Thomas E. Ouldridge

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All published works

Action	Title	Year	Authors
+ PDF Chat	Bit reset protocols that obey activity-constrained speed limits do not minimize work for a given speed	2025	Daan Mulder Thomas E. Ouldridge Pieter Rein ten Wolde
+	Autonomous learning of generative models with chemical reaction network ensembles	2025	William Poole Thomas E. Ouldridge Manoj Gopalkrishnan
+	Is stochastic thermodynamics the key to understanding the energy costs of computation?	2024	David H. Wolpert Jan Korbel Christopher W. Lynn Farita Tasnim Joshua A. Grochow Gülce Kardeş James B. Aimone Vijay Balasubramanian Eric DeGiuli David Doty
+ PDF Chat	The Interplay of Heterogeneity and Product Detachment in Templated Polymer Copying	2024	Jeremy E. B. Guntoro Benjamin J. Qureshi Thomas E. Ouldridge
+	Pipelined information flow in molecular mechanical circuits leads to increased error and irreversibility	2024	Ian Seet Thomas E. Ouldridge Jonathan P. K. Doye
+ PDF Chat	Recurrent neural chemical reaction networks that approximate arbitrary dynamics	2024	Alexander Dack Benjamin Qureshi Thomas E. Ouldridge Tomislav Plesa
+ PDF Chat	Information propagation in far-from-equilibrium molecular templating networks is optimised by pseudo-equilibrium systems with negligible dissipation	2024	Benjamin Qureshi Jenny M. Poulton Thomas E. Ouldridge
+ PDF Chat	Thermodynamics of deterministic finite automata operating locally and periodically	2023	Thomas E. Ouldridge David H. Wolpert
+ PDF Chat	Simulation of reversible molecular mechanical logic gates and circuits	2023	Ian Seet Thomas E. Ouldridge Jonathan P. K. Doye
+	Pipelined information flow in molecular mechanical circuits leads to increased error and irreversibility	2023	Ian Seet Thomas E. Ouldridge Jonathan P. K. Doye
+	Autonomous Learning of Generative Models with Chemical Reaction Network Ensembles	2023	William Poole Thomas E. Ouldridge Manoj Gopalkrishnan
+	Is stochastic thermodynamics the key to understanding the energy costs of computation?	2023	David H. Wolpert Jan Korbel Christopher W. Lynn Farita Tasnim Joshua A. Grochow Gülce Kardeş James B. Aimone Vijay Balasubramanian Eric DeGiuli David Doty
+	Exploiting bias in optimal finite-time copying protocols	2023	Daan Mulder Pieter Rein ten Wolde Thomas E. Ouldridge
+ PDF Chat	Minimal mechanism for cyclic templating of length-controlled copolymers under isothermal conditions	2022	Jordan Juritz Jenny M. Poulton Thomas E. Ouldridge
+ PDF Chat	Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling	2022	Jonathan P. K. Doye Ard A. Louis John S. Schreck Flavio Romano Ryan M. Harrison Majid Mosayebi Megan C. Engel Thomas E. Ouldridge
+	Simulation of reversible molecular mechanical logic gates and circuits	2022	Ian Seet Thomas E. Ouldridge Jonathan P. K. Doye
+	Detailed Balanced Chemical Reaction Networks as Generalized Boltzmann Machines	2022	William Poole Thomas E. Ouldridge Manoj Gopalkrishnan Erik Winfree
+	Thermodynamics of deterministic finite automata operating locally and periodically	2022	Thomas E. Ouldridge David H. Wolpert
+	A Universal Method for Analysing Copolymer Growth	2022	Benjamin J. Qureshi Jordan Juritz Jenny M. Poulton Adrian Beersing-Vasquez Thomas E. Ouldridge
+ PDF Chat	Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling	2021	Jonathan P. K. Doye Ard A. Louis John S. Schreck Flavio Romano Ryan M. Harrison Majid Mosayebi Megan C. Engel Thomas E. Ouldridge
+ PDF Chat	A Primer on the oxDNA Model of DNA: When to Use it, How to Simulate it and How to Interpret the Results	2021	Aditya Sengar Thomas E. Ouldridge Oliver Henrich Lorenzo Rovigatti Petr Šulc
+	Edge-effects dominate copying thermodynamics for finite-length molecular oligomers	2021	Jenny M. Poulton Thomas E. Ouldridge
+	oxDNA simulation setup files	2021	Aditya Sengar Thomas E. Ouldridge Lorenzo Rovigatti Oliver Henrich Petr Šulc Flavio Romano Jonathan P. K. Doye
+	oxDNA simulation setup files	2021	Aditya Sengar Thomas E. Ouldridge Lorenzo Rovigatti Oliver Henrich Petr Šulc Flavio Romano Jonathan P. K. Doye
+	What would it take to build a thermodynamically reversible Universal Turing machine? Computational and thermodynamic constraints in a molecular design	2021	Rory A. Brittain Nick S. Jones Thomas E. Ouldridge
+	Integral feedback in synthetic biology: Negative-equilibrium catastrophe	2021	Tomislav Plesa Alex Dack Thomas E. Ouldridge
+ PDF Chat	Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration	2020	Abhishek Deshpande Thomas E. Ouldridge
+	Implementing Non-Equilibrium Networks with Active Circuits of Duplex Catalysts	2020	Antti Lankinen Ismael Mullor Ruiz Thomas E. Ouldridge
+	Robust control of biochemical reaction networks via stochastic morphing	2019	Tomislav Plesa Guy‐Bart Stan Thomas E. Ouldridge Wooli Bae
+ PDF Chat	Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model	2019	Ryan M. Harrison Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	The Power of Being Explicit: Demystifying Work, Heat, and Free Energy in the Physics of Computation	2019	Thomas E. Ouldridge Rory A. Brittain Pieter Rein ten Wolde
+ PDF Chat	Physical Limitations of Work Extraction from Temporal Correlations	2019	Elan Stopnitzky Susanne Still Thomas E. Ouldridge Lee Altenberg
+ PDF Chat	Biochemical Szilard engines for memory-limited inference	2019	Rory A. Brittain Nick S. Jones Thomas E. Ouldridge
+	Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration	2019	Abhishek Deshpande Thomas E. Ouldridge
+ PDF Chat	Physical limitations of work extraction from temporal correlations	2019	Elan Stopnitzky Susanne Still Thomas E. Ouldridge Lee Altenberg
+ PDF Chat	Nonequilibrium correlations in minimal dynamical models of polymer copying	2019	Jenny M. Poulton Pieter Rein ten Wolde Thomas E. Ouldridge
+	Robust control of biochemical reaction networks via stochastic morphing	2019	Tomislav Plesa Guy‐Bart Stan Thomas E. Ouldridge Wooli Bae
+	Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration	2019	Abhishek Deshpande Thomas E. Ouldridge
+	Initialization files and data supporting https://arxiv.org/abs/1506.09008	2018	Ryan M. Harrison Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+	Initialization files and data supporting https://arxiv.org/abs/1506.09008	2018	Ryan M. Harrison Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+	Dummy Upload For Arxiv:1506.09008 Supplementary Data	2018	Thomas E. Ouldridge
+	Dummy Upload For Arxiv:1506.09008 Supplementary Data	2018	Thomas E. Ouldridge
+	Non-equilibrium correlations in minimal dynamical models of polymer copying	2018	Jenny M. Poulton Pieter Rein ten Wolde Thomas E. Ouldridge
+ PDF Chat	Coarse-grained simulation of DNA using LAMMPS	2018	Oliver Henrich Yair Augusto Gutiérrez Fosado Tine Curk Thomas E. Ouldridge
+ PDF Chat	Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly	2018	Pedro Fonseca Flavio Romano John S. Schreck Thomas E. Ouldridge Jonathan P. K. Doye Ard A. Louis
+	The power of being explicit: demystifying work, heat, and free energy in the physics of computation	2018	Thomas E. Ouldridge Rory A. Brittain Pieter Rein ten Wolde
+ PDF Chat	Geometric integrator for Langevin systems with quaternion-based rotational degrees of freedom and hydrodynamic interactions	2017	Ruslan L. Davidchack Thomas E. Ouldridge M. V. Tretyakov
+ PDF Chat	The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics	2017	Thomas E. Ouldridge
+ PDF Chat	High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits	2017	Abhishek Deshpande Thomas E. Ouldridge
+	High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits	2017	Abhishek Deshpande Thomas E. Ouldridge
+ PDF Chat	Designing the optimal bit: balancing energetic cost, speed and reliability	2017	Abhishek Deshpande Manoj Gopalkrishnan Thomas E. Ouldridge Nick S. Jones
+ PDF Chat	What we learn from the learning rate	2017	Rory A. Brittain Nick S. Jones Thomas E. Ouldridge
+ PDF Chat	Fundamental Costs in the Production and Destruction of Persistent Polymer Copies	2017	Thomas E. Ouldridge Pieter Rein ten Wolde
+ PDF Chat	Thermodynamics of Computational Copying in Biochemical Systems	2017	Thomas E. Ouldridge Christopher C. Govern Pieter Rein ten Wolde
+ PDF Chat	Multiscale simulations of anisotropic particles combining molecular dynamics and Green’s function reaction dynamics	2017	Adithya Vijaykumar Thomas E. Ouldridge Pieter Rein ten Wolde Peter G. Bolhuis
+	The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics	2017	Thomas E. Ouldridge
+ PDF Chat	Biochemical Machines for the Interconversion of Mutual Information and Work	2017	Thomas McGrath Nick S. Jones Pieter Rein ten Wolde Thomas E. Ouldridge
+ PDF Chat	Chemical Boltzmann Machines	2017	William Poole Andrés Ortiz-Muñoz Abhishek Behera Nick S. Jones Thomas E. Ouldridge Erik Winfree Manoj Gopalkrishnan
+	The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics	2017	Thomas E. Ouldridge
+	High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits	2017	Abhishek Deshpande Thomas E. Ouldridge
+ PDF Chat	Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors	2015	Majid Mosayebi Ard A. Louis Jonathan P. K. Doye Thomas E. Ouldridge
+ PDF Chat	Modelling DNA origami self-assembly at the domain level	2015	Frits Dannenberg Katherine E. Dunn Jonathan Bath Marta Kwiatkowska Andrew J. Turberfield Thomas E. Ouldridge
+	Coarse-grained modelling of strong DNA bending II: Cyclization	2015	Ryan M. Harrison Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	Introducing improved structural properties and salt dependence into a coarse-grained model of DNA	2015	Benedict Snodin Ferdinando Randisi Majid Mosayebi Petr Šulc John S. Schreck Flavio Romano Thomas E. Ouldridge Roman Tsukanov Eyal Nir Ard A. Louis
+ PDF Chat	DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization	2015	John S. Schreck Thomas E. Ouldridge Flavio Romano Petr Šulc Liam P. Shaw Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	Characterizing the bending and flexibility induced by bulges in DNA duplexes	2015	John S. Schreck Thomas E. Ouldridge Flavio Romano Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	New Langevin and gradient thermostats for rigid body dynamics	2015	Ruslan L. Davidchack Thomas E. Ouldridge M. V. Tretyakov
+ PDF Chat	Modelling Toehold-Mediated RNA Strand Displacement	2015	Petr Šulc Thomas E. Ouldridge Flavio Romano Jonathan P. K. Doye Ard A. Louis
+ PDF Chat	Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA	2015	Christian Matek Thomas E. Ouldridge Jonathan P. K. Doye Ard A. Louis
+	Fundamental Limits to Cellular Sensing	2015	Pieter Rein ten Wolde Nils B. Becker Thomas E. Ouldridge Andrew Mugler
+	Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice"	2015	Ryan M. Harrison Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	DNA nanotechnology: understanding and optimisation through simulation	2014	Thomas E. Ouldridge
+ PDF Chat	The Role of Loop Stacking in the Dynamics of DNA Hairpin Formation	2014	Majid Mosayebi Flavio Romano Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	The Robustness of Proofreading to Crowding-Induced Pseudo-Processivity in the MAPK Pathway	2014	Thomas E. Ouldridge Pieter Rein ten Wolde
+ PDF Chat	A nucleotide-level coarse-grained model of RNA	2014	Petr Šulc Flavio Romano Thomas E. Ouldridge Jonathan P. K. Doye Ard A. Louis
+	On the Connection between Computational and Biochemical Measurement	2014	Thomas E. Ouldridge Christopher C. Govern
+ PDF Chat	Simulating a burnt-bridges DNA motor with a coarse-grained DNA model	2013	Petr Šulc Thomas E. Ouldridge Flavio Romano Jonathan P. K. Doye Ard A. Louis
+ PDF Chat	DNA hybridization kinetics: zippering, internal displacement and sequence dependence	2013	Thomas E. Ouldridge Petr Šulc Flavio Romano Jonathan P. K. Doye Ard A. Louis
+ PDF Chat	Coarse-grained simulations of DNA overstretching	2013	Flavio Romano Debayan Chakraborty Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis
+ PDF Chat	Coarse-graining DNA for simulations of DNA nanotechnology	2013	Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis Flavio Romano Petr Šulc Christian Matek Benedict Snodin Lorenzo Rovigatti John S. Schreck Ryan M. Harrison
+ PDF Chat	Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble	2012	Thomas E. Ouldridge
+ PDF Chat	Sequence-dependent thermodynamics of a coarse-grained DNA model	2012	Petr Šulc Flavio Romano Thomas E. Ouldridge Lorenzo Rovigatti Jonathan P. K. Doye Ard A. Louis
+ PDF Chat	DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism	2012	Christian Matek Thomas E. Ouldridge Adam Levy Jonathan P. K. Doye Ard A. Louis
+ PDF Chat	The effect of topology on the structure and free energy landscape of DNA kissing complexes	2012	Flavio Romano Alexander Hudson Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis
+	Inferring bulk self-assembly properties from small simulations: multiple constituent species and systems in the grand canonical ensemble	2012	Thomas E. Ouldridge
+ PDF Chat	Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model	2011	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	DNA Nanotweezers Studied with a Coarse-Grained Model of DNA	2010	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	Extracting bulk properties of self-assembling systems from small simulations	2010	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye
+ PDF Chat	The self-assembly of DNA Holliday junctions studied with a minimal model	2009	Thomas E. Ouldridge Iain G. Johnston Ard A. Louis Jonathan P. K. Doye

Common Coauthors

Coauthor	Papers Together
Jonathan P. K. Doye	33
Ard A. Louis	27
Flavio Romano	20
Petr Šulc	11
Pieter Rein ten Wolde	11
Ryan M. Harrison	8
John S. Schreck	7
Jenny M. Poulton	6
Nick S. Jones	6
Manoj Gopalkrishnan	5
Rory A. Brittain	5
Lorenzo Rovigatti	5
Abhishek Deshpande	5
Majid Mosayebi	5
Tomislav Plesa	4
David H. Wolpert	4
Oliver Henrich	4
Ian Seet	4
William Poole	4
Aditya Sengar	3
Christian Matek	3
Joseph A. Paradiso	2
Erik Winfree	2
Gülce Kardeş	2
Jordan Juritz	2
James B. Aimone	2
Nahuel Freitas	2
Christopher W. Lynn	2
Susanne Still	2
Benjamin J. Qureshi	2
Abhishek Deshpande	2
Eric DeGiuli	2
Benjamin Qureshi	2
Andréa W. Richa	2
Jan Korbel	2
Brenda M. Rubenstein	2
Christopher C. Govern	2
Megan C. Engel	2
Wooli Bae	2
Paul M. Riechers	2
Matteo Marsili	2
Elan Stopnitzky	2
David Doty	2
Joshua A. Grochow	2
Benedict Snodin	2
Flavio Romano	2
Ruslan L. Davidchack	2
Farita Tasnim	2
Daan Mulder	2
M. V. Tretyakov	2

Commonly Cited References

Action	Title	Year	Authors	# of times referenced
+ PDF Chat	Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model	2011	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	25
+ PDF Chat	Sequence-dependent thermodynamics of a coarse-grained DNA model	2012	Petr Šulc Flavio Romano Thomas E. Ouldridge Lorenzo Rovigatti Jonathan P. K. Doye Ard A. Louis	20
+ PDF Chat	DNA Nanotweezers Studied with a Coarse-Grained Model of DNA	2010	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	18
+ PDF Chat	The role of collective motion in examples of coarsening and self-assembly	2008	Stephen Whitelam Edward H. Feng Michael F. Hagan Phillip L. Geissler	18
+ PDF Chat	DNA hybridization kinetics: zippering, internal displacement and sequence dependence	2013	Thomas E. Ouldridge Petr Šulc Flavio Romano Jonathan P. K. Doye Ard A. Louis	16
+ PDF Chat	Coarse-grained simulations of DNA overstretching	2013	Flavio Romano Debayan Chakraborty Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis	15
+ PDF Chat	DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism	2012	Christian Matek Thomas E. Ouldridge Adam Levy Jonathan P. K. Doye Ard A. Louis	14
+ PDF Chat	Thermodynamics of Computational Copying in Biochemical Systems	2017	Thomas E. Ouldridge Christopher C. Govern Pieter Rein ten Wolde	13
+ PDF Chat	Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles	2007	Stephen Whitelam Phillip L. Geissler	13
+ PDF Chat	Coarse-graining DNA for simulations of DNA nanotechnology	2013	Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis Flavio Romano Petr Šulc Christian Matek Benedict Snodin Lorenzo Rovigatti John S. Schreck Ryan M. Harrison	13
+ PDF Chat	Extracting bulk properties of self-assembling systems from small simulations	2010	Thomas E. Ouldridge Ard A. Louis Jonathan P. K. Doye	12
+ PDF Chat	The effect of topology on the structure and free energy landscape of DNA kissing complexes	2012	Flavio Romano Alexander Hudson Jonathan P. K. Doye Thomas E. Ouldridge Ard A. Louis	12
+ PDF Chat	Fundamental Costs in the Production and Destruction of Persistent Polymer Copies	2017	Thomas E. Ouldridge Pieter Rein ten Wolde	11
+ PDF Chat	The self-assembly of DNA Holliday junctions studied with a minimal model	2009	Thomas E. Ouldridge Iain G. Johnston Ard A. Louis Jonathan P. K. Doye	10
+ PDF Chat	Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link	2012	Cristiano De Michele Lorenzo Rovigatti Tommaso Bellini Francesco Sciortino	10
+ PDF Chat	Thermodynamics of information	2015	Juan M. R. Parrondo Jordan M. Horowitz Takahiro Sagawa	10
+ PDF Chat	Forward flux sampling for rare event simulations	2009	Rosalind J. Allen Chantal Valeriani Pieter Rein ten Wolde	8
+ PDF Chat	Mesoscopic modeling for nucleic acid chain dynamics	2005	Marta Sales‐Pardo Roger Guimerà André A. Moreira Jonathan Widom Luı́s A. Nunes Amaral	8
+ PDF Chat	The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics	2017	Thomas E. Ouldridge	8
+ PDF Chat	Biochemical Machines for the Interconversion of Mutual Information and Work	2017	Thomas McGrath Nick S. Jones Pieter Rein ten Wolde Thomas E. Ouldridge	7
+ PDF Chat	Stochastic thermodynamics, fluctuation theorems and molecular machines	2012	Udo Seifert	7
+ PDF Chat	A systematically coarse-grained model for DNA and its predictions for persistence length, stacking, twist, and chirality	2010	Alex Morriss-Andrews Jörg Rottler Steven S. Plotkin	7
+ PDF Chat	Imitating Chemical Motors with Optimal Information Motors	2013	Jordan M. Horowitz Takahiro Sagawa Juan M. R. Parrondo	7
+ PDF Chat	Second law and Landauer principle far from equilibrium	2011	Massimiliano Esposito J. van den Brand	7
+ PDF Chat	Sampling Rare Switching Events in Biochemical Networks	2005	Rosalind J. Allen Patrick B. Warren Pieter Rein ten Wolde	6
+ PDF Chat	Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA	2015	Christian Matek Thomas E. Ouldridge Jonathan P. K. Doye Ard A. Louis	6
+ PDF Chat	High-Precision Test of Landauer’s Principle in a Feedback Trap	2014	Yonggun Jun Momčilo Gavrilov John Bechhoefer	6
+ PDF Chat	Entropy production fluctuation theorem and the nonequilibrium work relation for free energy differences	1999	Gavin E. Crooks	6
+ PDF Chat	Langevin thermostat for rigid body dynamics	2009	Ruslan L. Davidchack Richard Handel M. V. Tretyakov	6
+ PDF Chat	DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization	2015	John S. Schreck Thomas E. Ouldridge Flavio Romano Petr Šulc Liam P. Shaw Ard A. Louis Jonathan P. K. Doye	6
+ PDF Chat	Kinetic versus Energetic Discrimination in Biological Copying	2013	Pablo Sartori Simone Pigolotti	6
+ PDF Chat	Efficiency of cellular information processing	2014	Andre C. Barato David Hartich Udo Seifert	6
+ PDF Chat	Minimal Energy Cost for Thermodynamic Information Processing: Measurement and Information Erasure	2009	Takahiro Sagawa Masahito Ueda	6
+ PDF Chat	Work and information processing in a solvable model of Maxwell’s demon	2012	Dibyendu Mandal Christopher Jarzynski	6
+ PDF Chat	Maxwell’s demon in biochemical signal transduction with feedback loop	2015	Sosuke Ito Takahiro Sagawa	5
+ PDF Chat	Model for assembly and gelation of four-armed DNA dendrimers	2006	Francis W. Starr Francesco Sciortino	5
+ PDF Chat	Stochastic thermodynamics of single enzymes and molecular motors	2011	Udo Seifert	5
+ PDF Chat	Landauer in the Age of Synthetic Biology: Energy Consumption and Information Processing in Biochemical Networks	2016	Pankaj Mehta Alex Lang David J. Schwab	5
+ PDF Chat	Notes on Landauer's principle, reversible computation, and Maxwell's Demon	2003	Charles H. Bennett	5
+ PDF Chat	Numerical Evidence for Nucleated Self-Assembly of DNA Brick Structures	2014	Aleks Reinhardt Daan Frenkel	5
+ PDF Chat	A nucleotide-level coarse-grained model of RNA	2014	Petr Šulc Flavio Romano Thomas E. Ouldridge Jonathan P. K. Doye Ard A. Louis	5
+ PDF Chat	Introducing improved structural properties and salt dependence into a coarse-grained model of DNA	2015	Benedict Snodin Ferdinando Randisi Majid Mosayebi Petr Šulc John S. Schreck Flavio Romano Thomas E. Ouldridge Roman Tsukanov Eyal Nir Ard A. Louis	5
+ PDF Chat	Single-molecule derivation of salt dependent base-pair free energies in DNA	2010	Josep Maria Huguet Cristiano Valim Bizarro Núria Forns Steven B. Smith Carlos Bustamante Félix Ritort	5
+ PDF Chat	Energetic costs of cellular computation	2012	Pankaj Mehta David J. Schwab	5
+ PDF Chat	The (absence of a) relationship between thermodynamic and logical reversibility	2005	O. J. E. Maroney	5
+ PDF Chat	Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble	2012	Thomas E. Ouldridge	5
+ PDF Chat	Simulating a burnt-bridges DNA motor with a coarse-grained DNA model	2013	Petr Šulc Thomas E. Ouldridge Flavio Romano Jonathan P. K. Doye Ard A. Louis	5
+ PDF Chat	Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors	2015	Majid Mosayebi Ard A. Louis Jonathan P. K. Doye Thomas E. Ouldridge	4
+ PDF Chat	From rigid base pairs to semiflexible polymers: Coarse-graining DNA	2007	Nils B. Becker Ralf Everaers	4
+	New Monte Carlo technique for studying phase transitions	1988	Alan M. Ferrenberg Robert H. Swendsen	4