44. Jian, T., Y. Zhou, P. Wang, W. Yang, P. Mu, X. Zhang, and C-L Chen. (In press). Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities.



43. Monahan, M., M. Homer, S. Zhang, R. Zheng, C-L Chen, J.J. De Yoreo, and B.M. Cossairt. (In press). Impact of nanoparticle size and surface chemistry on peptoid self-assembly.

42. Zhang, S., R. Sadre, B.A. Legg, H. Pyles, T. Perciano, E.W. Bethel, D. Baker, O. Rubel, and J.J. De Yoreo. (2022). Rotational dynamics and transition mechanisms of surface-adsorbed proteins. Proceedings of the National Academy of Sciences 119: 1-10. DOI: 10.1073/pnas.2020242119

41. Jin, B., F. Yan, X. Qi, B. Cai, J. Tao, X. Fu, S. Tan, P. Zhang, J. Pfaendtner, N.Y. Naser, F. Baneyx, X. Zhang, J.J. De Yoreo, and C-L Chen. (2022). Peptoid-directed formation of five-fold twinned Au nanostars through particle attachment and facet stabilization. Angewandte Chemie 61: 1-11. DOI: 10.1002.anie.202201980

40. Ziatdinov, M., A. Ghosh, and S.V. Kalinin. (2022). Physics makes the difference: Bayesian optimization and active learning via augmented Gaussian process. Machine Learning Science and Technology 3: 1-10. DOI: 10.1088/2632-2153/ac4baa

39. Qi, X., Y. Zhao, K. Lachowski, J. Boese, Y. Cai, O. Dollar, B. Hellner, L. Pozzo, J. Pfaendtner, J. Chun, F. Baneyx, and C.J. Mundy. (2022). Predictive theoretical framework for dynamic control of bioinspired hybrid nanoparticle self-assembly. ACS Nano 16: 1919-1928. DOI: 10.1021/acsnano.1c04923

38. Li, Z., D.K. Tran, M. Nguyen, T. Jian, F. Yan, S.A. Jenekhe, and C-L Chen. (2022). Amphiphilic peptoid directed self-assembly of oligoanilines into highly crystalline conducting nanotubes. Macro-Molecular Rapid Communications 43: 1-9. DOI: 10.1002/marc.202100639

37.Zhao, M., K.J. Lachowski, S. Zhang, S. Alamdari, J. Sampath, P. Mu, C.J. Mundy, J. Pfaendtner, J.J. De Yoreo, C-L Chen, L.D. Pozzo, and A.L. Ferguson. (2022). Hierarchical self-assembly pathways of peptoid helices and sheets. Biomacromolecules 23: 992-1008. DOI: 10.1021/acs.biomac.1c01385

36.Morozovska, A.N., E.A. Eliseev, A. Biswas, N.V. Morozovsky, and S.V. Kalinin. (2021). Effect of surface ionic screening on polarization reversal and phase diagrams in thin antiferroelectric films for information and energy storage. Physical Review Applied 16: 1-18. DOI: 10.1103/PhysRevApplied.16.044053


35.Biswas, A., A.N. Morozovska, M. Ziatdinov, E.A. Eliseev, and S.V. Kalinin. (2021). Multi-objective Bayesian optimization of ferroelectric materials with interfacial control for memory and energy storage applications. Journal of Applied Physics 130: 1-20. DOI: 10.1063/5.0068903

34.Zhao, M. (2021). Hierarchical assemblies of polypeptoids for rational design of advanced functional nanomaterials. Biopolymers 112: 1-14. DOI: 10.1002/bip.23469

33. Zhu, J., N. Avakyan, A. Kakkis, A. Hoffnagle, K.  Han, Y. Li, Z. Zhang, T. Choi, Y. Na, C-J Yu, and F.A. Tezcan. (2021). Protein assembly by design. Chemical Reviews 121: 13701-13796. DOI: 10.1021/acs.chemrev.1c00308

32. Li, Z., B. Cai, W. Yang, and C-L Chen. (2021). Hierarchical nanomaterials assembled from peptoids and other sequence-defined synthetic polymers. Chemical Reviews: 121: 14031-14087. DOI: 10.1021/acs.chemrev.1c00024

31. Lee, D.C., K.N. Guye, R.K. Paranji, K. Lachowski, L.D. Pozzo, D.S. Ginger, and S.H. Pun. (2021). Dual-stimuli responsive single-chain polymer folding via intrachain complexation of tetramethoxyazobenzene and β-cyclodextrin. Langmuir 37: 10126-10134. DOI: 10.1021/acs.langmuir.1c01442

30. Muckel, F., K.N. Guye, S.M. Gallagher, Y. Liu, and D.S. Ginger. (2021). Tuning hybrid exciton-photon fano resonances in two-dimensional organic-inorganic perovskite thin films. Nano Letters 21: 6124-6131. DOI: 10.1021/acs.nanolett.1c01504

29. Guye, K.N., H. Shen, M.Y. Yaman, G.Y. Liao, D. Baker, and D.S. Ginger. (2021). Importance of substrate-particle repulsion for protein-templated assembly of metal nanoparticles. Langmuir 37: 9111-9119. DOI: 10.1021/acs.langmuir.1c01194

28. Yaman, M.Y., K.N. Guye, M. Ziatdinov, H. Shen, D. Baker, S.V. Kalinin, and D.S. Ginger. (2021). Alignment of Au nanorods along de novo designed protein nanofibers studied with automated image analysis. Soft Matter 17: 6109-6115. DOI: 10.1039/D1SM00645B

27. Yang, W., Q. Yin, and C-L Chen. (2021). Designing sequence-defined peptoids for biomimetic control over inorganic crystallization. Chemistry of Materials 33: 3047-3065. DOI: 10.1021/acs.chemmater.1c00243

26. Prelesnik, J.L., 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. (2021). Ion-dependent protein-surface interactions from intrinsic solvent response. Proceedings of the National Academy of Sciences 118: 1-9. DOI: 10.1073/pnas.2025121118

25. Pushpavanam, K., B. Hellner, and F. Baneyx. (2021). Interrogating biomineralization one amino acid at a time: Amplification of mutational effects in protein-aided titania morphogenesis through reaction-diffusion control. Chemical Communications 57: 4803-4806. DOI: 10.1039/D1CC01521D

24. Pushpavanam, K., J. Ma, Y. Cai, N.Y. Naser, and F. Baneyx. (2021). Solid-binding proteins: Bridging synthesis, assembly, and function in hybrid and hierarchical materials fabrication. Annual Review of Chemical and Biomolecular Engineering. 12: 333-357. DOI: 10.1146/annurev-chembioeng-102020-015923

23. Wang, M., Y. Song, S. Zhang, X. Zhang, X. Cai, Y. Lin, J.J. De Yoreo, and C-L Chen. (2021). Programmable two-dimensional nanocrystals assembled from POSS-containing peptoids as highly efficient artificial light-harvesting systems. Science Advances 7: 1-8. DOI: 10.1126/sciadv.abg1448

22. Kalinin, S.V., S. Zhang, M. Valetti, H. Pyles, D. Baker, J.J. De  Yoreo, and M. Ziatdinov. (2021). Disentangling rotational dynamics and ordering transitions in a system of self-organizing protein nanorods via rotationally invariant latent representations. ACS Nano 15: 6471-6480. DOI: 10.1021/acsnano.0c08914

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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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


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

Controlling Mineralization with Protein-Functionalized Peptoid Nanotubes

Ma, J., B. Jin, K. Guye, Md.E. Chowdhury, C-L Chen, J.J. De Yoreo, and F. Baneyx

Learning and Predicting Photonic Responses of Plasmonic Nanoparticle Assemblies via Dual Variational Autoencoders

Yaman, M.Y., S.V. Kalinin, K.N. Guye, D.S. Ginger, and M. Ziatdinov

Designing Sequence-Defined  Peptoids for Fibrillar Self-Assembly and Silicification

Yang, W., Y. Zhou, B. Jin, X. Qi, B. Cai, Q. Yin, J. Pfaendtner, J.J. De Yoreo, and C-L Chen

Multivariate Analysis of Peptide-Driven Nucleation and Growth of Au Nanoparticles

Lachowski, K., K. Vaddi, L. Pozzo, F. Baneyx, and N. Naser.

Thermodynamic Basis for Stabilization of Helical Peptoids by Chiral Sidechains

Alamdari, S., K. Torkelson, X. Wang, C-L Chen, A. Ferguson, and J. Pfaendtner

Semi-Supervised Learning of Images with Strong Rotational Disorder: Assembling Nanoparticle Libraries

Ziatdinov, M.A., M.Y. Yaman, Y. Liu, D. Ginger, and S.V. Kalinin