Mesoscale fluid simulation with the Lattice Boltzmann method

PhDThis thesis describes investigations of several complex fluid effects., including hydrodynamic spinodal decomposition, viscous instability. and self-assembly of a cubic surfactant phase, by simulating them with a lattice Boltzmann computational model. The introduction describes what is meant by the term "complex fluid", and why such fluids are both important and difficult to understand. A key feature of complex fluids is that their behaviour spans length and time scales. The lattice Boltzmann method is presented as a modelling technique which sits at a "mesoscale" level intermediate between coarse-grained and fine-grained detail, and which is therefore ideal for modelling certain classes of complex fluids. The following chapters describe simulations which have been performed using this technique, in two and three dimensions. Chapter 2 presents an investigation into the separation of a mixture of two fluids. This process is found to involve several physical mechanisms at different stages. The simulated behaviour is found to be in good agreement with existing theory, and a curious effect, due to multiple competing mechanisms, is observed, in agreement with experiments and other simulations. Chapter 3 describes an improvement to lattice Boltzmann models of Hele-Shaw flow, along with simulations which quantitatively demonstrate improvements in both accuracy and numerical stability. The Saffman-Taylor hydrodynamic instability is demonstrated using this model. Chapter 4 contains the details and results of the TeraGyroid experiment, which involved extremely large-scale simulations to investigate the dynamical behaviour of a self-assembling structure. The first finite- size-effect- free dynamical simulations of such a system are presented. It is found that several different mechanisms are responsible for the assembly; the existence of chiral domains is demonstrated, along with an examination of domain growth during self-assembly. Appendix A describes some aspects of the implementation of the lattice Boltzmann codes used in this thesis; appendix B describes some of the Grid computing techniques which were necessary for the simulations of chapter 4. Chapter 5 summarises the work, and makes suggestions for further research and improvement.Huntsman Corporation Queen Mary University Schlumberger Cambridge Researc

Arrest of Stomatal Initials in Tradescantia Is Linked to the Proximity of Neighboring Stomata and Results in the Arrested Initials Acquiring Properties of Epidermal Cells

AbstractWe examined spatial relations of arrested stomatal initials and their differentiated state on leaves of the monocotyledon Tradescantia. The placement and proximity of stomata and arrested stomatal initials to the five nearest stomata were studied to test the hypothesis that if developing stomatal initials occur too close to one another, initials will arrest. The results showed that arrested stomatal initials were not randomly placed, but were closely associated with another stoma, most often in an adjacent cell file. The distance to their nearest stomatal neighbors was less than the equivalent distance between stomata that mature. After stomatal initials form, their position within or across cell files was not adjusted by cell division or expansion. Synergistic effects from several neighboring stomata could not be linked to stomatal arrest; rather, arrest was associated only with the nearest stomatal neighbor. Since the arrest of stomatal initials was distance dependent, a failure intrinsic to the arrested initials is not solely responsible for halting stomatal development. These data show that an inhibitory mechanism adjusts stomatal development to influence the final distribution of Tradescantia stomata. The pigmentation and expansion characteristics of arrested stomatal initials were like those of epidermal cells, indicating that the initials did not remain halted at a specific point in their development. The capacity of arrested initials to differentiate in the epidermal cell pathway indicates that they remain pluripotent after their initial specification and that the opportunity for patterning is long enough to permit their entry into the epidermal cell pathway

Simulating the Use of Alternative Fuels in a Turbofan Engine

The interest in alternative fuels for aviation has created a need to evaluate their effect on engine performance. The use of dynamic turbofan engine simulations enables the comparative modeling of the performance of these fuels on a realistic test bed in terms of dynamic response and control compared to traditional fuels. The analysis of overall engine performance and response characteristics can lead to a determination of the practicality of using specific alternative fuels in commercial aircraft. This paper describes a procedure to model the use of alternative fuels in a large commercial turbofan engine, and quantifies their effects on engine and vehicle performance. In addition, the modeling effort notionally demonstrates that engine performance may be maintained by modifying engine control system software parameters to account for the alternative fuel

Assessing the Effects of Icing the Body for 20 Minutes

Icing is one of the most inexpensive and convenient treatments available to reduce inflammation in sore and injured muscles. A commonly purported icing regimen follows a ?20 minutes on, 20 minutes off? cycle, so we investigated how much skeletal muscle cools during the 20-minute icing period. To model the temperature distribution, we used an axisymmetric geometry consisting of five layers: the ice, a plastic bag, skin, subcutaneous fat, and muscle. Our initial results showed cooling of the most superficial muscle tissue by approximately 15oC. We found that changes in properties such as density, specific heat, and conductivity did not affect temperature contours at the 20-minute time point; however, heating via perfusion, which was initially neglected, had a substantial effect on the final results. When blood flow was introduced into the model, the temperature of superficial muscle decreased only 3.5oC. We thus conclude that although icing is an effective means of cooling superficial layers of muscle, it is not particularly efficacious at increasing depths

Transcriptional effects of CRP* expression in Escherichia coli

<p>Abstract</p> <p>Background</p> <p><it>Escherichia coli </it>exhibits diauxic growth in sugar mixtures due to CRP-mediated catabolite repression and inducer exclusion related to phosphotransferase system enzyme activity. Replacement of the native <it>crp </it>gene with a catabolite repression mutant (referred to as <it>crp</it>*) enables co-utilization of glucose and other sugars in <it>E. coli</it>. While previous studies have examined the effects of expressing CRP* mutants on the expression of specific catabolic genes, little is known about the global transcriptional effects of CRP* expression. In this study, we compare the transcriptome of <it>E. coli </it>W3110 (expressing wild-type CRP) to that of mutant strain PC05 (expressing CRP*) in the presence and absence of glucose.</p> <p>Results</p> <p>The glucose effect is significantly suppressed in strain PC05 relative to strain W3110. The expression levels of glucose-sensitive genes are generally not altered by glucose to the same extent in strain PCO5 as compared to W3110. Only 23 of the 80 genes showing significant differential expression in the presence of glucose for strain PC05 are present among the 418 genes believed to be directly regulated by CRP. Genes involved in central carbon metabolism (including several TCA cycle genes) and amino acid biosynthesis, as well as genes encoding nutrient transport systems are among those whose transcript levels are most significantly affected by CRP* expression.</p> <p>We present a detailed transcription analysis and relate these results to phenotypic differences between strains expressing wild-type CRP and CRP*. Notably, CRP* expression in the presence of glucose results in an elevated intracellular NADPH concentration and reduced NADH concentration relative to wild-type CRP. Meanwhile, a more drastic decrease in the NADPH/NADP⁺ratio is observed for the case of CRP* expression in strains engineered to reduce xylose to xylitol via a heterologously expressed, NADPH-dependent xylose reductase. Altered expression levels of transhydrogenase and TCA cycle genes, among others, are consistent with these observations.</p> <p>Conclusion</p> <p>While the simplest model of CRP*-mediated gene expression assumes insensitivity to glucose (or cAMP), our results show that gene expression in the context of CRP* is very different from that of wild-type in the absence of glucose, and is influenced by the presence of glucose. Most of the transcription changes in response to CRP* expression are difficult to interpret in terms of possible systematic effects on metabolism. Elevated NADPH availability resulting from CRP* expression suggests potential biocatalytic applications of <it>crp* </it>strains that extend beyond relief of catabolite repression.</p