mathematical_biology

Phylogenetic inference turns molecular sequences into historical relationships. Classical likelihood-based methods excel in practice, yet the information geometry of alignment data relative to tree topology is rarely summarized in coordinates comparable across studies.

Allostery couples distant sites in a macromolecule: ligand binding at one pocket reshapes dynamics and thermodynamics elsewhere.

Many neural systems are hypothesized to operate near a critical point between ordered and disordered dynamics, balancing sensitivity and stability.

Evolutionary fitness landscapes encode how genotypes map to reproductive success. Rugged landscapes—with many local peaks and epistatic interactions—shape adaptation, evolvability, and the predictability of evolutionary paths.

Waddington’s epigenetic landscape metaphor remains the dominant intuitive picture for cell fate: stable types are valleys, differentiation is downhill flow, and reprogramming lifts cells across ridges.

We formalize a definition of life as the intersection of six necessary constraints: (L1) Shannon information capacity for self-description, (L2) Eigen error threshold for pattern preservation, (L3) thermal stability of covalent bonds, (L4) reversible