Preprints:
Jung, J.K., Dreyer, K.S., Dray, K.E., Muldoon, J.J., George, J., Shirman, S., Cabezas, M.D., D'Aquino, A.E., Verosloff, M.S., Seki, K., Rybnicky, G.A., Alam, K. K., Bagheri N. B., Jewett, M. C., Leonard, J. N., Mangan, N. M. Lucks, J. B., 2024. Developing, characterizing and modeling CRISPR-based point-of-use pathogen diagnostics. bioRxiv, pp.2024-07.
VanBelzen, J., Sakelaris, B., Brickner, D.G., Marcou, N., Riecke, H., Mangan, N. and Brickner, J.H., 2024. Chromatin endogenous cleavage provides a global view of RNA polymerase II transcription kinetics. bioRxiv, pp.2024-07.
J. D. George, S. Y. Jung, N. M. Mangan. "Walking into the complex plane to ‘order’ better time integrators." arXiv:2110.04402 [math.NA] 2021. (Video abstract for Undergraduate Research Conference)
VanBelzen, J., Sakelaris, B., Brickner, D.G., Marcou, N., Riecke, H., Mangan, N. and Brickner, J.H., 2024. Chromatin endogenous cleavage provides a global view of RNA polymerase II transcription kinetics. bioRxiv, pp.2024-07.
J. D. George, S. Y. Jung, N. M. Mangan. "Walking into the complex plane to ‘order’ better time integrators." arXiv:2110.04402 [math.NA] 2021. (Video abstract for Undergraduate Research Conference)
Peer Reviewed Publications
Karim, A.S., Brown, D.M., Archuleta, C.M., Grannan, S., Aristilde, L., Goyal, Y., Leonard, J.N., Mangan, N.M., Prindle, A., Rocklin, G.J. and Tyo, K.J., 2024. Deconstructing synthetic biology across scales: a conceptual approach for training synthetic biologists. Nature Communications, 15(1), p.5425.
K. P. Leisman, C. Owen, M. M. Warns, A. Tiwari, G. (Z.) Bian, S. M. Owens, C. Catlett, A. Shrestha, R. Poretsky, A. I. Packman, N. M. Mangan. "A modeling pipeline to relate municipal wastewater surveillance and regional public health data." Water Research, 252, 121178 (2024).
Tsuboyama, K., Dauparas, J., Chen, J., Laine, E., Mohseni Behbahani, Y., Weinstein, J.J., Mangan, N.M., Ovchinnikov, S. and Rocklin, G.J. Mega-scale experimental analysis of protein folding stability in biology and design. Nature, 620 (7973), pp.434-444. (2023)
H. Ribera, S. Shirman, A. V. Nguyen, N. M. Mangan. "Model selection of chaotic systems from data with hidden variables using sparse data assimiliation." Chaos 32, 063101 (2022).
Nyaanga, J., Shirman, S., Mangan, N.M. and Andersen, E.C., 2022. Characterization of larval growth in C. elegans cuticle mutants. MicroPubl Biol, 2022.
C. Fei, A, T. Wilson, N. M. Mangan, N. S. Wingreen, M. C. Jonikas. "Modelling the pyrenoid-based CO2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops." Nature Plants. Vol. 8, pg 583-595 (2022) (Blog post in Nature's Bioengineering Community)
N.W. Kennedy, C.E. Mills, C.H. Abrahamson, A. Archer, M.C. Jewett, N.M. Mangan, D. Tullman-Ercek. "Linking the Salmonella enterica 1, 2-propanediol utilization bacterial microcompartment shell to the enzymatic core via the shell protein PduB", Jornal of Bacteriology, e00576-21, 2022. (Preprint: bioRxiv:10.1101/2021.10.27.466122)
C.E. Mills, C. Waltmann, A.G. Archer, N.W. Kennedy, C.H. Abrahamson, A.D. Jackson, E.W. Roth, S. Shirman, M.C. Jewett, N.M. Mangan, D. Tullman-Ercek. "Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial
metabolosome morphology." Nature Communications, 13, 3746 (2022).
J. Nyaanga, C. Goss, G. Zhang, H. N. Ahmed, E. J. Andersen, I.R. Miller, J. K. Rozenich, I. L. Swarthout, J. A. Vaughn, N. M. Mangan, S. Shirman, E. C. Andersen. "Changes in body shape implicate cuticle stretch in C. elegans growth control." Cells & Development, Vol 170, 203780 (2022) (Preprint: bioRxiv: 10.1101/2021.04.01.438121)
K. Dray, J. J. Muldoon, N. M. Mangan, N. Bagheri, J. N. Leonard."GAMES: A dynamic model development workflow for rigorous characterization of synthetic genetic systems." ACS synthetic biology 11.2 (2022): 1009-1029. (Preprint: bioRxiv: 10.1101/2021.10.20.465216)
N. M. Mangan, T. Askham, S. L. Brunton, J. N. Kutz, J. L. Proctor, "Model Selection for hybrid dynamical systems via sparse regression," Proc. R. Soc. London A Math. Phys. Eng. Sci. Vol 475, No 2223 (2019).
C. Sun, N Mangan, M Dong, H. G. Winful, S. T. Cundiff, J. N. Kutz. "Stable numerical schemes for nonlinear dispersive equations with counter-propagation and gain dynamics," JOSA B. Vol. 26, No. 19, pp. 3263-3274. (2019)
C Jakobson, D Tullman-Ercek, N Mangan. “Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory.” Scientific Reports. Vol. 8, Article 8196, (2018)
T. G. Boatman, N. M. Mangan, T. Lawson, and R. J. Geider. "Inorganic carbon and pH dependency of Trichodesmium’s photosynthetic rates." Journal of Experimental Botany. (2018)
N. M. Mangan, J. N. Kutz, S. L. Brunton, and J. L. Proctor. "Model selection for dynamical systems via sparse regression and information criteria." Proc. R. Soc. London A Math. Phys. Eng. Sci. Vol 437, No 2204, (2017)
C. M. Jakobson, M. F. Slininger, D. Tullman-Ercek, and N. M. Mangan, “A Systems-Level Model Reveals That 1, 2-Propanediol Utilization Microcompartments Enhance Pathway Flux Through Intermediate Sequestration.,” PloS Comp. Bio., vol 13, no 5, p.e1005525, 2017.
M. Dong, N. M. Mangan, J. N. Kutz, S. T. Cundiff, H. G. Winful. "Traveling Wave Model for Frequency Comb Generation in Single Section Quantum Well Diode Lasers." IEEE Journal of Quantum Electronics 53 (6), 1-11, 2017
R. E. Brandt, N. M. Mangan, J. V. Li, Y. S. Lee, and T. Buonassisi. "Determining interface propterties limiting open-circuit voltage in heterojunction solar cells" J. Appl. Phys., vol 121, p. 185301, 2017.
N. M. Mangan, S. L. Brunton, J. L. Proctor, and J. N. Kutz, “Inferring biological networks by sparse identification of nonlinear dynamics,” IEEE Transactions on Mol. And Biol. and Multi-Scale Comm. Vol 2, No 1, 2017.
A. Polizzotti, A. Faghaninia, J. R. Poindexter, L. Nienhaus, V. Steinmann, R. LZ. Hoye, Al. Felten, A. Deyine, N. M. Mangan, J.-P. Correa-Baena, S. S. Shin, S. Jaffer, M. G. Bawendi, C. Lo, T. Buonassisi. "Improving Carrier Lifetime of Tin Sulfide via Prediction and Mitigation of Harmful Point Defects." J. Phys. Chem. Lett. Vol. 8, p. 3661-3667, 2017.
N. M. Mangan*, A. Flamholz*, R. D. Hood, R. Milo, and D. F. Savage, “pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism,” Proc. Natl. Acad. Sci., p. 201525145, 2016. (*authors contributed equally)
N. M. Mangan, R. E. Brandt, V. Steinmann, R. Jaramillo, C. Yang, J. R. Poindexter, R. Chakraborty, H. H. Park, X. Zhao, R. G. Gordon, and Tonio Buonassisi, “Framework to predict optimal buffer layer pairing for thin film solar cell absorbers: A case study for tin sulfide/zinc oxysulfide,” J. Appl. Phys., vol. 118, p. 115102, 2015.
D. B. Needleman, J. P. Mailoa, R. E. Brandt, N. M. Mangan, and T. Buonassisi, “Sensitivity Analysis of Optical Metrics for Spectral Splitting Photovoltaic Systems: A Case Study,” IEEE J. Photovoltaics, vol. 5, no. 5, pp. 1380–1388, 2015.
R. Chakraborty, V. Steinmann, N. M. Mangan, R. E. Brandt, J. R. Poindexter, R. Jaramillo, J. P. Mailoa, K. Hartman, A. Polizzotti, C. Yang, and others, “Non-monotonic effect of growth temperature on carrier collection in SnS solar cells,” Appl. Phys. Lett., vol. 106, no. 20, p. 203901, 2015.
M.-J. Sher, N. M. Mangan, M. J. Smith, Y.-T. Lin, S. Marbach, T. M. Schneider, S. Gradečak, M. P. Brenner, and E. Mazur, “Femtosecond-laser hyperdoping silicon in an SF6 atmosphere: Dopant incorporation mechanism,” J. Appl. Phys., vol. 117, no. 12, p. 125301, Mar. 2015.
Y.-T. Lin, N. Mangan, S. Marbach, T. M. Schneider, G. Deng, S. Zhou, M. P. Brenner, and E. Mazur, “Creating femtosecond-laser-hyperdoped silicon with a homogeneous doping profile,” Appl. Phys. Lett., vol. 106, no. 6, p. 62105, 2015.
N. Mangan and M. Brenner, “Systems analysis of the CO2 concentrating mechanism in cyanobacteria,” Elife, 2014.
N. Mangan, C. Reichhardt, and C. J. O. Reichhardt, “Reversible to irreversible flow transition in periodically driven vortices,” Phys. Rev. Lett., vol. 100, no. 18, 2008.
Y. Y. Kievsky, B. Carey, S. Naik, N. Mangan, D. Ben-Avraham, and I. Sokolov, “Dynamics of molecular diffusion of rhodamine 6G in silica nanochannels,” J. Chem. Phys., vol. 128, no. 15, 2008.
M. Reason, Y. Jin, H. A. McKay, N. Mangan, D. Mao, R. S. Goldman, X. Bai, and C. Kurdak, “Influence of N on the electronic properties of GaAsN alloy films and heterostructures,” J. Appl. Phys., vol. 102, no. 10, 2007.
K. P. Leisman, C. Owen, M. M. Warns, A. Tiwari, G. (Z.) Bian, S. M. Owens, C. Catlett, A. Shrestha, R. Poretsky, A. I. Packman, N. M. Mangan. "A modeling pipeline to relate municipal wastewater surveillance and regional public health data." Water Research, 252, 121178 (2024).
Tsuboyama, K., Dauparas, J., Chen, J., Laine, E., Mohseni Behbahani, Y., Weinstein, J.J., Mangan, N.M., Ovchinnikov, S. and Rocklin, G.J. Mega-scale experimental analysis of protein folding stability in biology and design. Nature, 620 (7973), pp.434-444. (2023)
H. Ribera, S. Shirman, A. V. Nguyen, N. M. Mangan. "Model selection of chaotic systems from data with hidden variables using sparse data assimiliation." Chaos 32, 063101 (2022).
Nyaanga, J., Shirman, S., Mangan, N.M. and Andersen, E.C., 2022. Characterization of larval growth in C. elegans cuticle mutants. MicroPubl Biol, 2022.
C. Fei, A, T. Wilson, N. M. Mangan, N. S. Wingreen, M. C. Jonikas. "Modelling the pyrenoid-based CO2-concentrating mechanism provides insights into its operating principles and a roadmap for its engineering into crops." Nature Plants. Vol. 8, pg 583-595 (2022) (Blog post in Nature's Bioengineering Community)
N.W. Kennedy, C.E. Mills, C.H. Abrahamson, A. Archer, M.C. Jewett, N.M. Mangan, D. Tullman-Ercek. "Linking the Salmonella enterica 1, 2-propanediol utilization bacterial microcompartment shell to the enzymatic core via the shell protein PduB", Jornal of Bacteriology, e00576-21, 2022. (Preprint: bioRxiv:10.1101/2021.10.27.466122)
C.E. Mills, C. Waltmann, A.G. Archer, N.W. Kennedy, C.H. Abrahamson, A.D. Jackson, E.W. Roth, S. Shirman, M.C. Jewett, N.M. Mangan, D. Tullman-Ercek. "Vertex protein PduN tunes encapsulated pathway performance by dictating bacterial
metabolosome morphology." Nature Communications, 13, 3746 (2022).
J. Nyaanga, C. Goss, G. Zhang, H. N. Ahmed, E. J. Andersen, I.R. Miller, J. K. Rozenich, I. L. Swarthout, J. A. Vaughn, N. M. Mangan, S. Shirman, E. C. Andersen. "Changes in body shape implicate cuticle stretch in C. elegans growth control." Cells & Development, Vol 170, 203780 (2022) (Preprint: bioRxiv: 10.1101/2021.04.01.438121)
K. Dray, J. J. Muldoon, N. M. Mangan, N. Bagheri, J. N. Leonard."GAMES: A dynamic model development workflow for rigorous characterization of synthetic genetic systems." ACS synthetic biology 11.2 (2022): 1009-1029. (Preprint: bioRxiv: 10.1101/2021.10.20.465216)
N. M. Mangan, T. Askham, S. L. Brunton, J. N. Kutz, J. L. Proctor, "Model Selection for hybrid dynamical systems via sparse regression," Proc. R. Soc. London A Math. Phys. Eng. Sci. Vol 475, No 2223 (2019).
C. Sun, N Mangan, M Dong, H. G. Winful, S. T. Cundiff, J. N. Kutz. "Stable numerical schemes for nonlinear dispersive equations with counter-propagation and gain dynamics," JOSA B. Vol. 26, No. 19, pp. 3263-3274. (2019)
C Jakobson, D Tullman-Ercek, N Mangan. “Spatially organizing biochemistry: choosing a strategy to translate synthetic biology to the factory.” Scientific Reports. Vol. 8, Article 8196, (2018)
T. G. Boatman, N. M. Mangan, T. Lawson, and R. J. Geider. "Inorganic carbon and pH dependency of Trichodesmium’s photosynthetic rates." Journal of Experimental Botany. (2018)
N. M. Mangan, J. N. Kutz, S. L. Brunton, and J. L. Proctor. "Model selection for dynamical systems via sparse regression and information criteria." Proc. R. Soc. London A Math. Phys. Eng. Sci. Vol 437, No 2204, (2017)
C. M. Jakobson, M. F. Slininger, D. Tullman-Ercek, and N. M. Mangan, “A Systems-Level Model Reveals That 1, 2-Propanediol Utilization Microcompartments Enhance Pathway Flux Through Intermediate Sequestration.,” PloS Comp. Bio., vol 13, no 5, p.e1005525, 2017.
M. Dong, N. M. Mangan, J. N. Kutz, S. T. Cundiff, H. G. Winful. "Traveling Wave Model for Frequency Comb Generation in Single Section Quantum Well Diode Lasers." IEEE Journal of Quantum Electronics 53 (6), 1-11, 2017
R. E. Brandt, N. M. Mangan, J. V. Li, Y. S. Lee, and T. Buonassisi. "Determining interface propterties limiting open-circuit voltage in heterojunction solar cells" J. Appl. Phys., vol 121, p. 185301, 2017.
N. M. Mangan, S. L. Brunton, J. L. Proctor, and J. N. Kutz, “Inferring biological networks by sparse identification of nonlinear dynamics,” IEEE Transactions on Mol. And Biol. and Multi-Scale Comm. Vol 2, No 1, 2017.
A. Polizzotti, A. Faghaninia, J. R. Poindexter, L. Nienhaus, V. Steinmann, R. LZ. Hoye, Al. Felten, A. Deyine, N. M. Mangan, J.-P. Correa-Baena, S. S. Shin, S. Jaffer, M. G. Bawendi, C. Lo, T. Buonassisi. "Improving Carrier Lifetime of Tin Sulfide via Prediction and Mitigation of Harmful Point Defects." J. Phys. Chem. Lett. Vol. 8, p. 3661-3667, 2017.
N. M. Mangan*, A. Flamholz*, R. D. Hood, R. Milo, and D. F. Savage, “pH determines the energetic efficiency of the cyanobacterial CO2 concentrating mechanism,” Proc. Natl. Acad. Sci., p. 201525145, 2016. (*authors contributed equally)
N. M. Mangan, R. E. Brandt, V. Steinmann, R. Jaramillo, C. Yang, J. R. Poindexter, R. Chakraborty, H. H. Park, X. Zhao, R. G. Gordon, and Tonio Buonassisi, “Framework to predict optimal buffer layer pairing for thin film solar cell absorbers: A case study for tin sulfide/zinc oxysulfide,” J. Appl. Phys., vol. 118, p. 115102, 2015.
D. B. Needleman, J. P. Mailoa, R. E. Brandt, N. M. Mangan, and T. Buonassisi, “Sensitivity Analysis of Optical Metrics for Spectral Splitting Photovoltaic Systems: A Case Study,” IEEE J. Photovoltaics, vol. 5, no. 5, pp. 1380–1388, 2015.
R. Chakraborty, V. Steinmann, N. M. Mangan, R. E. Brandt, J. R. Poindexter, R. Jaramillo, J. P. Mailoa, K. Hartman, A. Polizzotti, C. Yang, and others, “Non-monotonic effect of growth temperature on carrier collection in SnS solar cells,” Appl. Phys. Lett., vol. 106, no. 20, p. 203901, 2015.
M.-J. Sher, N. M. Mangan, M. J. Smith, Y.-T. Lin, S. Marbach, T. M. Schneider, S. Gradečak, M. P. Brenner, and E. Mazur, “Femtosecond-laser hyperdoping silicon in an SF6 atmosphere: Dopant incorporation mechanism,” J. Appl. Phys., vol. 117, no. 12, p. 125301, Mar. 2015.
Y.-T. Lin, N. Mangan, S. Marbach, T. M. Schneider, G. Deng, S. Zhou, M. P. Brenner, and E. Mazur, “Creating femtosecond-laser-hyperdoped silicon with a homogeneous doping profile,” Appl. Phys. Lett., vol. 106, no. 6, p. 62105, 2015.
N. Mangan and M. Brenner, “Systems analysis of the CO2 concentrating mechanism in cyanobacteria,” Elife, 2014.
N. Mangan, C. Reichhardt, and C. J. O. Reichhardt, “Reversible to irreversible flow transition in periodically driven vortices,” Phys. Rev. Lett., vol. 100, no. 18, 2008.
Y. Y. Kievsky, B. Carey, S. Naik, N. Mangan, D. Ben-Avraham, and I. Sokolov, “Dynamics of molecular diffusion of rhodamine 6G in silica nanochannels,” J. Chem. Phys., vol. 128, no. 15, 2008.
M. Reason, Y. Jin, H. A. McKay, N. Mangan, D. Mao, R. S. Goldman, X. Bai, and C. Kurdak, “Influence of N on the electronic properties of GaAsN alloy films and heterostructures,” J. Appl. Phys., vol. 102, no. 10, 2007.
Peer Reviewed Conference Proceedings:
R. E. Brandt, N. M. Mangan, J. V. Li, Y. S. Lee, T. Buonassisi. "Temperature-and intensity-dependent photovoltaic measurements to identify dominant recombination pathways." in Proceedings of the 43rd IEEE Photovoltaic Specialists Conference, 2016, pp 1997-2001.
N. Mangan and S. Mandre. Optimal distribution of riverine turbines in a linear array with systematic flow manipulation. XXIV ICTAM, 21-26th August 2016, Montreal, Canada.
S. Mandre, N. M. Mangan, T. Derecktor, and S. Winckler. A comparison of hydrokinetic turbines forming a vertical fence along the length of a river or tidal channel with a conventional rectangular turbine array. METS, 25-27th April 2016, Washington, D.C.
N. M. Mangan, R. E. Brandt, V. Steinmann, R. Jaramillo, J. V. Li, J. R. Poindexter, K. Hartman, L. Sun, R. G. Gordon, and T. Buonassisi, “A path to 10% efficiency for tin sulfide devices,” in Proceedings of the 40th IEEE Photovoltaic Specialist Conference, 2014, pp. 2373–2378.
J. R. Poindexter, R. E. Brandt, N. M. Mangan, and T. Buonassisi, “Extracting Mobility-Lifetime Product in Solar Cell Absorbers Using Quantum Efficiency Analysis,” MRS Proc., vol. 1771, p. mrss15-2131250, May 2015.
N. Mangan and S. Mandre. Optimal distribution of riverine turbines in a linear array with systematic flow manipulation. XXIV ICTAM, 21-26th August 2016, Montreal, Canada.
S. Mandre, N. M. Mangan, T. Derecktor, and S. Winckler. A comparison of hydrokinetic turbines forming a vertical fence along the length of a river or tidal channel with a conventional rectangular turbine array. METS, 25-27th April 2016, Washington, D.C.
N. M. Mangan, R. E. Brandt, V. Steinmann, R. Jaramillo, J. V. Li, J. R. Poindexter, K. Hartman, L. Sun, R. G. Gordon, and T. Buonassisi, “A path to 10% efficiency for tin sulfide devices,” in Proceedings of the 40th IEEE Photovoltaic Specialist Conference, 2014, pp. 2373–2378.
J. R. Poindexter, R. E. Brandt, N. M. Mangan, and T. Buonassisi, “Extracting Mobility-Lifetime Product in Solar Cell Absorbers Using Quantum Efficiency Analysis,” MRS Proc., vol. 1771, p. mrss15-2131250, May 2015.