| 2000 | Baccam, Prasith (Sid) | Genetic variation and evolution of equine infectious anemia virus rev quasispecies during long term persistent infection | Cornette | |
| 2000 | Pamuk, Serdal | Two dimensional models of tumor angiogenesis | Levine | |
| 2000 | Thompson, Heather | Investigating and representing inquiry in college Mathematics course | Keller | |
| 2001 | Dai, Jack Jie | Some results in probability and theoretical computer science | Athreya | |
| 2001 | Lee, Jeehyun | Optimization-based domain decomposition methods for multidisciplinary simulation | Gunzburger | |
| 2001 | Majumdar, Ruchira | On relationships between the Lypanov spectrum and the Morse spectrum | Kliemann | |
| 2001 | Vojtechovsky, Petr | Finite sample moufang loops | Smith, JDH | |
| 2002 | Becker, Joy | Computational complexity of digraph decomposition and the congruence extension property of algebras | Bergman | |
| 2002 | Choi, Ji Young | Multi-restricted numbers and powers of permutation representations | Smith, JDH | |
| 2002 | Chrysafinos, Konstantinos | Analysis and finite element approximation of parabolic saddle point problems and applications to control | Gunzburger | |
| 2002 | Ju, Lili | Probabilistic and parallel algorithms for centroidal Voroni tessalations with application to meshless computing and analysis on surfaces | Gunzburger | |
| 2002 | Zhu, Wenxiang | Modelling, analysis, numerical approximations of the forced Fisher's equation and related control problems | Gunzburger | Hou |
| 2003 | Calhoun-Lopez, Marcus | Numerical solutions of hyperbolic conservation laws: incorporating multi-resolution viscosity methods into finite element framework | Gunzburger | |
| 2003 | Candan, Tuncay | Oscillation behavior of Higher Order Functional Differential Equations with distributed deviating arguments | Dahiya | |
| 2003 | Kwon, Hee-Dae | Analysis and Approximation of Terminal-State Tracking Optimal Control Problems and Controllability Problems Constrained by Linear and Nonlinear Parabolic Partial Differential Equations | Hou | Gunzburger |
| 2003 | Malonza, David | Normal Forms for Couples Takens-Bogdanov Systems | Murdock | |
| 2003 | Zerr, Ryan | Partial dynamical systems and AF C*-algebras | Peters | |
| 2004 | Babyonyshev, Sergei | Metatheories of Deductive Systems | Pigozzi | Bergman |
| 2004 | Bhatt, Gyan Shyam | Nonseparable multivariate wavelets | Keinert | |
| 2004 | Kivunge, Benard Muthiani | Sedenion Extension Loops and Frames of Hypercomplex 2n-ons | Smith, JHD | |
| 2004 | Mutungi, Patrick Mugo | Simple Ternary Complex Grassmann Algebras | Smith, JHD | |
| 2004 | Yang, Sung-Dae | Shooting Methods for Numerical Solutions of Control Problems Constrained by Linear and Nonlinear Hyperbolic PDE’s | Hou | |
| 2005 | Aydinyan, Ruben | Loop transversal codes over finite rings | Smith, JDH | |
| 2005 | Campbell, Jessie | Enumeration and symmetry of edit spaces | Ashlock | |
| 2005 | Cui, Feng | Distance-based NMR structure determination and refinement | Wu, Z. | Jernigan |
| 2005 | Kim, Eun-Youn | Analysis of Game Playing Agents with Fingerprints | Ashlock | |
| 2005 | Kim, Joohyung | Classification of small class association schemes coming from certain combinatorial objects | Song | Long |
| 2005 | Maxwell, Mandi | Almost perfect nonlinear functions and related combinatorial structures | Song | Bergman |
| 2005 | Rajaram, Rajeev | Exact boundary controllability results for sandwich beam systems | Hansen | |
| 2005 | Wangsness, Amy | The matrix completion problem regarding various classes of PO,1-matrices | Hogben | |
| 2006 | Alm, Jeremy | Weak representation theory in the calculus of relations | Maddux | |
| 2006 | Chepkwony, Isaac | Analysis and control theory of some cochlear models | Hansen | |
| 2006 | Gunaratne, Ajith | A penalty function method for constrained molecular dynamics | Wu, Z. | |
| 2006 | Meyer, Kristen Ann | A new message authentication code based on the non-associativity of quasigroups | Bergman | |
| 2006 | Schonfeld, Justin | A modular data analysis pipeline for the discovery of novel RNA motifs | Ashlock | Voytas |
| 2006 | Wu, Di | Distance-based protein structure modeling | Wu, Z. | Jernigan |
| 2007 | Chung, Key One | Weak homomorphisms of coalgebras | Smith, JDH | |
| 2007 | Fiedler, James | Greco-Latin Squares as Bijections | Smith, JDH | |
| 2007 | Meng, Qiang | Topics in Pricing American-type Contracts | Weerasinghe | |
| 2007 | Rice, Theodore | Greedy Quasigroups and Greedy Algebras with Applications to Combinatorial Games | Smith, JDH | |
| 2007 | Vedell, Peter Thomas | Boundary value approaches to molecular dynamics simulation | Wu, Z. | |
| 2008 | Ahmed, Haseena | High-resolution alternating evolution schemes for hyperbolic conservation laws and Hamilton-Jacobi equations | Liu | |
| 2008 | Bhattacharyya, Gargi | Terwilliger algebras of wreath products of association schemes | Song | |
| 2008 | Dagli, Mehmet | Lie algebra decompositions with applications to quantum dynamics | D'Alessandro | Smith |
| 2008 | Drignei, Mihaela-Cristina | Inverse Sturm-Kiouville Problems using Multiple Spectra | Sacks | |
| 2008 | Halverson, Matthew | Asymptotic behavior of the solutions to a family of PDE's arising from the chemotaxis equations of Keller and Segal | Levine | Johnston |
| 2008 | Lee, Jangwoon (Leo) | Analysis and finite element approximations of stochastic optimal control problems constrained by stochastic elliptic partial differential equations | Hou | |
| 2008 | Mikkelson, Rana | Minimum rank of graphs that allow loops | Hogben | |
| 2008 | Shin, Jaemin | Inverse scattering problems for first-order systems | Sacks | |
| 2008 | Wang, Zhongming (Eric) | Development of level set methods for computing semi-classical limit in Schrodinger equations with various potentials | Liu | |
| 2008 | Xie, Xiaoliang | Large time-stepping methods for higher order time-dependent evolution equations | Liu | |
| 2008 | Xu, Ying | Modeling and direct numerical simulation of particle-laden turbulent flows | Luecke | Subramaniam |
| 2009 | Allen, Aaron | Stability results for damped multilayer composite beams and plates | Hansen | |
| 2009 | Alturk, Ahmet | Boundary functions for wavelets and their properties | Keinert | |
| 2009 | Guo. Xiaofang | Generic two-phase coexistence in quadratic contact process | Evans | |
| 2009 | Kurth, Chris Allen | Modular Forms and modular symbols for noncongruence groups | Long | |
| 2009 | Ming, Ju | Optimal control of stochastic flow | Hou | |
| 2009 | Pryporova, Olga | Types of convergences of matrices | Hogben | |