| AMBER 2016 reference manual DA Case, RM Betz, DS Cerutti, TE Cheatham, TA Darden, RE Duke, ... University of California: San Francisco, CA, USA, 1-923, 2016 | 136 | 2016 |
| AmberTools 16 DA Case, RM Betz, W Botello-Smith, DS Cerutti, TE Cheatham III, ... University of California, San Francisco, 2016 | 125 | 2016 |
| Theory and simulations for RNA folding in mixtures of monovalent and divalent cations HT Nguyen, N Hori, D Thirumalai Proceedings of the National Academy of Sciences 116 (42), 21022-21030, 2019 | 51 | 2019 |
| Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics HT Nguyen, N Hori, D Thirumalai Nature Chemistry, 1-11, 2022 | 50 | 2022 |
| Accurate small and wide angle x-ray scattering profiles from atomic models of proteins and nucleic acids HT Nguyen, SA Pabit, SP Meisburger, L Pollack, DA Case The Journal of chemical physics 141 (22), 2014 | 47 | 2014 |
| AMBER 2016 DA Case, RM Betz, W Botello-Smith, DS Cerutti, III T. E. Cheatham, ... University of California, San Francisco, 2016 | 45* | 2016 |
| Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations G Arad-Haase, SG Chuartzman, S Dagan, R Nevo, M Kouza, BK Mai, ... Biophysical journal 99 (1), 238-247, 2010 | 36 | 2010 |
| Charge Density of Cation Determines Inner versus Outer Shell Coordination to Phosphate in RNA HT Nguyen, D Thirumalai The Journal of Physical Chemistry B 124 (20), 4114-4122, 2020 | 19 | 2020 |
| Extracting water and ion distributions from solution x-ray scattering experiments HT Nguyen, SA Pabit, L Pollack, DA Case The Journal of chemical physics 144 (21), 2016 | 17 | 2016 |
| Top-hits for H1N1pdm identified by virtual screening using ensemble-based docking H Nguyen, L Le, TN Truong PLoS currents 3, RRN1030, 2011 | 14 | 2011 |
| Odd–even disparity in the population of slipped hairpins in RNA repeat sequences with implications for phase separation H Maity, HT Nguyen, N Hori, D Thirumalai Proceedings of the National Academy of Sciences 120 (24), e2301409120, 2023 | 12 | 2023 |
| Sizes, conformational fluctuations, and SAXS profiles for intrinsically disordered proteins ML Mugnai, D Chakraborty, A Kumar, HT Nguyen, W Zeno, ... bioRxiv, 2023.04. 24.538147, 2023 | 7 | 2023 |
| RNA encodes physical information I Seim, V Zhang, AP Jalihal, BM Stormo, SJ Cole, J Ekena, HT Nguyen, ... bioRxiv, 2024.12. 11.627970, 2024 | 2 | 2024 |
| Competition between stacking and divalent cation-mediated electrostatic interactions determines the conformations of short DNA sequences B Mondal, D Chakraborty, N Hori, HT Nguyen, D Thirumalai Journal of Chemical Theory and Computation 20 (7), 2934-2946, 2024 | 1 | 2024 |
| The Folding of Germ Granule mRNAs Controls Intermolecular Base Pairing in Germ Granules and Maintains Normal Fly Development S Tian, H Nguyen, Z Ye, S Rouskin, D Thirumalai, T Trcek bioRxiv, 2024.05. 31.596852, 2024 | 1 | 2024 |
| Minimal Models for RNA Simulations D Thirumalai, N Hori, HT Nguyen arXiv preprint arXiv:2501.00194, 2024 | | 2024 |
| Salt-dependent self-association of trinucleotide repeat RNA sequences H Maity, HT Nguyen, N Hori, D Thirumalai The Journal of Physical Chemistry Letters 15 (14), 3820-3827, 2024 | | 2024 |
| Impact of divalent ions on the conformations of single and double stranded DNA: A coarse-grained molecular dynamics study B Mondal, N Hori, D Chakraborty, HT Nguyen, D Thirumalai Biophysical Journal 122 (3), 212a, 2023 | | 2023 |
| Structure and dynamics of RNA in biomolecular condensate HT Nguyen, D Thirumalai Biophysical Journal 122 (3), 296a, 2023 | | 2023 |
| Liquid-Liquid Phase Separation of Repeat Disorder Sequences Leads to RNA Conformational and Dynamical Heterogeneity HT Nguyen, D Thirumalai Biophysical Journal 120 (3), 108a, 2021 | | 2021 |
Devarajan ThirumalaiUniversity of Texas at AustinVerified email at umd.edu