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Publications: Publications

PUBLICATIONS

71. Valleti, M., R.K. Vasudevan, M.A. Ziatdinov, and S.V. Kalinin. 2024. Deep kernel methods learn better: From cards to process optimization. Machine Learning Science & Technology 5(1): 015012. DOI: 10.1088/2632-2153/ad1a4f

70. Shao, L., D. Hu, S.-L. Zheng, T.K.H. Trinh, W. Zhou, H. Wang .Y. Zong, C. Li., and C-L Chen. (2024). Hierarchical self-assembly of multidimensional functional materials from sequence-defined peptoids. Angew. Chem. Int. Ed. (In press)

 

 

69Cai, Y., N. Naser, J. Ma, and. Baneyx. (2024). Precision loading and delivery of molecular cargo by size-controlled coacervation of gold nanoparticles functionalized with elastin-like peptides. (2024). Biomacromolecules 25:2390-2398.  DOI: 10.1021/acs.biomac.3c01312

68Zheng, R., M. Zhao, J.S. Du, T.R. Sudarshan, Y. Zhou, A.K. Paravastu, J. J. De Yoreo, A.L. Ferguson, and C-L Chen. (2024). Assembly of short amphiphilic peptoids into nanohelices with controllable supramolecular chirality. (2024). Nature Communications (In press).

 

 

67. Shen, H., E.M. Lynch, S. Akkineni, J.L. Watson, J. Decarreau, N.P. Bethel, I. Benna, W. Sheffler, D. Farrell, F. DiMaio, E. Derivery, J.J. De Yoreo, J. Kollman, and D. Baker. (2024). De novo design of pH-responsive self-assembling helical protein filaments. (2024). Nature Nanotechnology. DOI: 10.1038/s41565-024-01641-1

66. Smith, B.R., B. Pant, Y. Liu, J-C Yang, S. Jesse, A. Khojandi, S.V. Kalinin, Y. Cao, and R.K. Vasudevan. (2024). Physics-informed models of domain-wall dynamics as a route for autonomous domain wall design via reinforcement learning. (2024). Digital Discovery 3: 456-466. DOI: 10.1039/D3DD00126A

65. Cai, Y., X. Qi, J. Boese, Y. Zhao, B. Hellner, J. Chun, C. Mundy, and F. Baneyx. (2024). Towards predictive control of reversible nanoparticle assembly with solid-binding proteins. Soft Matter 20: 1935-1942. DOI: 10.1039/D4SM00094C

64. Du, J., Y. Bae, and J.J. De Yoreo. Non-classical crystallization in soft and organic materials. (2024). Nature Reviews Materials. DOI: 10.1038/s41578-023-00637-ys

63. Torkelson, K., N.Y. Naser, X. Qi, Z. Li, W. Yang, K. Pushpavanam, C-L Chen, F. Baneyx, and J. Pfaendtner. (2024). Rational design of novel biomimetic sequence-defined polymers for mineralization applications. Chemistry of Materials 36: 786-794. DOI: 10.1021/acs.chemmater.3c02216

62. Lachowski, K.J., H.T. Chiang, K. Torkelson, W. Zhou, S. Zhang, J. Pfaendtner, and L.D. Pozzo. (2023). Anisotropic gold nanomaterial synthesis using peptide facet specificity and timed intervention. Langmuir 39: 15878-15888. DOI: 10.1021/acs.langmuir.3c01577

61. Davila-Hernandez, F.A., B. Jin, H. Pyles, S. Zhang, Z. Wang, T.F. Huddy, A.K. Bera, A. Kang, C-L Chen, J.J. De Yoreo, and D. Baker. (2023). Directing polymorph specific calcium carbonate formation with de novo protein templates. Nature Communications 14: 1-11. DOI: 10.1038/s41467-023-43608-1

60. Yang, W., B. Cai, K.J. Lachowski, Q. Yin, J.J. De Yoreo, L.D. Pozzo, and C-L Chen. (2023). Insights into the biomimetic synthesis of 2D ZnO nanomaterials through peptoid engineering. Journal of Physical Chemistry Letters 14: 9732-9739. DOI: 10.1021/acs.jpclett.3c01882

59. Jin, B., Y. Chen, J. Tao, K.J. Lachowski, M.E. Bowden, Z. Zhang, L.D. Pozzo, N.M. Washton, K.T. Mueller, and J.J. De Yoreo. (2023). Multi-step nucleation of a crystalline silicate framework via a structurally precise prenucleation cluster. Angewandte Chemie 62: 1-7. DOI: 10.1002/anie.202303770

58. Schmid, S.Y., K. Lachowski, H.T. Chiang, L. Pozzo, J.J. De Yoreo, and S. Zhang. (2023). Mechanisms of biomolecular self-assembly investigated through in situ observations of structures and dynamics. Angewandte Chemie 62: 1-29. DOI: 10.1002/anie.202309725

57. Larson, H. and B. Cossairt. (2023). Indium-poly(carboxylic acid) ligand interactions modify InP quantum dot nucleation and growth. Chemistry of Materials 35: 6152-6160. DOI: 10.1021/acs.chemmater.3c01309

56. Alamdari, S. and J. Pfaendtner. (2023). Origins of conformational heterogeneity in peptoid helices formed by chiral N-1 phenylethyl sidechains. Journal of Physical Chemistry B 127: 6163-6170. DOI: 10.1021/acs.jpcb.3c02576

55. Alamdari, S., K. Torkelson, X. Wang, C-L Chen, A. Ferguson, and J. Pfaendtner. (2023). Thermodynamic basis for stabilization of helical peptoids by chiral sidechains. Journal of Physical Chemistry B 127: 6171-6183. DOI: 10.1021/acs.jpcb.3c01913

54. Zhao, M., S. Zhang, R. Zheng, S. Alamdari, C.J. Mundy, J. Pfaendtner, L. Pozzo, C-L Chen, J.J. De Yoreo, and A.L. Ferguson. (2023). Computational and experimental determination of the properties, structure, and stability of peptoid nanosheets and nanotubes. Biomacromolecules 24: 2618-2632. DOI: 10.1021/acs.biomac.3c00107

53. Yaman, M.Y., S.V. Kalinin, K.N. Guye, D.S. Ginger, and M. Ziatdinov. (2023). Learning and predicting photonic responses of plasmonic nanoparticle assemblies via dual variational autoencoders. Small 19: 2205893. DOI: 10.1002/smll.202205893

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

SUBMITTED PAPERS

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

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

Formation, Chemical Evolution, and Solidification of the Calcium Carbonate Dense Liquid Phase

Jin, B., Y. Chen, H. Pyles, M.D. Baer, B.A. Legg, Z. Wang, N.M. Washton, K.T. Mueller, D. Baker, C.J. Mundy, and J.J. De Yoreo

Physics and Chemistry from Parsimonious Representations: Image Analysis via Invariant Variational Autoencoders

Valleti, M., Y. Liu, and S.V. Kalinin

Towards Accelerating Physical Discovery via Non-Interactive and Interactive Multi-Fidelity Bayesian Optimization: Current Challenges and Future Opportunities

Biswas, A., S.M.P. Valleti, R. Vasudevan, M. Ziatdinov, and S. Kalinin

Active Deep Kernel Learning of Molecular Functionalities: Realizing Dynamic Structural Embeddings

Ghosh, A., M. Ziatdinov, and S.V. Kalinin

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