2018-Theoretical Ecology: 闵四教-226

Part III:  Theoretical Ecology-behavioral ecology and self-organization

This course will provide an overview of the theoretical principles and mathematical description of collective behaviors to living sysems. The range of subjects and approaches, from phenomenology to detailed calculations, will be of interest to students from theoretical ecology, applied mathematics, and computational biology. The topics to be covered will span the range of length scales from molecular to ecological systems, with emphasis on key paradigms. Introductory material on statistical mechanics will provide background for much of the course. The subsequent topics will include Brownian motion, Levy walks, anomalous transport, reaction-diffusion dynamics, pattern formation, Ising model, self-organizated patterning, and so on. 
The material is for your private use. Please do not distribute. PDFs of articles, in case we have them, are accessible via links below.

Suggested Readings for Lesson 1-6, PDF of Lecture [PDF]

  1. Vicsek T, Czirok A, Ben-Jacob E, Cohen I, & Shochet O (1995) Novel type of phase transition in a system of self-driven particles. Phys. Rev. Lett. 75:1226-1229.  [PDF]
  2. Klafter J & Sokolov IM (2005) Anomalous diffusion spreads its wings. Phys World 18(8):29-32. [PDF1] [PDF2]
  3. Einstein A (1905) Investigations on the theory of the Brownian movement. Ann. d. Phys. 17, 549-560 (1905). [PDF]
  4. Couzin ID, Krause J, James R, Ruxton GD, & Franks NR (2002) Collective memory and spatial sorting in animal groups. J. Theor. Biol. 218(1):1-11. [PDF]
  5. Couzin ID, Krause J, Franks NR, & Levin SA (2005) Effective leadership and decision-making in animal groups on the move.  Nature 433(7025):513-516. [PDF]
  6. De Jager, M., Weissing, F.J., Herman, P.M.J., Nolet, B., & Van de Koppel, J. (2011) Lévy walks evolve through feedback between movement strategies and environmental complexity. Science 332:1551-1553. [PDF]
  7. Turing AM, (1952) The chemical basis of morphogenesis. Phil. Trans. Roy. Soc. 237, 37-72 (1952). [PDF]
  8. Ouyang Q and H.L. Swinney, (1991) Transition from a uniform state to hexagonal and striped Turing patterns. Nature 352, 610-612. [PDF]
  9. Lee KJ, W.D. McCormick, Q. Ouyang, and H.L. Swinney, (1993) Pattern formation by interacting chemical fronts. Science 261, 192-194.
  10. Pascual M & Guichard F (2005) Criticality and disturbance in spatial ecological systems. Trends in Ecology & Evolution 20(2):88-95. [PDF]
  11. Attanasi A, et al. (2014) Finite-Size Scaling as a Way to Probe Near-Criticality in Natural Swarms. Phys. Rev. Lett. 113(23). [PDF]
  12. Chen X, Dong X, Be’er A, Swinney HL, & Zhang HP (2012) Scale-Invariant Correlations in Dynamic Bacterial Clusters. Phys. Rev. Lett. 108(14):148101. [PDF]
  13. Haimovici A, Tagliazucchi E, Balenzuela P, & Chialvo DR (2013) Brain Organization into Resting State Networks Emerges at Criticality on a Model of the Human Connectome. Phys. Rev. Lett. 110(17):178101. [PDF]
Suggested Readings for Lesson 7-12, PDF of Lecture [PDF]
  1. Brockmann D, Hufnagel L, & Geisel T (2006) The scaling laws of human travel. Nature 439(7075):462-465. [PDF]
  2. de Jager M, Weissing FJ, Herman PMJ, Nolet BA, & van de Koppel J (2011) Levy Walks Evolve Through Interaction Between Movement and Environmental Complexity. Science 332(6037):1551-1553. [PDF]
  3. Theraulaz G, et al. (2002) Spatial patterns in ant colonies. Proc. Natl. Acad. Sci. USA 99(15):9645-9649. [PDF]
  4. Reichenbach T, Mobilia M, & Frey E (2007) Mobility promotes and jeopardizes biodiversity in rock-paper-scissors games. Nature 448(7157):1046-1049. [PDF]
Suggested Readings for Lesson 13-18, PDF of Lecture [PDF]
  1. Viswanathan GM et al (2011) The physics of foraging, (Cambridge University Press, Cambridge) 164 p.
  2. Camazine S, et al. (2001) Self-organization in biological systems, (Princeton University Press, Princeton, N.J.; Oxford) pp viii, 538 p.
  3. Meinhardt H (2003) The algorithmic beauty of sea shells (Springer, Berlin; London) 3rd Ed pp xi, 236 p.
  4. Mitchell M (2009) Complexity: a guided tour (Oxford University Press, New York; Oxford) pp xvi, 349 p.
Please download the assignment at here [PDF].
Please submit to assignment to Quan-Xing Liu qxliu@sklec.ecnu.edu.cn entitled "your name+student ID".

Usefull links for students to learn
(1) Visualising scientific models with 3D computer graphics [video
(2) Bird flight a model for future flying robots [video] [video]
(3) Particle tracking using IDL [Link]
(4) JPIV [Link]
(5) Python cookbook [link]
(6) Trackpy [link]
(7) ImageJ track [link]; http://mosaic.mpi-cbg.de/?q=downloads/imageJ
(8) 图形处理python: http://scikit-learn.org/stable/; http://www.simpleitk.org/SimpleITK/resources/software.html; http://simplecv.org;  http://scikit-image.org/download.html
(9) Maine In-situ Sound & Color Lab; http://misclab.umeoce.maine.edu/software.php
(10) pgf&Tikz Latex; http://www.latexstudio.net/archives/category/tex-graphics/tikz-example
(11) https://www.r-graph-gallery.com/barplot/; R plot line.
(12) https://www.ted.com/talks/stefano_mancuso_the_roots_of_plant_intelligence 
(13) Youtube 资料下载 https://y2mate.com/youtube/v5TLu2kmQVU 
(14) 常用单位换算:https://www.translatorscafe.com/unit-converter/en/illumination/10-1/ 
(15) R statistics ,The Handbook of Biological Statistics. http://rcompanion.org/rcompanion/index.html 
(16) Sources of Remote Sensing Data, https://harvardforest.fas.harvard.edu/sources-remote-sensing-data
(16) Parallel Spectral Numerical Methods/Examples in Matlab and Python; https://en.wikibooks.org/wiki/Parallel_Spectral_Numerical_Methods/Examples_in_Matlab_and_Python
(18) R pacakge deSolve ode and PDE: http://desolve.r-forge.r-project.org/

Ecological data
1. Community Productivity and Invasibility: http://www.cedarcreek.umn.edu/research/data
2. Empirical Dynamic Modeling and Convergent Cross Mapping: https://cran.r-project.org/web/packages/rEDM/vignettes/rEDM-tutorial.html
3. Computational Model Library: https://www.comses.net/codebases/?page=2