MOLECULAR MASS MANIPULATION ENABLED BY GRAPHENE BASED NANOSTRUCTURES

The surge of interest in graphene, as epitomized by the Nobel Prize in Physics in 2010, is attributed to its extraordinary properties. Graphene is ultrathin, mechanically tough, and has amendable surface chemistry. These features make graphene and graphene based nanostructure an ideal candidate for the use of molecular mass manipulation. The controllable and programmable molecular mass manipulation is crucial in enabling future graphene based applications, however is challenging to achieve. This dissertation studies several aspects in molecular mass manipulation including mass transportation, patterning and storage. For molecular mass transportation, two methods based on carbon nanoscroll are demonstrated to be effective. They are torsional buckling instability assisted transportation and surface energy induced radial shrinkage. To achieve a more controllable transportation, a fundamental law of direction transport of molecular mass by straining basal graphene is studied. For molecular mass patterning, we reveal a barrier effect of line defects in graphene, which can enable molecular confining and patterning in a domain of desirable geometry. Such a strategy makes controllable patterning feasible for various types of molecules. For molecular mass storage, we propose a novel partially hydrogenated bilayer graphene structure which has large capacity for mass uptake. Also the mass release can be achieved by simply stretching the structure. Therefore the mass uptake and release is reversible. This kind of structure is crucial in enabling hydrogen fuel based technology. Lastly, spontaneous nanofluidic channel formation enabled by patterned hydrogenation is studied. This novel strategy enables programmable channel formation with pre-defined complex geometry.

High Precision Plasma Etch for Pattern Transfer: Towards Fluorocarbon Based Atomic Layer Etching

A basic requirement of a plasma etching process is fidelity of the patterned organic materials. In photolithography, a He plasma pretreatment (PPT) based on high ultraviolet and vacuum ultraviolet (UV/VUV) exposure was shown to be successful for roughness reduction of 193nm photoresist (PR). Typical multilayer masks consist of many other organic masking materials in addition to 193nm PR. These materials vary significantly in UV/VUV sensitivity and show, therefore, a different response to the He PPT. A delamination of the nanometer-thin, ion-induced dense amorphous carbon (DAC) layer was observed. Extensive He PPT exposure produces volatile species through UV/VUV induced scissioning. These species are trapped underneath the DAC layer in a subsequent plasma etch (PE), causing a loss of adhesion. Next to stabilizing organic materials, the major goals of this work included to establish and evaluate a cyclic fluorocarbon (FC) based approach for atomic layer etching (ALE) of SiO2 and Si; to characterize the mechanisms involved; and to evaluate the impact of processing parameters. Periodic, short precursor injections allow precise deposition of thin FC films. These films limit the amount of available chemical etchant during subsequent low energy, plasma-based Ar+ ion bombardment, resulting in strongly time-dependent etch rates. In situ ellipsometry showcased the self-limited etching. X-ray photoelectron spectroscopy (XPS) confirms FC film deposition and mixing with the substrate. The cyclic ALE approach is also able to precisely etch Si substrates. A reduced time-dependent etching is seen for Si, likely based on a lower physical sputtering energy threshold. A fluorinated, oxidized surface layer is present during ALE of Si and greatly influences the etch behavior. A reaction of the precursor with the fluorinated substrate upon precursor injection was observed and characterized. The cyclic ALE approach is transferred to a manufacturing scale reactor at IBM Research. Ensuring the transferability to industrial device patterning is crucial for the application of ALE. In addition to device patterning, the cyclic ALE process is employed for oxide removal from Si and SiGe surfaces with the goal of minimal substrate damage and surface residues. The ALE process developed for SiO2 and Si etching did not remove native oxide at the level required. Optimizing the process enabled strong O removal from the surface. Subsequent 90% H2/Ar plasma allow for removal of C and F residues.

Shaping the Dicot Fruit: Molecular and Genomic Approaches to Fruit Development

The fruit is one of the most complex and important structures produced by flowering plants, and understanding the development and maturation process of fruits in different angiosperm species with diverse fruit structures is of immense interest. In the work presented here, molecular genetics and genomic analysis are used to explore the processes that form the fruit in two species: The model organism Arabidopsis and the diploid strawberry Fragaria vesca. One important basic question concerns the molecular genetic basis of fruit patterning. A long-standing model of Arabidopsis fruit (the gynoecium) patterning holds that auxin produced at the apex diffuses downward, forming a gradient that provides apical-basal positional information to specify different tissue types along the gynoecium’s length. The proposed gradient, however, has never been observed and the model appears inconsistent with a number of observations. I present a new, alternative model, wherein auxin acts to establish the adaxial-abaxial domains of the carpel primordia, which then ensures proper development of the final gynoecium. A second project utilizes genomics to identify genes that regulate fruit color by analyzing the genome sequences of Fragaria vesca, a species of wild strawberry. Shared and distinct SNPs among three F. vesca accessions were identified, providing a foundation for locating candidate mutations underlying phenotypic variations among different F. vesca accessions. Through systematic analysis of relevant SNP variants, a candidate SNP in FveMYB10 was identified that may underlie the fruit color in the yellow-fruited accessions, which was subsequently confirmed by functional assays. Our lab has previously generated extensive RNA-sequencing data that depict genome-scale gene expression profiles in F. vesca fruit and flower tissues at different developmental stages. To enhance the accessibility of this dataset, the web-based eFP software was adapted for this dataset, allowing visualization of gene expression in any tissues by user-initiated queries. Together, this thesis work proposes a well-supported new model of fruit patterning in Arabidopsis and provides further resources for F. vesca, including genome-wide variant lists and the ability to visualize gene expression. This work will facilitate future work linking traits of economic importance to specific genes and gaining novel insights into fruit patterning and development.

PHYSICAL FACTORS IN B CELL ACTIN DYNAMICS AND ACTIVATION

Cells adapt to their changing world by sensing environmental cues and responding appropriately. This is made possible by complex cascades of biochemical signals that originate at the cell membrane. In the last decade it has become apparent that the origin of these signals can also arise from physical cues in the environment. Our motivation is to investigate the role of physical factors in the cellular response of the B lymphocyte. B cells patrol the body for signs of invading pathogens in the form of antigen on the surface of antigen presenting cells. Binding of antigen with surface proteins initiates biochemical signaling essential to the immune response. Once contact is made, the B cell spreads on the surface of the antigen presenting cell in order to gather as much antigen as possible. The physical mechanisms that govern this process are unexplored. In this research, we examine the role of the physical parameters of antigen mobility and cell surface topography on B cell spreading and activation. Both physical parameters are biologically relevant as immunogens for vaccine design, which can provide laterally mobile and immobile antigens and topographical surfaces. Another physical parameter that influences B cell response and the formation of the cell-cell junction is surface topography. This is biologically relevant as antigen presenting cells have highly convoluted membranes, resulting in variable topography. We found that B cell activation required the formation of antigen-receptor clusters and their translocation within the attachment plane. We showed that cells which failed to achieve these mobile clusters due to prohibited ligand mobility were much less activation competent. To investigate the effect of topography, we use nano- and micro-patterned substrates, on which B cells were allowed to spread and become activated. We found that B cell spreading, actin dynamics, B cell receptor distribution and calcium signaling are dependent on the topographical patterning of the substrate. A quantitative understanding of cellular response to physical parameters is essential to uncover the fundamental mechanisms that drive B cell activation. The results of this research are highly applicable to the field of vaccine development and therapies for autoimmune diseases. Our studies of the physical aspects of lymphocyte activation will reveal the role these factors play in immunity, thus enabling their optimization for biological function and potentially enabling the production of more effective vaccines.