Wolfram Science

Dawei Li: A Subsequent Study of Visualized Sequence Comparison Based on Ten Types of Viruses

Dawei Li presented an investigation of the behavior of gene sequences transcoded to base 4 digits and evolved according to a ECA rule. He attempted to discover a new model of the propagation of virii using NKS methods, saying that Dr. Wolfram's approach provides a non-traditional visualized model for sequence comparisons.

He began with 4 hypotheses:
1 DNA is not random; it has a rule.
2 There is an uncertain mode of nucleotide organization that each DNA sequence follow.
3 Simple rules can produce complex behaviors in living organisms.
4 It is not only appropriate to DNA/RNA, but also to protein sequences

He selected rule 84 because of its nested structure and investigated its effect on many gene sequences in a selection of viruses, including some SARS strains. He displayed an array of algorithmically-colored graphs of evolutions, with similar colors indicating closer similar behavior. A detailed analysis of the transformations of various sequences in the virus DNA followed. The overall results seemed to be that regions that produces nested structures on evolution may be related to the reproduction of the virus.

He finished extremely early and the audience peppered him with questions about the implications of his project. Many people seemed skeptical, but intrigued.

Loe Feijs: Reinventing Electronics in NKS

Engineering and Design lecture series

Loe Feijs of the Technical University of Eindhoven describes his work simulating electronic circuits with CA rules.

Loe explores the expressive power of CAs as an alternate basis for electrical engineering. As his first goal, he has designed several CA systems that attempt to emulate an RC phase-shift oscillator, with the assumption that if this is possible, more complex circuits will also be possible.

In his first attempt, each cell is assigned a voltage value. Rules define a diffusion and flow of voltage. This system was then extended to 2D with a graphical grid-based circuit specification (made using MS Paint!) and appropriate 2D rules. This system was successful at modeling a simple resistive system like a voltage divider. However, problems arose when trying to add a model for capacitor plates.

His second attempt utilized block CAs, and like the first used special colors to position the ground plane and input-level voltage, as well as to overlay voltmeters and ammeters. This method was again successful in modeling voltage dividers, and could also model capacitor plates using a special, larger rule. However, this model failed when trying to model FETs, but was instead able to model beam-deflection transistors, also known as vacuum tubes. This allowed the successful modeling of a phase-shift oscillator.

Margaret Eppstein: Predicting Naturalization versus Invasion using Stochastic CA Models

Natural Sciences lecture series

Margaret Eppstein of the University of Vermont discusses invasion vs. naturalization in plant models

Margaret talked about what makes plants invasive. Several ideas already exist to explain some of the phenomena: the enemy release hypothesis, evolution of increased competitive ability, the biotic resistance hypothesis and propagule pressure. Models include both positive feedback effects, like pollinators and the presence of symbionts, and negative feedback effects like predators and pathogens. A characteristic like soil chemistry can be both a positive and negative feedback effect.

However, the standard Lotka-Volterra models typically used fail to account for frequency-dependent feedback effects, as well as typically making the assumption of a mean field, meaning that the use of space is ignored.

Margaret has developed a new model that incorporates propagule pressure, and both frequency dependent and independent effects, as well as spatial scale. Her results show that it's important to consider space when modeling whether an exotic species can establish when invading a new environment, as well as both frequency-dependent and independent interactions. This is then modeled as a stochastic CA with a configurable cell neighborhood.

This new model may be a practical way to assess the invasive potential of new species, or to estimate range limits of invasive species.

Thomas Speller: "A Study within the Nanosystem Architecture Domain: Self-Assembly of Graphene"

Thomas Speller discussed a combination of shape grammars and cellular automata.  Shape grammars are apparently specifications of 2- or 3-dimensional forms, and are commonly used used in architectural schools. I wasn't familiar with the concept of shape grammars, but they appear to be a natural way to symbolically specify shapes.

He is interested in a domain study of graphene, a common structure in all biotic systems and many inanimate ones, which is becoming a popular subject of study among condensed matter physicists. He was generating shape grammars for graphene by using cellular automata to model the possible transitions between states.

He showed comparisons of different the results from different CAs pre-selected to model different physics processes, and showed that in each one, graphene-like structures were created. The difficulty in translating these processes to reality appears to be limiting the number of atoms that combine into separate aggregations before bonding with each other.