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Brandt, Erik G. "Interactions and dynamics in biophysical model systems /". Stockholm : Skolan för teknikvetenskap, Kungliga Tekniska högskolan, 2009. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-10300.
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Elmlund, Hans. "Protein structure dynamics and interplay : by single-particle electron microscopy". Doctoral thesis, Stockholm : Teknik och hälsa, Technology and Health, Kungliga Tekniska högskolan, 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4669.
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Dale, Michael Anthony Joseph. "Global Energy Modelling : A Biophysical Approach (GEMBA)". Thesis, University of Canterbury. Mechanical Engineering, 2010. http://hdl.handle.net/10092/5156.
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The aim of this thesis is to take a broad conceptual overview of the global energy system and investigate what the aims of sustainability might entail for such a system. The work presented uses a biophysical economic approach in that the dynamics of the global economy are investigated using the tool box of the physical sciences, including the laws of thermodynamics and the methods of energy analysis. Modern society currently uses approximately 500 exajoules (EJ = 10^18 J) of total primary energy supply (TPES) each year. This energy consumption has been increasing at roughly 2% per year for the past two hundred years. TPES is currently dominated by three non-renewable energy sources: coal, oil and gas which, together with energy from nuclear fission of uranium, make up around 85% of the energy market. Consumption of finite resources at a continuously growing rate is not sustainable in the long-term. A trend in policy direction is to seek a transition to renewable sources of energy. This thesis seeks to explore two questions: are the technical potentials of renewable energy sources enough to supply the current and/or projected demand for energy and what would be the effect on the physical resource economy of a transition to an energy supply system run entirely on renewable energy sources?
The Global Energy Model using a Biophysical Approach (GEMBA) methodology developed here is compared and contrasted with other approaches that are used to study the global energy-economy system, including the standard neoclassical economic approach used in such models as MESSAGE and MARKAL.
A number of meta-analyses have been conducted in support of the GEMBA model. These
include: meta-analysis of historic energy production from all energy sources; meta-analysis of global energy resources for all energy sources; meta-analysis of energy-return-on-investment (EROI) for all energy sources.
The GEMBA methodology uses a systems dynamic modelling approach utilising stocks and flows, feedback loops and time delays to capture the behaviour of the global energy-economy system. The system is decomposed into elements with simple behaviour that is known through energy analysis. The interaction of these elements is captured mathematically and run numerically via the systems dynamics software package, VenSim. Calibration of the model has been achieved using historic energy production data from 1800 to 2005. The core of the GEMBA methodology constitutes the description of a dynamic EROI function over the whole production cycle of an energy resource from initial development, through maturation to decline in production, in the case of non-renewable resources, or to the technical potential in the case of renewable resources.
Using the GEMBA methodology, the global energy-economy system is identified as a self-regulating system. The self-regulating behaviour acts to constrain the amount of total primary energy supply that the system can produce under a renewable-only regime. A number of analyses are conducted to test the sensitivity of the system to such changes as: an increase of the technical potential of renewable resources; technological breakthroughs which would significantly increase the EROI of renewable resources; a decrease in the capital intensity of renewable resources and; an increase in the energy intensity of the economy,
A statistical analysis reflecting the wide range of values of both the estimates of EROI and technical potentials of renewable energy sources has also been undertaken using a Monte Carlo approach.
The results from the modelling suggest that not all levels of energy demand projected by the WEA can be supplied by an energy system running solely on renewable energy. The Monte Carlo analyses suggest that reduction in total energy yield over current (2010) levels might occur with a 20-30% possibility. The middle and high growth scenarios from the WEA are greater than 95% of all scenarios modelled, hence seem unlikely to be sustained by an energy system running solely on renewable energy. This finding has implications for the future direction of both engineering and technology research as well as for energy policy. These implications are discussed.
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Pearson, Joshua Thomas. "A biophysical study of protein dynamics and protein-ligand interactions /". Thesis, Connect to this title online; UW restricted, 2006. http://hdl.handle.net/1773/8173.
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Stollar, Elliott Jonathan. "Biophysical and crystallographic investigation of homeodomain stability, dynamics, and recognition". Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.615778.
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Zerlaut, Yann. "Biophysical and circuit properties underlying population dynamics in neocortical networks". Thesis, Paris 6, 2016. http://www.theses.fr/2016PA066095/document.
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Le néocortex possède un état activé dans lequel l'activité corticalemanifeste un comportement complexe. Au niveau cellulaire, l'activitéest caractérisée par de fortes fluctuations sous-liminaires dupotential membranaire et une décharge irrégulière à bassefréquence. Au niveau du réseau, l'activité est marquée par un faibleniveau de synchronie et une dynamique chaotique. Néanmoins, c'est dansce régime que l'information est traitée de manière fiable par lesréseaux neuronaux. Ce régime est donc crucial pour le traitement del'information par le cortex. Dans cette thèse, nous contribuons à sacompréhension en examinant comment les propriétés biophysiques auniveau cellulaire combinées avec les propriétés d'architecture desréseaux façonnent cette dynamique asynchrone.Cette thèse repose sur les modèles de dynamique de réseaux appelésmodèles de champ moyen, un formalisme théorique qui décrit ladynamique de population grâce à une approche auto-consistante. Aucoeur de ce formalisme se trouve la fonction de transfertneuronale : la fonction entrée-sortie d'un neurone. La première partiede cette thèse s'attache à dériver des fonctions de transfertbiologiquement réalistes en incorporant des caractérisationsexpérimentales.Dans un premier temps, nous avons examiné in vitro comment lesneurones néocorticaux pyramidaux de la couche V du cortex visuelrépondent à des fluctuations du potentiel membranaire. Nous avonsobservé que les neurones individuels ne diffèrent pas seulement entermes d'excitabilité, mais qu'ils diffèrent aussi par leurssensibilités aux paramètres des fluctuations. Dans un deuxième temps,nous avons étudié de manière théorique comment l'intégrationdendritique dans des structures arborescentes façonne les fluctuationsau soma. Nous avons observé que, en fonction des propriétés del'activité présynaptique, différentes comodulations des paramètres desfluctuations pouvaient être obtenues. En combinant cette observationavec nos mesures expérimentales, nous avons observé que cela induisaitdes couplages différents entre activité synaptique et déchargeneuronale pour chaque neurone. Nous proposons donc que, puisque cemécanisme offre un moyen d'activer spécifiquement certains neurones enfonction des propriétés de l'entrée, l'hétérogénéité biophysiquepourrait contribuer à l'encodage de propriétés des stimuli dans lestraitements de l'information sensorielle.La deuxième partie de cette thèse examine comment les propriétésd'architecture des réseaux neuronaux se combinent avec les propriétésbiophysiques et affectent les réponses sensorielles via des effets dedynamiques de populations.Nous avons tout d'abord examiné de manière théorique comment un hautniveau d'activité spontanée impactait les réponses post-synaptiquesdans le cortex. Nous avons observé que la compétition entre lerecrutement dans le réseau cortical activé et les effets deconductances associés prédisaient une relation non-triviale entrel'intensité des stimuli et l'amplitude des réponses. Cette prédictionfut observée dans des enregistrements de réponses post-synaptiquesdans le cortex auditif du rat in vivo en réponse à des stimulicorticaux, thalamiques et auditifs.Pour finir, en tirant avantage des approches de champ moyen, nousavons construit un modèle grande échelle du réseau des couches II-IIIincluant le réseau des fibres horizontales. Nous avons examiné lespropriétés intégratives spatio-temporelles du modèle et nous les avonscomparées avec des mesures par imagerie optique de l'activitécérébrale chez le singe éveillé. En particulier, nous avonsreconstruit une expérience typique du traitement sensoriel: lemouvement apparent. Le modèle prédit un fort signal suppressif dont leprofil spatio-temporel correspond quantitativement à celui observé invivoThe neocortex of awake animals displays an activated state in whichcortical activity manifests highly complex, seemingly noisybehavior. At the level of single neurons the activity is characterizedby strong subthreshold fluctuations and irregular firing at lowrate. At the network level, the activity is weakly synchronized andexhibits a chaotic dynamics. Yet, it is within this regime thatinformation is processed reliably through neural networks. This regimeis thus crucial to neural computation. In this thesis, we contributeto its understanding by investigating how the biophysical propertiesat the cellular level combined with the properties of the networkarchitecture shapes this asynchronous dynamics.This thesis builds up on the so-called mean-field models of networkdynamics, a theoretical formalism that describes population dynamicsvia a self-consistency approach. At the core of this formalism lie theneuronal transfer function: the input-output description of individualneurons. The first part of this thesis focuses on derivingbiologically-realistic neuronal transfer functions. We firstformulate a two step procedure to incorporate biological details (suchas an extended dendritic structure and the effect of various ionicchannels) into this transfer function based on experimentalcharacterizations.First, we investigated in vitro how layer V pyramidal neocorticalneurons respond to membrane potential fluctuations on a cell-by-cellbasis. We found that, not only individual neurons strongly differ interms of their excitability, but also, and unexpectedly, in theirsensitivities to fluctuations. In addition, using theoreticalmodeling, we attempted to reproduce these results. The model predictsthat heterogeneous levels of biophysical properties such as sodiuminactivation, sharpness of sodium activation and spike frequencyadaptation account for the observed diversity of firing rateresponses.Then, we studied theoretically how dendritic integration in branchedstructures shape the membrane potential fluctuations at the soma. Wefound that, depending on the type of presynaptic activity, variouscomodulations of the membrane potential fluctuations could beachieved. We showed that, when combining this observation with theheterogeneous firing responses found experimentally, individual neuronsdifferentially responded to the different types of presynapticactivities. We thus propose that, because this mechanism offers a wayto produce specific activation as a function of the input properties,biophysical heterogeneity might contribute to the encoding of the stimulusproperties during sensory processing in neural networks.The second part of this thesis investigates how circuit properties,such as recurrent connectivity and lateral connectivity, combine withbiophysical properties to impact sensory responses through effectsmediated by population dynamics.We first investigated what was the effect of a high level of ongoingdynamics (the Up-state compared to the Down-state) on the scaling ofpost-synaptic responses. We found that the competition between therecruitment within the active recurrent network (in favor of highresponses in the Up-state) and the increased conductance level due tobackground activity (in favor of reduced responses in the Up-state)predicted a non trivial stimulus-response relationship as a functionof the intensity of the stimulation. This prediction was shown toaccurately capture measurements of post-synaptic membrane potentialresponses in response to cortical, thalamic or auditory stimulation inrat auditory cortex in vivo.Finally, by taking advantage of the mean-field approach, weconstructed a tractable large-scale model of the layer II-III networkincluding the horizontal fiber network. We investigate thespatio-temporal properties of this large-scale model and we compareits predictions with voltage sensitive dye imaging in awake fixatingmonkey
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Doerdelmann, Thomas. "Structural and Biophysical Studies of the Pitx2 Homeodomain". University of Cincinnati / OhioLINK, 2011. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1307443112.
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Pathmasiri, Wimal. "Structural and Biophysical Studies of Nucleic Acids". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8245.
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Reyns, Nathalie Brigitte. "Biophysical dispersal dynamics of the blue crab in Pamlico Sound, North Carolina". NCSU, 2004. http://www.lib.ncsu.edu/theses/available/etd-10312004-143755/.
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For many species such as the blue crab, Callinectes sapidus, successful estuarine recruitment to juvenile nursery habitats is dependent on the biophysical processes experienced during dispersal of the early life stages. The goal of this study was to determine how blue crab primary (postlarval) and secondary (early juvenile) dispersal occurs within a predominately wind-driven estuary, Pamlico Sound, North Carolina, USA. We (1) characterized circulation patterns in Pamlico Sound during the fall blue crab recruitment months over two consecutive years using current meters (2) sampled during multiple 24 h periods to relate spatiotemporal water column distributions of postlarval and early juveniles blue crabs with circulation patterns, and used a hydrodynamic model to recreate dispersal trajectories from eastern (inlet) to western sound nursery habitats and (3) examined the environmental (wind, diel cycle, tidal phase) and biological (ontogenetic, density-dependent) factors that contribute to early juvenile blue crab secondary dispersal from near-inlet nursery habitats. During our study, surface currents responded synchronously to wind-forcing by generally flowing in the same direction as the wind. Particle-tracking simulations suggested that dispersal from Oregon and Hatteras Inlets to across-sound nursery habitats resulted from the combined use of tidal and wind-driven currents. Simulation results and observed crab distributions further indicated that Oregon Inlet was the primary supplier of postlarval blue crabs (dispersing in surface waters at night) throughout Pamlico Sound, as postlarvae ingressing through Hatteras Inlet were not retained within our study area. Furthermore, Oregon Inlet supplied early juvenile blue crabs (dispersing in bottom waters at night) to northwestern sound habitats, while crabs from Hatteras Inlet dispersed to mid- and eastern-sound regions. Results from our study in near-inlet settlement habitats confirmed the importance of tides to mediating dispersal partway into Pamlico Sound, as early juvenile blue crabs responded to increasing conspecific density in settlement habitats by using flood-tide transport near the inlets to rapidly leave these habitats. Based on our findings, we make recommendations regarding the prioritization of nursery habitats for conservation and fisheries management.
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Chimatiro, Sloans Kalumba. "The biophysical dynamics of the Lower Shire River Floodplain fisheries in Malawi /". Connect to this title online, 2004. http://eprints.ru.ac.za/177/.
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Rohr, Tyler W. "Computational analysis of the biophysical controls on Southern Ocean phytoplankton ecosystem dynamics". Thesis, Massachusetts Institute of Technology, 2019. https://hdl.handle.net/1721.1/122325.
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Thesis: Ph. D., Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution), 2019Cataloged from PDF version of thesis.
Includes bibliographical references (pages 193-220).
Southern Ocean net community productivity plays an out sized role in regulating global biogeochemical cycling and climate dynamics. The structure of spatial-temporal variability in phytoplankton ecosystem dynamics is largely governed by physical processes but a variety of competing pathways complicate our understanding of how exactly they drive net population growth. Here, I leverage two coupled, 3-dimensional, global, numerical simulations in conjunction with remote sensing data and past observations, to improve our mechanistic understanding of how physical processes drive biology in the Southern Ocean. In Chapter 2, I show how different mechanistic pathways can control population dynamics from the bottom-up (via light, nutrients), as well as the top-down (via grazing pressure). In Chapters 3 and 4, I employ a higher resolution, eddy resolving, integration to explicitly track and examine closed eddy structures and address how they modify biomass at the mesoscale.
Chapter 3 considers how simulated eddies drive bottom-up controls on phytoplankton growth and finds that division rates are, on average, amplified in anticyclones and suppressed in cyclones. Anomalous division rates are predominately fueled by an anomalous vertical iron flux driven by eddy-induced Ekman Pumping. Chapter 4 goes on to describe how anomalous division rates combine with anomalous loss rates to drive anomalous net population growth. Biological rate-based mechanisms are then compared to the potential for anomalies to evolve strictly via physical transport (i.e. dilution, stirring, advection). All together, I identify and describe dramatic regional and seasonal variability in when, where, and how different mechanisms drive phytoplankton growth throughout the Southern Ocean. Better understanding this variability has broad implications to our understanding of how oceanic biogeochemisty will respond to, and likely feedback into, a changing climate.
Specifically, the uncertainty associated with this variability should temper recent proposals to artificially stimulate net primary production and the biological pump via iron fertilization. In Chapter 5 I argue that Southern Ocean Iron Fertilization fails to meet the basic tenets required for adoption into any regulatory market based framework.
by Tyler W. Rohr.
Ph. D.
Ph.D. Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences; and the Woods Hole Oceanographic Institution)
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Leekumjorn, Sukit. "Molecular Dynamics Simulations for the Study of Biophysical Processes on Biological Membranes". Diss., Virginia Tech, 2008. http://hdl.handle.net/10919/29180.
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Phospholipid bilayers constitute the primary structural element of biological membranes, and as such, they play a central role in biochemical and biophysical processes at the cellular level, including cell protection, intercellular interactions, trans-membrane transport, cell morphology, and protein function, to name a few. The properties of phospholipid bilayers are thus of great interest from both experimental and theoretical standpoints. Although experiments have provided much of the macroscopic functions and properties of biological membranes, insight into specific mechanisms at the molecular level are seldom accessible by conventional methods. To obtain a better understanding of biochemical and biophysical processes at the molecular level involving phospholipid bilayers, we apply molecular simulation methods to investigate the complexity of the membrane matrix using atomistic models. Here, we discuss three specific biological processes that are associated with biological membranes: 1) membrane stabilization, 2) membrane phase behavior, and 3) fatty acid-induced toxicity in cell membranes.
For membrane stabilization, molecular dynamics studies were performed for mixed phospholipid bilayers containing two of the most prevalent phospholipids (phosphatidylcholine and phosphatidylethanolamime) in biological membranes. We presented structural and dynamics properties of these systems, as well as the effect of stabilizing agents, such as trehalose, on their properties. Furthermore, we performed a comprehensive analysis of the phase transition of lipid bilayers and investigated the interactions of stabilizing agents (glucose or trehalose) with lipid bilayers under dehydrated conditions to understand the mechanisms for preservation of cellular systems.
For membrane phase behavior, a comprehensive study of the structural properties of saturated and monounsaturated lipid bilayers near the main phase transition were investigated using molecular dynamics simulations. In this study, we demonstrated that atomistic simulations are capable of capturing the phase transformation process of lipid bilayers, providing a valuable set of molecular and structural information at and near its transition state.
Lastly, the third study investigated the mechanism for fatty acid-induced toxicity by integrating in vitro and in silico experiments to reveal the biophysical interactions of saturated fatty acid (palmitate) with the cellular membranes and the role of trehalose and unsaturated fatty acids (oleate and linoleate) in preventing changes to the membrane structure. Knowledge gained from this study is essential in the prevention and treatment of obesity-associated cirrhosis diseases.Ph. D.
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Chimatiro, Sloans Kalumba. "The biophysical dynamics of the Lower Shire River Floodplain fisheries in Malawi". Thesis, Rhodes University, 2005. http://hdl.handle.net/10962/d1005086.
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Fishes of African floodplains typically comprise populations having short life cycles, relatively few age groups, more generalised feeding behaviour, and which experience spawning success that is strongly influenced by abiotic factors such as hydrological regime of the river, climatic seasonality and habitat characteristics. In addition, African river-floodplain ecosystems do not have appropriate predictive models for estimating yield in these ecosystems. While most predictive models developed to date for floodplain fisheries have taken into account morpho-edaphic factors, they have generally excluded climatic factors as a mega-determinant of the variability of floodplain fisheries. The principle aim of this thesis has been to develop a predictive management model that incorporates data on essential biological aspects of the target species, characteristics of the habitat as well as overall climatic factors, and thus allow for adaptive management of the fisheries in a continuously fluctuating floodplain environment. Lower Shire Floodplain (34 ⁰ 45’ – 35 ⁰ E and 16 ⁰ 00’-17 ⁰ 15’ S) in Malawi, one of the major rivers-floodplains in the Zambezi Basin, was used to test this type of model. The major hypothesis tested in this study was that “the dynamics of the fishery of Lower Shire Floodplain are driven by and adapted to the seasonal, but predictable, hydro-climatic regime of the floodplain”. The specific objectives were: to describe the floodplain’s climate and hydrological pattern; to develop a quantitative characterisation of the major habitats of the Lower Shire Floodplain; to assess the fishery in terms of size, gear utilisation, gear selectivity and yield; to assess the biological parameters of the target species, necessary for the management of the fishery; to analyse how water fluctuation in the floodplain affects the recruitment and life history of the two target species; and to develop of a predictive hydro-climatic model to benefit the management of the fisheries. The climate of the floodplain was characterised by low (765 ± 198 mm) and fairly variable (Cv = 27%) rainfall, which largely occurred between December and January. The area was generally humid (mean RH 68%), with mild to hot (25- 33ºC) and variable monthly mean diurnal (12ºC) temperature. Four quarterly hydro-climatic seasons were identified and comprised: Quarter 1 (Jul-Sep) characterised by hot, dry weather with a low flood regime; Quarter 2 (Oct-Dec) hot, windy, wet weather with low-but-rising flood regime; Quarter 3 (Jan-Mar) hot humid, wet weather with the flood regime at peak; and Quarter 4 (Apr-Jun) humid and cool weather with receding flood regime. The annual hydrograph of the floodplain was represented by four categories of flood regime as: low (Jul-Sept), low-but-rising (Oct-Dec), peak (Jan- Mar), and falling (Apr-Jun). The floodplain experienced a water deficit of 95.1 mm.year⁻¹, and it was hypothesised that ground water recharge maintained water in the floodplain the rest of the year. Three major habitats were identified in the floodplain. The river-floodplain, characterised by deep fast-flowing water, sandy substrate and little emergent vegetation; the permanently connected lagoons, were shallow (≤ 2 m) with sandymud bottom and slow flowing water; and the seasonally connected lagoons had slowflowing stagnant water, with comparatively more emergent and floating vegetation. Physicochemical characteristics of the habitats varied significantly with hydroclimatic seasons (one-way ANOVA, p ≤ 0.05), indicating the influence of flood regime, which joined the habitats in a non-equilibrial spatial distribution. Consequently, during receding and low flood regimes river-floodplain and permanently connected lagoons exhibited similar characteristics while all three habitats had similar characteristics during the rising and peak flood regimes. It was, therefore, concluded that in floodplains, habitats shift horizontally and vertically according to the water level. Gill nets, cast nets, long line, and fish traps accounted for 99% of the total count of gears, and hence considered the major fishing sectors. Two principal species in the floodplain were the catfish Clarias gariepinus and the cichlid Oreochromis mossambicus. Length-at-maximum-selectivity (ø) and length-at-50%-sexual-maturity (Lm₅₀) for each of the two species showed that although they were selected into the four fishing sectors at lengths above maturity, maximum selectivity into the long line occurred at a length before maturity for O. mossambicus. In addition, the width of the gamma selectivity function (σ) indicated that a considerable proportion of juveniles of the two species were also selected. Therefore, it was decided that management for the floodplain be centred on controlling over-fishing and preserving the spawner stock, by banning seine and mosquito nets, and closing river-floodplain and permanently connected lagoons to fishing during the low flood regime. There were significant seasonal variations in CPUE, lowest in the low flood, and highest during the peak flood regime. Sectioned otoliths were used to determine the age and growth of the two principal species in the floodplain. Marginal zone analysis revealed that annulus formation in all the species occurred during the period of low air and water temperatures, high evaporation and receding water levels, hence a high rate of desiccation and negative water budget. For O. mossambicus, maximum age reached was 6 years while in C. gariepinus it was 9 years. The 3-parameter von Bertalanffy growth model adequately described growth as lt = 177.6(1-e⁻·⁴⁴⁽t ⁺ ¹·⁴³⁾) mm TL for O. mossambicus and lt = 502.9(1-e⁻°·³¹⁽t ⁺ ¹·⁹²⁾) mm TL for C. gariepinus. Female O. mossambicus reached 50%-sexual-maturity at 109 mm SL, while males matured at 105 mm, and both male and female C. gariepinus reached Lm₅₀ at 249 mm SL. The breeding seasons of both O. mossambicus and Clarias gariepinus were between September and March, with modal peaks in January and November, respectively. The annual total mortality rates (Z) were 0.62 ± 0.18 yr⁻¹ for O. mossambicus and 0.93 ± 0.47 yr⁻¹ for C. gariepinus. The mean empirical estimates of natural mortality (M) were 0.46 yr⁻¹ for O. mossambicus and 0.50 year⁻¹ for C. gariepinus, and fishing mortality (F) was calculated as 0.16 yr⁻¹ for O. mossambicus and 0.43 yr⁻¹ for C. gariepinus. The overall exploitation level (Z/K) was 1.41 for O. mossambicus and 3.01 for C. gariepinus. Given that the Z/K ratio was >1, it was asserted that both O. mossambicus and C. gariepinus were mortality-dominated and fairly heavily exploited. However, potential for sustainable exploitation existed since both species showed signs of resilience due short longevity and high rate of natural mortality. Given the limitation of simple exponential models of fish mortality and growth under the situation of seasonal fluctuation of water levels, a simple predictive hydroclimatic- fisheries model was developed. The model predicted the life-history and production parameters fairly accurately (0.53 ≤ r² ≥ 0.98, p ≤ 0.05), and showed that environmental and biological events in the floodplain significantly (0.43 ≤ r² ≥ 0.91, p ≤ 0.05) followed the periodic function of time (day-of-the-year), hence, strongly seasonal. In addition, the flood-pulse preceded all the major biological events, with predicted phase lags established at 55.6º for peak flood, 157.2º, 260.1º, 334.6º and 341.4º for condition factor for O. mossambicus, recruitment, spawning period for O. mossambicus and C. gariepinus, respectively. Therefore, it was recommended that water obstruction on the Shire River must ensure sufficient water flow during the peak flood and spawning period to allow flooding and inundation of the floodplain in order to create habitat favourable for spawning and feeding as well as improve recruitment.
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Wadhwa, Vibhuti. "Biophysical approaches towards greater understanding of eukaryotic zinc sensing". The Ohio State University, 2020. http://rave.ohiolink.edu/etdc/view?acc_num=osu1593621283583113.
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Herrera-Valdez, Marco Arieli. "Geometry and nonlinear dynamics underlying excitability phenotypes in biophysical models of membrane potential". Diss., The University of Arizona, 2014. http://hdl.handle.net/10150/312741.
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The main goal of this dissertation was to study the bifurcation structure underlying families of low dimensional dynamical systems that model cellular excitability. One of the main contributions of this work is a mathematical characterization of profiles of electrophysiological activity in excitable cells of the same identified type, and across cell types, as a function of the relative levels of expression of ion channels coded by specific genes. In doing so, a generic formulation for transmembrane transport was derived from first principles in two different ways, expanding previous work by other researchers. The relationship between the expression of specific membrane proteins mediating transmembrane transport and the electrophysiological profile of excitable cells is well reproduced by electrodiffusion models of membrane potential involving as few as 2 state variables and as little as 2 transmembrane currents. Different forms of the generic electrodiffusion model presented here can be used to study the geometry underlying different forms of excitability in cardiocytes, neurons, and other excitable cells, and to simulate different patterns of response to constant, time-dependent, and (stochastic) time- and voltage-dependent stimuli. In all cases, an initial analysis performed on a deterministic, autonoumous version of the system of interest is presented to develop basic intuition that can be used to guide analyses of non-autonomous or stochastic versions of the model. Modifications of the biophysical models presented here can be used to study complex physiological systems involving single cells with specific membrane proteins, possibly linking different levels of biological organization and spatio-temporal scales.
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Piechnik, Stefan K. "A mathematical and biophysical modelling of cerebral blood flow and cerebrospinal fluid dynamics". Thesis, University of Cambridge, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.269226.
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Bansept, Florence. "Biophysical modeling of bacterial population dynamics and the immune response in the gut". Thesis, Sorbonne université, 2018. http://www.theses.fr/2018SORUS397.
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La première partie de cette thèse porte sur les dynamiques de colonisation d'une population bactérienne au début d'une infection intestinale. Le but est de déduire des paramètres biologiquement pertinents de données indirectes. Un modèle simple est étudié, et l'on discute de l'observable optimale pour caractériser la variabilité d'une distribution d'étiquettes génétiques. Des arguments biologiques et des incohérences entre des observables expérimentales avec le premier modèle motivent l'étude d'un second, où deux sous-populations se répliquent à des taux différents, mais on ne peut pas conclure clairement sur le jeu de données utilisé. La seconde partie porte sur les mécanismes de la réponse immunitaire. Le principal effecteur du système immunitaire adaptatif dans l'intestin, l'IgA (un anticorps), enchaîne les bactéries-filles en agrégats clonaux lors de la réplication. Nous avons contribué à prouver ce phénomène par un modèle qui prédit la réduction de la diversité bactérienne qui en découle. Au sein de l'hôte, l'interaction entre la croissance et la fragmentation des agrégats a pour conséquence le piégeage préférentiel des bactéries à croissance rapide, ce qui pourrait permettre au système immunitaire de réguler la composition du microbiote. A l'échelle de la population-hôte, et dans le contexte de l'évolution d'une résistance aux antibiotiques, si les bactéries sont transmises sous forme d'amas clonaux, alors la probabilité de transmettre une bactérie résistante est réduite dans une population immunisée. Ainsi, des outils de physique statistique nous permettent d'identifier des mécanismes génériques en biologieThe first part of this thesis focuses on the colonization dynamics of a bacterial population in early infection of the gut. The aim is to infer biologically relevant parameters from indirect data. We discuss the optimal observable to characterize the variability in genetic tags distributions. In a first one-population model, biological arguments and inconsistencies between several experimental observables lead to the study of a second model with two-subpopulations replicating at different rates. As expected, this model allows for broader possibilities in observables combination, even though no clear conclusion can be drawn as to a data set on Salmonella in mice. The second part concerns the mechanisms that make the immune response effective. The main effector of the immune system in the gut, IgA (an antibody), enchains daughter bacteria in clonal clusters upon replication. Our model predicting the ensuing reduction of diversity in the bacterial population contributes to evidence this phenomenon, called “enchained growth”. Inside the host, the interplay of cluster growth and fragmentation results in preferentially trapping faster-growing and potentially noxious bacteria away from the epithelium, which could be a way for the immune system to regulate the microbiota composition. At the scale of the hosts population, in the context of evolution of antibiotic resistance, if bacteria are transmitted via clonal clusters, the probability to transmit a resistant bacteria is reduced in immune populations. Thus we use statistical physics tools to identify some generic mechanisms in biology
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Rahmati, Vahid, Knut Kirmse, Dimitrije Marković, Knut Holthoff e Stefan J. Kiebel. "Inferring Neuronal Dynamics from Calcium Imaging Data Using Biophysical Models and Bayesian Inference". Saechsische Landesbibliothek- Staats- und Universitaetsbibliothek Dresden, 2016. http://nbn-resolving.de/urn:nbn:de:bsz:14-qucosa-203385.
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Calcium imaging has been used as a promising technique to monitor the dynamic activity of neuronal populations. However, the calcium trace is temporally smeared which restricts the extraction of quantities of interest such as spike trains of individual neurons. To address this issue, spike reconstruction algorithms have been introduced. One limitation of such reconstructions is that the underlying models are not informed about the biophysics of spike and burst generations. Such existing prior knowledge might be useful for constraining the possible solutions of spikes. Here we describe, in a novel Bayesian approach, how principled knowledge about neuronal dynamics can be employed to infer biophysical variables and parameters from fluorescence traces. By using both synthetic and in vitro recorded fluorescence traces, we demonstrate that the new approach is able to reconstruct different repetitive spiking and/or bursting patterns with accurate single spike resolution. Furthermore, we show that the high inference precision of the new approach is preserved even if the fluorescence trace is rather noisy or if the fluorescence transients show slow rise kinetics lasting several hundred milliseconds, and inhomogeneous rise and decay times. In addition, we discuss the use of the new approach for inferring parameter changes, e.g. due to a pharmacological intervention, as well as for inferring complex characteristics of immature neuronal circuits.
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Jackson, Beckford Shirlene R. "Biophysical Characterization of the Binding of Homologous Anthraquinone Amides to DNA". Digital Archive @ GSU, 2012. http://digitalarchive.gsu.edu/chemistry_diss/70.
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The synthesis of four homologous anthraquinones (AQ I-IV) bearing increasing lengths of polyethylene glycol (PEG) side chains and their binding to AT- and GC-rich DNA hairpins are reported. The molecules were designed such that the cationic charge is at a constant position and the ethylene glycol units chosen to allow significant increases in size with minimal changes in hydrophobicity. The mode and affinity of binding were assessed using circular dichroism (CD), nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), and isothermal titration calorimetry (ITC). The binding affinity decreased as the AQ chain length increased along the series with both AT- and GC-rich DNA. ITC measurements showed that the thermodynamic parameters of AQ I-IV binding to DNA exhibited significant enthalpy-entropy compensation. The enthalpy became more favorable while the entropy became less favorable. The correlation between enthalpy and entropy may involve not only the side chains, but also changes in the binding of water and associated counterions and hydrogen bonding.
The interactions of AQ I-IV with GC-rich DNA have been studied via molecular dynamics (MD) simulations. The geometry, conformation, interactions, and hydration of the complexes were examined. As the side chain lengthened, binding to DNA reduced the conformational space, resulting in an increase in unfavorable entropy. Increased localization of the PEG side chain in the DNA groove, indicating some interaction of the side chain with DNA, also contributed unfavorably to the entropy. The changes in free energy of binding due to entropic considerations (-3.9 to -6.3 kcal/mol) of AQ I-IV were significant.
The kinetics of a homologous series of anthraquinone threading intercalators, AQT I-IV with calf thymus DNA was studied using the stopped-flow. The threading mechanisms of the anthraquinones binding to DNA showed sensitivity to their side chain length. Fitting of the kinetic data led to our proposal of a two step mechanism for binding of AQT I, bearing the shortest side chain, and a three step mechanism for binding of the three longer homologs. Binding involves formation of an externally bound anthraquinone-DNA complex, followed by intercalation of the anthraquinone for AQT I-IV, then isomerization to another complex with similar thermodynamic stability for AQT II-IV.
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Talathi, Sachin S. "Biophysical modelling of synaptic plasticity and its function in the dynamics of neuronal networks". Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC IP addresses, 2006. http://wwwlib.umi.com/cr/ucsd/fullcit?p3214710.
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Thesis (Ph. D.)--University of California, San Diego, 2006.Title from first page of PDF file (viewed July 10, 2006). Available via ProQuest Digital Dissertations. Vita. Includes bibliographical references (p. 147-155).
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Ibrahim, Moustafa Ismaiel Omar. "Biophysical studies of the structure and backbone dynamics of gsPGK using NMR relaxation methods". Thesis, University of Sheffield, 2011. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.543234.
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Ni, Haibo. "Biophysical modelling of functional impacts of potassium channel mutations on human atrial and ventricular dynamics". Thesis, University of Manchester, 2017. https://www.research.manchester.ac.uk/portal/en/theses/biophysical-modelling-of-functional-impacts-of-potassium-channel-mutations-on-human-atrial-and-ventricular-dynamics(3372fd6a-850b-4f7d-893a-e2da28269ba8).html.
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Atrial fibrillation (AF) is the most common cardiac arrhythmia causing morbidity and mortality. Despite recent advances, developing effective and safe anti-AF pharmaceutical therapies remains challenging and is prone to adverse effects in the ventricles. Atrial-selective therapies are promising in managing AF. A better understanding of the role of the atrial-specific ion channels in the atrial arrhythmogenesis and contractility, as well as the anti-AF effects of blocking these channels is of interests. Also, a 3D ventricle-torso model capable of modelling ventricular electrical activities and the resulting electrocardiogram (ECG) is a valuable tool in evaluating the selectiveness and safety of an anti-AF pharmaceutical therapy. In part I, the role of an atrial-specific ion channel, IKur, in atrial electrical and mechanical activities and the potential of the current as a pharmaceutical target for anti-AF therapies were investigated in silico. The role of IKur in atrial arrhythmogenesis and mechanical contraction was revealed by elucidating the functional impacts of the KCNA5 mutations exerting either gain- or loss-in-function, on the atria. First, novel IKur models were developed and incorporated into multiscale biophysical models of human atrial electrophysiology to assess the effects of mutated IKur on atrial electrical dynamics. Then, a family of single cell human atrial electromechanical models was developed and incorporated into an updated 3D anatomical electromechanical model of human atria to clarify the effects of mutated IKur on the atrial contractile function. Finally, the antiarrhythmic effect of IKur block was assessed together with INa and other K+-current block. It was shown that the gain-of-function in IKur impaired atrial contractility and promoted atrial arrhythmogenesis by shortening the APD, whereas the down-regulated IKur exerted positive inotropic effects and increased the susceptibility of the atria to the genesis of early-afterdepolarisations. Both simulated IKur and INa block in human-AF demonstrated antiarrhythmic effects; the multi-channel block exerted synergistic anti-AF effects and enhanced the AF-selectivity of INa inhibitions. In Part II, a human ventricle-torso model was developed through proposing a new family of single cell ventricular models accounting for transmural, apicobasal and interventricular electrical heterogeneities and integrating an updated 3D biophysical and anatomical model of human ventricles with a heterogeneous anatomical model of a human torso. First, using the model, the role of heterogeneities in the genesis of T-wave was revealed. Then, ECG manifestations of bundle branch block and ventricular ischaemia were simulated. Finally, the platform was applied to investigate the impact of a long-QT-linked mutation (KCNQ1-G269S) on the ventricles and ECG. Good agreement between simulated and experimental/clinical ECG was reached under both normal and diseased conditions. It was shown that the apicobasal heterogeneity had a more pronounced effect on the T-wave than other heterogeneities. Simulations of the KCNQ1-G269S elucidated the causal link between the mutation and ECG manifestations of the patients.
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Ådén, Jörgen. "NMR studies of protein dynamics and structure". Doctoral thesis, Umeå universitet, Kemiska institutionen, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-36790.
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Enzymes are extraordinary molecules that can accelerate chemical reactions by several orders of magnitude. With recent advancements in structural biology together with classical enzymology the mechanism of many enzymes has become understood at the molecular level. During the last ten years significant efforts have been invested to understand the structure and dynamics of the actual catalyst (i. e. the enzyme). There has been a tremendous development in NMR spectroscopy (both hardware and pulse programs) that have enabled detailed studies of protein dynamics. In many cases there exists a strong coupling between enzyme dynamics and function. Here I have studied the conformational dynamics and thermodynamics of three model systems: adenylate kinase (Adk), Peroxiredoxin Q (PrxQ) and the structural protein S16. By developing a novel chemical shift-based method we show that Adk binds its two substrates AMP and ATP with an extraordinarily dynamic mechanism. For both substrate-saturated states the nucleotide-binding subdomains exchange between open and closed states, with the populations of these states being approximately equal. This finding contrasts with the traditional view of enzyme-substrate complexes as static low entropy states. We are also able to show that the individual subdomains in Adk fold and unfold in a non-cooperative manner. This finding is relevant from a functional perspective, since it allows a change in hydrogen bonding pattern upon substrate-binding without provoking global unfolding of the entire enzyme (as would be expected from a two-state folding mechanism). We also studied the structure and dynamics of the plant enzyme PrxQ in both reduced and oxidized states. Experimentally validated structural models were generated for both oxidation states. The reduced state displays unprecedented μs-ms conformational dynamics and we propose that this dynamics reflects local and functional unfolding of an α-helix in the active site. Finally, we solved the structure of S16 from Aquifex aeolicus and propose a model suggesting a link between thermostability and structure for a mesophilic and hyperthermophilic protein pair. A connection between the increased thermostability in the thermophilic S16 and residual structure in its unfolded state was discovered, persistent at high denaturant concentrations, thereby affecting the difference in heat capacity difference between the folded and unfolded state. In summary, we have contributed to the understanding of protein dynamics and to the coupling between dynamics and catalytic activity in enzymes.
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Streichan, Sebastian J. [Verfasser], e Karsten [Akademischer Betreuer] Kruse. "On biophysical aspects of growth and dynamics of epithelial tissues / Sebastian J. Streichan. Betreuer: Karsten Kruse". Saarbrücken : Saarländische Universitäts- und Landesbibliothek, 2011. http://d-nb.info/1051434068/34.
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Wild, Karen Ann. "The dynamics of the deep chlorophyll maximum in the vicinity of the Canary Islands (Spain)". Thesis, Bangor University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.481740.
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Gustafsson, Robert. "Biophysical characterization of the *5 protein variant of human thiopurine methyltransferase by NMR spectroscopy". Thesis, Linköpings universitet, Molekylär Bioteknik, 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:liu:diva-78526.
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Human thiopurine methyltransferase (TPMT) is an enzyme involved in the metabolism of thiopurine drugs, which are widely used in leukemia and inflammatory bowel diseases such as ulcerative colitis and Crohn´s disease. Due to genetic polymorphisms, approximately 30 protein variants are present in the population, some of which have significantly lowered activity. TPMT *5 (Leu49Ser) is one of the protein variants with almost no activity. The mutation is positioned in the hydrophobic core of the protein, close to the active site. Hydrogen exchange rates measured with NMR spectroscopy for N-terminally truncated constructs of TPMT *5 and TPMT *1 (wild type) show that local stability and hydrogen bonding patterns are changed by the mutation Leu49Ser. Most residues exhibit faster exchange rates and a lower local stability in TPMT *5 in comparison with TPMT *1. Changes occur close to the active site but also throughout the entire protein. Calculated overall stability is similar for the two constructs, so the measured changes are due to local stability. Protein dynamics measured with NMR relaxation experiments show that both TPMT *5 and TPMT *1 are monomeric in solution. Millisecond dynamics exist in TPMT *1 but not in TPMT *5, even though a few residues exhibit a faster dynamic. Dynamics on nanosecond to picosecond time scale have changed but no clear trends are observable.
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Piekielek, Nathan Brian. "Remote sensing grassland phenology in the greater Yellowstone ecosystem: biophysical correlates, land use effects and patch dynamics". Diss., Montana State University, 2012. http://etd.lib.montana.edu/etd/2012/piekielek/PiekielekN0812.pdf.
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Vegetation phenology refers to the seasonal timing of repeat biological events such as bud burst and primary-productivity and their relationship to climate. The spatial location and timing of phenology is relevant to a wide-variety of questions in ecology including the space use and population dynamics of migratory herbivores. Recent technological (remote sensing) and methodological (statistical smoothing algorithms and weighted-regression) advancement now allow for mapping spatial and temporal patterns of vegetation phenology across large spatial extents and at fine-temporal scales. It also allows for examination of vegetation response to climate. An understudied topic investigates how human activity (i.e. land use) modifies broad-scale patterns of phenology from their natural state. Land use effects on phenology is important in the context of parks and protected areas where human activity in surrounding areas can compromise biodiversity conservation goals. With this in mind, we posed the following research questions for a study-area within the Greater Yellowstone Ecosystem: 1) What are the biophysical correlates and likely drivers of landscape-scale grassland phenology under wildland conditions? 2) How do different types of land use modify grassland phenology from its wildland state? And, 3) Do spatial and temporal patterns of green forage patches produced with new tools and datasets display seasonal-dynamics that are consistent with current ecological understanding? To answer these questions we used the Normalized Difference Vegetation Index (NDVI) produced by the Moderate Resolution Imaging Spectroradiometer (MODIS) as input to the TIMESAT algorithm to produce estimates of grassland phenology. Our principle findings are that: 1) Seasonal variation in solar radiation, water availability, evaporative demand and temperature explained much of the variation in the timing of wildland grassland phenology; 2) All land use types extended the length of the growing season and agriculture increased two estimates of productivity; And, 3) New tools are capable of producing nearly-spatially and -temporally continuous maps of the pattern of green forage patches that are consistent with current ecological understanding. Results of the present study suggest that land use intensification in the Greater Yellowstone Ecosystem has the potential to alter landscape-scale ecosystem process with a variety of expected consequences for wildlife conservation and management.
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Khanna, Neha, e Neha Khanna@mdbc gov au. "Investigation of phytoplankton dynamics using time-series analysis of biophysical parameters in Gippsland Lakes, South-eastern Australia". RMIT University. Civil, Environmental and Chemical Engineering, 2007. http://adt.lib.rmit.edu.au/adt/public/adt-VIT20080226.123435.
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There is a need for ecological modelling to help understand the dynamics in ecological systems, and thus aid management decisions to maintain or improve the quality of the ecological systems. This research focuses on non linear statistical modelling of observations from an estuarine system, Gippsland Lakes, on the south-eastern coast of Australia. Feed forward neural networks are used to model chlorophyll time series from a fixed monitoring station at Point King. The research proposes a systematic approach to modelling in ecology using feed forward neural networks, to ensure: (a) that results are reliable, (b) to improve the understanding of dynamics in the ecological system, and (c) to obtain a prediction, if possible. An objective filtering algorithm to enable modelling is presented. Sensitivity analysis techniques are compared to select the most appropriate technique for ecological models. The research generated a chronological profile of relationships between biophysical parameters and chlorophyll level for different seasons. A sensitivity analysis of the models was used to understand how the significance of the biophysical parameters changes as the time difference between the input and predicted value changes. The results show that filtering improves modelling without introducing any noticeable bias. Partial derivative method is found to be the most appropriate technique for sensitivity analysis of ecological feed forward neural networks models. Feed forward neural networks show potential for prediction when modelled on an appropriate time series. Feed forward neural networks also show capability to increase understanding of the ecological environment. In this research, it can be seen that vertical gradient and temperature are important for chlorophyll levels at Point King at time scales from a few hours to a few days. The importance of chlorophyll level at any time to chlorophyll levels in the future reduces as the time difference between them increases.
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Tory, Monica C. "Colicin E1 channel peptide-membrane interactions, a biophysical approach to the molecular state, binding, and solvent dynamics". Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1997. http://www.collectionscanada.ca/obj/s4/f2/dsk2/ftp04/mq24512.pdf.
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GRAÇA, André. "Biophysical analysis of PS II – LHCII supercomplex : Understanding the LHCII phosphorylation-dependent dynamics along the thylakoid membrane". Thesis, Umeå universitet, Kemiska institutionen, 2018. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-149091.
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Bellaiche, Mathias Moussine Jacques. "Molecular mechanisms of protein self-assembly and aggregation". Thesis, University of Cambridge, 2018. https://www.repository.cam.ac.uk/handle/1810/277621.
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In this thesis, we investigate the mechanisms driving the self-assembly of peptides and proteins using computational and theoretical tools, always validating our results with experimental measures when possible. In the first part, Chapters 2-5, we focus on the Aβ system, a peptide whose aggregation is intimately linked with the development of Alzheimer's Disease. We begin by simulating the major alloforms of the peptide, Aβ_40 and Aβ_42, demonstrating that the two populate similar disordered ensembles and matching experimental data. Next we investigate how disordered Aβ_42 monomers interact with each other, finding that oligomerisation into amorphous aggregates is driven largely by hydrophobic, non-specific forces. We then move on to probing the aggregation of Aβ_42 into amyloid structures using a native-centric coarse-grained model, and explain the results with a novel Markov state analysis from which we are able to extract structural, kinetic and thermodynamic information on elongation reactions. Finally, we probe the interactions of Aβ_42 monomers with Aβ_42 fibrillar surfaces using a specially designed enhanced sampling scheme, which allows us to obtain enthalpy-driven binding thermodynamics consistent with experiments and to propose major polar binding modes. In the second part of the thesis, Chapters 6 and 7, we model the aggregation of two other self-assembling systems, viruses and a truncated form of the molecular chaperone Hsp70. We first develop a data analysis platform to extract information on the microscopic mechanisms of viral capsid self-assembly from experimental data, synthesising the results from several different systems to draw general evolutionary conclusions about the assembly mechanism. Finally, we model the oligomerisation of Hsp70 thermodynamically and kinetically, showing that its self-assembly is a highly cooperative reaction that is under strong structural constraints.
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Dean, Cayla Whitney. "Biophysical Interactions in the Straits of Florida: Turbulent Mixing Due to Diel Vertical Migrations of Zooplankton". NSUWorks, 2014. http://nsuworks.nova.edu/occ_stuetd/14.
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Diel vertical migrations (DVM) comprise the largest animal migration on the planet and are a phenomenon present in all bodies of water on Earth. A strong sound scattering layer undergoing DVM was observed in the Straits of Florida via a bottom-mounted Acoustic Doppler current profiler (ADCP) Workhorse Longranger 75 kHz (Teledyne RD Instruments) located at the 244 m isobath. ADCP average backscatter showed a clear periodicity corresponding with sunrise and sunset times indicating the presence of a nocturnal DVM. Analysis of the ADCP backscatter data indicated zooplankton swimming velocities were faster during sunrise than sunset times. In several cases the zooplankton swimming velocity appeared to be faster at the beginning of the descent, after which the swimming velocity decreased. Analysis of ADCP velocity data indicated a measureable decrease in the northward component of the current velocity field during migrations (sunrise and sunset) compared to three hours prior. This was presumably associated with an increase in drag due to turbulent friction associated with DVM. A non-hydrostatic computational fluid dynamics (CFD) model with injection of Lagrangian particles was utilized to simulate the effects of DVM on the velocity field and turbulence signature of the Florida Current. A domain simulating a section of the Florida Current was created and zooplankton were represented by particle injection with a discrete phase model. The model was run with and without particles, holding all other parameters the same, for comparison. Idealized temperature stratification and velocity profiles were set for both summer and winter conditions to observe seasonal differences. For each case, velocity and turbulence with particles were compared to results without particles to confirm the changes in profiles were due to the zooplankton (Lagrangian particles). In several cases there was an observable change in average x-velocity profiles due to the injection of particles into the domain. In all cases there was an observable increase in subgrid turbulent viscosity in the wake of the injected particles. This effect was much stronger in the winter case, most likely due to stratification of the water column which gave a near critical Richardson number. These results indicated that DVM does in fact have an effect on the velocity profile and turbulence signature in a strong current under certain conditions and that there was a seasonal difference due to stratification profiles.
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Reverey, Julia Franziska [Verfasser]. "Biophysical Studies of Processes Involved in Acanthamoeba Infections : Contact Lens Contamination, Adhesion, and Intracellular Dynamics / Julia Franziska Reverey". Kiel : Universitätsbibliothek Kiel, 2014. http://d-nb.info/1050388682/34.
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Stelzl, Lukas Sebastian. "Studying marcomolecular transitions by NMR and computer simulations". Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:6e4bbe06-fc58-471b-a932-d940fe78b9a5.
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Macromolecular transitions such as conformational changes and protein-protein association underlie many biological processes. Conformational changes in the N-terminal domain of the transmembrane protein DsbD (nDsbD) were studied by NMR and molecular dynamics (MD) simulations. nDsbD supplies reductant to biosynthetic pathways in the oxidising periplasm of Gram-negative bacteria after receiving reductant from the C-terminal domain of DsbD (cDsbD). Reductant transfer in the DsbD pathway happens via protein-protein association and subsequent thiol-disulphide exchange reactions. The cap loop shields the active-site cysteines in nDsbD from non-cognate oxidation, but needs to open when nDsbD bind its interaction partners. The loop was rigid in MD simulations of reduced nDsbD. More complicated dynamics were observed for oxidised nDsbD, as the disulphide bond introduces frustration which led to loop opening in some trajectories. The simulations of oxidised and reduced nDsbD agreed well with previous NMR spin-relaxation and residual dipolar coupling measurements as well as chemical shift-based torsion angle predictions. NMR relaxation dispersion experiments revealed that the cap loop of oxidised nDsbD exchanges between a major and a minor conformation. The differences in their conformational dynamics may explain why oxidised nDsbD binds its physiological partner cDsbD much tighter than reduced nDsbD. The redox-state dependent interaction between cDsbD and nDsbD is thought to enhance turnover. NMR relaxation dispersion experiments gave insight into the kinetics of the redox-state dependent interaction. MD simulations identified dynamic encounter complexes in the association of nDsbD with cDsbD. The mechanism of the conformational changes in the transport cycle of LacY were also investigated. LacY switches between periplasmic open and cytoplasmic open conformations to transport sugars across the cell membrane. Two mechanisms have been proposed for the conformational change, a rocker-switch mechanism based on rigid body motions and an “airlock” like mechanism in which the transporter would switch conformation via a fully occluded structure. In MD simulations using the novel dynamics importance sampling approach such a fully occluded structure was found. The simulations argued against a strict “rocker-switch” mechanism.
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Sukumaran, Madhav. "Biophysical investigations of AMPA receptor N-terminal domain structure and function reveal mechanisms underlying receptor assembly, dynamics, and allosteric potential". Thesis, University of Cambridge, 2014. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708278.
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Verspecht, Florence. "Temporal dynamics of the coastal water column". University of Western Australia. School of Environmental Systems Engineering, 2008. http://theses.library.uwa.edu.au/adt-WU2008.0097.
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Field measurements and numerical modelling of the shallow coastal waters offshore in south-western Australia were used to describe changes in the water column's vertical structure and the biological response on temporal scales of the order of hours and days. A cycle of chlorophyll a concentration, primary production, and photosystem II function on a diel timescale, which was related to changes in the solar irradiance and thermal structure, was identified. The diel cycle included (1) vertically well-mixed (or weakly linear) conditions in density and chlorophyll a early in the morning, resulting from vertical mixing through penetrative overnight convection; (2) depleted chlorophyll a concentration in the surface layer during the middle of the day due to photoinhibition; (3) an increased chlorophyll a concentration in the bottom layer by late afternoon due to optimum light conditions; and (4) the formation of a chlorophyll a break point (CBP) at the thermocline, which migrated downwards with the deepening surface mixed layer. On a longer timescale (days), moored acoustic instruments were used to derive echo level (EL), which approximated suspended particulate matter (SPM). Wind events ultimately controlled SPM, a conclusion based on (1) elevated EL during high windgenerated turbulence and bed shear stress, (2) positive time-lagged correlations between wind speed and EL at three field sites with different exposures to wave action, and (3) significant negative correlations between wind speed and depth-differentiated echo level (d(EL)/dz) at all sites. Sea breezes produced a similar response in EL through the water column to a small storm event, and wind-driven SPM resuspension resulted in a reduction in the sub-surface light climate (kd). Near-bed dissolved oxygen concentrations varied in accord with elevated wind speeds, EL and kd, highlighting a possible suppression of photosynthesis. One-dimensional modelling revealed that wind stirring was most often the dominant process in these waters. It was found that for a brief period during thermal stratification there was shear production of turbulent instabilities that migrated from the thermocline to the surface and the seabed. Convective cooling was not able to mix the water column entirely overnight without the addition of wind, and minimum wind speeds were determined for this complete vertical mixing. Bottom-generated turbulence was limited to a small region above the bed, and was deemed insignificant compared with mixing generated at the surface. Minimum wind speeds required for de-stratification and prevention of stratification were determined for summer, autumn and winter. A hypothetical desalination outfall was simulated for all seasons and it was concluded that positioning of the discharge at middepth was preferable compared to at the seabed. The results of this thesis advance the current knowledge of coastal biophysical oceanography and provide new insights into the temporal dynamics of the coastal water column of south-western Australia.
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Dutagaci, Bercem [Verfasser], Clemens [Akademischer Betreuer] Glaubitz e Peter [Akademischer Betreuer] Güntert. "Biophysical Studies of Lipid Membranes by Solid State NMR and Molecular Dynamics Simulations / Bercem Dutagaci. Gutachter: Clemens Glaubitz ; Peter Güntert. Betreuer: Clemens Glaubitz". Frankfurt am Main : Univ.-Bibliothek Frankfurt am Main, 2013. http://d-nb.info/1044772786/34.
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Denk, Jonas [Verfasser], e Erwin [Akademischer Betreuer] Frey. "Collective behavior in biophysical systems : from patterns in non-equilibrium protein systems to growth dynamics of cell populations / Jonas Denk ; Betreuer: Erwin Frey". München : Universitätsbibliothek der Ludwig-Maximilians-Universität, 2018. http://d-nb.info/1220631779/34.
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Hogben, Hannah J. "Coherent spin dynamics of radical pairs in weak magnetic fields". Thesis, University of Oxford, 2011. http://ora.ox.ac.uk/objects/uuid:61c4ab7e-406f-4193-949a-b5a70f43e3e1.
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The outcome of chemical reactions proceeding via radical pair (RP) intermediates can be influenced by the magnitude and direction of applied magnetic fields, even for interaction strengths far smaller than the thermal energy. Sensitivity to Earth-strength magnetic fields has been suggested as a biophysical mechanism of animal magnetoreception and this thesis is concerned with simulations of the effects of such weak magnetic fields on RP reaction yields. State-space restriction techniques previously used in the simulation of NMR spectra are here applied to RPs. Methods for improving the efficiency of Liouville-space spin dynamics calculations are presented along with a procedure to form operators directly into a reduced state-space. These are implemented in the spin dynamics software Spinach. Entanglement is shown to be a crucial ingredient for the observation of a low field effect on RP reaction yields in some cases. It is also observed that many chemically plausible initial states possess an inherent directionality which may be a useful source of anisotropy in RP reactions. The nature of the radical species involved in magnetoreception is investigated theoretically. It has been shown that European Robins are disorientated by weak radio-frequency (RF) fields at the frequency corresponding to the Zeeman splitting of a free electron. The potential role of superoxide and dioxygen is investigated and the anisotropic reaction yield in the presence of a RF-field, without a static field, is calculated. Magnetic field effect data for Escherichia coli photolyase and Arabidopsis thaliana cryptochrome 1, both expected to be magnetically sensitive, are satisfactorily modelled only when singlet-triplet dephasing is included. With a view to increasing the reaction yield anisotropy of a RP magnetoreceptor, a brief study of the amplification of the magnetic field experienced by a RP from nearby magnetite particles is presented. Finally in a digression from RPs, Spinach is used to determine the states expected to be immune from relaxation and therefore long-lived in NMR experiments on multi-spin systems.
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Babi, Almenar Javier. "Characterisation, biophysical modelling and monetary valuation of urban nature-based solutions as a support tool for urban planning and landscape design". Doctoral thesis, Università degli studi di Trento, 2021. http://hdl.handle.net/11572/288810.
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The recognition of nature in the resolution of societal challenges has been growing in relevance. This recognition has been associated with the development of new concepts from science and policy such as natural capital, ecosystem services, green infrastructure, and more recently Nature-Based Solutions (NBS). NBS intends to address societal challenges in an effective and adaptive form providing economic, social, and environmental benefits. The overall aim of this PhD thesis is to develop an environmental and economic assessment of NBS for highly urbanised territories based on rationales and models underpinning ecosystem services, urban/landscape ecology, and life cycle thinking approaches. This combined evaluation approach would help to better understand if NBS are cost-effective or not. The aim is developed according to four specific objectives.
The first objective corresponds to the characterisation of NBS in relation to urban contexts and the problematics that they can help to address or mitigate. To achieve this objective a critical review on the study of the relationship between NBS, ecosystem services (ES) and urban challenges (UC) was developed. As a main output, a graph of plausible cause-effect relationships between NBS, ES and UC is obtained. The graph represents a first step to support sustainable urban planning, moving from problems (i.e. urban challenges) to actions (i.e. NBS) to resolutions (i.e. ES).
The second objective corresponds to the definition of an adequate set of biophysical and monetary assessment methods and indicators to evaluate the value of NBS in urbanised contexts. To achieve this objective, a review of existing methods on ecosystem services valuation, life cycle cost analysis and life-cycle assessment are developed. The review takes into account specific constraints such as easiness to use and availability of data. At the end, potential methods and indicators were selected, which will be later integrated in the combined assessment framework.
The third objective corresponds to the design of a combined assessment framework integrating methods from life cycle assessment, landscape/urban ecology and ecosystem services that quantifies the environmental and economic value of NBS informing about the cost-effectiveness of its entire life cycle. To achieve this objective, a conceptual framework is developed. From it, a system dynamics model of ecosystem (dis)services is developed and coupled with a life cycle assessment method. The combined evaluation is tested with a relevant NBS type (i.e. urban forest) in a case study in the metropolitan area of Madrid.
The fourth objective is the development of a decision support (DSS) tool that integrates the assessment framework as part of iterative design processes in urban planning and landscape design. The DSS intends to enhance the interrelation between science, policy and planning/design. To achieve this objective a user-friendly web-based prototype DSS on NBS, called NBenefit$®, is developed. The prototype DSS provides the user a simple form of quantifying the provision of multiple ES and costs over the entire life cycle (implementation, operational life, and end-of-life) of NBS.
This thesis contributed to the characterisation of NBS and its environmental and economic assessment to inform urban planning and landscape design processes, allowing decisions that are more informed.Il riconoscimento della natura nella risoluzione delle sfide sociali è diventato sempre più importante. Questo riconoscimento è stato associato allo sviluppo di nuovi concetti provenienti dalla scienza e dalla politica, come il capitale naturale, i servizi ecosistemici, le infrastrutture verdi e, più recentemente, le soluzioni basate sulla natura (NBS). NBS intende affrontare le sfide della società in una forma efficace e adattabile fornendo benefici economici, sociali e ambientali. Lo scopo di ricerca di questa tesi di dottorato è quello di sviluppare una valutazione ambientale ed economica delle NBS per territori altamente urbanizzati basata su logiche e modelli che hanno alla base i servizi ecosistemici, l'ecologia urbana e paesaggistica e degli approcci di approcio life cycle. Questo quadro di valutazione combinato aiuterebbe a capire meglio se le NBS sono costo effetive e se contribuiscono a uno sviluppo resiliente e sostenibile. Questo scopo di ricerca è sviluppato secondo quattro obiettivi specifici. Il primo obiettivo corrisponde alla caratterizzazione delle NBS in relazione ai contesti urbani e alle problematiche che possono aiutare ad affrontare o mitigare. Per raggiungere questo obiettivo è stata sviluppata una revisione critica dell letteratura sullo studio della relazione tra NBS, servizi ecosistemici (ES) e sfide urbane (UC). Come risultato principale, si ottiene un grafico delle relazioni causa-effetto plausibili tra NBS, ES ed UC. Il grafico rappresenta un primo passo per supportare la pianificazione urbana sostenibile, passando dai problemi (es. UC) alle azioni (es. NBS) alle risoluzioni (es. ES). Il secondo obiettivo corrisponde alla definizione di un set di metodi e indicatori di valutazione biofisica e monetaria adeguate per valutare il valore della NBS in contesti urbanizzati. Per raggiungere questo obiettivo, viene sviluppata una revisione dei metodi esistenti sulla valutazione dei servizi ecosistemici, l'analisi dei costi del ciclo di vita e la valutazione del ciclo di vita. La revisione tiene conto di vincoli specifici come la facilità d'uso e la disponibilità dei dati. Alla fine, sono stati selezionati potenziali metodi e indicatori, che saranno successivamente integrati nel quadro di valutazione combinato. Il terzo obiettivo corrisponde alla progettazione del quadro di valutazione combinato, integrando metodi di valutazione del ciclo di vita, ecologia paesaggistica / urbana e servizi ecosistemici che quantifica il valore ambientale ed economico della NBS informando sull'efficacia in termini di costi del suo intero ciclo di vita. Per raggiungere questo obiettivo, prima viene sviluppato un quadro concettuale. Da esso, viene sviluppato un modello di dinamica di sistemi per calcolare i servizi (e disservici) ecosistemici, il quale è interrelazionato con un metodo di valutazione life cycle. Questa valutazione combinata viene testata con un tipo di NBS pertinente (foresta urbana) in un caso di studio nell'area metropolitana di Madrid. Il quarto obiettivo è lo sviluppo di uno strumento di supporto decisionale (DSS) che integri il quadro di valutazione come parte dei processi di progettazione iterativa nella pianificazione urbana e nella progettazione del paesaggio. Il DSS intende migliorare l'interrelazione tra scienza, politica e pianificazione / progettazione. Per raggiungere questo obiettivo è stato sviluppato Nbenefit$® un prototipo di DSS online per la valutazzione NBS di facile uso. Il prototipo DSS fornisce all'utente una forma semplice per quantificare multipli ES e costi (internalizatti o no) durante l'intero ciclo di vita (implementazione, vita operativa e fine vita) del NBS. In conclusione, questa tesi ha contribuito alla caratterizzazione di NBS e alla sua valutazione ambientale ed economica per informare i processi di pianificazione urbana e progettazione del paesaggio, consentendo decisioni più informate.
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Zietz, Burkhard. "An Ultrafast Spectroscopic and Quantum-Chemical Study of the Photochemistry of Bilirubin : Initial Processes in the Phototherapy for Neonatal Jaundice". Doctoral thesis, Umeå : Dept. of Chemistry, Umeå University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-672.
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Shen, Tongye. "Fluctuations and stochastic dynamics in molecular biophysics /". Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2002. http://wwwlib.umi.com/cr/ucsd/fullcit?p3061634.
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Klingelhoefer, Jochen W. "Biophysics of nanopores-multiscale molecular dynamics simulation studies". Thesis, University of Oxford, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.540136.
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Harrison, Ryan M. "Molecular biophysics of strong DNA bending and the RecQ DNA helicase". Thesis, University of Oxford, 2014. http://ora.ox.ac.uk/objects/uuid:f02fc167-b705-4275-a413-21d13b5d94c3.
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Molecular biophysics is a rapidly evolving field aimed at the physics-based investigation of the biomolecular processes that enable life. In this thesis, we explore two such processes: the thermodynamics of DNA bending, and the mechanism of the RecQ DNA helicase. A computational approach using a coarse-grained model of DNA is employed for the former; an experimental approach relying heavily on single-molecule fluorescence for the latter. There is much interest in understanding the physics of DNA bending, due to both its biological role in genome regulation and its relevance to nanotechnology. Small DNA bending fluctuations are well described by existing models; however, there is less consensus on what happens at larger bending fluctuations. A coarse-grained simulation is used to fully characterize the thermodynamics and mechanics of duplex DNA bending. We then use this newfound insight to harmonize experimental results between four distinct experimental systems: a 'molecular vise', DNA cyclization, DNA minicircles and a 'strained duplex'. We find that a specific structural defect present at large bending fluctuations, a 'kink', is responsible for the deviation from existing theory at lengths below about 80 base pairs. The RecQ DNA helicase is also of much biological and clinical interest, owing to its essential role in genome integrity via replication, recombination and repair. In humans, heritable defects in the RecQ helicases manifest clinically as premature aging and a greatly elevated cancer risk, in disorders such as Werner and Bloom syndromes. Unfortunately, the mechanism by which the RecQ helicase processes DNA remains poorly understood. Although several models have been proposed to describe the mechanics of helicases based on biochemical and structural data, ensemble experiments have been unable to address some of the more nuanced questions of helicase function. We prepare novel substrates to probe the mechanism of the RecQ helicase via single-molecule fluorescence, exploring DNA binding, translocation and unwinding. Using this insight, we propose a model for RecQ helicase activity.
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Brown, Peter N. "Biophysical and structural characterisation of protein-peptide interactions". Thesis, University of Edinburgh, 2010. http://hdl.handle.net/1842/3982.
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Proliferating cell nuclear antigen (PCNA) is an essential protein in the cell. It is involved in transcription and many types of DNA repair and replication. Homologues of this protein are found in all orders of life. The high level of conservation and essential nature of PCNA infers that it may be a potential drug target for anti-caner drugs in humans and also a potential anti-parasitic target. X-ray structures of PCNA from Homo sapiens (Hs), Schizosaccharomyces pombe (Sp) and Leishmania major (Lm) are now available and can be used as a template for structure based drug design. In this work PCNA from these three species have been prepared in milligram quantities for biochemical and biophysical studies. The previously unknown structure of LmPCNA has been solved in an uncomplexed form and also complexed with a dodecapeptide to a resolution of 3.0Å. A comparison of PCNA structures and their peptide complexes for the three species identifies structural differences which may be relevant in analysing thermodynamic contributions of binding. All eukaryotic PCNA molecules exist as ring shaped trimers which form around DNA. In this work the oligomeric state of LmPCNA has been determined to be hexameric both in solution and in the crystal. It has also been hypothesised that HsPCNA is hexameric however these would seem to form hexamers in which the trimeric rings associate “back-to-back” while LmPCNA trimers would seem to associate “face-to-face”. The binding affinities for these three PCNAs have been determined with a selection of peptides derived from the Hs p21 protein. This work has shown, using a selection of different techniques including Surface Plasmon Resonance (SPR), Isothermal Titration Calorimetry (ITC) and Dynamic Scanning Fluorimetry (DSF); that HsPCNA and SpPCNA have similar affinities for a 12mer peptide (Kd of ~1μM) however LmPCNA shows significantly weaker interactions (Kd of ~10μM). This is most likely due to divergence in the sequence and structure of LmPCNA. A systematic investigation by SPR on the effect of peptide linker length on binding has been carried out using a series of synthesised peptides with different lengths of chemical spacer. The series of streptavidin immobilised peptides show that longer spacers are required for the recovery of the PCNA peptide binding affinity. The results presented in this work indicate that a linker length of at least 20Å is required for measurable protein binding activity. This interaction is improved with longer peptide spacers.
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Morris, Eliza. "Mechanics and Dynamics of Biopolymer Networks". Thesis, Harvard University, 2014. http://dissertations.umi.com/gsas.harvard:11647.
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The three major mechanical components of cells are the biopolymers actin, microtubules, and intermediate filaments. Cellular processes are all highly reliant on the mechanics of the specific biopolymers and the networks they form, rendering necessary the study of both the kinetics and mechanics of the cytoskeletal components. Here, we study the in vitro mechanics of actin and composite actin/vimentin networks, and the effect of various actin-binding proteins on these networks.Engineering and Applied Sciences
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Worster, Katy Lynn. "Coordination dynamics of walking". Thesis, University of Colorado at Denver, 2015. http://pqdtopen.proquest.com/#viewpdf?dispub=3702117.
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Although coordination has been identified as a fundamental element necessary for the successful achievement of walking, this aspect of gait has yet to be embraced into instrumented gait analysis, perhaps in part due to the lack of a normative reference and unfamiliarity of mathematical methods that are best suited to capture this essential behavior. Therefore, this work focused on expanding clinical gait analysis techniques by validating nonlinear methods that describe the influence of neurological control on the musculoskeletal system. This body of work investigated the coordination dynamics during gait in both prospective and retrospective subjects free of gait pathology, subjects with spastic cerebral palsy, and subjects with a lower limb amputation using motion capture and mathematical models to help elucidate the complexities of gait and enhance therapeutic interventions. This investigation quantified coordination strategies employed by an unimpaired subject when presented with various walking conditions and challenges mimicking various inhibitions associated with performing the task of swing limb advancement. Two novel indices of coordination dynamics were created to provide a concise metric and ease their inclusion into future research applications. The first normative reference dataset of these coordination measures was created from a large cohort of unimpaired subjects. While there is presently not a gold standard method for quantifying coordination during gait, the exciting correlations between the proposed measures and select clinical performance tasks indicate the coordination measures quantify essential inter-segmental coordination dynamics of walking. The theoretical pendular software model created shows swing limb advancement is not a purely passive motion, but instead an actively controlled motion. Comparisons between the various cohorts revealed the proposed measures of coordination are more suitable for characterizing motor control strategies contributing to a gait pattern, quantify organization of individual segments, identify mechanisms of change, and reveal the loci of impairment(s). The proposed measures of coordination dynamics are capable of distinguishing between different gait pathologies and patterns associated with altered limb advancement during the swing period of gait. Results from this multidisciplinary work have the strong potential to directly impact the clinical treatment of persons with aberrant coordination dynamics during gait.
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Borek, Bartlomiej. "Dynamics of heterogeneous excitable media with pacemakers". Thesis, McGill University, 2012. http://digitool.Library.McGill.CA:80/R/?func=dbin-jump-full&object_id=107795.
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The heart is a heterogeneous excitable tissue embedded with pacemakers. To understand the fundamental rules governing its behaviour it is useful to investigate the interplay between structure and dynamics in simplified experimental and mathematical models. This thesis examines FitzHugh-Nagumo type reaction-diffusion equation models motivated by experiments with engineered cardiac tissue culture. The aim is to relate how the design properties of these systems determine the underlying spatiotemporal dynamics. First, a functional relation between randomly distributed heterogeneities and conduction velocity is proposed in two dimensional heterogeneous excitable media. The transitions to wave break are studied for two types of heterogeneities related to fibroblasts and collagen deposits. The effects of pacemakers are next considered with a theoretical study of the transitions in one-dimensional wave patterns of a pacemaker reset by a stimulus pulse from a distance. Reflected wave solutions are found near the apparent discontinuity in the phase transition curve of the system, and they grow into more multi-reflected trajectories for a coarser spatial discretization of the model. Finally, the dynamical regimes arising from the interaction of two pacemakers in heterogeneous excitable media are investigated. A novel chick culture is developed to exhibit dominant pacemaker dynamics. This stable rhythm undergoes transitions to more complex reentrant patterns following induction of new pacemakers by the application of the potassium channel blocker, E-4031. The dynamics are reproduced by the FitzHugh-Nagumo model, which further demonstrates the effects of pacemaker size and heterogeneity density on the transition to wave break and reentry. These findings may contribute to our understanding of the generic mechanisms governing the dynamics of wave propagation through heterogeneous excitable media with pacemakers, including healthy and diseased hearts.Le coeur est un tissu hétérogène excitable qui contient des générateurs de rythme. Pour comprendre les règles fondamentales qui dirigent son comportement, il est utile d'étudier l'interaction entre la structure et la dynamique des modèles expérimentaux et mathématiques simplifiés. Dans cette thèse, j'utilise des modèles d'équations de FitzHugh-Nagumo. Ces modèles sont motivés par l'expérimentation avec des tissus cardiaques modifiés pour étudier comment les propriétés des conceptions influencent la dynamique d'ondes. Tout d'abord, une relation fonctionelle entre la densité des hétérogénéités distribuées au hasard et la vitesse de conduction est proposée dans un modèle numérique de deux dimensions de média hétérogènes excitables. Les transitions à l'onde rupturée sont différentes pour deux types de substrats hétérogènes. Les effets des régions automatiques sont alors considérés avec une étude théorique des transitions dans les ondes unidimensionelles des générateurs de rythme réinitialisés par une seule impulsion d'une distance. Des solutions d'ondes réfléchies se trouvent près de la discontinuité apparente de la courbe de transition de phase du système et deviennent des trajectoires plus complexes pour une discrétisation spatiale plus grossière du modèle. Enfin, les modèles d'ondes résultant de l'interaction de deux générateurs de rythme dans des médias hétérogènes excitables sont étudiés. Une nouvelle culture de tissu cardiaque de poussin est développée pour présenter la dynamique dominante déterminée par un générateur de rythme. Ce rythme stable subit des transitions à des modèles d'ondes réentrants plus complexes suivant l'induction de nouveaux générateurs de rythme, par l'application du bloqueur des canaux potassiques, E-4031. La dynamique est reproduite par le modèle FitzHugh-Nagumo, prévoyant l'effet de la taille du générateur de rythme et la densité de l'hétérogèneité sur la transition de l'onde rupturée et à la réentrée. Ces résultants contribuent à notre compréhension des mécanismes de média hétérogènes excitables avec des générateurs de rythme, dont les coeurs sains et malades.
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Leftin, Avigdor. "Nuclear magnetic resonance probes of membrane biophysics: Structure and dynamics". Diss., The University of Arizona, 2010. http://hdl.handle.net/10150/305369.
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The phospholipid membrane is a self-assembled, dynamic molecular system that may exist alone in association with only water, or in complex systems comprised of multiple lipid types and proteins. In this dissertation the intra- and inter-molecular forces responsible for the atomistic, molecular and collective equilibrium structure and dynamics are studied by nuclear magnetic resonance spectroscopy (NMR). The multinuclear NMR measurements and various experimental techniques are able to provide data that enable the characterization of the hierarchical spatio-temporal organization of the phospholipid membrane. The experimental and theoretical studies conducted target membrane interactions ranging from model systems composed of only water and lipids, to multiple component domain forming membranes that are in association with peripheral and trans-membrane proteins. These measurements consisit of frequency spectrum lineshapes and nuclear-spin relaxation rates obtained using 2 H NMR, 13 C NMR, 31 P NMR and 1 H NMR. The changes of these experimental observables are interpreted within a statistical thermodynamic framework that allows the membrane structure, activation energies, and correlation times of motion to be determined. The cases presented demonstrate how fundamental principles of NMR spectroscopy may be applied to a host of membranes, leading to the biophysical characterization of membrane structure and dynamics.
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Šmít, Daniel. "Analysis of dynamical interactions of axon shafts and their biophysical modelling". Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066095/document.
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La fasciculation des axones joue un rôle essentiel dans le développement des réseaux neuronaux. Cependant, la dynamique de la fasciculation axonale, ainsi que les mécanismes biophysiques à l’œuvre dans ce processus, demeurent encore très mal compris. En vue d'étudier les mécanismes de fasciculation d'axones ex vivo, nous avons développé un système modèle simple, constitué par des explants d'épithélium olfactif de souris embryonnaires en culture, à partir desquels poussent les axones des neurones sensoriels olfactifs. Grâce à une étude en vidéomicroscopie, nous avons observé que ces axones interagissent de façon dynamique par leur fibre, à la manière de fermetures éclair pouvant se fermer ("zippering") ou s'ouvrir ("unzippering"), ce qui conduit respectivement à la fasciculation ou à la défasciculation des axones. Mettant à profit cette nouvelle préparation expérimentale pour l'étude des interactions dynamiques entre axones, nous avons développé une analyse biophysique détaillée des processus de zippering/unzippering.Nous mettons en évidence dans notre travail l'existence d'un mécanisme biophysique cohérent de contrôle des interactions locales entre fibres axonales. Ce mécanisme local est à mettre en relation avec les changements de la structure globale du réseau axonal (degré de fasciculation) qui s'opèrent sur une échelle temporelle plus longue. Enfin, nous discutons la signification fonctionnelle de nos observations et analyses, et proposons un nouveau rôles de la tension mécanique dans le développement du système nerveux : la régulation de la fasciculation des axones et, en conséquence, de la formation des cartes topologiques au sein des réseaux neuronauxWhile axon fasciculation plays a key role in the development of neural networks, very little is known about its dynamics and the underlying biophysical mechanisms. In a model system composed of neurons grown ex vivo from explants of embryonic mouse olfactory epithelia, we observed that axons dynamically interact with each other through their shafts, leading to zippering and unzippering behaviour that regulates their fasciculation. Taking advantage of this new preparation suitable for studying such interactions, we carried out a detailed biophysical analysis of zippering, occurring either spontaneously or induced by micromanipulations and pharmacological treatments.We show that there is a consistent mechanism which governs local interactions between axon shafts, supported by broad experimental evidence. This mechanism can be reconciled with changes in global structure of axonal network developing on slower time scale, analogically to well-studied relation between local relaxations, and topological changes and coarsening in two-dimensional liquid foams. We assess our observations and analysis in light of possible in vivo functional significance and propose a new role of mechanical tension in neural development: the regulation of axon fasciculation and consequently formation of neuronal topographic maps