Spacetime crystallography of a quantum mechanical biosphere

Alexander Wait
Biophysics Graduate Program
Church Lab, Harvard Medical School


The Quantum Coreworld consists of volumes of spacetime, called bricks, arranged in a torus around a spherical planetoid. In the Figure (below) the bricks are colored cubes. Bricks can be occupied by molecules which are described by a computational chemistry; these molecules undergo Brownian-motion during periodic fluctuations. Simultaneously new configurations of molecules, or motifs, enter the biosphere in the (green) bricks close to the planetoid and these molecules provide a source of nutrients and new diversity. The evolution of a coreworld is deterministically computed by a Quantum Virtual Machine (QVM). Bricks in the coreworld are further arranged into neighboring regions which can be distributed to different physical processors for simulation; (red) bricks are exchanged during fluctuations stitching together the various regions.

A crystallographer of real biological molecules must make difficult trade-offs between the resolution of a crystal (both in space and time) and the difficulty of crystallization. For the spacetime crystallographer designing an automaton that produces biologically plausible crystals, that can be computed in a reasonable time with available hardware, is analogous to the difficulty encountered by a real crystallographer. For this week's theory-lunch I will take you on a guided tour of my efforts to crystallize a quantum mechanical biosphere; the work combines digital evolution with current research in quantum information processing. In studying life as it might be I hope to convince you that we can also learn about life as it is.

A Quantum Coreworld after a fluctuation.


B O'Neill, "Digital Evolution", PLoS Biology 1:e18 2003. DOI: 10.1371/journal.pbio.0000018

David Mermin's notes - "puts the subject of quantum computation together in a way that will make sense to computer scientists unfamiliar with quantum mechanics and physicists, unfamiliar with computational complexity theory" - PDFs.

T Toffoli, "A pedestrian's introduction to spacetime crystallography", IBM Journal of Research and Development 48:13-29 2004. html.