Davoud Ebrahimi

Nanoscale elastic properties of montmorillonite upon water adsorption.

Smectites are an important group of clay minerals that experience swelling upon water adsorption. This paper uses molecular dynamics with the CLAYFF force field to simulate isothermal isobaric water adsorption of interlayer Wyoming Na-montmorillonite, a member of the smectite group. Nanoscale elastic properties of the clay-interlayer water system are calculated from the potential energy of the model system. The transverse isotropic symmetry of the elastic constant matrix was assessed by calculating Euclidean and Riemannian distance metrics. Simulated elastic constants of the clay mineral are compared with available results from acoustic and nanoindentation measurements.

Mesoscale properties of clay aggregates from potential of mean force representation of interactions between nanoplatelets

Face-to-face and edge-to-edge free energy interactions of Wyoming Na-montmorillonite platelets were studied by calculating potential of mean force along their center to center reaction coordinate using explicit solvent (i.e., water) molecular dynamics and free energy perturbation methods. Using a series of configurations, the Gay-Berne potential was parametrized and used to examine the meso-scale aggregation and properties of platelets that are initially random oriented under isothermal-isobaric conditions. Aggregates of clay were defined by geometrical analysis of face-to-face proximity of platelets with size distribution described by a log-normal function. The isotropy of the microstructure was assessed by computing a scalar order parameter. The number of platelets per aggregate and anisotropy of the microstructure both increases with platelet plan area. The system becomes more ordered and aggregate size increases with increasing pressure until maximum ordered state at confining pressure of 50 atm. Furt...

Atomic-scale modelling of elastic and failure properties of clays

The elastic and failure properties of a typical clay, illite, are investigated using molecular simulation. We employ a reactive (ReaxFF) and a non-reactive (ClayFF) force field to assess the elastic properties of the clay. As far as failure is concerned, ReaxFF was used throughout the study; however, some calculations were also performed with ClayFF. A crack parallel to the clay layers is found to have low fracture resistance when submitted to a tensile loading perpendicular to the crack. The mechanism of both yield and fracture failures is decohesion in the interlayer space. In contrast, under shear loading, the nanoscale failure mechanism is a stick-slip between clay layers. No fracture propagation is observed as the clay layers slide on top of each other. The low fracture resistance in mode I and the stick-slip failure in mode II are both the consequence of the lack of chemical bonds between clay layers where the cohesion is provided by non-covalent interactions. This work, which provides a description of the failure of clays at the microscopic scale, is the first step towards describing the failure of clays at a larger scale where the polycrystalline distribution of clay grains must be taken into account.

Synergistic Integration of Experimental and Simulation Approaches for the de Novo Design of Silk-Based Materials

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 Natures 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.

Predicting Silk Fiber Mechanical Properties through Multiscale Simulation and Protein Design

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.

EFFECT OF POLYDISPERSITY OF CLAY PLATELETS ON THE AGGREGATION AND MECHANICAL PROPERTIES OF CLAY AT THE MESOSCALE

The results from mesoscale simulations of the formation and evolution of microstructure for assemblies of Na-smectite particles based on assumed size distributions of individual clay platelets are presented here. The analyses predicted particle arrangements and aggregation (i.e. platelets linked in face-face configurations) and are used to link geometric properties of the microstructure and mechanical properties of the particle assemblies. Interactions between individual ellipsoidal clay platelets are represented using the Gay-Berne potential based on atomistic simulations of the free energy between two Na-smectite clay-platelets in liquid water, following a novel coarse-graining method developed previously. The current study describes the geometric (aggregate thickness, orientation, and porosity) and elastic properties in the ‘jammed states’ from the mesoscale simulations for selected ranges of clay particle sizes and confining pressures. The thickness of clay aggregates for monodisperse assemblies increases (with average stack thickness consisting of n = 3–8 platelets) with the diameter of the individualclay platelets and with the level of confining pressure. Aggregates break down at high confining pressures (50–300 atm) due to slippage between the platelets. Polydisperse simulations generate smaller aggregates (n = 2) and show much smaller effects of confining pressure. All assemblies show increased order with confining pressure, implying more anisotropic microstructure. The mesoscale simulations are also in good agreement with macroscopic compression behavior measured in conventional 1-D laboratory compression tests. The mesoscale assemblies exhibit cubic symmetry in elastic properties. The results for larger platelets (D = 1000 Å) are in good agreement with nano-indentation measurements on natural clays and shale samples.

Effect of Terminal Modification on the Molecular Assembly and Mechanical Properties of Protein-Based Block Copolymers

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.

Intracellular Pathways Involved in Bone Regeneration Triggered by Recombinant Silk–Silica Chimeras

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.

Predicting rates of in vivo degradation of recombinant spider silk proteins.

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

Mesoscale Modeling and Properties of Clay Aggregates

The clay phase of many natural soils comprises a micro-structure of clay aggregates. These can be formed during sedimentation, due to van der Waals attraction between negatively charged particle surfaces in saltwater environments, or can occur in partially saturated soils where colloidal iron acts as a cementing agent. In order to understand the formation of clay aggregates and their role in affecting properties at the macroscale/continuum level, we have carried out multiscale analyses, initially considering the formation and properties of the aggregates. Nanoscale numerical simulations consider interactions between two clay platelets. The analyses focus on Wyoming montmorillonite (Na-smectite) and use the CLAYFF force field to describe pairwise interactions between ions within the clay and surrounding bulk water (i.e., Coulombic and van der Waals forces). The analyses establish the potential of mean force at different spacings between the layers for edge-to-edge and face-to-face interactions. The results are then used to calibrate the Gay-Berne (GB) potential that represents each platelet as a single-site ellipsoidal body. It is then possible to simulate the process of aggregation for an assembly of clay platelets in mesoscale simulations. These simulations find that aggregates of Na-smectite typically form in face-to-face stacks with 3–8 platelets. The particle assemblies become more ordered and exhibit more pronounced elastic anisotropy at higher confining pressures. The computed elastic stiffness properties are in good agreement with previously measured nanoindentation moduli over a wide range of clay-packing densities.