Nicholas M. Fahrenkopf

Immobilization Mechanisms of Deoxyribonucleic Acid (DNA) to Hafnium Dioxide (HfO2) Surfaces for Biosensing Applications

Immobilization of biomolecular probes to the sensing substrate is a critical step for biosensor fabrication. In this work we investigated the phosphate-dependent, oriented immobilization of DNA to hafnium dioxide surfaces for biosensing applications. Phosphate-dependent immobilization was confirmed on a wide range of hafnium oxide surfaces; however, a second interaction mode was observed on monoclinic hafnium dioxide. On the basis of previous materials studies on these films, DNA immobilization studies, and density functional theory (DFT) modeling, we propose that this secondary interaction is between the exposed nucleobases of single stranded DNA and the surface. The lattice spacing of monoclinic hafnium dioxide matches the base-to-base pitch of DNA. Monoclinic hafnium dioxide is advantageous for nanoelectronic applications, yet because of this secondary DNA immobilization mechanism, it could impede DNA hybridization or cause nonspecific surface intereactions. Nonetheless, DNA immobilization on polycrystalline and amorphous hafnium dioxide is predominately mediated by the terminal phosphate in an oriented manner which is desirable for biosensing applications.

Biologically self-assembled memristive circuit elements

Both TiO2 and HfO2 are common materials for semiconductor fabrication that have shown memristive properties. Nanoparticles of these metal oxides have great prospect to provide nanoscale materials with tunable electronic properties for integration in advanced circuits such as neuromorphic networks based on memristive crossbar elements. We seek to take advantage of the unique interaction between the phosphate end-group of DNA and Ti02/Hf02 nanoparticles to enable a guided assembly of circuit elements via specific nucleotide sequences in a bottom-up fashion.

Octave-spanning coherent supercontinuum generation in silicon on insulator from 1.06 μm to beyond 2.4 μm

Efficient complementary metal-oxide semiconductor-based nonlinear optical devices in the near-infrared are in strong demand. Due to two-photon absorption in silicon, however, much nonlinear research is shifting towards unconventional photonics platforms. In this work, we demonstrate the generation of an octave-spanning coherent supercontinuum in a silicon waveguide covering the spectral region from the near- to shortwave-infrared. With input pulses of 18 pJ in energy, the generated signal spans the wavelength range from the edge of the silicon transmission window, approximately 1.06 to beyond 2.4 μm, with a −20 dB bandwidth covering 1.124–2.4 μm. An octave-spanning supercontinuum was also observed at the energy levels as low as 4 pJ (−35 dB bandwidth). We also measured the coherence over an octave, obtaining , in good agreement with the simulations. In addition, we demonstrate optimization of the third-order dispersion of the waveguide to strengthen the dispersive wave and discuss the advantage of having a soliton at the long wavelength edge of an octave-spanning signal for nonlinear applications. This research paves the way for applications, such as chip-scale precision spectroscopy, optical coherence tomography, optical frequency metrology, frequency synthesis and wide-band wavelength division multiplexing in the telecom window.

Ultra-Compact CMOS-Compatible Ytterbium Microlaser

We demonstrate a waveguide-coupled trench-based ytterbium microlaser, achieving a sub-milliwatt lasing threshold and a 1.9% slope efficiency within an ultra-compact 40-µm-radius cavity while maintaining full compatibility with a CMOS foundry process.

Novel approaches to biosensing and nano-biological interactions

Nanotechnology has recently been applied to a wide range of biological systems. In particular, there is a current push to examine the interface between the biological world and micro/nano-scale systems. Our research in this field has led to the development of novel strategies for spatial patterning of biomolecules, electrical and optical biosensing, nanomaterial delivery systems, single-cell manipulation, and the study of cellular interactions with nano-structured surfaces. Current work on these topics will be presented, including work on novel, semiconductor-based DNA detection methods and mechanical, atomic force microscopy (AFM)-based characterization of bacterial biofilms in threedimensional microfluidic systems.

Phosphate-dependent DNA Immobilization on Hafnium Oxide for Bio-Sensing Applications

Hafnium(IV) oxide (HfO 2 ) has replaced silicon oxide as a gate dielectric material in leading edge CMOS technology, providing significant improvement in gate performance for field effect transistors (FETs). We are currently exploring this high-k dielectric for its use in nucleic acid-based FET biosensors. Due to its intrinsic negative charge, label-free detection of DNA can be achieved in the gate region of high-sensitivity FET devices. Previous work has shown that phosphates and phosphonates coordinate specifically onto metal oxide substrates including aluminum and titanium oxides. This property can therefore be exploited for direct immobilization of biomolecules such as nucleic acids. Our work demonstrates that 5’ phosphate-terminated single stranded DNA (ssDNA) can be directly immobilized onto HfO 2 surfaces, without the need for additional chemical modification or crosslinking. Non-phosphorylated ssDNA does not form stable surface interactions with HfO 2 , indicating that immobilization is dependent upon the 5’ terminal phosphate. Further work has shown that surface immobilized ssDNA can be hybridized to complementary target DNA and that sequence-based hybridization specificity is preserved. These results suggest that the direct DNA-HfO 2 immobilization strategy can enable nucleic acid-based biosensing assays on HfO 2 terminated surfaces. This work will further enable high sensitivity electrical detection of biological targets utilizing transistor-based technologies.

A III-V field effect transistor (FET) with hafnium oxide gate dielectric for the detection of deoxyribonucleic acid (DNA) hybridization

Field-portable DNA biosensors have the potential to greatly improve diagnosis of disease, forensic DNA analysis, food safety monitoring, and biowarfare detection. These sensors detect hybridization of complementary strands of DNA, one immobilized onto the sensor substrate and the other free in solution. Most DNA sensors suffer from lack of portability or the inability to process large numbers of samples in parallel. Field effect transistor (FET) based DNA sensors, which detect hybridization by sensing negative charges on target DNA through the field effect, have the potential for both high throughput and portable detection [1].

High positional freedom SOI subwavelength grating coupler (SWG) for 300 mm foundry fabrication

We present an apodized, single etch-step, subwavelength grating (SWG) high positional freedom (HPF) grating coupler based on the 220 nm silicon-on-insulator (SOI) with 2μm BOX substrate. The grating coupler was designed for 1550 nm light with transverse electric (TE) polarization. It has a measured maximum coupling efficiency of -7.49 dB (17.8%) and a -1 dB/-3 dB bandwidth of ~14 nm/29.5 nm respectively. It was fabricated in a 300mm state of the art CMOS foundry. This work presents an SOI-based grating coupler with the highest-to the best of our knowledge- -1 dB single mode fiber lateral alignment of 21.4 μm × 10.1 μm.

Exploiting Phosphate Dependent DNA Immobilization on HfO 2 , ZrO 2 and AlGaN for Integrated Biosensors

A significant challenge for high throughput nucleic acid analysis and sequencing is to increase both throughput and sensitivity. Electrical detection methods are advantageous since they can be easily scaled to high density arrays, are highly sensitive, and do not require bulky optical equipment for readout. A focus of most nucleic acid based sensors is the detection of sequence-specific hybridization events between complementary strands of DNA or RNA. These hybridization events can be detected electrically, due to the intrinsic negative charge associated with the phosphate-rich nucleic acid backbone. Field effect transistors (FETs) and high electron mobility transistors (HEMTs) are ideal devices for detecting such hybridization events, due to their high sensitivity to changes in electrical field strength. A key concern for the construction of DNA-based FET and HEMT biosensors is the immobilization of probe oligonucleotides on the active region of the sensor. In previous work, our group has shown that single stranded DNA can be directly immobilized onto semiconductor materials without the need for complex surface chemistry or crosslinking strategies. In the present work, we have shown that the immobilization of single stranded DNA onto these materials is influenced by the terminal phosphate group of the DNA molecule, independent of backbone phosphates. This agrees with previous studies in which phosphates and phosphonates exhibited strong attachment to a variety of metal oxides. We have also shown that surface-immobilized DNA is available for hybridization and that hybridization is sequence specific. Phosphate-dependent immobilization was demonstrated for HfO 2 , AlGaN, and ZrO 2 surfaces using optical detection of DNA-DNA hybridization, as well as x-ray photoelectron spectroscopy (XPS) analysis of DNA-modified surfaces.