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1

DNA nanotechnology: understanding and optimisation through simulation

Ouldridge, Thomas E.

Journal:

Molecular Physics

Year:

2015

Language:

english

File:

PDF, 980 KB

english, 2015

2

Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA

Matek, Christian, Ouldridge, Thomas E., Doye, Jonathan P. K., Louis, Ard A.

Journal:

Scientific Reports

Year:

2015

Language:

english

File:

PDF, 868 KB

english, 2015

3

Coarse-grained simulation of DNA using LAMMPS

Henrich, Oliver, Gutiérrez Fosado, Yair Augusto, Curk, Tine, Ouldridge, Thomas E.

Journal:

The European Physical Journal E

Year:

2018

Language:

english

File:

PDF, 2.79 MB

english, 2018

4

In situ Generation of RNA Complexes for Synthetic Molecular Strand-Displacement Circuits in Autonomous Systems

Bae, Wooli, Stan, Guy-Bart V., Ouldridge, Thomas E.

Journal:

Year:

2020

File:

PDF, 3.55 MB

2020

5

DNA Nanotweezers Studied with a Coarse-Grained Model of DNA

Ouldridge, Thomas E., Louis, Ard A., Doye, Jonathan P. K.

Journal:

Physical Review Letters

Year:

2010

Language:

english

File:

PDF, 470 KB

english, 2010

6

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

Ouldridge, Thomas E., Louis, Ard A., Doye, Jonathan P. K.

Journal:

The Journal of Chemical Physics

Year:

2011

Language:

english

File:

PDF, 1.21 MB

english, 2011

7

DNA Cruciform Arms Nucleate through a Correlated but Asynchronous Cooperative Mechanism

Matek, Christian, Ouldridge, Thomas E., Levy, Adam, Doye, Jonathan P. K., Louis, Ard A.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 1.59 MB

english, 2012

8

[Springer Theses] Coarse-Grained Modelling of DNA and DNA Self-Assembly || Modelling a DNA Walker

Ouldridge, Thomas E.

Year:

2012

Language:

english

File:

PDF, 776 KB

english, 2012

9

[Springer Theses] Coarse-Grained Modelling of DNA and DNA Self-Assembly ||

Ouldridge, Thomas E.

Year:

2012

Language:

english

File:

PDF, 4.10 MB

english, 2012

10

Simulating a burnt-bridges DNA motor with a coarse-grained DNA model

Šulc, Petr, Ouldridge, Thomas E., Romano, Flavio, Doye, Jonathan P. K., Louis, Ard A.

Journal:

Natural Computing

Year:

2014

Language:

english

File:

PDF, 748 KB

english, 2014

11

Coarse-graining DNA for simulations of DNA nanotechnology

Doye, Jonathan P. K., Ouldridge, Thomas E., Louis, Ard A., Romano, Flavio, Šulc, Petr, Matek, Christian, Snodin, Benedict E. K., Rovigatti, Lorenzo, Schreck, John S., Harrison, Ryan M., Smith, William

Journal:

Physical Chemistry Chemical Physics

Year:

2013

Language:

english

File:

PDF, 9.28 MB

english, 2013

12

Optimizing DNA Nanotechnology through Coarse-Grained Modeling: A Two-Footed DNA Walker

Ouldridge, Thomas E., Hoare, Rollo L., Louis, Ard A., Doye, Jonathan P. K., Bath, Jonathan, Turberfield, Andrew J.

Journal:

Year:

2013

Language:

english

File:

PDF, 3.57 MB

english, 2013

13

A nucleotide-level coarse-grained model of RNA

Šulc, Petr, Romano, Flavio, Ouldridge, Thomas E., Doye, Jonathan P. K., Louis, Ard A.

Journal:

The Journal of Chemical Physics

Year:

2014

Language:

english

File:

PDF, 1.31 MB

english, 2014

14

Programmable energy landscapes for kinetic control of DNA strand displacement

Machinek, Robert R. F., Ouldridge, Thomas E., Haley, Natalie E. C., Bath, Jonathan, Turberfield, Andrew J.

Journal:

Nature Communications

Year:

2014

Language:

english

File:

PDF, 916 KB

english, 2014

15

The Robustness of Proofreading to Crowding-Induced Pseudo-Processivity in the MAPK Pathway

Ouldridge, Thomas E., Rein ten Wolde, Pieter

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 760 KB

english, 2014

16

The effect of topology on the structure and free energy landscape of DNA kissing complexes

Romano, Flavio, Hudson, Alexander, Doye, Jonathan P. K., Ouldridge, Thomas E., Louis, Ard A.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 982 KB

english, 2012

17

Inferring bulk self-assembly properties from simulations of small systems with multiple constituent species and small systems in the grand canonical ensemble

Ouldridge, Thomas E.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 780 KB

english, 2012

18

Coarse-grained simulations of DNA overstretching

Romano, Flavio, Chakraborty, Debayan, Doye, Jonathan P. K., Ouldridge, Thomas E., Louis, Ard A.

Journal:

The Journal of Chemical Physics

Year:

2013

Language:

english

File:

PDF, 1.34 MB

english, 2013

19

Sequence-dependent thermodynamics of a coarse-grained DNA model

Šulc, Petr, Romano, Flavio, Ouldridge, Thomas E., Rovigatti, Lorenzo, Doye, Jonathan P. K., Louis, Ard A.

Journal:

The Journal of Chemical Physics

Year:

2012

Language:

english

File:

PDF, 1.01 MB

english, 2012

20

The Role of Loop Stacking in the Dynamics of DNA Hairpin Formation

Mosayebi, Majid, Romano, Flavio, Ouldridge, Thomas E., Louis, Ard A., Doye, Jonathan P. K.

Journal:

Journal of Physical Chemistry B

Year:

2014

Language:

english

File:

PDF, 2.17 MB

english, 2014

21

Modelling Toehold-Mediated RNA Strand Displacement

Šulc, Petr, Ouldridge, Thomas E., Romano, Flavio, Doye, Jonathan P.K., Louis, Ard A.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 810 KB

english, 2015

22

[Springer Theses] Coarse-Grained Modelling of DNA and DNA Self-Assembly || A Novel DNA Model

Ouldridge, Thomas E.

Year:

2012

Language:

english

File:

PDF, 320 KB

english, 2012

23

The self-assembly of DNA Holliday junctions studied with a minimal model

Ouldridge, Thomas E., Johnston, Iain G., Louis, Ard A., Doye, Jonathan P. K.

Journal:

The Journal of Chemical Physics

Year:

2009

Language:

english

File:

PDF, 671 KB

english, 2009

24

Characterizing the bending and flexibility induced by bulges in DNA duplexes

Schreck, John S., Ouldridge, Thomas E., Romano, Flavio, Louis, Ard A., Doye, Jonathan P. K.

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 5.52 MB

english, 2015

25

Guiding the folding pathway of DNA origami

Dunn, Katherine E., Dannenberg, Frits, Ouldridge, Thomas E., Kwiatkowska, Marta, Turberfield, Andrew J., Bath, Jonathan

Journal:

Year:

2015

Language:

english

File:

PDF, 3.20 MB

english, 2015

26

Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors

Mosayebi, Majid, Louis, Ard A., Doye, Jonathan P.K., Ouldridge, Thomas E.

Journal:

Year:

2015

Language:

english

File:

PDF, 1.15 MB

english, 2015

27

DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

Schreck, John S., Ouldridge, Thomas E., Romano, Flavio, Šulc, Petr, Shaw, Liam P., Louis, Ard A., Doye, Jonathan P.K.

Journal:

Nucleic Acids Research

Year:

2015

Language:

english

File:

PDF, 2.04 MB

english, 2015

28

Direct Simulation of the Self-Assembly of a Small DNA Origami

Snodin, Benedict E. K., Romano, Flavio, Rovigatti, Lorenzo, Ouldridge, Thomas E., Louis, Ard A., Doye, Jonathan P.K.

Journal:

Year:

2016

Language:

english

File:

PDF, 3.95 MB

english, 2016

29

Fundamental Limits to Cellular Sensing

ten Wolde, Pieter Rein, Becker, Nils B., Ouldridge, Thomas E., Mugler, Andrew

Journal:

Journal of Statistical Physics

Year:

2016

Language:

english

File:

PDF, 1.22 MB

english, 2016

30

Biochemical Machines for the Interconversion of Mutual Information and Work

McGrath, Thomas, Jones, Nick S., ten Wolde, Pieter Rein, Ouldridge, Thomas E.

Journal:

Physical Review Letters

Year:

2017

Language:

english

File:

PDF, 380 KB

english, 2017

31

Modelling DNA origami self-assembly at the domain level

Dannenberg, Frits, Dunn, Katherine E., Bath, Jonathan, Kwiatkowska, Marta, Turberfield, Andrew J., Ouldridge, Thomas E.

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 1.69 MB

english, 2015

32

Introducing improved structural properties and salt dependence into a coarse-grained model of DNA

Snodin, Benedict E. K., Randisi, Ferdinando, Mosayebi, Majid, Šulc, Petr, Schreck, John S., Romano, Flavio, Ouldridge, Thomas E., Tsukanov, Roman, Nir, Eyal, Louis, Ard A., Doye, Jonathan P. K.

Journal:

The Journal of Chemical Physics

Year:

2015

Language:

english

File:

PDF, 4.42 MB

english, 2015

33

Multiscale simulations of anisotropic particles combining molecular dynamics and Green’s function reaction dynamics

Vijaykumar, Adithya, Ouldridge, Thomas E., ten Wolde, Pieter Rein, Bolhuis, Peter G.

Journal:

The Journal of Chemical Physics

Year:

2017

Language:

english

File:

PDF, 1.01 MB

english, 2017

34

Publisher’s Note: Biochemical Machines for the Interconversion of Mutual Information and Work [Phys. Rev. Lett. 118 , 028101 (2017)]

McGrath, Thomas, Jones, Nick S., ten Wolde, Pieter Rein, Ouldridge, Thomas E.

Journal:

Physical Review Letters

Year:

2017

Language:

english

File:

PDF, 21 KB

english, 2017

35

Coarse-Grained Modeling of RNA for Biology and Nanotechnology

Sulc, Petr, Romano, Flavio, Ouldridge, Thomas, Doye, Jonathan, Louis, Ard

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 47 KB

english, 2017

36

What we learn from the learning rate

Brittain, Rory A, Jones, Nick S, Ouldridge, Thomas E

Journal:

Journal of Statistical Mechanics Theory and Experiment

Year:

2017

Language:

english

File:

PDF, 1.59 MB

english, 2017

37

Thermodynamics of Computational Copying in Biochemical Systems

Ouldridge, Thomas E., Govern, Christopher C., ten Wolde, Pieter Rein

Journal:

Physical Review X

Year:

2017

Language:

english

File:

PDF, 419 KB

english, 2017

38

Fundamental Costs in the Production and Destruction of Persistent Polymer Copies

Ouldridge, Thomas E., Rein ten Wolde, Pieter

Journal:

Physical Review Letters

Year:

2017

Language:

english

File:

PDF, 234 KB

english, 2017

39

Designing the optimal bit: balancing energetic cost, speed and reliability

Deshpande, Abhishek, Gopalkrishnan, Manoj, Ouldridge, Thomas E., Jones, Nick S.

Journal:

Proceedings Mathematical Physical & Engineering Sciences

Year:

2017

Language:

english

File:

PDF, 959 KB

english, 2017

40

The importance of thermodynamics for molecular systems, and the importance of molecular systems for thermodynamics

Ouldridge, Thomas E.

Journal:

Natural Computing

Year:

2017

Language:

english

File:

PDF, 1.56 MB

english, 2017

41

DNA bipedal motor walking dynamics: an experimental and theoretical study of the dependency on step size

Khara, Dinesh C, Schreck, John S, Tomov, Toma E, Berger, Yaron, Ouldridge, Thomas E, Doye, Jonathan P K, Nir, Eyal

Journal:

Nucleic Acids Research

Year:

2017

Language:

english

File:

PDF, 3.51 MB

english, 2017

42

Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self-assembly

Fonseca, Pedro, Romano, Flavio, Schreck, John S., Ouldridge, Thomas E., Doye, Jonathan P. K., Louis, Ard A.

Journal:

The Journal of Chemical Physics

Year:

2018

Language:

english

File:

PDF, 4.10 MB

english, 2018

43

Nonequilibrium correlations in minimal dynamical models of polymer copying

Poulton, Jenny M., ten Wolde, Pieter Rein, Ouldridge, Thomas E.

Journal:

Proceedings of the National Academy of Sciences

Year:

2019

Language:

english

File:

PDF, 812 KB

english, 2019

44

Identifying physical causes of apparent enhanced cyclization of short DNA molecules with a coarse-grained model

Harrison, Ryan M., Romano, Flavio, Ouldridge, Thomas E., Louis, Ard A., Doye, Jonathan P.K.

Journal:

Journal of Chemical Theory and Computation

Year:

2019

Language:

english

File:

PDF, 7.14 MB

english, 2019

45

Biochemical Szilard engines for memory-limited inference

Brittain, Rory A, Jones, Nick S, Ouldridge, Thomas E

Journal:

New Journal of Physics

Year:

2019

Language:

english

File:

PDF, 3.56 MB

english, 2019

46

High rates of fuel consumption are not required by insulating motifs to suppress retroactivity in biochemical circuits

Deshpande, Abhishek, Ouldridge, Thomas E.

Journal:

Engineering Biology

Year:

2017

Language:

english

File:

PDF, 998 KB

english, 2017

47

Modelling DNA-strand displacement reactions in the presence of base-pair mismatches

Irmisch, Patrick, Ouldridge, Thomas E., Seidel, Ralf

Journal:

Journal of the American Chemical Society

Year:

2020

File:

PDF, 3.03 MB

2020

48

Optimizing enzymatic catalysts for rapid turnover of substrates with low enzyme sequestration

Deshpande, Abhishek, Ouldridge, Thomas E.

Journal:

Biological Cybernetics

Year:

2020

File:

PDF, 1.94 MB

2020

49

Self-Limiting Polymerization of DNA Origami Subunits with Strain Accumulation

Berengut, Jonathan F., Wong, Chak Kui, Berengut, Julian C., Doye, Jonathan P. K., Ouldridge, Thomas E., Lee, Lawrence K.

Journal:

Year:

2020

File:

PDF, 7.89 MB

2020