JD
Jonathan P. K. Doye
cond-mat.softq-bio.BMcond-mat.stat-mechphysics.bio-phphysics.chem-phMolecular Dynamics SimulationDNA nanotechnologyNucleic Acid Conformationself-assemblyDNA
On Valency
published · living versionsW_hy4un5bc·v1 · currentpublished
DNA nanotweezers studied with a coarse-grained model of DNA
with Thomas E. Ouldridge, Ard A. Louis
1 version
Preprints & journals
112 papers in the corpus · 1997–2025A patchy-particle three-dimensional octagonal quasicrystal.41467683 · Kowaguchi, Akie, Mehta, Savan, Doye, Jonathan P K et al.2025 · 2 citationsThe Journal of chemical physics. 2025;163(24)
Chirality transfer in lyotropic twist-bend nematics.41247211 · Ashkinazi, Anna, Chhabra, Hemani, El Moumane, Anouar et al.2025 · 1 citationThe Journal of chemical physics. 2025;163(19)
Controlling DNA-RNA strand displacement kinetics with base distribution.40478881 · Ratajczyk, Eryk J, Bath, Jonathan, Šulc, Petr et al.2025 · 9 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(23):e2416988122
A One-Component Patchy-Particle Icosahedral Quasicrystal.40168641 · Noya, Eva G, Doye, Jonathan P K2025 · 6 citationsACS nano. 2025;19(14):13714-13722
Reconfigurable nanomaterials folded from multicomponent chains of DNA origami voxels.39602517 · Luu, Minh Tri, Berengut, Jonathan F, Li, Jiahe et al.2024 · 16 citationsScience robotics. 2024;9(96):eadp2309
Pipelined information flow in molecular mechanical circuits leads to increased error and irreversibility.39562862 · Seet, Ian, Ouldridge, Thomas E, Doye, Jonathan P K2024 · 1 citationPhysical review. E. 2024;110(4-2):045310
Punctuated and continuous structural diversity of S-layers across the prokaryotic tree of life10.1101/2024.05.28.596244v1 · Johnston, E., Isbilir, B., Alva, V. et al.2024 · 17 citationsbioRxiv
Coarse-grained modeling of DNA-RNA hybrids.38497475 · Ratajczyk, Eryk J, Šulc, Petr, Turberfield, Andrew J et al.2024 · 22 citationsThe Journal of chemical physics. 2024;160(11)
Reconfigurable multi-component nanostructures built from DNA origami voxels10.1101/2024.03.10.584331v1 · Luu, M. T., Berengut, J., Daljit Singh, J. K. et al.2024 · 0 citationsbioRxiv
Simulation of reversible molecular mechanical logic gates and circuits.36932514 · Seet, Ian, Ouldridge, Thomas E, Doye, Jonathan P K2023 · 7 citationsPhysical review. E. 2023;107(2-1):024134
The oxDNA Coarse-Grained Model as a Tool to Simulate DNA Origami.37166713 · Doye, Jonathan P K, Fowler, Hannah, Prešern, Domen et al.2023 · 31 citationsMethods in molecular biology (Clifton, N.J.). 2023;2639:93-112
Reply to Ocklenburg and Mundorf: The interplay of developmental bias and natural selection.35787035 · Johnston, Iain G, Dingle, Kamaludin, Greenbury, Sam F et al.2022 · 6 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(28):e2205299119
Planar 2D wireframe DNA origami.35594345 · Wang, Xiao, Li, Shanshan, Jun, Hyungmin et al.2022 · 27 citationsScience advances. 2022;8(20):eabn0039
The interplay of supercoiling and thymine dimers in DNA.35188542 · Lim, Wilber, Randisi, Ferdinando, Doye, Jonathan P K et al.2022 · 13 citationsNucleic acids research. 2022;50(5):2480-2492
Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution.35275794 · Johnston, Iain G, Dingle, Kamaludin, Greenbury, Sam F et al.2022 · 128 citationsProceedings of the National Academy of Sciences of the United States of America. 2022;119(11):e2113883119
Characterizing the free-energy landscapes of DNA origamis.35129570 · Wong, Chak Kui, Tang, Chuyan, Schreck, John S et al.2022 · 16 citationsNanoscale. 2022;14(7):2638-2648
The free-energy landscape of a mechanically bistable DNA origami2201.08920v1 · Chak Kui Wong, Jonathan P. K. Doye2022 · 2 citationsAppl. Sci. 12, 5875 (2022)
Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling2111.10166v1 · Jonathan P. K. Doye, Ard A. Louis, John S. Schreck et al.2021 · 2 citationsFrontiers of Nanoscience, Vol. 21, Ch. 9, pp 195-210 (2022)
Massively Parallelized Molecular Force Manipulation with On-Demand Thermal and Optical Control.34762807 · Su, Hanquan, Brockman, Joshua M, Duan, Yuxin et al.2022 · 8 citationsJournal of the American Chemical Society. 2021;143(46):19466-19473
How to design an icosahedral quasicrystal through directional bonding.34408331 · Noya, Eva G, Wong, Chak Kui, Llombart, Pablo et al.2021 · 64 citationsNature. 2021;596(7872):367-371
Computational explorations in the space of one-component crystals.34011676 · Doye, Jonathan P K, Noya, Eva G2021 · 1 citationProceedings of the National Academy of Sciences of the United States of America. 2021;118(23)
Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation.33232603 · Berengut, Jonathan F, Wong, Chak Kui, Berengut, Julian C et al.2022 · 44 citationsACS nano. 2020;14(12):17428-17441
Computing the Elastic Mechanical Properties of Rodlike DNA Nanostructures.33164531 · Chhabra, Hemani, Mishra, Garima, Cao, Yijing et al.2021 · 24 citationsJournal of chemical theory and computation. 2020;16(12):7748-7763
Measuring internal forces in single-stranded DNA: Application to a DNA force clamp2007.13865v1 · Megan C. Engel, Flavio Romano, Ard A. Louis et al.2020 · 10 citationsJ. Chem. Theor. Comput. 16, 7764-7775 (2020)
Reconfigurable T-junction DNA Origami.32524699 · Young, Katherine G, Najafi, Behnam, Sant, William M et al.2020 · 4 citationsAngewandte Chemie (International ed. in English). 2020;59(37):15942-15946
Designer protein assemblies with tunable phase diagrams in living cells.32661377 · Heidenreich, Meta, Georgeson, Joseph M, Locatelli, Emanuele et al.2020 · 98 citationsNature chemical biology. 2020;16(9):939-945
Characterising DNA T-motifs by Simulation and Experiment2005.11545v1 · Behnam Najafi, Katherine G. Young, Jonathan Bath et al.2020 · 0 citationsarXiv
Design and synthesis of pleated DNA origami nanotubes with adjustable diameters.31728524 · Berengut, Jonathan F, Berengut, Julian C, Doye, Jonathan P K et al.2020 · 21 citationsNucleic acids research. 2019;47(22):11963-11975
Substrate conformational dynamics facilitate structure-specific recognition of gapped DNA by DNA polymerase.31544938 · Craggs, Timothy D, Sustarsic, Marko, Plochowietz, Anne et al.2020 · 47 citationsNucleic acids research. 2019;47(20):10788-10800
Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model.31282669 · Harrison, Ryan M, Romano, Flavio, Ouldridge, Thomas E et al.2019 · 33 citationsJournal of chemical theory and computation. 2019;15(8):4660-4672
TacoxDNA: A user-friendly web server for simulations of complex DNA structures, from single strands to origami.31301183 · Suma, Antonio, Poppleton, Erik, Matthies, Michael et al.2020 · 108 citationsJournal of computational chemistry. 2019;40(29):2586-2595
Force-Induced Unravelling of DNA Origami.29851456 · Engel, Megan C, Smith, David M, Jobst, Markus A et al.2019 · 62 citationsACS nano. 2018;12(7):6734-6747
DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size.29294083 · Khara, Dinesh C, Schreck, John S, Tomov, Toma E et al.2019 · 38 citationsNucleic acids research. 2018;46(3):1553-1561
Incorporating particle flexibility in a density functional description of nematics and cholesterics1801.10601v8 · Maxime M.C. Tortora, Jonathan P.K. Doye2018 · 16 citationsMol. Phys. 116, 2773-2791 (2018)
Rolling circle amplification shows a sinusoidal template length-dependent amplification bias.29237070 · Joffroy, Bastian, Uca, Yavuz O, Prešern, Domen et al.2019 · 84 citationsNucleic acids research. 2018;46(2):538-545
Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model.29083876 · Sharma, Rahul, Schreck, John S, Romano, Flavio et al.2019 · 50 citationsACS nano. 2017;11(12):12426-12435
Publisher's Note: "Perturbative density functional methods for cholesteric liquid crystals" [J. Chem. Phys. 146, 184504 (2017)].28571371 · Tortora, Maxime M C, Doye, Jonathan P K2019 · 0 citationsThe Journal of chemical physics. 2017;146(20):209902
Perturbative density functional methods for cholesteric liquid crystals1702.06377v4 · Maxime M.C. Tortora, Jonathan P.K. Doye2017 · 12 citationsJ. Chem. Phys. 146 (2017) 184504
Self-assembly of two-dimensional binary quasicrystals: a possible route to a DNA quasicrystal.27830657 · Reinhardt, Aleks, Schreck, John S, Romano, Flavio et al.2018 · 29 citationsJournal of physics. Condensed matter : an Institute of Physics journal. 2017;29(1):014006
Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation.27664220 · Sutthibutpong, Thana, Matek, Christian, Benham, Craig et al.2017 · 51 citationsNucleic acids research. 2016;44(19):9121-9130
DNA-stabilized Ag-Au bimetallic clusters: the effects of alloying and embedding on optical properties.27459508 · Palagin, Dennis, Doye, Jonathan P K2018 · 8 citationsPhysical chemistry chemical physics : PCCP. 2016;18(32):22311-22
Characterizing DNA Star-Tile-Based Nanostructures Using a Coarse-Grained Model.27010928 · Schreck, John S, Romano, Flavio, Zimmer, Matthew H et al.2017 · 40 citationsACS nano. 2016;10(4):4236-47
Design principles for rapid folding of knotted DNA nanostructures.26887681 · Kočar, Vid, Schreck, John S, Čeru, Slavko et al.2016 · 55 citationsNature communications. 2016;7:10803
Direct Simulation of the Self-Assembly of a Small DNA Origami.26766072 · Snodin, Benedict E K, Romano, Flavio, Rovigatti, Lorenzo et al.2016 · 99 citationsACS nano. 2016;10(2):1724-37
Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors.26575598 · Mosayebi, Majid, Louis, Ard A, Doye, Jonathan P K et al.2016 · 99 citationsACS nano. 2015;9(12):11993-2003
Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"1506.09005v1 · Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge et al.2015 · 7 citationsarXivon Valency
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA.26093573 · Snodin, Benedict E K, Randisi, Ferdinando, Mosayebi, Majid et al.2016 · 385 citationsThe Journal of chemical physics. 2015;142(23):234901
DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization.26056172 · Schreck, John S, Ouldridge, Thomas E, Romano, Flavio et al.2015 · 57 citationsNucleic acids research. 2015;43(13):6181-90
CO oxidation catalysed by Pd-based bimetallic nanoalloys.25820575 · Palagin, Dennis, Doye, Jonathan P K2016 · 29 citationsPhysical chemistry chemical physics : PCCP. 2015;17(42):28010-21
Modelling toehold-mediated RNA strand displacement.25762335 · Šulc, Petr, Ouldridge, Thomas E, Romano, Flavio et al.2016 · 67 citationsBiophysical journal. 2015;108(5):1238-47
Career total: 210 works. 112 are in this corpus.Showing the 50 most recent.
Profile built from the corpus for this byline.
Author records are still filling in while the Hub is in alpha. If this is your page, you'll be able to claim it soon. Spot a mistake? Tell us.