Related papers: Asymptotic hitting time for a simple evolutionary …
A complex network approach to protein folding is proposed. The graph object is the network of shortcut edges present in a native-state protein (SCN0). Although SCN0s are found via an intuitive message passing algorithm (S. Milgram,…
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…
Linear functions play a key role in the runtime analysis of evolutionary algorithms and studies have provided a wide range of new insights and techniques for analyzing evolutionary computation methods. Motivated by studies on separable…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
The conformational change of biological macromolecule is investigated from the point of quantum transition. A quantum theory on protein folding is proposed. Compared with other dynamical variables such as mobile electrons, chemical bonds…
In spite of decades of research, much remains to be discovered about folding: the detailed structure of the initial (unfolded) state, vestigial folding instructions remaining only in the unfolded state, the interaction of the molecule with…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
We propose a novel evolutionary algorithm on bit vectors which derives from the principles of information theory. The information-theoretic evolutionary algorithm (it-EA) iteratively updates a search distribution with two parameters, the…
We investigate the rate-length scaling law of protein folding, a key undetermined scaling law in the analytical theory of protein folding. We demonstrate that chain length is a dominant factor determining folding times, and that the…
Most research in the theory of evolutionary computation assumes that the problem at hand has a fixed problem size. This assumption does not always apply to real-world optimization challenges, where the length of an optimal solution may be…
Using a beta-hairpin protein as a representative example of two-state folders, we studied how the exploration of native-like states affects the folding kinetics. It has been found that the first-passage time (FPT) distributions are…
We prove that for any $\alpha$-mixing stationnary process the hitting time of any $n$-string $A_n$ converges, when suitably normalized, to an exponential law. We identify the normalization constant $\lambda(A_n)$. A similar statement holds…
A core feature of evolutionary algorithms is their mutation operator. Recently, much attention has been devoted to the study of mutation operators with dynamic and non-uniform mutation rates. Following up on this line of work, we propose a…
Hillclimbing is an essential part of any optimization algorithm. An important benchmark for hillclimbing algorithms on pseudo-Boolean functions $f: \{0,1\}^n \to \mathbb{R}$ are (strictly) montone functions, on which a surprising number of…
We introduce a quantity, the entropic susceptibility, that measures the thermodynamic importance-for the folding transition-of the contacts between amino acids in model proteins. Using this quantity, we find that only one equilibrium run of…
The probability distribution of sequences with maximum entropy that satisfies a given amino acid composition at each site and a given pairwise amino acid frequency at each site pair is a Boltzmann distribution with $\exp(-\psi_N)$, where…
We study the general fragmentation process starting from one element of size unity (E=1). At each elementary step, each existing element of size $E$ can be fragmented into $k\,(\ge 2)$ elements with probability $p_k$. From the continuous…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
Reaching a ground state of a spin system is analogous to a protein evolving into its native state. We study the ``folding'' times for various random Ising spin systems and determine characteristic temperatures that relate to the…