Yun Lyna Luo, PhD

Publications (click article titles to download PDFs)

Editorials / White Paper

1. The Need to Implement FAIR Principles in Biomolecular Simulations, Nature Methods 2024, arXiv:2407.16584
2. Reliability and Reproducibility Checklist for Molecular Dynamics Simulations, Commun Biol 2023, 6,268
3. Celebrating Benoit Roux's 60th Birthday: Quantifying Biology at the Membrane. J Comput Chem 2020, 41, 385-386

Software Update

4. Hwang W.*, et. al., CHARMM at 45: Enhancements in accessibility, functionality, and speed, J. Phys. Chem. B., 2024, 10.1021/acs.jpcb.4c04100

Viewpoint

5. Luo, Y.*, Mechanism-Based and Computational-Driven Covalent Drug Design. J. Chem. Inf. Model 2021, 61, 5307-5311

Book Chapters

6. Delemotte, L* & Luo, Y.*, Molecular Dynamics. Handbook of Ion Channels, 2^nd Edition, 2023.
7. Luo, Y.*, Lacroix, J.*, Ion Channels in Biophysics and Physiology: Methods & Challenges to Study Mechanosensitive Ion Channels. Adv Exp Med Biol 2021, 1349, 33-49.
8. Botello-Smith, W., Luo, Y.*, Concepts, Practices, and Interactive Tutorial for Allosteric Network Analysis of Molecular Dynamics Simulations. Methods Mol Biol 2021, 2302, 311-334.
9. Luo, Y.*, Lacroix, J., Prabhu, S., Antibody-Drug Conjugates: The 21st Century Magic Bullets for Cancer, Section V Case Studies, Chapter 12: Ado-Trastuzumab Emtansine, Springer, 2015.

Research articles

10. Li S., Wijerathne T., Bhatt A., Jiang W., Lacroix J.*, Han W.*, Luo Y.*, A two-step clockwork mechanism opens a proteo-lipidic pore in PIEZO2 channels, Nature Chemical Biology, 2026.
11. He, Xin, Lei Zhang, Yang Li, Song-Bai Liu, Zheng Li, Haojie Dong, Genevieve E Baker, et al. (2026) 2026. “Inhibition of ADSS2-Mediated de Novo AMP Biosynthesis Re-Sensitizes Acute Myeloid Leukemia to BH3 Mimetics.”. Nature Cancer 7 (6): 944-63. https://doi.org/10.1038/s43018-026-01184-5.
12. A Hernamdez, A Bhatt, I Revilla, JE Levine, SC Kosaraju*, YL Luo*, CholBindNet as an Interpretable Neural Networks for Cholesterol Binding Site Prediction, Commun Chem (2026).
13. Chung J, Bhatt A, Levine JE, Lin YC, Zhao M, MacKerell AD Jr*, Jo S*, Kosaraju SC*, Luo YL*. Docking-score landscapes shape active-learning performance across Vina, Glide, and SILCS. J Comput Aided Mol Des. 2026 Sep 11;40(1):231. doi: 10.1007/s10822-026-00927-x. 
14. Wijerathne Tharaka D, Chandrasekharan Aneesh, Bhatt Aashish, Luo Yun L, Lacroix Jérôme J (2026)  Yoda molecules agonize PIEZO2 eLife 15:RP111912 https://doi.org/10.7554/eLife.111912.1
15. PC Thai, MH Soria, JE Levine, CY Wen, YL Luo*, and SC Kosaraju*. Variational Generative Modeling for Forecasting Protein Diffusion from Molecular Dynamics. Proceedings of the 17th ACM International Conference on Bioinformatics, Computational Biology and Health Informatics. Association for Computing Machinery, New York, NY, USA, Article 81, 1–6. https://doi.org/10.1145/3807503.3819451 (2026)
16. JE Levine, YL Luo*, SC Kosaraju*, TSSR: Two-Stage Swap-Reward-Driven Reinforcement Learning for Character-Level SMILES Generation, arXiv:2601.04521
17. KH Kim, A Yaganapu, S Kosaraju, A Bhatt, YL Luo, SP Parsa, J Park, et.al., Prediction of bacterial protein-compound interactions with only positive samples, Bioinformatics. 2026 March; 42(3).
18. Zhang J., Bhatt A., Maksaev G., Luo Y.*, Yuan P.*, Lipid-mediated gating of a miniature mechanosensitive MscS channel from Trypanosoma cruzi, Nat. Commun., 2025
19. Wen C., Luo, Y.*, Madsen, J.*, Optimizing coarse-grained models for large-scale membrane protein simulations, Biophysical Reports, 2025
20. Guo J., Lei K., Liu J., Tong H., Luo Y.*, Han W.*, Li S*, “Cmem Builder: An Automated Tool for Curved Membrane Construction in Molecular Dynamics Simulations”, J. Chem.Theory and Comput. 2025.
21. Gong, David, et. al., Charles K Abrams, “Molecular Dynamics Simulation of GJC2 Mutants Reveal Pathogenic Mechanisms of PMLD1 and SPG44”, J. General Physiology  2025.
22. Lin Y., Lacroix J., Sterling J., Luo Y.,*, Dissecting current rectification through asymmetric nanopores, Biophys. J., 2025 (New and notable)
23. Wijerathne T., Bhatt A., Jiang W., Luo Y.*, Lacroix J.*, Mammalian PIEZO channels rectify anionic currents, Biophys. J., 2025
24. Kumar D., Harris A.*, Luo Y.*, Molecular permeation through large pore channels: computational approaches and insights, J. Physiology, 2025.
25. Edmond M., et. al., Luo Y., Barro-Soria R.*, Lipophilic compounds restore function of neurodevelopmental-associated KCNQ3 mutations, Commun. Biol. 2024.
26. Gaete P., et. al., Luo Y., Contreras J.*, Large-pore connexin hemichannels function like molecule transporters independent of ion conduction, PNAS, 2024, 121 (33) e2403903121
27. Li S.*, Wu B., Luo Y., Han W.*, Simulation of functional motion of super large biomolecules with a mixed-resolution model, J. Chem. Theory Comput., 2024
28. Dong H., et. al., Luo Y., Ling L.*, Targeting PRMT9 mediated arginine methylation suppresses cancer stem cell maintenance and elicits cGAS-mediated anti-cancer immunity, Nature Cancer, 2024
29. Baudry M., Wang Y., Bi X., Luo Y., et al., Identification and neuroprotective properties of NA-184, a calpain-2 inhibitor, Pharmacology Research & Perspectives, 2024
30. Jiang W., Wijerathne, T., Zhang H., Lin Y., Jo S., Im W., Lacroix J., Luo Y.*, Structural and thermodynamic framework for PIEZO1 modulation by small molecules, PNAS, 120, e2310933120, 2023 
31. Baudry M., Luo Y., Bi X., Calpain-2 inhibitors as therapy for traumatic brain injury, Neurotherapeutics, 20, 1592-1602, 2023
32. Jiang W.*, Lacroix J, Luo Y.* ,Importance of molecular dynamics equilibrium protocol on protein-lipid interaction near channel pore, Biophysical Reports, 2, 100080, 2022
33. Lin Y., Luo Y.*, Unifying Single-channel permeability from rare-event sampling and steady-state flux, Frontiers in Molecular Biosciences: Biological Modeling and Simulation, 2022
34. Jiang W., et. al., Lacroix J.*, Rohacs T.*, Luo Y.*, Crowding-induced opening of the mechanosensitive Piezo1 channel in silico. Commun. Biol. 4, 84, 2021
35. Jiang, W., Ling, Y., Luo, Y.*, Mechanical properties of anionic asymmetric bilayers from atomistic simulations, J. Chem. Phys., 2021
36. Jiang, W., Lin, Y., Botello-Smith, W., Contreras, J.*, Harris, A.*, Maragliano, L.*, Luo, Y.*, Free energy and kinetics of cAMP permeation through connexin26 hemichannel via applied voltage and milestoning, Biophys. J., 2021
37. Sterling J.*, Jiang W., Botello-Smith, W., Luo Y.*, Ion pairing and dielectric decrement in glycosaminoglycan brushes, J. Phys. Chem. B., 2021
38. Botello-Smith, W, Luo, Y.*, Investigating protein-protein allosteric network using current-flow scheme, J. Comput. Chem, 2020, 41, 552-560
39. Gaete PS, Lillo MA, López W, Liu Y, Jiang W, Luo Y, Harris AL, Contreras JE., A novel voltage-clamp/dye uptake assay reveals saturable transport of molecules through CALHM1 and connexin channels, J Gen Physiol. 2020, 2;152(11):e202012607.
40. Anderson S., et. al., Luo Y.*, Botello-Smith W.*, Andresen B.*, In silico prediction of ARB resistance: A first step in creating personalized ARB therapy. PLOS Comput. Biol., 2020.
41. Xie C., Jiang W., Lacroix J., Luo Y.*, Hao J*, Insight into Molecular Mechanism for Activin A-Induced Bone Morphogenetic Protein Signaling. Int. J. Mol. Sci. 2020, 21, 6498.
42. Sun J, et. al., Luo Y, Baudry M, Bi X.*, PKA and Ube3a regulate SK2 channel trafficking to promote synaptic plasticity in hippocampus: Implications for Angelman Syndrome, Sci. Rep. 2020, 10, 9824.
43. Botello-Smith W, Zhang H, Ozkan AD, Jiang W, Pham CN, Lacroix J* and Luo Y*, A molecular Mechanism for the Chemical Activation of the Mechanosensitive Piezo1 Channel, Nat. Commun., DOI: 10.1038/s41467-019-12501-1.
44. Zhu Y, et. al., Luo Y, Li L.*, Targeting PRMT1-mediated FLT3 methylation disrupts maintenance of MLL-rearranged acute lymphoblastic leukemia, Blood, DOI: 10.1182/blood.2019002457.
45. Botello-Smith W., Luo,Y.*, Robust determination of protein allosteric signaling pathways, J. Chem. Theory Comput., 2019, 15, 2116-2126.
46. Capuccino J., et. al., Luo Y.*, Contreras J.*, The connexin26 human mutation N14K disrupts cytosolic intersubunit interactions and promotes channel opening, J. Gen. Physiol., 2019, 151, 382-341.
47. Zhang H., Jiang W., Chatterjee P., Luo Y.*, Ranking reversible covalent drugs: from free energy perturbation to fragment docking, J. Chem. Inf. Model, 2019, 59, 2093-2102.
48. He X, et. al., Luo Y, Li L.*, PRMT1-mediated FLT3 arginine methylation promotes maintenance of FLT3-ITD+ acute myeloid leukemia, Blood, 2019, 134, 548-560.
49. Lacroix J.*, Botello-Smith W., Luo Y., Probing the gating mechanism of the mechanosensitive channel Piezo1 with the small molecule Yoda1, Nat. Commun., 2018, 9, 2029.
50. Fei Q., et. al., Lambros M.*, Luo Y.*, Molecular mechanism of resveratrol’s lipid membrane protection, Sci. Rep., 2018, 8, 1587.
51. Abrams C.*, et. al, Luo Y., Alterations at Arg76 of human connexin 46, a residue associated with cataract formation, cause loss of gap junction formation but preserve hemichannel function. Am. J. Physiol. Cell Physiol. 2018, 315, 623-635.
52. Chatterjee, P.*, Yadav, M., Chauhan, N., Huang, Y., Luo, Y., Cancer cell metabolism featuring Nrf2. Curr. Drug Discov. Technol. 2018, doi: 10.2174/1570163815666180911092443.
53. Liu M., et. al., Luo Y., Huang Y.*, Effects of bioactive constituents in the Traditional Chinese Medicinal formula Si-Wu-Tang on Nrf2 signaling and neoplastic cellular transformation, Phytomedicine, 2018, 40, 1-9.
54. Chatterjee P., Botello-Smith W., et. al., Luo Y.*, Can relative binding free energy predict selectivity of reversible covalent inhibitors? J. Am. Chem. Soc. 2017, 139, 17945-17952.
55. Botello-Smith W., et. al., Hao J.*, Luo Y.*, Polymodal allosteric regulation of type 1 serine/threonine kinase receptors via a conserved electrostatic lock, PLOS Comput. Biol., 2017, 13, e1005711.
56. Luo Y.*, Rossi A., Harris A., Computational Studies of Molecular Permeation through Connexin26 Channels, Biophys. J., 2016, 110, 584-599. 
57. Lopez W., Ramachandran J., Alsamarah A., Luo L., Harris A., Contreras J.*, Mechanism of gating by calcium in connexin hemichannels, Proc. Natl. Acad. Sci. U S A, 2016, 113, E7986-E7995.
58. Luo Y.*, Alsamarah A., Zhang K., Hao J.*, Development of New Therapeutic Agents for Fibrodysplasia Ossificans Progressiva. Curr Mol Med., 2016, 16, 4-11.
59. Alsamarah A., LaCuran A., Oelschlaeger P., Hao J., Luo Y.*, Uncovering molecular bases underlying bone morphogenetic protein receptor inhibitor selectivity. PLOS ONE, 2015, 10, e0132221.
60. Sun J., et. al., Luo Y., Baudry M., Bi X.*, UBE3A regulates synaptic plasticity and learning and memory by controlling SK2 channel endocytosis. Cell Rep., 2015, 12, 359-360.

Work Before WesternU

50. Jiang W., Phillips J., et. al., Luo Y., Schulten K.*, Roux B.*, Generalized scalable multiple copy algorithms for molecular dynamics simulations in NAMD. Comput. Phys. Commun., 2014, 185 (3), 908-916.
51. Venable R., Luo Y., Gawrisch K., Roux B., Pastor R.*, Simulations of Anionic Lipid Membranes: Development of Interaction-Specific Ion Parameters and Validation Using NMR Data. J. Phys. Chem. B. 2013 117 (35), 10183-10192.
52. Lopes P., Huang J., Shim J, Luo Y., Li H., Roux B.*, MacKerell A.*, Polarizable Force field for peptides and protein based the Classical Drude Oscillator. J. Chem. Theory Comput., 2013 9 (12), 5430-5449.
53. Y. Luo, W. Jiang, H. Yu, A. D. MacKerell, Jr., and B. Roux*, Calibrating the potential function for accurate ion pairing in molecular dynamics simulations of concentration electrolytes solutions. Faraday Discussions, 2013, 160, 135-149.
54. Jiang J., Luo L. (co-1^st), Maragliano L., Roux B.*, Calculation of Free Energy Landscape in Multi-Dimensions with Hamiltonian-Exchange Umbrella Sampling on Petascale Supercomputer. J. Chem. Theory Comput., 2012, 8 (11), 4672-4680.
55. Luo Y., Harder E., Faibish R., Roux B.*, Computer simulations of water flux and salt permeability of the reverse osmosis FT-30 aromatic polyamide membrane. J. Mem. Sci. 2011, 384 (1-2), 1-9.
56. Herrou J., Rotskoff G., Luo Y., Roux B., Crosson S.*, The structural basis of a protein partner switch that regulates stress-dependent transcription. Proc. Natl. Acad. Sci. U S A, 2012, 109 (21): E1415-23.
57. Luo Y., and Roux B.*, Simulation of osmotic pressure in concentrated aqueous salt solutions. J. Phys. Chem. Lett. 2010, 1 (1), 183–189
58. Luo Y., Egwolf B., Walters D., Roux B.*, Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter: I. Single ion potential of mean force calculations and diffusion coefficient. J. Phys. Chem. B, 2010, 114 (2), 952–958
59. Egwolf B., Luo Y., Walters D., Roux B., Ion selectivity of alpha-hemolysin with beta-cyclodextrin adapter:II. Multi ion effects studies with grand canonical monte carlo/brownian dynamics simulations. J. Phys. Chem. B, 2010, 114 (8), 2901–2909
60. Luo Y., et. al., Fan B.*, Cellular interaction through LewisX cluster: theoretical studies. J. Mol. Model, 2008, 14, 901-910.
61. Luo Y., et. al., Zhang Y.*, First synthesis of two deoxy Lewisx pentaosyl glycosphingolipids. Glycoconjugate J., 2008, 25, 335-344.
62. Barbault F., et. al. Fan B.*, Flexible computational docking studies of new aminoglycosides targeting RNA 16S bacterial ribosome site. Eur. J. Med. Chem. 2008, 43, 1648-56.
63. Luo Y., et. al., Zhang Y.*, Total synthesis of 4d-deoxy Lewisx pentasaccharide. Comptes Rendus Chimie, 2008, 11, 29-37.
64. Gourmala C, Luo Y., et. al, Fan B.*, Elucidation of the LewisX-LewisX carbohydrate interaction with molecular dynamics simulations. J. Mol. Struct.: THEOCHEM, 2007, 821, 22-29.

Patents 

• Protein arginine methyltransferase 9 inhibitors and methods of use, U.S. Patent 20240132887A1
• Calpain-2 selective inhibitor compounds for treatment of glaucoma, U.S. Patent 20210179543