Procedures for offline grid nesting in regional ocean models Evan Mason, Jeroen Molemaker, Alexander F. Shchepetkin, Francois Colas, James C. McWilliams, and Pablo Sangra Ocean modelling 35(1-2), 1-15. 2010

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Balanced and Unbalanced Routes to Dissipation in an Equilibrated Eady Flow. Molemaker, M.J. and J.C. McWilliams and X. Capet. J. Fluid Mech. 654: 35-63. 2010.

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Local balance and cross-scale flux of available potential energy. Molemaker, M.J. and J.C. McWilliams. J. Fluid Mech. 645, 295-314. 2010

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Linear Fluctuation growth during frontogenesis. McWilliams, J.C., and M.J. Molemaker, and E.I. Olafsdottir. J. Phys. Ocean. 39, 3111-3129: 2009.

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Cold Filamentary intensification and oceanic surface convergence lines. McWilliams, J.C., and F. Colas, and M.J. Molemaker. Geophys. Res. Lett. 36, L18602. doi:10.1029/2009GL039402: 2009.

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Low Viscosity Flow Simulations for Animation. Jeroen Molemaker, Jonathan M. Cohen, Sanjit Patel, Jun-yong Noh. Symposium on Computer Animation 2008. Award for Best Paper

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Mesoscale to Submesoscale Transition in the California Current System. Part I: Flow Structure, Eddy Flux, and Observational Tests. Xavier Capet, and James McWilliams, and M. Jeroen Molemaker, and Alexander Shchepetkin. J. Phys.Ocean. 38(1): 29. 2008.

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Mesoscale to Submesoscale Transition in the California Current System. Part II: Frontal Processes. Xavier Capet, and James McWilliams, and M. Jeroen Molemaker, and Alexander Shchepetkin. J. Phys.Ocean.. 38(1): 44. 2008.

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Mesoscale to Submesoscale Transition in the California Current System. Part III: Energy flux and balance. Xavier Capet, and James McWilliams, and M. Jeroen Molemaker, and Alexander Shchepetkin. J. Phys.Ocean. in press 2008.

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Baroclinic Instability and Loss of Balance. Molemaker, M.J. and J.C. McWilliams, and I. Yavneh. J. Phys Ocean 35, pp. 1505-1517. 2005.

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Routes to Dissipation in the Ocean: The 2D/3D Turbulence Conondrum. Peter Muller, James McWilliams and Jeroen Molemaker. in Marine Turbulence, Cambridge University Press, 397-405. 2005

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Ageostrophic, Anticyclonic Instability of a Geostrophic, Barotropic Boundary Current. James c. McWilliams and M. Jeroen Molemaker and Irad Yavneh. Phys. Fluids 16. 2004

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Practical Simulation of Surface Tension Flows. Jonathan M. Cohen and M. Jeroen Molemaker. SIGGRAPH 2004 sketches.

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Instability and Equilibration of Centrifugally-stable Stratified Taylor-Couette Flow. Molemaker, M.J, and J.C. McWilliams, and I. Yavneh, Phys. Rev. Lett. 86, 5270-5273. 2001 .

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From stirring to mixing of momentum: Cascades from balanced flows to dissipation in the oceanic interior. McWilliams, J.C., and M.J. Molemaker, and I. Yavneh. Aha Huliko'a Proceedings U. of Hawaii, 59-66. 2001.

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Non-axisymmetric instability of centrifugally stable, stratified Taylor-Couette flow. Yavneh, I., and J.C. McWilliams, and M.J. Molemaker. J. Fluid. Mech. 448, 1-21. 2001.

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Stability of a cold-core eddy in the presence of convection: hydrostatic versus non-hydrostatic modeling. Molemaker, M.J. and Dijkstra, H.A. J. Phys Ocean.30, (3) 475-494. 2000.

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Effects of turbulence and heterogeneous emissions on photochemically active species in the convective boundary layer. Maarten C. Krol, and M. Jeroen Molemaker, and Jordi Vila Guerau de Arellano. J. Geophys. Res-Atmos 105, (D5) 6871-6884. 2000.

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Multiple equilibria and stability of the North-Atlantic wind-driven circulation. Molemaker M.J. and Dijkstra, H.A. In: Numerical Methods for bifurcation problems and Large-scale dynamical systems. Ed: Doedel, E. and Tuckerman, L.S. Springer, New York, 303-318. 1999.

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Imperfections of the North Atlantic wind-driven ocean circulation: Continental geometry and windstress shape. Dijkstra H.A., Molemaker M.J. J. Mar Res.57: (1) 1-28 1999.

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Control of chemical reactions by convective turbulence in the boundary layer. Molemaker, M.J. and Vila-Guerau de Arellano, J. J. Atmos. Sci. 55, 568--579. 1998.

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Layer Formation in double-diffusive convection. Dijkstra H.A., and Molemaker M.J. and Kranenborg, E.J. In: Time-dependent Nonlinear Convection. ed: Tyvand, P.A. Computational Mechanics Publications, Boston. 1998

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The formation and evolution of a diffusive interface. Molemaker, M.J. and Dijkstra, H.A. J. Fluid Mech., 331, 199--222. 1997.

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Symmetry breaking and overturning oscillations in thermohaline driven flows. Dijkstra, H.A. and Molemaker, M.J. J. Fluid Mech., 331, 169--198. 1997.

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An efficient code to compute non parallel flows and their linear stability. Dijkstra, H.A., Molemaker, M.J., van der Ploeg, A., and Botta, E.F.F. Comp. Fluids, 24, 415-434. 1995

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Layer formation in a stably stratified liquid cooled from above. Molemaker, M.J. and Dijkstra, H.A. . In Double Diffusive Convection, volume 94 of Geophysical Monograph, 97-104. 1995

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Direct numerical simulation and large-eddy simulation of a non-premixed binary reaction in a turbulent convective boundary layer. Beets, C., Molemaker, M.J. and Vila Guerau de Arellano J. In Engineering Turbulence Modeling and Measurements 3.ed: W.Rodi and G. Bergeles. Elsevier science, Amsterdam, 279-282. 1995.

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Double diffusive and direct instabilities below growing sea ice. Molemaker, M.J. and Dijkstra, H.A. Int. J. Heat Mass Transfer, 37. 2547--2559. 1994

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