Related papers: Thermal Adaptation in Viruses and Bacteria
Using molecular dynamics computer simulations we investigate how the glass transition and the properties of the resulting glass depend on the cooling rate with which the sample has been quenched. This is done by studying a two component…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
We present an analysis of the role 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 compute the harmonic spectrum within the Gaussian…
The statistical properties of protein folding within the {\phi}^4 model are investigated. The calculation is performed using statistical mechanics and path integral method. In particular, the evolution of heat capacity in term of…
In this paper we revisit and adapt to viral evolution an approach based on the theory of branching process advanced by Demetrius, Schuster and Sigmund ("Polynucleotide evolution and branching processes", Bull. Math. Biol. 46 (1985)…
A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
The envelopes covering bacterial cytoplasm possess remarkable elastic properties. They are rigid enough to resist large pressures while being flexible enough to adapt to growth under environmental constraints. Similarly, the virus shells…
The dynamics of microbial communities is incredibly complex, determined by competition for metabolic substrates and cross-feeding of byproducts. Species in the community grow by harvesting energy from chemical reactions that transform…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
One of the many unresolved questions that revolves around the Covid-19 pandemic is whether local outbreaks can depend on ambient conditions like temperature and relative humidity. In this paper, we develop a model that tries to explain and…
A microscopic model for thermal excitation of vibrational ground state of a molecule interacting with a condensed medium is developed. The master equation for evolution of occupancies of the vibrational levels is derived. The rate constant…
The evolution and emergence of antibiotic resistance is a major public health concern. The understanding of the within-host microbial dynamics combining mutational processes, horizontal gene transfer and resource consumption, is one of the…
Considering high-temperature heating, the equations of transient heat conduction model require an adaptation, i.e. the dependence of thermophysical parameters of the model on the temperature is to be identified for each specific material to…
A study of a reacting boundary layer flow with heat transfer at conditions typical for configurations at elevated pressures has been performed using a set of direct numerical simulations. Effects of wall temperatures are investigated,…
Temperature is a widely used hyperparameter in various tasks involving neural networks, such as classification or metric learning, whose choice can have a direct impact on the model performance. Most of existing works select its value using…
Bacteria are often exposed to multiple stimuli in complex environments, and their efficient chemotactic decisions are critical to survive and grow in their native environments. Bacterial responses to the environmental stimuli depend on the…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
The response of ecosystems to perturbations is considered from a thermodynamic perspective by acknowledging that, as for all macroscopic systems and processes, the dynamics and stability of ecosystems is subject to definite thermodynamic…