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Lim, Chan-Ping Edwin. "Computational electromagnetic modeling for wireless channel characterization." Columbus, Ohio : Ohio State University, 2006. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1158607443.
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Zerbe, Brandon S. "Computational characterization of protein hot spots." Thesis, Boston University, 2012. https://hdl.handle.net/2144/31628.
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Thesis (Ph.D.)--Boston UniversityPLEASE NOTE: Boston University Libraries did not receive an Authorization To Manage form for this thesis or dissertation. It is therefore not openly accessible, though it may be available by request. If you are the author or principal advisor of this work and would like to request open access for it, please contact us at open-help@bu.edu. Thank you.
Protein hot spots provide a large portion of the binding free energy during interact ions, and detecting and characterizing these hot spot regions provides insight that can be used in the development of novel drugs for t he purpose of regulating pathological pathways. In t his dissertation, I first compare t he FTMap algorithm, which detects hot spots by identifying locations where different simulated solvent-sized molecules are consistently found to have favorable interactions, to experimental methods that detect hot spots by alternative means. Specifically, I show that FTMap detects the hot spots detected by alanine scanning, and I discover two roles for residues near hot spots in protein-protein interaction (PPI) complexes. Furthermore, additional insights into the binding energetics of PPis are uniquely provided by FTMap, and these insights are important for drug-design. FTMap is then shown to detect the hot spots identified by successful fragment-screening experiments, and the additional sites detected by FTMap are shown to provide insight into the optimal regions for ligand extension for the molecules identified by t he fragment-screening experiment. Since binding sites are composed of multiple hot spots, we have recently used FTMap for binding site detection. I examine the highly accurate binding site detection algorithm, show that the success of this algorithm is a consequence of only a portion of the scoring protocol, and develop a faster protocol for binding site detection based on this insight. I also quantitate the improvement in precision obtained by using multiple probes and argue t hat the principle biophysical considerations in hot spot detection are hydrophobicity and complexity. Finally, I develop a functional-group clustering algorithm, which is informative for evaluation of the binding locations of pre-determined chemical moieties. I then provide evidence that other approaches employing FTMap results may lead to insight into selectivity. I conclude with a discussion on the nature of hot spots, and I suggest that evolutionary studies of protein divergence should provide insight into the emergence of chemical-selectivity thus providing biophysical insight into the factors that drive selectivity within hot spots.
2031-01-01
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Igram, Dale J. "Computational Modeling and Characterization of Amorphous Materials." Ohio University / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1564347980986716.
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Wu, Shirley. "Characterization of protein function using automated computational methods /." May be available electronically:, 2009. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
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Jones, Charlotte Louise. "Synthesis, characterization and computational studies of boron-oxygen compounds." Thesis, Bangor University, 2016. https://research.bangor.ac.uk/portal/en/theses/synthesis-characterization-and-computational-studies-of-boronoxygen-compounds(8c2d8db8-e5e0-4582-8e4d-2abd5b72fa97).html.
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A total of twenty-one new non-metal cation polyborate salts are reported; nineteen of these contain the pentaborate anion, [B5O6(OH)4]-, one contains the triborate monoanion, [B3O3(OH)4]-, and one contains the heptaborate dianion, [B7O9(OH)5]2-. The crystal structures of ten salts containing these polyborate anions are reported: pyrrolidinium pentaborate (1), N-methylpyrrolidinium pentaborate.½ acetone (2.½CH3COCH3), N,N-dimethylpyrrolidinium pentaborate (3), 2-hydroxymethylpyrrolidinium pentaborate hemihydrate (4.½H2O), (2-hydroxyethyl)-N-methylpyrrolidinium pentaborate.0.3 hydrate (5.0.3H2O), 4-aminobenzylammonium pentaborate hemihydrate (9.½H2O), N,N-dimethyl-1-adamantylammonium pentaborate sesquihydrate (14.1.5H2O), N,N,N-trimethyl-1-adamantylammonium pentaborate trihydrate (15.3H2O), N,N,N-trimethyl-2-adamantylammonium pentaborate trihydrate (17.3H2O) and 4,4’-bipiperidinium heptaborate dihydrate (20.2H2O). The crystal structure of an additional amine-boric acid co-crystallized species is also reported. All of the synthesized compounds reported in Chapter 3 were characterized using spectroscopic (IR, multi-element NMR) and analytical (melting point, elemental analysis, thermal analysis, powder X-ray diffraction) techniques. The solid-state structures of the polyborate salts form giant H-bonded anionic lattices, with the ‘brickwall’ structure found to be sufficiently flexible to accommodate larger cations (within limits). When these limits are approached, they may be stretched further to accommodate the size of the cations by using ‘spacer’ molecules which increase the size of the lattice. It is only once the lattice cannot be stretched any further and/or when there are sufficient cation-anion interactions to dominate the energetics that polyborates other than pentaborates may be observed. The strength of the H-bonds found within polyborate salts were calculated using DFT theory; the results show that the α-reciprocal R22(8) H-bond interaction is the most energetically favoured (-21 kJ mol-1), which is also the most commonly observed interaction within the solid-state structures of pentaborate salts. The synthesis and characterization of Lewis base adducts of triorganoboroxines is also described within this thesis. Eight new adducts are reported, including the crystal structures of the triorganoboroxine.amine adducts of tri(4-chlorophenyl)boroxine.morpholine (30) and tri(4-chlorophenyl)boroxine.benzylamine (33). The Lewis acidity of the triorganoboroxines were also investigated and it was discovered that strongly electron-withdrawing pentafluorophenyl substituents greatly increase the Lewis acidity of the B atoms, resulting in a higher acceptor number.
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Kalaitzopoulos, Dimitrios. "Molecular characterization and computational analysis of constitutional chromosome rearrangements." Thesis, University of Cambridge, 2006. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614054.
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Briscoe, Adam. "Characterization and computational modelling of acrylic bone cement polymerisation." Thesis, University of Southampton, 2006. https://eprints.soton.ac.uk/64795/.
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Total joint replacement is one of the most successful surgical procedures and is a proven treatment for arthritis. Despite low failure rates, the wide application of the treatment means that large numbers of prostheses fail and must be revised. Improved pre-clinical testing methods for these orthopaedic devices may assist in developing new prostheses with improved clinical results. Computational modelling of biological systems is becoming increasingly accurate and is a much quicker and cheaper alternative to physical testing, but continued development is necessary to ensure computational models produce accurate and reliable predictions of implant behaviour. Acrylic bone cements have been used as a method of fixation for over 50 years but despite improvements in cement handling techniques and numerous attempts to improve the mechanical properties of the cement in other ways, the cement is often highlighted as the weak link in the joint replacement system. Aseptic loosening is cited as the cause for the majority of revision operations and cement degradation has been shown to be a contributor to the loosening process. In-vivo, cement is subject to cyclic loads and these are the primary cause of cement damage. Residual stresses generated during the polymerisation of the cement are now thought to play a significant role in cement failure. This thesis examines the development of residual stresses as a result of thermal and chemical changes during polymerisation of the cement. Experimental techniques for characterising the evolution of materials properties during the polymerisation reaction are discussed. Differential scanning calorimetry was used to measure the reaction variables such as the activation energy of polymerisation. The development of an ultrasonic rheometry technique for monitoring the mechanical property evolution within a bone cement specimen is discussed. Computational models were generated to predict the reaction behaviour of the cement in terms of the heat produced and the evolution of the physical properties of the curing mass. Some advantages and disadvantages of candidate mathematical models have been evaluated and are discussed, along with applications in several implant fixation scenarios. The model compared well with experimental data and was used to predict thermal necrosis in the bone surrounding both a hip resurfacing implant and a knee replacement. Using the output reaction path produced by the thermal model a mechanical model was also produced simulating the shrinkage and mechanical property evolution exhibited by the polymerising cement. Two material models were compared with and without the effects of plasticity. Residual stress magnitudes were assessed in comparison with published values and showed better agreement when plasticity was included. Peak stresses were observed to occur during polymerisation. The location of the peak stresses were compared with experimental data on pre-load crack locations in the literature and showed good agreement.
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Gaspar, Paulo Miguel da Silva. "Computational methods for gene characterization and genomic knowledge extraction." Doctoral thesis, Universidade de Aveiro, 2014. http://hdl.handle.net/10773/13949.
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Doutoramento conjunto MAPi em Ciências da ComputaçãoMotivation: Medicine and health sciences are changing from the classical symptom-based to a more personalized and genetics-based paradigm, with an invaluable impact in health-care. While advancements in genetics were already contributing significantly to the knowledge of the human organism, the breakthrough achieved by several recent initiatives provided a comprehensive characterization of the human genetic differences, paving the way for a new era of medical diagnosis and personalized medicine. Data generated from these and posterior experiments are now becoming available, but its volume is now well over the humanly feasible to explore. It is then the responsibility of computer scientists to create the means for extracting the information and knowledge contained in that data. Within the available data, genetic structures contain significant amounts of encoded information that has been uncovered in the past decades. Finding, reading and interpreting that information are necessary steps for building computational models of genetic entities, organisms and diseases; a goal that in due course leads to human benefits. Aims: Numerous patterns can be found within the human variome and exome. Exploring these patterns enables the computational analysis and manipulation of digital genomic data, but requires specialized algorithmic approaches. In this work we sought to create and explore efficient methodologies to computationally calculate and combine known biological patterns for various purposes, such as the in silico optimization of genetic structures, analysis of human genes, and prediction of pathogenicity from human genetic variants. Results: We devised several computational strategies to evaluate genes, explore genomes, manipulate sequences, and analyze patients’ variomes. By resorting to combinatorial and optimization techniques we were able to create and combine sequence redesign algorithms to control genetic structures; by combining the access to several web-services and external resources we created tools to explore and analyze available genetic data and patient data; and by using machine learning we developed a workflow for analyzing human mutations and predicting their pathogenicity.
Motivação: A medicina e as ciências da saúde estão atualmente num processo de alteração que muda o paradigma clássico baseado em sintomas para um personalizado e baseado na genética. O valor do impacto desta mudança nos cuidados da saúde é inestimável. Não obstante as contribuições dos avanços na genética para o conhecimento do organismo humano até agora, as descobertas realizadas recentemente por algumas iniciativas forneceram uma caracterização detalhada das diferenças genéticas humanas, abrindo o caminho a uma nova era de diagnóstico médico e medicina personalizada. Os dados gerados por estas e outras iniciativas estão disponíveis mas o seu volume está muito para lá do humanamente explorável, e é portanto da responsabilidade dos cientistas informáticos criar os meios para extrair a informação e conhecimento contidos nesses dados. Dentro dos dados disponíveis estão estruturas genéticas que contêm uma quantidade significativa de informação codificada que tem vindo a ser descoberta nas últimas décadas. Encontrar, ler e interpretar essa informação são passos necessários para construir modelos computacionais de entidades genéticas, organismos e doenças; uma meta que, em devido tempo, leva a benefícios humanos. Objetivos: É possível encontrar vários padrões no varioma e exoma humano. Explorar estes padrões permite a análise e manipulação computacional de dados genéticos digitais, mas requer algoritmos especializados. Neste trabalho procurámos criar e explorar metodologias eficientes para o cálculo e combinação de padrões biológicos conhecidos, com a intenção de realizar otimizações in silico de estruturas genéticas, análises de genes humanos, e previsão da patogenicidade a partir de diferenças genéticas humanas. Resultados: Concebemos várias estratégias computacionais para avaliar genes, explorar genomas, manipular sequências, e analisar o varioma de pacientes. Recorrendo a técnicas combinatórias e de otimização criámos e conjugámos algoritmos de redesenho de sequências para controlar estruturas genéticas; através da combinação do acesso a vários web-services e recursos externos criámos ferramentas para explorar e analisar dados genéticos, incluindo dados de pacientes; e através da aprendizagem automática desenvolvemos um procedimento para analisar mutações humanas e prever a sua patogenicidade.
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Dashti, Zahra Jalali Sefid. "Computational characterization of IRE-regulated genes in Glossina morsitans." Thesis, University of Western Cape, 2013. http://hdl.handle.net/11394/3325.
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Philosophiae Doctor - PhDBlood feeding is a habit exhibited by many insects. Considering the devastating impact of these insects on human health, it is important to focus research on understanding the biology behind blood-feeding, disease transmission and host-pathogen interactions. Such knowledge would pave the way for developing efficient preventative measures. Iron an important element for species survival, is at the center of events controlling tsetse’s fitness and reproductive success. Hence, targeting genes involved in iron trafficking and sequestration would present possible means of preventing disease transmission. Considering the dynamic and multi-factorial nature of iron metabolism, a well-coordinated regulatory system is expected to be at work. Despite extensive literature on the mechanism of iron regulation and key factors responsible in maintaining its homeostasis in human, less attention has been given to understand such system in insects, especially the blood-feeding insects. The availability of the genome sequences for several insect disease vectors allows for a more detailed analysis on the identification and characterization of events controlling and preventing iron-induced toxicity following a blood-meal. The International Glossina Genome Initiative (IGGI) has coordinated the sequencing and annotation of the Glossina morsitans genome that has led to the identification of 12220 genes. This knowledge-base along with current understanding of the IRE system in regulating iron metabolism, allowed for investigating the UTRs of Glossina genes for the presence of these elements. Using a combination of motif enrichment and IRE-stem loop structure prediction, an IRE-mediated regulation was inferred for 150 genes, among which, 72 were identified with 5’-IREs and 78 with 3’-IREs. Of the identified IRE-regulated genes, the ferritin heavy chain and MRCK-alpha are the only known genes to have IREs, while the rest are novel genes for which putative roles in regulating iron levels in tsetse fly have been assigned in this study. Moreover, the functional inference of the identified genes further points to the enrichment of transcription and translation. Furthermore, several hypothetical proteins with no defined functions were identified to be IRE-regulated. These include TMP007137, TMP009128, TMP002546, TMP002921, TMP003628, TMP004581, TMP008259, TMP012389, TMP005219, TMP005827, TMP007908, TMP009332, TMP01- 3384, TMP009102, TMP010544, TMP010707, TMP004292, TMP006517, TMP014030, TMP009821 and TMP003060 for which an iron-regulatory mechanism of action may be inferred. We further report 26 IRE-regulated secreted proteins in Glossina, that present good candidates for further investigation pertaining to the development of novel vector control strategies. Using the predicted data on the identified IRE-regulated genes and their functional classification, we derived at 29 genes with putative roles in iron trafficking, where several unknown and hypothetical proteins are included. Thus a novel role is inferred for these genes in cellular binding and transport in the context of iron metabolism. It is therefore possible that these genes may have evolved in Glossina, such that they compensate for the absence of an IRE- regulated mechanism for transferrin. Additionally, we propose 14 IRE-regulated genes involved in immune and stress response, which may indeed play crucial roles at the host pathogen interface through their possible mechanisms of iron sequestration. Using the subcellular localization analysis, we further categorized the putative IRE regulated genes into several subcellular localizations, where the majority of genes were found within the nucleus and the cytosol. The detection of the conserved motifs in a set of genes, is an interesting yet sophisticated area of research, that allows for identifying either co-regulated or orthologous genes, while further providing support for the putative function of a set of genes that would otherwise remain uncharacterized. This is based on the notion that co-regulated genes are often coexpressed to carry out a specific function. As such, 14 regulatory elements were identified in the 5’- and 3’-UTRs of IRE-regulated genes, involved in embryonic development and reproduction, inflammation and immune response, signaling pathways and neurogenesis as well as DNA repair. This study further proposes several IRE-regulated genes as targets for micro-RNA regulation through identifying micro-RNA binding sites in their 3’UTRs. Using a motif clustering approach we clustered IRE-regulated genes based on the number of motifs they share. Significantly co-regulated genes sharing two or more motifs were determined as critical targets for future investigation. The expression map of IRE-regulated genes was analyzed to better understand the events taking place from 3 hours to 15 days following a blood meal. Re-analysis of Anopheles microarray chip showed the significant expression of three cell envelope and transport genes as early response and six as late response to a blood meal, which could indeed be assigned a putative role in iron trafficking. Genes identified in this study with implications in iron metabolism, whose timely expression allows for maintaining iron homeostasis, represent good targets for future work. Considering the important role of evolution in species adaptation to habits such as Hematophagy, it is of importance to identify evolutionary signatures associated with these changes. To distinguish between evolutionary forces that are specific to iron-metabolism in blood-feeding insects and those that are found in other insects, the IRE-regulated genes were clustered into orthologous groups using several blood feeding and non-blood feeding insect species. Assessment of different evolutionary scenarios using the Maximum Likelihood (ML) approach, points to variations in the evolution of IRE-regulated genes between the two insect groups, whereby several genes indicate an increased mutation rate in the BF-insect group relative to their non-blood feeding insect counterparts. These include TMP003602 (phosphoinositide3-kinase), TMP009157 (ubiquitin-conjugating enzyme9), TMP010317 (general transcription factor IIH subunit1), TMP011104 (serine-pyruvate mitochondrial), TMP013137 (pentatricopeptide Transcription and translation), TMP013886 (tRNA(uridine-2-o-)-methyl-transferase-trm7) and TMP014187 (mediator 100kD). Additionally, we have indicated the presence of positively selected sites within seven blood-feeding IRE-regulated genes namely TMP002520 (nucleoporin), TMP008942 (eukaryotic translation initiation factor 3), TMP009871(bruno-3 transcript) , TMP010317 (general transcription factor IIH subunit1), TMP010673 (ferritin heavy-chain protein), TMP011104 (serine-pyruvate mitochondrial) and TMP011448 (brain chitinase and chia). Thus the results of this study provides an in depth understanding of iron metabolism in Glossina morsitans and confers important targets for future validations based on which innovative control strategies may be designed.
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Iyer, Kaushik A. "Quantitative characterization of thermophysical properties in computational heat transfer." Full text open access at:, 1993. http://content.ohsu.edu/u?/etd,273.
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Boatin, William. "Characterization of neuron models." Thesis, Available online, Georgia Institute of Technology, 2005, 2005. http://etd.gatech.edu/theses/available/etd-04182005-181732/.
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Thesis (M. S.)--Electrical and Computer Engineering, Georgia Institute of Technology, 2006.Dr. Robert H. Lee, Committee Member ; Dr. Kurt Wiesenfeld, Committee Member ; Dr Robert J. Butera, Committee Member.
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Alipour, Skandani Amir. "Computational and Experimental Nano Mechanics." Diss., Virginia Tech, 2014. http://hdl.handle.net/10919/64869.
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The many advances of nano technology extensively revolutionize mechanics. A tremendous need is growing to further bridge the gap between the classical mechanics and the nano scale for many applications at different engineering fields. For instance, the themes of interdisciplinary and multidisciplinary topics are getting more and more attention especially when the coherency is needed in diagnosing and treating terminal diseases or overcoming environmental threats. The fact that how mechanical, biomedical and electrical engineering can contribute to diagnosing and treating a tumor per se is both interesting and unveiling the necessity of further investments in these fields. This dissertation presents three different investigations in the area of nano mechanics and nano materials spanning from computational bioengineering to making mechanically more versatile composites.
The first part of this dissertation presents a numerical approach to study the effects of the carbon nano tubes (CNTs) on the human body in general and their absorbability into the lipid cell membranes in particular. Single wall carbon nano tubes (SWCNTs) are the elaborate examples of nano materials that departed from mere mechanical applications to the biomedical applications such as drug delivery vehicles. Recently, experimental biology provided detailed insights of the SWCNTs interaction with live organs. However, due to the instrumental and technical limitations, there are still numerous concerns yet to be addressed. In such situation, utilizing numerical simulation is a viable alternative to the experimental practices. From this perspective, this dissertation reports a molecular dynamics (MD) study to provide better insights on the effect of the carbon nano tubes chiralities and aspect ratios on their interaction with a lipid bilayer membrane as well as their reciprocal effects with surface functionalizing. Single walled carbon nano tubes can be utilized to diffuse selectively on the targeted cell via surface functionalizing. Many experimental attempts have smeared polyethylene glycol (PEG) as a biocompatible surfactant to carbon nano tubes. The simulation results indicated that SWCNTs have different time-evolving mechanisms to internalize within the lipid membrane. These mechanisms comprise both penetration and endocytosis. Also, this study revealed effects of length and chirality and surface functionalizing on the penetrability of different nano tubes.
The second part of the dissertation introduces a novel in situ method for qualitative and quantitative measurements of the negative stiffness of a single crystal utilizing nano mechanical characterization; nano indentation. The concept of negative stiffness was first introduced by metastable structures and later by materials with negative stiffness when embedded in a stiffer (positive stiffness) matrix. However, this is the first time a direct quantitative method is developed to measure the exact value of the negative stiffness for triglycine sulfate (TGS) crystals. With the advancements in the precise measuring devices and sensors, instrumented nano indentation became a reliable tool for measuring submicron properties of variety of materials ranging from single phase humongous materials to nano composites with heterogeneous microstructures. The developed approach in this chapter of the dissertation outlines how some modifications of the standard nano indentation tests can be utilized to measure the negative stiffness of a ferroelectric material at its Curie temperature.
Finally, the last two chapters outline the possible improvements in the mechanical properties of conventional carbon fiber composites by introducing 1D nano fillers to them. Particularly, their viscoelastic and viscoplastic behavior are studied extensively and different modeling techniques are utilized. Conventional structural materials are being replaced with the fiber-reinforced plastics (FRPs) in many different applications such as civil structures or aerospace and car industries. This is mainly due to their high strength to weight ratio and relatively easy fabrication methods. However, these composites did not reach their full potential due to durability limitations. The majorities of these limitations stem from the polymeric matrix or the interface between the matrix and fibers where poor adhesion fails to carry the desired mechanical loadings. Among such failures are the time-induced deformations or delayed failures that can cause fatal disasters if not taken care of properly. Many methodologies are offered so far to improve the FRPs' resistance to this category of time-induced deformations and delayed failures. Several researchers tried to modify the chemical formulation of polymers coming up with stiffer and less viscous matrices. Others tried to modify the adhesion of the fibers to the matrix by adding different chemically functional groups onto the fibers' surface. A third approach tried to modify the fiber to matrix adhesion and at the same time improve the viscous properties of the matrix itself. This can be achieved by growing 1D nano fillers on the fibers so that one side is bonded to the fiber and the other side embedded in the matrix enhancing the matrix with less viscous deformability. It is shown that resistance to creep deformation and stress relaxation of laminated composites improved considerably in the presence of the nano fillers such as multiwall carbon nano tubes (MWCNTs) and zinc oxide nano wires (ZnO- NWs). The constitutive behaviors of these hybrid composites were investigated further through the use of the time temperatures superposition (TTS) principle for the linear viscoelastic behavior and utilizing phenomenological models for the viscoplastic behavior.Ph. D.
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Roan, Esra. "Experimental and Multiscale Computational Approaches to the Nonlinear Characterization of Liver Tissue." University of Cincinnati / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1179425113.
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Castellano, Hereza Sergi. "Towards the characterization of the eukaryotic selenoproteome: a computational approach." Doctoral thesis, Universitat Pompeu Fabra, 2004. http://hdl.handle.net/10803/7076.
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Although the genome sequence and gene content are available for an increasing number of organisms, eukaryotic selenoproteins remain poorly characterized. In these proteins, selenium (Se) is incorporated in the form of selenocysteine(Sec), the 21st amino acid. Selenocysteine is cotranslationally inserted in response to UGA codons (a stop signal in the canonical genetic code). The alternative decoding is mediated by a stem-loop structure in the 3'UTR of selenoprotein mRNAs (the SECIS element). Selenium is implicated in male infertility, cancer and heart diseases, viral expression and ageing. In addition, most selenoproteins have homologues in which Sec is replaced by cysteine (Cys).Genome biologists rely on the high-quality annotation of genomes to bridge the gap from the sequence to the biology of the organism. However, for selenoproteins, which mediate the biological functions of selenium, the dual role of the UGA codon confounds both the automatic annotation pipelines and the human curators. In consequence, selenoproteins are misannotated in the majority of genome projects. Furthermore, the finding of novel selenoprotein families remains a difficult task in the newly released genome sequences.
In the last few years, we have contributed to the exhaustive description of the eukaryotic selenoproteome (set of eukaryotic selenoproteins) through the development of a number of ad hoc computational tools. Our approach is based on the capacity of predicting SECIS elements, standard genes and genes with a UGA codon in-frame in one or multiple genomes. Indeed, the comparative analysis plays an essential role because 1) SECIS sequences are conserved between close species (eg. human-mouse); and 2) sequence conservation across a UGA codon between genomes at further phylogenetic distance strongly suggests a coding function (eg. human-fugu). Our analysis of the fly, human and Takifugu and Tetraodon genomes have resulted in 9 novel selenoprotein families. Therefore, 20 distinct selenoprotein families have been described in eukaryotes to date. Most of these families are widely (but not uniformly) distributed across eukaryotes, either as true selenoproteins or Cys-homologues.
The correct annotation of selenoproteins is thus providing insight into the evolution of the usage of Sec. Our data indicate a discrete evolutionary distribution of selenoprotein in eukaryotes and suggest that, contrary to the prevalent thinking of an increase in the number of selenoproteins from less to more complex genomes, Sec-containing proteins scatter all along the complexity scale. We believe that the particular distribution of each family is mediated by an ongoing process of Sec/Cys interconversion, in which contingent events could play a role as important as functional constraints. The characterization of eukaryotic selenoproteins illustrates some of the most important challenges involved in the completion of the gene annotation of genomes. Notably among them, the increasing number of exceptions to our standard theory of the eukaryotic gene and the necessity of sequencing genomes at different evolutionary distances towards such a complete annotation.
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Adeniyi, Adebayo Azeez. "Computational studies, synthesis and characterization of ruthenium (ii) anticancer complexes." Thesis, University of Fort Hare, 2014. http://hdl.handle.net/10353/d1015577.
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This thesis is centred on the application of Ru-based complexes as a promising alternative to cis-platin in cancer chemotherapy. Cis-platin is known to be the most prescribed chemotherapy which has more than 70% application in cancer cases especially the testicular cancer. An insight is provided in Chapter One and Two into the literatures reports on the application of Ru(II)-based complexes in cancer chemotherapy. In order to address some of the pressing challenges in rational design of Ru-based anticancer complexes, section 3.3 and 3.4 deal with efforts to elucidate the complication of their chemistry and instability while in section 3.5 efforts are made to find solution to the lack of proper knowledge of their targets using different theoretical approaches as presented in Chapter Three. In addition to the theoretical study, this thesis also comprises of the synthesis of the bis-pyrazole derivatives type of ligands and the derivatives of their Ru(II)-based complexes as provided in Chapter Four and Five respectively. Also the computational methods were used to elucidate the structural and spectroscopic properties of the synthesised ligands and their Ru(II)-based complexes. The geometrical and electronic properties are studied in relation to the stability and the reported anticancer activities of Ru(II)-based complexes in section 3.3. In subsection 3.3.1, several quantum properties including the natural energy decomposition analysis (NEDA) and quantum theory of atoms in a molecule (QTAIM) are computed on three models of RAPTA-C complexes using DFT with hybrid functional and basis set with ECP and without ECP. The higher stability of Carbo-RAPTA-C and Oxalo-RAPTA-C over RAPTA-C comes from the lower exchange repulsion and higher polarization contributions to their stability which gives insight into experimental observation. A similar study was carried out in subsection 3.3.2 on half-sandwich Ru(II)-based anticancer complexes with 6-toluene and 6-trifluorotoluene.
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Jang, Jae Won. "Characterization of live modeling performance boundaries for computational structural mechanics /." Thesis, Connect to this title online; UW restricted, 2007. http://hdl.handle.net/1773/10178.
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Nair, Kalyani Sun Wei. "Multi-scale computational modeling and characterization of bioprinted tissue scaffolds /." Philadelphia, Pa. : Drexel University, 2008. http://hdl.handle.net/1860/2807.
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Michino, Mayako. "Developing new computational methods for characterization ORFS with unknown function." Thesis, Georgia Institute of Technology, 2003. http://hdl.handle.net/1853/25208.
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Rödelsperger, Christian [Verfasser]. "Computational characterization of genome-wide DNA-binding profiles / Christian Rödelsperger." Berlin : Freie Universität Berlin, 2011. http://d-nb.info/1026357837/34.
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He, Xiaoyin. "CHARACTERIZATION OF CORNEAL BIOMECHANICAL PROPERTIES USING EXPERIMENTAL AND COMPUTATIONAL METHODS." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1280178567.
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Fazelinia, Hossein Maranas Costas D. Cirino Patrick C. "Computational design and experimental characterization of proteins with novel functions." [University Park, Pa.] : Pennsylvania State University, 2009. http://etda.libraries.psu.edu/theses/approved/WorldWideIndex/ETD-4174/index.html.
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Hamid, Muhammad Raffay. "Unsupervised Activity Discovery and Characterization for Sensor-Rich Environments." Thesis, Georgia Institute of Technology, 2005. http://hdl.handle.net/1853/14131.
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This thesis presents an unsupervised method for discovering and analyzing the different
kinds of activities in an active environment. Drawing from natural language processing, a
novel representation of activities as bags of event n-grams is introduced, where the global
structural information of activities using their local event statistics is analyzed. It is demonstrated how maximal cliques in an undirected edge-weighted graph of activities, can be used in an unsupervised manner, to discover the different activity-classes. Taking on some work done in computer networks and bio-informatics, it is shown how to characterize these discovered activity-classes from a wholestic as well as a by-parts view-point. A definition of anomalous activities is formulated along with a way to detect them based on the difference of an activity instance from each of the discovered activity-classes. Finally, an information theoretic method to explain the detected anomalies in a human-interpretable form is presented. Results over extensive data-sets, collected from multiple active environments are
presented, to show the competence and generalizability of the proposed framework.
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Podowski, Raf M. "Applied bioinformatics for gene characterization /." Stockholm, 2006. http://diss.kib.ki.se/2006/91-7140-818-5/.
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Li, Chengkai. "Computational design of polymer nanocomposites." Thesis, Queensland University of Technology, 2022. https://eprints.qut.edu.au/230364/1/Chengkai_Li_Thesis.pdf.
Full textAbstract:
This project takes advantage of molecular dynamic simulation for the design of polymer nanocomposites. The newly synthesized low-dimensional carbon nanomaterials show unlimited potential in enhancing the mechanical performance of the polymer. The atomistic simulation approach enables a comprehensive characterization approach for the materials down to atomic level and establish in-detail insights into their mechanical behaviors usually beyond the reach of experiments. The obtained results and analysis establish a fundamental understanding of the enhancement mechanisms for the nanoscale reinforcements in polymer nanocomposites, which could eventually guide their design, fabrication, and engineering implementation.
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Pascual, Borràs Magdalena. "Computational Modelling of Polyoxometalates: Progress on Accurate NMR Characterization and Reactivity." Doctoral thesis, Universitat Rovira i Virgili, 2017. http://hdl.handle.net/10803/440510.
Full textAbstract:
Aquesta tesi es pot dividir en dues parts diferents: i) RMN i ii) la reactivitat. El factor comú d'ambdues seccions són els
polioxometal·lats (POMs). Els POMs són anions moleculars polimetàl·lics formats de l'agregació de blocs MO6
octaèdrics de metalls de transició en els seus estats d'oxidació més alts, i oxigen, que estan connectats per vèrtexs i
arestes.
La primera part està relacionada amb la caracterització dels POMs. En particular, es basa en el càlcul de paràmetres
d'espectroscòpia de ressonància magnètica nuclear (RMN). En primer lloc, s’ha estudiat el nucli 17O. S’ha establert
una estratègia basada en DFT per calcular i racionalitzar desplaçaments químics de 17O de polioxoanions amb alta
precisió. S’ha demostrat que els càlculs realitzats amb els funcionals de tipus GGA PBE, incloent spin-òrbit i
correccions d’escalatge, proporcionen un error mitjà absolut (MAE) <30 ppm, un valor petit tenint en compte el rang
dels desplaçaments químics de 17O en els POMs. També s’ha realitzar un estudi similar per a la determinació de
desplaçaments químics de 31P en els POMs amb mètodes DFT. S’ha descrit el primer polioxometalat que conté tal ·
li, el qual s’ha sintetitzat i determinat estructuralment. S’ha realitzar un estudi detallat de 203 / 205Tl de RMN per tal
de reproduir els valors experimentals. El δ (205Tl) es poden reproduir molt bé amb metodologia DFT.La segona part inclou l'estudi de la reactivitat dels POMs. Matt et. al. (Energy Environ. Sci. 2013, 6, 1504) va
dissenyar un pol·lioxometalat que contenia un fotosensibilitzador de Ir(III), capaç de fer evolucionar de manera eficient
H2. El mecanisme de recol·lecció de llum visible, la formació de les espècies amb càrrega separada i la reducció de
protons ha estat analitzat amb mètodes DFT i també amb mètodes Time-Dependent (TD-DFT). En l'última part, es
presenta un estudi computacional on s’investiga (a) els efectes de diferents lligands d'òxid en {M5O18}6- en vers la
reacció de protonolisis del enllaç M’-OR (b) els efectes de diferents metalls M' en la hidròlisi de el pol·lioxometalat
[(RO)M'W5O18]n-. Per últim s’ha realitzat un estudi experimental sobre la protonació del dímer, (TBA)6[(μ-O)
(TiW5O18) 2].Esta tesis se puede dividir en dos partes diferentes: i) RMN y ii) Reactividad. El factor común de ambas secciones son los polioxometalato (POMs). Los POMs son aniones polimetálicos moleculares formados por la agregación de bloques octaédricos MO6 formados por metales de transición, en sus estados de oxidación más altos, y oxígeno, que están conectados por vértices y bordes. La primera parte está relacionada con la caracterización de los POMs. En particular, se basa en el cálculo de parámetros de espectroscopia de resonancia magnética nuclear (RMN). Primero, nos centramos en el núcleo 17O. Se ha establecido una estrategia basada en metodología DFT para calcular con precisión y racionalizar los desplazamientos químicos de 17O en los POMs. Se ha demostrado que los cálculos realizados con el funcional PBE de tipo GGA, incluyendo correcciones de órbita y estalaje, proporcionan un error absoluto medio (MAE) <30 ppm, un valor pequeño considerando el amplio rango de desplazamientos químicos δ (17O) en POMs. También se ha realizado un estudio similar para la determinación de desplazamientos químicos de 31P en POMs. Se ha descrito el primer polioxometalato que contiene talio, el cual se ha sintetizado y determinado estructuralmente. Se ha realizado un estudio detallado de RMN de 203 / 205Tl para reproducir los valores experimentales. Los δ (205Tl) son reproducidos con metodología DFT.La segunda parte incluye estudios de reactividad de POMs. Matt et. al. (Energy Environ. Sci. 2013, 6, 1504) diseñó un polioxometalato con un foto sensibilizador de Ir (III) capaz de producir H2 de forma eficiente. El mecanismo de la recolección de luz visible, la formación de especies de carga separada y la reducción de protones ha sido analizado por DFT y DFT dependiente del tiempo (TD-DFT). En la última parte, se presenta un estudio computacional para investigar (a) los efectos de diferentes ligandos de {M5O18}6- sobre la protonolisis del enlace M'-OR y (b) los efectos de diferentes metales M' sobre la hidrólisis de [(RO)M'W5O18]n- con diferentes metaltes. Por último, se presenta un estudio experimental sobre la protonación del dímero (TBA)6[(μ-O)(TiW5O18)2].
This thesis can be divided in two different parts: i) NMR and ii) Reactivity. The common factor of both sections is Polyoxometalates (POMs). POMs are polymetallic molecular anions formed upon aggregation of octahedral MO6 blocks made of early transition metals (TMs), in their higher oxidation states, and oxygen, that are connected commonly by vertices and edges. The first part is related to the characterization of POMs. In particular, it is based on the calculation of nuclear magnetic resonance (NMR) spectroscopy parameters. First, we focused on 17O nuclei. We have established a DFT-based strategy to accurately compute and rationalize 17O NMR chemical shifts of polyoxoanions. We show that calculations performed with GGA-type PBE functional, including spin-orbit and scaling corrections, provide a mean absolute error value (MAE) <30 ppm, a small value considering the large range of δ(17O) chemical shifts in POMs. A study for the best DFT strategy for the determination of 31P NMR chemical shifts in POMs is also reported. We have described the first thallium containing polyoxometalate, which was synthetized and structurally determined. A detailed study of 203/205Tl NMR has been performed in order to reproduce the experimental values. The δ(205Tl) are really well reproduced with DFT methodology. However, in the spin-spin coupling, there are large differences between calculated and experimental 2J(205Tl-203Tl).
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Armaos, Alexandros 1989. "Computational characterization of protein-RNA interactions and implications for phase separation." Doctoral thesis, Universitat Pompeu Fabra, 2020. http://hdl.handle.net/10803/668546.
Full textAbstract:
Despite what was previously considered, the role of RNA is not only to carry the genetic
information from DNA to proteins. Indeed, RNA has proven to be implicated in more
complex cellular processes. Recent evidence suggests that transcripts have a regulatory
role on gene expression and contribute to the spatial and temporal organization of the
intracellular environment. They do so by interacting with RNA-binding proteins (RBPs)
to form complex ribonucleoprotein (RNP) networks, however the key determinants that
govern the formation of these complexes are still not well understood. In this work, I will
describe algorithms that I developed to estimate the ability of RNAs to interact with
proteins. Additionally, I will illustrate applications of computational methods to propose
an alternative model for the function of Xist lncRNA and its protein network.
Finally, I will show how computational predictions can be integrated with high
throughput approaches to elucidate the relationship between the structure of the RNA and
its ability to interact with proteins. I conclude by discussing open questions and future
opportunities for computational analysis of cell’s regulatory network.
Overall, the underlying goal of my work is to provide biologists with new insights into
the functional association between RNAs and proteins as well as with sophisticated tools
that will facilitate their investigation on the formation of RNP complexesA pesar de lo que se consideraba anteriormente, el papel del ARN no es solo transportar la información genética del ADN a las proteínas. De hecho, el ARN ha demostrado estar implicado en muchos procesos celulares más complejos. La evidencia reciente sugiere que los transcriptos tienen un papel regulador en la expresión génica y contribuyen a la organización espacial y temporal del entorno intracelular. Lo hacen interactuando con proteínas de unión a ARN (RBP) para formar redes complejas de ribonucleoproteína (RNP), sin embargo, los determinantes clave que rigen la formación de estos complejos aún no se conocen bien. En este trabajo, describiré algoritmos que he desarrollado para estimar la capacidad de los ARN de interactuar con las proteínas. Además, ilustraré aplicaciones de métodos computacionales para proponer una maquinaria alternativa para el Xist lncRNA y su red de interacciones. Finalmente, mostraré cómo las predicciones computacionales pueden integrarse con enfoques de alto rendimiento para dilucidar la relación entre la estructura del ARN y su capacidad para interactuar con las proteínas. Concluyo discutiendo preguntas abiertas y oportunidades futuras para el análisis computacional de la red reguladora de la célula. En general, el objetivo subyacente de mi trabajo es proporcionar a los biólogos nuevas ideas sobre la asociación funcional entre ARN y proteínas, así como herramientas sofisticadas que facilitarán su investigación sobre la formación de complejos RNP.
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Aronoff, Caroline Bradley. "A computational characterization of domain-based causal reasoning development in children." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/119744.
Full textAbstract:
Thesis: M. Eng., Massachusetts Institute of Technology, Department of Electrical Engineering and Computer Science, 2018.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 71-72).
To better understand human intelligence, we must first understand how humans use and learn from stories. One important aspect of how humans learn from stories is our ability to reason about cause and eect. Psychological evidence suggests that when children develop the ability to learn cause-and-eect relationships from stories, they do so in discrete stages where each new stage enables the child to incorporate new kinds of information. In this thesis, I attempt to shed light on the mechanisms that underlie the development of causal reasoning in children. I create a behavior-level model, an explanatory theory, and an explanation-level model that account for the developmental stages. I implement these models on top of the Genesis Story Understanding System. The result is a psychologically plausible explanation-level model that captures the observed causal reasoning behaviors of children at dierent stages of developments. The model also takes the observations from psychological evidence to another level by proposing mechanisms that enable such development in children.
by Caroline Bradley Aronoff.
M. Eng.
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Rezvanifar, Sayed Cyrus. "Computational Analysis and Anatomical Characterization of Trochlear Dysplasia in Patellar Instability." University of Akron / OhioLINK, 2019. http://rave.ohiolink.edu/etdc/view?acc_num=akron1571224864867381.
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Romagnoli, Alessandro. "Aerodynamic and thermal characterization of turbocharger turbines : experimental and computational evaluation." Thesis, Imperial College London, 2010. http://hdl.handle.net/10044/1/6134.
Full textAbstract:
Turbochargers are widely used in both passenger and commercial vehicle applications to increase power density, improved fuel economy leading to significant emissions reductions. In recent years, car manufacturers have introduced turbochargers widely in the diesel market in response to the stricter regulations in exhaust emissions. Although investment in turbocharger technology has made it possible to overcome issues related to reliability and cost, research is much needed in the area of design, testing methodologies and model development. This is particularly the case when considering unsteady flow effects. Computational codes are used by engine manufacturers to predict its performance and size components; prediction accuracy is crucial in this process. This thesis contributes to this process in several ways: steady modelling and heat transfer predictions. Furthermore, most aero-thermal design and analysis codes need data for validation; often the data available falls outside the range of conditions the engine experiences in reality leading to the need to interpolate and extrapolate excessively. The current work also contributes to this area by providing extensive experimental data in a large range of conditions. A further contribution of this work is the understanding of the turbine performance under pulsating flow; it shows that this performance deviates from the commonly used quasi-steady assumption in turbocharger/engine matching. A turbocharger is subjected to high temperature conditions; heat transfer within the turbine and the compressor severely affects the compressor performance at low rotational speeds and mass flow rates. Compressor maps provided by turbocharger manufacturers do not usually take into account the effects of heat transfer; this causes a mismatch when fitting the maps into engine codes which is detrimental to the overall engine performance prediction. The experimental investigation was conducted on three different turbine designs for an automotive turbocharger. The design progression was based on a commercial nozzleless unit modified into a variable geometry single as well as a twin-entry turbine configuration. The main geometrical parameters of these turbines were kept constant to allow equivalent performance assessment. The mixed-flow rotor used in this study consists of 12 blades with a constant inlet blade angle of +20°, a cone angle of 50° and a tip diameter of 95.2mm. The variable geometry stator consists of 15 vanes fitted into a ring mechanism, capable of pivoting in the range of 40° and 80° (with reference to the radial direction). The design progression into twin-entry turbine was completed by fitting a divider (accounting for only ≈6% of the overall internal volume) within volute. The turbine response for different vane angles (40° to 70°) and mass flow ratios between the two entries of the turbine was assessed. The turbine was tested under steady and pulsating flow conditions for two rotational speeds, 27.9 rev/s·√K and 43.0 rev/s·√K, a velocity ratio (U2/Cis) of 0.3 - 1.1 and a pulse frequency of 40 - 80Hz under both in-phase and out-of-phase conditions. A meanline aerodynamic model capable of predicting the performance parameters was developed for the nozzleless and the variable geometry single-entry turbine. The former was validated against experimental results spanning an equivalent speed range of 27.9 rev/s·√K and 53.8 rev/s·√K while the latter validated against one single speed (43.0 rev/s·√K) and three different vane angle settings (40°, 60° and 70°). The wide range of tests data from the Imperial College High Speed Dynamometer enabled the evaluation of the model in areas of the maps where currently no data exists. Based on the model prediction, a breakdown aerodynamic loss analysis was performed. As for the twin-entry turbine, the interaction between the two entries was investigated. Based on experimental evidence, a map-based method was developed to uniquely correlate the flow capacity within the entries for both partial and unequal admission. An investigation into the effects of heat transfer on a turbocharger was performed using a commercial turbocharger mounted on a 2.0 litre diesel engine. The global objective of these tests was to improve the understanding of heat transfer in turbochargers under realistic engine conditions. Measurements were obtained for engine speeds between 1000 and 3000 rpm at a step of 500 rpm – for each engine speed the load applied was varied from 16 to 250 Nm. In addition to the standard set of measurements needed to define the turbo operating point, the turbocharger was equipped with 17 thermocouples positioned in different locations in order to quantify the temperatures of the components constituting the turbocharger. A simplified 1-D heat transfer model was also developed and compared with experimental measurements. The algorithms calculate the heat transferred through the turbocharger, from the hot to the cold end by means of lump capacitances. The compressor performance deterioration from the adiabatic map was then predicted and based on the data generated by the model a multiple regression analysis was developed in order to assess the main parameters affecting the compressor non-adiabatic performance.
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Luxemburg, Michael. "Computational Modeling and Characterization of the Human Tri-Heteromeric GABAA Receptor." Thesis, KTH, Tillämpad fysik, 2019. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-256348.
Full textAbstract:
-aminobutyric acid receptors of type A (GABAARs) are the majorinhibitory neurotransmitter receptors in the human brain, andare modulated by a vast range of exogenous molecules, such assedatives and anesthetics. In the last year, the first cryo-electronmicroscopy (cryo-EM) images of the closed and desensitized statesof the GABAAR were released, enabling fruitful research throughsimulations of these complex proteins. This report investigatesthe characteristics of the two structures. Specifically, pore hydration,radius, and hydrophobicity is compared, and a major focuslies in the general anesthetic (GA) binding pockets in the transmembranedomain, as well as the ligands propofol, etomidate,and pentobarbital. Furthermore, different models for the missingstructure of the intracellular domain (ICD) are compared. Thestructures were simulated for 1 μs using GROMACS. Using multiplesequence alignment as the basis of different models with theheptapeptid SQPARAA in the place of the ICD, resulted in stablestructures with a backbone RMSD close to 2 Å after 1 μs. Thepores are shown to exhibit significant differences between the twostates, with heavier constriction at the 9’ site of the closed state,but also suspected faulty expansion of the pore near the top in thedesensitized state after equilibration. Two of the pockets in thedesensitized state further deviates from expectation, by being tooconstricted. The other pockets were large enough to bind ligandsin the desensitized state, but not in the closed state, as expected.The binding analysis of the GAs suggests that etomidate bindswith the phenyl ring pointing towards the ICD, and that pentobarbitalbinds with the head group pointing towards the pore. Italso suggests that the GAs can bind to every GA pocket, but thatmodulatory activity is dependent on consistently low binding energies,which varies between the ligands for the different pockets.-aminobutansyra receptorer av typ A (GABAARs) är de huvudsakligahämmande neurotransmittor-receptorerna i den mänskligahjärnan och moduleras av ett stort antal exogena molekyler, såsomsedativa läkemedel och anestetika. Under det senaste åretsläpptes de första bilderna från cryo-elektronmikroskopi (cryo-EM) av de stängda och desensibiliserade tillstånden i GABAAR,vilket möjliggjorde framgångsrik forskning genom simuleringarav dessa komplexa proteiner. Denna rapport undersöker egenskapernahos de två strukturerna. Specifikt jämförs hydrering avporen, porens radie och hydrofobicitet, medan huvudfokus liggerpå bindningsfickorna för generella anestetika (GA) i den transmembranadomänen, liksom på liganderna propofol, etomidat ochpentobarbital. Dessutom jämförs olika modeller för den saknadestrukturen hos den intracellulära domänen (ICD). Strukturernasimulerades i 1 μs med GROMACS. Användning av sekvensanpassningsom utgångspunkt för olika modeller med heptapeptidenSQPARAA som ersättning för ICD resulterade i stabila strukturermed RMSD för kolkedjan nära 2 Å efter 1 μs. Resultatenav karakterisering av poren visar signifikanta skillnader mellande två tillstånden med tydlig sammandragning vid 9’ positionen idet stängda tillståndet, men också misstänkt felaktig expansion avporen nära toppen i det desensibiliserade tillståndet efter ekvilibrering.Två av fickorna i det desensibiliserade tillståndet avvikervidare från förväntan, genom att vara för begränsade. De andrafickorna var tillräckligt stora för att binda ligander i det desensibiliseradetillståndet, men inte i det stängda, som förväntat. Bindningsanalysenav GA antyder att etomidat binder med fenylringenpekandes mot ICD och att pentobarbital binder med huvudgruppenpekandes mot poren. Analysen tyder också på att GAs kanbinda till varje GA-ficka, medan den modulerande aktiviteten ärberoende av konsekvent låga bindningsenergier, som varierar mellanliganderna för de olika fickorna.
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Freese, Peter (Peter Dale). "Biochemical and functional characterization of human RNA binding proteins." Thesis, Massachusetts Institute of Technology, 2018. http://hdl.handle.net/1721.1/115601.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Computational and Systems Biology Program, 2018.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references (pages 205-226).
RNA not only shuttles information between DNA and proteins but also carries out many other essential cellular functions. Nearly all steps of an RNA's life cycle are controlled by approximately one thousand RNA binding proteins (RBPs) that direct RNA splicing, cleavage and polyadenylation, localization, translation, and degradation. Despite the central role of RBPs in RNA processing and gene expression, they have been less well studied than DNA binding proteins, in part due to the historical dearth of technologies to probe RBP binding and activity in a high-throughput, comprehensive manner. In this thesis, I describe the affinity landscapes of the largest set of human RBPs to date elucidated through a highthroughput version of RNA Bind-N-Seq (RBNS), an unbiased in vitro assay that determines the primary sequence, secondary structure, and contextual preferences of an RBP. The 78 RBPs bound an unexpectedly low diversity of RNA motifs, implying convergence of binding specificity toward a small set of RNA motifs characterized by low compositional complexity. Offsetting the low diversity of sequence motifs, extensive preferences for contextual features beyond short linear motifs were observed, including bipartite motifs, flanking nucleotide content, and preference for or against RNA structure. These features likely refine which motif occurrences are selected in cells, enabling RBPs that bind the same linear motif to act on distinct subsets of transcripts. Additionally, RBNS data is integrated with complementary in vivo binding sites from enhanced crosslinking and immunoprecipitation (eCLIP) and functional (RNAi/RNA-seq) data produced through collaborative efforts with the ENCODE consortium. These data enable creation of "RNA maps" of RBP activity in pre-mRNA splicing and gene expression levels, either with (eCLIP) or without (RBNS) crosslinking-based assays. The mapping and characterization of RNA elements recognized by over 200 human RBPs is also presented in two human cell lines, K562 and HepG2 cells. Together, these novel data augment the catalog of functional elements encoded in the human genome to include those that act at the RNA level and provide a basis for how RBPs select their RNA targets, a fundamental requirement in more fully understanding RNA processing mechanisms and outcomes.
by Peter Freese.
Ph. D.
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Holmberg, Andreas. "Aeroacoustic Characterization using Multiport Methods." Doctoral thesis, KTH, MWL Strömningsakustik, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-105396.
Full textAbstract:
Noise is a major environmental pollutant, which can inict physical and psychologicalinjury. An important noise contribution stems from aeroacousticsources, which are found in e.g., ventilation ducts, engine exhaust systems andairplane engines.In this thesis, research methods for low Mach number aeroacoustic sourcesin ducts are developed. The basis of the methods is the ability to describe theintrinsic linear properties of the source as an N-port (multiport), where theoutput sound eld is related to the input sound eld and the generated soundeld, all consisting of plane waves. The methods presented are both numericaland experimental. The numerical method treats the passive properties, i.e.,scattering, attenuation and amplication of incident sound, while the experimentalmethod treats the active part (intrinsic sound generation) as well. Themethods are applied in the study of noise generation by a vortex mixer plate,placed in an airow of Mach 0.2, and in the study of acoustic-hydrodynamicinteraction in a T-junction of rectangular ducts.It is found that the accuracy of the experimental methods is signicantly increasedwhen the equations are over-determined, which is achieved by addingadditional microphones to the test rig. In the frequency range studied, themixer plate is found to generate less sound when made exible, without disturbingthe mixing quality.For the numerical method { based on the linearized Navier-Stokes equations,a model of the oscillation of the Reynolds stress (\turbulent damping")due to the acoustic eld is introduced. By comparing with experimental results,it is found that not using this model results in an over-prediction of theamplication at higher frequencies with several factors in magnitude, whileimplementing the model results in a much better agreement.QC 20121123
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Kallberg, Yvonne. "Bioinformatic methods in protein characterization /." Stockholm, 2002. http://diss.kib.ki.se/2002/91-7349-370-8/.
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Chanthasopeephan, Teeranoot Desai Jaydev Prataprai Lau Alan C. W. "Characterization of soft tissue cutting for haptic display : experiments and computational models /." Philadelphia, Pa. : Drexel University, 2006. http://hdl.handle.net/1860/1116.
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Koreck, Juergen. "Computational characterization of adhesive bond properties using guided waves in bonded plates." Thesis, Available online, Georgia Institute of Technology, 2006, 2006. http://etd.gatech.edu/theses/available/etd-08252006-064856/.
Full textAbstract:
Thesis (M. S.)--Civil and Environmental Engineering, Georgia Institute of Technology, 2007.Jacobs, Laurence, Committee Chair ; Qu, Jianmin, Committee Member ; Valle, Christine, Committee Co-Chair.
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Larsson, Pontus. "Computational Approaches to the Identification and Characterization of Non-Coding RNA Genes." Doctoral thesis, Uppsala universitet, Institutionen för cell- och molekylärbiologi, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-9518.
Full textAbstract:
Non-coding RNAs (ncRNAs) have emerged as highly diverse and powerful key players in the cell, the range of capabilities spanning from catalyzing essential processes in all living organisms, e.g. protein synthesis, to being highly specific regulators of gene expression. To fully understand the functional significance of ncRNAs, it is of critical importance to identify and characterize the repertoire of ncRNAs in the cell. Practically every genome-wide screen to identify ncRNAs has revealed large numbers of expressed ncRNAs and often identified species-specific ncRNA families of unknown function. Recent years' advancement in high-throughput sequencing techniques necessitates efficient and reliable methods for computational identification and annotation of genes. A major aim in the work underlying this thesis has been to develop and use computational tools for the identification and characterization of ncRNA genes. We used computational approaches in combination with experimental methods to study the ncRNA repertoire of the model organism Dictyostelium discoideum. We report ncRNA genes belonging to well-characterized gene families as well as previously unknown and potentially species-specific ncRNA families. The complicated task of de novo ncRNA gene prediction was successfully addressed by developing a method for nucleotide composition-based gene prediction using maximal-scoring partial sums and considering overlapping dinucleotides. We also report a substantial heterogeneity among human spliceosomal snRNAs. Northern blot analysis and cDNA cloning, as well as bioinformatical analysis of publicly available microarray data, revealed a large number of expressed snRNAs. In particular, U1 snRNA variants with several nucleotide substitutions that could potentially have dramatic effects on splice site recognition were identified. In conclusion, we have by using computational approaches combined with experimental analysis identified a rich and diverse ncRNA repertoire in the eukaryotes D. discoideum and Homo sapiens. The surprising diversity among the snRNAs in H. sapiens suggests a functional involvement in recognition of non-canonical introns and regulation of messenger RNA splicing.
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Damián, Ares Gonzalo. "Integrative computational modeling & in-vivo characterization of residual deformations in hemodynamics." Laboratório Nacional de Computação Científica, 2016. https://tede.lncc.br/handle/tede/230.
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This thesis is concerned with two major problems arising in the modeling of the cardiovascular system. The first topic consists in a comprehensive approach for the simulation of arterial blood flow and its effect on the stress state of the arterial wall, and the second topic is concerned with the in-vivo characterization of residual deformations in arterial wall tissues, based on data provided by medical images. Specifically, regarding the first topic, an original modeling framework is proposed for the treatment of hemodynamic problems with increased realism, featuring a combination of several modeling techniques in order to account for i) the fact that the initial (image-based) geometry corresponds to a configuration which is at equilibrium with an internal pressure acting over the lumen, and with tethering forces located at the artificial (axial) boundaries delimiting the arterial region of interest; ii) the fluid-structure interaction problem; iii) the complex constitutive behavior of the arterial wall; iv) the influence of surrounding tissues; v) the interaction of the vessel with the rest of the cardiovascular system; and iv) the influence of residual stresses. In order to tackle the issues described above, the preload mechanical problem is solved in a first stage, finding the zero-load material configuration which is employed to define suitable constitutive equations. This is performed by finding the solution for the mechanical equilibrium of the given image configuration considering the vessel at this state to be loaded by an internal baseline pressure and an axial traction (caused by tethering forces) at the artificial boundaries. It is worthwhile to mention that this axial traction is such that a previously defined pre-stretch level is considered on the equilibrium image configuration. Once the reference configuration is obtained, the complete 3D fluid-structure interaction simulation is carried out, coupled with a dimensionally reduced 1D model of the rest of the cardiovascular system. Strong coupling via fixed-point iterations is achieved for the fluid-structure interaction, while the dimensionally heterogeneous coupling is achieved through a Broyden method. Regarding the constitutive modeling, a fiber-reinforced hyperelastic constitutive law is considered. Furthermore, through the analysis of several numerical examples, the sensitivity with respect to the existence of the preload stresses is assessed to quantify the importance of this issue. These results indicate that the stress state of the arterial wall is strongly influenced by the existence of preload. Therefore, the consideration of such preload state is mandatory for the prediction of stresses in arterial tissue. For the second topic, a conceptual framework is presented for the in-vivo estimation of residual deformations and stresses. As a given data, a set of known configurations for an arterial segment is considered, which can potentially be obtained from medical imaging techniques. The mechanical equilibrium equations corresponding to such configurations are introduced through a variational approach, highlighting the role of the residual deformations and associated stresses. In this context, a cost functional is proposed to measure the imbalance of the mechanical setting arising from the consideration of inconsistent residual deformations, based on the generalized residuals of the associated variational equations. Then, the characterization of residual deformations becomes an optimization problem, focused on the minimization of this cost functional. For this purpose, a simple gradient descent method and an interior-point algorithm for constrained optimization are explored in this work. The proposed methodology is tested using three numerical examples based on manufactured solutions, a simple clamped bar, a thick-walled cylinder and a three-layered aorta artery. The obtained results are promising and suggest that the present method (or variants based on the present ideas), when coupled with adequate image acquisition techniques, could successfully lead to the in-vivo identification of residual deformations.
Esta tese aborda dois problemas de relevância na modelagem do sistema cardiovascular humano. O primeiro tema consiste no desenvolvimento de um enfoque abrangente para a simulação do escoamento sanguíneo e sua interação com a parede arterial, e o segundo tópico é a caracterização in-vivo de tensões e deformações residuais na parede arterial baseada em dados fornecidos por imagens médicas. De maneira específica, em relação ao primeiro tópico, um marco de modelagem é proposto para o tratamento de problemas hemodinâmicos com um alto grau de realismo, apresentando uma combinação de diferentes técnicas de modelagem para levar em conta i) o fato que as geometrias iniciais obtidas a partir de imagens médicas são correspondentes a um sistema de carregamentos não nulos, definido pela existência da pressão interna no lumen e de tensões axiais localizadas nos contornos artificiais do segmento arterial; ii) o problema de interação fluido-estrutura; iii) o complexo comportamento constitutivo da parede arterial; iv) a interação do segmento de interesse com o resto do sistema cardiovascular; e v) a influência dos tecidos circundantes; e vi) a existência de tensões residuais. Para a abordagem das questões descritas acima, o problema mecânico de precarregamento é resolvido em uma primeira etapa, encontrando a configuração material de carregamento nulo onde as equações constitutivas são usualmente definidas. Isto é realizado encontrando a solução do problema de equilíbrio mecânico da estrutura arterial dada, considerando que o vaso está submetido a um nível de pressão de base e uma tração axial nos contornos artificiais. Vale a pena ressaltar que esta tração axial é correspondente a um nível de pre-estiramento previamente definido. Uma vez que a configuração de referência é obtida, a simulação fluido-estrutura 3D é realizada, acoplada com um modelo dimensionalmente reduzido do resto do sistema cardiovascular. Um acoplamento forte através de iterações de ponto fixo é empregado para representar a interação fluido-estrutura, equanto o acoplamento entre modelos dimensionalmente heterogêneos é conseguido usando um método tipo Broyden. Em relação à modelagem constitutiva, um modelo hyperelástico reforçado com fibras é considerado. Além disso, através da análise de vários exemplos numéricos, a sensibilidade com relação à existência de precarregamentos é quantificada para remarcar a relevância desta questão. Tais resultados indicam que o estado de tensão da parede arterial é fortemente influenciado pela existência de precarregamentos. Assim sendo, levar em consideração esse estado de precarga é fundamental para a predição de tensões no tecido arterial. Em relação ao segundo tópico, um marco conceptual é apresentado para estimação de tensões e deformações residuais. Consideramos que os dados são um conjunto de configurações de um segmento arterial, as quais poderiam ser obtidas a partir do uso de técnicas de adquisição e , processamento e segmentação de imagens. Utilizando um enfoque variacional, são apresentadas as equações de equilíbrio mecânico para as configurações conhecidas, acentuando o papel desempenhado pelas deformações residuais. Neste contexto, apresenta-se um funcional custo que mede o desbalance mecânico que é originado se um campo de deformações residuais inconsistente é admitido. Este funcional custo está baseado no resíduo generalizado das equações variacionais previamente mencionadas. Como consequência, o problema de estimação de deformações residuais é transformado em um problema de otimização, no qual se procura minimizar o funcional custo proposto. Com este objetivo, neste trabalho de tese são considerados dois métodos, um método de gradiente e um algoritmo de ponto interior para problemas que apresentam restrições. A metodologia proposta é testada em três exemplos numéricos baseados em soluções manufaturadas: um barra engastada, um cilindro de parede grossa, e uma artéria aorta composta por três camadas. Os resultados obtidos são promissores e sugerem que o método apresentado (ou variantes baseadas nas ideias aqui mostradas) junto com técnicas adequadas para a adquisição de imagens podem conduzir à identificação in-vivo de deformações residuais.
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Desai, Ishani M. Eng Massachusetts Institute of Technology. "Designing structures with tree forks : mechanical characterization and generalized computational design approach." Thesis, Massachusetts Institute of Technology, 2020. https://hdl.handle.net/1721.1/127284.
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Thesis: M. Eng., Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, May, 2020Cataloged from the official PDF of thesis.
Includes bibliographical references (pages 80-83).
Timber structures have seen a resurgence in structural design in recent years due to a desire to reduce embodied carbon in the built environment. While many of these structures use standardized or regular elements, the recent revolution in digital fabrication has resulted in a variety of more complex and irregular timber forms, usually achieved through milling or other machine-driven production processes. However, the organic nature of wood has also inspired architects and engineers to harness naturally occurring formal variation, for example, in the geometries of tree forks and branches, to produce designs that are more directly responsive to their constitutive materials. Compared to conventional fabrication processes for timber, in which the material is often processed several times to achieve characteristics that are present in the original material, this approach embodies little waste in material and effort.
Naturally occurring branching tree forks seem to exhibit outstanding strength and material efficiency as a natural moment connection, which underpins previous research investigating their use in design. This thesis advances the use of tree forks as a natural connection in structures through two specific contributions. First, the paper establishes a flexible matching-based methodology for designing structures with a pre-existing library of tree fork nodes (based on actual available materials from salvaged trees, for example), balancing an initial target design, node matching quality, and structural performance. The methodology uses a combination of Iterative Closest Point and Hungarian Algorithms as a real-time computational approach for matching nodes in the library to nodes in the design.
The thesis presents results that systematically test this methodology by studying how matching quality varies depending on the number and species of tree forks available in the library and relates this back to the mechanical properties of tree branches found through physical testing. Second, mechanical laboratory testing of tree fork nodes of various tree species (available locally in the area) is presented to quantify the structural capacity of these connections and observe the behavior under tree fork load transfers. A structural score is developed to characterize the tolerance of tree fork nodes to imperfect matches in terms of structural capacity; these resulting geometries are compared to the previous matching-based scoring system. The resulting approach is projected forward as a framework for a more general computational approach for designing with existing material systems and geometries that can also be expanded beyond tree forks.
by Ishani Desai.
M. Eng.
M.Eng. Massachusetts Institute of Technology, Department of Civil and Environmental Engineering
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Souto, Nelson Mineiro. "Computational design of a mechanical test for material characterization by inverse analysis." Doctoral thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/15168.
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Doutoramento em Engenharia MecânicaWith the development of full-field measurements methods, recent material parameters identification strategies call upon the use of heterogeneous tests. The inhomogeneous strain fields developed during these tests lead to a more complete mechanical characterization of the sheet metals, allowing the substantial reduction of the number of tests in the experimental database needed for material parameters identification purposes. In the present work, an innovative design optimization process for the development of heterogeneous tests is presented. The main goal is the design of a mechanical test able to characterize the material behavior of thin metallic sheets under several stress and strain paths and amplitudes. To achieve this aim, the study was carried out with a virtual material, though derived from experimental data. An indicator of the mechanical interest of the test was proposed, and was used in an optimization procedure to design both the boundary conditions and the sample shape. On the one hand, the virtual behavior of a mild steel was characterized using a complex phenomenological model composed by the Yld2004-18p anisotropic yield criterion combined with a mixed isotropic-kinematic hardening law and a macroscopic rupture criterion. An efficient material parameters identification process based on finite element model updating type was implemented and the identified parameters set was validated by performing a deep drawing test leading either to full drawing or rupture of the blank. On the other hand, an indicator which rates the strain field of the experiment by quantifying the mechanical information of the test was formulated. The relevance of the indicator was stressed out by the numerical analysis of already known classical as well as heterogeneous tests and the results obtained were validated by a material parameter sensitivity study. Two different optimization approaches were used for designing the heterogeneous test, namely (i) a one-step procedure designing both specimen shape and loading path by using a tool and (ii) a sequential incremental technique designing the specimen shape and the loading path of the specimen considering local displacements. The results obtained revealed that the optimization approach proposed was very promising for designing a single experiment able to fully characterize the several strain paths and amplitudes encountered in sheet metal forming processes.
Devido ao desenvolvimento de métodos de medição global, recentes estratégias de identificação de parâmetros de material baseiam-se na informação obtida em testes mecânicos heterogéneos. Os campos de deformação desenvolvidos por estes testes permitem uma melhor caracterização mecânica de chapas metálicas, o que possibilita reduzir consideravelmente o número de testes mecânicos necessários num processo de identificação de parâmetros de modelos constitutivos complexos. No presente trabalho, uma metodologia de design recorrendo a optimização para desenvolver testes mecânicos heterógenos é apresentada. O seu principal objectivo consistiu na concepção de um teste mecânico capaz de caracterizar o comportamento mecânico de chapas metálicas para vários estados de tensão e deformação. Para isso, este estudo foi realizado considerando um material virtual obtido a partir de dados experimentais. Além disso, um indicador capaz de caracterizar testes mecânicos foi proposto para ser posteriormente utilizado na metodologia de optimização. Por um lado, o comportamento virtual de um aço macio foi caracterizado através de um modelo fenomenológico complexo composto pelo critério de plasticidade anisotrópico Yld2004-18p, combinado com uma lei de encruamento mista e com um critério macroscópico de ruptura. Para esta caracterização mecânica, um processo eficiente de identificação de parâmetros foi desenvolvido e o conjunto de parâmetros identificado foi validado comparando resultados experimentais e numéricos do processo de embutidura de um copo cilíndrico. Por outro lado, um indicador quantitativo para avaliar a informação do campo de deformação de testes mecânicos foi formulado e a sua performance foi avaliada através da análise numérica tanto de testes mecânicos clássicos como de testes heterogéneos. Relativamente à metodologia de optimização, duas abordagens diferentes foram consideradas para a concepção do teste mecânico heterógeno. A primeira abordagem consistiu num procedimento de etapa única projectando a forma do provete e o carregamento através da utilização de uma ferramenta. A segunda abordagem consistiu numa técnica incremental de varias etapas projectando a forma do provete e o caminho de deformação através da aplicação de carregamento por deslocamentos locais. Os resultados obtidos revelaram que a metodologia de optimização proposta permite a concepção de testes mecânicos capazes de caracterizar toda a gama de estados de deformação e níveis de deformação normalmente observados nos processos de conformação de chapas metálicas.
Grâce au développement des méthodes de mesure de champs, de nouvelles stratégies d’identification de paramètres matériau de lois de comportement mécanique sont proposées, fondées sur l’utilisation d’essais mécaniques hétérogènes. Les champs de déformation hétérogènes développés au cours de ces essais permettent une meilleure caractérisation du comportement mécanique des tôles métalliques et, par conséquent, de réduire considérablement le nombre d’essais nécessaires pour identifier les paramètres matériau de modèles phénoménologiques complexes. Mais comment concevoir ces essais? Dans ce travail, une méthodologie d’optimisation pour le développement d’essais mécaniques hétérogènes est présentée. L’objectif principal est la conception, par analyse inverse et en proposant un indicateur représentatif des états de déformation, d’un essai capable de caractériser le comportement mécanique des tôles métalliques pour plusieurs états de contrainte et déformation. Pour cela, cette étude a été réalisée en considérant un matériau virtuel (acier doux sous forme de tôle mince), obtenu à partir de données expérimentales. En outre, un indicateur qui caractérise les essais mécaniques a été proposé pour être utilisé dans la méthodologie d’optimisation. D’un côté, le comportement mécanique de l’acier doux a été représenté avec un modèle phénoménologique complexe composé du critère anisotrope de plasticité Yld2004-18p, combiné à une loi d’écrouissage mixte et un critère macroscopique de rupture. Pour cette loi de comportement, un procédé d’identification des paramètres du matériau a été développé et le jeu de paramètres identifiés a été validé en comparant des résultats expérimentaux et numériques de l’emboutissage d’un godet cylindrique. D’un autre côté, un indicateur quantitatif pour évaluer l’information du champ de déformation des essais mécaniques a été formulé et sa pertinence a été évaluée à travers l’analyse numérique d’essais classiques et hétérogènes de la littérature. Concernant la méthodologie d’optimisation, deux approches différentes ont été considérées pour la conception de l’essai mécanique hétérogène. La première approche est fondée sur une procédure en une seule étape, où l’optimisation de la forme de l’éprouvette et des conditions aux limites, imposées par un outil, a été effectuée. La seconde approche est fondée sur une technique incrémentale en plusieurs étapes, en optimisant la forme de l’éprouvette et le chemin de déformation, par l’application des déplacements locaux. Les résultats obtenus sont comparés et un essai est retenu pour identifier les paramètres matériau, en utilisant le matériau virtuel comme référence, afin d’illustrer la pertinence de la démarche.
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Seranthian, Kalay Arasan. "A Computational Study of Elastomer Friction and Surface Topography Characterization using Fractal Theory." University of Cincinnati / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1468512374.
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Al-Hajeri, Mohammad Hamad. "Characterization of the fluid flow associated with ceramic candle filters." Thesis, University of Nottingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.323258.
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Rizzo, Francesco. "Computational characterization of carbazole-benzonitrile derivatives for applications in Organic Light Emitting Diodes." Master's thesis, Alma Mater Studiorum - Università di Bologna, 2020. http://amslaurea.unibo.it/21022/.
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The technology of Organic Light-Emitting Diodes has reached such a high level of reliability that it can be used in various applications. The required light emission efficiency can be achieved by transforming the triplet excitons into singlet states through Reverse InterSystem Crossing (RISC), which is the main process of a general mechanism called thermally activated delayed fluorescence (TADF). In this thesis, we theoretically analyzed two carbazole-benzonitrile (donor-acceptor) derivatives, 2,5-di(9H-carbazol-9-yl)benzonitrile (p-2CzBN) and 2,3,4,5,6-penta(9H-carbazol-9-yl)benzonitrile (5CzBN), and addressed the problem of how donor-acceptor (D-A) or donor-acceptor-donor (D-A-D) flexible molecular architectures influence the nature of the excited states and the emission intensity. Furthermore, we analyzed the RISC rates as a function of the conformation of the carbazole lateral groups, considering the first electronic states, S0, S1, T1 and T2, involved in TADF process. The two prototype molecules, p-2CzBN and 5CzBN, have a similar energy gap between the first singlet and triplet states (∆EST, a key parameter in the RISC rate), but different TADF performances. Therefore, other parameters must be considered to explain their different behavior. The oscillator strength of p-2CzBN, never tested as emitter in OLEDs, is similar to that of 5CzBN, which is an active TADF molecule. We also note that the presence of a second T2 triplet state, lower in energy than S1 only in 5CzBN, and the reorganization energies, associated with RISC processes involving T1 and T2, are important factors in differentiating the rates in p-2CzBN and 5CzBN. For p-2CzBN, the RISC rate from T2 to S1 is surprisingly higher than that from T1 to S1, in disagreement with El-Sayed rules, due to a large reorganization energy associated to the T1 to S1, process; while the contrary occurs for 5CzBN. These insights are important for designing new TADF emitters based on the benzo-carbazole architecture.
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Nelson, George J. "Computational characterization of diffusive mass transfer in porous solid oxide fuel cell components." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31660.
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Thesis (Ph.D)--Mechanical Engineering, Georgia Institute of Technology, 2010.Committee Co-Chair: Haynes, Comas; Committee Co-Chair: Wepfer, William; Committee Member: Fedorov, Andrei; Committee Member: Liu, Meilin; Committee Member: Paredis, Chris; Committee Member: Teja, Amyn. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Fang, Lei. "COMPUTATIONAL MODELING, DESIGN, AND CHARACTERIZATION OF COCAINE-METABOLIZING ENZYMES FOR ANTI-COCAINE MEDICATION." UKnowledge, 2013. http://uknowledge.uky.edu/pharmacy_etds/39.
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Cocaine is a widely abused and addictive drug, resulting in serious medical and social problems in modern society. Currently, there is no FDA-approved medication specific for cocaine abuse treatment. The disastrous medical and social consequences of cocaine abuse have made the development of an anti-cocaine medication a high priority. However, despite decades of efforts, traditional pharmacodynamic approach has failed to yield a truly useful small-molecule drug due to the difficulties inherent in blocking a blocker like cocaine without affecting the normal functions of the transporters or receptors. An alternative approach, i.e. pharmacokinetic approach, is to interfere with the delivery of cocaine to its receptors/transporters and/or accelerate its metabolism in the body. It would be an ideal anti-cocaine medication to accelerate cocaine metabolism producing biologically inactive metabolites.
Two natural enzymes may catalyze hydrolysis of cocaine: human butyrylcholinesterase (BChE) and bacterial cocaine esterase (CocE). However, the wild-type enzymes are not suitable as anti-cocaine therapeutics, due to the low catalytic activity, thermoinstability, or short biological half-life. In this investigation, we performed integrated computational-experimental studies to rationally design and discover mutants of these enzymes in order to improve the catalytic activity, thermostability, and/or biological half-life. To rationally design desirable mutants of the enzymes, we have successfully developed computational models, including those for BChE gating, glycosylated BChE structure, BChE-substrate complex structures, BChE dimer/tetramer structures, CocE monomer/dimer structures, and CocE-substrate complex structures. Development of the computational models enabled us to rationally design new amino-acid mutations that may improve the catalytic activity, thermostability, and/or prolonged biological half-life. The computational design was followed by wet experimental tests, including both in vitro and in vivo experiments, leading to discovery of new enzyme forms with not only a high catalytic efficiency against cocaine, but also an improved thermostability and/or prolonged biological half-life. The identified new mutants of BChE and CocE are expected to be valuable candidates for development of a more efficient enzyme therapy for cocaine abuse. The encouraging outcomes of the present study also suggest that the structure-and-mechanism-based design and integrated computational-experimental approach is promising for rational drug design and discovery.
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Sontheimer, Jana. "Functional characterization of proteins involved in cell cycle by structure-based computational methods." Doctoral thesis, Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2012. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-86778.
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In the recent years, a rapidly increasing amount of experimental data has been generated by high-throughput technologies. Despite of these large quantities of protein-related data and the development of computational prediction methods, the function of many proteins is still unknown. In the human proteome, at least 20% of the annotated proteins are not characterized. Thus, the question, how to predict protein function from its amino acid sequence, remains to be answered for many proteins. Classical bioinformatics approaches for function prediction are based on inferring function from well-characterized homologs, which are identified based on sequence similarity. However, these methods fail to identify distant homologs with low sequence similarity. As protein structure is more conserved than sequence in protein families, structure-based methods (e.g. fold recognition) may recognize possible structural similarities even at low sequence similarity and therefore provide information for function inference. These fold recognition methods have already been proven to be successful for individual proteins, but their automation for high-throughput application is difficult due to intrinsic challenges of these techniques, mainly caused by a high false positive rate. Automated identification of remote homologs based on fold recognition methods would allow a signi cant improvement in functional annotation of proteins. My approach was to combine structure-based computational prediction methods with experimental data from genome-wide RNAi screens to support the establishment of functional hypotheses by improving the analysis of protein structure prediction results.
In the first part of my thesis, I characterized proteins from the Ska complex by computational methods. I showed the benefit of including experimental information to identify remote homologs: Integration of functional data helped to reduce the number of false positives in fold recognition results and made it possible to establish interesting functional hypotheses based on high con dence structural predictions. Based on the structural hypothesis of a GLEBS motif in c13orf3 (Ska3), I could derive a potential molecular mechanism that could explain the observed phenotype.
In the second part of my thesis, my goal was to develop computational tools and automated analysis techniques to be able to perform structure-based functional annotation in a high-throughput way. I designed and implemented key tools that were successfully integrated into a computational platform, called StrAnno, which I set up together with my colleagues. These novel computational modules include a domain prediction algorithm and a graphical overview that facilitates and accelerates the analysis of results.
StrAnno can be seen as a first step towards automatic functional annotation of proteins by structure-based methods. First, the analysis of long hit lists to identify promising candidates for further analysis is substantially facilitated by integration and combination of various sequence-based computational tools and data from functional databases. Second, the developed post-processing tools accelerate the evaluation of structural and functional hypotheses. False positives from the threading result lists are removed by various filters, and analysis of the possible true positives is greatly enhanced by the graphical overview. With these two essential benefits, fold recognition techniques are applicable to large-scale approaches. By applying this developed methodology to hits from a genome-wide cell cycle RNAi screen and evaluating structural hypotheses by molecular modeling techniques, I aimed to associate biological functions to human proteins and link the RNAi phenotype to a molecular function. For two selected human proteins, c20orf43 and HJURP, I could establish interesting structural and functional hypotheses. These predictions were based on templates with low sequence identity (10-20%). The uncharacterized human protein c20orf43 might be a E3 SUMO-ligase that could be involved either in DNA repair or rRNA regulatory processes. Based on the structural hypotheses of two domains of HJURP, I predicted a potential link to ubiquitylation processes and direct DNA binding. In addition, I substantiated the cell cycle arrest phenotype of these two genes upon RNAi knockdown.
Fold recognition methods are a promising alternative for functional annotation of proteins that escape sequence-based annotation due to their low sequence identity to well-characterized protein families. The structural and functional hypotheses I established in my thesis open the door to investigate the molecular mechanisms of previously uncharacterized proteins, which may provide new insights into cellular mechanisms.
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Kitanovski, Simo [Verfasser], and Daniel [Akademischer Betreuer] Hoffmann. "Computational identification and characterization of genotype-phenotype associations / Simo Kitanovski ; Betreuer: Daniel Hoffmann." Duisburg, 2021. http://d-nb.info/1230322779/34.
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Awan, Malik Shahzad K. "Performance characterization of computational resources for time-constrained job execution in P2P environments." Thesis, University of Warwick, 2013. http://wrap.warwick.ac.uk/57452/.
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Peer-to-peer (P2P) computing, involving the participation of thousands of general purpose, public computers, has established itself as a viable paradigm for executing looselycoupled, complex scientific applications requiring significant computational resources. The paradigm provides cheap, general-purpose computing resources with comparable computing power (FLOP/s) to an otherwise expensive supercomputer. The main characteristic of the paradigm is the volunteer participation of the general public, without any legal obligation, who dedicate their heterogeneous computational resources for advancing scientific research. The development of several middleware solutions have also furthered the application of P2P computing for solving complex scientific problems. The Berkeley Open Infrastructure for Network Computing (BOINC) is one of the most widely deployed middleware platforms in P2P systems, and has been deployed in more than 7.5 million general purpose computers for scientific computations, achieving an overall performance of 16,632.605 TeraFLOPS. ClimatePrediction.net, a large P2P project based on the BOINC middleware, involves more than 429,000 machines representing 200 different microprocessor architectures and running 21 distinct operating systems. The availability of such a large and diverse set of computational resources requires an in-depth investigation into the performance aspects of available computational resources in this dynamic P2P environment. This thesis analyses the performance data of ClimatePrediction.net primarily collected using two benchmarks, Dhrystone and Whetstone, which form part of the BOINC middleware. The results reveal a significant variation in integer and floating-point operational performance characterized by Dhrystone and Whetstone respectively for similar microprocessors, operating systems and hardware configurations. Under the BOINC environment, these performance results could be useful for: i) the selection of a suitable computing platform for executing time-constrained jobs; ii) calculating an incentive unit for rewarding project participants for their volunteer participation in large P2P projects to advance scientific research; and iii) efficient and effective utilization of available computational resources. However, the inconsistency in performance results of Dhrystone and Whetstone significantly affect their usefulness for the afore-mentioned three important applications areas, and highlight the need for reliability and consistency of performance results for obtaining maximum benefit in an uncontrolled and dynamic P2P environment. This thesis, based on the analysis of performance data of ClimatePrediction.net, identifies the key challenges associated with benchmarking in P2P environments. The thesis further suggests the design of a new light-weight P2P representative benchmark, by considering the source code of large P2P projects. The design outline of a new light-weight P2P representative benchmark – MalikStone – has been presented, whilst the results of MalikStone are compared with Dhrystone, Whetstone and CPU SPEC2006 and show its superiority in terms of consistency over both Dhrystone and Whetstone. For floating-point performance, MalikStone gave more representative results than Whetstone for Intel Corei5- 2400, Q9400, Q6600 and Pentium D processors with the standard deviation of repeated runs remaining less than 1 for each of the platforms. Similarly for integer operations, MalikStone also performed more consistently than Dhrystone with the standard deviation of repeated runs remaining less than 1 and gave more representative results for Corei5-2400, Q9400, Q6600 and Pentium D processors. In addition to the consistency in performance results, MalikStone captures broader performance characteristics by measuring floating-point, integer, bitwise-logic, string manipulation and programming construct operations. The performance results of MalikStone are further used for designing a new incentive unit – MalikCredit – for ensuring fairness in rewarding the project participants for their volunteer participation in large P2P projects to advance scientific research. MalikCredit is compared with BOINC’s existing incentive unit – Cobblestone, at three levels: 1) hourly level; 2) work-unit level; and 3) team-level; with the results showing fairness in rewards awarded using MalikCredit. This in turn is useful for retaining the existing project participants and attracting new volunteers for participating in large P2P projects, thereby, enhancing the application of P2P computing for solving scientific problems. A comparison of the credit values for the considered microprocessor architectures reveals that MalikCredit values are at least 2X more than Cobblestone values before normalization while the difference increases up to 3.3X for the fastest microprocessor, once normalization is applied to the claimed Cobblestones. The application of performance characterization done by MalikStone is further extended for scheduling computational resources by dynamically slicing the work-units keeping in view the available computational time of the resources and estimated execution time of the work-unit. The results of this new scheduling policy highlight their usefulness in maximizing the utilization of available computational resources when compared to BOINC’s traditional scheduling policies. The results have revealed that the policy improved the utilization of available computational resources by approximately 10% for the considered set of computational resources under the experimental setup considered in the case study (see Chapter 5). The findings of this thesis are envisaged to be primarily of significance to three main stakeholders: i) application developers; ii) project participants; and iii) project administrators. For application developers, the performance characterization done by MalikStone will be useful in exploiting the characteristics of underlying platforms for efficient execution, while at the same time supporting the improvement efforts for future versions of the software. The results will support project participants by informing them as to the amount of RAM, swap memory and main memory consumed during execution. The fairness in received rewards will encourage the existing project participants to continue participating in the lengthy execution of large P2P projects and will motivate the new volunteers to dedicate their computational resources to join large P2P projects. For the project administrators, the findings of this thesis will be useful in identifying suitable processor, operating system and hardware component configuration for best-case execution. In such a case the middleware might be instructed to postpone the allocation of work until a more effective architecture became available. Further, the newly proposed scheduling policy involving dynamic slicing of work-units based on the performance characterization of MalikStone could be deployed for improving the utilization of available computational resources. Finally, a few avenues of future research have been identified, which if explored could further enhance the appeal of this dynamic and uncontrolled P2P computing paradigm for cheaply solving complex and lengthy scientific problems that otherwise require enormous amount of financial cost as well as computational resources even exceeding that of traditional supercomputers.
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Chun, Byeongjae. "Characterization of nano-phase segregation in multicompartment micelle and its applications: Computational approaches." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/54416.
Full textAbstract:
Computational methodologies were employed to study a supramolecular micellar structure and its application, nanoreactor. This task was done through rigorous scale-up procedure using both atomistic and mesoscopic simulations. Primarily, density functional theory (DFT) calculation was used to characterize the smallest unit of complex molecules in the multicomponent mixture system. The following step involved transferring the information achieved by DFT calculation to larger scale simulation, such as molecular dynamics (MD) simulation. Lastly, based on the atomistic simulation results, we performed a series of dissipative particle dynamics (DPD) simulations to study a full body of polymeric multicompartment micelle. In the course of research, we built a systematic procedure to minimize the complexity of computation and efficiently characterize macromolecular structures and its application.
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Badieyan, Somayesadat. "Molecular Design and Mechanistic Characterization of Glycoside Hydrolases using Computational and Experimental Techniques." Diss., Virginia Tech, 2012. http://hdl.handle.net/10919/77989.
Full textAbstract:
Cellulase activity is due to the activity of multiple enzymes, including endoglucanases, cellobiohydrolases and glucosidases that work synergistically to solubilize crystalline cellulose efficiently. The dependence of hydrolysis reaction rate on temperature predicts that large increases in performance and decreased enzyme cost would be achieved if the enzymatic degradation could be operated at elevated temperatures. However there is always a tradeoff between the activity and stability of enzymes. So obtaining cellulases with high thermostability and simultaneously enhanced activity is a great challenge in the field of bioethanol production. In the studies presented in this dissertation, different computational techniques, such as Molecular Dynamics (MD), Molecular Docking, Quantum Mechanics (QM) and hybrid Quantum Mechanics and Molecular Mechanics (QM/MM), along with several site-directed mutagenesis and in vitro assays have been applied to the study and design of the activity and stability of cellulases. Using molecular dynamics to investigate the thermal unfolding of endoglucanases of family 5 of glycoside hydrolases (GH5), a good correlation between the optimum activity temperatures of cellulases and their structural fluctuations was revealed. These data led us to hypothesize that cellulase stability could be enhanced by redesign of enzyme dynamics through altering the amino acid composition in the highly flexible regions of an endoglucanase that would increase its local or global rigidity. Cellulase C, a GH5 member, was stabilized thermally and chemically by cross linking its highly flexible subdomain.
Family 1 of glycoside hydrolases were investigated by QM and hybrid QM/MM methods to analyze the role of non-catalytic polar residues at the active site of GH1 glucosidases that make hydrogen bonds to the glucose moiety at subsite -1. A tyrosine residue in simultaneous interaction with O5 of the glucose ring and the carboxylate group of the nucleophilic glutamate was found to play a significant role in the energy profile along the hydrolysis reaction coordinates. It was shown to reduce the energy barrier of the deglycosylation step by ~12 Kcal/mol. Exclusion of this tyrosine from QM calculation substantially influenced the preactivated structure of the glucose moiety in the enzyme-substrate complex and affected the structural distortion and charge distribution in transition states.Ph. D.
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Osborn, Tim H. "COMPUTATIONAL DESIGN AND CHARACTERIZATION OF SILICENE NANOSTRUCTURES FOR ELECTRICAL AND THERMAL TRANSPORT APPLICATIONS." Wright State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=wright1401712678.
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