111 research outputs found
Collected Papers (Papers of Mathematics or Applied Mathematics), Volume V
No full textThis volum includes 37 papers of mathematics or applied mathematics written by the author alone or in collaboration with the following co-authors: Cătălin Barbu, Mihály Bencze, Octavian Cira, Marian Niţu, Ion Pătraşcu, Mircea E. Şelariu, Rajan Alex, Xingsen Li, Tudor Păroiu, Luige Vlădăreanu, Victor Vlădăreanu, Ştefan Vlăduţescu, Yingjie Tian, Mohd Anasri, Lucian Căpitanu, Valeri Kroumov, Kimihiro Okuyama, Gabriela Tonţ, A. A. Adewara, Manoj K. Chaudhary, Mukesh Kumar, Sachin Malik, Alka Mittal, Neetish Sharma, Rakesh K. Shukla, Ashish K. Singh, Jayant Singh, Rajesh Singh, V.V. Singh, Hansraj Yadav, Amit Bhaghel, Dipti Chauhan, V. Christianto, Priti Singh, and Dmitri Rabounski
Protein Word Detection Using Text Segmentation Techniques
Get PDFLiterature in Molecular Biology is abundant with linguistic metaphors. There has been works in the past that attempt to draw parallels between linguistics and biology, driven by the fundamental premise that proteins have a language of their own. Since word detection is crucial to the decipherment of any unknown language, we attempt to establish a problem mapping from natural language text to protein sequences at the level of words. Towards this end, we explore the use of an unsupervised text segmentation algorithm for the task of extracting biological words” from protein sequences. We demonstrate the effectiveness of using domain knowledge to complement data-driven approaches in the text segmentation task, as well as in its biological counterpart. We also propose a novel extrinsic evaluation measure for protein words through protein family classification
Controlling the emergent microstructures in template-directed eutectic solidification for optical applications
Get PDFMesostructured materials with characteristic dimensions of the structure similar to or smaller than the wavelength of light exhibit enhanced optical properties. For successful use in the visible and near-infrared wavelength of light, these structures must be highly ordered and have characteristic features in the hundreds of nanometers to sub-micron size range. Usually, fabricating such structures require sophisticated lithographic techniques or self-assembly approaches, which are well-suited for only a certain class of materials and have limited dimensionality. Emerging work, however, is showing that performing self-assembly within a guiding template can result in the formation of mesostructures not present in either the template or the native self-organizing material. Achieving a diversity of morphologies that can be reconfigured via a simple external tuning knob, while using exactly the same template and material, will advance many fields, including optics, heat transport, and mechanics.
Such an external tuning knob could be the rate of solidification of eutectic alloys. In a eutectic system, multiple solid phases emerge, often in regular structures, as the melt solidifies and these phases could comprise of metals, organics, salts, ceramics, semiconductors, and polymers. The emergence of these microstructures can be controlled by various factors, including the rate of solidification, boundary effects, confinement, and applied thermal gradients. Further control on the emergence of these microstructures could be possible through templating. In this dissertation, particular emphasis is placed on determining the crucial aspects of template design parameters and studying their effects on the microstructure of solidifying eutectic materials.
Chapter 1 surveys the literature on directional solidification of eutectics and template-directed assembly, and establishes the criteria for selecting the starting eutectic and template materials for optical applications. In Chapter 2, molten salt eutectic material, AgCl-CsAgCl2, was explored as photonic crystals. Given the complex nature of thermal profile- and processing-dependent microstructural transition in AgCl-CsAgCl2 eutectic, the template-directed eutectic solidification was carried out using the model AgCl-KCl lamellar eutectic.
For templates with characteristic features much larger than the eutectic, for example, the cage structure template described in Chapter 3, the template design and composition determine the thermal profile during solidification, and thus, control the shape of the solidification front. This resulted in curving of the lamellae of AgCl-KCl eutectic.
A greater control on the emergence of template-directed eutectic microstructures is achieved in templates with characteristic features commensurate to the spacing of the solidifying eutectic. Using lithographically fabricated templates with arrays of pillars in various sizes and geometries, it was determined in Chapter 4 that the boundary effects of templates, substrates, and free surfaces control the orientation of eutectic lamellar microstructures. Understanding the pillar-template-directed orientation of the eutectic phases is an important first step towards designing new mesostructures. In Chapter 5 it was established that the pillar template geometry dictates the diffusion landscape of the solidifying eutectic, which leads to the emergence of symmetries not present in either the native eutectic or the template. This method leads to intricate and rather unexpected patterns, including Archimedean and quasi-crystalline tilings, with potential applications as non-reciprocal metasurfaces, magnetic spin-ice systems, and micro- and nano-lattices with enhanced mechanical properties. Further in Chapter 6 it was shown that for thin layers of eutectic, the pillars act as obstacles that drastically modify the lamellar spacing, which lead to the creation of lamellar faults and thus new morphologies at the pillars. Some of these emergent morphologies bear resemblance to split-ring structures, which are sought for optical metamaterials applications.
Through this dissertation, a thorough understanding of the emergence of template-directed eutectic microstructures has been established. The results summarized in Chapter 7 will form the fundamentals required in designing templates and selecting the eutectic solidification conditions to obtain a particular morphology and/or a diverse set of microstructures, which could further be reconfigured by externally tuning the rate of solidification. Further, these findings suggest that template-directed eutectic solidification is a powerful approach for fabricating mesostructures, which will find use in optical applications and many other modern technologies.Submission published under a 24 month embargo labeled 'U of I Access', the embargo will last until 2022-08-01The student, Ashish Ajit Kulkarni, accepted the attached license on 2020-06-11 at 19:08.The student, Ashish Ajit Kulkarni, submitted this Dissertation for approval on 2020-06-11 at 19:12.This Dissertation was approved for publication on 2020-06-12 at 11:17.DSpace SAF Submission Ingestion Package generated from Vireo submission #15426 on 2020-10-02 at 15:30:43Made available in DSpace on 2020-10-07T22:07:10Z (GMT). No. of bitstreams: 17
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Chapter-1 Adv Opt Mat paper.pdf: 76594 bytes, checksum: e8336ad1817e3efee535033a19ae9abf (MD5)
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Previous issue date: 2020-06-12Embargo set by: Seth Robbins for item 116187
Lift date: 2022-10-07T22:07:19Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemEmbargo set by: Seth Robbins for item 116187
Lift date: 2022-10-07T22:44:53Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemAuthor requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Onl
Multi-view methods for protein structure comparison using latent dirichlet allocation
No full textAbstract
Motivation: With rapidly expanding protein structure databases, efficiently retrieving structures similar to a given protein is an important problem. It involves two major issues: (i) effective protein structure representation that captures inherent relationship between fragments and facilitates efficient comparison between the structures and (ii) effective framework to address different retrieval requirements. Recently, researchers proposed vector space model of proteins using bag of fragments representation (FragBag), which corresponds to the basic information retrieval model.
Results: In this article, we propose an improved representation of protein structures using latent dirichlet allocation topic model. Another important requirement is to retrieve proteins, whether they are either close or remote homologs. In order to meet diverse objectives, we propose multi-viewpoint based framework that combines multiple representations and retrieval techniques. We compare the proposed representation and retrieval framework on the benchmark dataset developed by Kolodny and co-workers. The results indicate that the proposed techniques outperform state-of-the-art methods.
Availability: http://www.cse.iitm.ac.in/~ashishvt/research/protein-lda/.
Contact: [email protected]</jats:p
Functional site prediction by exploiting correlations between labels of interacting residues
No full text
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