Related papers: Alpha helices are more evolutionarily robust to en…
Methods from artificial intelligence (AI), in general, and machine learning, in particular, have kept conquering new territories in numerous areas of science. Most of the applications of these techniques are restricted to the classification…
The evolution of various competing cell types in tissues, and the resulting persistent tissue population, is studied numerically and analytically in a particle-based model of active tissues. Mutations change the properties of cells in…
A common view in evolutionary biology is that mutation rates are minimised. However, studies in combinatorial optimisation and search have shown a clear advantage of using variable mutation rates as a control parameter to optimise the…
Robustness, the insensitivity of some of a biological system's functionalities to a set of distinct conditions, is intimately linked to fitness. Recent studies suggest that it may also play a vital role in enabling the evolution of species.…
In classical evolutionary theory, genetic variation provides the source of heritable phenotypic variation on which natural selection acts. Against this classical view, several theories have emphasized that developmental variability and…
Evolution occurs in populations of reproducing individuals. It is well known that population structure can affect evolutionary dynamics. Traditionally, natural selection is studied between mutants that differ in reproductive rate, but are…
The main topic of this thesis is the analysis of evolution equations reflecting issues in ecology and population dynamics. In mathematical modelling, the impact of environmental elements and the interaction between species is read into the…
Many exoplanets have orbital characteristics quite different from those seen in our own solar system, including planets locked in orbital resonances and planets on orbits that are elliptical or highly inclined from their host star's spin…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
Decision trees and logistic regression are one of the most popular and well-known machine learning algorithms, frequently used to solve a variety of real-world problems. Stability of learning algorithms is a powerful tool to analyze their…
A minimal off-lattice model for alpha-helical proteins is presented. It is based on hydrophobicity forces and sequence independent local interactions. The latter are chosen so as to favor the formation of alpha-helical structure. They model…
Globular proteins are expected to assume folds with fixed secondary structures, alpha-helices and beta-sheets. Fold-switching proteins challenge this expectation by remodeling their secondary and/or tertiary structures in response to…
A convolutional neural network strongly robust to adversarial perturbations at reasonable computational and performance cost has not yet been demonstrated. The primate visual ventral stream seems to be robust to small perturbations in…
The inheritance of characteristics induced by the environment has often been opposed to the theory of evolution by natural selection. Yet, while evolution by natural selection requires new heritable traits to be produced and transmitted, it…
We present a sequence-based probabilistic formalism that directly addresses co-operative effects in networks of interacting positions in proteins, providing significantly improved contact prediction, as well as accurate quantitative…
Understanding how a stressor applied on a biological system shapes its evolution is key to achieving targeted evolutionary control. Here we present a toy model of two interacting lattice proteins to quantify the response to the selective…
Phenotypic plasticity and its evolution may help evolutionary rescue in a novel and stressful environment, especially if environmental novelty reveals cryptic genetic variation that enables the evolution of increased plasticity. However,…
In biological systems, expression dynamics that can provide fitted phenotype patterns with respect to a specific function have evolved through mutations. This has been observed in the evolution of proteins for realizing folding dynamics…
Traditionally evolution is seen as a process where from a pool of possible variations of a population (e.g. biological species or industrial goods) a few variations get selected which survive and proliferate, whereas the others vanish.…
Modern biomedicine is challenged to predict the effects of genetic variation. Systematic functional assays of point mutants of proteins have provided valuable empirical information, but vast regions of sequence space remain unexplored.…