Leveraging quantum computing for dynamic analyses of logical networks in systems biology.
Boolean networks
cortical area development network
gene-regulatory networks
quantum algorithms
quantum computing
systems biology
Journal
Patterns (New York, N.Y.)
ISSN: 2666-3899
Titre abrégé: Patterns (N Y)
Pays: United States
ID NLM: 101767765
Informations de publication
Date de publication:
10 Mar 2023
10 Mar 2023
Historique:
received:
06
09
2022
revised:
12
12
2022
accepted:
09
02
2023
entrez:
24
3
2023
pubmed:
25
3
2023
medline:
25
3
2023
Statut:
epublish
Résumé
The dynamics of cellular mechanisms can be investigated through the analysis of networks. One of the simplest but most popular modeling strategies involves logic-based models. However, these models still face exponential growth in simulation complexity compared with a linear increase in nodes. We transfer this modeling approach to quantum computing and use the upcoming technique in the field to simulate the resulting networks. Leveraging logic modeling in quantum computing has many benefits, including complexity reduction and quantum algorithms for systems biology tasks. To showcase the applicability of our approach to systems biology tasks, we implemented a model of mammalian cortical development. Here, we applied a quantum algorithm to estimate the tendency of the model to reach particular stable conditions and further revert dynamics. Results from two actual quantum processing units and a noisy simulator are presented, and current technical challenges are discussed.
Identifiants
pubmed: 36960443
doi: 10.1016/j.patter.2023.100705
pii: S2666-3899(23)00042-9
pmc: PMC10028428
doi:
Types de publication
Journal Article
Langues
eng
Pagination
100705Informations de copyright
© 2023 The Authors.
Déclaration de conflit d'intérêts
The authors declare no competing interests.
Références
Theory Biosci. 2012 Sep;131(3):181-91
pubmed: 22127955
IEEE Trans Nanobioscience. 2021 Jul;20(3):323-330
pubmed: 33690123
IEEE/ACM Trans Comput Biol Bioinform. 2011 Sep-Oct;8(5):1393-9
pubmed: 21778527
Front Physiol. 2020 Jul 31;11:848
pubmed: 32848827
Sci Adv. 2021 Jul 16;7(29):
pubmed: 34272246
Nat Commun. 2019 Nov 29;10(1):5464
pubmed: 31784527
Phys Rev A. 1995 Oct;52(4):R2493-R2496
pubmed: 9912632
Nat Commun. 2020 Aug 26;11(1):4256
pubmed: 32848126
Bioinformatics. 2010 May 15;26(10):1378-80
pubmed: 20378558
J Theor Biol. 1991 Apr 21;149(4):467-505
pubmed: 2062105
PLoS One. 2015 Jul 24;10(7):e0131832
pubmed: 26207376
Bioinformatics. 2011 Jun 1;27(11):1529-36
pubmed: 21471013
Sci Rep. 2021 Jun 23;11(1):13183
pubmed: 34162895
Phys Rev Lett. 2005 Apr 1;94(12):128701
pubmed: 15903968
Neuron. 2007 Oct 25;56(2):252-69
pubmed: 17964244
AMB Express. 2011 Dec 05;1:45
pubmed: 22141422
PLoS Comput Biol. 2010 Sep 16;6(9):
pubmed: 20862356
J Cell Sci. 2005 Nov 1;118(Pt 21):4947-57
pubmed: 16254242
Science. 2005 Oct 21;310(5747):449-51
pubmed: 16239464
BMC Syst Biol. 2012 Aug 07;6:96
pubmed: 22871178
J Theor Biol. 2008 Dec 7;255(3):269-77
pubmed: 18692073
Nat Commun. 2021 Jan 11;12(1):233
pubmed: 33431845
Nat Methods. 2021 Jul;18(7):715-719
pubmed: 34163087
Bioinformatics. 2006 Jul 15;22(14):e124-31
pubmed: 16873462
Nucleic Acids Res. 2011 Jan;39(Database issue):D561-8
pubmed: 21045058
Comput Struct Biotechnol J. 2020 Mar 10;18:571-582
pubmed: 32257043
Comput Struct Biotechnol J. 2021 Sep 15;19:5321-5332
pubmed: 34630946
Biology (Basel). 2017 Dec 18;6(4):
pubmed: 29258225
J Theor Biol. 1969 Mar;22(3):437-67
pubmed: 5803332
Cancers (Basel). 2021 Feb 10;13(4):
pubmed: 33578795
Phys Rev Lett. 2014 Nov 21;113(21):210501
pubmed: 25479481
Drug Discov Today. 2021 Jul;26(7):1680-1688
pubmed: 34119668