Related papers: Thermal Adaptation in Viruses and Bacteria
We developed a theory showing that under appropriate normalizations and rescalings, temperature response curves show a remarkably regular behavior and follow a general, universal law. The impressive universality of temperature response…
Molecular dynamics simulations are performed to study the temperature-dependent dynamics and structures of the hydration shells of elastin-like and collagen-like peptides. For both model peptides, it is consistently observed that, upon…
We analyze the dependence of thermal denaturation transition and folding rates of globular proteins on the number of amino acid residues, N. Using lattice Go models we show that DeltaT/T_F ~ N^-1, where T_F is the folding transition…
The 200 K protein dynamical transition is observed for the first time in the teraherz dielectric response. The complex dielectric permittivity $\epsilon$ = $\epsilon$' + i$\epsilon$" is determined in the 0.2 - 2.0 THz and 80-294 K ranges.…
Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a…
How do organisms recognize their environment by acquiring knowledge about the world, and what actions do they take based on this knowledge? This article examines hypotheses about organisms' adaptation to the environment from machine…
Many biological populations, such as bacterial colonies, have developed through evolution a protection mechanism, called bet-hedging, to increase their probability of survival under stressful environmental fluctutation. In this context, the…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
The time sequences of the molecular dynamics simulation for the folding process of a protein is analyzed with the inherent structure landscape which focuses on configurational dynamics of the system. Time dependent energy and entropy for…
Protein distributions measured under a broad set of conditions in bacteria and yeast were shown to exhibit a common skewed shape, with variances depending quadratically on means. For bacteria these properties were reproduced by temporal…
Biological systems are modular, and this modularity affects the evolution of biological systems over time and in different environments. We here develop a theory for the dynamics of evolution in a rugged, modular fitness landscape. We show…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
The mechanisms of cold- and pressure-denaturation of proteins are matter of debate and are commonly understood as due to water-mediated interactions. Here we study several cases of proteins, with or without a unique native state, with or…
The process of evolution by natural selection leads to phenotypes of increasing fitness. For cellular chemical reaction networks, this means optimising a variety of fitness functions such as robustness, precision, or sensitivity to external…
This paper introduces a stochastic adaptive dynamics model for the interplay of several crucial traits and mechanisms in bacterial evolution, namely dormancy, horizontal gene transfer (HGT), mutation and competition. In particular, it…
We introduce TemPL, a novel deep learning approach for zero-shot prediction of protein stability and activity, harnessing temperature-guided language modeling. By assembling an extensive dataset of 96 million sequence-host bacterial strain…
We present a two-species population model in a well-mixed environment where the dynamics involves, in addition to birth and death, changes due to environmental factors and inter-species interactions. The novel dynamical components are…
The emergence of self-replication and information transmission in life's origin remains unexplained despite extensive research on the topic. A hypothesis explaining the transition from a simple organic world to a complex RNA world is…