At SODA'10, Agarwal and Sharathkumar presented a streaming algorithm for approximating the minimum enclosing ball of a set of points in d-dimensional Euclidean space. Their algorithm requires one pass, uses O(d) space, and was shown to have approximation factor at most 1.3661. We prove that the same algorithm has approximation factor less than 1.22, which brings us much closer to a 1.207 lower bound given by Agarwal and Sharathkumar. We also apply this technique to the dynamic version of the minimum enclosing ball problem (in the non-streaming setting). We give an O(dn)-space data structure that can maintain a 1.22-approximate minimum enclosing ball in O(dlog n) expected amortized time per insertion/deletion. Finally, we prove that a 1+ϵ approximation to the problem can be found in (0.5+δ)/ϵ passes over the input, for an arbitrarily small constant δ, which is an improvement over the previous result that used 2/ϵ passes.

A theoretical analysis of the orientation of biofunctionalized thiolate has been made by changing the surface configuration. The results show that it is possible to match the experimental data by changing the molecular density and also that it is possible to match the experimental data using only hollow sites in the gold surface as placements for the molecules. Some configurations that match available data using only hollow sites positions have been suggested. Moving away from the (sqrt(3) x sqrt(3)) R30° configuration result in a large energy gain for Bor Capped.

The structures, vibrational frequencies, and potential energy functions of several molecules in their ground and excited electronic states were determined using various spectroscopic and theoretical methods. High-level ab initio and density functional theory (DFT) calculations were utilized to investigate the previously reported structures and vibrational spectra of 1,3- disilacyclobutane (13DSCB) and its 1,1,3,3-d4 (13DSCB-d4) isotopomer. These calculations confirmed the finding from earlier microwave work that the CSiC angles of the 13DSCB ring are unexpectedly larger than the SiCSi angles. The calculated vibrational spectra using density functional theory agreed well with the experimental data and showed CH2 modes to have unusually low values. The calculations also confirmed that the individual molecules in the vapor phase are puckered whereas in the solid they become planar. The one-dimensional potential energy surfaces (PESs) for the ring inversion vibration of 2-cyclohexen-1-one and its 2,6,6-d3 isotopomer in its ground and singlet S1(n,π*) electronic states were determined using ultraviolet cavity ringdown spectroscopy (CRDS). The CRDS data allowed several of the quantum states of the ring inversion vibration to be determined for both the ground and excited electronic states, and the data were fit very well with PESs with high barriers to inversion. The infrared and Raman spectra and DFT calculations were utilized to complete a vibrational assignment of 2CHO and 2CHO-d3. A remarkable agreement was seen between the experimental and calculated spectra. The fluorescence excitation spectra (FES) and the single-vibronic level fluorescence (SVLF) spectra of jet-cooled 1,4-dihydronaphthalene (14DHN) were acquired to determine its ring-puckering potential energy function for the ground and singlet S1(π,π*) electronic states. Ultraviolet, infrared, and Raman spectra were also recorded to complement the analysis. The potential energy functions showed that the molecule is planar in both the ground and S1(π,π*) states. A complete vibrational assignment was carried out for 14DHN using the infrared and Raman data and aided by DFT calculations. The ab intio calculations carried out on 2-methyl-2-cyclopenten-1-one (2MCP) showed that the molecule can have 3 different conformers. Infrared and Raman spectra of the liquid-phase molecule were recorded and analyzed to complement the theoretical calculations.

All living creatures, despite their profound diversity, share a common architectural building block: the cell. Cells are the basic functional units of life, yet are themselves comprised of numerous components with distinct mechanical characteristics. It is well established that cells have the ability to sense and respond to externally applied forces. However, the detailed mechanism of mechanosensation is still not clearly understood, and is an active area of research involving experimental and theoretical works. Mathematical modeling of the mechanical stimulus correlating to different experimental stimulation procedures forms the first step to understanding the mechanosensation in cellular system. In this thesis, a continuum -based computational model of living cells that explicitly incorporate the material properties of various cellular components are developed. In the constitutive modeling of cell, the continuum standard linear solid viscoelastic model (SLS), its natural extension for large scale deformation standard Neo-Hookean solid viscoelastic model (SnHS) as well as polymer mechanics- based dynamic shear modulus model was introduced. Finite element simulations of three widely used experiments- atomic force microscopy (AFM), magnetic twisting cytometry (MTC) and micropipette aspiration in the quantification of cell properties were carried out to verify the developed constitutive model. From the results of AFM finite element simulation, it was observed that the force-deformation and strain-relaxation curves obtained fit the experimental results very well. The influences of cytoplasm shear modulus which varies due to the formation of stress fiber, and cortex shear modulus which alters with the actin filament concentration factors and load frequency were systematically studied. Similarly, in magnetic twisting cytometry (MTC) simulation, the role of cytoplasm material properties, constant/sinusoidal forcing rates and various frequencies on the overall mechanical response of a cell was obtained. Numerical results are validated against experiments results. Micropipette aspiration simulation was also carried out in which the typical creep deformation test was carried out to study the viscoelastic behavior of the cell. Based on the results from finite element simulation, the effect of pipette radius, effect of cortex shear modulus and effect of pressure rate have been derived for the interpretation of the mechanical parameters from the micropipette aspiration.

Prediction of functions of genes in a genome is a key step in all genome sequencing projects. Sequences that carry out important functions are likely to be conserved between evolutionarily distant species and can be identified using cross-species comparisons. In the absence of completed genomes and the accompanying high-quality annotations, expressed sequence tags (ESTs) from random cDNA clones are the primary tools for functional genomics. EST datasets are fragmented and redundant, necessitating clustering of ESTs into groups that are likely to have been derived from the same genes. EST clustering helps reduce the search space for sequence homology searching and improves the accuracy of function predictions using EST datasets. This dissertation is a case study that describes clustering of Bos taurus and Sus scrofa EST datasets, and utilizes the EST clusters to make computational function predictions using a comparative genomics approach. We used a novel EST clustering method, TAMUClust, to cluster bovine ESTs and compare its performance to the bovine EST clusters from TIGR Gene Indices (TGI) by using bovine ESTs aligned to the bovine genome assembly as a gold standard. This comparison study reveals that TAMUClust and TGI are similar in performance. Comparisons of TAMUClust and TGI with predicted bovine gene models reveal that both datasets are similar in transcript coverage. We describe here the design and implementation of an annotation pipeline for predicting functions of the Bos taurus (cattle) and Sus scrofa (pig) transcriptomes. EST datasets were clustered into gene families using Ensembl protein family clusters as a framework. Following clustering, the EST consensus sequences were assigned predicted function by transferring annotations of the Ensembl vertebrate protein(s) they are grouped to after sequence homology searches and phylogenetic analysis. The annotations benefit the livestock community by helping narrow down the gamut of direct experiments needed to verify function.

In an effort to partially mimic the complex interaction between nerve growth factor (NGF) and its membrane-bound tyrosine kinase A receptor (TrkA), several small organic molecules with functionalities similar to the side-chains of the amino acid residues of NGF critical to binding were devised. These molecules were studied computationally using the program Affinity. Each molecule was individually docked onto one of the binding sites on TrkA as determined by mutagenesis studies and the x-ray crystal structure obtained from the Protein Data Bank. One of the strategies to enhance binding of active peptidomimetics to their target proteins is to link them together to form either homodimers or heterodimers. However, these dimers have low solubility in water and mimic only residues that are close together on the protein. Triethylene oxide- and hexaethylene oxide-based linker molecules were designed to circumvent these limitations. The increased polarity will improve the watersolubility and the added lengths, which can be controlled and varied by simple chemical manipulations, will allow for mimicking critical residues that are farther apart on the protein.

The structures, vibrational frequencies, and potential energy functions of several molecules in their ground and excited electronic states were determined using various spectroscopic and theoretical methods. High-level ab initio and density functional theory (DFT) calculations were utilized to investigate the previously reported structures and vibrational spectra of 1,3- disilacyclobutane (13DSCB) and its 1,1,3,3-d4 (13DSCB-d4) isotopomer. These calculations confirmed the finding from earlier microwave work that the CSiC angles of the 13DSCB ring are unexpectedly larger than the SiCSi angles. The calculated vibrational spectra using density functional theory agreed well with the experimental data and showed CH2 modes to have unusually low values. The calculations also confirmed that the individual molecules in the vapor phase are puckered whereas in the solid they become planar. The one-dimensional potential energy surfaces (PESs) for the ring inversion vibration of 2-cyclohexen-1-one and its 2,6,6-d3 isotopomer in its ground and singlet S1(π,π*) electronic states were determined using ultraviolet cavity ringdown spectroscopy (CRDS). The CRDS data allowed several of the quantum states of the ring inversion vibration to be determined for both the ground and excited electronic states, and the data were fit very well with PESs with high barriers to inversion. The infrared and Raman spectra and DFT calculations were utilized to complete a vibrational assignment of 2CHO and 2CHO-d3. A remarkable agreement was seen between the experimental and calculated spectra. The fluorescence excitation spectra (FES) and the single-vibronic level fluorescence (SVLF) spectra of jet-cooled 1,4-dihydronaphthalene (14DHN) were acquired to determine its ring-puckering potential energy function for the ground and singlet S1(π,π*) electronic states. Ultraviolet, infrared, and Raman spectra were also recorded to complement the analysis. The potential energy functions showed that the molecule is planar in both the ground and S1(π,π*) states. A complete vibrational assignment was carried out for 14DHN using the infrared and Raman data and aided by DFT calculations. The ab intio calculations carried out on 2-methyl-2-cyclopenten-1-one (2MCP) showed that the molecule can have 3 different conformers. Infrared and Raman spectra of the liquid-phase molecule were recorded and analyzed to complement the theoretical calculations.

<p>This thesis examines the intonation patterns of Modern Greek with regard to different interpretations of the sentence types (declarative, interrogative, imperative).</p><p>14 utterances are produced by Greek native speakers (2 men and 2 women) so as to express various speech acts: STATEMENT, QUESTION, COMMAND and REQUEST.</p><p>The acquisition of the F0 curve for each utterance by means of the Wavesurfer tool leads to an analysis of the pitch movements and their alignments.</p><p>After the F0 curves are analyzed and illustrated using the Excel program we are able to compare and group them. Thus, we come up with 5 different intonation patterns. After a second-level comparison based on the fact that some of the F0 curves were similar but they differed only as far as the final pitch movement is concerned, we ended up with 3 fundamental categories of intonation patterns: Category I whose main feature is the rising pitch movement aligned to the onset of the stressed syllables. This category includes only sentences that denote Statement so we can call it the STATEMENT category. Category II’s main characteristic is a dipping pitch movement aligned to the head of the utterance that is the stress of the verb or a particle that signifies negation (/min/, /den/). Sentences meaning Command or Request belong to this category. Lastly, Category III’s intonation pattern consists of peaking pitch movements aligned to the initial and final stressed syllables. Interrogative sentences belong to this category no matter their interpretation.</p><p>A secondary goal of the thesis is to examine to which extent intonation can be a safe criterion for the “correct” interpretation of a sentence. A de facto presumption that since the ratio between the number of utterances (14) and the different intonation patterns (5) is not 1:1 there can always be misunderstandings among speakers, is basically verified by the results of our perception test conducted to Greek native speakers: Greek native speakers were able to identify most of the speech acts that were expressed by the most common (default) sentence type (i.e. imperative sentence for COMMAND and interrogative for QUESTION) however there were combinations that they had difficulties to identify, such as interrogative sentences that were denoting other than QUESTION, e.g. REQUEST or STATEMENT.Ending, a perception test conducted to Flemish speakers (subjects that were native speakers of another language than Greek) showed that they were more successful in sentences that meant STATEMENT and QUESTION but they could hardly identify an interrogative sentence that meant other than QUESTION and they also confused between COMMAND and REQUEST. This implies that the intonation used to convey different interpretations is basically language-dependent.</p><p>Concluding, this study offers a description of the intonation patterns (based on pitch movements) regarding the 3 sentence types with 4 different interpretations. Our findings prove that the intonation for some cases (i.e. for sentences that express COMMAND or STATEMENT) seems to be structure-independent and for others structure-dependent (cf. the interrogative sentences). Additionally, the fact that the negation can play an important role for the choice of intonation pattern (as shown for the case of COMMAND and STATEMENT) could be considered as a structure-dependent feature of intonation. This approach contrasts the approach used for many years in the traditional Grammar according to which the structure alone (sentence type) defines the meaning that is to be conveyed.</p>

Thèse doctorat : Informatique : Villeurbanne, INSA : 2007. / Thèse rédigée en anglais. Résumé étendu en français. Titre provenant de l'écran-titre. Bibliogr. p. 192-202.

Thesis (Ph.D.)--University of Delaware, 2009. / Principal faculty advisor: John Case, Dept. of Computer & Information Sciences. Includes bibliographical references.