Publications

  1. An Affordable Topography-Based Protocol for Assigning a Residue’s Character on a Hydropathy (PARCH) Scale, J. Ji, B. Carpentier, A. Chakraborty, and S. Nangia, JCTC 2023 (ASAP).
  2. Lipidation Alters the Structure and Hydration of Myristoylated Intrinsically Disordered Proteins, J. Ji, Md. S. Hossain, E. N. Krueger, Z. Zhang, S. Nangia, B. Carpentier, M. Martel, S. Nangia, D. Mozhdehi, Biomacromolecules, 24, 1244–1257 (2023).
  3. Self-Defensive Antimicrobial Surfaces Using Polymyxin-Loaded Poly(styrene sulfonate) Microgels, X. Xiao, J. Ji, W. Zhao, H. Wang, S. Nangia, H. Wang, M. Libera, ACS Biomaterials Science & Engineering, 8, 4827–4837 (2022).
  4. Unique structural features of claudin‐5 and claudin‐15 lead to functionally distinct tight junction strand architecture, N. Rajagopal, S. Nangia, Annals of the New York Academy of Sciences (2022).
  5. Joint Profile Characteristics of Long-Latency Transient Evoked and Distortion Otoacoustic Emissions, D. Pacheco, N.Rajagopal, B. A. Prieve, S. Nangia, American Journal of Audiology, 31, 684-697 (2022).
  6. Salt Destabilization of Cationic Colistin Complexation within Polyanionic Microgels, X. Xiao, J. Ji, W. Zhao, S. Nangia, M. Libera, Macromolecules, 55, 1736-1746 (2022).
  7. Adaptive Recombinant Nanoworms from Genetically Encodable Star Amphiphiles, M.  S. Hossain, J. Ji, C. J. Lynch, M. Guzman, S. Nangia, D. Mozhdehi, Biomacromolecules, 23, 863-876 (2021). Featured on the cover!
  8. Persister control by leveraging dormancy associated reduction of antibiotic efflux, S. Roy, A. A. Bahar, H. Gu, S. Nangia, K. Sauer, D. Ren, PLoS Pathogens, 17, e1010144 (2021).
  9. Development of the computational antibiotic screening platform (CLASP) to aid in the discovery of new antibiotics, Y. Dai, H. Ma, M. Wu, T. A. Welsch, S. R. Vora, D. Ren, S. Nangia, Soft Matter, 17, 2725-2736 (2021).
  10. High-level antibiotic tolerance of a clinically isolated Enterococcus faecalis strain, H. Gu, S. Roy, X. Zheng, T. Gao, H. Ma, Z. Soultan, C. Fortner, S. Nangia, D. Ren, Applied and Environmental Microbiology, 87, e02083-20 (2020).
  11. Molecular mechanism of ultrasound interaction with a blood-brain barrier model  V. H. Man, M. S. Li, P. Derreumaux, J. Wang, T. T. Nguyen, S. Nangia, P. H. Nguyen, Journal of Chemical Physics, 153, 045104  (2020).
  12. Paracellular Gatekeeping: What Does It Take for an Ion to Pass Through a Tight Junction Pore?  F. J. Irudaynathan and  S. Nangia, Langmuir, 36, 6757–6764  (2020). Featured on the cover!
  13. Interaction of amphiphilic coumarin with DPPC/DPPS lipid bilayer: effects of concentration and alkyl tail length, P.. Kalyanram, H. Ma,  S. Marshall, C. Goudreau, A. Cartaya, T.  Zimmermann, I. Stadler, S. Nangia and A. Gupta, Physical Chemistry Chemical Physics  (2020).
  14. Predicting selectivity of paracellular pores for biomimetic applications, N. Rajagopal, A. J. Durand, and S. Nangia, Molecular Systems Design & Engineering  (2020).
  15. Computational Nanoscopy of Tight Junctions at the Blood–Brain Barrier Interface, N. Rajagopal, F. J. Irudayanathan, and S. Nangia, International Journal of Molecular Science, 20, 5583 (2019). Invited (Review) Article.
  16. Obtaining Protein Association Energy Landscape for Integral Membrane Proteins, N. Rajagopal and S. Nangia, Journal of Chemical Theory and Computation, 15, 11, 6444-6455 (2019). Featured on the cover!
  17. The ghrelin O-acyltransferase structure reveals a catalytic channel for transmembrane hormone acylation, M. B Campaña, F. J. Irudayanathan, T. R. Davis, K. R. McGovern-Gooch, R. Loftus, M.  Ashkar, N. Escoffery, M. Navarro, M. A Sieburg, S. Nangia, and J. L. Hougland, Journal of Biological Chemistry, 294, 14166-14174 (2019).
  18. The influence of water on choline-based ionic liquids, E. E. L. Tanner, K. M. Piston, H. Ma, K. N. Ibsen, S. Nangia, S. Mitragotri, ACS Biomateraterial Science and Engineering 5, 3645–3653 (2019).
  19. Palmitoylation of claudin-5 proteins Influences their lipid domain affinity and tight junction assembly at the blood-brain barrier interface,  N. Rajagopal, F. J. Irudayanathan, and S. Nangia,  Journal of Physical Chemistry B, 123, 983–993 (2019).
  20. Development of effective stochastic potential method using random matrix theory for efficient conformational sampling of semiconductor nanoparticles at non-zero temperatures,  J. Scher, M. Bayne, A. Srihari, S. Nangia, and A. Chakraborty, Journal of Chemical Physics, 149, 014103 (2018).
  21. Self-assembly simulations of classic claudins–insights into the pore structure, selectivity and higher-order complexes,  F. J. Irudayanathan,  X. Wang, N. Wang, S. Willsey, I. Seddon, and S. Nangia,  Journal of Physical Chemistry B, 122, 7463–7474 (2018). Featured on the cover!
  22. Mechanism of Antibacterial Activity of Choline-Based Ionic Liquids (CAGE), Kelly N. Ibsen, H. Ma, A. Banerjee, E. E. L. Tanner, S. Nangia, and S. Mitragotri, ACS Biomaterials Science and Engineering 4, 2370–2379 (2018).
  23. Dynamics of OmpF trimer formation in the bacterial outer membrane of Escherichia coli, H. Ma, A. Khan, and S. Nangia, Langmuir, 34, 5623–5634 (2018).  Featured on the cover!
  24. Architecture of the paracellular channels formed by Claudins of the blood-brain barrier tight junctions, F. J. Irudayanathan, N. Wang, X. Wang , and S. Nangia, Annals of the New York Academy of Sciences, 1749-6632 (2017).
  25. Modeling diversity in structures of bacterial outer membrane lipids, H. Ma, D. D. Cummins, N. B. Edelstein, J. Gomez, A. Khan, M. D. Llewellyn, T. Picudella, S. R. Willsey, and S. Nangia, Journal of Chemical Theory and Computation, 13, 811–824 (2017).
  26. Drug-specific design of telodendrimer architecture for effective Doxorubicin encapsulation, W. Jiang, X. Wang, D. Guo, J. Luo, and S. Nangia, Journal of Physical Chemistry B, 120, 9766–9777 (2016).
  27. Molecular architecture of the blood-brain barrier tight junction proteins–A Synergistic Computational and in vitro Approach, F. J. Irudayanathan, J. P. Trasatti, P. Karande, and S. Nangia, Journal of Physical Chemistry B, 120, 77-88 (2016).
  28. Combinatorial approaches to evaluate nanodiamonds uptake and induced cellular fate, R. Eldawud, M. Reitzig, J. Opitz, Y. Rojanasakul, W. Jiang, S. Nangia, and C. Dinu, Nanotechnology, 27 (2016).
  29. Simulating gram-negative bacterial outer membrane: A coarse grain model, H. Ma, F. J. Irudayanathan, W. Jiang, and S. Nangia, Journal of Physical Chemistry B, 119, 14668–14682 (2015). Featured on the cover!
  30. Signaling factor interactions with polysaccharide aggregates of bacterial biofilms, S. C. DeSalvo, Y. Liu, G. Choudhary, D. Ren, S. Nangia, and R. Sureshkumar, Langmuir, 31, 1958-1966 (2015).
  31. Multiscale approach to investigate self-assembly of telodendrimer based nanocarriers for anticancer drug-delivery, W. Jiang, J. Luo, and S. Nangia, Langmuir, 31, 4270-4280 (2015).
  32. Optical signature of formation of protein corona in the firefly luciferase-CdSe quantum dot complex, J.M. Elward, F.J. Irudayanathan, S. Nangia, and A. Chakraborty, Journal of Chemical Theory and Computation, 10, 5534-5524 (2014). Featured on the cover of JCTC!
  33. A structure–property relationship study of the well-dfined telodendrimers to improve hemocompatibility of nanocarriers for anticancer drug delivery, C. Shi, D. Yuan , S. Nangia, G. Xu, K. Lam, and J. Luo, Langmuir, 28, 17666–17671 (2014).
  34. Effects of nanoparticle charge and shape anisotropy on translocation through cell membranes, S. Nangia and R. Sureshkumar, Langmuir, 28, 17666–17671 (2012). Featured on the cover of Langmuir!
  35. Theoretical advances in the dissolution studies of mineral-water interfaces, S. Nangia and B. J. Garrison, Thoeretical Chemistry Accounts, 127, 271-284 (2010). Invited feature Article.
  36. Role of intrasurface hydrogen bonding on silica dissolution, S. Nangia and B. J. Garrison, J. Phys. Chem. C 114, 2267-2272 (2010).
  37. Advanced Monte Carlo approach to study evolution of quartz surface during the dissolution process, S. Nangia and B. J. Garrison, J. Am. Chem. Soc. 131, 9538-9546 (2009).
  38. Ab-initio study of dissolution and precipitation reaction from edge, kink, and surface sites of quartz as a function of pH, S. Nangia and B. J. Garrison, Mol. Phys. 107 , 831-843 (2009).
  39. Ab Initio investigation of dissolution mechanisms in aluminosilicate minerals, C. P. Morrow, S. Nangia and B. J. Garrison, J. Phys. Chem. A 113, 1343-1352 (2009).
  40. Reaction rates and dissolution mechanisms of quartz as a function of pH, S. Nangia and B. J. Garrison, J. Phys. Chem. A 112, 2027-2033 (2008).
  41. Study of a family of 40 hydroxylated beta-cristobalite surfaces using empirical potential energy functions, S. Nangia, N. M. Washton, K. T. Mueller, J. D. Kubicki, and B. J. Garrison, J. Phys. Chem. C 111, 5169-5177 (2007).
  42. Direct calculation of coupled diabatic potential-energy surfaces for ammonia and mapping of a four-dimensional conical intersection seam, S. Nangia and D. G. Truhlar, J. Chem. Phys. 124, 124309-13 (2006).
  43. Non-Born-Oppenheimer molecular dynamics, A. W. Jasper, S. Nangia, CY. Zhu, and D. G. Truhlar, Acc. Chem. Res. 39, 101-108 (2006).
  44. A new form of MgTa2O6 obtained by the molten salt method, A. K. Ganguly, S. Nangia, M. Thirumal, and P. L. Gai, J. Chem. Sci. 118, 37-42 (2006).
  45. Can a single-reference approach provide a balanced description of ground and excited states? A comparison of the completely renormalized equation-of-motion coupled-cluster method with multireference quasidegenerate perturbation theory near a conical intersection and along a photodissociation coordinate in ammonia, S. Nangia and D. G. Truhlar, M. J. McGuire, and P. Piecuch, J. Phys. Chem A 109, 11643-11646 (2005).
  46. Introductory lecture: Nonadiabatic effects in chemical dynamics, A. W. Jasper, CY. Zhu, S. Nangia, and D. G. Truhlar, Faraday Discus. 127, 1-22 (2004).
  47. Coherent switching with decay of mixing: An improved treatment of electronic coherence for non-Born-Oppenheimer trajectories, CY. Zhu, S. Nangia, A. W. Jasper, and D. G. Truhlar, J. Chem. Phys. 121, 7658-7670 (2004).
  48. Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method, S. Nangia, A. W. Jasper, T. F. Miller III, and D. G. Truhlar, J. Chem. Phys. 120, 3586-3597 (2004).