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PUBLISHED PAPERS USING PARAMESH

S.K. Antiochos, P.J. MacNeice, D.S. Spicer and J.A. Klimchuk, "The Dynamic Formation of Prominence Condensations", Astrophysical Journal, vol. 512, p.985-991, (1999).

Peter MacNeice, Kevin M. Olson, Clark Mobarry, Rosalinda deFainchtein and Charles Packer, "PARAMESH : A parallel adaptive mesh refinement community toolkit.", Computer Physics Communications, vol. 126, p.330-354, (2000).

S.K. Antiochos, P.J. MacNeice and D.S. Spicer, "The Thermal Non-Equilibrium of Prominences", to appear in Astrophysical Journal Letters (2000).

K. C. B. New, D.-I. Choi, J. M. Centrella, P. MacNeice, M. F. Huq, and K. Olson, "Three-dimensional adaptive evolutions of gravitational waves in numerical relativety", Phys. Rev., vol. D62, 084039 (2000).

B. Fryxell, K. Olson, P. Ricker, F. X. Timmes, M. Zingale, D. Q. Lamb, P. MacNeice, R. Rosner, J. W. Truran, and H. Tufo, "FLASH: An Adaptive Mesh Hydrodynamics Code for Modeling Astrophysical Thermonuclear Flashes", Astrophysical Journal Suppl., vol. 131, p. 273-334, (2000).

F. X. Timmes, M. Zingale, K. Olson, B. Fryxell, P. Ricker, A. C. Calder, L. J. Dursi, H. Tufo, P. MacNeice, J. W. Truran, and R. Rosner, "On the Cellular Structure of Carbon Detonations", Astrophysical Journal, vol. 543, pp. 938-954, (2000).

M. Zingale, F. X. Timmes, A. Calder, J. Dursi, B, Fryxewll, D. Lamb, K. Olson, P. Ricker, R. Rosner, J. Truran, and H. Tufo, "Direct Simulations of Nuclear Flames with the FLASH Code", in Proceedings of the AAS 195th Meeting, (2000).

J. Dursi, J. Niemeyer, A. Calder, B. Fryxell, D. Lamb, K. Olson, P. Ricker, R. Rosner, F. Timmes, H. Tufo, and M. Zingale, "Compressed Reactive Turbulence and Supernovae Ia Recollapse using the FLASH code", in Proceeding of the AAS 195th Meeting, (2000).

K. M. Olson, P. MacNeice, B. Fryxell, P. Ricker, F. X. Timmes, and M. Zingale, "PARAMESH: A Parallel, Adaptive Mesh Refinement Toolkit and Performance of the ASCI/FLASH code", in Proceeding of the AAS 195th Meeting, (2000).

B. Fryxell, M. Zingale, F. X, Timmes, K. Olson. D. Lamb, A. Calder, J. Dursi, P. Ricker, R. Rosner, and H. Tufo, "Helium Burning on Neutron Stars: 2-dimensional Results", in Proceedings of the AAS 195th Meeting, (2000).

P. M. Ricker, B. Fryxell, K. Olson, F. X. Timmes, M. Zingale, D. Q. Lamb, P. MacNeice, R. Rosner, and H. Tufo, "FLASH: A Multidimensional Hydrodynamics Code for Modeling Astrophysical Thermonuclear Flashes", in Proceeding of the AAS 195th Meeting, (2000).

R. Rosner, A. Calder, J. Dursi, B. Fryxell, D. Q. Lamb, J. C. Niemeyer, K. Olson. F. X. Timmes, J. W. Truran, H. Tufo, Y. N. Young, M. Zingale, E. Lusk, and R. Stevens, "Flash code: Studying Astrophysical Thermonuclear Flashes", Computing in Science and Engineering, vol. 2, issue 2, pp. 33-41, (2000)

A. C. Calder, B. C. Curtiss, L. J. Dursi, B. Fryxell, G. Henry, P. MacNeice, K. Olson, P. Ricker, F. X. Timmes, H. M. Tufo, J. W. Truran. and M. Zingale, "High-Performance Reactive Fluid Flow Simulations Useing Adaptive Mesh Refinement on Thousands of Processors", Gordon-Bell Prize Winning Paper, Super Computing 2000, IEEE Computer Society, (2000)

M. Zingale, F. X. Timmes, B. Fryxell, D. Q. Lamb, K. Olson, A. C. Calder, L. J. Dursi, P. Ricker, R. Rosner, P. MacNeice, and H. M. Tufo, "Helium Detonations on Neutron Stars", Astrophysical Journal Suppl., vol. 133, pp. 195-220, (2001)

B. Fryxell, M. Zingale, F. X. Timmes, D. Q. Lamb, K. Olson, A. C. Calder, L. J. Dursi, P. Ricker, R. Rosner, J. W. Truran, P. MacNeice, and H. Tufo., 2001, `Numerical Simulations of Thermonuclear Flashes on Neutron Stars', Nuclear Physics A, vol. 688, 172.

A. C. Calder, B. Fryxell, T. Plewa, R. Rosner, L. J. Dursi, V. G. Weirs, T. Dupont, H. F. Robey, J. O. Kane, B. A. Remington, R. P. Drake, G. Dimonte, M. Zingale, F. X. Timmes, K. Olson, P. Ricker, P. MacNeice, and H. M. Tufo, "On Validating an Astrophysical Simulation Code", Astrophysical Journal Suppl., vol. 143, pp. 201-229, (2002).

M. Zingale, L. J. Dursi, J. ZuHone, A. C. Calder, B. Fryxell, T. Plewa, J. W. Truran, A. Caceres, K. Olson, P. M. Ricker, K. Riley, R. Rosner, A. Siegel, F. X. Timmes, and N. Vladimirova, "Mapping Initial Hydrostatic Models in Godunov Codes", Astrophysical Journal Suppl., vol. 143, pp. 539-565, (2002).

M. Zingale, S. E. Woosley, A. Cumming,  A. Calder, L. J. Dursi,, B. Fyxell, K. Olson, P. Ricker, R. Rosner, and F. X. Timmes, `Investigations of Pointwise Ignition of Helium Deflagrations on Neutron Stars', 3D Stellar Evolution, ASP Conference Proceedings, vol. 293, 22-26 July 2002 at University of California Davis, Livermore California, eds. S. Turcotte, S. C. Keller, and R. M. Cavallo, ISBN:1-58381-140-0, 2003, p. 329.

D. Spadaro, A. F. Lanza, A. C. Lanzafame, J. T. Karpen, S. K. Antiochos, J. A. Klimchuk, and P. J. MacNeice, "A Transient Heating Model for Coronal Structure and Dynamics", Astrophysical Journal, vol. 582, pp. 486-494.

L. J. Dursi, M. Zingale, A. C. Calder, B. Fryxell, F. X. Timmes, N. Vladimorova, R. Rosner, A. Caceres, D. Q. Lamb, K. Olson, P. M. Ricker, K. Riley, A. Siegel, and J. W. Truran, "The Response of Model and Astrophysical Thermonuclear Flames to Curvature and Stretch", Astrophysical Journal, vol. 595, pp. 955-979, (2003).

M. Bruggen,"Simulations of Buoyant Bubbles in Galaxy Clusters", Astrophysical Journal, vol. 592, pp. 839-845, (2003).

U. Becciani, V. Antonuccio, A. Costa, and D. Ferro, "FLY: A Treecode for Adaptive Mesh Refinement", in ASP Conf. Ser. Vol. 295, Atronomical Data Analysis Software and Systems XII, eds. H. E. Payne, R. I. Jedrzejewski, and R. N. Hook (SanFrancisco: ASP), p. 423, (2003).

K. Hendrikson, L. Shen, D. K. P. Yue, D.G. Dommeruth, and P. Adams, "Simulation of Steep Breaking Waves and Spray Sheets Around a Ship: The Last Frontier in Computational Ship Hydrodynamics", The Resource, Fall 2003, p. 2, (2003).

S. Heinz, E. Churazov, W. Forman, C. Jones, and U. G. Briel, "Ram pressure stripping of the formation of cold fronts", Mon. Not. of the Royal Astron. Soc., vol. 346, issue 1, P. 13 (2003).

K. Robinson, L. J. Dursi, P. M. Ricker, R. Rosner, A. C. Calder, M. Zingale, J. W. Truran, T. Linde, A. Caceres, B. Fryxell, K. Olson, K. Riley, A. Siegel, and N. Vladimorova, "Morphology of Rising Hydrodynamic and Magnetohydrodynamic Bubbles from Numerical Simulations", Astrophysical Journal, vol. 601, pp. 621-643, (2004).

P. MacNeice, S. K. Antiochos , A. Phillips, D. S. Spicer, C. R. DeVore, and K. Olson, `A Numerical Study of the Breakout Model for Coronal Mass Ejection Initiation', ApJ, vol. 614, 1028 2004.

M. Ruszkowski, M. Bruggen,  and M. C. Begelman,  ‘ Three-dimensional simulations of viscous dissipation in the intracluster medium’, 2004, ApJ, vol. 615, issue 2, 675.

C. Zanni, A. Ferrari, S. Massaglia,  G. Bodo, and P. Rossi, ‘On the MHD acceleration of Astrophysical jets’, 2004,  Astro. And Space Sci., vol. 293, issue 1, 99.

B. J. Lynch, S. K. Antiochos, P. J. MacNeice, T. H. Zurbuchen, and L. A. Fisk, 2004, ‘ Observable Properties of the Breakout Model for Coronal Mass Ejections’, ApJ, vol. 617,  L589.

M. Benna, P. R. Mahaffy, P.  MacNeice,  and K. Olson, `A Multiscale Central Difference Scheme Applied to Magnetohydrodynamic Simulation of Cometary Atmospheres' 2004, ApJ, vol. 617, 656.

D.-I. Choi, J. D. Brown, B. Imbiriba, J. M. Centrella, P. MacNeice, "Interface Conditions for Wave Propagation Through Mesh Refinement Boundaries", Journal of Computational Physics, vol. 193, p. 398 (2004).

A. Alexakis, A. C. Calder, A. Heger, E. F. Brown, L. J. Dursi, J. W. Truran, D. Q. Lamb, F. X. Timmes, B. Fryxell, M. Zingale, P. M. Ricker, and K. Olson, 2004, `On Heavy Element Enrichment in Classical Novae', ApJ, 602, 931.

B. Imbiriba, J. Baker, D. Choi, J. Centrella, D. R. Fisk, J. D. Brown, J. R. van Metre, and K. Olson `Evolving a puncture black hole with fixed mesh refinement', 2004, Phys. Rev. D, vol. 70, issue 12, id. 124024.

K. Olson and P. MacNeice  2005, `An Overview of the PARAMESH AMR Sotware Package and Some of Its Applications', Adaptive Mesh Refinement - Theory and Applications, Proceedings of the Chicago Workshop on Adaptive Mesh Refinement Methods, Sept. 3-5, 2003, Series: Lecture Notes in Computational Science and Engineering, vol. 41, eds. T. Pewa, T. Linde, G. V. Weirs Parallel Computation, (Berlin: Springer).

A. D. Phillips, P. J. MacNeice, and S. K. Antiochos, 2005, ‘The role of magnetic helicity in coronal mass ejections’, ApJ, vol. 624, L129.

G. Weirs, D. Vikram, T. Plewa, C. Tomkins,  and M. Marr-Lyon, ‘Validating the FLASH Code: Vortex-Dominated Flows’, 2005, Astro. and Space Sci., vol. 298. Issue 1-2.  341.

A. C. Calder,  ‘Laboratory Expoeriments for Simulation Code Validation:: A Case Study’, 2005, Astro. And Space Sci., vol. 298, Issue 1-2, 25.

R. Banderjee, R. E. Pudritz,  and L. Holmes,  ‘The formation and evolution of protostellar discs; three-dimensional adaptive mesh refinement hydrosimulations of collapsing, rotating Bonnor-Ebert spheres’, 2004, MNRAS, vol. 355, issue 1, 248.

Olson, K., 2006, PARAMESH: A Parallel Adaptive Grid Tool, in Parallel Computational Fluid Dynamics 2005: Theory and Applications: Proceedings of the Parallel CFD Conference, College Park, MD, U.S.A., eds. A. Deane, A. Ecer, G. Brenner, D. Emerson, J. McDonough, J. Periaux, N. Satofuka, and D. Tromeur-Dervout (Elsevier).

Heath, D., Krause, M., and Alexander, P., 2007, “Chemical enrichment of the intracluster medium FR II radio sources”, MNRAS, vol. 374, 787.

Joung, M. K. R. and MacLow, M.-M., 2006, “Turbulent Structure of Stratified Supernova-driven Interstellar Medium”, ApJ, vol.  653, 1266.

Almgren, A.S, Bell, J. B., Rendleman, C. A., and Zngale, M., 2006, “Low Mach Number Modeling of Type Ia Supernovae. II. Energy Evolution”, ApJ, vol. 649,     927.

Escala, Andres,2006, “On the Fueling of Massive Black Holes and the Properties of Their Host Spheroids”, ApJ, vol. 648, L13-L16.

Dursi, L. J. and Timmes, F.  X., 2006, “Local Ignition in Carbon-Oxygen White    Dwarfs. I. One-Zone Ignition and Spherical Shock Ignition of Detonations, ApJ,     vol. 641, 1071.

Banerjee, R. and Pudritz, R. E., 2006, “Outflow and Jets from Collapsing Magnetic Cloud  Cores”, ApJ, vol. 641, 949.

Zhang, W. and MacFedyen, A. I., 2006, “RAM: A Relativistic Adaptive Mesh Hydrodynamics Code”, ApJS, vol. 164, 255.

Magra, T., 2006, “Dynamic and Topological Features of Photospheric and Coronal Activities Produced by Flux Emergence in the Sun”, ApJ, vol, 653, 1499.

Baker, J. G., Centrella, J.,  Choi, D., Koppitz, M., vanMetre, J. R.,  and Miller, M. C., 2006, “Getting a Kick Out of Numerical Relativity”, ApJ, vol. 653, L93.

Patsourakos, S. and Klimchuk, J. A., 2006, “Nonthermal Spectral Line Broadening and the Nanoflare Model”,  ApJ, vol. 647, 1452.

Sparado, D., Lanza, A. F., Karpen, J. T., and Antiochos, S. K., 2006, “A Transient Heating Model for the Structure and Dynamics of the Solar Transition Region”,  ApJ, vol. 642, 579.

Iliev, I. T. et al., 2006, “Cosmological Radiative Transfer Codes Comparison Project I: The Static Density Field Tests, MNRAS, vol. 371,  1057.

De Val-Borro, M. et al., 2006,”A comparative study of the disc-planet interaction”, MNRAS, vol. 370, 539.

Banerjee, R., Pudritz, R. E., and Anderson, D. A., 2006, “Supersonic turbulence, filarmentary accretion and the rapid assembly of massive stars and discs”,     MNRAS, vol. 373, 1091.

Welsch, B, T., DeVore, C. R., and Antiochos, S. K., 2005, “Magnetic Reconnection Models of Prominence Formation”, ApJ, vol. 634, 1395.

Patsourakos, S. and Klimchuk, J. A., 2005, "Coronal Loop Heating by Nanoflares: The Field-Aligned Distribution of the Heating on Loop Observations”,  ApJ, vol.     628, 1023.

Heitman, K., Ricker, P. M., Warren. M. S., and Habib, S., 2005, “Robustness of Cosmological Simulations. I. Large-Scale Structure”, ApJ., vol. 160, 28.

Heinz, S. and Churazov, E., 2005, “Heating the Bubbly Gas of  Galaxy Clusters with Weak Shocks and Sound Waves”, ApJ, vol. 634, L141.

Tang, S. and Wang, Q. D., 2005, “ Supernova Blast Waves in Low-Density Hot Media: A Mechanism for Spatially Distributed Heating”, ApJ, vol. 628, 205.

Kasen, D. and Plewa, T., 2005, “Spectral Signatures of Gravitationally Confiined Thermonuclear Supernova Explosions”, ApJ, vol. 622, L41.

Becciani, U., Comparato, M., and Antonuccio, V., 2006, “FLY MPI-2: a parallel tree code for LSS”, JCP, vol. 174,  605.

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