Molecular Simulation

During my Ph.D. I developed and applied enhanced sampling methods such as metadynamics and parallel bias metadynamics to probe the interfacial phenomena that govern biological processes at the microscale. This work combined molecular dynamics simulation with experiment to understand biomolecules in various contexts such as peptoid self-assembly, protein behavior at the air-water interface, and biomolecular adsorption to mineral surfaces.

Publications

Origins of conformational heterogeneity in peptoid helices formed by chiral N-1-phenylethyl sidechains

S Alamdari, J Pfaendtner · The Journal of Physical Chemistry B, 2023

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Thermodynamic basis for the stabilization of helical peptoids by chiral sidechains

S Alamdari, K Torkelson, X Wang, CL Chen, AL Ferguson, J Pfaendtner · The Journal of Physical Chemistry B, 2023

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Computational and experimental determination of the properties, structure, and stability of peptoid nanosheets and nanotubes

M Zhao, S Zhang, R Zheng, S Alamdari, CJ Mundy, J Pfaendtner, LD Pozzo, CL Chen, JJ De Yoreo, AL Ferguson · Biomacromolecules, 2023

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Peptide mimic of the marine sponge protein silicatein fabricates ultrathin nanosheets of silicon dioxide and titanium dioxide

K Strunge, N Hoinkis, H Lutz, S Alamdari, SJ Roeters, H Lu, J Pfaendtner, T Weidner · Langmuir, 2022

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Hierarchical self-assembly pathways of peptoid helices and sheets

M Zhao, KJ Lachowski, S Zhang, S Alamdari, J Sampath, P Mu, CJ Mundy, J Pfaendtner, JJ De Yoreo, CL Chen, LD Pozzo, AL Ferguson · Biomacromolecules, 2022

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Substitution of distal and active site residues reduces product inhibition of E1 from Acidothermus cellulolyticus

SR Summers^*, S Alamdari^*, CJ Kraft, R Brunecky, J Pfaendtner, JL 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

S Alamdari, J Sampath, A Prakash, LD Gibson, J Pfaendtner · Foundations of Molecular Modeling and Simulation, 2021

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Orientation and conformation of proteins at the air–water interface from integrative molecular dynamics simulations and sum frequency generation spectroscopy

S Alamdari, SJ Roeters, TW Golbek, L Schmüser, T Weidner, J 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

J Sampath, S Alamdari, J Pfaendtner · Chemistry of Materials, 2020

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MARTINI-compatible coarse-grained model for the mesoscale simulation of peptoids

M Zhao, J Sampath, S Alamdari, G Shen, CL Chen, CJ Mundy, J Pfaendtner, AL 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

S Summers, C Kraft, S Alamdari, J Pfaendtner, JL Kaar · ACS Sustainable Chemistry & Engineering, 2020

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Sequence–structure–binding relationships reveal adhesion behavior of the Car9 solid-binding peptide

B Hellner, S Alamdari, H Pyles, S Zhang, A Prakash, KG Sprenger, JJ De Yoreo, D Baker, J Pfaendtner, F 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

S Alamdari, J Pfaendtner · Molecular Systems Design & Engineering, 2020

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Ice-binding site of surface-bound type III antifreeze protein partially decoupled from water

D Verreault, S Alamdari, SJ Roeters, R Pandey, J Pfaendtner, T Weidner · Physical Chemistry Chemical Physics, 2018

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