Related papers: Asymptotic hitting time for a simple evolutionary …
We study the thermodynamic behavior of a simple off-lattice model for protein folding. The model is two-dimensional and has two different ``amino acids''. Using numerical simulations of all chains containing eight or ten monomers, we…
We propose and analyze a self-adaptive version of the $(1,\lambda)$ evolutionary algorithm in which the current mutation rate is part of the individual and thus also subject to mutation. A rigorous runtime analysis on the OneMax benchmark…
We develop a theoretical approach to the protein folding problem based on out-of-equilibrium stochastic dynamics. Within this framework, the computational difficulties related to the existence of large time scale gaps in the protein folding…
We propose a new method based on discrete Fourier analysis to analyze the time evolutionary algorithms spend on plateaus. This immediately gives a concise proof of the classic estimate of the expected runtime of the $(1+1)$ evolutionary…
Protein sequences serve as a natural record of the evolutionary constraints that shape their functional structures. We show that it is possible to use only sequence information to go beyond predicting native structures and global stability…
We study folding in 16-monomer heteropolymers on the square lattice. For a given sequence, thermodynamic properties and stability of the native state are unique. However, the kinetics of folding depends on the model of dynamics adopted for…
We assume that the protein folding process follows two autonomous steps: the conformational search for the native, mainly ruled by the hydrophobic effect; and, the final adjustment stage, which eventually gives stability to the native. Our…
For genetic algorithms using a bit-string representation of length~$n$, the general recommendation is to take $1/n$ as mutation rate. In this work, we discuss whether this is really justified for multimodal functions. Taking jump functions…
The authors address the problem of downhill protein folding in the framework of a simple statistical mechanical model, which allows an exact solution for the equilibrium and a semianalytical treatment of the kinetics. Focusing on protein…
The OneMax problem, alternatively known as the Hamming distance problem, is often referred to as the "drosophila of evolutionary computation (EC)", because of its high relevance in theoretical and empirical analyses of EC approaches. It is…
Two proteins, one belonging to the mainly alpha class and the other belonging to the alpha/beta class, are selected to test a kinetic mechanism for protein folding. Targeted molecular dynamics is applied to generate folding pathways for…
We analyse the performance of well-known evolutionary algorithms (1+1)EA and (1+$\lambda$)EA in the prior noise model, where in each fitness evaluation the search point is altered before evaluation with probability $p$. We present refined…
We simulate neutral evolution of proteins imposing conservation of the thermodynamic stability of the native state in the framework of an effective model of folding thermodynamics. This procedure generates evolutionary trajectories in…
The protein folding problem has attracted an increasing attention from physicists. The problem has a flavor of statistical mechanics, but possesses the most common feature of most biological problems -- the profound effects of evolution. I…
While most theoretical run time analyses of discrete randomized search heuristics provide bounds on the expected number of evaluations to find the global optimum, we consider the anytime performance of evolutionary and…
Growing experimental evidence shows that proteins follow one or a few distinct paths when folding. We propose in this paper a procedure to parametrize these observed pathways, and from this parametrization construct effective Hamiltonians…
The thermodynamics of proteins indicate that folding/unfolding takes place either through stable intermediates or through a two-state process without intermediates. The rather short folding times of the two-state process indicate that…
This paper extends the runtime analysis of non-elitist evolutionary algorithms (EAs) with fitness-proportionate selection from the simple OneMax function to the linear functions. Not only does our analysis cover a larger class of fitness…
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 study the statistical properties of a simple genetic regulatory network that provides heterogeneity within a population of cells. This network consists of a binary genetic switch in which stochastic flipping between the two switch states…