Publications

We present the results of large scale molecular dynamics simulations aimed at understanding the origins of high friction coefficients in pure metals, and their concomitant reduction in alloys and composites. We utilize a series of targeted simulations to demonstrate that different slip mechanisms are active in the two systems, leading to differing frictional behavior. Specifically, we show that in pure metals, sliding occurs along the crystallographic slip planes, whereas in alloys shear is accommodated by grain boundaries. In pure metals, there is significant grain growth induced by the applied shear stress and the slip planes are commensurate contacts with high friction. However, the presence of dissimilar atoms in alloys suppresses grain growth and stabilizes grain boundaries, leading to low friction via grain boundary sliding. Graphic Abstract: [Figure not available: see fulltext.]

The efficient and controlled assembly of complex structures from macromolecular building blocks is a critical open question in both biological systems and nanoscience. Using molecular dynamics simulations we study the self-assembly of tubular structures from model macromolecular monomers with multiple binding sites on their surfaces [Cheng et al., Soft Matter, 2012, 8, 5666-5678]. In this work we add chirality to the model monomer and a lock-and-key interaction. The self-assembly of free monomers into tubules yields a pitch value that often does not match the chirality of the monomer (including achiral monomers). We show that this mismatch occurs because of a twist deformation that brings the lateral interaction sites into alignment when the tubule pitch differs from the monomer chirality. The energy cost for this deformation is small as the energy distributions substantially overlap for small differences in the pitch and chirality. In order to control the tubule pitch by preventing the twist deformation, the interaction between the vertical surfaces must be increased without resulting in kinetically trapped structures. For this purpose, we employ lock-and-key interactions and obtain good control of the self-assembled tubule pitch. These results explain some fundamental features of microtubules. The vertical interaction strength is larger than the lateral in microtubules because this yields a controlled assembly of tubules with the proper pitch. We also generally find that the control of the assembly into tubules is difficult, which explains the wide range of pitch values and protofilament numbers observed in microtubule assembly. © The Royal Society of Chemistry.

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Large-scale molecular dynamics simulations are used to simulate a layer of nanoparticles floating on the surface of a liquid. Both a low viscosity liquid, represented by Lennard-Jones monomers, and a high viscosity liquid, represented by linear homopolymers, are studied. The organization and diffusion of the nanoparticles are analyzed as the nanoparticle density and the contact angle between the nanoparticles and liquid are varied. When the interaction between the nanoparticles and liquid is reduced the contact angle increases and the nanoparticles ride higher on the liquid surface, which enables them to diffuse faster. In this case the short-range order is also reduced as seen in the pair correlation function. For the polymeric liquids, the out-of-layer fluctuation is suppressed and the short-range order is slightly enhanced. However, the diffusion becomes much slower and the mean square displacement even shows sub-linear time dependence at large times. The relation between diffusion coefficient and viscosity is found to deviate from that in bulk diffusion. Results are compared to simulations of the identical nanoparticles in 2-dimensions. © 2012 American Institute of Physics.

Understanding the complex self-assembly of biomacromolecules is a major outstanding question. Microtubules are one example of a biopolymer that possesses characteristics quite distinct from standard synthetic polymers that are derived from its hierarchical structure. In order to understand how to design and build artificial polymers that possess features similar to those of microtubules, we have initially studied the self-assembly of model monomers into a tubule geometry. Our model monomer has a wedge shape with lateral and vertical binding sites that are designed to form tubules. We used molecular dynamics simulations to study the assembly process for a range of binding site interaction strengths. In addition to determining the optimal regime for obtaining tubules, we have calculated a diagram of the structures that form over a wide range of interaction strengths. Unexpectedly, we find that the helical tubules form, even though the monomer geometry is designed for nonhelical tubules. We present the detailed dynamics of the tubule self-assembly process and show that the interaction strengths must be in a limited range to allow rearrangement within clusters. We extended previous theoretical methods to treat our system and to calculate the boundaries between different structures in the diagram. © 2012 The Royal Society of Chemistry.

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