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Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
Scaling theory generates transferable (even universal) algebraic and geometrical relations between the amino acid sequences and the aggregation functions of the three titled radically different proteins. In addition to the two…
A possible explanation based on first principles for the appearance of the Omicron variant of the SARS-CoV-2 virus is proposed involving coinfection with HIV. The gist is that the resultant HIV-induced immunocompromise allows SARS-CoV-2…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
Designing novel proteins with desired functions is crucial in biology and chemistry. However, most existing work focus on protein sequence design, leaving protein sequence and structure co-design underexplored. In this paper, we propose…
Nowadays, evidence is mounting that the race of living organisms for adaptation to the chemicals synthesized by their neighbours may drive community structures. Particularly, some bacterial infections and plant invasions disruptive of the…
An important question in genome evolution is whether there exist fragile regions (rearrangement hotspots) where chromosomal rearrangements are happening over and over again. Although nearly all recent studies supported the existence of…
We model the competition between recombination and point mutation in microbial genomes, and present evidence for two distinct phases, one uniform, the other genetically diverse. Depending on the specifics of homologous recombination, we…
The native three dimensional structure of a single protein is determined by the physico chemical nature of its constituent amino acids. The twenty different types of amino acids, depending on their physico chemical properties, can be…
In this paper, we address the problem of identifying protein functionality using the information contained in its aminoacid sequence. We propose a method to define sequence similarity relationships that can be used as input for…
Molecular diffusion measurements are widely used to probe microstructure in materials and living organisms noninvasively. The precise relation of diffusion metrics to microstructure remains a major challenge: In complex samples, it is often…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
We consider a class of birth/death like process corresponding to coupled biochemical reactions and consider the problem of quantifying the variance of the molecular species in terms of the rates of the reactions. In particular, we address…
Since the largest 2014-2016 Ebola virus disease outbreak in West Africa, understanding of Ebola virus infection has improved, notably the involvement of innate immune mediators. Amongst them, collectins are important players in the…
The fundamental models of epidemiology describe the progression of an infectious disease through a population using compartmentalized differential equations, but do not incorporate population-level heterogeneity in infection susceptibility.…
Bacterial growth environment strongly influences the efficacy of antibiotic treatment, with slow growth often being associated with decreased susceptibility. Yet in many cases the connection between antibiotic susceptibility and pathogen…
We discuss a realistic scenario, accounting for the existence of sub-micrometric protein domains in cell membranes. At the biological level, such membrane domains have been shown to be specialized, in order to perform a determined…
We introduce a protein language model for determining the complete sequence of a peptide based on measurement of a limited set of amino acids. To date, protein sequencing relies on mass spectrometry, with some novel edman degregation based…
Motile organisms can form stable agglomerates such as cities or colonies. In the outbreak of a highly contagious disease, the control of large-scale epidemic spread depends on factors like the number and size of agglomerates, travel rate…
A modified, deterministic SEIR model is developed for the 2014 Ebola epidemic occurring in the West African nations of Guinea, Liberia, and Sierra Leone. The model describes the dynamical interaction of susceptible and infected populations,…