A.A. Louis: Publications

161.	Visualising Feature Learning in Deep Neural Networks by Diagonalizing the Forward Feature Map Yoonsoo Nam, Chris Mingard, Seok Hyeong Lee, Soufiane Hayou, Ard Louis | arxiv abstract | pdf |
160.	Controlling DNA-RNA strand displacement kinetics with base distribution Eryk J Ratajczyk, Jonathan Bath, Petr Sulc, Jonathan P K Doye, Ard A Louis, and Andrew J Turberfield | biorxiv abstract| pdf
159.	Exploiting the equivalence between quantum neural networks and perceptrons Chris Mingard, Jessica Pointing, Charles London, Yoonsoo Nam, and Ard A. Louis | arxiv abstract | pdf |
158.	An exactly solvable model for emergence and scaling laws Yoonsoo Nam, Nayara Fonseca, Seok Hyeong Lee, and Ard Louis | arxiv abstract | pdf |
157.	Coarse-grained modelling of DNA-RNA hybrids Eryk J. Ratajczyk, Petr Šulc, Andrew J. Turberfield, Jonathan P.K. Doye, Ard A. Louis J. Chem. Phys. 160, 115101 (2024) | arxiv abstract | pdf | Scilight article highlighting our work
156.	Non-Poissonian bursts in the arrival of phenotypic variation can strongly affect the dynamics of adaptation Nora S. Martin, Steffen Schaper, Chico Q. Camargo, and Ard A. Louis Molecular Biology and Evolution 41, 6 (2024). | BioRxiv abstract | pdf |
155.	Exploring simplicity bias in 1D dynamical systems Kamaludin Dingle, Mohammad Alaskandarani, Boumediene Hamzi, and Ard A. Louis Entropy 26 (5), 426 (2024) | arxiv abstract | pdf |
154.	Bias in the arrival of variation can dominate over natural selection in Richard Dawkins' biomorphs Nora S. Martin, Chico Q. Camargo, and Ard A. Louis, PLOS Computational Biology, 20, e1011893. (2024) | BioRxiv abstract | pdf |
153.	Do deep neural networks have an inbuilt Occam's razor? Chris Mingard, Henry Rees, Guillermo Valle-Pérez, Ard A. Louis | arxiv abstract | pdf |
152.	Maximum Mutational Robustness in Genotype-Phenotype Maps Follows a Self-similar Blancmange-like Curve Vaibhav Mohanty, Sam F Greenbury, Tasmin Sarkany, Shyam Narayanan, Kamaludin Dingle, Sebastian E Ahnert, Ard A Louis J. Roy. Soc. Interface 20, 20230169 (2023). | Biorxiv abstract | pdf | phys.org news story| Science alert story | Livescience story |
151.	Predicting phenotype transition probabilities via conditional algorithmic probability approximations Kamaludin Dingle, Javor K. Novev, Sebastian E. Ahnert, and Ard A. Louis J. Roy. Soc. Interface, 19 (197), 20220694 (2023). | Biorxiv abstract | pdf |
150.	Robustness and Stability of Spin Glass Ground States to Perturbed Interactions Vaibhav Mohanty and Ard A. Louis Phys. Rev. E. 107, 014126 (2023) | arxiv abstract | pdf |
149.	Designing the self-assembly of arbitrary shapes using minimal complexity building blocks Joakim Bohlin, Andrew J. Turberfield, Ard A. Louis, Petr Šulc ACS Nano 17, 6, 5387 (2023) | arxiv abstract| featured on the cover:
148.	The structure of genotype-phenotype maps makes fitness landscapes navigable Sam F. Greenbury, Ard A. Louis, and Sebastian E. Ahnert Nature Ecology and Evolution 6,1742 (2022) | biorxiv abstract | pdf |github repository| |Nature Ecology Evolution Commentary |
147.	Free energy landscapes of DNA and its assemblies: perspectives from coarse-grained modelling Jonathan P. K. Doye, Ard A. Louis, John S. Schreck, Flavio Romano, Ryan M. Harrison, Majid Mosayebi, Megan C. Engel, Thomas E. Ouldridge Frontiers of Nanoscience 21, 195 (2022) | arrxiv abstract | pdf |
146.	Reply to Ocklenburg and Mundorf: The interplay of developmental bias and natural selection Iain G Johnston, Kamaludin Dingle, Sam F. Greenbury, Chico Q. Camargo, Jonathan P. K. Doye, Sebastian E. Ahnert, Ard A. Louis PNAS 119, e2205299119 (2022) | biorxiv abstract|
145.	The long and winding road to understanding organismal construction: Reply to comments on "From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics" Susanna Manrubia, José A. Cuesta, Jacobo Aguirre, Sebastian E. Ahnert, Lee Altenberg, Alejandro V. Cano, Pablo Catalán, Ramon Diaz-Uriarte, Santiago F. Elena, Juan Antonio García-Martín, Paulien Hogeweg, Bhavin S. Khatri, Joachim Krug, Ard A. Louis, Nora S. Martin, Joshua L. Payne, Matthew J. Tarnowski, Marcel Weiß Physics of life reviews 42, 19-24 (2022) | arxiv abstract | pdf |
144.	Symmetry and simplicity spontaneously emerge from the algorithmic nature of evolution Iain G Johnston, Kamaludin Dingle, Sam F. Greenbury, Chico Q. Camargo, Jonathan P. K. Doye, Sebastian E. Ahnert, Ard A. Louis PNAS 119, e2113883119 (2022). | biorxiv abstract| combined pdf | github repository | | Chico's Twitter thread | Press release | NY Times news story | Oxford U news story| Oxford Physics news story | Le Monde story | Pour La Science article |
143.	The interplay of supercoiling and thymine dimers in DNA Wilber Lim, Ferdinando Randisi, Jonathan PK Doye, Ard Louis Nucl. Acids. Res. 50, 2480 (2022) | biorxiv abstract | pdf |
142.	Why Flatness Correlates With Generalization For Deep Neural Networks Shuofeng Zhang, Isaac Reid, Guillermo Valle-Pérez, and Ard A. Louis | arxiv abstract | pdf |
141.	Double-descent curves in neural networks: a new perspective using Gaussian processes Ouns El Harzli, Bernardo Cuenca Grau, Guillermo Valle-Pérez, and Ard A. Louis Proceedings of the AAAI Conference on Artificial Intelligence. 38 11856 (2024). | arxiv abstract | pdf |
140.	Generalization bounds for deep learning Guillermo Valle-Pérez and Ard A. Louis | arxiv abstract | pdf |
139.	Phenotype bias determines how RNA structures occupy the morphospace of all possible shapes Kamaludin Dingle, Fatme Ghaddar, Petr Sulc, and Ard A. Louis Molecular Biology and Evolution, 39, msab280 (2021) | biorxiv abstract | pdf |
138.	Is SGD a Bayesian sampler? Well, almost Chris Mingard, Guillermo Valle-Pérez, Joar Skalse, Ard A. Louis Journal of Machine Learning 22 (79), 1-64 (2021) | arxiv abstractv | pdf |
137.	Measuring internal forces in single-stranded DNA: Application to a DNA force clamp Megan C. Engel, Flavio Romano, Ard A. Louis, Jonathan P.K. Doye J. Chem. Theory Comput. 16, 7765 (2020). | arxiv abstract | pdf |
136.	Reconfigurable T‐junction DNA Origami Katherine G. Young, Behnam Najafi, William M. Sant, Sonia Contera, Ard A. Louis, Jonathan P. K. Doye, Andrew J. Turberfield, Jonathan Bath Angewante Chemie, 132, 16076 (2020). | arxiv abstract | pdf |
135.	Characterising DNA T-motifs by Simulation and Experiment Behnam Najafi, Katherine G Young, Jonathan Bath, Ard A Louis, Jonathan PK Doye, Andrew J Turberfiel | arxiv abstractv | pdf |
134.	The oxDNA coarse-grained model as a tool to simulate DNA origami Jonathan P. K. Doye, Hannah Fowler, Domen Prešern, Joakim Bohlin, Lorenzo Rovigatti, Flavio Romano, Petr Šulc, Chak Kui Wong, Ard A. Louis, John S. Schreck, Megan C. Engel, Michael Matthies, Erik Benson, Erik Poppleton, Benedict E. K. Snodin n: Valero, J. (eds) DNA and RNA Origami. Methods in Molecular Biology, vol 2639. Humana, New York | arxiv abstract | |
133.	Boolean Threshold Networks as Models of Genotype-Phenotype Maps C.Q. Camargo and A. A. Louis Complex Networks XI pp 143 (2020) | arxiv abstract | pdf |
132.	From genotypes to organisms: State-of-the-art and perspectives of a cornerstone in evolutionary dynamics Susanna Manrubia, José A. Cuesta, Jacobo Aguirre, Sebastian E. Ahnert, Lee Altenberg, Alejandro V. Cano, Pablo Catalán, Ramon Diaz-Uriarte, Santiago F. Elena, Juan Antonio García-Martín, Paulien Hogeweg, Bhavin S. Khatri, Joachim Krug, Ard A. Louis, Nora S. Martin, Joshua L. Payne, Matthew J. Tarnowski, Marcel Weiß | arxiv abstract | pdf |
131.	Generic predictions of output probability based on complexities of inputs and outputs Kamaludin Dingle, Guillermo Valle-Pérez,Ard A. Louis Sci. Rep. 10, 4415 (2020) | arxiv abstract | pdf |
130.	Neural networks are a priori biased towards Boolean functions with low entropy Chris Mingard, Joar Skalse, Guillermo Valle-Pérez, David Martínez-Rubio, Vladimir Mikulik, Ard A. Louis | arxiv abstract | pdf |
129.	Rational design of hidden thermodynamic driving through DNA mismatch repair Natalie EC Haley, Thomas E Ouldridge, Alessandro Geraldini, Ard A Louis, Jonathan Bath, Andrew J Turberfield Nature Communications 11, 2562 (2020) | bioarxiv abstract | pdf |
128.	TacoxDNA: A user friendly web server for simulations of complex DNA structures, from single strands to origami Antonio Suma, Erik Poppleton, Michael Matthies, Petr Šulc, Flavio Romano, Ard A. Louis, Jonathan P. K. Doye, Cristian Micheletti, Lorenzo Rovigatti J. Comp. Chem 40, 2586 (2019) | arxiv abstract |pdf| featured on the cover:
127.	Identifying Physical Causes of Apparent Enhanced Cyclization of Short DNA Molecules with a Coarse-Grained Model Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge,Ard A. Louis, Jonathan P. K. Doye J. Chem. Theory Comput 15, 8 (2019) | arxiv abstract | pdf |
126.	Coarse-grained modelling of the structural properties of DNA origami Benedict E K Snodin, John S Schreck, Flavio Romano, Ard A Louis, Jonathan P K Doye Nuc. Acids Res., 47, 1585 (2019) | arxiv abstract | pdf |
125.	A touch of awe: crafting meaning from the wonder of the cosmos Steve Paulson, Paul Davies, Ard Louis, and Lucianne Walkowicz Ann. NY Acad. Sci. 1436 46 (2018) | arxiv abstract | pdf |
124.	Deep learning generalizes because the parameter-function map is biased towards simple functions Guillermo Valle Pérez, Chico Q. Camargo, Ard A. Louis | arxiv abstract | pdf |
123.	Force-induced unravelling of DNA Origami Megan C. Engel, David M. Smith, Markus A. Jobst, Martin Sajfutdinow, Tim Liedl, Flavio Romano, Lorenzo Rovigatti, Ard A. Louis and Jonathan P. K. Doye ACS Nano 12, 6734 (2018) | arxiv abstract | pdf|
122	Input–output maps are strongly biased towards simple outputs K. Dingle, C. Q. Camargo and A. A. Louis Nature Comm. 9, 761 (2018) |Arxiv abstract | pdf| Oxford blog post on simplicity bias | Phys.org blog post on simplicity bias | Nature Physics article highlighting our work |
121.	Introduction to molecular simulation P Sulc, JPK Doye, AA Louis Quantitative Biology: Computational Methods and Examples, ed. B. Munsky, W.S. Hlavacek and L.S. Tsimring, MIT Press (2018) | arxiv abstract | pdf |
120.	Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly P Fonseca, F Romano, JS Schreck, TE Ouldridge, JPK Doye, AA Louis J. Chem. Phys. 148, 134910 (2018) | arxiv abstract | pdf|
119.	Characterizing the Motion of Jointed DNA Nanostructures Using a Coarse-Grained Model Rahul Sharma, John S. Schreck, Flavio Romano, Ard A. Louis and Jonathan P.K. Doye ACS Nano, 11, 23426 (2017) | arxiv abstract | pdf|
	2016
118.	Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation Thana Sutthibutpong, Christian Matek, Craig Benham, Gabriel G. Slade, Agnes Noy, Charles Laughton, Jonathan P. K. Doye, Ard A. Louis and Sarah A. Harris Nucl. Acids Res 44, 9121 (2016) | arxiv abstract | pdf|
117.	Contingency, convergence and hyper-astronomical numbers in biological evolution Ard A. Louis Studies in History and Philosophy of Biological and Biomedical Sciences 58, 107 (2016) | arxiv abstract | pdf|
116.	Characterizing DNA star-tile-based nanostructures using a coarse-grained model John S. Schreck, Flavio Romano, Matthew Zimmer, Ard A. Louis, and Jonathan P.K. Doye ACS Nano 10, 4236 (2016) | arxiv abstract | pdf|
115.	Coarse-grained modelling of strong DNA bending II: Cyclization Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye | arxiv abstract | pdf|
114.	Coarse-grained modelling of strong DNA bending I: Thermodynamics and comparison to an experimental "molecular vice" Ryan M. Harrison, Flavio Romano, Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye | arxiv abstract | pdf|
113.	Direct simulation of the self-assembly of a small DNA origami B.E.K. Snodin, F. Romano, L. Rovigatti, T.E. Ouldridge, A.A. Louis and J.P.K. Doye ACS Nano 10 1724 (2016) | arxiv abstract | pdf|
112.	Genetic correlations greatly increase mutational robustness and can both reduce and enhance evolvability Sam F. Greenbury, Steffen Schaper, Sebastian E. Ahnert, and Ard A. Louis PLoS Comp. Biol. 12(3): e1004773 (2016) | arxiv abstract | pdf|
	2015
111.	The structure of the genotype-phenotype map strongly constrains the evolution of non-coding RNA Kamaludin Dingle, Steffen Schaper, and Ard A. Louis Interface Focus 5: 20150053 (2015) | arxiv abstract | pdf|
110.	Coarse-grained modelling of supercoiled RNA Christian Matek, Petr Šulc, Ferdinando Randisi, Jonathan P. K. Doye, Ard A. Louis J. Chem. Phys. 143, 243122 (2015) | arxiv abstract | pdf|
109.	Introducing Improved Structural Properties and Salt Dependence into a Coarse-Grained Model of DNA Benedict E. K. Snodin, Ferdinando Randisi, Majid Mosayebi, Petr Sulc, John S. Schreck, Flavio Romano, Thomas E. Ouldridge, Roman Tsukanov, Eyal Nir, Ard A. Louis, Jonathan P. K. Doye J. Chem. Phys. 142, 234901 (2015) | arxiv abstract | pdf | (this paper was selected as a featured article and also for the journal cover )
108.	Taylor dispersion of colloidal particles in narrow channels Jimaan Sane', Johan T. Padding and Ard A. Louis Mol. Phys 113, 2538 (2015) | arxiv abstract | pdf reprint |
107.	Force-Induced Rupture of a DNA Duplex: From Fundamentals to Force Sensors Majid Mosayebi, Ard A. Louis, Jonathan P. K. Doye, Thomas E. Ouldridge ACS Nano (2015) | arxiv abstract | pdf reprint |
106.	Characterizing the bending and flexibility induced by bulges in DNA duplexes John S. Schreck, Thomas E. Ouldridge, Flavio Romano, Ard A. Louis, Jonathan P. K. Doye J. Chem. Phys. 142, 165101 (2015) | arxiv abstract | pdf reprint | (this paper was selected for the journal cover ).
105.	Modelling toehold-mediated RNA strand displacement Petr Šulc, Thomas E. Ouldridge, Flavio Romano, Jonathan P. K. Doye, Ard A. Louis Biophys. J. 108, 1238 (2015) | arxiv abstract | pdf reprint | (this paper was selected for the journal cover and the subject of a Biophysical Society blog post ).
104.	DNA hairpins primarily promote duplex melting rather than inhibiting hybridization John S. Schreck, Thomas E. Ouldridge, Flavio Romano, Petr Sulc, Liam Shaw, Ard A. Louis, Jonathan P. K. Doye Nuc. Acids Res. 43, 6181 (2015) | arxiv abstract | pdf reprint |
103.	Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA Christian Matek, Thomas E. Ouldridge, Jonathan P. K. Doye, Ard A. Louis Scientific Reports 5, 7655 (2015) | arxiv abstract | pdf reprint |
	2014
102.	The role of loop stacking in the dynamics of DNA hairpin formation Majid Mosayebi, Flavio Romano, Thomas E. Ouldridge, Ard A. Louis, Jonathan P. K. Doye J. Phys. Chem. B, 118, 14326 (2014) | arxiv abstract | pdf reprint |
101.	A nucleotide-level coarse-grained model of RNA Petr Sulc, Flavio Romano, Thomas E. Ouldridge, Jonathan P. K. Doye, Ard A. Louis J. Chem. Phys.140, 235102 (2014) | arxiv abstract | pdf reprint | (this paper was selected for the journal cover ).
100.	A tractable genotype-phenotype map for the self-assembly of protein quaternary structure Sam F. Greenbury, Iain G. Johnston, Ard A. Louis, Sebastian E. Ahnert J. R. Soc. Interface 11, 20140249 (2014) | arxiv abstract | pdf reprint | (This paper was one of the top ten most cited papers in 2014 for Royal Society Interface. )
99.	The arrival of the frequent: how bias in genotype-phenotype maps can steer populations to local optima Steffen Schaper and Ard A. Louis PLoS ONE 9(2): e86635 (2014) | arxiv abstract | pdf reprint | Oxford Science Blogpost
98.	Graph Automorphisms and Topological Characterization of Complex Networks by Algorithmic Information Content Hector Zenil, Fernando Soler-Toscano, Kamaludin Dingle, and Ard A. Louis Physica A 404, 341 (2014) | arxiv abstract | pdf reprint |
97.	Simulating a burnt-bridges DNA motor with a coarse-grained DNA model Petr Šulc, Thomas E. Ouldridge, Flavio Romano, Jonathan P. K. Doye, and Ard A. Louis Natural Computing 13, 535 (2014) | arxiv abstract | pdf reprint |
	2013
96.	Coarse-graining DNA for simulations of DNA nanotechnology Jonathan P.K. Doye, Thomas E. Ouldridge, Ard A. Louis, Flavio Romano, Petr Sulc, Christian Matek, Benedict E.K. Snodin, Lorenzo Rovigatti, John S. Schreck, Ryan M. Harrison, William P.J. Smith Phys. Chem. Chem. Phys. 15 20395 (2013) | arxiv abstract | pdf reprint | on the PCCP cover and highlighted as a Hot Article by Soft Matter
95.	Zigzag transitions and nonequilibrium pattern formation in colloidal chains Arthur V. Straube, Roel P. A. Dullens, Lutz Schimansky-Geier, and Ard A. Louis J. Chem. Phys. 139, 134908 (2013) | arxiv abstract | pdf reprint |
94.	Dynamics of solutes with hydrodynamic interactions: Comparison of several mesoscale simulation methods Guillaume Batot, Vincent Dahirel, Guillaume Meriguet, Ard Louis, and Marie Jardat Phys. Rev. E 88, 043304 (2013) | arxiv abstract | pdf reprint |
93.	On the biophysics and kinetics of toehold-mediated DNA strand displacement Niranjan Srinivas, Thomas E. Ouldridge, Petr Sulc, Joseph M. Schaeffer, Bernard Yurke, Ard A. Louis, Jonathan P. K. Doye, and Erik Winfree Nucl. Acids Res. 41 10641 (2013) | arxiv abstract | pdf reprint |
92.	DNA hybridization kinetics: zippering, internal displacement and sequence dependence Thomas E. Ouldridge, Petr Šulc, Flavio Romano, Jonathan P. K. Doye, and Ard A. Louis Nucl. Acids Res. 41, 8886 (2013) | arxiv abstract | pdf reprint |
91.	Optimizing DNA nanotechnology through coarse-grained modelling: A two-footed DNA walker Thomas E. Ouldridge, Rollo Hoare, Ard A. Louis, Jonathan P. K. Doye, Jonathan Bath, and Andrew J. Turberfield ACS Nano 7, 2479 (2013). | arxiv abstract | pdf reprint |
90.	Coarse-grained simulations of DNA overstretching Flavio Romano, Debayan Chakraborty, Jonathan P. K. Doye, Thomas E. Ouldridge, Ard. A. Louis, J. Chem. Phys. 138, 085101 (2013) | arxiv abstract | pdf reprint |
89.	Viscous fingering at ultralow interfacial tension Siti Aminah Setu, Ioannis Zacharoudiou, Gareth J. Davies, Denis Bartolo, Sebastien Moulinet, Ard A. Louis, Julia M. Yeomans and Dirk G.A.L. Aarts Soft Matter 9, 10599 (2013) | arxiv abstract | pdf reprint |
	2012
88.	Effect of Bending Rigidity on the Knotting of a Polymer under Tension Richard Matthews, Ard A. Louis, and Christos N. Likos ACS Macro Lett. 1, 1352 (2012) | arxiv abstract | pdf reprint |
87.	Sequence-dependent thermodynamics of a coarse-grained DNA model Petr Sulc, Flavio Romano, Thomas E. Ouldridge, Lorenzo Rovigatti, Jonathan P. K. Doye, Ard A. Louis J. Chem. Phys. 137, 135101 (2012) (this paper was selected for the journal cover ). | arxiv abstract | pdf reprint |
86.	DNA cruciform arms nucleate through a correlated but non-synchronous cooperative mechanism Christian Matek, Thomas E. Ouldridge, Alex Levy, Jonathan P. K. Doye, and Ard A. Louis J. Phys. Chem B 116, 11616 (2012) | arxiv abstract | pdf reprint |
85.	The effect of topology on the structure and free energy landscape of DNA kissing complexes Flavio Romano, Alex Hudson, Jonathan P.K. Doye, Thomas E. Ouldridge, and Ard A. Louis J. Chem. Phys. 136, 215102 (2012) | arxiv abstract | pdf reprint |
84.	How Peclet number affects microstructure and transient cluster aggregation in sedimenting colloidal suspensions A. Moncho Jorda, A.A. Louis and J.T. Padding J. Chem. Phys. 136, 064517 (2012) | arxiv abstract | pdf reprint |
83.	Formation of dodecagonal quasicrystals in two-dimensional systems of patchy particles Marjolein N. van der Linden, Jonathan P. K. Doye, and Ard A. Louis J. Chem. Phys. 136, 054904 (2012). | arxiv abstract | pdf reprint |
82.	Epistasis can lead to fragmented neutral networks and contingency in evolution Steffen Schaper, Iain G. Johnston, and Ard A. Louis Proceedings of the Royal Society B 279, 1777 (2012) | arxiv abstract | pdf reprint |
	2011
81.	Extracting short-ranged interactions from structure factors Ard A. Louis, Mol. Phys. 109, 2945 (2011) | arxiv abstract | pdf reprint |
80.	Evolutionary Dynamics in a Simple Model of Self-Assembly Iain G. Johnston, Sebastian E. Ahnert, Jonathan K. P. Doye and Ard A. Louis, Phys. Rev. E. 83, 066105 (2011) | arxiv abstract | pdf reprint |
79.	Templated self-assembly of patchy particles Alexander J. Williamson, Alex W. Wilber, Jonathan P. K. Doye, and Ard A. Louis Soft Matter 7, 3423 (2011). | arxiv abstract | pdf reprint | highlighted as a Hot Article by Soft Matter
78.	Confinement of knotted polymers in a slit R. Matthews, A.A. Louis, J.M. Yeomans Mol. Phys. 109, 1289 (2011) | arxiv abstract | pdf reprint |
77.	Reentrant phase behaviour for systems with competition between phase separation and self-assembly Aleks Reinhardt, Alexander J. Williamson, Jonathan P. K. Doye, Jesús Carrete, Luis M. Varela, and Ard A. Louis J. Chem. Phys. 134, 104905 (2011) | arxiv abstract | pdf reprint |
76.	Structural and thermodynamic properties of a coarse-grained model of DNA Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye J. Chem. Phys. 134, 085101 (2011) | arxiv abstract | pdf reprint | (this paper was a featured article on the journal cover ).
75.	Pattern Formation in Colloidal Explosions Arthur V. Straube, Ard A. Louis. Jorg Baumgartl, Clemens Bechinger, and Roel P. A. Dullens Europhys. Lett. 94, 48008 (2011). | arxiv abstract | pdf reprint |
	2010
74.	Is water an amniotic Eden or a corrosive Hell? Emerging perspectives on the strangest fluid in the Universe. Simon Conway Morris and Ard .A. Louis in Water and Life, eds. J. D. Barrow, S. Conway Morris, J.L. Finney, C.L. Harper and R.M. Lynden-Bell (CRC Press (2010))
73.	Complex dynamics of knotted filaments in shear flow Richard Matthews, Ard A. Louis and Julia M. Yeomans Europhys. Lett. 92, 34003 (2010). | arxiv abstract | pdf reprint |
72.	The effect of scale-free topology on the robustness and evolvability of gene regulatory networks Sam F. Greenbury, Iain G. Johnston, Matthew A. Smith, Jonathan P.K. Doye and Ard A. Louis J. Theor. Biol. 267, 48 (2010) | arxiv abstract | pdf reprint |
71.	The stability of a crystal with diamond structure for patchy particles with tetrahedral symmetry E. G. Noya, C. Vega, J. P. K. Doye, A. A. Louis J. Chem. Phys. 132, 234511 (2010) | arxiv abstract | pdf reprint |
70.	DNA nanotweezers studied with a coarse-grained model of DNA Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye Phys. Rev. Lett. 104, 178101 (2010) | arxiv abstract | pdf reprint |
69.	Coarse-graining dynamics by telescoping down time-scales: comment for Faraday FD144 A.A. Louis Faraday Discuss. 144, 323 (2010) | arxiv abstract | pdf reprint |
68.	No free lunch for effective potentials: general comment for Faraday FD144: A.A. Louis Faraday Discuss. 144, 323 (2010) | arxiv abstract | pdf reprint |
67.	Self-assembly, modularity and physical complexity S. E. Ahnert, I. Johnston, T. M. A. Fink, J. P. K. Doye, and A. A. Louis Phys. Rev. E 82 026117 (2010) | arxiv abstract | pdf reprint |
66.	Modelling the Self-Assembly of Virus Capsids Iain G. Johnston, Ard A. Louis and Jonathan P.K. Doye J. Phys.: Condensed Matter, 22 , 104101 (2010) | arxiv abstract | pdf reprint | (this paper was selected for journal cover and as one of the journal's Highlights of 2010)
65.	Extracting bulk properties of self-assembling systems from small simulations Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye J. Phys.: Condensed Matter, 22, 104102 (2010) special issue: | arxiv abstract | pdf reprint |
64.	The effects of inter-particle attractions on colloidal sedimentation A. Moncho Jorda', A. A. Louis and J. T. Padding Phys. Rev. Lett. 104, 068301 (2010) | arxiv abstract | pdf reprint | (this paper was selected as an Editor's Suggestion" in PRL)
63.	Effect of topology on dynamics of knots in polymers under tension Richard Matthews, Ard A. Louis and Julia M. Yeomans Europhys. Lett. 89, 20001 (2010) | arxiv abstract | pdf reprint |
62.	The crossover from single file to Fickian diffusion Jimaan Sane', Johan T. Padding and Ard A. Louis Faraday Discuss. 144, 285 (2010) | arxiv abstract | pdf reprint |
	2009
61.	Monodisperse self-assembly in a model with protein-like interactions Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis, Anna C. F. Lewis J. Chem. Phys. 131, 175102 (2009) | arxiv abstract | pdf reprint |
60.	Self-assembly of monodisperse clusters: Dependence on target geometry Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis J. Chem. Phys. 131, 175101 (2009) | arxiv abstract | pdf reprint | (note, paper was selected on the front cover of the 7 November 2009 issue of J. Chem. Phys, and was one of the most downloaded papers for November 2009.
59.	Hydrodynamics of confined colloidal fluids in two dimensions Jimaan Sane', Johan T. Padding and Ard A. Louis Phys. Rev. E 79, 051402 (2009) | arxiv abstract | pdf reprint |
58.	The self-assembly and evolution of homomeric protein complexes Gabriel Villar, Alex Wilber, Alex J. Williamson, Parvinder Thiara, Jonathan J.P.K. Doye, Ard A. Louis, Mara N. Jochum, Anna C.F. Lewis and Emmanuel D. Levy Phys. Rev. Lett. 102, 118106 (2009) | arxiv abstract | pdf reprint |
57.	Knot controlled ejection of a polymer from a virus capsid Richard Matthews, Ard A. Louis and Julia M. Yeomans Phys. Rev. Lett. 102, 088101 (2009) | arxiv abstract | pdf reprint | (this paper was selected as an Editor's Suggestion in PRL)
56.	The self-assembly of DNA Holliday junctions studied with a minimal model Thomas E. Ouldridge, Iain G. Johnston, Ard A. Louis, Jonathan P. K. Doye J. Chem. Phys. 130, 065101 (2009) | arxiv abstract | pdf reprint |
	2008
55.	Density profiles and solvation forces for a Yukawa fluid in a slit pore S. Karanikas, J. Dzubiella, A. Moncho-Jorda', and A. A. Louis J. Chem. Phys. 128, 204704 (2008) | arxiv abstract | pdf reprint |
54.	The interplay between hydrodynamic and Brownian fluctuations in sedimenting colloidal suspensions J.T. Padding and A.A. Louis Phys. Rev. E 77, 011402 (2008) | arxiv abstract | pdf reprint |
	2007
53.	Phase diagram of model anisotropic particles with octahedral symmety E. G. Noya, C. Vega, J. P. K. Doye, A. A. Louis J. Chem. Phys. 127, 054501 (2007) | arxiv abstract | pdf reprint |
52.	Measuring colloidal interactions with confocal microscopy C. Patrick Royall, Ard. A. Louis, and Hajime Tanaka J. Chem. Phys. 127, 044507 (2007) | arxiv abstract | pdf reprint|
51.	Representability problems for coarse-grained water potentials Margaret E. Johnson, Teresa Head-Gordon, Ard A. Louis J. Chem. Phys. 126, 144509 (2007) | arxiv abstract | pdf reprint|
50.	Controlling crystallization and its absence: proteins, colloids and patchy models J.P.K. Doye, A.A. Louis, I-C. Lin, L.R. Allen, E.G. Noya, A.W. Wilber, H.C. Kok, R. Lyus Phys. Chem. Chem. Phys. 9, 2197 (2007) |arxiv abstract | pdf reprint | (note: this article was featured on the front cover of the 14 May 2007 issue. It was also the most downloaded PCCP article for May 2007.
49.	Reversible self-assembly of patchy particles into monodisperse clusters Alex W. Wilber, Jonathan P. K. Doye, Ard A. Louis, Mark A. Miller, Eva G. Noya, Pauline Wong J. Chem. Phys. 127, 085106 (2007) | arxiv abstract | pdf reprint|
	2006
48.	Hydrodynamic interactions and Brownian forces in colloidal suspensions: Coarse-graining over time and length-scales J.T. Padding and A.A. Louis Phys. Rev. E 74, 031402 (2006) | arxiv abstract | pdf reprint|
47.	Phase separation of a model binary polymer solution in an external field Chris I. Addison, Pierre-Arnaud Artola, Jean-Pierre Hansen, and Ard A. Louis, J. Phys. Chem. B 110, 3661 (2006) (Special issue in honour of Mike Klein ) | arxiv abstract | pdf reprint|
	2005
46.	Polymer solutions: from hard monomers to soft polymers J.-P. Hansen, C.I. Addison and A.A. Louis, J. Phys. Condens. Matter 17, S3185 (2005) | arxiv abstract | pdf reprint |
45.	Stick boundary conditions and rotational velocity auto-correlation functions for colloidal particles in a coarse-grained representation of the solvent J.T. Padding, H. Löwen, A. Wysocki, and A.A. Louis, J. Phys. Condens. Matter 17, S3393 (2005) | arxiv abstract | pdf reprint |
44.	Coarse-graining diblock copolymer solutions: a macromolecular version of the Widom-Rowlinson model C.I. Addison, J.P. Hansen, V. Krakoviack and A. A. Louis, Mol. Phys. 103, 2045 (2005) (Special issue in honour of Ben Widom ) | arxiv abstract | pdf reprint |
43.	From concentration profiles to polymer osmotic equations of state C.I. Addison, J.P. Hansen, and A. A. Louis, ChemPhysChem. 6, 1760 (2005) (Special issue in honour of Michele Parrinello ) | arxiv abstract | pdf reprint |
42.	A density--functional study of interfacial properties of colloid--polymer mixtures A. Moncho Jorda, J. Dzubiella, J. P. Hansen, and A. A. Louis, J. Phys. Chem. B 109, 6640 (2005). (Special issue in honour of David Chandler) | arxiv abstract | pdf reprint|
	2004
41.	Dynamic colloidal stabilization by nanoparticle halos S. Karanikas and A. A. Louis, Phys. Rev. Lett. 93, 248303 (2004) see also Jiwen Liu and Erik Luijten, Phys. Rev. Lett. 93, 247802 (2004) or cond-mat/0411278 | arxiv abstract | pdf reprint|
40.	Hydrodynamic and Brownian Fluctuations in Sedimenting Suspensions J.T. Padding and A. A. Louis, Phys. Rev. Lett. 93, 220601 (2004) | arxiv abstract | pdf reprint|
39.	Influence of solvent quality on polymer solutions: a Monte Carlo study of bulk and interfacial properties C.I. Addison, A. A. Louis, and J-.P. Hansen, J. Chem. Phys. 121, 612 (2004) | arxiv abstract | pdf reprint|
38.	Inhibition of protein crystallization by evolutionary negative design J.P.K. Doye, A. A. Louis,and M. Vendruscolo, Physical Biology 1, P9-P13 (2004) | arxiv abstract | pdf reprint|
37.	Phase separation of a multiple occupancy lattice gas R. Finken, J.-P. Hansen, A.A. Louis, J. Phys. A: Math. Gen. 37, 577 (2004) | arxiv abstract | pdf reprint|
36.	Thermodynamic perturbation theory of the phase behaviour of colloid / interacting polymer mixtures B. Rotenberg, J. Dzubiella, J.-P. Hansen, A. A. Louis, Mol. Phys. 102, 1 (2004) | arxiv abstract | pdf reprint|
	2003
35.	Effect of polymer-polymer interactions on the surface tension of colloid-polymer mixtures A. Moncho-Jorda, B. Rotenberg, A. A. Louis, J. Chem. Phys. 119, 12667 (2003) | arxiv abstract | pdf reprint|
34.	The Asakura-Oosawa model in the protein limit: the role of many-body interactions A. Moncho-Jorda, A. A. Louis, P. G. Bolhuis, R. Roth J. Phys.: Condensed Matter, 15, S3429 (2003) special issue Effective many-body interactions and correlations in soft matter | arxiv abstract | pdf reprint|
33.	Influence of solvent quality on effective pair potentials between polymers in solution V. Krakoviack, J. P. Hansen,and A. A. Louis, Phys. Rev. E 67, 041801 (2003) | arxiv abstract | pdf reprint|
32.	Non-monotonic variation with salt concentration of the second virial coefficient in protein solutions E. Allahyarov, H. Löwen, J.P. Hansen, and A.A. Louis, Phys. Rev. E 67, 051494 (2003) | arxiv abstract | pdf reprint|
31.	Phase separation of penetrable core mixtures R. Finken, J.-P. Hansen, A. A. Louis, J. Stat. Phys. 110 , 1015 (2003). (Special issue in honour of Prof. Michael E. Fisher ) | arxiv abstract | pdf reprint|
30.	Colloid-polymer mixtures in the protein limit P.G. Bolhuis, E.J. Meijer, and A.A. Louis, Phys. Rev. Lett. 90, 068304 (2003) | arxiv abstract | pdf reprint|
	2002
29.	Influence of polymer excluded volume on the phase behavior of colloid--polymer mixtures P.G. Bolhuis, A.A. Louis, and J.P. Hansen, Phys. Rev. Lett. 89, 128302 (2002) | arxiv abstract | pdf reprint|
28.	Beware of density dependent pair potentials J. Phys.: Condens. Matter 14, 9187 (2002). (Special issue in honour of professor Jean-Pierre Hansen) | arxiv abstract | pdf reprint|
27.	Exotic fluids and crystals of soft polymeric colloids C N Likos, N Hoffmann, H Lowen and A A Louis, J. Phys.: Condens. Matter 14 7681 (2002). (Special issue in honour of Prof. Peter Pusey) | arxiv abstract | pdf reprint|
26.	Polymer induced depletion potentials in polymer-colloid mixtures A.A. Louis, P.G. Bolhuis, E.J. Meijer, and J.P. Hansen, J. Chem. Phys. 117, 1893 (2002) | arxiv abstract | pdf reprint|
25.	Density profiles and surface tensions of polymers near colloidal surfaces A.A. Louis, P.G. Bolhuis, E.J. Meijer, and J.P. Hansen, J. hem. Phys. 116 , 10547 (2002) | arxiv abstract | pdf reprint|
24.	Coarse-graining polymers as soft colloids A.A. Louis, P.G. Bolhuis, R. Finken, V. Krakoviack, E.J. Meijer,and J.P. Hansen, Physica A 306, 251 (2002) | arxiv abstract | pdf reprint|
23.	Effective forces in colloidal mixtures: from depletion attraction to accumulation repulsion A.A. Louis, E. Allahyarov, H. Löwen and R.Roth Phys. Rev. E 65 061407 (2002) | arxiv abstract | pdf reprint|
22.	Combining quantum and classical density functional theory for ion-electron mixtures. A.A. Louis, H. Xu, J.A. Anta J. Non-Cryst. Solids 312-314C, 60 (2002) | arxiv abstract | pdf reprint|
21.	Relating monomer to centre-of-mass distribution functions in polymer solutions V. Krakoviack, J. P. Hansen, A. A. Louis, Europhysics Letters 58, 53 (2002) | arxiv abstract | pdf reprint|
20.	How to derive and parameterize effective potentials in colloid-polymer mixtures P.G. Bolhuis and A.A. Louis, Macromolecules 35, 1860 (2002) | arxiv abstract | pdf reprint|
19.	Discrete charge patterns, Coulomb correlations and interactions in protein solutions E. Allahyarov, H. Löwen, A.A. Louis, and J.P. Hansen, Europhys. Lett. 57, 731 (2002) | arxiv abstract | pdf reprint|
	2001
18.	Theory of asymmetric non-additive binary hard-sphere mixtures R. Roth, R. Evans, and A. A. Louis, Phys. Rev. E 64, 051202 (2001) | arxiv abstract | pdf reprint|
17.	"Many-body interactions and correlations in coarse-grained descriptions of polymer solutions" P.G. Bolhuis, A.A. Louis, and J.P. Hansen, Phys. Rev. E. 64, 021801 (2001) | arxiv abstract | pdf reprint|
16.	Effective potentials for polymers and colloids: Beyond the van der Waals picture of fluids?" A.A. Louis, Phil. Trans. Roy. Soc. A 359 , 939 (2001) | arxiv abstract | pdf reprint|
15.	Generalized effective depletion potentials A.A. Louis,and R. Roth J. Phys.: Condens. Matter 33 L777 (2001) | arxiv abstract | pdf reprint|
14.	Accurate effective pair potentials for polymer solutions P.G. Bolhuis, A.A. Louis, J.P. Hansen, and E.J. Meijer, J. Chem. Phys. 114, 4296 (2001) | arxiv abstract | pdf reprint|
	2000
13.	Mean Field Fluid Behavior of the Gaussian Core Model A.A. Louis, P.G. Bolhuis, and J.P. Hansen, Phys. Rev. E. 62, 7961 (2000) | arxiv abstract | pdf reprint|
12.	Can Polymer Coils be modeled as Soft Colloids? A. A. Louis, P.G. Bolhuis, J.P. Hansen, E.J. Meijer, Phys. Rev. Lett. 85, 2522 (2000) | arxiv abstract | pdf reprint|
11.	Fluid-solid phase-separation in hard-sphere mixtures is unrelated to bond-percolation A. A. Louis, Phys. Rev. Lett. 84, 1840 (2000) (comment) | arxiv abstract | pdf reprint|
10.	Probing Ion-Ion and Electron-Ion Correlations in Liquid Metals within the Quantum Hypernetted Chain Approximation J.A. Anta and A.A. Louis, Phys. Rev. B. 61, 11400 (2000) | arxiv abstract | pdf reprint|
9.	Crystallization and phase-separation in non-additive binary hard-sphere mixtures A. A. Louis, R. Finken and J.P. Hansen, Phys. Rev. E. 61, R1028 (2000) | arxiv abstract | pdf reprint|
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