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.

Preferential binding effects on protein structure and dynamics revealed by coarse-grained Monte Carlo simulation

The effect of preferential binding of solute molecules within an aqueous solution on the structure and dynamics of the histone H3.1 protein is examined by a coarse-grained Monte Carlo simulation. The knowledge-based residue-residue and hydropathy-index-based residue-solvent interactions are used as input to analyze a number of local and global physical quantities as a function of the residue-solvent interaction strength (f). Results from simulations that treat the aqueous solution as a homogeneous effective solvent medium are compared to when positional fluctuations of the solute molecules are explicitly considered. While the radius of gyration (R_g) of the protein exhibits a non-monotonic dependence on solvent interaction over a wide range of f within an effective medium, an abrupt collapse in R_g occurs in a narrow range of f when solute molecules rapidly bind to a preferential set of sites on the protein. The structure factor S(q) of the protein with wave vector (q) becomes oscillatory in the collapsed state, which reflects segmental correlations caused by spatial fluctuations in solute-protein binding. Spatial fluctuations in solute binding also modify the effective dimension (D) of the protein in fibrous (D ∼ 1.3), random-coil (D ∼ 1.75), and globular (D ∼ 3) conformational ensembles as the interaction strength increases, which differ from an effective medium with respect to the magnitude of D and the length scale.

Asymmetry in structural response of inner and outer transmembrane segments of CorA protein by a coarse-grain model

Structure of CorA protein and its inner (i.corA) and outer (o.corA) transmembrane (TM) components are investigated as a function of temperature by a coarse-grained Monte Carlo simulation. Thermal response of i.corA is found to differ considerably from that of the outer component, o.corA. Analysis of the radius of gyration reveals that the inner TM component undergoes a continuous transition from a globular conformation to a random coil structure on raising the temperature. In contrast, the outer transmembrane component exhibits an abrupt (nearly discontinuous) thermal response in a narrow range of temperature. Scaling of the structure factor shows a globular structure of i.corA at a low temperature with an effective dimension D ∼ 3 and a random coil at a high temperature with D ∼ 2. The residue distribution in o.corA is slightly sparser than that of i.corA in a narrow thermos-responsive regime. The difference in thermos-response characteristics of these components (i.corA and o.corA) may reflect their unique transmembrane functions.

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.

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.

Aggregation and network formation in self-assembly of protein (H3.1) by a coarse-grained Monte Carlo simulation

Multi-scale aggregation to network formation of interacting proteins (H3.1) are examined by a knowledge-based coarse-grained Monte Carlo simulation as a function of temperature and the number of protein chains, i.e., the concentration of the protein. Self-assembly of corresponding homo-polymers of constitutive residues (Cys, Thr, and Glu) with extreme residue-residue interactions, i.e., attractive (Cys-Cys), neutral (Thr-Thr), and repulsive (Glu-Glu), are also studied for comparison with the native protein. Visual inspections show contrast and similarity in morphological evolutions of protein assembly, aggregation of small aggregates to a ramified network from low to high temperature with the aggregation of a Cys-polymer, and an entangled network of Glu and Thr polymers. Variations in mobility profiles of residues with the concentration of the protein suggest that the segmental characteristic of proteins is altered considerably by the self-assembly from that in its isolated state. The global motion of proteins and Cys polymer chains is enhanced by their interacting network at the low temperature where isolated chains remain quasi-static. Transition from globular to random coil transition, evidenced by the sharp variation in the radius of gyration, of an isolated protein is smeared due to self-assembly of interacting networks of many proteins. Scaling of the structure factor S(q) with the wave vector q provides estimates of effective dimension D of the mass distribution at multiple length scales in self-assembly. Crossover from solid aggregates (D ∼ 3) at low temperature to a ramified fibrous network (D ∼ 2) at high temperature is observed for the protein H3.1 and Cys polymers in contrast to little changes in mass distribution (D ∼ 1.6) of fibrous Glu- and Thr-chain configurations.

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.

Electronic properties of a graphene device with peptide adsorption: insight from simulation

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.

The effect of single wall carbon nanotube metallicity on genomic DNA-mediated chirality enrichment

Achieving highly enriched single wall carbon nanotubes (SWNTs) is one of the major hurdles today because their chirality-dependent properties must be uniform and predictable for use in nanoscale electronics. Due to the unique wrapping and groove-binding mechanism, DNA has been demonstrated as a highly specific SWNT dispersion and fractionation agent, with its enrichment capabilities depending on the DNA sequence and length as well as the nanotube properties. Salmon genomic DNA (SaDNA) offers an inexpensive and scalable alternative to synthetic DNA. In this study, SaDNA enrichment capabilities were tested on SWNT separation with varying degrees of metallicity that were formulated from mixtures of commercial metallic (met-) and semiconducting (sem-) abundant SWNTs. The results herein demonstrate that the degree of metallicity of the SWNT sample has a significant effect on the SaDNA enrichment capabilities, and this effect is modeled based on deconvolution of the near-infrared (NIR) absorption spectra and verified with photoluminescence emission (PLE) measurements. Using molecular dynamics and circular dichroism, the preferential SaDNA mediated separation of the (6, 5) sem-tube is shown to be largely influenced by the presence of met-SWNTs.

Random coil to globular thermal response of a protein (H3.1) with three knowledge-based coarse-grained potentials

The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (R(g)) with the temperature (T) occurs, however, depends on the potential, i.e. ΔT(MJ) ≈ 0.013-0.020, ΔT(BT) ≈ 0.018-0.026, and ΔT(BFKV) ≈ 0.006-0.013 (in reduced unit). Unlike MJ and BT potentials, results from the BFKV potential show an anomaly where the magnitude of R(g) decreases on raising the temperature in a range ΔT(A) ≈ 0.015-0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) ∝ q(-1/ν), with the wave vector, q=2π/λ, and the wavelength, λ, reveals a systematic change in the effective dimension (D(e)∼1/ν) of the histone with all potentials (MJ, BT, BFKV): D(e)∼3 in the globular structure with D(e)∼2 for the random coil. Reproducibility of the general yet unique (monotonic) structural transition of the protein H3.1 with the temperature (in contrast to non-monotonic structural response of a similar but different protein H2AX) with three interaction sets shows that the knowledge-based contact potential is viable tool to investigate structural response of proteins. Caution should be exercise with the quantitative comparisons due to differences in transition regimes with these interactions.

A novel nano-configuration for thermoelectrics: helicity induced thermal conductivity reduction in nanowires

In this article, we propose a novel helical nano-configuration towards the designing of high ZT thermoelectric materials. Non-equilibrium molecular dynamics (NEMD) simulations for 'model' bi-component nanowires indicate that a significant reduction in thermal conductivity, similar to that of flat superlattice nanostructures, can be achieved using a helical geometric configuration. The reduction is attributed to a plethora of transmissive and reflective phonon scattering events resulting from the steady alteration of phonon propagating direction that emerges from the continuous rotation of the helical interface. We also show that increasing the relative mass ratio of the two components lowers the phonon energy transmission at the interface due to differences in vibrational frequency spectra, thereby relatively 'easing' the phonon energy propagation along the helical pathway. While the proposed mechanisms result in a reduced lattice thermal conductivity, the continuous nature of the bi-component nanowire would not be expected to significantly reduce its electrical counterpart, as often occurs in superlattice/alloy nanostructures. Hence, we postulate that the helical configuration of atomic arrangement provides an attractive and general framework for improved thermoelectric material assemblies independent of the specific chemical composition.

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 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.

Conformational temperature-dependent behavior of a histone H2AX: a coarse-grained Monte Carlo approach via knowledge-based interaction potentials

Histone proteins are not only important due to their vital role in cellular processes such as DNA compaction, replication and repair but also show intriguing structural properties that might be exploited for bioengineering purposes such as the development of nano-materials. Based on their biological and technological implications, it is interesting to investigate the structural properties of proteins as a function of temperature. In this work, we study the spatial response dynamics of the histone H2AX, consisting of 143 residues, by a coarse-grained bond fluctuating model for a broad range of normalized temperatures. A knowledge-based interaction matrix is used as input for the residue-residue Lennard-Jones potential.We find a variety of equilibrium structures including global globular configurations at low normalized temperature (T* = 0.014), combination of segmental globules and elongated chains (T* = 0.016,0.017), predominantly elongated chains (T* = 0.019,0.020), as well as universal SAW conformations at high normalized temperature (T* ≥ 0.023). The radius of gyration of the protein exhibits a non-monotonic temperature dependence with a maximum at a characteristic temperature (T(c)* = 0.019) where a crossover occurs from a positive (stretching at T* ≤ T(c)*) to negative (contraction at T* ≥ T(c)*) thermal response on increasing T*.

Importance of interfaces in governing thermal transport in composite materials: modeling and experimental perspectives

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.

Scaffolding of an antimicrobial peptide (KSL) by a scale-down coarse-grained approach

A coarse-grained approach with enhanced representation of amino acid (involving four components, i.e. a central alpha carbon and its side group along with C and N terminals) is used to study the multi-scale assembly of an antimicrobial peptide (KSL) in an explicit solvent (in a scale-down hierarchy of Eby et al. [Phys. Chem. Chem. Phys., 2011, 13, 1123-1130]). Both local (mobility, solvent-surrounding, energy profiles) and global (variation of the root mean square displacement of peptides and its gyration radius with time steps, radial distribution function, and structure factors) physical quantities are analyzed as a function of the solvent quality (i.e. the solvent-residue interaction strength). We find that the mobility of the interacting side group (lysine) decays as the number of its surrounding solvent constituents grows systematically on increasing the interaction strength. Pinning of lysine directs the underlying segmental conformation that propagates to larger scale scaffolding. The radial distribution function (a measure of the correlated peptide assembly) decays with the distance (faster with stronger solvent interaction). Scaling of the structure factor (S(q)) of peptide assembly with the wave vector q = 2π/λ (λ is the wavelength), S(q) ∝q(-1/ν) provides an insight into its multi-scale mass (N) distribution. The effective dimension D(e) = 1/ν of the peptide assembly over the spatial distribution (R) can be estimated using N∝R(D(e)). On scales larger than the size (i.e. the radius of gyration R(g)) of the peptide, D(e) ≈ 1.303 ± 0.070 to D(e) ≈ 1.430 ± 0.096, a rather fibrous morphology appears perhaps due to directed pinning while the morphology appears like an ideal chain, D(e) ≈ 1.809 ± 0.017 to D(e) ≈ 1.978 ± 0.017, at a smaller scale R≤R(g).

Molecular dynamics simulations of thermal transport in porous nanotube network structures

Carbon nanotube based 3D nanostructures have shown a lot of promise towards designing next generation of multi-functional systems, such as nano-electronic devices. Motivated by their recent successful experimental synthesis as well as characterization, and realizing that thermal dissipation is an important concern in proposed devices because of ever-increasing power density, we have investigated the phononic thermal transport behavior in 3D porous nanotube network structures using reverse non-equilibrium molecular dynamics simulations. Based on our study, the length scale associated with the distance between nanotube junctions emerges as the most dominating parameter that governs phonon scattering (hence the characteristic mean free path) and the heat flow in these nanostructures at molecular length scales. However, because of their spatial inhomogeneity, we show that the aerial density of carbon nanotubes (normal to heat flow) is also of critical importance in determining their system-level thermal conductivity. Based on our findings, we postulate that both parameters should be considered while designing nano-devices where thermal management is relevant.

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.

Kapitza resistance in the lattice Boltzmann-Peierls-Callaway equation for multiphase phonon gases

The interface thermal resistance becomes more and more important as device miniaturization for better performance renders a large surface-to-volume ratio and invariably requires a device design with multiple materials inducing thermal interfaces across the material heterogeniety. Toward developing a comprehensive computational methodology for thermal transport prediction, incorporating the interface effects in a heterogeneous medium, a novel boundary collision rule is devised in the lattice Boltzmann computational scheme to realize a thermal interface between phonon gases with dissimilar dispersion relations. Consistent with the Callaway collision operator for Umklapp process, the interface phonon collision process is regarded as a linear relaxation mechanism toward the local pseudo-equilibrium phonon distribution, which is uniquely defined by the energy conservation principle. The Kapitza length and the interface thermal resistance are determined by the relaxation parameter and the local phonon properties. The implementation of the proposed mesoscopic boundary collision rule in the lattice Boltzmann computational framework provides a methodology of predicting the thermal properties of a heterogeneus medium incorporating both normal and Umklapp collision processes of phonon.

Globular structure of a human immunodeficiency virus-1 protease (1DIFA dimer) in an effective solvent medium by a Monte Carlo simulation

A coarse-grained model is used to study the structure and dynamics of a human immunodeficiency virus-1 protease (1DIFA dimer) consisting of 198 residues in an effective solvent medium on a cubic lattice by Monte Carlo simulations for a range of interaction strengths. Energy and mobility profiles of residues are found to depend on the interaction strength and exhibit remarkable segmental symmetries in two monomers. Lowest energy residues such as Arg(41) and Arg(140) (most electrostatic and polar) are not the least mobile; despite the higher energy, the hydrophobic residues (Ile, Leu, and Val) are least mobile and form the core by pinning down the local segments for the globular structure. Variations in the gyration radius (R(g)) and energy (E(c)) of the protein show nonmonotonic dependence on the interaction strength with the smallest R(g) around the largest value of E(c). Pinning of the conformations by the hydrophobic residues at high interaction strength seems to provide seed for the protein chain to collapse.

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.

Polarization at metal-biomolecular interfaces in solution

Metal surfaces in contact with water, surfactants and biopolymers experience attractive polarization owing to induced charges. This fundamental physical interaction complements stronger epitaxial and covalent surface interactions and remains difficult to measure experimentally. We present a first step to quantify polarization on even gold (Au) surfaces in contact with water and with aqueous solutions of peptides of different charge state (A3 and Flg-Na3) by molecular dynamics simulation in all-atomic resolution and a posteriori computation of the image potential. Attractive polarization scales with the magnitude of atomic charges and with the length of multi-poles in the aqueous phase such as the distance between cationic and anionic groups. The polarization energy per surface area is similar on aqueous Au {1 1 1} and Au {1 0 0} interfaces of approximately -50 mJ m(-2) and decreases to -70 mJ m(-2) in the presence of charged peptides. In molecular terms, the polarization energy corresponds to -2.3 and -0.1 kJ mol(-1) for water in the first and second molecular layers on the metal surface, and to between -40 and 0 kJ mol(-1) for individual amino acids in the peptides depending on the charge state, multi-pole length and proximity to the surface. The net contribution of polarization to peptide adsorption on the metal surface is determined by the balance between polarization by the peptide and loss of polarization by replaced surface-bound water. On metal surfaces with significant epitaxial attraction of peptides such as Au {1 1 1}, polarization contributes only 10-20% to total adsorption related to similar polarity of water and of amino acids. On metal surfaces with weak epitaxial attraction of peptides such as Au {1 0 0}, polarization is a major contribution to adsorption, especially for charged peptides (-80 kJ mol(-1) for peptide Flg-Na(3)). A remaining water interlayer between the metal surface and the peptide then reduces losses in polarization energy by replaced surface-bound water. Computed polarization energies are sensitive to the precise location of the image plane (within tenths of Angstroms near the jellium edge). The computational method can be extended to complex nanometre and micrometer-size surface topologies.

Bioassembled layered silicate-metal nanoparticle hybrids

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.

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.

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.

Residue energy and mobility in sequence to global structure and dynamics of a HIV-1 protease (1DIFA) by a coarse-grained Monte Carlo simulation

Energy, mobility, and structural profiles of residues in a specific sequence of human immunodeficiency virus (HIV)-1 protease chain and its global conformation and dynamics are studied by a coarse-grained computer simulation model on a cubic lattice. HIV-1 protease is described by a chain of 99 residues (nodes) in a specific sequence (1DIFA) with N- and C-terminals on the lattice, where empty lattice sites represent an effective solvent medium. Internal structures of the residues are ignored but their specificities are captured via an interaction (epsilon(ij)) matrix (residue-residue, residue-solvent) of the coefficient (fepsilon(ij)) of the Lennard-Jones potential. Simulations are performed for a range of interaction strength (f) with the solvent-residue interaction describing the quality of the solvent. Snapshots of the protein show considerable changes in the conformation of the protein on varying the interaction. From the mobility and energy profiles of the residues, it is possible to identify the active (and not so active) segments of the protein and consequently their role in proteolysis. Contrary to interaction thermodynamics, the hydrophobic residues possess higher configurational energy and lower mobility while the electrostatic and polar residues are more mobile despite their lower interaction energy. Segments of hydrophobic core residues, crucial for the structural evolution of the protein are identified-some of which are consistent with recent molecular dynamics simulation in context to possible clinical observations. Global energy and radius of gyration of the protein exhibit nonmonotonic dependence on the interaction strength (f) with opposite trends, e.g., rapid transition into globular structure with higher energy. Variations of the rms displacement of the protein and that of a tracer residue, Gly(49), with the time steps show how they slow down on increasing the interaction strength.

Toward understanding amino acid adsorption at metallic interfaces: a density functional theory study

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.

Enrichment of (6,5) single wall carbon nanotubes using genomic DNA

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.

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.

Conformation of a coarse-grained protein chain (an aspartic acid protease) model in effective solvent by a bond-fluctuating Monte Carlo simulation

In a coarse-grained description of a protein chain, all of the 20 amino acid residues can be broadly divided into three groups: Hydrophobic (H) , polar (P) , and electrostatic (E) . A protein can be described by nodes tethered in a chain with a node representing an amino acid group. Aspartic acid protease consists of 99 residues in a well-defined sequence of H , P , and E nodes tethered together by fluctuating bonds. The protein chain is placed on a cubic lattice where empty lattice sites constitute an effective solvent medium. The amino groups (nodes) interact with the solvent (S) sites with appropriate attractive (PS) and repulsive (HS) interactions with the solvent and execute their stochastic movement with the Metropolis algorithm. Variations of the root mean square displacements of the center of mass and that of its center node of the protease chain and its gyration radius with the time steps are examined for different solvent strength. The structure of the protease swells on increasing the solvent interaction strength which tends to enhance the relaxation time to reach the diffusive behavior of the chain. Equilibrium radius of gyration increases linearly on increasing the solvent strength: A slow rate of increase in weak solvent regime is followed by a faster swelling in stronger solvent. Variation of the gyration radius with the time steps suggests that the protein chain moves via contraction and expansion in a somewhat quasiperiodic pattern particularly in strong solvent.

High-resolution electron microscopy of montmorillonite and montmorillonite/epoxy nanocomposites

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.

Correlation of the β-sheet crystal size in silk fibers with the protein amino acid sequence

Low voltage transmission electron microscopy (LVTEM) and wide angle X-ray scattering (WAXS) are used to independently determine the size of the β-sheet crystalline regions in Bombyx mori silk fibers. The peak in the size distributions of the major and minor axes of the anisotropic crystallites measured from the LVTEM images compare well with the average sizes as determined by Scherrer analysis of the X-ray fiber diagrams. These values are then discussed in the context of the B. mori fibroin heavy chain amino acid sequence, and the underlying mechanism for the organism's control on fiber crystallite size, and therefore mechanical properties, is proposed.

Multiscale mode dynamics of a tethered membrane

Stochastic dynamics of a tethered membrane with a bond-fluctuating coarse-grained Monte Carlo simulation shows, in addition to diffusion, nondiffusive behavior sensitive to the type of membrane, its size, and quality of the solvent. Motion of the membrane's center node is described by the variation of the mean-square displacement (R{n}{2}) with time step (t) , i.e., R{n}{2} proportional, variantt{2nu} with the exponent nu approximately 18-16 in the short time followed by subdiffusive power laws (i.e., nu approximately 15,110 ) in the intermediate time regimes before reaching diffusion nu=1. The crossover between in-plane wrinkle modes is identified from the segmental (node) motion of the membrane.

Study of the ordered structures of poly(styrene-b-vinyl4pyridine) in a solution state by using small-angle X-ray scattering and generalized indirect Fourier transform

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.

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.

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.

Thermally Induced α-Helix to β-Sheet Transition in Regenerated Silk Fibers and Films

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.