Publications

Publications

† = Graduate student coauthor
* = Undergraduate student coauthor

Submitted

  • In vivo measurement of tissue-specific bias in protein degradation pathways
    Speirs M., Naylor B., Anderson C.†, Cutler K., Peelor F., Hamilton K. L., Millier B.,  Transtrum M.K. Anderson J., Price J.C.
  • Automatic detection of instances of focused crowd involvement at recreational events
    Todd E.*, Cook M.R.†, Pedersen K.†, Butler B.B.†, Zhao X.*, Liu C.*, Gee K.L.,  Transtrum M.K., Woolworth D.S., .
  • Symbolic Regression for Data-Driven Dynamic Model Refinement in Power Systems
    Saric A.T., Saric A.A.,  Transtrum M.K., Stankovic A.M.
  • Analysis Workflow for Transient Dynamics with Physics- and Data-Driven Models
    Saric A.T., Saric A.A.,  Transtrum M.K., Stankovic A.M.
  • Data-Driven Classification, Reduction, Parameter Identification and State Estimation in Hybrid Power Systems
    Saric A.T.,  Transtrum M.K., Stankovic A.M.
  • Analysis of Magnetic Vortex Dissipation in Sn-Segregated Boundaries in Nb3Sn SRF Cavities
    Carlson J.*, Pack A.R.  Transtrum M.K., Lee J., Seidman D.N., Liarte D.B., Sitaraman N., Senanian A., Sethna J.P., Arias T.A., Posen S.
    pdf
  • Ab Initio Study of Antisite Defects in Nb3Sn: Phase Diagram and Impact on Superconductivity
    Sitaraman N.S., Carlson J.*, Pack A.R. Porter R.D., Liepe M.U.,  Transtrum M.K., Arias T.A.
    pdf
  • Manifold boundaries give "gray-box" approximations of complex models
     Transtrum M.K.
  • Information topology identifies emergent model classes
     Transtrum M.K., Hart G., Qiu P.
    pdf
  • Performance theory: A complete metabolic theory of ecology
    Hansen L.D., Hansen C.W.,  Transtrum M.K., Hart G.L.W.

2020

  1. K-Means clustering of inputs to a geospatial model for optimizing acoustic data collection
    Butler B.B.†, Pedersen K.†, Maekawa C.*, Gee K.L., Todd E.*,  Transtrum M.K..
    Proceedings on Meetings in Acoustics (accepted)
  2. Probabilistic Extension of Flexible Hybrid State Estimation for Cyber-Physical Systems
    Svenda V.G., Stankovic A.M., Saric A.T.,  Transtrum M.K.
    International Journal of Electrical Power and Energy Systems (accepted)
  3. Vortex nucleation in superconductors within time-dependent Ginzburg-Landau theory in two and three dimensions: Role of surface defects and material inhomogeneities
    Pack A.R., Carlson J.* , Wadsworth S.*,  Transtrum M.K.
    Phys. Rev. B 101 144504 (2020)
    pdf DOI
  4. Flexible Hybrid State Estimation for Power Systems with Communication Irregularities
    Svenda V.G., Stankovic A.M., Saric A.T.,  Transtrum M.K.
    IET Generation, Transmission & Distribution (accepted)
  5. Data-driven Symbolic Regression for Identification of Nonlinear Dynamics in Power Systems
    Stankovic A.M., Saric A.A., Saric A.T.,  Transtrum M.K.
    IEEE Power and Energy Society General Meeting, Montreal, 2020
  6. Interleaving Physics- and Data-Driven Models for Power Systems Transient Dynamics
    Stankovic A.M., Saric A.A., Saric A.T.,  Transtrum M.K.
    Power Systems Computation Conference, Porto, Portugal, 2020
    Electric Power Systems Research 189 106824
    DOI

2019

  1. Probabilistic Network Observability of a Hybrid Power System with Communication Irregularities
    Svenda V.G., Stankovic A.M., Saric A.T.,  Transtrum M.K.
    North American Power Symposium (NAPS), Wichita, KS, 2019
  2. Network Reduction of Transient Stability Models using Partial Response Matching
    Francis B.L.†, Nuttal J.R*, Transtrum M.K., Saric A.T., Stankovic A.M.
    North American Power Symposium (NAPS), Wichita, KS, 2019
  3. Ab Initio Calculations on the Growth and Superconducting Properties of Nb₃Sn
    Sitaraman N.S., Arias, T., Cueva, P., Kelley M.M., Muller D.A., Carlson J.*, Pack A.R.  Transtrum M.K., Liepe M., Porter R.D., Sun Z
    International Conference on RF Superconductivity (19th), Dresden, Germany, 2019
    pdf
  4. Classifying crowd behavior at collegiate basketball games using acoustic data
    Butler B.A.*, Pedersen K.†, Cook M.R.†, Wadsworth S.W.*, Todd E.*, Stark D.*, Gee K.L.,  Transtrum M.K. Warnick S.
    Proceedings on Meetings in Acoustics 35 055006 (2018) 
    DOI pdf
  5. Machine learning-based ensemble model predictions of outdoor ambient sound levels
    Pederson K†, Gee K.L.,  Transtrum M.K. Butler B.A., James M.M., Salton A.R.
    Proceedings of Meetings on Acoutstics 35 022002 (2018)
    DOI pdf
  6. Unwinding the model manifold: choosing similarity measures to remove local minima in sloppy dynamical systems
    Francis B.L.†, Transtrum M.K. 
    Physical Review E 100 012206 
    DOI pdf
  7. Data Classification and Parameter Identification in Power Systems by Manifold Learning
    Saric A.T., Transtrum M.K., Stankovic A.M.
    IEEE Power and Energy Society Powertech, Milan (2019).
  8. Modeling magnetic correlations in magnetite nanoparticle assemblies using x-ray magnetic scattering data
    Rackham J., Newbold B., Kotter S., Smith D., Dalton G., Harrison R., Reid A.H.,  Transtrum M.K., Chesnel K
    AIP Advances  9 035033 (2019) 
    DOI pdf
  9. 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) 
    DOI
     See also a longer version here

2018

  1. 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) 
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. Experimental design and model reduction in systems biology 
    Jeong J., Zhuang Q., Transtrum M.K. Zhou E., Qiu P.
     Quantitative Biology 6(4) 287-306, 2018 
    DOI pdf
  8. 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
  9. Titration Calorimetry: From Concept to Application
    Hansen L.D., Transtrum M.K., Quinn C.F 
    Springer Briefs in Molecular Science
    DOI pdf
  10.  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

2017

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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)
  6. 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
  7. 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

2016

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems
    Transtrum M.K., Qiu P.
    PLoS Computational Biology 12(5): e1004915 (2016)
    DOI pdf

2015

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. Enzyme kinetics determined by single-injection isothermal titration calorimetry
     Transtrum M.K., Hansen, L.D., Quinn, C.
     Methods  76 194-200 (2015)
    DOI pdf

2014

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

2013

  1. 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
  2. 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).
  3. 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

2012

  1. Geodesic acceleration and the small-curvature approximation for nonlinear least squares
     Transtrum M.K. and Sethna J.P.
    arXiv:1207.4999
  2. Improvements to the Levenberg-Marquardt algorithm for nonlinear least squares minimization
     Transtrum M.K. and Sethna J.P.
    arXiv:1201.5885
  3. 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
  4. 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

2011

  1. 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.)
  2. 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
  3. 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
  4. 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 

2010

  1. 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

2009

  1. 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

2007

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

2006

  1. 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

2005

  1. 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 and Dissertations

Doctoral Dissertations

  1. Information Geometry and Model Reduction in Oscillatory and Networked Systems
    Benjamin Francis. Dissertation. (2020)
    pdf
  2. Superconductivity at its Limit: Simulating Superconductor Dynamics Near the Superconducting Superheating Field in Eilenberger and Ginzburg-Landau Theory
    Alden Pack. Dissertation. (2020)
    pdf

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. Computational Simulations of Temperature-Dependent Dynamics in Type II Superconductors Using a Material Specific Formulation of Ginzburg Landau Theory
    Aiden Harbick (William and Mary). Thesis. (2020)
    pdf

  2. Simulations of Magnetic Vortex Nucleation at Grain Boundaries in RF Superconducting Cavities
    Jared Carlson. Thesis. (2019)
    pdf

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

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

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

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

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

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

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