Publications & Archive
R2D emerged from a long-running research program in muscle, molecular motors, thermodynamics, and multiscale biological mechanics. The conventional scientific record of that work and the developing R2D archive serve different purposes.
Muscle and Molecular Motor Research
For more than two decades, my research has examined how molecular-scale events become mechanical behavior at the scale of muscle.
This work includes the molecular mechanisms of muscle contraction and regulation, the mechanochemistry of myosin molecular motors, muscle thermodynamics, ensemble mechanics, single-molecule and whole-cell measurements, and multiscale models of biological systems.
A recurring question has been how randomly fluctuating molecular motors can collectively generate the deterministic force, shortening, and power measured at the scale of a muscle fiber.
That question ultimately led beyond muscle. Muscle provides an unusually useful scientific system because chemistry, thermodynamics, statistical mechanics, and mechanics can all be measured on the same physical system while the definition of the scientific object changes with scale.
The peer-reviewed publications documenting this research program can be found through Google Scholar.
From Muscle to R2D
The development of R2D began with a problem exposed by muscle: the mathematics that describes a muscle fiber cannot simply be assigned to one of its subordinate molecular components.
A myosin molecule and a muscle fiber are different scientific objects. Each has its own states, transitions, constraints, and readable observables.
R2D formalizes this boundary dependence by defining microstate and macrostate at the boundary where they are distinguished. Changing scale therefore does not merely coarse-grain the same object. It changes the mathematical state domain and, with it, the object being described.
The resulting framework has since been developed beyond muscle into a general mathematical interface for examining scientific structure across physics, chemistry, biology, and geometry.
R2D Archive and Continuing Development
Formal versions of R2D are archived on Zenodo.
Zenodo provides permanent, citable records of the framework at defined stages of development. These archived releases include the R2D Canon and subsequent formal developments and applications.
The distinction between the archive and this website is intentional:
- Zenodo preserves fixed scholarly versions.
- R2DScience.org presents the current framework and makes it easier to navigate and use.
- The Canon remains the authoritative mathematical source.
- Applications show how the framework develops when it is run against specific scientific problems.
As R2D develops, major formal releases will continue to be deposited on Zenodo so that earlier formulations remain permanently available and citable.
Current Canon
The current Canon is the master statement of the R2D framework.
It is intended both for human readers and as a source document for AI. Future releases will be made available in formats suitable for reading, archiving, and machine interrogation.
Citation and Contact
For questions about the research program, publications, or the R2D archive: