Vahid Ganjalizadeh | University of California, Santa Cruz (original) (raw)

Papers by Vahid Ganjalizadeh

Nature Communications, 2022

Many sensors operate by detecting and identifying individual events in a time-dependent signal wh... more Many sensors operate by detecting and identifying individual events in a time-dependent signal which is challenging if signals are weak and background noise is present. We introduce a powerful, fast, and robust signal analysis technique based on a massively parallel continuous wavelet transform (CWT) algorithm. The superiority of this approach is demonstrated with fluorescence signals from a chip-based, optofluidic single particle sensor. The technique is more accurate than simple peak-finding algorithms and several orders of magnitude faster than existing CWT methods, allowing for real-time data analysis during sensing for the first time. Performance is further increased by applying a custom wavelet to multi-peak signals as demonstrated using amplification-free detection of single bacterial DNAs. A 4x increase in detection rate, a 6x improved error rate, and the ability for extraction of experimental parameters are demonstrated. This cluster-based CWT analysis will enable high-performance, real-time sensing when signal-to-noise is hardware limited, for instance with low-cost sensors in point of care environments.

Conference on Lasers and Electro-Optics

Chip-based single molecule detection requires ultra-sensitive devices and robust signal processin... more Chip-based single molecule detection requires ultra-sensitive devices and robust signal processing methods. A new wavelet-based signal processing method is introduced that improves detection and error rates on an optofluidic platform by 2x and 3x, respectively. © 2019 The Author(s)

Conference on Lasers and Electro-Optics

High fidelity interference patterns from multimode interference waveguides are needed for multipl... more High fidelity interference patterns from multimode interference waveguides are needed for multiplexed optofluidic biosensors. Spot pattern fidelity can be optimized by careful design of the single-mode waveguides used to excite the multimode waveguides.

2019 IEEE Photonics Conference (IPC), 2019

Three-dimensional hydrodynamic focusing promises to enhance detection capabilities of optofluidic... more Three-dimensional hydrodynamic focusing promises to enhance detection capabilities of optofluidic sensors, enabling low concentration interrogation with higher confidence, critical for disease diagnosis. Novel 3DHDF designs with optofluidic channel diameters in the range of ten microns are evaluated, predicting detection enhancement of up to 3.54 times.

IEEE Photonics Technology Letters, 2021

Optofluidic sensors have enabled single molecule sensing using planar, waveguide dependent multi-... more Optofluidic sensors have enabled single molecule sensing using planar, waveguide dependent multi-spot fluorescence excitation. Here, we demonstrate a new approach to single-particle fluorescence sensing using free-space, top-down illumination of liquid-core antiresonant reflecting optical waveguide (ARROW) devices using two different multi-spot excitation techniques. First, the liquid core ARROW waveguide is excited with a focused beam through a slit pattern milled into an opaque aluminum film, showing comparable performance for single bead fluorescence detection as in-plane, multi-mode interference waveguide based excitation. The second top-down illumination technique images the spot pattern from a Y-splitter SiO2 waveguide chip directly onto the detection device for efficient power utilization and circumventing the need for an opaque cover, producing a further 2.7times2.7\times 2.7times improvement in signal-to-noise ratio. The two top-down approaches open up new possibilities for chip-based op...

Producing high fidelity multi-spot patterns from a long ARROW-based multimode interference wavegu... more Producing high fidelity multi-spot patterns from a long ARROW-based multimode interference waveguide is important for optofluidic biosensors that rely on optical multiplexing. We have found that spot pattern fidelity is affected by input waveguide geometry and etching parameters.

Micromachines

Optofluidic devices are capable of detecting single molecules, but greater sensitivity and specif... more Optofluidic devices are capable of detecting single molecules, but greater sensitivity and specificity is desired through hydrodynamic focusing (HDF). Three-dimensional (3D) hydrodynamic focusing was implemented in 10-μm scale microchannel cross-sections made with a single sacrificial layer. HDF is achieved using buffer fluid to sheath the sample fluid, requiring four fluid ports to operate by pressure driven flow. A low-pressure chamber, or pit, formed by etching into a substrate, enables volumetric flow ratio-induced focusing at a low flow velocity. The single layer design simplifies surface micromachining and improves device yield by 1.56 times over previous work. The focusing design was integrated with optical waveguides and used in order to analyze fluorescent signals from beads in fluid flow. The implementation of the focusing scheme was found to narrow the distribution of bead velocity and fluorescent signal, giving rise to 33% more consistent signal. Reservoir effects were o...

IEEE Photonics Technology Letters

Multimode interference (MMI) waveguides can be used to create wavelength-dependent spot patterns ... more Multimode interference (MMI) waveguides can be used to create wavelength-dependent spot patterns which enables simultaneous analyte detection on a single optofluidic chip, useful for disease diagnostics. The fidelity of such multi-spot patterns is important for high sensitivity and accurate target identification. Buried rib structures have been incorporated into these SiO2-based waveguides to improve environmental stability. Through experiments and simulation, this letter explores design parameters for a buried MMI rib waveguide based on anti-resonant reflecting optical waveguides in order to produce high-fidelity spot patterns. Optimal rib heights and widths are reported in the context of available microfabrication etch technology and performance for an optimized biosensor is shown.

Microfluidics and Nanofluidics

3D hydrodynamic focusing was implemented with channel cross-section dimensions smaller than 10 μm... more 3D hydrodynamic focusing was implemented with channel cross-section dimensions smaller than 10 μm. Microchannels were formed using sacrificial etching of two photoresist layers on a silicon wafer. The photoresist forms a plus-shaped prismatic focusing fluid junction which was coated with plasma-enhanced chemical-vapor-deposited oxide. Buffer fluid carried to the focusing junction envelopes an intersecting sample fluid, resulting in 3D focusing of the sample stream. The design requires four fluid ports and operates across a wide range of fluid velocities through pressure-driven flow. The focusing design was integrated with optical waveguides to interrogate fluorescing particles and confirm 3D focusing. Particle diffusion away from a focused stream was characterized.

Optics letters, Jan 15, 2018

Liquid-core waveguide-based optofluidic devices have proven to be valuable tools for analysis of ... more Liquid-core waveguide-based optofluidic devices have proven to be valuable tools for analysis of biological samples in fluid. They have enabled single bioparticle sensitivity while maintaining in-plane detection via light-induced fluorescence. The incorporation of multi-spot excitation with multimode interference (MMI) waveguides has enabled spatially and spectrally multiplexed detection of single viruses on an oxide-based optofluidic platform. Here, we introduce a new way of MMI-based multiplexing where multiple analysis channels are placed within a single multi-spot pattern. This stacked channel design enables both velocity and spectral multiplexing of single particles. The principle is demonstrated with differentiated detection of single H3N2 and H1N1 viruses on a polydimethylsiloxane platform.

IEEE journal of quantum electronics, 2018

Multimode interference (MMI) waveguides can be used for multiplexing and de-multiplexing optical ... more Multimode interference (MMI) waveguides can be used for multiplexing and de-multiplexing optical signals. High fidelity, wavelength dependent multi-spot patterns from MMI waveguides are useful for sensitive and simultaneous identification of multiple targets in multiplexed fluorescence optofluidic biosensors. Through experiments and simulation, this paper explores design parameters for an MMI rib anti-resonant reflecting optical waveguide (ARROW) in order to produce high fidelity spot patterns at the liquid core biomarker excitation region. Width and etch depth of the single excitation rib waveguide used to excite the MMI waveguide are especially critical because they determine the size of the input optical mode which is imaged at the MMI waveguide's output. To increase optical throughput into the MMI waveguide when light is coupled in from an optical fiber, tapers in the waveguide width can be used for better mode matching.

Micromachines

Optofluidic, lab-on-a-chip fluorescence sensors were fabricated using buried anti-resonant reflec... more Optofluidic, lab-on-a-chip fluorescence sensors were fabricated using buried anti-resonant reflecting optical waveguides (bARROWs). The bARROWs are impervious to the negative water absorption effects that typically occur in waveguides made using hygroscopic, plasma-enhanced chemical vapor deposition (PECVD) oxides. These sensors were used to detect fluorescent microbeads and had an average signal-to-noise ratio (SNR) that was 81.3% higher than that of single-oxide ARROW fluorescence sensors. While the single-oxide ARROW sensors were annealed at 300 • C to drive moisture out of the waveguides, the bARROW sensors required no annealing process to obtain a high SNR.

2014 Second RSI/ISM International Conference on Robotics and Mechatronics (ICRoM), 2014

This paper presents a novel structure for absolute capacitive pressure sensor which utilizes vert... more This paper presents a novel structure for absolute capacitive pressure sensor which utilizes vertically arranged comb fingers to reach high sensitivity with wide dynamic range. High sensitivity is one of the important factors in pressure sensors, which usually is achieved by decreasing air-gap within sensing electrodes and thin membrane in capacitive types, but in this paper a comb-grid structure is employed instead to improve the sensitivity. Due to the out-of-plane configuration of comb-fingers, capacitance variation is affected by both changing in lateral overlapped area and also distance within the electrodes simultaneously, which provides two extra degrees of freedom in manipulation and optimization of the sensor behavior in comparison with conventional capacitive pressure sensors. Design optimizations and analysis are derived by energy method which is in fine agreement with Finite Element Analysis (FEA) performed by ANSYS. Variation in sensing electrode area is also carried out to optimize the sensitivity. The results show a sensitivity of 66 fF/kPa at area ratio of 10% and membrane size of 1 × 1 mm2. Full scale pressure range of 160 kPa at area ratio of 70% and membrane size of 500 μm × 500 μm is achieved. We found that, higher sensitivities are achieved by horizontally decrement in air gap.

2014 International Conference on Optical MEMS and Nanophotonics, 2014

This paper demonstrates a novel optofluidic pressure sensor. Since optofluidics is becoming an em... more This paper demonstrates a novel optofluidic pressure sensor. Since optofluidics is becoming an emerging technology which combines the advantages of optics and microfluidics, it is used to bring new benefits to traditional pressure sensors. In this study, an external pressure causes deformation on a microring resonator which yields wavelength shift in the resonating. Whole structure is based on polydimethylsiloxane (PDMS) to ensure compatibility with microfluidic chips. Numerical simulations are performed to determine wavelength shift due to applied pressure. Maximum radial displacement of 2.5 μm is observed for an applied pressure of 25 kPa. A sensitivity of 2 nm/kPa is achieved.

Nature Communications

Many sensors operate by detecting and identifying individual events in a time-dependent signal wh... more Many sensors operate by detecting and identifying individual events in a time-dependent signal which is challenging if signals are weak and background noise is present. We introduce a powerful, fast, and robust signal analysis technique based on a massively parallel continuous wavelet transform (CWT) algorithm. The superiority of this approach is demonstrated with fluorescence signals from a chip-based, optofluidic single particle sensor. The technique is more accurate than simple peak-finding algorithms and several orders of magnitude faster than existing CWT methods, allowing for real-time data analysis during sensing for the first time. Performance is further increased by applying a custom wavelet to multi-peak signals as demonstrated using amplification-free detection of single bacterial DNAs. A 4x increase in detection rate, a 6x improved error rate, and the ability for extraction of experimental parameters are demonstrated. This cluster-based CWT analysis will enable high-perf...

This paper demonstrates a novel optofluidic pressure sensor. Since optofluidics is becoming an em... more This paper demonstrates a novel optofluidic pressure sensor. Since optofluidics is becoming an emerging technology which combines the advantages of optics and microfluidics, it is used to bring new benefits to traditional pressure sensors. In this study, an external pressure causes deformation on a microring resonator which yields wavelength shift in the resonating. Whole structure is based on polydimethylsiloxane (PDMS) to ensure compatibility with microfluidic chips. Numerical simulations are performed to determine wavelength shift due to applied pressure. Maximum radial displacement of 2.5 μm is observed for an applied pressure of 25 kPa. A sensitivity of 2 nm/kPa is achieved.

Nature Communications, 2022

Many sensors operate by detecting and identifying individual events in a time-dependent signal wh... more Many sensors operate by detecting and identifying individual events in a time-dependent signal which is challenging if signals are weak and background noise is present. We introduce a powerful, fast, and robust signal analysis technique based on a massively parallel continuous wavelet transform (CWT) algorithm. The superiority of this approach is demonstrated with fluorescence signals from a chip-based, optofluidic single particle sensor. The technique is more accurate than simple peak-finding algorithms and several orders of magnitude faster than existing CWT methods, allowing for real-time data analysis during sensing for the first time. Performance is further increased by applying a custom wavelet to multi-peak signals as demonstrated using amplification-free detection of single bacterial DNAs. A 4x increase in detection rate, a 6x improved error rate, and the ability for extraction of experimental parameters are demonstrated. This cluster-based CWT analysis will enable high-performance, real-time sensing when signal-to-noise is hardware limited, for instance with low-cost sensors in point of care environments.

Conference on Lasers and Electro-Optics

Chip-based single molecule detection requires ultra-sensitive devices and robust signal processin... more Chip-based single molecule detection requires ultra-sensitive devices and robust signal processing methods. A new wavelet-based signal processing method is introduced that improves detection and error rates on an optofluidic platform by 2x and 3x, respectively. © 2019 The Author(s)

Conference on Lasers and Electro-Optics

High fidelity interference patterns from multimode interference waveguides are needed for multipl... more High fidelity interference patterns from multimode interference waveguides are needed for multiplexed optofluidic biosensors. Spot pattern fidelity can be optimized by careful design of the single-mode waveguides used to excite the multimode waveguides.

2019 IEEE Photonics Conference (IPC), 2019

Three-dimensional hydrodynamic focusing promises to enhance detection capabilities of optofluidic... more Three-dimensional hydrodynamic focusing promises to enhance detection capabilities of optofluidic sensors, enabling low concentration interrogation with higher confidence, critical for disease diagnosis. Novel 3DHDF designs with optofluidic channel diameters in the range of ten microns are evaluated, predicting detection enhancement of up to 3.54 times.

IEEE Photonics Technology Letters, 2021

Optofluidic sensors have enabled single molecule sensing using planar, waveguide dependent multi-... more Optofluidic sensors have enabled single molecule sensing using planar, waveguide dependent multi-spot fluorescence excitation. Here, we demonstrate a new approach to single-particle fluorescence sensing using free-space, top-down illumination of liquid-core antiresonant reflecting optical waveguide (ARROW) devices using two different multi-spot excitation techniques. First, the liquid core ARROW waveguide is excited with a focused beam through a slit pattern milled into an opaque aluminum film, showing comparable performance for single bead fluorescence detection as in-plane, multi-mode interference waveguide based excitation. The second top-down illumination technique images the spot pattern from a Y-splitter SiO2 waveguide chip directly onto the detection device for efficient power utilization and circumventing the need for an opaque cover, producing a further 2.7times2.7\times 2.7times improvement in signal-to-noise ratio. The two top-down approaches open up new possibilities for chip-based op...

Producing high fidelity multi-spot patterns from a long ARROW-based multimode interference wavegu... more Producing high fidelity multi-spot patterns from a long ARROW-based multimode interference waveguide is important for optofluidic biosensors that rely on optical multiplexing. We have found that spot pattern fidelity is affected by input waveguide geometry and etching parameters.

Micromachines

Optofluidic devices are capable of detecting single molecules, but greater sensitivity and specif... more Optofluidic devices are capable of detecting single molecules, but greater sensitivity and specificity is desired through hydrodynamic focusing (HDF). Three-dimensional (3D) hydrodynamic focusing was implemented in 10-μm scale microchannel cross-sections made with a single sacrificial layer. HDF is achieved using buffer fluid to sheath the sample fluid, requiring four fluid ports to operate by pressure driven flow. A low-pressure chamber, or pit, formed by etching into a substrate, enables volumetric flow ratio-induced focusing at a low flow velocity. The single layer design simplifies surface micromachining and improves device yield by 1.56 times over previous work. The focusing design was integrated with optical waveguides and used in order to analyze fluorescent signals from beads in fluid flow. The implementation of the focusing scheme was found to narrow the distribution of bead velocity and fluorescent signal, giving rise to 33% more consistent signal. Reservoir effects were o...

IEEE Photonics Technology Letters

Multimode interference (MMI) waveguides can be used to create wavelength-dependent spot patterns ... more Multimode interference (MMI) waveguides can be used to create wavelength-dependent spot patterns which enables simultaneous analyte detection on a single optofluidic chip, useful for disease diagnostics. The fidelity of such multi-spot patterns is important for high sensitivity and accurate target identification. Buried rib structures have been incorporated into these SiO2-based waveguides to improve environmental stability. Through experiments and simulation, this letter explores design parameters for a buried MMI rib waveguide based on anti-resonant reflecting optical waveguides in order to produce high-fidelity spot patterns. Optimal rib heights and widths are reported in the context of available microfabrication etch technology and performance for an optimized biosensor is shown.

Microfluidics and Nanofluidics

3D hydrodynamic focusing was implemented with channel cross-section dimensions smaller than 10 μm... more 3D hydrodynamic focusing was implemented with channel cross-section dimensions smaller than 10 μm. Microchannels were formed using sacrificial etching of two photoresist layers on a silicon wafer. The photoresist forms a plus-shaped prismatic focusing fluid junction which was coated with plasma-enhanced chemical-vapor-deposited oxide. Buffer fluid carried to the focusing junction envelopes an intersecting sample fluid, resulting in 3D focusing of the sample stream. The design requires four fluid ports and operates across a wide range of fluid velocities through pressure-driven flow. The focusing design was integrated with optical waveguides to interrogate fluorescing particles and confirm 3D focusing. Particle diffusion away from a focused stream was characterized.

Optics letters, Jan 15, 2018

Liquid-core waveguide-based optofluidic devices have proven to be valuable tools for analysis of ... more Liquid-core waveguide-based optofluidic devices have proven to be valuable tools for analysis of biological samples in fluid. They have enabled single bioparticle sensitivity while maintaining in-plane detection via light-induced fluorescence. The incorporation of multi-spot excitation with multimode interference (MMI) waveguides has enabled spatially and spectrally multiplexed detection of single viruses on an oxide-based optofluidic platform. Here, we introduce a new way of MMI-based multiplexing where multiple analysis channels are placed within a single multi-spot pattern. This stacked channel design enables both velocity and spectral multiplexing of single particles. The principle is demonstrated with differentiated detection of single H3N2 and H1N1 viruses on a polydimethylsiloxane platform.

IEEE journal of quantum electronics, 2018

Multimode interference (MMI) waveguides can be used for multiplexing and de-multiplexing optical ... more Multimode interference (MMI) waveguides can be used for multiplexing and de-multiplexing optical signals. High fidelity, wavelength dependent multi-spot patterns from MMI waveguides are useful for sensitive and simultaneous identification of multiple targets in multiplexed fluorescence optofluidic biosensors. Through experiments and simulation, this paper explores design parameters for an MMI rib anti-resonant reflecting optical waveguide (ARROW) in order to produce high fidelity spot patterns at the liquid core biomarker excitation region. Width and etch depth of the single excitation rib waveguide used to excite the MMI waveguide are especially critical because they determine the size of the input optical mode which is imaged at the MMI waveguide's output. To increase optical throughput into the MMI waveguide when light is coupled in from an optical fiber, tapers in the waveguide width can be used for better mode matching.

Micromachines

Optofluidic, lab-on-a-chip fluorescence sensors were fabricated using buried anti-resonant reflec... more Optofluidic, lab-on-a-chip fluorescence sensors were fabricated using buried anti-resonant reflecting optical waveguides (bARROWs). The bARROWs are impervious to the negative water absorption effects that typically occur in waveguides made using hygroscopic, plasma-enhanced chemical vapor deposition (PECVD) oxides. These sensors were used to detect fluorescent microbeads and had an average signal-to-noise ratio (SNR) that was 81.3% higher than that of single-oxide ARROW fluorescence sensors. While the single-oxide ARROW sensors were annealed at 300 • C to drive moisture out of the waveguides, the bARROW sensors required no annealing process to obtain a high SNR.

2014 Second RSI/ISM International Conference on Robotics and Mechatronics (ICRoM), 2014

This paper presents a novel structure for absolute capacitive pressure sensor which utilizes vert... more This paper presents a novel structure for absolute capacitive pressure sensor which utilizes vertically arranged comb fingers to reach high sensitivity with wide dynamic range. High sensitivity is one of the important factors in pressure sensors, which usually is achieved by decreasing air-gap within sensing electrodes and thin membrane in capacitive types, but in this paper a comb-grid structure is employed instead to improve the sensitivity. Due to the out-of-plane configuration of comb-fingers, capacitance variation is affected by both changing in lateral overlapped area and also distance within the electrodes simultaneously, which provides two extra degrees of freedom in manipulation and optimization of the sensor behavior in comparison with conventional capacitive pressure sensors. Design optimizations and analysis are derived by energy method which is in fine agreement with Finite Element Analysis (FEA) performed by ANSYS. Variation in sensing electrode area is also carried out to optimize the sensitivity. The results show a sensitivity of 66 fF/kPa at area ratio of 10% and membrane size of 1 × 1 mm2. Full scale pressure range of 160 kPa at area ratio of 70% and membrane size of 500 μm × 500 μm is achieved. We found that, higher sensitivities are achieved by horizontally decrement in air gap.

2014 International Conference on Optical MEMS and Nanophotonics, 2014

This paper demonstrates a novel optofluidic pressure sensor. Since optofluidics is becoming an em... more This paper demonstrates a novel optofluidic pressure sensor. Since optofluidics is becoming an emerging technology which combines the advantages of optics and microfluidics, it is used to bring new benefits to traditional pressure sensors. In this study, an external pressure causes deformation on a microring resonator which yields wavelength shift in the resonating. Whole structure is based on polydimethylsiloxane (PDMS) to ensure compatibility with microfluidic chips. Numerical simulations are performed to determine wavelength shift due to applied pressure. Maximum radial displacement of 2.5 μm is observed for an applied pressure of 25 kPa. A sensitivity of 2 nm/kPa is achieved.

Nature Communications

Many sensors operate by detecting and identifying individual events in a time-dependent signal wh... more Many sensors operate by detecting and identifying individual events in a time-dependent signal which is challenging if signals are weak and background noise is present. We introduce a powerful, fast, and robust signal analysis technique based on a massively parallel continuous wavelet transform (CWT) algorithm. The superiority of this approach is demonstrated with fluorescence signals from a chip-based, optofluidic single particle sensor. The technique is more accurate than simple peak-finding algorithms and several orders of magnitude faster than existing CWT methods, allowing for real-time data analysis during sensing for the first time. Performance is further increased by applying a custom wavelet to multi-peak signals as demonstrated using amplification-free detection of single bacterial DNAs. A 4x increase in detection rate, a 6x improved error rate, and the ability for extraction of experimental parameters are demonstrated. This cluster-based CWT analysis will enable high-perf...

This paper demonstrates a novel optofluidic pressure sensor. Since optofluidics is becoming an em... more This paper demonstrates a novel optofluidic pressure sensor. Since optofluidics is becoming an emerging technology which combines the advantages of optics and microfluidics, it is used to bring new benefits to traditional pressure sensors. In this study, an external pressure causes deformation on a microring resonator which yields wavelength shift in the resonating. Whole structure is based on polydimethylsiloxane (PDMS) to ensure compatibility with microfluidic chips. Numerical simulations are performed to determine wavelength shift due to applied pressure. Maximum radial displacement of 2.5 μm is observed for an applied pressure of 25 kPa. A sensitivity of 2 nm/kPa is achieved.