Publications by authors named "Thomas Ouldridge"

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Thermodynamic limits in far-from-equilibrium molecular templating networks.
Benjamin Qureshi, Jenny M Poulton, Thomas E Ouldridge

Newton· January 2026

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Biochemical surface patterning in microfluidic devices.
Kate Collins, Claire E Stanley, Thomas E Ouldridge

Curr Opin Biotechnol· December 2025

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Design of DNA strand displacement reactions.
Križan Jurinović, Merry Mitra, Rakesh Mukherjee, Thomas E Ouldridge

Curr Opin Biotechnol· December 2025

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Setting a direction for molecular recognition.
Thomas E Ouldridge, Rakesh Mukherjee

Nat Nanotechnol· October 2025

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Overcoming the Speed Limit of Four-Way DNA Branch Migration with Bulges in Toeholds.
Samia Bakhtawar, Francesca Smith, Aditya Sengar, Guy-Bart V Stan, John Goertz, Thomas E Ouldridge

Nano Lett· September 2025

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Information propagation through enzyme-free catalytic templating of DNA dimerization with weak product inhibition.
Javier Cabello-Garcia, Rakesh Mukherjee, Wooli Bae, Guy-Bart V Stan, Thomas E Ouldridge

Nat Chem· August 2025

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Bit reset protocols that obey activity-constrained speed limits do not minimize work for a given speed.
Daan Mulder, Thomas E Ouldridge, Pieter Rein Ten Wolde

Phys Rev E· April 2025

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The interplay of heterogeneity and product detachment in templated polymer copying.
Jeremy E B Guntoro, Benjamin J Qureshi, Thomas E Ouldridge

J Chem Phys· February 2025

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Autonomous learning of generative models with chemical reaction network ensembles.
William Poole, Thomas E Ouldridge, Manoj Gopalkrishnan

J R Soc Interface· January 2025

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Is stochastic thermodynamics the key to understanding the energy costs of computation?
David H Wolpert, Jan Korbel, Christopher W Lynn, Farita Tasnim, Joshua A Grochow, Thomas E Ouldridge

Proc Natl Acad Sci U S A· November 2024

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Pipelined information flow in molecular mechanical circuits leads to increased error and irreversibility.
Ian Seet, Thomas E Ouldridge, Jonathan P K Doye

Phys Rev E· October 2024

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Strong sequence-dependence in RNA/DNA hybrid strand displacement kinetics.
Francesca G Smith, John P Goertz, Križan Jurinović, Molly M Stevens, Thomas E Ouldridge

Nanoscale· September 2024

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Kinetic Proofreading Can Enhance Specificity in a Nonenzymatic DNA Strand Displacement Network.
Rakesh Mukherjee, Aditya Sengar, Javier Cabello-García, Thomas E Ouldridge

J Am Chem Soc· July 2024

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Evaluating DFHBI-Responsive RNA Light-Up Aptamers as Fluorescent Reporters for Gene Expression.
Alicia Climent-Catala, Ivan Casas-Rodrigo, Suhasini Iyer, Rodrigo Ledesma-Amaro, Thomas E Ouldridge

ACS Synth Biol· December 2023

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A universal method for analyzing copolymer growth.
Benjamin Qureshi, Jordan Juritz, Jenny M Poulton, Adrian Beersing-Vasquez, Thomas E Ouldridge

J Chem Phys· March 2023

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Simulation of reversible molecular mechanical logic gates and circuits.
Ian Seet, Thomas E Ouldridge, Jonathan P K Doye

Phys Rev E· February 2023

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The stability and number of nucleating interactions determine DNA hybridization rates in the absence of secondary structure.
Sophie Hertel, Richard E Spinney, Stephanie Y Xu, Thomas E Ouldridge, Richard G Morris

Nucleic Acids Res· August 2022

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Synthetic biology and bioelectrochemical tools for electrogenetic system engineering.
Joshua M Lawrence, Yutong Yin, Paolo Bombelli, Alberto Scarampi, Marko Storch, Thomas E Ouldridge

Sci Adv· May 2022

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Building an RNA-Based Toggle Switch Using Inhibitory RNA Aptamers.
Alicia Climent-Catala, Thomas E Ouldridge, Guy-Bart V Stan, Wooli Bae

ACS Synth Biol· February 2022

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Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions.
Jordan Juritz, Jenny M Poulton, Thomas E Ouldridge

J Chem Phys· February 2022

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Kinetics of RNA and RNA:DNA Hybrid Strand Displacement.
Hao Liu, Fan Hong, Francesca Smith, John Goertz, Thomas Ouldridge

ACS Synth Biol· November 2021

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Quasi-robust control of biochemical reaction networks via stochastic morphing.
Tomislav Plesa, Guy-Bart Stan, Thomas E Ouldridge, Wooli Bae

J R Soc Interface· April 2021

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Handhold-Mediated Strand Displacement: A Nucleic Acid Based Mechanism for Generating Far-from-Equilibrium Assemblies through Templated Reactions.
Javier Cabello-Garcia, Wooli Bae, Guy-Bart V Stan, Thomas E Ouldridge

ACS Nano· February 2021

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Generation of RNA Complexes for Synthetic Molecular Strand-Displacement Circuits in Autonomous Systems.
Wooli Bae, Guy-Bart V Stan, Thomas E Ouldridge

Nano Lett· January 2021

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Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation.
Jonathan F Berengut, Chak Kui Wong, Julian C Berengut, Jonathan P K Doye, Thomas E Ouldridge

ACS Nano· December 2020

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