Résumé

Profile

Name
Akin Budi
Qualifications
PhD Project
Title of Thesis
On the Effects of External Stresses on Protein Conformation
Supervisors
Prof. Irene Yarovsky and Prof. Ian Snook
Research Group
Computational Physics
Consultant
Dr. Herbert Treutlein (Cytopia Pty. Ltd.)
Description of Project
Computational studies of biological macromolecules response under external stress
Research Interests
  • Computational modelling of materials to investigate their structural and dynamical properties, in particular their suitability for hydrogen storage materials
  • Embedded Atom Method potential development
  • Computational study of aluminium-based nanoclusters as potential hydrogen storage materials
  • Protein dynamics and their response to stress
  • Methods used include classical molecular dynamics, classical force fields, and reactive force fields
Summary of Responsibilities
  • Postdoctoral fellow in the Computational Physics group
  • Specialised lectures at Honours level in the Advanced Materials course
  • Postgraduate consultation
Current and Recent Research Projects
Journal Articles
  1. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Comparative Study of Insulin Chain-B in Isolated and Monomeric Environments under External Stress" J. Phys. Chem. B, 112(26):7916-7924 (2008)
  2. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Effect of Frequency on Insulin Response to Electric Field Stress" J. Phys. Chem. B, 111(20):5748-5756 (2007)
  3. F.S. Legge, A. Budi, H. Treutlein, I. Yarovsky, "Protein Flexibility: Multiple Molecular Dynamics Simulations of Insulin Chain B" Biophys. Chem., 119(2):146-157 (2006)
  4. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Electric Field Effects on Insulin Chain-B Conformation" J. Phys. Chem. B, 109(47):22641-22648 (2005)
  5. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Protein Response to Electric Field Stress" Proceedings of the 16th Australian Institute of Physics Congress 2005 Canberra, Australia (2005) ISBN 0-9598064-8-2
  6. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Effect of External Stresses on Protein Conformation: A Computer Modelling Study" Eur. Biophys. J., 33(2):121-129 (2004)
  7. G. Bryant, S. Martin, A. Budi, W. van Megen, "Accurate Measurement of Small Polydispersities in Colloidal Suspensions" Langmuir, 19(3):616-621 (2003)
Due to copyright restrictions, I can't put full text access to most of the above journals on this website. However, if you write to me and ask nicely, I will give you the reprint/preprint.
Conferences Papers/Publications
  1. A. Budi, D.J. Henry, J.D. Gale, I. Yarovsky, "Development of Computational Methods for Studying Hydrogen Interactions With Light Metal Nanostructures" 17th World Hydrogen Energy Conference, Brisbane, Australia (2008)
  2. A. Budi, D.J. Henry, J.D. Gale, I. Yarovsky, "EAM Potential Development for Aluminium-Based Light Metal Nanostructures" 2008 International Conference On Nanoscience and Nanotechnology, Melbourne, Australia (2008)
  3. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "On The Effects of Stresses on Protein Conformation" Molecular Modelling 2007, Melbourne, Australia (2007)
  4. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "On The Effects of Stresses on Protein Conformation" Workshop: Interaction Energies and the Structure of Surfaces and Nano-structures, Melbourne, Australia (2007)
  5. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Protein Misfolding Due to External Stress: A Theoretical Study" 10th Molecular Modelling Workshop, Perth, Australia (2006)
  6. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Protein Response to Electric Field Stress" 31th Annual Lorne Conference on Protein Structure and Function, Lorne, Australia (2006)
  7. F.S. Legge, A. Budi, H. Treutlein, I. Yarovsky, "Protein Flexibility: Multiple Molecular Dynamics Simulations of Insulin Chain B" 30th Annual Lorne Conference on Protein Structure and Function, Phillip Island, Australia (2005)
  8. F.S. Legge, A. Budi, H. Treutlein, I. Yarovsky, "Protein Flexibility: Multiple Molecular Dynamics Simulations of Insulin Chain B" Biomolecular Dynamics and Interactions Symposium, Melbourne, Australia (2005)
  9. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Computer Simulation Study of Electric Field and Temperature Effects on Insulin Chain B" 29th Annual Lorne Conference on Protein Structure and Function, Lorne, Australia (2004)
  10. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Detailed Structural Analysis of the Transition Pathway of Stressed Insulin Using the Conformational Analysis Tool PEPCAT" 28th Annual Lorne Conference on Protein Structure and Function, Lorne, Australia (2003)
  11. A. Budi, F.S. Legge, H. Treutlein, I. Yarovsky, "Unfolding Pathways of Chemically and Thermally Stressed Insulin: A Molecular Dynamics Study" Bioactive Discovery in the new millenium, International Modelling conference, Lorne, Australia (2003)
  12. Y. Berry, A. Budi, J. Carver, H. Treutlein, I. Yarovsky, "Response of Proteins to External Non-Ionising Radiation: An Experimental and Computer Modelling Investigation" The 26th Annual Conference of the Australian Society for Biophysics, Melbourne, Australia (2002)
  13. B.H. Budi, I.K. Snook, "Molecular Dynamics Investigation of Thin Films" Proceedings of the 6th Australian Molecular Modelling Conference, p. 43 (2000)
Please go to the presentations section to see a preview and download the presentations.
Professional Affiliations
Awards
  • Stanley Martin Memorial Prize, RMIT University, Applied Physics, 1998
  • Dean's List, RMIT University, Faculty of Applied Science, 1999
  • AK & DA Connor Award, RMIT University, Applied Physics, 1999
  • Walter Boas Memorial Prize, RMIT University, Applied Physics, 2000

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