On the biophysics and kinetics of toehold-mediated DNA strand displacement N Srinivas, TE Ouldridge, P Šulc, JM Schaeffer, B Yurke, AA Louis, ... Nucleic acids research 41 (22), 10641-10658, 2013 | 528 | 2013 |
Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model TE Ouldridge, AA Louis, JPK Doye The Journal of chemical physics 134 (8), 085101, 2011 | 504 | 2011 |
Sequence-dependent thermodynamics of a coarse-grained DNA model P Šulc, F Romano, TE Ouldridge, L Rovigatti, JPK Doye, AA Louis The Journal of chemical physics 137 (13), 135101, 2012 | 338 | 2012 |
Introducing improved structural properties and salt dependence into a coarse-grained model of DNA BEK Snodin, F Randisi, M Mosayebi, P Šulc, JS Schreck, F Romano, ... The Journal of chemical physics 142 (23), 234901, 2015 | 329 | 2015 |
DNA hybridization kinetics: zippering, internal displacement and sequence dependence TE Ouldridge, P Šulc, F Romano, JPK Doye, AA Louis Nucleic acids research 41 (19), 8886-8895, 2013 | 258 | 2013 |
Programmable energy landscapes for kinetic control of DNA strand displacement RRF Machinek, TE Ouldridge, NEC Haley, J Bath, AJ Turberfield Nature Communications 5, 2014 | 225 | 2014 |
Coarse-graining DNA for simulations of DNA nanotechnology JPK Doye, TE Ouldridge, AA Louis, F Romano, P Šulc, C Matek, ... Physical Chemistry Chemical Physics 15 (47), 20395-20414, 2013 | 223 | 2013 |
DNA nanotweezers studied with a coarse-grained model of DNA TE Ouldridge, AA Louis, JPK Doye Physical Review Letters 104 (17), 178101, 2010 | 221 | 2010 |
Guiding the folding pathway of DNA origami KE Dunn, F Dannenberg, TE Ouldridge, M Kwiatkowska, AJ Turberfield, ... Nature, 2015 | 196 | 2015 |
A nucleotide-level coarse-grained model of RNA P Šulc, F Romano, TE Ouldridge, JPK Doye, AA Louis The Journal of chemical physics 140 (23), 235102, 2014 | 150 | 2014 |
Optimizing DNA nanotechnology through coarse-grained modeling: a two-footed DNA walker TE Ouldridge, RL Hoare, AA Louis, JPK Doye, J Bath, AJ Turberfield ACS nano 7 (3), 2479-2490, 2013 | 111 | 2013 |
Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors M Mosayebi, AA Louis, JPK Doye, TE Ouldridge ACS nano, 2015 | 104 | 2015 |
Thermodynamics of Computational Copying in Biochemical Systems TE Ouldridge, CC Govern, PR ten Wolde Physical Review X 7 (2), 021004, 2017 | 103 | 2017 |
Fundamental Limits to Cellular Sensing PR ten Wolde, NB Becker, TE Ouldridge, A Mugler Journal of Statistical Physics 162 (5), 1395-1424, 2016 | 102 | 2016 |
Direct simulation of the self-assembly of a small DNA origami BEK Snodin, F Romano, L Rovigatti, TE Ouldridge, AA Louis, JPK Doye ACS nano 10 (2), 1724-1737, 2016 | 95 | 2016 |
Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA C Matek, TE Ouldridge, JPK Doye, AA Louis Scientific reports 5, 2015 | 90 | 2015 |
Design of hidden thermodynamic driving for non-equilibrium systems via mismatch elimination during DNA strand displacement NEC Haley, TE Ouldridge, IM Ruiz, A Geraldini, AA Louis, J Bath, ... Nature Communications 11 (1), 1-11, 2020 | 88 | 2020 |
Coarse-grained simulations of DNA overstretching F Romano, D Chakraborty, JPK Doye, TE Ouldridge, AA Louis The Journal of chemical physics 138 (8), 085101, 2013 | 88 | 2013 |
Modeling DNA-strand displacement reactions in the presence of base-pair mismatches P Irmisch, TE Ouldridge, R Seidel Journal of the American Chemical Society 142 (26), 11451-11463, 2020 | 79 | 2020 |
Extracting bulk properties of self-assembling systems from small simulations TE Ouldridge, AA Louis, JPK Doye Journal of Physics: Condensed Matter 22 (10), 104102, 2010 | 71 | 2010 |