Barry L. Farmer

Modeling of thermal transport in pillared-graphene architectures.

Carbon nanotubes (CNT) and graphene are considered as potential future candidates for many nano/microscale integrated devices due to their superior thermal properties. Both systems, however, exhibit significant anisotropy in their thermal conduction, limiting their performance as three-dimensional thermal transport materials. From thermal management perspective, one way to tailor this anisotropy is to consider designing alternative carbon-based architectures. This paper investigates the thermal transport in one such novel architecture-a pillared-graphene (PG) network nanostructure which combines graphene sheets and carbon nanotubes to create a three-dimensional network. Nonequilibrium molecular dynamics simulations have been carried out using the AIREBO potential to calculate the thermal conductivity of pillared-graphene structures along parallel (in-plane) as well as perpendicular (out-of-plane) directions with respect to the graphene plane. The resulting thermal conductivity values for PG systems are discussed and compared with simulated values for pure CNT and graphite. Our results show that in these PG structures, the thermal transport is governed by the minimum interpillar distance and the CNT-pillar length. This is primarily attributed to scattering of phonons occurring at the CNT-graphene junctions in these nanostructures. We foresee that such architecture could potentially be used as a template for designing future structurally stable microscale systems with tailorable in-plane and out-of-plane thermal transport.

Adsorption mechanism of single amino acid and surfactant molecules to Au {111} surfaces in aqueous solution: design rules for metal-binding molecules

The adsorption mechanism of twenty amino acids and four surfactants was examined on a {111} surface of gold in dilute aqueous solution using molecular dynamics simulation with a broadly applicable intermolecular potential CHARMM–METAL. All molecules are attracted to the surface between −3 and −26 kcal mol−1. The adsorption strength correlates with the degree of coordination of polarizable atoms (O, N, C) to multiple epitaxial sites. Therefore, the molecular size and geometry rather than the specific chemistry determine the adsorption energy. Large molecules with planar sp2 hybridized groups (Arg, Trp, Gln, Tyr, Asn, and PPh3) adsorb most strongly, followed by molecules with polar sp3 hybridized groups, and short molecules with sp3 hybridized alkyl groups exhibit least attraction. Conformationally flexible, extended molecules such as hexadecyltrimethylammonium bromide (CTAB) also showed significant attraction to the metal surface related to accommodation in epitaxial grooves and coordination with numerous epitaxial sites. Computational results are consistent with combinatorial binding experiments, observations in the growth and stabilization of metal nanoparticles, and ab initio data. The mechanism of adsorption conforms to soft epitaxy observed for peptides on metal surfaces (H. Heinz et al., J. Am. Chem. Soc., 2009, 131, 9704) and enables the de novo design of molecules for binding to a given metal surface. In addition to soft epitaxy, contributions to adsorption are possible by covalent bonding and induced charges.

Preferential Binding of Peptides to Graphene Edges and Planes

Peptides identified from combinatorial peptide libraries have been shown to bind to a variety of abiotic surfaces. Biotic-abiotic interactions can be exploited to create hybrid materials with interesting electronic, optical, or catalytic properties. Here we show that peptides identified from a combinatorial phage display peptide library assemble preferentially to the edge or planar surface of graphene and can affect the electronic properties of graphene. Molecular dynamics simulations and experiments provide insight into the mechanism of peptide binding to the graphene edge.

Biomimetic Chemosensor: Designing Peptide Recognition Elements for Surface Functionalization of Carbon Nanotube Field Effect Transistors

Single-wall carbon nanotube field effect transistors (SWNT-FETs) are ideal candidates for fabricating sensors due to their unique electronic properties and have been widely investigated for chemical and biological sensing applications. The lack of selectivity of SWNT-FETs has prompted extensive research on developing ligands that exhibit specific binding as selective surface coating for SWNTs. Herein we describe the rational design of a peptide recognition element (PRE) that is capable of noncovalently attaching to SWNTs as well as binding to trinitrotoluene (TNT). The PRE contains two domains, a TNT binding domain derived from the binding pocket of the honeybee odor binding protein ASP1, and a SWNT binding domain previously identified from the phage peptide display library. The PRE structure in the presence of SWNT was investigated by performing classical all-atom molecular dynamics simulations, circular dichroism spectroscopy, and atomic force microscopy. Both computational and experimental analyses demonstrate that the peptide retains two functional domains for SWNT and TNT binding. The binding motif of the peptide to SWNT and to TNT was revealed from interaction energy calculations by molecular dynamics simulations. The potential application of the peptide for the detection of TNT is theoretically predicted and experimentally validated using a SWNT-FET sensor functionalized with a designer PRE. Results from this study demonstrate the creation of chemosensors using designed PRE as selective surface coatings for targeted analytes.

Molecular dynamics simulation study of norbornene–POSS polymers

Abstract Atomistic molecular dynamics simulations have been used to delineate the effects of introducing polyhedral oligomeric silsesquioxane (POSS) moieties substituted by cyclopentyl and cyclohexyl rings as pendant groups on polynorbornene. Simulations were also performed on polynorbornene for comparison. Calculated volume–temperature behavior and X-ray scattering profiles matched well with experimental results. Most importantly, the effects of incorporating the POSS moieties into the polymer have been identified via simulations. These were judged on the basis of the increase in the glass transition temperature, retardation of the chain dynamics and improvements in the calculated elastic tensile, bulk and shear moduli of the POSS containing polymers compared to the norbornene homopolymer. The most important conclusion from the study is that aggregation of the POSS moieties is not required for the beneficial effects to be realized. Indeed, the simulations show that there is no tendency for aggregation to occur among the POSS moieties if they are well dispersed to begin with over the time scale of the simulation. Packing features are delineated with the aid of intermolecular site–site radial distribution functions. In addition, the mean squared displacement of the POSS moieties in the polymer matrix was found to be very small at all temperatures leading to a slowing of the segmental dynamics of the polymer chain, and thereby imparting the macroscopically observed stiffness. It is reasoned that the chief source of reinforcement arises from the POSS moieties behaving as strong anchor points in the polymeric matrix. This has more to do with the ponderous nature of these moieties versus any specific intermolecular interactions.

Structure of a Peptide Adsorbed on Graphene and Graphite

Noncovalent functionalization of graphene using peptides is a promising method for producing novel sensors with high sensitivity and selectivity. Here we perform atomic force microscopy, Raman spectroscopy, infrared spectroscopy, and molecular dynamics simulations to investigate peptide-binding behavior to graphene and graphite. We studied a dodecamer peptide identified with phage display to possess affinity for graphite. Optical spectroscopy reveals that the peptide forms secondary structures both in powder form and in an aqueous medium. The dominant structure in the powder form is α-helix, which undergoes a transition to a distorted helical structure in aqueous solution. The peptide forms a complex reticular structure upon adsorption on graphene and graphite, having a helical conformation different from α-helix due to its interaction with the surface. Our observation is consistent with our molecular dynamics calculations, and our study paves the way for rational functionalization of graphene using biomolecules with defined structures and, therefore, functionalities.

Interaction energy and surface reconstruction between sheets of layered silicates

Interactions between two layered silicate sheets, as found in various nanoscale materials, are investigated as a function of sheet separation using molecular dynamics simulation. The model systems are periodic in the xy plane, open in the z direction, and subjected to stepwise separation of the two silicate sheets starting at equilibrium. Computed cleavage energies are 383 mJ /m(2) for K-mica, 133 mJ /m(2) for K-montmorillonite (cation exchange capacity=91), 45 mJ /m(2) for octadecylammonium (C(18))-mica, and 40 mJ /m(2) for C(18)-montmorillonite. These values are in quantitative agreement with experimental data and aid in the molecular-level interpretation. When alkali ions are present at the interface between the silicate sheets, partitioning of the cations between the surfaces is observed at 0.25 nm separation (mica) and 0.30 nm separation (montmorillonite). Originally strong electrostatic attraction between the two silicate sheets is then reduced to 5% (mica) and 15% (montmorillonite). Weaker van der Waals interactions decay within 1.0 nm separation. The total interaction energy between sheets of alkali clay is less than 1 mJ /m(2) after 1.5 nm separation. When C(18) surfactants are present on the surfaces, the organic layer (>0.8 nm) acts as a spacer between the silicate sheets so that positively charged ammonium head groups remain essentially in the same position on the surfaces of the two sheets at any separation. As a result, electrostatic interactions are efficiently shielded and dispersive interactions account for the interfacial energy. The flexibility of the hydrocarbon chains leads to stretching, disorder, and occasional rearrangements of ammonium head groups to neighbor cavities on the silicate surface at medium separation (1.0-2.0 nm). The total interaction energy amounts to less than 1 mJ /m(2) after 3 nm separation.

MBO(N)D: A multibody method for long-time molecular dynamics simulations

A modeling approach that can significantly speed up the dynamics simulation of large molecular systems is presented herein. A multigranular modeling approach, whereby different parts of the molecule are modeled at different levels of detail, is enabled by substructuring. Substructuring the molecular system is accomplished by collecting groups of atoms into rigid or flexible bodies. Body flexibility is modeled by a truncated set of body‐based modes. This approach allows for the elimination of the high‐frequency harmonic motion while capturing the low‐frequency anharmonic motion of interest. This results in the use of larger integration step sizes, substantially reducing the computational time required for a given dynamic simulation. The method also includes the use of a multiple time scale (MTS) integration scheme. Speed increases of 5‐ to 30‐fold over atomistic simulations have been realized in various applications of the method.

Relation between packing density and thermal transitions of alkyl chains on layered silicate and metal surfaces.

Self-assembled layers of alkyl chains grafted onto the surfaces of layered silicates, metal, and oxidic nanoparticles are utilized to control interactions with external media by tuning the packing density of the chains on the surface, head group functionality, and chain length. Characterization through experiment and simulation shows that the orientation of the alkyl layers and reversible phase transitions on heating are a function of the cross-sectional area of the alkyl chains in relation to the available surface area per alkyl chain. On even surfaces, a packing density less than 0.2 leads to nearly parallel orientation of the alkyl chains on the surface, a high degree of conformational disorder, and no reversible melting transitions. A packing density between 0.2 and 0.75 leads to intermediate inclination angles, semicrystalline order, and reversible melting transitions on heating. A packing density above 0.75 results in nearly vertical alignment of the surfactants on the surface, a high degree of crystalline character, and absence of reversible melting transitions. Curved surfaces can be understood by the same principle, taking into account a local radius of curvature and a distance-dependent packing density on the surface. In good approximation, this simple model is independent from the length of the alkyl chains (a minimum length of C10 is required to form sufficiently distinctive patterns), the chemical nature of the surface, and of the surfactant head group. These structural details primarily determine the functionality of alkyl modified surfaces and the temperature of thermal transitions.

Influence of the shape of nanostructured metal surfaces on adsorption of single peptide molecules in aqueous solution.

Self-assembly and function of biologically modified metal nanostructures depend on surface-selective adsorption; however, the influence of the shape of metal surfaces on peptide adsorption mechanisms has been poorly understood. The adsorption of single peptide molecules in aqueous solution (Tyr(12) , Ser(12) , A3, Flg-Na(3) ) is investigated on even {111} surfaces, stepped surfaces, and a 2 nm cuboctahedral nanoparticle of gold using molecular dynamics simulation with the CHARMM-METAL force field. Strong and selective adsorption is found on even surfaces and the inner edges of stepped surfaces (-20 to -60 kcal/mol peptide) in contrast to weaker and less selective adsorption on small nanoparticles (-15 to -25 kcal/mol peptide). Binding and selectivity appear to be controlled by the size of surface features and the extent of co-ordination of epitaxial sites by polarizable atoms (N, O, C) along the peptide chain. The adsorption energy of a single peptide equals a fraction of the sum of the adsorption energies of individual amino acids that is characteristic of surface shape, epitaxial pattern, and conformation constraints (often β-strand and random coil). The proposed adsorption mechanism is supported and critically evaluated by earlier sequence data from phage display, dissociation constants of small proteins as a function of nanoparticle size, and observed shapes of peptide-stabilized nanoparticles. Understanding the interaction of single peptides with shaped metal surfaces is a key step towards control over self-organization of multiple peptides on shaped metal surfaces and the assembly of superstructures from nanostructures.