A.A. Louis: Publications

96.	Graph Automorphisms and Topological Characterization of Complex Networks by Algorithmic Information Content Hector Zenil, Fernando Soler-Toscano, Kamaludin Dingle, and Ard A. Louis | arxiv abstract | pdf reprint |
95.	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 | arxiv abstract | pdf reprint |
94.	DNA hybridization kinetics: zippering, internal displacement and sequence dependence Thomas E. Ouldridge, Petr Šulc, Flavio Romano, Jonathan P. K. Doye, and Ard A. Louis | arxiv abstract | pdf reprint |
93.	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 | arxiv abstract | pdf reprint |
92.	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 to appear in ACS nano: early as Article ASAP | arxiv abstract | pdf reprint |
91.	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 |
90.	3D Nature of the Saffman-Taylor Instability Siti Aminah Setu, Ioannis Zacharoudiou, Gareth J. Davies, Denis Bartolo, Sebastien Moulinet, Ard A. Louis, Julia M. Yeomans and Dirk G.A.L. Aarts | arxiv abstract | pdf reprint |
	2012
89.	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 |
88.	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 |
87.	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 |
86.	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 |
85.	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 |
84.	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 |
83.	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
82.	Extracting short-ranged interactions from structure factors Ard A. Louis, Mol. Phys. 109, 2945 (2011) | arxiv abstract | pdf reprint |
81.	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 |
80.	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
79.	Confinement of knotted polymers in a slit R. Matthews, A.A. Louis, J.M. Yeomans Mol. Phys. 109, 1289 (2011) | arxiv abstract | pdf reprint |
78.	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 |
77.	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 selected for the journal cover ).
76.	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
75.	Is water an amniotic Eden or a corrosive Hell? Emerging perspectives on the strangest fluid in the Universe. S. Conway Morris and A.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))
74.	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 |
73.	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 |
72.	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 |
71.	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 |
70.	Coarse-graining dynamics by telescoping down time-scales: comment for Faraday FD144 A.A. Louis Faraday Discuss. 144, 323 (2010) | arxiv abstract | pdf reprint |
69.	No free lunch for effective potentials: general comment for Faraday FD144: A.A. Louis Faraday Discuss. 144, 323 (2010) | arxiv abstract | pdf reprint |
68.	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 |
67.	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)
66.	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 |
65.	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)
64.	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 |
63.	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
62.	Coarse-graining dynamics for convection-diffusion of colloids: Taylor dispersion Jimaan Sane', Johan T. Padding and Ard A. Louis | arxiv abstract | pdf reprint |
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|
	previous century
8.	The structure of colloid-polymer mixtures A. A. Louis, R. Finken and J.P. Hansen, Europhysics Letters, 46, 741 (1999) | arxiv abstract | pdf reprint|
7.	Electron-Ion Structure Factors and the General Accuracy of Linear Response A. A. Louis,and N. W. Ashcroft, J. Non-Crystalline Solids 250-252, 9 (1999) | arxiv abstract | pdf reprint|
6.	Extending Linear Response: Inferences from Electron-Ion Structure Factors A. A. Louis,and N. W. Ashcroft, Phys. Rev. Lett. 81, 4456 (1998) | arxiv abstract | pdf reprint|
5.	"Quantum Dissipation from Phonons; Metallic Hydrogen; Electron-Ion Mixtures" PhD Thesis: Theoretical Physics,Cornell University (1998) ||
4.	Metallization of Fluid Hydrogen, W. J. Nellis, A. A. Louis, N. W. Ashcroft, Phil. Trans. R. Soc. A. 356 119-135 (1998) --A general introduction Bill Nellis' experiment and how all this relates to the planet Jupiter can be found by clicking here. | arxiv abstract | pdf reprint|
3.	Atomic Tunneling from a STM/AFM tip: Dissipative Quantum Effects from Phonons., Ard A. Louis,and James P. Sethna, Phys. Rev. Lett. 74 , 1363 (1995) An introduction to our work (lots of pretty pictures!) for a more general audience can be found by clicking  here | arxiv abstract | pdf reprint|
2.	Phase separation in a binary hard-core mixture: An exact result., Daan Frenkel and Ard A. Louis, Phys. Rev. Lett. 68, 3363 (1992) | pdf reprint|
1.	Entropic Phase Separation (postscript -- no figs) Ard A. Louis, Undergraduate Thesis, University of Utrecht (1992) Any elementary textbook on statistical mechanics will try to convince you that energy is everything w.r.t. phase separation. The goal of this thesis is to show otherwise (i.e. Entropy is Everything! ). | |