Improving the quality of finite volume meshes through genetic optimisation

Author's accepted version. The final publication is available at Springer via http://dx.doi.org/10.1007/s00366-015-0423-0Mesh quality issues can have a substantial impact on the solution process in Computational Fluid Dynamics (CFD), leading to poor quality solutions, hindering convergence and in some cases, causing the solution to diverge. In many areas of application, there is an interest in automated generation of finite volume meshes, where a meshing algorithm controlled by pre- specified parameters is applied to a pre-existing CAD geometry. In such cases the user is typically confronted with a large number of controllable parameters, and ad- justing these takes time and perserverence. The process can however be regarded as a multi-input and possi- bly multi-objective optimisation process which can be optimised by application of Genetic Algorithm tech- niques. We have developed a GA optimisation code in the language Python, including an implementation of the NGSA-II multi-objective optimisation algorithm, and applied to control the mesh generation process us- ing the snappyHexMesh automated mesher in Open- FOAM. We demonstrate the results on three selected cases, demonstrating significant improvement in mesh quality in all cases

Another integrable case in the Lorenz model

A scaling invariance in the Lorenz model allows one to consider the usually discarded case sigma=0. We integrate it with the third Painlev\'e function.Comment: 3 pages, no figure, to appear in J. Phys.

Engineering stochasticity in gene expression

Stochastic fluctuations (noise) in gene expression can cause members of otherwise genetically identical populations to display drastically different phenotypes. An understanding of the sources of noise and the strategies cells employ to function reliably despite noise is proving to be increasingly important in describing the behavior of natural organisms and will be essential for the engineering of synthetic biological systems. Here we describe the design of synthetic constructs, termed ribosome competing RNAs (rcRNAs), as a means to rationally perturb noise in cellular gene expression. We find that noise in gene expression increases in a manner proportional to the ability of an rcRNA to compete for the cellular ribosome pool. We then demonstrate that operons significantly buffer noise between coexpressed genes in a natural cellular background and can even reduce the level of rcRNA enhanced noise. These results demonstrate that synthetic genetic constructs can significantly affect the noise profile of a living cell and, importantly, that operons are a facile genetic strategy for buffering against noise

Observable Properties of Orbits in Exact Bumpy Spacetimes

We explore the properties of test-particle orbits in "bumpy" spacetimes - stationary, reflection-symmetric, asymptotically flat solutions of Einstein equations that have a non-Kerr (anomalous) higher-order multipole-moment structure but can be tuned arbitrarily close to the Kerr metric. Future detectors should observe gravitational waves generated during inspirals of compact objects into supermassive central bodies. If the central body deviates from the Kerr metric, this will manifest itself in the emitted waves. Here, we explore some of the features of orbits in non-Kerr spacetimes that might lead to observable signatures. As a basis for this analysis, we use a family of exact solutions proposed by Manko & Novikov which deviate from the Kerr metric in the quadrupole and higher moments, but we also compare our results to other work in the literature. We examine isolating integrals of the orbits and find that the majority of geodesic orbits have an approximate fourth constant of the motion (in addition to the energy, angular momentum and rest mass) and the resulting orbits are tri-periodic to high precision. We also find that this fourth integral can be lost for certain orbits in some oblately deformed Manko-Novikov spacetimes. However, compact objects will probably not end up on these chaotic orbits in nature. We compute the location of the innermost stable circular orbit (ISCO) and find that the behavior of orbtis near the ISCO can be qualitatively different depending on whether the ISCO is determined by the onset of an instability in the radial or vertical direction. Finally, we compute periapsis and orbital-plane precessions for nearly circular and nearly equatorial orbits in both the strong and weak field, and discuss weak-field precessions for eccentric equatorial orbits.Comment: 42 pages, 20 figures, accepted by Phys. Rev. D, v2 has minor changes to make it consistent with published versio

Bacteriological and Physicochemical Quality of Drinking Water and Hygiene- Sanitation Practices of the Consumers in Bahir Dar City, Ethiopia

BACKGROUND: Lack of safe drinking water, basic sanitation, and hygienic practices are associated with high morbidity and mortality from excreta related diseases. The aims of this study were to determine the bacteriological and physico-chemical quality of drinking water and investigate the hygiene and sanitation practices of the consumers in Bahir Dar City, Ethiopia. METHODS: A cross sectional prospective study was conducted in Bahir Dar City from October-December, 2009. Water samples were collected from 35 private taps and 35 household water containers for bacteriological analysis. The turbidity, pH, temperature and turbidity were measured immediately after collection. Finally, the hygiene-sanitation practices of the consumers were surveyed using interview. RESULTS: Twenty seven (77.1%) of the household water samples had high total coliforms counts. Twenty (57.1%) household water samples and 9 (25.7%) of the tap water samples had no residual free chlorine. Sixteen (45.7%) household water samples had very high risk score to thermotolerant coliforms. Eight (22.9%) tap water samples had low risk score for total coliforms whereas 21(60%) tap water had very low risk score for thermotolerant coliforms. Twelve (34.3%) of the consumers collect water without contact with their hand and 9(25.7%) wash their hands with soap after visiting toilet. CONCLUSION: Water supplies at tap and household water containers were contaminated with bacteria. Poor sanitation, low level of hygiene, uncontrolled treatment parameters are the causes for contamination. Control of physico-chemical parameters and promoting good hygiene and sanitation are recommended. KEYWORDS: Bacteriology, physicochemical, tap water, household, Bahir Da

Adiabatic quantum computation along quasienergies

The parametric deformations of quasienergies and eigenvectors of unitary operators are applied to the design of quantum adiabatic algorithms. The conventional, standard adiabatic quantum computation proceeds along eigenenergies of parameter-dependent Hamiltonians. By contrast, discrete adiabatic computation utilizes adiabatic passage along the quasienergies of parameter-dependent unitary operators. For example, such computation can be realized by a concatenation of parameterized quantum circuits, with an adiabatic though inevitably discrete change of the parameter. A design principle of adiabatic passage along quasienergy is recently proposed: Cheon's quasienergy and eigenspace anholonomies on unitary operators is available to realize anholonomic adiabatic algorithms [Tanaka and Miyamoto, Phys. Rev. Lett. 98, 160407 (2007)], which compose a nontrivial family of discrete adiabatic algorithms. It is straightforward to port a standard adiabatic algorithm to an anholonomic adiabatic one, except an introduction of a parameter |v>, which is available to adjust the gaps of the quasienergies to control the running time steps. In Grover's database search problem, the costs to prepare |v> for the qualitatively different, i.e., power or exponential, running time steps are shown to be qualitatively different. Curiously, in establishing the equivalence between the standard quantum computation based on the circuit model and the anholonomic adiabatic quantum computation model, it is shown that the cost for |v> to enlarge the gaps of the eigenvalue is qualitatively negligible.Comment: 11 pages, 2 figure

The role of quantum fluctuations in the optomechanical properties of a Bose-Einstein condensate in a ring cavity

We analyze a detailed model of a Bose-Einstein condensate trapped in a ring optical resonator and contrast its classical and quantum properties to those of a Fabry-P{\'e}rot geometry. The inclusion of two counter-propagating light fields and three matter field modes leads to important differences between the two situations. Specifically, we identify an experimentally realizable region where the system's behavior differs strongly from that of a BEC in a Fabry-P\'{e}rot cavity, and also where quantum corrections become significant. The classical dynamics are rich, and near bifurcation points in the mean-field classical system, the quantum fluctuations have a major impact on the system's dynamics.Comment: 11 pages, 11 figures, submitted to PR

Delay of Disorder by Diluted Polymers

We study the effect of diluted flexible polymers on a disordered capillary wave state. The waves are generated at an interface of a dyed water sugar solution and a low viscous silicon oil. This allows for a quantitative measurement of the spatio-temporal Fourier spectrum. The primary pattern after the first bifurcation from the flat interface are squares. With increasing driving strength we observe a melting of the square pattern. It is replaced by a weak turbulent cascade. The addition of a small amount of polymers to the water layer does not affect the critical acceleration but shifts the disorder transition to higher driving strenghs and the short wave length - high frequency fluctuations are suppressed

On vacuum gravitational collapse in nine dimensions

We consider the vacuum gravitational collapse for cohomogeneity-two solutions of the nine dimensional Einstein equations. Using combined numerical and analytical methods we give evidence that within this model the Schwarzschild-Tangherlini black hole is asymptotically stable. In addition, we briefly discuss the critical behavior at the threshold of black hole formation.Comment: 4 pages, 4 figure