Properties of selected mutations and genotypic landscapes under Fisher's Geometric Model

The fitness landscape - the mapping between genotypes and fitness - determines properties of the process of adaptation. Several small genetic fitness landscapes have recently been built by selecting a handful of beneficial mutations and measuring fitness of all combinations of these mutations. Here we generate several testable predictions for the properties of these landscapes under Fisher's geometric model of adaptation (FGMA). When far from the fitness optimum, we analytically compute the fitness effect of beneficial mutations and their epistatic interactions. We show that epistasis may be negative or positive on average depending on the distance of the ancestral genotype to the optimum and whether mutations were independently selected or co-selected in an adaptive walk. Using simulations, we show that genetic landscapes built from FGMA are very close to an additive landscape when the ancestral strain is far from the optimum. However, when close to the optimum, a large diversity of landscape with substantial ruggedness and sign epistasis emerged. Strikingly, landscapes built from different realizations of stochastic adaptive walks in the same exact conditions were highly variable, suggesting that several realizations of small genetic landscapes are needed to gain information about the underlying architecture of the global adaptive landscape.Comment: 51 pages, 8 figure

Front-end electronics for ATLAS pixel detector

Large advances have been made over the last years in the development of rad-soft readout chip prototypes, closing the first phase of the ATLAS pixel [2] demonstrator programme. The next step of this programme is aimed at realizing a full scale pixel front-end chip using two rad-hard technologies. The DMILL chip has been received in Oct. 99 and the deep submicron design is currently under development. Measurements on the DMILL ATLAS pixel Front-end chip are presented

Boko Haram: Terrorist Organization, Freedom Fighters or Religious Fanatics? An Analysis of Boko Haram Within Nigeria, an Australian Perspective and the Need for Counter Terrorism Responses that Involves Prescribing them as a Terrorist Organization.

The adoption of Sharia law and the creation of an Islamic government are prominent motivations for religious terrorism within the current climate. Throughout history, Nigeria has been exposed to ethno religious violence and political discontent and has recently seen an escalation in associated violence threatening its sovereignty, territorial integrity, peace and stability. This paper explores Boko Haram, a Nigerian Islamist sect, responsible for numerous attacks in northern and central Nigeria on infrastructure and people. The origins and ideological motivations of this group are examined and compared to the current wave of religious terrorism in relation to tactics, leadership and objectives. Parallels and relationships are drawn between Boko Haram and other proscribed terrorist organizations such as al-Qa’ida, al-Qa’ida in the Islamic Maghreb (AQIM) and the Somalian al Shabaab. This paper defines Boko Haram as a terrorist organization, as opposed to religious fanatics or freedom fighters, other common views about this group. This paper takes an Australian legislative approach to defining terrorism and terrorist organizations and examines Boko Haram against a contemporary terrorist organization proscribed by the Australian Government, AQIM, to substantiate claims that this organization demonstrates features common among terrorist organizations. Future prospects of this group, including potential expansion and listing them as a terrorist organization by the Australian government for national security, are presented

Chemical and statistical soot modeling

The combustion of petroleum based fuels like kerosene, gasoline, or diesel leads to the formation of several kind of pollutants. Among them, soot particles are particularly bad for their severe consequences on human health. Over the past decades, strict regulations have been placed on car and aircraft engines in order to limit these particulate matter emissions. Designing low emission engines requires the use of predictive soot models which can be applied to the combustion of real fuels. Towards this goal, the present work addresses the formation of soot particles both from a chemical and statistical point of view. As a first step, a chemical model is developed to describe the formation of soot precursors from the combustion of several components typically found in surrogates, including n-heptane, iso-octane, benzene, and toluene. The same mechanism is also used to predict the formation of large Polycyclic Aromatic Hydrocarbons (PAH) up to cyclopenta[cd]pyrene (C_(18)H_(10)). Then, a new soot model which represents soot particles as fractal aggregates is used. In this model, a soot particle is described by three variables: its volume (V), its surface area (S), and the number of hydrogen sites on the surface (H). The Direct Quadrature Method of Moments (DQMOM) is used as a precise representation of the population of soot particles which includes small spherical particles and large aggregates. This model is shown to predict accurately the formation of soot in a wide range of flames including premixed and counter flow diffusion flames, low and high temperature flames and for a wide range of fuels from ethylene to iso-octane. Finally, this model predicts several aggregate properties like the primary particle diameter and gives insight into the reactivity of the soot surface

Effects of dissipation rate and diffusion rate of the progress variable on local fuel burning rate in premixed turbulent flames

The validity of the premixed flamelet equations and the dependence of the fuel burning rate on the parameters involved in these equations have been investigated using a large series of direct numerical simulations of turbulent premixed flames in the thin reaction zones (TRZ) and the distributed reaction zones (DRZ) regimes. Methane, toluene, n-heptane, and iso-octane fuels were considered over a wide range of unburnt conditions and turbulence characteristics. Flames with unity and non-unity Lewis numbers were investigated separately to isolate turbulence-chemistry interaction from differential diffusion effects. In both cases, the flamelet equations, which rely on the assumption of a thin reaction zone, are locally valid throughout the TRZ regime, more precisely up to a Karlovitz number at the reaction zone of 10 (based on the definition used in this paper). Consistent with this result, in the unity Lewis number limit, the fuel burning rate is strongly correlated with the dissipation rate of the progress variable, the only parameter in the flamelet equations. In the non-unity Lewis number case, the burning rate is a strong function of both the dissipation rate and the diffusion rate, both of which are parameters in the flamelet equations. In particular, the correlation with these parameters is significantly better than with curvature or tangential strain rate

A fast, low-memory, and stable algorithm for implementing multicomponent transport in direct numerical simulations

Implementing multicomponent diffusion models in reacting-flow simulations is computationally expensive due to the challenges involved in calculating diffusion coefficients. Instead, mixture-averaged diffusion treatments are typically used to avoid these costs. However, to our knowledge, the accuracy and appropriateness of the mixture-averaged diffusion models has not been verified for three-dimensional turbulent premixed flames. In this study we propose a fast,efficient, low-memory algorithm and use that to evaluate the role of multicomponent mass diffusion in reacting-flow simulations. Direct numerical simulation of these flames is performed by implementing the Stefan-Maxwell equations in NGA. A semi-implicit algorithm decreases the computational expense of inverting the full multicomponent ordinary diffusion array while maintaining accuracy and fidelity. We first verify the method by performing one-dimensional simulations of premixed hydrogen flames and compare with matching cases in Cantera. We demonstrate the algorithm to be stable, and its performance scales approximately with the number of species squared. Then, as an initial study of multicomponent diffusion, we simulate premixed, three-dimensional turbulent hydrogen flames, neglecting secondary Soret and Dufour effects. Simulation conditions are carefully selected to match previously published results and ensure valid comparison. Our results show that using the mixture-averaged diffusion assumption leads to a 15% under-prediction of the normalized turbulent flame speed for a premixed hydrogen-air flame. This difference in the turbulent flame speed motivates further study into using the mixture-averaged diffusion assumption for DNS of moderate-to-high Karlovitz number flames.Comment: 36 pages, 14 figure

Vorticity isotropy in high Karlovitz number premixed flames

The isotropy of the smallest turbulent scales is investigated in premixed turbulent combustion by analyzing the vorticity vector in a series of high Karlovitz number premixed flame direct numerical simulations. It is found that increasing the Karlovitz number and the ratio of the integral length scale to the flame thickness both reduce the level of anisotropy. By analyzing the vorticity transport equation, it is determined that the vortex stretching term is primarily responsible for the development of any anisotropy. The local dynamics of the vortex stretching term and vorticity resemble that of homogeneous isotropic turbulence to a greater extent at higher Karlovitz numbers. This results in small scale isotropy at sufficiently high Karlovitz numbers and supports a fundamental similarity of the behavior of the smallest turbulent scales throughout the flame and in homogeneous isotropic turbulence. At lower Karlovitz numbers, the vortex stretching term and the vorticity alignment in the strain-rate tensor eigenframe are altered by the flame. The integral length scale has minimal impact on these local dynamics but promotes the effects of the flame to be equal in all directions. The resulting isotropy in vorticity does not reflect a fundamental similarity between the smallest turbulent scales in the flame and in homogeneous isotropic turbulence

Subfilter scalar-flux vector orientation in homogeneous isotropic turbulence

The geometric orientation of the subfilter-scale scalar-flux vector is examined in homogeneous isotropic turbulence. Vector orientation is determined using the eigenframe of the resolved strain-rate tensor. The Schmidt number is kept sufficiently large so as to leave the velocity field, and hence the strain-rate tensor, unaltered by filtering in the viscous-convective subrange. Strong preferential alignment is observed for the case of Gaussian and box filters, whereas the sharp-spectral filter leads to close to a random orientation. The orientation angle obtained with the Gaussian and box filters is largely independent of the filter width and the Schmidt number. It is shown that the alignment direction observed numerically using these two filters is predicted very well by the tensor-diffusivity model. Moreover, preferred alignment of the scalar gradient vector in the eigenframe is shown to mitigate any probable issues of negative diffusivity in the tensor-diffusivity model. Consequentially, the model might not suffer from solution instability when used for large eddy simulations of scalar transport in homogeneous isotropic turbulence. Further a priori tests indicate poor alignment of the Smagorinsky and stretched vortex model predictions with the exact subfilter flux. Finally, strong filter dependence of subfilter scalar-flux orientation suggests that explicit filtering may be preferable to implicit filtering in large eddy simulations

A cost-effective semi-implicit method for the time integration of fully compressible reacting flows with stiff chemistry

We present a simple method to remove the stiffness associated with the chemical source terms in the fully compressible Navier-Stokes equations when the classical fourth order Runge-Kutta scheme is used

On filtering in the viscous-convective subrange for turbulent mixing of high Schmidt number passive scalars

In the present work, we investigate the possibility of performing velocity-resolved, scalar-filtered (VR-SF) numerical simulations of turbulent mixing of high Schmidt number scalars, by using a Large Eddy Simulation (LES)-type filter in the viscous-convective subrange. The only requirement for this technique is the large scale separation between the Kolmogorov and Batchelor length scales, which is a direct outcome of the high Schmidt number of the scalar. The present a priori analysis using high fidelity direct numerical simulation data leads to two main observations. First, the missing triadic interactions between (resolved) velocity and (filtered-out) scalar modes in the viscous-convective subrange do not affect directly the large scales. Second, the magnitude of the subgrid term is shown to be extremely small, which makes it particularly susceptible to numerical errors associated with the scalar transport scheme. A posteriori tests indicate that upwinded schemes, generally used for LES in complicated geometries, are sufficiently dissipative to overwhelm any contribution from the subgrid term. This renders the subgrid term superfluous, and as a result, VR-SF simulations run without subgrid scalar flux models are able to preserve large scale transport characteristics with remarkable accuracy