Populations in statistical genetic modelling and inference

What is a population? This review considers how a population may be defined in terms of understanding the structure of the underlying genetics of the individuals involved. The main approach is to consider statistically identifiable groups of randomly mating individuals, which is well defined in theory for any type of (sexual) organism. We discuss generative models using drift, admixture and spatial structure, and the ancestral recombination graph. These are contrasted with statistical models for inference, principle component analysis and other `non-parametric' methods. The relationships between these approaches are explored with both simulated and real-data examples. The state-of-the-art practical software tools are discussed and contrasted. We conclude that populations are a useful theoretical construct that can be well defined in theory and often approximately exist in practice

SAS Macros for Analysis of Unreplicated 2^k and 2^k-p Designs with a Possible Outlier

Many techniques have been proposed for judging the significance of effects in unreplicated 2^k and 2^k-p designs. However, relatively few methods have been proposed for analyzing unreplicated designs with possible outliers. Outliers can be a major impediment to valid interpretation of data from unreplicated designs. This paper presents SAS macros which automate a manual method for detecting an outlier and performing an analysis of data from an unreplicated 2^k or 2^k-p design when an outlier is present. This method was originally suggested by Cuthbert Daniel and is based on the normal or half normal plot of effects. This automated version was shown in simulation studies to perform better than other procedures proposed to do the same thing.

Source Galerkin Calculations in Scalar Field Theory

In this paper, we extend previous work on scalar $\phi^4$ theory using the Source Galerkin method. This approach is based on finding solutions $Z[J]$ to the lattice functional equations for field theories in the presence of an external source $J$. Using polynomial expansions for the generating functional $Z$, we calculate propagators and mass-gaps for a number of systems. These calculations are straightforward to perform and are executed rapidly compared to Monte Carlo. The bulk of the computation involves a single matrix inversion. The use of polynomial expansions illustrates in a clear and simple way the ideas of the Source Galerkin method. But at the same time, this choice has serious limitations. Even after exploiting symmetries, the size of calculations become prohibitive except for small systems. The calculations in this paper were made on a workstation of modest power using a fourth order polynomial expansion for lattices of size $8^2$,$4^3$,$2^4$ in $2D$, $3D$, and $4D$. In addition, we present an alternative to the Galerkin procedure that results in sparse matrices to invert.Comment: 31 pages, latex, figures separat

Anti-Americanism and Public Opinion in the European Union

The term “anti-Americanism” has become common coinage in public and academic debate, the more so since the election of President G. W. Bush, and especially since 9/11. Yet little is known of its causes and impact. Defining it as opposition to US policy, and using 2003 and 2005 Eurobarometer data we examine individuals` attitudes to the US in five policy dimensions for EU members. We find that over a third of EU voters either approved or disapproved of the US in all five dimensions. We also find there are differences in attitude to US policy related to age, policy preferences and nationality. And, although anti-Americanism is associated with a preference for greater European independence, perhaps surprisingly it is also linked to a desire for a less federal and hence less powerful Europe.european union; federalism; anti-americanism

New Numerical Method for Fermion Field Theory

A new deterministic, numerical method to solve fermion field theories is presented. This approach is based on finding solutions $Z[J]$ to the lattice functional equations for field theories in the presence of an external source $J$. Using Grassmann polynomial expansions for the generating functional $Z$, we calculate propagators for systems of interacting fermions. These calculations are straightforward to perform and are executed rapidly compared to Monte Carlo. The bulk of the computation involves a single matrix inversion. Because it is not based on a statistical technique, it does not have many of the difficulties often encountered when simulating fermions. Since no determinant is ever calculated, solutions to problems with dynamical fermions are handled more easily. This approach is very flexible, and can be taylored to specific problems based on convenience and computational constraints. We present simple examples to illustrate the method; more general schemes are desirable for more complicated systems.Comment: 24 pages, latex, figures separat

Molecular Simulations of Ultrafast Radiation Induced Melting at Metal-Semiconductor Interfaces

Understanding radiation induced ultrafast melting at material interfaces is essential in designing robust electronic devices for aviation/space applications and in laser machining. While it is difficult to achieve the spatial and temporal resolution required to quantify the phenomenon experimentally, simulations can provide the detailed mechanisms of the structural changes that happen during phase transition. In this work, we use molecular simulations to study the effect of radiation damage on silicon carbide (SiC) - tungsten (W) interfaces which is of interest in high power electronics. A multi-scale approach is involved wherein the reactions at the interfaces are quantified using ab-initio molecular dynamics (MD) simulations and classical MD simulations are employed to understand the structural and diffusional changes across the material interface. Finally, coarse-grained Lennard-Jones type models are used to study the larger scale mechanisms and structures obtained due to the induced damages. We show that the response of the material to radiation damage depends on factors such as energy of the incident radiation, thermal properties, and molecular structure of the material

Molecular Dynamics Investigation of the Structural and Mechanical Properties of Off-Stoichiometric Epoxy Resins

We carried out molecular dynamics (MD) simulations to measure the mechanical properties of various off-stoichiometric polymers regarding amine to epoxy ratios (r) and to understand the stiffness of the polymers in terms of their structures. The aerospace-grade API-60 epoxy resin is used as an adhesive bond for assembling large-scale composite structures via the co-curing-ply bonding method. This method will produce a reliable and certifiable composite joint without additional fasteners. Calculated Young's modulus was measured from the uniaxial tension simulation with several high strain rates, and the experimental modulus was estimated by extrapolating the simulation results. We found that the stiffness was associated with molecular packing caused by chemical cross-linking. We also found that the number of network clusters gradually decreased as the ratio approached r = 1.0, which made the tighter cluster and the system much stiffer with an increase in the molecular weight and the degree of cross-linking. Structural properties such as Rg, MSD were measured to figure out the degree of stiffness with respect to the r