Publications Scientifiques

* M. Potters, T. Vaillant, F. Bouchet, Sampling microcanonical measures of the 2D Euler equations using Creutz’s algorithm: a phase transition from disorder to order when energy is increased, in press J. Stat. Mech. 2013

• M. Champion, A. Alastuey, T. Dauxois an S. Ruffo, Gravitation in the microcanonical ensemble: Appropriate scaling leading to extensivity and thermalization, submitted to J. Stat. Phys. (2012), arXiv:1210.5592.

• Everaers, Ralf,Topological versus rheological entanglement length in primitive-path analysis protocols, tube models, and slip-link models, PHYSICAL REVIEW E Volume: 86 Issue: 2 Article Number: 022801 DOI: 10.1103/PhysRevE.86.022801 Part 1, August 13, 2012
  

• Gupta, Shamik; Potters, Max; Ruffo, Stefano, One-dimensional lattice of oscillators coupled through power-law interactions: Continuum limit and dynamics of spatial Fourier modes, PHYSICAL REVIEW E Volume: 85 Issue: 6 Article Number: 066201 DOI: 10.1103/PhysRevE.85.066201 Part 2, June 4, 2012

• Bouchet, Freddy; Venaille, Antoine, Statistical mechanics of two-dimensional and geophysical flows, PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS Volume: 515 Issue: 5 Pages: 227-295 DOI: 10.1016/j.physrep.2012.02.001, June 2012

• de Buyl, Pierre; Fanelli, Duccio; Ruffo, Stefano, Phase transitions of quasistationary states in the Hamiltonian Mean Field model, CENTRAL EUROPEAN JOURNAL OF PHYSICS Volume: 10 Issue: 3 Pages: 652-659 DOI: 10.2478/s11534-012-0010-6, June 2012

• Magi, Alberto; Tattini, Lorenzo; Benelli, Matteo; et al., WNP: a novel algorithm for gene products annotation from weighted functional networks, PloS one Volume: 7 Issue: 6 Pages: e38767 DOI: 10.1371/journal.pone.0038767, (2012) Epub June 28, 2012

• Bouchet, Freddy; Touchette, Hugo, Non-classical large deviations for a noisy system with non-isolated attractors, JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT Article Number: P05028 DOI: 10.1088/1742-5468/2012/05/P05028, May 2012

• Patelli, Aurelio; Gupta, Shamik; Nardini, Cesare; et al., Linear response theory for long-range interacting systems in quasistationary states, PHYSICAL REVIEW E Volume: 85 ssue: 2 Article Number: 021133 DOI: 10.1103/PhysRevE.85.021133 Part 1, February 23, 2012

• Nardini, Cesare; Gupta, Shamik; Ruffo, Stefano; et al., Kinetic theory for non-equilibrium stationary states in long-range interacting systems, JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT Article Number: L01002 DOI: 10.1088/1742-5468/2012/01/L01002, January 2012

• Everaers, Ralf; Rosa, Angelo Multi-scale modeling of diffusion-controlled reactions in polymers: Renormalisation of reactivity parameters, JOURNAL OF CHEMICAL PHYSICS Volume: 136 Issue: 1 Article Number: 014902 DOI: 10.1063/1.3673444, January 7, 2012
  

• Cesare Nardini, Shamik Gupta, Stefano Ruffo, Thierry Dauxois, Freddy Bouchet, Kinetic theory of nonequilibrium stochastic long-range systems: Phase transition and bistability, J. Stat. Mech. Theory Exp. P12010 (2012)

• S. Gupta, A. Campa and S. Ruffo, Overdamped dynamics of long-range systems on a one-dimensional lattice: Dominance of the mean-field mode and phase transition, Phys. Rev. E, 86, 061130 (2012).

• Nadiga, Balasubramanya T.; Bouchet, Freddy, The equivalence of the Lagrangian-averaged Navier-Stokes-alpha model and the rational large eddy simulation model in two dimensions, PHYSICS OF FLUIDS Volume: 23 Issue: 9 Article Number: 095105 DOI: 10.1063/1.3632084, September 2011

• Venaille, Antoine; Bouchet, Freddy, Solvable Phase Diagrams and Ensemble Inequivalence for Two-Dimensional and Geophysical Turbulent Flows, JOURNAL OF STATISTICAL PHYSICS Volume: 143 Issue: 2 Pages: 346-380 DOI: 10.1007/s10955-011-0168-0, April 2011

• Venaille, Antoine; Bouchet, Freddy, Are oceanic rings and jets statistical equilibrium states ?, Bajer, K; Kopec, J; Kursa, M; et al., 13th European Turbulence Conference (ETC) Location: Univ Warsaw, Warsaw, POLAND Date: September 12-15, 2011, 13TH EUROPEAN TURBULENCE CONFERENCE (ETC13): GEOPHYSICAL AND MAGNETOHYDRODYNAMIC TURBULENCE Book Series: Journal of Physics Conference Series Volume: 318 Article Number: 072024 DOI: 10.1088/1742-6596/318/7/072024 (2011)

• Meyer, Sam; Becker, Nils B.; Syed, Sajad Hussain; et al., From crystal and NMR structures, footprints and cryo-electron-micrographs to large and soft structures: nanoscale modeling of the nucleosomal stem, NUCLEIC ACIDS RESEARCH Volume: 39 Issue: 21 Pages: 9139-9154 DOI: 10.1093/nar/gkr573, November 2011

• Jost, Daniel; Zubair, Asif; Everaers, Ralf, Bubble statistics and positioning in superhelically stressed DNA, Physical Review E, Volume 84, Issue 3, Article Number 031912, DOI: 10.1103/PhysRevE.84.031912, Part 1, September 12 2011

• Volk R.; Calzavarini E.; Lévêque E.; et al., Dynamics of inertial particles in a turbulent von Karman flow, JOURNAL OF FLUID MECHANICS Volume: 668 Pages: 223-235 DOI: 10.1017/S0022112010005690 (2011)

• Salort J; Roche PE; and E. Lévêque, Mesoscale equipartition of kinetic energy in quantum turbulence, EPL Volume: 94 Issue: 2 Article Number: 24001 (2011)

• Vosskuhle, Michel; Pumir, Alain; Leveque, Emmanuel, Estimating the Collision Rate of Inertial Particles in a Turbulent Flow: Limitations of the "Ghost Collision" Approximation, Conference: 13th European Turbulence Conference (ETC) Location: Univ Warsaw, Warsaw, Poland, September 12-15, 2011 - Journal of Physics Conference Series Volume: 318, Article Number: 052024, DOI: 10.1088/1742-6596/318/5/052024, 2011

• Bouchet, Freddy; Gupta, Shamik; Mukamel, David, Thermodynamics and dynamics of systems with long-range interactions, 12th International Summer School on Fundamental Problems in Statistical Physics Location: European Ctr Foresta, Leuven, BELGIUM, August 31-September 11, 2009 - PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS Volume: 389 Issue: 20 Special Issue: SI Pages: 4389-4405 DOI: 10.1016/j.physa.2010.02.024, October 15, 2010

• Bouchet, Freddy; Corvellec, Marianne, Invariant measures of the 2D Euler and Vlasov equations, JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT Article Number: P08021 DOI: 10.1088/1742-5468/2010/08/P08021, August 2010

• Bouchet, Freddy; Morita, Hidetoshi, Large time behavior and asymptotic stability of the 2D Euler and linearized Euler equations, PHYSICA D-NONLINEAR PHENOMENA Volume: 239 Issue: 12 Pages: 948-966 DOI: 10.1016/j.physd.2010.01.020, June 15, 2010

• Olivetti, Alain; Barre, Julien; Marcos, Bruno; et al., Breathing Dynamics for Systems of Interacting Particles in the Microcanonical and Canonical Descriptions, transport theory and Statistical Physics, Volume: 39 Issue: 5-7 Special Issue: SI Pages: 524-551 DOI: 10.1080/00411450.2011.567857 (2010)

• A. Cahuzac, J. Boudet, P. Borgnat and E. Leveque Smoothing algorithms for the mean-flow extraction in large-eddy simulation of complex turbulent flows, Phys. Fluids 22, 125104, (2010)

• Ji-Xuan Hou, Carsten Svaneborg, Ralf Everaers, and Gary S. Grest, Stress Relaxation in Entangled Polymer Melts, Phys. Rev. Lett. 105, 068301 (2010)

• Sajad Hussain Syed, Damien Goutte-Gattat, Nils Becker, Sam Meyer, Manu Shubhdarshan Shukla, Jeffrey J. Hayes, Ralf Everaers, Dimitar Angelov, Jan Bednar, Stefan Dimitrov, Single-base resolution mapping of H1–nucleosome interactions and 3D organization of the nucleosome, Proceedings of the National Academy of Sciences, (2010)

• Rosa A, Becker NB, Everaers R, Looping Probabilities in Model Interphase Chromosomes, BIOPHYSICAL JOURNAL, Volume: 98, Issue: 11, Pages: 2410-2419 (2010)

• N.B. Becker, A. Rosa and R. Everaers, The radial distribution function of worm-like chains, Eur. Phys. J. E Volume 32, Number 1, May 2010

• Daniel Jost and Ralf Everaers, Prediction of RNA multiloop and pseudoknot conformations from a lattice-based, coarse-grain tertiary structure model, J. Chem. Phys. 132, 095101 (2010)

• A. Naso and A. Prosperetti, The interaction between a solid particle and a turbulent flow, New J. Phys. 12, 033040 (2010)

• A. Naso, R. Monchaux, P.-H. Chavanis and B. Dubrulle, Statistical mechanics of Beltrami flows in axisymmetric geometry: Theory reexamined, Phys. Rev. E 81, 066318 (2010)

• A. Naso, S. Thalabard, G. Collette, P.-H. Chavanis and B. Dubrulle, Statistical mechanics of Beltrami flows in axisymmetric geometry: Equilibria and bifurcations, J. Stat. Mech. P06019 (2010)

• Becker, Nils B.; Everaers, Ralf, DNA nanomechanics: How proteins deform the double helix, JOURNAL OF CHEMICAL PHYSICS Volume: 130 Issue: 13 Article Number: 135102 DOI: 10.1063/1.3082157, April 7, 2009

• Jost, Daniel; Everaers, Ralf, A Unified Poland-Scheraga Model of Oligo- and Polynucleotide DNA Melting: Salt Effects and Predictive Power, BIOPHYSICAL JOURNAL Volume: 96 Issue: 3 Pages: 1056-1067 DOI: 10.1529/biophysj.108.134031, February 4, 2009

• Jost, Daniel; Everaers, Ralf, Genome wide application of DNA melting analysis, JOURNAL OF PHYSICS-CONDENSED MATTER Volume: 21 Issue: 3 Article Number: 034108 DOI: 10.1088/0953-8984/21/3/034108, January 21, 2009

• N. B. Becker and R. Everaers Comment on "Remeasuring the Double Helix", Science 325 (5940), 538-b, (2009)

• A. V. Klopper, Carsten Svaneborg and Ralf Everaers, Microphase separation in cross-linked polymer blends. Efficient replica RPA post-processing of simulation data for homopolymer networks, Eur. Phys. J. E 28, 89-96 (2009)

• Nils B. Becker and Ralf Everaers, DNA nanomechanics: How proteins deform the double helix, J. Chem. Phys. 130, 135102 (2009)

• Roche PE, Barenghi CF, Leveque E, Quantum turbulence at finite temperature: The two-fluids cascade, Source: EPL Volume: 87 Issue: 5 Article Number: 54006 (2009)

• Calzavarini E, Volk R, Bourgoin M, Leveque E, Pinton JF, Toschi F, Acceleration statistics of finite-sized particles in turbulent flow: the role of Faxen forces, JOURNAL OF FLUID MECHANICS, Volume: 630, Pages: 179-189, (2009)

• Rosa, Angelo; Everaers, Ralf,Structure and Dynamics of Interphase Chromosomes, PLOS COMPUTATIONAL BIOLOGY Volume: 4 Issue: 8 Article Number: e1000153 DOI: 10.1371/journal.pcbi.1000153, August 22, 2008

• Svaneborg, Carsten; Everaers, Ralf; Grest, Gary S.; et al., Connectivity and entanglement stress contributions in strained polymer networks, MACROMOLECULES Volume: 41 Issue: 13 Pages: 4920-4928 DOI: 10.1021/ma800018f, July 8, 2008

• Nariya Uchida, Gary S. Grest, and Ralf Everaers, Viscoelasticity and primitive path analysis of entangled polymer liquids: From F-actin to polyethylene, J. Chem. Phys. 128, 044902 (2008)

• Pasichnyk, I.; Everaers, R.; Maggs, A. C., Simulating Van der Waals interactions in water/hydrocarbon-based complex fluids, JOURNAL OF PHYSICAL CHEMISTRY B Volume: 112 Issue: 6 Pages: 1761-1764 DOI: 10.1021/jp077401m, february 14, 2008

• Uchidaa, Nariya; Grest, Gary S.; Everaers, Ralf, Viscoelasticity and primitive path analysis of entangled polymer liquids: From F-actin to polyethylene, JOURNAL OF CHEMICAL PHYSICS Volume: 128 Issue: 4 Article Number: 044902 DOI: 10.1063/1.2825597, January 28, 2008