Tailoring GaN Semiconductor Surfaces with Biomolecules

Effects of surface properties of GaN semiconductors on cell behavior

In recent years, semiconductors have aroused great interest in connecting, observing and influencing the behavior of biological elements, and it is possible to use semiconductor-cell compound interfaces to discover new signal transduction in the biological field. Among them, III-V nitride semiconductors, represented by gallium nitride (GaN), are used as substrates to form semiconductor-biology interfaces with cells, providing a platform for studying the effects of semiconductors on cell behavior. The interfaces between GaN substrate and cells play an important role in detecting and manipulating cell behaviors and provide a new opportunity for studying cell behavior and developing diagnostic systems. Hence, it is necessary to understand how the properties of the GaN substrate directly influence the behavior of biological tissues, and to create editable biological interfaces according to the needs. This paper reviews the synergism between GaN semiconductors and biological cells. The electrical properties, persistent photoconductivity (PPC), nanostructures, and chemical functionalization of GaN on the promotion of cell behaviors, such as growth, adhesion, differentiation, and signal transduction, are emphatically introduced. The purpose of this study is to provide guidance to explore the detection and regulation methods of cell behavior based on semiconductors and promote the application of them in the field of bioelectronics, such as biochips, biosensors, and implantable systems.

Tuning Microbial Activity via Programmatic Alteration of Cell/Substrate Interfaces

A wide portfolio of advanced programmable materials and structures has been developed for biological applications in the last two decades. Particularly, due to their unique properties, semiconducting materials have been utilized in areas of biocomputing, implantable electronics, and healthcare. As a new concept of such programmable material design, biointerfaces based on inorganic semiconducting materials as substrates introduce unconventional paths for bioinformatics and biosensing. In particular, understanding how the properties of a substrate can alter microbial biofilm behavior enables researchers to better characterize and thus create programmable biointerfaces with necessary characteristics on demand. Herein, the current status of advanced microorganism-inorganic biointerfaces is summarized along with types of responses that can be observed in such hybrid systems. This work identifies promising inorganic material types along with target microorganisms that will be critical for future research on programmable biointerfacial structures.

Hyperthermia treatment of cancer cells by the application of targeted silk/iron oxide composite spheres

Magnetic iron oxide nanoparticles (IONPs) are one of the most extensively studied materials for theranostic applications. IONPs can be used for magnetic resonance imaging (MRI), delivery of therapeutics, and hyperthermia treatment. Silk is a biocompatible material and can be used for biomedical applications. Previously, we produced spheres made of H2.1MS1 bioengineered silk that specifically carried a drug to the Her2-overexpressing cancer cells. To confer biocompatibility and targeting properties to IONPs, we blended these particles with bioengineered spider silks. Three bioengineered silks (MS1Fe1, MS1Fe2, and MS1Fe1Fe2) functionalized with the adhesion peptides F1 and F2, were constructed and investigated to form the composite spheres with IONPs carrying a positive or negative charge. Due to its highest IONP content, MS1Fe1 silk was used to produce spheres from the H2.1MS1:MS1Fe silk blend to obtain a carrier with cell-targeting properties. Composite H2.1MS1:MS1Fe1/IONP spheres made of silks blended at different ratios were obtained. Although the increased content of MS1Fe1 silk in particles resulted in an increased affinity of the spheres to IONPs, it decreased the binding of the composite particles to cancer cells. The H2.1MS1:MS1Fe1 particles prepared at a ratio of 8:2 and loaded with IONPs exhibited the ability to bind to the targeted cancer cells similar to the control spheres without IONPs. Moreover, when exposed to the alternating magnetic field, these particles generated 2.5 times higher heat. They caused an almost three times higher percentage of apoptosis in cancer cells than the control particles. The blending of silks enabled the generation of cancer-targeting spheres with a high affinity for iron oxide nanoparticles, which can be used for anti-cancer hyperthermia therapy.

Flexible perylenediimide/GaN organic-inorganic hybrid system with exciting optical and interfacial properties

We report the band gap tuning and facilitated charge transport at perylenediimide (PDI)/GaN interface in organic–inorganic hybrid nanostructure system over flexible titanium (Ti) foil. Energy levels of the materials perfectly align and facilitate high efficiency charge transfer from electron rich n-GaN to electron deficient PDI molecules. Proper interface formation resulted in band gap tuning as well as facilitated electron transport as evident in I–V characteristics. Growth of PDI/GaN hybrid system with band gap tuning from ultra-violet to visible region and excellent electrical properties open up new paradigm for fabrication of efficient optoelectronics devices on flexible substrates.

Exploration of M(100)-2×1 (M=Si, Ge) surface termination through hydrogen passivation using ethane and ammonia-borane derivatives: A theoretical approach

Termination process of Si(100)-2 × 1 as well as Ge(100)-2 × 1 reconstructed surfaces have been explored comprehensively through the dehydrogenation of ethane and ammonia-borane and their several analogues by employing density functional theory (DFT). From our study, it is evident that the termination of Si-surface via the dehydrogenation of aforementioned ethane and NH₃BH₃ derivatives is more feasible compared to Ge-surface. For ethane, the investigation shows that the substitution of non-participating hydrogens with +I group (electron donating) causes an enhancement in the kinetic and thermodynamic feasibility of the termination process, whereas the implementation of -I substituent (electron withdrawing) makes an adverse effect. While exploring the termination of Si- as well as Ge-surfaces through the dehydrogenation of NH₃BH₃ and its derivatives, it is noticed that from both the kinetic as well as thermodynamic perspectives, the termination processes are more feasible than that of ethane and its derivatives. We have further examined the detailed mechanism of each termination process by analyzing the geometrical parameters and NPA charges. From bonding evaluation, it is evident that the hydrogen abstraction from ethane by both the surfaces is symmetric in nature, where both the hydrogens show slightly positive charge. But for NH₃BH₃ the hydrogen abstraction process becomes asymmetric, where the boron associated hydrogen is abstracted as hydride by the electrophilic surface Si (Ge) and the hydrogen bonded with the N-centre is abstracted as proton by the nucleophilic surface Si (Ge). Overall, the present theoretical work reveals one of the efficient chemical processes for terminating Si as well as Ge(100)-2 × 1 reconstructed surfaces through the formation of non-polar SiH bonds.

Towards a comprehensive understanding of the Si(100)-2×1 surface termination through hydrogen passivation using methylamine and methanol: a theoretical approach

Using density functional theory, we explored the termination process of Si (100)-2 × 1 reconstructed surface mechanistically through the dehydrogenation of small molecules, considering methyl amine and methanol as terminating reagents. At first, both the terminating reagents form two types of adduct through adsorption on the Si (100)-2 × 1 surface, one in chemisorption mode and the other via physisorption, from which the dehydrogenation process is initiated. By analyzing the activation barriers, it was observed that termination of the Si-surface through the dehydrogenation is kinetically almost equally feasible using either reagent. We further examined in detail the mechanism for each termination process by analyzing geometrical parameters and natural population analysis charges. From bonding evaluation, it is evident that hydrogen abstraction from adsorbates on the Si-surface is asymmetric in nature, where one hydrogen is abstracted as hydride by the electrophilic surface Si and the other hydrogen is abstracted as proton by the neucleophilic surface Si. Moreover, it was also observed that hydride transfer from adsorbate to the Si-surface occurs first followed by proton transfer. Overall, our theoretical interpretation provides a mechanistic understanding of the Si (100)-2 × 1 reconstructed surface termination by amine and alcohol that will further motivate researchers to design different types of decorated semiconductor devices. Graphical Abstract Surface termination process of Si(100)-2×1 through formation of non-polar Si-H bonds via dehydrogenation of methylamine and methanol as terminating reagents.

Group III nitride nanomaterials for biosensing

Biosensing has found wide applications in biological and medical research, and in clinical diagnosis, environmental monitoring and other analytical tasks. Recognized as novel and outstanding transducing materials because of their superior and unique physical/chemical properties, group III nitride (III-nitride) nanomaterials have been introduced into biosensor development with remarkable advancements achieved in the past few decades. This paper presents the first comprehensive review on biosensor development with III-nitride nanomaterials. The review starts with the introduction of the material properties and biocompatibility of III-nitrides that are useful for biosensing. The focus is then placed on surface treatments of III-nitrides, which lay the foundation for biosensing, and on biosensing mechanisms where the exceptional properties of III-nitride nanomaterials lead to superior biosensing performance. From a practical point of view, techniques for biosensor fabrication are then summarized. Finally, existing biosensing applications and future directions are discussed.

Cell-Capture and Release Platform Based on Peptide-Aptamer-Modified Nanowires

Nanowires have attracted much attention due to their potential bioapplications, such as delivery of drugs or sensing devices. Here we report the development of a unique cell-capture and release platform based on nanowires. The combination of nanowires, surface-binding peptides, and cell-targeting aptamers leads to specific and efficient capture of cancer cells. Moreover, the binding processes are reversible, which is not only useful for downstream analysis but also for reusability of the substrate. Our work provides a new method in the design of the cell-capture and release platform, which may open up new opportunities of developing cell-separation and diagnosis systems based on cell-capture techniques.

Adsorption and adhesion of common serum proteins to nanotextured gallium nitride

As the broader effort towards device and material miniaturization progresses in all fields, it becomes increasingly important to understand the implications of working with functional structures that approach the size scale of molecules, particularly when considering biological systems. It is well known that thin films and nanostructures feature different optical, electrical, and mechanical properties from their bulk composites; however, interactions taking place at the interface between nanomaterials and their surroundings are less understood. Here, we explore interactions between common serum proteins - serum albumin, fibrinogen, and immunoglobulin G - and a nanotextured gallium nitride surface. Atomic force microscopy with a carboxyl-terminated colloid tip is used to probe the 'activity' of proteins adsorbed onto the surface, including both the accessibility of the terminal amine to the tip as well as the potential for protein extension. By evaluating the frequency of tip-protein interactions, we can establish differences in protein behaviour on the basis of both the surface roughness as well as morphology, providing an assessment of the role of surface texture in dictating protein-surface interactions. Unidirectional surface features - either the half-unit cell steppes of as-grown GaN or those produced by mechanical polishing - appear to promote protein accessibility, with a higher frequency of protein extension events taking place on these surfaces when compared with less ordered surface features. Development of a full understanding of the factors influencing surface-biomolecule interactions can pave the way for specific surface modification to tailor the bio-material interface, offering a new path for device optimization.

Identifying Affinity Classes of Inorganic Materials Binding Sequences via a Graph-Based Model

Rapid advances in bionanotechnology have recently generated growing interest in identifying peptides that bind to inorganic materials and classifying them based on their inorganic material affinities. However, there are some distinct characteristics of inorganic materials binding sequence data that limit the performance of many widely-used classification methods when applied to this problem. In this paper, we propose a novel framework to predict the affinity classes of peptide sequences with respect to an associated inorganic material. We first generate a large set of simulated peptide sequences based on an amino acid transition matrix tailored for the specific inorganic material. Then the probability of test sequences belonging to a specific affinity class is calculated by minimizing an objective function. In addition, the objective function is minimized through iterative propagation of probability estimates among sequences and sequence clusters. Results of computational experiments on two real inorganic material binding sequence data sets show that the proposed framework is highly effective for identifying the affinity classes of inorganic material binding sequences. Moreover, the experiments on the structural classification of proteins (SCOP) data set shows that the proposed framework is general and can be applied to traditional protein sequences.

Surface characterization of gallium nitride modified with peptides before and after exposure to ionizing radiation in solution

An aqueous surface modification of gallium nitride was employed to attach biomolecules to the surface. The modification was a simple two-step process using a single linker molecule and mild temperatures. The presence of the peptide on the surface was confirmed with X-ray photoelectron spectroscopy. Subsequently, the samples were placed in water baths and exposed to ionizing radiation to examine the effects of the radiation on the material in an environment similar to the body. Surface analysis confirmed degradation of the surface of GaN after radiation exposure in water; however, the peptide molecules successfully remained on the surface following exposure to ionizing radiation. We hypothesize that during radiation exposure of the samples, the radiolysis of water produces peroxide and other reactive species on the sample surface. Peroxide exposure promotes the formation of a more stable layer of gallium oxyhydroxide which passivates the surface better than other oxide species.

Adsorption sequence of multifunctional groups: a study on the reaction pathway and the adsorption structure of homocysteine on the Ge(100) surface

We investigated the adsorption mechanism of homocysteine (HS-CH2-CH2-CH(NH2)-COOH) on the Ge(100) surface along with its electronic structures and adsorption geometries to determine the sequence of adsorption of this amino acid's functional groups using core-level photoemission spectroscopy (CLPES) in conjunction with density functional theory (DFT) calculations. We found that the "SH-dissociated OH-dissociated N-dative-bonded structure" and the "SH-dissociated OH-dissociation-bonded structure" were preferred at a monolayer (ML) coverage of 0.30 (lower coverage) and 0.60 (higher coverage), respectively. The "SH-dissociated OH-dissociated N-dative-bonded structure" was the most stable structure. Moreover, we systematically confirmed the sequence of adsorption of the functional groups of the homocysteine molecule on the Ge(100) surface, which is thiol group (-SH), carboxyl group (-COOH), and amine group (-NH2).

Cell behavior on gallium nitride surfaces: peptide affinity attachment versus covalent functionalization

Gallium nitride is a wide band gap semiconductor that demonstrates a unique set of optical and electrical properties as well as aqueous stability and biocompatibility. This combination of properties makes gallium nitride a strong candidate for use in chemical and biological applications such as sensors and neural interfaces. Molecular modification can be used to enhance the functionality and properties of the gallium nitride surface. Here, gallium nitride surfaces were functionalized with a PC12 cell adhesion promoting peptide using covalent and affinity driven attachment methods. The covalent scheme proceeded by Grignard reaction and olefin metathesis while the affinity driven scheme utilized the recognition peptide isolated through phage display. This study shows that the method of attaching the adhesion peptide influences PC12 cell adhesion and differentiation as measured by cell density and morphological analysis. Covalent attachment promoted monolayer and dispersed cell adhesion while affinity driven attachment promoted multilayer cell agglomeration. Higher cell density was observed on surfaces modified using the recognition peptide. The results suggest that the covalent and affinity driven attachment methods are both suitable for promoting PC12 cell adhesion to the gallium nitride surface, though each method may be preferentially suited for distinct applications.

Direct grafting of long-lived luminescent indicator dyes to GaN light-emitting diodes for chemical microsensor development

Two new methods for covalent functionalization of GaN based on plasma activation of its surface are presented. Both of them allow attachment of sulfonated luminescent ruthenium(II) indicator dyes to the p- and n-type semiconductor as well as to the surface of nonencapsulated chips of GaN light-emitting diodes (blue LEDs). X-ray photoelectron spectroscopy analysis of the functionalized semiconductor confirms the formation of covalent bonds between the GaN surface and the dye. Confocal fluorescence microscopy with single-photon-timing (SPT) detection has been used for characterization of the functionalized surfaces and LED chips. While the ruthenium complex attached to p-GaN under an oxygen-free atmosphere gives significantly long mean emission lifetimes for the indicator dye (ca. 2000 ns), the n-GaN-functionalized surfaces display surprisingly low values (600 ns), suggesting the occurrence of a quenching process. A photoinduced electron injection from the dye to the semiconductor conduction band, followed by a fast back electron transfer, is proposed to be responsible for the excited ruthenium dye deactivation. This process invalidates the use of the n-GaN/dye system for sensing applications. However, for p-GaN/dye materials, the luminescence decay accelerates in the presence of O(2). The moderate sensitivity is attributed to the fact that only a monolayer of indicator dye is anchored to the semiconductor surface but serves as a demonstrator device. Moreover, the luminescence decays of the functionalized LED chip measured with excitation of either an external (laser) source or the underlying LED emission (from p-GaN/InGaN quantum wells) yield the same mean luminescence lifetime. These results pave the way for using advanced LEDs to develop integrateable optochemical microsensors for gas analysis.

Assembly kinetics of nanocrystals via peptide hybridization

The assembly kinetics of colloidal semiconductor quantum dots (QDs) on solid inorganic surfaces is of fundamental importance for implementation of their solid-state devices. Herein an inorganic binding peptide, silica binding QBP1, was utilized for the self-assembly of nanocrystal quantum dots on silica surface as a smart molecular linker. The QD binding kinetics was studied comparatively in three different cases: first, QD adsorption with no functionalization of substrate or QD surface; second, QD adsorption on QBP1-modified surface; and, finally, adsorption of QBP1-functionalized QD on silica surface. The surface modification of QDs with QBP1 enabled 79.3-fold enhancement in QD binding affinity, while modification of a silica surface with QBP1 led to only 3.3-fold enhancement. The fluorescence microscopy images also supported a coherent assembly with correspondingly increased binding affinity. Decoration of QDs with inorganic peptides was shown to increase the amount of surface-bound QDs dramatically compared to the conventional methods. These results offer new opportunities for the assembly of QDs on solid surfaces for future device applications.

Material binding peptides for nanotechnology

Remarkable progress has been made to date in the discovery of material binding peptides and their utilization in nanotechnology, which has brought new challenges and opportunities. Nowadays phage display is a versatile tool, important for the selection of ligands for proteins and peptides. This combinatorial approach has also been adapted over the past decade to select material-specific peptides. Screening and selection of such phage displayed material binding peptides has attracted great interest, in particular because of their use in nanotechnology. Phage display selected peptides are either synthesized independently or expressed on phage coat protein. Selected phage particles are subsequently utilized in the synthesis of nanoparticles, in the assembly of nanostructures on inorganic surfaces, and oriented protein immobilization as fusion partners of proteins. In this paper, we present an overview on the research conducted on this area. In this review we not only focus on the selection process, but also on molecular binding characterization and utilization of peptides as molecular linkers, molecular assemblers and material synthesizers.

Phage display: selecting straws instead of a needle from a haystack

An increasing number of peptides with specific binding affinity to various protein and even non-protein targets are being discovered from phage display libraries. The power of this method lies in its ability to efficiently and rapidly identify ligands with a desired target property from a large population of phage clones displaying diverse surface peptides. However, the search for the needle in the haystack does not always end successfully. False positive results may appear. Thus instead of specific binders phage with no actual affinity toward the target are recovered due to their propagation advantages or binding to other components of the screening system, such as the solid phase, capturing reagents, contaminants in the target sample or blocking agents, rather than the target. Biopanning experiments on different targets performed in our laboratory revealed some previously identified and many new target-unrelated peptide sequences, which have already been frequently described and published, but not yet recognized as target-unrelated. Distinguishing true binders from false positives is an important step toward phage display selections of greater integrity. This article thoroughly reviews and discusses already identified and new target-unrelated peptides and suggests strategies to avoid their isolation.

Sensing by means of nonlinear optics with functionalized GaAs/AlGaAs photonic crystals

We report on specific functionalization of GaAs/AlGaAs photonic structures for molecular sensing via the optical second harmonic generation signal in the visible range exhibited by these nanostructures. Functionalization has been achieved by peptides selected by the phage display technology, revealing specific recognition for semiconducting surfaces. These small peptides when biotinylated serve for controlled placement of biotin onto the substrate to capture then streptavidin. Functionalization (with biotinylated peptide) and molecular recognition (of streptavidin) events both result in enhancing the nonlinear optical response of the samples. Adsorption and infiltration of biomolecules into the GaAs/AlGaAs photonic structure were monitored by atomic force and scanning electron microscopy combined with Energy Dispersive X-ray spectroscopy. We demonstrate that once functionalized with specific peptides, photonic structures could be used as miniature biosensors down to femtomolar detection sensitivity, by monitoring changes in the second harmonic signal when molecules are captured. Our results prove the outstanding sensitivity of the nonlinear approach in biosensing with photonic crystal waveguides as compared to linear absorption techniques on the same samples. The present work is expected to pioneer development of a new class of extremely small affinity-based biosensors with high sensitivity and demonstrates that photonic structures support device functionality that includes strongly confined and localized nonlinear radiation emission and detection processes.

Selection and mass spectrometry characterization of peptides targeting semiconductor surfaces

We report on elaboration of 12-mer peptides that reveal specific recognition for the following semiconductor (SC) surfaces: GaAs(100), InAs(100), GaN(0001), ZnSe(100), ZnTe(100), GaAs(111)A, GaSb(100), CdSe(100). A M13 bacteriophage library was used to screen 10(9) different 12-mer peptides against these substrates to finally isolate, in maximum six amplification cycles, peptides that bind to the target surfaces. The specific peptides for the InAs and ZnSe surfaces were obtained. Contrary, for the other SC surfaces several peptides with high affinities have been isolated. Aiming for a better specificity, when the phage display has been conducted through six cycles, the screening procedure got dominated by a phage present in the M13 bacteriophage library and the SVSVGMKPSPRP peptide has been selected for different SCs. The high amplification potential of this phage has been observed previously with different targets. Thus, precaution should be undertaken in defining adhesion peptides with the phage display technique and real affinity of the obtained biolinkers should be studied with other methods. We employed mass spectrometry (MALDI-TOF/TOF) to demonstrate the preferential attachment (or not) of the SVSVGMKPSPRP peptide to the different SC surfaces. This allows us to define a realistic selection of the expressed peptides presenting affinity for the studied eight SC surfaces. We demonstrate that with increasing the dielectric constants of the employed solvents, adhesion of the SVSVGMKPSPRP peptide onto GaN(0001) is hindered.

Coverage dependence of the adsorption structure of alanine on Ge(100)

The variations with coverage and annealing temperature in the adsorption structure of alanine on Ge(100) have been investigated using high-resolution core-level photoemission spectroscopy (HRCLPES). The C 1s, N 1s, and O 1s core-level spectra at a low initial coverage show that both the carboxyl and amine groups of the alanine molecules participate in bonding with the Ge(100) surface in an "intrarow O-H dissociated and N dative bonded structure". However, at higher coverage we found that in addition to this structure an "O-H dissociation structure" is present. Moreover, we systematically monitored the variation of the bonding features of alanine adsorbed on Ge(100) with annealing temperature and thus were able to track the desorption processes. By analyzing the C 1s, N 1s, and O 1s spectra at 420 K, we conclude that the principal adsorption structure at this temperature is the "O-H dissociation structure" because of the disconnection of Ge-N dative bonding. At higher temperatures, the "O-H dissociation structure" is converted into various fragments such as Ge oxide (or Ge-CO), Ge nitride (Ge cyanide), and Ge carbide.

Intrarow adsorption structure of glycine on Ge(100)

The adsorption structure of glycine on Ge(100) was investigated using scanning tunneling microscopy (STM), density functional theory (DFT) calculations, and high-resolution core-level photoemission spectroscopy (HRCLPES). We found a major adsorption feature of glycine on Ge(100) in the STM images. This feature appeared as a bright protrusion between two dimer rows with a dark adjacent dimer. The position of the bright protrusion located in the middle of the two dimer rows indicates a multibonding adsorption structure. The results of the theoretical calculations confirm that the adsorption structure of glycine on Ge(100) (between two possible multibonding adsorption structures) is an "intrarow O-H dissociated and N dative bonded structure". In the HRCLPES experiments, we found an N 1s peak (at 399.5 eV) and two O 1s peaks (at 531.1 and 532.0 eV), which represent strong evidence that the adsorption configuration of glycine on Ge(100) is composed of both O-H dissociation and N dative bonding. All our STM, DFT, and HRCLPES results suggest that the adsorption structure of glycine molecules on Ge(100) is an "intrarow O-H dissociated and N dative bonded structure".