Dissertations / Theses: 'Structural cell model'

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Dennison, Kelly J. "Development of a structural model of human T-cell leukemia virus type-I protease." Thesis, Georgia Institute of Technology, 2002. http://hdl.handle.net/1853/30060.

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Granja, Vasquez Jochen. "Analysis of Secreted Phosphoprotein-24 and its Effects During Osteoblast Differentiation in a Mesenchymal Stem Cell Model." VCU Scholars Compass, 2009. http://scholarscompass.vcu.edu/etd/1884.

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Musculoskeletal diseases, in particular osteoporosis, are increasingly becoming more prevalent in the U.S. due to the ageing population (Figure1). It is estimated that one-sixth of 300 million people in U.S. suffer from bone disorders or loss. About 10 million of those people above age 50 suffer from osteoporosis. Patients that suffer from osteoporosis have high morbidity and mortality rates. For instance, patients have decreased bone mineral density (BMD), a measurement of bone density that reflects the strength of bone as represented by calcium content. A decrease in BMD typically leads to an increased risk of bone fractures. In particular, hip fractures have an associated 20% mortality rate 1 year after injury among senior citizens 1. Patients that suffer from musculoskeletal diseases and from bone injuries, not associated with disease, account for 130 million hospital visit per year. Not to mention, 245 billion dollars of healthcare expenditure 2. Over that last 30 years, there has been much improvement in the field of bone research and its application to medicine. It has changed the quality of life and prolonged the life expectancy of patients suffering from bone disease. However, many details remain unknown about the underlying mechanism that control bone metabolism, formation, and healing. Furthermore, current effective therapies to combat bone disorders have limitations including unwanted side effects and prohibitive costs. For example, treatment with glucocorticoids which is a known inducer of osteoblastogenesis in vitro has been shown to produce an osteoporotic phenotype in vivo. Recognizing the importance of bone health and its affordability to the public makes the advancement of therapeutic targets work worth doing. Work in this field will eventually lead to the prevention, treatment, and cure for bone disease. A potential therapeutic candidate that maybe involved directly or indirectly with bone formation is secreted phosphoprotein-24 (Spp24). The following research aims to establish an importance and role for Spp24 in bone differentiation. A novel antibody that detects Spp24 which we have developed and characterized, has allowed us to feasibly study the protein. Our results demonstrate localization of Spp24 in different tissue, the processing of the protein during osteoblastogenesis, and have allowed us to conceptualize possible functions based on our data.

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Maluš, Miroslav. "Komplexní model turbulence pro různé velikosti cel." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2021. http://www.nusl.cz/ntk/nusl-442416.

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This diploma thesis is about creating a program to model turbulent cells of different sizes on the chosen transmission path. The initial part of the work is devoted to the formation of atmospheric turbulence and the mathematical description of the extent of turbulence and its effect on optical waves. The methods of the turbulence generation and their physical description of formation are described below. The practical part is devoted to the created program in the MATLAB.

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Santana, Bonilla Alejandro, Rafael Gutierrez, Sandonas Leonardo Medrano, Daijiro Nozaki, Alessandro Paolo Bramanti, and Gianaurelio Cuniberti. "Structural distortions in molecular-based quantum cellular automata: a minimal model based study." Royal Society of Chemistry, 2014. https://tud.qucosa.de/id/qucosa%3A36371.

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Molecular-based quantum cellular automata (m-QCA), as an extension of quantum-dot QCAs, offer a novel alternative in which binary information can be encoded in the molecular charge configuration of a cell and propagated via nearest-neighbor Coulombic cell–cell interactions. Appropriate functionality of m-QCAs involves a complex relationship between quantum mechanical effects, such as electron transfer processes within the molecular building blocks, and electrostatic interactions between cells. The influence of structural distortions of single m-QCA are addressed in this paper within a minimal model using an diabatic-to-adiabatic transformation. We show that even small changes of the classical square geometry between driver and target cells, such as those induced by distance variations or shape distortions, can make cells respond to interactions in a far less symmetric fashion, modifying and potentially impairing the expected computational behavior of the m-QCA.

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Minassian, Anuka [Verfasser], and Peter [Gutachter] Kloppenburg. "Stem Cell Therapy For Stroke. Modulation of structural and functional adjustments after stem cell implantation in a mouse model of cortical stroke / Anuka Minassian ; Gutachter: Peter Kloppenburg." Köln : Universitäts- und Stadtbibliothek Köln, 2018. http://d-nb.info/1200096991/34.

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Börsum, Jakob. "Estimating Causal Effects Of Relapse Treatment On The Risk For Acute Myocardial Infarction Among Patients With Diffuse Large B-Cell Lymphoma." Thesis, Uppsala universitet, Statistiska institutionen, 2021. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-447241.

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This empirical register study intends to estimate average causal effects of relapse treatment on the risk for acute myocardial infarction (AMI) among patients with Diffuse B-Cell Lymphoma (DLBCL) within the potential outcome framework. The report includes a brief introduction to causal inference and survival anal- ysis and mentions specific causal parameters of interest that will be estimated. A cohort of 2887 Swedish DLBCL patients between 2007 and 2014 were included in the study where 560 patients suffered a relapse. The relapse treatment is hypothesised to be cardiotoxic and induces an increased risk of heart diseases. The identifiability assumptions need to hold to estimate average causal effects and are assessed in this report. The patient cohort is weighted using inverse probability of treatment and censoring weights and potential marginal survival curves are estimated from marginal structural Cox models. The resulting point estimate indicates a protective causal effect of relapse treatment on AMI but estimated bootstrap confidence intervals suggest no significant effect on the 5% significance level.

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Mason, Nena Lundgreen. "The Anatomy of Porcine and Human Larynges: Structural Analysis and High Resolution Magnetic Resonance Imaging of the Recurrent Laryngeal Nerve." BYU ScholarsArchive, 2015. https://scholarsarchive.byu.edu/etd/5783.

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The recurrent laryngeal nerve (RLN) innervates all the intrinsic muscles of the larynx that are responsible for human vocalization and language. The RLN runs along the tracheoesophageal groove bilaterally and is often accidentally damaged or transected during head and neck surgical procedures. RLN palsy and vocal cord paralysis are the most common and serious post op complications of thyroid surgeries. Patients who suffer from RLN injury can develop unilateral or bilateral vocal fold paralysis (BVFP). Theoretically, selective reinnervation of the posterior cricoarytenoid muscle would be the best treatment for BVFP. The phrenic nerve has been shown in several studies to be the best candidate to anastomose to the distal end of a severed RLN to restore glottal abduction. Successful PCA reinnervation has been sporadically achieved in both human patients and in animal models. Another notable ramification of recurrent laryngeal nerve injury is vocal instability caused by the alteration of mechanical properties within the larynx. In phonosurgery, alterations to the position and framework of the laryngeal apparatus are made to improve voice quality. Accurate and realistic synthetic models are greatly needed to predict the outcome of various adjustments to vocal cord tension and position that could be made surgically. Despite the sporadically successful attempts at PCA reinnervation, thus far, there are still several deficits in our anatomical familiarity and technological capability, which hinder the regularity of successful PCA reinnervation surgeries and our capacity to generate synthetic models of the human larynx that are both realistic and functional. We will address three of these deficits in this project using the porcine larynx as a model. Firstly, we will identify the anatomical variations of the porcine recurrent laryngeal nerve branches. A microscribe digitizer will be used to create three-dimensional mapping of the recurrent laryngeal nerve branches that are relevant to the posterior cricoarytenoid muscle and the abduction of the vocal folds. Secondly, we will develop a magnetic resonance imaging technique to correlate recurrent laryngeal nerve branching patterns with high-resolution MR images that can be used to determine the branching patterns present in a given specimen without surgery. Lastly, we will determine the distribution and composition of different tissue types found within human vocal folds. High resolution MRI, and Mallory's trichrome and H&E histological staining will be used to distinguish and identify the tissue composition of the vocal folds and surrounding laryngeal structures. Detailed information regarding vocal fold tissue composition and histological geometry will enable laryngeal modelers to select more sophisticated and life-like materials with which to construct synthetic vocal fold models.

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Silparasetty, Shobha Lavanya. "Cloning of "Animal Cryptochrome" cDNA from the Model Organism CHLAMYDOMONAS REINHARDTII for Functional Analysis of Its Protein Product." TopSCHOLAR®, 2009. http://digitalcommons.wku.edu/theses/117.

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reinhardtii, a unicellular green alga, is a model organism to study the circadian clock. Cryptochromes are the blue light photoreceptors that entrain the clock in some organisms. The CPH1 protein of C. reinhardtii resembles the cryptochromes of the plant model Arabidopsis, but whether CPH1 entrains the circadian clock in C. reinhardtii is not yet known. Recent reports have suggested the existence of one more cryptochrome in C. reinhardtii, which resembles the cryptochromes of animals. However, the amino acid sequence of this protein shows even higher sequence similarity with the 6-4 DNA photolyase of Arabidopsis. DNA photolyases are involved in the repair of UV light-induced DNA damage using the energy of blue light. In order to determine, if the “animal cryptochrome” gene of C. reinhardtii actually encodes a 6-4 DNA photolyase rather than a photoreceptor, an experimental design was developed to test whether the protein product is able to rescue an E. coli mutant defective in its DNA photolyase gene. The design is as follows: In a first step, the coding region of the “animal cryptochrome” cDNA is cloned. In a second step, the cDNA is inserted in-frame into an E. coli expression vector. In a third step, the construct is transformed into an E. coli photolyase mutant, its expression induced, and the strain tested for better survival after UV light exposure. To accomplish the first step, the cloning of “animal cryptochrome” cDNA, total RNA was successfully extracted from C. reinhardtii 4 hrs into the light phase of a 12 h light/12 h dark cycle and reverse transcribed into cDNA using oligo(dT) primers. After initially unsuccessful attempts at amplifying animal cryptochrome from cDNA or genomic template with a variety of primers and conditions, a short fragment with the expected size of 186 bp was amplifiable with both templates. However, even this fragment was not reliably obtained in every PCR assay. Because of this difficulty, real-time PCR was finally performed in the presence of DMSO (Dimethylsulfoxide) and Betaine. These two adjuvants were reported to improve amplifications particularly for GC-rich templates. C. reinhardtii DNA is especially GC-rich with an average of 64% Gs and Cs. The improved conditions allowed the reliable amplification of the 186 bp fragment from genomic template. It also enabled the amplification of a larger fragment of 528 bp from the same template. The results suggest that a combination of 5% DMSO and 1M Betaine is optimal for the amplification of C. reinhardtii DNA and thus can serve as the basis for successful amplification of the entire 1788 bp coding region of the animal cryptochrome cDNA.

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Orlová, Lucie. "Výpočtové modelování mechanických zkoušek živočišné buňky." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2021. http://www.nusl.cz/ntk/nusl-443747.

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Předkládaná diplomová práce se zabývá stavbou živých živočišných buněk a jejich odezvou na mechanické zatěžování. Zobecněným zaměřením práce je popis mechanického chování buňky nejenom ve fyziologickém, ale i v patologickém stavu. Výchozím předpokladem pro úspěšné řešení zadané úlohy je vysoce interdisciplinární přístup kombinující výpočtové přístupy mechaniky těles (v~tomto případě metodu konečných prvků) s lékařským výzkumem. Nejdůležitějším bodem při tvorbě výpočtového modelu, pomocí něhož je možné aproximovat chování živé buňky při zatížení, je zejména identifikace mechanicky významných komponent a~jejich materiálových parametrů. V tomto případě jsou jako mechanicky význačné identifikovány spojité součásti jádro, membrána a cytoplazma, které jsou nově propojeny s prvky diskrétními (mitochondriální sítí) v hybridním modelu, jehož platnost je ověřena pomocí experimentálních dat. Tento model slouží jako podklad k vyhodnocení míry vlivu mitochondrií na celkovou tuhost buňky.

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Yamamoto, Akihisa. "Mesoscopic structural dynamics and mechanics of cell membrane models." 京都大学 (Kyoto University), 2015. http://hdl.handle.net/2433/198928.

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Borges, Rutz Ricardo. "Mathematical models of physiologically structured cell populations." Doctoral thesis, Universitat Autònoma de Barcelona, 2012. http://hdl.handle.net/10803/96187.

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En aquesta tesi es té en compte un model no lineal de creixement de població de cèl·lules que s'estructuren pel seu contingut de ciclina i cinases depenents de ciclina (CDK). Aquest model condueix a un sistema no lineal d'equacions en derivades parcials de primer ordre amb termes no locals. Per estudiar aquest sistema utilitzem la teoria de semigrups lineals positius i la formulació semilineal, que són eines molt poderoses per fer front a l'anàlisi d'aquest tipus de models, tant des del punt de vista del problema de valor inicial, com de l'existència i l'estabilitat d'estats estacionaris. El model que es considera a la tesi descriu la següent situació biològica: les cèl·lules s'estructuren en relació amb el contingut d'un determinat grup de proteïnes anomenades ciclines i CDK i es divideixen en dos tipus: proliferants i quiescents. Les cèl·lules proliferants creixen i es divideixen, donant a lloc al final del cicle cel·lular a noves cèl·lules, o bé van cap al compartiment de les quiescents, mentre que les cèl·lules quiescents no envelleixen ni es divideixen, ni canvien el seu contingut de ciclina, però o tornen cap al compartiment de proliferació o bé romanen en l’estat de repòs. D'altra banda, tant les cèl·lules proliferants com les quiescents poden experimentar l'apoptosi, la mort cel·lular programada. L'únic terme no lineal en el model és un terme de reclutament de cèl·lules quiescents cap a la fase de proliferació. En aquest treball demostrem l'existència global, unicitat i positivitat de les solucions del problema de valor inicial. Reescrivint el nostre sistema en una forma abstracta podem demostrar que un cert operador lineal és el generador infinitesimal d'un semigrup positiu fortament continu. D'altra banda s'utilitza la formulació semilineal estàndard per a l’equació no lineal abstracta i obtenim una única solució global positiva per a qualsevol condició inicial positiva a L1. També es prova l'existència i unicitat d'un estat estacionari no trivial del nostre sistema sota hipòtesis adequades. Com es fa sovint en situacions similars, el problema és relacionat amb provar l'existència (i unicitat) d'un vector propi positiu normalitzat. Això correspon als vectors propis del valor propi dominant d'un determinat operador lineal positiu parametritzat pel valor de la variable de feedback. L'existència tant del valor propi dominant i de (l’únic) vector propi positiu està donat per una versió del teorema de Perron- Frobenius en dimensió infinita. També s’inclouen simulacions numèriques basades en la integració al llarg de les línies característiques. Amb l'ajuda d'aquestes simulacions numèriques trobem inestabilitat de l'estat estacionari per a valors de paràmetres compatibles amb els que donen inestabilitat en el model de dimensió finita. També s'inclou la demostració de l'existència de solucions independents del contingut de ciclina per a una elecció molt particular dels valors dels paràmetres i funcions que defineixen el model. Finalment s'utilitza la formulació anomenada cumulativa (o en retard) de la dinàmica de poblacións estructurades. En particular s'ha considerat una versió diferent del model estudiat abans, on es suposa que el pas de proliferants a quiescents només pot ocórrer una sola vegada, enfocament oposat al primer model on aquestes transicions poden ocórrer infinites vegades. A més a més, també suposem que hi ha un valor particular x del contingut de ciclina que separa les cèl·lules que encara no es poden dividir de les altres que sí que poden dividir-se. L'equació del model resulta ser una equació amb retard que relaciona els valors actuals d'aquestes variables amb la seva història (el seu valor en el passat). Fent servir aquest enfocament, es pot provar l'existència i unicitat de solucions del problema de valor inicial, i el principi d'estabilitat lineal a través d'una formulació semilineal en el marc dels semigrups duals.
In this thesis we consider a nonlinear cell population model where cells are structured with respect to the content of cyclin and cyclin dependent kinases (CDK). This model leads to a first order nonlinear partial differential equations system with non local terms. To study this system we use the theory of positive linear semigroups and the semilinear formulation, which are very powerful tools to deal with the analysis of this kind of models, both from the point of view of the initial value problem as well as the existence and stability of steady states. The model considered in the thesis describes the following biological situation: cells are structured with respect to the content of a certain group of proteins called cyclin and CDK and are distributed into two types: proliferating and quiescent cells. The proliferating cells grow and divide, giving birth at the end of the cell cycle to new cells, or else transit to the quiescent compartment, whereas quiescent cells do not age nor divide nor change their cyclin content but either transit back to the proliferating compartment or else stay in the quiescent compartment. Moreover, both proliferating and quiescent cells may experiment apoptosis, i.e. programmed cell death. The only nonlinear term is a recruitment term of quiescent cells going back to the proliferating phase. In this work we start proving global existence, uniqueness and positiveness of the solutions of the initial value problem. We rewrite our system in an abstract form and show that some linear operator is the infinitesimal generator of a positive strongly continuous semigroup. On the other hand we use the standard semilinear formulation for the nonlinear (abstract) equation and obtain a unique global positive solution for any positive initial condition in L1. We also prove the existence and uniqueness of a nontrivial steady state of our system under suitable hypotheses. As it is often done in similar situations, the problem is related to proving the existence (and uniqueness) of a positive normalized eigenvector. This eigenvector corresponds to the dominant eigenvalue of a certain positive linear operator parameterized by the value of the (one dimensional) feedback variable G. The existence of both dominant eigenvalue and (unique) positive eigenvector is given by a version of the infinite dimensional Perron-Frobenius theorem. We include numerical simulations based on the integration along characteristic lines. With the help of these numerical simulations we find instability of the steady state for parameter values compatible with the ones which give instability in the finite dimensional model. We also include a computation showing the existence of cyclin-independent solutions for a very particular choice of the parameter values and functions defining the model. Finally we use the so-called cumulative or delayed formulation of the structured population dynamics. In particular we have considered a different version of the model studied before, where one assumes that proliferating cells can become quiescent only once opposed to the other approach where these transitions can occur infinitely many times and moreover, we also assume that there is a particular value x of the cyclin content that separates cells which still cannot divide from the others which are able to divide. The model equation turns out to be a delay equation relating the current values of these variables with their history (their value in the past). Using this approach, one can prove existence and uniqueness of solutions of the initial value problem, and the linear stability principle by means of a semi-linear formulation in the framework of dual semigroups.

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Al-wattar, Tahseen Abdulridha Ali. "Developing equivalent solid model for lattice cell structure using numerical approaches." Wright State University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=wright1610335304435815.

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Shaw, Alexander George. "Developing models of the mammalian cell S phase." Thesis, University of Manchester, 2011. https://www.research.manchester.ac.uk/portal/en/theses/developing-models-of-the-mammalian-cell-s-phase(3df7caaf-fd64-4bd2-b500-802f1a2c8ce2).html.

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The accurate replication of the mammalian genome is a complex and logistically challenging process. The entirety of the genome must undergo a single duplication with as little error as possible. This must occur in a coordinated fashion and over suitably short time scale so as to allow timely cellular division within a cell cycle that is typically around 24 hours in a human cell. A great wealth of knowledge already exists describing various aspects of the S phase, during which this replication of the genome occurs. This data has been gathered over a variety of model systems, ranging from inferences from the replicative mechanics of SV40 through to direct observations of replication in mammalian cells.In order integrate this data and determine the value of inferences from different data sources, quantitative models of the mammalian cell S phase are required. This study documents the development of several such models and the exploration of the influences that experimentally determined parameters and different mechanistic theories can have on the behaviour of a simulated S phase. Of particular exploratory interest were the modes of activating replication of replicon clusters, with the aim of simulating experimentally observed dynamics. Additionally, the study also aimed to investigate the variation of replication fork rates and the density of origins of replication, along with the relationship that occurs between the two during both replicational stress and during a normal S phase. Through an iterative series of models, relevant parameters and key theories are sequentially explored so as to better understand the S phase. Particularly influential parameters were identified and studied in detail, with experimental determination where necessary in order to more accurately inform the model system. Conclusions concerning the behaviour of the system and the potential impact of the results were drawn upon the completion of each level of modelling and experimental work.To conclude the study, a linear model simulating the genome of the MRC5 cell line was used to estimate the modes activation of DNA replication along chromosomes in order to recreate experimentally observed replication dynamics. Experimentally determined profiles of replication fork rates and the density of origin firing were also determined for the MRC5 cell line, and were used to populate the model with accurate and appropriate data. Using the model to simulate S phase through a variety of behavioural parameters, realistic S phase dynamics were found to occur through a combination of de novo activation of replicon clusters and a specific probability of neighbour activation by completed clusters. These derived mechanics, when performed on a system correctly parameterised with suitable data, can simulate experimentally observed phenomena. The development of the model highlighted the requirements of data fit for purpose, and the study also stresses the need for critical consideration of inferences made between different model systems.

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Ye, Zhou. "Effect of Nanoscale Surface Structures on Microbe-Surface Interactions." Diss., Virginia Tech, 2017. http://hdl.handle.net/10919/85387.

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Bacteria in nature predominantly grow as biofilms on living and non-living surfaces. The development of biofilms on non-living surfaces is significantly affected by the surface micro/nano topography. The main goal of this dissertation is to study the interaction between microorganisms and nanopatterned surfaces. In order to engineer the surface with well-defined and repeatable nanoscale structures, a new, versatile and scalable nanofabrication method, termed Spun-Wrapped Aligned Nanofiber lithography (SWAN lithography) was developed. This technique enables high throughput fabrication of micro/nano-scale structures on planar and highly non-planar 3D objects with lateral feature size ranging from sub-50 nm to a few microns, which is difficult to achieve by any other method at present. This nanolithography technique was then utilized to fabricate nanostructured electrode surfaces to investigate the role of surface nanostructure size (i.e. 115 nm and 300 nm high) in current production of microbial fuel cells (MFCs). Through comparing the S. oneidensis attachment density and current density (normalized by surface area), we demonstrated the effect of the surface feature size which is independent of the effect on the surface area. In order to better understand the mechanism of microorganism adhesion on nanostructured surfaces, we developed a biophysical model that calculates the total energy of adhered cells as a function of nanostructure size and spacing. Using this model, we predict the attachment density trend for Candida albicans on nanofiber-textured surfaces. The model can be applied at the population level to design surface nanostructures that reduce cell attachment on medical catheters. The biophysical model was also utilized to study the motion of a single Candida albicans yeast cell and to identify the optimal attachment location on nanofiber coated surfaces, thus leading to a better understanding of the cell-substrate interaction upon attachment.
Ph. D.

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Cruickshank, Mark. "Analysis of CR2/CD21 transcriptional regulation by chromatin structural variation and notch activity in human cell models." University of Western Australia. School of Biomedical, Biomolecular and Chemical Sciences, 2007. http://theses.library.uwa.edu.au/adt-WU2007.0115.

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[Truncated abstract] Human complement receptor 2 (CR2/CD21) is a cell surface glycoprotein detected on specific cells involved in immunity, which binds complement C3 cleavage fragments, cellular ligands IFN-? and CD23 as well as the EBV coat protein, gp350/220. During the early stages of B-cell development CR2/CD21 is silenced. Expression is initiated on immature B-cells escaping negative selection. During peripheral maturation CR2/CD21 is up-regulated with B-cell sub-populations showing distinctive surface levels (comparatively low, intermediate or high). CR2/CD21 is silenced upon terminal plasmacytic differentiation. Appropriate timing and expression level of CR2/CD21 is important for the development of a healthy B-cell repertoire. Previous studies have identified sequences within the proximal promoter and first intron of CR2/CD21 that cooperate within native chromatin to control cell-specific silencing. Further, analysis of cultured human cells has revealed chromatin structural variation causing DNase I hypersensitivity at these regulatory sites in a CR2/CD21-expressing mature B-cell line (Raji) which are absent in a non-lymphoid cell type (K562). The primary focus of the present study involved characterising chromatin structural variation over previously recognized DNase I hypersensitive regions at the CR2/CD21 locus in human cells to understand how chromatin structure might regulate developmental expression of CR2/CD21. ... These studies provide evidence that notch signaling influences CR2/CD21 expression in human cell lines. First, in vivo binding of CBF1 to CR2/CD21 sequences in the proximal promoter and CRS implies that CR2/CD21 is a direct target of notch activation. Second, the effect of exogenous notch signalling molecules on CR2/CD21 proximal promoter activity was modulated by factors binding tandem E-boxes near the transcriptional start site suggesting that the notch pathway may also influence CR2/CD21 expression via control of HLH molecules. Third, initiation of CR2/CD21 expression was observed in a nonexpressing pre-B cell line (Reh) by co-culture with stromal cells expressing a notch ligand (OP9-DL) but not control stroma (OP9-GFP). Together, these findings support a role for notch regulation of B-cell maturation and invite speculation that initiation of CR2/CD21 expression following negative selection of immature B-cells involves crosstalk between HLH transcriptional regulators and the notch pathway. Furthermore, the Reh/OP9-DL co-culture system may provide a model to directly study the relationship between cell signalling molecules, transcription factor regulation, chromatin structural variation and differentiation of B-cells.

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Callow, Philip Austin. "Cationic lipid : DNA complexes - their structure and interactions with model cell membranes." Thesis, King's College London (University of London), 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400591.

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Daukste, Liene. "Mathematical Modelling of Cancer Cell Population Dynamics." Thesis, University of Canterbury. Department of Mathematics and Statistics, 2012. http://hdl.handle.net/10092/10057.

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Mathematical models, that depict the dynamics of a cancer cell population growing out of the human body (in vitro) in unconstrained microenvironment conditions, are considered in this thesis. Cancer cells in vitro grow and divide much faster than cancer cells in the human body, therefore, the effects of various cancer treatments applied to them can be identified much faster. These cell populations, when not exposed to any cancer treatment, exhibit exponential growth that we refer to as the balanced exponential growth (BEG) state. This observation has led to several effective methods of estimating parameters that thereafter are not required to be determined experimentally. We present derivation of the age-structured model and its theoretical analysis of the existence of the solution. Furthermore, we have obtained the condition for BEG existence using the Perron-Frobenius theorem. A mathematical description of the cell-cycle control is shown for one-compartment and two-compartment populations, where a compartment refers to a cell population consisting of cells that exhibit similar kinetic properties. We have incorporated into our mathematical model the required growing/aging times in each phase of the cell cycle for the biological viability. Moreover, we have derived analytical formulae for vital parameters in cancer research, such as population doubling time, the average cell-cycle age, and the average removal age from all phases, which we argue is the average cell-cycle time of the population. An estimate of the average cell-cycle time is of a particular interest for biologists and clinicians, and for patient survival prognoses as it is considered that short cell-cycle times correlate with poor survival prognoses for patients. Applications of our mathematical model to experimental data have been shown. First, we have derived algebraic expressions to determine the population doubling time from single experimental observation as an alternative to empirically constructed growth curve. This result is applicable to various types of cancer cell lines. One option to extend this model would be to derive the cell cycle time from a single experimental measurement. Second, we have applied our mathematical model to interpret and derive dynamic-depicting parameters of five melanoma cell lines exposed to radiotherapy. The mathematical result suggests there are shortcomings in the experimental methods and provides an insight into the cancer cell population dynamics during post radiotherapy. Finally, a mathematical model depicting a theoretical cancer cell population that comprises two sub-populations with different kinetic properties is presented to describe the transition of a primary culture to a cell line cell population.

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Xiao, Long. "A structural micromechanical model of large deformation behavior of red blood cells." Connect to online resource, 2008. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:1458440.

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Magzoub, Mazin. "Cell-penetrating peptides in model membrane systems : interaction, structure induction and membrane effects /." Stockholm : Institutionen för biokemi och biofysik, Univ, 2004. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-247.

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Williams, Katherine Spring. "Anti-Cancer Treatment and the Cell Cycle: Cellular-Level Mathematical Models." Diss., The University of Arizona, 2016. http://hdl.handle.net/10150/613282.

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This dissertation presents a collection of mathematical models for cellular response to the most common forms of anti-cancer therapy (radiation and chemotherapy) and the role of the cell cycle in this response. These models have application to improving cancer therapy through: optimization of dose and scheduling of agents already in clinical use; better predictive methods for selecting the most promising among new drug candidates or candidate combinations; and combination therapy with newer agents that target the cell cycle or cellular metabolism. The cellular pharmacodynamic models are based on the key concept of "cellular damage" that results from exposure to therapy and has distinct kinetics from cell kill. Damage is lethal only if it exceeds a cell's tolerance threshold at one or more checkpoints in the cell cycle (for apoptosis) or at any time point (for necrosis). This is the "peak damage" model. Each mechanism of cell kill, each agent in combination therapy, and each cycle in fractionated therapy increases the damage function (the "additive damage" model). The overall framework is termed the "peak additive damage model." This model framework is first tested on 128 independent in vitro dose-response data sets for radiation alone. It outperforms previously proposed models, including the widely-used linear-quadratic model. The peak additive damage model is then applied to radiochemotherapy. Its performance is superior to the previously proposed independent cell kill model when tested with 218 data sets for fixed-schedule exposure against. For varying-schedule exposures, cell heterogeneity and cycle asynchrony necessitate a cell-cycle-phase-structured model that divides the population into cohorts with different responses, still determined for each cohort by the peak additive damage model, that are then averaged. This model simultaneously predicts dose-response and cell cycle distribution data, and is tested with such data from the literature. Finally, a first step is taken towards allowing for microenvironmental input into cellular response, by developing a model for the cell cycle that is driven by metabolic inputs and external growth factors. Overall, the models presented here have great flexibility to be extended to complex schedules, any number of agents, and agents with metabolic or cell-cycle targets.

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Krbálek, Jaroslav. "Určování elastických parametrů pro modely izolovaných buněk." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2010. http://www.nusl.cz/ntk/nusl-229369.

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This diploma thesis focuses on computational modeling of the cell mechanical tests. The goal of this thesis is to build a cell model and to simulate compression test on this model. If necessary, the model should be adjusted so the model reflects real cell behavior. It was created the cell model reflecting cytoplasm, nucleus, membrane and cell cytoskeleton. Cytoskeleton was modeled as tensegrity structure. After this, the pressure test was simulated on this model. The behavior of the cell model and real cell was compared using the stress force. The stress force - cell deformation curve was markedly different for the cell model and the real cell. For this reason, the cytoplasm material model was adjusted. The difference between the curves was acceptable after this modification. It was found during computations that the cytoskeleton model influence on the cell load is minimal. These results does not reflects real cell behavior, which means that the model is considered inadequate for performing stress load simulation.

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Reynolds, Catherine Jane. "T cell receptor structure and cytokine responses in lung targeted inflammatory models." Thesis, Imperial College London, 2008. http://hdl.handle.net/10044/1/11884.

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Redfearn, James C. "A Comprehensive Model of the Structure and Function of the FtsZ Ring of Escherichia coli." Kent State University / OhioLINK, 2016. http://rave.ohiolink.edu/etdc/view?acc_num=kent1460475643.

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林德華 and Tak-wah Lam. "Topological data structure and algorithms for cell-complex based non-manifold form feature modeling." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 1994. http://hub.hku.hk/bib/B3121244X.

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Lam, Tak-wah. "Topological data structure and algorithms for cell-complex based non-manifold form feature modeling /." Hong Kong : University of Hong Kong, 1994. http://sunzi.lib.hku.hk/hkuto/record.jsp?B19672214.

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KC, Rabi. "Study of Some Biologically Relevant Dynamical System Models: (In)stability Regions of Cyclic Solutions in Cell Cycle Population Structure Model Under Negative Feedback and Random Connectivities in Multitype Neuronal Network Models." Ohio University / OhioLINK, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou16049254273607.

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27

Zhao, Lingyin. "Generalized Frequency Plane Model of Integrated Electromagnetic Power Passives." Diss., Virginia Tech, 2004. http://hdl.handle.net/10919/27692.

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The challenge to put power electronics on the same cost reduction spiral as integrated signal electronics has yet to be met. In the ongoing work for achieving complete power electronic converter integration, it has proven to be essential to develop a technology for integration of electromagnetic power passives. This integration will enable the incorporation of resonant circuits, transformers, EMI filters and the like into the integrated power electronics modules. These integrated electromagnetic power passives have been realized in terms of distributed structures, utilizing magnetic layers, conductive layers and dielectric layers. Because of the compact structures and the special implementation techniques of these integrated modules, the high frequency parasitic resonance are normally significant and may have negative impact on the performance and EMI characteristics. However, the existing modeling technique can only predict the fundamental resonant frequency and showed neither the causes of the high frequency resonance nor how to calculate those accurately. In this dissertation, comprehensive research work towards higher order electromagnetic modeling of integrated passive components is presented. Firstly, an L-C cell is identified as the basic building block of integrated passives such as an integrated series resonator. As an essential mistake in the structure evolution process of the original resonant transmission line primitive, the well-known conventional transmission line equivalent circuit as well as the equations are not applicable for the unbalanced current in an integrated passive module. For this particular application, a generalized transmission structure theory that applies to both balanced and unbalanced current has to be developed. The impedances of a generalized transmission structure with various loads and interconnections have been studied. An open-circuited load and a short-circuited load lead to series resonance and parallel resonance, respectively. The equations are substantiated with experimental results. Some preliminary study indicates the advantages of this unbalanced current passives integration technique. Since the existing integrated passive components are no other than some combination of this generalized transmission line primitive, the theoretical analysis may be applied to the further modeling of all integrated passive components. As the extension of the generalized two-conductor transmission structure model developed for the two-conductor approach, the generalized multi-conductor transmission structure theory has been proposed. As multiple L-C cells are putting in parallel, magnetic and capacitive coupling between cells cannot be neglected. To determine the capacitance between two adjacent conductors on top of the same dielectric substrate, Schwarz-Christoffel transformation and its inverse transformation have been applied with the calculation results verified by measurement. Based on the original voltage and current equations written in matrix form, modal analysis has been conducted to solve the equations. All these provide the basis for any further modeling of an integrated passive structure. Based on the basic L-C cell structure, this dissertation proposes an alternative multi-cell approach to the integration of reactive components and establishes the principles for its design and operation. It achieves the 3-D integration and has a PCB-mount chip-like structure which may have the potential to be more manufacturable, modularizable and mechanically robust. Different functional equivalents can be obtained by different PCB interconnections. The experimental results confirm the functionality as integrated reactive components for applications such as high frequency resonators. To apply the multi-conductor generalized transmission structure model to practical integrated passives structures, three typical cases have been studied: spiral-winding structure integrated series resonator, multi-cell structure integrated series resonator and integrated RF EMI filter. All these structures can be treated as one or more multi-conductor transmission structures connected in certain patterns. Different connection patterns only determine the voltage and current boundary conditions with which the equations can be solved. After obtaining the voltages and currents at each point, the impedance or transfer gain of a structure can be obtained. The MATLAB calculation results correlate well with the measurement results. The calculation sensitivities with respect to variation of various parameters are also discussed and causes of resonance at different frequency range are identified. The proposed generalized transmission structure model based on matrix modal analysis is rather complex and takes a lot of computer time especially when the number of turns is large. Furthermore, the operating frequency of an integrated resonant module is normally around its 1st resonant frequency and up to the 2nd resonant frequency. Therefore, a more simplistic higher order lumped element model which covers the operating range up to the 2nd resonant frequency may be good enough for the general design purpose. A higher order equivalent circuit model for integrated series resonant modules as an example of integrated power passives is presented in this dissertation. Inter-winding capacitance is also considered compared to the conventional 1st order approximation model. This model has been verified by small-signal test results and can be easily implemented into the design algorithm as part of the high frequency design considerations. The wide band modeling and proposed new structure mentioned above provide a comprehensive basis for better design of integrated passive components. As a general frequency plane modeling approach, the work presented in this dissertation may be extended to other passive structures, such as multi-layer capacitors, planar magnetics, etc..
Ph. D.

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Rosich, Oliva Albert. "Sensor placement for fault diagnosis based on structural models: application to a fuel cell stak system." Doctoral thesis, Universitat Politècnica de Catalunya, 2011. http://hdl.handle.net/10803/53635.

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The present work aims to increase the diagnosis systems capabilities by choosing the location of sensors in the process. Therefore, appropriate sensor location will lead to better diagnosis performance and implementation easiness. The work is based on structural models ands some simplifications are considered in order to only focus on the sensor placement analysis. Several approaches are studied to solve the sensor placement problem. All of them find the optimal sensor configuration. The sensor placement techniques are applied to a fuel cell stack system. The model used to describe the behaviour of this system consists of non-linear equations. Furthermore, there are 30 candidate sensors to improve the diagnosis specifications. The results obtained from this case study are used to strength the applicability of the proposed approaches.
El present treball té per objectiu incrementar les prestacions dels diagnosticadors mitjançant la localització de sensors en el procés. D'aquesta manera, instal·lant els sensors apropiats s'obtenen millors diagnosticador i més facilitats d'implementació. El treball està basat en models estructurals i contempla una sèrie de simplificacions per tal de entrar-se només en la problemàtica de la localització de sensors. S'utilitzen diversos enfocs per tal de resoldre la localització de sensors, tot ells tenen com objectiu trobar la configuració òptima de sensors. Les tècniques de localització de sensors són aplicades a un sistema basat en una pila de combustible. El model d'aquest sistema està format per equacions no lineals. A més, hi ha la possibilitat d'instal·lar fins a 30 sensors per tal de millorar la diagnosis del sistema. Degut a aquestes característiques del sistema i del model, els resultats obtinguts mitjançant aquest cas d'estudi reafirmen l'aplicabilitat dels mètodes proposats.

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Clark, Francis. "A computational study of gene structure and splicing in model eukaryote organisms /." St. Lucia, Qld, 2003. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe17395.pdf.

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Garvey, Cathryn E. "Cloning, Expression, and Characterization of Ara h 3, a Major Peanut Allergen." ScholarWorks@UNO, 2012. http://scholarworks.uno.edu/td/1565.

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Abstract There are eight foods that contribute to food allergies in the western world and peanut is the most common. Currently, there are no medical treatments that can cure an individual of food allergy, so avoidance of the allergic food is the only option. In the United States, there are three immunodominant allergic proteins accountable for patient sensitization to peanut, Arachis hypogea 1, 2, and 3 (Ara h 1, Ara h 2, Ara h 3). Therefore, research into why peanuts are more allergic than other foods that have homologous proteins is critical and may be obtained by studying the structural and allergenic properties of individual allergens and the changes that occur due to food processing. In this study, the basic and acidic subunits of Ara h 3 were cloned, expressed, and purified, and compared with each other and with the native Ara h 3 purified from peanut for differences in binding to IgE from peanut allergic individuals. Also, an in vitro Maillard reaction was performed on purified native raw Ara h 3 and patient serum IgE western blots were performed. This study concluded that an in vitro Maillard reaction enhanced IgE binding to Ara h 3, IgE binding to native Ara h 3 was in most cases higher than to the recombinant Ara h 3 subunits, and recognition of the acidic subunit was much higher than the and basic subunits in both the recombinant and native forms of the protein were investigated. Keywords:

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31

Leon, Ronald P. "Structural and functional analysis of MCM helicases in eukaryotic DNA replication /." Connect to full text via ProQuest. Limited to UCD Anschutz Medical Campus, 2007.

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Thesis (Ph.D. in Biophysics & Genetics, Program in Molecular Biology) -- University of Colorado Denver, 2007.
Typescript. Includes bibliographical references (leaves 90-98). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;

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32

Derivi, Alexandre Guimarães. "Correlações eletrostáticas e de tamanho em um modelo de cela para dispersões coloidais." reponame:Biblioteca Digital de Teses e Dissertações da UFRGS, 2008. http://hdl.handle.net/10183/12664.

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Dispersões coloidais estão presentes em muitas aplicações industriais e biológicas, tais como indústria de alimentos, cosméticos, produtos farmacêuticos e nanoestruturas. Devido a efeitos entrópicos, macromoléculas, quando imersas em uma solução de partículas pequenas, tendem a se aglomerar. Para evitar este fenômeno, cargas são adicionadas à superfície do colóide. Conseqüentemente, para manter o sistema neutro, a solução contém uma série de pequenos contraíons que neutralizam a carga do colóide. A inclusão de cargas pode evitar a aglomeração dos colóides, mas incorpora ao problema uma série de novos efeitos de natureza eletrostática. Todos estes efeitos, bem como o comportamento termodinâmico do sistema, no entanto, podem ser compreendidos analisando-se a distribuição de contraíons ao redor do colóide. Uma teoria muito simples que fornece esta distribuição de contraíons é a teoria de Poisson Boltzmann, na qual os contraíons são partículas pontuais e as interações eletrostáticas entre os íons são obtidas via potencial médio criado por todos os íons sobre um determinado contraíon, desconsiderando, desta forma, as correlações. Nesta tese respondemos à pergunta: quando correlações eletrostáticas e de tamanho são relevantes? Propusemos que correlações eletrostáticas são relevantes quando as interações eletrostáticas entre íos superam os efeitos entrópicos, ou seja, quando o parâmetro de plasma está acima de um certo limiar, G2d > 2. Sugerimos, também, que o tamanho dos íons torna-se relevante quando a fração de volume dos contraíons na superfície do colóide está acima de um limiar, ou seja, fs > 0,2. As duas propostas são testadas comparando-se os resultados obtidos via teoria de Poisson Boltzmann com os resultados provenientes de simulações. Em seguida, empregamos a teoria de Debye-Hückel Buraco Cavidade para incorporar correlações eletrostáticas. Comparamos os resultados obtidos via esta teoria com os resultados de simulações. Mostramos que a incorporação dos efeitos de correlações eletrostáticas resultam em um maior número de contraíos próximos à superfície do macroíon do que o observado via teoria de Poisson Boltzmann. Depois, introduzimos duas teorias de funcionais de densidade ponderada que incluem efeitos de correlações de tamanho: funcional de densidade ponderada com um peso baseado na teoria Debye-Hückel Buraco Cavidade e uma funcional de densidade ponderada com um peso constante. Comparamos os resultados obtidos através destas duas teorias com simulações, e observamos que a segunda teoria apresenta uma melhor concordância com as simulações. De maneira geral, as correlações de tamanho deixam os íons mais afastados do colóide do que o predito via teoria de Poisson Boltzmann. Finalmente, propusemos uma combinação da teoria Debye-Hückel-Buraco-Cavidade e funcional de densidade ponderada com um peso constante para tratar de problemas onde tanto correlações eletrostáticas como de tamanho se façam presentes. Observamos que para G2d < 2 e fs < 0,2 a teoria mista fornece os mesmos resultados que a teoria de Poisson Boltzmann; para G2d > 2 e fs < 0,2 a teoria mista fornece os mesmos resultados que a teoria Debye-Hückel-Buraco-Cavidade, pois somente correlações eletrostáticas são relevantes; para G2d < 2 e fs > 0,2 a teoria mista oferece o mesmo resultado que a teoria funcional de densidade ponderada com um peso constante; para G2d ≈ 2 e fs ≈ 0,2 ocorre uma compensação entre efeitos e a teoria mista fornece o mesmo resultado que a teoria de Poisson Boltzmann. Para G2d > 2 and fs > 0,2 efeitos de tamanho dominam e a teoria mista oferece os mesmos resultados que a teoria da funcional de densidade ponderada com umpeso constante.
Colloidal dispersions are present in many industrial and biological applications going from food, cosmetics, pharmaceutical and nanostructures. Due to entropic effects the large macromolecules in a solvent made of small particles, agglomerate. In order to avoid this effect, charged groups are added to the colloidal surface. Consequently in order to keep the charge neutrality the solution is full of counterions. The addition of charges might stop agglomeration but adds a number of new phenomena that are deeply related to the distribution of the counterions around the macroion. One simple theory that describes this distribution is the Poisson Boltzmann approach in which the counterions are assumed to be point ions and where the electrostatic interactions between the counterions are taken into account as the average field on a singel ions, ignoring correlations. In this thesis we address the question; when does electrostatic correlations and the size of the counterions are relevant? We propose that electrostatic correlations are relevant when the electrostatic interactions between the ions are bigger than the entropic effects. This assumption can be expressed by the plasma parameter being above a certain threshold, G2d > 2. We also propose that the size of the counterions become relevant when the volume fraction of ions at the surface of the colloid is above a certain threshold fs > 0.2. This two propositions are tested comparing results obtained with the PB theory with simulations. We then propose a theory to take into account the electrostatic correlations, the Debye-Hückel-Hole-Cavity and test this approach with simulations. The electrostatic correlation leads to more ions close to the colloid than the Poisson Boltzmann predicts. Next, we present two different approaches to account for size effects, the Weight Density Approximation based in the Debye-Hückel-Hole-Cavity theory and the Weight Density Approximation based in a constant weight. Comparison with simulations show that the second approach gives a better agreement. The size correlations leads to less ions close to the colloid than the Poisson Boltzmann approach predicts. Finally we propose a combination of the Debye-Hückel-Hole-Cavity and the Weight Density Approximation based in a constant weight to be the theory able to take into account both electrostatic and size correlations. Our result shows that for G2d <2 and fs <0.2 electrostatic and size correlations are irrelevant so Poisson Boltzmann is a good approach; for G2d > 2 and fs < 0.2 electrostatic correlations dominates and Debye-Hückel-Hole-Cavity gives a good approach; G2d < 2 and fs > 0.2 the Weight Density Approximation based in a constant weight gives the correct behavior; for G2d ≈ 2 and fs ≈ 0.2 the electrostatic correlation effects cancel the size effects and Poisson Boltzmann gives a good approximation. For G2d > 2 and fs > 0.2 size effects dominate.

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Chen, Song. "Design, synthesis and characterization of A-D-A structural porphyrin small molecules for bulk heterojunction organic solar cell applications." HKBU Institutional Repository, 2017. https://repository.hkbu.edu.hk/etd_oa/477.

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Bulk heterojunction organic solar cells (BHJ OSCs) have been recognized as one of the most promising next generation green technology alternatives to inorganic solar cells because of the low-cost, lightweight, flexibility. Specifically, the use of small molecules instead of polymers as donors in BHJ OSC have been developed very fast recently because small molecules can be facilely synthesized and easily purified, and have a determined molecular structure without batch-to-batch variations. To date, those among the most efficient small molecules were constructed as acceptor-donor-acceptor (A-D-A) structural configuration from electron-rich units such as benzodithiophene (BDT), dithienosilole (DTS), oligothiophene units, and electron-deficient units such as benzothiadiazole (BT), diketopyrrolopyrrole (DPP), isoindigo (IID) and perylenediimide (PDI). Surprisingly, porphyrins were rarely studied either in polymers or π-conjugated small molecules as donor materials, though they have unique chemistry together with excellent photochemical and electrochemical properties, such as facile functionalization of the periphery and the variation of the central atom (metal ions), strong UV-visible absorption, ultrafast photoinduced charge separation in porphyrin-fullerene systems. In this research work, we design, synthesize and characterize new porphyrin-based small molecules with acceptor-donor-acceptor (A-D-A) configuration for bulk heterojunction organic solar cells, and investigate their structure-property relationships, specifically the effect of peripheral and backbone alkyl side-chains, π-conjugated linkers as well as electron-deficient ending units on the charge mobility, film morphology and solar cell performances. In Chapter 1, a general review on the historic and recent development of BHJ OSCs was given first, including the major components and working principle of OSC, the versatile organic semiconductors and their performances in OSCs. In chapter 2, six A-D-A structural porphyrin small molecules were designed and synthesized, in which different peripheral alkyl substitutions are attached to the meso-position of porphyrin core (CS-I, CS-II, CS-III, CS-4, CS-5 and CS-6), and 3-ethylrhodanine is used as terminal group. Their UV-visible absorption in solid, energy level, blend film morphology, charge mobility and cell performance are dependent on the different peripheral substitutions. The active layer consists of these six small molecules as donor materials and PC71BM as the acceptor material with an optimized film thickness. Although all six molecules show similar optical spectrum in solutions, the introduction of linear alkyl side chains can promote thin-film nanostructural order, especially shown to shorten π-π stacking distances between backbones and increase the correlation lengths of both π-π stacking and lamellar spacing, leading to higher efficiency in this serial. Among them, the highest power conversion efficiency of 9.09% has been achieved by CS-4 based devices. In chapter 3, another two new A-D-A porphyrin small molecules (PTTR and PTTCNR) have been developed, which are similar in structure to CS-I, II and III, except that the linker is phenylethynyl in CS-I, II and III, whereas it is terthiophenylethynyl in PTTR and PTTCNR. The highest power conversion efficiency of 8.21% is achieved by PTTCNR, corresponding to a JSC of 14.30 mA cm−2, VOC of 0.82 V, and FF of 70.01%. The excellent device performances can be ascribed to the conjugated structure of porphyrin with 3,3''-dihexyl-terthiophene and the aliphatic 2-octylundecyl peripheral substitutions, which not only effectively increase the solar flux coverage between the conventional Soret and Q bands of porphyrin unit, but also optimize molecular packing through polymorphism associated with side-chain and the π-conjugated backbones, and form the blend films with [6,6]-phenyl-C71-butyric acid methyl ester (PC71BM) characteristics of bi-continuous, interpenetrating networks required for efficient charge separation and transportation.;In chapter 4, we designed and synthesized a new dimeric porphyrin donor molecule (CS-DP) containing A-π2-D-π1-D-π2-A architecture by coupling of two zinc porphyrin cores through ethynyl linker. Interestingly, it can harvests the photons up to deep near-infrared (NIR) region in the absorption spectrum. From the past decades, it has been found that developing donor molecules with the absorption spectral in NIR region is a challenging key factor to get the high performance BHJ OSCs. Solar cell devices employing CS-DP as a donor exhibit a highest power conversion efficiency of 8.23%, corresponding to JSC = 15.14 mA cm-2, VOC = 0.781 mV and FF = 69.8% under AM 1.5G solar radiation. The high efficiency of this molecule is attributed to a panchromatic IPCE action spectrum from 300 nm to 1000 nm. Also, this performance is best for the reported deep NIR organic solar cells based on single small molecule and PC71BM system so far. We envision that this new small bandgap dimeric porphyrin is very promising to use in ternary and multi-junction applications as well as NIR photodetectors. In chapter 5, a series of new A-D-A structural porphyrin small molecules (CS-10, CS-11 and CS-12) have been prepared, that contain the same meso-thienyl-thioalkyl substituted porphyrin core and 3-ethylrhodanine ending unit, but varies with different numbers of phenylethynyl linker. Using them as donors for solution-processed organic solar cells, the device based on CS-10 featuring single phenyl ethynyl π-linker exhibits high power conversion efficiency (PCE) of 7.0%. The results indicate that meso-thienyl-thioalkyl substitution and controlled π-linker length is beneficial to tune the optoelectronic properties, film morphology and consequently performance of porphyrin-based BHJ OSCs. In chapter 6, two symmetrical tetra-meso-substituted porphyrin molecules (ZnP and CuP) have been prepared in gram-scale through the direct condensation of pyrrole and 4-[bis(4-methoxyphenyl)amino]benzaldehyde. Its Zn(II) and Cu(II) complexes exhibit excellent thermal and electrochemical stability, specifically, high hole mobility and very favorable energetics for hole extraction that render them attractive for implementation as new hole transporting materials in organometallic halide perovskite solar cells (PSCs). As expected, the use of ZnP as HTM in PSCs affords a competitive PCE of 17.78%, which is comparable to the most powerful HTM of Spiro-OMeTAD (18.59%) under the same working conditions. Meanwhile, the metal centers affect somewhat the photovoltaic performances that CuP as HTM produces a relative lower PCE of 15.36%. Notably, the perovskite solar cells employing ZnP show longer stability than that of Spiro-OMeTAD. Moreover, the two porphyrin-based HTMs can be prepared from relatively cheap raw materials with a facile synthetic route. The results demonstrate that ZnP and CuP can be a new class of HTMs for efficient and stable perovskite solar cells. To the best of our knowledge, this is the highest performance for porphyrin-based perovskite solar cells with PCE > 17%. The dissertation was completed with conclusions and outlooks in chapter 7.

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34

Hall, Catherine Jane. "Comparisons of solution structures of free and IL-1β bound Fab suggests a model for B cell receptor signalling." Thesis, University of Leicester, 2010. http://hdl.handle.net/2381/28119.

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Therapeutic antibodies are an important and growing class of biotherapeutics with the potential to treat a range of major human diseases. Structural knowledge of the complexes formed between antibodies and target proteins would provide valuable information about the mode of action of the therapeutic and potentially reveal a structural mechanism underlying antigen induced B cell receptor signalling. Often the Fab fragment of the antibody is used in therapeutics, however, there are currently no NMR-based structures available for Fab or Fab/antigen complexes, presumably due to the difficulties of producing suitable samples and obtaining NMR data for large proteins and complexes. The work described here illustrates the development of approaches that have made it possible to obtain high quality NMR-based structures for the gIC8 Fab alone and in complex with its antigen, IL-1β, including the development of approaches that allow the measurement of reliable RDC data. Expression and purification of a [superscript 15]N/[superscript 13]C/[superscript 2]H-labelled gIC8 Fab fragment allowed for collection of triple resonance data for the free Fab and over 90% of the visible backbone resonances to be assigned. A refined homology model of the free gIC8 Fab and a docked and refined structure for the gIC8 Fab/IL-1β complex were obtained using experimental NMR restraints. Comparisons made between the free and bound Fab structures highlight small antigen induced changes in domain orientation, which suggest a mechanism for B cell receptor signalling. The work reported here shows that NMR spectroscopy can be used as a tool to obtain detailed structural data for large Fab and Fab-target protein complexes and provide an improved understanding of how antibodies interact with their target proteins.

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Kovari, Daniel T. "Investigations of the spreading and closure mechanisms of phagocytosis in J774a.1 macrophages." Diss., Georgia Institute of Technology, 2015. http://hdl.handle.net/1853/54882.

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Phagocytosis is the process by which cells engulf foreign bodies. It is the hallmark behavior of white blood cells, being the process through which those cells ingest and degrade pathogens and debris. To date a large amount of research has focused on documenting the existence and role of biochemical components involved with phagocytosis. Scores of signaling molecules have been implicated in the complex signal cascade which drives the process. These molecules are small (typically no larger than 5 nanometers) and operate in a crowded, chemically “noisy,” environment, yet they coordinate the cell's activity over comparatively expansive distances (as large as 20 micrometers). How these molecular processes scale-up to coordinate the activities of the cell over such massive distances is largely unknown. Using a planar analog of phagocytosis termed “frustrated phagocytosis,” we experimentally demonstrate that phagocytosis occurs in three distinct phases: initial cell-antigen binding, symmetric spreading, and late-stage contraction. Initial binding and symmetric spreading appears to be both mechanically and chemically similar to the quasi-universal cellular behaviors of adhesion and migration. Adhesion and migration have received extensive attention from the biophysics community in recent years. Leveraging these similarities, we adapt the biomechanical frameworks used in models of migration to phagocytosis. We show that macroscopic properties such as a cell's effective viscosity and membrane cortical tension can be used to model cell behavior during phagocytosis. Our experiments reveal that late-stage contraction distinguishes frustrated phagocytosis from other spreading behaviors. This contraction is myosin dependent. Additionally we demonstrate, for the first time, that late-stage contraction corresponds with formation of a contractile F-actin belt. Based on the dynamic contraction model (DC) developed to explain actin structure during cell migration we propose a DC model of phagocytosis which posits that contractile belt formation is the result of a late-stage myosin activity coupled with F-actin.

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Bauer, David. "Využití tensegritních struktur pro modelování mechanického chování hladkých svalových buněk." Master's thesis, Vysoké učení technické v Brně. Fakulta strojního inženýrství, 2011. http://www.nusl.cz/ntk/nusl-229836.

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The master’s thesis deals with the computational modelling of the mechanical testing of isolated smooth muscle cells. The main aims are to create computational model of a cell, to simulate single-axis tensile test and to modify the model so that the model reflects real mechanical response. The model of the cell includes cytoplasm, nucleus, cell membrane and cytoskeleton which is modelled as a tensegrite structure. On this model the tensile test was simulated in case of the cell with cytoskeleton and the cell with distributed the cytoskeleton. Force-elongation curves, which were obtained from this simulation, were compared with experimental data which were taken from literature. Tensile properties were measured on freshly isolated cells from rat thoracic aorta, cultured cells, and cells treated with cytochalasin D to disrupt their actin filaments. It was found that the cytoskeleton influence on the cell load in computational model was smaller than in the real cell. Therefore the model was modified by changing material propreties and geometry so that the model of the cell corresponded with the different types of experimentally measured cells.

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Chang, Samuel Fu-Min. "A development and evaluation of the new pastoral structure and lay person training model among the Taiwan cell group church." Online full text .pdf document, available to Fuller patrons only, 2002. http://www.tren.com.

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38

Schuster, Simon [Verfasser], and Stefan [Akademischer Betreuer] Zahler. "Models for angiogenesis on micro-structured surfaces : a novel view on endothelial cell biology / Simon Schuster. Betreuer: Stefan Zahler." München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2016. http://d-nb.info/109312492X/34.

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Aquino, José Miguel Redondo de. "Methods for the prediction of effective properties of metal foams." Master's thesis, Universidade de Aveiro, 2016. http://hdl.handle.net/10773/22354.

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Mestrado em Engenharia Mecânica
Given their unique properties, there is an increasing interest in using metal foams. In order to expand the usage of these materials, there is a great need to accurately characterize their effective properties. However, there is a great difficulty in predicting the properties of these inhomogeneous materials due to their irregularities and micro defects. The scope of this work is precisely to find analytical models or numerical methods that can describe the behaviour of metallic foams in an elastic regime. To do this, numerical methods and analytical models provided by previous works, were used. To apply the numerical methods, it was necessary to model representative unitcell geometries. Based on previous works results, the selected geometries were the Kelvin and the Weaire-Phelan structures. With these it was possible to model closed-cell and open-cell representative unit-cells. The open and closed-cell geometries were then subjected to three numerical methods, symmetry boundary conditions with a prescribed force, symmetry boundary conditions with an imposed displacement and asymptotic expansion homogenization. The two methods that use symmetry boundary conditions were analysed in Femap software and the Asymptotic Expansion Homogenization, which uses periodic boundary conditions, was analysed with main-FRAN program. It is known that the relative density is the characteristic that has bigger influence on metal foams stiffness. As the analytical models relate the relative Young’s modulus with the relative density, in this work this relation was also obtained for each numerical method. The numerical results were then compared to the analytical models and to experimental results.
Dadas as suas propriedades únicas, existe um interesse crescente em utilizar espumas metálicas. De forma a globalizar a utilização destes materiais, há uma grande necessidade de caracterizar com precisão as suas propriedades efetivas. Contudo, há uma grande dificuldade em prever as propriedades destes materiais não-homogéneos devido às suas irregularidades e microdefeitos. O âmbito deste trabalho é precisamente encontrar modelos analíticos ou métodos numéricos que consigam descrever o comportamento das espumas metálicas em regime elástico. Para isso foram usados métodos numéricos e modelos analíticos providenciados por trabalhos precedentes. Para aplicar os métodos numéricos foi necessário, modelar as geometrias das células unitárias representativas. Com base nos resultados de trabalhos já existentes, as geometrias selecionadas foram as estruturas de Kelvin e de Weaire-Phelan. Com estas geometrias definidas, foi possível modelar células representativas unitárias de célula aberta e de célula fechada. Após definidas, as geometrias de célula aberta e célula fechada foram submetidas a três métodos numéricos, condições de fronteira de simetria com uma força prescrita, condições de fronteira de simetria com deslocamento imposto e homogeneização por expansão assimptótica. Os dois métodos que usam condições de fronteira simétricas foram analisados no programa Femap, o procedimento de homogeneização por expansão assimptótica, que usa condições de fronteira periódicas, foi analisado através do programa mainFRAN. Sabe-se que a densidade relativa é a característica que tem maior influência sobre a rigidez das espumas metálicas. Como os modelos analíticos relacionam o módulo de Young relativo com a densidade relativa, neste trabalho esta relação também foi obtida para cada método numérico. Os resultados numéricos foram então comparados com modelos analíticos e com resultados experimentais.

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LUCO, DAYANE P. "Padronização de técnicas de isolamento de células de Langerhans imaturas e desenvolvimento de um modelo tridimensional de pele humana para testes de sensibilidade in vitro." reponame:Repositório Institucional do IPEN, 2014. http://repositorio.ipen.br:8080/xmlui/handle/123456789/23179.

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Submitted by Claudinei Pracidelli (cpracide@ipen.br) on 2014-12-19T17:52:28Z No. of bitstreams: 0
Made available in DSpace on 2014-12-19T17:52:28Z (GMT). No. of bitstreams: 0
Dissertação (Mestrado em Tecnologia Nuclear)
IPEN/D
Instituto de Pesquisas Energeticas e Nucleares - IPEN-CNEN/SP

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UREÑA, MARTÍN Carlos. "Study of Caveolae Mechanotransduction Under 3D Compressive Stresses : Comparative Analysis of 2 Models Mimicking Structural and Mechanical Tumor Characteristics." Thesis, Université Paris-Saclay (ComUE), 2019. http://www.theses.fr/2019SACLS525.

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La mécanique et le stress compressif jouent un rôle important dans la progression tumorale. Récemment, plusieurs approches ont été développées pour tester le stress en compression dans des modèles 3D in vitro. Dans le présent travail, nous montrons d’abord la pertinence de la compression dans l’organisation des fibroblastes associés au cancer (CAF), en enveloppant les cellules cancéreuses lors d’une compression isotrope 3D dans des capsules d’alginate creux. Dans ce système, les CAF couvrent les cellules cancéreuses en présence de compression selon un processus impliquant vraisemblablement une réorganisation du dépôt de fibronectine et non un réarrangement passif des deux sphéroïdes. Dans la deuxième partie de ce travail, nous avons étudié la réaction des composants de la cavéole au stress en compression.Les cavéoles sont des invaginations de la membrane plasmique capables d'amortir la tension de la membrane, protégeant ainsi la cellule de son éclatement. Nous montrons ici comment les cavéoles réduisent leur présence lors de la compression3D à court terme et comment cette compression inhibe l'activation de STAT1 et STAT3 induite par l'interféron. De plus, les effets à long terme des contraintes de compression sur les sphéroïdes entraînent également la perte du composant cavéole EHD2, une ATPase centrale pour la stabilité des cavéoles sur la membrane. Enfin, nous avons trouvé différentes voies avec une transcription modifiée du gène après un stress compressif. Parmi eux, nous avons caractérisé l'effet de la perte decavéoline-1 sur la libération d'exosomes sous compression 3D
Mechanics and compressive stress play an important role in tumor progression. Recently, several approaches have been developed to test compressive stress in 3D in vitro models. In the present work, we first show the relevance of compression in the organization of cancer associated fibroblasts (CAFs), enwrapping cancer cells upon 3D isotropic compression in capsules of hollow alginate. In this system, CAFs cover cancer cells in the presence of compression by a process which most likely involves fibronectin deposition reorganization, and not a passive rearrangement of the two spheroids. In the second part of this work, we investigated the response of caveolae components to compressive stress. Caveolae are plasma membrane invaginations which are able to buffer membrane tension, thus protecting the cell from bursting. Here, we show how caveolae reduce their presence under 3D short term compression, and how this compression inhibits interferon induced STAT1 and STAT3 activation. Moreover, long term effects of compressive stress in spheroids result also in loss of the caveolae component EHD2, acentral ATPase for caveolae stability on the membrane. Lastly, we found different pathways with altered gene transcription after compressive stress. Among them, we characterized the effect of caveolin-1 loss on the release of exosomes under 3Dcompression

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Manifacier, Ian. "Understanding adherent cell mechanics and the influence of substrate rigidity." Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM4106/document.

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L’ingénierie tissulaire est une stratégie médicale qui repose sur la régénération de tissu par les cellules avec ou sans matériaux. Pour maîtriser cette synthèse, il faut comprendre la cellule comme une part intégrante du tissu. Hormis ses interactions biochimiques avec son support, la cellule interagit également mécaniquement avec son environnement. Elle s’accroche à ce dernier et évalue sa dureté pour adapter sa réponse biologique. Dans cette étude, j’ai développé des modèles numériques pour analyser l’influence de la rigidité du substrat sur le comportement mécanique de la cellule, sur sa structure contractile interne et les efforts qu’elle génère. En d’autres termes, j’ai essayé de comprendre comment la cellule ressent la rigidité de son environnement. De plus, au lieu de me focaliser sur les propriétés mécaniques quantitatives, j’ai cherché à développer un modèle conceptuel simplifié plus proche de la structure cellulaire
Tissue engineering is a medical strategy based on utilizing cells and materials to regenerate a new tissue. Yet, it involves intertwined interactions that allow cells to act as integrated parts of an organ. In addition to chemical reactions, the cell interacts mechanically with its environment by sensing its rigidity. Here, we used several computational models to understand how substrate rigidity affects a cell’s structure as it adheres and spreads on it. In other words we tried to understand the way a cell feels how soft or hard it surrounding is, how it affects its internal structure and the forces that transit within it. In addition, instead of focusing on mechanical properties, we developed a simplified, yet coherent conceptual understanding of the cellular structure

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43

Planas, Iglesias Joan 1980. "On the study of 3D structure of proteins for developing new algorithms to complete the interactome and cell signalling networks." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/104152.

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Proteins are indispensable players in virtually all biological events. The functions of proteins are determined by their three dimensional (3D) structure and coordinated through intricate networks of protein-protein interactions (PPIs). Hence, a deep comprehension of such networks turns out to be crucial for understanding the cellular biology. Computational approaches have become critical tools for analysing PPI networks. In silico methods take advantage of the existing PPI knowledge to both predict new interactions and predict the function of proteins. Regarding the task of predicting PPIs, several methods have been already developed. However, recent findings demonstrate that such methods could take advantage of the knowledge on non-interacting protein pairs (NIPs). On the task of predicting the function of proteins,the Guilt-by-Association (GBA) principle can be exploited to extend the functional annotation of proteins over PPI networks. In this thesis, a new algorithm for PPI prediction and a protocol to complete cell signalling networks are presented. iLoops is a method that uses NIP data and structural information of proteins to predict the binding fate of protein pairs. A novel protocol for completing signalling networks –a task related to predicting the function of a protein, has also been developed. The protocol is based on the application of GBA principle in PPI networks.
Les proteïnes tenen un paper indispensable en virtualment qualsevol procés biològic. Les funcions de les proteïnes estan determinades per la seva estructura tridimensional (3D) i són coordinades per mitjà d’una complexa xarxa d’interaccions protiques (en anglès, protein-protein interactions, PPIs). Axí doncs, una comprensió en profunditat d’aquestes xarxes és fonamental per entendre la biologia cel•lular. Per a l’anàlisi de les xarxes d’interacció de proteïnes, l’ús de tècniques computacionals ha esdevingut fonamental als darrers temps. Els mètodes in silico aprofiten el coneixement actual sobre les interaccions proteiques per fer prediccions de noves interaccions o de les funcions de les proteïnes. Actualment existeixen diferents mètodes per a la predicció de noves interaccions de proteines. De tota manera, resultats recents demostren que aquests mètodes poden beneficiar-se del coneixement sobre parelles de proteïnes no interaccionants (en anglès, non-interacting pairs, NIPs). Per a la tasca de predir la funció de les proteïnes, el principi de “culpable per associació” (en anglès, guilt by association, GBA) és usat per extendre l’anotació de proteïnes de funció coneguda a través de xarxes d’interacció de proteïnes. En aquesta tesi es presenta un nou mètode pre a la predicció d’interaccions proteiques i un nou protocol basat per a completar xarxes de senyalització cel•lular. iLoops és un mètode que utilitza dades de parells no interaccionants i coneixement de l’estructura 3D de les proteïnes per a predir interaccions de proteïnes. També s’ha desenvolupat un nou protocol per a completar xarxes de senyalització cel•lular, una tasca relacionada amb la predicció de les funcions de les proteïnes. Aquest protocol es basa en aplicar el principi GBA a xarxes d’interaccions proteiques.

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Ferrer, Savall Jordi. "Individual-based modeling of Plasmodium falciparum erythrocyte infection in in vitro cultures." Doctoral thesis, Universitat Politècnica de Catalunya, 2010. http://hdl.handle.net/10803/6597.

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La malària és encara avui en dia una malaltia que causa aproximadament un milió de morts a l'any a tot el món. La seva eradicació suposa un gran repte per a la humanitat i per a la comunitat científica, en particular. El cultiu in vitro del paràsit és essencial per al desenvolupament de nous medicaments. Els mètodes de cultiu actuals es basen en l'heurística i requereixen millores.
En aquesta tesi es presenta una aproximació teòrica al procés d'infecció a eritròcits en cultius in vitro amb Plasmodium falciparum, un dels protozous paràsits causants de la malària. El treball està centrat en la construcció i avaluació de models d'una complexitat adequada per tractar els problemes específics detectats pels experts en l'àmbit, i inclou també la formulació d'algorismes de simulació i el disseny de protocols experimentals.
Aquest tipus de treball requereix de la col·laboració multidisciplinària. La visió dels experts en malària es complementa amb la modelització i simulació, que permet la comprovació dels supòsits preestablerts, la comprensió de fenòmens observats i la millora dels mètodes de cultiu actuals. Així doncs, cal establir i desenvolupar eines que permetin crear, analitzar i compartir models amb grups que estudien la malària des d'altres perspectives. En aquesta tesi, s'ha optat per la modelització basada en l'individu (IbM) i orientada a la reproducció de múltiples patrons (PoM). El model s'ha formulat seguint l'ODD, un protocol estàndard en el camp de l'ecologia teòrica, que s'ha adaptat a la representació de comunitats microbianes.
Els models basats en l'individu (IbMs) defineixen un conjunt de normes que regeixen el comportament de cada cèl·lula i les seves interaccions amb les altres cèl·lules i amb el seu entorn immediat. A partir d'aquestes regles, i tenint en compte una certa diversitat dins de la població i un cert grau d'aleatorietat en els processos individuals, els IbMs mostren explícitament el comportament emergent del sistema en conjunt. Complementàriament, s'han aplicat conceptes propis de la termodinàmica per tal d'entendre
l'aparició de patrons macroscòpics a partir de l'estructura de la població (per exemple de la distribució de les fases d'infecció entre els glòbuls vermells infectats).
Aquesta recerca ha comportat la la creació i aplicació del model i simulador INDISIM-RBC, que ha demostrat ser una bona eina per millorar la comprensió dels cultius estudiats. Es tracta d'un model mecanicista, basat en l'individu, que reprodueix quantitativament els patrons observats en cultius reals a diferents nivells de descripció, i que en prediu el comportament sota determinades condicions.
Hem demostrat que INDISIM-RBC pot ser emprat per a estudiar en detall alguns aspectes del cultiu del paràsit causant de la malària que calia aclarir. Permet realitzar experiments virtuals i així impulsar noves línies de recerca i explorar noves tècniques de cultiu. En particular, INDISIM-RBC s'ha utilitzat per millorar els protocols experimentals actuals del cultius estàtics, definint la geometria òptima de l'hematòcrit i els protocols de subcultiu més adequats per als cultius continus.
El treball realitzat en malària s'ha comparat amb la investigació duta a terme pel grup de recerca em relació amb d'altres comunitats microbianes. D'aquesta manera, podem estudiar les propietats emergents dels sistemes microbians en general en relació als efectes de la individualitat de la cèl·lula, la diversitat de les poblacions, l'heterogeneïtat en el medi, o el caràcter local de les interaccions, entre d'altres. Aquesta visió general proporciona eines conceptuals que poden ser emprades per refinar l'anàlisi dels processos d'infecció sota estudi.
Malaria is still a major burden that causes approximately one million deaths annually worldwide. Its eradication supposes a great challenge to the humanity and to the scientific community, in particular. In vitro cultivation of the parasite is essential for the development of new drugs. Current culture methods are based on heuristics and demand for specific improvements.
The present thesis is a theoretical approach to in vitro cultivation of the protozoan parasite Plasmodium falciparum infecting human red blood cells. It mainly focuses on the process of building a model of appropriate complexity to deal with the specific demands above mentioned, but it also includes the formulation and implementation of algorithms, and the design and execution of experimental trials.
This kind of work requires multidisciplinary collaboration: the insight of the experts in malaria research is complemented with modeling and simulation, which allows for checking settled assumptions, increasing the understanding on the system and improving the current culturing methods.
The use of tools for building, analyzing and sharing models is an imperative to this end. In this thesis, Pattern-oriented Modeling (PoM) has been adopted as the most appropriate way for raising of models and the ODD protocol (Objectives, Design Concepts and Details) has been proposed as the standard tool for communicating them.
Individual-based Modeling (IbM) has been used to tackle malaria culture systems. IbMs define a set of rules governing each cell, its interactions with others and with its immediate surroundings. From this set of rules, and taking into account diversity within the population and a certain degree of randomness in the individual processes, IbMs explicitly show the emerging behavior of the system as a whole. Methods from statistical thermodynamics have been applied to understand the emergence of macroscopic patterns from the population structure (e.g. distribution of infection stages among infected red blood cells).
The research resulted in the development of the model and simulator INDISIM-RBC, which has proved to be a good tool to improve understanding of the cultures under study. It is a mechanistically rich individual-based model and it quantitatively reproduces and predicts several patterns observed in real cultures at different levels of description.
We demonstrated that INDISIM-RBC can be used to study in detail several aspects of malaria cultivation that remained unclear, as well as to perform virtual experiments. Consequently, it can be used to open novel lines of research and to examine potential experimental techniques. INDISIM-RBC has also been used to improve the current experimental culturing protocols in static cultivation by obtaining the optimal geometry of the hematocrit layer and subcultivation periods in the continuous cultures.
This study on malaria has been compared to the research carried out by the group regarding other microbial communities. Thereby studying general emerging properties of microbial systems in general, with regard to the effect of cell individuality, heterogeneity and diversity, the local nature of interactions; and biological and spatial complexity. In doing so, the acquired holistic view has been used to develop tools that allow for a better characterization and study of the infection process, in particular.

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45

Birkholz, Oleg [Verfasser], and M. [Akademischer Betreuer] Kamlah. "Modeling transport properties and electrochemical performance of hierarchically structured lithium-ion battery cathodes using resistor networks and mathematical half-cell models / Oleg Birkholz ; Betreuer: M. Kamlah." Karlsruhe : KIT-Bibliothek, 2021. http://d-nb.info/123814814X/34.

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Wang, Hui-Shan Amy. "Arsenic in drinking water caused ultra-structural damage in urinary bladder but did not affect expression of DNA damage repair genes or repair of DNA damage in transitional cells." Diss., Virginia Tech, 2007. http://hdl.handle.net/10919/28773.

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Arsenic is a human carcinogen associated with urinary bladder transitional cell carcinoma and other cancers. Arsenic is also a strong comutagen and cocarcinogen. One possible mode of action for arsenic carcinogenesis/cocarcinogenesis is inhibition of DNA damage repair. In laboratory animals, urinary bladder transitional cell carcinoma has only been observed in dimethylarsinic acid [DMA(V)]-exposed F344 rats. The goal of the present studies was to investigate inhibition of DNA repair as a mode of action for arsenic carcinogenesis/ cocarcinogenesis in the urinary bladder. Methods were first developed to harvest only transitional cells, the target cell type of arsenic carcinogenesis, suitable for RNA extraction or for DNA damage detection by Comet assay. Morphological studies established that DMA(V) in drinking water at 40 ppm was cytotoxic to the urothelium of Sprague-Dawley and F344 rats, and mitochondria were targeted by DAM(V). To investigate whether DMA(V) decreases the expression of DNA repair genes, mRNA levels of DNA repair genes in transitional cells were next measured in F344 rats exposed to up to 100 ppm DMA(V) in drinking water for 4 weeks. The mRNA levels of Ataxia Telangectasia mutant (ATM), X-ray repair cross-complementing group 1 (XRCC1), excision repair cross-complementing group 3/Xeroderma Pigmentosum B (ERCC3/XPB), and DNA polymerase beta genes were not altered, as measured by real time RT PCR. These results suggested either that DMA(V) affects DNA repair without affecting the baseline expression of DNA repair genes or that DMA(V) does not affect DNA repair in the bladder. Arsenic effects on DNA repair were further investigated in F344 rats given 100 ppm DMA(V) or arsenate in drinking water for 1 week. DNA damage levels in transitional cells and micronuclei frequency (MN) in bone marrow were measured. Dimethylarsinic acid did not affect in vivo cyclophosphamide-induced DNA damage, and neither DMA(V) nor arsenate inhibited in vitro repair of hydrogen peroxide- or formaldehyde-induced DNA damage, as measured by Comet assay. Neither DMA(V) nor arsenate increased MN or elevated in vivo cyclophosphamide-increased MN. These results suggest inhibition of DNA repair by arsenic, in the transitional epithelium, may not be a major mechanism responsible for carcinogensis/cocarcinogenesis in the bladder.
Ph. D.

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47

Strachala, Dávid. "Modifikace struktury křemíkových solárních článků." Master's thesis, Vysoké učení technické v Brně. Fakulta elektrotechniky a komunikačních technologií, 2014. http://www.nusl.cz/ntk/nusl-221019.

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The aim of the work is to create a coherent overview of the silicon monocrystaline solar cell in terms of the physical principle of the structure and sequence of technological operations necessary for its production. The effect of individual manufacturing steps is discussed in relation to the requirement of decreasing recombination, optical and ohmic losses of the monocrystalline solar cell. Due to a theoretical assumption, one-dimensional model of solar cell was created in a PC1D software that was later optimized to achieve the highest possible efficiency. Using the available technologies, final model of the solar cell is manufactured in Solartec company and in the end of the work compared with the output of simulation.

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Beckmann, Christoph [Verfasser], and Christoph V. [Akademischer Betreuer] Suschek. "Comparative Evaluation of Organic and Synthetic Matrix Structures Combined with Adipose Tissue-Derived Multipotent Cells in a Murine Skin Wound Model / Christoph Beckmann. Gutachter: Christoph V. Suschek." Düsseldorf : Universitäts- und Landesbibliothek der Heinrich-Heine-Universität Düsseldorf, 2015. http://d-nb.info/1076625371/34.

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Nevalainen, J. (Jukka). "Utilisation of the structure of the retinal nerve fiber layer and test strategy in visual field examination." Doctoral thesis, University of Oulu, 2010. http://urn.fi/urn:isbn:9789514262012.

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Abstract The aim of this study was to create a mathematical model of the retinal nerve fiber layer and of the entire hill of vision, and to compare different perimetric methods and test grids in the detection of visual field loss in glaucoma and optic neuritis. A mathematical model of the retinal nerve fiber layer was developed, based on traced nerve fiber bundle trajectories extracted from 55 fundus photographs of 55 human subjects. The model resembled the typical retinal nerve fiber layer course within 20° eccentricity from the foveola. The standard deviation of the calculated corresponding angular location at the optic nerve head circumference ranged from less than 1° up to 18° (mean 8.8°). A smooth mathematical model of the hill of vision was created, based on 81 ophthalmologically healthy subjects. The model fit R2 was 0.72. Applying individually condensed test grids in 41 glaucomatous eyes of 41 patients enhanced remarkably the detection of progression. Seven out of 11 (64%) of the progressive scotomata detected by spatially condensed grids would have been missed by the conventional 6° × 6° grid. In 20 eyes of 20 patients with advanced glaucoma, the comparability of visual field areas obtained with semi-automated kinetic perimetry and automated static perimetry was satisfactory and within the range of the test-retest reliability of automated static perimetry. Using a standardized grid of 191 static targets within the central 30° visual field, the most common finding in 100 eyes of 99 patients with acute optic neuritis were central scotomas, accounting for 41% of all visual field defects in affected eyes. In conclusion, a model of the retinal nerve fiber layer was developed, which provided a detailed location specific estimate of the magnitude of the variability on the courses of retinal nerve fiber bundle trajectories in the human retina. A smooth mathematical model of the hill of vision with a satisfactory model fit was described for the 80° visual field. Individually condensed grids enabled the detection of a glaucomatous visual field progression more frequently and also earlier than conventional grids. Semi-automated kinetic perimetry was found to be a valuable alternative to automated static perimetry in monitoring advanced glaucomatous visual field loss. Using a grid with a higher spatial resolution may enhance the detection of small central visual field loss in optic neuritis.

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Lu, Biao. "Evaluation of physico-chemical properties of biorefinery-derived amphiphilic molecules and their effects on multi-scale biological models." Thesis, Compiègne, 2015. http://www.theses.fr/2015COMP2218/document.

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Abstract:

Aujourd'hui, un grand nombre de nouvelles molécules peuvent être synthétisées à partir de la biomasse. Les tensioactifs dérivés de sucre sont notamment considérés comme une alternative aux tensioactifs fossiles en raison de leur biodégradabilité et de leur biocompatibilité. Cependant, les études associant la caractérisation physico-chimique et les propriétés biologiques de ce type de tensio-actifs sont limitées. Il est ainsi difficile de prédire les propriétés d'un tensioactif à partir de sa structure chimique. L'établissement d'une méthodologie permettant de relier la structure des surfactants à leurs propriétés apparait pertinent. Dans ce travail, quatre surfactants dérivés de sucre ayant chacun une chaîne C8 liée à une tête glucose ou maltose par un groupe amide ont été caractérisés par leurs propriétés tensio-actives dans différentes solutions (eau et milieu biologique). Leurs interactions avec des protéines ont également été analysées. Concernant l'évaluation des propriétés biologiques, des tests de cytotoxicité/irritation ont été effectués sur trois modèles in-vitro : 1) modèle cellulaire 20 (cellules L929 cultivées en monocouche), Il) modèle cellulaire 30 (cellules L929 cultivées dans un gel de collagène), Ill) épiderme humain reconstitué. Les résultats indiquent que les quatre surfactants synthétisés présentent de bonnes propriétés tensio-actives et trois d'entre eux sont moins cytotoxiques que des tensioactifs de référence. Plusieurs hypothèses permettant de relier la structure chimique des molécules à leurs propriétés physico-chimiques et biologiques ont été proposées. Des travaux futurs permettront d'enrichir la base de données sur les relations structure-propriétés des tensioactifs issus de la biomasse, et de l'utiliser pour synthétiser des surfactants présentant des propriétés adaptées aux applications envisagées
Nowadays, a wide variety of new molecules can derive from biomass. Among them, the family of sugar-based surfactants, which are considered as alternatives to fossil-based surfactants, due to their relatively high biodegradability and biocompatibility, exhibit interesting properties both in terms of their self-assembly and their ability to induce biological responses. In the study, for the purpose to analyse these properties, different methodologies have been established. In this work, physico-chemistry and cellular biology methodologies are associated to analyse the properties of pre-selected molecules characterized by gradua) structure modifications. Firstly, we have screened synthesized sugar-based surfactants according to their solubility and their ability to reduce surface tension of water. Four pre-selected molecules, with a C8 chain linked to a glucose or maltose head through an amide functional group, either under the form of carbamoyl (carbohydrate scaffold bearing the carbonyl) or alkylcarboxamide (the alkyl chain bearing the carbonyl), were then dissolved in water/ cell culture media for surface tension measurements. Their behaviors in solutions were characterized by Krafft points, Critical Micellar Concentrations or self-assembling properties through different methods. To evaluate the cytotoxic/ irritant effects of these molecules on cells and tissues, 3 in-vitro models were established: I) 2D cell culture mode! (L929 cell monolayer) II) 3D ce!! culture mode! (L929 cells embedded in collagen gel) and III) Reconstituted human epidermis (differentiated human keratinocytes). Corresponding experiments were carried out on these models with increasing complexity. Results show that the synthesized sugar-based surfactants, GlulamideC8, Glu6amideC8, Glu6amideC8' and MallamideC8 can reduce the surface tension of water solution to the came level as standard surfactants (Tween 20 and Hecameg). In the meantime, GlulamideC8, Glu6amideC8' and MallamideC8 present Iess cytotoxicity effects on L929 cells both in the monolayer model and the 3D mode! than Tween 20 and Hecameg. All synthesized and standard surfactants (GlulamideC8, Glu6amideC8, Gu6amideC8', MallamideC8, Tween 20 and Hecameg) have no significant cytotoxic/ irritant effects on reconstituted human epidermis at 1000 ig/mL after 48 h of topical application. Discussions have been made according to the results of experiments to establish possible structures/ physico-chemical properties - cytotoxicity relationships of these surfactants

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Dissertations / Theses on the topic 'Structural cell model'

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