Presented by Dr Tim Moroney (QUT)
3 May 2012, Room 442, Priestley Building (67), UQ St Lucia Campus
Abstract
I will present several problems in applied mathematics that we have identified as suitable for GPU acceleration. Preliminary testing in MATLAB is encouraging, but suggests that overheads are significant. This motivates us to consider a C++ solution. I will discuss a GPU library for C++ with MATLAB-like syntax which is currently under development, and which allows easy porting of MATLAB code to the faster C++ environment.
After the seminar, please join us for drinks and pizza at the Pizza Café on the UQ St Lucia campus.
Presented by Peter Baxter (CARM, UQ)
20 Oct 2011, M313, QUT Gardens Point Campus
The white-backed woodpecker is critically endangered in Sweden due to lack of suitable habitat. Possible recovery actions - releasing captive-bred birds and manipulating the structure and species composition of forests - can be implemented at a variety of intensities and over a period of decades. I will describe a forest-woodpecker model and its use with simulated annealing to identify management strategies that meet management targets at low cost.
We will have afternoon tea before the talk: from 3.30pm in O614.
Presented by Matthew Simpson
1 Sep 2011, UQ St Lucia Campus, 67-442
Continuum diffusion models are often used to represent the collective motion of cell populations. Most previous studies have simply used linear diffusion to represent collective cell spreading, while others found that degenerate nonlinear diffusion provides a better match to experimental cell density profiles. In the cell modeling literature there is no guidance available with regard to which approach is more appropriate for representing the spreading of cell populations. Furthermore, there is no knowledge of particular experimental measurements that can be made to distinguish between situations where these two models are appropriate. Here we provide a link between individual-based and continuum models using a multi-scale approach in which we analyze the collective motion of a population of interacting agents in a generalized lattice-based exclusion process. For round agents that occupy a single lattice site, we find that the relevant continuum description of the system is a linear diffusion equation, whereas for elongated rod-shaped agents that occupy L adjacent lattice sites we find that the relevant continuum description is connected to the porous media equation (pme). The exponent in the nonlinear diffusivity function is related to the aspect ratio of the agents. Our work provides a physical connection between modeling collective cell spreading and the use of either the linear diffusion equation or the pme to represent cell density profiles. Results suggest that when using continuum models to represent cell population spreading, we should take care to account for variations in the cell aspect ratio because different aspect ratios lead to different continuum models. This is joint work with Dr Ruth Baker (Oxford) and Dr Scott McCue (QUT).
We'll have afternoon tea before the talk, from 3.40pm in 69-704.
Presented by Vivien Challis
18 Aug 2011, QUT Gardens Point Campus, B-505
The release of NVIDIA's CUDA architecture and language CUDA C puts the use of massively parallel Graphics Processing Units (GPUs) within the reach of the scientific programmer, placing large computational power at their finger tips for little cost. I'll give an introduction to GPUs and NVIDIA's language CUDA C, in particular showing some simple examples. I'll also outline my progress re-writing our Fortran 90 topology optimisation algorithm to run on the GPU architecture.
Afternoon tea will be held before the talk from 3.30pm in O-614.
Presented by Assoc Prof Dann Mallet, Queensland University of Technology.
4 Aug 2011, Room 442, Priestley Mathematics Building (Building 67), The University of Queensland.
Chlamydia trachomatis, an obligate intracellular bacterial pathogen that infects the genital and ocular mucosa of humans causing sexually transmitted disease and trachoma, is estimated to cause 70-75% of endocervical infections in women. These infections are asymptomatic and may persist for months to years. Chronic pain, pelvic inflammatory disease, infertility and ectopic pregnancy are among the serious consequences of C. trachomatis genital tract infections in women, which together contribute to the most costly outcomes of any sexually transmitted infection besides HIV/AIDS. The health care costs rise to an estimated $US4 billion in the United States of America alone.
C. trachomatis is an intracellular, complex and multi-functional process pathogen, unique among prokaryotes because of a biphasic developmental cycle of replication in which the organism exists in two distinctive forms; the Elementary Body (EB), which is the infectious form, and the Reticulate Body (RB), which is the replicating structure. The host immune system, conditions in the genital mucosa and the menstrual cycle all play significant roles in the clearance of Chlamydia throughout the infection period.
In vitro, modelling all the factors mentioned above is not straightforward. There are also several differences in the Chlamydia infection of laboratory animals such as mice (among the best animal models), compared with the infection in humans such as length of infection and the immune-evasion mechanism. Therefore mathematical models describing the interaction between C. trachomatis and the immune system are extremely useful mechanisms for obtaining further insights into the dynamics of the infection process, and the subsequent effects and possible effective control strategies.
In this seminar I will present a summary of the work to date on the mathematical modelling of Chlamydia trachomatis within the host. This will essentially comprise a discussion of the work of Wilson and coworkers that is largely ordinary differential equation based, and the work of my own group which is generally concerned with investigating spatial effects and the immune system response in chlamydial infection, carried out using partial differential equation and hybrid cellular automata based methods.
After Dann's talk some of us will go to The Pizza Cafe for drinks and pizza - everyone is welcome to join us.
Presented by Dr Cathy Holmes, The University of Queensland.
7 Apr 2011, S-Block, room S-314, Queensland University of Technology.
Coupled limit cycle oscillators arise in many different contexts in biology, chemistry, physics and engineering. This talk is about the collective behaviour of arrays of nanomechanical oscillators interacting via a common field. If the oscillators are identical multistability leading to hysteresis is a common feature of the dynamics of the system. This behaviour can be understood by deriving and analysing amplitude equations for the dominant oscillatory motion. For nonidentical oscillators detuning can desynchronize the oscillators. Using coupled amplitude equations we explore the mechanism for the loss of synchronization.
Presented by Prof Graeme Pettet, Queensland University of Technology.
24 Mar 2011, Room 442, Priestley Mathematics Building (Building 67), The University of Queensland.
Chemotactic or haptotactic cell migration mechanisms are commonly observed or hypothesised in a range of tissue invasion problems such as angiogenesis, tumour metastasis and embryogenesis. Mathematical models employed to describe such phenomena usually result in smooth-fronted travelling waves. Although of interest, such waves do not typically capture the sharp transitions between tissue type or cell populations that may be observed. Here we will demonstrate that for typical systems of Advection-Reaction-Diffusion models used in these contexts, geometric singular perturbation techniques can be employed to demonstrate the potential existence of shock-like solutions in addition to the usual smooth-fronted solutions.
