Related papers: Asymptotic hitting time for a simple evolutionary …
It is known that the evolutionary algorithm $(1+1)$-EA with mutation rate $c/n$ optimises every monotone function efficiently if $c<1$, and needs exponential time on some monotone functions (HotTopic functions) if $c\geq 2.2$. We study the…
In many real-world optimization problems, the objective function evaluation is subject to noise, and we cannot obtain the exact objective value. Evolutionary algorithms (EAs), a type of general-purpose randomized optimization algorithm,…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
In a seminal paper in 2013, Witt showed that the (1+1) Evolutionary Algorithm with standard bit mutation needs time $(1+o(1))n \ln n/p_1$ to find the optimum of any linear function, as long as the probability $p_1$ to flip exactly one bit…
While the theoretical analysis of evolutionary algorithms (EAs) has made significant progress for pseudo-Boolean optimization problems in the last 25 years, only sporadic theoretical results exist on how EAs solve permutation-based…
The one-fifth success rule is one of the best-known and most widely accepted techniques to control the parameters of evolutionary algorithms. While it is often applied in the literal sense, a common interpretation sees the one-fifth success…
While the theoretical analysis of evolutionary algorithms (EAs) has made significant progress for pseudo-Boolean optimization problems in the last 25 years, only sporadic theoretical results exist on how EAs solve permutation-based…
Understanding how evolutionary algorithms perform on constrained problems has gained increasing attention in recent years. In this paper, we study how evolutionary algorithms optimize constrained versions of the classical LeadingOnes…
How proteins fold remains a central unsolved problem in biology. While the idea of a folding code embedded in the amino acid sequence was introduced more than 6 decades ago, this code remains undefined. While we now have powerful predictive…
To gain a better theoretical understanding of how evolutionary algorithms (EAs) cope with plateaus of constant fitness, we propose the $n$-dimensional Plateau$_k$ function as natural benchmark and analyze how different variants of the $(1 +…
Mechanical stretching of six proteins is studied through molecular dynamics simulations. The model is Go-like, with Lennard-Jones interactions at native contacts. Low temperature unfolding scenarios are remarkably complex and sensitive to…
In this paper, we mathematically describe the time evolution of protein folding features via Iori et al.'s heteropolymer model. More specifically, we identify that the folding amino acid chain evolve according to a power law $D \sim…
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…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…
The determination of the folding mechanisms of proteins is critical to understand the topological change that can propagate Alzheimer and Creutzfeld-Jakobs diseases, among others. The computational community has paid considerable attention…
We study unbiased $(1+1)$ evolutionary algorithms on linear functions with an unknown number $n$ of bits with non-zero weight. Static algorithms achieve an optimal runtime of $O(n (\ln n)^{2+\epsilon})$, however, it remained unclear whether…
Folding kinetics of a lattice model of protein is studied. It uses the Random Energy Model for the intrachain couplings and a temperature dependent free energy of solvation derived from a realistic hydration model of apolar solutes. The…
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…
We study evolutionary algorithms in a dynamic setting, where for each generation a different fitness function is chosen, and selection is performed with respect to the current fitness function. Specifically, we consider Dynamic BinVal, in…
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…