HPC Researcher Profile

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Methodology of Genomic Signature Analysis (GSA). The specific aim of our project was to Re-analyse the WTCCC Genome Wide Association Study data using a novel computational approach geared to identifying genomic signatures useful for predicting Crohn’s disease risk.

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'Computational Studies of Photocatalytic Activities of Titanium Dioxide Surfaces for Solar Fuel Production'. Here are the papers from the use of the HPC cluster.
1.

 Vertically aligned nanorod-like rutile TiO2 single crystal nanowire bundles with superior electron transport and photoelectrocatalytic properties
Haimin Zhang, Xiaolu Liu, Yibing Li, Qingfeng Sun, Yun Wang, Barry J. Wood, Porun Liu, Dongjiang Yang and Huijun Zhao
Journal of Materials Chemistry, accepted. DOI: 10.1039/C2JM15546J (IF=5.10)

2.

Structure, Reactivity, Photoactivity and Stability of Ti-O Based Materials: A Theoretical Comparison
Yun Wang, Tao Sun, Dongjiang Yang, Hongwei Liu, Haimin Zhang, Xiangdong Yao and Huijun Zhao
Physical Chemistry Chemical Physics, accepted. DOI: 10.1039/C2CP23143C (IF=3.45 )

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A Facile Vapor Phase Hydrothermal Method for Direct Growth of Titanate Nanotubes on Titanium Substrate via a Distinctive Nanosheet Rolled-up Mechanism
Porun Li, Haimin Zhang, Hongwei Liu, Yun Wang, Xiangdong Yao, Guangshan Zhu, Shanqing Zhang, Huijun Zhao
Journal of the American Chemical Society, 2011, 133, 19032 (IF=9.02 )

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Facile Fabrication of Anatase TiO2 Microspheres on Solid Substrates and Surface
Crystal Facets Transformation from {001} to {101}
Haimin Zhang, Porun Liu, Feng Li, Hongwei Liu, Yun Wang, Shanqing Zhang,
Mingxing Guo, Huiming Cheng, and Huijun Zhao
Chemistry - A European Journal, 2011, 17, 5949 (IF=5.48)

5.

Anatase TiO2 Crystal Facet Growth: Mechanistic Role of Hydrofluoric Acid and Photoelectrocatalytic Activity
Haimin Zhang, Yun Wang, Porun Liu, Yanhe Han, Xiangdong Yao, Jin Zou, Huiming Cheng and Huijun Zhao
ACS Applied Materials & Interfaces, 2011. 3, 2472 (New Journal)

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Origin of Reactivity Diversity of Lattice Oxygen in Titanates
Yun Wang, Hongwei Liu, Haimin Zhang, Porun Liu, Xiangdong Yao, Shanqing Zhang and Huijun Zhao
Chemical Physics Letters, 2011. 511, 82 (IF=2.28)

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A selective etching phenomenon on {001} faceted anatase titanium dioxide single crystal surface by hydrofluoric acid
Yun Wang, Haimin Zhang, Yanhe Han, Porun Liu, Xiangdong Yao and Huijun Zhao
Chemical Communications, 2011, 47, 2829 (IF=5.79, Times Cited 2)

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Research is mostly focused on galectins. Using gowonda for molecular docking and molecular dynamics.

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from Nov 2010 - July 2011, Barbara was working in Debra Benhardt's group in the QMNC doing molecular dynamics simulations using the cluster. Barbara investigated various theoretical results in non-equilibrium fluid dynamics associated with the Fluctuation Theorem.

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Work on genome-wide association studies, analysing huge SNP array datasets using PLINK. Performed multiple pathway analyses using software such as MAGENTA and ALIGATOR. Will be submitting the thesis in the next couple of weeks and will hopefully get a paper out on the pathway analyses in the next couple of months.

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run the Blast package on NR data base to extract Position Specific Scoring Matrix (PSSM)

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Numerical modelling of the South China Sea using the Regional Ocean Modelling System (ROMS) through Griffith Centre for Coastal Management

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research involves developing a computational program which uses the layered finite element method to solve the failure analysis of reinforced concrete plates and shells. Currently using the cluster to develop a finite element computational tool written in Fortran. This tool is called RCEPFA and is used to perform failure analysis of reinforced concrete plates and shells. RCEPFA was created as part of Griffith University A/Prof Hong Guan's thesis. The research involves further developing this tool to fix any bugs and perform code optimisation. In order to run and test RCEPFA , the Oracle Solaris Studio Fortran compiler will be used.

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Vehicle routing and logistics, and optimisation collaborations with Griffith Researcher

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non-equilibrium molecular dynamics simulations and free energy calculations

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perform simulations of ion trajectories in static electrostatic fields, mainly using fortran 77 and gcc compilers but also MPI framework for parallel computing. use Matlab in parallel

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running some algorithm experiments

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use VASP program and rebuild the quantum structure and atom system

Thermal effects control the structure of the Cu(100)-c(2×2)N surface\\
 Yun Wang,1 Tao Sun,1 Yajun Li,2 Huijun Zhao1\*\\
 1. Centre for Clean Environment and Energy, and Griffith School of Environment,  Gold Coast Campus, Griffith University, QLD 4222, Australia\\
 "Structure, Reactivity, Photoactivity and Stability of Ti-O Based Materials: A Theoretical Comparison"\\
 Author(s): Wang, Yun; Sun, Tao; Yang, Dongjiang; Liu, Hongwei; Zhang, Haimin; Yao, Xiangdong; Zhao, Huijun

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run Bioinformatics software:
-R/Bioconductor (simpleaffy, aroma.affymetrix)

• Affymetrix Power Tools
  for the normalization and processing of microarray experiment data.

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Visiting student at QMNC performing Fortran compilations

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working on attaining a protein structure of a novel Zebrafish protein (Drgal1-L2) homologous to human galectin-1. Galectins are family of small carbohydrate binding proteins, which are capable of mediating numerous cellular interactions and molecular events. Drgal1-L2 is of particular interest to our group for drug design and discovery targeted towards human galectin-1 implicated in cancer and immune disorders, as well as providing an insight into the evolution of such proteins in terms of their role in vascular biology, immunobiology and neurobiology.
I was recently successful in solving the crystal structure of Drgal1-L2 and comparing it against known human galectin-1 structures. While some progress has been made to associate structural landmarks with functional attributes, there is a growing need to establish whether Drgal1-L2 and galectin-1 differ in terms of their behavior; e.g. folding to adopt subtle changes in structure with dramatic effects on function. This information can be more generally applied to assisting biologists and chemists alike in understanding novel structural characteristics and molecular dynamics which govern the biological laws of attraction between complex carbohydrate structures.
Simulation of molecular dynamics is a computationally expensive process which demands a high level of computational power.

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Numerical simulations of electrical propagation through the heart using C++ with the Petsc libraries

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researching two mathematical modelling projects requiring the use of powerful computing. The first is to model the electric field in the heart (along with my PhD student Josef Barnes) and the second is to use computational fluid dynamics software to model blood flow in coronary arteries.

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run Matlab code to test large Image data

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Will be mainly converting GPU and MPI programs from local ICT cluster to Gowanda, assisting academics in conversion.

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Analysis of amplicon libraries from Next generation sequencing

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Part of Debra Bernhardt's group interested in non-equilibrium molecular dynamics simulations and free energy calculations.

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MD simulation software GROMOSXX and GROMOS++ (analysis software).

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Advancement of the Scaled Boundary Finite Element Method in Wave-structure Interaction in Ocean Engineering. Currently using gowonda for intensive memory requirement results from matlab coding of the Scaled Boundary Finite Element Method

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matlab calculations through a python script.

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Research project about finding molecular transition states

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Parallel Optimisation Techniques

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Malaria Drug Resistance & Chemotherapy Laboratory . using models to investigate the effectiveness of various intervention strategies in achieving elimination of malaria from the simulated community.

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(1) Dynamical downscaling of coastal ocean circulation for the South East Queensland coasts.
Type of research: Numerical modelling on HPC (a community ocean model)
Publication: No papers have been published regarding this topic.
(2) A coastal management decision support system.
Type of research: Setting up a cloud-based decision support system focusing on regional coastal forecasts for Queensland.
No papers have been published regarding this topic.
A presentation at an international conference regarding this topic this April in New Caledonia.

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