1,720,974 research outputs found
Experiments on the bacterial nucleoid of Escherichia coli viewed as a physical entity
No full textIn this thesis we focus on the compaction of DNA within Escherichia coli and aim to gain some understanding of the physical mechanism behind its spatial organization in the cell. Chapter I is a brief review of the current knowledge of nucleoid structure. We discuss a model for DNA compaction in the living Escherichia coli cell, for which this thesis has provided evidence. In this model the formation of the nucleoid is presented as the phase separation of supercoiled DNA in a suspension of proteins. Chapter II is a brief introduction to excluded-volume interactions and ends with an exposition of recent theoretical calculations that explain how the phase separation between DNA and proteins within E. coli may occur. In chapter III, a comparison between E. coli nucleoids isolated by the detergent and osmotic shock methods is presented. In chapter IV the presence of polyethylene glycol (PEG) was used to study the effect of polymeric depletion interactions on the dimensions of nucleoids isolated by osmotic shock. We derive the free energy of isolated nucleoids when compacted into the intracellular dimensions. A discussion of these results with reference to the phase separation theory developed by Odijk (1998) is given and we conclude that depletion can be the force behind the formation of the bacterial nucleoid. Based on dynamic light scattering (DLS) experiments we show that within isolated nucleoids the supercoil segments exhibit a fast dynamics. In chapter V the process of expansion of nucleoids released by osmotic shock is studied. In our experiments, nucleoids initially expanded quite fast, followed by a long intermediate period. The average exponent characterizing the dynamics of the intermediate phase is indicative of a process driven by excluded-volume. Nevertheless, there are substantial variations between the individual measurements, which are not fully understood. In Chapter VI we directly monitor the movement of DNA segments within isolated nucleoids. We conclude that the isolated nucleoid has a gel-like structure where supercoil segments show confined Brownian motion. The observed diffusion constant substantiates the DLS experiments preformed in Chapter IV.Applied Science
Statistical mechanics of protein solutions
No full textWe study theoretically thermodynamic properties of spherical globular proteins in aqueous solution with added monovalent salt. We show how one can determine an effective interaction potential between the proteins from experimental data as a function of salt concentration and we apply this to the protein lysozyme at a solution pH of 7.5 and ionic strengths between 0.05 M and 2 M. It turns out that apart from steric and electrostatic repulsions, there is also an attractive interaction between the proteins. We then develop a method, which we name the optimized Baxter model (OBM), to determine thermodynamic properties of the protein solution, also at large volume fractions of proteins. We apply this method to predict the osmotic compressibility of the protein solution as a function of protein concentration and we show that the predictions compare fairly well with experimental data of lysozyme at several salt concentrations. Since both the OBM and the effective interaction between the proteins are only approximate, we use the OBM to predict thermodynamic properties of a model system with known interaction potential, and we compare these predictions with results from computer simulations to see how accurate the OBM actually is. We also look at the phase equilibrium between a protein solution and protein crystals. We use the OBM to determine the osmotic pressure and the chemical potential of the solution and we show that one can explain the ionic-strength dependence of the chemical potential with a simple model for the crystal. We apply the same method to crystals of silicotungstate in equilibrium with the solution phase. Finally, we predict the first-order correction in the density of the collective diffusion coefficient and we compare the predictions to experimental results on lysozyme.Applied Science
Impact of nonuniform counterion condensation on the growth of linear charged micelles
No full textApplied Science
Polymer nematic gel under tension, Appendix in "Liquid crystalline epoxide thermosets" S. Jahromi, W.A.G. Kuipers, B. Norder, and W.J. Mijs.
No full textApplied Science
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