Curriculum Vitae
Feel free to contact me if you would like a copy of any manuscripts. A more up-to-date list of my publications can be found on google scholar. For code please check out my github.
A copy of my CV can be found here.
Publications
*equal contribution
Microsoft Research
19. K. E. Wu, K. K. Yang, R. van den Berg, S. Alamdari, J. Y. Zou, A. X. Lu, A. P. Amini, "Protein structure generation via folding diffusion" Nature Communications, 2024
18. S. Alamdari, N. Thakkar, R. van den Berg, A. X. Lu, N. Fusi., A. P. Amini, K. K. Yang "Protein generation with evolutionary diffusion: sequence is all you need" bioRxiv, 2023
University of Washington
17. S. Alamdari and J. Pfaendtner. "Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N-1-Phenylethyl Sidechains" J. Phys. Chem. B, 2023 [doi]
16. S. Alamdari, K. Torkelson, X. Wang, C. L. Chen, A. L. Ferguson, J. Pfaendtner "Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains"J. Phys. Chem. B, 2023 [doi]
15. M. Zhao, S. Zhang, R. Zheng, S. Alamdari, C. J. Mundy, J. Pfaendtner, L. D. Pozzo, C. L. Chen, J. J. De Yoreo, A. L. Ferguson. "Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes" Biomacromolecules, 2023 [doi]
14. K. Strunge, N. Hoinkis, H. Lutz, S. Alamdari, S. J. Roeters, H. Lu, J. Pfaendtner, T. Weidner. "Peptide Mimic of the Marine Sponge Protein Silicatein Fabricates Ultrathin Nanosheets of Silicon Dioxide and Titanium Dioxide" Langmuir, 2022 [doi]
13. M. Zhao, K. Lachowski, S. Zhang, S. Alamdari, J. Sampath, P. Mu, C. J. Mundy, J. Pfaendtner, J. De Yoreo, C. L. Chen, L. D. Pozzo, A. L. Ferguson, "Hierarchical Self-Assembly Pathways of Polypeptoid Helices and Sheets” Biomacromolecules, 2022. [doi]
12. S. Summers*, S. Alamdari*, Casey J. Kraft, R. Brunecky, J. Pfaendtner, J. L. Kaar, “Amino Acid Substitution of Distal and Active Site Residues Reduce Product Inhibition of E1 Endocellulase from Acidothermus Cellulolyticus” Protein Eng. Des. Sel., 2021. [doi]
11. S. Alamdari*, J. Sampath*, A. Prakash, L. Gibson, J. Pfaendtner, “Efficient sampling of high-dimensional free energy landscapes: A Review of Parallel Bias Metadynamics”, Foundations of Molecular Modeling and Simulation. 2021. [doi]
10. S. J. Roeters*, T. Golbek*, M. Bregnhøj*, T. Drace, S. Alamdari, W. Roseboom, G. Kramer, S. Woutersen, J. Pfaendtner, T. Boesen, T. Weidner “The Ice Nucleating Protein inaZ is Activated by Low Temperature” Nat. Commun. 2021 [doi] (Editor's Highlight)
9. N. Thompson, T. A. Cohen, S. Alamdari, G. A. Williamson, V. C. Holmberg, D. A. C. Beck. “DiffCapAnalyzer: A Python Package for Quantitative Analysis of Total Differential Capacity Data” J. Open Source Softw. 2020 [doi]
8. S. Alamdari*, S. Roeters*, T. Golbek, L. Schmüser, T. Weidner, J. Pfaendtner “Orientation and Conformation of Proteins at the Air-Water Interface Determined from Integrative Molecular Dynamics Simulations and Sum Frequency Generation Spectroscopy” Langmuir. 2020 [doi]
7. J. Sampath*, S. Alamdari*, J. Pfaendtner “Closing the Gap Between Modeling and Experiments in the Self-assembly of Biomolecules at Interfaces and in Solution” Chem. Mat. 2020 [doi]
6. M. Zhao, J. Sampath, S. Alamdari, G. Shen, C. L. Chen, C. J. Mundy, J. Pfaendtner, A. L. Ferguson, “A MARTINI-compatible coarse-grained model for the mesoscale simulation of peptoids” J. Phys. Chem. B. 2020 [doi]
5. S. Summers, Casey Kraft, S. Alamdari, J. Pfaendtner, J. Karr “Enhanced Activity and Stability of Acidothermus cellulolyticus Endoglucanase 1 in Ionic Liquids via Engineering Active Site Residues and Non-native Disulfide Bridges” ACS Sustain. Chem. Eng. 2020 [doi]
4. B. Hellner, S. Alamdari, H. Pyles, S. Zhang, A. Prakash, K. Sprenger, J. De Yoreo, D. Baker, J. Pfaendtner, F. Baneyx, “Sequence-structure-binding relationships reveal adhesion behavior of the Car9 solid-binding peptide: an integrated experimental and simulation study” J. Am. Chem. Soc. 2020 [doi]
3. S. Alamdari, J. Pfaendtner, “Impact of glutamate carboxylation in the adsorption of the α-1 domain of osteocalcin to hydroxyapatite and titania” Mol. Syst. Des. Eng. 2020 [doi] (Featured Front Cover Art)
2. D. Verreault, S. Alamdari, S. J. Roeters, R. Pandey, J. Pfaendtner, T. Weidner, “Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water”, Phys. Chem. Chem. Phys. 2018 [doi]
Arizona State University
1. G. Wang, C. Robert, A. Suslu, B. Chen, S. Yang, S. Alamdari, I. C. Gerber, T. Amand, X. Marie, B. Urbaszek, S. Tongay, “Spin-orbit engineering in transition metal dichalcogenide alloy monolayers”, Nat. Commun. 2015 [doi]