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Wolfram Summer School

June 24–July 14, 2018
Bentley University, Waltham, MA

Alumni

Robert Oppenheimer

Class of 2014

Bio

Robert is currently finishing a bachelor of science and arts, majoring in biology, economics, and anthropology at the University of Sydney, Australia. He comes from a wool-growing family in regional New South Wales. He has loved learning about evolutionary and ecological theory, as well as working in the field trapping Tasmanian devils and tracking small marsupials in the Simpson Desert.

During Rob's degree he led a team of undergraduates in an annual, international competition for student research in synthetic biology (iGEM). He is now learning more about bionanotechnology as a member of the first Australian BIOMOD team, and will spend the next year at the Victor Chang Institute, Sydney, looking at biological nanomachines like the bacterial flagella motor.

Robbie has a particular interest in education and science communication, for instance, creating a science-writing competition for Australian high-school students (strangenature.org). He gets excited about stuff like—taking life into space, creating the first synthetic cell, understanding the thermodynamic basis of natural selection, theories of ecological economics, ethnographies of science, and poetry slams.

Project

Cooperativity is a key organizing principle in chemistry and biology without which the complex molecular systems required for life could not function.... [T]here seems to be no accessible theoretical model to guide us as to what advantage might be expected even for a simplified, ideal system.

Whitty, A. "Cooperativity and Biological Complexity." Nature Chemical Biology 4 (2008): 435–439.

Cooperativity involves nonlinear interactions between elements in a system.

Examples of cooperativity include the folding of chainlike organic molecules (nucleic acids, proteins, phospholipids), the binding of ligands to receptor proteins, or the increasing affinity of hemoglobin for oxygen as additional oxygen molecules bind to it. Understanding the basic rules for local interactions will offer insight into basic questions such as Levinthal's paradox—the observation that a folding protein randomly sampling all possible conformations would take longer to fold than the current age of the universe, coupled with the observation that proteins typically fold in milliseconds.

Boids ("bird-oids") is a computer simulation of the interaction between agents in a space with two or more dimensions.

This type of model has been used to model a range of biological phenomena, including flocks of birds, schools of fish, swarming bacteria, and ferromagnetic alignment.

There are three key features of any boids model:

  • Cohesion, the attraction to the average position of nearby elements,
  • Alignment, the adjustment of velocity and direction to the average of nearby elements, and
  • Separation, the repulsion from elements in a close range.

In this project I will create and explore a model that replaces boids with simple chains.

The chains are idealised organic polymers and will carry information that determines their interactions with other chains, for instance, in the form of a positive or negative charge. Thus each link in the chain will have its own rules for local interactions, as in the models of boids. In this model the position, velocity, orientation, and angles in a chain will have random initial conditions and will vary over time as the chain interacts with its neighbors.

I intend to explore this model with three main parameters: Energy (E), the total kinetic activity of the system; Intensity (I), the strength of the interaction between elements; and Range (R), the distance over which this interaction acts.

My project will attempt to model simultaneously the interactions within and between many chains over time.

Favorite Outer Totalistic r=1, k=2 2D Cellular Automaton

Rule 242500