PSI Structures Research Articles

Carbon-stabilized porous silicon biosensor for the ultrasensitive label-free electrochemical detection of bacterial RNA gene fragments

Herein, we report a carbon-stabilized porous silicon (pSi)-based electrochemical biosensing platform for the label- and amplification-free detection of bacterial 16S rRNA gene fragments that facilitates pan-bacterial detection. The sensing approach combines thermally carbonized pSi (THCpSi) structures as novel porous electrochemical transducers, and a highly sensitive sensing mechanism based on partial blockage of the pores caused by hybridization of 16S rRNA gene fragment to the DNA capture probe immobilized within the pores. Pore blockage upon RNA hybridization was quantified via differential pulse voltammetry as a decrease in the oxidation current of the redox pair ([Fe(CN)6]3/4−) added to the measuring solution. The use of carbon-stabilized pSi to build the biosensor has additional benefits: it favors high density of the immobilized bioreceptors and a large electroactive surface area, both further enhancing the overall sensitivity of the biosensor. The easily adjustable pSi morphology is key to design diagnostic tools fit-for-purpose. By tailoring the pore diameter, pore blockage upon analyte hybridization can be maximized, thus enhancing sensitivity. By tailoring film thickness, the surface area can be adjusted to optimize the amount of immobilized bioreceptors and the electroactive surface area. An excellent sensing performance was achieved by building the biosensor on THCpSi structures featuring a 27 nm pore diameter and a 1.6 μm film thickness, whose external surface was coated with a thin layer of silicon nitride (Si3N4), the latter contributing to maximize the pore blockage. The biosensor achieved a limit of detection of 2.3 pM when tested in 5% fetal bovine serum.

Reduction kinetics of porous silicon synthesis for lithium battery anodes

Porous silicon (pSi) microparticles can be favorably employed as the high-capacity and stable anode materials in all formats of lithium-based batteries. Magnesiothermic reduction reaction (MRR) of low-cost silica produces pSi structures at relatively low temperatures; however, yield and reduction selectivity are currently limited. Herein, we conduct MRR kinetic studies using the Ginstling–Brounstein (GB) and Jander diffusion models under dynamic (via reactor rotation) and static conditions (D-MRR and S-MRR, respectively) at various reduction temperatures and times. The reduction rate and nominal kinetic constants for the d-MRR are found to be more than three times greater than those for the S-MRR, possibly because of the enhanced mass transfer rate in the d-MRR. d-MRR results in superior precursor conversion and pSi yield than S-MRR. The apparent activation energy for d-MRR is approximately 180 kJ mol–1 by GB model. The pSi microparticles are mesoporous (pore size = 23.7 nm, pore volume = 0.30 cm3 g–1) and comprise interconnected primary silicon nanoparticles (SiNPs) (diameter = 30 nm). Therefore, a pSi/C composite anode demonstrates significantly enhanced cycling stability compared with conventional solid SiNP/C composites. Overall, d-MRR is a highly efficient and scalable production process for pSi microparticles for use in high-capacity anodes for advanced lithium-based batteries.

Wafer-Scale Fabrication and Transfer of Porous Silicon Films as Flexible Nanomaterials for Sensing Application.

Flexible sensors are highly advantageous for integration in portable and wearable devices. In this work, we propose and validate a simple strategy to achieve whole wafer-size flexible SERS substrate via a one-step metal-assisted chemical etching (MACE). A pre-patterning Si wafer allows for PSi structures to form in tens of microns areas, and thus enables easy detachment of PSi film pieces from bulk Si substrates. The morphology, porosity, and pore size of PS films can be precisely controlled by varying the etchant concentration, which shows obvious effects on film integrity and wettability. The cracks and self-peeling of Psi films can be achieved by the drying conditions after MACE, enabling transfer of Psi films from Si wafer to any substrates, while maintaining their original properties and vertical alignment. After coating with a thin layer of silver (Ag), the rigid and flexible PSi films before and after transfer both show obvious surface-enhanced Raman scattering (SERS) effect. Moreover, flexible PSi films SERS substrates have been demonstrated with high sensitivity (down to 2.6 × 10−9 g/cm2) for detection of methyl parathion (MPT) residues on a curved apple surface. Such a method provides us with quick and high throughput fabrication of nanostructured materials for sensing, catalysis, and electro-optical applications.

High-conversion reduction synthesis of porous silicon for advanced lithium battery anodes

For practical implementation of high-capacity silicon anodes, porous silicon (pSi) structures have demonstrated outstanding cycling stability against the large volume changes typical of solid silicon particles. The conventional magnesiothermic reduction (MR) of silica under static conditions limits the yield of pSi and sometimes produces low-purity of pSi owing to limited mass transfer and many side reactions. Hence, we devise a rotational MR (R-MR) system with rapid magnesium transport in which a uniform Mg/SiO2 molar ratio is readily achievable, and a short reaction time can be applied. Compared to conventional MR, the R-MR process has an extremely high yield (∼90 wt%) of pSi at almost complete conversion of precursor, whereas side reactions are substantially suppressed. Mg 2p X-ray photoelectron spectroscopy analysis of the reduction product reveals that pSi yield is well correlated with the conversion of Mg to MgO. The carbon-coated pSi/C samples and their hybrids with graphite (pSi/C@Gr) composites demonstrate stable cycling performance for 300−600 cycles at high capacity with high cycling efficiency (∼99.9%). Therefore, high-conversion R-MR can be a very efficient and scalable process for obtaining pSi for use in carbon composites (such as pSi/C and pSi/C@Gr) that offer outstanding cycling performance in high-capacity anodes for high-energy LIBs.

PSI of the Colonial Alga Botryococcus braunii Has an Unusually Large Antenna Size.

PSI is an essential component of the photosynthetic apparatus of oxygenic photosynthesis. While most of its subunits are conserved, recent data have shown that the arrangement of the light-harvesting complexes I (LHCIs) differs substantially in different organisms. Here we studied the PSI-LHCI supercomplex of Botryococccus braunii, a colonial green alga with potential for lipid and sugar production, using functional analysis and single-particle electron microscopy of the isolated PSI-LHCI supercomplexes complemented by time-resolved fluorescence spectroscopy in vivo. We established that the largest purified PSI-LHCI supercomplex contains 10 LHCIs (∼240 chlorophylls). However, electron microscopy showed heterogeneity in the particles and a total of 13 unique binding sites for the LHCIs around the PSI core. Time-resolved fluorescence spectroscopy indicated that the PSI antenna size in vivo is even larger than that of the purified complex. Based on the comparison of the known PSI structures, we propose that PSI in B. braunii can bind LHCIs at all known positions surrounding the core. This organization maximizes the antenna size while maintaining fast excitation energy transfer, and thus high trapping efficiency, within the complex.

Designing A Zener Diode Using Ag2O(1-X)Zno(X)/Psi Structures Deposited by Laser Induced Plasma Technique

In this paper Zener diode was designed by mixing three mixing ratios of Ag2O(1-x)ZnO(x), where x is 0.5, 0.3, and 0.1, that are deposited on a p-type porous silicon using laser induced plasma technique at room temperature (RT). The results of the Zener diode showed a decrease in knee and Zener voltage when the mixing ratio of Ag2O(1-x)ZnO(x) structure was increased. Nanofilms of 200nm thickness were prepared from pure ZnO and Ag2O as well as Ag2O(1-x)ZnO(x) with three maxing ratios and deposited on glass slides at RT to analyze the structure and optical properties. The structures of Ag2O and Ag2O(1-x)ZnO(x) showed high absorbance in the visible region with redshift in spectra when the mixing ratio was increased, while ZnO had a high absorbance in the ultraviolet region. It is concluded that when the value of x increases the energy gap value for the Ag2O(1-x)ZnO(x) structure decreases.

Performance Evaluation of Crack-Like ZnO/PSi Nanostructure Chemical Solution Sensor via Electrochemical Impedance Technique

Electrochemical impedance spectroscopy (EIS) has been broadly used to investigate a variety of other electrochemical systems, including electrodeposition, corrosion, fuel cells and batteries. Here, a new approach to characterize chemical sensors based on the ZnO/porous Si (PSi) nanostructure arrays via an EIS technique is reported. ZnO nanostructures were successfully synthesized on the PSi structures using the free-catalytic thermal immersion method. Detailed characterization of this nanostructure was carried out by atomic force microscopy, field emission scanning electron microscopy and EIS. EIS analysis was used for two classified groups; polar and non-polar solvents. The performance evaluation of ZnO/PSi nanostructure sensors showed rapid and high response compared to a PSi nanostructure that may attribute to the regular morphology and suitable thickness for sensing.

Porous Silicon Nanostructures as Effective Faradaic Electrochemical Sensing Platforms

AbstractThe electrochemical performance of porous silicon (pSi) stabilized via thermal decomposition of acetylene gas is investigated for the first time. In this study, pSi undergoes two thermal treatments at either 525 or 800 °C, which result in hydrogen‐terminated thermally hydrocarbonized pSi (THCpSi) and hydroxyl‐terminated thermally carbonized pSi (TCpSi), respectively, the latter upon dipping in hydrofluoric acid to activate the surface termination. Electrochemical characterization, using cyclic voltammetry, chronocoulometry, and electrochemical impedance spectroscopy in the presence of several redox pairs, [Fe(CN)6]3/4−, [Ru(NH3)6]2/3+, and hydroquinone/quinone, is used to demonstrate the versatility and high stability to degradation of carbon‐stabilized pSi nanostructures and their excellent electrochemical performance. Added to the large surface area, adjustable pore morphology and tailorable surface chemistry of THCpSi and TCpSi, these nanostructures demonstrate fast electron‐transfer kinetics, providing key advantages over conventional carbon electrodes. The versatile surface chemistry of THCpSi and TCpSi offer various possibilities to introduce multiple functional groups depending on the nature of the bioreceptor to be immobilized. For proof of principle, the use of a THCpSi‐based immunosensor to detect MS2 bacteriophage is demonstrated by means of electrochemical impedance spectroscopy, showing a detection limit of 4.9 pfu mL−1. Carbon‐stabilized pSi structures represent a new class of nanostructured electrodes for biosensing applications.

Recent Advances in Porous Silicon Based Optical Biosensors

Abstract PSi structures have unique physical and optical properties, which are being exploited for a numerous biomedical applications including biosensing, bioimaging, tissue engineering, and drug delivery. Different PSi optical structures can be fabricated to improve the sensitivity of the optical measurements. A very high surface area per volume of PSi can be used for the higher loading of target analytes in a small sensor area, which helps in increasing sensitivity and allows the miniaturization of biosensor. The specificity of PSi biosensor to the target analyte can be inferred by immobilizing the corresponding bioreceptor such as DNA, enzyme, or antibody via different conjugation chemistries. Finally, PSi is biocompatible material that offers additional advantage in comparison to other sensing platforms for in vivo implantable biosensing applications. This paper reviews fabrication, surface modification, biofunctionalization, and optical biosensing applications of PSi structures with special emphasis on in vivo and PSi photonic particles biosensing.

Porous Silicon Nanostructured Materials for Sensing Applications: Molecular Assembling and Electrochemical or Optical Evaluation

ABSTRACTPorous silicon (PSi) combines the potential of miniaturization with a very large surface area. The PSi surface can be chemically modified resulting in a high sensitivity (low detection threshold) device for chemical and biomolecular sensing. In previous work, we have shown that redox proteins and fluorescent ligands can be infiltrated into PSi (PSiMc) structures. The hybrid devices have shown interesting new properties produced by the coupling of the individual properties of PSi nanostructures and the modifiers. In this work, we have obtained a PSiMc/redox protein bioelectrode, which presents a quasi-reversible electrochemical response. This effect was attributed to the semiconducting nature of the PSi substrate and to the functional groups of the crosslinking molecules (MPTS), which together produce a capacitive effect on the device. On the other hand, the chemical modification of PSiMc with fluorescent ligands allowed us to fabricate fluorescent PSi hybrid nanostructures, which were tested for the detection of environmental pollutants such as heavy metals (specifically Hg2+). We found that the selectivity of this optical device depends on the selected recognizing molecule. The captured metal induces the formation of a metallic complex that shows higher fluorescence compared with the sensor device. These results demonstrate the viability of using porous silicon as optical sensors and electrochemical biosensors. The infiltration of fluorescent recognizing molecules and proteins into the PSi matrix were evaluated by specular reflectance, FTIR spectroscopy, fluorescence spectroscopy and cyclic voltammetry.

TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures.

The NIH Protein Structure Initiative centers, such as the Joint Center for Structural Genomics (JCSG), have developed highly efficient technological platforms that are capable of experimentally determining the three-dimensional structures of hundreds of proteins per year. However, the overwhelming majority of the almost 5000 protein structures determined by these centers have yet to be described in the peer-reviewed literature. In a high-throughput structural genomics environment, the process of structure determination occurs independently of any associated experimental characterization of function, which creates a challenge for the annotation and analysis of structures and the publication of these results. This challenge has been addressed by developing TOPSAN (`The Open Protein Structure Annotation Network'), which enables the generation of knowledge via collaborations among globally distributed contributors supported by automated amalgamation of available information. TOPSAN currently provides annotations for all protein structures determined by the JCSG in addition to preliminary annotations on a large number of structures from the other PSI production centers. TOPSAN-enabled collaborations have resulted in insightful structure-function analysis for many proteins and have led to numerous peer-reviewed publications, as exemplified by the articles included in this issue of Acta Crystallographica Section F.

In vivo evaluation of safety of nanoporous silicon carriers following single and multiple dose intravenous administrations in mice

Porous silicon (pSi) is being extensively studied as an emerging material for use in biomedical applications, including drug delivery, based on the biodegradability and versatile chemical and biophysical properties. We have recently introduced multistage nanoporous silicon microparticles (S1MP) designed as a cargo for nanocarrier drug delivery to enable the loaded therapeutics and diagnostics to sequentially overcome the biological barriers in order to reach their target. In this first report on biocompatibility of intravenously administered pSi structures, we examined the tolerability of negatively (−32.5 ± 3.1 mV) and positively (8.7 ± 2.5 mV) charged S1MP in acute single dose (10 7, 10 8, 5 × 10 8 S1MP/animal) and subchronic multiple dose (10 8 S1MP/animal/week for 4 weeks) administration schedules. Our data demonstrate that S1MP did not change plasma levels of renal (BUN and creatinine) and hepatic (LDH) biomarkers as well as 23 plasma cytokines. LDH plasma levels of 145.2 ± 23.6, 115.4 ± 29.1 vs. 127.0 ± 10.4; and 155.8 ± 38.4, 135.5 ± 52.3 vs. 178.4 ± 74.6 were detected in mice treated with 10 8 negatively charged S1MP, 10 8 positively charged S1MP vs. saline control in single and multiple dose schedules, respectively. The S1MPs did not alter LDH levels in liver and spleen, nor lead to infiltration of leukocytes into the liver, spleen, kidney, lung, brain, heart, and thyroid. Collectively, these data provide evidence of a safe intravenous administration of S1MPs as a drug delivery carrier.

Ligands in PSI structures

Approximately 65% of PSI structures report some type of ligand(s) that is bound in the crystal structure. Here, a description is given of how such ligands are handled and analyzed at the JCSG and a survey of the types, variety and frequency of ligands that are observed in the PSI structures is also compiled and analyzed, including illustrations of how these bound ligands have provided functional clues for annotation of proteins with little or no previous experimental characterization. Furthermore, a web server was developed as a tool to mine and analyze the PSI structures for bound ligands and other identifying features.

Detection and light enhancement of glucose oxidase adsorbed on porous silicon microcavities

AbstractPorous silicon (PSi) structure is used as support material to detect protein infiltration and to induce fluorescence and second harmonic light enhancement from glucose oxidase (GOX). Functionalization and protein infiltration is monitored by specular reflectometry. Optical response enhancement of PSi microcavity structures compared to PSi single layers or Bragg mirrors is observed, when GOX is impregnated. Penetration of organic molecules along the PSi microcavity structure is demonstrated by energy dispersive X‐ray profile. Enhanced fluorescence emission of GOX when adsorbed on PSi microcavity is evidenced by multi‐photon microscopy (MPM). Second harmonic light generation is observed at some particular pores of PSi and subsequent resonance enhancement of the signal arising from the GOX adsorbed within the pores is detected. Our work evidences an improved device functionality of GOX‐PSi microcavities due to strongly confined and localized light emission within these structures. This opens the way towards the application of PSi microcavity structures as amended biosensors based on their locally enhanced optical response. The second main achievement lies in the novelty of the used techniques. In contrast to the specular reflectometry used to monitor the macroscopic optical response of PSi structures, MPM presents a valuable alternative microscopic technique probing individual pores. (© 2009 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)

Assessing functional novelty of PSI structures via structure-function analysis of large and diverse superfamilies

AbstractThe structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing representative structures for many structurally uncharacterised protein families. As suggested by the recent assessment of the Protein Structure Initiative (Structural Genomics Initiative, funded by the NIH), doubts have arisen as to whether Structural Genomics as initially planned were really beneficial to our understanding of biological issues, and in particular of protein function.A few protein domain superfamilies have been shown to account for unexpectedly large numbers of proteins encoded in fully sequenced genomes. These large superfamilies are generally very diverse, spanning a wide range of functions, both in terms of molecular activities and biological processes. Some of these superfamilies, such as the Rossmann-fold P-loop nucleotide hydrolases or the TIM-barrel glycosidases, have been the subject of extensive structural studies which in turn have shed light on how evolution of the sequence and structure properties produce functional diversity amongst homologues. Recently, the Structure-Function Linkage Database (SFLD) has been setup with the aim of helping the study of structure-function correlations in such superfamilies. Since the evolutionary success of these large superfamilies suggests biological importance, several Structural Genomics Centers have focused on providing full structural coverage for representatives of all sequence families in these superfamilies.In this work we evaluate structure/function diversity in a set of these large superfamilies and attempt to assess the quality and quantity of biological information gained from Structural Genomics.

Assessing functional novelty of PSI structures via structure-function analysis of large and diverse superfamilies

The structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing representative structures for many structurally uncharacterised protein families. As suggested by the recent assessment of the Protein Structure Initiative (Structural Genomics Initiative, funded by the NIH), doubts have arisen as to whether Structural Genomics as initially planned were really beneficial to our understanding of biological issues, and in particular of protein function.A few protein domain superfamilies have been shown to account for unexpectedly large numbers of proteins encoded in fully sequenced genomes. These large superfamilies are generally very diverse, spanning a wide range of functions, both in terms of molecular activities and biological processes. Some of these superfamilies, such as the Rossmann-fold P-loop nucleotide hydrolases or the TIM-barrel glycosidases, have been the subject of extensive structural studies which in turn have shed light on how evolution of the sequence and structure properties produce functional diversity amongst homologues. Recently, the Structure-Function Linkage Database (SFLD) has been setup with the aim of helping the study of structure-function correlations in such superfamilies. Since the evolutionary success of these large superfamilies suggests biological importance, several Structural Genomics Centers have focused on providing full structural coverage for representatives of all sequence families in these superfamilies.In this work we evaluate structure/function diversity in a set of these large superfamilies and attempt to assess the quality and quantity of biological information gained from Structural Genomics.

Functionalization of nanostructured porous silicon microcavities for glucose oxidase detection

Abstract Stable porous silicon microcavities (PSiMcs) are designed in order to detect the confined glucose oxidase (GOX) at low concentration. A chemical pathway is proposed to functionalize and stabilize porous silicon structures that are primordial for further effective molecular confinement. The procedure avoids the preliminary thermal oxidation of the PSi surface and consists of a direct surface oxidation during the silanization process, an amino activation by a linker that also prevents further oxidation, and the binding of the GOX enzyme. Functionalization and protein confinement are monitored by the narrow resonance peaks in the near-infrared region (700–1000 nm) of the engineered meso- and macroporous microcavities. Protein penetration along the entire, large pore sized structure is demonstrated. The protein retains its native form within the properly functionalized PSi structures, which are ideal for molecular sensing also due to their high quality factor. A detection resolution of 25 nM GOX has been determined, thus demonstrating the high quality sensing of our functionalized porous silicon microcavity structures.

Some Ill Considered Comments on the Protein Structure Initiative

Some Ill Considered Comments on the Protein Structure Initiative

Nano crystalline porous silicon as large-area electrode for electrochemical synthesis of polypyrrole

Polypyrrole (pPy) films were electrochemically synthesized over the surface of nano-crystalline porous silicon (pSi), platinum (Pt) and polished silicon (Si) substrates. As evidenced by the SEM pictures and the potential time-transient characteristics the polymerized growth is relatively porous, smooth and faster over pSi substrates in comparison to the Pt and polished Si surfaces. The polymerization charge on pSi substrate is significantly enhanced and the high accessible surface area of nano-pSi/pPy structure resulted in an improved redox performance of pPy. Impedance study revealed no change in the diffusion control process for pSi/pPy and Pt/pPy electrodes whereas an increase in Faradaic resistance for pSi/pPy electrode is noticed. Redox properties of pPy on n- and p-type pSi structures were studied using cyclic voltametry and electrochemical impedance spectroscopy. FESEM was used to study the surface morphology and to further compliment the electrochemical performance of the electrode.

A novel approach for the preparation of acrylate–siloxane particles with core–shell structure

AbstractIt is well known that polysiloxane has excellent properties, such as water repellency, low surface energy, biocompatibility, etc. Its application, however, is subject to some limit due to poor cohesiveness and poor film‐forming properties. Recently, many efforts have been made to overcome such flaws. It is found that polyacrylate is in common consideration for its good cohesiveness and excellent film‐forming properties. This is why there have been so many descriptions of core–shell PSi–PA (PSi, polysiloxane as core; PA, polyacrylate as shell) particles in the literature. Unfortunately, their hydrophobicity is considerably different; therefore, the reversed morphological PA–PSi particles are scarcely available. In the work reported here, core‐shell PA–PSi structures with poly(butyl methacrylate) (PA) as the core and PSi as the shell were successfully prepared by dispersion polymerization. Characterization of the PA–PSi particles was carried out using transmission electron microscopy, particle size analysis, X‐ray photoelectron spectroscopy and static contact angle measurements. Copyright © 2006 Society of Chemical Industry