Theoretical Studies of Bimolecular Interactions Under Non-equilibrium Conditions

The computational resources provided for project e90 were used to develop and apply innovative computational techniques to investigate biomolecular interactions and function under non-equilibrium conditions through several collaborative projects (listed as Challenges). The outcomes from these studies elucidated system behaviour in different conditions and help formulate rational design principles for efficient and nontoxic biomedical materials and nanodevices.

Principal investigator

Nevena Todorova
Magnifying glass

Area of science

Chemical Sciences, Geosciences, Molecular modelling of biomaterials

Systems used


Applications used

Partner Institution: RMIT University| Project Code: e90/pawsey03000

The Challenge

Individual project challenges:
1) Exploring structure, dynamics and self-assembly of apolipoprotein A-I (ApoA-I)
2) Exploring small molecule analyte interactions with functionalised gold nanoparticle surfaces for chemical sensing
3) Investigating DNA Origami protection and molecular interfacing through engineered sequence-defined peptoids
4) Investigating the role of sequence on the conformation of star-shaped “Structurally Nanoengineered Antimicrobial Peptide Polymers” (SNAPPs) on their biological activity

The Solution

To address all challenges advanced multiscale computational techniques are being employed to provide atomistic insight into the structure, dynamics and interactions mechanisms of our systems in solutions. This information is crucial for the fundamental understanding of the molecular systems in question. and enable rational design of novel biomaterials for medical applications.

The Outcome

The Pawsey Supercomputing Centre provides the computational resources needed for the running and analysing our simulation data. These resources are crucial for the successful completion of the projects.

List of Publications

1. S. Wang, M. A Gray, S. Xuan, Y. Lin, J. Byrnes, A. I Nguyen, N. Todorova, M. M Stevens, C. R Bertozzi, R. N Zuckermann, O. Gang “DNA origami protection and molecular interfacing through engineered sequence-defined peptoids” Proceedings of the National Academy of Sciences, Vol. 117 (12), pp. 6339-6348 (2020)
2. N. Todorova, A. Bentvelzen, I. Yarovsky ”Electromagnetic field modules aggregation propensity of amyloid peptides” Journal of Chemical Physics, Vol. 152 (3), pp. 035104 (2020)
3. N. Kim, M. R Thomas, M S Bergholt, I. J Pence, H. Seong, P. Charchar, N. Todorova, A. Nagelkerke, A. Belessiotis-Richards, D J Payne, A. Gelmi, I. Yarovsky, M. M Stevens “Surface enhances Raman scattering artificial nose for high dimensionality fingerprinting” Nature Communications, Vol. 11 (1), pp. 1-12 (2020)
4. N Todorova, I Yarovsky “The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations” Australian Journal of Chemistry, Vol. 72, pp. 574–584 (2019)

Figure 1. MD simulations of the interactions of PE1 and PE4 with dsDNA. Molecular representation of the most visited binding sites and structures of (A) PE1 and (B) PE4 with dsDNA (blue: peptoid backbone, red: Nae residues, and green: Nte residues).