Embedded Files
In Progress
"H2A.Z facilitates Sox2-nucleosome interaction by promoting DNA and histone H3 tail mobility, "Moos, Helen; Patel, Rutika; Flaherty, Sophie; Loverde, Sharon; Nikolova, Evgenia, in prep. Bioarxiv, preprint.
Peer-Reviewed
"Mapping Allosteric Communication in the Nucleosome with Conditional Activity," Augustine Onyema, Chukwuebuka Dikeocha*, Rutika Patel, Jonathan Moussa, Sharon M. Loverde, JCIM, 2026. Link. *undergraduate student
CONDACT (CONDitional ACTivity) code:
Github: https://github.com/CUNY-CSI-Loverde-Laboratory/conditional_activity
Trajectories: https://zenodo.org/records/17193099
"Structural and Thermodynamic Impact of Oncogenic Mutations on the Nucleosome Core Particle," Augustine Onyema*, Chris DiForte*, Rutika Patel, Sebastien Poget, and Sharon M. Loverde, Biophysical Journal, 2025. Link.
Trajectories: https://zenodo.org/records/15725116
"Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling," Rutika Patel and Sharon M. Loverde, JCTC, 2025. Link.
"The need to implement FAIR principles in biomolecular simulations," Amaro et al. Nature Methods, 22, 641-645, 2025. Link.
"Unveiling Nucleosome Dynamics: A Comparative Study Using All-Atom and Coarse-Grained Simulations Enhanced by Principal Component Analysis," Abhik Ghosh Moulick, Rutika Patel, Augustine Onyema, and Sharon M. Loverde, JCP, 162, 6, 2025. Link.
Github: https://github.com/CUNY-CSI-Loverde-Laboratory/GhoshMoulick_2024-
Trajectories: https://zenodo.org/records/14033991
"Conformational dynamics of the nucleosomal histone H2B tails revealed by molecular dynamics simulations," Rutika Patel, Augustine Onyema, Phu Tang, and Loverde, S. M., JCIM, 2024. Link.
Github: https://github.com/CUNY-CSI-Loverde-Laboratory/H2B_N_terminal_tails
"Sequence Dependence in Nucleosome Dynamics," Khatua, Prabir, Tang, Phu, Ghoshmoulick, Abhik, Patel, Rutika, Manandhar, Anjela, and Loverde, S.M., JPCB, 2024. Link.
Github: https://github.com/CUNY-CSI-Loverde-Laboratory/NUCLEOSOME_SEQUENCE_DEPENDENCE and https://github.com/CUNY-CSI-Loverde-Laboratory/PCA
"Molecular Dynamics Simulations of Polylectrolyte Complexes," Tania Rajpersaud, Sara Tabendeh, Lorraine Leon, and Loverde, S. M., Biomacromolecules, 2024. Link.
Github: https://github.com/CUNY-CSI-Loverde-Laboratory/Rajpersaud_Biomacromolecules_2023
"Exploration of the Nucleation Pathway for Supramolecular Fibers," Tang, Phu, Khatua, Prabir, Carnevale, Enzo, Loverde, S.M., JCIM, 2023. Link.
Github: https://github.com/CUNY-CSI-Loverde-Laboratory/Tang_JCIM_2023
10. "PEO-b-PBD diblock copolymers induce packing defects in lipid : hybrid membranes and improve insertion rates of natively folded peptides, " Steinkühler, Já ; Jacobs, Miranda; Boyd, Margrethe; Loverde, Sharon M.; Kamat, Neha, Biomacromolecules, 2022. Link.
11. "Domain Formation in Charged Polymer Vesicles," Kaushik Chakraborty, Prabir Khatua, Wataru Shinoda, Sharon M. Loverde, Macromolecules, 54, 9258-9267 (2021). Link.
Github: https://github.com/CUNY-CSI-Loverde-Laboratory/Chakraborty_Loverde_Macromolecules_2021
12. "The Interaction of Supramolecular Anticancer Nanotubes with Phospholipid Membranes," Phu Tang*, Anjela Manandhar*, William Hu**, Myungshim Kang, and Sharon M. Loverde, Nanoscale Advances, 3, 370-382 (2021).*Co-first authors **High school author Link.
13. "Interaction of Camptothecin with Model Cellular Membranes ," Phu K. Tang, Kaushik Chakraborty, William Hu*, Myungshim Kang and Sharon M. Loverde, Journal of Chemical Theory and Computation, 16, 3373-3384 (2020). *High school author Link.
14. "Molecular Simulation of the Shape Deformation of a Polymersome," Kaushik Chakrabory, Wataru Shinoda, and Sharon M. Loverde, Soft Matter, 16, 3234-3244 (2020). Link.
Github: https://github.com/CUNY-CSI-Loverde-Laboratory/Chakraborty_Loverde_SoftMatter_2020
15. "Rational Coarse Grained Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes," Anjela Manandhar, Kaushik Chakraborty, Phu Tang, Myungshim Kang, Pengcheng Zhang, Honggang Cui, and Sharon M. Loverde, Journal of Physical Chemistry B, 123, 10582-10593 (2019). Link.
16. "Molecular Dynamics Simulations of Phospholipid Bilayers With Polycaprolactone," Michaela Drenscko and Sharon M. Loverde, Molecular Simulation, 45, 859-867 (2019). Link.
17. "Molecular Mechanism for the Role of the H2A and H2B Histone Tails in Nucleosome Repositioning," Kaushik Chakraborty, Myungshim Kang, and Sharon M. Loverde, Journal of Physical Chemistry B, 122, 11827- 11840 (2018). Link.
18. "Molecular Dynamics Simulations of Supramolecular Anticancer Nanotubes," Myungshim Kang, Kaushik Chakraborty, and Sharon M. Loverde, Journal of Chemical Information and Modeling, 56, 1164-1168 (2018). Link.
19. "Nucleotide State Effect on the Protofilament Conformation of Tubulin Octamers," Anjela Manandhar, Myungshim Kang, Kaushik Chakraborty, and Sharon M. Loverde, Journal of Physical Chemistry B, 122, 6164-6178, (2018). Link
20. "Glassy Worm-Like Micelles in Solvent and Shear-Mediated Shape Transitions," Kaushik Chakraborty, Kandaswamy Vijayan, Andre Brown, Dennis E. Discher, Sharon M. Loverde, Soft Matter, 2018, DOI: 10.1039/C8SM00080H. Link
21. "Isomeric Control of the Mechanical Properties of Supramolecular Filament Hydrogels," Yi-An Lin,Myungshim Kang, Wei-Chiang Chen,Yu-Chuan Ou, Andrew G. Cheetham, Pei-Hsun Wu, Denis Wirtz, Sharon M. Loverde and Honggang Cui, Biomaterials Science, 6, 216-224 (2018). Link
22. "Coarse-grained molecular dynamics studies of the structure and stability of peptide-based drug amphiphile filaments," Myungshim Kang, Honggang Cui, and Sharon M. Loverde, Soft Matter, 13, 7721-7730 (2017). DOI: 10.1039/c7sm00943g (2017). Link
23. "Molecular Simulations of Peptide Amphiphiles," Anjela Manandhar, Myungshim Kang, Kaushik Chakraborty, Phu Tang, and Sharon M. Loverde, Organic and Biomolecular Chemistry, 15, 7993-8005 (2017). Link
24. "Asymmetric Breathing Motions of Nucleosomal DNA and the Role of Histone Tails," Kaushik Chakraborty and Sharon M. Loverde, Journal of Chemical Physics, 147, 065101 (2017). Link
25. "Characterization of Hydrophobic Collapse of Polystyrene in Water Using Free Energy Techniques," Mihaela Drenscko and Sharon M. Loverde, Molecular Simulation, 43, 234-241 (2017). Link
26. “π-π Stacking Mediated Chirality in Functional Supramolecular Filaments,” Myungshim Kang, Pengcheng Zhang, Honggang Cui, Sharon M. Loverde, Macromolecules, 49 (3), 993-1001 (2016). Link
27. “TCR triggering by pMHC ligands tethered on surfaces via poly(ethylene glycol) depends on polymer length,” Zhengyu Ma, D. N. Lebard *, S. M. Loverde *, K. A. Sharp, M. L. Klein, D. E. Discher, T. H. Finkel, Plos One, 11, e112292 (2014). Link
28. “Molecular Simulation of the Concentration-Dependent Interaction of Hydrophobic Drugs with Model Membranes,” Myungshim Kang and Sharon M. Loverde, Journal of Physical Chemistry B, 118, 11965-11972 (2014). Link
29. "Molecular Simulation of the Transport of Drugs across Model Membranes," Sharon M. Loverde, Journal of Physical Chemistry Letters, 5, 1669-1675 (2014). Link
30. "Computer Simulation of Polymer and Biopolymer Self-Assembly for Drug Delivery," Sharon M. Loverde, Molecular Simulation, 40, 794-801 (2014). Link
31. "Probing the Structure of PEGylated-lipid Assemblies by Coarse-grained Molecular Dynamics," Wataru Shinoda, D. E. Discher, M. L. Klein, S. M. Loverde, Soft Matter, 9, 11549-11556 (2013). Link
32. "Filomicelles in nanomedicine–from flexible, fragmentable, and ligand-targetable drug carrier designs to combination therapy for brain tumors," N. S. Oltra, J. Swift, A. Mahmud, K. Rajagopal, S. Loverde, D. Discher, J. Mater. Chem. B. (2013). Link
33. “Nanoparticle Shape Improves Delivery: Rational Coarse Grain Molecular Dynamics (rCG-MD) of Taxol in Worm-Like PEG-PCL Micelles,” S. M. Loverde, M. L. Klein, D. E. Discher, Adv. Mater., 24, 3823-3830 (2012). Link
34. “Curvature, Rigidity, and Pattern Formation in Functional Polymer Micelles and Vesicles – from Dynamic Visualization to Molecular Simulation,” S. M. Loverde, D. A. Pantano, D. A. Christian, A. Mahmud, M. L. Klein, D. E. Discher, Current Opinion in Solid State and Materials Science, 15, 277-284 (2011). Special Issue in Functional Gels and Membranes. Link
35. “Rugged Energy Landscapes underlie Phase Transitions and Rigidities of Worm-like Micelles and Vesicles made with Polycaprolactone-Based Diblock Copolymers”, K. Rajagopal, A. Mahmud, D. A. Christian, J. D. Pajerowski, S. M. Loverde, and D. E. Discher, Macromolecules, 43, 9736–9746 (2010). Link
36. “Curvature driven molecular demixing in the budding and breakup of mixed component worm-like micelles,” S. M. Loverde, V. Ortiz, R. D. Kamien, M. L. Klein, and D. E. Discher, Soft Matter, 6, 1419-1425 (2010). Cover Article. Link
37. “Asymmetric Charge Patterning on Surfaces and Interfaces: Formation of Hexagonal Domains,” S. M. Loverde, M. O. de la Cruz, Journal of Chemical Physics, 127, 164707 (2007). Link
38. “Charged Particles on Surfaces: Coexistence of Dilute Phases and Periodic Structures at Interfaces”, S. M. Loverde, F. J. Solis, and M. O. de la Cruz, Physical Review Letters, 98, 237802 (2007). Link
39. “Competing Interactions in Two Dimensional Coulomb Systems: Surface Charge Heterogeneities in Co-assembled Cationic-Anionic Incompatible Mixtures,” S. M. Loverde, Y. S. Velichko, M. O. de la Cruz, Journal of Chemical Physics, 124, 144702 (2006). Link
40. “Monte Carlo Simulation of Reversibly Associating Ideal Chains,” S. M. Loverde, A. V. Ermoshkin, M. O. de la Cruz, J. of Polymer Science B., 43, 796-804 (2005). Link
40. “Subloops, Barkhausen Noise, and Disorder Induced Critical Behavior,” J. H. Carpenter, K. A. Dahmen, J. P. Sethna, G. Friedman, S. Loverde, and A. Vanderveld , Journal of Applied Physics, 89, 6799-6801 (2001). Link
Preprints
"Ion Condensation Structure on Patterned Surfaces," Y. S. Velichko, F.J. Solis, S. M. Loverde, and M. Olvera de la Cruz, http://arxiv.org/abs/0704.3717. Link
Book Chapters
"Degradable Poly(ethylene oxide)-/block/-polycaprolactone Worm-like Micelles: From Phase Transitions and Molecular Simulation to Persistent Circulation and Shrinking Tumors,” N. S. Oltra, S. M. Loverde, T. Harada, A. Mahmud, K. Rajagopoal, and D. E. Discher. Degradable Polymers and Materials, Principles and Practice (2nd Edition), 2012. Link
Myungshim Kang, Dennis Lam*, Dennis E. Discher, Sharon M. Loverde, Molecular Modeling for Micellar Drug Delivery, in Computational Pharmaceutics: Application of Molecular Modeling in Drug Delivery (eds. Defang Ouyang and Sean C. Smith) Wiley, 2015. Link *Undergraduate Author
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