Mark Transtrum > Publications

Publications

    * = Undergraduate student coauthor
    = Graduate student coauthor

    Submitted

  • Transtrum M.K., Francis B.L., Saric A.T., Stankovic A.M., Simultaneous Global Identification of Dynamic and Network Parameters in Transient Stability Studies

  • Svenda V.G., Stankovic A.M., Saric A.T., Transtrum M.K., Hybrid Power System State Estimatino with Time Stamping, Communication Irregularities and Co-Simulation

  • Pare P.E., Grimsman D., Wilson A., Transtrum M.K., Warnick S., Model Boundary Approximation Method as a unifying Framework for Balanced Truncation and Singular Perturbation Approximation

  • Mattingly H.M., Transtrum M.K., Abbott M.C., Machta B.B., Rational Ignorance: Simpler models learn more from finite data

  • Saric A.T., Transtrum M.K., Stankovic A.M., Derivation of Dynamic Equivalents for Power System Areas from Boundary Measurements

  • Hunt C.A., Erdemir A., Gabhann F.M., Lytton W.W., Sander E.A., Transtrum M.K., Mulugeta W, Mechanistic Models, Model Mechanisms, and Computational Models of Explanation for Biological Phenomena

  • Transtrum M.K., Manifold boundaries give "gray-box" approximations of complex models

  • Transtrum M.K., Hart G., Qiu P. Information topology identifies emergent model classes (pdf).

  • Hansen L.D., Hansen C.W., Transtrum M.K., Hart G.L.W., Performance theory: A complete metabolic theory of ecology

    2017

  1. Mason M., Scampicchio M., Quinn C.F., Transtrum M.K., Hansen L.D., Kenealey J.D., Stability and Reusability of Invertase Immobilized on Nylon-6 Nanofiber Membrane Measured by Isothermal Titration Calorimetry (ITC). JFS: Food Engineering, Materials Science, and Nanotechnology (In Press).

  2. Saric A.T., Transtrum M.K., Stankovic A.M., Information Geometry for Model Identification and Parameter Estimation in Renewable Energy--DFIG Plant Case. IET Generation, Transmission & Distribution (In Press)

  3. Transtrum M.K. Saric A.T., Stankovic A.M., Information Geometry Approach to Verification of Dynamic Models in Power System. IEEE Transactions on Power Systems (In Press)

  4. Stankovic A.S., Svenda V., Saric A.T., Transtrum M.K., Hybrid Power System State Estimation with Irregular Sampling. IEEE Power in Energy and Society General Meeting, Chicago, 2017.

  5. Youn C.C., Saric A.T., Transtrum M.K. Stankovic A.M., Information Geometry for Model Reduction of Dynamic Loads in Power Systems. IEEE Power in Energy and Society Powertech, Manchester (2017).

  6. Liarte D.B., Posen S., Transtrum M.K., Catelani G., Liepe M., Sethna J.P., Theoretical estimates of maximum fields in superconducting resonant radio frequency cavities: Stability theory, disorder, and laminates. Superconductor Science and Technology 30 033002 (2017).
    DOI: 10.1088/1361-6668/30/3/033002 (pdf)

  7. 2016

  8. Mathis A.D., Naylor B.C., Carson R.H., Evans E., Harwell J., Knecht J., Hexem E., Peelor F.F., Miller B.F., Hamilton K.L., Transtrum M.K., Biman B.T., Price J.C. Mechanisms of in vivo ribosome maintenance respond to nutrient signals. Molecular and Cellular Proteomics (in press).
    DOI: 10.1074/mcp.M116.063255

  9. White A.*, Tolman M., Thames H.D., Withers H.R., Mason K., Transtrum M.K., The limitations of model-based experimental design and parameter estimation in sloppy systems PLoS Computational Biology 12(12): e1005227 (2016)
    DOI: 10.1371/journal.pcbi.1005227 (pdf)

  10. Liarte D.B., Transtrum M.K., Sethna J.P., Ginzburg-Landau theory of the superheating field anisotropy of layered superconductors Physical Review B 94 144504, (2016)
    DOI: (10.1103/PhysRevB.94.144504) (pdf)

  11. Transtrum M.K. Saric A.T., Stankovic A.M., Measurement-Directed Reduction of Dynamic Models in Power Systems. IEEE Transactions on Power Systems. In press.
    DOI: 10.1109/TPWRS.2016.2611511

  12. Saric A.T., Transtrum M.K., Stankovic A.M., Dynamic Model Estimation for Power System Areas from Boundary Measurements. IEEE Power in Energy and Society General Meeting, Boston, 2016. (pdf)

  13. Transtrum M.K., Saric A.T., Stankovic A.M., Information Geometry for Model Verification in Energy Systems. Power Systems Computation Conference, Genoa, 2016.
    DOI:10.1109/PSCC.2016.7540968 (pdf)

  14. Transtrum M.K., Qiu P., Bridging Mechanistic and Phenomenological Models of Complex Biological Systems. PLoS Computational Biology 12(5): e1004915 (2016)
    DOI: 10.1371/journal.pcbi.1004915 (pdf)

  15. 2015

  16. Hansen L.D., Transtrum M.K., Quinn C., Demarse N., Enzyme-catalyzed and binding reaction kinetics determined by titration calorimetry. BBA General Subjects 1840, 957-966 (2015)
    DOI: 10.1016/j.bbagen.2015.12.018 (pdf)

  17. Posen S., Transtrum M.K., Catelani G., Liepe M.U., Sethna J.P., Shielding superconductors with thin films as applied to rf cavities for particle accelerators. Phys. Rev. Applied 4, 044019 (2015)
    DOI: 10.1103/PhysRevApplied.4.044019 (pdf).

  18. Transtrum M.K., Machta B., Brown K., Daniels, B.C., Myers C.R., Sethna, J.P., Sloppiness and Emergent Theories in Physics, Biology, and Beyond. J. Chem. Phys. 143 010901 (2015) (pdf).

  19. Pare P.E., Wilson A., Transtrum M.K., Warnick S, A unified view of balanced truncation and singular perturbation approximations. American Control Conference, Chicago, 2015.
    DOI:10.1109/ACC.2015.7171025 (pdf)

  20. Mannakee B.K., Ragsdale A.P., Transtrum M.K., Gutenkunst R.N. Sloppiness and the geometry of parameter space. in Uncertainty in Biology Volume 17 of the series Studies in Mechanobiology, Tissue Engineering and Biomaterials.
    DOI:10.1007/978-3-319-21296-8_11 (pdf)

  21. Transtrum M.K., Hansen, L.D., Quinn, C. Enzyme kinetics determined by single-injection isothermal titration calorimetry. Methods 76 194-200 (2015) (pdf).

  22. 2014

  23. Transtrum M.K., Qiu P. Model reduction by manifold boundaries. Physical Review Letters 113 098701 (2014) (pdf)

  24. 2013

  25. Posen S., Catelani G., Liepe M., Sethna J.P., and Transtrum M.K. Theoretical field limit for muli-layer superconductors. arXiv:1309.3239. See also, Response to comment on theoretical RF field limits of multilayer coating structures of superocnductor resonant cavities.

  26. Machta B.B., Chachra R., Transtrum M.K., Sethna J.P. Parameter Space Compression Underlies Emergent Theories and Predictive Models. Science 342, 604-607 (2013). See also BYU News release, BYU Radio Interview of Transtrum by Marcus Smith (beginning at the 8:18 mark), Physicists unify the structure of scientific theories in the Cornell Chronicle (Anne Ju); Jesse Silverberg's Huffington Post blog and Kathryn McGill's vblog Soft Matters with Jim Sethna from The Physics Factor; and (Unedited) Interview of Sethna by Steven Reiner, Stony Brook School of Journalism (Mobile version).

  27. Sheu T., Molkentine J., , Transtrum M.K., Buchholz T.A., Withers H.R., Thames H.D., Mason K.A. Use of the LQ model with large fraction sizes results in underestimation of isoeffect doses. Radiotherapy and Oncology. 109 21-25 (2013) (pdf)

  28. 2012

  29. Transtrum M.K. and Sethna J.P. Geodesic acceleration and the small-curvature approximation for nonlinear least squares. arXiv:1207.4999

  30. Transtrum M.K. and Sethna J.P. Improvements to the Levenberg-Marquardt algorithm for nonlinear least squares minimization. arXiv:1201.5885

  31. Chachra R., Transtrum M.K., and Sethna J.P. Structural susceptibility and separation of time scales in the van der Pol oscillator. Physical Review E. 86 026712, (2012)
    DOI: 10.1103/PhysRevE.86.026712, (pdf)

  32. Transtrum M.K. and Qiu P. Optimal Experiment Selection for Parameter Estimation in Biological Differential Equation Models. BMC Bioinformatics. 13 1, 181, (2012) (pdf)
    DOI: 10.1186/1471-2105-13-181

    2011

  33. Transtrum M.K., Chen Y.J., Machta B.B., Gutenkunst T., and Sethna J.P. Contribution to discussion on "Riemann manifold Langevin and Hamiltonian Monte Carlo Methods". Journal of the Royal Statistical Society: B. 72 2, 123-214, (2011) (pdf) (Discussion on page 199.)

  34. Chachra R., Transtrum M.K., and Sethna J.P. Comment on "Sloppy models, parameter uncertainty, and the role of experimental design". Molecular Biosystems. 10 1039, (2011) (pdf)

  35. Transtrum M.K., Machta B.B., and Sethna J.P. The geometry of nonlinear least squares with applications to sloppy models and optimization. Physical Review E. 83 036701, (2011) (pdf)

  36. Transtrum M.K., Catelani G., and Sethna J.P. Superheating field of superconductors within Ginzburg Landau theory. Physical Review B. 83 094505, (2011) (pdf)

  37. 2010 and earlier

  38. Transtrum M.K., Machta B.B., and Sethna J.P. Why are nonlinear fits to data so challenging? Physical Review Letters. 104 060201, (2010) (pdf)

  39. Junkermeier C., Transtrum M.K. , and Berrondo M. An Analytic iterative approach to solving the time-independent Schrodinger equation. International Journal of Quantum Chemistry. 109, 982-998, (2009) (pdf)

  40. Van Huele J.F.S. and Transtrum M.K. Beyond the quantum in Snyder space. In: Beyond the Quantum. 235-243, (2007)

  41. Transtrum M.K. and Van Huele J.F.S. A perturbative approach to Snyder space with applications. Journal of Physics A-Mathematical and General. 39, 14985-14996, (2006) (pdf)

  42. Transtrum M.K. and Van Huele J.F.S. Commutation Relations for functions of operators. Journal of Mathematical Physics. 46, 063510, (2005) (pdf)

Transtrum Group Theses

    Undergraduate Theses

  1. "Computational Models of Film and Bulk Superconductors in Time Varying Magnetic Fields", Alden Pack. Thesis (2015). (pdf)

  2. "Improving the Efficiency of the Levenberg-Marquardt Algorithm Using Partial-Rank Jacobian Updates", Michael Zarian. Thesis (2016). (pdf)

  3. "Adaptation in Enzyme Networks: Searching for Minimal Mechanisms", Merril Asp. Thesis. (2016) (pdf)