Publications and Preprints

Google Scholar Citation Report; Self-archiving policies.

In preparation and in submission

Published in refereed journals

• B. W. Oakley, G. Bonner, and J.-L.T., Optimal spatially-dependent diffusion tensors, Nonlinearity 36, 6777–6797, 2023.
• F. M. Ventrella, N. Pujara, G. Boffetta, M. Cencini, J.-L.T., and F. De Lillo, Microswimmer trapping in surface waves with shear, Proceedings of the Royal Society A 479, 20230280, 2023.
• N. Pujara and J.-L.T., Wave-averaged motion of small particles in surface gravity waves: effect of particle shape on orientation, drift, and dispersion, Physical Review Fluids 8, 074801, July 2023.
• G. Bonner, J.-L.T., and B. Valko, On a random entanglement problem, IMA Journal of Applied Mathematics 87(6), 1090–1120, December 2022.
• J.-L.T. and J. Guo, Anisotropic active Brownian particle with a fluctuating propulsion force, Physical Review E 106(1), L012603, July 2022.
• J.-L.T., The mathematics of burger flipping, Physica D 439, 133410, November 2022.
• G. Di Labbio, J.-L.T., and L. Kadem, Braids in the heart: Global measures of mixing for cardiovascular flows, Flow 2, E12, May 2022.
• A. Klünker, K. Padberg-Gehle, and J.-L.T., Open-flow mixing and transfer operators, Philosophical Transactions of the Royal Society A 380, 202110028, April 2022.
• J.-L.T., Moving forward by shaking sideways, Symmetry 14(3), 620, March 2022.
• K. Ma, N. Pujara, and J.-L.T., Reaching for the surface: Spheroidal microswimmers in surface gravity waves, Physical Review Fluids 7, 014310, 2022.
• J.-L.T., Nonuniform mixing, Physical Review Fluids 6(9), 090501, September 2021.
• H. Chen and J.-L.T., Shape matters: A Brownian microswimmer in a channel, Journal of Fluid Mechanics 916, A15–37, 2021.
• B. W. Oakley, J.-L.T., and C. R. Doering, On mix-norms and the rate of decay of correlations, Nonlinearity 34(6), 3762–3782, June 2021.
• Y. Feng, Y. Feng, G. Iyer, and J.-L.T., Phase separation in the advective Cahn–Hilliard equation, Journal of Nonlinear Science 30(6), 2821–2845, 2020.
• M. Filippi, M. Budišić, M. R. Allshouse, S. Atis, J.-L.T., and T. Peacock, Using braids to quantify interface growth and coherence in a rotor-oscillator flow, Physical Review Fluids 5, 054504, May 2020.
• H. Wen and J.-L.T., Winding of a Brownian particle around a point vortex, Philosophical Transactions of the Royal Society A 377, 20180347, September 2019. [Matlab code]
• T. Morrell, S. Spagnolie, and J.-L.T., Velocity fluctuations in a dilute suspension of viscous vortex rings, Physical Review Fluids 4 (4), 044501, April 2019.
• G. Chaudhary, R. Ewoldt, and J.-L.T., Unraveling hagfish slime, Journal of the Royal Society Interface 16 (150), 20180710, 2019. [Matlab code]
• R. Sturman and J.-L.T., Lyapunov exponents for the random product of two shears, Journal of Nonlinear Science, 29 (2), 593–620, April 2019.
• J.-L.T., The mathematics of taffy pullers, Mathematical Intelligencer 40 (1), 26–35, 2018.
• F. Marcotte, C. R. Doering, J.-L.T., and W. R. Young, Optimal heat transfer and optimal exit times, SIAM Journal on Applied Mathematics 78 (1), 591–608, 2018.
• H. Aref et al., Frontiers of chaotic advection, Reviews of Modern Physics 89, 025007, June 2017.
• P. Mueller and J.-L.T., Fluid transport and mixing by an unsteady microswimmer, Physical Review Fluids 2, 013103, January 2017.
• S. E. Spagnolie, C. Wahl, J. Lukasik, and J.-L.T., Microorganism billiards, Physica D 341, 33–44, February 2017.
• D. Sondak, C. Hawley, S. Heng, R. Vinsonhaler, E. Lauga, and J.-L.T., Can phoretic particles swim in two dimensions?, Physical Review E 94, 062606, December 2016.
• J.-L.T., Distribution of particle displacements due to swimming microorganisms, Physical Review E 92, 023023, August 2015.
• M. Budišić and J.-L.T., Finite-time braiding exponents, Chaos 25, 087407, 2015.
• S. E. Tumasz and J.-L.T., Estimating topological entropy from the motion of stirring rods, Procedia IUTAM 7, 117–126, 2013.
• S. E. Tumasz and J.-L.T., Topological entropy and secondary folding, Journal of Nonlinear Science 23 (3), 511–524, June 2013.
• J. G. Puckett, F. Lechenault, K. E. Daniels, and J.-L.T., Trajectory entanglement in dense granular materials, Journal of Statistical Mechanics: Theory and Experiment 2012 (6), P06008, June 2012.
• J.-L.T., Using multiscale norms to quantify mixing and transport, Nonlinearity 84 (3), R1–R44, February 2012. Review article
• M. R. Allshouse and J.-L.T., Detecting coherent structures using braids, Physica D 241 (2), 95–105, January 2012.
• M. D. Finn and J.-L.T., Topological optimization of rod-stirring devices, SIAM Review 53 (4), 723–743, December 2011.
• B. Thomases, M. Shelley, and J.-L.T., A Stokesian viscoelastic flow: Transition to oscillations and mixing, Physica D 240 (20), 1602–1614, October 2011.
• J.-L.T., E. Gouillart, and O. Dauchot, Moving walls accelerate mixing, Physical Review E 84 (3), 036113, September 2011.
• E. Lanneau and J.-L.T., On the minimum dilatation of braids on the punctured disc, Geometriae Dedicata 152 (1), 165–182, June 2011. [Mathematica code]
• Z. Lin, J.-L.T., and C. R. Doering, Optimal stirring strategies for passive scalar mixing, Journal of Fluid Mechanics 675, 465–476, May 2011.
• E. Lanneau and J.-L.T., On the minimum dilatation of pseudo-Anosov homeomorphisms on surfaces of small genus, Annales de l'Institut Fourier 61 (1), 105–144, 2011.
  A note on the title of the published version [click].
  In the proofs, the copy editors inserted the typo 'homeTRomorphism' in the title. We caught that and flagged it, but in the final version they only changed it to 'homeRomorphism'. This is deeply embarassing, but since we never saw the final version before it appeared there was not much to be done.
• Z. Lin, J.-L.T., and S. Childress, Stirring by squirmers, Journal of Fluid Mechanics 669, 167–177, February 2011.
• E. Gouillart, O. Dauchot, and J.-L.T., Measures of mixing quality in open flows with chaotic advection, Physics of Fluids 23 (1), 013604, January 2011.
• J.-L.T. and C. R. Doering, The Mixing efficiency of open flows, Physica D 240 (2), 180–186, January 2011.
• J.-L.T. and S. Childress, Stirring by swimming bodies, Physics Letters A 374 (34), 3487–3490, July 2010.
• L. Ó Náraigh and J.-L.T., Nonlinear dynamics of phase separation in thin films, Nonlinearity 23, 1559–1583, July 2010.
• E. Gouillart, J.-L.T., and O. Dauchot, Rotation shields chaotic mixing regions from no-slip walls, Physical Review Letters 104, 204502, May 2010.
• J.-L.T., Braids of entangled particle trajectories, Chaos 20, 017516, January 2010. Featured as a Research Highlight in Chaos; Most downloaded article from February to June 2010.
• E. Gouillart, O. Dauchot, J.-L.T., and S. Roux, Open-flow Mixing: Experimental Evidence for Strange Eigenmodes, Physics of Fluids 21 (2), 023603, 2009.
• L. Ó Náraigh and J.-L.T., Bounds on the Mixing Enhancement for a Stirred Binary Fluid, Physica D 237, 2673–2684, 2008.
• E. Gouillart, O. Dauchot, B. Dubrulle, S. Roux, and J.-L.T., Slow Decay of Concentration Variance Due to No-slip Walls in Chaotic Mixing, Physical Review E 78, 026211, August 2008. Featured in PRE's kaleidoscope.
• J.-L.T., M. D. Finn, E. Gouillart, and T. Hall, Topology of Chaotic Mixing Patterns, Chaos 18, 033123, September 2008.
• T. Okabe, B. Eckhardt, J.-L.T., and C. R. Doering, Mixing Effectiveness Depends on the Source Distribution: Simulation Results, Journal of Statistical Mechanics: Theory and Experiments 2008 (7), P07018, July 2008.
• J.-L.T. and G. A. Pavliotis, Optimizing the Source Distribution in Fluid Mixing, Physica D 237 (7), 918–929, June 2008.
• L. Ó Náraigh and J.-L.T., Dynamical Effects and Phase Separation in Cooled Binary Fluid Films, Physical Review E 76, 035303, September 2007.
• E. Gouillart, N. Kuncio, O. Dauchot, B. Dubrulle, S. Roux, and J.-L.T., Walls Inhibit Chaotic Mixing, Physical Review Letters 99, 114501, 2007. Featured as a Physics World and Sciences et Avenir news item.
• T. A. Shaw, J.-L.T., and C. R. Doering, Stirring up Trouble: Multi-scale Mixing Measures for Steady Scalar Sources, Physica D 231 (2), 143-164, July 2007.
• M. D. Finn and J.-L.T., Topological Entropy of Braids on the Torus, SIAM Journal on Applied Dynamical Systems 6, 79-98, 2007.
• L. Ó Náraigh and J.-L.T., Bubbles and Filaments: Stirring a Cahn–Hilliard Fluid, Physical Review E 75, 016216, January 2007.
• J.-L.T. and M. D. Finn, Topology, Braids, and Mixing in Fluids, Philosophical Transactions of the Royal Society A 364, 3251-3266, December 2006.
• A. Roy, L. Mahadevan, and J.-L.T., Fall and Rise of a Viscoelastic Filament, Journal of Fluid Mechanics 563, 283-292, September 2006.
• M. D. Finn, J.-L.T., and E. Gouillart, Topological Chaos in Spatially Periodic Mixers, Physica D 221 (1), 92-100, September 2006.
• C. R. Doering and J.-L.T., Multiscale Mixing Efficiencies for Steady Sources, Physical Review E 74 (2), 025301(R), August 2006.
• E. Gouillart, J.-L.T., and M. D. Finn, Topological Mixing with Ghost Rods, Physical Review E 73, 036311, March 2006.
• J.-L.T., Measuring Topological Chaos, Physical Review Letters 94 (8), 084502, March 2005.
• J.-L.T., C. R. Doering, and J. D. Gibbon, A Bound on Mixing Efficiency for the Advection-Diffusion Equation, Journal of Fluid Mechanics 521, 105-114, December 2004.
• J.-L.T., Stretching and Curvature along Material Lines in Chaotic Flows, Physica D 198 (3-4), 169-181, November 2004.
• J.-L.T., The Strange Eigenmode in Lagrangian Coordinates, Chaos 14 (3), 531-538, September 2004.
• E. A. Spiegel and J.-L.T., Higher-order Continuum Approximation for Rarefied Gases, Physics of Fluids 15 (11), 3558-3567, November 2003.
• J.-L.T. and S. Childress, Chaotic Mixing in a Torus Map, Chaos 13 (2), 502-507, June 2003.
• J.-L.T., Advection-Diffusion in Lagrangian Coordinates, Physics Letters A 309 (5-6), 415-422, March 2003.
• J.-L.T., Finite Extension of Polymers in Turbulent Flow, Physics Letters A 308 (5-6), 445-450, March 2003.
• J.-L.T. and A. H. Boozer, The Onset of Dissipation in the Kinematic Dynamo, Physics of Plasmas 10 (1), 259-265, January 2003.
• J.-L.T., Derivatives and Constraints in Chaotic Flows: Asymptotic Behaviour and a Numerical Method, Physica D 172 (1-4), 139-161, November 2002.
• J.-L.T., Covariant Time Derivatives for Dynamical Systems, Journal of Physics A 34 (29), 5875-5885, July 2001.
• J.-L.T. and P. J. Morrison, The Twisted Top, Physics Letters A 283 (5-6), 335-341, May 2001.
• J.-L.T. and A. H. Boozer, Geometrical Constraints on Finite-time Lyapunov Exponents in Two and Three Dimensions, Chaos 11 (1), 16-28, March 2001.
• J. P. Smith, J.-L.T., and W. Horton, Dynamical Range of the WINDMI Model: An exploration of possible magnetospheric plasma states, Journal of Geophysical Research - Space Physics 105 (A6), 12983-12996, June 2000.
• J.-L.T. and P. J. Morrison, Classification and Casimir Invariants of Lie-Poisson Brackets, Physica D 136 (3-4), 205-244, February 2000.
• J.-L.T. and W. Horton, Energy-conserving Truncations for Convection with Shear Flow, Physics of Fluids 8 (7), 1715-1719, July 1996.

Conference proceedings, unpublished preprints, and others

• J.-L.T., Ineffective diffusivity, Journal of Fluid Mechanics 972, F1. October 2023.
• J.-L.T., The complexity of entanglements, SIAM News, December 2014.
• J.-L.T. and Marko Budišić, Braidlab: A Software Package for Braids and Loops.
• J.-L.T., Lecture Notes on Braids and Dynamics. [pdf] [djvu]
• J.-L.T., Distribution of particle displacements in biomixing, Oberwolfach Reports 11 (1) 240–242 (2014).
• N. J. Balmforth, P. J. Morrison, and J.-L.T., Pattern formation in Hamiltonian systems with continuous spectra; a normal-form single-wave model, in submission.
• K. Obuse and J.-L.T., A low-Reynolds-number treadmilling swimmer near a semi-infinite wall, to appear in IMA Volume on Natural Locomotion in Fluids and on Surfaces: Swimming, Flying, and Sliding edited by Stephen Childress, Anette (Peko) Hosoi, William W. Schultz, and Z. Jane Wang.
• A. Gilbert, I. Klapper, J.-L.T., and J. Wang, Special Issue: Fluid Dynamics: From Theory to Experiment (Preface), Physica D 240 (1), 1565–1566, October 2011.
• J.-L.T., Chaos in the Gulf, Science 330, 458–459, October 2010.
• J.-L.T., E. Lanneau, and S. Matz, The Cat's Cradle, Stirring, and Topological Complexity, Dynamical Systems Magazine, April 2009.
• M. D. Finn and J.-L.T., Topological Chaos in Flows on Surfaces of Arbitrary Genus , Paper presented at the International Congress of Theoretical and Applied Mathematics, Adelaide, Australia, 25–29 August 2008.
• J.-L.T., E. Gouillart, and O. Dauchot, Speeding Up Mixing with Moving Walls, Paper presented at the International Congress of Theoretical and Applied Mathematics, Adelaide, Australia, 25–29 August 2008.
• J.-L.T. and K. Kamhawi, Chaotic Geodesics, in Chaos, Complexity, and Transport: Theory and Applications, 2008 (World Scientific, Singapore). (Proceedings of the Conference CCT'07, Le Pharo, Marseille, 4–8 June 2007.)
• L. Ó Náraigh and J.-L.T., Nonlinear Dynamics of Phase Separation in Ultra-thin Films, unpublished preprint.
• J.-L.T., Scalar Decay in Chaotic Mixing, in Transport and Mixing in Geophysical Flows, Lecture Notes in Physics 744, 3-35, 2008 (Springer, Berlin). (Proceedings of the Gran Combin Summer School, Valle d'Aosta, Italy, 14-24 June 2004.)
• J.-L.T., E. Gouillart, and M. D. Finn, The Size of Ghost Rods, Proceedings of the Workshop on Analysis and Control of Mixing with Applications to Micro and Macro Flow Processes, CISM, Udine, Italy, 27 June–1 July 2005 (Springer-Verlag, 2006).
• S. Sadokierski and J.-L.T., Heat Transfer in Underground Rail Tunnels, unpublished preprint.
• J.-L.T. and K. Kamhawi, Transport in Thin Gravity-driven Flow over a Curved Substrate, unpublished preprint.
• Book Review: Turbulent Flows by Stephen Pope. Geophysical and Astrophysical Fluid Dynamics, 2004.
• Book Review: Nonlinear Dynamics and Chaos: Where do we go from here? John Hogan, Alan Champneys, Bernd Krauskopf, Mario di Bernardo, Eddie Wilson, Hinke Osinga, and Martin Homer (editors). UK Nonlinear News, May 2003.
• S. Hong, J.-L.T., L. Fréchette, and V. Modi, Numerical Study of Mixing in Microchannels with Patterned Zeta Potential Surfaces, Paper presented at IMECE 2003, ASME International Mechanical Engineering Congress & Exposition, Washington, D.C., November 16-21, 2003.
• J.-L.T., Differential Constraints in Chaotic Flows on Curved Manifolds, unpublished preprint.
• E. A. Spiegel and J.-L.T., Continuum Equations for Stellar Dynamics, Stellar Astrophysical Fluid Dynamics: Proceedings of the Chateau de Mons meeting in honour of Douglas Gough's 60th birthday (Cambridge University Press, 2003), pp. 377-391.
• J.-L.T., Classification, Casimir Invariants, and Stability of Lie-Poisson Systems, Ph.D. Thesis, The University of Texas at Austin, December 1998 (Supervisor: Philip J. Morrison).
• J.-L.T. and P. J. Morrison, Invariants and Labels in Lie-Poisson Systems, Proceedings of the 13th Florida Workshop in Nonlinear Dynamics and Chaos in Astrophysics, Annals of the New York Academy of Sciences 867, 109-119, December 1998.
• J.-L.T., Long-wave Instability in Double-diffusive Marangoni Convection, Proceedings of the 1996 Summer program in Geophysical Fluid Dynamics, Woods Hole, MA. Edited by Steve Meacham.
• J.-L.T., Modeling Shear Flow in Rayleigh–Benard Convection, Master's Thesis, The University of Texas at Austin, August 1995 (Supervisor: C. Wendell Horton).

Last modified: 0:09 12 December 2023

Background: Coarsening of a binary fluid (Simulations by Lennon Ó Náraigh)

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