Le but de ce travail est de fournir une amélioration de la connaissance sur le phénomène de la réduction de la traînée induite par polymère en considérant certains aspects de sa simulation numérique et les changements qui se produisent dans la cinématique de l’écoulement. Dans un premier temps, les transformations du type racine carrée et kernel racine-k pour le tenseur de conformation du modèle FENE-P ont été implémentées afin d’assurer la positivité du tenseur de conformation. Cependant, ces approches divergent en raison du caractère non-borné du tenseur de conformation. Cette contrainte n’a pas été respectée, même avec l’inclusion de diffusion artificielle. L’effet d’amortissement de la diffusion artificielle a permis d’assurer la stabilité numérique, mais il aboutit à une réduction de la traînée relative de 22% à 42% plus faible que prévue par les approches standards. Dans un second temps, les modes hyperboliques, paraboliques et elliptiques des écoulements turbulents viscoélastiques ont été évalués en utilisant de différents critères de classification d’écoulements. Certains avantages concernant les critères objectifs ont été discutés. On a observé que les domaines hyperboliques contribuent de manière significative à la cinématique de l’écoulement. Enfin, on a observé une tendance des domaines elliptiques et hyperboliques à devenir paraboliques et que cette tendance augmente avec l’élasticité. / The purpose of this work is to provide an enhancement of the knowledge about the polymer-induced drag reduction phenomenon by considering some aspects of its numerical simulation and the changes that occur in the flow kinematics. In the first part, the square root and kernel root-k formulations for the conformation tensor in the FENE-P model were implemented and showed to preserve the positiveness of the conformation tensor. However, they led to numerical divergence due to the loss of boundedness of the conformation tensor. This constraint was violated even with the inclusion of artificial diffusion. The damping effect of artificial diffusion helped to ensure numerical stability, but led to relative drag reduction from 22% to 42% lower than expected from traditional methods. In the second part, the hyperbolic, parabolic and elliptic modes of turbulent viscoelastic flows were evaluated by means of different flow classification criteria. Some advantages of considering objective criteria were discussed. It was shown that the hyperbolic domains significantly contribute to the flow kinematics. Finally, a tendency of both elliptic and hyperbolic domains to become parabolic was observed and found to increase with the elasticity.

<p>Phospholipase C β (PLCβ) is an enzyme that plays a key role in cardiovascular function by hydrolyzing phosphatidylinositides (PIs) at the plasma membrane in response to the activation of G protein-coupled receptors at the membrane. PLCβ normally has low basal activity, and its activation is driven by direct binding of the heterotrimeric G protein subunits Gβγ and Gαq. Recent work from our lab and others has shown that the PH domain and first two EF-hands (EF1/2) are conformationally dynamic in solution. This opens up a potential avenue in looking at the dyamics of PLCβ as structures only depict the lipase in a more compact globular shape. We want to address how these known conformational changes PLCβ interacts with the membrane and protein-protein interactions necessary for fuction. In this study, we are using an intramolecular disulfide crosslink to stabilize defined conformational states of PLCβ. These conformational variants will be assessed for their basal activity and their ability to interact with liposomes. In addition, we are laying the initial groundwork to use these variants in single molecule tracking experiments on supported lipid bilayers. These experiments will provide significant insights into how the conformational state of PLCβ contributes to membrane binding and Gβγ stimulation at the membrane interface.</p>

UHRF1 is an essential epigenetic regulator implicated in the maintenance of DNA methylation. While its functional state has been suggested to be allosterically regulated by phosphatidylinositol 5-phosphate and dependent on purification conditions and tags coupled to the protein, the expression system might have a broader impact on UHRF1s interaction properties. We hypothesized that the translation kinetics defined by the expression host has an impact on the folding process of the protein, which ultimately affects its structure and function. To test this idea, the cDNA of UHRF1 was recoded in order to generate optimized and harmonized sequences that were expected to alter the overall translation speed. Both proteins were expressed in Escherichia coli BL21-DE3 and their interaction profiles with H3K9me3 and unmodified H3 peptides were determined by microscale thermophoresis assays. The dissociation constants were compared by ttests in order to evaluate a possible change in the interaction properties of the optimized and harmonized proteins, compared to non-optimized UHRF1 expressed in E. coli BL21-DE3. While no difference was found for the interaction of optimized UHRF1 with the H3K9me3 peptide, a significant difference was found for its interaction with the unmodified H3 peptide. Moreover, both the interactions of harmonized UHRF1 with H3K9me3 and unmodified H3 peptides were determined to change. For this reason, we concluded that translation kinetics dependent on the expression system impacts the functional state of UHRF1. To further study this phenomenon, we expressed the consensus sequence of UHRF1 in Escherichia coli BL21-Codon Plus-(DE3)-RIL, a bacterial strain that is enriched with arginine, isoleucine, and leucine tRNA isoacceptors. Differences in its interaction profile with histone peptides were found when compared with UHRF1 expressed in Escherichia coli BL21-DE3. Since the major difference between these strains is the abundance of tRNAs, we obtained further findings that support our initial hypothesis. Additionally, the interaction profiles from the consensus UHRF1 protein were determined in the presence of PI5P to get an insight into how this phosphoinositide might impact the final structure and function of UHRF1. MST measurements and limited proteolysis assays led us to the idea of a partially open conformation for the UHRF1 expressed in E. coli BL21-DE3 and E.coli Codon Plus-(DE3)-RIL.

Graduation date: 1992

A semiflexible polymer confined to a spherical surface is used as a basic model for understanding DNA conformation in restricted space. By means of Monte Carlo simulation for a bead-rod chain generated on a spherical surface, we find an ordered helicoidal phase at sufficiently high surface density and determine the critical density of the isotropic-helicoidal phase transition for various persistence lengths. We verify that the excluded volume effect is the key factor to cause the helicoidal state. In addition to Monte Carlo simulations, we utilize the model of wormlike chain with Onsager's excluded volume interaction and examine the Landau expansion of the free energy involving both the orientational and spatial order parameters. We also analytically figure out the critical density and transition gap for various ratios of persistence lengths of the polymer chain and the radius of spherical surface. The results from both simulation and analysis are consistent with each other.

A semiflexible polymer confined to a spherical surface is used as a basic model for understanding DNA conformation in restricted space. By means of Monte Carlo simulation for a bead-rod chain generated on a spherical surface, we find an ordered helicoidal phase at sufficiently high surface density and determine the critical density of the isotropic-helicoidal phase transition for various persistence lengths. We verify that the excluded volume effect is the key factor to cause the helicoidal state. In addition to Monte Carlo simulations, we utilize the model of wormlike chain with Onsager's excluded volume interaction and examine the Landau expansion of the free energy involving both the orientational and spatial order parameters. We also analytically figure out the critical density and transition gap for various ratios of persistence lengths of the polymer chain and the radius of spherical surface. The results from both simulation and analysis are consistent with each other.

Diss. (sammanfattning) Stockholm : Karol. inst., 2004. / Härtill 5 uppsatser.

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by Poon Hoi To. / Thesis (M.Phil.)--Chinese University of Hong Kong, 1981. / Bibliography: leaves 40-41.