Publications

in preparation

Dasetty, S., Coffman, R., Bidone, T.C., Ferguson, A.L. Resolution of minimum free energy activation pathway of 𝛼𝐼𝐼𝑏𝛽3 using deep generative modeling and finite temperature string method.

submitted

Tribello, G.A., Bonomi, M., Bussi, G., Camilloni, C.,Armstrong, B.I., Arsiccio, A. Aureli, S., Ballabio, F., Bernetti, M., Bonati, L., Brookes, S.G.H., Brotzakis, Z.F., Capelli, R., Ceriotti, M., Chan, K.-T., Cossio, P., Dasetty, S., Donadio, D., Ensing, B., Ferguson, A.L., Gale, J.D., Gervasio, F.L., Giorgino, T., Herringer, N.S.M., Hocky, G.M., Hoff, S.E., Invernizzi, M., Languin-Catto¨en, O., Leone, V., Limongelli, V., Lopez-Acevedo, O., Marinelli, F., Martinez, P.F., Angelos, M.M., Murtada, M.H., Parrinello, M., Piaggi, P.M., Pietropaolo, A., Pietrucci, F., Pipolo, S., Pritchard, C., Raiteri, P., Raniolo, S., Rapetti, D., Rizzi, V., Rydzewski, J., Salvalaglio, M., Schran, C., Seal, A., Shayesteh Zadeh, A., F. D. Silva, T., Spiwok, V., Stirnemann, G., Sucerquia, D., Tiwary, P., Valsson, O., Vendruscolo, M., Voth, G.A., White, A.D., Wu., J., PLUMED Tutorials: a collaborative, community-driven learning ecosystem.(submitted, 2024). Preprint DOI:https://doi.org/10.48550/arXiv.2412.03595

Wu, J., Dasetty, S., Beckett, D., Wang, Y., Skóra, T., Bidone, T.C., Ferguson, A.L., Voth, G.A. Data-Driven Equation-Free Dynamics Applied to Many-Protein Complexes: The Microtubule Tip Relaxation (submitted, 2024). Preprint DOI:https://biorxiv.org/cgi/content/short/2024.10.10.617682v1

Wang, Y. Jang, H.-J., Topel, M., Dasetty, S., Liu, Y., Ibrahim, M., Van Buren, J., Rozyyev, V., Ouyang, E., Zhuang, W., Pu, H., Lee, S.S.S. Elam, J.W., Ferguson, A.L., Darling, S.B., Chen, J. Reversible ppt-level detection of perfluorooctane sulfonic acid in tap water using field-effect transistor sensors (submitted, 2024). Preprint DOI:https://doi.org/10.26434/chemrxiv-2024-6q6q5

Published

2024

  1. Rico PF, Schneider L, Perez-Lemus G, Alessandri R, Dasetty S, Menéndez CA, Wu Y, Jin Y, Nguyen T, Parker J, Ferguson AL, Whitmer J, de Pablo JJ. PySAGES: flexible, advanced sampling methods accelerated with GPUs. npj Comput. Mater. (2024). DOI:https://doi.org/10.1038/s41524-023-01189-z

    2. 2023

  2. Dasetty S, Bidone, TC., Ferguson AL. Data-driven prediction of $\alpha_{IIb}\beta_{3}$ integrin activation pathways using nonlinear manifold learning and deep generative modeling. Biophys. J.: Special Issue in Machine Learning (2023). DOI:https://doi.org/10.1016/j.bpj.2023.12.009

  3. Dasetty S, Topel M., Tang Y., Wang Y., Jonas E., Darling S., Chen J., Ferguson AL. Data-driven discovery of linear molecular probes with optimal selective affinity for PFAS in water. J. Chem. Eng. Data: Special Issue in Machine Learning (2023). DOI:https://doi.org/10.1021/acs.jced.3c00404

  4. Herringer N.S.M, Dasetty S, Gandhi D, Lee J and Ferguson AL, Permutationally Invariant Networks for Enhanced Sampling (PINES): Discovery of Multi-Molecular and Solvent-Inclusive Collective Variables. arXiv preprint https://arxiv.org/pdf/2308.08680.pdf DOI:https://doi.org/10.48550/arXiv.2308.08680

  5. Dasetty S, Zajac J, Zhang Y, Sarupria S. EMI Series Exploitation of active site flexibility-low temperature activity relation for engineering broad range temperature active enzymes. Molecular Systems Design & Engineering. Mol. Syst. Des. Eng. (2023). DOI:https://doi.org/10.1039/D3ME00013C

2022

  1. Dasetty S., Coropceanu I., Portner J., Li J., de Pablo J. J., Talapin D.V. and Ferguson A.L. Active Learning of Polarizable Nanoparticle Phase Diagrams for the Guided Design of Triggerable Self-Assembling Superlattices. Mol. Syst. Des. Eng. (2022). DOI:https://doi.org/10.1039/D1ME00187F (Featured in MSDE recent HOT articles collection)

2021

  1. Wang W., Dasetty S., Sarupria S., Blenner M. Rational engineering of low temperature activity in thermoalkalophilic Geobacillus thermocatenulatus lipase. Biochem. Eng. J. 2021 Jun 16. DOI:https://doi.org/10.1016/j.bej.2021.108093

  2. Dasetty S. Sarupria S. Advancing Rational Control of Peptide–Surface Complexes. The Journal of Physical Chemistry B. 2021 Mar 4. DOI:https://doi.org/10.1021/acs.jpcb.0c10740

<2020

  1. Dasetty S., Meza-Morales PJ, Getman RB, Sarupria S. Simulations of interfacial processes: recent advances in force field development. Current Opinion in Chemical Engineering. 2019 Mar 1;23:138-45. DOI:https://doi.org/10.1016/j.coche.2019.04.003

  2. Dasetty S., Barrows JK, Sarupria S. Adsorption of amino acids on graphene: assessment of current force fields. Soft matter. 2019;15(11):2359-72. DOI:https://doi.org/10.1039/C8SM02621A

  3. Dasetty S., Blenner M.A., Sarupria S. Engineering Lipases: walking the fine line between activity and stability. Materials Research Express. 2017 Nov;4(11):114008. DOI:https://doi.org/10.1088/2053-1591/aa9946

  4. Sengupta B, Gregory WE, Zhu J, Dasetty S., Karakaya M, Brown JM, Rao AM, Barrows JK, Sarupria S, Podila R. Influence of carbon nanomaterial defects on the formation of protein corona. RSC advances. 2015;5(100):82395-402. DOI:https://doi.org/10.1039/C5RA15007H

  5. Sahoo PK, Prajwal BP, Dasetty S., John M, Newalkar BL, Choudary NV, Ayappa KG. Influence of exhaust gas heating and L/D ratios on the discharge efficiencies for an activated carbon natural gas storage system. Applied energy. 2014 Apr 15;119:190-203. DOI:https://doi.org/10.1016/j.apenergy.2013.12.057