Quantifying Cooperativity in Mutated Collagen

Many biological systems can be considered coupled systems, arising from the interconnected structure of on (or more) molecular/protein components. An important characteristic of any such “built up” macromolecule is the need for synergistic behavior between the individual components. In nature, this behavior is evident, e.g., the double stranded constitution of DNA is a well-known fact; however, it is the highly cross-linked helical structure that shows potential as a structural material at a nanoscale. Similarly, in a synthetic environment cooperativity has been demonstrated in a small sample, i.e., polyelectrolytes and hydrogen graphene oxides. The integration of different components to functional materials requires an intimate knowledge of the mechanical cooperativity of the system. This cooperativity can be seen as the optimization of contact, adhesion and/or deformation. Mechanical cooperativity can be thought of as the equivalent behavior between components and the system. This concept is well understood; however, the difficulty arises in quantifying cooperativity. We have recently developed metrics based on the gyration tensor of individual molecules to explore the use of universal shape ratios to conclude whether the system is behaving as a cohesive unit. Cooperativity can then be objectively defined by invariants derived from the gyration tensor of each chain. These metrics include the slip (an indication of size), the differential anisotropy (shape configuration), and skewness (orientation of the pair). Here, we apply this framework to a simple tropocollagen molecule using full atomistic molecular dynamics. In a natural state, the triple helix is a highly cooperative macromolecule. By introducing known mutations (e.g., those that result in osteogenesis imperfecta) we track and quantify the change in cooperativity. We then link the change in cooperativity to known effects of mechanical behavior with severity of the mutation, inferring changes in mechanical stability with purely geometric measures. Such a molecular-shape-based analysis can potentially be adapted to assess the health and stability of other biological systems

Mechanical properties and interface of carbon/metal nanocomposites

The recent discovery of graphene and its associated thermal, electrical, and mechanical properties has motivated further investigation of similar two-dimensional (2D) systems, including all-carbon allotropes of graphene. The high strength and atomistic thickness of such 2D systems make them promising for composite materials. However, there is intrinsic weakness at the interface, typically characterized by noncovalent interactions. Here, we present two nanocomposite studies: mechanical properties of graphdiyne/copper composites and defect engineering of graphene/copper interfaces.One emerging allotrope of graphene is so-called graphdiyne, a one atom-thick carbon network which can be constructed by connecting two adjacent hexagonal rings with uniformly distributed diacetylenic linkages. This allotrope has demonstrated a set of distinguished properties and is considered a promising material, which can meet the increasing requirements to carbon-based nanomaterials. There are a few reports of the mechanical behavior of isolated graphdiyne. However, currently graphdiyne has only successfully been synthesized on copper substrates, and the composite behavior of the material has not been investigated. Here, we combine copper/graphdiyne nanocomposites with varied numbers of layers of graphdiyne sheets, as well as sandwich-structured copper/graphdiyne layers to determine mechanical properties. Using full atomistic molecular dynamics, the elastic stiffness and limit states of these nanocomposite materials are investigated through direct tensile loads. We present theoretical methods to estimate the parameters to mechanically characterize copper/graphdiyne nanocomposites. Second, we present a simple model of graphene/copper, subject to shear stress transfer across the carbon/metal interface. The weak van der Waals interaction governs the strength of the system. To increase the strength of the interface, vacancy defects are introduced into the graphene, to “rough up” the potential landscape and facilitate stress transfer. Although the strength of the graphene is decreased, the stiffness is only marginally affected, and the response of the composite system can be improved. Such defect engineering can potentially be used to enhance the compatibility of carbon/metal nanostructures

Nanomechanical coupling of mechanomutable polyelectrolytes

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering, 2012.Cataloged from PDF version of thesis.Includes bibliographical references (p. 255-282).Nanotechnology has advanced to the point where almost any molecular functional group can be introduced into a composite material system. However, emergent properties attained via the combination of arbitrary components - e.g., the complexation of two weak polyelectrolytes - is not yet predictive, and thus cannot be rationally engineered. Predictive and reliable quantification of material properties across scales is necessary to enable the design and development of advanced functional (and complex) materials. There is a vast amount of experimental study which characterize the strength of electrostatic interactions, topology, and viscoelastic properties of polyelectrolyte multilayers (PEMs), but very little is known about the fundamental molecular interactions that drive system behavior. Here, we focus on two specific weak polyelectrolytes - poly(acrylic acid) (PAA) and poly(allylamine hydrochloride) (PAH) - that undergo electrostatic complexation, and can be manipulated as function of pH. While the driving mechanism investigated here is ionic interactions, the findings and atomistic approaches are applicable to a variety of systems such as hydrogen bonded polypeptides (e.g., protein structures), as well as similar polyelectrolyte systems (e.g., PSS, PDMA, etc.). Specifically, in this dissertation, the coupling of electrostatic cross-links and weak interactions, polyelectrolyte persistence length and molecular rigidity of PAA and PAH is investigated with full atomistic precision. Large-scale molecular dynamics (MD) simulations indicate the stiffening of PEMs cannot be explained by increased electrostatic cross-linking alone, but rather the effect is amplified by the increase in molecular rigidity due to self-repulsion. Based on MD simulations, a general theoretical model for effective electrostatic persistence length is proposed for highly flexible polyelectrolytes and charged macromolecules through the introduction of an electrostatic contour length which can applied to other chemical species. A focus on adhesion reveals the effective cross-linking strength exceeds the strength of ionic interaction alone, due to secondary effects (e.g., H-bonding, steric effects, etc.) Moreover, a derived elastic model for complexation reveals a critical bound for cross-link density and stiffness, indicating the required conditions to induce cooperative mechanical behavior. The key insight is that these critical conditions can be further extended for the coupling of flexible molecules in general, such as proteins or flexible nanoribbons. The results demonstrate how nanoscale control can lead to uniquely tunable mechanomutable materials from designed functional building blocks. While PEM systems are currently being developed for biosensor, membrane, and tissue engineering technologies, the results presented herein provide a basis to tune the properties of such systems at the nanoscale, thereby engineering system behavior and performance across scales. Understanding the bounds of mechanical performance of two specific polyelectrolyte species, and their joint interaction through complexation, provides a basis for coupling molecules with various functionalities. Similar to complete understanding the limitations of a steel beam in construction of a bridge, the systematic delineation of polyelectrolyte complexation allows quantitative prediction of larger-scale systems.by Steven W. Cranford.Ph.D

Self-folding and aggregation of amyloid nanofibrils

Amyloids are highly organized protein filaments, rich in β-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.United States. Office of Naval Research (Grant NN00014-08-1-0844)National Science Foundation (U.S.). Materials Research Science and Engineering Centers (Program) (Grant DMR-0819762)United States. Army Research Office. Multidisciplinary University Research Initiative (Grant W911NF-09-1-0541

A single degree of freedom ‘lollipop’ model for carbon nanotube bundle formation

Current carbon nanotube (CNT) synthesis methods include the production of ordered, free-standing vertically aligned arrays, the properties of which are partially governed by interactions between adjacent tubes. Using material parameters determined by atomistic methods, here we represent individual CNTs by a simple single degree of freedom ‘lollipop’ model to investigate the formation, mechanics, and self-organization of CNT bundles driven by weak van der Waals interactions. The computationally efficient simple single degree of freedom model enables us to study arrays consisting of hundreds of thousands of nanotubes. The effects of nanotube parameters such as aspect ratio, bending stiffness, and surface energy, on formation and bundle size, as well as the intentional manipulation of bundle pattern formation, are investigated. We report studies with both single wall carbon nanotubes (SWCNTs) and double wall carbon nanotubes (DWCNTs) with varying aspect ratios (that is, varying height). We calculate the local density distributions of the nanotube bundles and show that there exists a maximum attainable bundle density regardless of an increase in surface energy for nanotubes with given spacing and stiffness. In addition to applications to CNTs, our model can also be applied to other types of nanotube arrays (e.g. protein nanotubes, polymer nanofilaments).National Science Foundation (U.S.). Materials Research Science and Engineering Centers (Program) (Award DMR-0819762

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.National Science Foundation (U.S.) (MRSEC Program under award number DMR- 0819762

Assessing Material Fragility using Nanoscale Incremental Dynamic Analysis

A new methodology to assess material failure subjected to stochastic loads is proposed, titled Nanoscale Incremental Dynamic Analysis (NIDA), which is adopted from performance-based assessment in structural engineering. Using full atomistic molecular dynamics, proof-of-concept simulations produce the material fragility curve of a simple carbon nanotube