Publications

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Sandia's scientific and engineering expertise in the fields of computational biology, high-performance prosthetic limbs, biodetection, and bioinformatics has been applied to specific problems at the forefront of cancer research. Molecular modeling was employed to design stable mutations of the enzyme L-asparaginase with improved selectivity for asparagine over other amino acids with the potential for improved cancer chemotherapy. New electrospun polymer composites with improved electrical conductivity and mechanical compliance have been demonstrated with the promise of direct interfacing between the peripheral nervous system and the control electronics of advanced prosthetics. The capture of rare circulating tumor cells has been demonstrated on a microfluidic chip produced with a versatile fabrication processes capable of integration with existing lab-on-a-chip and biosensor technology. And software tools have been developed to increase the calculation speed of clustered heat maps for the display of relationships in large arrays of protein data. All these projects were carried out in collaboration with researchers at the University of Texas M. D. Anderson Cancer Center in Houston, TX.

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We perform pressure-driven non-equilibrium molecular dynamics (MD) simulations to drive a 1.0 M NaCI electrolyte through a dipole-lined smooth nanopore of diameter 12 A penetrating a model membrane. We show that partial, about 70-80%, CI- rejection is achieved at a ~68 atmosphere pressure. At the high water flux achieved in these model nanopores, which are particularly pertinent to atomistically smooth carbon nanotube membranes that permit fast water transport, the ion rejection ratio decreases with increasing water flux. The computed potential of mean force of Cl- frozen inside the nanopore reveals a barrier of 6.4 kcal/mol in 1.0 M NaCI solution. The Cl- permeation occurs despite the barrier, and this is identified as a dynamical effect, with ions carried along by the water flux. Na +-CI- ion-pairing or aggregation near the pore entrance and inside the pore, where the dielectric screening is weaker than in bulk water, is critical to Cl- permeation. We also consider negative charges decorating the rim and the interior of the pore instead of dipoles, and find that, with sufficient pressure, CI- from a 1.0 M NaCI solution readily passes through such nanopores. © 2009 American Scientific Publishers.

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A molecular-scale interpretation of interfacial processes is often downplayed in the analysis of traditional water treatment methods. However, such an approach is critical for the development of enhanced performance in traditional desalination and water treatments. Water confined between surfaces, within channels, or in pores is ubiquitous in technology and nature. Its physical and chemical properties in such environments are unpredictably different from bulk water. As a result, advances in water desalination and purification methods may be accomplished through an improved analysis of water behavior in these challenging environments using state-of-the-art microscopy, spectroscopy, experimental, and computational methods.

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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.

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We report on our studies of the structural properties of a hydrogen molecule dissolved in liquid water. The radial distribution function, coordination number and coordination number distribution are calculated using different representations of the interatomic forces within molecular dynamics (MD), Monte Carlo (MC) and ab initio molecular dynamics (AIMD) simulation frameworks. Although structural details differ in the radial distribution functions generated from the different force fields, all approaches agree that the average and most probable number of water molecules occupying the inner hydration sphere around hydrogen is 16. Furthermore, all results exclude the possibility of clathrate-like organization of water molecules around the hydrophobic molecular hydrogen solute.

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.