Professional Education

  • Doctor of Philosophy, University of Minnesota Twin Cities (2015)
  • Master of Technology, Indian Institute of Technology, Kharagpur (2010)
  • Bachelor of Technology, Indian Institute of Technology, Kharagpur (2010)

Stanford Advisors

All Publications

  • Enhanced broadband fluorescence detection of nucleic acids using multipolar gap-plasmons on biomimetic Au metasurfaces NANOSCALE Narasimhan, V., Siddique, R., Hoffmann, M., Kumar, S., Choo, H. 2019; 11 (29): 13750–57


    Recent studies on metal-insulator-metal-based plasmonic antennas have shown that emitters could couple with higher-order gap-plasmon modes in sub-10-nm gaps to overcome quenching. However, these gaps are often physically inaccessible for functionalization and are not scalably manufacturable. Here, using a simple biomimetic batch-fabrication, a plasmonic metasurface is created consisting of closely-coupled nanodisks and nanoholes in a metal-insulator-metal arrangement. The quadrupolar mode of this system exhibits strong broadband resonance in the visible-near-infrared regime with minimal absorptive losses and effectively supresses quenching, making it highly suitable for broadband plasmon-enhanced fluorescence. Functionalizing the accessible insulator nanogap, analytes are selectively immobilized onto the plasmonic hotspot enabling highly-localized detection. Sensing the streptavidin-biotin complex, a 91-, 288-, 403- and 501-fold fluorescence enhancement is observed for Alexa Fluor 555, 647, 750 and 790, respectively. Finally, the detection of single-stranded DNA (gag, CD4 and CCR5) analogues of genes studied in the pathogenesis of HIV-1 between 10 pM-10 μM concentrations and then CD4 mRNA in the lysate of transiently-transfected cells with a 5.4-fold increase in fluorescence intensity relative to an untransfected control is demonstrated. This outcome promises the use of biomimetic Au metasurfaces as platforms for robust detection of low-abundance nucleic acids.

    View details for DOI 10.1039/c9nr03178b

    View details for Web of Science ID 000477704400042

    View details for PubMedID 31140518

  • Glucose Sensing Using Surface-Enhanced Raman-Mode Constraining ANALYTICAL CHEMISTRY Yang, D., Afroosheh, S., Lee, J., Cho, H., Kumar, S., Siddique, R. H., Narasimhan, V., Yoon, Y., Zayak, A. T., Choo, H. 2018; 90 (24): 14269–78


    Diabetes mellitus is a chronic disease, and its management focuses on monitoring and lowering a patient's glucose level to prevent further complications. By tracking the glucose-induced shift in the surface-enhanced Raman-scattering (SERS) emission of mercaptophenylboronic acid (MPBA), we have demonstrated fast and continuous glucose sensing in the physiologically relevant range from 0.1 to 30 mM and verified the underlying mechanism using numerical simulations. Bonding of glucose to MPBA suppresses the "breathing" mode of MPBA at 1071 cm-1 and energizes the constrained-bending mode at 1084 cm-1, causing the dominant peak to shift from 1071 to 1084 cm-1. MPBA-glucose bonding is also reversible, allowing continuous tracking of ambient glucose concentrations, and the MPBA-coated substrates showed very stable performance over a 30 day period, making the approach promising for long-term continuous glucose monitoring. Using Raman-mode-constrained, miniaturized SERS implants, we also successfully demonstrated intraocular glucose measurements in six ex vivo rabbit eyes within ±0.5 mM of readings obtained using a commercial glucose sensor.

    View details for DOI 10.1021/acs.analchem.8b03420

    View details for Web of Science ID 000454182800026

    View details for PubMedID 30369240

  • High-performance flexible metal-on-silicon thermocouple SCIENTIFIC REPORTS Assumpcao, D., Kumar, S., Narasimhan, V., Lee, J., Choo, H. 2018; 8: 13725


    We have demonstrated metal-on-silicon thermocouples with a noticeably high Seebeck coefficient and an excellent temperature-sensing resolution. Fabrication of the thermocouples involved only simple photolithography and metal-liftoff procedures on a silicon substrate. The experimentally measured Seebeck coefficient of our thermocouple was 9.17 × 10-4 V/°K, which is 30 times larger than those reported for standard metal thin-film thermocouples and comparable to the values of alloy-based thin-film thermocouples that require sophisticated and costly fabrication processes. The temperature-voltage measurements between 20 to 80 °C were highly linear with a linearity coefficient of 1, and the experimentally demonstrated temperature-sensing resolution was 0.01 °K which could be further improved up to a theoretical limit of 0.00055 °K. Finally, we applied this approach to demonstrate a flexible metal-on-silicon thermocouple with enhanced thermal sensitivity. The outstanding performance of our thermocouple combined with an extremely thin profile, bending flexibility, and simple, highly-compatible fabrication will proliferate its use in diverse applications such as micro-/nanoscale biometrics, energy management, and nanoscale thermography.

    View details for DOI 10.1038/s41598-018-32169-9

    View details for Web of Science ID 000444501200005

    View details for PubMedID 30214053

    View details for PubMedCentralID PMC6137040

  • Multifunctional biophotonic nanostructures inspired by the longtail glasswing butterfly for medical devices NATURE NANOTECHNOLOGY Narasimhan, V., Siddique, R., Lee, J., Kumar, S., Ndjamen, B., Du, J., Hong, N., Sretavan, D., Choo, H. 2018; 13 (6): 512-+


    Numerous living organisms possess biophotonic nanostructures that provide colouration and other diverse functions for survival. While such structures have been actively studied and replicated in the laboratory, it remains unclear whether they can be used for biomedical applications. Here, we show a transparent photonic nanostructure inspired by the longtail glasswing butterfly (Chorinea faunus) and demonstrate its use in intraocular pressure (IOP) sensors in vivo. We exploit the phase separation between two immiscible polymers (poly(methyl methacrylate) and polystyrene) to form nanostructured features on top of a Si3N4 substrate. The membrane thus formed shows good angle-independent white-light transmission, strong hydrophilicity and anti-biofouling properties, which prevent adhesion of proteins, bacteria and eukaryotic cells. We then developed a microscale implantable IOP sensor using our photonic membrane as an optomechanical sensing element. Finally, we performed in vivo testing on New Zealand white rabbits, which showed that our device reduces the mean IOP measurement variation compared with conventional rebound tonometry without signs of inflammation.

    View details for DOI 10.1038/s41565-018-0111-5

    View details for Web of Science ID 000434715700022

    View details for PubMedID 29713074

    View details for PubMedCentralID PMC5992053

  • Self-directed Transport on Nanostructured Plasmonic Sensors MINIATURE FLUIDIC DEVICES FOR RAPID BIOLOGICAL DETECTION Kumar, S., Oh, S. H., Escobedo, C., Brolo, A. G. 2018: 105–22
  • Surface-Enhanced Raman Spectroscopy-Based Label-Free Insulin Detection at Physiological Concentrations for Analysis of Islet Performance ACS SENSORS Cho, H., Kumar, S., Yang, D., Vaidyanathan, S., Woo, K., Garcia, I., Shue, H. J., Yoon, Y., Ferreri, K., Choo, H. 2018; 3 (1): 65–71


    Label-free optical detection of insulin would allow in vitro assessment of pancreatic cell functions in their natural state and expedite diabetes-related clinical research and treatment; however, no existing method has met these criteria at physiological concentrations. Using spatially uniform 3D gold-nanoparticle sensors, we have demonstrated surface-enhanced Raman sensing of insulin in the secretions from human pancreatic islets under low and high glucose environments without the use of labels such as antibodies or aptamers. Label-free measurements of the islet secretions showed excellent correlation among the ambient glucose levels, secreted insulin concentrations, and measured Raman-emission intensities. When excited at 785 nm, plasmonic hotspots of the densely arranged 3D gold-nanoparticle pillars as well as strong interaction between sulfide linkages of the insulin molecules and the gold nanoparticles produced highly sensitive and reliable insulin measurements down to 100 pM. The sensors exhibited a dynamic range of 100 pM to 50 nM with an estimated detection limit of 35 pM, which covers the reported concentration range of insulin observed in pancreatic cell secretions. The sensitivity of this approach is approximately 4 orders of magnitude greater than previously reported results using label-free optical approaches, and it is much more cost-effective than immunoassay-based insulin detection widely used in clinics and laboratories. These promising results may open up new opportunities for insulin sensing in research and clinical applications.

    View details for DOI 10.1021/acssensors.7b00864

    View details for Web of Science ID 000423782600008

    View details for PubMedID 29322773

  • Template-Stripped Multifunctional Wedge and Pyramid Arrays for Magnetic Nanofocusing and Optical Sensing ACS APPLIED MATERIALS & INTERFACES Kumar, S., Johnson, T. W., Wood, C. K., Qu, T., Wittenberg, N. J., Otto, L. M., Shaver, J., Long, N. J., Victora, R. H., Edel, J. B., Oh, S. 2016; 8 (14): 9319–26


    We present large-scale reproducible fabrication of multifunctional ultrasharp metallic structures on planar substrates with capabilities including magnetic field nanofocusing and plasmonic sensing. Objects with sharp tips such as wedges and pyramids made with noble metals have been extensively used for enhancing local electric fields via the lightning-rod effect or plasmonic nanofocusing. However, analogous nanofocusing of magnetic fields using sharp tips made with magnetic materials has not been widely realized. Reproducible fabrication of sharp tips with magnetic as well as noble metal layers on planar substrates can enable straightforward application of their material and shape-derived functionalities. We use a template-stripping method to produce plasmonic-shell-coated nickel wedge and pyramid arrays at the wafer-scale with tip radius of curvature close to 10 nm. We further explore the magnetic nanofocusing capabilities of these ultrasharp substrates, deriving analytical formulas and comparing the results with computer simulations. These structures exhibit nanoscale spatial control over the trapping of magnetic microbeads and nanoparticles in solution. Additionally, enhanced optical sensing of analytes by these plasmonic-shell-coated substrates is demonstrated using surface-enhanced Raman spectroscopy. These methods can guide the design and fabrication of novel devices with applications including nanoparticle manipulation, biosensing, and magnetoplasmonics.

    View details for DOI 10.1021/acsami.5b12157

    View details for Web of Science ID 000374274900056

    View details for PubMedID 26837912

    View details for PubMedCentralID PMC4832397

  • Nanohole Array-Directed Trapping of Mammalian Mitochondria Enabling Single Organelle Analysis ANALYTICAL CHEMISTRY Kumar, S., Wolken, G. G., Wittenberg, N. J., Arriaga, E. A., Oh, S. 2015; 87 (24): 11973–77


    We present periodic nanohole arrays fabricated in free-standing metal-coated nitride films as a platform for trapping and analyzing single organelles. When a microliter-scale droplet containing mitochondria is dispensed above the nanohole array, the combination of evaporation and capillary flow directs individual mitochondria to the nanoholes. Mammalian mitochondria arrays were rapidly formed on chip using this technique without any surface modification steps, microfluidic interconnects, or external power sources. The trapped mitochondria were depolarized on chip using an ionophore with results showing that the organelle viability and behavior were preserved during the on-chip assembly process. Fluorescence signal related to mitochondrial membrane potential was obtained from single mitochondria trapped in individual nanoholes revealing statistical differences between the behavior of polarized vs depolarized mammalian mitochondria. This technique provides a fast and stable route for droplet-based directed localization of organelles-on-a-chip with minimal limitations and complexity, as well as promotes integration with other optical or electrochemical detection techniques.

    View details for DOI 10.1021/acs.analchem.5b03604

    View details for Web of Science ID 000366871500007

    View details for PubMedID 26593329

    View details for PubMedCentralID PMC4809531

  • Fine tuning of nanopipettes using atomic layer deposition for single molecule sensing ANALYST Sze, J. Y., Kumar, S., Ivanov, A. P., Oh, S., Edel, J. B. 2015; 140 (14): 4828–34


    Nanopipettes are an attractive single-molecule tool for identification and characterisation of nucleic acids and proteins in solutions. They enable label-free analysis and reveal individual molecular properties, which are generally masked by ensemble averaging. Having control over the pore dimensions is vital to ensure that the dimensions of the molecules being probed match those of the pore for optimization of the signal to noise. Although nanopipettes are simple and easy to fabricate, challenges exist, especially when compared to more conventional solid-state analogues. For example, a sub-20 nm pore diameter can be difficult to fabricate and the batch-to-batch reproducibility is often poor. To improve on this limitation, atomic layer deposition (ALD) is used to deposit ultrathin layers of alumina (Al2O3) on the surface of the quartz nanopipettes enabling sub-nm tuning of the pore dimensions. Here, Al2O3 with a thickness of 8, 14 and 17 nm was deposited onto pipettes with a starting pore diameter of 75 ± 5 nm whilst a second batch had 5 and 8 nm Al2O3 deposited with a starting pore diameter of 25 ± 3 nm respectively. This highly conformal process coats both the inner and outer surfaces of pipettes and resulted in the fabrication of pore diameters as low as 7.5 nm. We show that Al2O3 modified pores do not interfere with the sensing ability of the nanopipettes and can be used for high signal-to-noise DNA detection. ALD provides a quick and efficient (batch processing) for fine-tuning nanopipettes for a broad range of applications including the detection of small biomolecules like RNA, aptamers and DNA-protein interactions at the single molecule level.

    View details for DOI 10.1039/c5an01001b

    View details for Web of Science ID 000357209200011

    View details for PubMedID 26066550

  • Millimeter-Sized Suspended Plasmonic Nanohole Arrays for Surface-Tension-Driven Flow-Through SERS CHEMISTRY OF MATERIALS Kumar, S., Cherukulappurath, S., Johnson, T. W., Oh, S. 2014; 26 (22): 6523–30


    We present metallic nanohole arrays fabricated on suspended membranes as an optofluidic substrate. Millimeter-sized suspended nanohole arrays were fabricated using nanoimprint lithography. We demonstrate refractive-index-based tuning of the optical spectra using a sucrose solution for the optimization of SERS signal intensity, leading to a Raman enhancement factor of 107. Furthermore, compared to dead-ended nanohole arrays, suspended nanohole arrays capable of flow-through detection increased the measured SERS signal intensity by 50 times. For directed transport of analytes, we present a novel methodology utilizing surface tension to generate spontaneous flow through the nanoholes with flow rates of 1 μL/min, obviating the need for external pumps or microfluidic interconnects. Using this method for SERS, we obtained a 50 times higher signal as compared to diffusion-limited transport and could detect 100 pM 4-mercaptopyridine. The suspended nanohole substrates presented herein possess a uniform and reproducible geometry and show the potential for improved analyte transport and SERS detection.

    View details for DOI 10.1021/cm5031848

    View details for Web of Science ID 000345550600025

    View details for PubMedID 25678744

    View details for PubMedCentralID PMC4311951

  • Electron Tomography of Cryo-Immobilized Plant Tissue: A Novel Approach to Studying 3D Macromolecular Architecture of Mature Plant Cell Walls In Situ PLOS ONE Sarkar, P., Bosneaga, E., Yap, E. G., Das, J., Tsai, W., Cabal, A., Neuhaus, E., Maji, D., Kumar, S., Joo, M., Yakovlev, S., Csencsits, R., Yu, Z., Bajaj, C., Downing, K. H., Auer, M. 2014; 9 (9): e106928


    Cost-effective production of lignocellulosic biofuel requires efficient breakdown of cell walls present in plant biomass to retrieve the wall polysaccharides for fermentation. In-depth knowledge of plant cell wall composition is therefore essential for improving the fuel production process. The precise spatial three-dimensional (3D) organization of cellulose, hemicellulose, pectin and lignin within plant cell walls remains unclear to date since the microscopy techniques used so far have been limited to two-dimensional, topographic or low-resolution imaging, or required isolation or chemical extraction of the cell walls. In this paper we demonstrate that by cryo-immobilizing fresh tissue, then either cryo-sectioning or freeze-substituting and resin embedding, followed by cryo- or room temperature (RT) electron tomography, respectively, we can visualize previously unseen details of plant cell wall architecture in 3D, at macromolecular resolution (∼ 2 nm), and in near-native state. Qualitative and quantitative analyses showed that wall organization of cryo-immobilized samples were preserved remarkably better than conventionally prepared samples that suffer substantial extraction. Lignin-less primary cell walls were well preserved in both self-pressurized rapidly frozen (SPRF), cryo-sectioned samples as well as high-pressure frozen, freeze-substituted and resin embedded (HPF-FS-resin) samples. Lignin-rich secondary cell walls appeared featureless in HPF-FS-resin sections presumably due to poor stain penetration, but their macromolecular features could be visualized in unprecedented details in our cryo-sections. While cryo-tomography of vitreous tissue sections is currently proving to be instrumental in developing 3D models of lignin-rich secondary cell walls, here we confirm that the technically easier method of RT-tomography of HPF-FS-resin sections could be used immediately for routine study of low-lignin cell walls. As a proof of principle, we characterized the primary cell walls of a mutant (cob-6) and wild type Arabidopsis hypocotyl parenchyma cells by RT-tomography of HPF-FS-resin sections, and detected a small but significant difference in spatial organization of cellulose microfibrils in the mutant walls.

    View details for DOI 10.1371/journal.pone.0106928

    View details for Web of Science ID 000342030300049

    View details for PubMedID 25207917

    View details for PubMedCentralID PMC4160213

  • A patterned recombinant human IgM guides neurite outgrowth of CNS neurons SCIENTIFIC REPORTS Xu, X., Wittenberg, N. J., Jordan, L. R., Kumar, S., Watzlawik, J. O., Warrington, A. E., Oh, S., Rodriguez, M. 2013; 3: 2267


    Matrix molecules convey biochemical and physical guiding signals to neurons in the central nervous system (CNS) and shape the trajectory of neuronal fibers that constitute neural networks. We have developed recombinant human IgMs that bind to epitopes on neural cells, with the aim of treating neurological diseases. Here we test the hypothesis that recombinant human IgMs (rHIgM) can guide neurite outgrowth of CNS neurons. Microcontact printing was employed to pattern rHIgM12 and rHIgM22, antibodies that were bioengineered to have variable regions capable of binding to neurons or oligodendrocytes, respectively. rHIgM12 promoted neuronal attachment and guided outgrowth of neurites from hippocampal neurons. Processes from spinal neurons followed grid patterns of rHIgM12 and formed a physical network. Comparison between rHIgM12 and rHIgM22 suggested the biochemistry that facilitates anchoring the neuronal surfaces is a prerequisite for the function of IgM, and spatial properties cooperate in guiding the assembly of neuronal networks.

    View details for DOI 10.1038/srep02267

    View details for Web of Science ID 000322153700002

    View details for PubMedID 23881231

    View details for PubMedCentralID PMC3721078

  • Nanopore-Induced Spontaneous Concentration for Optofluidic Sensing and Particle Assembly ANALYTICAL CHEMISTRY Kumar, S., Wittenberg, N. J., Oh, S. 2013; 85 (2): 971–77


    Metallic nanopore arrays have emerged as optofluidic platforms with multifarious sensing and analytical capabilities such as label-free surface plasmon resonance (SPR) sensing of molecular binding interactions and surface-enhanced Raman spectroscopy (SERS). However, directed delivery of analytes through open nanopores using traditional methods such as external electric fields or pressure gradients still remains difficult. We demonstrate that nanopore arrays have an intrinsic ability to promote flow through them via capillary flow and evaporation. This passive "nano-drain" mechanism is utilized to concentrate biomolecules on the surface of nanopores for improved detection sensitivity or create ordered nanoscale arrays of beads and liposomes. Without using any external pump or fluidic interconnects, we can concentrate and detect the presence of less than a femtomole of streptavidin in 10 μL of sample using fluorescence imaging. Liposome nanoarrays are also prepared in less than 5 min and used to detect lipid-protein interactions. We also demonstrate label-free SPR detection of analytes using metallic nanopore arrays. This method provides a fast, simple, transportable, and small-volume platform for labeled as well as label-free plasmonic analysis while improving the detection time and sensitivity.

    View details for DOI 10.1021/ac302690w

    View details for Web of Science ID 000313668400046

    View details for PubMedID 23214989

    View details for PubMedCentralID PMC3568508