{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,10]],"date-time":"2026-02-10T19:50:37Z","timestamp":1770753037251,"version":"3.50.0"},"reference-count":32,"publisher":"American Association for the Advancement of Science (AAAS)","funder":[{"name":"Zhejiang Lab","award":["2021RD0AB01"],"award-info":[{"award-number":["2021RD0AB01"]}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["designated grant by trustee Mr. WANG Wei"],"award-info":[{"award-number":["designated grant by trustee Mr. WANG Wei"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["spj.science.org"],"crossmark-restriction":true},"short-container-title":["Intell Comput"],"published-print":{"date-parts":[[2024,1]]},"abstract":"<jats:p>Nuclear electric resonance (NER) offers a method of controlling nuclear spins using electric field gradients (EFGs), which is a critical concept in quantum computing. In this study, we focus on nitrogen atoms in DNA, which have a nuclear spin of 1 and are influenced by EFGs. Utilizing molecular dynamics simulations, quantum chemical computations, and theoretical analyses, we studied the characteristics of EFGs in the context of DNA. Our results show that the orientation patterns of the EFGs at the positions of nitrogen atoms in DNA bases vary with different types of bases and nitrogen atom sites. Consequently, the genetic and structural information of DNA is encoded into the direction of the nitrogen nuclear spins. Furthermore, the interaction and evolution of these nitrogen nuclear spins with surrounding nuclear spins suggest the potential for quantum computing of genetic information. Our findings not only provide new insights into quantum phenomena in biological systems but also lay the groundwork for expanding the theoretical foundations of DNA quantum computing and offer innovative approaches for the design of future biocompatible quantum computers.<\/jats:p>","DOI":"10.34133\/icomputing.0094","type":"journal-article","created":{"date-parts":[[2024,11,21]],"date-time":"2024-11-21T08:31:58Z","timestamp":1732177918000},"update-policy":"https:\/\/doi.org\/10.34133\/aaas_crossmark_01","source":"Crossref","is-referenced-by-count":2,"title":["Encoding Genetic and Structural Information in DNA Using Electric Field Gradients and Nuclear Spins"],"prefix":"10.34133","volume":"3","author":[{"ORCID":"https:\/\/orcid.org\/0009-0003-4069-3155","authenticated-orcid":false,"given":"Yu","family":"Zheng","sequence":"first","affiliation":[{"name":"School of Electronics, \rPeking University, Beijing 100871, China."}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0009-0009-7341-4072","authenticated-orcid":true,"given":"Quansheng","family":"Ren","sequence":"additional","affiliation":[{"name":"School of Electronics, \rPeking University, Beijing 100871, China."}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"221","published-online":{"date-parts":[[2024,12,12]]},"reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.7973651"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1002\/sstr.202100051"},{"key":"e_1_3_3_4_2","doi-asserted-by":"crossref","unstructured":"Lipton RJ. DNA based computers. Providence (RI): American Mathematical Society; 1996.","DOI":"10.1090\/dimacs\/027"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1021\/ja047628k"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1038\/35003155"},{"issue":"4","key":"e_1_3_3_7_2","doi-asserted-by":"crossref","first-page":"1385","DOI":"10.1073\/pnas.97.4.1385","article-title":"Molecular computation: RNA solutions to chess problems","volume":"97","author":"Faulhammer D","year":"2000","unstructured":"Faulhammer D, Cukras AR, Lipton RJ, Landweber LF. Molecular computation: RNA solutions to chess problems. Proc Natl Acad Sci USA. 2000;97(4):1385\u20131389.","journal-title":"Proc Natl Acad Sci USA"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1126\/science.278.5337.446"},{"issue":"2","key":"e_1_3_3_9_2","doi-asserted-by":"crossref","first-page":"R27","DOI":"10.1088\/0957-4484\/17\/2\/R01","article-title":"DNA computing: Applications and challenges","volume":"17","author":"Ezziane Z","year":"2005","unstructured":"Ezziane Z. DNA computing: Applications and challenges. Nanotechnology. 2005;17(2):R27.","journal-title":"Nanotechnology"},{"key":"e_1_3_3_10_2","unstructured":"Chen J Wang Y Deaton R. Large scale genomic monitoring or profiling using a DNA-based memory and microarrays. Paper presented at: Proceedings of the 24th Army Science Conference; 2004; Orlando FL USA."},{"issue":"2","key":"e_1_3_3_11_2","doi-asserted-by":"crossref","first-page":"74","DOI":"10.3991\/ijim.v11i2.6564","article-title":"DNA computing: Challenges and application","volume":"11","author":"El-Seoud SA","year":"2017","unstructured":"El-Seoud SA, Mohamed R, Ghoneimy S. DNA computing: Challenges and application. Int J Interact Mobile Technol. 2017;11(2):74\u201387.","journal-title":"Int J Interact Mobile Technol"},{"issue":"2","key":"e_1_3_3_12_2","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1109\/TMBMC.2023.3272230","article-title":"Quantum computation by biological systems","volume":"9","author":"D\u2019Acunto M","year":"2023","unstructured":"D\u2019Acunto M. Quantum computation by biological systems. IEEE Trans Mol Biol Multi-Scale Commun. 2023;9(2):257\u2013262.","journal-title":"IEEE Trans Mol Biol Multi-Scale Commun"},{"issue":"1","key":"e_1_3_3_13_2","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.cplett.2007.01.054","article-title":"Triplet\u2013singlet spin communication between DNA nucleotides serves the basis for quantum computing","volume":"436","author":"Tulub AA","year":"2007","unstructured":"Tulub AA, Stefanov VE. Triplet\u2013singlet spin communication between DNA nucleotides serves the basis for quantum computing. Chem Phys Lett. 2007;436(1-3):258\u2013262.","journal-title":"Chem Phys Lett"},{"key":"e_1_3_3_14_2","unstructured":"Pitk\u00e4nen M. The notion of wave genome and DNA as topological quantum computer. 2010."},{"key":"e_1_3_3_15_2","unstructured":"Deaton R. DNA and quantum computers. Paper presented at: Proceedings of the 3rd Annual Conference on Genetic and Evolutionary Computation; 2001; San Francisco CA USA."},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1038\/s41586-020-2057-7"},{"key":"e_1_3_3_17_2","doi-asserted-by":"crossref","unstructured":"Asaad S. Electrical control and quantum chaos with a high-spin nucleus in silicon. Cham (Switzerland): Springer Nature; 2021.","DOI":"10.1007\/978-3-030-83473-9"},{"issue":"17","key":"e_1_3_3_18_2","doi-asserted-by":"crossref","first-page":"13374","DOI":"10.1039\/D3CP06207D","article-title":"Nuclear spin alignment of sodium ions via electric field gradients in phospholipid membranes","volume":"26","author":"Zheng Y","year":"2024","unstructured":"Zheng Y, Ren Q. Nuclear spin alignment of sodium ions via electric field gradients in phospholipid membranes. Phys Chem Chem Phys. 2024;26(17):13374\u201313382.","journal-title":"Phys Chem Chem Phys"},{"key":"e_1_3_3_19_2","doi-asserted-by":"crossref","unstructured":"Macke TJ Case DA. Modeling unusual nucleic acid structures. New York (NY): ACS Publications; 1998.","DOI":"10.1021\/bk-1998-0682.ch024"},{"issue":"1","key":"e_1_3_3_20_2","doi-asserted-by":"crossref","first-page":"55","DOI":"10.1038\/nmeth.3658","article-title":"Parmbsc1: A refined force field for DNA simulations","volume":"13","author":"Ivani I","year":"2016","unstructured":"Ivani I, Dans PD, Noy A, P\u00e9rez A, Faustino I, Hospital A, Walther J, Andrio P, Go\u00f1i R, Balaceanu A, et al. Parmbsc1: A refined force field for DNA simulations. Nat Methods. 2016;13(1):55\u201358.","journal-title":"Nat Methods"},{"key":"e_1_3_3_21_2","unstructured":"Der Spoel V. GROMACS 2021.3 Source code. Zenodo."},{"issue":"30","key":"e_1_3_3_22_2","doi-asserted-by":"crossref","first-page":"9882","DOI":"10.1021\/jp1035663","article-title":"Molecular dynamics of DNA: Comparison of force fields and terminal nucleotide definitions","volume":"114","author":"Ricci CG","year":"2010","unstructured":"Ricci CG, de Andrade AS, Mottin M, Netz PA. Molecular dynamics of DNA: Comparison of force fields and terminal nucleotide definitions. J Phys Chem B. 2010;114(30):9882\u20139893.","journal-title":"J Phys Chem B"},{"issue":"10","key":"e_1_3_3_23_2","doi-asserted-by":"crossref","first-page":"5584","DOI":"10.1039\/C9CP06844A","article-title":"Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects","volume":"22","author":"Long MP","year":"2020","unstructured":"Long MP, Alland S, Martin ME, Isborn CM. Molecular dynamics simulations of alkaline earth metal ions binding to DNA reveal ion size and hydration effects. Phys Chem Chem Phys. 2020;22(10):5584\u20135596.","journal-title":"Phys Chem Chem Phys"},{"issue":"2","key":"e_1_3_3_24_2","doi-asserted-by":"crossref","first-page":"926","DOI":"10.1063\/1.445869","article-title":"Comparison of simple potential functions for simulating liquid water","volume":"79","author":"Jorgensen WL","year":"1983","unstructured":"Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML. Comparison of simple potential functions for simulating liquid water. J Chem Phys. 1983;79(2):926\u2013935.","journal-title":"J Chem Phys"},{"issue":"12","key":"e_1_3_3_25_2","doi-asserted-by":"crossref","first-page":"1463","DOI":"10.1002\/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H","article-title":"LINCS: A linear constraint solver for molecular simulations","volume":"18","author":"Hess B","year":"1997","unstructured":"Hess B, Bekker H, Berendsen HJ, Fraaije JG. LINCS: A linear constraint solver for molecular simulations. J Comput Chem. 1997;18(12):1463\u20131472.","journal-title":"J Comput Chem"},{"issue":"19","key":"e_1_3_3_26_2","doi-asserted-by":"crossref","first-page":"8577","DOI":"10.1063\/1.470117","article-title":"A smooth particle mesh Ewald method","volume":"103","author":"Essmann U","year":"1995","unstructured":"Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG. A smooth particle mesh Ewald method. J Chem Phys. 1995;103(19):8577\u20138593.","journal-title":"J Chem Phys"},{"issue":"3","key":"e_1_3_3_27_2","doi-asserted-by":"crossref","first-page":"R55","DOI":"10.1016\/S0969-2126(99)80033-1","article-title":"New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations","volume":"7","author":"Darden T","year":"1999","unstructured":"Darden T, Perera L, Li L, Pedersen L. New tricks for modelers from the crystallography toolkit: The particle mesh Ewald algorithm and its use in nucleic acid simulations. Structure. 1999;7(3):R55\u2013R60.","journal-title":"Structure"},{"key":"e_1_3_3_28_2","unstructured":"Frisch MJ Trucks GW Schlegel HB Scuseria GE Robb MA Cheeseman JR Scalmani G Barone V Menucci B Petersson GA et\u00a0al. Gaussian 09 revision A. Wallingford (CT): Gaussian Inc.; 2009."},{"issue":"7","key":"e_1_3_3_29_2","doi-asserted-by":"crossref","first-page":"496","DOI":"10.1139\/v07-069","article-title":"EFGShield\u2014A program for parsing and summarizing the results of electric field gradient and nuclear magnetic shielding tensor calculations","volume":"85","author":"Adiga S","year":"2007","unstructured":"Adiga S, Aebi D, Bryce DL. EFGShield\u2014A program for parsing and summarizing the results of electric field gradient and nuclear magnetic shielding tensor calculations. Can J Chem. 2007;85(7-8):496\u2013505.","journal-title":"Can J Chem"},{"issue":"3","key":"e_1_3_3_30_2","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41592-019-0686-2","article-title":"SciPy 1.0: Fundamental algorithms for scientific computing in Python","volume":"17","author":"Virtanen P","year":"2020","unstructured":"Virtanen P, Gommers R, Oliphant TE, Haberland M, Reddy T, Cournapeau D, Burovski E, Peterson P, Weckesser W, Bright J, et al. SciPy 1.0: Fundamental algorithms for scientific computing in Python. Nat Methods. 2020;17(3):261\u2013272.","journal-title":"Nat Methods"},{"issue":"5","key":"e_1_3_3_31_2","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1016\/S0960-0779(01)00072-8","article-title":"Dynamics of classical quadrupole moment I","volume":"13","author":"Tokita M","year":"2002","unstructured":"Tokita M, Kawabata S. Dynamics of classical quadrupole moment I. Chaos, Solitons Fractals. 2002;13(5):997\u20131015.","journal-title":"Chaos, Solitons Fractals"},{"key":"e_1_3_3_32_2","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1119\/1.1969509","article-title":"Discussion of quadrupole precession","volume":"31","author":"Raich JC","year":"1963","unstructured":"Raich JC, Good RH Jr. Discussion of quadrupole precession. Am J Phys. 1963;31:356\u2013362.","journal-title":"Am J Phys"},{"issue":"4","key":"e_1_3_3_33_2","doi-asserted-by":"crossref","first-page":"516","DOI":"10.1119\/1.1986606","article-title":"Comparison of the magnetic dipole and electric quadrupole spin precessions","volume":"40","author":"Ley-Koo E","year":"1972","unstructured":"Ley-Koo E. Comparison of the magnetic dipole and electric quadrupole spin precessions. Am J Phys. 1972;40(4):516\u2013525.","journal-title":"Am J Phys"}],"container-title":["Intelligent Computing"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/spj.science.org\/doi\/pdf\/10.34133\/icomputing.0094","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,12]],"date-time":"2024-12-12T20:53:20Z","timestamp":1734036800000},"score":1,"resource":{"primary":{"URL":"https:\/\/spj.science.org\/doi\/10.34133\/icomputing.0094"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,1]]},"references-count":32,"alternative-id":["10.34133\/icomputing.0094"],"URL":"https:\/\/doi.org\/10.34133\/icomputing.0094","relation":{},"ISSN":["2771-5892"],"issn-type":[{"value":"2771-5892","type":"electronic"}],"subject":[],"published":{"date-parts":[[2024,1]]},"assertion":[{"value":"2024-04-14","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-07-08","order":1,"name":"revised","label":"Revised","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-09-09","order":2,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2024-12-12","order":3,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}],"article-number":"0094"}}