53. M.Y. Yaman, S.V. Kalinin, K.N. Guye, D.S. Ginger, and M. Ziatdinov. (In press). Learning and predicting photonic responses of plasmonic nanoparticle assemblies via dual variational autoencoders. Small.

​

52. Biswas, A., R. Vasudevan, M. Ziatdinov, and S.V. Kalinin. (2023). Optimizing training trajectories in variational autoencoders via latent Bayesian optimization approach. Machine Learning Science and Technology 4: 1-15. DOI: 10.1088/2632-2153/acb316.

​

​

51. Alberstein, R.G., J.L. Prelesnik, E. Nazouki, S. Zhang, J.J. De Yoreo, J. Pfaendtner, F.A. Tezcan, and C.J. Mundy. (2023). Discrete orientations of interfacial waters direct crystallization of mica-binding proteins. Journal of Physical Chemistry Letters 14: 80-87. DOI: 10.1021/acs.jpclett.2c02948.

​

​

50. Yang, W., Y. Zhou, B. Jin, X. Qi, B. Cai, Q. Yin, J. Pfaendtner, J.J. De Yoreo, and C-L Chen. (2023). Designing sequence-defined peptoids for fibrillar self-assembly and silicification. Journal of Colloid and Interface Science 634: 450-459. DOI: 10.1016/j.jcis.2022.11.136.

​

​

49. Shao, L., J. Ma, J.L. Prelesnik, Y. Zhou, M. Nguyen, M. Zhao, S.A. Jenekhe, S.V. Kalinin, A.L. Ferguson, J. Pfaendtner, C.J. Mundy, J.J. De Yoreo, F. Baneyx, and C-L Chen. (2022). Hierarchical materials from high information content macromolecular building blocks: Construction, dynamic interventions, and prediction. Chemical Reviews 122: 17397-17478. DOI: 10.1021/acs/chemrev.2c00220.

​

​

48. Valetti, M., R.K. Vasudevan, M.A. Ziatdinov, and S.V. Kalinin. (2022). Bayesian optimization in continuous spaces via virtual process embeddings. Digital Discovery 1: 910-925. DOI: 10.1039/D2DD00065B.

 

 

47. Ma, J. B. Jin, K.N. Guye, M.E. Chowdhury, N.Y. Naser, C-L Chen, J.J. De Yoreo, and F. Baneyx. (2022). Controlling mineralization with protein-functionalized peptoid nanotubes. Advanced Materials: 1-11. DOI: 10.1002/adma.202207543.

 

 

46. Vaddi,  K., H.T. Chiang, and L.D. Pozzo. (2022). Autonomous retrosynthesis of gold nanoparticles via spectral shape matching. Digital Discovery 1: 502-510. DOI: 10.1039/D2DD00025C.

​

​

45. Lachowski, K., K. Vaddi,  N. Naser, F. Baneyx, and L.D. Pozzo. (2022). Multivariate analysis of peptide-driven nucleation and growth of Au nanoparticles. Digital Discovery 1: 427-439. DOI: 10.1039/D2DD00017B.

 

 

44. Jian, T., Y. Zhou, P. Wang, W. Yang, P. Mu, X. Zhang, X. Zhang, and C-L Chen. (2022). Highly stable and tunable peptoid/hemin enzymatic mimetics with natural peroxidase-like activities. Nature Communications 13: 1-13. DOI: 10.1038/s41467-022-30285-9.

 

 

43. Monahan, M., M. Homer, S. Zhang, R. Zheng, C-L Chen, J.J. De Yoreo, and B.M. Cossairt. (2022). Impact of nanoparticle size and surface chemistry on peptoid self-assembly. ACS Nano 16: 8095-8106. DOI: 10.1021/acsnano.2c01203. 

​

​

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