Antonov, J., D. Seidov, T. Boyer, R. Locarnini, A. Mishonov, H. Garcia, O. Baranova, M. Zweng, and D. Johnson. 2010. World Ocean Atlas 2009: Volume 2, Salinity. S. Levitus, ed., US Government Printing Office, Washington, DC, 184 pp, ftp://ftp.nodc.noaa.gov/pub/WOA09/DOC/woa09_vol2_text.pdf.
Bleck, R. 2002. An oceanic general circulation model framed in hybrid isopycnic-Cartesian coordinates. Ocean Modelling 4:55–88, https://doi.org/10.1016/S1463-5003(01)00012-9.
Bleck, R., and S.G. Benjamin. 1993. Regional weather prediction with a model combining terrain-following and isentropic coordinates: Part 1. Model description. Monthly Weather Review 121(6):1,770–1,785, https://doi.org/10.1175/1520-0493(1993)121<1770:RWPWAM>2.0.CO;2.
Bleck, R., and D.B. Boudra. 1981. Initial testing of a numerical ocean circulation model using a hybrid (quasi–isopycnic) vertical coordinate. Journal of Physical Oceanography 11(6):755–770, https://doi.org/10.1175/1520-0485(1981)011<0755:ITOANO>2.0.CO;2.
Bonjean, F., and G.S. Lagerloef. 2002. Diagnostic model and analysis of the surface currents in the tropical Pacific Ocean. Journal of Physical Oceanography 32(10):2,938–2,954, https://doi.org/10.1175/1520-0485(2002)032<2938:DMAAOT>2.0.CO;2.
Booij, N., R.C. Ris, and L.H. Holthuijsen. 1999. A third-generation wave model for coastal regions: Part I. Model description and validation. Journal of Geophysical Research 104:7,649–7,666, https://doi.org/10.1029/98JC02622.
Chatterjee, A., D. Shankar, S.S.C. Shenoi, G.V. Reddy, G.S. Michael, M. Ravichandran, V.V. Gopalkrishna, E.R. Rao, T.U. Bhaskar, and V.N. Sanjeevan. 2012. A new atlas of temperature and salinity for the North Indian Ocean. Journal of Earth System Science 121(3):559–593, https://doi.org/10.1007/s12040-012-0191-9.
Chen, S., M. Flatau, T.G. Jensen, T. Shinoda, J. Schmidt, P. May, J. Cummings, M. Liu, P.E. Ciesielski, C.W. Fairall, and others. 2015. A study of CINDY/DYNAMO MJO suppressed phase. Journal of Atmospheric Science 72:3,755–3,779, https://doi.org/10.1175/JAS-D-13-0348.1.
Fairall, C.W., E.F. Bradley, J.S. Godfrey, G.A. Wick, J.B. Edson, and G.S. Young. 1996a. Cool-skin and warm-layer effects on sea surface temperature. Journal of Geophysical Research 101(C1):1,295–1,308, https://doi.org/10.1029/95JC03190.
Fairall, C.W., E.F. Bradley, D.P. Rogers, J.B. Edson, and G.S. Young. 1996b. Bulk parameterization of air-sea fluxes for Tropical Ocean-Global Atmosphere Coupled-Ocean Atmosphere Response Experiment. Journal of Geophysical Research 101(C2):3,747–3,764, https://doi.org/10.1029/95JC03205.
Gordon, A.L., E.L. Shroyer, A. Mahadevan, D. Sengupta, and M. Freilich. 2016. Bay of Bengal: 2013 northeast monsoon upper-ocean circulation. Oceanography 29(2):82–91, https://doi.org/10.5670/oceanog.2016.41.
Haidvogel, D.B., H. Arango, W.P. Budgell, B.D. Cornuelle, E. Curchitser, E. Di Lorenzo, K. Fennel, W.R. Geyer, A.J. Hermann, L. Lanerolle, and others. 2008. Ocean forecasting in terrain-following coordinates: Formulation and skill assessment of the Regional Ocean Modeling System. Journal of Computational Physics 227(7):3,595–3,624, https://doi.org/10.1016/j.jcp.2007.06.016.
Haidvogel, D.B., H.G. Arango, K. Hedstrom, A. Beckmann, P. Malanotte-Rizzoli, and A.F. Shchepetkin. 2000. Model evaluation experiments in the North Atlantic Basin: Simulations in nonlinear terrain-following coordinates. Dynamics of Atmospheres and Oceans 32(3):239–281, https://doi.org/10.1016/S0377-0265(00)00049-X.
Han, W. 2005. Origins and dynamics of the 90-day and 30–60 day variations in the equatorial Indian Ocean. Journal of Physical Oceanography 35:708–728, https://doi.org/10.1175/JPO2725.1.
Han, W., and J.P. McCreary Jr. 2001. Modeling salinity distributions in the Indian Ocean. Journal of Geophysical Research 106:859–877, https://doi.org/10.1029/2000JC000316.
Jensen, T.G. 1993. Equatorial variability and resonance in a wind-driven Indian Ocean model. Journal of Geophysical Research 98:22,533–22,552, https://doi.org/10.1029/93JC02565.
Jensen, T.G. 2001. Arabian Sea and Bay of Bengal exchange of salt and tracers in an ocean model. Geophysical Research Letters 28:3,967–3,970, https://doi.org/10.1029/2001GL013422.
Jensen, T.G. 2003. Cross-equatorial pathways of salt and tracers from the northern Indian Ocean: Modelling results. Deep Sea Research Part II 50:2,111–2,128, https://doi.org/10.1016/S0967-0645(03)00048-1.
Jensen, T.G., T. Shinoda, S. Chen, and M. Flatau. 2015. Ocean response to CINDY/DYNAMO MJOs in air-sea coupled COAMPS. Journal of the Meteorological Society of Japan 93A:157–178, https://doi.org/10.2151/jmsj.2015-049.
Kantha, L.H., and C.A. Clayson. 2004. On the effect of surface gravity waves on mixing in the oceanic mixed layer. Ocean Modelling 6:101–124, https://doi.org/10.1016/S1463-5003(02)00062-8.
Large, W.G., J.C. McWilliams, and S.C. Doney. 1994. Oceanic vertical mixing: A review and a model with a nonlocal boundary layer parameterization. Reviews of Geophysics 32(4):363–403, https://doi.org/10.1029/94RG01872.
Locarnini, R.A., A.V. Mishonov, J.I. Antonov, T.P. Boyer, H.E. Garcia, O.K. Baranova, M.M. Zweng, and D.R. Johnson. 2010. World Ocean Atlas 2009: Volume 1, Temperature. S. Levitus, ed., NOAA Atlas NESDIS, 68, 184 pp, ftp://ftp.nodc.noaa.gov/pub/WOA09/DOC/woa09_vol1_text.pdf.
Love, B.S., A.J. Matthews, and G.S. Lister, 2011. The diurnal cycle of precipitation over the Maritime Continent in a high-resolution atmospheric model. Quarterly Journal of the Royal Meteorology Society 137:934–947, https://doi.org/10.1002/qj.809.
Matsuno, T. 1966. Quasi-geostrophic motions in the equatorial area. Journal of the Meteorological Society of Japan 44:25–43.
McCreary, J.P., W. Han, D. Shankar, and S.R. Shetye, 1996. Dynamics of the East India Coastal Current: Part 2. Numerical solutions. Journal of Geophysical Research 101:13,993–14,010, https://doi.org/10.1029/96JC00560.
Mellor, G.L., and T. Yamada. 1982. Development of a turbulence closure model for geophysical fluid problems. Reviews of Geophysics and Space Physics 20:851–875, https://doi.org/10.1029/RG020i004p00851.
Metzger, E.J., H.E. Hurlburt, X. Xu, J.F. Shriver, A.L. Gordon, J. Sprintall, R.D. Susanto, and H.M. van Aken. 2010. Simulated and observed circulation in the Indonesian Seas: 1/12° global HYCOM and the INSTANT observations. Dynamics of Atmospheres and Oceans 50:275–300, https://doi.org/10.1016/j.dynatmoce.2010.04.002.
Metzger, E.J., O.M. Smedstad, P.G. Thoppil, H.E. Hurlburt, J.A. Cummings, A.J. Wallcraft, L. Zamudio, D.S. Franklin, P.G. Posey, M.W. Phelps, and others. 2014. US Navy operational global ocean and Arctic ice prediction systems. Oceanography 27(3):32–43, https://doi.org/10.5670/oceanog.2014.66.
Murty, V.S.N., Y.V.B. Sarma, D.P. Rao, and C.S. Murty. 1992. Water characteristics, mixing and circulation in the Bay of Bengal during southwest monsoon. Journal of Marine Research 50:207–228, https://doi.org/10.1357/002224092784797700.
Pant, V., M.S. Girishkumar, T.V.S. Udaya Bhaskar, M. Ravichandran, F. Papa, and V.P. Thangaprakash. 2015. Observed interannual variability of near-surface salinity in the Bay of Bengal. Journal of Geophysical Research 120:3,315–3,329, https://doi.org/10.1002/2014JC010340.
Praveen Kumar, B., J. Vialard, M. Lengaigne, V.S. Murty, and M.J. McPhaden. 2012. TropFlux: Air-sea fluxes for the global tropical oceans: Description and evaluation. Climate Dynamics 38:1,521–1,543, https://doi.org/10.1007/s00382-011-1115-0.
Qiu, B., M. Mao, and Y. Kashino. 1999. Intraseasonal variability in the Indo-Pacific throughflow and regions surrounding the Indonesian seas. Journal of Physical Oceanography 29:1,599–1,618, https://doi.org/10.1175/1520-0485(1999)029<1599:IVITIP>2.0.CO;2.
Saha, S., S. Moorthi, H.-L. Pan, X. Wu, J. Wang, S. Nadiga, P. Tripp, R. Kistler, J. Woollen, D. Behringer, and others. 2010. The NCEP climate forecast system reanalysis. Bulletin of the American Meteorological Society 91:1,015–1,057, https://doi.org/10.1175/2010BAMS3001.1.
Shchepetkin, A.F., and J.C. McWilliams. 2003. A method for computing horizontal pressure-gradient force in an oceanic model with a nonaligned vertical coordinate. Journal of Geophysical Research 108(C3), 3090, https://doi.org/10.1029/2001JC001047.
Shchepetkin, A.F., and J.C. McWilliams. 2005. The Regional Oceanic Modeling System (ROMS): A split-explicit, free-surface, topography-following-coordinate oceanic model. Ocean Modelling 9(4):347–404, https://doi.org/10.1016/j.ocemod.2004.08.002.
Shchepetkin, A.F., and J.C. McWilliams. 2009. Computational kernel algorithms for fine-scale, multiprocess, longtime oceanic simulations. Handbook of Numerical Analysis 14:121–183, https://doi.org/10.1016/S1570-8659(08)01202-0.
Sengupta, D., G.N. Bharath Raj, and S.S.C. Shenoi. 2006. Surface freshwater from Bay of Bengal runoff and Indonesian Throughflow to the tropical Indian Ocean. Geophysical Research Letters 33, L22609, https://doi.org/10.1029/2006GL027573.
Shinoda, T., W. Han, E.J. Metzger, and H. Hurlburt. 2012. Seasonal variation of the Indonesian Throughflow in Makassar Strait. Journal of Physical Oceanography 42:1,099–1,123, https://doi.org/10.1175/JPO-D-11-0120.1.
Smith, W.H.F., and D.T. Sandwell. 1997. Global sea floor topography from satellite altimetry and ship depth soundings. Science 277:1,956–1,962, https://doi.org/10.1126/science.277.5334.1956.
Thoppil, P.G., E.J. Metzger, H.E. Hurlburt, O.M. Smedstad, and H. Ichikawa. 2016. The current system east of the Ryukyu Islands as revealed by a global ocean reanalysis. Progress in Oceanography 141:239–258, https://doi.org/10.1016/j.pocean.2015.12.013.
Vinayachandran, P.N., Y. Masumoto, T. Mikawa, and T. Yamagata. 1999. Intrusion of the Southwest Monsoon Current into the Bay of Bengal. Journal of Geophysical Research 104:11,077–11,085, https://doi.org/10.1029/1999JC900035.
Vinayachandran, P.N., D. Shankar, S. Vernekar, K.K. Sandeep, P. Amol, C.P. Neema, and Abhisek Chatterjee. 2013. A summer monsoon pump to keep the Bay of Bengal salty. Geophysical Research Letters 40:1,777–1,782, https://doi.org/10.1002/grl.50274.
Wijesekera, H.W., T.G. Jensen, E. Jarosz, W.J. Teague, E.J. Metzger, D.W. Wang, S.U.P. Jinadasa, K. Arulananthan, L.R. Centurioni, and H.J. Fernando. 2015. Southern Bay of Bengal currents and salinity intrusions during the northeast monsoon. Journal of Geophysical Research 120:6,897–6,913, https://doi.org/10.1002/2015JC010744.
Yu, L., J.J. O’Brien, and J. Yang. 1991. On the remote forcing of the circulation in the Bay of Bengal. Journal of Geophysical Research 96:20,449–20,454, https://doi.org/10.1029/91JC02424.