A. Maritan

A Tale of Two Chains: Geometries of a Chain Model and Protein Native State Structures

The paper compares simulations of polymer chains and experimental data on protein structures to analyze their geometries and reconcile differences through symmetry considerations.

Amino acid characteristics in protein native state structures

The paper analyzes side chain protrusion statistics in protein structures to understand amino acid behavior in native states.

III. Geometrical framework for thinking about globular proteins: turns in proteins

The paper introduces a geometrical framework to understand protein turns by defining them as isolated local poking interactions, identifying their structural classes and amino acid preferences.

Emergent Ecological Patterns and Modelling of Gut Microbiomes in Health and in Disease

This study investigates ecological patterns in gut microbiomes to determine if they can distinguish healthy from diseased states, using metagenomics data and population dynamics models.

Sperm length evolution in relation to body mass is shaped by multiple trade-offs in tetrapods

This study investigates how sperm length evolves in relation to body mass in tetrapods, finding that trade-offs with sperm competition and clutch size shape this relationship.

II. Geometrical framework for thinking about globular proteins: the power of poking

The paper benchmarks a geometrical model of protein structure using structural data and simulations, showing that symmetry and geometry can explain protein complexity through poking interactions.

A geometrical framework for thinking about proteins

The paper introduces a geometrical model of proteins based on symmetry and geometry, showing it aligns with experimental data and explains protein structure and function.

A scale-invariant log-normal droplet size distribution below the critical concentration for protein phase separation

The paper investigates droplet size distributions in protein phase separation and finds they follow a scale-invariant log-normal function, suggesting universal behavior and a method to estimate critical concentration.

Marginally compact phase and ordered ground states in a model polymer with side spheres

This study investigates the phase behavior of a polymer model with side spheres, revealing a marginally compact phase with ordered structures and first-order transitions.

Spontaneous dimensional reduction and novel ground state degeneracy in a simple chain model

The paper studies a homopolymer model of a linear chain molecule, finding a first-order phase transition, ground state degeneracy, spontaneous dimensional reduction, and a two-layer structure composed of helices and strands connected by loops.

Building blocks of protein structures - Physics meets Biology

This paper derives the geometry of protein building blocks using physics and mathematics without sequence or chemistry, showing a perfect fit with quantum chemistry and implications for artificial life.

Statistical Physics of DNA melting: Unveiling the artificial corrections for self-complementary sequences

This paper derives a statistical physics framework for DNA hybridization and melting, showing that self-complementary sequences do not require artificial entropic corrections.

Constrained proteome allocation affects coexistence inmodels of competitive microbial communities

The paper develops a new framework integrating proteome allocation into microbial community models to better understand coexistence dynamics.

Inferring macro-ecological patterns from local species’ occurrences

This paper introduces a framework to infer biodiversity patterns at large scales using presence-absence data, showing improved accuracy compared to existing methods.

Adaptive metabolic strategies in consumer-resource models

The paper introduces adaptive metabolic strategies into consumer-resource models to explain microbial growth and community dynamics without relying on specific molecular mechanisms.

Biodiversity of Tropical Forests

This paper introduces a framework to estimate biodiversity in tropical forests, showing that previous methods overestimate species counts and revealing hyper-rarity as a buffer against mass extinctions.