Publications
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Publications while at MSR
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Protein structure generation via folding diffusion
Kevin E Wu, Kevin K Yang, Rianne van den Berg, Sarah Alamdari, James Y Zou, Alex X Lu, Ava P Amini
Nature Communications, 2024
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code
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Protein generation with evolutionary diffusion: sequence is all you need
Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Alex Xijie Lu, Nicolo Fusi, Ava Pardis Amini, Kevin K Yang
bioRxiv, 2023
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code
* Featured in TechCrunch
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Publications while at UW
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Origins of Conformational Heterogeneity in Peptoid Helices Formed by Chiral N-1-Phenylethyl Sidechains
Sarah Alamdari and Jim Pfaendtner
J. Phys. Chem. B, 2023
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Thermodynamic Basis for the Stabilization of Helical Peptoids by Chiral Sidechains
Sarah Alamdari, Kaylyn Torkelson, Xiaoqian Wang, Chun-Long Chen, Andrew L. Ferguson, Jim Pfaendtner
J. Phys. Chem. B, 2023
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Computational and Experimental Determination of the Properties, Structure, and Stability of Peptoid Nanosheets and Nanotubes
Mingfei Zhao, Shuai Zhang, Renyu Zheng, Sarah Alamdari, Christopher J Mundy, Jim Pfaendtner, Lilo D Pozzo, Chun-Long Chen, James J De Yoreo, Andrew L Ferguson
Biomacromolecules, 2023
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Peptide Mimic of the Marine Sponge Protein Silicatein Fabricates Ultrathin Nanosheets of Silicon Dioxide and Titanium Dioxide
Kris Strunge, Nina Hoinkis, Helmut Lutz, Sarah Alamdari, Steven J Roeters, Hao Lu, Jim Pfaendtner, Tobias Weidner
Langmuir, 2022
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Hierarchical Self-Assembly Pathways of Peptoid Helices and Sheets
Mingfei Zhao, Kacper J Lachowski, Shuai Zhang, Sarah Alamdari, Janani Sampath, Peng Mu, Christopher J Mundy, Jim Pfaendtner, James J De Yoreo, Chun-Long Chen, Lilo D Pozzo, Andrew L Ferguson
Biomacromolecules, 2022
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Ice-nucleating proteins are activated by low temperatures to control the structure of interfacial water
Steven J Roeters*, Thaddeus W Golbek*, Mikkel Bregnhøj*, Taner Drace, Sarah Alamdari, Winfried Roseboom, Gertjan Kramer, Tina Šantl-Temkiv, Kai Finster, Jim Pfaendtner, Sander Woutersen, Thomas Boesen, Tobias Weidner
Nature Communications, 2021
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bioRxiv
*Featured in 2021 Editor's Highlight
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Substitution of distal and active site residues reduces product inhibition of E1 from Acidothermus Cellulolyticus
Samantha R Summers*, Sarah Alamdari*, Casey J Kraft, Roman Brunecky, Jim Pfaendtner, Joel L Kaar
Protein Engineering, Design and Selection, 2021
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Efficient Sampling of High-Dimensional Free Energy Landscapes: A Review of Parallel Bias Metadynamics
Sarah Alamdari*, Janani Sampath*, Arushi Prakash, Luke D Gibson, Jim Pfaendtner
Foundations of Molecular Modeling and Simulation (Book Chapter), 2021
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DiffCapAnalyzer: A Python Package for Quantitative Analysis of Total Differential Capacity Data
Nicole L Thompson, Theodore A Cohen, Sarah Alamdari, Chih-Wei Hsu, Grant A Williamson, David A. C. Beck, Vincent C Holmberg
Journal of Open Source Software, 2020
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Orientation and conformation of proteins at the air–water interface determined from integrative molecular dynamics simulations and sum frequency generation spectroscopy
Sarah Alamdari*, Steven J Roeters*, Thaddeus W Golbek, Lars Schmüser, Tobias Weidner, Jim Pfaendtner
Langmuir, 2020
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Closing the gap between modeling and experiments in the self-assembly of biomolecules at interfaces and in solution
Janani Sampath*, Sarah Alamdari*, Jim Pfaendtner
Chemistry of Materials, 2020
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MARTINI-compatible coarse-grained model for the mesoscale simulation of peptoids
Mingfei Zhao, Janani Sampath, Sarah Alamdari, Gillian Shen, Chun-Long Chen, Christopher J Mundy, Jim Pfaendtner, Andrew L Ferguson
The Journal of Physical Chemistry B, 2020
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Enhanced Activity and Stability of Acidothermus cellulolyticus Endoglucanase 1 in Ionic Liquids via Engineering Active Site Residues and Non-Native Disulfide Bridges
Samantha Summers, Casey Kraft, Sarah Alamdari, Jim Pfaendtner, Joel L Kaar
ACS Sustainable Chemistry & Engineering, 2020
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Sequence–structure–binding relationships reveal adhesion behavior of the Car9 solid-binding peptide: an integrated experimental and simulation study
Brittney Hellner, Sarah Alamdari, Harley Pyles, Shuai Zhang, Arushi Prakash, Kayla G Sprenger, James J De Yoreo, David Baker, Jim Pfaendtner, François Baneyx
Journal of the American Chemical Society, 2020
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Impact of glutamate carboxylation in the adsorption of the α-1 domain of osteocalcin to hydroxyapatite and titania
Sarah Alamdari, Jim Pfaendtner
Molecular systems design & engineering, 2020
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* Selected front cover art
* Featured in UW IT press release
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Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water
Dominique Verreault, Sarah Alamdari, Steven J Roeters, Ravindra Pandey, Jim Pfaendtner, Tobias Weidner
Physical Chemistry Chemical Physics, 2018
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Publication while at ASU
Spin-orbit engineering in transition metal dichalcogenide alloy monolayers
Gang Wang, Cedric Robert, Aslihan Suslu, Bin Chen, Sijie Yang, Sarah Alamdari, Iann C Gerber, Thierry Amand, Xavier Marie, Sefaattin Tongay, Bernhard Urbaszek
Nature communications, 2015
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