Ashkan Fakharzadeh
Postdoctoral Research Associate
Home Department: Biochemistry
Office Address: 3055 Beckman Institute, 405 N. Mathews Avenue, Urbana, Illinois 61801
Email Address: afakhar@illinois.edu
Phone:(217)-300-0380
Research Interests
- Development of Multi-scale Simulation Methods
- Enhanced sampling techniques, Path-finding algorithms
- Conformational Transitions in Membrane Transporter and Membrane Proteins
- EAATs, MFS transporters, GPCRs
- Nucleic Acids
- Nonequilibrium Statistical Mechanics
Publications
Comparative Study of the Bending Free Energies of C- and G-Based DNA: A-, B-, and Z-DNA and Associated Mismatched Trinucleotide
Repeats. A. Fakharzadeh, M. Moradi, C. Sagui, C. Roland. Journal of Chemical Information and Modeling, 65 (11), 5672-5689.
Conformational free energy landscape of a glutamate transporter and microscopic details of its transport mechanism. S. Thangapandian, A. Fakharzadeh, M. Moradi, E. Tajkhorshid. Proceedings of the National Academy of Sciences, 122 (10), e2416381122.
Structure and Dynamics of DNA and RNA Double Helices Formed by d(CTG), d(GTC), r(CUG), and r(GUC) Trinucleotide Repeats and Associated DNA-RNA Hybrids. A. Fakharzadeh, J. Qu, F. Pan, C. Sagui, C. Roland. The Journal of Physical Chemistry B, 127 (37), 7907-7924.
Addressing the embeddability problem in transition rate estimation. C. Goolsby, J. Losey, A. Fakharzadeh, Y. Xu, MC. Duker, M. Sherman, D. Matteson, M. Moradi. The Journal of Physical Chemistry A, 127 (27), 5745-5759.
RNA as a major-groove ligand: RNA-RNA and RNA-DNA triplexes formed by GAA and UUC or TTC sequences. J. Zhang, A. Fakharzadeh, C. Roland, C. Sagui. ACS omega, 7 (43), 38728-38743.
Novel eGZ-motif formed by regularly extruded guanine bases in a left-handed Z-DNA helix as a major motif behind CGG trinucleotide repeats. A. Fakharzadeh, J. Zhang, C. Roland, C. Sagui. Nucleic Acids Research, 50 (9), 4860-4876.
Construction of DNA/RNA triplex helices based on GAA/TTC trinucleotide repeats. J. Zhang, A. Fakharzadeh, F. Pan, C. Roland, C. Sagui. Bio-protocol, 11 (18), e4155-e4155.
Atypical structures of GAA/TTC trinucleotide repeats underlying Friedreich's ataxia: DNA triplexes and RNA/DNA hybrids. J. Zhang, A. Fakharzadeh, F. Pan, C. Roland, C. Sagui. Nucleic Acids Research, 48 (17), 9899-9917.
Effective Riemannian diffusion model for conformational dynamics of biomolecular systems. A. Fakharzadeh, M. Moradi. The Journal of Physical Chemistry Letters, 7 (24), 4980-4987.
