PUBLICATIONS

21. Ma, J., B. Cai, S. Zhang, T. Jian, J.J. De Yoreo, C-L Chen, and F. Baneyx. (2021). Nanoparticle-mediated assembly of peptoid naonsheets functionalized with solid-binding proteins: Designing heterostructures for hierarchy. Nano Letters 21: 1636-1642. DOI: 10.1021/acs.nanolett.0c04285

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20. Monahan, M., B. Cai, T. Jian, S. Zhang, G. Zhu, C-L Chen, J.J. De Yoreo, and B. Cossairt. (2021). Peptoid-directed assembly of CdSe Nanoparticles. Nanoscale 13: 1273-1282. DOI: 10.1039/D0NR07509D

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19. Ziatdinov, M.,  S. Zhang, O. Dollar, J. Pfaendtner, C.J. Mundy, X. Li, H. Pyles, D. Baker, J.J. De Yoreo, and S.V. Kalinin. (2021). Quantifying the dynamics of protein self-organization using deep learning analysis of atomic force microscopy data. Nano Letters 21: 158-165. DOI: 10.1021/acs.nanolett.0c03447

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18. Cai, B., Z. Li, and C-L Chen. (2021). Programming amphiphilic peptoid oligomers for hierarchical assembly and inorganic crystallization. Accounts of Chemical Research 54: 81-91. DOI: 10.1021/acs.accounts.0c00533

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17. Alamdari, S., S.J. Roeters, T.W. Golbek, L. Schmüser, T. Weidner, and J. Pfaendtner. (2020). Orientation and conformation of proteins at the air-water interface determined from integrative molecular dynamics simulations and sum frequency generation spectroscopy. Langmuir 36: 11855-11865. DOI: 10.1021/acs.langmuir.0c01881

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16. Sampath, J., S. Alamdari, and J. Pfaendtner. (2020). Closing the gap between modeling and experiments in the self-assembly of biomolecules at interfaces and in solution. Chemistry of Materials 32: 8043-8059. DOI: 10.1021/acs.chemmater.0c01891

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15. Zhao, M., J. Sampath, S. Alamdari, G. Shen, C- Chen, C.J. Mundy, J. Pfaendtner, and A.L. Ferguson. (2020). MARTINI-compatible coarse-grained model for the mesoscale simulation of peptoids. The Journal of Physical Chemistry B 124: 7745-7764. DOI: 10.1021/acs.jpcb.0c04567

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14. Wang, M., Y. Song, P. Mu, X. Cai, Y. Lin, and C-L Chen. (2020). Peptoid-based programmable 2D nanomaterial sensor for selective and sensitive detection of H2S in live cells. ACS Applied Bio Materials 3: 6039-6048. DOI: 10.1021/acsabm.0c00657

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13. Ritchhart, A., M. Monahan, J. Mars, M.F. Toney, J.J. De Yoreo, and B.M. Cossairt. (2020). Covalently linked, two-dimensional quantum dot assemblies. Langmuir 36: 9944-9951. DOI: 10.1021/acs.langmuir.0c01668

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12. Zhang, S., R.G. Alberstein, J.J. De Yoreo, and F.A. Tezcan. (2020). Assembly of a patchy protein into variable 2D lattices via tunable multiscale interactions. Nature Communications 11: 1-12. DOI: 10.1038/s41467-020-17562-1

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11. Zhang, S., J. Chen, J.Liu, H. Pyles, D. Baker, C-L Chen, and J.J. De Yoreo. (2020). Engineering biomolecular self-assembly at solid-liquid interfaces. Advanced Materials (online). DOI: 10.1002/adma.201905784

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10. Hellner, B., A.E. Stegmann, K. Pushpavanam, M.J. Bailey, and F. Baneyx. (2020). Phase control of nanocrystalline inclusions in bioprecipitated titania with a panel of mutant silica-binding proteins. Langmuir 36: 8503-8510. DOI: 10.1021/acs.langmuir.0c01108

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9. Liu, J., B. Cai, L. Cui, and C-L Chen. (2020). Peptoid-based hierarchically-structured biomimetic nanomaterials: Synthesis, characterization and applications. Science China Materials 63: 1099-1112. DOI: 10.1007/s40843-020-1296-8

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8. Sampath, J., A. Kullman, R. Gebhart, G. Drobny, and J. Pfaendtner. (2020). Molecular recognition and specificity of biomolecules to titanium dioxide from molecular dynamics simulations. npj Computational Materials 6: 1-8. DOI: 10.1038/s41524-020-0288-7

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7. Li, X., D. Kim, S.M. Neumayer, M. Ahmadi, and S.V. Kalinin. (2020). Estimating presiach density via subset selection. IEEE Access 8: 61767-61774. DOI: 10.1109/ACCESS.2020.2983364

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6. Hellner, B., S. Alamdari, H. Pyles, S. Zhang, A. Prakash, K.G. Sprenger, J.J. De Yoreo, D. Baker, J. Pfaendtner, and F. Baneyx. (2020). Sequence-structure-binding relationships reveal adhesion behavior of the Car9 solid-binding peptide: An integrated experimental and simulation study. Journal of the American Chemical Society 142: 2355-2363. DOI: 10.1021/jacs.9b11617

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5. Luo, Y., Y. Song, M. Wang, T. Jian, S. Ding, P. Mu, Z. Liao, Q. Shi, X. Cai, H. Jin, D. Du, W-J Dong, C-L Chen, and Y. Lin. (2019). Bioinspired peptoid nanotubes for targeted tumor cell imaging and chemo-photodynamic therapy. Small 15: 1-8. DOI: 10.1002/smll.201902485

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4. Sampath, J. and J. Pfaendtner. (2019). Amphiphilic peptide binding on crystalline vs. amorphous silica from molecular dynamics simulations. Molecular Physics 117: 3642-3650. DOI: 10.1080/00268976.2019.1657192

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3. Pyles, H., S. Zhang, J.J. De Yoreo, and D. Baker. (2019). Controlling protein assembly on inorganic crystals through designed protein interfaces. Nature 571: 251-256. DOI: 10.1038/s41586-019-1361-6

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2. Hellner, B., S.B. Lee, A. Subramaniam, V.R. Subramanian, and F. Baneyx. (2019). Modeling the cooperative adsorption of solid-binding proteins on silica: Molecular insights from surface plasmon resonance measurements. Langmuir 35: 5013-5020. DOI: 10.1021/acs.langmuir.9b00283

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1. Dunakey, S.J.G., B.L. Coyle, A. Thomas, M. Xu, B.J.F. Swift, and F. Baneyx. (2019). Selective labeling and decoration of the ends and sidewalls of single-walled carbon nanotubes using mono- and bispecific solid-binding fluorescent proteins. Bioconjugate Chemistry 30: 959-965. DOI: 10.1021/acs.bioconjchem.9b00097

SUBMITTED PAPERS

The following papers have been submitted for publication in peer-reviewed journals.

Programmable Two-Dimensional Nanocrystals Assembled from POSS-Containing Peptoids as Highly Efficient Artificial Light-Harvesting Systems. 
Wang, M., S. Yang, S. Zhang, X. Zhang, X. Cai, Y. Lin, J.J. De Yoreo, and C-L Chen

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Ion-Dependent Protein-Surface Interactions from Intrinsic Solvent Response
Prelesnik, J., R.G. Alberstein, S. Zhang, H. Pyles, D. Baker, J. Pfaendtner, J.J. De Yoreo, F.A. Tezcan, R.C. Remsing, and C.J. Mundy

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Solid-Binding Proteins: Bridging Synthesis and Function in Hybrid and Hierarchical Materials Fabrication

Pushpavanam, K., J. Ma, Y. Cai, N.Y. Naser, and F. Baneyx

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Decoding Biomineralization One Amino Acid at a Time: Influence of Silica-Binding Proteins on the Morphology of Bioprecipitated Titania in a Diffusion-Controlled Setup

Pushpavanam, K., B. Hellner, and F. Baneyx

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Rotational States and Transition Mechanisms of Surface-Adsorbed Proteins

Zhang, S., R. Sadre, B.A. Legg, H. Pyles, T. Perciano, E.W. Bethel, D. Baker, O. Rübel, and J.J. De Yoreo

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Strong Coupling Between Silver Nanoparticles and Hybrid Photon-Exciton Fano Resonances in Two-Dimensional Organic-Inorganic Perovskite Thin Films

Muckel, F., K.N. Guye, S.M. Gallagher, Y. Liu, and D.S. Ginger

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Exploring Particle Dynamics During Self-Organization Processes via Rotationally Invariant Latent Representations

Kalinin, S.V., S. Zhang, M. Valleti, H. Pyles, D. Baker, J.J. De Yoreo, and M. Ziatdinov

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Hierarchical Nanomaterials Assembled from Sequence-Defined Synthetic Polymers

Li, Z., B. Cai, W. Yang, and C-L Chen