Related papers: Asymptotic hitting time for a simple evolutionary …

Naturally evolving proteins gradually accumulate mutations while continuing to fold to thermodynamically stable native structures. This process of neutral protein evolution is an important mode of genetic change, and forms the basis for the…

We inquire how structure emerges during the process of protein folding. For this we scrutinise col- lective many-atom motions during all-atom molecular dynamics simulations. We introduce, develop and employ various topological techniques,…

In this study we evaluate, at full atomic detail, the folding processes of two small helical proteins, the B domain of protein A and the Villin headpiece. Folding kinetics are studied by performing a large number of ab initio Monte Carlo…

We propose a new way to self-adjust the mutation rate in population-based evolutionary algorithms in discrete search spaces. Roughly speaking, it consists of creating half the offspring with a mutation rate that is twice the current…

Single-molecule atomic force spectroscopy probes elastic properties of titin, ubiquitin and other relevant proteins. We explain bioprotein folding dynamics under both length- and force-clamp by modeling polyprotein modules as particles in a…

Natural protein sequences contain a record of their history. A common constraint in a given protein family is the ability to fold to specific structures, and it has been shown possible to infer the main native ensemble by analyzing…

For the vast majority of naturally occurring, small, single domain proteins folding is often described as a two-state process that lacks detectable intermediates. This observation has often been rationalized on the basis of a nucleation…

Extending previous analyses on function classes like linear functions, we analyze how the simple (1+1) evolutionary algorithm optimizes pseudo-Boolean functions that are strictly monotone. Contrary to what one would expect, not all of these…

We consider the simple exclusion process in the integer segment $ [1, N]$ with $k\le N/2$ particles and spatially inhomogenous jumping rates. A particle at site $x\in [ 1, N]$ jumps to site $x-1$ (if $x\ge 2$) at rate $1-\omega_x$ and to…

Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…

We have used numerical simulations to investigate how the properties of motor proteins control the dynamical behavior of a driven flexible filament. The filament is pinned at one end and positioned on top of a patch of anchored motor…

Assuming that mutation and fixation processes are reversible Markov processes, we prove that the equilibrium ensemble of sequences obeys a Boltzmann distribution with $\exp(4N_e m(1 - 1/(2N)))$, where $m$ is Malthusian fitness and $N_e$ and…

Evolutionally conserved quantity that specifies folding nuclei is pursued by a case study for a small protein (PDB code: 1ten). First it is demonstrated that the sequences of amino acids at folding nuclei are not conserved. Then 3D…

The folding dynamics of small single-domain proteins is a current focus of simulations and experiments. Many of these proteins are 'two-state folders', i.e. proteins that fold rather directly from the denatured state to the native state,…

We investigate spin-1/2 electrons with local Hubbard interaction and variable range hopping amplitudes which decay like~$\sinh(\kappa)/\sinh(\kappa r)$. Assuming integrability the Asymptotic Bethe Ansatz approach allows us to derive the…

The folding of a protein towards its native state is a rather complicated process. However there are empirical evidences that the folding time correlates with the contact order, a simple measure of the spatial organisation of the native…

We study the asymptotic behavior of the $N$-clock model, a nearest neighbors ferromagnetic spin model on the $d$-dimensional cubic $\varepsilon$-lattice in which the spin field is constrained to take values in a discretization…

We give a detailed analysis of the cost used by the (1+1)-evolutionary algorithm. The problem has been approached in the evolutionary algorithm literature under various views, formulation and degree of rigor. Our asymptotic approximations…

Predicting protein properties is paramount for biological and medical advancements. Current protein engineering mutates on a typical protein, called the wild-type, to construct a family of homologous proteins and study their properties.…

The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…