Related papers: Thermal Adaptation in Viruses and Bacteria
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level…
We present an analysis of the effects of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we computed the harmonic spectrum within the…
A systematic expansion of the many-body master equation for active matter, in which motors power configurational changes as in the cytoskeleton, is shown to yield a description of the steady state and responses in terms of an effective…
The rise of trait-based ecology has led to an increased focus on the distribution and dynamics of traits in communities. However, a general theory of trait-based ecology, that can apply across different scales (e.g., species that differ in…
Many biological populations exhibit diversity in their strategy for survival and reproduction in a given environment, and microbes are an example. We explore the fate of different strategies under sustained environmental change by…
Quantitative models of associative learning that explain the behavior of real animals with high precision have turned out very difficult to construct. We do this in the context of the dynamics of the thermal preference of C. elegans. For…
The time dependence of the temperature during the reheating process is studied. We consider the thermal feedback effects of the produced particles on the effective dissipation rate of the inflaton field, which can lead to enhanced…
The metabolic processes complexity is at the heart of energy conversion in living organisms and forms a huge obstacle to develop tractable thermodynamic metabolism models. By raising our analysis to a higher level of abstraction, we develop…
Water plays a fundamental role in protein stability. However, the effect of the properties of water on the behaviour of proteins is only partially understood. Several theories have been proposed to give insight into the mechanisms of cold…
Related groups of microbes are widely distributed across Earth's habitats, implying numerous dispersal and adaptation events over evolutionary time. However, to date, relatively little is known about the characteristics and mechanisms of…
Biological organisms have evolved a wide range of immune mechanisms to defend themselves against pathogens. Beyond molecular details, these mechanisms differ in how protection is acquired, processed and passed on to subsequent generations…
Generative models of complex systems often require post-hoc parameter adjustments to produce useful outputs. For example, energy-based models for protein design are sampled at an artificially low ''temperature'' to generate novel,…
As pathogens spread in a population of hosts, immunity is built up and the pool of susceptible individuals is depleted. This generates selective pressure, to which many human RNA viruses, such as influenza virus or SARS-CoV-2, respond with…
We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
Thermal response of a protein (CoVE) conformation is studied by a coarse-grained Monte Carlo simulation. Three distinct segments, the N-terminal, Trans-membrane, and C-terminal are verified from its specific contact profile. The radius of…
The signaling apparatus mediating bacterial chemotaxis can adapt to a wide range of persistent external stimuli. In many cases, the bacterial activity returns to its pre-stimulus level exactly and this "perfect adaptability" is robust…
The Darwinian paradigm of biological evolution is based on the separability of the variation and selection processes. As a result, the population thinking had always been an integral part of the Darwinian approach. I propose an alternative…
Body size or mass is one of the main factors underlying food webs structure. A large number of evolutionary models have shown that indeed, the adaptive evolution of body size (or mass) can give rise to hierarchically organised trophic…
In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…
We introduce a graph generating model aimed at representing the evolution of protein interaction networks. The model is based on the hypotesis of evolution by duplications and divergence of the genes which produce proteins. The obtained…