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A Suite of Tutorials for the WESTPA 2.0 Rare-Events Sampling Software [Article v2.0].
Bogetti AT, Leung JMG, Russo JD, Zhang S, Thompson JP, Saglam AS, Ray D, Mostofian B, Pratt AJ, Abraham RC, Harrison PO, Dudek M, Torrillo PA, DeGrave AJ, Adhikari U, Faeder JR, Andricioaei I, Adelman JL, Zwier MC, LeBard DN, Zuckerman DM, Chong LT. Bogetti AT, et al. Living J Comput Mol Sci. 2023;5(1):1655. doi: 10.33011/livecoms.5.1.1655. Living J Comput Mol Sci. 2023. PMID: 37200895 Free PMC article.
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.
Dommer A, Casalino L, Kearns F, Rosenfeld M, Wauer N, Ahn SH, Russo J, Oliveira S, Morris C, Bogetti A, Trifan A, Brace A, Sztain T, Clyde A, Ma H, Chennubhotla C, Lee H, Turilli M, Khalid S, Tamayo-Mendoza T, Welborn M, Christensen A, Smith DG, Qiao Z, Sirumalla SK, O'Connor M, Manby F, Anandkumar A, Hardy D, Phillips J, Stern A, Romero J, Clark D, Dorrell M, Maiden T, Huang L, McCalpin J, Woods C, Gray A, Williams M, Barker B, Rajapaksha H, Pitts R, Gibbs T, Stone J, Zuckerman DM, Mulholland AJ, Miller T 3rd, Jha S, Ramanathan A, Chong L, Amaro RE. Dommer A, et al. Among authors: bogetti a. Int J High Perform Comput Appl. 2023 Jan;37(1):28-44. doi: 10.1177/10943420221128233. Epub 2022 Oct 2. Int J High Perform Comput Appl. 2023. PMID: 36647365 Free PMC article.
WESTPA 2.0: High-Performance Upgrades for Weighted Ensemble Simulations and Analysis of Longer-Timescale Applications.
Russo JD, Zhang S, Leung JMG, Bogetti AT, Thompson JP, DeGrave AJ, Torrillo PA, Pratt AJ, Wong KF, Xia J, Copperman J, Adelman JL, Zwier MC, LeBard DN, Zuckerman DM, Chong LT. Russo JD, et al. Among authors: bogetti at. J Chem Theory Comput. 2022 Feb 8;18(2):638-649. doi: 10.1021/acs.jctc.1c01154. Epub 2022 Jan 19. J Chem Theory Comput. 2022. PMID: 35043623 Free PMC article.
#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol.
Dommer A, Casalino L, Kearns F, Rosenfeld M, Wauer N, Ahn SH, Russo J, Oliveira S, Morris C, Bogetti A, Trifan A, Brace A, Sztain T, Clyde A, Ma H, Chennubhotla C, Lee H, Turilli M, Khalid S, Tamayo-Mendoza T, Welborn M, Christensen A, Smith DGA, Qiao Z, Sirumalla SK, O'Connor M, Manby F, Anandkumar A, Hardy D, Phillips J, Stern A, Romero J, Clark D, Dorrell M, Maiden T, Huang L, McCalpin J, Woods C, Gray A, Williams M, Barker B, Rajapaksha H, Pitts R, Gibbs T, Stone J, Zuckerman D, Mulholland A, Miller T 3rd, Jha S, Ramanathan A, Chong L, Amaro R. Dommer A, et al. Among authors: bogetti a. bioRxiv [Preprint]. 2021 Nov 15:2021.11.12.468428. doi: 10.1101/2021.11.12.468428. bioRxiv. 2021. PMID: 34816263 Free PMC article. Updated. Preprint.
AI-driven multiscale simulations illuminate mechanisms of SARS-CoV-2 spike dynamics.
Casalino L, Dommer AC, Gaieb Z, Barros EP, Sztain T, Ahn SH, Trifan A, Brace A, Bogetti AT, Clyde A, Ma H, Lee H, Turilli M, Khalid S, Chong LT, Simmerling C, Hardy DJ, Maia JD, Phillips JC, Kurth T, Stern AC, Huang L, McCalpin JD, Tatineni M, Gibbs T, Stone JE, Jha S, Ramanathan A, Amaro RE. Casalino L, et al. Among authors: bogetti at. Int J High Perform Comput Appl. 2021 Sep;35(5):432-451. doi: 10.1177/10943420211006452. Int J High Perform Comput Appl. 2021. PMID: 38603008 Free PMC article.
18 results