Joseph M. Mahaffy SDSU
Math 636: Mathematical Modeling Fall 2018
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Math 636 - PNAS Reports

Early this semester, you are going to write a review based on articles from the journal Proceedings of the National Academy of Sciences (PNAS). You will select an article from this journal, then write a report (2-5 pages) on this article. In particular, you will begin with a summary of what the authors showed in their article, then you will detail the mathematical modeling required to demonstrate their results or some aspect of the mathematical modeling. The article that you choose must be less than 5 years old and each student must select a unique article. (Exceptions to this rule can be made for reasons, such as particular interest or advice from a future advisor.) You will email me the details on the article that you have selected (title, PNAS issue, date, pages, etc.), then I will post it below, so others will not select the same article. Be sure to attach a PDF version of the article so that I can have it in my files. You can change your mind, but you must let me know so that I can update the list for other students. Articles will be assigned on a first come, first serve basis. (I will try very hard to update this page daily with any changes.) I will check that each of you choose a unique article. Your review will be due Thur. Sept. 27.

Student and PNAS Article

  1. Zariluz Alvarado -- Guillermo Lorenzoa , Michael A. Scottb , Kevin Tewc , Thomas J. R. Hughesd,1, Yongjie Jessica Zhange , Lei Liue , Guillermo Vilanovaa , and Hector Gomez, "Tissue-scale, personalized modeling and simulation of prostate cancer growth,” www.pnas.org/cgi/doi/10.1073/pnas.1615791113.
  2. Gabriel Arias -- Daniel S. Falster, Remko A. Duursma, and Richard G. FitzJohn, "How functional traits influence plant growth and shade tolerance across the life cycle", www.pnas.org/cgi/doi/10.1073/pnas.1714044115.
  3. Bryce Chudomelka -- Adrianna C. Jenkins, Pierre Karashchuk, Lusha Zhu, and Ming Hsu, "Predicting human behavior toward members of different social groups," www.pnas.org/cgi/doi/10.1073/pnas.1719452115.
  4. Wen-Jian Chung -- Shou-Li Li, Ottar N. Bjørnstad, Matthew J. Ferraria, Riley Mummaha, Michael C. Runge , Christopher J. Fonnesbeck , Michael J. Tildesley, William J. M. Probert , and Katriona Shea, "Essential information: Uncertainty and optimal control of Ebola outbreaks," www.pnas.org/cgi/doi/10.1073/pnas.1617482114.
  5. Chuck Connors -- Daniel Floryan, Tyler Van Buren, and Alexander J. Smits, "Efficient cruising for swimming and flying animals is dictated by fluid drag," www.pnas.org/cgi/doi/10.1073/pnas.18059411.
  6. Christopher Ewing -- Seong-Eun Kim, Michael K. Behr, Demba Ba, and Emery N. Brown, "State-space multitaper time-frequency analysis," www.pnas.org/cgi/doi/10.1073/pnas.1702877115.
  7. Andrea Fontanelli -- R. Sahli, G. Pallares, C. Ducottet, I. E. Ben Ali, S. Al Akhrass, M. Guibert, and J. Scheibert, "Evolution of real contact area under shear and the value of static friction of soft materials," www.pnas.org/cgi/doi/10.1073/pnas.1706434115.
  8. Eric Geels -- Caroline H. Brighton, Adrian L. R. Thomas, and Graham K. Taylor, "Terminal attack trajectories of peregrine falcons are described by the proportional navigation guidance law of missiles," www.pnas.org/cgi/doi/10.1073/pnas.1714532114.
  9. Oliver Gorton -- Roberta Amato, Lucas Lacasa, Albert Díaz-Guilera, Andrea Baronchelli, "The dynamics of norm change in the cultural evolution of language," www.pnas.org/cgi/doi/10.1073/pnas.172105911.
  10. Robert Harrison -- Alicia N. M. Kraay, Andrew F. Brouwer, Nan Lin, Philip A. Collender, Justin V. Remais, and Joseph N. S. Eisenberg, "Modeling environmentally mediated rotavirus transmission: The role of temperature and hydrologic factors," |www.pnas.org/cgi/doi/10.1073/pnas.1719579115.
  11. Nhat Hoang -- Steven Brunton, Joshua Proctor, and Nathan Kutz, "Discovering governing equations from data by sparse identification of nonlinear dynamics system," www.pnas.org/cgi/doi.org/10.1073/pnas.1517384113.
  12. Basile Hurat -- Philip S. Chodrow, "Structure and information in spatial segregation," |www.pnas.org/cgi/doi/10.1073/pnas.1708201114.
  13. Chris Lehnig -- Qian Zhang, Kaiyuan Sun, Matteo Chinazzi, Ana Pastore y Piontti, Natalie E. Dean, Diana Patricia Ro, Stefano Merler, Dina Mistry, Piero Poletti, Luca Rossi, Margaret Bray, M. Elizabeth Halloran, Ira M. Longini Jr., and Alessandro Vespignani, "Spread of Zika virus in the Americas," www.pnas.org/cgi/doi/10.1073/pnas.1620161114.
  14. Pu Li -- Sam Palmer, Luca Albergante, Clare C. Blackburn , and T. J. Newman, "Thymic involution and rising disease incidence with age," www.pnas.org/cgi/doi/10.1073/pnas.1714478115.
  15. Ryan Ly -- Wenrui Hao, Hannah M. Komar, Phil A. Hart, Darwin L. Conwell, Gregory B. Lesinski, and Avner Friedman, "Mathematical model of chronic pancreatitis," www.pnas.org/cgi/doi/10.1073/pnas.1620264114.
  16. Katelyn McNair -- Rasmus Skytte Eriksen, Sine L. Svenningsen, Kim Sneppen, and Namiko Mitarai, "A growing microcolony can survive and support persistent propagation of virulent phages," www.pnas.org/cgi/doi/10.1073/pnas.1708954115.
  17. Ashleigh Meyers -- Anwesha Chaudhury, Lorette Noiret, and John M. Higgins, "White blood cell population dynamics for risk stratification of acute coronary syndrome," www.pnas.org/cgi/doi/10.1073/pnas.1709228114.
  18. John Morgan -- Habib Ammari, Thomas Boulier, Josselin Garnier, and Han Wang, "Shape recognition and classification in electro-sensing," www.pnas.org/cgi/doi/10.1073/pnas.1406513111 .
  19. Jon Parsons -- Chad Giusti, Eva Pastalkova, Carina Curto, and Vladimir Itskov, "Clique topology reveals intrinsic geometric structure in neural correlations," www.pnas.org/cgi/doi/10.1073/pnas.1506407112.
  20. Jesus Perez Cuarenta -- Sen Pei, Sasikiran Kandula, Wan Yang, and Jeffrey Shaman, "Forecasting the spatial transmission of influenza in the United States," www.pnas.org/cgi/doi/10.1073/pnas.1708856115.
  21. Molly Poole -- Mario Herrero, Petr Havlík, Hugo Valin, An Notenbaert, Mariana C. Rufino, Philip K. Thornton, Michael Blümmel, Franz Weiss, Delia Grace, and Michael Obersteiner, "Biomass use, production, feed efficiencies, and greenhouse gas emissions from global livestock systems," www.pnas.org/cgi/doi/10.1073/pnas.1308149110.
  22. Geneva Porter -- Wajeeha Aziz, Wen Wang, Sebmen Kesaf, Alsayed Abdelhamid Mohamed, Yugo Fukazawa, Ryuichi Shigemoto, "Distinct kinetics of synaptic structural plasticity, memory formation, and memory decay in massed and spaced learning," www.pnas.org/cgi/doi/10.1073/pnas.1303317110.
  23. Abdullah Sahin -- Pedro Flombaum, José L. Gallegos , Rodolfo A. Gordillo, José Rincón, Lina L. Zabala, Nianzhi Jiao, David M. Karl, William K. W. Li, Michael W. Lomas, Daniele Veneziano, Carolina S. Vera, Jasper A. Vrugt, and Adam C. Martiny, "Present and future global distributions of the marine Cyanobacteria Prochlorococcus and Synechococcus," www.pnas.org/cgi/doi/10.1073/pnas.1307701110.
  24. Dartanyon Shivers -- Yu Xiea and Xiang Zhou, "Modeling individual-level heterogeneity in racial residential segregation," www.pnas.org/cgi/doi/10.1073/pnas.1202218109.
  25. Christopher Smith -- Richard P. Mann and Dirk Helbing, "Optimal incentives for collective intelligence," www.pnas.org/cgi/doi/10.1073/pnas.1618722114.
  26. Tina Stuckey -- Ruian Ke, Hui Li, Shuyi Wang, Wenge Ding, Ruy M. Ribeiro, Elena E. Giorgi, Tanmoy Bhattacharya, Richard J. O. Barnard, Beatrice H. Hahn, George M. Shaw, and Alan S. Perelson, "Superinfection and cure of infected cells as mechanisms for hepatitis C virus adaptation and persistence," | www.pnas.org/cgi/doi/10.1073/pnas.1805267115 .
  27. Peter Uhl-- Jessica M. Conway and Alan S. Perelson, "Post-treatment control of HIV infection," www.pnas.org/cgi/doi/10.1073/pnas.1419162112.
  28. Maurice Umukoro -- A. Demetri Pananos, Thomas M. Bury, Clara Wang, Justin Schonfeld, Sharada P. Mohanty, Brendan Nyhan, Marcel Salathé, and Chris T. Bauch, "Critical dynamics in population vaccinating behavior," www.pnas.org/cgi/doi/10.1073/pnas.1704093114.
  29. Lyndsay Walker -- Kai Lou, Steve Granick, and François Amblard, "How to better focus waves by considering symmetry and information loss," www.pnas.org/cgi/doi/10.1073/pnas.1803652115.

 

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