Related papers: Structurally constrained protein evolution: result…

We study the evolution of domain wall networks appearing after phase transitions in the early Universe. They exhibit interesting dynamical scaling behaviour which is not yet well understood, and are also simple models for the more…

Many biological processes are supported by special molecules, called motor proteins or molecular motors, that transport cellular cargoes along linear protein filaments and can reversibly associate to their tracks. Stimulated by these…

Most social, technological and biological networks are embedded in a finite dimensional space, and the distance between two nodes influences the likelihood that they link to each other. Indeed, in social systems, the chance that two…

In a stochastic process, noise often modifies the picture offered by the mean field dynamics. In particular, when there is an absorbing state, the noise erases a stable fixed point of the mean field equation from the stationary…

Homeostasis of protein concentrations in cells is crucial for their proper functioning, and this requires concentrations (at their steady-state levels) to be stable to fluctuations. Since gene expression is regulated by proteins such as…

Evolution is a dynamic process. The two classical forces of evolution are mutation and selection. Assuming small mutation rates, evolution can be predicted based solely on the fitness differences between phenotypes. Predicting an…

Binding interactions between proteins and other molecules mediate numerous cellular processes, including metabolism, signaling, and regulation of gene expression. These interactions evolve in response to changes in the protein's chemical or…

In this work we develop a microscopic physical model of early evolution, where phenotype,organism life expectancy, is directly related to genotype, the stability of its proteins in their native conformations which can be determined exactly…

The spread of infectious disease and the evolution of antigenically distinct strains are often modeled separately, despite strong feedbacks mediated by host immune memory and heterogeneous contacts. To tackle this challenging problem, we…

The primary aim of this work is to explore how proteins point mutations impact their marginal stability and, hence, their evolvability. With this purpose, we show that the use of four classic notions, namely, those from Leibniz & Kant…

Mapping between sequence and structure is currently an open problem in structural biology. Despite many experimental and computational efforts it is not clear yet how the structure is encoded in the sequence. Answering this question may…

Several recent works have shown that protein structure can predict site-specific evolutionary sequence variation. In particular, sites that are buried and/or have many contacts with other sites in a structure have been shown to evolve more…

The role of the selection pressure and mutation amplitude on the behavior of a single-species population evolving on a two-dimensional lattice, in a periodically changing environment, is studied both analytically and numerically. The…

We show that a neural network originally designed for language processing can learn the dynamical rules of a stochastic system by observation of a single dynamical trajectory of the system, and can accurately predict its emergent behavior…

A theoretical framework is developed to study the dynamics of protein folding. The key insight is that the search for the native protein conformation is influenced by the rate r at which external parameters, such as temperature, chemical…

We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…

Protein structure tokenization converts 3D structures into discrete or vectorized representations, enabling the integration of structural and sequence data. Despite many recent works on structure tokenization, the properties of the…

The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…

Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…

The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have…