Christopher Roland

Mechanical properties, defects and electronic behavior of carbon nanotubes

Abstract Using state-of-the-art classical and quantum simulations, we have studied the mechanical and electronic response of carbon nanotubes to external deformations, such as strain and bending. In strained nanotubes the spontaneous formation of double pentagon–heptagon defect pairs is observed. Tubes containing these defects are energetically preferred to uniformly stretched tubes at strains greater than 5%. These defects act as nucleation centers for the formation of dislocations in the originally ideal graphitic network and constitute the onset of further deformations of the carbon nanotube. In particular, plastic or brittle behaviors can occur depending upon the external conditions and tube symmetry. We have also investigated the effects that the presence of addimers has on strained carbon nanotubes. The main result is the formation of a new class of defects that wrap themselves about the circumference of the nanotube. These defects are shown to modify the geometrical structure and to induce the formation of nanotube-based quantum dots. Finally, we computed transport properties for various ideal and mechanically deformed carbon nanotubes. High defect densities are shown to greatly affect transport in individual nanotubes, while small diameter bent armchair nanotubes mantam thier basic electrical properties even in presence of large deformations with no defects involved.

Carbon Nanotube Based Magnetic Tunnel Junctions

Spin-coherent quantum transport in carbon nanotube magnetic tunnel junctions is investigated theoretically. A spin-valve effect is found for metallic, armchair tubes, with a magnetoconductance ratio ranging up to 20%. Because of the finite length of the nanotube junctions, transport is dominated by resonant transmission. The magnetic tunnel junctions are found to have distinctly different transport behavior depending on whether or not the length of the tubes is commensurate with a 3N+1 rule, with N the number of basic carbon repeat units along the nanotube length.

Adaptively biased molecular dynamics for free energy calculations

We present an adaptively biased molecular dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using nonequilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential and is inspired by the metadynamics method. The ABMD method has several useful features, including a small number of control parameters and an O(t) numerical cost with molecular dynamics time t. The ABMD method naturally allows for extensions based on multiple walkers and replica exchange, where different replicas can have different temperatures and/or collective variables. This is beneficial not only in terms of the speed and accuracy of a calculation, but also in terms of the amount of useful information that may be obtained from a given simulation. The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment.

Thin film deposition: fundamentals and modeling

We review some of the principles of thin film growth. We begin with a description of the growth modes of films and relate the different structures to the thermodynamic driving forces and to kinetics. The influence of misfit strain, surface free energies, and interface energies are discussed in detail. In particular, we treat the instability of a moving crystal-vapor surface resulting from stress, and the stabilizing influence of step energies in the case where the surface is coincident with a low-index orientation below its surface roughening transition temperature. The introduction of defects by strain, high growth rates, and shadowing instabilities are described. A Monte Carlo model of Al is developed; the model parameters are derived from molecular dynamics calculations of atomic level energetics and kinetics. Anisotropies in surface energies and surface mobilities are found to be large, and have a strong influence on film structures. An extension of the model to polycrystalline films is included. Some of the issues involved in metallization of silicon devices are discussed using results from this model.

Conformations and free energy landscapes of polyproline peptides

The structure of the proline amino acid allows folded polyproline peptides to exist as both left- (PPII) and right-handed (PPI) helices. We have characterized the free energy landscapes of hexamer, nanomer, and tridecamer polyproline peptides in gas phase and implicit water as well as explicit hexane and 1-propanol for the nanomer. To enhance the sampling provided by regular molecular dynamics, we used the recently developed adaptively biased molecular dynamics method, which describes Landau free energy maps in terms of relevant collective variables. These maps, as a function of the collective variables of handedness, radius of gyration, and three others based on the peptide torsion angle ω, were used to determine the relative stability of the different structures, along with an estimate of the transition pathways connecting the different minima. Results show the existence of several metastable isomers and therefore provide a complementary view to experimental conclusions based on photo-induced electron transfer experiments with regard to the existence of stable heterogeneous subpopulations in PPII polyproline.

GROWTH OF CARBON NANOTUBES : A MOLECULAR DYNAMICS STUDY

Abstract Molecular dynamics with realistic many-body atomic potentials was used to study the growth of carbon nanotubes. Analysis of the bond switching and ring migration processes has led to an identification of tube growth mechanisms. Wide tubes, initially open, were found to grow straight maintaining an all-hexagonal structure, while narrow tubes were found to develop permanent pentagonal rings that lead to tube closure upon further deposition. Continued deposition on the top of a closed tube yields a disordered cap structure, implying that open tubes are critical for defect-free growth.

Electronic and field emission properties of boron nitride/carbon nanotube superlattices

BN/C nanotube superlattices are quasi one-dimensional heterostructures that show unique physical properties derived from their peculiar geometry. Using state-of-the-art ab initio calculations, we show that BN/C systems can be used for effective band-offset nanodevice engineering, polarization-based devices, and robust field emitters with an efficiency enhanced by up to two orders of magnitude over carbon nanotube systems.

Reaction path ensemble of the B–Z-DNA transition: a comprehensive atomistic study

Since its discovery in 1979, left-handed Z-DNA has evolved from an in vitro curiosity to a challenging DNA structure with crucial roles in gene expression, regulation and recombination. A fundamental question that has puzzled researchers for decades is how the transition from B-DNA, the prevalent right-handed form of DNA, to Z-DNA is accomplished. Due to the complexity of the B–Z-DNA transition, experimental and computational studies have resulted in several different, apparently contradictory models. Here, we use molecular dynamics simulations coupled with state-of-the-art enhanced sampling techniques operating through non-conventional reaction coordinates, to investigate the B–Z-DNA transition at the atomic level. Our results show a complex free energy landscape, where several phenomena such as over-stretching, unpeeling, base pair extrusion and base pair flipping are observed resulting in interconversions between different DNA conformations such as B-DNA, Z-DNA and S-DNA. In particular, different minimum free energy paths allow for the coexistence of different mechanisms (such as zipper and stretch–collapse mechanisms) that previously had been proposed as independent, disconnected models. We find that the B–Z-DNA transition—in absence of other molecular partners—can encompass more than one mechanism of comparable free energy, and is therefore better described in terms of a reaction path ensemble.

A Statistical Analysis of the PPII Propensity of Amino Acid Guests in Proline-Rich Peptides

There has been considerable debate about the intrinsic PPII propensity of amino-acid residues in denatured polypeptides. Experimentally, the propensity scale is based on the behavior of guest amino-acid residues placed in the middle of polyproline hosts. We have used classical molecular dynamics simulations, with state-of-the-art force fields to carry out a comprehensive analysis of the conformational equilibria of the proline-based host oligopeptides with single guests. The tracked structural characteristics include the PPII content, the cis/trans isomerization of the prolyl bonds, the puckering of the pyrrolidine rings of the proline residues, and the secondary structural motifs. We find no evidence for an intrinsic PPII propensity in any of the guest amino acids other than proline. Instead, the PPII content as derived from experiments may be explained in terms of: 1), a local correlation between the dihedral angles of the guest amino acid and the proline residue immediately preceding it; and 2), a nonlocal correlation between the cis/trans states of the peptide bonds. In terms of the latter, we find that the presence of a guest (other than proline, tyrosine, or tryptophan) increases the trans content of most of the prolyl bonds, which results in an effective increase of the peptide PPII content. With respect to the local dihedral correlations, we find that these are well described in terms of the so-called odds-ratio statistic. Expressed in terms of free energy language, the PPII content based on the odds-ratio of the relevant residues correlate well with the experimentally measured PPII content.

Ab initio calculation of electrostatic multipoles with Wannier functions for large-scale biomolecular simulations

It has long been known that accurate electrostatics is a key issue for improving current force fields for large-scale biomolecular simulations. Typically, this calls for an improved and more accurate description of the molecular electrostatic potential, which eliminates the artifacts associated with current point charge-based descriptions. In turn, this involves the partitioning of the extended molecular charge distribution, so that charges and multipole moments can be assigned to different atoms. As an alternate to current approaches, we have investigated a charge partitioning scheme that is based on the maximally localized Wannier functions. This has the advantage of partitioning the charge, and placing it around the molecule in a chemically meaningful manner. Moreover, higher order multipoles may all be calculated without any undue numerical difficulties. Tests on isolated molecules and water dimers, show that the molecular electrostatic potentials generated by such a Wannier-function based approach are in excellent agreement with the density functional-based calculations.