Publications


= Graduate student coauthor
* = Undergraduate student coauthor

    2018

  1. 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 (In Press)
    DOI pdf

  2. 2017

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

  4. 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 (In Press)
    DOI

  5. 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

  6. 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

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

  8. 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 in Energy and Society Powertech, Manchester (2017).
    DOI, pdf

  9. 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

  10. 2016

  11. 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

  12. 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

  13. 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

  14. 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

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

  16. 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

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

  18. 2015

  19. 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

  20. 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.

  21. 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.

  22. 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

  23. 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

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

  25. 2014

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

  27. 2013

  28. 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

  29. 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).

  30. 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

  31. 2012

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

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

  34. 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

  35. 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

  36. 2011

  37. 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.)

  38. 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

  39. 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

  40. 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

  41. 2010

  42. 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

  43. 2009

  44. 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

  45. 2007

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

  47. 2006

  48. 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

  49. 2005

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

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

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

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

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

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