Final report : LDRD project 79824 carbon nanotube sorting via DNA-directed self-assembly.

Single-wall carbon nanotubes (SWNTs) have shown great promise in novel applications in molecular electronics, biohazard detection, and composite materials. Commercially synthesized nanotubes exhibit a wide dispersion of geometries and conductivities, and tend to aggregate. Hence the key to using these materials is the ability to solubilize and sort carbon nanotubes according to their geometric/electronic properties. One of the most effective dispersants is single-stranded DNA (ssDNA), but there are many outstanding questions regarding the interaction between nucleic acids and SWNTs. In this work we focus on the interactions of SWNTs with single monomers of nucleic acids, as a first step to answering these outstanding questions. We use atomistic molecular dynamics simulations to calculate the binding energy of six different nucleotide monophosphates (NMPs) to a (6,0) single-wall carbon nanotube in aqueous solution. We find that the binding energies are generally favorable, of the order of a few kcal/mol. The binding energies of the different NMPs were very similar in salt solution, whereas we found a range of binding energies for NMPs in pure water. The binding energies are sensitive to the details of the association of the sodium ions with the phosphate groups and also to the average conformations of the nucleotides. We use electronic structure (Density Functional Theory (DFT) and Moller-Plesset second order perturbation to uncorrelated Hartree Fock theory (MP2)) methods to complement the classical force field study. With judicious choices of DFT exchange correlation functionals, we find that DFT, MP2, and classical force field predictions are in qualitative and even quantitative agreement; all three methods should give reliable and valid predictions. However, in one important case, the interactions between ions and metallic carbon nanotubes--the SWNT polarization-induced affinity for ions, neglected in most classical force field studies, is found to be extremely large (on the order of electron volts) and may have important consequences for various SWNT applications. Finally, the adsorption of NMPs onto single-walled carbon nanotubes were studied experimentally. The nanotubes were sonicated in the presence of the nucleotides at various weight fractions and centrifuged before examining the ultraviolet absorbance of the resulting supernatant. A distinct Langmuir adsorption isotherm was obtained for each nucleotide. All of the nucleotides differ in their saturation value as well as their initial slope, which we attribute to differences both in nucleotide structure and in the binding ability of different types or clusters of tubes. Results from this simple system provide insights toward development of dispersion and separation methods for nanotubes: strongly binding nucleotides are likely to help disperse, whereas weaker ones may provide selectivity that may be beneficial to a separation process

Development of a model colloidal system for rheology simulation.

The objective of the experimental effort is to provide a model particle system that will enable modeling of the macroscopic rheology from the interfacial and environmental structure of the particles and solvent or melt as functions of applied shear and volume fraction of the solid particles. This chapter describes the choice of the model particle system, methods for synthesis and characterization, and results from characterization of colloidal dispersion, particle film formation, and the shear and oscillatory rheology in the system. Surface characterization of the grafted PDMS interface, dispersion characterization of the colloids, and rheological characterization of the dispersions as a function of volume fraction were conducted

Bio-inspired nanocomposite assemblies as smart skin components.

There is national interest in the development of sophisticated materials that can automatically detect and respond to chemical and biological threats without the need for human intervention. In living systems, cell membranes perform such functions on a routine basis, detecting threats, communicating with the cell, and triggering automatic responses such as the opening and closing of ion channels. The purpose of this project was to learn how to replicate simple threat detection and response functions within artificial membrane systems. The original goals toward developing 'smart skin' assemblies included: (1) synthesizing functionalized nanoparticles to produce electrochemically responsive systems within a lipid bilayer host matrices, (2) calculating the energetics of nanoparticle-lipid interactions and pore formation, and (3) determining the mechanism of insertion of nanoparticles in lipid bilayers via imaging and electrochemistry. There are a few reports of the use of programmable materials to open and close pores in rigid hosts such as mesoporous materials using either heat or light activation. However, none of these materials can regulate themselves in response to the detection of threats. The strategies we investigated in this project involve learning how to use programmable nanomaterials to automatically eliminate open channels within a lipid bilayer host when 'threats' are detected. We generated and characterized functionalized nanoparticles that can be used to create synthetic pores through the membrane and investigated methods of eliminating the pores either through electrochemistry, change in pH, etc. We also focused on characterizing the behavior of functionalized gold NPs in different lipid membranes and lipid vesicles and coupled these results to modeling efforts designed to gain an understanding of the interaction of nanoparticles within lipid assemblies

Resolving fundamental limits of adhesive bonding in microfabrication.

As electronic and optical components reach the micro- and nanoscales, efficient assembly and packaging require the use of adhesive bonds. This work focuses on resolving several fundamental issues in the transition from macro- to micro- to nanobonding. A primary issue is that, as bondline thicknesses decrease, knowledge of the stability and dewetting dynamics of thin adhesive films is important to obtain robust, void-free adhesive bonds. While researchers have studied dewetting dynamics of thin films of model, non-polar polymers, little experimental work has been done regarding dewetting dynamics of thin adhesive films, which exhibit much more complex behaviors. In this work, the areas of dispensing small volumes of viscous materials, capillary fluid flow, surface energetics, and wetting have all been investigated. By resolving these adhesive-bonding issues, we are allowing significantly smaller devices to be designed and fabricated. Simultaneously, we are increasing the manufacturability and reliability of these devices

Solution behavior of PEO : the ultimate biocompatible polymer.

Poly(ethylene oxide) (PEO) is the quintessential biocompatible polymer. Due to its ability to form hydrogen bonds, it is soluble in water, and yet is uncharged and relatively inert. It is being investigated for use in a wide range of biomedical and biotechnical applications, including the prevention of protein adhesion (biofouling), controlled drug delivery, and tissue scaffolds. PEO has also been proposed for use in novel polymer hydrogel nanocomposites with superior mechanical properties. However, the phase behavior of PEO in water is highly anomalous and is not addressed by current theories of polymer solutions. The effective interactions between PEO and water are very concentration dependent, unlike other polymer/solvent systems, due to water-water and water-PEO hydrogen bonds. An understanding of this anomalous behavior requires a careful examination of PEO liquids and solutions on the molecular level. We performed massively parallel molecular dynamics simulations and self-consistent Polymer Reference Interaction Site Model (PRISM) calculations on PEO liquids. We also initiated MD studies on PEO/water solutions with and without an applied electric field. This work is summarized in three parts devoted to: (1) A comparison of MD simulations, theory and experiment on PEO liquids; (2) The implementation of water potentials into the LAMMPS MD code; and (3) A theoretical analysis of the effect of an applied electric field on the phase diagram of polymer solutions

Final report :LDRD project 84269 supramolecular structures of peptide-wrapped carbon nanotubes.

Carbon nanotubes (CNT) are unique nanoscale building blocks for a variety of materials and applications, from nanocomposites, sensors and molecular electronics to drug and vaccine delivery. An important step towards realizing these applications is the ability to controllably self-assemble the nanotubes into larger structures. Recently, amphiphilic peptide helices have been shown to bind to carbon nanotubes and thus solubilize them in water. Furthermore, the peptides then facilitate the assembly of the peptide-wrapped nanotubes into supramolecular, well-aligned fibers. We investigate the role that molecular modeling can play in elucidating the interactions between the peptides and the carbon nanotubes in aqueous solution. Using ab initio methods, we have studied the interactions between water and CNTs. Classical simulations can be used on larger length scales. However, it is difficult to sample in atomistic detail large biomolecules such as the amphiphilic peptide of interest here. Thus, we have explored both new sampling methods using configurational-bias Monte Carlo simulations, and also coarse-grained models for peptides described in the literature. An improved capability to model these inorganichiopolymer interfaces could be used to generate improved understanding of peptide-nanotube self-assembly, eventually leading to the engineering of new peptides for specific self-assembly goals

Modeling biomembranes.

Understanding the properties and behavior of biomembranes is fundamental to many biological processes and technologies. Microdomains in biomembranes or ''lipid rafts'' are now known to be an integral part of cell signaling, vesicle formation, fusion processes, protein trafficking, and viral and toxin infection processes. Understanding how microdomains form, how they depend on membrane constituents, and how they act not only has biological implications, but also will impact Sandia's effort in development of membranes that structurally adapt to their environment in a controlled manner. To provide such understanding, we created physically-based models of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these models were applied to phenomena such as microdomain formation, membrane fusion, pattern formation, and protein insertion. Because lipid dynamics and self-organization in membranes occur on length and time scales beyond atomistic MD, we used coarse-grained models of double tail lipid molecules that spontaneously self-assemble into bilayers. DFT provided equilibrium information on membrane structure. Experimental work was performed to further help elucidate the fundamental membrane organization principles

Modeling biomembranes.

Understanding the properties and behavior of biomembranes is fundamental to many biological processes and technologies. Microdomains in biomembranes or ''lipid rafts'' are now known to be an integral part of cell signaling, vesicle formation, fusion processes, protein trafficking, and viral and toxin infection processes. Understanding how microdomains form, how they depend on membrane constituents, and how they act not only has biological implications, but also will impact Sandia's effort in development of membranes that structurally adapt to their environment in a controlled manner. To provide such understanding, we created physically-based models of biomembranes. Molecular dynamics (MD) simulations and classical density functional theory (DFT) calculations using these models were applied to phenomena such as microdomain formation, membrane fusion, pattern formation, and protein insertion. Because lipid dynamics and self-organization in membranes occur on length and time scales beyond atomistic MD, we used coarse-grained models of double tail lipid molecules that spontaneously self-assemble into bilayers. DFT provided equilibrium information on membrane structure. Experimental work was performed to further help elucidate the fundamental membrane organization principles

Bio-inspired nanocomposite assemblies as smart skin components.

There is national interest in the development of sophisticated materials that can automatically detect and respond to chemical and biological threats without the need for human intervention. In living systems, cell membranes perform such functions on a routine basis, detecting threats, communicating with the cell, and triggering automatic responses such as the opening and closing of ion channels. The purpose of this project was to learn how to replicate simple threat detection and response functions within artificial membrane systems. The original goals toward developing 'smart skin' assemblies included: (1) synthesizing functionalized nanoparticles to produce electrochemically responsive systems within a lipid bilayer host matrices, (2) calculating the energetics of nanoparticle-lipid interactions and pore formation, and (3) determining the mechanism of insertion of nanoparticles in lipid bilayers via imaging and electrochemistry. There are a few reports of the use of programmable materials to open and close pores in rigid hosts such as mesoporous materials using either heat or light activation. However, none of these materials can regulate themselves in response to the detection of threats. The strategies we investigated in this project involve learning how to use programmable nanomaterials to automatically eliminate open channels within a lipid bilayer host when 'threats' are detected. We generated and characterized functionalized nanoparticles that can be used to create synthetic pores through the membrane and investigated methods of eliminating the pores either through electrochemistry, change in pH, etc. We also focused on characterizing the behavior of functionalized gold NPs in different lipid membranes and lipid vesicles and coupled these results to modeling efforts designed to gain an understanding of the interaction of nanoparticles within lipid assemblies