Switchable X-Ray Orbital Angular Momentum from an Artificial Spin Ice.

Artificial spin ices (ASI) have been widely investigated as magnetic metamaterials with exotic properties governed by their geometries. In parallel, interest in x-ray photon orbital angular momentum (OAM) has been rapidly growing. Here we show that a square ASI with a patterned topological defect, a double edge dislocation, imparts OAM to scattered x rays. Unlike single dislocations, a double dislocation does not introduce magnetic frustration, and the ASI equilibrates to its antiferromagnetic (AFM) ground state. The topological charge of the defect differs with respect to the structural and magnetic order; thus, x-ray diffraction from the ASI produces photons with even and odd OAM quantum numbers at the structural and AFM Bragg conditions, respectively. The magnetic transitions of the ASI allow the AFM OAM beams to be switched on and off by modest variations of temperature and applied magnetic field. These results demonstrate ASIs can serve as metasurfaces for reconfigurable x-ray optics that could enable selective probes of electronic and magnetic properties.

Thermal anisotropy in nano-crystalline MoS2 thin films.

In this work, we grow thin MoS2 films (50-150 nm) uniformly over large areas (>1 cm(2)) with strong basal plane (002) or edge plane (100) orientations to characterize thermal anisotropy. Measurement results are correlated with molecular dynamics simulations of thermal transport for perfect and defective MoS2 crystals. The correlation between predicted (simulations) and measured (experimental) thermal conductivity are attributed to factors such as crystalline domain orientation and size, thereby demonstrating the importance of thermal boundary scattering in limiting thermal conductivity in nano-crystalline MoS2 thin films. Furthermore, we demonstrate that the cross-plane thermal conductivity of the films is strongly impacted by exposure to ambient humidity.

Binding of solvated peptide (EPLQLKM) with a graphene sheet via simulated coarse-grained approach.

Binding of a solvated peptide A1 ((1)E (2)P (3)L (4)Q (5)L (6)K (7)M) with a graphene sheet is studied by a coarse-grained computer simulation involving input from three independent simulated interaction potentials in hierarchy. A number of local and global physical quantities such as energy, mobility, and binding profiles and radius of gyration of peptides are examined as a function of temperature (T). Quantitative differences (e.g., the extent of binding within a temperature range) and qualitative similarities are observed in results from three simulated potentials. Differences in variations of both local and global physical quantities suggest a need for such analysis with multiple inputs in assessing the reliability of both quantitative and qualitative observations. While all three potentials indicate binding at low T and unbinding at high T, the extent of binding of peptide with the temperature differs. Unlike un-solvated peptides (with little variation in binding among residues), solvation accentuates the differences in residue binding. As a result the binding of solvated peptide at low temperatures is found to be anchored by three residues, (1)E, (4)Q, and (6)K (different from that with the un-solvated peptide). Binding to unbinding transition can be described by the variation of the transverse (with respect to graphene sheet) component of the radius of gyration of the peptide (a potential order parameter) as a function of temperature.

Thermal rectification in three-dimensional asymmetric nanostructure.

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.

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.

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 ß-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.

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.

Poly(2-hydroxyethyl methacrylate) for enzyme immobilization: impact on activity and stability of horseradish peroxidase.

On the basis of their versatile structure and chemistry as well as tunable mechanical properties, polymer brushes are well-suited as supports for enzyme immobilization. However, a robust surface design is hindered by an inadequate understanding of the impact on activity from the coupling motif and enzyme distribution within the brush. Herein, horseradish peroxidase C (HRP C, 44 kDa), chosen as a model enzyme, was immobilized covalently through its lysine residues on a N-hydroxysuccinimidyl carbonate-activated poly(2-hydroxyethyl methacrylate) (PHEMA) brush grafted chemically onto a flat impenetrable surface. Up to a monolayer coverage of HRP C is achieved, where most of the HRP C resides at or near the brush-air interface. Molecular modeling shows that lysines 232 and 241 are the most probable binding sites, leading to an orientation of the immobilized HRP C that does not block the active pocket of the enzyme. Michaelis-Menten kinetics of the immobilized HRP C indicated little change in the K(m) (Michaelis constant) but a large decrease in the V(max) (maximum substrate conversion rate) and a correspondingly large decrease in the k(cat) (overall catalytic rate). This indicates a loss in the percentage of active enzymes. Given the relatively ideal geometry of the HRPC-PHEMA brush, the loss of activity is most likely due to structural changes in the enzyme arising from either secondary constraints imposed by the connectivity of the N-hydroxysuccinimidyl carbonate linking moiety or nonspecific interactions between HRP C and DSC-PHEMA. Therefore, a general enzyme-brush coupling motif must optimize reactive group density to balance binding with neutrality of surroundings.

Supramolecular assembly of a biomineralizing antimicrobial peptide in coarse-grained Monte Carlo simulations.

Monte Carlo simulations are used to model the self-organizing behavior of the biomineralizing peptide KSL (KKVVFKVKFK) in the presence of phosphate. Originally identified as an antimicrobial peptide, KSL also directs the formation of biosilica through a hypothetical supramolecular template that requires phosphate for assembly. Specificity of each residue and the interactions between the peptide and phosphate are considered in a coarse-grained model. Both local and global physical quantities are calculated as the constituents execute their stochastic motion in the presence and absence of phosphate. Ordered peptide aggregates develop after simulations reach thermodynamic equilibrium, wherein phosphates form bridging ligands with lysines and are found interdigitated between peptide molecules. Results demonstrate that interactions between the lysines and phosphate drive self-organization into lower energy conformations of interconnected peptide scaffolds that resemble the supramolecular structures of polypeptide- and polyamine-mediated silica condensation systems. Furthermore, the specific phosphate-peptide organization appears to mimic the zwitterionic structure of native silaffins (scaffold proteins of diatom shells), suggesting a similar template organization for silica deposition between the in vitro KSL and silaffin systems.

Single mode phonon energy transmission in functionalized carbon nanotubes.

Although the carbon nanotube (CNT) features superior thermal properties in its pristine form, the chemical functionalization often required for many applications of CNT inevitably degrades the structural integrity and affects the transport of energy carriers. In this article, the effect of the side wall functionalization on the phonon energy transmission along the symmetry axis of CNT is studied using the phonon wave packet method. Three different functional groups are studied: methyl (-CH(3)), vinyl (-C(2)H(3)), and carboxyl (-COOH). We find that, near Γ point of the Brillouin zone, acoustic phonons show ideal transmission, while the transmission of the optical phonons is strongly suppressed. A positive correlation between the energy transmission coefficient and the phonon group velocity is observed for both acoustic and optical phonon modes. On comparing the transmission due to functional groups with equivalent point mass defects on CNT, we find that the chemistry of the functional group, rather than its molecular mass, has a dominant role in determining phonon scattering, hence the transmission, at the defect sites.

Role of solvent selectivity in the equilibrium surface composition of monolayers formed from a solution containing mixtures of organic thiols.

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.

Biofunctionalization and immobilization of a membrane via peptide binding (CR3-1, S2) by a Monte Carlo simulation.

A coarse-grained computer simulation model is used to study the immobilization of a dynamic tethered membrane (representation of a clay platelet) in a matrix of mobile peptide chains CR3-1: 1Trp-2Pro-3Ser-4Ser-5Tyr-6Leu-7Ser-8Pro-9Ile-10Pro-11Tyr-12Ser and S2: 1His-2Gly-3Ile-4Asn-5Thr-6Thr-7Lys-8Pro-9Phe-10Lys-11Ser-12Val on a cubic lattice. Each residue interacts with the membrane nodes with appropriate interaction and executes their stochastic motion with the Metropolis algorithm. Density profiles, binding energy of each residue, mobility, and targeted structural profile are analyzed as a function of peptide concentration. We find that the binding of peptides S2 is anchored by lysine residues (7Lys, 10Lys) while peptides CR3-1 do not bind to membrane. The membrane slows down as peptides S2 continues to bind leading to its eventual pinning. How fast the immobilization of the membrane occurs depends on peptide concentration. Binding of peptide S2 modulates the morphology of the membrane. The immobilization of membrane occurs faster if peptides S2 are replaced by the homopolymer of lysine ([Lys]12 of the same molecular weight), the strongest binding residue. The surface of membrane can be patterned with somewhat reduced roughness with the homopolymer of lysine than that with peptide S2

In Silico Discovery and Validation of Neuropeptide-Y-Binding Peptides for Sensors.

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.

Nature of molecular interactions of peptides with gold, palladium, and Pd-Au bimetal surfaces in aqueous solution.

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].

Advancing Peptide-Based Biorecognition Elements for Biosensors Using in-Silico Evolution.

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.

Imaging the magnetic structures of artificial quasicrystal magnets using resonant coherent diffraction of circularly polarized X-rays.

Unraveling nanoscale spin structures has long been an important activity addressing various scientific interests, that are also readily adaptable to technological applications. This has invigorated the development of versatile nanoprobes suitable for imaging specimens under native conditions. Here we have demonstrated the resonant coherent diffraction of an artificial quasicrystal magnet with circularly polarized X-rays. The nanoscale magnetic structure was revealed from X-ray speckle patterns by comparing with micromagnetic simulations, as a step toward understanding the intricate relationship between the chemical and spin structures in an aperiodic quasicrystal lattice. Femtosecond X-ray pulses from free electron lasers are expected to immediately extend the current work to nanoscale structure investigations of ultrafast spin dynamics, surpassing the present spatio-temporal resolution.

Dynamics of alkyl ammonium intercalants within organically modified montmorillonite: Dielectric relaxation and ionic conductivity.

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.

In silico carbon molecular beam epitaxial growth of graphene on the h-BN substrate: carbon source effect on van der Waals epitaxy.

Against the presumption that hexagonal boron-nitride (h-BN) should provide an ideal substrate for van der Waals (vdW) epitaxy to grow high quality graphene films, carbon molecular beam epitaxy (CMBE) techniques using solid carbon sublimation have reported relatively poor quality of the graphene. In this article, the CMBE growth of graphene on the h-BN substrate is numerically studied in order to identify the effect of the carbon source on the quality of the graphene film. The carbon molecular beam generated by the sublimation of solid carbon source materials such as graphite and glassy carbon is mostly composed of atomic carbon, carbon dimers and carbon trimers. Therefore, the graphene film growth becomes a complex process involving various deposition characteristics of a multitude of carbon entities. Based on the study of surface adsorption and film growth characteristics of these three major carbon entities comprising graphite vapour, we report that carbon trimers convey strong traits of vdW epitaxy prone to high quality graphene growth, while atomic carbon deposition is a surface-reaction limited process accompanied by strong chemisorption. The vdW epitaxial behaviour of carbon trimers is found to be substantial enough to nucleate and develop into graphene like planar films within a nanosecond of high flux growth simulation, while reactive atomic carbons tend to impair the structural integrity of the crystalline h-BN substrate upon deposition to form an amorphous interface between the substrate and the growing carbon film. The content of reactive atomic carbons in the molecular beam is suspected to be the primary cause of low quality graphene reported in the literature. A possible optimization of the molecular beam composition towards the synthesis of better quality graphene films is suggested.

Peptide interactions with zigzag edges in graphene.

Recognition and manipulation of graphene edges enable the control of physical properties of graphene-based devices. Recently, the authors have identified a peptide that preferentially binds to graphene edges from a combinatorial peptide library. In this study, the authors examine the functional basis for the edge binding peptide using experimental and computational methods. The effect of amino acid substitution, sequence context, and solution pH value on the binding of the peptide to graphene has been investigated. The N-terminus glutamic acid residue plays a key role in recognizing and binding to graphene edges. The protonation, substitution, and positional context of the glutamic acid residue impact graphene edge-binding. Our findings provide insights into the binding mechanisms and the design of peptides for recognizing and functionalizing graphene edges.

Biotic-Abiotic Interactions: Factors that Influence Peptide-Graphene Interactions.

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.