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Academic literature on the topic 'DNA Sensing Element'

Author: Grafiati
Published: 6 September 2023

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Journal articles on the topic "DNA Sensing Element"

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Williams, Ryan M., Amanda R. Kulick, Srilakshmi Yedlapalli, Louisa Battistella, Cyrus J. Hajiran, and Letha J. Sooter. "In VitroSelection of a Single-Stranded DNA Molecular Recognition Element Specific for Bromacil." Journal of Nucleic Acids 2014 (2014): 1–8. http://dx.doi.org/10.1155/2014/102968.

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Bromacil is a widely used herbicide that is known to contaminate environmental systems. Due to the hazards it presents and inefficient detection methods, it is necessary to create a rapid and efficient sensing device. Towards this end, we have utilized a stringentin vitroselection method to identify single-stranded DNA molecular recognition elements (MRE) specific for bromacil. We have identified one MRE with high affinity (Kd=9.6 nM) and specificity for bromacil compared to negative targets of selection and other pesticides. The selected ssDNA MRE will be useful as the sensing element in a field-deployable bromacil detection device.
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Bowman, Teresa V., and Eirini Trompouki. "Sensing Stemness." Current Stem Cell Reports 7, no. 4 (October 6, 2021): 219–28. http://dx.doi.org/10.1007/s40778-021-00201-w.

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Abstract Purpose of Review Hematopoietic stem cells (HSCs) are formed embryonically during a dynamic developmental process and later reside in adult hematopoietic organs in a quiescent state. In response to their changing environment, HSCs have evolved diverse mechanisms to cope with intrinsic and extrinsic challenges. This review intends to discuss how HSCs and other stem cells co-opted DNA and RNA innate immune pathways to fine-tune developmental processes. Recent Findings Innate immune receptors for nucleic acids like the RIG-I-like family receptors and members of DNA sensing pathways are expressed in HSCs and other stem cells. Even though the “classic” role of these receptors is recognition of foreign DNA or RNA from pathogens, it was recently shown that cellular transposable element (TE) RNA or R-loops activate such receptors, serving as endogenous triggers of inflammatory signaling that can shape HSC formation during development and regeneration. Summary Endogenous TEs and R-loops activate RNA and DNA sensors, which trigger distinct inflammatory signals to fine-tune stem cell decisions. This phenomenon could have broad implications for diverse somatic stem cells, for a variety of diseases and during aging.
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Booth, Marsilea Adela, Sally Ann Harbison, and Jadranka Travas-Sejdic. "Developing Polypyrrole-Based Oligonucleotide Biosensors." Materials Science Forum 700 (September 2011): 215–18. http://dx.doi.org/10.4028/www.scientific.net/msf.700.215.

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Many medical, forensic science, environmental and general scientific difficulties may be aided by the existence of suitable biosensors such as gene sensors, body fluid detection DNA sensors, disease detection DNA sensors etc. The sensor technology described here uses the conducting polymer polypyrrole (PPy) as both sensing element and transducer of sensing events. Stability and reproducibility are necessary characteristics of practical biosensors. The stability of polymers can be investigated using electrical impedance spectroscopy (EIS). This work discusses research focused towards creating a stable, reproducible sensor surface for oligonucleotide detection. The effect of electropolymerisation conditions (electropolymerisation method, solvent and electrolyte used), post-growth treatment (cycling and EIS experiments), and the sensing-environment conditions on sensor stability and applicability will be discussed.
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Cao, Zhong, Zhong Liang Xiao, Yun Lin Dai, Masao Kamahori, and Maki Shimoda. "Electrical Characteristics of Extended Gate FET Sensing Chip Constructed for Detection of DNA." Advanced Materials Research 97-101 (March 2010): 4189–92. http://dx.doi.org/10.4028/www.scientific.net/amr.97-101.4189.

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An extended gate field effect transistor (EGFET) sensing chip has been constructed by using one gold plate electrode for molecule recognition and FET part for signal transduction. By using a 70.7mV DC voltage onto a Ag/AgCl reference electrode, the electrical characteristics of immobilization of the oligonucleotide probe of P1 and hybridization with the target single strand DNA of P2 on the EGFET sensing chip were examined in detail. The electrical signals on the change of a threshold voltage (VT) shift at a constant ID (3000μA) in VG-ID characteristic were obtained, and the VT shift value due to hybridization was calculated to be 12 mV, which may be attributed to the decreased negative charges after hybridization occurred at the gate surface. The surface density of hybridized dsDNA on gold surface of the FET was evaluated to be about 1 × 1012 molecules/cm2, indicating that the EGFET was a promising sensing element for biochip.
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Balaji, Aditya, Songlin Yang, Jeslyn Wang, and Jin Zhang. "Graphene Oxide-Based Nanostructured DNA Sensor." Biosensors 9, no. 2 (May 30, 2019): 74. http://dx.doi.org/10.3390/bios9020074.

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Quick detection of DNA sequence is vital for many fields, especially, early-stage diagnosis. Here, we develop a graphene oxide-based fluorescence quenching sensor to quickly and accurately detect small amounts of a single strand of DNA. In this paper, fluorescent magnetic nanoparticles (FMNPs) modified with target DNA sequence (DNA-t) were bound onto the modified graphene oxide acting as the fluorescence quenching element. FMNPs are made of iron oxide (Fe3O4) core and fluorescent silica (SiO2) shell. The average particle size of FMNPs was 74 ± 6 nm and the average thickness of the silica shell, estimated from TEM results, was 30 ± 4 nm. The photoluminescence and magnetic properties of FMNPs have been investigated. Target oligonucleotide (DNA-t) was conjugated onto FMNPs through glutaraldehyde crosslinking. Meanwhile, graphene oxide (GO) nanosheets were produced by a modified Hummers method. A complementary oligonucleotide (DNA-c) was designed to interact with GO. In the presence of GO-modified with DNA-c, the fluorescence intensity of FMNPs modified with DNA-t was quenched through a FRET quenching mechanism. Our study indicates that FMNPs can not only act as a FRET donor, but also enhance the sensor accuracy by magnetically separating the sensing system from free DNA and non-hybridized GO. Results indicate that this sensing system is ideal to detect small amounts of DNA-t with limitation detection at 0.12 µM.
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Ida, Jeunice, Soo Chan, Jörn Glökler, Yee Lim, Yee Choong, and Theam Lim. "G-Quadruplexes as An Alternative Recognition Element in Disease-Related Target Sensing." Molecules 24, no. 6 (March 19, 2019): 1079. http://dx.doi.org/10.3390/molecules24061079.

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G-quadruplexes are made up of guanine-rich RNA and DNA sequences capable of forming noncanonical nucleic acid secondary structures. The base-specific sterical configuration of G-quadruplexes allows the stacked G-tetrads to bind certain planar molecules like hemin (iron (III)-protoporphyrin IX) to regulate enzymatic-like functions such as peroxidase-mimicking activity, hence the use of the term DNAzyme/RNAzyme. This ability has been widely touted as a suitable substitute to conventional enzymatic reporter systems in diagnostics. This review will provide a brief overview of the G-quadruplex architecture as well as the many forms of reporter systems ranging from absorbance to luminescence readouts in various platforms. Furthermore, some challenges and improvements that have been introduced to improve the application of G-quadruplex in diagnostics will be highlighted. As the field of diagnostics has evolved to apply different detection systems, the need for alternative reporter systems such as G-quadruplexes is also paramount.
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Hashim, U., Soon Weng Chong, and Wei-Wen Liu. "Fabrication of Silicon Nitride Ion Sensitive Field-Effect Transistor for pH Measurement and DNA Immobilization/Hybridization." Journal of Nanomaterials 2013 (2013): 1–9. http://dx.doi.org/10.1155/2013/542737.

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The fabrication of ion sensitive field-effect transistor (ISFET) using silicon nitride (Si3N4) as the sensing membrane for pH measurement and DNA is reported. For the pH measurement, the Ag/AgCl electrode was used as the reference electrode, and different pH values of buffer solution were used in the ISFET analysis. The ISFET device was tested with pH buffer solutions of pH2, pH3, pH7, pH8, and pH9. The results show that the IV characteristic of ISFET devices is directly proportional and the device’s sensitivity was 43.13 mV/pH. The ISFET is modified chemically to allow the integration with biological element to form a biologically active field-effect transistor (BIOFET). It was found that the DNA immobilization activities which occurred on the sensing membrane caused the drain current to drop due to the negatively charged backbones of the DNA probes repelled electrons from accumulating at the conducting channel. The drain current was further decreased when the DNA hybridization took place.
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Allegra, Alessandro, Claudia Petrarca, Mario Di Gioacchino, Giuseppe Mirabile, and Sebastiano Gangemi. "Electrochemical Biosensors in the Diagnosis of Acute and Chronic Leukemias." Cancers 15, no. 1 (December 26, 2022): 146. http://dx.doi.org/10.3390/cancers15010146.

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Until now, morphological assessment with an optical or electronic microscope, fluorescence in situ hybridization, DNA sequencing, flow cytometry, polymerase chain reactions, and immunohistochemistry have been employed for leukemia identification. Nevertheless, despite their numerous different vantages, it is difficult to recognize leukemic cells correctly. Recently, the electrochemical evaluation with a nano-sensing interface seems an attractive alternative. Electrochemical biosensors measure the modification in the electrical characteristics of the nano-sensing interface, which is modified by the contact between a biological recognition element and the analyte objective. The implementation of nanosensors is founded not on single nanomaterials but rather on compilating these components efficiently. Biosensors able to identify the molecules of deoxyribonucleic acid are defined as DNA biosensors. Our review aimed to evaluate the literature on the possible use of electrochemical biosensors for identifying hematological neoplasms such as acute promyelocytic leukemia, acute lymphoblastic leukemia, and chronic myeloid leukemia. In particular, we focus our attention on using DNA electrochemical biosensors to evaluate leukemias.
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Ramsay, Joshua P., Tahlia R. Bastholm, Callum J. Verdonk, Dinah D. Tambalo, John T. Sullivan, Liam K. Harold, Beatrice A. Panganiban, et al. "An epigenetic switch activates bacterial quorum sensing and horizontal transfer of an integrative and conjugative element." Nucleic Acids Research 50, no. 2 (December 14, 2021): 975–88. http://dx.doi.org/10.1093/nar/gkab1217.

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Abstract Horizontal transfer of the integrative and conjugative element ICEMlSymR7A converts non-symbiotic Mesorhizobium spp. into nitrogen-fixing legume symbionts. Here, we discover subpopulations of Mesorhizobium japonicum R7A become epigenetically primed for quorum-sensing (QS) and QS-activated horizontal transfer. Isolated populations in this state termed R7A* maintained these phenotypes in laboratory culture but did not transfer the R7A* state to recipients of ICEMlSymR7A following conjugation. We previously demonstrated ICEMlSymR7A transfer and QS are repressed by the antiactivator QseM in R7A populations and that the adjacently-coded DNA-binding protein QseC represses qseM transcription. Here RNA-sequencing revealed qseM expression was repressed in R7A* cells and that RNA antisense to qseC was abundant in R7A but not R7A*. Deletion of the antisense-qseC promoter converted cells into an R7A*-like state. An adjacently coded QseC2 protein bound two operator sites and repressed antisense-qseC transcription. Plasmid overexpression of QseC2 stimulated the R7A* state, which persisted following curing of this plasmid. The epigenetic maintenance of the R7A* state required ICEMlSymR7A-encoded copies of both qseC and qseC2. Therefore, QseC and QseC2, together with their DNA-binding sites and overlapping promoters, form a stable epigenetic switch that establishes binary control over qseM transcription and primes a subpopulation of R7A cells for QS and horizontal transfer.
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Li, Yong, Tomoki Kimura, John H. Laity, and Glen K. Andrews. "The Zinc-Sensing Mechanism of Mouse MTF-1 Involves Linker Peptides between the Zinc Fingers." Molecular and Cellular Biology 26, no. 15 (August 1, 2006): 5580–87. http://dx.doi.org/10.1128/mcb.00471-06.

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ABSTRACT Mouse metal response element-binding transcription factor-1 (MTF-1) regulates the transcription of genes in response to a variety of stimuli, including exposure to zinc or cadmium, hypoxia, and oxidative stress. Each of these stresses may increase labile cellular zinc, leading to nuclear translocation, DNA binding, and transcriptional activation of metallothionein genes (MT genes) by MTF-1. Several lines of evidence suggest that the highly conserved six-zinc finger DNA-binding domain of MTF-1 also functions as a zinc-sensing domain. In this study, we investigated the potential role of the peptide linkers connecting the four N-terminal zinc fingers of MTF-1 in their zinc-sensing function. Each of these three linkers is unique, completely conserved among all known vertebrate MTF-1 orthologs, and different from the canonical Cys2His2 zinc finger TGEKP linker sequence. Replacing the RGEYT linker between zinc fingers 1 and 2 with TGEKP abolished the zinc-sensing function of MTF-1, resulting in constitutive DNA binding, nuclear translocation, and transcriptional activation of the MT-I gene. In contrast, swapping the TKEKP linker between fingers 2 and 3 with TGEKP had little effect on the metal-sensing functions of MTF-1, whereas swapping the canonical linker for the shorter TGKT linker between fingers 3 and 4 rendered MTF-1 less sensitive to zinc-dependent activation both in vivo and in vitro. These observations suggest a mechanism by which physiological concentrations of accessible cellular zinc affect MTF-1 activity. Zinc may modulate highly specific, linker-mediated zinc finger interactions in MTF-1, thus affecting its zinc- and DNA-binding activities, resulting in translocation to the nucleus and binding to the MT-I gene promoter.
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Book chapters on the topic "DNA Sensing Element"

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Kumar, Pramod, and Sushil Kumar. "Detection of Bio-Relevant Metal Ions by Luminescent Ru(II)-Polypyridyl Based Sensors." In Ruthenium - an Element Loved by Researchers [Working Title]. IntechOpen, 2021. http://dx.doi.org/10.5772/intechopen.96453.

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Biorelevant metal ions such as Cu2+ and Fe2+/Fe3+ participate in various biological events which include electron transfer reactions, delivery and uptake of oxygen, DNA and RNA syntheses, and enzymatic catalysis to maintain fundamental physiological processes in living organisms. So far, several analytical techniques have been investigated for their precise detection; however, luminescence-based sensing is often superior due to its high sensitivity, selectivity, fast and easy operation and convenient cellular imaging. Owing to their immense photophysical and photochemical properties stemming from large Stokes shift, absorption in visible region, good photostability and long excited state lifetimes, Ru(II)-polypyridyl-based complexes have gained increasing interest as luminophores. Over past few decades, several Ru(II)-polypyridyl based chemosensors have rapidly been developed for detection of different biorelevant and other metal ions. The main object of this book chapter is to cover a majority of Ru(II)-polypyridyl based chemosensors showing a selective and sensitive detection of bio-relevant Cu2+ and Fe2+/Fe3+ ions. The photophysical properties of Ru(II) complexes, detection of metal ions, sensing mechanism and applications of these sensors are discussed at a length.
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Tripathi, Abhay Dev, Soumya Katiyar, and Avinash K. Chaurasia. "Nanomaterials for Biosensing Applications." In Recent Advances in Biosensor Technology, edited by Abha Mishra, 1–29. BENTHAM SCIENCE PUBLISHERS, 2023. http://dx.doi.org/10.2174/9789815123739123010004.

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A biosensor is a device that detects the presence of analytes with its biological receptor entity, having unique specificities corresponding to their analytes. Most of these analytes are usually physical in nature, such as DNA, proteins, antibodies, and antigens, but they may also be simple compounds, including glucose, H2O2, toxins, and so on. Biosensors’ significance rises in providing real-time quantitative and qualitative information on analyte composition. The sensing mechanism involves the transduction of target binding interactions into optical, electrochemical signals, etc ., which can be amplified and detected. Nanomaterials (NMs) have shown significant potential in biological sensing-these allow close interactions with target biomolecules due to their extremely small size and suitable surface modifications. Nanomaterials appear to be potential possibilities because of their capacity to immobilize a greater number of bioreceptor units in confined devices and even act as a transduction element, allowing for enhanced sensitivity and reduced detection limits down to specific molecules. Nanomaterials have been widely used for in vitro detection of disease-related molecular biomarkers and imaging, contrasts to map out the distribution of biomarkers in vivo. This chapter summarizes nanomaterials such as gold nanoparticles, quantum dots, polymeric nanoparticles, carbon nanotubes, nanodiamonds, and graphene nanostructured materials that are currently being researched or utilized as biosensors.
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Conference papers on the topic "DNA Sensing Element"

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Lee, Hee-Jo, Hyun-Seok Lee, Kyung-Hwa Yoo, and Jong-Gwan Yook. "DNA sensing based on single element planar double split-ring resonator." In 2009 IEEE MTT-S International Microwave Symposium Digest (MTT). IEEE, 2009. http://dx.doi.org/10.1109/mwsym.2009.5166039.

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Li, Leslie, Richard Burton, and Greg Schoenau. "Feasibility Study on the Use of Dynamic Neural Networks (DNN’s) for Modeling a Variable Displacement Load Sensing Pump." In ASME 2006 International Mechanical Engineering Congress and Exposition. ASMEDC, 2006. http://dx.doi.org/10.1115/imece2006-15588.

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The feasibility of using a particular form of neural networks, defined as Dynamic Neural Units (DNU's), to model a pump in a load sensing system is investigated in this paper. Because of the highly complex structure of the pump, its compensators and controlling elements, simulation of load-sensing pump systems pose many challenges to researchers. Several models of pumps, compensators and valves have been developed and published in the literature but they are overly simplified or are in an extremely complex form. One modeling approach which can capture the nonlinear dynamic properties of the pump yet still retain reasonable simplicity in its basic form is to use neural network technology. Previous studies have shown some limited success in using feed forward neurons with dynamic properties being introduced using time delays. A problem referred to a error accumulation has prevented these neural based models from being practical dynamic representations of load sensing systems. Based on the topology of the biological neural systems several new structures, Dynamic Neural Units (DNU's) have been developed. Only one DNU is necessary to capture or represent some of the dynamics of a plant, which a static (feed forward) neuron cannot do. The main advantage of the dynamic neuron is that it reduces the network dimension and the amount of computational requirement and has the potential to avoid this error accumulation problem. The use of Dynamic Neural Networks with Dynamic Neural Units in simulating a variable displacement pump is presented in this paper. Only the pump portion of the load sensing pump system is considered due to problems of interacting operating points. A DNU structure and a DNN (which is comprised of DNU's) are introduced. The simulation results establishes the feasibility of using a Dynamic Neural Networks with DNU's to model a simulated nonlinear hydraulic system such as a load sensing pump.
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Lopez-Reyna, C. E., and J. N. Zemel. "The Road to Smart Transducer Technology." In ASME 2002 International Mechanical Engineering Congress and Exposition. ASMEDC, 2002. http://dx.doi.org/10.1115/imece2002-33179.

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The past decade has seen three distinct trends emerge in sensor technologies. The first is biosensing wherein measurements as diverse as detecting aromas in food processing to highly sophisticated detection of DNA and proteins have become staples of contemporary engineering efforts. The second important trend is the continuing decrease in the physical size of sensing elements embodied by the replacement of “micro” by “nano” in fabrication and technology. These two efforts in biosensing and the decreasing size of electronic and sensing components have transformed not only virtually every area of research, development and engineering, they are powerfully influencing many aspects of everyday life. The third trend, and the one that will be examined in this paper, involves efforts to fuse information technology with sensing technologies. The rubric “smart transducer technologies” has been given to these activities to connote this fusion.
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Choi, Junseo, Bahador Farshchian, and Sunggook Park. "Fabrication of Perforated Conical Nanopores in Freestanding Polymer Membranes Using Nanoimprint Lithography and Pressed Self-Perfection Method." In ASME 2012 International Mechanical Engineering Congress and Exposition. American Society of Mechanical Engineers, 2012. http://dx.doi.org/10.1115/imece2012-87669.

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Nanopores have proven to be an important sensing element in biosensors to detect and analyze single biomolecules such as DNAs, RNAs, or proteins. The charged biomolecules are driven by an electric field and detected as transient current blocks associated with their translocation through the pores. While protein nanopores, such as alpha-hemolysin and MspA protein nanopores embedded within a lipid bilayer membrane [1], promise to be a rapid, sensitive and label-free sensing paradigm, their duration of usage is too short to perform repetitive experiments due to the mechanical instability of the lipid bilayer. A variety of methods have been developed to prepare synthetic nanopores, which can substrate for protein nanopores, including a direct milling with a focused high-energy electron or ion beam in insulating substrates, an ion track etching in polymer substrates, and an anodizing in aluminum substrates. However, those methods do not allow for control over both the size and location of pores and the high yield of production.
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Maschmann, Matthew R., Gregory J. Ehlert, and Jeffery W. Baur. "Piezoresistive Reponse of Aligned Carbon Nanotube Arrays for Flow Sensing Applications." In ASME 2011 Conference on Smart Materials, Adaptive Structures and Intelligent Systems. ASMEDC, 2011. http://dx.doi.org/10.1115/smasis2011-5096.

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We investigate the electromechanical sensing capabilities of aligned carbon nanotube (CNT) arrays as a means for a lightweight and simple electromechanical transduction element. CNT array heights of 25 and 350 μm are examined using a modified dynamic mechanical analyzer (DMA) to impart multiple strain-based test configurations while simultaneously measuring electrical resistance. Observed gauge factors range from 12.5 for the 25μm array to greater than 190 for the 350 μm array, with a peak sensitivity of 13,750 ohms/gram force achieved for the 350 μm array. The electromechanical response observed was independent of the examined frequency range, suggesting high fidelity sensory capabilities. Results of this study serve as a preliminary proof of concept for using CNT arrays as a transduction mechanism for a proposed artificial hair sensor for small air vehicles.
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