Characterization of materials and fabrication of active matrix thin film transistor arrays for electrical interfacing of biological materials

Electrical interfacing between semiconductor devices and biological materials has been studied for live cell probing which will make it possible to perform direct electrical sensing of cells. To extend the applicability of extracellular and planar microelectrode arrays, recently vertically aligned nanofibers (VACNFs) have been integrated with micro electrode arrays (MEA) for applications such as cell membrane mimics, gene delivery arrays, neuroelectrochemical interfacing arrays, superhydrophobic switches, and intracellular probes. The main drawback of VACNF-MEA devices are the low density of electrodes and passive addressing approach. In order to increase the number of elements of an MEA and enable both stimulation and recording on the same platform, an actively addressed thin film transistor (TFT) array platform was developed. Active matrix-TFTs are highly functional devices which have been used widely as backplanes in display electronics field over the past few decades.VACNFs were integrated onto the TFT array (TFT-VACNF) as they enhance the electrical sensitivity to the cell relative to standard planar arrays; furthermore, the vertical electrodes provide the potential for intracellular sensing within individual cells. This device platform provides great potential as an advanced microelectrode array for direct cell sensing, probing, and recording with a high electrode density and active addressability. In this study, VACNFs were successfully integrated onto TFT devices to demonstrate a new microelectrode array platform. The materials and processes of the TFT structure were designed to be compatible with the requisite high-temperature (~700°C) and direct current Plasma Enhanced Chemical Vapor Deposition (dc-PECVD) VACNF growth process.To extend the applicability of utilizing these vertical electrodes, this dissertation describes: the characterization and optimization of each layer for the TFT; the fabrication process and issues for active matrix TFT array; the critical device integration issues of VACNFs onto active matrix TFT arrays are elaborated; and the initial and final device characteristics are reported

Opportunistic Interference Mitigation Achieves Optimal Degrees-of-Freedom in Wireless Multi-cell Uplink Networks

We introduce an opportunistic interference mitigation (OIM) protocol, where a user scheduling strategy is utilized in $K$-cell uplink networks with time-invariant channel coefficients and base stations (BSs) having $M$ antennas. Each BS opportunistically selects a set of users who generate the minimum interference to the other BSs. Two OIM protocols are shown according to the number $S$ of simultaneously transmitting users per cell: opportunistic interference nulling (OIN) and opportunistic interference alignment (OIA). Then, their performance is analyzed in terms of degrees-of-freedom (DoFs). As our main result, it is shown that $KM$ DoFs are achievable under the OIN protocol with $M$ selected users per cell, if the total number $N$ of users in a cell scales at least as $\text{SNR}^{(K-1)M}$. Similarly, it turns out that the OIA scheme with $S$($<M$) selected users achieves $KS$ DoFs, if $N$ scales faster than $\text{SNR}^{(K-1)S}$. These results indicate that there exists a trade-off between the achievable DoFs and the minimum required $N$. By deriving the corresponding upper bound on the DoFs, it is shown that the OIN scheme is DoF optimal. Finally, numerical evaluation, a two-step scheduling method, and the extension to multi-carrier scenarios are shown.Comment: 18 pages, 3 figures, Submitted to IEEE Transactions on Communication

rMAPS: RNA map analysis and plotting server for alternative exon regulation.

RNA-binding proteins (RBPs) play a critical role in the regulation of alternative splicing (AS), a prevalent mechanism for generating transcriptomic and proteomic diversity in eukaryotic cells. Studies have shown that AS can be regulated by RBPs in a binding-site-position dependent manner. Depending on where RBPs bind, splicing of an alternative exon can be enhanced or suppressed. Therefore, spatial analyses of RBP motifs and binding sites around alternative exons will help elucidate splicing regulation by RBPs. The development of high-throughput sequencing technologies has allowed transcriptome-wide analyses of AS and RBP-RNA interactions. Given a set of differentially regulated alternative exons obtained from RNA sequencing (RNA-seq) experiments, the rMAPS web server (http://rmaps.cecsresearch.org) performs motif analyses of RBPs in the vicinity of alternatively spliced exons and creates RNA maps that depict the spatial patterns of RBP motifs. Similarly, rMAPS can also perform spatial analyses of RBP-RNA binding sites identified by cross-linking immunoprecipitation sequencing (CLIP-seq) experiments. We anticipate rMAPS will be a useful tool for elucidating RBP regulation of alternative exon splicing using high-throughput sequencing data