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Numerical Simulation of Photoinduced Force Microscopy
ABSTRACT OF THE THESISNumerical Simulation of Photoinduced Force MicroscopyByMohammad AlmajhadiMaster of Science in Electrical and Computer EngineeringUniversity of California, Irvine, 2016Professor H. Kumar Wickramasinghe, Chair In this thesis we introduce a method of imaging: photoinduced force microscopy (PiFM). In this method, the images are accomplished by detecting tip-sample force at the near field which is optically excited. The origin of this force is related to the dipole momentum of the tip and its image in the sample. The dipole momentum strength is function of the polarizability of the sample under test; the polarizability is a wavelength dependent. Therefore, driving sample at resonance will give higher force than off resonance. This polarizability contains the spectroscopic information about the sample. By tuning the excited laser over broad range of frequency spectra, sample can by identified by comparing the resulting force measurement to a well-known absorption curve. PiFM Spatial resolution is well below 10nm and it is limited only by the tip geometry. This is because the field is spatially confined and the gradient of tip-sample force is proportional to z-4 where z is the distance away from the tip. Finite Element Method (FEM) is utilized to calculate the force gradient, and the tip-sample force. The probe is attached to the end of a cantilever vibrating at one or two mechanical frequencies. Simultaneously, topographic and optical imaging process can be done by detecting them at different mechanical frequencies. In fact, the force will shift the mechanical frequencies, and this shift will be detected through quad-photodetector and the extracted signal will be translated into an image
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Nanoprobe Platform For Quantifying Gene Expression Levels in Single Living Cell
Dissecting the regulation of gene expression processes is fundamental to understand how cells function. Techniques used to obtain our current view of gene expressions rely on isolating mRNAs from large numbers of cells, which often associates with a loss or damage of the material, as well as the loss of spatial information. Also, individual cells within a population are unlikely to behave all in the same way, and current standard techniques are unable to detect cell-to-cell differences that can result from genetic variation, biological noise and different characteristics of genes within a population.To solve these limitations, we developed a sensitive and non-destructive method and apparatus for tracking gene expressions on single cell level within a population of cells, either on a collagen cell culture gel or in a microfluidic environment. The developed bench-top instrument utilizes a modified AFM (Atomic Force Microscopy) probes for in situ extraction of mRNA molecules from single cells. The modified coaxial AFM probe serves as nanotweezer, and wherein the application of an alternating potential between the inner and outer electrodes of the co-axial cable creates a dielectrophoretic force for attracting target molecules toward the tip-end. For adherent cell lines, the samples are cultured on collagen gel for select-and-probe analysis. An integrated microfluidic/nanoprobe platform is also developed for gene expression analysis of suspension cells on single cell level.This system directly targets and samples down to a few molecules within a single living cell, without the need for purification and averaging typically of conventional technologies. By providing reliable and exceptional sensitivity to identify differences between individual cells in a seemingly homogeneous population, the system creates possibilities for assaying the genomic analysis in living cells and tracking them in response to external stimuli. This technique has potential impacts on understanding the heterogeneity of transcriptional responses as well as its implications for cell function and disease. It is going to have broad application areas ranging from systems biology to cancer research
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Study of near-field circular dichroic optical forces on plasmonic nanostructures
Plasmonic nanostructures and nanoparticle assemblies with spatial symmetry breaking interact with right- and left-handed circularly polarized (RCP and LCP, respectively) lights differently. The difference between absorption of RCP and LCP by these nanostructures is called circular dichroism (CD). Compared to their molecular counterparts, broken symmetry nanostructures demonstrate orders of magnitude higher CDs, making them suitable for promising applications in photonic devices, such as circular polarizers and devices with negative refractive index, as well as in pharmaceutical sciences for enantioselectivity enhancement of chiral molecules. Although CD is useful information in characterization of these devices, since it is a far-field quantity, it cannot retrieve the underlying near-field interactions. Understanding the near-field interactions, however, is necessary in designing novel photonic devices with different applications. In this thesis, we investigate the near-field circular dichroic forces on plasmonic nanoparticle assemblies at nanoscale using photoinduced force microscopy (PiFM). We first introduce a PiFM technique based on gold nanoparticles (AuNPs) and silicon tip. Conventionally, gold-coated silicon tips are used in PiFM, which causes some anisotropy-induced distortions in the images because of the irregularities of gold grains on the silicon tip. This is especially important in CD studies as these asymmetries can create fake signals. Using AuNPs and silicon tip, we demonstrate much more accurate and distortion-free images, as well as an order of magnitude enhancement in signal-to-noise ratio. We then use this PiFM technique to study the near-field circular dichroic forces on different AuNP assemblies. We show that while two different mirror-symmetric (structurally achiral) assemblies can have zero CD, their near-field circular dichroic force maps can be different depending on their rotational symmetry. We finally demonstrate a metasurface, made of broken symmetry ramp-shaped nanostructures, which exhibits giant CD at the visible frequencies using a simple fabrication technique based on gradient focused-ion beam milling, addressing complicated fabrication challenges to create 3-D asymmetric nanostructures
Going Beyond Counting First Authors in Author Co-citation Analysis
The present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Variations on the Author
“Variations on the Author” discusses two of Eduardo Coutinho’s recent films (Um Dia na Vida, from 2010, and Últimas Conversas, posthumously released in 2015) and their contribution to the general question of documentary authorship. The director’s filmography is characterized by a consistent yet self-effacing form of authorial self-inscription: Coutinho often features as an interviewer that rather than express opinions propels discourses; an interviewer that is good at listening. This mode of self-inscription characterizes him as an author who is not expressive but who is nonetheless markedly present on the screen. In Um Dia na Vida, however, Coutinho is completely absent form the image, while Últimas Conversas, on the contrary, includes a confessional prologue that moves the director from the margins to the center of his films. This article examines the ways in which these works stand out in the filmography of a director who offers new insights into the notion of cinematic authorship
Appropriate Similarity Measures for Author Cocitation Analysis
We provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
We conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
koamabayili/VECTRON-author-checklist: VECTRON author checklist
We have done our best to complete the author checklist relating to the use of animals in the hut study. Note that the objective for the hut study was to evaluate the IRS treatment applications for residual efficacy against Anopheles mosquitoes, including the local An. coluzzii mosquito population. Cows were only used to attract mosquitoes into the huts and no tests were carried out directly on the cows. The author checklist is intended for use with studies where experiments are carried out on animals, which is why we have had such difficulty in completing this for the hut study, as many of the questions do not relate to how the cows were used
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