دورية أكاديمية
#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol.
| العنوان: | #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol. |
|---|---|
| المؤلفون: | Dommer A; UC San Diego, La Jolla, CA, USA., Casalino L; UC San Diego, La Jolla, CA, USA., Kearns F; UC San Diego, La Jolla, CA, USA., Rosenfeld M; UC San Diego, La Jolla, CA, USA., Wauer N; UC San Diego, La Jolla, CA, USA., Ahn SH; UC San Diego, La Jolla, CA, USA., Russo J; Oregon Health & Science University, Portland, OR, USA., Oliveira S; University of Bristol, UK., Morris C; UC San Diego, La Jolla, CA, USA., Bogetti A; University of Pittsburgh, Pittsburgh, PA, USA., Trifan A; Argonne National Laboratory, Lemont, IL, USA.; University of Illinois at Urbana-Champaign, Urbana, IL, USA., Brace A; Argonne National Laboratory, Lemont, IL, USA.; University of Chicago, Chicago, IL, USA., Sztain T; UC San Diego, La Jolla, CA, USA.; Freie Universitat Berlin., Clyde A; Argonne National Laboratory, Lemont, IL, USA.; University of Chicago, Chicago, IL, USA., Ma H; Argonne National Laboratory, Lemont, IL, USA., Chennubhotla C; University of Pittsburgh, Pittsburgh, PA, USA., Lee H; Brookhaven National Lab and Rutgers University., Turilli M; Brookhaven National Lab and Rutgers University., Khalid S; University of Oxford, UK., Tamayo-Mendoza T; Entos, Inc., San Diego, CA, USA., Welborn M; Entos, Inc., San Diego, CA, USA., Christensen A; Entos, Inc., San Diego, CA, USA., Smith DG; Entos, Inc., San Diego, CA, USA., Qiao Z; California Institute of Technology, Pasadena, CA, USA., Sirumalla SK; Entos, Inc., San Diego, CA, USA., O'Connor M; Entos, Inc., San Diego, CA, USA., Manby F; Entos, Inc., San Diego, CA, USA., Anandkumar A; California Institute of Technology, Pasadena, CA, USA.; NVIDIA Corp, Santa Clara, CA, USA., Hardy D; University of Illinois at Urbana-Champaign, Urbana, IL, USA., Phillips J; University of Illinois at Urbana-Champaign, Urbana, IL, USA., Stern A; NVIDIA Corp, Santa Clara, CA, USA., Romero J; NVIDIA Corp, Santa Clara, CA, USA., Clark D; NVIDIA Corp, Santa Clara, CA, USA., Dorrell M; Pittsburgh Supercomputing Center, Pittsburgh, PA, USA., Maiden T; Pittsburgh Supercomputing Center, Pittsburgh, PA, USA., Huang L; Texas Advanced Computing Center, Austin, TX, USA., McCalpin J; Texas Advanced Computing Center, Austin, TX, USA., Woods C; University of Bristol, UK., Gray A; NVIDIA Corp, Santa Clara, CA, USA., Williams M; University of Bristol, UK., Barker B; Oracle for Research, Austin, TX, USA., Rajapaksha H; Oracle for Research, Austin, TX, USA., Pitts R; Oracle for Research, Austin, TX, USA., Gibbs T; NVIDIA Corp, Santa Clara, CA, USA., Stone J; University of Illinois at Urbana-Champaign, Urbana, IL, USA.; NVIDIA Corp, Santa Clara, CA, USA., Zuckerman DM; Oregon Health & Science University, Portland, OR, USA., Mulholland AJ; University of Bristol, UK., Miller T 3rd; Entos, Inc., San Diego, CA, USA.; California Institute of Technology, Pasadena, CA, USA., Jha S; Brookhaven National Lab and Rutgers University., Ramanathan A; Argonne National Laboratory, Lemont, IL, USA., Chong L; University of Pittsburgh, Pittsburgh, PA, USA., Amaro RE; UC San Diego, La Jolla, CA, USA. |
| المصدر: | The international journal of high performance computing applications [Int J High Perform Comput Appl] 2023 Jan; Vol. 37 (1), pp. 28-44. Date of Electronic Publication: 2022 Oct 02. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: Sage Science Press Country of Publication: United States NLM ID: 100911700 Publication Model: Print-Electronic Cited Medium: Print ISSN: 1094-3420 (Print) Linking ISSN: 10943420 NLM ISO Abbreviation: Int J High Perform Comput Appl Subsets: PubMed not MEDLINE |
| أسماء مطبوعة: | Original Publication: Thousand Oaks, CA : Sage Science Press, c1998- |
| مستخلص: | We seek to completely revise current models of airborne transmission of respiratory viruses by providing never-before-seen atomic-level views of the SARS-CoV-2 virus within a respiratory aerosol. Our work dramatically extends the capabilities of multiscale computational microscopy to address the significant gaps that exist in current experimental methods, which are limited in their ability to interrogate aerosols at the atomic/molecular level and thus obscure our understanding of airborne transmission. We demonstrate how our integrated data-driven platform provides a new way of exploring the composition, structure, and dynamics of aerosols and aerosolized viruses, while driving simulation method development along several important axes. We present a series of initial scientific discoveries for the SARS-CoV-2 Delta variant, noting that the full scientific impact of this work has yet to be realized. Competing Interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship, and/or publication of this article. (© The Author(s) 2022.) |
| التعليقات: | Update of: bioRxiv. 2021 Nov 15;:. (PMID: 34816263) |
| References: | Parallel Comput. 2016 Jul;55:17-27. (PMID: 27274603) Cell. 2020 Apr 16;181(2):281-292.e6. (PMID: 32155444) J Chem Phys. 2021 Nov 28;155(20):204103. (PMID: 34852495) Nat Commun. 2021 Jun 8;12(1):3433. (PMID: 34103506) Sci Data. 2022 Jun 17;9(1):327. (PMID: 35715420) J Chem Theory Comput. 2014 Jul 8;10(7):2658-2667. (PMID: 25246856) Nature. 2020 Dec;588(7838):498-502. (PMID: 32805734) Biochem Soc Trans. 2018 Jun 19;46(3):707-719. (PMID: 29802217) Science. 2020 Mar 13;367(6483):1260-1263. (PMID: 32075877) J Phys Chem B. 2013 Sep 5;117(35):10183-92. (PMID: 23924441) Annu Rev Biophys. 2017 May 22;46:43-57. (PMID: 28301772) J Phys Chem B. 2018 Feb 1;122(4):1484-1494. (PMID: 29293344) J Mol Graph. 1996 Feb;14(1):33-8, 27-8. (PMID: 8744570) Am J Physiol Lung Cell Mol Physiol. 2019 Oct 1;317(4):L498-L509. (PMID: 31389736) Biochim Biophys Acta Biomembr. 2018 Jun;1860(6):1309-1317. (PMID: 29474890) Clin Infect Dis. 2022 May 30;74(10):1722-1728. (PMID: 34358292) Protein Eng. 1999 Jun;12(6):439-46. (PMID: 10388840) Sci Rep. 2019 Nov 22;9(1):17350. (PMID: 31758042) Eur Phys J B. 2021;94(7):144. (PMID: 34720710) J Chem Theory Comput. 2015 Apr 14;11(4):1864-74. (PMID: 26574392) Elife. 2019 Apr 01;8:. (PMID: 30932812) J Chem Theory Comput. 2016 Jan 12;12(1):405-13. (PMID: 26631602) J Comput Chem. 2009 Oct;30(13):2157-64. (PMID: 19229944) J Chem Theory Comput. 2009 Aug 20;5(9):2353-2370. (PMID: 20161005) Science. 2020 Oct 9;370(6513):203-208. (PMID: 32817270) Mol Cell Proteomics. 2018 Nov;17(11):2164-2176. (PMID: 30097532) J Chem Theory Comput. 2020 Nov 10;16(11):6763-6775. (PMID: 32990438) J R Soc Interface. 2018 Feb;15(139):. (PMID: 29491178) J Comput Chem. 2005 Dec;26(16):1781-802. (PMID: 16222654) J Chem Phys. 2020 Jul 28;153(4):044130. (PMID: 32752662) J Chem Theory Comput. 2015 Feb 10;11(2):800-9. (PMID: 26392815) High Perform Comput (2016). 2016 Jun;9945:188-206. (PMID: 29202130) Comput Struct Biotechnol J. 2021 Dec 11;20:139-147. (PMID: 34934478) J Chem Theory Comput. 2013 Sep 10;9(9):3878-88. (PMID: 26592383) Nat Struct Mol Biol. 2020 Dec;27(12):1202-1208. (PMID: 33177698) Science. 2021 Dec 24;374(6575):1621-1626. (PMID: 34751595) Glycobiology. 2019 Apr 1;29(4):320-331. (PMID: 30689864) J Autoimmun. 2021 Nov;124:102715. (PMID: 34399188) J Chem Inf Model. 2022 Jan 10;62(1):116-128. (PMID: 34793155) PLoS Comput Biol. 2014 Jul 17;10(7):e1003720. (PMID: 25032790) J Chem Phys. 2020 Sep 28;153(12):124111. (PMID: 33003742) Elife. 2021 Mar 23;10:. (PMID: 33755013) J Chem Theory Comput. 2022 Feb 8;18(2):638-649. (PMID: 35043623) Science. 2020 Nov 27;370(6520):1089-1094. (PMID: 33082295) Science. 2021 Aug 27;373(6558):. (PMID: 34446582) Nature. 2020 Dec;588(7837):327-330. (PMID: 32942285) J Comput Chem. 2011 Nov 15;32(14):3135-41. (PMID: 21815173) Comput Struct Biotechnol J. 2021;19:5140-5148. (PMID: 34490059) J Chem Phys. 2020 Oct 7;153(13):134110. (PMID: 33032406) Indoor Air. 2021 Mar;31(2):314-323. (PMID: 32979298) Nat Chem. 2021 Jul;13(7):651-659. (PMID: 34031561) J Am Chem Soc. 2019 Dec 26;141(51):19953-19958. (PMID: 31805762) J Am Chem Soc. 2019 Apr 24;141(16):6519-6526. (PMID: 30892023) Chem Sci. 2018 Dec 27;10(8):2360-2372. (PMID: 30881664) Parallel Comput. 2020 May;102:. (PMID: 34824485) J Phys Chem B. 2010 Jun 17;114(23):7830-43. (PMID: 20496934) ACS Cent Sci. 2020 Oct 28;6(10):1722-1734. (PMID: 33140034) Proteins. 2010 Jul;78(9):2029-40. (PMID: 20455260) BMC Bioinformatics. 2018 Dec 21;19(Suppl 18):484. (PMID: 30577777) Biophys J. 1996 Jan;70(1):97-110. (PMID: 8770190) Brief Bioinform. 2021 Mar 22;22(2):1499-1507. (PMID: 33634309) Nat Chem. 2021 Oct;13(10):963-968. (PMID: 34413500) J Phys Chem A. 2021 Feb 25;125(7):1642-1649. (PMID: 33577732) Nat Methods. 2017 Jan;14(1):71-73. (PMID: 27819658) J Comput Chem. 2013 Sep 30;34(25):2135-45. (PMID: 23832629) Glycobiology. 2005 Aug;15(8):791-804. (PMID: 15814823) Lancet Respir Med. 2020 Sep;8(9):914-924. (PMID: 32717211) ACS Cent Sci. 2021 Jan 27;7(1):200-209. (PMID: 33532579) |
| معلومات مُعتمدة: | BB/L01386X/1 United Kingdom BB_ Biotechnology and Biological Sciences Research Council; P41 GM104601 United States GM NIGMS NIH HHS; R01 GM115805 United States GM NIGMS NIH HHS; R01 GM132826 United States GM NIGMS NIH HHS |
| فهرسة مساهمة: | Keywords: AI; COVID-19; Delta; GPU; HPC; SARS-CoV-2; aerosols; computational virology; deep learning; molecular dynamics; multiscale simulation; weighted ensemble |
| تواريخ الأحداث: | Date Created: 20230117 Latest Revision: 20240216 |
| رمز التحديث: | 20240216 |
| مُعرف محوري في PubMed: | PMC9527558 |
| DOI: | 10.1177/10943420221128233 |
| PMID: | 36647365 |
| قاعدة البيانات: | MEDLINE |
Full Text Finder | تدمد: | 1094-3420 |
|---|---|
| DOI: | 10.1177/10943420221128233 |