Tesi: "Biophysical transition"

1

Colledge, Vicki Louise. "Stuructural and biophysical investigations of bacillus subtillis transition-state regulators". Thesis, University of York, 2010. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.535053.

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2

Valba, Olga. "Statistical analysis of networks and biophysical systems of complex architecture". Phd thesis, Université Paris Sud - Paris XI, 2013. http://tel.archives-ouvertes.fr/tel-00919606.

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Complex organization is found in many biological systems. For example, biopolymers could possess very hierarchic structure, which provides their functional peculiarity. Understating such, complex organization allows describing biological phenomena and predicting molecule functions. Besides, we can try to characterize the specific phenomenon by some probabilistic quantities (variances, means, etc), assuming the primary biopolymer structure to be randomly formed according to some statistical distribution. Such a formulation is oriented toward evolutionary problems.Artificially constructed biological network is another common object of statistical physics with rich functional properties. A behavior of cells is a consequence of complex interactions between its numerous components, such as DNA, RNA, proteins and small molecules. Cells use signaling pathways and regulatory mechanisms to coordinate multiple processes, allowing them to respond and to adapt to changing environment. Recent theoretical advances allow us to describe cellular network structure using graph concepts to reveal the principal organizational features shared with numerous non-biological networks.The aim of this thesis is to develop bunch of methods for studying statistical and dynamic objects of complex architecture and, in particular, scale-free structures, which have no characteristic spatial and/or time scale. For such systems, the use of standard mathematical methods, relying on the average behavior of the whole system, is often incorrect or useless, while a detailed many-body description is almost hopeless because of the combinatorial complexity of the problem. Here we focus on two problems.The first part addresses to statistical analysis of random biopolymers. Apart from the evolutionary context, our studies cover more general problems of planar topology appeared in description of various systems, ranging from gauge theory to biophysics. We investigate analytically and numerically a phase transition of a generic planar matching problem, from the regime, where almost all the vertices are paired, to the situation, where a finite fraction of them remains unmatched.The second part of this work focus on statistical properties of networks. We demonstrate the possibility to define co-expression gene clusters within a network context from their specific motif distribution signatures. We also show how a method based on the shortest path function (SPF) can be applied to gene interactions sub-networks of co-expression gene clusters, to efficiently predict novel regulatory transcription factors (TFs). The biological significance of this method by applying it on groups of genes with a shared regulatory locus, found by genetic genomics, is presented. Finally, we discuss formation of stable patters of motifs in networks under selective evolution in context of creation of islands of "superfamilies".

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3

Nauseef, Jones Trevor. "An investigation of the molecular and biophysical properties of metastatic cells". Diss., University of Iowa, 2015. https://ir.uiowa.edu/etd/3150.

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Prostate cancer presents a significant paradox: it is very common, yet rarely fatal. To wit, the prostate is the most common non-skin tissue for cancer diagnosis in men in the United States. Despite its high incidence, fatal malignancy occurs in only a small fraction of diagnosed men. The fatal cases are characteristically defined by distant spread in the body, also known as metastasis. In order to metastasize a cancer cell must complete several sequential steps. These include degradation of and invasion through the epithelial basement membrane, typically through the loss of static intracellular adhesions with fellow epithelial cells; entrance into the blood stream (intravasation); survival within circulation; exit from the blood stream upon arrival at a new tissue (extravasation); and survival and colonization at the secondary site. At the time of diagnosis, it is not currently possible to accurately predict future metastasis and thereby clinicians cannot delineate those men at high risk for fatal disease from the vast majority of men who are likely to experience an indolent disease course. Consequently, we examined the behavior of cancer cells in several steps of the metastatic cascade. In doing so, we uncovered both molecular and biophysical characteristics of cancer cells that may facilitate successful metastatic dissemination and tumor outgrowth. Epithelial-to-mesenchymal transition (EMT) is physiological process of transdifferentiation that is normally initiated during vertebrate development, but has recently been implicated in tumor development, progression, and metastases. The EMT program results in dramatic changes, including the exchange of epithelial for mesenchymal markers, altered cellular morphology, and gain of motility. EMT-like cellular alterations have been implicated most strongly in the metastasis steps of invasion and survival of cells at primary tumors sites. How EMT-like changes may facilitate survival and growth in the microenvironment of a micrometastatic niche has been less clearly elucidated. Consequently, we evaluated how EMT-like changes may affect the survival and subsequent outgrowth of prostate cancer cell lines following restrictive growth conditions. We observed that EMT-like cells as compared to their more epithelial counterparts displayed enhanced maintenance of their proliferative potential following extended culture in nutrient restriction. This phenotype depended on an EMT-associated increase in autophagy. Notably, the post-stress outgrowth phenotype could be conferred through a paracrine signaling mechanism that may involve autophagy-derived exosome-like extracellular vesicles. These studies demonstrated that EMT-like cells have a resistance to nutrient restriction through enhanced autophagy and may have uncovered a novel autophagy-dependent exosomal secretion pathway. Metastatic efficiency is thought to be strongly limited by the destruction of circulating tumor cells by the hemodynamic shear forces within the vasculature. However, such a persistent belief has little appropriate published experimental evidence. We developed an in vitro assay to expose cells to fluid shear stress (FSS). By monitoring the viability of the cells, we determined that transformed cells had a highly conserved ability to resist even very high FSS. The mechanism depended on the capacity to patch membrane defects, extracellular calcium, and a dynamic cytoskeleton. We also observed a stiffening of cancer cell membranes after exposure to FSS. Taken together, these studies expand the understanding of how cancer cells survive in circulation and indicate that metastatic efficiency is less limited by hemodynamic forces than previously thought. The steps of hematogenous metastasis between intravasation and extravasation necessitate the existence of circulating tumor cells (CTCs). Collection, enumeration, and study of CTCs have the potential to serve as a "liquid biopsy" of the metastatic cascade. In prostate cancer, the enumeration of CTCs by detection of the expression of epithelial markers has displayed limited clinical utility. We hypothesized that the prognostic value of CTC number may be enhanced by detection of cells which have undergone the pro-metastatic EMT-like program. We developed a flow cytometry-based experimental assay for enumeration of CTCs using epithelial (EpCAM) and mesenchymal-like (N-cadherin) surface proteins. We detected from prostatectomy patients before and after surgery events expressing EpCAM, N-cadherin, and both. However, the detection of background events from healthy control subjects was unacceptably high. These studies support the idea of mesenchymal-like tumor cells in circulation, but will require further assay development for reliable conclusions to be drawn. In sum, the work described above has provided descriptive and mechanistic insight to molecular and biophysical properties that may facilitate prostate cancer metastasis. It is our hope that these data will result in the development of relevant preventative, diagnostic, and therapeutic clinical strategies for prostate cancer.

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4

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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5

Wang, Yin 1951. "Influences of membrane biophysical properties on the Metarhodopsin I to Metarhodopsin II transition in visual excitation". Diss., The University of Arizona, 1997. http://hdl.handle.net/10150/282520.

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Current biophysical studies of membrane proteins are centered on the relation of their structures to key biological functions of membranes in terms of lipid-protein interactions. The conformational transition of rhodopsin from Metarhodopsin I to Metarhodopsin II (Meta I-Meta II) is the triggering event for the visual process. Meta II is the activated form of the visual receptor and binds a signal transducing G protein (transducin), followed by two amplification stages which lead to generation of a visual nerve impulse. Herein, flash photolysis and surface plasmon resonance (SPR) spectroscopy techniques have been used to monitor the Meta I-Meta II transition of rhodopsin in various membrane recombinants. The flash photolysis experiments clearly show a substantial shift to the left of the Meta I-Meta II equilibrium for rhodopsin in egg phosphatidylcholine recombinant membranes. Investigation of the influences on rhodopsin function by non-lamellar forming lipids reveals a characteristic relationship between the Gibbs free energy change for the Meta I-Meta II equilibrium of rhodopsin and the intrinsic curvature of the lipid bilayer. Complementary SPR studies suggest a protrusion of the protein at the activated Meta II state which may be associated with exposure of recognition sites for the signal transducing G protein on the cytoplasmic surface of rhodopsin. All the experimental results obtained here are consistent with the hypothesis of a new flexible surface biomembrane model. The Meta II state is favored by a negative spontaneous curvature of the bilayer, corresponding to an imbalance of the lateral forces within the polar head groups and acyl chains. The mean curvature of membrane bilayer in the Meta II state reflects the small spontaneous curvature of the lipid bilayer in the vicinity of protein. Relief of the lipid curvature frustration in the Meta II state energetically couples the lipids to the photoexcitation of rhodopsin. Consideration of the various energetic contributions suggests the bilayer curvature free energy provides a reservoir of work in the modulation of rhodopsin function in the visual process. These studies that biophysical properties of the liquid-crystalline lipid bilayer are important in relation to protein function and may be relevant to the biomedical investigations of visual dysfunction.

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6

Stam, Carson A. "Using Biophysical Geospatial and Remotely Sensed Data to Classify Ecological Sites and States". DigitalCommons@USU, 2012. https://digitalcommons.usu.edu/etd/1389.

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Monitoring and identifying the state of rangelands on a landscape scale can be a time consuming process. In this thesis, remote sensing imagery has been used to show how the process of classifying different ecological sites and states can be done on a per pixel basis for a large landscape. Twenty-seven years' worth of remotely sensed imagery was collected, atmospherically corrected, and radiometrically normalized. Several vegetation indices were extracted from the imagery along with derivatives from a digital elevation model. Dominant vegetation components from five major ecological sites in Rich County, Utah, were chosen for study. The vegetation components were Aspen, Douglas-fir, Utah juniper, mountain big sagebrush, and Wyoming big sagebrush. Training sites were extracted from within map units with a majority of one of the five ecological sites. A Random Forests decision tree model was developed using an attribute table populated with spectral biophysical variables derived from the training sites. The overall out-of-bag accuracy for the Random Forests model was 97.2%. The model was then applied to the predictor spectral and biophysical variables to spatially map the five major vegetation components for all of Rich County. Each vegetation class had greater than 90% accuracies except for Utah juniper at 81%. This process is further explained in chapter 2. As a follow-on effort, we attempted to classify vegetation ecological states within a single ecological site (Wyoming big sagebrush). This was done using field data collected by previous studies as training data for all five ecological states documented for our chosen ecological site. A Maximum Likelihood classifier was applied to four years of Landsat 5 Thematic Mapper imagery to map each ecological state to pixels coincident to the map units correlated to the Wyoming big sagebrush ecological site. We used the Mahalanobis distance metric as an indicator of pixel membership to the Wyoming big sagebrush ecological site. Overall classification accuracy for the different ecological states was 64.7% for pixels with low Mahalanobis distance and less than 25% for higher distances.

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7

Drew, Elliot Dudley. "Biophysical and computational characterisation of the disorder-to-order structural transition of the small hydrophilic endoplasmic-reticulum associated protein, SHERP". Thesis, Birkbeck (University of London), 2018. http://bbktheses.da.ulcc.ac.uk/366/.

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This thesis explores the disorder-to-order structural transition of the small hydrophilic endoplasmic reticulum associated protein (SHERP). SHERP has been shown to be essential to the life cycle of Leishmania major, a parasite responsible for leishmaniasis which kills tens of thousands every year. The protein is almost entirely disordered in solution, but undergoes a dramatic increase in helicity upon binding to anionic lipids or detergents. Although the ordered structure of SHERP had previously been solved by solution nuclear magnetic resonance spectroscopy in the presence of sodium dodecyl sulphate (SDS), both the nature of the disordered ensemble of the protein and the organisation of the SHERP/detergent complex were unknown. Using a combination of synchrotron radiation circular dichroism spectroscopy (SRCD), small angle X-ray scattering (SAXS) and molecular dynamics (MD), several projects were carried out exploring the disorder-to-order structural transition of SHERP in the presence of SDS. The effectiveness of sequence-based predictors to estimate the effect of single mutants was explored, with a number of mutants expressed and characterised by SRCD and MD. A mutant, the "permutant", was designed with the aim of decreasing the disorder of the protein in solution while maintaining amino acid composition, by introduction of multiple potential i → i4 salt bridges created by permutations of the wild-type sequence. Molecular dynamics simulations of the wild-type and "permutant" construct found a dramatic increase in salt bridge formation, and in vitro characterisation of the "permutant" construct showed it had significantly greater helical character than the wild-type in the absence of SDS. The disordered ensemble of SHERP was characterised by replica exchange MD, SRCD and SAXS. Good agreement was found between simulation and experiment, with a predominantly unfolded ensemble deficient in secondary structure described by our results. The changes that occur upon SHERP binding to SDS were also characterised. MD simulation of the SHERP-SDS complex showed that the protein bound among the head-groups of the SDS micelle, and the helical content and helix-turn-helix structure was retained. It also allowed identification of several cationic side-chains which formed stabilising salt bridges with the sulphates of SDS. The complex was then characterised in vitro, by SAXS and CD spectroscopy. The addition of the protein led to a doubling in micelle length, with multiple SHERP molecules found to bind to the anionic head-groups in the shell of the micelle. The residues identified during the MD simulation were substituted with alanine to make a series of mutants with increasing negative charge. Significant decreases in helicity, micelle length and the numbers of protein bound occurred as negative charge increased, possibly caused by decreased affinity of the protein for the micelle causing less protein molecules to bind per micelle, leading to a decreased chance of stabilising protein-protein interactions resulting in partial folding of the protein. These results demonstrate the importance of charge-charge interactions in the disorder-to-order structural transition of SHERP, and provide structural context for future functional work on this protein.

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8

Kettner, Claudia, Angela Köppl e Sigrid Stagl. "List of well-being indicators". European Commission, bmwfw, 2012. http://epub.wu.ac.at/4714/1/WWWforEurope_WPS_no002_MS30.pdf.

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This milestone presents a pool of available indicators and indicator systems which go beyond the narrow concepts of national economic accounts as well as a structuring of the indicators and indices according to central areas of well-being. The milestone builds the basis for Task 202.2, where a subset of indicators will be selected based on different theoretical frameworks, e.g. services / functionings, needs. Some of the indicators will be included in the macro-economic models in order to account for key dimensions of sustainability.
Series: WWWforEurope

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9

Kettner, Claudia, Angela Köppl e Sigrid Stagl. "Towards an operational measurement of socio-ecological performance". European Commission, bmwfw, 2014. http://epub.wu.ac.at/4718/1/WWWforEurope_WPS_no052_MS29.pdf.

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Questioning GDP as dominant indicator for economic performance has become commonplace. For economists economic policy always aims for a broader array of goals (like income, employment, price stability, trade balance) alongside income, with income being the priority objective. The Stiglitz-Sen-Fitoussi Commission argued for extending and adapting key variables of macroeconomic analysis. International organisations such as the EC, OECD, Eurostat and UN have proposed extended arrays of macroeconomic indicators (see 'Beyond GDP', 'Compendium of wellbeing indicators', 'GDP and Beyond', 'Green Economy', 'Green Growth', 'Measuring Progress of Societies'). Despite these high profile efforts, few wellbeing and environmental variables are in use in macroeconomic models. The reasons for the low uptake of socio-ecological indicators in macroeconomic models range from path dependencies in modelling, technical limitations, indicator lists being long and unworkable, choices of indicators appearing ad hoc and poor data availability. In this paper we review key approaches and identify a limited list of candidate variables and - as much as possible - offer data sources.
Series: WWWforEurope

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10

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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11

Gori, Matteo. "Phase transitions theory and applications to biophysics". Thesis, Aix-Marseille, 2016. http://www.theses.fr/2016AIXM4111.

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Les études et les résultats présentés dans ce manuscrit ont pour but de développer une meilleure compréhension des principes à la base de l'auto-organisation dans les systèmes biologiques. La théorie topologique des transitions de phase est l'un des approches possibles pour fournir une généralisation de la description des transitions de phase dans les systèmes petits ou mésoscopiques. Cette théorie a été rigoureusement enracinée dans deux théorèmes: un contre exemple à l'un de ces théorèmes a été récemment découvert. La première partie de ce manuscrit est donc consacré à mieux comprendre ce «contre-exemple » pour verifier si et comment la théorie peut être sauvé.Dans la deuxieme parte de ce manuscrit les résultats des recherches théoriques, numériques et expérimentales sur la condensation à la Fr "ohlich sont reportés. Ceci est une condition préalable à l'activation des oscillations dipolaires géantes qui entraînent des interactions électrodynamiques à long portée entre les molécules coresonnantes. Dans cette thèse, on montre que les interactions à longue portée affectent sensiblement les propriétés de diffusion des molécules en solution. Une empreinte des interactions à long portée pourrait être un phénomène de «transition» en ce qui concerne le coefficient de diffusion en fonction d'un paramètre de contrôle proportionnel à l’intensité d'interaction. Simulations analogues ont été réalisées afin de valider une approche expérimentale visant à trouver une telle «empreinte» dans les systèmes avec interactions à longue portée
The studies and results reported in this manuscript are aimed to develop a deeper understanding of the principles at the basis of self-organization in biological system.The Topological Theory of phase transitions is one of the possible approaches to provide a generalization of description of phase transitions in small or mesoscopic systems. This theory has been rigorously rooted in two theorems: a counterexample to one of these theorems has been recently found. The first part of this manuscript is devoted to investigation of the "counterexample" to understand if and how the theory can be saved. In the second part of this manuscript the results of theoretical, numerical and experimental investigations on Fr"ohlich-like condensation for normal modes of biomolecules are reported. This is a prerequisite for the activation of giant dipole oscillations in biomolecules which entail long-range electrodynamic interactions between coresonant molecules. In this thesis is shown that long-range interactions markedly affect the self-diffusion properties of molecules in solution. A fingerprint of long-range interactions could be a "transitional" phenomenon concerning the self-diffusion coefficient as a function of a control parameter proportional to interaction strength. Analogous simulations have been performed to validate an experimental approach aimed at finding such "fingerprint" in systems with built-in long-range interactions

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12

Desnos, Hugo. "Amélioration des procédures de cryoconservation de type congélation-lente par simulation et caractérisation des effets de composés chitooligosaccharides". Thesis, Lyon, 2019. http://www.theses.fr/2019LYSE1048/document.

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Les méthodes d’amélioration des procédures de cryoconservation sont traditionnellement basées sur l’empirisme. Pour s’en démarquer, nous sommes repartis des modèles biophysiques développés pour décrire les procédures en s’appuyant sur 2 méthodes. La 1ère méthode a consisté au développement de techniques de simulation des procédures en caractérisant l’utilisation du Snomax dans l’appareil DSC. Nous avons montré que le contrôle de la température de nucléation (Tn) est possible en choisissant les conditions expérimentales (volume d’échantillon et concentration en Snomax) qui influencent les probabilités de présence de 3 sous-populations d’INA des protéines de P. syringae. La possibilité d’effectuer des simulations a pu être validée pour certaines plages de surfusion dans les solutions de cryoconservation. Ceci a permis la caractérisation des effets physiques influencés par Tn et qui interviennent au cours des procédures et d’alimenter les modèles biophysiques de cryoconservation. La 2ème méthode a consisté à la modification de la composition des solutions afin de réduire le recours au DMSO (cytotoxique) en utilisant des composés de type oligosaccharides : les COS. Après vérification de la biocompatibilité des COS avec des cellules embryonnaires, la caractérisation de l’influence thermodynamique des COS a été effectuée. Il a été montré que les COS sont des cryostabilisateurs qui se lient à une petite quantité de molécule d’eau et n’en affecte pas les propriétés physicochimiques. Les COS peuvent donc être introduits dans le milieu extracellulaire sans risque d’accélérer la déshydratation cellulaire. De plus, il a été montré qu’ils favorisent la gélification du milieu extracellulaire, laquelle est fonction de la proportion massique d’eau en solution résiduelle. Cette gélification fige une partie du système ce qui favorise sa stabilisation au passage des zones de températures à risques de recristallisation
We wished to move aside classical cryopreservation procedure improvements that are based on empiricism and to focus on existing biophysical models in order to describe procedures. We based our study on two methods. The first method consisted in developing the methods for the simulations of procedures, by characterizing the use of Snomax in a DSC device. This study highlighted that the nucleation temperature (Tn) control is possible under precise experimental conditions (sample volume and Snomax concentration) that influence the presence probability of 3 INA subpopulations of the P. syringae protein aggregates. The possibility to simulate the cryopreservation procedures has been achieved for some supercooling ranges within complex cryopreservation solutions. Consequently, it has been possible to characterize the physical effects influenced by Tn and involved within procedures. These results will participate in supplying cryopreservation biophysical models. The second method aimed to modify the composition of cryopreservative solutions in order to reduce the DMSO use (because of its cytotoxicity), using extracellular CPA components: the chitooligosaccharides COS. Subsequent to the biocompatibility verification of the COS with embryonic cells, the thermodynamic influence of the COS has been characterized. Therefore, it has been demonstrated that COS are cryostabilizers that link themselves to a small number of water molecules and does not influence its physicochemical properties. Consequently, COS can be added within the extracellular space without any risk to accelerate the cell dehydration. It has been demonstrated that COS favor the gelation of the extracellular space and that this gelation relies on the mass proportion of water in the residual solution. This gelation immobilizes a part of the system and therefore favor its stabilization when the temperature reaches the risky recrystallization range

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13

Tjhung, Elsen. "Phenomenology and simulations of active fluids". Thesis, University of Edinburgh, 2013. http://hdl.handle.net/1842/8017.

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Active fluids are an interesting new class of non-equilibrium systems in physics. In such fluids, the system is forced out of equilibrium by the individual active particles - in contrast to driven systems where the system is forced out of equilibrium by some external forces. Some biological examples of active fluids are bacterial suspensions and actomyosin solutions inside eukaryotic cells. In the case of bacterial suspensions, the fluid is stirred internally by the swimming bacteria and as a consequence of this, active fluids can have some interesting physics of their own such as hydrodynamic instabilities and spontaneous symmetry breaking. Here, in particular, we study how such instabilities may arise and how they may lead to a non-equilibrium steady state. We also study numerically a droplet of active matter as a simple representation of cell extract comprising actomyosin solution bounded by a cell membrane. It is widely believed that cell motility is driven only by actin polymerization pushing against the cell membrane. However, we show that even in the absence of actin polymerization, actin-myosin contraction alone can also generate a unidirectional motion. This happens due to the spontaneous breakdown of a discrete symmetry at large enough activity (i.e. actomyosin contraction). This non-equilibrium phase transition from stationary to motile state is somewhat similar to the second order phase transition in equilibrium thermodynamics. Finally, we studied the behaviour of an active droplet on a two-dimensional surface to mimic cell crawling. Whereas cell migration in 3D environment maybe driven mainly by actin-myosin contraction (described above), cell crawling on a 2D surface is driven mainly by actin polymerisation. Here we find that localised actin polymerisation can cause protrusion in the cell membrane which is qualitatively similar to lamellipodium formation in cell crawling.

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14

Finnerty, Gerald Thomas. "Factors determining the transition to seizure in the tetanus toxin model of epilepsy". Thesis, Imperial College London, 1993. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.361453.

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15

Alrabghi, Ghadah. "THE PHYSICAL PROPERTIES OF PHOSPHOLIPID AND TRIGLYCERIDE MONOLAYERS: PHASE TRANSITIONS, MORPHOLOGY AND COLLAPSE". Kent State University / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=kent1436273087.

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16

Tripathi, Swarnendu. "Conformational Transition Mechanisms of Flexible Proteins". Kent State University / OhioLINK, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=kent1281491004.

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17

Gutierrez, Cori Omar. "Relationship and feedback between LULC changes and hydroclimatic variability in Amazonia". Electronic Thesis or Diss., Sorbonne université, 2024. http://www.theses.fr/2024SORUS123.

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La forêt amazonienne joue un rôle essentiel en tant que régulateur du système climatique et principal puits de carbone terrestre. Il contrôle les processus hydroclimatiques et atténue les effets des sécheresses grâce au couplage végétation-atmosphère. En fait, les forêts amazoniennes peuvent potentiellement affecter les régimes de précipitations grâce à des processus biophysiques tels que le recyclage de l'eau. Cependant, ces capacités ont été réduites au cours des dernières décennies en raison des perturbations du système climat-végétation ainsi que de l'intensification des sécheresses. Cela a accentué un processus de transition biophysique d'un écosystème à prédominance forestière vers une savane. Par conséquent, compte tenu de ces complexités, il est extrêmement important de comprendre la direction des changements.À l'aide de plusieurs ensembles de données et du modèle couplé ORCHIDEE-LMDZ, cette thèse approfondit l'étude des interactions entre l'hydroclimatologie et la végétation amazonienne. En outre, il cherche à élargir notre compréhension des modifications du système végétation-atmosphère et de ses liens avec le climat et des changements du LULC. De même, en tenant compte des taux croissants de déforestation, il étudie les effets et les rétroactions résultant d'un scénario de perte forestière à grande échelle sur les processus hydrologiques.Les résultats montrent que, dans le sud-ouest de l'Amazonie, les forêts passant d'un état influencé par la disponibilité énergétique à un état dépendant de la disponibilité en eau tout au long de l'année. Pendant la saison des pluies, la croissance de la végétation est principalement influencée par la disponibilité en énergie plutôt que par la disponibilité en eau. Cependant, en dehors de cette période, les forêts réagissent positivement aux précipitations et au stockage terrestre de l'eau, ce qui suggère que la végétation dépend principalement de l'approvisionnement hydrique. Toutefois, une analyse spatiale révèle que la déforestation récente modifie ces transitions et déstabilise l'équilibre naturel du système climat-végétation.La nature de ces déséquilibres en Amazonie n'est pas complètement claire. En examinant les liens entre les flux d'eau/énergie et les conditions de végétation, nous explorons si ces changements sont inhérents au climat ou résultent de processus anthropiques. 67% du sud-ouest a connu une transition vers un état majoritairement sec en raison du climat (forçage externe), tandis que 21% a connu une transition vers un état dominé par la déforestation (forçage interne). Cependant, les moteurs externes et internes entraînent simultanément des changements. En quantifiant les forçages, nous montrons que les synergies ont amené 74% du sud-ouest de l'Amazonie à un état de stress hydrique élevé. Or, ces dernières années, 30% des changements sont strictement dominés par des forçages internes. Cela suggère que les processus internes jouent un rôle croissant dans la transition vers des états caractérisés par un stress hydrique forestier élevé, particulièrement là où la déforestation et la pression anthropique augmentent.À l'aide du modèle couplé ORCHIDEE-LMDZ, les effets de la déforestation projetée de l'Amazonie d'ici 2050 sur le cycle de l'eau et la sécheresse sont examinés. La déforestation diminue les précipitations, réduit l'évapotranspiration et augmente le ruissellement. De plus, elle accentue le stress hydrique, notamment dans le sud-ouest de l'Amazonie (retour positif). La demande en eau dans l'atmosphère, à la surface et même dans la zone racinaire du sol s'intensifie pendant la saison sèche. Pendant la saison des pluies, le déficit d'humidité atmosphérique devient encore plus aigu vers les Andes tropicales, sur la région de l'Altiplano. Ces résultats permettent de mieux comprendre les effets possibles du déboisement massif sur la disponibilité en eau et la résilience de l'Amazonie dans un contexte où les changements se produisent à un rythme accéléré
The Amazon rainforest plays a vital role by functioning as a regulator of the climate system and as the main terrestrial carbon sink. It drives hydroclimatic processes and mitigates the effects of droughts through vegetation-atmosphere coupling. Indeed, Amazon forests have the potential to impact rainfall patterns through biophysical processes like water recycling. However, these capacities have been reduced during the last decades due to disturbances in the climate-vegetation system together with the intensification of droughts. All this has accentuated a process of biophysical transition from a predominantly forested ecosystem to a Savanna. Therefore, given these complexities, understanding the direction of changes is of vital importance.Using multiple datasets and the coupled ORCHIDEE and LMDZ models, this thesis delves into the study of the interactions between Amazon hydroclimatology and vegetation. In addition, it seeks to expand our understanding of modifications in the vegetation-atmosphere system and its links with climate and LULC changes. Likewise, taking into account the increasing rates of deforestation, it investigates the effects and feedback resulting from a large-scale forest loss scenario on hydrological processes.The results show that, over the southwestern Amazon, forests undergo a transition from being influenced by energy availability to depending on water availability throughout the year. During the rainy season, vegetation growth is primarily influenced by energy availability rather than water availability. Nevertheless, outside of this period, forests respond positively to precipitation and terrestrial water storage, suggesting that vegetation is primarily dependent on water supply. However, a spatial analysis reveals that recent deforestation modifies these transitions and destabilizes the natural balance in the climate-vegetation system.The nature of these imbalances in the Amazon is not entirely clarified. Through an approach based on the relationships of water/energy fluxes and vegetation conditions over the last four decades, it is explored whether these changes are intrinsic to climate variability or are driven by anthropogenic processes. 67% of the southwestern Amazon has experienced a transition towards a predominantly dry state due to climatic factors (external forcing), while 21% has transitioned towards a state dominated by deforestation (internal forcing). However, external and internal forcings are not independent processes, as both mechanisms drive changes simultaneously. By weighing the magnitudes of these forcings, we show that the synergies have led 74% of the southwestern Amazon toward a state of greater water stress. Nevertheless, during recent years, although combined external-internal processes continue to exert significant control over changes, 30% of these are strictly dominated by internal forcing. This suggests that internal processes are playing an increasingly relevant role in the transition towards a state characterized by high forest water stress, especially in areas where deforestation and anthropogenic pressure are increasing.Using the coupled ORCHIDEE and LMDZ models, the effects of projected Amazon deforestation by 2050 on the hydrological cycle and dryness are examined. Deforestation decreases precipitation, reduces evapotranspiration and increases runoff. Furthermore, deforestation accentuates water stress especially in the southwestern Amazon (positive feedback). Water demands in the atmosphere, on the land surface and even in the soil root zone intensify during the dry season. During the wet season, the deficit of specific atmospheric humidity becomes even more acute towards the tropical Andes over the Altiplano region. These findings provide a more thorough understanding of the possible effects of massive forest removal on the water availability and resilience of the Amazon in a context where changes are occurring at an accelerated rate

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18

Laarraj, Mohcine. "Nanocalorimètre dynamique pseudo-différentiel à haute sensibilité pour l'étude thermodynamique et cinétique de la transition vitreuse". Thesis, Université Grenoble Alpes (ComUE), 2016. http://www.theses.fr/2016GREAY029/document.

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Cette thèse décrit la réalisation d’un nanocalorimètre dynamique différentiel pour l’étude de la transition vitreuse. Le capteur microfabriqué, la chaine de mesure de bas niveau de bruit et de grande stabilité, ainsi que l’environnement thermique du capteur sont décrits en détails. La méthode de mesure utilisée est une méthode fréquentielle dans laquelle l’amplitude et la phase de la température oscillante sont mesurées avec une grande résolution. La résolution du nanocalorimètre sur le module de la capacité calorifique complexe est de ∆|C_p^* |/|C_p^* |  ± 0,001 %, et sur la phase de l’oscillation de température est de ∆φ/φ  ± 0,0005 %. La résolution est environ mille fois plus élevée que celle des calorimètres à modulation de température commerciaux. Les potentialités du nanocalorimètre pour l’étude d’effets thermodynamiques et cinétiques fins sont démontrées sur un modèle de polymère vitreux, le poly(acétate de vinyle). Des effets nouveaux et trop tenus pour être détectés avec des calorimètres classiques ont été mesurés. Le module de la capacité calorifique complexe et la phase de l’oscillation de température présentent des relaxations temporelles de faible variation dans l’état de liquide surfondu comme dans l’état vitreux. De plus, le dégel des degrés de libertés internes structuraux du polymère peut, suivant l’histoire thermique suivie par le matériau, se réaliser en deux étapes lors du réchauffement. Ce double dégel n’est visible que sur la dérivée en température du module de la capacité calorifique complexe. En conclusion, la résolution, la stabilité et la répétabilité du nanocalorimètre sont particulièrement adaptées à des mesures nanocalorimétriques fines pour l’étude thermodynamique et cinétique de systèmes complexes hors équilibres dont les verres font partie
This thesis reports the working principle and the building up of a dynamic differential nanocalorimeter to the study of the glass transition. The micro-fabricated sensor, the low noise and highly stable measurement chain, as well as the thermal environment of the sensor are described in details. The measurement method is a spectroscopic method in which the amplitude and phase of the oscillating temperature are measured with a high resolution at different frequencies. The resolution of the nanocalorimeter on the measurement of the complex heat capacity module is ∆|C_p^* |/|C_p^* |  ± 0,001 %, and on the phase of the temperature oscillation is ∆φ/φ  ± 0, 0005 %. This resolution is about one thousand times higher than that of the commercial temperature modulated calorimeters. The potentialities of the nanocalorimeter for the study of fine thermodynamic and kinetic effects are demonstrated on a model of glassy polymer, the poly(vinyl acetate). New effects which are too fine to be detected by conventional calorimeters have been measured. The modulus of the complex heat capacity and the phase of the temperature oscillation exhibit small relaxational effects of low amplitude either in the super-cooled liquid state or in the glassy state. In addition, according to the thermal history followed by the material, the structural recovery of this polymer can take place in two steps during the heating. These two steps are visible only on the temperature derivative of the modulus of the complex heat capacity. In conclusion, resolution, stability and repeatability of the nanocalorimeter are particularly suitable for fine thermodynamic and kinetic study on out of equilibrium complex systems such as glasses

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19

Miermont, Agnès. "Severe osmotic compression of the yeast Saccharomyces cerevisiae". Phd thesis, Université Paris-Diderot - Paris VII, 2013. http://tel.archives-ouvertes.fr/tel-00864602.

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Les cellules ont développé plusieurs voies de signalisation et de réponses transcriptionnelles pour réguler leur taille et coordonner leur croissance et leurs divisions cellulaires. L'intérieur des cellules est naturellement surchargé par des macromolécules. Cet encombrement macromoléculaire, appelé crowding, a été intensément étudié in vitro et est connu pour affecter la cinétique des réactions. Cependant, l'étude des effets d'encombrement in vivo est plus difficile en raison du haut niveau de complexité et d'hétérogénéité à l'intérieur d'une cellule. Au cours de cette thèse, nous nous sommes intéressés aux effets de changement du volume cellulaire sur la cinétique de réactions biochimiques chez la levure Saccharomyces cerevisiae. Pour cela, nous avons induit des stress osmotiques pour comprimer la cellule et étudier l'impact du crowding sur les cinétiques de signalisation. La réduction du volume cellulaire augmente la viscosité interne et peut retarder le fonctionnement de plusieurs voies de signalisation et de processus cellulaires. En augmentant progressivement le niveau de compression, on observe un ralentissement des processus biologiques jusqu'à un point où l'adaptation cellulaire est abolie. Ceci a été observé pour la translocation nucléaire de facteurs de transcription (Hog1, Msn2, Crz1, Mig1 et Yap1) ainsi que pour la mobilité des protéines Abp1 et Sec7. Nous montrons aussi que la compression altère la capacité de plusieurs protéines à diffuser dans le cytoplasme de différents types cellulaires. Nous proposons que ces altérations cinétiques induites par l'augmentation de la viscosité intracellulaire ne soient pas sans rappeler une transition vitreuse. Ces résultats suggèrent l'importance d'un encombrement macromoléculaire optimal permettant aux cellules de fonctionner correctement.

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Gerbelli, Barbara Bianca. "Propriedades estruturais e elásticas de fases lamelares: O efeito da composição da membrana". Universidade de São Paulo, 2012. http://www.teses.usp.br/teses/disponiveis/43/43134/tde-12032013-102341/.

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Neste trabalho, é apresentado um estudo sistemático de uma fase lamelar composta de lecitina á qual é incorporado um co-surfactante de uso comercial (Simulsol), que consiste de uma mistura de ácidos graxos etoxilados. Foi realizado um estudo estrutural, utilizando a técnica de espalhamento de raios X em baixo ângulo (SAXS) em amostras inseridas em capilares, variando a composição da membrana, desde 100% de lecitina até 100% de Simulsol, ao longo da linha de diluição, para cada composição. Os resultados experimentais de espalhamento foram analisados usando um método que permite o ajuste direto da intensidade de espalhamento e um procedimento de otimização que fornece o perfil de densidade eletrônica da bicamada. Com esse método de análise, além de parâmetros estruturais tais como, periodicidade lamelar e espessura da bicamada obtém-se o parâmetro de Caillé, que relaciona as constantes elásticas que caracterizam a flexibilidade do sistema lamelar. As propriedades termodinâmicas do sistema lamelar foram investigadas para duas composições de membrana, em experimentos onde o potencial químico da água é controlado. A combinação dos resultados obtidos nos estudos estruturais e termodinâmicos permitiu a determinação do módulo de compressibilidade da fase lamelar e da constante de rigidez da membrana. A incorporação do co-surfactante aumenta a contribuição de interações de natureza entrópica relacionada às flutuações da membrana, que resultam na estabilização da fase lamelar para distâncias de separação entre as membranas muito maiores do que as observadas no sistema lamelar composto apenas por lecitina. Para pequenas distâncias de separação entre as bicamadas, observa-se superposição de regiões polares de bicamadas vizinhas, que são acompanhadas de mudanças no comportamento do parâmetro de Caillé, e consequentemente no comportamento das constantes de compressibilidade e na constante de rigidez. No regime diluído, a incorporação de moléculas anfifílicas com apenas uma cadeia carbônica resulta na redução significativa da constante de rigidez da membrana de lecitina de ~ 20kBT para ~0,5kBT.
In this work we present a systematic study of structural properties of a lamelar phase composed of lecithin when a commercial cosurfactant(Simulsol) which is a mixture of etoxylated fatty acids. The study was carried out using small angle X ray scattering with samples encapsulated in glass capillaries, varying membrane composition from 100% of lecithin to 100% of Simulsol, through the dilution line, for each composition. The experimental results were analyzed using a method that fits directly the scattered intensity and, by means of an optimization procedure, gives the electronic density profile of the lipid bilayer. From the analysis of experimental data, in addition to the structural parameters, such as the lamellar period and membrane thickness,we obtain the Caillè parameter, which relates the elastic constants that characterizes the flexibility of the lamellar system. Thermodynamic properties of the lamellar system were also investigated, for two membrane compositions, by controlling the water chemical potential. The combination of results obtained in structural and thermodynamic studies allowed determination of the compressibility modulus of the lamellar phase and the membrane rigidity constant. The incorporation of co-surfactant to the membrane increases the contribution of entropic interactions arising from membrane fluctuations resulting in the stabilization of lamellar phase for larger membrane separation distances than observed for the lamellar system composed of lecithin only. For small membrane separation distances, a superposition of polar region of neighbor bilayers is observed, with related changes in the behavior of Caillè parameter, and consequently in the behavior of compressibility and membrane rigidity constants. In diluted regime, the incorporation of amphiphilic molecules with a single carbonic chain results in a significant reduction in lecithin membrane rigidity, from ~20kBT to ~ 0,5 kBT .

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21

Ho, Chian Sing. "Inquiry of Lipid Membranes Interacting with Functional Peptides and Polyphenol Drug Molecules". Scholar Commons, 2016. http://scholarcommons.usf.edu/etd/6255.

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Cellular membranes are important targets for many membrane-active peptides and drug compounds. Here we are interested in deciphering how lipid membranes are perturbed by several membrane-active molecules, including the transmembrane domain of the influenza M2 protein (M2TM), aggregates formed by a synthetic polyglutamine peptide, and three polyphenol compounds (i.e., tamoxifen, genistein, and verapamil). We employ phase-separated ternary lipid model membranes in the form of giant unilamellar vesicles (GUVs) to simulate raft-like structures that have been proposed to govern many important processes in plasma membranes (e.g., intracellular singling and trafficking). Specifically, we use fluorescent microscopy to interrogate how those membrane additives modulate the phase behavior of free-standing GUVs, as well as the miscibility transition temperature (Tm). We find that M2TM increases Tm and causes vesicle budding; polyglutamine aggregates disrupt lipid membranes; and the three polyphenol compounds exert disparate effects on GUV Tm.

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22

Li, Yan. "The Metabolic Transitions Regulated by the Estrogen-related Receptor (ERR) in Drosophila melanogaster". VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/559.

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In multicellular organism, bioenergetic metabolism is strictly regulated toward efficient generation of ATP. However, in certain situations, such as in limiting oxygen or in the rapidly proliferating system like growing juvenile or cancer cells, organisms apply the metabolic strategy that favors the production of biomass (e.g., nucleotides, amino acids, and lipids) over efficiency of ATP generation. The conserved estrogen-related receptors (ERRs) are master regulators in controlling metabolic homeostasis, and good candidates for mediating the metabolic transition induced by hypoxia and development. First, we investigate how dERR influences hypoxic adaptation in Drosophila melanogaster. We find that dERR is required for a competent hypoxic response alone, or together with hypoxia inducible factor (HIF), which is the main transcription factor modulating the hypoxic adaptation. We show that dERR binds to dHIFα and participates in the HIF-dependent transcriptional program in hypoxia. In addition, dERR acts in the absence of dHIFα in hypoxia and a significant portion of HIF-independent transcriptional responses can be attributed to dERR actions, including up-regulation of glycolytic transcripts. These results indicate that competent hypoxic responses arise from complex interactions between HIF-dependent and -independent mechanisms, and that dERR plays a central role in both of these programs. Secondly, we examine how dERR modulates metabolic transition toward the fatty acid oxidation at late L3 larva stage. We show that dERR is essential for the expression of an uncharacterized long-chain-fatty-acid acyl-CoA synthetase, CG4500, which is subject to induction by starvation. Furthermore, late L3 larvae of dERR mutants exhibit altered lipid profiles with elevated medium-chain and long-chain fatty acids. Together, with the previous finding that ERR directs an early switch toward glycolysis in the embryo, our studies indicate that ERR is a master regulator of programmed metabolic shifts through Drosophila development.

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23

Trueman, Steven F. "Insights Into ER Translocation Channel Gating. Structural Regulation of the Transition Between the Closed and Open Channel Conformations: A Dissertation". eScholarship@UMMS, 2011. https://escholarship.umassmed.edu/gsbs_diss/576.

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The transition between the closed and open conformations of the Sec61 complex permits nascent protein insertion into the translocation channel. A critical event in this structural transition is the opening of the lateral translocon gate that is formed by four transmembrane (TM) spans (TM2, TM3, TM7 and TM8 in Sec61p) to expose the signal sequence-binding (SSB) site. To gain mechanistic insight into lateral gate opening, mutations were introduced into a lumenal loop (L7) that connects TM7 and TM8. The sec61 L7 mutants were found to have defects in both the posttranslational and cotranslational translocation pathways due to a kinetic delay in channel gating. The translocation defect caused by L7 mutations could be suppressed by the prl class of sec61 alleles that reduce the fidelity of signal sequence recognition. The prl mutants are proposed to act by destabilizing the closed conformation of the translocation channel. Our results indicate that the equilibrium between the open and closed conformations of the protein translocation channel maintains a balance between translocation activity and signal sequence recognition fidelity. In the opening of the translocation channel, both the lateral and lumenal gate must open in a coordinated fashion for efficient protein translocation to occur. The lumenal gate is composed of a short helix of the loop preceding the second TM span, referred to as the plug helix, and six hydrophobic pore ring residues which form the constriction ring in the center of the channel. We identified three lateral gate polar residues and three hydrophobic residues from the plug domain that affect channel gating. Mutagenesis of the lateral gate polar cluster residues yields either a gain of function (prl phenotype) or a loss of function (translocation defect) phenotype. The combination of polar cluster mutations with each other or with plug domain mutations which cause a prl phenotype resulted in the mutually suppressive or additive phenotypes in double mutant strains. Cooperation between these residues is made possible through a structural link which connects the two translocation channel gates at their interface. The structural link provides a mechanism for the channel to coordinate the movement of multiple domains in the channel gating conformational change. Translocation assays demonstrated that this mechanism of gating regulation is particularly important for efficient protein translocation of substrates using the posttranslational translocation pathway. Our results indicate that residues from the plug and lateral gate domain form a regulatory cluster of residues responsible for efficient translocation channel gating.

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24

Scarlett, Michael A. "Can a comprehensive transition plan to barefoot running be the solution to the injury epidemic in American endurance runners?" Scholarship @ Claremont, 2018. http://scholarship.claremont.edu/cmc_theses/1830.

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Fossils belonging to the genus Homo, dating as far back as two million years ago, exhibit uniquely efficient features suggesting that early humans had evolved to become exceptional endurance runners. Although they did not have the cushion or stability-control features provided in our modern day running shoes, our early human ancestors experienced far less of the running-related injuries we experience today. The injury rate has been estimated as high as 90% annually for Americans training for a marathon and as high as 79% annually for all American endurance runners. There is an injury epidemic in conventionally shod populations that does not exist in the habitually unshod or minimally shod populations around the world. This has led many to conclude that the recent advent of highly technological shoes might be the problem. Although current literature has been inconclusive, there are two main limitations in virtually all of the studies: 1) transition phases of less than three months and 2) transition phases without rehabilitation exercises. These two aspects are key to the treatment of the structural consequences on the muscles and tendons of the foot and calf that habitually shod individuals have faced. This study includes a discussion of the cumulative consequences that lifelong shoe usage has on the development of the feet and lower legs. I propose a 78-week study that addresses the limitations of past studies by implementing a gradual, 32-week, multi-shoe transition complemented by an evidence-based rehabilitation program. I believe that this approach will restore strength and elasticity to muscles and tendons that have been inhibited by lifelong usage of overconstructed shoes and adequately prepare runners for the increased demand brought on by a changing running mechanic. This comprehensive, multifaceted transition plan to a fully minimalist shoe will provide novel insight into the ongoing barefoot debate. Can this approach finally demonstrate the proposed benefits of losing the shoes?

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25

Kistler, Kurt Andrew. "Using Quantum Mechanics to Investigate the Photophysical Properties of the DNA and RNA Bases and their Fluorescent Analogs". Diss., Temple University Libraries, 2010. http://cdm16002.contentdm.oclc.org/cdm/ref/collection/p245801coll10/id/73855.

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Chemistry
Ph.D.
The ability of the nucleic acids to absorb ultraviolet light and remain relatively photostable is a property upon which life depends. The nucleobases, which are the primary chromophores, when irradiated display rapid radiationless decay back to the ground state, in general faster than is needed for photoreaction. Fluorescent analogs of these bases have structures similar to the nucleic acid bases, but display much longer excited state lifetimes. Theoretical investigations using quantum mechanical methods can provide insight into the precise mechanisms of these decay processes, and to the molecular specifics that contribute to them. The results of multi-reference configuration interaction (MRCI) ab initio investigations into these mechanisms are presented, with emphasis on cytosine and its fluorescent analog 5-methyl-2-pyrimidinone (5M2P). A comprehensive picture of the potential energy surfaces of these two bases is given, including stationary points and conical intersections, where radiationless transitions are promoted, between up to three state surfaces, as well as pathways connecting these points for each base. Cytosine is shown to have two different energetically accessible radiationless decay channels. The fluorescence of 5M2P is also demonstrated theoretically, with mechanism proposed. The potential energy surfaces of the two bases have many close similarities, with the different photophysical properties being attributed to subtle energetic differences between the two bases. Nonadiabatic coupling and the geometric phase effect are analyzed in detail near conical intersections in cytosine, including in a region close to a three-state conical intersection. A substituent effect study on the 2-pyrimidinone ring system shows that the presence, position and orientation of the amino group in cytosine is central to its photophysical properties, particularly its high absorption energy, and can be explained with a simple Frontier Molecular Orbital model. The effects of water solvent on the excitation energies of cytosine and uracil are theoretically investigated using two multi-reference ab initio methods, a quantum mechanical molecular mechanics method using MRCI (MRCI-QM/MM), and the fragment molecular orbital multiconfiguration self-consistent field method (FMO-MCSCF). The solvatochromic shifts calculated from both methods agree well with other more expensive methods and experimental data. The effects of water on the photophysical pathways of cytosine is also investigated using MRCI-QM/MM, including considerations of solvent reorganization. Results show that the overall effect of water on the decay mechanisms is small, with neither decay channel being significantly blocked or favored.
Temple University--Theses

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26

Lopes, Pedro [Verfasser], e Hans Robert [Akademischer Betreuer] Kalbitzer. "Conformational Transitions of the Ras Protein Involved in Macromolecular Interactions and Modulated by Small Compounds. A Biophysical Approach Using NMR and X-Ray Crystallography at Ambient and High Pressures / Pedro Lopes ; Betreuer: Hans Robert Kalbitzer". Regensburg : Universitätsbibliothek Regensburg, 2018. http://d-nb.info/1182033377/34.

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27

Koirala, Deepak P. "Mechanochemistry, Transition Dynamics and Ligand-Induced Stabilization of Human Telomeric G-Quadruplexes at Single-Molecule Level". Kent State University / OhioLINK, 2014. http://rave.ohiolink.edu/etdc/view?acc_num=kent1397919270.

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28

Caleman, Carl. "Towards Single Molecule Imaging - Understanding Structural Transitions Using Ultrafast X-ray Sources and Computer Simulations". Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-7915.

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29

Darcy, Michael Augusto. "High Force Applications of DNA Origami Devices". The Ohio State University, 2021. http://rave.ohiolink.edu/etdc/view?acc_num=osu1619092851712077.

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30

Karjalainen, Eeva-Liisa. "The choreography of protein vibrations : Improved methods of observing and simulating the infrared absorption of proteins". Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2011. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-60415.

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The work presented in this thesis has striven toward improving the capability to study proteins using infrared (IR) spectroscopy. This includes development of new and improved experimental and theoretical methods to selectively observe and simulate protein vibrations. A new experimental method of utilising adenylate kinase and apyrase as helper enzymes to alter the nucleotide composition and to perform isotope exchange in IR samples was developed. This method enhances the capability of IR spectroscopy by enabling increased duration of measurement time, making experiments more repeatable and allowing investigation of partial reactions and selected frequencies otherwise difficult to observe. The helper enzyme mediated isotope exchange allowed selective observation of the vibrations of the catalytically important phosphate group in a nucleotide dependent protein such as the sarcoplasmic reticulum Ca2+-ATPase. This important and representative member of P-type ATPases was further investigated in a different study, where a pathway for the protons countertransported in the Ca2+-ATPase reaction cycle was proposed based on theoretical considerations. The transport mechanism was suggested to involve separate pathways for the ions and the protons. Simulation of the IR amide I band of proteins enables and supports structure-spectra correlations. The characteristic stacking of beta-sheets observed in amyloid structures was shown to induce a band shift in IR spectra based on simulations of the amide I band. The challenge of simulating protein spectra in aqueous medium was also addressed in a novel approach where optimisation of simulated spectra of a large set of protein structures to their corresponding experimental spectra was performed. Thereby, parameters describing the most important effects on the amide I band for proteins could be determined. The protein spectra predicted using the optimised parameters were found to be well in agreement with experiment.

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 5: Manuscript.

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Huang, Yan. "Synthesis, Kinetic and Photocatalytic Studies of Porphyrin-Ruthenium-Oxo Complexes". TopSCHOLAR®, 2010. http://digitalcommons.wku.edu/theses/182.

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Macrocyclic ligand-complexed transition metal-oxo intermediates are the active oxidizing species in a variety of important biological and catalytic oxidation reactions. Many transition metal catalysts have been designed to mimic the predominant oxidation catalysts in Nature, namely the cytochrome P450 enzymes. Ruthenium porphyrin complexes have been the center of the research and have successfully been utilized, as catalysts, in major oxidation reactions such as the hydroxylation of alkanes. This study focuses on kinetic and photocatalytic studies of oxidation reactions with wellcharacterized high-valent ruthenium-oxo porphyrin complexes. The trans-dioxoruthenium(VI) porphyrins have been among the best characterized metal-oxo intermediates and their involvement as the active oxidant in the hydrocarbon oxidation have been extensively studied. Following the literature known methods, a series of trans-dioxoruthenium(VI) porphyrin complexes (3a-b) were synthesized and spectroscopically characterized by UV-vis, IR and lH-NMR. In addition to the well-known chemical methods, we developed a novel photochemical approach for generation of trans-dioxoruthenium(VI) porphyrins with visible light. The fast kinetic study of two-electron oxidations of para-substituted phenyl methyl sulfides by these dioxoruthenium(VI) species was conducted by using stopped-flow spectroscopy. Results showed that the decay of trans--dioxoruthenium(VI) porphyrins in the presence of reactive sulfides follows a biexponential process. The reactivity order in the series of dioxoruthenium complexes follows TPFPP> TPP> TMP, consistent with expectations based on the electrophilic nature of high-valent metal-oxo species. Moreover, the sulfoxidation reactions are 3 to 4 orders of magnitude faster than the well-known epoxidation reactions. In addition, several ruthenium porphyrins were used as the catalysts in the competitive oxidation reactions to identify the kinetically competent oxidants during catalytic turnover conditions. The photocatalytic studies of aerobic oxidation reactions of hydrocarbons catalyzed by a bis-porphyrin-ruthenium(lV) fl-OXO dimer using atmospheric oxygen as oxygen source in the absence of co-reductants were investigated as well. The ruthenium(lV) fl-OXO bisporphyrin (6a) was found to catalyze aerobic oxidation of a variety of organic substrates efficiently. By comparison, 6a was found to be more efficient photocatalyst than the well-known 3a under identical conditions. A KIE at 298K was found to be larger than those observed in autoxidation processes, suggesting a nonradical mechanism that involved the intermediacy of ruthenium(V)-oxo species as postulated.

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32

He, Enuo. "Stochastic modelling of the cell cycle". Thesis, University of Oxford, 2012. http://ora.ox.ac.uk/objects/uuid:04185cde-85af-4e24-8d06-94b865771cf1.

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Precise regulation of cell cycle events by the Cdk-control network is essential for cell proliferation and the perpetuation of life. The unidirectionality of cell cycle progression is governed by several critical irreversible transitions: the G1-to-S transition, the G2-to-M transition, and the M-to-G1 transition. Recent experimental and theoretical evidence has pulled into question the consensus view that irreversible protein degradation causes the irreversibility of those transitions. A new view has started to emerge, which explains the irreversibility of cell cycle transitions as a consequence of systems-level feedback rather than of proteolysis. This thesis applies mathematical modelling approaches to test this proposal for the Mto- G1 transition, which consists of two consecutive irreversible substeps: the metaphase-to-anaphase transition, and mitotic exit. The main objectives of the present work were: (i) to develop deterministic models to identify the essential molecular feedback loops and to examine their roles in the irreversibility of the M-to-G1 transition; (ii) to present a straightforward and reliable workflow to translate deterministic models of reaction networks into stochastic models; (iii) to explore the effects of noise on the cell cycle transitions using stochastic models, and to compare the deterministic and the stochastic approaches. In the first part of this thesis, I constructed a simplified deterministic model of the metaphase-to-anaphase transition, which is mainly regulated by the spindle assembly checkpoint (the SAC). Based on the essential feedback loops causing the bistability of the transition, this deterministic model provides explanations for three open questions regarding the SAC: Why is the SAC not reactivated when the kinetochore tension decreases to zero at anaphase onset? How can a single unattached kinetochore keep the SAC active? How is the synchronized and abrupt destruction of cohesin triggered? This deterministic model was then translated into a stochastic model of the SAC by treating the kinetochore microtubule attachment at prometaphase as a noisy process. The stochastic model was analyzed and simulation results were compared to the experimental data, with the aim of explaining the mitotic timing regulation by the SAC. Our model works remarkably well in qualitatively explaining experimental key findings and also makes testable predictions for different cell lines with very different number of chromosomes. The noise generated from the chemical interactions was found to only perturb the transit timing of the mitotic events, but not their ultimate outcomes: all cells eventually undergo anaphase, however, the time required to satisfy the SAC differs between cells due to stochastic effects. In the second part of the thesis, stochastic models of mitotic exit were created for two model organisms, budding yeast and mammalian cells. I analyzed the role of noise in mitotic exit at both the single-cell and the population level. Stochastic time series simulations of the models are able to explain the phenomenon of reversible mitotic exit, which is observed under specific experimental conditions in both model organisms. In spite of the fact that the detailed molecular networks of mitotic exit are very different in budding yeast and mammalian cells, their dynamic properties are similar. Importantly, bistability of the transitions is successfully captured also in the stochastic models. This work strongly supports the hypothesis that uni-directional cell cycle progression is a consequence of systems-level feedback in the cell cycle control system. Systems-level feedback creates alternative steady states, which allows cells to accomplish irreversible transitions, such as the M-to-G1 transition studied here. We demonstrate that stochastic models can serve as powerful tools to capture and study the heterogeneity of dynamical features among individual cells. In this way, stochastic simulations not only complement the deterministic approach, but also help to obtain a better understanding of mechanistic aspects. We argue that the effects of noise and the potential needs for stochastic simulations should not be overlooked in studying dynamic features of biological systems.

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33

Zhan, Hongli. "Biophysical characterization of the allosteric transition in lactose repressor protein (LacI)". Thesis, 2005. http://hdl.handle.net/1911/18842.

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Allosteric transition, the basis of signal transduction and central to the function of regulatory proteins (e.g., transcriptional factors), is widely involved in biological systems with conformational change as a key characteristic. Although end-state structures are known for many proteins, less is known about the underlying detailed mechanism of the allosteric transition. We have used LacI as a model system to investigate this process at the atomic level. The work in this thesis focuses on three regions of LacI: the core pivot region, the N-subdomain monomer-monomer interface, and the hinge region. Characterization of representative mutants (L148F, S151P, P320A, and Q60G/L148F) demonstrated that the core pivot region exerts long-range effects on LacI function. For L148F and S151P, operator and inducer binding are altered in an inverse fashion with binding for one ligand strengthened, and binding for the other ligand weakened. Further characterization of L148F and S 151P has indicated that the conformational equilibrium is shifted towards the induced state in L148F and towards the repressed end in S151P. This conclusion is supported by detailed thermodynamic ligand binding assays and UV difference spectra. Detailed unfolding/refolding studies further suggest that the intrinsic ligand-binding properties of L148F and S151P are altered. Global fitting of all ligand-binding data is underway to further characterize these shifts. Our data for K84 hydrophobic variants (K84A/L) disclose impeded allosteric response to inducer, a state that is supported by a unique pattern in UV difference spectra. Operator release kinetics for K84A/L in response to IPTG suggest that two inducer molecules are required to release operator DNA. Characterization of 13 substitutions at V52, including binding to operator sequence variants, indicates a dominant role of the protein-operator interaction in LacI allostery and high affinity operator binding. Moreover, subsets of mutants that decouple inducer binding and conformational change were identified. In summary, this thesis work emphasizes the key role of several regions in LacI allostery, identifies several LacI allosteric intermediates, and discloses intermediates trapped along the allosteric pathway by mutation that correlate with points along the TMD simulation.

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34

Csiszar, Susan A. "The role of water in structural transitions of biophysical systems". 2005. http://link.library.utoronto.ca/eir/EIRdetail.cfm?Resources__ID=362568&T=F.

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35

Lettieri, Steven A. "Phase transitions in models of ion-specific protein solutions". 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3354770.

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36

Li, Xiaofei Gunton James D. Gunton James D. Rickman Jeffery M. Vavylonis Dimitrios Chaudhury Manoj K. "A study of phase transitions in globular protein solutions using Monte Carlo simulation". 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3373079.

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37

Blouin, George C. "Alkyl isocyanides as transition state analogs for ligand entry and exit in globins". Thesis, 2008. http://hdl.handle.net/1911/22179.

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There are two competing models for ligand entry and exit in globins. In the histidine gate model, a channel from the heme iron to the solvent opens by the outward rotation of the His(E7) side chain (7 th residue of the E-helix). In the multiple paths model, ligands diffuse through the protein matrix and exit at multiple points at its surface. Previous workers solved crystal structures to identify channels in myoglobin (Mb) with n-alkyl isocyanides (CNRs), a long flexible ligand that acts as a molecular "Ariadne's thread." When bound to Mb, a CNR points either toward solvent through an opened His(E7) (out conformation) or into the back of the distal pocket (in conformation). To measure the in/out equilibrium in solution, FTIR spectra have been collected for wild-type and mutant MbCNRs. The fraction of CNRs that point in (Fin) is regulated by the distal pocket volume, the freedom of the His(E7) side chain to rotate outward, and an unfavorable hydrophobic effect for CNRs that point outward into solvent. The relative importance of distal histidine flexibility and pocket volume on diatomic ligand binding with Mb has been assessed by correlating F in for bound CNRs with O2 and NO binding parameters. These correlations indicate strongly that: (1) CNRs and diatomic ligands use the histidine gate; (2) the volume of the binding pocket regulates non-covalent ligand capture and covalent bond formation with the iron atom; (3) the "baseball glove" model of ligand binding to Mb applies for all ligands; and (4) CNRs serve as useful transition state analogs for the diatomic ligand binding reactions of all globins.

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38

"Experimental characterization and molecular dynamics simulation of the allosteric transition in the Escherichia coli lactose repressor". Thesis, 2009. http://hdl.handle.net/1911/61933.

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The lactose repressor protein (LacI), a prototypic negative transcriptional regulator in E. coli, relies on an allosteric conformational change for its function. Targeted molecular dynamics (TMD) simulation of this LacI transition predicts that residues located in/near the inducer binding pocket, especially D149 and S193, play a critical role in the early stage of this allosteric process. Single mutants at D149 and S193, characterized by a series of biochemical and biophysical experiments, present limited information about LacI allostery. In contrast, double mutants are much more informative: D149A/S193A exhibits wild-type properties, which exclude the requirement for inter-residue hydrogen bond formation in the allosteric response. However, D149C/S193C purified from cell extracts shows decreased sensitivity to inducer binding, while retaining wild-type binding affinities for both operator and inducer. By manipulating cysteine oxidation, the more reduced state of D149C/S193C responds to inducer more similarly to wild-type protein, whereas the more oxidized state displays diminished inducer sensitivity. D149C/S193C exhibits near wild-type binding parameters for operator DNA and inducer, with comparable rate constants for binding to IPTG and dissociation from operator DNA. These features of D149C/S193C indicate that the novel disulfide bond formed in this mutant impedes the allosteric transition, consistent with the role of this region predicted by TMD simulation. V150C/V192C displays wild-type binding properties, presumably due to its reduced state. Interestingly, S151C/V192C in a partially oxidized state displays wild-type DNA and IPTG binding affinities, and retains normal response to IPTG binding. These data suggest that mobility of the entire flexible loop (residues 149-156) may not be the crucial element for Lad allosteric regulation. Further, a molecular dynamics simulation method was used to probe the motions that are necessary for the conformational change in LacI. The results of this simulation indicate that the backbone of residue 149 is the feature that may play a critical role in LacI allosteric regulation. In summary, biochemical characterization and computational simulation of multiple LacI mutants provide evidence for the functional roles of specific residues (and their interaction) and shed light on LacI allostery.

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39

Freddolino, Peter L. "Application of all-atom and coarse-grained molecular dynamics simulations to long timescale structural transitions of proteins /". 2009. http://gateway.proquest.com/openurl?url_ver=Z39.88-2004&rft_val_fmt=info:ofi/fmt:kev:mtx:dissertation&res_dat=xri:pqdiss&rft_dat=xri:pqdiss:3362787.

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Thesis (Ph.D.)--University of Illinois at Urbana-Champaign, 2009.
Source: Dissertation Abstracts International, Volume: 70-06, Section: B, page: 3363. Adviser: Klaus Schulten. Includes bibliographical references (leaves 179-201) Available on microfilm from Pro Quest Information and Learning.

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40

"Computational Approaches to Simulation and Analysis of Large Conformational Transitions in Proteins". Doctoral diss., 2017. http://hdl.handle.net/2286/R.I.46316.

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abstract: In a typical living cell, millions to billions of proteins—nanomachines that fluctuate and cycle among many conformational states—convert available free energy into mechanochemical work. A fundamental goal of biophysics is to ascertain how 3D protein structures encode specific functions, such as catalyzing chemical reactions or transporting nutrients into a cell. Protein dynamics span femtosecond timescales (i.e., covalent bond oscillations) to large conformational transition timescales in, and beyond, the millisecond regime (e.g., glucose transport across a phospholipid bilayer). Actual transition events are fast but rare, occurring orders of magnitude faster than typical metastable equilibrium waiting times. Equilibrium molecular dynamics (EqMD) can capture atomistic detail and solute-solvent interactions, but even microseconds of sampling attainable nowadays still falls orders of magnitude short of transition timescales, especially for large systems, rendering observations of such "rare events" difficult or effectively impossible. Advanced path-sampling methods exploit reduced physical models or biasing to produce plausible transitions while balancing accuracy and efficiency, but quantifying their accuracy relative to other numerical and experimental data has been challenging. Indeed, new horizons in elucidating protein function necessitate that present methodologies be revised to more seamlessly and quantitatively integrate a spectrum of methods, both numerical and experimental. In this dissertation, experimental and computational methods are put into perspective using the enzyme adenylate kinase (AdK) as an illustrative example. We introduce Path Similarity Analysis (PSA)—an integrative computational framework developed to quantify transition path similarity. PSA not only reliably distinguished AdK transitions by the originating method, but also traced pathway differences between two methods back to charge-charge interactions (neglected by the stereochemical model, but not the all-atom force field) in several conserved salt bridges. Cryo-electron microscopy maps of the transporter Bor1p are directly incorporated into EqMD simulations using MD flexible fitting to produce viable structural models and infer a plausible transport mechanism. Conforming to the theme of integration, a short compendium of an exploratory project—developing a hybrid atomistic-continuum method—is presented, including initial results and a novel fluctuating hydrodynamics model and corresponding numerical code.
Dissertation/Thesis
Doctoral Dissertation Physics 2017

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41

Bhattacharya, Rupak. "Structure and Dynamics of Interfacial Molecular Membranes". Thesis, 2013. https://etd.iisc.ac.in/handle/2005/3413.

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This thesis describes the study on structure and dynamics of various kinds of molecular membranes in general. We have studied the morphological transition of colloidal as well as biologically relevant membranes and qualitatively argued regarding the interplay between structure and dynamics. Systematic measurements have been performed to address the issue of ambiguous behavior of molecules under stress when its confined at the interface. The structural and dynamical effect on interfacial membranes have been studied for soft colloidal free standing langmuir monolayer as well as for the quasi two dimensional lipid membranes on solid supports. For organic nanoparticle monolayer we have observed a correlation between the nanoparticle raft dynamics and the underlying morphological transition. In this study we have also found a non-monotonic behavior of dynamical heterogeneity with time which is unusual for a colloidal system in common and beyond the prediction of Mode Coupling Theory. In the case of lipid membrane, we have given an experimental evidence of lipid molecular rearrangement process at molecular level when its perturbed by foreign entities. Using sophisticated X-Ray scattering techniques, we were able to capture the subtle changes happening in the assembly of lipid molecules in a planar bilayer structure when it interacts with molecules having biological relevance. In the next level we have used lipid membranes as an active plat-form to study the physical interaction with several kinds of nanoparticles and explored the mechanism of active participation of lipid molecules in self assembly process. Besides with the help of Fluorescence Correlation Spectroscopy, we have also studied the effect of nanoparticles assemblies on the dynamics of lipid molecules itself. In Chapter 1, we have provided the background along with a brief review of the existing literature for understanding the results represented in the subsequent chapters. This includes discussion on the various physical properties of our systems of interest, including dynamic behavior of colloidal particles in different concentration regime and a detailed theoretical understanding regarding the glass transition and jamming transition for a highly dense colloidal packing. In this section we have also discussed the advantages of interfacial microrheology technique over conventional bulk rheology in terms of efficiency and sensitivity. Here we have also pointed out the formulation of the multi-particle tracking method for achieving different parameters which are correlated in space and time for a given system. Followed by that the Dynamical Susceptibility and the anomaly in Van Hove correlation function, for a heterogeneous system has been argued thoroughly. Towards the end we have discussed about the general features of another type of two dimensional membrane i.e. the lipid membrane at interface. Using raft theory we have also tried to give a plausible explanation of the dynamical heterogeneity of the real cell membrane which is mimicked by the model supported lipid membrane. Here we have argued about the structural six fold symmetry of a compact monolayer. Finally in the last part we have summarized the theoretical aspects of the lipid molecule mediated self assembly process and the how the lipid diffusion plays a vital role in it. Chapter 2 deals with the aspect of measuring the morphological transition and its effect on the dynamics for a two dimensional membrane at air/water interface. It starts with the discussion on the synthesis method for various types of organic molecule grafted nanoparticles like Cadmium Selenide(CdSe Quantum Dots) and Gold Nanoparticle(Au NPs) of different size and properties and followed by a preparation method of 2D film at air/water interface and on solid substrate using Langmuir-Blodgett method. In this chapter we have discussed about the basic principles of several experimental tools like Brewster Angle Microscopy(BAM), Laser Scanning Confocal Microscopy(LSCM), Atomic Force Microscopy(AFM), Thermogravimetric Analysis(TGA), X Ray Reflectivity(XRR), Grazing Incidence Diffraction(GID), Fluorescence Correlation Spectroscopy(FCS) etc. Chapter 3 explains the main aspects of the microscopic dynamics in dense amorphous nanoparticle monolayer at the air-water interface. In this study we have found a transition in mechanical properties, tracked down through the systematic variation of isothermal compressibility(�) with increasing two dimensional packing fraction of nanoparticle rafts up to the area fraction of Φ∼0.82 using Laser Scanning Confocal Microscope. Here we have used multi particle tracking method for a close packed gold monolayer with CdSe tracer to estimate different dynamical properties like Mean Square Displacement(MSD), Dynamical Heterogeneity etc. These calculations indeed point out the non-monotonic variation of the amplitude in the four-point dynamic susceptibility (χ4), a signature of spatio-temporal extension of correlated domains. Along with that we have also observed the anomaly in trend for the inherent relaxation time τ∗with increasing area fraction(Φ). Interestingly the variation in χ4exactly follows the systematic we found for the isothermal compressibility( �) with increasing Φ and that indicates the connection between the observed macroscopic transitions in mechanical properties and the microscopic dynamical phase transitions. Finally we have given a possible explanation of these kind of events in terms of the interaction between this sterically stabilized nanoparticle domains with the help of interpenetration of the capping long chain polymers of the neighboring nanoparticle. Chapter 4 opens up the possibilities of probing the hidden features of biomembranes at molecular scale with the help of very precise techniques based on synchrotron X ray diffraction. Here we have studied the rearrangement of the lipid molecules of an artificial membrane on a solid support as an effect of ad-sorption of organic branched molecules. In this work we have used non toxic PETIM dendrimers of two different generations, i.e. G3and G4which differs a lot in terms of size, no of termination groups, molecular weights and protonation states. Our initial measurements shows quantitatively the in-plane and out of plane symmetry breaking of the lipid bilayer as a result of the interaction with these two types of molecules. The molecular adsorption effect was quantified in terms of thickness reduction and the change in the scattering length density(SLD) or the electron density of the top layer in out of plane reflectivity model. Interestingly both the dendrimers showed different behavior and the interaction reflected in terms of membrane penetration was found stronger for higher generation. On the other hand the GID measurement indicates an enhancement of the in plane unit cell dimension and associated parameters of the arrangement of lipid molecules as a result of interaction with dendrimers. The combined XRR and GID measurements indicate a local fluidization of lipid packing as an outcome of charged branched molecules adsorption on the membrane surface. Chapter 5 is summarizes the lipid mediated self assembly process of nanoparticles on a bilayer and how the interaction changes the local properties of the bilayer represented by the molecular diffusivity. In this study we have used particles of wide variety of features in terms of size, charge, functionality, polarity etc and found a quite dramatic effect in the nanoparticle adsorption event on a solid supported Lαphased DMPC lipid bilayer. We have also seen that de-pending on the concentration and amount of surface charge the nanoparticles form two dimensional regular self assembled patterns on the bilayer surface. In FCS measurement, we have also found a second group of dynamics ( distribution of diffusivity) along with the normal bilayer diffusion which has been identified as the diffusion of the lipid molecules where nanoparticles are adsorbed. The inherent increment in diffusivity supports the argument of local fluidization in lipid membrane in presence of charged nanoparticle as we have observed in our XRR and GID data described in chapter 4. Chapter 6 contains the summary and the future perspective of the work presented here.

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42

Bhattacharya, Rupak. "Structure and Dynamics of Interfacial Molecular Membranes". Thesis, 2013. http://etd.iisc.ernet.in/2005/3413.

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Abstract (sommario):

This thesis describes the study on structure and dynamics of various kinds of molecular membranes in general. We have studied the morphological transition of colloidal as well as biologically relevant membranes and qualitatively argued regarding the interplay between structure and dynamics. Systematic measurements have been performed to address the issue of ambiguous behavior of molecules under stress when its confined at the interface. The structural and dynamical effect on interfacial membranes have been studied for soft colloidal free standing langmuir monolayer as well as for the quasi two dimensional lipid membranes on solid supports. For organic nanoparticle monolayer we have observed a correlation between the nanoparticle raft dynamics and the underlying morphological transition. In this study we have also found a non-monotonic behavior of dynamical heterogeneity with time which is unusual for a colloidal system in common and beyond the prediction of Mode Coupling Theory. In the case of lipid membrane, we have given an experimental evidence of lipid molecular rearrangement process at molecular level when its perturbed by foreign entities. Using sophisticated X-Ray scattering techniques, we were able to capture the subtle changes happening in the assembly of lipid molecules in a planar bilayer structure when it interacts with molecules having biological relevance. In the next level we have used lipid membranes as an active plat-form to study the physical interaction with several kinds of nanoparticles and explored the mechanism of active participation of lipid molecules in self assembly process. Besides with the help of Fluorescence Correlation Spectroscopy, we have also studied the effect of nanoparticles assemblies on the dynamics of lipid molecules itself. In Chapter 1, we have provided the background along with a brief review of the existing literature for understanding the results represented in the subsequent chapters. This includes discussion on the various physical properties of our systems of interest, including dynamic behavior of colloidal particles in different concentration regime and a detailed theoretical understanding regarding the glass transition and jamming transition for a highly dense colloidal packing. In this section we have also discussed the advantages of interfacial microrheology technique over conventional bulk rheology in terms of efficiency and sensitivity. Here we have also pointed out the formulation of the multi-particle tracking method for achieving different parameters which are correlated in space and time for a given system. Followed by that the Dynamical Susceptibility and the anomaly in Van Hove correlation function, for a heterogeneous system has been argued thoroughly. Towards the end we have discussed about the general features of another type of two dimensional membrane i.e. the lipid membrane at interface. Using raft theory we have also tried to give a plausible explanation of the dynamical heterogeneity of the real cell membrane which is mimicked by the model supported lipid membrane. Here we have argued about the structural six fold symmetry of a compact monolayer. Finally in the last part we have summarized the theoretical aspects of the lipid molecule mediated self assembly process and the how the lipid diffusion plays a vital role in it. Chapter 2 deals with the aspect of measuring the morphological transition and its effect on the dynamics for a two dimensional membrane at air/water interface. It starts with the discussion on the synthesis method for various types of organic molecule grafted nanoparticles like Cadmium Selenide(CdSe Quantum Dots) and Gold Nanoparticle(Au NPs) of different size and properties and followed by a preparation method of 2D film at air/water interface and on solid substrate using Langmuir-Blodgett method. In this chapter we have discussed about the basic principles of several experimental tools like Brewster Angle Microscopy(BAM), Laser Scanning Confocal Microscopy(LSCM), Atomic Force Microscopy(AFM), Thermogravimetric Analysis(TGA), X Ray Reflectivity(XRR), Grazing Incidence Diffraction(GID), Fluorescence Correlation Spectroscopy(FCS) etc. Chapter 3 explains the main aspects of the microscopic dynamics in dense amorphous nanoparticle monolayer at the air-water interface. In this study we have found a transition in mechanical properties, tracked down through the systematic variation of isothermal compressibility(�) with increasing two dimensional packing fraction of nanoparticle rafts up to the area fraction of Φ∼0.82 using Laser Scanning Confocal Microscope. Here we have used multi particle tracking method for a close packed gold monolayer with CdSe tracer to estimate different dynamical properties like Mean Square Displacement(MSD), Dynamical Heterogeneity etc. These calculations indeed point out the non-monotonic variation of the amplitude in the four-point dynamic susceptibility (χ4), a signature of spatio-temporal extension of correlated domains. Along with that we have also observed the anomaly in trend for the inherent relaxation time τ∗with increasing area fraction(Φ). Interestingly the variation in χ4exactly follows the systematic we found for the isothermal compressibility( �) with increasing Φ and that indicates the connection between the observed macroscopic transitions in mechanical properties and the microscopic dynamical phase transitions. Finally we have given a possible explanation of these kind of events in terms of the interaction between this sterically stabilized nanoparticle domains with the help of interpenetration of the capping long chain polymers of the neighboring nanoparticle. Chapter 4 opens up the possibilities of probing the hidden features of biomembranes at molecular scale with the help of very precise techniques based on synchrotron X ray diffraction. Here we have studied the rearrangement of the lipid molecules of an artificial membrane on a solid support as an effect of ad-sorption of organic branched molecules. In this work we have used non toxic PETIM dendrimers of two different generations, i.e. G3and G4which differs a lot in terms of size, no of termination groups, molecular weights and protonation states. Our initial measurements shows quantitatively the in-plane and out of plane symmetry breaking of the lipid bilayer as a result of the interaction with these two types of molecules. The molecular adsorption effect was quantified in terms of thickness reduction and the change in the scattering length density(SLD) or the electron density of the top layer in out of plane reflectivity model. Interestingly both the dendrimers showed different behavior and the interaction reflected in terms of membrane penetration was found stronger for higher generation. On the other hand the GID measurement indicates an enhancement of the in plane unit cell dimension and associated parameters of the arrangement of lipid molecules as a result of interaction with dendrimers. The combined XRR and GID measurements indicate a local fluidization of lipid packing as an outcome of charged branched molecules adsorption on the membrane surface. Chapter 5 is summarizes the lipid mediated self assembly process of nanoparticles on a bilayer and how the interaction changes the local properties of the bilayer represented by the molecular diffusivity. In this study we have used particles of wide variety of features in terms of size, charge, functionality, polarity etc and found a quite dramatic effect in the nanoparticle adsorption event on a solid supported Lαphased DMPC lipid bilayer. We have also seen that de-pending on the concentration and amount of surface charge the nanoparticles form two dimensional regular self assembled patterns on the bilayer surface. In FCS measurement, we have also found a second group of dynamics ( distribution of diffusivity) along with the normal bilayer diffusion which has been identified as the diffusion of the lipid molecules where nanoparticles are adsorbed. The inherent increment in diffusivity supports the argument of local fluidization in lipid membrane in presence of charged nanoparticle as we have observed in our XRR and GID data described in chapter 4. Chapter 6 contains the summary and the future perspective of the work presented here.

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Tesi sul tema "Biophysical transition"

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