N-body and methods with similarly high computational density are a source of many high-profile speedups, since they can approach the theoretical limits of the GPU’s computing capabilities.
These are just a sample of the numerous papers on compute-intensive methods such as N-body.
Gravitational Simulation
Burtscher, Martin and Keshav Pingali. An efficient CUDA implementation of the tree-based Barnes-Hut n-body algorithm. In GPU Gems Emerald Edition, Wen-Mei Hwu, ed., Morgan-Kaufmann, 2011, pp. 75-92. http://cs.txstate.edu/~burtscher/papers/gcg11.pdf
Harris, Mark, Lars Nyland and Jan Prins. Fast n-body simulation with CUDA. In GPU Gems 3, Addison-Wesley, 2007, pp. 677-695. https://developer.nvidia.com/gpugems/gpugems3/part-v-physics-simulation/chapter-31-fast-n-body-simulation-cuda
Molecular Modeling
Götz, Andreas, Mark J. Williamson, Dong Xu, Duncan Poole, Scott Le Grand, and Ross C. Walker. Routine microsecond molecular dynamics simulations with AMBER on GPUs – Part I : Generalized Born, J. Chem. Theory Comput. 2012, 8 (5), 1542−1555.
Hwu, Wen-Mei and David Kirk. Programming Massively Parallel Processors. Morgan-Kaufmann, 2010, pp. 173-188.
Hardy, David J., John E. Stone, Kirby L. Vandivort, David Gohara, Christopher Rodrigues, and Klaus Schulten. Fast molecular electrostatics algorithms on GPUs. In GPU Computing Gems, Chapter 4, pp. 43-58, Elsevier, 2011.
Stone, John E., James C. Phillips, Peter L. Freddolino, David J. Hardy, Leonardo G. Trabuco, and Klaus Schulten. Accelerating molecular modeling applications with graphics processors. Journal of Computational Chemistry 28: 2618-2640, 2007.
https://doi.org/10.1002/jcc.20829
Stone, John E., David J. Hardy, Barry Isralewitz, and Klaus Schulten. GPU algorithms for molecular modeling. In Scientific Computing with Multicore and Accelerators, Jack Dongarra, David A. Bader, and Jakob Kurzak, ed., Chapman & Hall / CRC Press, Chapter 16, pp. 351-371, 2010.
Boids
da Silva, A. R., Lages, W. S., and Chaimowicz, L. 2009. Boids that see: Using self-occlusion for simulating large groups on GPUs. ACM Comput. Entertain. 7, 4, Article 51 (December 2009), 20 pages. DOI = 10.1145/1658866.1658870 https://doi.org/10.1145/1658866.1658870