Micro to macro scale simulation coupling for stray light analysis.

Stray light in an optical system is unwanted parasitic light that may degrade performance. It can originate from different sources and may lead to different problems in the optical system such as fogging, ghost images for imagers, or inaccurate measurements for time of flight applications. One of the root causes is the reflectivity of the sensor itself. In this paper we present a new optical simulation methodology to analyze the stray light contribution due to the sensor reflectivity by coupling electromagnetic simulation (to calculate the pixels' bidirectional reflectance distribution function, also named BRDF) and ray-tracing simulation (for stray light analysis of the camera module). With this simulation flow we have been able to reproduce qualitatively red ghost images observed on different sensors in our laboratory.

Efficient layout-aware statistical analysis for photonic integrated circuits.

Fabrication variability significantly impacts the performance of photonic integrated circuits (PICs), which makes it crucial to quantify the impact of fabrication variations before the final fabrication. Such analysis enables circuit and system designers to optimize their designs to be more robust and obtain maximum yield when designing for manufacturing. This work presents a simulation methodology, Reduced Spatial Correlation Matrix-based Monte-Carlo (RSCM-MC), to efficiently study the impact of spatially correlated fabrication variations on the performance of PICs. First, a simple and reliable method to extract physical correlation lengths, variability parameters that define the inverse of the spatial frequencies of width and height variations over a wafer, is presented. Then, the process of generating correlated variations for MC simulations using RSCM-MC methodology is presented. The methodology generates correlated variations by first creating a reduced correlation matrix containing spatial correlations between all the circuit components, and then processing it using Cholesky decomposition to obtain correlated variations for all circuit components. These variations are then used to conduct MC simulations. The accuracy and the computation performance of the proposed methodology are compared with other layout-dependent Monte-Carlo simulation methodologies, such as Virtual wafer-based Monte-Carlo (VW-MC). A Mach-Zehnder lattice filter is used to study the accuracy, and a second-order Mach-Zehnder filter and a 16x16 optical switch matrix system are used to compare the computational performance.

Performance prediction for silicon photonics integrated circuits with layout-dependent correlated manufacturing variability.

This work develops an enhanced Monte Carlo (MC) simulation methodology to predict the impacts of layout-dependent correlated manufacturing variations on the performance of photonics integrated circuits (PICs). First, to enable such performance prediction, we demonstrate a simple method with sub-nanometer accuracy to characterize photonics manufacturing variations, where the width and height for a fabricated waveguide can be extracted from the spectral response of a racetrack resonator. By measuring the spectral responses for a large number of identical resonators spread over a wafer, statistical results for the variations of waveguide width and height can be obtained. Second, we develop models for the layout-dependent enhanced MC simulation. Our models use netlist extraction to transfer physical layouts into circuit simulators. Spatially correlated physical variations across the PICs are simulated on a discrete grid and are mapped to each circuit component, so that the performance for each component can be updated according to its obtained variations, and therefore, circuit simulations take the correlated variations between components into account. The simulation flow and theoretical models for our layout-dependent enhanced MC simulation are detailed in this paper. As examples, several ring-resonator filter circuits are studied using the developed enhanced MC simulation, and statistical results from the simulations can predict both common-mode and differential-mode variations of the circuit performance.

Fiber-chip edge coupler with large mode size for silicon photonic wire waveguides.

Fiber-chip edge couplers are extensively used in integrated optics for coupling of light between planar waveguide circuits and optical fibers. In this work, we report on a new fiber-chip edge coupler concept with large mode size for silicon photonic wire waveguides. The coupler allows direct coupling with conventional cleaved optical fibers with large mode size while circumventing the need for lensed fibers. The coupler is designed for 220 nm silicon-on-insulator (SOI) platform. It exhibits an overall coupling efficiency exceeding 90%, as independently confirmed by 3D Finite-Difference Time-Domain (FDTD) and fully vectorial 3D Eigenmode Expansion (EME) calculations. We present two specific coupler designs, namely for a high numerical aperture single mode optical fiber with 6 µm mode field diameter (MFD) and a standard SMF-28 fiber with 10.4 µm MFD. An important advantage of our coupler concept is the ability to expand the mode at the chip edge without leading to high substrate leakage losses through buried oxide (BOX), which in our design is set to 3 µm. This remarkable feature is achieved by implementing in the SiO2 upper cladding thin high-index Si3N4 layers. The Si3N4 layers increase the effective refractive index of the upper cladding near the facet. The index is controlled along the taper by subwavelength refractive index engineering to facilitate adiabatic mode transformation to the silicon wire waveguide while the Si-wire waveguide is inversely tapered along the coupler. The mode overlap optimization at the chip facet is carried out with a full vectorial mode solver. The mode transformation along the coupler is studied using 3D-FDTD simulations and with fully-vectorial 3D-EME calculations. The couplers are optimized for operating with transverse electric (TE) polarization and the operating wavelength is centered at 1.55 µm.

Precise control of the coupling coefficient through destructive interference in silicon waveguide Bragg gratings.

We present waveguide Bragg gratings with misaligned sidewall corrugations on a silicon-on-insulator platform. The grating strength can be tuned by varying the misalignment between the corrugations on the two sidewalls. This approach allows for a wide range of grating coupling coefficients to be achieved with precise control, and substantially reduces the effects of quantization error due to the finite mask grid size. The experimental results are in very good agreement with simulations using the finite-difference time-domain (FDTD) method.

The use of aluminum nanostructures as platforms for metal enhanced fluorescence of the intrinsic emission of biomolecules in the ultra-violet.

We consider the possibility of using aluminum nanostructures for enhancing the intrinsic emission of biomolecules. We used the finite-difference time-domain (FDTD) method to calculate the effects of aluminum nanoparticles on nearby fluorophores that emit in the ultra-violet (UV). We find that the radiated power of UV fluorophores is significantly increased when they are in close proximity to aluminum nanostructures. We show that there will be increased localized excitation near aluminum particles at wavelengths used to excite intrinsic biomolecule emission. We also examine the effect of excited-state fluorophores on the near-field around the nanoparticles. Finally we present experimental evidence showing that a thin film of amino acids and nucleotides display enhanced emission when in close proximity to aluminum nanostructured surfaces. Our results suggest that biomolecules can be detected and identified using aluminum nanostructures that enhance their intrinsic emission. We hope this study will ignite interest in the broader scientific community to take advantage of the plasmonic properties of aluminum and the potential benefits of its interaction with biomolecules to generate momentum towards implementing fluorescence-based bioassays using their intrinsic emission.

On the Feasibility of Using the Intrinsic Fluorescence of Nucleotides for DNA Sequencing.

There is presently a worldwide effort to increase the speed and decrease the cost of DNA sequencing as exemplified by the goal of the National Human Genome Research Institute (NHGRI) to sequence a human genome for under $1000. Several high throughput technologies are under development. Among these, single strand sequencing using exonuclease appear very promising. However, this approach requires complete labeling of at least two bases at a time, with extrinsic high quantum yield probes. This is necessary because nucleotides absorb in the deep ultra-violet (UV) and emit with extremely low quantum yields. Hence intrinsic emission from DNA and nucleotides is not being exploited for DNA sequencing. In the present paper we consider the possibility of identifying single nucleotides using their intrinsic emission. We used the finite-difference time-domain (FDTD) method to calculate the effects of aluminum nanoparticles on nearby fluorophores that emit in the UV. We find that the radiated power of UV fluorophores is significantly increased when they are in close proximity to aluminum nanostructures. We show that there will be increased localized excitation near aluminum particles at wavelengths used to excite intrinsic nucleotide emission. Using FDTD simulation we show that a typical DNA base when coupled to appropriate aluminum nanostructures leads to highly directional emission. Additionally we present experimental results showing that a thin film of nucleotides show enhanced emission when in close proximity to aluminum nanostructures. Finally we provide Monte Carlo simulations that predict high levels of base calling accuracy for an assumed number of photons that is derived from the emission spectra of the intrinsic fluorescence of the bases. Our results suggest that single nucleotides can be detected and identified using aluminum nanostructures that enhance their intrinsic emission. This capability would be valuable for the ongoing efforts towards the $1000 genome.

Flow cytometry with gold nanoparticles and their clusters as scattering contrast agents: FDTD simulation of light-cell interaction.

The formulation of the finite-difference time-domain (FDTD) approach is presented in the framework of its potential applications to in-vivo flow cytometry based on light scattering. The consideration is focused on comparison of light scattering by a single biological cell alone in controlled refractive-index matching conditions and by cells labeled by gold nanoparticles. The optical schematics including phase contrast (OPCM) microscopy as a prospective modality for in-vivo flow cytometry is also analyzed. The validation of the FDTD approach for the simulation of flow cytometry may open up a new avenue in the development of advanced cytometric techniques based on scattering effects from nanoscale targets.

Aluminum nanoparticles as substrates for metal-enhanced fluorescence in the ultraviolet for the label-free detection of biomolecules.

We use finite-difference time-domain calculations to show that aluminum nanoparticles are efficient substrates for metal-enhanced fluorescence (MEF) in the ultraviolet (UV) for the label-free detection of biomolecules. The radiated power enhancement of the fluorophores in proximity to aluminum nanoparticles is strongly dependent on the nanoparticle size, fluorophore-nanoparticle spacing, and fluorophore orientation. Additionally, the enhancement is dramatically increased when the fluorophore is between two aluminum nanoparticles of a dimer. Finally, we present experimental evidence that functionalized forms of amino acids tryptophan and tyrosine exhibit MEF when spin-coated onto aluminum nanostructures.

Systematic Computational Study of the Effect of Silver Nanoparticle Dimers on the Coupled Emission from Nearby Fluorophores.

We use the finite-difference time-domain method to predict how fluorescence is modified if the fluorophore is located between two silver nanoparticles of a dimer system. The fluorophore is modeled as a radiating point dipole with orientation defined by its polarization. When a fluorophore is oriented perpendicular to the metal surface, there is a large increase in total power radiated through a closed surface containing the dimer system, in comparison to the isolated fluorophore and the case of a fluorophore near a single nanoparticle. The increase in radiated power indicates increases in the relative radiative decay rates of the emission near the nanoparticles. The angle-resolved far-field distributions of the emission in a single plane are also computed. This is informative as many experimental conditions involve collection optics and detectors that collect the emission along a single plane. For fluorophores oriented perpendicular to the metal surfaces, the dimer systems lead to significant enhancements in the fluorescence emission intensity in the plane. In contrast, significant emission quenching occurs if the fluorophores are oriented parallel to the metal surfaces. We also examine the effect of the fluorophore on the near-field around the nanoparticles and correlate our results with surface plasmon excitations.

Uniform illumination and rigorous electromagnetic simulations applied to CMOS image sensors.

This paper describes a new methodology we have developed for the optical simulation of CMOS image sensors. Finite Difference Time Domain (FDTD) software is used to simulate light propagation and diffraction effects throughout the stack of dielectrics layers. With the use of an incoherent summation of plane wave sources and Bloch Periodic Boundary Conditions, this new methodology allows not only the rigorous simulation of a diffuse-like source which reproduces real conditions, but also an important gain of simulation efficiency for 2D or 3D electromagnetic simulations. This paper presents a theoretical demonstration of the methodology as well as simulation results with FDTD software from Lumerical Solutions.

Computational study of fluorescence scattering by silver nanoparticles.

We study the nature of fluorescence scattering by a radiating fluorophore placed near a metal nanoparticle with the finite-difference time-domain method. Angle-resolved light-scattering distributions are contrasted with those that result when ordinary plane waves are scattered by the nanoparticle. For certain sized nanoparticles and fluorophore dipoles oriented parallel to the metal surface, we find that the highest scattered fluorescence emission is directed back toward the fluorophore, which is very different from plane-wave scattering. The largest enhancements of far-field radiation are found when the dipole is oriented normal to the surface. We also examined the effect of the fluorophore on the near field around the particle. The fields can be enhanced or quenched compared to the isolated fluorophore and exhibit strong dependence on fluorophore orientation, as well as interesting spatial variations around the nanoparticle.