Epigenetic modelling

The field of epigenetics looks at changes in the chromosomal structure that affect gene expression without altering DNA sequence. A large-scale modelling project to better understand these mechanisms is gaining momentum. Early advances in genetics led to the all-genetic paradigm: phenotype (an organism's characteristics/behaviour) is determined by genotype (its genetic make-up). This was later amended and expressed by the well-known formula P = G + E, encompassing the notion that the visible characteristics of a living organism (the phenotype, P) is a combination of hereditary genetic factors (the genotype, G) and environmental factors (E). However, this method fails to explain why in diseases such as schizophrenia we still observe differences between identical twins. Furthermore, the identification of environmental factors (such as smoking and air quality for lung cancer) is relatively rare. The formula also fails to explain cell differentiation from a single fertilized cell. In the wake of early work by Waddington, more recent results have emphasized that the expression of the genotype can be altered without any change in the DNA sequence. This phenomenon has been tagged as epigenetics. To form the chromosome, DNA strands roll over nucleosomes, which are a cluster of nine proteins (histones), as detailed in Figure 1. Epigenetic mechanisms involve inherited alterations in these two structures, eg through attachment of a functional group to the amino acids (methyl, acetyl and phosphate). These 'stable alterations' arise during development and cell proliferation and persist through cell division. While information within the genetic material is not changed, instructions for its assembly and interpretation may be. Modelling this new paradigm, P = G + E + EpiG, is the object of our study.

Evaluation framework to assess benefits and harms of bone-anchored prosthesis

Bone-anchored prostheses are increasingly acknowledged as viable alternative method of attachment of artificial limb compared to socket-suspended prostheses. To date, a few osseointegration fixations are commercially available. Several devices are at different stages of development particularly in Europe and the US. Clearly, the current momentum experienced worldwide is creating a need for a standardized evaluation framework to assess the benefits and safety of each procedure.

Two-dimensional bow and stern flows in a finite-depth fluid with constant vorticity

This thesis is concerned with two-dimensional free surface flows past semi-infinite surface-piercing bodies in a fluid of finite-depth. Throughout the study, it is assumed that the fluid in question is incompressible, and that the effects of viscosity and surface tension are negligible. The problems considered are physically important, since they can be used to model the flow of water near the bow or stern of a wide, blunt ship. Alternatively, the solutions can be interpreted as describing the flow into, or out of, a horizontal slot. In the past, all research conducted on this topic has been dedicated to the situation where the flow is irrotational. The results from such studies are extended here, by allowing the fluid to have constant vorticity throughout the flow domain. In addition, new results for irrotational flow are also presented. When studying the flow of a fluid past a surface-piercing body, it is important to stipulate in advance the nature of the free surface as it intersects the body. Three different possibilities are considered in this thesis. In the first of these possibilities, it is assumed that the free surface rises up and meets the body at a stagnation point. For this configuration, the nonlinear problem is solved numerically with the use of a boundary integral method in the physical plane. Here the semi-infinite body is assumed to be rectangular in shape, with a rounded corner. Supercritical solutions which satisfy the radiation condition are found for various values of the Froude number and the dimensionless vorticity. Subcritical solutions are also found; however these solutions violate the radiation condition and are characterised by a train of waves upstream. In the limit that the height of the body above the horizontal bottom vanishes, the flow approaches that due to a submerged line sink in a $90^\circ$ corner. This limiting problem is also examined as a special case. The second configuration considered in this thesis involves the free surface attaching smoothly to the front face of the rectangular shaped body. For this configuration, nonlinear solutions are computed using a similar numerical scheme to that used in the stagnant attachment case. It is found that these solution exist for all supercritical Froude numbers. The related problem of the cusp-like flow due to a submerged sink in a corner is also considered. Finally, the flow of a fluid emerging from beneath a semi-infinite flat plate is examined. Here the free surface is assumed to detach from the trailing edge of the plate horizontally. A linear problem is formulated under the assumption that the elevation of the plate is close to the undisturbed free surface level. This problem is solved exactly using the Wiener-Hopf technique, and subcritical solutions are found which are characterised by a train of sinusoidal waves in the far field. The nonlinear problem is also considered. Exact relations between certain parameters for supercritical flow are derived using conservation of mass and momentum arguments, and these are confirmed numerically. Nonlinear subcritical solutions are computed, and the results are compared to those predicted by the linear theory.

Where is spatial information and science in your world?

Skills in spatial sciences are fundamental to understanding our world in context. Increasing digital presence and the availability of data with accurate spatial components has allowed almost everything researchers and students do to be represented in a spatial context. Representing outcomes and disseminating information has moved from 2D to 4D with time series animation. In the next 5 years industry will not only demand QUT graduates have spatial skills along with analytical skills, graduates will be required to present their findings in spatial visualizations that show spatial, spectral and temporal contexts. Domains such as engineering and science will no longer be the leaders in spatial skills as social sciences, health, arts and the business community gain momentum from place-based research including human interactions. A university that can offer students a pathway to advanced spatial investigation will be ahead of the game.

Meeting the challenges of neuroimaging genetics

As research encompassing neuroimaging and genetics gains momentum, extraordinary information will be uncovered on the genetic architecture of the human brain. However, there are significant challenges to be addressed first. Not the least of these challenges is to accomplish the sample size necessary to detect subtle genetic influences on the morphometry and function of the healthy brain. Aside from sample size, image acquisition and analysis methods need to be refined in order to ensure optimum sensitivity to genetic and complementary environmental influences. Then there is the vexing issue of interpreting the resulting data. We describe how researchers from the east coast of Australia and the west coast of America have embarked upon a collaboration to meet these challenges using data currently being collected from a large-scale twin study, and offer some opinions about future directions in the field.

Architecture for service profiling

Service oriented architecture is gaining momentum. However, in order to be successful, the proper and up-to-date description of services is required. Such a description may be provided by service profiling mechanisms, such as one presented in this article. Service profile can be defined as an up-to-date description of a subset of non-functional properties of a service. It allows for service comparison on the basis of non-functional parameters, and choosing the service which is most suited to the needs of a user. In this article the notion of a service profile along with service profiling mechanism is presented as well as the architecture of a profiling system. © 2006 IEEE.

An investigation into challenges facing distributed teams: Case of South Australian construction projects

There is increasing momentum within the construction industry to deploy distributed teams on projects, yet the major challenges that companies face for managing teams in distributed arrangements have yet to be explored in the construction context. Driven by such need, this study is intended to present an account of the major challenges encountered throughout the life cycle of offshore outsourcing arrangements within the South Australian construction industry. To this end, the study describes the observations made within the natural contexts of one construction project in terms of the challenges to the success of deploying distributed teams for outsourcing of works. Discussions remain in dialogue with relevant theories and the pertinent literature to explain the interpretations and lessons learned and to underpin the conclusions made. It is contended that this study contributes to the field by providing an illuminating insight into potential challenges facing distributed teams being implemented in outsourcing tasks in construction projects. Discussions also offer practical guidelines for construction project managers and assist them in dealing with potential challenges of offshore outsourcing through the lenses of distributed team working principles.

Identifying opportunity spaces for design research in South America: Working with grassroots and community groups

As design research continues to gain momentum in South America, design researchers and practitioners in the region have begun to consider how to the field may address regionally-specific issues, including on-going political struggles. By bringing approaches such as Participatory Design and Adversarial Design that consider political aspects of design, local researchers have explored various forms that these two approaches could take that are tailored to the needs and values of different communities across the region. This paper focuses on identifying opportunities for developing design research projects in community-based and grassroots-oriented contexts. The paper presents the findings of our study about the understanding and experience of design researchers and experts who have been working closely with community groups and grassroots organisations in South America. Five themes emerged, highlighting opportunities and challenges related to positioning contemporary design research in the region, integration of adversarial perspectives into design processes, leveraging local obstacles through creativity, and the potential of building capacity within community groups and grassroots organisations for sustainability and autonomy.

Modelling of the evaporation of a droplet suspended in a binary atmosphere

The process of spray drying is applied in a number of contexts. One such application is the production of a synthetic rock used for storage of nuclear waste. To establish a framework for a model of the spray drying process for this application, we here develop a model describing evaporation from droplets of pure water, such that the model may be extended to account for the presence of colloid within the droplet. We develop a spherically-symmetric model and formulate continuum equations describing mass, momentum, and energy balance in both the liquid and gas phases from first principles. We establish appropriate boundary conditions at the surface of the droplet, including a generalised Clapeyron equation that accurately describes the temperature at the surface of the droplet. To account for experiment design, we introduce a simplified platinum ball and wire model into the system using a thin wire problem. The resulting system of equations is transformed in order to simplify a finite volume solution scheme. The results from numerical simulation are compared with data collected for validation, and the sensitivity of the model to variations in key parameters, and to the use of Clausius–Clapeyron and generalised Clapeyron equations, is investigated. Good agreement is found between the model and experimental data, despite the simplicity of the platinum phase model.

Spatial B-jump at sudden channel enlargements with abrupt drop

An analytical and experimental study of the hydraulic jump in stilling basins with abrupt drop and sudden enlargement, called the spatial B-jump here, is carried out for finding the sequent depth ratio and resulting energy dissipation. The spatial B-jump studied has its toe downstream of the expansion section, and the stream lines at the toe are characterized by downward curvature. An expression is obtained for the sequent depth ratio based on the momentum equation with suitable assumptions for the extra pressure force term because of the abrupt drop in the bed and sudden enlargement in the basin width. Predictions compare favorably with experiments. It is shown that the spatial B-jump needs less tailwater depth, thereby enhancing the stability of the jump when compared either with spatial jump, which forms in sudden expanding channels, or with B-jump, which forms in a channel with an abrupt drop in bed. It is also shown that there is a significant increase in relative energy loss for the spatial B-jump compared to either the spatial jump or B-jump alone.

Unsteady Compressible Boundary-Layer Flow On The Stagnation Line Of An Infinite Swept Cylinder

Numerical solutions of flow and heat transfer process on the unsteady flow of a compressible viscous fluid with variable gas properties in the vicinity of the stagnation line of an infinite swept cylinder are presented. Results are given for the case where the unsteady temperature field is produced by (i) a sudden change in the wall temperature (enthalpy) as the impulsive motion is started and (ii) a sudden change in the free-stream velocity. Solutions for the simultaneous development of the thermal and momentum boundary layers are obtained by using quasilinearization technique with an implicit finite difference scheme. Attention is given to the transient phenomenon from the initial flow to the final steady-state distribution. Results are presented for the skin friction and heat transfer coefficients as well as for the velocity and enthalpy profiles. The effects of wail enthalpy parameter, sweep parameter, fluid properties and transpiration cooling on the heat transfer and skin friction are considered.

Superconductivity in the nonadiabatic limit

Isotope-shift exponent (cu) and the pressure coefficient of superconducting transition temperature (beta) have been studied in the nonadiabatic limit. We have considered the effect of nonadiabaticity in both within and beyond the Migdal-Eliashberg formalism. It reveals from our study that the pressure coefficient of superconducting transition is high for the low-T-c region and low for the high-T-c region and the minimum value of alpha is obtained where the transition temperature is maximum. Lowest value of isotope-shift exponent is obtained for small momentum exchange between the electrons and the bosonic field. Qualitative variation of beta with temperature is consistent with the experimental results of the hole doped superconductors for small momentum exchange.

Unsteady free convection flow in the stagnation-point region of a three-dimensional body

The unsteady free convection flow in the stagnation-point region of a heated three-dimensional body placed in an ambient fluid is studied under boundary layer approximations. We have considered the case where there is an initial steady state that is perturbed by a step-change in the wall temperature. The non-linear coupled partial differential equations governing the free convection flow are solved numerically using a finite difference scheme. The presented results show the temporal development of the momentum and thermal boundary layer characteristics.

Mixed Convection Boundary Layer Flow Past a Horizontal Circular Cylinder Embedded in a Bidisperse Porous Medium

Adopting a two-temperature and two-velocity model, appropriate to a bidisperse porous medium (BDPM) proposed by Nield and Kuznetsov (2008), the classical steady, mixed convection boundary layer flow about a horizontal, isothermal circular cylinder embedded in a porous medium has been theoretically studied in this article. It is shown that the boundary layer analysis leads to expressions for the flow and heat transfer characteristics in terms of an inter-phase momentum parameter, a thermal diffusivity ratio, a thermal conductivity ratio, a permeability ratio, a modified thermal capacity ratio, and a buoyancy or mixed convection parameter. The transformed partial differential equations governing the flow and heat transfer in the f-phase (the macro-pores) and the p-phase (the remainder of the structure) are solved numerically using a very efficient implicit finite-difference technique known as Keller-box method. A good agreement is observed between the present results and those known from the open literature in the special case of a traditional Darcy formulation (monodisperse system).

Inducing nonlocal reactions with a local probe

The scanning tunneling microscope (STM) has evolved continually since its invention, as scientists have expanded its use to encompass atomic-scale manipulation, momentum-resolved electronic characterization, localized chemical reactions (bond breaking and bond making) in adsorbed molecules, and even chain reactions at surfaces. This burgeoning field has recently expanded to include the use of the STM to inject hot electrons into substrate surface states; the injected electrons can travel laterally and induce changes in chemical structure in molecules located up to 100 nm from the STM tip. We describe several key demonstrations of this phenomenon, including one appearing in this issue of ACS Nano by Chen et al. Possible applications for this technique are also discussed, including characterizing the dispersion of molecule−substrate interface states and the controlled patterning of molecular overlayers.