Monday, March 11, 2024
links for "Cellular Automata and Edge of Chaos" lecture
Devin Acker's Elementary CA Demo
Cellular Automata rules lexicon at MCell.
Cellular Automata Rules
Cellab
New Kind of Science Applets
Wolfram CA Demos
Langton's Lambda Parameter
Edge Of Chaos CA
Lambda Parameter Applet
Labels: #cellularAutomata, #complexity, #Computation, #edgeOfChaos, #selfOrganization, Class Links
Monday, February 26, 2024
Links for "Boolean Networks and Self-Organization" lecture
Random Boolean Networks Tutorial by Carlos Gershenson
Random Boolean Networks Demo by Wolfram
BooleSim by Mathias Bock
Discrete Dynamics Lab
Booleannet tool for simulating biological regulatory networks in a boolean formalism by Istvan Albert.
CANA Control and Redundancy in Boolean Networks by Rion Correia and CASCI.
Muramator Robot
Spontaneous Order and Self Organization @ Scholarpedia
Labels: #BooleanNetworks, #cellularAutomata, #edgeOfChaos, #self-organization, Class Links
Companion Links for chaos and logistic map lecture
Wolfram demo for the Logistic map and detailed study.
Java Code for Time Series of Logistic Map
GDScript Code for Logistic Map
Andrew Clem ~ Chaos theory contains a very nice explanation of the logistic map and the white bands of periodic behavior inside the chaotic range. Try r=3.84 in the demo used in class, to see a cycle of 3 arise.
See also The birth of period 3, revisited.
Applications of constrained chaos:
Two-dimensional constrained chaos and industrial revolution cycles: "Since the 1760s, at least three industrial revolutions have occurred. To explain this phenomenon, we introduce two-dimensional (2D) constrained chaos. Using a model of innovation dynamics, we show that an industrial-revolution-like technology burst, driven by investment/saving motives for R&D activities, recurs about every one hundred years if the monopolistic use of a new technology lasts about 8 y." Full paper @PNAS.
Non-equilibrium early-warning signals for critical transitions in ecological systems. "We employ landscape-flux theory from nonequilibrium statistical mechanics as a general framework to quantify the global stability of ecological systems and provide warning signals for critical transitions." Full paper @ PNAS.
Labels: #chaos, #logisticMap
Sunday, February 25, 2024
Lecture Notes (Chapter 4): Self-organization and emergent complex behavior
Labels: #DynamicalSystems, #evolvability, #geneRegulation, #robustness, #self-organization
Monday, February 19, 2024
Companion links for "Dynamical Systems and Attractor Behavior" lecture
Turing Reaction-Diffusion Model of Morphogenesis by Kele W. Cable: a demo by Chris Jennings .
Graphics Research on Reaction-Diffusion
synthetic texture using reaction-diffusion
Reaction-Diffusion in gene expression of digit determination (in mouse)
Validation of predicted patternsin Turing diffusion (in abiological droplets)
Revising the Turing model with biological evidence (in zebrafish)
Turing-type polyamide membranes for water purification
Expanding theoretical models (ABM and others)
Reaction-Diffusion in various areas.
3-Body Gravitational Problem 3-Body Problem in JavaScript
Lorenz Attractor Demo
Wolfram Projects Demo
Plotting Edward Lorenz's 1963 "Deterministic Nonperiodic Flow" in a 3-dimensional space using mplot3d.
Sensitive dependence on initial conditions in the Lorenz Attractor (Python code). Wolfram Sensitivity To Initial Conditions Demo.
Labels: #Attractors, #chaos, #DynamicalSystems, #Dynamics, #ReactionDiffusion, #Turing
Saturday, February 17, 2024
Toward first artificial plant genome
Labels: #artificialGenome, #genomics, #SyntheticBiology
Monday, February 12, 2024
Companion links for Self-Similarity and L-Systems Lecture
- The Koch Curve Fractal, and a generator.
- The Koch Snowflake, and a demo and another.
L-Systems
- A good description and demos by Chris Jennings
- Source Code from Gary Flake's Computational Beauty of Nature Book
- Generate an L-System. An alternative generator, and Another HTML Generator.
- Code for a L-System Explorer
- The Algorithmic Beauty of Plants
- Self-similar syncopations: Fibonacci, L-systems, limericks and ragtime.
- Musical L-Systems by Stelios Manousakis and the Symbolic Composer
3D Genbots using L-systems
The GOLEM Project.
See also the research pages pages of Karl Sims, Jordan Pollack, Hod Lipson, Josh Bongard, and Dario Floreano.
Labels: #development, #fractals, #Lsystems, #morphogenesis, Class Links
Links for "Modeling Principles of Organization" lecture
- Fibonacci numbers in Nature. The Romanesco Vegetable.
- Fibonacci Spiral Demo. Another Demo.
- Fibonacci Music
The magic of Fibonacci numbers by Arthur Benjamin
Peter Hilton (1923-2010) discusses intriguing number tricks that can be explained by analysing the properties of Fibonacci numbers and the related Lucas numbers. The explanations themselves benefit from further explanations which, in their turn, lead to further discoveries. Recorded at Imperial College London during the 1996 London Mathematical Society Popular Lecture series.
D'Arcy Thompson
- In retrospect: On Growth and Form by Phillip Ball.
- D'Arcy Thompson's Affine Fish Transformations @ Wolfram
- S.J. Gould. [1971] "D'Arcy Thompson and the Science of Form". New Literary History, 2 (2): 229-258
- W. Arthur [2006]. "D'Arcy Thompson and the theory of transformations".Nature Reviews Genetics 7, 401-406.
- Geometry of Growth and Form: Commentary on D'Arcy Thompson
- Java applet for shell sketching
Patterns of Life – D’Arcy Thompson, Structuralism and the Shape of Life
Treasures of the Library 5. D'Arcy Thompson, On growth and form
BLOOMS: Strobe Animated Sculptures Invented by John Edmark from Charlie Nordstrom on Vimeo. "This series of 3D printed sculptures was designed in such a way that the appendages match Fibonacci's Sequence, a mathematical sequence that manifests naturally in objects like sunflowers and pinecones. When the sculptures are spun at just the right frequency under a strobe light, a rather magical effect occurs: the sculptures seem to be animated or alive!"
Labels: #DArcyThompson, #Fibonacci, #modeling, #morphogenesis, #recursion, ClassLinks
Sunday, February 11, 2024
Lecture notes (Chapter 3): Modeling the World and Systems Approach to Life
Labels: #artificallife, #computationalBiology, #Hertz, #information, #modeling, #SystemsBiology, #SystemsScience
Friday, February 02, 2024
Diversity of information pathways drives sparsity in real-world networks
Labels: #ComplexSystems, #information, #thermodynamics
Monday, January 29, 2024
Links for Information Lecture 2
Information Theory Tutorial
Letter frequency in English
Word and Letter Frequency in English
Entropy of English
Text Mechanic - Text Manipulation Tools
1952 – “Theseus” Maze-Solving Mouse @ cyberneticzoo.com
Claude Shannon Demonstrating Theseus
Labels: #entropy, #information, #life
viruslike entities found in human gut microbes
Lecture Notes (Chapter 2): The Logical Mechanisms of Life
Labels: #ArtificialLife, #BiologicalTheory, #ComplexSystems, #GeneralSystems, #SystemsScience, #Theory
Sunday, January 21, 2024
Lecture notes (chapter 1): What is Life?
Labels: #artificallife, #bioinspiredcomputing, #ComplexSystems, #evolutionarysystems, #life
Sunday, September 10, 2023
Genomic Complexity or Variation in Drastic Fitness Changes
Labels: #dna, #evolution, #EvolutionarySystems #Polyploidy #Fitness #GenomeComplexity #Gemome, #GenomicComplexity
Tuesday, April 18, 2023
Multilevel cultural evolution: From new theory to practical applications
Labels: #complexity, #evolution, #MUltilevelSelection
Evolutionary Advantages of RNA Editing
Image from Christofi, T., Zaravinos, A. RNA editing in the forefront of epitranscriptomics and human health. J Transl Med 17, 319 (2019)
Labels: #adaptation, #evolution, #RNA, #RNAEditing
Friday, March 03, 2023
Organoid intelligence
Labels: #AI, #Brain, #organoids, #SyntheticBiology
Thursday, March 02, 2023
Lane formation in Crowd Dynamics
Labels: #Crowddynamics, #Crowds, #self-organization
Wednesday, February 08, 2023
Ants Revisit the Shortest Path Problem
Labels: #ants, #optimization, #ShortestPaths
Thursday, April 07, 2022
How Cells Conquer Mazes
Labels: #CellBiology, #Dynamics, #Movement, #Pathfinding
Monday, March 14, 2022
Engineered Biological Switches
Labels: #dna, #MolecularComputers, #Switches
Thursday, March 03, 2022
How We Can Make Sense of Chaos
Labels: #chaos, #DynamicalSystems
Monday, January 18, 2021
3D underwater collective behaviors in a fish-inspired robot swarm
Labels: #collectivebehavior, #collectiveIntelligence, #Robotics, #Swarms
Tuesday, January 14, 2020
Programmable organisms
Labels: #BioRobots, #ProgrammableMatter
Friday, October 18, 2019
Self-healing, path solving mould
Labels: #Intelligence, #SlimeMould
Saturday, March 23, 2019
Robotic collectives inspired by biological cells
Labels: #collectiveIntelligence, #Robotics
Tuesday, December 18, 2018
A neural data structure for novelty detection
Labels: #bioinspired computing, #NoveltyDetection, #Olfaction
Thursday, July 05, 2018
Programming self-organizing multicellular structures
Labels: #self-organization, #SyntheticBiology
Thursday, May 03, 2018
Fractal-like hierarchical organization of bone
Labels: #fractals
Saturday, October 14, 2017
Robot that can change its texture on the fly
Thursday, August 31, 2017
Octopus embodiment and intelligence
Labels: #Embodiment, #Intelligence, #Octopus
Wednesday, June 28, 2017
mathematical sculptors create compelling forms
Friday, March 03, 2017
DNA Fountain enables a robust and efficient storage architecture
Labels: #Computation, #dna
Wednesday, February 22, 2017
Studying swarms of ants could help speed up your commute
Labels: #collectivebehavior, #collectiveIntelligence, #Swarms