dynamics, we characterize the mechanical properties of a free (unconfined chain) and explore the effect of confinement radius (R), free chain length (L) and temperature (T) on the effective compressive stiffness of carbyne chains and demonstrate that the stiffness can be tuned over an order of magnitude (from approximately 0.54 kcal mol(-1) Å(2) to 46 kcal mol(-1) Å(2)) by geometric control. Confinement may inherently stabilize the chains, potentially providing a platform for the synthesis of extraordinarily long chains (tens of nanometers) with variable compressive response.

Nanotube dispersion and polymer conformational confinement in a nanocomposite fiber: a joint computational experimental study.

A combination of computational and experimental methods was implemented to understand and confirm that conformational changes of a polymer [specifically polyacrylonitrile (PAN)] vary with the dispersion quality and confinement between single-wall carbon nanotubes (SWNT) in the composite fibers. A shear-flow gel-spinning approach was utilized to produce PAN-based composite fibers with high concentration (i.e., loading of 10 wt %) of SWNT. Dispersion qualities of SWNT ranging from low to high were identified in the fibers, and their effects on the structural morphologies and mechanical properties of the composites were examined. These results show that, as the SWNT dispersion quality in terms of distribution in the fiber and exfoliation increases, PAN conformations were confined to the extended-chain form. Full atomistic computational results show that the surface interaction energy between isolated PAN and SWNT was not preferred, leading to the self-agglomeration of PAN. However, confinement of the polymer chains between SWNT bundles or individual tubes (i.e., molecular crowding) resulted in large increases in the PAN-SWNT interaction energy. In other words, the crowding of polymer chains by the SWNT at high concentrations can promote extended-chain conformational development during fiber spinning. This was also evidenced experimentally by the observance of significantly improved PAN orientation and crystallization in the composite. Ultimately this work provides fundamental insight toward the specific structural changes capable at the polymer/nanotube interface which are important toward improvement of the effective contribution of the SWNT to the mechanical performance of the composite.

Compliant threads maximize spider silk connection strength and toughness.

Millions of years of evolution have adapted spider webs to achieve a range of functionalities, including the well-known capture of prey, with efficient use of material. One feature that has escaped extensive investigation is the silk-on-silk connection joints within spider webs, particularly from a structural mechanics perspective. We report a joint theoretical and computational analysis of an idealized silk-on-silk fibre junction. By modifying the theory of multiple peeling, we quantitatively compare the performance of the system while systematically increasing the rigidity of the anchor thread, by both scaling the stress-strain response and the introduction of an applied pre-strain. The results of our study indicate that compliance is a virtue-the more extensible the anchorage, the tougher and stronger the connection becomes. In consideration of the theoretical model, in comparison with rigid substrates, a compliant anchorage enormously increases the effective adhesion strength (work required to detach), independent of the adhered thread itself, attributed to a nonlinear alignment between thread and anchor (contact peeling angle). The results can direct novel engineering design principles to achieve possible load transfer from compliant fibre-to-fibre anchorages, be they silk-on-silk or another, as-yet undeveloped, system.

Thermal stability of idealized folded carbyne loops.

Self-unfolding items provide a practical convenience, wherein ring-like frames are contorted into a state of equilibrium and subsequently  pop up' or deploy when perturbed from a folded structure. Can the same process be exploited at the molecular scale? At the limiting scale is a closed chain of single atoms, used here to investigate the limits of stability of such folded ring structures via full atomistic molecular dynamics. Carbyne is a one-dimensional carbon allotrope composed of sp-hybridized carbon atoms. Here, we explore the stability of idealized carbyne loops as a function of chain length, curvature, and temperature, and delineate an effective phase diagram between folded and unfolded states. We find that while overall curvature is reduced, in addition to torsional and self-adhesive energy barriers, a local increase in curvature results in the largest impedance to unfolding.

Synergetic material and structure optimization yields robust spider web anchorages.

Millions of years of evolution have adapted spider webs to achieve a range of properties, including the well-known capture of prey, with efficient use of materials. One feature that remains poorly understood is the attachment disc, a network of silk fibers that mechanically anchors a web to its environment. Experimental observations suggest that one possible attachment disc adheres to a substrate through multiple symmetrically branched structures composed of sub-micrometer scale silk fibers. Here, a theoretical model is used to explore the adaptation of the strength of attachment of such an anchorage, and complementary mesoscale simulations are applied to demonstrate a novel mechanism of synergetic material and structural optimization, such that the maximum anchorage strength can be achieved regardless of the initial anchor placement or material type. The optimal delamination (peeling) angle is facilitated by the inherent extensibility of silk, and is attained automatically during the process of delamination. This concept of self-optimizing peeling angle suggests that attachment discs do not require precise placement by the spider, irrespective of adhesion strength. Additional hierarchical branching of the anchorage increases efficiency, where both the delamination force and toughness modulus increase with a splitting of the cross-sectional area.

Increasing silk fibre strength through heterogeneity of bundled fibrils.

Can naturally arising disorder in biological materials be beneficial? Materials scientists are continuously attempting to replicate the exemplary performance of materials such as spider silk, with detailed techniques and assembly procedures. At the same time, a spider does not precisely machine silk-imaging indicates that its fibrils are heterogeneous and irregular in cross section. While past investigations either focused on the building material (e.g. the molecular scale protein sequence and behaviour) or on the ultimate structural component (e.g. silk threads and spider webs), the bundled structure of fibrils that compose spider threads has been frequently overlooked. Herein, I exploit a molecular dynamics-based coarse-grain model to construct a fully three-dimensional fibril bundle, with a length on the order of micrometres. I probe the mechanical behaviour of bundled silk fibrils with variable density of heterogenic protrusions or globules, ranging from ideally homogeneous to a saturated distribution. Subject to stretching, the model indicates that cooperativity is enhanced by contact through low-force deformation and shear 'locking' between globules, increasing shear stress transfer by up to 200 per cent. In effect, introduction of a random and disordered structure can serve to improve mechanical performance. Moreover, addition of globules allows a tuning of free volume, and thus the wettability of silk (with implications for supercontraction). These findings support the ability of silk to maintain near-molecular-level strength at the scale of silk threads, and the mechanism could be easily adopted as a strategy for synthetic fibres.

Materiomics: an -omics approach to biomaterials research.

The past fifty years have seen a surge in the use of materials for clinical application, but in order to understand and exploit their full potential, the scientific complexity at both sides of the interface--the material on the one hand and the living organism on the other hand--needs to be considered. Technologies such as combinatorial chemistry, recombinant DNA as well as computational multi-scale methods can generate libraries with a very large number of material properties whereas on the other side, the body will respond to them depending on the biological context. Typically, biological systems are investigated using both holistic and reductionist approaches such as whole genome expression profiling, systems biology and high throughput genetic or compound screening, as already seen, for example, in pharmacology and genetics. The field of biomaterials research is only beginning to develop and adopt these approaches, an effort which we refer to as "materiomics". In this review, we describe the current status of the field, and its past and future impact on the biomedical sciences. We outline how materiomics sets the stage for a transformative change in the approach to biomaterials research to enable the design of tailored and functional materials for a variety of properties in fields as diverse as tissue engineering, disease diagnosis and de novo materials design, by combining powerful computational modelling and screening with advanced experimental techniques.

Extended graphynes: simple scaling laws for stiffness, strength and fracture.

The mono-atomistic structure and chemical stability of graphene provides a promising platform to design a host of novel graphene-like materials. Using full atomistic first-principles based ReaxFF molecular dynamics, here we perform a systematic comparative study of the stability, structural and mechanical properties of graphynes - a variation of the sp(2) carbon motif wherein the characteristic hexagons of graphene are linked by sp(1) acetylene (single- and triple-bond) carbyne-like chains. The introduction of acetylene links introduces an effective penalty in terms of stability, elastic modulus (i.e., stiffness), and failure strength, which can be predicted as a function of acetylene repeats, or, equivalently, lattice spacing. We quantify the mechanical properties of experimental accessible graphdiyne, with a modulus on the order of 470 to 580 GPa and a ultimate strength on the order of 36 GPa to 46 GPa (direction dependent). We derive general scaling laws for the cumulative effects of additional acetylene repeats, formulated through a simple discrete spring-network framework, allowing extrapolation of mechanical performance to highly extended graphyne structures. Onset of local tensile buckling results in a transitional regime characterized by a severe reduction of strength (ultimate stress), providing a new basis for scaling extended structures. Simple fracture simulations support the scaling functions, while uncovering a "two-tier" failure mode for extended graphynes, wherein structural realignment facilitates stress transfer beyond initial failure. Finally, the specific modulus and strength (normalized by areal density) is found to be near-constant, suggesting applications for light-weight, yet structurally robust molecular components.

Selective hydrogen purification through graphdiyne under ambient temperature and pressure.

Graphdiyne, a recently synthesized one-atom-thick carbon allotrope, is atomistically porous - characterized by a regular "nanomesh"- and suggests application as a separation membrane for hydrogen purification. Here we report a full atomistic reactive molecular dynamics investigation to determine the selective diffusion properties of hydrogen (H(2)) amongst carbon monoxide (CO) and methane (CH(4)), a mixture otherwise known as syngas, a product of the gasification of renewable biomass (such as animal wastes). Under constant temperature simulations, we find the mass flux of hydrogen molecules through a graphdiyne membrane to be on the order of 7 to 10 g cm(-2) s(-1) (between 300 K and 500 K), with carbon monoxide and methane remaining isolated. Using a simple Arrhenius relation, we determine the energy required for permeation on the order of 0.11 ± 0.03 eV for single H(2) molecules. We find that addition of marginal applied force (approximately 1 to 2 pN per molecule, representing a controlled pressure gradient, ΔP, on the order of 100 to 500 kPa) can successfully enhance the separation of hydrogen gas. Addition of larger driving forces (50 to 100 pN per molecule) is required to selectively filter carbon monoxide or methane, suggesting that, under near-atmospheric conditions, only hydrogen gas will pass such a membrane. Graphdiyne provides a unique, chemically inert and mechanically stable platform facilitating selective gas separation at nominal pressures using a homogeneous material system, without a need for chemical functionalization or the explicit introduction of molecular pores.

Nonlinear material behaviour of spider silk yields robust webs.

Natural materials are renowned for exquisite designs that optimize function, as illustrated by the elasticity of blood vessels, the toughness of bone and the protection offered by nacre. Particularly intriguing are spider silks, with studies having explored properties ranging from their protein sequence to the geometry of a web. This material system, highly adapted to meet a spider's many needs, has superior mechanical properties. In spite of much research into the molecular design underpinning the outstanding performance of silk fibres, and into the mechanical characteristics of web-like structures, it remains unknown how the mechanical characteristics of spider silk contribute to the integrity and performance of a spider web. Here we report web deformation experiments and simulations that identify the nonlinear response of silk threads to stress--involving softening at a yield point and substantial stiffening at large strain until failure--as being crucial to localize load-induced deformation and resulting in mechanically robust spider webs. Control simulations confirmed that a nonlinear stress response results in superior resistance to structural defects in the web compared to linear elastic or elastic-plastic (softening) material behaviour. We also show that under distributed loads, such as those exerted by wind, the stiff behaviour of silk under small deformation, before the yield point, is essential in maintaining the web's structural integrity. The superior performance of silk in webs is therefore not due merely to its exceptional ultimate strength and strain, but arises from the nonlinear response of silk threads to strain and their geometrical arrangement in a web.

Tuning the mechanical properties of graphene oxide paper and its associated polymer nanocomposites by controlling cooperative intersheet hydrogen bonding.

The mechanical properties of pristine graphene oxide paper and paper-like films of polyvinyl alcohol (PVA)-graphene oxide nanocomposite are investigated in a joint experimental-theoretical and computational study. In combination, these studies reveal a delicate relationship between the stiffness of these papers and the water content in their lamellar structures. ReaxFF-based molecular dynamics (MD) simulations elucidate the role of water molecules in modifying the mechanical properties of both pristine and nanocomposite graphene oxide papers, as bridge-forming water molecules between adjacent layers in the paper structure enhance stress transfer by means of a cooperative hydrogen-bonding network. For graphene oxide paper at an optimal concentration of ~5 wt % water, the degree of cooperative hydrogen bonding within the network comprising adjacent nanosheets and water molecules was found to optimally enhance the modulus of the paper without saturating the gallery space. Introducing PVA chains into the gallery space further enhances the cooperativity of this hydrogen-bonding network, in a manner similar to that found in natural biomaterials, resulting in increased stiffness of the composite. No optimal water concentration could be found for the PVA-graphene oxide nanocomposite papers, as dehydration of these structures continually enhances stiffness until a final water content of ~7 wt % (additional water cannot be removed from the system even after 12 h of annealing).

Self-folding and aggregation of amyloid nanofibrils.

Amyloids are highly organized protein filaments, rich in ß-sheet secondary structures that self-assemble to form dense plaques in brain tissues affected by severe neurodegenerative disorders (e.g. Alzheimer's Disease). Identified as natural functional materials in bacteria, in addition to their remarkable mechanical properties, amyloids have also been proposed as a platform for novel biomaterials in nanotechnology applications including nanowires, liquid crystals, scaffolds and thin films. Despite recent progress in understanding amyloid structure and behavior, the latent self-assembly mechanism and the underlying adhesion forces that drive the aggregation process remain poorly understood. On the basis of previous full atomistic simulations, here we report a simple coarse-grain model to analyze the competition between adhesive forces and elastic deformation of amyloid fibrils. We use simple model system to investigate self-assembly mechanisms of fibrils, focused on the formation of self-folded nanorackets and nanorings, and thereby address a critical issue in linking the biochemical (Angstrom) to micrometre scales relevant for larger-scale states of functional amyloid materials. We investigate the effect of varying the interfibril adhesion energy on the structure and stability of self-folded nanorackets and nanorings and demonstrate that these aggregated amyloid fibrils are stable in such states even when the fibril-fibril interaction is relatively weak, given that the constituting amyloid fibril length exceeds a critical fibril length-scale of several hundred nanometres. We further present a simple approach to directly determine the interfibril adhesion strength from geometric measures. In addition to providing insight into the physics of aggregation of amyloid fibrils our model enables the analysis of large-scale amyloid plaques and presents a new method for the estimation and engineering of the adhesive forces responsible of the self-assembly process of amyloid nanostructures, filling a gap that previously existed between full atomistic simulations of primarily ultra-short fibrils and much larger micrometre-scale amyloid aggregates. Via direct simulation of large-scale amyloid aggregates consisting of hundreds of fibrils we demonstrate that the fibril length has a profound impact on their structure and mechanical properties, where the critical fibril length-scale derived from our analysis of self-folded nanorackets and nanorings defines the structure of amyloid aggregates. A multi-scale modeling approach as used here, bridging the scales from Angstroms to micrometres, opens a wide range of possible nanotechnology applications by presenting a holistic framework that balances mechanical properties of individual fibrils, hierarchical self-assembly, and the adhesive forces determining their stability to facilitate the design of de novo amyloid materials.

In silico assembly and nanomechanical characterization of carbon nanotube buckypaper.

Carbon nanotube sheets or films, also known as 'buckypaper', have been proposed for use in actuating, structural and filtration systems, based in part on their unique and robust mechanical properties. Computational modeling of such a fibrous nanostructure is hindered by both the random arrangement of the constituent elements as well as the time- and length-scales accessible to atomistic level molecular dynamics modeling. Here we present a novel in silico assembly procedure based on a coarse-grain model of carbon nanotubes, used to attain a representative mesoscopic buckypaper model that circumvents the need for probabilistic approaches. By variation in assembly parameters, including the initial nanotube density and ratio of nanotube type (single- and double-walled), the porosity of the resulting buckypaper can be varied threefold, from approximately 0.3 to 0.9. Further, through simulation of nanoindentation, the Young's modulus is shown to be tunable through manipulation of nanotube type and density over a range of approximately 0.2-3.1 GPa, in good agreement with experimental findings of the modulus of assembled carbon nanotube films. In addition to carbon nanotubes, the coarse-grain model and assembly process can be adapted for other fibrous nanostructures such as electrospun polymeric composites, high performance nonwoven ballistic materials, or fibrous protein aggregates, facilitating the development and characterization of novel nanomaterials and composites as well as the analysis of biological materials such as protein fiber films and bulk structures.