Skip to main content

Publications

All Publications

Author(s)Title/JournalYearTopic Areas
D. L. ChoppIntroduction to High Performance Scientific Computing, SIAM2019Numerical Methods
A. Caruso, F. Boano, L. Ridolfi, D. L. Chopp, A. PackmanBiofilm-Induced Bioclogging Produces Sharp Interfaces in Hyporheic Flow, Redox Conditions and Microbial Community Structure, Geophysical Research Letters, 44:4917-49252017Biofilms
A. Sadeghirad, D. L. Chopp, X. Ren, E. Fang, J. LuaA Novel Hybrid Approach for Level Set Characterization and Tracking of Non-Planar 3D Cracks in the Extended Finite Element Method, Engineering Fracture Mechanics, 160:1-142016Level Set Method, eXtended Finite Element Method, Fracture Mechanics
R. Kublik and D. L. ChoppA Locally Adaptive Time-Stepping Algorithm for the Solution to Reaction-Diffusion Equations on Branched Structures, Advances in Computational Mathematics, 42(3):621-6492016Numerical Methods, Computational Neuroscience
X. Li, D.L. Chopp, W.A. Russin, P.T. Brannon, M. R. Parsek, A.I. PackmanIn Situ Biomineralization and Particle Deposition Distinctively Mediate Biofilm Susceptibility to Chlorine, Applied and Environmental Microbiology, 82(10):2886-28922016Biofilms
X. Li, D.L. Chopp, W.A. Russin, P.T. Brannon, M. R. Parsek, A.I. PackmanSpatial Patterns of Carbonate Biomineralization in Biofilms, Applied and Environmental Microbiology, 81(21):7403-74102015Biofilms
X. Li, J.L. Song, A. Culotti, W. Zhang, D.L. Chopp, N. Lu, A.I. PackmanMethods for Characterizing the Co-Development of Biofilm and Habitat Heterogeneity, Journal of Visualized Experiments, 972015Biofilms
B. V. Merkey and D. L. ChoppModeling the Impact of Interspecies Competition on Performance of a Microbial Fuel Cell, Bulletin of Mathematical Biology, 76(6):1429-14532014Level Set Method, Biofilms
B. S. Tseng, W. Zhang, J. J. Harrison, T. P. Quach, J. L. Song, J. Penterman, P. K. Singh, D. L. Chopp, A. I. Packman, and M. R. Parsek. The Extracellular Matrix Protects Pseudomonas aerguinosa Biofilms by Limiting the Penetration of Tobramycin, Environmental Microbiology, 15(10):2865-28782013Biofilms
A. A. Davila, D. W. Buck, D. L. Chopp, C. M. Connor, S. Persing, V. Rawlani, and J. Y. S. KimA Novel Prospective Three-Dimensional Analysis of Nasolabial Fold Augmentation, Aesthetic Surgery Journal, 32(4):488-4942012Plastic Surgery
B. V. Merkey and D. L. ChoppThe Performance of a Microbial Fuel Cell Depends Strongly on Anode Geometry: A Multidimensional Modeling Study, Bulletin of Mathematical Biology, 74:834-8572012Biofilms, Level Set Method
D. L. Chopp, V. Rawlani, M. Ellis, S. A. Johnson, S. Khan, K. Bethke, N. Hansen, J. YS KimA Geometric Analysis of Mastectomy Incisions: Optimizing Intraoperative Breast Volume, Canadian Journal of Plastic Surgery, 19(2):45-502011Plastic Surgery
R. Duddu, D. L. Chopp, and P. VoorheesDiffusional Evolution of Precipitates in Elastic Media Using the Extended Finite Element and the Level Set Methods, Journal of Computational Physics, 230(4):1249-12642011Materials Science, Level Set Method
J. Shi, D. L. Chopp, J. Lua, N. Sukumar, and T. BelytschkoAbaqus Implementation of Extended Finite Element Method Using a Level Set Representation for Three-Dimensional Fatigue Crack Growth and LIfe Predictions, Engineering Fracture Mechanics, 77(14):2840-28632010Level Set Method, eXtended Finite Element Method, Fracture Mechanics
B. L. Vaughan, B. G. Smith, D.L. ChoppThe Influence of Fluid Flow on Modeling Quorum Sensing in Bacterial Biofilms, Bulletin of Mathematical Biology, 72(5):1143-11652010Level Set Method, Biofilms
D. L. ChoppAnother look at velocity extensions in the level set method. SIAM Journal of Scientific Computing, 31(5):3255-32732009Level Set Method
B. Merkey, B. E. Rittmann, and D.L. ChoppModeling How Soluble Microbial Products (SMP) Support Heterotrophs in Autotroph-Based Biofilms, Journal of Theoretical Biology, 259:670-6832009Level Set Method, Biofilms
R. Duddu, D.L. Chopp, and B. MoranA Two-Dimensional Continuum Model of Biofilm Growth Incorporating Fluid Flow and Shear Stress Based Detachment, Biotechnology and Bioengineering, 103(1):92-1042009Level Set Method, Biofilms
N. Sukumar, D. L. Chopp, E. Béchet, N. MöesThree-dimensional non-planar crack growth by a coupled extended finite element and fast marching method, International Journal of Numerical Methods in Engineering, 76(5):727-7482008Level Set Method, eXtended Finite Element Method, Fracture Mechanics
M. J. Rempe, N. Spruston, W. L. Kath, and D. L. ChoppCompartmental neural simulations with spatial adaptivity. Journal of Computational Neuroscience, 25(3):465-4802008Computational Neuroscience, Numerical Methods
R. Duddu, S. Bordas, D. L. Chopp, and B. MoranA combined extended finite element and level set method for biofilm growth. International Journal of Numerical Methods in Engineering, 74(5):848-8702008Level Set Method, Biofilms
B. G. Smith, B. L. Vaughan, and D. L. ChoppThe extended finite element method for boundary layer problems in biofilm growth, Communications in Applied Mathematics and Computational Science, 2(1):35-562007Level Set Method, Biofilms, eXtended Finite Element Method
M. J. Kirisits, J. Margolis, B. L. Purevdorj-Gage, B. Vaughan, D. L. Chopp, P. Stoodley, and M. R. ParsekThe influence of the hydrodynamic environment on quorum sensing in Pseudomonas aeruginosa biofilms, Journal of Bacteriology, 189(22):8357-83602007Biofilms, Level Set Method
B. L. Vaughan, Jr., B. G. Smith, and D. L. ChoppA comparison of the extended finite element method with the immersed interface method for elliptic equations with discontinuous coefficients and singular sources. Communications in Applied Mathematics and Computational Science, 1(1):207-2282006eXtended Finite Element Method
J. D. Shrout, D. L. Chopp, C. L. Just, M. Hentzer, M. Givskov, and M. R. ParsekThe impact of quorum sensing and swarming motility on Pseudomonas aeruginosa biofilm formation is nutritionally conditional. Molecular Microbiology, 62(5):1264-12772006Biofilms
A. Tongen and D. L. ChoppSimulation of multigrain thin film growth. Interfaces and Free Boundaries, 8:1-192006Materials Science, Level Set Method
M. J. Rempe and D. L. ChoppA predictor-corrector algorithm for reaction-diffusion equations associated with neural activity on branched structures. SIAM Journal of Scientific Computing, 28(6):2139-21612006Numerical Methods, Computational Neuroscience
M. Torres, D. L. Chopp, and T. WalshLevel set methods to compute minimal surfaces in a medium with exclusions (voids). Interfaces and Free Boundaries, 7(2)2005Differential Geometry, Level Set Method
S. Kodambaka, D. L. Chopp, I. Petrov, and J. E. GreeneCoalescence kinetics of two-dimensional TiN islands on atomically-smooth TiN(001) and TiN(111) terraces. Surface Science, 540(2-3):L611-L6162003Materials Science, Level Set Method
M. Stolarska and D. L. ChoppModeling spiral cracking due to thermal cycling in integrated circuits. International Journal of Numerical Methods in Engineering, 41(20):2381-24102003Level Set Method, Fracture Mechanics
D. L. Chopp, M. J. Kirisits, M. R. Parsek, and B. MoranThe dependence of quorum sensing on the depth of a growing biofilm. Bulletin of Mathematical Biology, 65(6):1053-10792003Biofilms
D. L. Chopp and J. A. VellingFoliations of hyperbolic space by constant mean curvature surfaces sharing ideal boundary. Journal of Experimental Mathematics, 12(3):339-3502003Level Set Method, Differential Geometry
D. L. Chopp and N. SukumarFatigue crack propagation of multiple coplanar cracks with the coupled extended finite element/fast marching method. International Journal of Engineering Science, 41(8):845-8692003Level Set Method, eXtended Finite Element Method, Fracture Mechanics
N. Sukumar, D. L. Chopp, and B. MoranExtended finite element for three-dimensional fatigue crack propagation, Engineering Fracture Mechanics, 70(1):29-482003Level Set Method, eXtended Finite Element Method, Fracture Mechanics
D. L. Chopp, M. J. Kirisits, M. R. Parsek, and B. MoranA mathematical model of quorum sensing in a growing P. aeruginosa biofilm. Journal of Industrial Microbiology and Biotechnology, 29(6):339-3462002Biofilms
K. A. Smith, F. J. Solis, and D. L. ChoppA projection method for motion of triple junctions by level sets. Interfaces and Free Boundaries, 4(3):263-2762002Level Set Method
H. Ji, D. L. Chopp, and J. E. DolbowA hybrid extended finite element/level set method for modeling phase transformations. International Journal for Numerical Methods in Engineering, 54(8):1209-12332001Level Set Method, eXtended Finite Element Method, Materials Science
D. L. ChoppReplacing iterative algorithms with single-pass algorithms. Proceedings of the National Academy of Sciences, 98(20):10992-109932001Level Set Method
D. L. ChoppSome improvements of the fast marching method, SIAM Journal of Scientific Computing, 23(1):230-2442001Level Set Method
M. Stolarska, D. L. Chopp, N. Möes, and T. BelytschkoModelling crack growth by level sets in the extended finite element method, International Journal for Numerical Methods in Engineering, 51(8):943-9602001Level Set Method, eXtended Finite Element Method, Fracture Mechanics
F. H. Baumann, D. L. Chopp, G. H. Gilmer, J. E. Greene, H. Huang, S. Kodambaka, P. O'Sullivan, and T. Diaz de la RubiaMulti-scale modelling of thin film deposition: Applications to Si device processing, Materials Research Society Bulletin, 26(3), 2001Materials Science
N. Sukumar, D. L. Chopp, N. Möes, and T. BelytschkoModelling holes and inclusions by level sets in the extended finite element method. Computer Methods in Applied Mechanics and Engineering, 190(46-47):6183-62002001Level Set Method, Fracture Mechanics
D. L. ChoppA level-set method for simulating island coarsening. Journal of Computational Physics, 162:104-1222000Level Set Method, Materials Science
D. L. Chopp and J. A. SethianMotion by intrinsic Laplacian of curvature. Interfaces and Free Boundaries, 1(1):107-1231999Level Set Method, Differential Geometry
D. L. Chopp, L. C. Evans, and H. IshiiWaiting time effects for Gauss curvature flows. Indiana University Math Journal, 48(1):311-3341999Level Set Method, Differential Geometry
S. Angenent, T. Ilmanen, and D.L. ChoppA computed example of nonuniqueness of mean curvature flow in R3. Communications on Partial Differential Equations, 20(11-12):1937-19581995Level Set Method, Differential Geometry
D. L. ChoppNumerical computation of self-similar solutions for mean curvature flow. Journal of Experimental Mathematics, 3(1):1-151994Level Set Method, Differential Geometry
D. L. Chopp and J. A. SethianFlow under curvature: Singularity formation, minimal surfaces, and geodesics, Journal of Experimental Mathematics, 2(4):235-2551993Level Set Method, Differential Geometry
D. L. ChoppComputing minimal surfaces via level set curvature flow, Journal of Computational Physics, 106(1):77-911993Level Set Method, Differential Geometry
D. L. ChoppDeformable Models: Biomedical and Clinical Applications, chapter Simulating Bacterial Biofilms. Springer2007Biofilms, Level Set Method
D. L. ChoppHandbook of Biomedical Image Analysis, volume 1, chapter Recent Advances in the Level Set Method. Kluwer Academic2005Level Set Method
D. L. ChoppState of the Art PDE and Level Sets Algorithms, Approaches to Static and Motion Imagery Segmentation, chapter Level Set Extensions, Flow and Crack Propagation. Kluwer Academic2002Level Set Method
J. S. Suri, D. L. Chopp, and S. LaxminarayanState of the Art PDE and Level Sets Algorithms, Approaches to Static and Motion Imagery Segmentation, chapter The Future of PDEs and Level Sets. Kluwer Academic2002Level Set Method
M. Stolarska, D. L. Chopp, N. Moës, and T. BelytschkoModelling crack growth by level sets. In the 14th European Conference on Fracture2002Level Set Method, eXtended Finite Element Method, Fracture Mechanics
J. E. Dolbow, H. Ji, and D. L. ChoppAdvances in the hybrid finite element / level set method for phase transformations. In the 5th World Congress on Computational Mechanics2002Level Set Method, Materials Science
J. A. Sethian and D. L. ChoppPhysics and geometry of flow under curvature: Singularity formation, minimal surfaces, geodesics, and surface tension. In DeGruyter Trento Conference on Mean Curvature Flow1994Level Set Method, Differential Geometry
J. A. Sethian and D. L. ChoppFlow under mean curvature: Singularity formation and minimal surfaces. In Computational Crystal Growers Workshop1992Level Set Method, Differential Geometry