Publications


= Graduate student coauthor
* = Undergraduate student coauthor

    2019

  1. Model Boundary Approximation Method as a unifying Framework for Balanced Truncation and Singular Perturbation Approximation
    Pare P.E., Grimsman D., Wilson A., Transtrum M.K., Warnick S.
    IEEE Transactions on Automatic Control (accepted)
    See also a longer version here

  2. 2018

  3. Optimal Experimental Design for Machine Learning Using the Fisher Information
    Neilsen T.B., Van Komen D.F., Transtrum M.K., Allen M.B.
    Proceedings on Meetings in Acoustics (accepted)

  4. Effect of extreme temperatures on soil: A calorimetric approach
    Hansen L.D., Barros N., Transtrum M.K., Rodriguez-Anon J.A., Proupin J., Pineiro V., Arias-Gonzalez A., Gartzia N
    Thermochimica Acta (accepted)
    DOI pdf

  5. Data-Driven Dynamic Equivalents for Power System Areas from Boundary Measurements
    Saric A.T., Transtrum M.K., Stankovic A.M.
    IEEE Transactions on Power Systems 34.1 360-370 (2019)
    DOI

  6. Influence of Communication Irregularities and Co-simulation on Hybrid Power System State Estimation
    Svenda V.G., Stankovic A.M., Saric A.T., Transtrum M.K.
    IEEE PES Innovative Smart Grid Technologies Conference (ISGT) Europe , Sarajevo, 2018

  7. Geometrically Motivated Reparameterization for Identifiability Analysis in Power Systems Models
    Transtrum M.K., Francis B.L., Youn C.C., Saric A.T., Stankovic A.M.
    North American Power Symposium (NAPS), Fargo, ND, 2018

  8. Simultaneous Global Identification of Dynamic and Network Parameters in Transient Stability Studies
    Transtrum M.K., Francis B.L., Saric A.T., Stankovic A.M.
    IEEE Power and Energy Society General Meeting, Portland, 2018

  9. Experimental design and model reduction in systems biology
    Jeong J., Zhuang Q., Transtrum M.K. Zhou E., Qiu P.
    Quantitative Biology (In press)

  10. The Spectrum of Mechanism-Oriented Models and Methods for Explanations of Biological Phenomena
    Hunt C.A., Erdemir A., Gabhann F.M., Lytton W.W., Sander E.A., Transtrum M.K., Mulugeta W.
    Processes 6, 56 (2018)
    DOI pdf

  11. Titration Calorimetry: From Concept to Application
    Hansen L.D., Transtrum M.K., Quinn C.F
    Springer Briefs in Molecular Science
    DOI pdf

  12. Maximizing the information learned from finite data selects a simple model
    Mattingly H.M., Transtrum M.K., Abbott M.C., Machta B.B.
    Proceedings of the National Academy of Sciences 115 (8), 1760-1765 (2018)
    DOI pdf

  13. 2017

  14. Calorimetric Methods for Measuring Stability and Reusability of Membrane Immobilized Enzymes
    Mason M., Scampicchio M., Quinn C.F., Transtrum M.K., Baker N., Hansen L.D., Kenealey J.D.
    JFS: Food Engineering, Materials Science, and Nanotechnology 83.2 326-331 (2018)
    DOI pdf

  15. Information Geometry for Model Identification and Parameter Estimation in Renewable Energy--DFIG Plant Case
    Saric A.T., Transtrum M.K., Stankovic A.M.
    IET Generation, Transmission, and Distribution 12(6) 1294 (2018)
    DOI pdf

  16. Information Geometry Approaches to Verification of Dynamic Models in Power System
    Transtrum M.K., Saric A.T., Stankovic A.M.
    IEEE Transactions on Power Systems 33.1 440-450 (2018)
    DOI pdf

  17. SRF Theory Developments from the Center for Bright Beams
    Liarte D.B., Arias T., Hall D.L., Liepe M., Sethna J.P., Sitaraman N., Pack A., Transtrum M.K.
    18th Int. Conf. on RF Superconductivity, Lanzhou, China (2017)
    pdf

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

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

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

  21. 2016

  22. Mechanisms of in vivo ribosome maintenance respond to nutrient signals
    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.
    Molecular and Cellular Proteomics, 16.2, 243-254 (2017)
    DOI pdf

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

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

  25. Measurement-Directed Reduction of Dynamic Models in Power Systems
    Transtrum M.K. Saric A.T., Stankovic A.M.
    IEEE Transactions on Power Systems. 32.3, 2243-2253 (2017).
    DOI pdf

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

  27. Information Geometry for Model Verification in Energy Systems
    Transtrum M.K., Saric A.T., Stankovic A.M.
    Power Systems Computation Conference, Genoa, 2016
    DOI pdf

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

  29. 2015

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

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

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

  33. A unified view of balanced truncation and singular perturbation approximations
    Pare P.E., Wilson A., Transtrum M.K., Warnick S
    American Control Conference, Chicago, 2015
    DOI pdf

  34. Sloppiness and the geometry of parameter space
    Mannakee B.K., Ragsdale A.P., Transtrum M.K., Gutenkunst R.N.
    Uncertainty in Biology Volume 17 of the series Studies in Mechanobiology, Tissue Engineering and Biomaterials
    DOI pdf

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

  36. 2014

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

  38. 2013

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

  40. Parameter Space Compression Underlies Emergent Theories and Predictive Models
    Machta B.B., Chachra R., Transtrum M.K., Sethna J.P.
    Science 342, 604-604 (2013)
    DOI pdf
    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).

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

  42. 2012

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

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

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

  46. Optimal Experiment Selection for Parameter Estimation in Biological Differential Equation Models
    Transtrum M.K. and Qiu P.
    BMC Bioinformatics. 13 1, 181, (2012)
    DOI pdf

  47. 2011

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

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

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

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

  52. 2010

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

  54. 2009

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

  56. 2007

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

  58. 2006

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

  60. 2005

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

Transtrum Group Theses

Masters Theses

  1. Computational Exploration of Vortex Nucleation In Type II Superconductors Using a Finite Element Method in Ginzburg-Landau Theory
    Alden Pack. Thesis. (2017)
    pdf

Undergraduate Theses

  1. K-Means Clustering Analysis of Geospatial Features: Optimizing the Acquisition of Training Data
    Brooks Butler. Thesis. (2018)
    pdf

  2. Parameter Reduction of the Hodgkin-Huxley Model of Action Potential Propagation
    Tyler Bahr. Thesis. (2018)
    pdf

  3. Algorithms for Inferring the Information Topology of Statistical Mechanics Models
    Kolten Barfuss. Thesis. (2017)
    pdf

  4. Model Reduction on the WNT Pathway Leads to Biological Adaptation
    Casie Gaza (Linfield College). Thesis. (2017)
    pdf

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

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

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