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McGregor, Juliette Elizabeth. "Imaging dynamic biological processes." Thesis, University of Cambridge, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.609205.
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Reichenbach, Tobias. "Dynamic patterns of biological systems." Diss., lmu, 2008. http://nbn-resolving.de/urn:nbn:de:bvb:19-84101.
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Magi, Ross. "Dynamic behavior of biological membranes." Thesis, The University of Utah, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3680576.
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Biological membranes are important structural units in the cell. Composed of a lipid bilayer with embedded proteins, most exploration of membranes has focused on the proteins. While proteins play a vital role in membrane function, the lipids themselves can behave in dynamic ways which affect membrane structure and function. Furthermore, the dynamic behavior of the lipids can affect and be affected by membrane geometry. A novel fluid membrane model is developed in which two different types of lipids flow in a deforming membrane, modelled as a two-dimensional Riemannian manifold that resists bending. The two lipids behave like viscous Newtonian fluids whose motion is determined by realistic physical forces. By examining the stability of various shapes, it is shown that instability may result if the two lipids forming the membrane possess biophysical qualities, which cause them to respond differently to membrane curvature. By means of numerical simulation of a simplified model, it is shown that this instability results in curvature induced phase separation. Applying the simplified model to the Golgi apparatus, it is hypothesized that curvature induced phase separation may occur in a Golgi cisterna, aiding in the process of protein sorting.
In addition to flowing tangentially in the membrane, lipids also flip back and forth between the two leaflets in the bilayer. While traditionally assumed to occur very slowly, recent experiments have indicated that lipid flip-flop may occur rapidly. Two models are developed that explore the effect of rapid flip-flop on membrane geometry and the effect of a pH gradient on the distribution of charged lipids in the leaflets of the bilayer. By means of a stochastic model, it is shown that even the rapid flip-flop rates observed are unlikely to be significant inducers of membrane curvature. By means of a nonlinear Poisson- Boltzmann model, it is shown that pH gradients are unlikely to be significant inducers of bilayer asymmetry under physiological conditions.
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Waheed, Qaiser. "Molecular Dynamic Simulations of Biological Membranes." Doctoral thesis, KTH, Teoretisk biologisk fysik, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-102268.
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Biological membranes mainly constituent lipid molecules along with some proteins and steroles. The properties of the pure lipid bilayers as well as in the presence of other constituents (in case of two or three component systems) are very important to be studied carefully to model these systems and compare them with the realistic systems. Molecular dynamic simulations provide a good opportunity to model such systems and to study them at microscopic level where experiments fail to do. In this thesis we study the structural and dynamic properties of the pure phospholipid bilayers and the phase behavior of phospholipid bilayers when other constituents are present in them. Material and structural properties like area per lipid and area compressibility of the phospholipids show a big scatter in experiments. These properties are studied for different system sizes and it was found that the increasing undulations in large systems effect these properties. A correction was applied to area per lipid and area compressibility using the Helfrich theory in Fourier space. Other structural properties like order of the lipid chains, electron density and radial distribution functions are calculated which give the structure of the lipid bilayer along the normal and in the lateral direction. These properties are compared to the X-ray and neutron scattering experiments after Fourier transform. Thermodynamic properties like heat capacity and heat of melting are also calculated from derivatives of energies available in molecular dynamics. Heat capacity on the other hand include quantum effect and are corrected for that by applying quantum correction using normal mode analysis for a simple as well as ambiguous system like water. Here it is done for SPC/E water model. The purpose of this study is to further apply the quantum corrections on macromolecules like lipids by using this technique. Furthermore the phase behavior of two component systems (phospholipids/cholesterol) is also studied. Phase transition in these systems is observed at different cholesterol concentrations as a function of temperature by looking at different quantities (as an order parameter) like the order of chains, area per molecule and partial specific area. Radial distribution functions are used to look at the in plane structure for different phases having a different lateral or positional order. Adding more cholesterol orders the lipid chains changing a liquid disordered system into a liquid ordered one and turning a solid ordered system into a liquid ordered one. Further more the free energy of domain formation is calculated to investigate the two phasecoexistence in binary systems. Free energy contains two terms. One is bulk freeenergy which was calculated by the chemical potential of cholesterol moleculein a homogeneous system which is favorable for segregation. Second is thefree energy of having an interface which is calculated from the line tension of the interface of two systems with different cholesterol concentration which in unfavorable for domain formation. The size of the domains calculated from these two contributions to the free energy gives the domains of a few nm in size. Though we could not find any such domains by directly looking at our simulations.QC 20120913
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Jones, E. Y. "Structural and dynamic studies on biological macromolecules." Thesis, University of Oxford, 1985. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.371551.
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Abul-Haija, Yousef Mustafa Yousef. "Dynamic supramolecular hydrogels with adaptive biological functionality." Thesis, University of Strathclyde, 2015. http://oleg.lib.strath.ac.uk:80/R/?func=dbin-jump-full&object_id=25997.
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Bunyapaiboonsri, Taridaporn. "Dynamic combinatorial chemistry : Exploration using biological receptors." Université Louis Pasteur (Strasbourg) (1971-2008), 2003. http://www.theses.fr/2003STR13065.
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La chimie combinatoire dynamique a été récemment introduite comme une approche nouvelle et attractive pour générer et cribler un grand nombre de bibliothèques de composés en une seule étape. Basé sur l'interconnexion réversible entre les composés de la bibliothèque, le processus d'auto-ajustement donne accès à la sélection et à l'amplification du meilleur inhibiteur en présence d'une cible. Au cours de cette thèse, nous avons choisi deux cibles biologiques qui nous ont permis d'explorer l'approche de la chimie combinatoire dynamique. La réversibilité du système a été rendue possible en utilisant l'échange de disulfures ou la formation réversible d'acyl hydrazones. Premièrement, une bibliothèque dynamique d'inhibiteurs d'acétylcholinestérase a été générée grâce à l'échange de disulfures. Nous avons observé la réversibilité du système à l'aide de la spectroscopie de RMN. A partir d'un mélange initial de 5 homodisulfures en présence d'un agent réducteur, une bibliothèque contenant 15 composantes a été obtenue. Les composantes de cette bibliothèque ont été mises en évidence par SM-ES et par EC. Deuxièmement, une bibliothèque combinatoire dynamique d'inhibiteurs d'acétylcholinesterase a été générée en se basant sur la formation réversible d'acyl-hydrazones. Le processus pré-équilibré a été utilisé pour obtentir d'une bibliothèque dynamique composée de 66 espèces possibles, à partir de 13 unités de bases. Nous avons ensuite identifié l'inhibiteur très puissant (IC50 et Ki de l'ordre de nM), en utilisant la méthode de la déconvolution dynamique. Finalement, le processus pré-équilibré combiné à la technique de la déconvolution dynamique a été employé pour identifier les inhibiteurs de la HPr kinase/phosphatase. Ainsi, nous avons pu préparer une bibliothèque dynamique constituée de 440 composés possibles, en une seule étape, à partir de 21 unités de bases. Le ligand hétérocyclique bis-cationique s'est révélé un inhibiteur relativement puissant (IC50 de l'ordre de mM)Dynamic combinatorial chemistry (DCC) has recently been introduced as a new and attractive approach for generating and screening large numbers of library compounds in one step. Based upon the reversible interconnection between library components, the self-adjusting process give access to selection and amplification of the best binder in the presence of a target. In this thesis, two biological targets were chosen to explore the DCC approach. The reversibility of the system was achieved using disulfide interchange or reversible acyl hydrazone formation. Firstly, a dynamic library of acetylcholinesterase inhibitors was generated through disulfide exchange. The reversibility of the system was observed by NMR spectroscopy. Upon scrambling 5 initial homodisulfides in the presence of a reducing agent, a 15-compound library was produced. The library components were analyzed by ESI-MS and CE. Secondly, a dynamic combinatorial library of acetylcholinesterase inhibitors was further generated through reversible acyl hydrazone formation. The pre-equilibrated process was applied to produce a dynamic library composed of 66 possible species, from a set of 13 initial aldehyde and hydrazide building blocks. Using a technique called dynamic deconvolution, a highly potent inhibitor was identified with IC50 in the nanomolar range. Finally, the pre-equilibrated process combined with the dynamic deconvolution technique was further studied to identify HPr kinase/phosphatase inhibitors. From a set of 21 initial aldehyde and hydrazide builiding blocks, a dynamic library of 440 possible compounds was formed in one operation. A bis-cationic heterocyclic ligand was identified as a relatively potent inhibitor, displaying an IC50 in the micromolar range
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Romanel, Alessandro. "Dynamic Biological Modelling: a language-based approach." Doctoral thesis, Università degli studi di Trento, 2010. https://hdl.handle.net/11572/368272.
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Systems biology investigates the interactions and relationships among the components of biological systems to understand how they globally work. The metaphor “cells as computations†, introduced by Regev and Shapiro, opened the realm of biological modelling to concurrent languages. Their peculiar characteristics led to the development of many different bio-inspired languages that allow to abstract and study specific aspects of biological systems. In this thesis we present a language based on the process calculi paradigm and specifically designed to account for the complexity of signalling networks. We explore a new design space for bio-inspired languages, with the aim to capture in an intuitive and simple way the fundamental mechanisms governing protein-protein interactions. We develop a formal framework for modelling, simulating and analysing biological systems. An implementation of the framework is provided to enable in-silico experimentation.
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Cavallo, Antonio. "Four dimensional particle tracking in biological dynamic processes." [S.l.] : [s.n.], 2002. http://deposit.ddb.de/cgi-bin/dokserv?idn=964904667.
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Lewis, Mark A. "Analysis of dynamic and stationary biological pattern formation." Thesis, University of Oxford, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.276976.
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Tomazou, Marios. "Towards light based dynamic control of synthetic biological systems." Thesis, Imperial College London, 2014. http://hdl.handle.net/10044/1/44243.
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For the field of synthetic biology, the adaptation of principles, from the well established traditional engineering disciplines, like mechanical and electrical engineering, in order to realise complex synthetic biological circuits, is an intriguing prospect. These principles can enable a forward engineering, rational design and implementation approach, where a system's properties can be predicted or designed in silico followed by the manufacturing of the in vivo system, that can be tested, used or redesigned in the most efficient possible way. Achieving control over these circuits, is one of the important topics of the field, for these applications to become robust and render useful functions applicable to energy, medicine, pharmaceuticals and agriculture industries. In this work, I attempt to explore light, as a promising control 'dial' for synthetic circuitry. Light is fast, economic compared to chemicals, it can be interfaced with electronics, it is reversible in its effect and can be applied at a fine spatio-temporal resolution. These characteristics, are absent from the classically used chemical inducers, meaning that light, can open new possibilities for the user to control synthetic systems, or even facilitate the cell to cell communication, within population based networks. This work, is a contribution towards harnessing the advantages of light, for achieving control over synthetic circuits. More specifically, I start with the detailed theoretical and experimental study of the Cph8 two component system, a synthetic chimeric receptor which is responsive to red light. This is done, in order to develop a sufficient theoretical understanding of it, through detailed mechanistic modelling, in order to connect the specific system with the toggle switch and the dual feedback oscillator, in an optimal way and achieve control of these devices through light. The developed model, was able to highlight the main aspects and mechanisms inherent to its structure, describe most of the observations from the experimental system, to also make quantitative predictions. The second part of this work, was the development of novel promoters, that can be regulated by a commonly used transcription factor, such as LacI, but also, light responsive regulators like OmpR and CcaR. This yielded a direct way to integrate light and chemical inputs, into a single output, while the dual regulation, allowed to connect and modulate the toggle switch without the need of additional transcription factors. The latter, a light tuneable toggle switch, showed indications that it can function as a memory controller that can be reset by light. Finally, I show the design and modelling of a light tuneable dual feedback oscillator, where light of one wavelength can be used to tune the amplitude, while another wavelength can tune the period. The developed models and synthetic circuits are expected to contribute towards implementing finely tuned and controlled synthetic circuits through light.
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Lindell, Per Ingemar. "Dynamic operation of mammalian cell fed-batch bioreactors." Thesis, Massachusetts Institute of Technology, 1992. http://hdl.handle.net/1721.1/16509.
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Hall, Dennis A. (Dennis Alan) 1970. "Dynamic nuclear polarization of biological systems at high magnetic fields." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/9635.
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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1998.Includes bibliographical references.
Dynamic nuclear polarization methods were studied at high magnetic field strength and were applied to improve the sensitivity of the nuclear magnetic resonance spectroscopy of biological solids. Studies of the dynamics of electron-nuclear polarization transfer via the solid effect and thermal mixing at 5 Tesla are described for two systems: the free radical BDPA doped into polystyrene and the nitroxide TEMPO in a water:glycerol matrix. A model for thermal mixing at high magnetic fields in paramagnetic systems such as TEMPO which exhibit partially inhomogeneous EPR lines is developed in which electron-electron cross relaxation across the EPR line is explicitly included. The TEMPO/water/glycerol matrix is exploited for polarization transfer to biological solutes. As a demonstration, enhancements of up to two orders of magnitude were exhibited in the high-resolution "1N magic-angle spinning spectra of the protein T4- lysozyme. The potential of this method as a general signal enhancement tool for biological systems is assessed. These dynamic nuclear polarization experiments at 5 Tesla require high-power microwave irradiation at or near the EPR frequency. To that end, a cyclotron resonance maser, or gyrotron, is described. This 140 GHz gyrotron, which under conventional operation produces millisecond pulses, has been adapted to operate at -100 W in a quasi-CW mode for tens of seconds, the time required for electron-nuclear polarization transfer.
by Dennis A. Hall.
Ph.D.
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You, Chang Hun. "Learning patterns in dynamic graphs with application to biological networks." Pullman, Wash. : Washington State University, 2009. http://www.dissertations.wsu.edu/Dissertations/Summer2009/c_you_072309.pdf.
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Thesis (Ph. D.)--Washington State University, August 2009.Title from PDF title page (viewed on Aug. 19, 2009). "School of Electrical Engineering and Computer Science." Includes bibliographical references (p. 114-117).
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O'Neill, George C. "Dynamic electrophysiological connectomics." Thesis, University of Nottingham, 2016. http://eprints.nottingham.ac.uk/33502/.
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The human brain can be divided into multiple areas, each responsible for different aspects of behaviour. For a century we have been developing techniques to non-invasively map these areas and their associated functions, a discipline now known as neuroimaging. In recent years the field has undergone a paradigm shift to investigate how the brain communicates with itself; it is widely regarded that healthy brain function relies upon efficient connectivity between different functional areas, and the neuroimaging field has been revolutionised by our ability to estimate this connectivity. Studies into communication between spatially separate locations in the brain have revealed a series of robust functional networks which govern mental processes. However these studies have been based on the temporal averaging of minutes or even hours of data to give us a generalised ’snapshot’ of connectivity. Increasing evidence shows us that these connections are dynamic in space, time and frequency and so the next generation of of neuroimaging methods, which capture this 5-dimensional connectivity will prove to be key tools in the investigation of brain networks and ultimately their breakdown in disease. In this thesis we introduce novel methods to capture non-stationarity using magnetoencephalography (MEG), an imaging modality which measures the changes in extracranial magnetic fields associated with neuronal current flow. MEG is a direct measurement of neural activity and has an excellent temporal resolution, which makes it attractive for non-invasively tracking dynamic functional connections. However there are many technical limitations which can confound assessment of functional connectivity which have to be addressed. In Chapters 2 and 3 we introduce the theory behind MEG; specifically how it is possible to measure the femtoTelsa changes in magnetic field generated by the brain and how to project these data to generate a 3-dimensional picture of current in the brain. Chapter 4 reviews some of popular methods of assessing functional connectivity and how to control for the influence of artefactual functional connections erroneously produced during source projection. Chapter 5 introduces a pipeline to assess functional connections across time, space and frequency and in Chapter 6 we apply this pipeline to show that resting state networks, measured using ’static’ metrics are in fact comprised of a series of rapidly forming and dissolving subnetwork connections. Finally, Chapter 7 introduces a pipeline to track dynamic network behaviour simultaneously across the entire brain volume and shows that networks can be characterised by their temporal signatures of connectivity.
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Gupta, Apoorv. "Dynamic regulation of bacterial metabolic pathways using autonomous, pathway-independent control strategies." Thesis, Massachusetts Institute of Technology, 2017. http://hdl.handle.net/1721.1/112511.
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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2017.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 86-91).
Metabolic engineering efforts have so far focused on strain optimization through careful metabolic modeling and tinkering with host genomes, through gene knockouts or knockins, to direct flux in desired channels. These efforts have borne fruit with the development of large manufacturing processes for numerous chemicals. The next challenge for metabolic engineering, however, lies in tackling issues associated with construction of more complex pathways, such as those that directly interfere with host metabolism, have branchpoints with promiscuous enzymes, or synthesize toxic intermediates or products. Dynamic metabolic engineering has emerged as a new frontier for tool development to allow regulation and control of native and cellular pathways during the course of a production run. Advantages in dynamic strategies are especially apparent in the aforementioned examples where traditional static strategies of gene knockouts or knockins are not an option. Instead, it is necessary to be able to control when certain genes are expressed, such as to build biomass before switching on growth-limiting production pathways, or accumulating intermediates to drive the reaction of a promiscuous enzyme along a certain branch. In this thesis, we propose enzyme control strategies that are independent of any biosynthetic pathway of interest. Therefore, they can theoretically be applied to a wide variety of contexts in a "plug-and-play" fashion to control pathway enzyme expression. After initial work to understand the limitations of nutrient starvation strategies to induce genetic circuits, we decided to use quorum sensing circuitry to create circuits that can be autonomously induced. We used parts of the Esa QS system (derived from Pantoea stewartii) to create circuit variants in the Lscherichia cohi genome, which switch off expression of the targeted gene at various times and cell densities. Switching times were varied by modulating the expression of the AHL synthase, and therefore the production rate of AHL, the quorum sensing molecule. Switching dynamics were characterized and ranked for the entire library of circuit variants using fluorescent reporters. The characterized device was used to identify optimal switching times for redirection of glycolytic fluxes into heterologous pathways, resulting in a 5.5-fold boost in myo-inositol (MI) and increasing glucaric acid titers from unmeasurable quantities up to >0.8 g/L. With a focus on industrial application, consistency of device performance was verified in benchtop bioreactors, achieving nearly 10-fold and 5-fold boosts in specific titers of myoinositol and glucaric acid, respectively. To demonstrate broad utility and "off-the-shelf" applicability, the control module was applied to dynamic downregulation of flux into aromatic amino acid biosynthesis to accumulate the industrially-relevant intermediate, shikimate, resulting in an increase in titers from unmeasurable quantities to >100 mg/L. Finally, this QS device was coupled with a MI-biosensor circuit to institute two layers of dynamic regulation and further improve glucaric acid titers. Production trials in these composite strains resulted in the highest glucaric titers (-2 g/L) reported to date from E. coli K-strains. This work reports the first completely autonomous dynamic regulation module and its application in bioproduction of multiple products from different metabolic pathways. We envision that the strategy presented here may be adapted to any pathway context and gene of interest. With increased prevalence of dynamic regulation, the relevant strategies may become standardized for general use.
by Apoorv Gupta.
Ph. D.
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Valtorta, Davide. "Dynamic torsion test for the mechanical characterization of soft biological tissues." kostenfrei, 2007. http://e-collection.ethbib.ethz.ch/view/eth:29354.
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Maksym, Geoffrey N. "Computer controlled oscillator for dynamic testing of biological soft tissue strips." Thesis, McGill University, 1993. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=69742.
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A computer controlled tissue strip oscillator has been constructed for the advanced study of lung parenchyma mechanics. The data acquisition and control are facilitated on a 486 personal computer. The tissue is maintained by a continuously circulating bath of Krebs-Ringer solution at 37$ sp circ$C bubbled with a 95% O$ sb2$ and 5% CO$ sb2$ gas mixture. The oscillator has a useful bandwidth to 20 Hz at 0.5 cm amplitude and step response with no overshoot at all amplitudes. The movement range of the motor is 5 cm with resolution 13.6 $ mu$m. The force resolution is 66 $ mu$N with a range of 0.25 N. A tissue preconditioning protocol was developed as a standard maneuver to be conducted prior to applying length perturbations about specific operating stresses. The tissue strip oscillator has been successfully tested on dog lung tissue strips.
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Berry, Richard M. "Possible dynamic roles for the electrostatic force in biological membrane systems." Thesis, University of Oxford, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.316866.
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Winkler, Pamina M. "Novel planar photonic antennas to address the dynamic nanoarchitecture of biological membranes." Doctoral thesis, Universitat Politècnica de Catalunya, 2020. http://hdl.handle.net/10803/670293.
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The cell membrane is the encompassing protective shield of every cell and it is composed of a multitude of proteins, lipids and other molecules. The organization of the cell membrane is inextricably intertwined with its function, and sensitive to perturbations from the underlying actin cytoskeleton and the extracellular environment at the nano- and the mesoscale. Elucidating the dynamic interplay between lipids and proteins diffusing on the cell membrane, forming transient domains and (re)organizing them according to signals from the juxtaposed inner and outer meshwork, is of paramount interest in fundamental cell biology. The overarching goal of this thesis is to gain deeper insight into how lipids and proteins dynamically organize in biological membranes at the nanoscale.
Photonic nano-antennas are metallic nanostructures that localize and enhance the incident optical radiation into highly confined nanometric regions (< 20 nm), leading to greatly enhanced light-matter interactions. In this thesis, we exploit an innovative design of planar gold nano-antenna arrays of different gap sizes (10-45 nm) and embedded in nanometric-size boxes. To elucidate nanoscale diffusion dynamics in biological membranes with high spatiotemporal resolution and single-molecule detection sensitivity, we further combine our nanogap antenna arrays with fluorescence correlation spectroscopy (FCS) in a serial and multiplexed manner.
In this dissertation, we first describe the fabrication process of these planar gold nanogap antennas and characterize their performance by means of electron microscopy and FCS of individual molecules in solution. We demonstrate giant fluorescence enhancement factors of up to 104-105 times provided by our planar nanogap antennas in ultra-confined detection volumes and with single molecule detection sensitivity in the micromolar range.
Second, we apply these planar plasmonic nano-antennas in combination with FCS for assessing the dynamic organization of mimetic lipid membranes at the nanoscale. For a ternary composition of the model membranes that include unsaturated and saturated lipids together with cholesterol, we resolve transient nanoscopic heterogeneities as small as 10 nm in size, coexisting in both macroscopically phase-separated lipid phases.
Third, we add a Hyaluronic Acid (HA) layer on top of the model lipid membranes to emulate the effect of the extracellular environment surrounding native biological membranes. We extend our nano-antenna-FCS approach with atomic force microscopy and spectroscopy. We reveal a distinct influence of HA on the nanoscale lipid organization of mimetic membranes composed of lipids constituting the more ordered lipid phase. Our results indicate a synergistic effect of cholesterol and HA re-organizing biological membranes at the nanoscale.
Fourth, we apply our planar nano-antenna platform combined with FCS to elucidate the nanoscale dynamics of different lipids in living cells. With our nanogap antennas we were able to breach into the sub-30 nm spatial scale on living cell membranes for the first time. We provide compelling evidence of short-lived cholesterol-induced ~10 nm nanodomain partitioning in living plasma membranes.
Fifth, we demonstrate the multiplexing capabilities of our planar gold nanogap antenna platform combined with FCS in a widefield illumination scheme combined with sCMOS camera detection. Our approach allows recording of fluorescence signal from more than 200 antennas simultaneously. Moreover, we demonstrate multiplexed FCS recording on 50 nano-antennas simultaneously, both in solution as well as in living cells, with a temporal resolution in the millisecond range. The dissertation finishes with a brief discussion of the main results achieved in this research and proposes new avenues for future research in the field.La membrana plasmática separa el entorno intracelular del extracelular y está compuesta por una multitud de diferentes proteínas y lípidos. Su organización está fuertemente interconectada a su función, y es sensible a perturbaciones tanto de la actina cortical posicionada internamente en proximidad con la membrana, así como de una red extracelular en contacto próximo con la membrana exterior. Estas perturbaciones ocurren a distintas escalas temporales y espaciales, llegando a unos pocos nanómetros. Dada la estrecha relación entre la organización de la membrana y su función biológica, es tremendamente importante entender como lípidos y proteínas se organizan dinámicamente a la escala nanométrica y como se ven afectados por su entorno. El objetivo principal de esta tesis doctoral se centra en alcanzar este entendimiento. Las antenas fotónicas son nano-estructuras metálicas que incrementan la radiación electromagnética en regiones nanométricas (< 20 nm) del espacio. En esta tesis doctoral, hemos fabricado y utilizado plataformas con matrices de antenas en oro, y con regiones de confinamiento entre 10-45 nm. Además, hemos combinado estas antenas con la técnica de ¿fluorescence correlation spectroscopy (FCS)¿ a fin de obtener información espaciotemporal a la nano-escala en membranas biológicas, junto a la sensibilidad de detectar moléculas individuales a altas concentraciones. En esta disertación, describimos primero la fabricación de antenas fotónicas y caracterizamos su rendimiento utilizando técnicas de microscopía electrónica y FCS de moléculas individuales en solución. Nuestros resultados demuestran factores de incremento de la fluorescencia entre 104-105, en regiones ultra-confinadas, y una capacidad para detectar moléculas individuales en rango de concentraciones de micro-molares. Una vez validadas nuestras herramientas, nos enfocamos en su uso para el estudio dinámico de la organización de membranas lipídicas miméticas a escala nanométrica. En el caso de composiciones ternarias de lípidos insaturados, saturados y colesterol, hemos descubierto la existencia de heterogeneidades nanoscópicas y transitorias que coexisten tanto en las regiones ordenadas como desordenadas de las membranas lipídicas. El siguiente capítulo contiene resultados enfocados a estudiar el efecto del entorno extracelular en la organización dinámica de este tipo de capas lipídicas. Para ello, y como modelo, preparamos membranas lipídicas cubiertas de ácido hialurónico (HA), un componente abundantemente expresado en la matriz extracelular. Combinando FCS con microscopia y espectroscopia de fuerzas atómicas, logramos resolver la influencia de HA a escala nanométrica en la organización de la fase ordenada de las membranas lipídicas. Nuestros resultados indican la existencia de un efecto sinérgico entre HA y colesterol en el reordenamiento de la membrana a la nano-escala. El siguiente tema de investigación en esta tesis doctoral se enfoca a la aplicación de antenas fotónicas y FCS para el estudio de dominios lipídicos enriquecidos de colesterol en la membrana plasmática de células vivas. La utilización de estas antenas nos ha permitido, por primera vez, remontar la barrera de 30 nm, y demostrar de manera inequívoca la existencia de dominios enriquecidos en colesterol en células vivas con una resolución espacial de 10 nm. Finalmente, hemos demostrado la capacidad de multiplexado de nuestras antenas fotónicas, combinando una iluminación y detección en campo amplio utilizando una camera sCMOS. Describimos la implementación de nuestro esquema, así como también medidas que demuestran la detección simultánea de fluorescencia en más de 200 antenas. De manera importante, demostramos la obtención de curvas de FCS en 50 antenas simultáneamente, tanto en solución como en células vivas. Esta disertación culmina con una breve discusión de los resultados más importantes de esta investigación en el futuro
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Li, Yang Ph D. Massachusetts Institute of Technology. "In vitro model of injury/cytokine-induced cartilage catabolism modulated by dynamic compression, growth factors, and glucocorticoids." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/81669.
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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013.Cataloged from PDF version of thesis.
Includes bibliographical references.
The degradation of articular cartilage is the hallmark in the pathogenesis of osteoarthritis (OA). It still remains largely unknown which precise mechanisms initiate cartilage degradation. However, risks factors include traumatic joint injury that results in immediate upregulation of inflammatory cytokines within the joint, as well as direct mechanical damage to the cartilage, factors known to contribute to the onset of OA and its progression. The first aim of this thesis focused on elucidating the importance of post-injury mechanical loading of cartilage. An in vitro model was used to simulate aspects of joint injury: mechanically damaged cartilage was co-cultured in the presence of inflammatory cytokines (TNF-Q and IL-6). Intermittent dynamic compression was then applied to simulate different strain levels known to exist in vivo after joint injury. Strain-dependent modulation of aggrecan biosynthesis and degradation, aggrecanase cleavage of aggrecan, chondrocyte gene expression profiles and changes in cell viability (apoptosis) were observed. Results imply that appropriate biomechanical stimuli can be beneficial during rehabilitation for post traumatic OA (PTOA) treatment. In the second aim, a combination therapy of insulin-like growth factor-1 (IGF-1) and the glucocorticoid dexamethasone (Dex) was tested as a potential therapeutic for PTOA. The effects of this combination were examined at the transcriptional and protein levels in the presence of IL-i a. Our results showed that the combination of IGF- 1 and Dex significantly improved aggrecan biosynthesis, blocked aggrecan and collagen proteolysis and loss, and rescued cell viability. These dramatic results could not be achieved by using either IGF-1 or Dex alone, thus providing strong support for the concept and use of a combination therapy for PTOA treatment. Dex is used to relieve inflammation and pain for short term OA treatment; however, it has not been studied as a potential disease-modifying drug for OA. In the last aim, the pro-survival role of Dex was investigated at the signaling, gene expression, and protein levels. Results suggest that Dex inhibits caspase-dependent apoptosis pathways, possibly through suppression of the phosphorylation of JNK and NF-kB/ixB signaling pathways. Taken together, these studies support the use of glucocorticoid treatment for inflammation-related cartilage cell death such as that found in PTOA.
by Yang Li.
Ph.D.
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R, Kyvik Adriana. "Self-assembled monolayers for biological applications: design, processing, characterization and biological studies." Doctoral thesis, Universitat Autònoma de Barcelona, 2019. http://hdl.handle.net/10803/666882.
Full textAbstract:
Self-assembled monolayers (SAMs) on gold surfaces have been designed, processed,
characterized and used for specific biological studies. The studies performed include
the control of lipid bilayer diffusion, cell adhesion and vascularization studies and
also the creation of antimicrobial surfaces.
More specifically, dynamic SAMs on surfaces whose properties can be modified
with an electrochemical external stimulus have been developed and used to interrogate
biological systems. The developed platform has been applied to two different
applications to overcome present challenges when performing biological studies.
Firstly, in Chapter 2, the design and synthesis of all the molecules needed to
develop an electroactive platform, its processing as SAMs and the optimization of
the surface confined redox process between a non-reactive Hydroquinone (HQ)
termination and its corresponding reactive Benzoquinone (BQ) is reported. Two
different interfacial reactions taking place on the electroactivated surfaces were
studied in detail; the Diels-Alder (DA) and the Michael Addition (MA) interfacial
reactions, with cyclopentadiene (Cp) or thiol tagged molecules, respectively. The
comparative study between DA and MA as surface functionalization strategies with a
temporal control reveal that even though MA is not commonly used for this purpose
it offers an attractive strategy for stimulus activated functionalization for biological
applications.
In Chapter 3, the developed platform has been used to achieve a temporal control
of cell adhesion and in this way mimic in vivo conditions more accurately. Cell
adhesion plays fundamental roles in biological functions and as such, it is important
to control cell adhesion on materials used for biomedical applications. Towards this
aim, the dynamic interface developed has been used to immobilize cell adhesion promoting
peptides through the two different interfacial reactions, namely the DA and
the MA reaction, and a comparative study has been carried out. Moreover, a study
involving immobilized VEGF-mimicking peptide Qk has been conducted demonstrating
the possibility of using the novel peptide for directing cell differentiation into
tubular networks for in vitro platforms, by attaching them on a surface.
In Chapter 4, we have used the developed electroactive interface to control the
dynamics of lipid bilayers as cell membrane models, designed for transmembrane
protein characterization in a more in vivo like environment. Specifically, electroactive
SAMs have been used to control the moment in which tethering of lipid bilayer
deposited on them occurs and consequently decrease its diffusion. In this way,
proteins and lipids can maintain their fluidity until tethering is desired, a useful
platform for transmembrane protein characterization.
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Finally, in Chapter 5, a surface biofunctionalization strategy also based on SAMs
has been used to produce a bactericidal surface by successfully immobilizing novel
antimicrobial proteins produced by recombinant DNA technology. This is relevant in
view of the verge of an imminent antibiotics crisis. To confirm the antimicrobial activity
and biofilm growth prevention of these surfaces, a biofilm assay was performed
demonstrating that proteins retain their antimicrobial effect when immobilized.
All these strategies open new possibilities for controlled biomolecule immobilization
for fundamental biological studies and for applications in biotechnology, in the
interface of materials science and biology.
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Kisiday, John D. (John David) 1970. "In vitro culture of a chondrocyte-seeded peptide hydrogel and the effects of dynamic compression." Thesis, Massachusetts Institute of Technology, 2003. http://hdl.handle.net/1721.1/29614.
Full textAbstract:
Thesis (Ph. D. in Bioengineering)--Massachusetts Institute of Technology, Biological Engineering Division, 2003.Includes bibliographical references.
Emerging medical technologies for effective and lasting repair of articular cartilage include delivery of cells or cell-seeded scaffolds to a defect site to initiate de novo tissue regeneration. Biocompatible scaffolds assist in providing a template for cell distribution and extracellular matrix accumulation in a three-dimensional geometry. In these studies, a self-assembling peptide hydrogel is evaluated as a potential scaffold for cartilage repair using a model bovine cell source. A seeding technique is developed for 3-D encapsulation of chondrocytes in a peptide hydrogel. The chondrocyte-seeded peptide hydrogel was then evaluated cellular activities in vitro under standard culture conditions and also when subjected to dynamic compression. During 4 weeks of culture in vitro, chondrocytes seeded within the peptide hydrogel retained their morphology and developed a cartilage-like ECM rich in proteoglycans and type II collagen, indicative of a stable chondrocyte phenotype. Time dependent accumulation of this ECM was paralleled by increases in material stiffness, indicative of deposition of mechanically-functional neo-tissue. Culture of chondrocyte-seeded peptide hydrogels in ITS-supplemented medium was investigated as an alternative to high serum culture. Low serum (0.2%), ITS-supplemented medium was found to maintain high levels of cell division and extracellular matrix synthesis and accumulation, as seen in high serum culture. Furthermore, low serum, ITS medium induced minimal chondrocyte de-differentiation on the surface of the hydrogel. This is in contrast to high serum culture, where surface de-differentiation and subsequent proliferation led to a 5-10 cell thick layer that stained positive for type I collagen.
(cont.) The effects of dynamic compression of chondrocyte-seeded peptide hydrogels were evaluated over long-term culture. A non-continuous loading protocol was identified in which proteoglycan, but not protein, synthesis increased over static, free-swelling culture. Increases in GAG matrix accumulation were observed after at least 8 days of loading, while hydroxyproline accumulation was unaffected by dynamic compression. These data demonstrated dynamic compression differentially regulated the synthesis of proteoglycans. Analysis of GAG loss to the medium indicated peak proteoglycan catabolism occurred immediately after the initiation of loading. This phenomenon was further explored using a modified loading protocol that increased GAG loss to the medium. Peak GAG loss to the medium was 2-fold higher than previously observed, resulting in GAG accumulation values significantly less than controls. Hydroxyproline accumulation was minimally affected by loading, demonstrating that dynamic compression also differentially regulated the catabolism of proteoglycans. Proteoglycan catabolism was not predominantly due to physical disruption accumulated extracellular matrix or loss of newly-synthesized molecules. Instead, the presence of MMPs in the medium that coincided with GAG loss suggest a potential enzymatic mechanism. These results demonstrate the potential of a self-assembling peptide hydrogel as a scaffold for the synthesis and accumulation of a true cartilage-like extracellular matrix ...
John D. Kisiday.
Ph.D.in Bioengineering
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Al-Atar, Eman. "Dynamic modeling and process design of a membrane enhanced biological phosphorus removal process." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/31205.
Full textAbstract:
The design and operation of the membrane enhanced biological phosphorus removal (MEBPR) process was studied in the current research to utilize the utmost capacity of the membrane system for operating the process under high influent loads. The study was conducted in two parts. In the first part, a dynamic model was calibrated to predict data collected from the UBC MEBPR pilot plant. Then the calibrated model was utilized in simulation studies to develop guidelines for the design and operation of a UCT-type MEBPR process under high flowrates without jeopardizing the effluent quality. The Technical University of Delft model combined with ASM2d model (TUDP) which is developed for conventional biological phosphorus systems was found sufficient to describe the process behavior of the MEBPR process. The trend of the measured concentration profiles were reasonably predicted, but the exact concentration values for the anoxic nitrate and the effluent ortho-phosphate were not predicted. The calibrated model for the MEBPR process was able to predict the measured data collected from the UBC conventional enhanced biological phosphorus removal (CEBPR) process without changing any of the model parameters except for the rate of polyphosphate formation, k[sub pp], which was increased from 0.1 to 0.2 g P/(g COD • d) to better predict the anoxic ortho-phosphate concentrations. Simulation studies for the UCT-type MEBPR process showed that the sludge mass distribution in the bioreactor zones of the anaerobic and the aerobic zone are critical for the bio-P removal and the nitrification processes respectively. Appropriate design of the bioreactor zone volumes is important to ensure proper sludge mass distribution in the biological zones. A constant influent volatile fatty acid to total phosphorus concentration was also found important for an efficient bio-P removal process. The aerobic recycle flow was found to be most important for reducing the effluent nitrate concentration while minimizing nitrate leakage to the anaerobic zone. Based on the experimental results and the simulation studies carried out in the current project, a set of guidelines for the design and operation of a UCT-type MEBPR process and the application of process control were developed to achieve stable process performance for nutrient removal under high flowrate operation.Applied Science, Faculty of
Chemical and Biological Engineering, Department of
Graduate
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Li, Song. "Integrate qualitative biological knowledge for gene regulatory network reconstruction with dynamic Bayesian networks." [Ames, Iowa : Iowa State University], 2007.
Find full text
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Martin, Misfeld. "The influence of biological mediators on the dynamic function of the aortic root." Thesis, Imperial College London, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.411045.
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Kästner, Claudia [Verfasser]. "Ultra-Small Silver Nanoparticles - Dynamic Behavior in Aqueous and Biological Environments / Claudia Kästner." Berlin : Freie Universität Berlin, 2018. http://d-nb.info/1196805822/34.
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Cardillo, Giulia. "Fluid Dynamic Modeling of Biological Fluids : From the Cerebrospinal Fluid to Blood Thrombosis." Thesis, Institut polytechnique de Paris, 2020. http://www.theses.fr/2020IPPAX110.
Full textAbstract:
Dans cette thèse, trois modèles mathématiques ont été proposés, avec l’objectif de modéliser autant d’aspects complexes de la biomédecine, dans lesquels la dynamique des fluides du système joue un rôle fondamental: i) les interactions fluide-structure entre la pulsatilité du liquide céphalo-rachidien et la moelle épinière (modélisation analytique); ii) dispersion efficace d’un médicament dans l’espace sous-arachnoïdien (modélisation numérique); et iii) la formation et l’évolution d’un thrombus au sein du système cardiovasculaire (modélisation numérique).Le liquide céphalorachidien est un fluide aqueux qui entoure le cerveau et la moelle épinière afin de les protéger. Une connaissance détaillée de la circulation du liquide céphalorachidien et de son interaction avec les tissus peut être importante dans l’étude de la pathogenèse de maladies neurologiques graves, telles que la syringomyélie, un trouble qui implique la formation de cavités remplies de liquide (seringues) dans la moelle épinière.Par ailleurs, dans certains cas, des analgésiques - ainsi que des médicaments pour le traitement de maladies graves telles que les tumeurs et les infections du liquide céphalorachidien - doivent être administrés directement dans le liquide céphalorachidien. L’importance de connaître et de décrire l’écoulement du liquide céphalorachidien, ses interactions avec les tissus environnants et les phénomènes de transport qui y sont liés devient claire. Dans ce contexte, nous avons proposé: un modèle capable de décrire les interactions du liquide céphalo-rachidien avec la moelle épinière, considérant cela, pour la première fois, comme un milieu poreux imprégné de différents fluides (sang capillaire et veineux et liquide céphalo-rachidien); et un modèle capable d’évaluer le transport d’un médicament dans l’espace sousarachnoïdien, une cavité annulaire remplie de liquide céphalo-rachidien qui entoure la moelle épinière.Avec le troisième modèle proposé, nous entrons dans le système cardiovasculaire.Dans le monde entière, les maladies cardiovasculaires sont la cause principale de mortalité. Parmi ceux-ci, nous trouvons la thrombose, une condition qui implique la formation d’un caillot à l’intérieur d’un vaisseau sanguin, qui peut causer sa occlusion. À cet égard, un modèle numérique a été développé qui étudie la formation et l’évolution des thrombus, en considérant simultanément les aspects chimico-biomécaniques et dynamiques des fluides du problème. Dans le modèle proposé pour la première fois, l'importance du rôle joué par les gradients de contrainte de cisaillement dans le processus de thrombogenèse est pris en compte.Les modèles sélectionnés ont fourni des résultats intéressants. Tout d’abord, l’étude des interactions fluide-structure entre le liquide céphalo-rachidien et la moelle épinière a mis en évidence es conditions pouvant induire l’apparition de la syringomyélie. Il a été observé comment la déviation des valeurs physiologiques du module d’Young de la moelle épinière, les pressions capillaires dans l’interface moelle-espace sousarachnoïdien et la perméabilité des compartiments capillaire et veineux, conduisent à la formation de seringues.Le modèle de calcul pour l’évaluation de la dispersion pharmacologique dans l’espace sousarachnoïdien a permis une estimation quantitatif de la diffusivité effective du médicament, une quantité qui peut aider à l’optimisation des protocoles d’injections intrathécales.Le modèle de thrombogenèse a fourni un instrument capable d’étudier quantitativement l’évolution des dépôts de plaquettes dans la circulation sanguine. En particulier, les résultats ont fourni des informations importantes sur la nécessité de considérer le rôle de l’activation mécanique et de l’agrégation des plaquettes aux côtés de la substance chimiqueIn the present thesis, three mathematical models are described. Three different biomedical issues, where fluid dynamical aspects are of paramount importance, are modeled: i) Fluid-structure interactions between cerebro-spinal fluid pulsatility and the spinal cord (analytical modeling); ii) Enhanced dispersion of a drug in the subarachnoid space (numerical modeling); and iii) Thrombus formation and evolution in the cardiovascular system (numerical modeling).The cerebrospinal fluid (CSF) is a liquid that surrounds and protects the brain and the spinal cord. Insights into the functioning of cerebrospinal fluid are expected to reveal the pathogenesis of severe neurological diseases, such as syringomyelia that involves the formation of fluid-filled cavities (syrinxes) in the spinal cord.Furthermore, in some cases, analgesic drugs -- as well drugs for treatments of serious diseases such as cancers and cerebrospinal fluid infections -- need to be delivered directly into the cerebrospinal fluid. This underscores the importance of knowing and describing cerebrospinal fluid flow, its interactions with the surrounding tissues and the transport phenomena related to it. In this framework, we have proposed: a model that describes the interactions of the cerebrospinal fluid with the spinal cord that is considered, for the first time, as a porous medium permeated by different fluids (capillary and venous blood and cerebrospinal fluid); and a model that evaluates drug transport within the cerebrospinal fluid-filled space around the spinal cord --namely the subarachnoid space--.The third model deals with the cardiovascular system. Cardiovascular diseases are the leading cause of death worldwide, among these diseases, thrombosis is a condition that involves the formation of a blood clot inside a blood vessel. A computational model that studies thrombus formation and evolution is developed, considering the chemical, bio-mechanical and fluid dynamical aspects of the problem in the same computational framework. In this model, the primary novelty is the introduction of the role of shear micro-gradients into the process of thrombogenesis.The developed models have provided several outcomes. First, the study of the fluid-structure interactions between cerebro-spinal fluid and the spinal cord has shed light on scenarios that may induce the occurrence of Syringomyelia. It was seen how the deviation from the physiological values of the Young modulus of the spinal cord, the capillary pressures at the SC-SAS interface and the permeability of blood networks can lead to syrinx formation.The computational model of the drug dispersion has allowed to quantitatively estimate the drug effective diffusivity, a feature that can aid the tuning of intrathecal delivery protocols.The comprehensive thrombus formation model has provided a quantification tool of the thrombotic deposition evolution in a blood vessel. In particular, the results have given insight into the importance of considering both mechanical and chemical activation and aggregation of platelets
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Swensen, Adam Clayton. "Investigation of Dynamic Biological Systems Using Direct Injection and Liquid Chromatography Mass Spectrometry." BYU ScholarsArchive, 2016. https://scholarsarchive.byu.edu/etd/6574.
Full textAbstract:
In biological systems, small changes can have significant impacts. It is, therefore, very important to be able to identify these changes in order to understand what is occurring in the organism. In many cases, this is not an easy task. Mass spectrometry has proven to be a very useful tool in elucidating biological changes even at a very small scale. Several different mass spectrometry based techniques have been developed to discover and investigate complex biological changes. Some of these techniques, such as proteomics, have been through years of development and have advanced to the point that anyone can complete complex analyses of global protein identification and measurement with relative ease. Other techniques are still developing and still have some ground to cover in terms of experimental outcome and ease of execution. Herein we show improvements we have made in high-throughput high-resolution mass spectrometry based techniques to identify and quantify small molecules that are involved in significant biological changes. To begin, we show that our improved high-resolution mass spectrometry based lipidomics techniques are capable of identifying small changes in diseased states that are associated with inflammation, mitochondrial shape and function, and cancer. With our techniques we have been able to extract, identify, and quantify several thousand unique lipid species from complex samples with confidence. Our initial studies looked at global lipidome profiles of differing tissue types from human and mouse biopsies. This was then adapted to compare the global lipidomes of diseased states against healthy states in asthmatic lung tissue, cigarette smoke treated cells, high fat high sugar (HFHS) stressed animals (with and without additional treatment), and in signaling lipids associated with cell death resistance and growth signaling in pancreatic cancer. As a result of our success with lipidomic method improvement we then adapted our techniques and knowledge for use in elucidating small molecule signaling peptides and oxidation changes in proteins. We were able to show that our improved liquid chromatography mass spectrometry based small molecule assays are capable of identifying and quantifying small peptides and protein modifications that would otherwise be undetectable using traditional techniques. This work resulted in the development of a scalable method to detect and quantify the small iron-regulatory hormone known as hepcidin from a variety of samples such as blood, urine, and cell-culture media. We were also instrumental in evaluating and revising a new ultra-high pressure liquid chromatography (UHPLC) system that allows for better separation of analytes from complex mixtures for identification and quantification. Through these advances we hope to aid researchers and clinicians to enable them to use mass spectrometry to further our knowledge about the small but significant changes that regulate complex biological systems.
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Guner, Ugur. "Identification of topological and dynamic properties of biological networks through diverse types of data." Diss., Georgia Institute of Technology, 2011. http://hdl.handle.net/1853/41116.
Full textAbstract:
It is becoming increasingly important to understand biological networks in order to understand complex diseases, identify novel, safer protein targets for therapies and design efficient drugs. 'Systems biology' has emerged as a discipline to uncover biological networks through genomic data. Computational methods for identifying these networks become immensely important and have been growing in number in parallel to increasing amount of genomic data under the discipline of 'Systems Biology'.
In this thesis we introduced novel computational methods for identifying topological and dynamic properties of biological networks. Biological data is available in various forms. Experimental data on the interactions between biological components provides a connectivity map of the system as a network of interactions and time series or steady state experiments on concentrations or activity levels of biological constituents will give a dynamic picture of the web of these interactions. Biological data is scarce usually relative to the number of components in the networks and subject to high levels of noise. The data is available from various resources however it can have missing information and inconsistencies. Hence it is critical to design intelligent computational methods that can incorporate data from different resources while considering noise component.
This thesis is organized as follows; Chapter 1 and 2 will introduce the basic concepts for biological network types. Chapter 2 will give a background on biochemical network identification data types and computational approaches for reverse engineering of these networks. Chapter 3 will introduce our novel constrained total least squares approach for recovering network topology and dynamics through noisy measurements. We proved our method to be superior over existing reverse engineering methods. Chapter 4 is an extension of chapter 3 where a Bayesian parameter estimation algorithm is presented that is capable of incorporating noisy time series and prior information for the connectivity of network. The quality of prior information is critical to be able to infer dynamics of the networks. The major drawback of prior connectivity data is the presence of false negatives, missing links. Hence, powerful link prediction methods are necessary to be able to identify missing links. At this junction a novel link prediction method is introduced in Chapter 5. This method is capable of predicting missing links in a connectivity data. An application of this method on protein-protein association data from a literature mining database will be demonstrated. In chapter 6 a further extension into link prediction applications will be given. An interesting application of these methods is the drug adverse effect prediction. Adverse effects are the major reason for the failure of drugs in pharmaceutical industry, therefore it is very important to identify potential toxicity risks in the early drug development process. Motivated by this chapter 6 introduces our computational framework that integrates drug-target, drug-side effect, pathway-target and mouse phenotype-mouse genes data to predict side effects. Chapter 7 will give the significant findings and overall achievements of the thesis. Subsequent steps will be suggested that can follow the work presented here to improve network prediction methods.
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Loya, Adil. "Large scale dynamic molecular modelling of metal oxide nanoparticles in engineering and biological fluids." Thesis, University of Hertfordshire, 2015. http://hdl.handle.net/2299/15336.
Full textAbstract:
Nanoparticles (NP) offer great merits over controlling thermal, chemical and physical properties when compared to their micro-sized counterparts. The effectiveness of the dispersion of the NP is the key aspect of the applications in nanotechnology. The project studies the characterization and modification of functional NPs aided by the means of large scale molecular thermal dynamic computerized dispersing simulations, in the level of Nanoclusters (NC). Carrying out NP functionality characterisation in fluids can be enhanced, and analysed through computational simulation based on their interactions with fluidic media; in terms of thermo-mechanical, dynamic, physical, chemical and rheological properties. From the engineering perspective, effective characterizations of the nanofluids have also been carried out based on the particles sizes and particle-fluids Brownian motion (BM) theory. The study covered firstly, investigation of the pure CuO NP diffusion in water and hydrocarbon fluids, secondly, examination of the modified CuO NP diffusion in water. In both cases the studies were put under experiments and simulations for data collection and comparison. For simulation the COMPASS forcefield, smoothed particle hydrodynamic potential (SPH) and discrete particle dynamics potential (DPD) were implemented through the system. Excellent prediction of BM, Van der Waals interaction, electrostatic interaction and a number of force-fields in the system were exploited. The experimental results trend demonstrated high coherence with the simulation results. At first the diffusion coefficient was found to be 1.7e-8m2/s in the study of CuO NC in water based fluidic system. Secondly highly concurrent simulation results (i.e. data for viscosity and thermal conductivity) have been computed to experimental coherence. The viscosity trend of MD simulation and experimental results show a high level of convergence for temperatures between 303-323K. The simulated thermal conductivity of the water-CuO nanofluid was between 0.6—0.75W•m−1•K−1, showing a slight increase following a rise in temperature from 303 to 323 K. Moreover, the alkane-CuO nanofluid experimental and simulated work was also carried out, for analysing the thermo-physical quantities. The alkane-CuO nanofluid viscosity was found 0.9—2.7mpas and thermal conductivity is between 0.1—0.4W•m−1•K−1. Finally, the successful modification of the NPs on experimental and simulation platform has been analysed using different characterization variables. Experimental modification data has been quantified by using Fourier Transformation Infrared (FTIR) peak response, from particular ranges of interest i.e. 1667-1609cm-1 and 1668-1557cm-1. These FTIR peaks deduced Carboxylate attachment on the surface of NPs. Later, MD simulation was approached to mimic experimental setup of modification chemistry and similar agglomerations were observed as during experimental conditions. However, this approach has not been presented before; therefore this study has a significant impact on describing the agglomeration of modified NPs on simulation and experimental basis. Henceforth, the methodology established for metal oxide nanoparticle dispersion simulation is a novelty of this work.
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Zhang, Bai. "Modeling and Characterization of Dynamic Changes in Biological Systems from Multi-platform Genomic Data." Diss., Virginia Tech, 2011. http://hdl.handle.net/10919/29111.
Full textAbstract:
Biological systems constantly evolve and adapt in response to changed environment and external stimuli at the molecular and genomic levels. Building statistical models that characterize such dynamic changes in biological systems is one of the key objectives in bioinformatics and computational biology. Recent advances in high-throughput genomic and molecular profiling technologies such as gene expression and and copy number microarrays provide ample opportunities to study cellular activities at the individual gene and network levels. The aim of this dissertation is to formulate mathematically dynamic changes in biological networks and DNA copy numbers, to develop machine learning algorithms to learn these statistical models from high-throughput biological data, and to demonstrate their applications in systems biological studies.
The first part (Chapters 2-4) of the dissertation focuses on the dynamic changes taking placing at the biological network level. Biological networks are context-specific and dynamic in nature. Under different conditions, different regulatory components and mechanisms are activated and the topology of the underlying gene regulatory network changes. We report a differential dependency network (DDN) analysis to detect statistically significant topological changes in the transcriptional networks between two biological conditions. Further, we formalize and extend the DDN approach to an effective learning strategy to extract structural changes in graphical models using l1-regularization based convex optimization. We discuss the key properties of this formulation and introduce an efficient implementation by the block coordinate descent algorithm. Another type of dynamic changes in biological networks is the observation that a group of genes involved in certain biological functions or processes coordinate to response to outside stimuli, producing distinct time course patterns. We apply the echo stat network, a new architecture of recurrent neural networks, to model temporal gene expression patterns and analyze the theoretical properties of echo state networks with random matrix theory.
The second part (Chapter 5) of the dissertation focuses on the changes at the DNA copy number level, especially in cancer cells. Somatic DNA copy number alterations (CNAs) are key genetic events in the development and progression of human cancers, and frequently contribute to tumorigenesis. We propose a statistically-principled in silico approach, Bayesian Analysis of COpy number Mixtures (BACOM), to accurately detect genomic deletion type, estimate normal tissue contamination, and accordingly recover the true copy number profile in cancer cells.Ph. D.
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Sundaraj, Kenneth. "Real-time dynamic simulation and 3D interaction of biological tissue : application to medical simulators." Grenoble INPG, 2004. http://www.theses.fr/2004INPG0012.
Full textAbstract:
L'avènement de l'imagerie médicale et de nouvelles techniques opératoires a bouleversé les méthodes de travail des médecins. Mais ce changement nécessitera une formation renforcée des praticiens et chirurgiens. C'est pourquoi le dévelopment d'outils appropriés comme les simulateurs médico-chirurgicaux se fait de plus en plus ressentir. Dans ce cadre, nous nous sommes intéressés au problème de la modélisation des phénomènes de déformation de tissu biologique et à la détection des collisions dans un environment virtuel. Dans un premier temps, nous présentons les différents modèles physiques existants et les différentes méthodes de résolution numérique associées aux objets déformable. Nous proposons ensuite un modèle développé pour la simulation de tissu biologique, en présentant successivement les aspects liés à la formulation du modèle, à la résolution du modèle, et au traitement des interactions physiques. Ce modèle, basé sur l'utilisation du principe de Pascal, permet de modéliser de manière relativement satisfaisante des corps biologiques, tout en permettant une simulation interactive. Dans un deuxième temps, nous présentons les différents algorithmes existants pour la détectionde collision, ainsi que la difficulté d'adapter ces algorithmes aux simulateurs médicaux où les objets déformables complexes forment la base du modèle. Nous proposons ensuite les algorithmes développés pour traiter ce problème dans le cadre des simulateurs médicaux. Ces algorithmes présentent des caractéristiques de robustesse numérique et d'efficacité supérieures á l'existant, et permettent de traiter des corps déformables. Nous appliquons ces résultats dans le cadre de deux simulateur medicaux
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Tesson, Karen Jane. "Dynamic networks : an interdisciplinary study of network organization in biological and human social systems." Thesis, University of Bath, 2006. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.434065.
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Jumpathong, Watthanachai. "The dynamic interplay between DNA damage and metabolism : the metabolic fate and transport of DNA lesions and novel DNA damage derived from intermediary metabolism." Thesis, Massachusetts Institute of Technology, 2014. http://hdl.handle.net/1721.1/93772.
Full textAbstract:
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Biological Engineering, 2014.This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections.
Cataloged from student-submitted PDF version of thesis.
Includes bibliographical references.
The work presented in this thesis explores two novel and complementary facets of endogenous DNA damage: the development of biomarkers of inflammation based on metabolites of DNA damage products and the formation of DNA adducts by electrophilic products of intermediary metabolism. From the first perspective, endogenous DNA damage generated by reactive oxygen and nitrogen species from inflammation and oxidative stress has shown strong mechanistic links to the pathophysiology of cancer and other human diseases, with the damage products reflecting all types of damage chemistries including oxidation, deamination, halogenation, nitration and alkylation. However, the use of DNA damage products as biomarkers has been limited by poor understanding of the damage actually arising in tissues and a lack of appreciation of the fate of DNA damage products from the moment of formation at the site of damage to release from cells to final excretion from the body. The goal of the work presented in the first part of this thesis was to investigate the metabolic fates of the base propenal products arising from 4'-oxidation of 2'-deoxyribose in DNA, one of the most common products of DNA oxidation, and to define base propenal metabolites as potential biomarkers of oxidative stress. This project was approached with systematic metabolite profiling, starting with prediction of potential base propenal metabolites based on a priori knowledge of its chemical reactivity as an [alpha],[beta]-unsaturated aldehyde toward glutathione (GSH) in non-enzymatic reactions and in rat liver cell extracts. Of 15 potential candidates predicted and identified from these in vitro studies, analysis of urine samples from rats given intravenous doses (IV) of thymine propenal revealed three major metabolites: thymine propenoic acid and two mercapturic acid derivatives, which accounted for ~6% of the injected dose. An additional four metabolites, including conjugates with GSH, cysteinylglycine and cysteine, were observed in bile and accounted for ~22% of the dose. One of the major metabolites detected in urine and bile, a bis-mercapturic acid adduct of reduced thymine propenal was detected as a background excretory product in saline-treated rats and was significantly elevated after oxidative stress caused by treatment with bleomycin and CCl₄. Our observations suggest that metabolism and disposition of damaged biomolecules should be considered as crucial factors in the development of biomarkers relevant to inflammation and oxidative stress. The second part of this thesis addresses the complementary hypothesis that electrophilic metabolites generated endogenously from intermediary metabolism can react with DNA to form adducts. This concept is illustrated here with glyoxylate from the glyoxylate metabolic cycle, whicvh plays a key role as an alternative to the TCA cycle in plants, bacteria, protists and fungi under changing conditions of environmental nutrients. The goal of this project was to characterize DNA adducts caused by glyoxylate in the mycobacterium M. smegmatis, with the studies motivated by the higher-than-expected mutation rate of mycobacteria during dormancy induced by nutrient deprivation and a shift to utilization of the glyoxylate cycle. Initially, in vitro reactions of 2'-deoxyguanosine (dG) with glyoxylate yielded N²-carboxyhydroxymethyl dG (N²-CHMdG) as the only adduct. However, the adduct proved to be unstable, so a reduction-based analytical method was developed to yield the stable amine derivative, N2-carboxymethyl dG (N²-CMdG). This stable adduct was used to develop an isotope-dilution chromatography-coupled tandem mass spectrometry method to quantify N²-CHMdG as N²-CMdG in calf thymus DNA treated with glyoxylate in vitro. This analytical method was then applied to quantify and compare the level N2-CMdG in (1) wild-type M. smegmatis grown in rich medium (7H9) or in minimal M9 medium supplemented with acetate, the latter inducing a switch from the TCA cycle to the glyoxylate cycle; and (2) the isocitrate dehydrogenase (ICD)-deficient mutant of M. smegmatis. Mycobacteria grown in the acetate medium experienced a 2-fold increase in the adduct compared to those grown in 7H9. Similarly, the adduct increased 2-fold in the ICD mutant compared to wild-type M. smegmatis grown in 7H9. The results support the idea that shifts in intermediary metabolism can lead to DNA damage that may cause mutations associated with nutrient deprivation in mycobacteria, with implications for the genetic toxicology of other metabolism-derived electrophiles.
by Watthanachai Jumpathong.
Ph. D.
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Abuzayan, Khaled Jebril. "Physical and neurophysiological factors influencing dynamic balance." Thesis, Liverpool John Moores University, 2010. http://researchonline.ljmu.ac.uk/5965/.
Full textAbstract:
Static and dynamic balance are essential in daily and sports life. Many factors have been identified as influencing static balance control, two of which are carrying additional weight and localized muscle fatigue but their influence on dynamic balance in sport activities has not been fully established. Therefore, the aim of this thesis was to investigate the characteristics of dynamic balance in sport related activities, with specific reference to the influence of body mass changes and muscular fatigue. Study one: The objectives of study one (methodological study, n = 5) were to apply the extrapolated Centre of Mass (XCoM) method and other relevant variables (centre of pressure, CoP; Centre of Mass, CoM; shear forces, Fh; kinetic energy, KE; momentum, P; and angular impulse, AI) to investigate sport related activities such as hopping and jumping. Many studies have represented the CoP data without mentioning its accuracy so several experiments were done to establish the agreement between the CoP and the projected CoM in a static condition. It was found that there was an inaccuracy with the average difference about 4mm. This meant that the angular impulse could not be reliably calculated. Its horizontal component, representing the Friction Torque (Q), could be reliably computed for dynamic balance. The implementation of the XCoM method was found to be practical for evaluating both static and dynamic balance. The general findings were that the CoP, the CoM, the XCoM, Fh, and Qwere more informative than the other variables (e.g. KE, P, and AI) during static and dynamic balance. The XCoM method was found to be applicable to dynamic balance as well as static balance. Study 2: The objectives of study two (baseline study, n =20) were to implement Matlab procedures for quantifying selected static and dynamic balance variables, establish baseline data of selected variables which characterize static and dynamic balance activities in a population of healthy young adult males, and to examine any trial effects on these variables. The results indicated that the implementation of Matlab procedures for quantifying selected static and dynamic balance variables was practical and enabled baseline data to be established for selected variables. There was no significant trial effect. Recommendations were made for suitable tests to be used in later studies. Specifically it was found that one foot-tiptoes tests either in static or dynamic balance are too challenging for most participants in normal circumstances. A one foot-flat eyes open test was considered to be representative and challenging for static balance, while adding further vertical jump and landing tests (two feet flat and one foot flat vertical jump) to the horizontal jumping and hopping for dynamic balance was considered to be more representative of sports situations. The main differences between horizontal and vertical jumping were in anterior-posterior direction. Study 3: The objectives of study three (differentiation study, n =20) were to establish the influence of physical (external added weight) and neurophysiological (fatigue) factors on static and dynamic balance in sport related activities. This was typified statically by the Romberg test (one foot flat, eyes open) and dynamically by jumping and hopping in both horizontal and vertical directions. Statically, added weight increased body's inertia and therefore decreased body sway in anterior-posterior direction though not significantly. Dynamically, added weight significantly increased body sway in both mideo-lateral and anterior-posterior directions, indicating instability, and the use of the counter rotating segments mechanism to maintain balance was demonstrated. Fatigue on the other hand significantly increased body sway during static balance as a neurophysiological adaptation primarily to the inverted pendulum mechanism. Dynamically, fatigue significantly increased body sway in both mideo-lateral and anterior-posterior directions again indicating instability but with a greater use of counter rotating segments mechanism. Differential adaptations for each of the two balance mechanisms (inverted pendulum and counter rotating segments) were found between one foot flat and two feet flat dynamic conditions, as participants relied more heavily on the first in the one foot flat conditions and relied more on the second in the two feet flat conditions. Conclusion: Results from this thesis are expected to aid towards advancing the understanding of balance in sport related activities, and can provide a solid foundation for future work in this area. In particular, a method was established to assess static and dynamic balance, baseline data for these associations was provided, and differential adaptations to physical or neurophysiological constraints were found. Valuable associations between specific variables and the first two mechanisms of balance were demonstrated.
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Jang, Seunghee Shelly. "Parameter estimation of stochastic nonlinear dynamic processes using multiple experimental data sets : with biological applications." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/7294.
Full textAbstract:
The dynamic behavior of many chemical and biological processes is defined by a set of nonlinear differential equations that constitute a model. These models typically contain parameters that need to be estimated using experimental data. A number of factors such as sampling intervals, number of measurements and noise level characterize the quality of data, and have a direct effect on the quality of estimated parameters. The quality of experimental data is rather poor in many processes due to instrument limitations or other physical and economical constraints. Traditional parameter estimation methods either yield inaccurate results or are not applicable when applied to such data. Despite this, it is common practice to apply them on a merged data set obtained by pooling together data from multiple experiments. Considering the difficulties in maintaining consistent experimental conditions, straightforward integration of multiple data sets will not provide the best estimates of parameters.
In this thesis, a new approach to estimate parameters of nonlinear dynamic models using multiple experimental data is proposed. The approach uses Bayesian inference, and sequentially updates prior probability distribution of parameters for systematic integration of multiple data sets. An expression for posterior probability distribution of parameters conditional on all experimental data sets is derived. This expression is often analytically intractable; therefore two instances of numerical approximation method called Markov Chain Monte Carlo - Metropolis-Hastings (MH) algorithm and Gibbs sampler (GS) - are implemented. The two algorithms form inner and outer levels of iterations, where the MH algorithm is used in the inner level to estimate conditional probability distributions of individual parameters, which is used in the outer level in conjunction with the GS to estimate joint probability distributions of the parameters.
The proposed method is applied to three nonlinear biological processes to estimate probability distribution of parameters with a small number of irregular samples. The approximated probability distribution provides a straightforward tool to calculate confidence interval of parameter estimates and is robust to initial guess of parameter value. Correlation among model parameters, quality of each model, and the approach taken to optimize the high cost of MCMC sampling are discussed.
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Zehraoui, Abderrahman. "ENHANCED BIOLOGICAL OXIDATION OF HYDROPHOBIC COMPOUNDS UNDER DYNAMIC LOAD IN A TRICKLE BED AIR BIOFILTER." University of Cincinnati / OhioLINK, 2013. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1384849490.
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Goel, Gautam. "Dynamic flux estimation a novel framework for metabolic pathway analysis /." Diss., Atlanta, Ga. : Georgia Institute of Technology, 2009. http://hdl.handle.net/1853/31769.
Full textAbstract:
Thesis (Ph.D)--Biomedical Engineering, Georgia Institute of Technology, 2010.Committee Chair: Voit, Eberhard O.; Committee Member: Butera, Robert; Committee Member: Chen, Rachel; Committee Member: Kemp, Melissa; Committee Member: Neves, Ana Rute. Part of the SMARTech Electronic Thesis and Dissertation Collection.
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Vester, Diana [Verfasser], and Udo [Verfasser] Reichl. "Molecular biological analysis of dynamic interactions between influenza viruses and host cells : host cell proteomes and viral replication dynamics / Diana Vester ; Udo Reichl." Magdeburg : Universitätsbibliothek, 2011. http://d-nb.info/1047202816/34.
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Harding, Theodor. "A prototype dynamic model for the co-treatment of a high strength simple-organic industrial effluent and coal-mine drainage." Doctoral thesis, Faculty of Engineering and the Built Environment, 2020. http://hdl.handle.net/11427/32660.
Full textAbstract:
This research study's the use of biological sulfate reduction technologies for the treatment of Sasol Secunda's coal-mine drainage (CMD) using Fischer-Tropsch Reaction Water (FTRW) as a cost-efficient carbon source. The research aims to develop a prototype dynamic model that describes this co-treatment of FTRW and CMD in both a continuously stirred tank reactor (CSTR) biological sulfate reduction (BSR) system and a BSR gas-lift (BSR-GL) integrated system. The BSR-GL system recovers elemental sulfur (S0 ) from the H2S produced and stripped from the BSR unit. Furthermore, this study aims to use the prototype model for a quantitative comparison of the CSTR-BSR and BSR-GL systems. Two bench-scale 5-litre CSTR-BSR and a 20-litre BSR-GL system were operated, under varying feed COD concentrations and hydraulic retention times (HRTs), to generate datasets for use in verification and a rudimentary validation of the prototype model. The BSR-GL integrated system includes 1) a 1-litre H2S gas reactive absorption (ABS) unit utilising an aqueous ferric solution for the recovery of elemental sulfur (S0 ) from sulfide and 2) ferrous biological oxidation reactor to regenerate ferric from the ferrous for re-supply to the ABS unit. The datasets generated in the experimental study allowed for the identification, mathematical modelling and reaction verification of 32 components that interact as reactants and products in 23 reactions observed in the two BSR systems. The prototype model is presented in a mass and charge balanced Gujer matrix that includes, i) 5 SRB mediated processes, ii) 2 liquid-gas mass transfer processes, iii) 3 processes describing the ABS and Fe2+ bio-oxidation units, iv) 4 processes describing sulfide and elemental sulfur oxidation and v) the S0 and poly-sulfide aqueous equilibrium and vi) 9 processes describing death regeneration and BPO hydrolysis. This prototype model was implemented in the DHI WEST® software for initial stage simulation trials. The experimental datasets allowed for the first-stage estimation of the best-fit reaction rate equations and the calibration of the kinetic parameters related to the 23 reactions, using MATLAB® curve fitting toolbox. A pre-processor that describe the pH and equilibrium chemistry of the components of the artificially prepared FTRW+CMD feed mixture batches under varying total concentrations have also been developed in this research. This was done to generated influent file to the DHI WEST® simulations that incorporated the dynamics related to the FTRW+CMD feed mixtures. The sulfate utilisation rate (gSO4 -2 .l-1 .d-1 ) of the GL-BSR and CSTR-BSR systems were compared to determine which system had the best sulfate removal. The results were found to be as follows; a. On comparison it was found that the sulfate substrate utilisation rate for the CSTR_BSR system is 39.28% of that of the BSR-GL_N2 system, where both systems were fed at feed mixture of COD of 2500mgCOD/l, where the COD:SO4 2- was 0.7, b. For the same systems fed a feed mixture of COD at 5000mgCOD/l (COD:SO4 2- = 0.7), the sulfate substrate utilisation rate for the CSTR_BSR system was found to be 17.86% less than that of the BSR_GLN2 system. c. Finally, it was also found that the substrate utilisation rate for the CSTR_BSR system was 30.06% less than that of the BSR_GLN2 system at Se of 4gCOD/l, for both systems fed substrate at 5000mgCOD/l. Thus, it can be concluded that the sulfate substrate utilisation rate for the BSR-GL system is higher than that of the CSTR_BSR system, for systems fed COD feed mixtures at 2.5 or 5gCOD/l where both systems have the same effluent substrate concentrations. However, the difference in the comparative substrate utilisation rate is less at higher feed substrate concentrations. This is the influence of substrate inhibition on the active SRB biomass, which increases with higher effluent substrate concentrations. Finally, this research found that the use of gas-lift reactor technologies is superior to CSTR technologies in the treatment of coal-mine drainage utilising biological sulfate reduction (BSR). The CSTR-BSR system, fed sulfate between 1.6 to 14gSO4 2- /l, produced effluent with high dissolved H2S concentrations, on average 285mgS/l and maximum at >600mgS/l. Releasing this effluent to the environment would be hazardous to aquatic and human health and corrosive to infrastructure. As such, the effluent from the CSTR-BSR system requires further treatment to stabilise the water for any use. The BSR-GL technology allows for the conversion of the H2S produced during BSR reactions to form elemental sulfur, which is a resource recovered from this process, thus complying to the circular economy aim of this study.
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Schneider, Nils [Verfasser], and Matthias [Akademischer Betreuer] Meier. "Development of microfluidic and biological technologies for quantitative and dynamic analysis of gene expression in single cells." Freiburg : Universität, 2018. http://d-nb.info/1189583208/34.
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Yamada, Ayako. "Dynamic self-organization of biomolecules in relation to their biological significance : single giant DNA and phospholipid molecules." 京都大学 (Kyoto University), 2008. http://hdl.handle.net/2433/136864.
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Lee, Sang-Hyun. "The dynamic nuclear transport regulation of NF-kB and IkBS." free to MU campus, to others for purchase, 2002. http://wwwlib.umi.com/cr/mo/fullcit?p3060116.
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Abdullah, Syed Zaki. "Investigation of effect of dynamic operational conditions on membrane fouling in a membrane enhanced biological phosphorus removal process." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/264.
Full textAbstract:
The membrane bioreactor (MBR) is becoming increasingly popular for wastewater treatment, mainly due to its capability of producing high quality effluent with a relatively small footprint. However, high plant maintenance and operating costs due to membrane fouling limit the wide spread application of MBRs. Membrane fouling generally depends on the interactions between the membrane and, the activated sludge mixed liquor, which in turn, are affected by the chosen operating conditions. The present research study aimed to explore the process performance and membrane fouling in the membrane enhanced biological phosphorus removal (MEBPR) process under different operating conditions by, (1) comparing two MEBPRs operated in parallel, one with constant inflow and another with a variable inflow, and by, (2) operating the MEBPRs with different solids retention times (SRT).
On-line filtration experiments were conducted simultaneously in both MEBPR systems by using test membrane modules. From the transmembrane pressure (TMP) data of the test membrane modules, it was revealed that fouling propensities of the MEBPR mixed liquors were similar in both parallel reactors under the operating conditions applied, although the fouling propensity of the aerobic mixed liquors of both reactors increased when the SRT of the reactors was reduced.
Routinely monitored reactor performance data suggest that an MEBPR process with a varying inflow (dynamic operating condition) performs similarly to an MEBPR process with steady operating conditions at SRTs of 10 days and 20 days. Mixed liquor characterization tests were conducted, including critical flux, capillary suction time (CST), time to filter (TTF) and, bound and soluble extracellular polymeric substances (EPS) were quantified, to evaluate their role on membrane fouling. The tests results suggest that the inflow variation in an MEBPR process did not make a significant difference in any of the measured parameters.
With decreased SRT, an increase in the concentrations of EPS was observed, especially the bound protein, and the bound and soluble humic-like substances. This suggests that these components of activated sludge mixed liquors may be related to membrane fouling. No clear relationship was observed between membrane fouling and other measured parameters, including critical flux, normalized CST and normalized TTF.Applied Science, Faculty of
Civil Engineering, Department of
Graduate
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Abdullah, Syed. "Investigation of effect of dynamic operational conditions on membrane fouling in a membrane enhanced biological phosphorus removal process." Thesis, University of British Columbia, 2007. http://hdl.handle.net/2429/264.
Full textAbstract:
The membrane bioreactor (MBR) is becoming increasingly popular for wastewater treatment, mainly due to its capability of producing high quality effluent with a relatively small footprint. However, high plant maintenance and operating costs due to membrane fouling limit the wide spread application of MBRs. Membrane fouling generally depends on the interactions between the membrane and, the activated sludge mixed liquor, which in turn, are affected by the chosen operating conditions. The present research study aimed to explore the process performance and membrane fouling in the membrane enhanced biological phosphorus removal (MEBPR) process under different operating conditions by, (1) comparing two MEBPRs operated in parallel, one with constant inflow and another with a variable inflow, and by, (2) operating the MEBPRs with different solids retention times (SRT).
On-line filtration experiments were conducted simultaneously in both MEBPR systems by using test membrane modules. From the transmembrane pressure (TMP) data of the test membrane modules, it was revealed that fouling propensities of the MEBPR mixed liquors were similar in both parallel reactors under the operating conditions applied, although the fouling propensity of the aerobic mixed liquors of both reactors increased when the SRT of the reactors was reduced.
Routinely monitored reactor performance data suggest that an MEBPR process with a varying inflow (dynamic operating condition) performs similarly to an MEBPR process with steady operating conditions at SRTs of 10 days and 20 days. Mixed liquor characterization tests were conducted, including critical flux, capillary suction time (CST), time to filter (TTF) and, bound and soluble extracellular polymeric substances (EPS) were quantified, to evaluate their role on membrane fouling. The tests results suggest that the inflow variation in an MEBPR process did not make a significant difference in any of the measured parameters.
With decreased SRT, an increase in the concentrations of EPS was observed, especially the bound protein, and the bound and soluble humic-like substances. This suggests that these components of activated sludge mixed liquors may be related to membrane fouling. No clear relationship was observed between membrane fouling and other measured parameters, including critical flux, normalized CST and normalized TTF.
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Secrier, Maria [Verfasser], and Lars [Akademischer Betreuer] Steinmetz. "Visualization and analysis strategies for dynamic gene-phenotype relationships and their biological interpretation / Maria Secrier ; Betreuer: Lars Steinmetz." Heidelberg : Universitätsbibliothek Heidelberg, 2013. http://d-nb.info/1177249510/34.
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An, Ran. "Using a Combinatorial Peptide Ligand Library to Reduce the Dynamic Range of Protein Concentrations in Complicated Biological Samples." The Ohio State University, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=osu1388765432.
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Figueiredo, Daniel Oliveira. "Differential dynamic logic and applications." Master's thesis, Universidade de Aveiro, 2015. http://hdl.handle.net/10773/16841.
Full textAbstract:
Mestrado em Matemática e AplicaçõesNa área industrial e habitual usar ferramentas discretas em sistemas cuja evolução e contínua e regida pelas leis da mecânica. Estes sistemas que apresentam tanto comportamento contínuo como discreto são conhecidos como sistemas híbridos. A lógica diferencial dinâmica e uma lógica desenvolvida recentemente para trabalhar com estes sistemas. Neste trabalho, apresentamos a lógica diferencial dinâmica como uma generalização da lógica dinâmica (e, consequentemente, da lógica modal). Também são apresentadas algumas aplicações e discutida a utilidade destas lógicas nas áreas da mecânica e da biologia. Embora o uso de ferramentas computacionais seja comum e os resultados até agora obtidos sejam satisfatórios, os exemplos apresentados mostram que a lógica diferencial dinâmica pode ser usada como uma alternativa, assim como um complemento, na biologia sintética
In industry, it is often used discrete tools in system which behavior is continuous and modeled by the laws of mechanics. These systems which display both continuous and discrete dynamic behavior are known as hybrid systems. Di erential dynamic logic is a logic recently developed in order to reasoning about hybrid systems. In this work, we present the di erential dynamic logic as a generalization of dynamic logic (and consequently of modal logic). We also present some applications and we discuss about the utility of using these logics in the areas of mechanics and molecular biology. Although computational tools have been applied to reasoning about biological regulatory networks with satisfactory results, our examples show that di erential dynamic logic can be used as an alternative, or even as a complement, in synthetic biology.
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Allen, Michael D. "Biological links between cofactors metabolism, signaling and dynamic relationships between iron, manganese, and chlorophyll in the green alga Chlamydomonas reinhardtii /." Diss., Restricted to subscribing institutions, 2008. http://proquest.umi.com/pqdweb?did=1619423491&sid=1&Fmt=2&clientId=1564&RQT=309&VName=PQD.
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