1
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Uguz I, Ohayon D, Yilmaz S, Griggs S, Sheelamanthula R, Fabbri JD, McCulloch I, Inal S, Shepard KL. Complementary integration of organic electrochemical transistors for front-end amplifier circuits of flexible neural implants. Sci Adv 2024; 10:eadi9710. [PMID: 38517957 PMCID: PMC10959418 DOI: 10.1126/sciadv.adi9710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 02/14/2024] [Indexed: 03/24/2024]
Abstract
The ability to amplify, translate, and process small ionic potential fluctuations of neural processes directly at the recording site is essential to improve the performance of neural implants. Organic front-end analog electronics are ideal for this application, allowing for minimally invasive amplifiers owing to their tissue-like mechanical properties. Here, we demonstrate fully organic complementary circuits by pairing depletion- and enhancement-mode p- and n-type organic electrochemical transistors (OECTs). With precise geometry tuning and a vertical device architecture, we achieve overlapping output characteristics and integrate them into amplifiers with single neuronal dimensions (20 micrometers). Amplifiers with combined p- and n-OECTs result in voltage-to-voltage amplification with a gain of >30 decibels. We also leverage depletion and enhancement-mode p-OECTs with matching characteristics to demonstrate a differential recording capability with high common mode rejection rate (>60 decibels). Integrating OECT-based front-end amplifiers into a flexible shank form factor enables single-neuron recording in the mouse cortex with on-site filtering and amplification.
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Affiliation(s)
- Ilke Uguz
- Columbia University, New York, NY, USA
| | - David Ohayon
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
- Institute of Functional Intelligent Materials (IFIM), National University of Singapore, 117544, Singapore
| | | | - Sophie Griggs
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Rajendar Sheelamanthula
- Physical Science and Engineering Division, KAUST Solar Center, KAUST, Thuwal 23955-6900, Saudi Arabia
| | | | - Iain McCulloch
- Department of Chemistry, Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
- Physical Science and Engineering Division, KAUST Solar Center, KAUST, Thuwal 23955-6900, Saudi Arabia
| | - Sahika Inal
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
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2
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Ribeiro JF, Shepard KL, Ruther P. Editorial: Problems, strategies, and developments for high-density long-term chronic intracortical neural interfaces and their application. Front Neurosci 2024; 18:1373451. [PMID: 38414846 PMCID: PMC10896840 DOI: 10.3389/fnins.2024.1373451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/29/2024] Open
Affiliation(s)
- João Filipe Ribeiro
- Microtechnology for Neuroelectronics Lab, Istituto Italiano di Tecnologia, Neuroscience and Brain Technologies, Genova, Italy
| | - Kenneth L. Shepard
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY, United States
| | - Patrick Ruther
- Department of Microsystems Engineering (IMTEK), University of Freiburg, Freiburg, Germany
- BrainLinks-BrainTools Center, University of Freiburg, Freiburg, Germany
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3
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Lee Y, Buchheim J, Hellenkamp B, Lynall D, Yang K, Young EF, Penkov B, Sia S, Stojanovic MN, Shepard KL. Carbon-nanotube field-effect transistors for resolving single-molecule aptamer-ligand binding kinetics. Nat Nanotechnol 2024:10.1038/s41565-023-01591-0. [PMID: 38233588 DOI: 10.1038/s41565-023-01591-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 12/11/2023] [Indexed: 01/19/2024]
Abstract
Small molecules such as neurotransmitters are critical for biochemical functions in living systems. While conventional ultraviolet-visible spectroscopy and mass spectrometry lack portability and are unsuitable for time-resolved measurements in situ, techniques such as amperometry and traditional field-effect detection require a large ensemble of molecules to reach detectable signal levels. Here we demonstrate the potential of carbon-nanotube-based single-molecule field-effect transistors (smFETs), which can detect the charge on a single molecule, as a new platform for recognizing and assaying small molecules. smFETs are formed by the covalent attachment of a probe molecule, in our case a DNA aptamer, to a carbon nanotube. Conformation changes on binding are manifest as discrete changes in the nanotube electrical conductance. By monitoring the kinetics of conformational changes in a binding aptamer, we show that smFETs can detect and quantify serotonin at the single-molecule level, providing unique insights into the dynamics of the aptamer-ligand system. In particular, we show the involvement of G-quadruplex formation and the disruption of the native hairpin structure in the conformational changes of the serotonin-aptamer complex. The smFET is a label-free approach to analysing molecular interactions at the single-molecule level with high temporal resolution, providing additional insights into complex biological processes.
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Affiliation(s)
- Yoonhee Lee
- Department of Electrical Engineering, Columbia University, New York, NY, USA
- Division of Electronics & Information System, ICT Research Institute, Daegu Gyeongbuk Institute of Science and Technology (DGIST), Daegu, Republic of Korea
| | - Jakob Buchheim
- Department of Electrical Engineering, Columbia University, New York, NY, USA
- Deutsches Zentrum für Luft- und Raumfahrt e.V. (DLR), Institute of Quantum Technologies, Ulm, Germany
| | - Björn Hellenkamp
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - David Lynall
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Kyungae Yang
- Department of Medicine, Columbia University, New York, NY, USA
| | - Erik F Young
- Quicksilver Biosciences, Inc., New York, NY, USA
| | - Boyan Penkov
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Samuel Sia
- Department of Biomedical Engineering, Columbia University, New York, NY, USA
| | | | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY, USA.
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4
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Uguz I, Ohayon D, Arslan V, Sheelamanthula R, Griggs S, Hama A, Stanton JW, McCulloch I, Inal S, Shepard KL. Flexible switch matrix addressable electrode arrays with organic electrochemical transistor and pn diode technology. Nat Commun 2024; 15:533. [PMID: 38225257 PMCID: PMC10789794 DOI: 10.1038/s41467-023-44024-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 11/28/2023] [Indexed: 01/17/2024] Open
Abstract
Due to their effective ionic-to-electronic signal conversion and mechanical flexibility, organic neural implants hold considerable promise for biocompatible neural interfaces. Current approaches are, however, primarily limited to passive electrodes due to a lack of circuit components to realize complex active circuits at the front-end. Here, we introduce a p-n organic electrochemical diode using complementary p- and n-type conducting polymer films embedded in a 15-μm -diameter vertical stack. Leveraging the efficient motion of encapsulated cations inside this polymer stack and the opposite doping mechanisms of the constituent polymers, we demonstrate high current rectification ratios ([Formula: see text]) and fast switching speeds (230 μs). We integrate p-n organic electrochemical diodes with organic electrochemical transistors in the front-end pixel of a recording array. This configuration facilitates the access of organic electrochemical transistor output currents within a large network operating in the same electrolyte, while minimizing crosstalk from neighboring elements due to minimized reverse-biased leakage. Furthermore, we use these devices to fabricate time-division-multiplexed amplifier arrays. Lastly, we show that, when fabricated in a shank format, this technology enables the multiplexing of amplified local field potentials directly in the active recording pixel (26-μm diameter) in a minimally invasive form factor with shank cross-sectional dimensions of only 50×8 [Formula: see text].
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Affiliation(s)
- Ilke Uguz
- Electrical Engineering Department, Columbia University, New York, 10027, NY, USA.
| | - David Ohayon
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Volkan Arslan
- Electrical Engineering Department, Columbia University, New York, 10027, NY, USA
| | | | - Sophie Griggs
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Adel Hama
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - John William Stanton
- Electrical Engineering Department, Columbia University, New York, 10027, NY, USA
| | - Iain McCulloch
- Physical Science and Engineering Division, KAUST, Thuwal, 23955-6900, Saudi Arabia
- Department of Chemistry, University of Oxford, Oxford, OX1 3TA, UK
| | - Sahika Inal
- Organic Bioelectronics Laboratory, Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal, 23955-6900, Saudi Arabia
| | - Kenneth L Shepard
- Electrical Engineering Department, Columbia University, New York, 10027, NY, USA
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5
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Hillebrandt S, Moon CK, Taal AJ, Overhauser H, Shepard KL, Gather MC. High-Density Integration of Ultrabright OLEDs on a Miniaturized Needle-Shaped CMOS Backplane. Adv Mater 2023:e2300578. [PMID: 37470219 DOI: 10.1002/adma.202300578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 05/24/2023] [Accepted: 07/03/2023] [Indexed: 07/21/2023]
Abstract
Direct deposition of organic light-emitting diodes (OLEDs) on silicon-based complementary metal-oxide-semiconductor (CMOS) chips has enabled self-emissive microdisplays with high resolution and fill-factor. Emerging applications of OLEDs in augmented and virtual reality (AR/VR) displays and in biomedical applications, e.g., as brain implants for cell-specific light delivery in optogenetics, require light intensities orders of magnitude above those found in traditional displays. Further requirements often include a microscopic device footprint, a specific shape and ultrastable passivation, e.g., to ensure biocompatibility and minimal invasiveness of OLED-based implants. In this work, up to 1024 ultrabright, microscopic OLEDs are deposited directly on needle-shaped CMOS chips. Transmission electron microscopy and energy-dispersive X-ray spectroscopy are performed on the foundry-provided aluminum contact pads of the CMOS chips to guide a systematic optimization of the contacts. Plasma treatment and implementation of silver interlayers lead to ohmic contact conditions and thus facilitate direct vacuum deposition of orange- and blue-emitting OLED stacks leading to micrometer-sized pixels on the chips. The electronics in each needle allow each pixel to switch individually. The OLED pixels generate a mean optical power density of 0.25 mW mm-2 , corresponding to >40 000 cd m-2 , well above the requirement for daylight AR applications and optogenetic single-unit activation in the brain.
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Affiliation(s)
- Sabina Hillebrandt
- Organic Semiconductor Centre, SUPA School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK
- Humboldt Centre for Nano- and Biophotonics, Department of Chemistry, University of Cologne, Greinstr. 4-6, 50939, Cologne, Germany
| | - Chang-Ki Moon
- Organic Semiconductor Centre, SUPA School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK
- Humboldt Centre for Nano- and Biophotonics, Department of Chemistry, University of Cologne, Greinstr. 4-6, 50939, Cologne, Germany
| | | | | | | | - Malte C Gather
- Organic Semiconductor Centre, SUPA School of Physics and Astronomy, University of St Andrews, North Haugh, St Andrews, KY16 9SS, UK
- Humboldt Centre for Nano- and Biophotonics, Department of Chemistry, University of Cologne, Greinstr. 4-6, 50939, Cologne, Germany
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6
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Zeng N, Jung T, Sharma M, Eichler G, Fabbri J, Cotton RJ, Spinazzi E, Youngerman B, Carloni L, Shepard KL. A Wireless, Mechanically Flexible, 25μm-Thick, 65,536-Channel Subdural Surface Recording and Stimulating Microelectrode Array with Integrated Antennas. 2023 IEEE Symp VLSI Technol Circuits (2023) 2023; 2023:10.23919/vlsitechnologyandcir57934.2023.10185321. [PMID: 37671168 PMCID: PMC10478373 DOI: 10.23919/vlsitechnologyandcir57934.2023.10185321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/07/2023]
Abstract
This paper presents a fully wireless microelectrode array (MEA) system-on-chip (SoC) with 65,536 electrodes for non-penetrative cortical recording and stimulation, featuring a total sensing area of 6.8mm×7.4mm with a 26.5μm×29μm electrode pitch. Sensing, data telemetry, and powering are monolithically integrated on a single chip, which is made mechanically flexible to conform to the surface of the brain by substrate removal to a total thickness of 25μm allowing it to be contained entirely in the subdural space under the skull.
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7
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Poggio E, Vallese F, Hartel AJW, Morgenstern TJ, Kanner SA, Rauh O, Giamogante F, Barazzuol L, Shepard KL, Colecraft HM, Clarke OB, Brini M, Calì T. Perturbation of the host cell Ca 2+ homeostasis and ER-mitochondria contact sites by the SARS-CoV-2 structural proteins E and M. Cell Death Dis 2023; 14:297. [PMID: 37120609 PMCID: PMC10148623 DOI: 10.1038/s41419-023-05817-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2023] [Revised: 04/11/2023] [Accepted: 04/18/2023] [Indexed: 05/01/2023]
Abstract
Coronavirus disease (COVID-19) is a contagious respiratory disease caused by the SARS-CoV-2 virus. The clinical phenotypes are variable, ranging from spontaneous recovery to serious illness and death. On March 2020, a global COVID-19 pandemic was declared by the World Health Organization (WHO). As of February 2023, almost 670 million cases and 6,8 million deaths have been confirmed worldwide. Coronaviruses, including SARS-CoV-2, contain a single-stranded RNA genome enclosed in a viral capsid consisting of four structural proteins: the nucleocapsid (N) protein, in the ribonucleoprotein core, the spike (S) protein, the envelope (E) protein, and the membrane (M) protein, embedded in the surface envelope. In particular, the E protein is a poorly characterized viroporin with high identity amongst all the β-coronaviruses (SARS-CoV-2, SARS-CoV, MERS-CoV, HCoV-OC43) and a low mutation rate. Here, we focused our attention on the study of SARS-CoV-2 E and M proteins, and we found a general perturbation of the host cell calcium (Ca2+) homeostasis and a selective rearrangement of the interorganelle contact sites. In vitro and in vivo biochemical analyses revealed that the binding of specific nanobodies to soluble regions of SARS-CoV-2 E protein reversed the observed phenotypes, suggesting that the E protein might be an important therapeutic candidate not only for vaccine development, but also for the clinical management of COVID designing drug regimens that, so far, are very limited.
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Affiliation(s)
- Elena Poggio
- Department of Biology, University of Padova, Padova, Italy
| | - Francesca Vallese
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Andreas J W Hartel
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Travis J Morgenstern
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA
| | - Scott A Kanner
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Oliver Rauh
- Membrane Biophysics, Department of Biology, Technical University of Darmstadt, Darmstadt, Germany
| | - Flavia Giamogante
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Lucia Barazzuol
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Henry M Colecraft
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
- Department of Molecular Pharmacology and Therapeutics, Columbia University Irving Medical Center, New York, NY, USA
- Doctoral Program in Neurobiology and Behavior, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - Oliver Biggs Clarke
- Department of Anesthesiology, Columbia University Irving Medical Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | - Marisa Brini
- Department of Biology, University of Padova, Padova, Italy
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy
| | - Tito Calì
- Department of Biomedical Sciences, University of Padova, Padova, Italy.
- Study Center for Neurodegeneration (CESNE), University of Padova, Padova, Italy.
- Padova Neuroscience Center (PNC), University of Padova, Padova, Italy.
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8
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Rabinowitz J, Hartel AJW, Dayton H, Fabbri JD, Jo J, Dietrich LEP, Shepard KL. Charge Mapping of Pseudomonas aeruginosa Using a Hopping Mode Scanning Ion Conductance Microscopy Technique. Anal Chem 2023; 95:5285-5292. [PMID: 36920847 PMCID: PMC10359948 DOI: 10.1021/acs.analchem.2c05303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
Scanning ion conductance microscopy (SICM) is a topographic imaging technique capable of probing biological samples in electrolyte conditions. SICM enhancements have enabled surface charge detection based on voltage-dependent signals. Here, we show how the hopping mode SICM method (HP-SICM) can be used for rapid and minimally invasive surface charge mapping. We validate our method usingPseudomonas aeruginosaPA14 (PA) cells and observe a surface charge density of σPA = -2.0 ± 0.45 mC/m2 that is homogeneous within the ∼80 nm lateral scan resolution. This biological surface charge is detected from at least 1.7 μm above the membrane (395× the Debye length), and the long-range charge detection is attributed to electroosmotic amplification. We show that imaging with a nanobubble-plugged probe reduces perturbation of the underlying sample. We extend the technique to PA biofilms and observe a charge density exceeding -20 mC/m2. We use a solid-state calibration to quantify surface charge density and show that HP-SICM cannot be quantitatively described by a steady-state finite element model. This work contributes to the body of scanning probe methods that can uniquely contribute to microbiology and cellular biology.
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Affiliation(s)
- Jake Rabinowitz
- Department of Electrical Engineering, Columbia University, New York, New York 10027, United States
| | - Andreas J W Hartel
- Department of Electrical Engineering, Columbia University, New York, New York 10027, United States.,Department of Biology, Columbia University, New York, New York 10027, United States
| | - Hannah Dayton
- Department of Biology, Columbia University, New York, New York 10027, United States
| | - Jason D Fabbri
- Department of Electrical Engineering, Columbia University, New York, New York 10027, United States
| | - Jeanyoung Jo
- Department of Biology, Columbia University, New York, New York 10027, United States
| | - Lars E P Dietrich
- Department of Biology, Columbia University, New York, New York 10027, United States
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, New York 10027, United States
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9
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Pollmann EH, Yin H, Uguz I, Dubey A, Wingel KE, Choi JS, Moazeni S, Gilhotra Y, Pavlovsky VA, Banees A, Boominathan V, Robinson J, Veeraraghavan A, Pieribone VA, Pesaran B, Shepard KL. Subdural CMOS optical probe (SCOPe) for bidirectional neural interfacing. bioRxiv 2023:2023.02.07.527500. [PMID: 36798295 PMCID: PMC9934536 DOI: 10.1101/2023.02.07.527500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Optical neurotechnologies use light to interface with neurons and can monitor and manipulate neural activity with high spatial-temporal precision over large cortical extents. While there has been significant progress in miniaturizing microscope for head-mounted configurations, these existing devices are still very bulky and could never be fully implanted. Any viable translation of these technologies to human use will require a much more noninvasive, fully implantable form factor. Here, we leverage advances in microelectronics and heterogeneous optoelectronic packaging to develop a transformative, ultrathin, miniaturized device for bidirectional optical stimulation and recording: the subdural CMOS Optical Probe (SCOPe). By being thin enough to lie entirely within the subdural space of the primate brain, SCOPe defines a path for the eventual human translation of a new generation of brain-machine interfaces based on light.
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10
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Jang SS, Dubnik S, Hon J, Hellenkamp B, Lynall DG, Shepard KL, Nuckolls C, Gonzalez RL. Characterizing the Conformational Free-Energy Landscape of RNA Stem-Loops Using Single-Molecule Field-Effect Transistors. J Am Chem Soc 2023; 145:402-412. [PMID: 36547391 PMCID: PMC10025942 DOI: 10.1021/jacs.2c10218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We have developed and used single-molecule field-effect transistors (smFETs) to characterize the conformational free-energy landscape of RNA stem-loops. Stem-loops are one of the most common RNA structural motifs and serve as building blocks for the formation of complex RNA structures. Given their prevalence and integral role in RNA folding, the kinetics of stem-loop (un)folding has been extensively characterized using both experimental and computational approaches. Interestingly, these studies have reported vastly disparate timescales of (un)folding, which has been interpreted as evidence that (un)folding of even simple stem-loops occurs on a highly rugged conformational energy landscape. Because smFETs do not rely on fluorophore reporters of conformation or mechanical (un)folding forces, they provide a unique approach that has allowed us to directly monitor tens of thousands of (un)folding events of individual stem-loops at a 200 μs time resolution. Our results show that under our experimental conditions, stem-loops (un)fold over a 1-200 ms timescale during which they transition between ensembles of unfolded and folded conformations, the latter of which is composed of at least two sub-populations. The 1-200 ms timescale of (un)folding we observe here indicates that smFETs report on complete (un)folding trajectories in which unfolded conformations of the RNA spend long periods of time wandering the free-energy landscape before sampling one of several misfolded conformations or the natively folded conformation. Our findings highlight the extremely rugged landscape on which even the simplest RNA structural elements fold and demonstrate that smFETs are a unique and powerful approach for characterizing the conformational free-energy of RNA.
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Affiliation(s)
- Sukjin S. Jang
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Sarah Dubnik
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Jason Hon
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Björn Hellenkamp
- Department of Electrical Engineering, Columbia University, 3000 Broadway, New York, 10027, USA
| | - David G. Lynall
- Department of Electrical Engineering, Columbia University, 3000 Broadway, New York, 10027, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, 3000 Broadway, New York, 10027, USA
| | - Colin Nuckolls
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, 3000 Broadway, New York, NY 10027, USA
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11
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Uguz I, Shepard KL. Spatially controlled, bipolar, cortical stimulation with high-capacitance, mechanically flexible subdural surface microelectrode arrays. Sci Adv 2022; 8:eabq6354. [PMID: 36260686 PMCID: PMC9581492 DOI: 10.1126/sciadv.abq6354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
Most neuromodulation approaches rely on extracellular electrical stimulation with penetrating electrodes at the cost of cortical damage. Surface electrodes, in contrast, are much less invasive but are challenged by the lack of proximity to axonal processes, leading to poor resolution. Here, we demonstrate that high-density (40-μm pitch), high-capacitance (>1 nF), single neuronal resolution PEDOT:PSS electrodes can be programmed to shape the charge injection front selectively at depths approaching 300 micrometers with a lateral resolution better than 100 micrometers. These electrodes, patterned on thin-film parylene substrate, can be subdurally implanted and adhere to the pial surface in chronic settings. By leveraging surface arrays that are optically transparent with PEDOT:PSS local interconnects and integrated with depth electrodes, we are able to combine surface stimulation and recording with calcium imaging and depth recording to demonstrate these spatial limits of bidirectional communication with pyramidal neurons in mouse visual cortex both laterally and at depth from the surface.
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12
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Elloian J, Jadwiszczak J, Arslan V, Sherman JD, Kessler DO, Shepard KL. Flexible ultrasound transceiver array for non-invasive surface-conformable imaging enabled by geometric phase correction. Sci Rep 2022; 12:16184. [PMID: 36171424 PMCID: PMC9519534 DOI: 10.1038/s41598-022-20721-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Accepted: 09/16/2022] [Indexed: 11/12/2022] Open
Abstract
Ultrasound imaging provides the means for non-invasive real-time diagnostics of the internal structure of soft tissue in living organisms. However, the majority of commercially available ultrasonic transducers have rigid interfaces which cannot conform to highly-curved surfaces. These geometric limitations can introduce a signal-quenching air gap for certain topographies, rendering accurate imaging difficult or impractical. Here, we demonstrate a 256-element flexible two-dimensional (2D) ultrasound piezoelectric transducer array with geometric phase correction. We show surface-conformable real-time B-mode imaging, down to an extreme radius of curvature of 1.5 cm, while maintaining desirable performance metrics such as high signal-to-noise ratio (SNR) and minimal elemental cross-talk at all stages of bending. We benchmark the array capabilities by resolving reflectors buried at known locations in a medical-grade tissue phantom, and demonstrate how phase correction can improve image reconstruction on curved surfaces. With the current array design, we achieve an axial resolution of ≈ 2 mm at clinically-relevant depths in tissue, while operating the array at 1.4 MHz with a bandwidth of ≈ 41%. We use our prototype to image the surface of the human humerus at different positions along the arm, demonstrating proof-of-concept applicability for real-time diagnostics using phase-corrected flexible ultrasound probes.
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Affiliation(s)
- Jeffrey Elloian
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, NY, 10027, USA
| | - Jakub Jadwiszczak
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, NY, 10027, USA
| | - Volkan Arslan
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, NY, 10027, USA
| | - Jeffrey D Sherman
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, NY, 10027, USA
| | - David O Kessler
- Department of Emergency Medicine, Morgan Stanley Children's Hospital of New York Presbyterian at Columbia University Medical Center, New York, 10032, USA
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, NY, 10027, USA. .,Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Avenue, New York, NY, 10027, USA.
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13
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Zhang Y, Muthuraman P, Andino-Pavlovsky V, Uguz I, Elloian J, Shepard KL. Augmented ultrasonography with implanted CMOS electronic motes. Nat Commun 2022; 13:3521. [PMID: 35725979 PMCID: PMC9209459 DOI: 10.1038/s41467-022-31166-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Accepted: 06/07/2022] [Indexed: 11/09/2022] Open
Abstract
Modern clinical practice benefits significantly from imaging technologies and much effort is directed toward making this imaging more informative through the addition of contrast agents or reporters. Here, we report the design of a battery-less integrated circuit mote acting as an electronic reporter during medical ultrasound imaging. When implanted within the field-of-view of a brightness-mode (B-mode) ultrasound imager, this mote transmits information from its location through backscattered acoustic energy which is captured within the ultrasound image itself. We prototype and characterize the operation of such motes in vitro and in vivo. Performing with a static power consumption of less than 57 pW, the motes operate at duty cycles for receiving acoustic energy as low as 50 ppm. Motes within the same field-of-view during imaging have demonstrated signal-to-noise ratios of more than 19.1 dB at depths of up to 40 mm in lossy phantom. Physiological information acquired through such motes, which is beyond what is measurable with endogenous ultrasound backscatter and which is biogeographically located within an image, has the potential to provide an augmented ultrasonography.
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Affiliation(s)
- Yihan Zhang
- Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA.,School of Integrated Circuits, Peking University, Beijing, P. R. China
| | - Prashant Muthuraman
- Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA
| | | | - Ilke Uguz
- Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA
| | - Jeffrey Elloian
- Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA.
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14
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Jadwiszczak J, Sherman J, Lynall D, Liu Y, Penkov B, Young E, Keneipp R, Drndić M, Hone JC, Shepard KL. Mixed-Dimensional 1D/2D van der Waals Heterojunction Diodes and Transistors in the Atomic Limit. ACS Nano 2022; 16:1639-1648. [PMID: 35014261 PMCID: PMC9526797 DOI: 10.1021/acsnano.1c10524] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Inverting a semiconducting channel is the basis of all field-effect transistors. In silicon-based metal-oxide-semiconductor field-effect transistors (MOSFETs), a gate dielectric mediates this inversion. Access to inversion layers may be granted by interfacing ultrathin low-dimensional semiconductors in heterojunctions to advance device downscaling. Here we demonstrate that monolayer molybdenum disulfide (MoS2) can directly invert a single-walled semiconducting carbon nanotube (SWCNT) transistor channel without the need for a gate dielectric. We fabricate and study this atomically thin one-dimensional/two-dimensional (1D/2D) van der Waals heterojunction and employ it as the gate of a 1D heterojunction field-effect transistor (1D-HFET) channel. Gate control is based on modulating the conductance through the channel by forming a lateral p-n junction within the CNT itself. In addition, we observe a region of operation exhibiting a negative static resistance after significant gate tunneling current passes through the junction. Technology computer-aided design (TCAD) simulations confirm the role of minority carrier drift-diffusion in enabling this behavior. The resulting van der Waals transistor architecture thus has the dual characteristics of both field-effect and tunneling transistors, and it advances the downscaling of heterostructures beyond the limits of dangling bonds and epitaxial constraints faced by III-V semiconductors.
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Affiliation(s)
- Jakub Jadwiszczak
- Department of Electrical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Jeffrey Sherman
- Department of Electrical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - David Lynall
- Department of Electrical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Yang Liu
- Department of Mechanical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Boyan Penkov
- Department of Electrical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Erik Young
- Department of Electrical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Rachael Keneipp
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - James C Hone
- Department of Mechanical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, 500 West 120th Street, New York, New York 10027, United States
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Avenue, New York, New York 10027, United States
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15
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Taal AJ, Lee C, Choi J, Hellenkamp B, Shepard KL. Toward implantable devices for angle-sensitive, lens-less, multifluorescent, single-photon lifetime imaging in the brain using Fabry-Perot and absorptive color filters. Light Sci Appl 2022; 11:24. [PMID: 35075116 PMCID: PMC8786868 DOI: 10.1038/s41377-022-00708-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 05/17/2023]
Abstract
Implantable image sensors have the potential to revolutionize neuroscience. Due to their small form factor requirements; however, conventional filters and optics cannot be implemented. These limitations obstruct high-resolution imaging of large neural densities. Recent advances in angle-sensitive image sensors and single-photon avalanche diodes have provided a path toward ultrathin lens-less fluorescence imaging, enabling plenoptic sensing by extending sensing capabilities to include photon arrival time and incident angle, thereby providing the opportunity for separability of fluorescence point sources within the context of light-field microscopy (LFM). However, the addition of spectral sensitivity to angle-sensitive LFM reduces imager resolution because each wavelength requires a separate pixel subset. Here, we present a 1024-pixel, 50 µm thick implantable shank-based neural imager with color-filter-grating-based angle-sensitive pixels. This angular-spectral sensitive front end combines a metal-insulator-metal (MIM) Fabry-Perot color filter and diffractive optics to produce the measurement of orthogonal light-field information from two distinct colors within a single photodetector. The result is the ability to add independent color sensing to LFM while doubling the effective pixel density. The implantable imager combines angular-spectral and temporal information to demix and localize multispectral fluorescent targets. In this initial prototype, this is demonstrated with 45 μm diameter fluorescently labeled beads in scattering medium. Fluorescent lifetime imaging is exploited to further aid source separation, in addition to detecting pH through lifetime changes in fluorescent dyes. While these initial fluorescent targets are considerably brighter than fluorescently labeled neurons, further improvements will allow the application of these techniques to in-vivo multifluorescent structural and functional neural imaging.
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Affiliation(s)
- Adriaan J Taal
- Columbia University - Department of Electrical Engineering, 500W. 120th St., Mudd 1310, New York, 10027, NY, USA
| | - Changhyuk Lee
- Columbia University - Department of Electrical Engineering, 500W. 120th St., Mudd 1310, New York, 10027, NY, USA
- Korea Institute of Science and Technology - Brain Science Institute, 5 Hwarang-ro 14-gil, Seongbuk-gu, Seoul, 02792, Republic of Korea
| | - Jaebin Choi
- Columbia University - Department of Electrical Engineering, 500W. 120th St., Mudd 1310, New York, 10027, NY, USA
| | - Björn Hellenkamp
- Columbia University - Department of Electrical Engineering, 500W. 120th St., Mudd 1310, New York, 10027, NY, USA
| | - Kenneth L Shepard
- Columbia University - Department of Electrical Engineering, 500W. 120th St., Mudd 1310, New York, 10027, NY, USA.
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16
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Kim H, Kim YD, Wu T, Cao Q, Herman IP, Hone J, Guo J, Shepard KL. Electroluminescence of atoms in a graphene nanogap. Sci Adv 2022; 8:eabj1742. [PMID: 35061537 PMCID: PMC8782453 DOI: 10.1126/sciadv.abj1742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 11/29/2021] [Indexed: 06/01/2023]
Abstract
Here, we report light emission from single atoms bridging a graphene nanogap that emit bright visible light based on fluorescence of ionized atoms. Oxygen atoms in the gap shows a peak emission wavelength of 569 nm with a full width at half maximum (FWHM) of 208 nm. The energy states produced by these ionized oxygen atoms bridging carbon atoms in the gap also produce a large negative differential resistance (NDR) in the transport across the gap with the highest peak-to-valley current ratio (PVR = 45) and highest peak current density (~90 kA/cm2) ever reported in a solid-state tunneling device. While tunneling transport has been previously observed in graphene nanogaps, the bridging of ionized oxygen observed here shows a low excess current, leading to the observed PVR. On the basis of the highly reproducible light emission and NDR from these structures, we demonstrate a 65,536-pixel light-emitting nanogap array.
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Affiliation(s)
- Hyungsik Kim
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Young Duck Kim
- Department of Physics, Kyung Hee University, Seoul, Republic of Korea
- Department of Information Display, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Tong Wu
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA
| | - Qingrui Cao
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA
- Department of Physics, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Irving P. Herman
- Department of Applied Physics and Applied Mathematics, Columbia University, New York, NY, USA
| | - James Hone
- Department of Mechanical Engineering, Columbia University, New York, NY, USA
| | - Jing Guo
- Department of Electrical and Computer Engineering, University of Florida, Gainesville, FL, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA
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17
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Costa T, Shi C, Tien K, Elloian J, Cardoso FA, Shepard KL. An Integrated 2D Ultrasound Phased Array Transmitter in CMOS With Pixel Pitch-Matched Beamforming. IEEE Trans Biomed Circuits Syst 2021; 15:731-742. [PMID: 34260357 DOI: 10.1109/tbcas.2021.3096722] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Emerging non-imaging ultrasound applications, such as ultrasonic wireless power delivery to implantable devices and ultrasound neuromodulation, require wearable form factors, millisecond-range pulse durations and focal spot diameters approaching 100 μm with electronic control of its three-dimensional location. None of these are compatible with typical handheld linear array ultrasound imaging probes. In this work, we present a 4 mm × 5 mm 2D ultrasound phased array transmitter with integrated piezoelectric ultrasound transducers on complementary metal-oxide-semiconductor (CMOS) integrated circuits, featuring pixel-level pitch-matched transmit beamforming circuits which support arbitrary pulse duration. Our direct integration method enabled up to 10 MHz ultrasound arrays in a patch form-factor, leading to focal spot diameter of ∼200 μm, while pixel pitch-matched beamforming allowed for precise three-dimensional positioning of the ultrasound focal spot. Our device has the potential to provide a high-spatial resolution and wearable interface to both powering of highly-miniaturized implantable devices and ultrasound neuromodulation.
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18
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Shi C, Andino-Pavlovsky V, Lee SA, Costa T, Elloian J, Konofagou EE, Shepard KL. Application of a sub-0.1-mm 3 implantable mote for in vivo real-time wireless temperature sensing. Sci Adv 2021; 7:7/19/eabf6312. [PMID: 33962948 PMCID: PMC8104878 DOI: 10.1126/sciadv.abf6312] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 03/18/2021] [Indexed: 05/17/2023]
Abstract
There has been increasing interest in wireless, miniaturized implantable medical devices for in vivo and in situ physiological monitoring. Here, we present such an implant that uses a conventional ultrasound imager for wireless powering and data communication and acts as a probe for real-time temperature sensing, including the monitoring of body temperature and temperature changes resulting from therapeutic application of ultrasound. The sub-0.1-mm3, sub-1-nW device, referred to as a mote, achieves aggressive miniaturization through the monolithic integration of a custom low-power temperature sensor chip with a microscale piezoelectric transducer fabricated on top of the chip. The small displaced volume of these motes allows them to be implanted or injected using minimally invasive techniques with improved biocompatibility. We demonstrate their sensing functionality in vivo for an ultrasound neurostimulation procedure in mice. Our motes have the potential to be adapted to the distributed and localized sensing of other clinically relevant physiological parameters.
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Affiliation(s)
- Chen Shi
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | | | - Stephen A Lee
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Tiago Costa
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
- Department of Microelectronics, Delft University of Technology, 2628 CD Delft, Netherlands
| | - Jeffrey Elloian
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Elisa E Konofagou
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
- Department of Radiology, Columbia University, New York, NY 10032, USA
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA.
- Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA
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19
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Taal AJ, Rabinowitz J, Shepard KL. mr-EBL: ultra-high sensitivity negative-tone electron beam resist for highly selective silicon etching and large-scale direct patterning of permanent structures. Nanotechnology 2021; 32:245302. [PMID: 33706291 DOI: 10.1088/1361-6528/abeded] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 03/11/2021] [Indexed: 06/12/2023]
Abstract
Electron beam lithography (EBL) is the state-of-the-art technique for rapid prototyping of nanometer-scale devices. Even so, processing speeds remain limited for the highest resolution patterning. Here, we establish Mr-EBL as the highest throughput negative tone electron-beam-sensitive resist. The 10μC cm-2dose requirement enables fabricating a 100 mm2photonic diffraction grating in a ten minute EBL process. Optimized processing conditions achieve a critical resolution of 75 nm with 3× faster write speeds than SU-8 and 1-2 orders of magnitude faster write speeds than maN-2400 and hydrogen silsesquioxane. Notably, these conditions significantly differ from the manufacturers' recommendations for the recently commercialized Mr-EBL resist. We demonstrate Mr-EBL to be a robust negative etch mask by etching silicon trenches with aspect ratios of 10 and near-vertical sidewalls. Furthermore, our optimized processing conditions are suitable to direct patterning on integrated circuits or delicate nanofabrication stacks, in contrast to other negative tone EBL resists. In conclusion, Mr-EBL is a highly attractive EBL resist for rapid prototyping in nanophotonics, MEMS, and fluidics.
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Affiliation(s)
- Adriaan J Taal
- Electrical Engineering, Columbia University, New York, United States of America
| | - Jake Rabinowitz
- Electrical Engineering, Columbia University, New York, United States of America
| | - Kenneth L Shepard
- Electrical Engineering, Columbia University, New York, United States of America
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20
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Sherman JD, Elloian J, Jadwiszczak J, Shepard KL. On the Temperature Dependence of the Piezoelectric Response of Prepoled Poly(vinylidene fluoride) Films. ACS Appl Polym Mater 2020; 2:5110-5120. [PMID: 34142087 PMCID: PMC8205423 DOI: 10.1021/acsapm.0c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
There is growing interest in integrating piezoelectric materials with complementary metal-oxide-semiconductor (CMOS) technology to enable expanded applications. A promising material for ultrasound transducer applications is polyvinylidene fluoride (PVDF), a piezoelectric polymer. One of the challenges with PVDF is that its piezoelectric properties can deteriorate when exposed to temperatures in excess of 70 °C for extended periods of time during fabrication. Here, we report on the effects of both shortening annealing times and providing this heating non-uniformly, as is characteristic of some processing conditions, on the piezoelectric coefficient (d 33) of PVDF films for various thicknesses. In this case, no degradation in the d 33 was observed at temperatures below 100 °C for anneal times of under one minute when this heating is applied through one side of the film, making PVDF compatible with many bonding and photolithographic processing steps required for CMOS integration. More surprisingly, for one-sided heating to temperatures between 90 °C and 110 °C, we observed a transient enhancement of the d 33 by nearly 40% that lasted for several hours after these anneals. We attribute this effect to induced strain in these films.
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Affiliation(s)
- Jeffrey D Sherman
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, New York 10027, United States
| | - Jeffrey Elloian
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, New York 10027, United States
| | - Jakub Jadwiszczak
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, New York 10027, United States
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, 500 W 120th St., New York, New York 10027, United States
- Department of Biomedical Engineering, Columbia University, 1210 Amsterdam Avenue, New York, New York 10027, United States
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21
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Moreaux LC, Yatsenko D, Sacher WD, Choi J, Lee C, Kubat NJ, Cotton RJ, Boyden ES, Lin MZ, Tian L, Tolias AS, Poon JKS, Shepard KL, Roukes ML. Integrated Neurophotonics: Toward Dense Volumetric Interrogation of Brain Circuit Activity-at Depth and in Real Time. Neuron 2020; 108:66-92. [PMID: 33058767 PMCID: PMC8061790 DOI: 10.1016/j.neuron.2020.09.043] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/18/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022]
Abstract
We propose a new paradigm for dense functional imaging of brain activity to surmount the limitations of present methodologies. We term this approach "integrated neurophotonics"; it combines recent advances in microchip-based integrated photonic and electronic circuitry with those from optogenetics. This approach has the potential to enable lens-less functional imaging from within the brain itself to achieve dense, large-scale stimulation and recording of brain activity with cellular resolution at arbitrary depths. We perform a computational study of several prototype 3D architectures for implantable probe-array modules that are designed to provide fast and dense single-cell resolution (e.g., within a 1-mm3 volume of mouse cortex comprising ∼100,000 neurons). We describe progress toward realizing integrated neurophotonic imaging modules, which can be produced en masse with current semiconductor foundry protocols for chip manufacturing. Implantation of multiple modules can cover extended brain regions.
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Affiliation(s)
- Laurent C Moreaux
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Dimitri Yatsenko
- Vathes LLC, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Wesley D Sacher
- Kavli Nanoscience Institute, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA; Max Planck Institute for Microstructure Physics, Halle, Germany
| | - Jaebin Choi
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Changhyuk Lee
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA; Center for BioMicrosystems, Brain Science Institute, Korea Institute of Science and Technology, Korea
| | - Nicole J Kubat
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA
| | - R James Cotton
- Shirley Ryan AbilityLab, Northwestern University, Chicago, IL 60611, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Edward S Boyden
- Howard Hughes Medical Institute, Cambridge, MA, USA; McGovern Institute, MIT, Cambridge, USA; Koch Institute, MIT, Cambridge, USA; Departments of Brain and Cognitive Sciences, Media Arts and Sciences, and Biological Engineering, MIT, Cambridge, USA
| | - Michael Z Lin
- Departments of Neurobiology and Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - Lin Tian
- Department of Biochemistry and Molecular Medicine, School of Medicine, University of California, Davis, CA 95616, USA
| | - Andreas S Tolias
- Vathes LLC, Houston, TX 77030, USA; Center for Neuroscience and Artificial Intelligence and Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA; Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
| | - Joyce K S Poon
- Max Planck Institute for Microstructure Physics, Halle, Germany; Department of Electrical and Computer Engineering, University of Toronto, 10 King's College Rd., Toronto, ON M5S 3G4, Canada
| | - Kenneth L Shepard
- Departments of Electrical Engineering and Biomedical Engineering, Columbia University, New York, NY 10027, USA
| | - Michael L Roukes
- Division of Physics, Mathematics and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA; Kavli Nanoscience Institute, California Institute of Technology, Pasadena, CA 91125, USA; Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA 91125, USA; Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
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22
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Choi J, Taal AJ, Meng WL, Pollmann EH, Stanton JW, Lee C, Moazeni S, Moreaux LC, Roukes ML, Shepard KL. Fully Integrated Time-Gated 3D Fluorescence Imager for Deep Neural Imaging. IEEE Trans Biomed Circuits Syst 2020; 14:636-645. [PMID: 32746353 PMCID: PMC7528638 DOI: 10.1109/tbcas.2020.3008513] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
This paper presents a device for time-gated fluorescence imaging in the deep brain, consisting of two on-chip laser diodes and 512 single-photon avalanche diodes (SPADs). The edge-emitting laser diodes deliver fluorescence excitation above the SPAD array, parallel to the imager. In the time domain, laser diode illumination is pulsed and the SPAD is time-gated, allowing a fluorescence excitation rejection up to O.D. 3 at 1 ns of time-gate delay. Each SPAD pixel is masked with Talbot gratings to enable the mapping of 2D array photon counts into a 3D image. The 3D image achieves a resolution of 40, 35, and 73 μm in the x, y, and z directions, respectively, in a noiseless environment, with a maximum frame rate of 50 kilo-frames-per-second. We present measurement results of the spatial and temporal profiles of the dual-pulsed laser diode illumination and of the photon detection characteristics of the SPAD array. Finally, we show the imager's ability to resolve a glass micropipette filled with red fluorescent microspheres. The system's 420 μm-wide cross section allows it to be inserted at arbitrary depths of the brain while achieving a field of view four times larger than fiber endoscopes of equal diameter.
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23
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Choi J, Taal AJ, Meng WL, Pollmann EH, Stanton JW, Lee C, Moazeni S, Moreaux LC, Roukes ML, Shepard KL. Fully Integrated Time-Gated 3D Fluorescence Imager for Deep Neural Imaging. IEEE Trans Biomed Circuits Syst 2020; 14:636-645. [PMID: 32746353 DOI: 10.1109/biocas.2019.8919018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
This paper presents a device for time-gated fluorescence imaging in the deep brain, consisting of two on-chip laser diodes and 512 single-photon avalanche diodes (SPADs). The edge-emitting laser diodes deliver fluorescence excitation above the SPAD array, parallel to the imager. In the time domain, laser diode illumination is pulsed and the SPAD is time-gated, allowing a fluorescence excitation rejection up to O.D. 3 at 1 ns of time-gate delay. Each SPAD pixel is masked with Talbot gratings to enable the mapping of 2D array photon counts into a 3D image. The 3D image achieves a resolution of 40, 35, and 73 μm in the x, y, and z directions, respectively, in a noiseless environment, with a maximum frame rate of 50 kilo-frames-per-second. We present measurement results of the spatial and temporal profiles of the dual-pulsed laser diode illumination and of the photon detection characteristics of the SPAD array. Finally, we show the imager's ability to resolve a glass micropipette filled with red fluorescent microspheres. The system's 420 μm-wide cross section allows it to be inserted at arbitrary depths of the brain while achieving a field of view four times larger than fiber endoscopes of equal diameter.
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24
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Shi C, Costa T, Elloian J, Zhang Y, Shepard KL. A 0.065-mm 3 Monolithically-Integrated Ultrasonic Wireless Sensing Mote for Real-Time Physiological Temperature Monitoring. IEEE Trans Biomed Circuits Syst 2020; 14:412-424. [PMID: 32012022 DOI: 10.1109/tbcas.2020.2971066] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Accurate monitoring of physiological temperature is important for many biomedical applications, including monitoring of core body temperature, detecting tissue pathologies, and evaluating surgical procedures involving thermal treatment such as hyperthermia therapy and tissue ablation. Many of these applications can benefit from replacing external temperature probes with injectable wireless devices. Here we present such a device for real-time in vivo temperature monitoring that relies on "chip-as-system" integration. With an on-chip piezoelectric transducer and measuring only 380 μm × 300 μm × 570 μm, the 0.065-mm3 monolithic device, in the form of a mote, harvests ultrasound energy for power and transmits temperature data through acoustic backscattering. Containing a low-power temperature sensor implemented with a subthreshold oscillator and consuming 0.813 nW at 37 °C, the mote achieves line sensitivity of 0.088 °C/V, temperature error of +0.22/-0.28 °C, and a resolution of 0.0078 °C rms. A long-term measurement with the mote reveals an Allan deviation floor of <138.6 ppm, indicating the feasibility of using the mote for continuous physiological temperature monitoring.
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25
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Cornell WC, Zhang Y, Bendebury A, Hartel AJ, Shepard KL, Dietrich LE. Phenazine oxidation by a distal electrode modulates biofilm morphogenesis. Biofilm 2020; 2:100025. [PMID: 33447810 PMCID: PMC7798475 DOI: 10.1016/j.bioflm.2020.100025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 05/02/2020] [Accepted: 05/03/2020] [Indexed: 11/20/2022] Open
Abstract
Microbes living in biofilms, dense assemblages of cells, experience limitation for resources such as oxygen when cellular consumption outpaces diffusion. The pathogenic bacterium Pseudomonas aeruginosa has strategies for coping with hypoxia that support cellular redox balancing in biofilms; these include (1) increasing access to oxygen by forming wrinkles in the biofilm surface and (2) electrochemically reducing endogenous compounds called phenazines, which can shuttle electrons to oxidants available at a distance. Phenazine-mediated extracellular electron transfer (EET) has been shown to support survival for P. aeruginosa cells in anoxic liquid cultures, but the physiological relevance of EET over a distance for P. aeruginosa biofilms has remained unconfirmed. Here, we use a custom-built electrochemistry setup to show that phenazine-mediated electron transfer at a distance inhibits wrinkle formation in P. aeruginosa biofilms. This result demonstrates that phenazine-dependent EET to a distal oxidant affects biofilm morphogenesis.
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Affiliation(s)
- William Cole Cornell
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Yihan Zhang
- Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA
| | - Anastasia Bendebury
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
| | - Andreas J.W. Hartel
- Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, 10027, USA
- Corresponding authors.
| | - Lars E.P. Dietrich
- Department of Biological Sciences, Columbia University, New York, NY, 10027, USA
- Corresponding authors.
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26
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Thimot J, Kim K, Shi C, Shepard KL. A 27-Mbps, 0.08-mm 3 CMOS Transceiver with Simultaneous Near-field Power Transmission and Data Telemetry for Implantable Systems. Proc Cust Integr Circuits Conf 2020; 2020. [PMID: 34305311 DOI: 10.1109/cicc48029.2020.9075888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
This paper describes an inductively powered 27-Mbps, 0.08-mm3 CMOS transceiver with integrated RF receiver coils for simultaneous two-way, near-field data telemetry and power transmission for implantable systems. A four-coil inductive link operates at a 27-MHz carrier for power and a 700-MHz carrier for data telemetry with the antennae taking an area of only 2 mm by 2 mm. Amplitude-shift-keying (ASK) modulation is used for data downlink at 6.6 kbps and load-shift keying (LSK) backscattering is used for data uplink at 27 Mbps. The transceiver consumes 2.7 mW and can power a load consuming up to an additional 1.5 mW. Implemented in a 0.18-um silicon-on-insulator (SOI) technology, post-processing steps are used to decrease chip thickness to approximately 15um, making the chip flexible with a tissue-like form factor and removing the effects of the substrate on coil performance. Power harvesting circuitry, including passive rectifier, voltage regulator, RF limiter, ASK and LSK modulator, clock generator, and digital controller are positioned adjacent to the coils and limited to an area of 0.5 mm by 2mm. Complete transceiver functionality of the system has been achieved with overall power transfer efficiency (PTE) of 1.04% through 1 mm of tissue phantom between reader and implant.
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Affiliation(s)
- Jordan Thimot
- Bioelectronic Systems Lab, Department of Electrical Engineering, Columbia University, New York NY
| | - Kukjoo Kim
- Bioelectronic Systems Lab, Department of Electrical Engineering, Columbia University, New York NY
| | - Chen Shi
- Bioelectronic Systems Lab, Department of Electrical Engineering, Columbia University, New York NY
| | - Kenneth L Shepard
- Bioelectronic Systems Lab, Department of Electrical Engineering, Columbia University, New York NY
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27
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Abstract
Single-walled carbon nanotubes (SWCNTs) are well-established transporters of electronic current, electrolyte, and ions. In this work, we demonstrate an electrically actuated biomimetic ion pump by combining these electronic and nanofluidic transport capabilities within an individual SWCNT device. Ion pumping is driven by a solid-state electronic input, as Coulomb drag coupling transduces electrical energy from solid-state charge along the SWCNT shell to electrolyte inside the SWCNT core. Short-circuit ionic currents, measured without an electrolyte potential difference, exceed 1 nA and scale larger with increasing ion concentrations through 1 M, demonstrating applicability under physiological (∼140 mM) and saltwater (∼600 mM) conditions. The interlayer coupling allows ionic currents to be tuned with the source-drain potential difference and electronic currents to be tuned with the electrolyte potential difference. This combined electronic-nanofluidic SWCNT device presents intriguing applications as a biomimetic ion pump or component of an artificial membrane.
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Affiliation(s)
- Jake Rabinowitz
- Department of Electrical Engineering, Columbia University, NY 10027, USA
| | - Charishma Cohen
- Department of Electrical Engineering, Columbia University, NY 10027, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, NY 10027, USA
- Department of Biomedical Engineering, Columbia University, NY 10027, USA
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28
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Choi J, Taal AJ, Pollmann EH, Lee C, Kim K, Moreaux LC, Roukes ML, Shepard KL. A 512-Pixel, 51-kHz-Frame-Rate, Dual-Shank, Lens-less, Filter-less Single Photon Avalanche Diode CMOS Neural Imaging Probe. IEEE J Solid-State Circuits 2019; 54:2957-2968. [PMID: 31798187 PMCID: PMC6886722 DOI: 10.1109/jssc.2019.2941529] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We present an implantable single photon shank-based imager, monolithically integrated onto a single CMOS IC. The imager comprises of 512 single photon avalanche diodes distributed along two shanks, with a 6-bit depth in-pixel memory and an on-chip digital-to-time converter. To scale down the system to a minimally invasive form factor, we substitute optical filtering and focusing elements with a time-gated, angle-sensitive detection system. The imager computationally reconstructs the position of fluorescent sources within a three-dimensional volume of 3.4 mm × 600 µm × 400 µm.
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Affiliation(s)
- Jaebin Choi
- Electrical Engineering Department, Columbia University, New York, NY, USA
| | - Adriaan J Taal
- Electrical Engineering Department, Columbia University, New York, NY, USA
| | - Eric H Pollmann
- Electrical Engineering Department, Columbia University, New York, NY, USA
| | - Changhyuk Lee
- Brain Science Institute, Korea Institute of Science and Technology, Seoul, South Korea
| | - Kukjoo Kim
- Electronics and Telecommunications Research Institute, Daejeon, South Korea
| | | | | | - Kenneth L Shepard
- Bioelectronic Systems Laboratories, Columbia University, New York, NY, USA
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29
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Chien CC, Shekar S, Niedzwiecki DJ, Shepard KL, Drndic M. Single-Stranded DNA Translocation Recordings through Solid-State Nanopores on Glass Chips at 10 MHz Measurement Bandwidth. ACS Nano 2019; 13:10545-10554. [PMID: 31449393 PMCID: PMC6904932 DOI: 10.1021/acsnano.9b04626] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Accurate and low-cost analysis of biomolecules is important for many applications. This work seeks to further improve the measurement bandwidths achievable with solid-state nanopores, which have emerged as an important platform for this analysis. We report single-stranded DNA translocation recordings at a bandwidth of 10 MHz copolymers of 80 (C20A20C20A20), 90 (C30A30C30), and 200 (C50A50C50A50) nucleotides through Si nanopores with effective diameters of 1.4-2.1 nm and effective membrane thicknesses 0.5-8.9 nm. By optimizing glass chips with thin nanopores and by integrating them with custom-designed amplifiers based on complementary metal-oxide-semiconductor technology, this work demonstrates detection of translocation events as brief as 100 ns with a signal-to-noise ratio exceeding seven at a measurement bandwidth of 10 MHz. We also report data robustness and variability across 13 pores of similar size and thickness, yielding a current blockade between 30 and 60% with a mean ionic current blockade (ΔI) of ∼3-9 nA and a characteristic dwell time of ∼2-21 ns per nucleotide. These measurements show that characteristic translocation rates are at least 10 times faster than previously recorded. We detect transient intraevent fluctuations, multiple current levels within translocation events, and variability of DNA translocation event signatures and durations.
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Affiliation(s)
- Chen-Chi Chien
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Siddharth Shekar
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - David J. Niedzwiecki
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
- Goeppert LLC, Pennovation Works, 3401 Grays Ferry Avenue, Philadelphia PA 19146, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Marija Drndic
- Department of Physics and Astronomy, University of Pennsylvania, Philadelphia, PA 19104, USA
- Address correspondence to
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30
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Shekar S, Jayant K, Rabadan MA, Tomer R, Yuste R, Shepard KL. A miniaturized multi-clamp CMOS amplifier for intracellular neural recording. Nat Electron 2019; 2:343-350. [PMID: 31850397 PMCID: PMC6913532 DOI: 10.1038/s41928-019-0285-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Accepted: 07/17/2019] [Indexed: 05/28/2023]
Abstract
Intracellular electrophysiology is a foundational method in neuroscience and uses electrolyte-filled glass electrodes and benchtop amplifiers to measure and control transmembrane voltages and currents. Commercial amplifiers perform such recordings with high signal-to-noise ratios (SNRs) but are often expensive, bulky, and not easily scalable to many channels due to reliance on board-level integration of discrete components. Here, we present a monolithic complementary-metal-oxide-semiconductor (CMOS) multi-clamp amplifier integrated circuit capable of recording both voltages and currents with performance exceeding that of commercial benchtop instrumentation. Miniaturization enables high-bandwidth current mirroring, facilitating the synthesis of large-valued active resistors with lower noise than their passive equivalents. This enables the realization of compensation modules that can account for a wide range of electrode impedances. We validate the amplifier's operation electrically, in primary neuronal cultures, and in acute slices, using both high-impedance sharp and patch electrodes. This work provides a solution for low-cost, high-performance and scalable multi-clamp amplifiers.
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Affiliation(s)
- Siddharth Shekar
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Krishna Jayant
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
- NeuroTechnology Center, Columbia University, New York, NY 10027, USA
| | - M Angeles Rabadan
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- NeuroTechnology Center, Columbia University, New York, NY 10027, USA
| | - Raju Tomer
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- NeuroTechnology Center, Columbia University, New York, NY 10027, USA
| | - Rafael Yuste
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
- NeuroTechnology Center, Columbia University, New York, NY 10027, USA
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
- Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
- NeuroTechnology Center, Columbia University, New York, NY 10027, USA
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31
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Rabinowitz J, Edwards MA, Whittier E, Jayant K, Shepard KL. Nanoscale Fluid Vortices and Nonlinear Electroosmotic Flow Drive Ion Current Rectification in the Presence of Concentration Gradients. J Phys Chem A 2019; 123:8285-8293. [PMID: 31264868 DOI: 10.1021/acs.jpca.9b04075] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ion current rectification (ICR) is a transport phenomenon in which an electrolyte conducts unequal currents at equal and opposite voltages. Here, we show that nanoscale fluid vortices and nonlinear electroosmotic flow (EOF) drive ICR in the presence of concentration gradients. The same EOF can yield negative differential resistance (NDR), in which current decreases with increasing voltage. A finite element model quantitatively reproduces experimental ICR and NDR recorded across glass nanopipettes under concentration gradients. The model demonstrates that spatial variations of electrical double layer properties induce the nanoscale vortices and nonlinear EOF. Experiments are performed in conditions directly related to scanning probe imaging and show that quantitative understanding of nanoscale transport under concentration gradients requires accounting for EOF. This characterization of nanopipette transport physics will benefit diverse experimentation, pushing the resolution limits of chemical and biophysical recordings.
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Affiliation(s)
| | - Martin A Edwards
- Department of Chemistry , University of Utah , Salt Lake City , Utah 84112 , United States
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32
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Hartel AJW, Shekar S, Ong P, Schroeder I, Thiel G, Shepard KL. High bandwidth approaches in nanopore and ion channel recordings - A tutorial review. Anal Chim Acta 2019; 1061:13-27. [PMID: 30926031 PMCID: PMC6860018 DOI: 10.1016/j.aca.2019.01.034] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/05/2019] [Indexed: 01/01/2023]
Abstract
Transport processes through ion-channel proteins, protein pores, or solid-state nanopores are traditionally recorded with commercial patch-clamp amplifiers. The bandwidth of these systems is typically limited to 10 kHz by signal-to-noise-ratio (SNR) considerations associated with these measurement platforms. At high bandwidth, the input-referred current noise in these systems dominates, determined by the input-referred voltage noise of the transimpedance amplifier applied across the capacitance at the input of the amplifier. This capacitance arises from several sources: the parasitic capacitance of the amplifier itself; the capacitance of the lipid bilayer harboring the ion channel protein (or the membrane used to form the solid-state nanopore); and the capacitance from the interconnections between the electronics and the membrane. Here, we review state-of-the-art applications of high-bandwidth conductance recordings of both ion channels and solid-state nanopores. These approaches involve tightly integrating measurement electronics fabricated in complementary metal-oxide semiconductors (CMOS) technology with lipid bilayer or solid-state membranes. SNR improvements associated with this tight integration push the limits of measurement bandwidths, in some cases in excess of 10 MHz. Recent case studies demonstrate the utility of these approaches for DNA sequencing and ion-channel recordings. In the latter case, studies with extended bandwidth have shown the potential for providing new insights into structure-function relations of these ion-channel proteins as the temporal resolutions of functional recordings matches time scales achievable with state-of-the-art molecular dynamics simulations.
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Affiliation(s)
- Andreas J W Hartel
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
| | - Siddharth Shekar
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Peijie Ong
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Darmstadt, Germany
| | - Kenneth L Shepard
- Bioelectronic Systems Laboratory, Department of Electrical Engineering, Columbia University, New York City, 10027, NY, USA.
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33
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Lee C, Taal AJ, Choi J, Kim K, Tien K, Moreaux L, Roukes ML, Shepard KL. A 512-Pixel 3kHz-Frame-Rate Dual-Shank Lensless Filterless Single-Photon-Avalanche-Diode CMOS Neural Imaging Probe. Dig Tech Pap IEEE Int Solid State Circuits Conf 2019; 2019:198-200. [PMID: 34321707 DOI: 10.1109/isscc.2019.8662408] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Changhyuk Lee
- Columbia University, New York, NY.,KIST, Seoul, Korea
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34
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Shekar S, Chien CC, Hartel A, Ong P, Clarke OB, Marks A, Drndic M, Shepard KL. Wavelet Denoising of High-Bandwidth Nanopore and Ion-Channel Signals. Nano Lett 2019; 19:1090-1097. [PMID: 30601669 PMCID: PMC6904930 DOI: 10.1021/acs.nanolett.8b04388] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Recent work has pushed the noise-limited bandwidths of solid-state nanopore conductance recordings to more than 5 MHz and of ion channel conductance recordings to more than 500 kHz through the use of integrated complementary metal-oxide-semiconductor (CMOS) integrated circuits. Despite the spectral spread of the pulse-like signals that characterize these recordings when a sinusoidal basis is employed, Bessel filters are commonly used to denoise these signals to acceptable signal-to-noise ratios (SNRs) at the cost of losing many of the faster temporal features. Here, we report improvements to the SNR that can be achieved using wavelet denoising instead of Bessel filtering. When combined with state-of-the-art high-bandwidth CMOS recording instrumentation, we can reduce baseline noise levels by over a factor of 4 compared to a 2.5 MHz Bessel filter while retaining transient properties in the signal comparable to this filter bandwidth. Similarly, for ion-channel recordings, we achieve a temporal response better than a 100 kHz Bessel filter with a noise level comparable to that achievable with a 25 kHz Bessel filter. Improvements in SNR can be used to achieve robust statistical analyses of these recordings, which may provide important insights into nanopore translocation dynamics and mechanisms of ion-channel function.
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Affiliation(s)
| | - Chen-Chi Chien
- Department of Physics and Astronomy , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
| | | | | | - Oliver B Clarke
- Department of Physiology and Cellular Biophysics , Columbia University , New York , New York 10032 , United States
| | - Andrew Marks
- Department of Physiology and Cellular Biophysics , Columbia University , New York , New York 10032 , United States
| | - Marija Drndic
- Department of Physics and Astronomy , University of Pennsylvania , Philadelphia , Pennsylvania 19104 , United States
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35
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Jayant K, Wenzel M, Bando Y, Hamm JP, Mandriota N, Rabinowitz JH, Plante IJL, Owen JS, Sahin O, Shepard KL, Yuste R. Flexible Nanopipettes for Minimally Invasive Intracellular Electrophysiology In Vivo. Cell Rep 2019; 26:266-278.e5. [PMID: 30605681 PMCID: PMC7263204 DOI: 10.1016/j.celrep.2018.12.019] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/23/2018] [Accepted: 12/04/2018] [Indexed: 12/01/2022] Open
Abstract
Intracellular recordings in vivo remains the best technique to link single-neuron electrical properties to network function. Yet existing methods are limited in accuracy, throughput, and duration, primarily via washout, membrane damage, and movement-induced failure. Here, we introduce flexible quartz nanopipettes (inner diameters of 10-25 nm and spring constant of ∼0.08 N/m) as nanoscale analogs of traditional glass microelectrodes. Nanopipettes enable stable intracellular recordings (seal resistances of 500 to ∼800 MΩ, 5 to ∼10 cells/nanopipette, and duration of ∼1 hr) in anaesthetized and awake head-restrained mice, exhibit minimal diffusional flux, and facilitate precise recording and stimulation. When combined with quantum-dot labels and microprisms, nanopipettes enable two-photon targeted electrophysiology from both somata and dendrites, and even paired recordings from neighboring neurons, while permitting simultaneous population imaging across cortical layers. We demonstrate the versatility of this method by recording from parvalbumin-positive (Pv) interneurons while imaging seizure propagation, and we find that Pv depolarization block coincides with epileptic spread. Flexible nanopipettes present a simple method to procure stable intracellular recordings in vivo.
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Affiliation(s)
- Krishna Jayant
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA; Department of Biological Sciences, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA.
| | - Michael Wenzel
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
| | - Yuki Bando
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
| | - Jordan P Hamm
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
| | - Nicola Mandriota
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Jake H Rabinowitz
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Ilan Jen-La Plante
- Department of Chemistry, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA
| | - Jonathan S Owen
- Department of Chemistry, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA
| | - Ozgur Sahin
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; Department of Physics, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA; Department of Biomedical Engineering, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
| | - Rafael Yuste
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA; NeuroTechnology Center, Columbia University, New York, NY 10027, USA; Kavli Institute for Brain Science, Columbia University, New York, NY 10027, USA
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36
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Robinson JT, Pohlmeyer E, Gather MC, Kemere C, Kitching JE, Malliaras GG, Marblestone A, Shepard KL, Stieglitz T, Xie C. Developing Next-generation Brain Sensing Technologies - A Review. IEEE Sens J 2019; 19:10.1109/jsen.2019.2931159. [PMID: 32116472 PMCID: PMC7047830 DOI: 10.1109/jsen.2019.2931159] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Advances in sensing technology raise the possibility of creating neural interfaces that can more effectively restore or repair neural function and reveal fundamental properties of neural information processing. To realize the potential of these bioelectronic devices, it is necessary to understand the capabilities of emerging technologies and identify the best strategies to translate these technologies into products and therapies that will improve the lives of patients with neurological and other disorders. Here we discuss emerging technologies for sensing brain activity, anticipated challenges for translation, and perspectives for how to best transition these technologies from academic research labs to useful products for neuroscience researchers and human patients.
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Affiliation(s)
- Jacob T. Robinson
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
- Department of Neuroscience, Baylor College of Medicine, Houston, TX 77030, USA
| | - Eric Pohlmeyer
- John Hopkins University Applied Physics Laboratory, Laurel, MD 20723, USA
| | - Malte C. Gather
- SUPA, School of Physics & Astronomy, University of St Andrews, St Andrews KY16 9SS Scotland, UK
| | - Caleb Kemere
- Department of Electrical and Computer Engineering, Rice University, Houston, TX 77005, USA
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - John E. Kitching
- Time and Frequency Division, NIST, 325 Broadway, Boulder, Colorado 80305, USA
| | - George G. Malliaras
- Electrical Engineering Division, Department of Engineering, University of Cambridge, Cambridge CB3 0FA, UK
| | - Adam Marblestone
- MIT Media Lab, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Thomas Stieglitz
- Institute of Microsystem Technology, Laboratory for Biomedical Microtechnology, D-79110 Freiburg, Germany
- Cluster of Excellence BrainLinks-BrainTools, University of Freiburg, 79110 Freiburg, Germany
- Bernstein Center Freiburg, University of Freiburg, 79104 Freiburg, Germany
| | - Chong Xie
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712, USA
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37
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Tsai D, Sawyer D, Bradd A, Yuste R, Shepard KL. Addendum: A very large-scale microelectrode array for cellular-resolution electrophysiology. Nat Commun 2018; 9:4497. [PMID: 30356050 PMCID: PMC6200797 DOI: 10.1038/s41467-018-06969-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
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38
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Lee Y, Trocchia SM, Warren SB, Young EF, Vernick S, Shepard KL. Electrically Controllable Single-Point Covalent Functionalization of Spin-Cast Carbon-Nanotube Field-Effect Transistor Arrays. ACS Nano 2018; 12:9922-9930. [PMID: 30260623 PMCID: PMC6887518 DOI: 10.1021/acsnano.8b03073] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Single-point-functionalized carbon-nanotube field-effect transistors (CNTFETs) have been used to sense conformational changes and binding events in protein and nucleic acid structures from intrinsic molecular charge. The key to utilizing these devices as single-molecule sensors is the ability to attach a single probe molecule to an individual device. In contrast, with noncovalent attachment approaches such as those based on van der Waals interactions, covalent attachment approaches generally deliver higher stability but have traditionally been more difficult to control, resulting in low yield. Here, we present a single-point-functionalization method for CNTFET arrays based on electrochemical control of a diazonium reaction to create sp3 defects, combined with a scalable spin-casting method for fabricating large arrays of devices on arbitrary substrates. Attachment of probe DNA to the functionalized device enables single-molecule detection of DNA hybridization with complementary target, verifying the single-point functionalization. Overall, this method enables single-point defect generation with 80% yield.
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Affiliation(s)
- Yoonhee Lee
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Scott M. Trocchia
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | | | - Erik F. Young
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Sefi Vernick
- Agricultural Research Organization, Volcani Center, Institute of Agricultural Engineering, Bet Dagan, Israel
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
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39
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Tsai D, Yuste R, Shepard KL. Correction to "Statistically Reconstructed Multiplexing for Very Dense, High-Channel-Count Acquisition Systems". IEEE Trans Biomed Circuits Syst 2018; 12:1215-1216. [PMID: 30130234 PMCID: PMC6986344 DOI: 10.1109/tbcas.2018.2851843] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Presents corrections to the paper, "Statistically reconstructed multiplexing for very dense, high-channel-count acquisition systems," (Tsai, D., et al), IEEE Trans. Biomed. Circuits Syst., vol. 8, no. 1, pp. 13-23, Feb. 2018.
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Affiliation(s)
- David Tsai
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
| | - Rafael Yuste
- Department of Biological Sciences, Columbia University, New York, NY 10027, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027, USA
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40
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Fleischer DA, Shekar S, Dai S, Field RM, Lary J, Rosenstein JK, Shepard KL. CMOS-Integrated Low-Noise Junction Field-Effect Transistors for Bioelectronic Applications. IEEE Electron Device Lett 2018; 39:931-934. [PMID: 30666084 PMCID: PMC6338421 DOI: 10.1109/led.2018.2844545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this work, we present a CMOS-integrated low-noise junction field-effect transistor (JFET) developed in a standard 0.18 pm CMOS process. These JFETs reduce input-referred flicker noise power by more than a factor of 10 when compared to equally sized n-channel MOS devices by eliminating oxide interfaces in contact with the channel. We show that this improvement in device performance translates into a factor-of-10 reduction in the input-referred noise of integrated CMOS operational amplifiers when JFET devices are used at the input, significant for many applications in bioelectronics.
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Affiliation(s)
- Daniel A Fleischer
- Electrical Engineering Department, Columbia University, New York, NY 10027 USA (
| | - Siddharth Shekar
- Electrical Engineering Department, Columbia University, New York, NY 10027 USA (
| | - Shanshan Dai
- School of Engineering, Brown University, Providence, RI 02912 USA
| | | | | | | | - Kenneth L Shepard
- Electrical Engineering Department, Columbia University, New York, NY 10027 USA (
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41
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Kim YD, Gao Y, Shiue RJ, Wang L, Aslan B, Bae MH, Kim H, Seo D, Choi HJ, Kim SH, Nemilentsau A, Low T, Tan C, Efetov DK, Taniguchi T, Watanabe K, Shepard KL, Heinz TF, Englund D, Hone J. Ultrafast Graphene Light Emitters. Nano Lett 2018; 18:934-940. [PMID: 29337567 DOI: 10.1021/acs.nanolett.7b04324] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Ultrafast electrically driven nanoscale light sources are critical components in nanophotonics. Compound semiconductor-based light sources for the nanophotonic platforms have been extensively investigated over the past decades. However, monolithic ultrafast light sources with a small footprint remain a challenge. Here, we demonstrate electrically driven ultrafast graphene light emitters that achieve light pulse generation with up to 10 GHz bandwidth across a broad spectral range from the visible to the near-infrared. The fast response results from ultrafast charge-carrier dynamics in graphene and weak electron-acoustic phonon-mediated coupling between the electronic and lattice degrees of freedom. We also find that encapsulating graphene with hexagonal boron nitride (hBN) layers strongly modifies the emission spectrum by changing the local optical density of states, thus providing up to 460% enhancement compared to the gray-body thermal radiation for a broad peak centered at 720 nm. Furthermore, the hBN encapsulation layers permit stable and bright visible thermal radiation with electronic temperatures up to 2000 K under ambient conditions as well as efficient ultrafast electronic cooling via near-field coupling to hybrid polaritonic modes under electrical excitation. These high-speed graphene light emitters provide a promising path for on-chip light sources for optical communications and other optoelectronic applications.
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Affiliation(s)
- Young Duck Kim
- Department of Physics, Kyung Hee University , Seoul 02447, Republic of Korea
| | | | - Ren-Jye Shiue
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Lei Wang
- Kavli Institute at Cornell for Nanoscale Science , Ithaca, New York 14853, United States
| | - Burak Aslan
- Department of Applied Physics, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Myung-Ho Bae
- Korea Research Institute of Standards and Science , Daejeon 34113, Republic of Korea
- Department of Nano Science, University of Science and Technology , Daejeon 34113, Republic of Korea
| | | | - Dongjea Seo
- Department of Materials Science and Engineering, Yonsei University , Seoul 120-749, Republic of Korea
| | - Heon-Jin Choi
- Department of Materials Science and Engineering, Yonsei University , Seoul 120-749, Republic of Korea
| | - Suk Hyun Kim
- Department of Applied Physics, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Andrei Nemilentsau
- Department of Electrical and Computer Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Tony Low
- Department of Electrical and Computer Engineering, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | | | - Dmitri K Efetov
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology , 08860 Castelldefels, Barcelona, Spain
| | - Takashi Taniguchi
- National Institute for Materials Science , 1-1 Namiki, Tsukuba 305-0044, Japan
| | - Kenji Watanabe
- National Institute for Materials Science , 1-1 Namiki, Tsukuba 305-0044, Japan
| | | | - Tony F Heinz
- Department of Applied Physics, Stanford University , Stanford, California 94305, United States
- SLAC National Accelerator Laboratory , Menlo Park, California 94025, United States
| | - Dirk Englund
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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42
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Hon J, Daly NS, Trocchia SM, Nuckolls C, Shepard KL, Gonzalez RL. High Temporal- and Spatial-Resolution Studies of a Helix-to-Coil Transition that Controls the Switching Mechanism of a Riboswitch. Biophys J 2018. [DOI: 10.1016/j.bpj.2017.11.2402] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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43
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Tsai D, Yuste R, Shepard KL. Statistically Reconstructed Multiplexing for Very Dense, High-Channel-Count Acquisition Systems. IEEE Trans Biomed Circuits Syst 2018; 12:13-23. [PMID: 29377795 PMCID: PMC5835400 DOI: 10.1109/tbcas.2017.2750484] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Multiplexing is an important strategy in multichannel acquisition systems. The per-channel antialiasing filters needed in the traditional multiplexing architecture limit its scalability for applications requiring high channel density, high channel count, and low noise. A particularly challenging example is multielectrode arrays for recording from neural systems. We show that conventional approaches must tradeoff recording density and noise performance, at a scale far from the ideal goal of one-to-one mapping between neurons and sensors. We present a multiplexing architecture without per-channel antialiasing filters. The sparsely sampled data are recovered through a compressed sensing strategy, involving statistical reconstruction and removal of the undersampled thermal noise. In doing so, we replace large analog components with digital signal processing blocks, which are much more amenable to scaled CMOS implementation. The resulting statistically reconstructed multiplexing architecture recovers input signals at significantly improved signal-to-noise ratios when compared to conventional multiplexing with antialiasing filters at the same per-channel area. We implement the new architecture in a 65 536-channel neural recording system and show that it is able to recover signals with performance comparable to conventional high-performance, single-channel systems, despite a more than four-orders-of-magnitude increase in channel density.
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44
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Rauh O, Hansen UP, Mach S, Hartel AJW, Shepard KL, Thiel G, Schroeder I. Extended beta distributions open the access to fast gating in bilayer experiments-assigning the voltage-dependent gating to the selectivity filter. FEBS Lett 2017; 591:3850-3860. [PMID: 29106736 PMCID: PMC5747313 DOI: 10.1002/1873-3468.12898] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Revised: 10/17/2017] [Accepted: 10/27/2017] [Indexed: 01/02/2023]
Abstract
Lipid bilayers provide many benefits for ion channel recordings, such as control of membrane composition and transport molecules. However, they suffer from high membrane capacitance limiting the bandwidth and impeding analysis of fast gating. This can be overcome by fitting the deviations of the open‐channel noise from the baseline noise by extended beta distributions. We demonstrate this analysis step‐by‐step by applying it to the example of viral K+ channels (Kcv), from the choice of the gating model through the fitting process, validation of the results, and what kinds of results can be obtained. These voltage sensor‐less channels show profoundly voltage‐dependent gating with dwell times in the closed state of about 50 μs. Mutations assign it to the selectivity filter.
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Affiliation(s)
- Oliver Rauh
- Plant Membrane Biophysics, Technische Universität Darmstadt, Germany
| | - Ulf-Peter Hansen
- Department of Structural Biology, Christian-Albrechts-University of Kiel, Germany
| | - Sebastian Mach
- Plant Membrane Biophysics, Technische Universität Darmstadt, Germany
| | - Andreas J W Hartel
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University, New York, NY, USA
| | - Gerhard Thiel
- Plant Membrane Biophysics, Technische Universität Darmstadt, Germany
| | - Indra Schroeder
- Plant Membrane Biophysics, Technische Universität Darmstadt, Germany
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45
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Jayant K, Hirtz JJ, Plante IJL, Tsai DM, De Boer WDAM, Semonche A, Peterka DS, Owen JS, Sahin O, Shepard KL, Yuste R. Targeted intracellular voltage recordings from dendritic spines using quantum-dot-coated nanopipettes. Nat Nanotechnol 2017; 12:335-342. [PMID: 27941898 PMCID: PMC5901699 DOI: 10.1038/nnano.2016.268] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/02/2016] [Indexed: 05/21/2023]
Abstract
Dendritic spines are the primary site of excitatory synaptic input onto neurons, and are biochemically isolated from the parent dendritic shaft by their thin neck. However, due to the lack of direct electrical recordings from spines, the influence that the neck resistance has on synaptic transmission, and the extent to which spines compartmentalize voltage, specifically excitatory postsynaptic potentials, albeit critical, remains controversial. Here, we use quantum-dot-coated nanopipette electrodes (tip diameters ∼15-30 nm) to establish the first intracellular recordings from targeted spine heads under two-photon visualization. Using simultaneous somato-spine electrical recordings, we find that back propagating action potentials fully invade spines, that excitatory postsynaptic potentials are large in the spine head (mean 26 mV) but are strongly attenuated at the soma (0.5-1 mV) and that the estimated neck resistance (mean 420 MΩ) is large enough to generate significant voltage compartmentalization. Nanopipettes can thus be used to electrically probe biological nanostructures.
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Affiliation(s)
- Krishna Jayant
- Department of Electrical Engineering, Columbia University, New York, New York 10027, USA
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- NeuroTechnology Center, Columbia University, New York, New York 10027, USA
- Kavli Institute of Brain Science, Columbia University, New York, New York 10027, USA
- Correspondence and requests for materials should be addressed to K.J.,
| | - Jan J. Hirtz
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- NeuroTechnology Center, Columbia University, New York, New York 10027, USA
- Kavli Institute of Brain Science, Columbia University, New York, New York 10027, USA
| | - Ilan Jen-La Plante
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - David M. Tsai
- Department of Electrical Engineering, Columbia University, New York, New York 10027, USA
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- NeuroTechnology Center, Columbia University, New York, New York 10027, USA
- Kavli Institute of Brain Science, Columbia University, New York, New York 10027, USA
| | - Wieteke D. A. M. De Boer
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- NeuroTechnology Center, Columbia University, New York, New York 10027, USA
- Kavli Institute of Brain Science, Columbia University, New York, New York 10027, USA
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Alexa Semonche
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
| | - Darcy S. Peterka
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- NeuroTechnology Center, Columbia University, New York, New York 10027, USA
- Kavli Institute of Brain Science, Columbia University, New York, New York 10027, USA
| | - Jonathan S. Owen
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Ozgur Sahin
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- NeuroTechnology Center, Columbia University, New York, New York 10027, USA
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, New York 10027, USA
- NeuroTechnology Center, Columbia University, New York, New York 10027, USA
- Kavli Institute of Brain Science, Columbia University, New York, New York 10027, USA
- Department of Biomedical Engineering, New York, New York 10027, USA
| | - Rafael Yuste
- Department of Biological Sciences, Columbia University, New York, New York 10027, USA
- NeuroTechnology Center, Columbia University, New York, New York 10027, USA
- Kavli Institute of Brain Science, Columbia University, New York, New York 10027, USA
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46
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Amiri H, Shepard KL, Nuckolls C, Hernández Sánchez R. Single-Walled Carbon Nanotubes: Mimics of Biological Ion Channels. Nano Lett 2017; 17:1204-1211. [PMID: 28103039 PMCID: PMC5301282 DOI: 10.1021/acs.nanolett.6b04967] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2016] [Revised: 01/06/2017] [Indexed: 05/22/2023]
Abstract
Here we report on the ion conductance through individual, small diameter single-walled carbon nanotubes. We find that they are mimics of ion channels found in natural systems. We explore the factors governing the ion selectivity and permeation through single-walled carbon nanotubes by considering an electrostatic mechanism built around a simplified version of the Gouy-Chapman theory. We find that the single-walled carbon nanotubes preferentially transported cations and that the cation permeability is size-dependent. The ionic conductance increases as the absolute hydration enthalpy decreases for monovalent cations with similar solid-state radii, hydrated radii, and bulk mobility. Charge screening experiments using either the addition of cationic or anionic polymers, divalent metal cations, or changes in pH reveal the enormous impact of the negatively charged carboxylates at the entrance of the single-walled carbon nanotubes. These observations were modeled in the low-to-medium concentration range (0.1-2.0 M) by an electrostatic mechanism that mimics the behavior observed in many biological ion channel-forming proteins. Moreover, multi-ion conduction in the high concentration range (>2.0 M) further reinforces the similarity between single-walled carbon nanotubes and protein ion channels.
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Affiliation(s)
- Hasti Amiri
- Department of Chemistry and Department of Electrical
Engineering, Columbia University, New York, New York 10027, United States
| | - Kenneth L. Shepard
- Department of Chemistry and Department of Electrical
Engineering, Columbia University, New York, New York 10027, United States
- E-mail:
| | - Colin Nuckolls
- Department of Chemistry and Department of Electrical
Engineering, Columbia University, New York, New York 10027, United States
- E-mail:
| | - Raúl Hernández Sánchez
- Department of Chemistry and Department of Electrical
Engineering, Columbia University, New York, New York 10027, United States
- E-mail:
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47
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Vernick S, Trocchia SM, Warren SB, Young EF, Bouilly D, Gonzalez RL, Nuckolls C, Shepard KL. Electrostatic Control of DNA Hydridization Kinetics Studied with the Single-Molecule Field-Effect Transistor. Biophys J 2017. [DOI: 10.1016/j.bpj.2016.11.1794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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48
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Bouilly D, Hon J, Daly NS, Trocchia S, Vernick S, Yu J, Warren S, Wu Y, Gonzalez RL, Shepard KL, Nuckolls C. Single-Molecule Reaction Chemistry in Patterned Nanowells. Nano Lett 2016; 16:4679-85. [PMID: 27270004 PMCID: PMC5176326 DOI: 10.1021/acs.nanolett.6b02149] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
A new approach to synthetic chemistry is performed in ultraminiaturized, nanofabricated reaction chambers. Using lithographically defined nanowells, we achieve single-point covalent chemistry on hundreds of individual carbon nanotube transistors, providing robust statistics and unprecedented spatial resolution in adduct position. Each device acts as a sensor to detect, in real-time and through quantized changes in conductance, single-point functionalization of the nanotube as well as consecutive chemical reactions, molecular interactions, and molecular conformational changes occurring on the resulting single-molecule probe. In particular, we use a set of sequential bioconjugation reactions to tether a single-strand of DNA to the device and record its repeated, reversible folding into a G-quadruplex structure. The stable covalent tether allows us to measure the same molecule in different solutions, revealing the characteristic increased stability of the G-quadruplex structure in the presence of potassium ions (K(+)) versus sodium ions (Na(+)). Nanowell-confined reaction chemistry on carbon nanotube devices offers a versatile method to isolate and monitor individual molecules during successive chemical reactions over an extended period of time.
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Affiliation(s)
- Delphine Bouilly
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027 United
States
| | - Jason Hon
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027 United
States
| | - Nathan S. Daly
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027 United
States
| | - Scott Trocchia
- Department of Electrical Engineering, Columbia University, 500 W. 120th Street, New York, New York 10027 United
States
| | - Sefi Vernick
- Department of Electrical Engineering, Columbia University, 500 W. 120th Street, New York, New York 10027 United
States
| | - Jaeeun Yu
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027 United
States
| | - Steven Warren
- Department of Electrical Engineering, Columbia University, 500 W. 120th Street, New York, New York 10027 United
States
| | - Ying Wu
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027 United
States
| | - Ruben L. Gonzalez
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027 United
States
- E-mail:
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, 500 W. 120th Street, New York, New York 10027 United
States
- E-mail:
| | - Colin Nuckolls
- Department of Chemistry, Columbia University, 3000 Broadway, New York, New York 10027 United
States
- E-mail:
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49
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Shekar S, Niedzwiecki DJ, Chien CC, Ong P, Fleischer DA, Lin J, Rosenstein JK, Drndić M, Shepard KL. Measurement of DNA Translocation Dynamics in a Solid-State Nanopore at 100 ns Temporal Resolution. Nano Lett 2016; 16:4483-9. [PMID: 27332998 PMCID: PMC5312517 DOI: 10.1021/acs.nanolett.6b01661] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Despite the potential for nanopores to be a platform for high-bandwidth study of single-molecule systems, ionic current measurements through nanopores have been limited in their temporal resolution by noise arising from poorly optimized measurement electronics and large parasitic capacitances in the nanopore membranes. Here, we present a complementary metal-oxide-semiconductor (CMOS) nanopore (CNP) amplifier capable of low noise recordings at an unprecedented 10 MHz bandwidth. When integrated with state-of-the-art solid-state nanopores in silicon nitride membranes, we achieve an SNR of greater than 10 for ssDNA translocations at a measurement bandwidth of 5 MHz, which represents the fastest ion current recordings through nanopores reported to date. We observe transient features in ssDNA translocation events that are as short as 200 ns, which are hidden even at bandwidths as high as 1 MHz. These features offer further insights into the translocation kinetics of molecules entering and exiting the pore. This platform highlights the advantages of high-bandwidth translocation measurements made possible by integrating nanopores and custom-designed electronics.
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Affiliation(s)
- Siddharth Shekar
- Department of Electrical Engineering, Columbia University , New York, New York 10027, United States
| | - David J Niedzwiecki
- Department of Physics and Astronomy, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Chen-Chi Chien
- Department of Physics and Astronomy, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Peijie Ong
- Department of Applied Physics and Applied Mathematics, Columbia University , New York, New York 10027, United States
| | - Daniel A Fleischer
- Department of Electrical Engineering, Columbia University , New York, New York 10027, United States
| | | | - Jacob K Rosenstein
- School of Engineering, Brown University , Providence, Rhode Island 02912, United States
| | - Marija Drndić
- Department of Physics and Astronomy, University of Pennsylvania , Philadelphia, Pennsylvania 19104, United States
| | - Kenneth L Shepard
- Department of Electrical Engineering, Columbia University , New York, New York 10027, United States
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50
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Warren SB, Vernick S, Romano E, Shepard KL. Complementary Metal-Oxide-Semiconductor Integrated Carbon Nanotube Arrays: Toward Wide-Bandwidth Single-Molecule Sensing Systems. Nano Lett 2016; 16:2674-9. [PMID: 26999579 PMCID: PMC5319850 DOI: 10.1021/acs.nanolett.6b00319] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
There is strong interest in realizing genomic molecular diagnostic platforms that are label-free, electronic, and single-molecule. One attractive transducer for such efforts is the single-molecule field-effect transistor (smFET), capable of detecting a single electronic charge and realized with a point-functionalized exposed-gate one-dimensional carbon nanotube field-effect device. In this work, smFETs are integrated directly onto a custom complementary metal-oxide-semiconductor chip, which results in an array of up to 6000 devices delivering a measurement bandwidth of 1 MHz. In a first exploitation of these high-bandwidth measurement capabilities, point functionalization through electrochemical oxidation of the devices is observed with microsecond temporal resolution, which reveals complex reaction pathways with resolvable scattering signatures. High-rate random telegraph noise is detected in certain oxidized devices, further illustrating the measurement capabilities of the platform.
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Affiliation(s)
- Steven B. Warren
- Department of Electrical Engineering, Columbia University, New York, NY 10027
| | - Sefi Vernick
- Department of Electrical Engineering, Columbia University, New York, NY 10027
| | - Ethan Romano
- Department of Electrical Engineering, Columbia University, New York, NY 10027
| | - Kenneth L. Shepard
- Department of Electrical Engineering, Columbia University, New York, NY 10027
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