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For: Ouldridge TE. DNA nanotechnology: understanding and optimisation through simulation. Mol Phys 2014. [DOI: 10.1080/00268976.2014.975293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Number Cited by Other Article(s)
1
Qiao YP, Ren CL, Ma YQ. Two Different Ways of Stress Release in Supercoiled DNA Minicircles under DNA Nick. J Phys Chem B 2023;127:4015-4021. [PMID: 37126597 DOI: 10.1021/acs.jpcb.2c08618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
2
Atitey K. DEGBOE: Discrete time Evolution modeling of Gene mutation through Bayesian inference using qualitative Observation of mutation Events. J Biomed Inform 2022;134:104197. [PMID: 36084801 PMCID: PMC9809132 DOI: 10.1016/j.jbi.2022.104197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 08/02/2022] [Accepted: 09/01/2022] [Indexed: 01/05/2023]
3
van den Berg MP, Scamman WC, Stubbs JM. Monte Carlo molecular simulation of solution and surface-bound DNA hybridization of short oligomers at varying surface densities. Biophys Chem 2022;284:106784. [DOI: 10.1016/j.bpc.2022.106784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/11/2022] [Accepted: 02/19/2022] [Indexed: 11/27/2022]
4
KOH HEEYUEN, LEE JAEGYUNG, LEE JAEYOUNG, KIM RYAN, TABATA OSAMU, JIN-WOO KIM, KIM DONYUN. Design Approaches and Computational Tools for DNA Nanostructures. IEEE OPEN JOURNAL OF NANOTECHNOLOGY 2021;2:86-100. [PMID: 35756857 PMCID: PMC9232119 DOI: 10.1109/ojnano.2021.3119913] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
5
Plesa T, Stan GB, Ouldridge TE, Bae W. Quasi-robust control of biochemical reaction networks via stochastic morphing. J R Soc Interface 2021;18:20200985. [PMID: 33849334 PMCID: PMC8086924 DOI: 10.1098/rsif.2020.0985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 03/18/2021] [Indexed: 01/09/2023]  Open
6
Haley NEC, Ouldridge TE, Mullor Ruiz I, Geraldini A, Louis AA, Bath J, Turberfield AJ. Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement. Nat Commun 2020;11:2562. [PMID: 32444600 PMCID: PMC7244503 DOI: 10.1038/s41467-020-16353-y] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 04/15/2020] [Indexed: 11/09/2022]  Open
7
O’Brien J, Murugan A. Temporal Pattern Recognition through Analog Molecular Computation. ACS Synth Biol 2019;8:826-832. [PMID: 30836003 DOI: 10.1021/acssynbio.8b00503] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
8
Sieradzan AK, Golon Ł, Liwo A. Prediction of DNA and RNA structure with the NARES-2P force field and conformational space annealing. Phys Chem Chem Phys 2018;20:19656-19663. [PMID: 30014063 DOI: 10.1039/c8cp03018a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
9
Shi Z, Castro CE, Arya G. Conformational Dynamics of Mechanically Compliant DNA Nanostructures from Coarse-Grained Molecular Dynamics Simulations. ACS NANO 2017;11:4617-4630. [PMID: 28423273 DOI: 10.1021/acsnano.7b00242] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
10
Joshi H, Kaushik A, Seeman NC, Maiti PK. Nanoscale Structure and Elasticity of Pillared DNA Nanotubes. ACS NANO 2016;10:7780-91. [PMID: 27400249 DOI: 10.1021/acsnano.6b03360] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
11
Dans PD, Walther J, Gómez H, Orozco M. Multiscale simulation of DNA. Curr Opin Struct Biol 2016;37:29-45. [DOI: 10.1016/j.sbi.2015.11.011] [Citation(s) in RCA: 99] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Revised: 11/23/2015] [Accepted: 11/25/2015] [Indexed: 01/05/2023]
12
Jacobs WM, Frenkel D. Self-Assembly of Structures with Addressable Complexity. J Am Chem Soc 2016;138:2457-67. [DOI: 10.1021/jacs.5b11918] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
13
Softley T. Announcement of the winner of the Longuet-Higgins Early Career Researcher Prize 2014. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1082702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
14
Naômé A, Laaksonen A, Vercauteren DP. A Coarse-Grained Simulation Study of the Structures, Energetics, and Dynamics of Linear and Circular DNA with Its Ions. J Chem Theory Comput 2015;11:2813-26. [DOI: 10.1021/acs.jctc.5b00113] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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