Department Publications

2020s

2024

95. Impact of submicron Nb₃Sn stoichiometric surface defects on high-field superconducting radiofrequency cavity performance

    Sarah A. Willson, Aiden V. Harbick^†, Liana Shpani, Van Do, Helena Lew-Kiedrowska, Matthias U. Liepe, Mark K. Transtrum, and S. J. Sibener

    Phys. Rev. Res. 6 (4), 043133 (2024).
    
96. Maximum entropy temperature selection via the equipartition theorem

    Jacob R. Nuttall^‡, Tracianne B. Neilsen, and Mark K. Transtrum

    185th Meeting of the Acoustical Society of America, (Sydney, Australia, December 2023). Proc. Meet. Acoust. 52 (1), 070004 (2024).
    
97. Information Geometry in Underwater Acoustics: Tutorial, Case Study, and Outlook

    Jay C. Spendlove^†, Michael C. Mortenson^†, Tracianne B. Neilsen, and Mark K. Transtrum

    J. Theor. Comput. Acoust. 32 (3), 2450011 (2024).
    
98. Learning Seabed Properties and Sensitivities from Ship Noise Spectrograms

    Michael C. Mortenson^†, Tracianne B. Neilsen, Mark K. Transtrum, and David P. Knobles

    OCEANS 2024 (Singapore, April 2024).
    
99. Toward a dynamic national transportation noise map: Modeling temporal variability of spectral traffic noise emission levels

    Mylan R. Cook^†, Kent L. Gee, Mark. K. Transtrum, and Shane V. Lympany

    J. Acoust. Soc. Am. 156 (3), 1693-1706 (2024).
    
100. Information geometry analysis example for absolute and relative transmission loss in a shallow ocean

     Jay C. Spendlove^†, Tracianne B. Neilsen, and Mark K. Transtrum

     JASA Express Letters 4 (7), 076001 (2024).
     
101. The training process of many deep networks explores the same low-dimensional manifold

     Jialin Mao, Itay Griniasty, Han Kheng Teoh, Rahul Ramesh, Rubing Yang, Mark K. Transtrum, James P. Sethna, and Pratik Chaudhari

     Proc. Natl. Acad. Sci. U. S. A. 121 (12), e2310002121 (2024).
     
102. Data-driven decomposition of crowd noise from indoor sporting events

     Mitchell C. Cutler^‡, Mylan R. Cook^†, Mark K. Transtrum, and Kent L. Gee

     J. Acoust. Soc. Am. 155 (2), 962-970 (2024).
     

2023

87. Sloppy model analysis identifies bifurcation parameters without normal form analysis

    Christian N. K. Anderson^† and Mark K. Transtrum

    Phys. Rev. E 108 (6), 064215 (2023).
    
88. Sloppy model analysis identifies bifurcation parameters without normal form analysis

    Christian N. K. Anderson^† and Mark K. Transtrum

    Phys. Rev. E 108 (6), 064215 (2023).
    
89. Toward a dynamic national transportation noise map: Modeling temporal variability of traffic volume

    Mylan R. Cook^†, Kent L. Gee, Mark. K. Transtrum, and Shane V. Lympany

    J. Acoust. Soc. Am. 154 (5), 2950-2958 (2023).
    
90. Recurrence Quantification Analysis of Crowd Sound Dynamics

    Shannon Proksch, Majerle Reeves, Kent Gee, Mark Transtrum, Chris Kello, and Ramesh Balasubramaniam

    Cogn. Sci. 47 (10), e13363 (2023).
    
91. Field-dependent nanospin ordering in monolayers of Fe₃O₄ nanoparticles throughout the superparamagnetic blocking transition

    Johnathon Rackham^†, Brittni Pratt^†, Dalton Griner^‡, Dallin Smith^‡, Yanping Cai^†, Roger G. Harrison, … Mark K. Transtrum, and Karine Chesnel (2 other authors)

    Phys. Rev. B 108 (10), 104415 (2023).
    
92. Feature selection for a continental-scale geospatial model of environmental sound levels

    Katrina Pedersen^†, Mark K. Transtrum, Kent L. Gee, Shane V. Lympany, Michael M. James, and Alexandria R. Salton

    J. Acoust. Soc. Am. 154 (2), 1168-1178 (2023).
    
93. Enhanced Surface Superconductivity of Niobium by Zirconium Doping

    Nathan S. Sitaraman, Zeming Sun, Benjamin L. Francis^†, Ajinkya C. Hire, Thomas Oseroff, Zhaslan Baraissov, … and Mark K. Transtrum (4 other authors)

    Phys. Rev. Applied 20 (1), 014064 (2023).
    
94. K-Means Clustering of 51 Geospatial Layers Identified for Use in Continental-Scale Modeling of Outdoor Acoustic Environments

    Katrina Pedersen^†, Ryan R. Jensen, Lucas K. Hall, Mitchell C. Cutler^‡, Mark K. Transtrum, Kent L. Gee, and Shane V. Lympany

    Appl. Sci.-Basel 13 (14), 8123 (2023).
    
95. ZrNb(CO) RF Superconducting Thin Film with High Critical Temperature in the Theoretical Limit

    Zeming Sun, Thomas Oseroff, Zhaslan Baraissov, Darrah K. Dare, Katrina Howard, Benjamin Francis^†, … Mark K. Transtrum, … (7 other authors)

    Adv. Electron. Mater. 9 (8), 2300151 (2023).
    
96. An app for nationwide dynamic traffic noise prediction

    Mylan Cook^†, Kent Gee, Mark Transtrum, and Shane Lympany

    INTER-NOISE and NOISE-CON Congress and Conference Proceedings, NOISE-CON23, (Grand Rapids, MI, May 2023).
97. Accurate broadband gradient estimates enable local sensitivity analysis of ocean acoustic models

    Michael C. Mortenson^†, Tracianne B. Neilsen, Mark K. Transtrum, and David P. Knobles

    J. Theor. Comput. Acoust. 31 (2), 2250015 (2023).
    
98. Information geometry for multiparameter models: new perspectives on the origin of simplicity

    Katherine N Quinn, Michael C Abbott, Mark K Transtrum, Benjamin B Machta, and James P Sethna

    Rep. Prog. Phys. 86 (3), 035901 (2023).
    

2022

75. Toward improving road traffic noise characterization: A reduced-order model for representing hourly traffic volume dynamics

    Mylan R. Cook^†, Kent L. Gee, Mark K. Transtrum, Shane V. Lympany, and Matthew F. Calton

    181st Meeting of the Acoustical Society of America, (Seattle, WA, December 2021).
    
76. Selecting simple, transferable models with the supremum principle

    Cody Petrie^‡, Christian Anderson^†, Casie Maekawa^‡, Travis Maekawa^‡, and Mark K. Transtrum

    Phys. Rev. Res. 4 (3), L032044 (2022).
    
77. Utilizing Nonequilibrium Isotope Enrichments to Dramatically Increase Turnover Measurement Ranges in Single Biopsy Samples from Humans

    Bradley C. Naylor^†, Christian N. K. Anderson^†, Marcus Hadfield^‡, David H. Parkinson^‡, Austin Ahlstrom^‡, Austin Hannemann^‡, Chad R. Quilling^‡, Kyle J. Cutler^‡, … Mark K. Transtrum, … (8 other authors)

    J. Proteome Res. 21 (11), 2703-2714 (2022).
    
78. Bayesian, frequentist, and information geometric approaches to parametric uncertainty quantification of classical empirical interatomic potentials

    Yonatan Kurniawan^†, Cody L. Petrie^‡, Kinamo J. Williams^‡, Mark K. Transtrum, Ellad B. Tadmor, Ryan S. Elliott, Daniel S. Karls, and Mingjian Wen

    J. Chem. Phys. 156 (21), 214103 (2022).
    
79. Integration of Physics- and Data-Driven Power System Models in Transient Analysis After Major Disturbances

    Aleksandar A. Sarić, Mark K. Transtrum, Andrija T. Sarić, and Aleksandar M. Stanković

    IEEE Syst. J. 17 (1), 479-490 (2022).
    
80. Application of a spectral-based wind noise reduction method to acoustical measurements

    Mylan R. Cook^†, Kent L. Gee, Mark K. Transtrum, Shane V. Lympany, and Matt Calton

    181st Meeting of the Acoustical Society of America, (Seattle, WA, December 2021). Proc. Meet. Acoust. 45, 045002 (2022).
    
81. Modeling Live Crowd Emotion Dynamics for State Estimation and Prediction

    Brooks A. Butler^†, Philip E. Paré^†, Mark K. Transtrum, and Sean Warnick

    2021 IEEE Conference on Control Technology and Applications, (San Diego, CA, Aug 2021).
    
82. State Estimation Model Reduction through the Manifold Boundary Approximation Method

    Vanja G. Svenda, Mark K Transtrum, Benjamin L. Francis, Andrija T. Saric, and Aleksandar M Stankovic

    IEEE Trans. Power Syst. 37 (1), 272-281 (2022).
    

2021

67. Piecemeal Reduction of Models of Large Networks

    Benjamin L. Francis^†, Mark K. Transtrum, Andrija T. Sarić, and Aleksandar M. Stanković

    2021 60th IEEE Conference on Decision and Control (CDC), (Austin, TX, December 2021).
    
68. Validating two geospatial models of continental-scale environmental sound levels

    Katrina Pedersen^†, Mark K. Transtrum, Kent L. Gee, Shane V. Lympany, Michael M. James, and Alexandria R. Salton

    JASA Express Letters 1 (12), 122401 (2021).
    
69. Simultaneous Determination of Equilibrium Constants, Enthalpy Changes and Stoichiometries by Titration Calorimetry

    Lee D. Hansen, Mark K. Transtrum, and Jason D. Kenealey

    Chapter 5 in Gibbs Energy and Helmholtz Energy: Liquids, Solutions and Vapours, edited by Emmerich Wilhelm and Trevor Letcher, Royal Society of Chemistry (2021).
    
70. Automatic classification and reduction of wind noise in spectral data

    Mylan R. Cook^†, Kent L. Gee, Mark K. Transtrum, Shane V. Lympany, and Matt Calton

    JASA Express Letters 1 (6), 063602 (2021).
    
71. Examining wind noise reduction effects of windscreens and microphone elevation in outdoor acoustical measurements

    Zachary Jones^†, Mylan R. Cook^†, Kent L. Gee, Mark K. Transtrum, Shane V. Lympany, Matthew F. Calton, and Michael M. James

    179th Meeting of the Acoustical Society of America, Acoustics Virtually Everywhere (December 2020). Proc. Meet. Acoust. 42 (1), 045007 (2021).
    
72. Symbolic Regression for Data-Driven Dynamic Model Refinement in Power Systems

    Andrija T. Sarić, Aleksandar A. Sarić, Mark K. Transtrum, and Aleksandar M. Stanković

    IEEE Trans. Power Syst. 36 (3), 2390-2402 (2021).
    
73. Data-Driven Classification, Reduction, Parameter Identification and State Extension in Hybrid Power Systems

    Andrija T. Sarić, Mark K. Transtrum, and Aleksandar M. Stanković

    IEEE Trans. Power Syst. 36 (3), 2222-2233 (2021).
    
74. Effect of the density of states at the Fermi level on defect free energies and superconductivity: A case study of Nb₃Sn

    Nathan S. Sitaraman, Michelle M. Kelley, Ryan D. Porter, Matthias U. Liepe, Tomás A. Arias, Jared Carlson^†, Alden R. Pack^†, Mark K. Transtrum, … (1 other authors)

    Phys. Rev. B 103 (11), 115106 (2021).
    
75. Analysis of magnetic vortex dissipation in Sn-segregated boundaries in Nb₃Sn superconducting RF cavities

    Jared Carlson, Alden Pack, Mark K. Transtrum, Jaeyel Lee, David N. Seidman, Danilo B. Liarte, … (6 other authors)

    Phys. Rev. B 103 (2), 024516 (2021).
    

2020

58. Automatic detection of instances of focused crowd involvement at recreational events

    Eric Todd^‡, Mylan R. Cook^†, Katrina Pedersen^†, David S. Woolworth, Brooks A. Butler^‡, Xin Zhao^‡, Colt Liu^‡, Kent L. Gee, Mark K. Transtrum, … (1 other authors)

    178th Meeting of the Acoustical Society of America, (San Diego, CA, December 2019). Proc. Meet. Acoust. 39, 040003 (2020).
    
59. Interleaving physics- and data-driven models for power system transient dynamics

    Aleksandar M. Stanković, Aleksandar A. Sarić, Andrija T. Sarić, and Mark K. Transtrum

    Electr. Power Syst. Res. 189, 106824 (2020).
    
60. Probabilistic extension of flexible hybrid state estimation for cyber-physical systems

    Vanja G. Švenda, Aleksandar M. Stanković, Andrija T. Sarić, and Mark K. Transtrum

    Int. J. Electr. Power Energy Syst. 122, 106179 (2020).
    
61. K-Means clustering of inputs to a geospatial model for optimizing acoustic data collection

    Brooks A. Butler^‡, Katrina Pedersen^†, Casie Maekawa, Kent L. Gee, Mark K. Transtrum, Michael M. James, and Alexandria R. Salton

    176th Meeting of Acoustical Society of America, 2018 Acoustics Week in Canada (Victoria, Canada, November 2018). Proc. Meet. Acoust. 35 (1), 055008 (2020).
    
62. Data-driven Symbolic Regression for Identification of Nonlinear Dynamics in Power Systems

    Alex M. Stanković, Aleksandar A. Sarić, Andrija T. Sarić, and Mark K. Transtrum

    2020 IEEE Power & Energy Society General Meeting, (Montreal, Canada, August 2020).
    
63. Vortex nucleation in superconductors within time-dependent Ginzburg-Landau theory in two and three dimensions: Role of surface defects and material inhomogeneities

    Alden R. Pack^†, Jared Carlson^‡, Spencer Wadsworth^‡, and Mark K. Transtrum

    Phys. Rev. B 101 (14), 144504 (2020).
    
64. Flexible hybrid state estimation for power systems with communication irregularities

    V. G. Švenda, A. M. Stanković, A. T. Sarić, and M. K. Transtrum

    IET Gener. Transm. Distrib. 14 (11), 2111-2119 (2020).
    

2010s

2019

51. Network Reduction in Transient Stability Models using Partial Response Matching

    Benjamin L. Francis^‡, Jacob R. Nuttall^‡, Mark K. Transtrum, Andrija T. Sarić, and Aleksandar M. Stanković

    2019 North American Power Symposium (NAPS), (Wichita, Kansas, October 2019).
    
52. Model Boundary Approximation Method as a Unifying Framework for Balanced Truncation and Singular Perturbation Approximation

    P. E. Paré, D. Grimsman, A. T. Wilson, M. K. Transtrum, and S. Warnick

    IEEE Trans. Autom. Control 64 (11), 4796-4802 (2019).
    
53. Machine learning-based ensemble model predictions of outdoor ambient sound levels

    Katrina Pedersen^†, Mark K. Transtrum, Kent L. Gee, Brooks A. Butler^‡, Michael M. James, and Alexandria R. Salton

    176th Meeting of Acoustical Society of America; 2018 Acoustics Week in Canada, (Victoria, Canada, November 2018). Proc. Meet. Acoust. 35 (1), 022002 (2019).
    
54. Classifying crowd behavior at collegiate basketball games using acoustic data

    Brooks A. Butler^‡, Katrina Pedersen^†, Mylan R. Cook^†, Spencer G. Wadsworth^‡, Eric Todd^‡, Dallen Stark^‡, Kent L. Gee, Mark K. Transtrum, … (1 other authors)

    176th Meeting of Acoustical Society of America; 2018 Acoustics Week in Canada, (Victoria, Canada, November 2018). Proc. Meet. Acoust. 35 (1), 055006 (2019).
    
55. Data Classification and Parameter Identification in Power Systems by Manifold Learning

    Andrija T. Sarić, Mark K. Transtrum, and Aleksandar M. Stanković

    2019 IEEE Milan PowerTech, (Milan, Italy, June 2019).
    
56. Unwinding the model manifold: Choosing similarity measures to remove local minima in sloppy dynamical systems

    Benjamin L. Francis^† and Mark K. Transtrum

    Phys. Rev. E 100 (1), 012206 (2019).
    
57. Modeling inter-particle magnetic correlations in magnetite nanoparticle assemblies using x-ray magnetic scattering data

    Johnathon Rackham^†, Brittni Newbold^‡, Steve Kotter^‡, Dallin Smith^‡, Dalton Griner^‡, Roger Harrison, … Mark Transtrum, and Karine Chesnel (1 other authors)

    AIP Advances 9 (3), 035033 (2019).
    
58. Optimal experimental design for machine learning using the Fisher information

    Tracianne B. Neilsen, David F. Van Komen^‡, Mark K. Transtrum, Makenzie B. Allen^‡, and David P. Knobles

    Proc. Meet. Acoust. 35 (1), 055004 (2019).
    
59. Data-Driven Dynamic Equivalents for Power System Areas from Boundary Measurements

    Andrija T. Sarić, Mark T. Transtrum, and Aleksandar M. Stanković

    IEEE Trans. Power Syst. 34 (1), 360-370 (2019).
    

2018

42. Simultaneous Global Identification of Dynamic and Network Parameters in Transient Stability Studies

    Mark K. Transtrum, Benjamin L. Francis^†, Andrija T. Saric, and Aleksandar M. Stankovic

    2018 IEEE Power & Energy Society General Meeting (PESGM). (Portland, OR, August 2018).
    
43. Influence of Communication Irregularities and Co-simulation on Hybrid Power System State Estimation

    Vanja G. Švenda, Alex M. Stanković, Andrija T. Sarić, and Mark K. Transtrum

    2018 IEEE PES Innovative Smart Grid Technologies Conference Europe (ISGT-Europe). (Sarajevo, Bosnia-Herzegovina, October 2018).
    
44. Effect of extreme temperatures on soil: A calorimetric approach

    Lee D. Hansen, Nieves Barros, Mark K. Transtrum, Jose A. Rodríguez-Añón, Jorge Proupín, Verónica Piñeiro, Ander Arias-González, and Nahia Gartzia

    Thermochim. Acta 670, 128-135 (2018).
    
45. Geometrically Motivated Reparameterization for Identifiability Analysis in Power Systems Models

    Mark K. Transtrum, Benjamin L. Francis^†, Clifford C. Youn, Andrija T. Saric, and Aleksander M. Stankovic

    2018 North American Power Symposium (NAPS). (Fargo, ND, September 2018).
    
46. The Spectrum of Mechanism-Oriented Models and Methods for Explanations of Biological Phenomena

    C. Anthony Hunt, Ahmet Erdemir, William W. Lytton, Feilim Mac Gabhann, Edward A. Sander, Mark K. Transtrum, and Lealem Mulugeta

    Processes 6 (5), 56 (2018).
    
47. Experimental design and model reduction in systems biology

    Jenny E. Jeong, Qinwei Zhuang, Mark K. Transtrum, Enlu Zhou, and Peng Qiu

    Quant. Biol. 6 (4), 287-306 (2018).
    
48. Titration Calorimetry: From Concept to Application

    Lee D. Hansen, Mark K. Transtrum, and Colette F. Quinn

    Springer (2018)
    
49. Maximizing the information learned from finite data selects a simple model

    Henry H. Mattingly, Mark K. Transtrum, Michael C. Abbott, and Benjamin B. Machta

    Proc. Natl. Acad. Sci. U. S. A. 115 (8), 1760-1765 (2018).
    
50. Calorimetric Methods for Measuring Stability and Reusability of Membrane Immobilized Enzymes

    Marco Mason^†, Matteo Scampicchio, Colette F. Quinn, Mark K. Transtrum, Nicholas Baker^‡, Lee D. Hansen, and Jason D. Kenealey

    J. Food Sci. 83 (2), 326-331 (2018).
    
51. Hybrid power system state estimation with irregular sampling

    Aleksandar M. Stanković, Vanja Švenda, Andrija T. Sarić, and Mark K. Transtrum

    Power & Energy Society General Meeting, IEEE (Chicago, IL, July 2017)
    
52. SRF Theory Developments from the Center for Bright Beams

    D. B. Liarte, T. Arias, D. L. Hall, M. Liepe, J. P. Sethna, N. Sitaraman, A. Pack^†, and M. K. Transtrum

    18th International Conference on RF Superconductivity, (Lanzhou, China, 2017).
    
53. Information Geometry Approach to Verification of Dynamic Models in Power Systems

    M. K. Transtrum, A. T. Saric, and A. M. Stankovic

    IEEE Trans. Power Syst. 33 (1), 440-450 (2018).
    

2017

30. Information geometry for model identification and parameter estimation in renewable energy – DFIG plant case

    Andrija T. Sarić, Mark K. Transtrum, and Aleksandar M. Stanković

    IET Gener. Transm. Distrib. 12 (6), 1294-1302 (2017).
    
31. Information geometry for model reduction of dynamic loads in power systems

    Clifford C. Youn, Andrija T. Sarić, Mark K. Transtrum, and Aleksandar M. Stanković

    2017 IEEE Manchester PowerTech (Manchester, UK, June 2017).
    
32. Mechanisms of in vivo ribosome maintenance change in response to nutrient signals

    Andrew D. Mathis^†, Bradley C. Naylor^†, Richard H. Carson^†, Eric Evans^‡, Justin Harwell^‡, Jared Knect^‡, Eric Hexem^‡, … Mark K. Transtrum, … (5 other authors)

    Mol. Cell. Proteomics 16 (2), 243-254 (2017).
    
33. Theoretical estimates of maximum fields in superconducting resonant radio frequency cavities: stability theory, disorder, and laminates

    Danilo B. Liarte, Sam Posen, Mark K. Transtrum, Gianluigi Catelani, Matthias Liepe, and James P. Sethna

    Supercond. Sci. Technol. 30 (3), 033002 (2017).
    

2016

26. The Limitations of Model-Based Experimental Design and Parameter Estimation in Sloppy Systems

    Andrew White^‡, Malachi Tolman^†, Howard D. Thames, Hubert Rodney Withers, Kathy A. Mason, and Mark K. Transtrum

    PLoS Comput. Biol. 12, 1-12 (2016).
    
27. Ginzburg-Landau theory of the superheating field anisotropy of layered superconductors

    Danilo B. Liarte, Mark K. Transtrum, and James P. Sethna

    Phys. Rev. B 94 (14), 144504 (2016).
    
28. Measurement-Directed Reduction of Dynamic Models in Power Systems

    Mark K. Transtrum , Andrija T. Saric, and Aleksandar M. Stankovic

    IEEE Trans. Power Syst. 32 (3), 2243-2253 (2016).
    
29. Dynamic Model Estimation for Power System Areas from Boundary Measurements

    Andrija T. Sarić, Mark K. Transtrum, and Aleksandar M. Stanković

    IEEE Power in Energy and Society General Meeting, (Boston, MA, July 2016).
    
30. Information geometry for model verification in energy systems

    Mark K. Transtrum, Andrija T. Saric, and Alex M. Stankovic

    2016 Power Systems Computation Conference (PSCC), (Genova, Italy, June 2016).
    
31. Bridging Mechanistic and Phenomenological Models of Complex Biological Systems

    Mark K. Transtrum and Peng Qiu

    PLoS Comput. Biol. 12 (5), 1-34 (2016).
    
32. Enzyme-catalyzed and binding reaction kinetics determined by titration calorimetry

    Lee D. Hansen, Mark K. Transtrum, Colette Quinn, and Neil Demarse

    Biochim. Biophys. Acta-Gen. Subj. 1860 (5), 957-966 (2016).
    

2015

19. Shielding Superconductors with Thin Films as Applied to rf Cavities for Particle Accelerators

    Sam Posen, Mark K. Transtrum, Gianluigi Catelani, Matthias U. Liepe, and James P. Sethna

    Phys. Rev. Applied 4, 044019 (2015).
    
20. Sloppiness and the Geometry of Parameter Space

    Brian K. Mannakee, Aaron P. Ragsdale, Mark K. Transtrum, and Ryan N. Gutenkunst

    Uncertainty in Biology, Volume 17 of the series Studies in Mechanobiology, Tissue Engineering and Biomaterials
    
21. A unified view of Balanced Truncation and Singular Perturbation Approximations

    Philip E. Paré, Alma T. Wilson, Mark K. Transtrum, and Sean C. Warnick

    American Control Conference, (Chicago, IL, July 2015), pp 1984-1989.
    
22. Perspective: Sloppiness and emergent theories in physics, biology, and beyond

    Mark K. Transtrum, Benjamin B. Machta, Kevin S. Brown, Bryan C. Daniels, Christopher R. Myers, and James P. Sethna

    J. Chem. Phys. 143 (1), 010901 (2015).
    
23. Enzyme kinetics determined by single-injection isothermal titration calorimetry

    Mark K. Transtrum, Lee D. Hansen, and Colette Quinn

    Methods 76, 194-200 (2015).
    

2014

14. Model Reduction by Manifold Boundaries

    Mark K. Transtrum and Peng Qiu

    Phys. Rev. Lett. 113, 098701 (2014).
    

2013

13. Parameter Space Compression Underlies Emergent Theories and Predictive Models

    Benjamin B. Machta, Ricky Chachra, Mark K. Transtrum, and James P. Sethna

    Science 342 (6158), 604-607 (2013).
    
14. Use of the LQ model with large fraction sizes results in underestimation of isoeffect doses

    Tommy Sheu, Jessica Molkentine, Mark K. Transtrum, Thomas A. Buchholz, Hubert Rodney Withers, Howard D. Thames, and Kathy A. Mason

    Radiother. Oncol. 109 (1), 21-25 (2013).
    

2012

11. Structural susceptibility and separation of time scales in the van der Pol oscillator

    Ricky Chachra, Mark K. Transtrum, and James P. Sethna

    Phys. Rev. E 86 (2), 026712 (2012).
    
12. Optimal experiment selection for parameter estimation in biological differential equation models

    Mark K Transtrum and Peng Qiu

    BMC Bioinformatics 13 (1), 181 (2012).
    

2011

9. Comment on “Sloppy models, parameter uncertainty, and the role of experimental design”

   Ricky Chachra, Mark K. Transtrum, and James P. Sethna

   Mol. BioSyst. 7, 2522 (2011).
   
10. Superheating field of superconductors within Ginzburg-Landau theory

    Mark K. Transtrum, Gianluigi Catelani, and James P. Sethna

    Phys. Rev. B 83 (9), 094505 (2011).
    
11. Geometry of nonlinear least squares with applications to sloppy models and optimization

    Mark K. Transtrum, Benjamin B. Machta, and James P. Sethna

    Phys. Rev. E 83 (3), 036701 (2011).
    
12. Riemann manifold Langevin and Hamiltonian Monte Carlo methods

    Mark K. Transtrum, Yanjiun Chen, Benjamin B. Machta, James P. Sethna, and Ryan Gutenkunst

    Read before The Royal Statistical Society at a meeting organized by the Research Section (October 2010). See discussion on page 199. J. Roy. Stat. Soc. B 73 (2), 123-214 (2011).
    

2010

5. Why are Nonlinear Fits to Data so Challenging?

   Mark K. Transtrum, Benjamin B. Machta, and James P. Sethna

   Phys. Rev. Lett. 104 (6), 060201 (2010).
   

2000s

2009

4. An Analytic Iterative Approach to Solving the Time-Independent Schrodinger Equation

   Chad Junkermeier^†, Mark Transtrum^‡, and Manuel Berrondo

   Int. J. Quantum Chem. 109 (5), 982-998 (2009).
   

2007

3. Beyond the quantum in Snyder space

   J. F. S. Van Huele and M. K. Transtrum^‡

   Beyond the Quantum, (June 2006,Leiden, The Netherlands), 235-243.
   

2006

2. A perturbative approach to Snyder space with applications

   Mark K. Transtrum^‡ and Jean-François S. Van Huele

   J. Phys. A 39 (48), 14985-14996 (2006).
   

2005

1. Commutation relations for functions of operators

   Mark K. Transtrum and Jean-François S. Van Huele

   J. Math. Phys. 46 (6), 063510 (2005).
   

^‡Undergraduate Student Author

^†Graduate Student Author