TO
Thomas E. Ouldridge
physics.bio-phcond-mat.softq-bio.BMcond-mat.stat-mechq-bio.MNphysics.chem-phDNAMolecular Dynamics Simulationsynthetic biologybiophysics
On Valency
published · living versionsW_hy4un5bc·v1 · currentpublished
DNA nanotweezers studied with a coarse-grained model of DNA
with Ard A. Louis, Jonathan P. K. Doye
1 version
Preprints & journals
96 papers in the corpus · 2008–2026Recurrent neural chemical reaction networks trained to switch dynamical behaviours through learned bifurcations.42869459 · Dack, Alexander, Plesa, Tomislav, Ouldridge, Thomas E2026 · 0 citationsJournal of the Royal Society, Interface. 2026;23(243)
Topologically-constrained toehold-mediated strand displacement10.26434/chemrxiv.15009472/v1 · Andrew Stannard, Aditya Sengar, Alexander H. Clowsley et al.2026 · 0 citationsChemRxiv
Fuel-Driven Catalytic Molecular Templating.42584610 · Mitra, Merry, Mukherjee, Rakesh, Jurinović, Križan et al.2026 · 1 citationJournal of the American Chemical Society. 2026;148(31):33027-33038
Recurrent neural chemical reaction networks that approximate arbitrary dynamics.42025162 · Dack, Alexander, Qureshi, Benjamin, Ouldridge, Thomas E et al.2026 · 1 citationCell systems. 2026;17(5):101572
Far-from-equilibrium assembly of multimers through DNA-based catalytic templating10.64898/2026.04.13.718267v2 · Mukherjee, R., Mitra, M., Jurinovic, K. et al.2026 · 1 citationbioRxiv
A versatile method to pattern surfaces within microfluidic devices10.64898/2026.02.19.706879v2 · Collins, K., Stanley, C. E., Ouldridge, T. E.2026 · 0 citationsbioRxiv
Thermodynamic limits in far-from-equilibrium molecular templating networks.41503379 · Qureshi, Benjamin, Poulton, Jenny M, Ouldridge, Thomas E2026 · 2 citationsNewton ((New York, N.Y.). 2026;2(1):None
Design of DNA strand displacement reactions.41349497 · Jurinović, Križan, Mitra, Merry, Mukherjee, Rakesh et al.2025 · 7 citationsCurrent opinion in biotechnology. 2025;97:103396
Biochemical surface patterning in microfluidic devices.41242019 · Collins, Kate, Stanley, Claire E, Ouldridge, Thomas E2025 · 5 citationsCurrent opinion in biotechnology. 2025;96:103390
Setting a direction for molecular recognition.40973807 · Ouldridge, Thomas E, Mukherjee, Rakesh2026 · 0 citationsNature nanotechnology. 2025;20(10):1359-1360
Overcoming the Speed Limit of Four-Way DNA Branch Migration with Bulges in Toeholds.40906898 · Bakhtawar, Samia, Smith, Francesca, Sengar, Aditya et al.2025 · 4 citationsNano letters. 2025;25(37):13772-13779
Information propagation through enzyme-free catalytic templating of DNA dimerization with weak product inhibition.40473818 · Cabello-Garcia, Javier, Mukherjee, Rakesh, Bae, Wooli et al.2025 · 13 citationsNature chemistry. 2025;17(8):1179-1187
Bit reset protocols that obey activity-constrained speed limits do not minimize work for a given speed.40411036 · Mulder, Daan, Ouldridge, Thomas E, Wolde, Pieter Rein Ten2025 · 3 citationsPhysical review. E. 2025;111(4-1):044141
The interplay of heterogeneity and product detachment in templated polymer copying.39918127 · Guntoro, Jeremy E B, Qureshi, Benjamin J, Ouldridge, Thomas E2025 · 5 citationsThe Journal of chemical physics. 2025;162(5)
Autonomous learning of generative models with chemical reaction network ensembles.39837479 · Poole, William, Ouldridge, Thomas E, Gopalkrishnan, Manoj2025 · 7 citationsJournal of the Royal Society, Interface. 2025;22(222):20240373
Is stochastic thermodynamics the key to understanding the energy costs of computation?39471216 · Wolpert, David H, Korbel, Jan, Lynn, Christopher W et al.2026 · 52 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(45):e2321112121
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
Strong sequence-dependence in RNA/DNA hybrid strand displacement kinetics.39235130 · Smith, Francesca G, Goertz, John P, Jurinović, Križan et al.2024 · 16 citationsNanoscale. 2024;16(37):17624-17637
Kinetic Proofreading Can Enhance Specificity in a Nonenzymatic DNA Strand Displacement Network.38951503 · Mukherjee, Rakesh, Sengar, Aditya, Cabello-García, Javier et al.2024 · 17 citationsJournal of the American Chemical Society. 2024;146(28):18916-18926
Thermodynamic limits on general far-from-equilibrium molecular templating networks2404.02791v2 · Benjamin Qureshi, Jenny M. Poulton, Thomas E. Ouldridge2024 · 2 citationsarXiv
The Role of Sequence Information in Minimal Models of Molecular Assembly2402.19225v2 · Jeremy Guntoro, Thomas Ouldridge2024 · 0 citationsarXiv
Exploiting bias in optimal finite-time copying protocols2312.14682v2 · Daan Mulder, Pieter Rein ten Wolde, Thomas E. Ouldridge2023 · 3 citationsPhys. Rev. Research 7, L012026 (2025)
Evaluating DFHBI-Responsive RNA Light-Up Aptamers as Fluorescent Reporters for Gene Expression.37991880 · Climent-Catala, Alicia, Casas-Rodrigo, Ivan, Iyer, Suhasini et al.2023 · 8 citationsACS synthetic biology. 2023;12(12):3754-3765
A universal method for analyzing copolymer growth.36922142 · Qureshi, Benjamin, Juritz, Jordan, Poulton, Jenny M et al.2023 · 6 citationsThe Journal of chemical physics. 2023;158(10):104906
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
A Universal Method for Analysing Copolymer Growth2211.02498v2 · Benjamin J. Qureshi, Jordan Juritz, Jenny M. Poulton et al.2022 · 0 citationsarXiv
Thermodynamics of deterministic finite automata operating locally and periodically2208.06895v3 · Thomas E. Ouldridge, David H. Wolpert2022 · 10 citationsarXiv
The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.35880577 · Hertel, Sophie, Spinney, Richard E, Xu, Stephanie Y et al.2022 · 23 citationsNucleic acids research. 2022;50(14):7829-7841
Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines2205.06313v1 · William Poole, Thomas Ouldridge, Manoj Gopalkrishnan et al.2022 · 4 citationsarXiv
Synthetic biology and bioelectrochemical tools for electrogenetic system engineering.35507663 · Lawrence, Joshua M, Yin, Yutong, Bombelli, Paolo et al.2022 · 42 citationsScience advances. 2022;8(18):eabm5091
Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions.35183080 · Juritz, Jordan, Poulton, Jenny M, Ouldridge, Thomas E2022 · 10 citationsThe Journal of chemical physics. 2022;156(7):074103
Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers.35133150 · Climent-Catala, Alicia, Ouldridge, Thomas E, Stan, Guy-Bart V et al.2022 · 20 citationsACS synthetic biology. 2022;11(2):562-569
Mechanisms underlying sequence-dependent DNA hybridisation rates in the absence of secondary structure10.1101/2021.12.17.473246v1 · Hertel, S., Spinney, R., Xu, S. et al.2021 · 2 citationsbioRxiv
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)
Kinetics of RNA and RNA:DNA Hybrid Strand Displacement.34752075 · Liu, Hao, Hong, Fan, Smith, Francesca et al.2022 · 60 citationsACS synthetic biology. 2021;10(11):3066-3073
A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results2104.11567v1 · Aditya Sengar, Thomas E. Ouldridge, Oliver Henrich et al.2021 · 72 citationsFront. Mol. Biosci. 8, 693710 (2021)
Quasi-robust control of biochemical reaction networks via stochastic morphing.33849334 · Plesa, Tomislav, Stan, Guy-Bart, Ouldridge, Thomas E et al.2021 · 6 citationsJournal of the Royal Society, Interface. 2021;18(177):20200985
Integral feedback in synthetic biology: Negative-equilibrium catastrophe2102.10668v3 · Tomislav Plesa, Alex Dack, Thomas E. Ouldridge2021 · 5 citationsarXiv
What would it take to build a thermodynamically reversible Universal Turing machine? Computational and thermodynamic constraints in a molecular design2102.03388v1 · Rory A. Brittain, Nick S. Jones, Thomas E. Ouldridge2021 · 0 citationsarXiv
Handhold-Mediated Strand Displacement: A Nucleic Acid Based Mechanism for Generating Far-from-Equilibrium Assemblies through Templated Reactions.33470806 · Cabello-Garcia, Javier, Bae, Wooli, Stan, Guy-Bart V et al.2021 · 38 citationsACS nano. 2021;15(2):3272-3283
In situ Generation of RNA Complexes for Synthetic Molecular Strand-Displacement Circuits in Autonomous Systems.33275434 · Bae, Wooli, Stan, Guy-Bart V, Ouldridge, Thomas E2021 · 18 citationsNano letters. 2021;21(1):265-271
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
Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration.33044662 · Deshpande, Abhishek, Ouldridge, Thomas E2021 · 6 citationsBiological cybernetics. 2020;114(6):653-668
Modeling DNA-Strand Displacement Reactions in the Presence of Base-Pair Mismatches.32496760 · Irmisch, Patrick, Ouldridge, Thomas E, Seidel, Ralf2021 · 107 citationsJournal of the American Chemical Society. 2020;142(26):11451-11463
Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts2005.11433v1 · Antti Lankinen, Ismael Mullor Ruiz, Thomas E. Ouldridge2020 · 3 citationsarXiv
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement.32444600 · Haley, Natalie E C, Ouldridge, Thomas E, Mullor Ruiz, Ismael et al.2020 · 103 citationsNature communications. 2020;11(1):2562
Robust control of biochemical reaction networks via stochastic morphing1908.10779v1 · Tomislav Plesa, Guy-Bart Stan, Thomas E. Ouldridge et al.2019 · 0 citationsarXiv
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
Physical limitations of work extraction from temporal correlations.31108699 · Stopnitzky, Elan, Still, Susanne, Ouldridge, Thomas E et al.2019 · 9 citationsPhysical review. E. 2019;99(4-1):042115
Nonequilibrium correlations in minimal dynamical models of polymer copying.30659156 · Poulton, Jenny M, Ten Wolde, Pieter Rein, Ouldridge, Thomas E2019 · 25 citationsProceedings of the National Academy of Sciences of the United States of America. 2019;116(6):1946-1951
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