Luis Ruiz

Processable Cyclic Peptide Nanotubes with Tunable Interiors

A facile route to generate cyclic peptide nanotubes with tunable interiors is presented. By incorporating 3-amino-2-methylbenzoic acid in the D,L-alternating primary sequence of a cyclic peptide, a functional group can be presented in the interior of the nanotubes without compromising the formation of high aspect ratio nanotubes. The new design of such a cyclic peptide also enables one to modulate the nanotube growth process to be compatible with the polymer processing window without compromising the formation of high aspect ratio nanotubes, thus opening a viable approach toward molecularly defined porous membranes.

Tailoring the water structure and transport in nanotubes with tunable interiors

Self-assembly of cyclic peptide nanotubes (CPNs) in polymer thin films has opened up the possibility of creating separation membranes with tunable nanopores that can differentiate molecules at the sub-nanometer level. While it has been demonstrated that the interior chemistry of the CPNs can be tailored by inserting functional groups in the nanopore lumen (mCPNs), a design strategy for picking the chemical modifications that lead to particular transport properties has not been established. Drawing from the knowledgebase of functional groups in natural amino acids, here we use molecular dynamics simulations to elucidate how bioinspired mutations influence the transport of water through mCPNs. We show that, at the nanoscale, factors besides the pore size, such as electrostatic interactions and steric effects, can dramatically change the transport properties. We recognize a novel asymmetric structure of water under nanoconfinement inside the chemically functionalized nanotubes and identify that the small non-polar glycine-mimic groups that minimize the steric constraints and confer a hydrophobic character to the nanotube interior are the fastest transporters of water. Our computationally developed experiments on a realistic material system circumvent synthetic challenges, and lay the foundation for bioinspired principles to tailor artificial nanochannels for separation applications such as desalination, ion-exchange and carbon capture.

Critical length scales and strain localization govern the mechanical performance of multi-layer graphene assemblies

Multi-layer graphene assemblies (MLGs) or fibers with a staggered architecture exhibit high toughness and failure strain that surpass those of the constituent single sheets. However, how the architectural parameters such as the sheet overlap length affect these mechanical properties remains unknown due in part to the limitations of mechanical continuum models. By exploring the mechanics of MLG assemblies under tensile deformation using our established coarse-grained molecular modeling framework, we have identified three different critical interlayer overlap lengths controlling the strength, plastic stress, and toughness of MLGs, respectively. The shortest critical length scale L(C)(S) governs the strength of the assembly as predicted by the shear-lag model. The intermediate critical length L(C)(P) is associated with a dynamic frictional process that governs the strain localization propensity of the assembly, and hence the failure strain. The largest critical length scale L(C)(T) corresponds to the overlap length necessary to achieve 90% of the maximum theoretical toughness of the material. Our analyses provide the general guidelines for tuning the constitutive properties and toughness of multilayer 2D nanomaterials using elasticity, interlayer adhesion energy and geometry as molecular design parameters.

Regulating Ion Transport in Peptide Nanotubes by Tailoring the Nanotube Lumen Chemistry.

We use atomistic nonequilibrium molecular dynamics simulations to demonstrate how specific ionic flux in peptide nanotubes can be regulated by tailoring the lumen chemistry through single amino acid substitutions. By varying the size and polarity of the functional group inserted into the nanotube interior, we are able to adjust the Na(+) flux by over an order of magnitude. Cl(-) is consistently denied passage. Bulky, nonpolar groups encourage interactions between the Na(+) and the peptide backbone carbonyl groups, disrupting the Na(+) solvation shell and slowing the transport of Na(+). Small groups have the opposite effect and accelerate flow. These results suggest that relative ion flux and selectivity can be precisely regulated in subnanometer pores by molecularly defining the lumen according to biological principles.

Multiscale modeling of elasticity and fracture in organic nanotubes

AbstractCyclic peptide nanotubes (CPNs) have unique chemical and mechanical features that squarely position them to tackle persistent challenges in sensor technologies, tissue scaffolds, templates for organic and hybrid electronics, and ultrasmall electromechanical systems. These self-assembled hierarchical nanostructures are highly organized at the nanoscale and feature exceptional thermodynamical stability arising from the collective action of secondary interactions, in particular intersubunit hydrogen-bond networks. Understanding the elasticity and fracture behavior of CPNs through a multiscale analysis is crucially important for developing science-based approaches for designing the molecular subunits and hierarchical assemblies of these materials. In pursuit of addressing this need, a methodology is proposed for linking atomistic simulation results into coarser descriptions of these self-assembling soft nanostructures. This approach involves estimation of the free-energy landscape of the system along ...

ATOMISTIC MODELING AND MECHANICS OF SELF-ASSEMBLED ORGANIC NANOTUBES

Organic building blocks inspired by biological systems are promising for fabricating nanostructured materials for a broad range of applications such as antimicrobials, biosensors, electronics, and biomaterials. Self-assembling cyclic peptide organic nanotubes have shown great promise for these applications due to their precise structural features, diverse chemical functionalization capabilities and exceptional stability arising from arrangement of hydrogen bonds into cooperative clusters. Mechanical behavior of organic nanotubes is important for various possible applications ranging from subnanoporous selective membranes to molecular templates for electronics. However, large-scale deformation mechanisms of organic nanotubes have not been studied thus far. Here we investigate the mechanisms involved in the large deformation and failure of self-assembled organic nanotubes, focusing on geometry effects characteristic of protein nanostructures. We carry out molecular dynamics simulations to assess the role of hydrogen bonds as weak interactions in the context of deformation and failure processes involving bending and shear loads. Mechanisms of failure are found to depend on the cross-sectional geometry and the deformation rate, where a transition to localized shear failure is observed at high-strain rates. Our results provide important physical insight into the mechanics of organic nanotubes central to emerging applications of self-assembling peptides in biomedicine and biotechnology.

Thermodynamics versus Kinetics Dichotomy in the Linear Self- Assembly of Mixed Nanoblocks

We report classical and replica exchange molecular dynamics simulations that establish the mechanisms underpinning the growth kinetics of a binary mix of nanorings that form striped nanotubes via self-assembly. A step-growth coalescence model captures the growth process of the nanotubes, which suggests that high aspect ratio nanostructures can grow by obeying the universal laws of self-similar coarsening, contrary to systems that grow through nucleation and elongation. Notably, striped patterns do not depend on specific growth mechanisms, but are governed by tempering conditions that control the likelihood of depropagation and fragmentation.

Molecular modeling of the microstructure of soft materials

In this chapter, we will present a contemporary review of the hitherto numerical characterization of nanowires (NWs). The bulk of the research reported in the literatures concern metallic NWs including Al, Cu, Au, Ag, Ni, and their alloys NWs. Research has also been reported for the investigation of some nonmetallic NWs, such as ZnO, GaN, SiC, SiO2. A plenty of researches have been conducted regarding the numerical investigation of NWs. Issues analyzed include structural changes under different loading situations, the formation and propagation of dislocations, and the effect of the magnitude of applied loading on deformation mechanics. Efforts have also been made to correlate simulation results with experimental measurements. However, direct comparisons are difficult since most simulations are carried out under conditions of extremely high strain/loading rates and small simulation samples due to computational limitations. Despite of the immense numerical studies of NWs, a significant work still lies ahead in terms of problem formulation, interpretation of results, identification and delineation of deformation mechanisms, and constitutive characterization of behavior. In this chapter, we present an introduction of the commonly adopted experimental and numerical approaches in studies of the deformation of NWs in Section 1. An overview of findings concerning perfect NWs under different loading situations, such as tension, compression, torsion, and bending are presented in Section 2. In Section 3, we will detail some recent results from the authors’ own work with an emphasis on the study of influences from different pre-existing defect on NWs. Some thoughts on future directions of the computational mechanics of NWs together with Conclusions will be given in the last section.

Molecular modeling of the microstructure of soft materials: Healing, memory, and toughness mechanisms

In this chapter, we will present a contemporary review of the hitherto numerical characterization of nanowires (NWs). The bulk of the research reported in the literatures concern metallic NWs including Al, Cu, Au, Ag, Ni, and their alloys NWs. Research has also been reported for the investigation of some nonmetallic NWs, such as ZnO, GaN, SiC, SiO2. A plenty of researches have been conducted regarding the numerical investigation of NWs. Issues analyzed include structural changes under different loading situations, the formation and propagation of dislocations, and the effect of the magnitude of applied loading on deformation mechanics. Efforts have also been made to correlate simulation results with experimental measurements. However, direct comparisons are difficult since most simulations are carried out under conditions of extremely high strain/loading rates and small simulation samples due to computational limitations. Despite of the immense numerical studies of NWs, a significant work still lies ahead in terms of problem formulation, interpretation of results, identification and delineation of deformation mechanisms, and constitutive characterization of behavior. In this chapter, we present an introduction of the commonly adopted experimental and numerical approaches in studies of the deformation of NWs in Section 1. An overview of findings concerning perfect NWs under different loading situations, such as tension, compression, torsion, and bending are presented in Section 2. In Section 3, we will detail some recent results from the authors’ own work with an emphasis on the study of influences from different pre-existing defect on NWs. Some thoughts on future directions of the computational mechanics of NWs together with Conclusions will be given in the last section.