31. A. Krasley+, S. Chakraborty+, L. Vukovic*, A. Beyene* Mechanisms of Catechol-Induced Optical Modulations in ssDNA Functionalized Single Wall Carbon Nanotubes, accepted (2024).

30. D. Wilson+, S. Chakraborty+, U. H. Sweety, H. Sharifan, J. A. Hernandez, J. C. White, L. Vukovic*, M. Narayan*. An atomic, molecular and cellular understanding of PFDA-associated structural, functional and behavioral outcomes across biological assemblies, Environmental Science and Ecotechnology, accepted (2024).

29. S. S. Nalige, P. Galonska, P. Kelich, L. Sistemich, C. Herrmann, L. Vukovic, S. Kruss, M. Havenith. THz coupling in carbon nanotube sensors modulates their fluorescence, Nat. Commun., 15, 6770 (2024).

28. G. Molina-Aguirre, S. Chakraborty, J. Kosmrlj, L. Vukovic*, B. Pinter*. Photophysics of molecular probes for amyloid-beta detection: computational insights into roles of probe linker and functional groups, J. Phys. Chem. A, 128, 7055-7067 (2024).

27. P. Kelich, J. Adams, S. Jeong, N. Navarro, M. P. Landry, L. Vukovic*. Predicting Serotonin Detection with DNA-Carbon Nanotube Sensors Across Multiple Spectral Wavelengths, J. Chem. Inf. Model.,10, 3992-4001 (2024).

26. A. Karim, A. Yadav, U. H. Sweety, J. Kumar, S. Delgado, J. A. Hernandez, J. C. White, L. Vukovic, M. Narayan. Interfacial interactions between nanoplastics and biological systems: Towards an atomic and molecular understanding of plastics-driven cellular dyshomeostasis, ACS Appl. Mater. Interfaces, 16, 20, 25740-25756 (2024).

25. A. Yadav, L. Vukovic*, M. Narayan*. An Atomic and Molecular Insight into how PFOA Reduces alpha-Helicity, Compromises Substrate Binding, and Creates New Binding Pockets in a Model Globular Protein, J. Am. Chem. Soc.,146, 18, 12766-12777 (2024).

24. S. An, Y. Suh, P. Kelich, D. Lee, L. Vukovic, S. Jeong. Directed Evolution of Near-infrared Serotonin Nanosensors with Machine Learning-based Screening, Nanomaterials, 14, 247 (2024).

23. P. Girnt, G. Molina-Aguirre, D. Gomez Bustos, C. Sandoval-Pauker, L. Vukovic, B. Pinter. Fusion position-dependent aromatic transitions of ligand backbone rings for controlling the redox energetics of photoredox catalysts, Inorg. Chem. 63, 2586-2596 (2024).

22. Q. Wang, N. Liu, Y. Deng, Y. Guan, H. Xiao, T. A. Nitka, H. Yang, A. Yadav, L. Vukovic, I. I. Mathews, X. Chen, C.-Y. Kim. Triepoxide formation by a flavin-dependent monooxygensase in monensin biosynthesis, Nat. Commun. 14, 6273 (2023).

21. S. Chakraborty, E. Ebarguen, K. E. Chacon, M. Petkovic, L. Vukovic*. Base Stacking and Sugar Orientations Contribute to Chiral Recognition of Single-Walled Carbon Nanotubes by Short ssDNAs, J. Phys. Chem. C, 127, 19759-19768 (2023).

20. J. Y. K. Wong, A. Ekanayake, S. Kharchenko, S. Kirberger, R. Qiu, P. Kelich, S. Sarkar, J. Li, K. Fernandez, E. Alvizo-Paez, E. R. Alvizo-Paez, J. Miao, S. Kalhor-Monfared, J. J. Dwyer, H. Kangm H. Choi, J. M. Nuss, J. Vederas, Y.-S. Lin, M. S. Macauley, L. Vukovic, W. Pomerantz, R. Derda. Genetically-Encoded Discovery of Perfluoroaryl-Macrocycles that Bind to Albumin and Exhibit Extended Circulation in-vivo, Nat. Commun. 14, 5654 (2023).

19. A. Yadav+, P. Kelich+, N. E. Kallmyer, N. F. Reuel*, L. Vukovic*. Characterizing the Interactions of Cell Membrane-Disrupting Peptides with Lipid-Functionalized Single-Walled Carbon Nanotube Systems for Antimicrobial Screening, ACS Appl. Mater. Interfaces, 15, 24084 - 24096 (2023). (+ authors contributed equally)

18. P. Kelich+, H. Zhao+, J. R. Orona, L. Vukovic*. BinderSpace: A Package for Sequence Space Analyses for Datasets of Affinity-Selected Oligonucleotides and Peptide-Based Molecules, J. Comput. Chem. 44, 1836-1844 (2023). (+ authors contributed equally)

17. D. A. Hastman+, P. Chaturvedi+, E. Oh, J. S. Melinger, I. L. Medintz, L. Vuković*, S. A. Díaz*. Mechanistic understanding of DNA denaturation in nanoscale thermal gradients created by femtosecond excitation of gold nanoparticles, ACS Appl. Mater. Interfaces, 14, 3404-3417 (2022). (+ authors contributed equally)

16. P. Kelich+, S. Jeong+, N. Navarro+, J. Adams, X. Sun, H. Zhao, M. Landry*, L. Vuković*. Discovery of DNA-Carbon Nanotube Sensors for Serotonin with Machine Learning and Near-Infrared Fluorescence Spectroscopy, ACS Nano, 16, 736-745 (2022). (+ authors contributed equally)

15. P. Chaturvedi, P. Kelich, T. A. Nitka, L. Vuković*. Computational modeling of virucidal inhibition mechanism for broad-spectrum antiviral nanoparticles and HPV16 capsid segments, J. Phys. Chem. B, 125, 13122-13131 (2021).

14. A. Ekanayake, L. Sobze, P. Kelich, J. Youk, N. Bennett, R. Mukherjee, A. Bhardwaj, F. Wuest, L. Vuković, R. Derda. Genetically encoded fragment-based discovery from phage-displayed macrocyclic libraries with genetically-encoded unnatural pharmacophores, J. Am. Chem. Soc. 143, 5497-5507 (2021).

13. A. A. Alizadehmojarad*, B. Fazelabdolabadi, L. Vuković*, Surfactant-controlled mobility of oil droplets in mineral nanopores, Langmuir, 36, 12061 (2020).

12. P. Chaturvedi, Y. Han, P. Král*, L. Vuković*, Adaptive evolution of peptide inhibitors for mutating SARS-CoV-2, Adv. Theory Simul. 3, 2000156 (2020).

11. A. A. Alizadehmojarad, X, Zhou, A. G. Beyene, K. E. Chacon, Y. Sung, R. L. Pinals, M. P. Landry*, L. Vuković*, Binding affinity and conformational preferences influence kinetic stability of short oligonucleotides on carbon nanotubes, Adv. Mat. Inter. 7, 2000353 (2020).

10. S. T. Jones, V. Cagno, M. Janecek, D. Ortiz, N. Gasilova, J. Piret, M. Gasbarri, D. A. Constant, Y. Han, L. Vuković, P. Král, L. Kaiser, S. Huang, S. Constant, K. Kirkegaard, G. Boivin, F. Stellacci, C. Tapparel, Modified cyclodextrins as broad-spectrum antivirals, Science Advances, 6 , eaax9318 (2020).

9. P. Chaturvedi, L. Vuković*, Structural properties of small single-stranded circular nucleic acids, J. Phys. Chem. B, 123 , 8216 (2019).

8. T. A. Nitka, P. Král, L. Vuković*, Configurations of nanocubes floating and clustering on liquid surfaces, J. Phys. Chem. Lett., 10, 3592 (2019).

7. R. Nissler, F. Mann, P. Chaturvedi, J. Horlebein, D. Meyer, L. Vuković, S. Kruss, Quantification of the number of adsorbed DNA molecules on single-walled carbon nanotubes, J. Phys. Chem. C, 123, 4837 (2019).

6. A G. Beyene+, A. A. Alizadehmojarad+, G. Dorlhiac, A. M. Streets, P. Král, L. Vuković*, M. P. Landry*, Ultralarge modulation of fluorescence by neuromodulators in carbon nanotubes with self-assembled oligonucleotide rings, Nano Lett. 18 , 6995 (2018). (+ co-first authors)

5. E. Polo, T. T. Nitka, E. Neubert, L. Erpenbeck, L. Vuković, S. Kruss, Control of integrin affinity by confining RGD peptides on fluorescent carbon nanotubes, ACS Appl. Mater. Interfaces, 10, 17693-17703 (2018).

4. V. Cagno, P. Andreozzi, M. D'Alicarnasso, P. J. Silva, M. Mueller, M. Galloux, R. Le Goffic, S. T. Jones, M. Vallino, J. Hodek, J. Weber, S. Sen , Dr. E. R. Janecek, A. Bekdemir, B. Sanavio, C. Martinelli, M. Donalisio, M.-A. Rameix-Welti, Y. Han, L. Kaiser, L. Vuković, P. Král , C. Tapparel, S. Krol, D. Lembo, F. Stellacci, Inducing irreversible viral changes: a novel approach towards broad-spectrum virucidal drugs, Nature Materials, 17, 195-203 (2018).

3. S. Gorle, Y. Pan, Z. Sun, L. S. Shlyakhtenko, R. S. Harris, Y. L. Lyubchenko*, L. Vuković*, Computational Model and Dynamics of Monomeric Full-Length APOBEC3G, ACS Central Science, 3, 1180-1188 (2017).

2. T. Udayabhaskararao, T. Altantzis, L. Houben, M. Coronado-Puchau, J. Langer, R. Popovitz-Biro, L. M. Liz-Marzán, L. Vuković, P. Král, S. Bals, R. Klajn, Tunable Porous Nanoallotropes Prepared from Binary Nanoparticle Superlattices Self-Assembled at the Solvent-Air Interface, Science, 358, 514-518 (2017).

1. S. Kruss, D. P. Salem, L. Vuković, B. Lima, E. R. Vander Ende, E. S. Boyden, M. S. Strano. High Resolution Imaging of Cellular Dopamine Efflux Using a Fluorescent Nanosensor Array, Proc. Natl. Acad. Sci. USA 114, 1789-1794 (2017) .

25. S. Sen, L. Vuković*, P. Král*, Computational screening of nanoparticles coupling to AB40 peptides and fibrils, Sci. Rep. 9, 17804 (2019).

24. L. Zheng, H. Zhao, Y. Han, L. Vuković, J. Mecinović, P. Král, and W. T. S. Huck, Catalytic transport of molecular cargo using diffusive binding along a polymer track, Nat. Chem. 11, 359 (2019).

23. S. Mondal, G. Jacoby, M. R. Sawaya, Z. A. Arnon, L. Adler-Abramovich, L. Vuković, P. Rehak, L. J. W. Shimon, P. Král, R. Beck, D. Eisenberg, and E. Gazit, Transition of metastable cross-alpha crystals into cross-betta fibrils by beta-turn flipping, J. Am. Chem. Soc. 141, 363 (2019).

22. S. Shaham-Niv, P. Rehak, D. Zaguri, A. Levin, L. Adler-Abramovich, L. Vuković, P. Král, E. Gazit, Differential inhibition of metabolite amyloid formation by generic fibrillation-modifying polyphenols, Comm. Chem. 1, 25 (2018).

21. S. Sen, Y. Han, P. Rehak, L. Vuković*, and P. Král*, Computational Studies of Micellar and Nanoparticle Nanomedicines, Chem. Soc. Rev., 47, 3849-3860 (2018).

20. S. Shaham-Niv, P. Rehak, L. Vuković, L. Adler-Abramovich, P. Král, E. Gazit, Formation of apoptosis-inducing amyloid fibrils by tryptophan, Isr. J. Chem. 57, 729-737 (2017).

19. Y. Zhang*, L. Vuković*, T. Rudack*, W. Han, K. Schulten, Recognition of poly-ubiquitins by the proteasome through protein re-folding guided by electrostatic and hydrophobic interactions. J. Phys. Chem. B 120, 8137-8146 (2016). (* equal contribution)

18. L. Vuković, C. Chipot, D. L. Makino, E. Conti, K. Schulten, Molecular mechanism of processive 3' to 5' RNA translocation in the active subunit of the RNA exosome complex. J. Am. Chem. Soc. 138, 4069-4078 (2016).

17. X. Wang, L. Vuković, H. R. Koh, K. Schulten, S. Myong, Dynamic profiling of double-stranded RNA binding proteins. Nucl. Acids Res. 43, 7566-7576 (2015).

16. M. Landry, L. Vuković, S. Kruss, G. Bisker, A. M. Landry, R. Jain, K. Schulten, M. S. Strano, Comparative dynamics and sequence dependence of DNA and RNA binding to single walled carbon nanotubes, J. Phys. Chem. C, 119, 10048-10058 (2015).

15. Y. Qiu, H. Niu, L. Vuković, P. Sung, S. Myong, Molecular mechanism of resolving trinucleotide repeat hairpin by helicases, Structure, 23, 1018-1027 (2015).

14. L. Vuković, H. R. Koh, S. Myong, K. Schulten, Substrate recognition and specificity of double-stranded RNA binding proteins. Biochemistry, 53, 3457 (2014).

13. C. R. James, A. M. Rush, T. Insley, L. Vuković, P. Král, N. C. Gianneschi, Poly(oligonucleotide). J. Am. Chem. Soc. 136, 11216 (2014).

12. L. Vuković, E. Vokac, P. Král, Molecular Friction-Induced Electroosmotic Phenomena in Thin Neutral Nanotubes. J. Phys. Chem. Lett. 5, 2131 (2014).

11. L. Vuković, A. Madriaga, A. Kuzmis, A. Banerjee, A. Tang, K. R. Tao, N. Shah, P. Král, H. Onyuksel, Solubilization of Therapeutic Agents in Micellar Nanomedicines. Langmuir, 29, 15747 (2013).

10. L. Vuković, C. F. Burmeister, P. Král, G. Groenhof, Control Mechanisms of Photoisomerization in Protonated Schiff Bases. J. Phys. Chem. Lett., 4, 1005 (2013).

9. H. Chan, A. Demortiere, L. Vuković, P. Král, C. Petit, Colloidal Nanocube Supercrystals Stabilized by Multipolar Coulombic Coupling. ACS Nano, 6, 4203 (2012).

8. J. W. Bae, R. M. Pearson, N. Patra, S. Sunoqrot, L. Vuković, P. Král, S. Hong, Dendron-mediated Self-assembly of Highly PEGylated Block Copolymers: A Potential Nanocarrier Platform. Chem. Comm. 47, 10302 (2011).

7. L. Vuković, S. P. Drake, F. A. Khatib, A. Madriaga, K. S. Brandenburg, P. Král, H. Onyuksel, Highly PEGylated Sterically Stabilized Micelles in Aqueous Media. J. Am. Chem. Soc. 133, 13481 (2011).

6. J. He, X.-M. Lin, H. Chan, L. Vuković, P. Král, H. Jaeger, Diffusion and Filtration Properties of Self-Assembled Gold Nanocrystal Membranes. Nano Letters 11, 2430 (2011).

5. P. Král, L. Vuković, N. Patra, B. Wang, A. Titov, Control of rotary motion at the nanoscale: Motility. self-assembly, actuation, J. Nanosci. Lett. 1, 128 (2011).

4. L. Vuković and P. Král, Coulombically Driven Rolling of Nanorods on Water. Phys. Rev. Lett. 103, 246103 (2009), highlighted in Nature Nanotechnology (2009) and Virtual Journal of Nanoscale Sci. & Technol. Vol. 21, Issue 25.

3. B. Wang, L. Vuković, and P. Král, Nanoscale Rotary Motors Driven by Electron Tunneling. Phys. Rev. Lett. 101, 186808 (2008), highlighted in Nature Nanotechnology (2008).

2. L. Vukovic, C. J. Jameson, D. N. Sears, Intermolecular hyperfine tensor for Xe@O2. Density and temperature dependence of Xe chemical shifts in oxygen gas. Mol. Phys. 104 , 1217 (2006).

1. D. N. Sears, L. Vukovic, C. J. Jameson, Xe nuclear magnetic resonance line shapes in channels decorated with paramagnetic centers. J. Chem. Phys. 125, 114708 (2006).