Probe microscopy methods and applications in imaging of biological materials.

Atomic force microscopy is an emerging tool for investigating the biomolecular aspects of cellular interactions; however, cell and tissue analyses must frequently be performed in aqueous environment, over rough surfaces, and on complex adhesive samples that complicate the imaging process and readily facilitate the blunting or fouling of the AFM probe. In addition, the shape and surface chemistry of the probe determine the quality and types of data that can be acquired from biological materials, with certain information becoming available only within a specific range of tip lengths or diameters, or through the assistance of specific chemical or biological functionalization procedures. Consequently, a broad range of probe modification techniques has been developed to extend the capabilities and overcome the limitations of biological AFM measurements, including the fabrication of AFM tips with specialized morphologies, surface coating with biologically affine molecules, and the attachment of proteins, nucleic acids and cells to AFM probes. In this review, we underline the importance of probe choice and modification for the AFM analysis of biomaterials, discuss the recent literature on the use of non-standard AFM tips in life sciences research, and consider the future utility of tip functionalization methods for the investigation of fundamental cell and tissue interactions.

Permanent tuning of optical resonant modes of chalcogenide-coated microresonators.

Chalcogenide materials are promising for optical resonant mode tuning of whispering gallery mode (WGM) microresonators due to their high nonlinearity. In this study, this phenomenon was demonstrated for Ge2Sb2Te5-coated toroidal microresonators using an optical postprocess, which utilizes the intrinsically photosensitive property of the Ge2Sb2Te5 coating. A signal laser was used to illuminate the resonator for permanent tuning of the WGMs in a sensitive manner. 0.01 nm and 0.02 nm permanent tuning of the WGMs was recorded for 5 nm and 10 nm coated resonators, respectively. This technique enables resonance matching of coupled optical resonators, which could pave the way for optoelectronic circuitries employing multiple optical microresonators.

Reversible decryption of covert nanometer-thick patterns in modular metamaterials.

Continuous development of security features is mandatory for the fight against forgery of valuable documents and products, the most notable example being banknotes. Such features demonstrate specific properties under certain stimuli such as fluorescent patterns glowing under ultraviolet light. These security features should also be hard to copy by unlicensed people and be interrogated by anyone using easily accessible tools. To this end, this Letter demonstrates the development of an ideal security feature enabled by the realization of modular metamaterials based on metal-dielectric-metal cavities that consist of two separate parts: metal nanoparticles on an elastomeric substrate and a bottom mirror coated with a thin dielectric. Patterns generated by creating nanometer-thick changes in the dielectric layer are invisible (encrypted) and can only be detected (decrypted) by sticking the elastomeric patch on. The observed optical effects such as visibility and colors can only be produced with the correct combination of materials and film thicknesses, making the proposed structures a strong alternative to compromised security features.

A comparison of peptide amphiphile nanofiber macromolecular assembly strategies.

Supramolecular peptide nanofibers that are composed of peptide amphiphile molecules have been widely used for many purposes from biomedical applications to energy conversion. The self-assembly mechanisms of these peptide nanofibers also provide convenient models for understanding the self-assembly mechanisms of various biological supramolecular systems; however, the current theoretical models that explain these mechanisms do not sufficiently explain the experimental results. In this study, we present a new way of modeling these nanofibers that better fits with the experimental data. Molecular dynamics simulations were applied to create model fibers using two different layer models and two different tilt angles. Strikingly, the fibers which were modeled to be tilting the peptide amphiphile molecules and/or tilting the plane were found to be more stable and consistent with the experiments.

Colorimetric detection of ultrathin dielectrics on strong interference coatings.

Metal films covered with ultrathin lossy dielectrics can exhibit strong interference effects manifested as the broad absorption of the incident light resulting in distinct surface colors. Despite their simple bilayer structures, such surfaces have only recently been scrutinized and applied mainly to color printing. Here, we report the use of such surfaces for colorimetric detection of ultrathin dielectrics. Upon deposition of a nanometer-thick dielectric on the surface, the absorption peak red shifts, changing the surface color. The color contrast between the bare and dielectric-coated surfaces can be detected by the naked eye. The optical responses of the surfaces are characterized for nanometer-thick SiO2, Al2O3, and bovine serum albumin molecules. The results suggest that strong interference surfaces can be employed as biosensors.

Force and time-dependent self-assembly, disruption and recovery of supramolecular peptide amphiphile nanofibers.

Biological feedback mechanisms exert precise control over the initiation and termination of molecular self-assembly in response to environmental stimuli, while minimizing the formation and propagation of defects through self-repair processes. Peptide amphiphile (PA) molecules can self-assemble at physiological conditions to form supramolecular nanostructures that structurally and functionally resemble the nanofibrous proteins of the extracellular matrix, and their ability to reconfigure themselves in response to external stimuli is crucial for the design of intelligent biomaterials systems. Here, we investigated real-time self-assembly, deformation, and recovery of PA nanofibers in aqueous solution by using a force-stabilizing double-pass scanning atomic force microscopy imaging method to disrupt the self-assembled peptide nanofibers in a force-dependent manner. We demonstrate that nanofiber damage occurs at tip-sample interaction forces exceeding 1 nN, and the damaged fibers subsequently recover when the tip pressure is reduced. Nanofiber ends occasionally fail to reconnect following breakage and continue to grow as two individual nanofibers. Energy minimization calculations of nanofibers with increasing cross-sectional ellipticity (corresponding to varying levels of tip-induced fiber deformation) support our observations, with high-ellipticity nanofibers exhibiting lower stability compared to their non-deformed counterparts. Consequently, tip-mediated mechanical forces can provide an effective means of altering nanofiber integrity and visualizing the self-recovery of PA assemblies.

Multivalent Presentation of Cationic Peptides on Supramolecular Nanofibers for Antimicrobial Activity.

Noncovalent and electrostatic interactions facilitate the formation of complex networks through molecular self-assembly in biomolecules such as proteins and glycosaminoglycans. Self-assembling peptide amphiphiles (PA) are a group of molecules that can form nanofibrous structures and may contain bioactive epitopes to interact specifically with target molecules. Here, we report the presentation of cationic peptide sequences on supramolecular nanofibers formed by self-assembling peptide amphiphiles for cooperative enhanced antibacterial activity. Antibacterial properties of self-assembled peptide nanofibers were significantly higher than soluble peptide molecules with identical amino acid sequences, suggesting that the tandem presentation of bioactive epitopes is important for designing new materials for bactericidal activity. In addition, bacteria were observed to accumulate more rapidly on peptide nanofibers compared to soluble peptides, which may further enhance antibacterial activity by increasing the number of peptide molecules interacting with the bacterial membrane. The cationic peptide amphiphile nanofibers were observed to attach to bacterial membranes and disrupt their integrity. These results demonstrate that short cationic peptides show a significant improvement in antibacterial activity when presented in the nanofiber form.

Supramolecular Peptide Nanofiber Morphology Affects Mechanotransduction of Stem Cells.

Chirality and morphology are essential factors for protein function and interactions with other biomacromolecules. Extracellular matrix (ECM) proteins are also similar to other proteins in this sense; however, the complexity of the natural ECM makes it difficult to study these factors at the cellular level. The synthetic peptide nanomaterials harbor great promise in mimicking specific ECM molecules as model systems. In this work, we demonstrate that mechanosensory responses of stem cells are directly regulated by the chirality and morphology of ECM-mimetic peptide nanofibers with strictly controlled characteristics. Structural signals presented on l-amino acid containing cylindrical nanofibers (l-VV) favored the formation of integrin ß1-based focal adhesion complexes, which increased the osteogenic potential of stem cells through the activation of nuclear YAP. On the other hand, twisted ribbon-like nanofibers (l-FF and d-FF) guided the cells into round shapes and decreased the formation of focal adhesion complexes, which resulted in the confinement of YAP proteins in the cytosol and a corresponding decrease in osteogenic potential. Interestingly, the d-form of twisted-ribbon like nanofibers (d-FF) increased the chondrogenic potential of stem cells more than their l-form (l-FF). Our results provide new insights into the importance and relevance of morphology and chirality of nanomaterials in their interactions with cells and reveal that precise control over the chemical and physical properties of nanostructures can affect stem cell fate even without the incorporation of specific epitopes.

Wafer-scale arrays of high-Q silica optical microcavities.

On-chip high-Q microcavities possess significant potential in terms of integration of optical microresonators into functional optoelectronic devices that could be used in various applications, including biosensors, photonic-integrated circuits, or quantum optics experiments. Yet, despite the convenience of fabricating wafer-scale integrated microresonators with moderate Q values using standard microfabrication techniques, surface-tension-induced microcavities (STIMs), which have atomic-level surface roughness enabling the observation of Q values larger than 106, could only be produced using individual thermal treatment of every single microresonator within the devised area. Here, we demonstrate a facile method for large-scale fabrication of silica STIMs of various morphologies. Q values exceeding 106 are readily obtained using this technique. This study represents a significant advancement toward fabrication of wafer-scale optoelectronic circuitries.

Perfectly absorbing ultra thin interference coatings for hydrogen sensing.

Here we numerically demonstrate a straightforward method for optical detection of hydrogen gas by means of absorption reduction and colorimetric indication. A perfectly absorbing metal-insulator-metal (MIM) thin film interference structure is constructed using a silver metal back reflector, silicon dioxide insulator, and palladium as the upper metal layer and hydrogen catalyst. The thickness of silicon dioxide allows the maximizing of the electric field intensity at the Air/SiO2 interface at the quarter wavelengths and enabling perfect absorption with the help of highly absorptive palladium thin film (∼7 nm). While the exposure of the MIM structure to H2 moderately increases reflection, the relative intensity contrast due to formation of metal hydride is extensive. By modifying the insulator film thickness and hence the spectral absorption, the color is tuned and eye-visible results are obtained.

Rounding corners of nano-square patches for multispectral plasmonic metamaterial absorbers.

Multispectral metamaterial absorbers based on metal-insulator-metal nano-square patch resonators are studied here. For a geometry consisting of perfectly nano-square patches and vertical sidewalls, double resonances in the visible regime are observed due to simultaneous excitation of electric and magnetic plasmon modes. Although slightly modifying the sizes of the square patches makes the resonance wavelengths simply shift, rounding corners of the square patches results in emergence of a third resonance due to excitation of the circular cavity modes. Sidewall angle of the patches are also observed to affect the absorption spectra significantly. Peak absorption values for the triple resonance structures are strongly affected as the sidewall angle varies from 90 to 50 degrees. Rounded corners and slanted sidewalls are typical imperfections for lithographically fabricated metamaterial structures. The presented results suggest that imperfections caused during fabrication of the top nano-structures must be taken into account when designing metamaterial absorbers. Furthermore, it is shown that these fabrication imperfections can be exploited for improving resonance properties and bandwidths of metamaterials for various potential applications such as solar energy harvesting, thermal emitters, surface enhanced spectroscopies and photodetection.

Self-assembled peptide nanofiber templated one-dimensional gold nanostructures exhibiting resistive switching.

An amyloid-like peptide molecule self-assembling into one-dimensional nanofiber structure in ethanol was designed and synthesized with functional groups that can bind to gold ions. The peptide nanofibers were used as templates for nucleation and growth of one-dimensional gold nanostructures in the presence of ascorbic acid as reducing agent. We performed multistep seed-mediated synthesis of gold nanoparticles by changing peptide/gold precursor and peptide/reducing agent ratios. Gold nanostructures with a wide range of morphologies such as smooth nanowires, noodle-like one-dimensional nanostructures, and uniform aggregates of spherical nanoparticles were synthesized by use of an environmentally friendly synthesis method. Nanoscale electrical properties of gold-peptide nanofibers were investigated using atomic force microscopy. Bias dependent current (IV) measurements on thin films of gold-peptide nanofiber hybrid revealed tunneling dominated transport and resistive switching. Gold-peptide nanofiber composite nanostructures can provide insight into electrical conduction in biomolecular/inorganic composites, highlighting their potential applications in electronics and optics.

Amyloid inspired self-assembled peptide nanofibers.

Amyloid peptides are important components in many degenerative diseases as well as in maintaining cellular metabolism. Their unique stable structure provides new insights in developing new materials. Designing bioinspired self-assembling peptides is essential to generate new forms of hierarchical nanostructures. Here we present oppositely charged amyloid inspired peptides (AIPs), which rapidly self-assemble into nanofibers at pH 7 upon mixing in water caused by noncovalent interactions. Mechanical properties of the gels formed by self-assembled AIP nanofibers were analyzed with oscillatory rheology. AIP gels exhibited strong mechanical characteristics superior to gels formed by self-assembly of previously reported synthetic short peptides. Rheological studies of gels composed of oppositely charged mixed AIP molecules (AIP-1 + 2) revealed superior mechanical stability compared to individual peptide networks (AIP-1 and AIP-2) formed by neutralization of net charges through pH change. Adhesion and elasticity properties of AIP mixed nanofibers and charge neutralized AIP-1, AIP-2 nanofibers were analyzed by high resolution force-distance mapping using atomic force microscopy (AFM). Nanomechanical characterization of self-assembled AIP-1 + 2, AIP-1, and AIP-2 nanofibers also confirmed macroscopic rheology results, and mechanical stability of AIP mixed nanofibers was higher compared to individual AIP-1 and AIP-2 nanofibers self-assembled at acidic and basic pH, respectively. Experimental results were supported with molecular dynamics simulations by considering potential noncovalent interactions between the amino acid residues and possible aggregate forms. In addition, HUVEC cells were cultured on AIP mixed nanofibers at pH 7 and biocompatibility and collagen mimetic scaffold properties of the nanofibrous system were observed. Encapsulation of a zwitterionic dye (rhodamine B) within AIP nanofiber network was accomplished at physiological conditions to demonstrate that this network can be utilized for inclusion of soluble factors as a scaffold for cell culture studies.

Nanomechanical characterization by double-pass force-distance mapping.

We demonstrate high speed force-distance mapping using a double-pass scheme. The topography is measured in tapping mode in the first pass and this information is used in the second pass to move the tip over the sample. In the second pass, the cantilever dither signal is turned off and the sample is vibrated. Rapid (few kHz frequency) force-distance curves can be recorded with small peak interaction force, and can be processed into an image. Such a double-pass measurement eliminates the need for feedback during force-distance measurements. The method is demonstrated on self-assembled peptidic nanofibers.

Photonic bandgap infrared spectrometer.

We propose and demonstrate an infrared (IR) absorption spectrometer, made with a spatially variable photonic bandgap (PBG) structure, a blackbody source, and a simple IR detector, to identify the IR molecular fingerprints of analyte molecules. The PBG-based structure consists of thermally evaporated, IR transparent, high-refractive-index chalcogenide quarter-wave stacks (QWS) with a cavity layer. Spatial variation of the very sharp transmission peak due to the QWS cavity mode allows the structure to be used as a variable IR filter. Our proposed IR-PBG spectrometer can be used for detection and identification of volatile organic compounds.

Two-dimensional X-ray photoelectron spectroscopy for composite surface analysis.

We describe a method for obtaining two-dimensional X-ray photoelectron spectroscopic data derived from the frequency dependence of the XPS peaks recorded under electrical square-wave pulses, which control and affect the binding energy positions via the electrical potentials developed as a result of charging. By using cross-correlations between various peaks, our technique enables us to elucidate electrical characteristics of surface structures of composite samples and bring out various correlations between hidden/overlapping peaks.

Electro-optic and electro-absorption characterization of InAs quantum dot waveguides.

Optical properties of multilayer InAs quantum dot waveguides, grown by molecular beam epitaxy, have been studied under applied electric field. Fabry-Perot measurements at 1515 nm on InAs/GaAs quantum dot structures yield a significantly enhanced linear electro-optic efficiency compared to bulk GaAs. Electro-absorption measurements at 1300 nm showed increased absorption with applied field accompanied with red shift of the spectra. Spectral shifts of up to 21% under 18 Volt bias was observed at 1320 nm.

A figure of merit for optimization of nanocrystal flash memory design.

Nanocrystals can be used as storage media for carriers in flash memories. The performance of a nanocrystal flash memory depends critically on the choice of nanocrystal size and density as well as on the choice of tunnel dielectric properties. The performance of a nanocrystal memory device can be expressed in terms of write/erase speed, carrier retention time and cycling durability. We present a model that describes the charge/discharge dynamics of nanocrystal flash memories and calculate the effect of nanocrystal, gate, tunnel dielectric and substrate properties on device performance. The model assumes charge storage in quantized energy levels of nanocrystals. Effect of temperature is included implicitly in the model through perturbation of the substrate minority carrier concentration and Fermi level. Because a large number of variables affect these performance measures, in order to compare various designs, a figure of merit that measures the device performance in terms of design parameters is defined as a function of write/erase/discharge times which are calculated using the theoretical model. The effects of nanocrystal size and density, gate work function, substrate doping, control and tunnel dielectric properties and device geometry on the device performance are evaluated through the figure of merit. Experimental data showing agreement of the theoretical model with the measurement results are presented for devices that has PECVD grown germanium nanocrystals as the storage media.

The Predictor Role of the Aqueduct Cerebrospinal Fluid Flow on Endoscopic Third Ventriculostomy: Explication on Assumption Physical Model.

AIM: To evaluate the cerebrospinal fluid (CSF) flow dynamics in the aqueductus sylvii of patients with obstructive hydrocephalus who underwent endoscopic third ventriculostomy (ETV) and to predict ventriculostomy patency via aqueduct flow measurements. MATERIAL AND METHODS: Twenty-four patients with obstructive hydrocephalus caused by primary aqueduct stenosis who underwent ETV were included in the study. All the patients underwent conventional and cine magnetic resonance imaging before and after treatment. The flow of CSF in the aqueduct of Sylvius and prepontine cistern was assessed, and the diameter of the third ventricle was also measured. Increase in the aqueduct flow velocity after a successful ETV was supported by the assumption physical model that highlights a possible mechanism that explains the clinical findings. RESULTS: The flow pattern and velocity in the prepontine cistern and aqueduct were normal in 17 out of 24 patients who responded to ETV clinically. However, seven patients who did not respond to ETV had an abnormal flow pattern in both the prepontine cistern and aqueduct. CONCLUSION: The flow pattern in the aqueduct was normalised and velocity was increased compared with those of preoperative values after a successful ETV. The flow of CSF in the prepontine cistern is routinely used for ventriculostomy patency assessment. In addition, aqueduct measurements may be useful in predicting ventriculostomy patency. The physical model provides valuable insights on a possible mechanism that affected the experimental data.

Biocompatible Electroactive Tetra(aniline)-Conjugated Peptide Nanofibers for Neural Differentiation.

Peripheral nerve injuries cause devastating problems for the quality of patients' lives, and regeneration following damage to the peripheral nervous system is limited depending on the degree of the damage. Use of nanobiomaterials can provide therapeutic approaches for the treatment of peripheral nerve injuries. Electroactive biomaterials, in particular, can provide a promising cure for the regeneration of nerve defects. Here, a supramolecular electroactive nanosystem with tetra(aniline) (TA)-containing peptide nanofibers was developed and utilized for nerve regeneration. Self-assembled TA-conjugated peptide nanofibers demonstrated electroactive behavior. The electroactive self-assembled peptide nanofibers formed a well-defined three-dimensional nanofiber network mimicking the extracellular matrix of the neuronal cells. Neurite outgrowth was improved on the electroactive TA nanofiber gels. The neural differentiation of PC-12 cells was more advanced on electroactive peptide nanofiber gels, and these biomaterials are promising for further use in therapeutic neural regeneration applications.