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Integrated Angle-insensitive Nano-plasmonic Filters for Ultraminiaturized Fluorescence Microarray in a 65-nm Digital CMOS Process Lingyu Hong, Hao Li, Haw Yang, and Kaushik Sengupta ACS Photonics, Just Accepted Manuscript • DOI: 10.1021/acsphotonics.8b00440 • Publication Date (Web): 12 Sep 2018 Downloaded from http://pubs.acs.org on September 13, 2018
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Integrated Angle-insensitive Nano-plasmonic Filters for Ultra-miniaturized Fluorescence Microarray in a 65-nm Digital CMOS Process Lingyu Hong1 , Hao Li2 , Haw Yang2 , and Kaushik Sengupta1 1
Department of Electrical Engineering, 2 Department of Chemistry, Princeton University, Prince-
ton, NJ, 08544, USA
Abstract: In this work, we demonstrate for the first time massively parallelizable nanoplasmonic structures and integration of electronics in the same substrate in CMOS. We adopt the same ‘fabless’ approach in today’s semiconductor industry with absolutely ‘no change’ of either fabrication or processing, and show that copper interconnects in an industry standard digital CMOS process (65-nm node) can be exploited to allow sub-wavelength optical field processing in a massively scalable fashion. We demonstrate this in the context of eliminating all external optics and enabling the first optics-free fully integrated CMOS fluorescencebased biosensor array with massively multiplexed bio-molecular sensing capability for DNAs with surface sensitivity comparable to commercial fluorescence readers. The angle and scattering insensitive nature of the filter, relying on coupled surface-plasmon polariton modes, allows us to eliminate all external optics and miniaturize the entire 96-sensor array system including a LED source within 0.1 cc of volume. The system demonstrates detection sensitivity around 1 molecule/µm2 or zepto moles of quantum dot based fluorophores on the chip surface. The electronic-nanophotonic co-design approach allows us to optimally partition optical and electronic filtering, enabling us to detect fluorescence signal 77 dB lower than the
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excitation. CMOS-based nano-optical systems can lead to novel chip-scale optical sensors for in-vitro and in-vivo applications.
Keywords: CMOS, plasmonics, nanoplasmonics, nano-optics, copper, biosensor, DNA, microarray.
The ability to sense bio-molecules (DNAs, RNAs, proteins) with high sensitivity and specificity in a massively multiplexed fashion in an ultra-miniaturized and ultra low power system, small enough to fit inside a pill, can revolutionize personalized medicine and low-cost diagnostics
1–6
,
prevention of epidemic diseases, and also enable complex bio-molecular sensing modalities in-vivo that current technologies fail to address 7–9 . Currently, such detection systems are typically based on affinity-reaction (such as specific antigen-antibody for enzyme-linked-immunoabsorbent-assay (ELISA), DNA-cDNA) and signals are detected by fluorescence reporters 10–15 . This typically requires complex optical instrumentation including multiple filters, lenses, discrete photodetectors and mechanical scanners arranged in collimated optics making such systems bulky and expensive. This is particularly true for systems to reach surface detection sensitivities of the level of 1 fluorophore/µm2 and below (sub-pM levels of target biomolecules), where the background excitation can be between 106 − 107 times larger than the fluorescence signal.
In these new class of miniaturized sensing systems, complementary-metal-oxide semiconductor (CMOS) can play a significant role in enabling massively multiplexed biosensing due to its scalability, yield, and ability to integrate complex systems at low cost
16–27
. At optical frequen-
cies, while the performance of CMOS image sensors have caught up with classic CCD detectors 2 ACS Paragon Plus Environment
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in recent years, fully integrated, multiplexed, and external-optics-free fluorescence sensing has not been demonstrated in CMOS.
In this work, we present the first demonstration of sub-wavelength optical field manipulation in a digital commercial CMOS foundry process along with the full integration of a multiplexed fluorescence sensor that reaches surface sensitivity of 1 fluorophore/µm2 . While prior works have shown CMOS-compatible nano-optical structures in copper or otherwise 28–32 , here we adopt an absolutely ‘no-change’ approach to CMOS fabrication and demonstrate for the first time optical nanostructures exploiting the lowest copper interconnect layers in an industry-standard 65-nm CMOS foundry process typically used for digital processors and wireless integrated circuits (ICs). These integrated filters allow angle-insensitive filtering of background excitation enabling the removal of all external optical elements, therefore allowing the detection of immobilized fluorophores directly on the chip surface. The IC integrates all the necessary nano-optical filters and electronic circuitry including photo-detection, low-noise readout and signal processing for 96-multiplexed sensor array into a 2 × 1mm2 CMOS chip. To further leverage the angle insensitiveness of the on-chip filter, we employed a low-cost mm-sized UV LED for fluorescence excitation along with proper packaging of the chip with bio-interface, thereby miniaturizing the complete 96-sensor fluorescence sensing system into a total volume of ∼0.1 cc, eliminating all external optical or mechanical components 33 .
The key enabler of the presented ultra-miniaturized 96-sensor fluorescence reader chip is the on-chip copper-based sub-wavelength nano-plasmonic filter. Unlike prior plasmonic filters that are
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based on resonant plasmon coupling, such as the structures proposed for RGB color filtering
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34–36
,
the presented filter exploits the differential propagation loss of coupled surface plasmon modes in the sub-wavelength waveguide array structure. This unique design achieves a very high extinction ratio (40-50 dB) required for high-sensitivity fluorescence detection, and it simultaneously enables the filter to be insensitive to angles of incidence or complex fluorescence dipole excitation condition. This is key to on-chip miniaturization of a benchtop fluorescence reader where stray and scattered incident light is inevitable and fluorophores emit for a wide range of angles of incidence. Such integrated angle-insensitive design eliminates all external collimating optics 37, 38 , and achieves detection sensitivity orders of magnitude higher than filter-less fluorescence detection systems based on fluorescence lifetime detection with complex picosecond-level laser synchronization 39, 40 .
In this work, we present the complete design, theory and measurement results of the onchip copper-based nano-plasmonic filter and demonstrate the entire fluorescence reader system showing the multiplexing ability in detecting very low levels of fluorescence signals in both nucleic assays. While we experimentally demonstrate the sensor performance with fluorescence labels on the sensor surface and with DNA assays, the high sensitivity of the sensor in detecting fluorescence labels on the surface can be utilized for high sensitivity immunoassays as well with a standard protein chemistry. Furthermore, we show the scalability of fabrication of optical nanostructures in massively parallelized fashion which can be an enabling technology for future complex nanooptical systems. Miniaturized fluorescence sensing systems in a CMOS process can enable new sensing modalities for a wide range of bio-molecular sensing applications, both in-vitro and in4 ACS Paragon Plus Environment
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vivo.
CMOS-Nano-optics Integration and System-level Opportunities
The embedded multi-layer electronic interconnects (∼ 10-12 layers) realized with copper in modern day CMOS are used here to serve the dual role of interconnects and optical signal processing. With semiconductor device scaling, the feature size of the copper-based interconnect layers has also entered the deep-subwavelength regime at or below 100 nm for nodes smaller than 65-nm transistor feature size
41
. Design of these nano-structures in a CMOS process must be compli-
ant with design rule checks (DRCs) of the foundry to ensure high yield and tight process control of fabrication. This includes minimum feature sizes, minimum spacings, minimum areas as well as metal density requirements for stability of the planarization process. However, a close cointegration and co-design approach of the on-chip nano-optical structures in close proximity to the integrated electronics in the same substrate enables new system level capabilities that remain obfuscated in the partitioned approach. As an example, while the nano-plasmonic filters presented in this work achieve nearly 50 dB of extinction ratio between the excitation and fluorescence emission, the massive multiplexing ability allows us to sense the background to achieve another 27 dB of electronic filtering at the signal processing level at the backend, allowing an end-to-end detection capability of fluorescence power (Pf ) even 77 dB below the excitation light (Pl ) (See Supporting Information for calculation). In the past two decades, exploiting nanoscale metallic structures to manipulate and guide light has made tremendous progress in enabling sub-diffraction waveguiding 42–44 , nanofocusing 45, 48 , improved photovoltaic devices 46, 47 , plasmon modulation 49 ,
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flat lenses with meta-surfaces 50, 51 , and plasmon resonance-based enhancements for Raman spectroscopy and biosensing
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. Leveraging existing CMOS technology to manipulate light at the
visible and NIR at nano-scale with integrated photon detection and complex signal processing circuitry can enable a new class of multi-functional optical system on chips (SoCs) with extreme miniaturization, low-power to operate and extremely low cost upon mass manufacturing 55, 56 .
Integrated Copper-based Angle-Insensitive Nano-plasmonic Filter
Design In a classical fluorescence set-up, both fluorescence signal and laser excitation are collimated to allow the usage of a high-performance multi-layer fluorescence emission filter which typically works within a small range of angles 37, 38 . In this miniaturized sensor platform without optical collimation (Fig. 1), the radiation from the fluorescent dipoles on the chip surface interacts with the integrated filters in a complex fashion for a wide range of incident angles
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. In
addition, in order to retain the ultra-miniaturized form factor for point-of-care in-vitro and even in-vivo diagnostics, it is preferable to use LED as opposed to bulky laser system for fluorescence excitation. In this work, the filter needs to handle the near-grazing excitation light as well as the scattered light from the assay and other necessary structures of the CMOS chip (e.g. the bonding pads). Therefore, the angle insensitive characteristic of the filter with extinction ratios (≥ 45dB) becomes a critical and differentiating factor for chip-scale fluorescence sensing. This precludes any resonant filter structures (interference-based or resonant plasmonic coupling
34, 35
). In this
work, we exploit the differential loss of the coupled sub-wavelength waveguiding through the copper nano-structures with the dominant coupled surface plasmon polariton (SPP) modes to achieve
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angle-insensitive filter characteristics.
In the 65-nm industry standard CMOS process, the lowest metal layers in close proximity to the transistors have the smallest feature sizes (≈ 100 nm width, ≈ 130 nm spacing). The nanoplasmonic filter is designed to be an array of vertical sub-wavelength slab waveguides realized with the 4th − 7th copper interconnect layers and the via layers in between, in total measuring 1.41 µm in vertical length in the direction of the optical mode propagation (Fig. 2a). Electronic signals are extracted from the photon-detection circuitry and transferred to the edge of the chip using the 1st − 3rd interconnect layers and are transmitted externally. The entire optical path, filters and the electronic routing are co-designed to ensure optimal performance by maximizing light collection efficiency (minimizing circuits routing metal layers on top of the active photon-detection area) and minimizing light leakage from the sides of the chip.
The metallic nanostructures fabricated in standard CMOS are examined under scanning electron microscope (SEM) after the top passivation layers are removed by focused ion beam (FIB), as shown in Fig. 2b-Fig. 2d. The fabricated metallic nanostructures show exceptional consistency with the original design. The high yield of the CMOS fabrication process for both optical and electronic functionalities is exploited to enable a continuous global filter sheet across the entire array, allowing seamless scaling in the number of sensing sites for multiplexed fluorescence detection.
Operating Principle Fig. 3(a) shows the simulated normal incidence transmission spectrum for the y-polarization (perpendicular to the slabs) and x-polarization (parallel to the slabs), respectively. The parameters of the filter structure are shown in Fig. 2, the dielectric constant of copper 7 ACS Paragon Plus Environment
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Figure 1: (a) 96-sensor multiplexed fluorescence sensor chip fabricated in standard 65nm CMOS with integrated nano-plasmonic filters, photon detection, readout and signal processing circuitry. (b) The array architecture showing the 12x8 sensors with nano-plasmonic filters on top and the optical shield surrounding the filters to prevent light leakage into chip. (c) The structure of the photodiode with the optically shielded reference diode, and the in-pixel readout circuitry co-designed with the integrated nano-plasmonic filter. 8 ACS Paragon Plus Environment
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Figure 2: (a) The structure and dimension of the integrated nano-plasmonic filter, implemented in 65 nm CMOS process with minimum metal linewidth of 100 nm and spacing of 130 nm. (b)(d) SEM images of the interconnect layers serving the dual functionalities of integrated optical filtering and electronic routing for the photon-detection circuitry underneath the filter.
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across the wavelengths of interest is obtained from
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and the dielectric material surrounding the
filter structure is assumed to be glass. The simulation is performed for one unit cell of the structure applying periodic boundary conditions using Finite Difference Time Domain (FDTD) method. To comply with the design rule checks of the CMOS fabrication process, the filter is designed to allow light to pass for one polarization along y for minimum area requirement of each copper nanostructure. As can be seen, the filter shows nearly 60 dB extinction ratio between 405 nm and 800 nm. Due to the sub-wavelength spacing between the slabs, light with parallel polarization (along x) are largely blocked across the wavelength of interest. We choose quantum dots as the fluorescence tag for their photo-stability, stronger emission and higher Stokes shift 61, 62 and they have become standardized for assay chemistry. Fig. 3(a) also shows the fluorescence excitation and emission spectrum of the chosen Qdot 800 fluorescent tag which can be efficiently excited at around 400 nm and emits at around 800 nm, compatible with the filter performance 63 . In principle, the filter can be designed to process both polarizations with different geometric shapes (such as sub-wavelength nano-pillar arrays and etc.) and therefore double the photon collection efficiency. In this work, since the filter blocks the parallel polarization at 405 nm excitation wavelength, it removes the need for any external polarizer as well. Additionally, although theoretically process variation can have some effect on the optical performance of the filter. The non-resonant absorptive nature of the filter design enable the optical performance to preserve. As shown in Fig 3(b), the simulated extinction ratio keeps its value at 55-65 dB for 10% metal line-width variation.
A modal analysis of the periodic, sub-wavelength copper waveguide array is carried out to explain the filtering principle. A 2-dimensional (2D) waveguide array which shares similar princi10 ACS Paragon Plus Environment
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ple of operation is first considered. In this 2D system as shown in Fig. 4a, the structure is periodic along y dimension with unit cell pitch of 230 nm, the structure is assumed to be infinite along x and the modes propagates along -z. Due to the periodicity of the system, coupled waveguide modes are excited which is characterized by the Bloch wave vector along y dimension (k// ), depending on the excitation condition (incident angles for plane-wave excitations or different dipole excitations). To study the quality of the modes, we first consider the case when k// = 0, corresponding to plane wave excitation normal to the surface of the filter along z dimension. Expectedly, the waveguide supports different orders of TE and TM modes. Fig. 4b-Fig. 4e show the simulated absolute values of Hx and Ex field distributions for the TM and TE modes for 405 nm fluorescence excitation and 800 nm fluorescence emission wavelengths, and Fig. 4f summarizes the effective mode index and the propagation losses of the modes.
As can be seen, the fundamental TM modes (T M0 ) for both 405 nm and 800 nm wavelengths that have an effective index larger than the refractive index of the dielectric media SiO2 are known as the surface plasmon polariton (SPP) modes, which do not ‘cut-off’ as the dimensions of the waveguide system scale down. The loss of the SPP modes, therefore, mainly depends on the dielectric behavior of copper at these frequencies, which experiences significant propagation loss at 405 nm (∼ 35.24dB/µm) compared to wavelengths near 800 nm (∼ 0.95dB/µm ). This nonresonant characteristic is critical for sensitive detection in presence of uncollimated and scattered excitation and fluorescence.
It is critical to understand the effect of the cavity modes represented by various types of
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Figure 3: (a) Simulated transmission spectra for the nano-plasmonic filter at normal incidence for polarizations perpendicular and parallel to the copper waveguide slabs. The spectra show ∼ 60 dB extinction ratio between 800 nm and 405 nm wavelengths for perpendicular polarization and almost complete blockage for parallel polarization across the wavelengths of interest. The absorption and emission spectrum of the chosen quantum dot fluorophore (Qdot 800) are shown inside the figure and they match the implemented filter performance. (b) Simulated filter extinction ratio with 10% metal line width process variation showing robustness of the filtering process. 12 ACS Paragon Plus Environment
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Figure 4: (a) Simplified structure of the 2D waveguide array model. (b),(c),(d),(e) Simulated mode profiles of the TM and TE modes of the lowest three orders including the SPP mode. (f) Summary of the effective mode index (propagation constant normalized by the wave-vector k0 in vacuum).
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TE and higher order TM modes, when extinction ratios as high as 50 dB are being considered as shown in the Fig. 4. In contract to the SPP modes whose mode loss is primarily determined by the material loss for different wavelengths (Fig. 5a), the loss of these cavity modes are also affected strongly by the geometry and dimensions of the waveguide with respect to the wavelength (Fig. 5b). As can been seen, while the T M0 mode loss for 800 nm is orders of magnitude lower than that at 405 nm, the reverse is true for the T E0 mode. For optimal filter performance, the cavity modes must be suppressed to the largest extent possible. In this work, the spacing among the waveguide slabs is chosen to be 130 nm, the minimum allowable dimension in the implemented 65nm CMOS technology, thereby keeping the loss of both the cavity and SPP modes at the excitation wavelength of 405 nm high. Sub-wavelength spacing is key to ensure that background excitation is rejected regardless of which modes are excited, hence the robust high-performance optical filtering. Expectedly, migrating to finer technology node (such as a 32 nm CMOS) will further enhance the filter performance due to stronger elimination of T E0 mode for 405 nm.
Angle-insensitive Filter Characteristics As mentioned above, for chip-scale fluorescence-sensing, the filter needs to suppress the near-grazing and scattered excitation light and also allow fluorescence emission from a variety of incident angles to pass efficiently. For the same periodic structure shown in Fig. 4a, the coupled modes are characterized by the modal order, complex propagation constant as well as the Bloch wave vector k// along y dimension, and the electric or magnetic field satisfys u(y + nΛ) = u(y) exp(jnΛk// ), where Λ is the pitch of the waveguide array (230 nm). For the 2D waveguide array structure, the solution of the complex propagation constant (β) can be derived analytically. 14 ACS Paragon Plus Environment
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Figure 5: The coupled SPP (T M0 ) modes and cavity modes (T E0 ) have distinct losses as functions of wavelength and waveguide spacing at kx =ky =0 (normal incidence). The implemented minimum spacing of 130 nm in 65 nm CMOS ensures both SPP and cavity modes experience high propagation losses at 405 nm, critical for angle-insensitive filtering.
1 1 k2 2 k1 TM mode : cos(k// Λ) − cos(k1 a) cos(k2 b) + ( + ) sin(k1 a) sin(k2 b) = 0 2 2 k1 1 k2 1 k2 k1 TE mode : cos(k// Λ) − cos(k1 a) cos(k2 b) + ( + ) sin(k1 a) sin(k2 b) = 0 2 k1 k2
Where k1 =
(1) (2)
p p 1 k02 − β 2 and k2 = 2 k02 − β 2 , 1 and 2 are the dielectric constants of
copper and SiO2 respectively, a and b are the slab thickness of copper and SiO2 respectively, and − Λπ < k//
