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Wearable sensors for human health, performance, and state monitoring, which have a linear response to the binding of biomarkers found in sweat, saliva, or urine, are of current interest for many applications. A critical part of any device is a biological recognition element (BRE) that is able to bind a biomarker at the surface of a sensor with a high affinity and selectivity to produce a measurable signal response. In this study, we discover and compare 12-mer peptides that bind to neuropeptide Y (NPY), a stress and human health biomarker, using independent and complimentary experimental and computational approaches. The affinities of the NPY-binding peptides discovered by both methods are equivalent and below the micromolar level, which makes them suitable for application in sensors. The in silico design protocol for peptide-based BREs is low cost, highly efficient, and simple, suggesting its utility for discovering peptide binders to a variety of biomarker targets.

Sensors for human health and performance monitoring require biological recognition elements (BREs) at device interfaces for the detection of key molecular biomarkers that are measurable biological state indicators. BREs, including peptides, antibodies, and nucleic acids, bind to biomarkers in the vicinity of the sensor surface to create a signal proportional to the biomarker concentration. The discovery of BREs with the required sensitivity and selectivity to bind biomarkers at low concentrations remains a fundamental challenge. In this study, we describe an in-silico approach to evolve higher sensitivity peptide-based BREs for the detection of cardiac event marker protein troponin I (cTnI) from a previously identified BRE as the parental affinity peptide. The P2 affinity peptide, evolved using our in-silico method, was found to have ∼16-fold higher affinity compared to the parent BRE and ∼10 fM (0.23 pg/mL) limit of detection. The approach described here can be applied towards designing BREs for other biomarkers for human health monitoring.

Understanding the factors that influence the interaction between biomolecules and abiotic surfaces is of utmost interest in biosensing and biomedical research. Through phage display technology, several peptides have been identified as specific binders to abiotic material surfaces, such as gold, graphene, silver, and so forth. Using graphene-peptide as our model abiotic-biotic pair, we investigate the effect of graphene quality, number of layers, and the underlying support substrate effect on graphene-peptide interactions using both experiments and computation. Our results indicate that graphene quality plays a significant role in graphene-peptide interactions. The graphene-biomolecule interaction appears to show no significant dependency on the number of graphene layers or the underlying support substrate.

In this work, to explain doping behavior of single-layer graphene upon HSSYWYAFNNKT (P1) and HSSAAAAFNNKT (P1-3A) adsorption in field-effect transistors (GFETs), we applied a combined computational approach, whereby peptide adsorption was modeled by molecular dynamics simulations, and the lowest energy configuration was confirmed by density functional theory calculations. On the basis of the resulting structures of the hybrid materials, electronic structure and transport calculations were investigated. We demonstrate that π-π stacking of the aromatic residues and proximate peptide backbone to the graphene surface in P1 have a role in the p-doping. These results are consistent with our experimental observation of the GFET's p-doping even after a 24-h annealing procedure. Upon substitution of three of the aromatic residues to Ala in (P1-3A), a considerable decrease from p-doping is observed experimentally, demonstrating n-doping as compared to the nonadsorbed device, yet not explained based on the atomistic MD simulation structures. To gain a qualitative understanding of P1-3A's adsorption over a longer simulation time, which may differ from aromatic amino acid residues' swift anchoring on the surface, we analyzed equilibrated coarse-grain simulations performed for 500 ns. Desorption of the Ala residues from the surface was shown computationally, which could in turn affect charge transfer, yet a full explanation of the mechanism of n-doping will require elucidation of differences between various aromatic residues as dependent on peptide composition, and inclusion of effects of the substrate and environment, to be considered in future work.

Previously, thermal rectification has been reported in several low-dimensional shape-asymmetric nanomaterials. In this Letter, we demonstrate that a three-dimensional crystalline material with an asymmetric shape also displays as strong thermal rectification as low-dimensional materials do. The observed rectification is attributed to the stronger temperature dependence of vibration density of states in the narrower region of the asymmetric material, resulting from the small number of atomic degrees of freedom directly interacting with the thermostat. We also demonstrate that the often reported "device shape asymmetry" is not a sufficient condition for thermal rectification. Specifically, the size asymmetry in boundary thermal contacts is equally important toward determining the magnitude of thermal rectification. When the boundary thermal contacts retain the same size asymmetry as the nanomaterial, the overall system displays notable thermal rectification, in accordance with existing literature. However, when the wider region of the asymmetric nanomaterial is partially thermostatted by a smaller sized contact, thermal rectification decreases dramatically and even changes direction.

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.

Thermal management in polymeric composite materials has become increasingly critical in the air-vehicle industry because of the increasing thermal load in small-scale composite devices extensively used in electronics and aerospace systems. The thermal transport phenomenon in these small-scale heterogeneous systems is essentially controlled by the interface thermal resistance because of the large surface-to-volume ratio. In this review article, several modeling strategies are discussed for different length scales, complemented by our experimental efforts to tailor the thermal transport properties of polymeric composite materials. Progress in the molecular modeling of thermal transport in thermosets is reviewed along with a discussion on the interface thermal resistance between functionalized carbon nanotube and epoxy resin systems. For the thermal transport in fiber-reinforced composites, various micromechanics-based analytical and numerical modeling schemes are reviewed in predicting the transverse thermal conductivity. Numerical schemes used to realize and scale the interface thermal resistance and the finite mean free path of the energy carrier in the mesoscale are discussed in the frame of the lattice Boltzmann-Peierls-Callaway equation. Finally, guided by modeling, complementary experimental efforts are discussed for exfoliated graphite and vertically aligned nanotubes based composites toward improving their effective thermal conductivity by tailoring interface thermal resistance.

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.

We have developed a simple model to quantify the effect of solvent selectivity on the surface composition of two-component self-assembled monolayers formed from solutions containing mixtures of organic thiols. The coarse-grained molecular model incorporates the relevant intermolecular interactions in the solution and monolayer to yield an expression for the free energy of monolayer formation. Minimization of the free energy results in a simple and analytically tractable expression for the monolayer composition as a function of solvent selectivity (defined as the difference in the Flory-type interaction parameters of the two organic thiols in the solution) and the degree of incompatibility between the adsorbate molecules. A comparison of our theory to experiments on the formation of two-component self-assembled monolayers from solution indicates that the coarse-grained molecular model captures the trends in the experimental data quite well.

Here we report on the bioenabled assembly of layered nanohybrids using peptides identified with regard to their affinity to the nanoparticle surface. A dodecamer peptide termed M1, determined from a phage peptide display library, was found to bind to the surface of a layered aluminosilicate (montmorillonite, MMT). Fusion of a metal binding domain to the M1 peptide or the M1 peptide by itself was able to direct the growth of metal nanoparticles, such as gold and cobalt-platinum, respectively, on the MMT. This method of producing hybrid nanoclay materials will have utility in catalytic, optical, biomedical, and composite materials applications.

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.

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.

We investigated molecular interactions involved in the selective binding of several short peptides derived from phage-display techniques (8-12 amino acids, excluding Cys) to surfaces of Au, Pd, and Pd-Au bimetal. The quantitative analysis of changes in energy and conformation upon adsorption on even {111} and {100} surfaces was carried out by molecular dynamics simulation using an efficient computational screening technique, including 1000 explicit water molecules and physically meaningful peptide concentrations at pH = 7. Changes in chain conformation from the solution to the adsorbed state over the course of multiple nanoseconds suggest that the peptides preferably interact with vacant sites of the face-centered cubic lattice above the metal surface. Residues that contribute to binding are in direct contact with the metal surfaces, and less-binding residues are separated from the surface by one or two water layers. The strength of adsorption ranges from 0 to -100 kcal/(mol peptide) and scales with the surface energy of the metal (Pd surfaces are more attractive than Au surfaces), the affinity of individual residues versus the affinity of water, and conformation aspects, as well as polarization and charge transfer at the metal interface (only qualitatively considered here). A hexagonal spacing of approximately 1.6 A between available lattice sites on the {111} surfaces accounts for the characteristic adsorption of aromatic side groups and various other residues (including Tyr, Phe, Asp, His, Arg, Asn, Ser), and a quadratic spacing of approximately 2.8 A between available lattice sites on the {100} surface accounts for a significantly lower affinity to all peptides in favor of mobile water molecules. The combination of these factors suggests a "soft epitaxy" mechanism of binding. On a bimetallic Pd-Au {111} surface, binding patterns are similar, and the polarity of the bimetal junction can modify the binding energy by approximately 10 kcal/mol. The results are semiquantitatively supported by experimental measurements of the affinity of peptides and small molecules to metal surfaces as well as results from quantum-mechanical calculations on small peptide and surface fragments. Interfaces were modeled using the consistent valence force field extended for Lennard-Jones parameters for fcc metals which accurately reproduce surface and interface energies [Heinz, H.; Vaia, R. A.; Farmer, B. L.; Naik, R. R. J. Phys. Chem. C 2008, 112, 17281-17290].

In examining adsorption of a few selected single amino acids on Au and Pd cluster models by density functional theory calculations, we have shown that specific side-chain binding affinity to the surface may occur because of a combination of effects, including charge transfer. Larger binding was calculated at the Pd interface. In addition, the interplay between amino acid solvation and adsorption at the interface was considered from first principles. This analysis serves as the first step toward gaining a more accurate understanding of specific interactions at the interface of biological-metal nanostructures than has been attempted in the past.

Single wall carbon nanotubes (SWNTs) have attracted attention because of their potential in a vast range of applications, including transistors and sensors. However, immense technological importance lies in enhancing the purity and homogeneity of SWNTs with respect to their chirality for real-world electronic applications. In order to achieve optimal performance of SWNTs, the diameter, type, and chirality have to be effectively sorted. Any employed strategy for sorting SWNTs has to be scalable, nondestructible, and economical. In this paper, we present a solubilization and chirality enrichment study of commercially available SWNTs using genomic DNA. On the basis of the comparison of the photoluminescence (PL) and near-infrared absorption measurements from the SWNTs dispersed with salmon genomic DNA (SaDNA) and d(GT)20, we show that genomic DNA specifically enriches (6,5) tubes. Circular dichroism and classical all-atom molecular dynamics simulations reveal that the genomic double-stranded SaDNA prefers to interact with (6,5) SWNTs as compared to (10,3) tubes, meanwhile single-stranded d(GT)20 shows no or minimal chirality preference. Our enrichment process demonstrates enrichment of >86% of (6,5) SWNTs from CoMoCat nanotubes using SaDNA.

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.

The structures of the mesophases and their subunits (micelles) of poly(styrene-b-vinyl4pyridine) (PS-b-P4VP) in a toluene solution were studied by using small-angle X-ray scattering (SAXS), transmission electron microscopy (TEM), and generalized indirect Fourier transform (GIFT) methods. The structures of PS-b-P4VP, such as the individual micelle, the face-centered cubic (fcc) and body-centered cubic (bcc), and the lamellar, were identified. The SAXS from the PS-b-P4VP solution showed a good contrast for the micelle, even in a low concentration of 0.25 wt %. As the concentration increases, the fcc and both fcc and bcc appear for the packing of the micelles of PS(3.3K)-b-P4VP(4.7K) and PS(12K)-b-P4VP(11.8K), respectively. The lamellar structure was also identified, with a further increase in the concentration for PS(3.3K)-b-P4VP(4.7K). These structures were also identified via TEM images.

The low-frequency (0.01 Hz-10 MHz) dynamic characteristics of alkyl quaternary ammonium exchanged montmorillonite (SC20A) were investigated to determine the correlation between temperature-dependent changes in the interlayer structure and collective mobility of the surfactant. From 25 to 165 degrees C, SC20A exhibits two interlayer transitions, one ascribed to the melting of the intercalated alkyl chains of the surfactant (20-40 degrees C) and another associated with an abrupt decrease in the interlayer's coefficient of thermal expansion (100 degrees C). For this temperature range, the excess surfactant and residual electrolytes present in commercially manufactured SC20A enhance the direct current conductivity and increase low-frequency space-charge polarization, which is believed to occur across percolation paths established by the surfaces of the SC20A crystallites. In contrast, a higher-frequency relaxation, which was less sensitive to process history and impurity content, is ascribed to relaxation within the interlayer at the surfactant-aluminosilicate interface electrostatic couple. The temperature dependence of these dielectric relaxations indicated a drastic increase in mobility as the interlayer organic phase transitions from static and glasslike into molten and mobile. Overall, SC20A displayed features of alternating current universality, including time-temperature superposition, common in other types of disordered ion-conducting media. The presence of long-range transport and its sensitivity to low amounts of impurities imply that from a dynamic perspective the local environment of the surfactants are substantially diverse and a minority fraction, such as at the edge of the crystallite (gallery and aluminosilicate layer), may dominate the lower-frequency dielectric response.

The structure of thin films cast from regenerated solutions of Bombyx mori cocoon silk in hexafluoroisopropyl alcohol (HFIP) was studied by synchrotron X-ray diffraction during heating. A solid-state conformational transition from an alpha-helical structure to the well-known beta-sheet silk II structure occurred at a temperature of approximately 140 degrees C. The transition appeared to be homogeneous, as both phases do not coexist within the resolution of the current study. Modulated differential scanning calorimetry (DSC) of the films showed an endothermic melting peak followed by an exothermic crystallization peak, both occurring near 140 degrees C. Oriented fibers were also produced that displayed this helical molecular conformation. Subsequent heating above the structural transition temperature produced oriented beta-sheet fibers very similar in structure to B. mori cocoon fibers. Heat treatment of silk films at temperatures well below their degradation temperature offers a controllable route to materials with well-defined structures and mechanical behavior.

With the use of high-resolution transmission electron microscopy the structure and morphology of montmorillonite (MMT), a material of current interest for use in polymer nanocomposites, was characterized. Using both imaging theory and experiment, the procedures needed to generate lattice images from MMT were established. These procedures involve careful control of the microscope's objective lens defocus to maximize contrast from features of a certain size, as well as limiting the total dose of electrons received by the sample. Direct images of the MMT lattice were obtained from neat Na+ MMT, organically modified MMT, and organically modified MMT/epoxy nanocomposites. The degree of crystallinity and turbostratic disorder were characterized using electron diffraction and high-resolution electron microscopy (HREM). Also, the extent of the MMT sheets to bend when processed into an epoxy matrix was directly visualized. A minimum radius of curvature tolerable for a single MMT sheet during bending deformation was estimated to be 15 nm, and from this value a critical failure strain of 0.033 was calculated. HREM can be used to improve the understanding of the structure of polymer nanocomposites at the nanometer-length scale.

Oxygen quenching of pyrene has been studied in a diverse series of polymers. Most measurements were made using homo- or copolymers containing a poly(dimethylsiloxane) region. Systematic variations in the polymer properties have been made in order to delineate the structural features important for satisfactory use as supports for oxygen sensors. In particular, quenching behavior was examined as a function of the type and amount of copolymer cross-linkers; these were added to produce domains of different polarity and rigidity that would segregate the sensor molecule. A domain model (Xu, W.; et al. Anal. Chem. 1994, 66, 4133-4141) was used to explain the variations in oxygen-quenching properties as a function of additives and cross-linkers. The relative affinity of the different domains for the pyrene and the efficacy of the domains for oxygen quenching controls the overall behavior of the sensing response.