Papers › Quantifying biomolecular diffusion with a "spherical cow" model
Quantifying biomolecular diffusion with a "spherical cow" model
Frederico Campos Freitas, Sandra Byju, Asem Hassan, Ronaldo Junio de Oliveira, Paul C. Whitford
The archive published only this paper's code-link row. Authors, date and abstract are from arXiv's metadata (CC0), read from the Kaggle arXiv metadata snapshot of 2026-09-12 where its title matched the archive's; the title is the archive's.
The dynamics of biological polymers, including proteins, RNA, and DNA, occur in very high-dimensional spaces. Many naturally-occurring polymers can navigate a vast phase space and rapidly find their lowest free energy (folded) state. Thus, although the search process is stochastic, it is not completely random. Instead, it is best described in terms of diffusion along a downhill free energy landscape. In this context, there have been many efforts to use simplified representations of the energetics, for which the potential energy is chosen to be a relatively smooth function with a global minima that corresponds to the folded state. That is, instead of including every type of physical interaction, the broad characteristics of the landscape are encoded in approximate energy functions. We describe a particular class of models, called structure-based models, that can be used to explore the diffusive properties of biomolecular folding and conformational rearrangements. These energy functions may be regarded as the "spherical cow" for modeling molecular biophysics. We discuss the physical principles underlying these models and provide an entry-level tutorial, which may be adapted for use in curricula for physics and non-physics majors.
Code
Repository list and official/mentioned flags are the archive's, frozen 2025-07-28. Reachability, where shown, is from one Syntology probe window (2026-09-16 to 2026-09-18); repositories not probed show nothing. GitHub stars are not tracked.
Code Syntology ran Syntology
Not run by Syntology. Nothing on this page verifies that the listed code works.
Results from the paper archive 2025-07-28
No leaderboard rows for this paper in the archive.
Report a problem or propose a change · a person checks every report against the paper or source before anything changes; decisions are listed on /corrections