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Huang G, Tian L, Liu KK, Hu B, Xu F, Lu TJ, Naik RR, Singamaneni S. Elastoplastic Deformation of Silk Micro- and Nanostructures. ACS Biomater Sci Eng 2016; 2:893-899. [DOI: 10.1021/acsbiomaterials.6b00177] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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52
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Kim S, Russell M, Kulkarni DD, Henry M, Kim S, Naik RR, Voevodin AA, Jang SS, Tsukruk VV, Fedorov AG. Activating "Invisible" Glue: Using Electron Beam for Enhancement of Interfacial Properties of Graphene-Metal Contact. ACS NANO 2016; 10:1042-1049. [PMID: 26741645 DOI: 10.1021/acsnano.5b06342] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Interfacial contact of two-dimensional graphene with three-dimensional metal electrodes is crucial to engineering high-performance graphene-based nanodevices with superior performance. Here, we report on the development of a rapid "nanowelding" method for enhancing properties of interface to graphene buried under metal electrodes using a focused electron beam induced deposition (FEBID). High energy electron irradiation activates two-dimensional graphene structure by generation of structural defects at the interface to metal contacts with subsequent strong bonding via FEBID of an atomically thin graphitic interlayer formed by low energy secondary electron-assisted dissociation of entrapped hydrocarbon contaminants. Comprehensive investigation is conducted to demonstrate formation of the FEBID graphitic interlayer and its impact on contact properties of graphene devices achieved via strong electromechanical coupling at graphene-metal interfaces. Reduction of the device electrical resistance by ∼50% at a Dirac point and by ∼30% at the gate voltage far from the Dirac point is obtained with concurrent improvement in thermomechanical reliability of the contact interface. Importantly, the process is rapid and has an excellent insertion potential into a conventional fabrication workflow of graphene-based nanodevices through single-step postprocessing modification of interfacial properties at the buried heterogeneous contact.
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Tian L, Luan J, Liu KK, Jiang Q, Tadepalli S, Gupta MK, Naik RR, Singamaneni S. Plasmonic Biofoam: A Versatile Optically Active Material. NANO LETTERS 2016; 16:609-616. [PMID: 26630376 DOI: 10.1021/acs.nanolett.5b04320] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Owing to their ability to confine and manipulate light at the nanoscale, plasmonic nanostructures are highly attractive for a broad range of applications. While tremendous progress has been made in the synthesis of size- and shape-controlled plasmonic nanostructures, their integration with other materials and application in solid-state is primarily through their assembly on rigid two-dimensional (2D) substrates, which limits the plasmonically active space to a few nanometers above the substrate. In this work, we demonstrate a simple method to create plasmonically active three-dimensional biofoams by integrating plasmonic nanostructures with highly porous biomaterial aerogels. We demonstrate that plasmonic biofoam is a versatile optically active platform that can be harnessed for numerous applications including (i) ultrasensitive chemical detection using surface-enhanced Raman scattering; (ii) highly efficient energy harvesting and steam generation through plasmonic photothermal heating; and (iii) optical control of enzymatic activity by triggered release of biomolecules encapsulated within the aerogel. Our results demonstrate that 3D plasmonic biofoam exhibits significantly higher sensing, photothermal, and loading efficiency compared to conventional 2D counterparts. The design principles and processing methodology of plasmonic aerogels demonstrated here can be broadly applied in the fabrication of other functional foams.
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54
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Schmucker AL, Tadepalli S, Liu KK, Sullivan CJ, Singamaneni S, Naik RR. Plasmonic paper: a porous and flexible substrate enabling nanoparticle-based combinatorial chemistry. RSC Adv 2016. [DOI: 10.1039/c5ra21977a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
The physical properties and manipulation of the nanomaterials immobilized on paper substrate offers tremendous potential for a variety of applications.
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Merrill NA, McKee EM, Merino KC, Drummy LF, Lee S, Reinhart B, Ren Y, Frenkel AI, Naik RR, Bedford NM, Knecht MR. Identifying the Atomic-Level Effects of Metal Composition on the Structure and Catalytic Activity of Peptide-Templated Materials. ACS NANO 2015; 9:11968-11979. [PMID: 26497843 DOI: 10.1021/acsnano.5b04665] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Bioinspired approaches for the formation of metallic nanomaterials have been extensively employed for a diverse range of applications including diagnostics and catalysis. These materials can often be used under sustainable conditions; however, it is challenging to control the material size, morphology, and composition simultaneously. Here we have employed the R5 peptide, which forms a 3D scaffold to direct the size and linear shape of bimetallic PdAu nanomaterials for catalysis. The materials were prepared at varying Pd:Au ratios to probe optimal compositions to achieve maximal catalytic efficiency. These materials were extensively characterized at the atomic level using transmission electron microscopy, extended X-ray absorption fine structure spectroscopy, and atomic pair distribution function analysis derived from high-energy X-ray diffraction patterns to provide highly resolved structural information. The results confirmed PdAu alloy formation, but also demonstrated that significant surface structural disorder was present. The catalytic activity of the materials was studied for olefin hydrogenation, which demonstrated enhanced reactivity from the bimetallic structures. These results present a pathway to the bioinspired production of multimetallic materials with enhanced properties, which can be assessed via a suite of characterization methods to fully ascertain structure/function relationships.
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Bhimanapati GR, Lin Z, Meunier V, Jung Y, Cha J, Das S, Xiao D, Son Y, Strano MS, Cooper VR, Liang L, Louie SG, Ringe E, Zhou W, Kim SS, Naik RR, Sumpter BG, Terrones H, Xia F, Wang Y, Zhu J, Akinwande D, Alem N, Schuller JA, Schaak RE, Terrones M, Robinson JA. Recent Advances in Two-Dimensional Materials beyond Graphene. ACS NANO 2015; 9:11509-39. [PMID: 26544756 DOI: 10.1021/acsnano.5b05556] [Citation(s) in RCA: 877] [Impact Index Per Article: 97.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The isolation of graphene in 2004 from graphite was a defining moment for the "birth" of a field: two-dimensional (2D) materials. In recent years, there has been a rapidly increasing number of papers focusing on non-graphene layered materials, including transition-metal dichalcogenides (TMDs), because of the new properties and applications that emerge upon 2D confinement. Here, we review significant recent advances and important new developments in 2D materials "beyond graphene". We provide insight into the theoretical modeling and understanding of the van der Waals (vdW) forces that hold together the 2D layers in bulk solids, as well as their excitonic properties and growth morphologies. Additionally, we highlight recent breakthroughs in TMD synthesis and characterization and discuss the newest families of 2D materials, including monoelement 2D materials (i.e., silicene, phosphorene, etc.) and transition metal carbide- and carbon nitride-based MXenes. We then discuss the doping and functionalization of 2D materials beyond graphene that enable device applications, followed by advances in electronic, optoelectronic, and magnetic devices and theory. Finally, we provide perspectives on the future of 2D materials beyond graphene.
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Bedford NM, Hughes ZE, Tang Z, Li Y, Briggs BD, Ren Y, Swihart MT, Petkov VG, Naik RR, Knecht MR, Walsh TR. Sequence-Dependent Structure/Function Relationships of Catalytic Peptide-Enabled Gold Nanoparticles Generated under Ambient Synthetic Conditions. J Am Chem Soc 2015; 138:540-8. [DOI: 10.1021/jacs.5b09529] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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58
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Freeman R, Boekhoven J, Dickerson MB, Naik RR, Stupp SI. Biopolymers and supramolecular polymers as biomaterials for biomedical applications. MRS BULLETIN 2015; 40:1089-1101. [PMID: 26989295 PMCID: PMC4790466 DOI: 10.1557/mrs.2015.270] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Protein- and peptide-based structural biopolymers are abundant building blocks of biological systems. Either in their natural forms, such as collagen, silk or fibronectin, or as related synthetic materials they can be used in various technologies. An emerging area is that of biomimetic materials inspired by protein-based biopolymers, which are made up of small molecules rather than macromolecules and can therefore be described as supramolecular polymers. These materials are very useful in biomedical applications because of their ability to imitate the extracellular matrix both in architecture and their capacity to signal cells. This article describes important features of the natural extracellular matrix and highlight how these features are being incorporated into biomaterials composed of biopolymers and supramolecular polymers. We particularly focus on the structures, properties, and functions of collagen, fibronectin, silk, and the supramolecular polymers inspired by them as biomaterials for regenerative medicine.
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Tadepalli S, Kuang Z, Jiang Q, Liu KK, Fisher MA, Morrissey JJ, Kharasch ED, Slocik JM, Naik RR, Singamaneni S. Peptide Functionalized Gold Nanorods for the Sensitive Detection of a Cardiac Biomarker Using Plasmonic Paper Devices. Sci Rep 2015; 5:16206. [PMID: 26552720 PMCID: PMC4639779 DOI: 10.1038/srep16206] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Accepted: 09/16/2015] [Indexed: 12/13/2022] Open
Abstract
The sensitivity of localized surface plasmon resonance (LSPR) of metal nanostructures to adsorbates lends itself to a powerful class of label-free biosensors. Optical properties of plasmonic nanostructures are dependent on the geometrical features and the local dielectric environment. The exponential decay of the sensitivity from the surface of the plasmonic nanotransducer calls for the careful consideration in its design with particular attention to the size of the recognition and analyte layers. In this study, we demonstrate that short peptides as biorecognition elements (BRE) compared to larger antibodies as target capture agents offer several advantages. Using a bioplasmonic paper device (BPD), we demonstrate the selective and sensitive detection of the cardiac biomarker troponin I (cTnI). The smaller sized peptide provides higher sensitivity and a lower detection limit using a BPD. Furthermore, the excellent shelf-life and thermal stability of peptide-based LSPR sensors, which precludes the need for special storage conditions, makes it ideal for use in resource-limited settings.
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Choi J, Chen H, Li F, Yang L, Kim SS, Naik RR, Ye PD, Choi JH. Nanomanufacturing of 2D Transition Metal Dichalcogenide Materials Using Self-Assembled DNA Nanotubes. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:5520-5527. [PMID: 26313027 DOI: 10.1002/smll.201501431] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/23/2015] [Indexed: 06/04/2023]
Abstract
2D transition metal dichalcogenides (TMDCs) are nanomanufactured using a generalized strategy with self-assembled DNA nanotubes. DNA nanotubes of various lengths serve as lithographic etch masks for the dry etching of TMDCs. The nanostructured TMDCs are studied by atomic force microscopy, photoluminescence, and Raman spectroscopy. This parallel approach can be used to manufacture 2D TMDC nanostructures of arbitrary geometries with molecular-scale precision.
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61
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Kim S, Russell M, Henry M, Kim SS, Naik RR, Voevodin AA, Jang SS, Tsukruk VV, Fedorov AG. Dynamic modulation of electronic properties of graphene by localized carbon doping using focused electron beam induced deposition. NANOSCALE 2015; 7:14946-14952. [PMID: 26302897 DOI: 10.1039/c5nr04063a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We report on the first demonstration of controllable carbon doping of graphene to engineer local electronic properties of a graphene conduction channel using focused electron beam induced deposition (FEBID). Electrical measurements indicate that an "n-p-n" junction on graphene conduction channel is formed by partial carbon deposition near the source and drain metal contacts by low energy (<50 eV) secondary electrons due to inelastic collisions of long range backscattered primary electrons generated from a low dose of high energy (25 keV) electron beam (1 × 10(18) e(-) per cm(2)). Detailed AFM imaging provides direct evidence of the new mechanism responsible for dynamic evolution of the locally varying graphene doping. The FEBID carbon atoms, which are physisorbed and weakly bound to graphene, diffuse towards the middle of graphene conduction channel due to their surface chemical potential gradient, resulting in negative shift of Dirac voltage. Increasing a primary electron dose to 1 × 10(19) e(-) per cm(2) results in a significant increase of carbon deposition, such that it covers the entire graphene conduction channel at high surface density, leading to n-doping of graphene channel. Collectively, these findings establish a unique capability of FEBID technique to dynamically modulate the doping state of graphene, thus enabling a new route to resist-free, "direct-write" functional patterning of graphene-based electronic devices with potential for on-demand re-configurability.
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62
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Kim SS, Kuang Z, Ngo YH, Farmer BL, Naik RR. Biotic-Abiotic Interactions: Factors that Influence Peptide-Graphene Interactions. ACS APPLIED MATERIALS & INTERFACES 2015; 7:20447-20453. [PMID: 26305504 DOI: 10.1021/acsami.5b06434] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Understanding the factors that influence the interaction between biomolecules and abiotic surfaces is of utmost interest in biosensing and biomedical research. Through phage display technology, several peptides have been identified as specific binders to abiotic material surfaces, such as gold, graphene, silver, and so forth. Using graphene-peptide as our model abiotic-biotic pair, we investigate the effect of graphene quality, number of layers, and the underlying support substrate effect on graphene-peptide interactions using both experiments and computation. Our results indicate that graphene quality plays a significant role in graphene-peptide interactions. The graphene-biomolecule interaction appears to show no significant dependency on the number of graphene layers or the underlying support substrate.
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63
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Potyrailo RA, Bonam RK, Hartley JG, Starkey TA, Vukusic P, Vasudev M, Bunning T, Naik RR, Tang Z, Palacios MA, Larsen M, Le Tarte LA, Grande JC, Zhong S, Deng T. Towards outperforming conventional sensor arrays with fabricated individual photonic vapour sensors inspired by Morpho butterflies. Nat Commun 2015; 6:7959. [PMID: 26324320 PMCID: PMC4569698 DOI: 10.1038/ncomms8959] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 07/01/2015] [Indexed: 12/18/2022] Open
Abstract
Combining vapour sensors into arrays is an accepted compromise to mitigate poor selectivity of conventional sensors. Here we show individual nanofabricated sensors that not only selectively detect separate vapours in pristine conditions but also quantify these vapours in mixtures, and when blended with a variable moisture background. Our sensor design is inspired by the iridescent nanostructure and gradient surface chemistry of Morpho butterflies and involves physical and chemical design criteria. The physical design involves optical interference and diffraction on the fabricated periodic nanostructures and uses optical loss in the nanostructure to enhance the spectral diversity of reflectance. The chemical design uses spatially controlled nanostructure functionalization. Thus, while quantitation of analytes in the presence of variable backgrounds is challenging for most sensor arrays, we achieve this goal using individual multivariable sensors. These colorimetric sensors can be tuned for numerous vapour sensing scenarios in confined areas or as individual nodes for distributed monitoring. Individual vapour sensors often suffer from poor selectivity, which hinders their broad applicability. Here, Potyrailo et al. fabricate individual sensors inspired by the Morpho butterfly capable of selectively detecting vapours in mixtures and with a variable moisture background.
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64
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Silva JE, Geryak R, Loney DA, Kottke PA, Naik RR, Tsukruk VV, Fedorov AG. Stick-slip water penetration into capillaries coated with swelling hydrogel. SOFT MATTER 2015; 11:5933-5939. [PMID: 26119374 DOI: 10.1039/c5sm00660k] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We have observed intriguing stick-slip behavior during capillary pressure driven filling of borosilicate microtubes coated with hydrogel on their inner wall. Swelling of hydrogel upon exposure to a translating waterfront is accompanied by "stick-and-slip" motion. This results in the macroscopic filling velocity for water penetration into glass capillaries coated with poly(N-isopropylacrylamide) (PNIPAM) being constant throughout the filling process, and reduced by three orders of magnitude when compared to filling of uncoated capillaries. A simple scaling analysis is used to introduce a possible explanation by considering the mechanisms responsible for pinning and unpinning of the contact line. The explanation assumes that the time scale for water diffusion into a hydrogel film and the resulting swelling/change of the local meniscus contact angle define the duration of each "stick" event. The "slip" length scale is in turn established by the elastocapillary deformation of dry hydrogel at the pinning point of the contact line. The sequential dynamics of these processes then determine the rate of water filling into a swelling capillary. Collectively, these experimental and theoretical results provide a new conceptual framework for liquid motion confined by soft, dynamically evolving polymer interfaces, in which the system creates an energy barrier to further motion through elasto-capillary deformation, and then lowers the barrier through diffusive softening. This insight has implications for optimal design of microfluidic and lab-on-a-chip devices based on stimuli-responsive smart polymers.
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65
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Slocik JM, Drummy LF, Dickerson MB, Crouse CA, Spowart JE, Naik RR. Bioinspired High-Performance Energetic Materials Using Heme-Containing Crystals. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2015; 11:3539-3544. [PMID: 25940859 DOI: 10.1002/smll.201403659] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Revised: 03/12/2015] [Indexed: 06/04/2023]
Abstract
Synthetic hemozoin crystals (β-hematin) are assembled with aluminium nanoparticles (nAl) to create a nanomaterial composite that is highly energetic and reactive. The results here demonstrate that hemozoin rapidly oxidizes the nAl fuel to release large amounts of energy (+12.5 ± 2.4 kJ g(-1) ).
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66
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Briggs BD, Bedford NM, Seifert S, Koerner H, Ramezani-Dakhel H, Heinz H, Naik RR, Frenkel AI, Knecht MR. Atomic-scale identification of Pd leaching in nanoparticle catalyzed C-C coupling: effects of particle surface disorder. Chem Sci 2015; 6:6413-6419. [PMID: 30090261 PMCID: PMC6054123 DOI: 10.1039/c5sc01424g] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 07/23/2015] [Indexed: 11/21/2022] Open
Abstract
C-C coupling reactions are of great importance in the synthesis of numerous organic compounds, where Pd nanoparticle catalyzed systems represent new materials to efficiently drive these reactions. Despite their pervasive utility, the catalytic mechanism of these particle-based reactions remains highly contested. Herein we present evidence of an atom leaching mechanism for Stille coupling under aqueous conditions using peptide-capped Pd nanoparticles. EXAFS analysis revealed Pd coordination changes in the nanoparticle consistent with Pd atom abstraction, where sizing analysis by SAXS confirmed particle size changes associated with a leaching process. It is likely that recently discovered highly disordered surface Pd atoms are the favored catalytic active sites and are leached during oxidative addition, resulting in smaller particles. Probing the mechanism of nanoparticle-driven C-C coupling reactions through structural analyses provides fundamental information concerning these active sites and their reactivity at the atomic-scale, which can be used to improve catalytic performance to meet important sustainability goals.
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67
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Rose DP, Ratterman ME, Griffin DK, Hou L, Kelley-Loughnane N, Naik RR, Hagen JA, Papautsky I, Heikenfeld JC. Adhesive RFID Sensor Patch for Monitoring of Sweat Electrolytes. IEEE Trans Biomed Eng 2015. [PMID: 25398174 DOI: 10.1109/tbme.2014.2369910.1109/tbme.2014.2369991] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Wearable digital health devices are dominantly found in rigid form factors such as bracelets and pucks. An adhesive radio-frequency identification (RFID) sensor bandage (patch) is reported, which can be made completely intimate with human skin, a distinct advantage for chronological monitoring of biomarkers in sweat. In this demonstration, a commercial RFID chip is adapted with minimum components to allow potentiometric sensing of solutes in sweat, and surface temperature, as read by an Android smartphone app with 96% accuracy at 50 mM Na(+) (in vitro tests). All circuitry is solder-reflow integrated on a standard Cu/polyimide flexible-electronic layer including an antenna, but while also allowing electroplating for simple integration of exotic metals for sensing electrodes. Optional paper microfluidics wick sweat from a sweat porous adhesive allowing flow to the sensor, or the sensor can be directly contacted to the skin. The wearability of the patch has been demonstrated for up to seven days, and includes a protective textile which provides a feel and appearance similar to a standard Band-Aid. Applications include hydration monitoring, but the basic capability is extendable to other mM ionic solutes in sweat (Cl(-), K(+), Mg(2+), NH4(+), and Zn(2+)). The design and fabrication of the patch are provided in full detail, as the basic components could be useful in the design of other wearable sensors.
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68
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Bedford NM, Ramezani-Dakhel H, Slocik JM, Briggs BD, Ren Y, Frenkel AI, Petkov V, Heinz H, Naik RR, Knecht MR. Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts. ACS NANO 2015; 9:5082-92. [PMID: 25905675 DOI: 10.1021/acsnano.5b00168] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then elucidated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences.
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69
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Martin JA, Mirau PA, Chushak Y, Chávez JL, Naik RR, Hagen JA, Kelley-Loughnane N. Single-Round Patterned DNA Library Microarray Aptamer Lead Identification. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:137489. [PMID: 26075138 PMCID: PMC4446497 DOI: 10.1155/2015/137489] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/12/2014] [Revised: 04/22/2015] [Accepted: 04/27/2015] [Indexed: 06/04/2023]
Abstract
A method for identifying an aptamer in a single round was developed using custom DNA microarrays containing computationally derived patterned libraries incorporating no information on the sequences of previously reported thrombin binding aptamers. The DNA library was specifically designed to increase the probability of binding by enhancing structural complexity in a sequence-space confined environment, much like generating lead compounds in a combinatorial drug screening library. The sequence demonstrating the highest fluorescence intensity upon target addition was confirmed to bind the target molecule thrombin with specificity by surface plasmon resonance, and a novel imino proton NMR/2D NOESY combination was used to screen the structure for G-quartet formation. We propose that the lack of G-quartet structure in microarray-derived aptamers may highlight differences in binding mechanisms between surface-immobilized and solution based strategies. This proof-of-principle study highlights the use of a computational driven methodology to create a DNA library rather than a SELEX based approach. This work is beneficial to the biosensor field where aptamers selected by solution based evolution have proven challenging to retain binding function when immobilized on a surface.
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70
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Naik RR, Singh AK, Mali AM, Khirade MF, Bapat SA. A tumor deconstruction platform identifies definitive end points in the evaluation of drug responses. Oncogene 2015; 35:727-37. [PMID: 25915841 DOI: 10.1038/onc.2015.130] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/16/2015] [Accepted: 03/20/2015] [Indexed: 02/07/2023]
Abstract
Tumor heterogeneity and the presence of drug-sensitive and refractory populations within the same tumor are almost never assessed in the drug discovery pipeline. Such incomplete assessment of drugs arising from spatial and temporal tumor cell heterogeneity reflects on their failure in the clinic and considerable wasted costs in the drug discovery pipeline. Here we report the derivation of a flow cytometry-based tumor deconstruction platform for resolution of at least 18 discrete tumor cell fractions. This is achieved through concurrent identification, quantification and analysis of components of cancer stem cell hierarchies, genetically instable clones and differentially cycling populations within a tumor. We also demonstrate such resolution of the tumor cytotype to be a potential value addition in drug screening through definitive cell target identification. Additionally, this real-time definition of intra-tumor heterogeneity provides a convenient, incisive and analytical tool for predicting drug efficacies through profiling perturbations within discrete tumor cell subsets in response to different drugs and candidates. Consequently, possible applications in informed therapeutic monitoring and drug repositioning in personalized cancer therapy would complement rational design of new candidates besides achieving a re-evaluation of existing drugs to derive non-obvious combinations that hold better chances of achieving remission.
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71
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Tapp M, Sullivan R, Dennis P, Naik RR, Milam VT. Spectroscopic studies of nucleic acid additions during seed-mediated growth of gold nanoparticles. JOURNAL OF MATERIALS RESEARCH 2015; 30:666-676. [PMID: 25960601 PMCID: PMC4423617 DOI: 10.1557/jmr.2014.409] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
The effect of adding nucleic acids to gold seeds during the growth stage of either nanospheres or nanorods was investigated using UV-Vis spectroscopy to reveal any oligonucleotide base or structure-specific effects on nanoparticle growth kinetics or plasmonic signatures. Spectral data indicate that the presence of DNA duplexes during seed ageing drastically accelerated nanosphere growth while the addition of single-stranded polyadenine at any point during seed ageing induces nanosphere aggregation. For seeds added to a gold nanorod growth solution, single-stranded polythymine induces a modest blue-shift in the longitudinal peak wavelength. Moreover, a particular sequence comprised of 50% thymine bases was found to induce a faster, more dramatic blue-shift in the longitudinal peak wavelength compared to any of the homopolymer incubation cases. Monomeric forms of the nucleic acids, however, do not yield discernable spectral differences in any of the gold suspensions studied.
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72
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Rose DP, Ratterman ME, Griffin DK, Hou L, Kelley-Loughnane N, Naik RR, Hagen JA, Papautsky I, Heikenfeld JC. Adhesive RFID Sensor Patch for Monitoring of Sweat Electrolytes. IEEE Trans Biomed Eng 2014; 62:1457-65. [PMID: 25398174 DOI: 10.1109/tbme.2014.2369991] [Citation(s) in RCA: 189] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Wearable digital health devices are dominantly found in rigid form factors such as bracelets and pucks. An adhesive radio-frequency identification (RFID) sensor bandage (patch) is reported, which can be made completely intimate with human skin, a distinct advantage for chronological monitoring of biomarkers in sweat. In this demonstration, a commercial RFID chip is adapted with minimum components to allow potentiometric sensing of solutes in sweat, and surface temperature, as read by an Android smartphone app with 96% accuracy at 50 mM Na(+) (in vitro tests). All circuitry is solder-reflow integrated on a standard Cu/polyimide flexible-electronic layer including an antenna, but while also allowing electroplating for simple integration of exotic metals for sensing electrodes. Optional paper microfluidics wick sweat from a sweat porous adhesive allowing flow to the sensor, or the sensor can be directly contacted to the skin. The wearability of the patch has been demonstrated for up to seven days, and includes a protective textile which provides a feel and appearance similar to a standard Band-Aid. Applications include hydration monitoring, but the basic capability is extendable to other mM ionic solutes in sweat (Cl(-), K(+), Mg(2+), NH4(+), and Zn(2+)). The design and fabrication of the patch are provided in full detail, as the basic components could be useful in the design of other wearable sensors.
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Tian L, Tadepalli S, Park SH, Liu KK, Morrissey JJ, Kharasch ED, Naik RR, Singamaneni S. Bioplasmonic calligraphy for multiplexed label-free biodetection. Biosens Bioelectron 2014; 59:208-15. [PMID: 24727607 PMCID: PMC4044868 DOI: 10.1016/j.bios.2014.03.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2014] [Revised: 03/13/2014] [Accepted: 03/21/2014] [Indexed: 10/25/2022]
Abstract
Printable multi-marker biochips that enable simultaneous quantitative detection of multiple target biomarkers in point-of-care and resource-limited settings are a holy grail in the field of biodiagnostics. However, preserving the functionality of biomolecules, which are routinely employed as recognition elements, during conventional printing approaches remains challenging. In this article, we introduce a simple yet powerful approach, namely plasmonic calligraphy, for realizing multiplexed label-free bioassays. Plasmonic calligraphy involves a regular ballpoint pen filled with biofunctionalized gold nanorods as plasmonic ink for creating isolated test domains on paper substrates. Biofriendly plasmonic calligraphy approach serves as a facile method to miniaturize the test domain size to few mm(2), which significantly improves the sensitivity of the plasmonic biosensor compared to bioplasmonic paper fabricated using immersion approach. Furthermore, plasmonic calligraphy also serves as a simple and efficient means to isolate multiple test domains on a single test strip, which facilitates multiplexed biodetection and multi-marker biochips. Plasmonic calligraphy, which can be potentially automated by implementing with a robotic arm, serves as an alternate path forward to overcome the limitations of conventional ink-jet printing.
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Kim S, Kulkarni DD, Davis R, Kim SS, Naik RR, Voevodin AA, Russell M, Jang SS, Tsukruk VV, Fedorov AG. Controlling the physicochemical state of carbon on graphene using focused electron-beam-induced deposition. ACS NANO 2014; 8:6805-6813. [PMID: 24988046 DOI: 10.1021/nn5011073] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Focused electron-beam-induced deposition (FEBID) is a promising nanolithography technique using "direct-write" patterning by carbon line and dot deposits on graphene. Understanding interactions between deposited carbon molecules and graphene enables highly localized modification of graphene properties, which is foundational to the FEBID utility as a nanopatterning tool. In this study, we demonstrate a unique possibility to induce dramatically different adsorption states of FEBID-produced carbon deposits on graphene, through density functional theory calculations and complementary Raman experiments. Specifically, an amorphous carbon deposit formed by direct irradiation of high energy primary electrons exhibits unusually strong interactions with graphene via covalent bonding, whereas the FEBID carbon formed due to low-energy secondary electrons is only weakly interacting with graphene via physisorption. These observations not only are of fundamental importance to basic physical chemistry of FEBID carbon-graphene interactions but also enable the use of selective laser-assisted postdeposition ablation to effectively remove the parasitically deposited, physisorbed carbon films for improving FEBID patterning resolution.
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Schmucker AL, Dickerson MB, Rycenga M, Mangelson BF, Brown KA, Naik RR, Mirkin CA. Combined chemical and physical encoding with silk fibroin-embedded nanostructures. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2014; 10:1485-1489. [PMID: 24376130 DOI: 10.1002/smll.201302923] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 10/16/2013] [Indexed: 06/03/2023]
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