Sarah Alamdari

I am currently a data scientist at Microsoft Research where I apply generative deep learning methods to study protein design.

I completed my PhD in Chemical Engineering at University of Washington under the supervision of Jim Pfaendtner as an NSF GRFP Fellow. During my PhD I applied and developed computational methods to probe interfacial phenomena that govern biological processes at the microscale, informing their behavior at the macroscale. Previously, I was a FURI undergraduate researcher synthesizing 2D materials in the Tongay Research Group and graduated Magna Cum Laude in Chemical Engineering at Arizona State University.

I am passionate about equitable access and representation in the computational research space, one of the most underrepresented spaces within STEM. I am a first-gen college student and grew up in a Colombian/Iranian immigrant household. Like so many other first-gen students the journey to becoming a computational researcher a has not been straightforward, or easy. This has driven me to increase equitable access to academia and provide underserved students the tools, guidance, and mentorship they need to be successful through working with Techbridge Girls and in helping jumpstart the COMSEF Scholars REU program

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Research

My broader research interests lie at the intersection of computational biology, deep learning, and molecular simulation. I am motivated to gain a deeper understanding of the fundamental driving forces in biological systems, with the goal of expediting rational and efficient design of new bioinspired technologies.

Publications

Publications while at UW

* denotes equal contribution

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
link
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
link
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
link / bioRxiv
*Featured in 2021 Editor's Highlight
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
link
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
link
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
link / code
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
link / talk
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
link
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
link
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
link
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
link
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
link
* Selected front cover art
* Featured in UW IT press release
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
link

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
link

source code,