| 2008? | Scott A. Hill. | Holding and slack in a deterministic bus-route model. | Submitted to Transportation Science. |
| 2006 | Daniel P. Knudsen, John T. Arsenault, Scott A. Hill, Donald M. O'Malley, and Jorge V. José. | Locomotive network modeling based on identified neurons in zebrafish. | Neurocomputing |
| 2005 | Scott A. Hill, Melissa A. Borla, Jorge V. José, and Donald M. O'Malley. | Neurokinematic modeling of complex swimming patterns of the larval zebrafish. | Neurocomputing |
| 2005 | Scott A. Hill. | Numerical analysis of a time-headway bus route model. | Physica A |
| 2003 | Scott A. Hill and Gene F. Mazenko. | Granular clustering in a hydrodynamic simulation. | Physical Review E |
| 2001 | Scott A. Hill and Gene F. Mazenko. | Nonlinear hydrodynamical approach to granular materials. | Physical Review E |
| 1997 | Scott Hill and William K. Wootters | Entanglement of a pair of quantum bits. | Physical Review Letters |