Related papers: Synonymous codon usage and selection on proteins
We extend well-known comparative results under expected utility to models of non-expected utility by providing novel conditions on local utility functions. We illustrate how our results parallel, and are distinct from, existing results for…
Comonotonicity (``same variation'') of random variables minimizes hedging possibilities and has been widely used, e.g., in Gilboa and Schmeidler's ambiguity models. This paper investigates anticomonotonicity (``opposite variation'';…
In subdivided populations, migration acts together with selection and genetic drift and determines their evolution. Building up on a recently proposed method, which hinges on the emergence of a time scale separation between local and global…
Cultural traits such as words, names, decorative styles, and technical standards often assume arbitrary values and are thought to evolve neutrally. But neutral evolution cannot explain why some traits come and go in cycles of popularity…
BACKGROUND: An important question is whether evolution favors properties such as mutational robustness or evolvability that do not directly benefit any individual, but can influence the course of future evolution. Functionally similar…
The relationship between a neuron's complex inputs and its spiking output defines the neuron's coding strategy. This is frequently and effectively modeled phenomenologically by one or more linear filters that extract the components of the…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
The complex dynamics of gene expression in living cells can be well-approximated using Boolean networks. The average sensitivity is a natural measure of stability in these systems: values below one indicate typically stable dynamics…
Organisms are equipped with regulatory systems that display a variety of dynamical behaviours ranging from simple stable steady states, to switching and multistability, to oscillations. Earlier work has shown that oscillations in protein…
A major goal of molecular evolutionary biology is to identify loci or regions of the genome under selection versus those evolving in a neutral manner. Correct identification allows accurate inference of the evolutionary process and thus…
Many enhanced sampling methods, such as Umbrella Sampling, Metadynamics or Variationally Enhanced Sampling, rely on the identification of appropriate collective variables. For proteins, even small ones, finding appropriate collective…
Many proteins in cells are capable of sensing and responding to piconewton scale forces, a regime in which conformational changes are small but significant for biological processes. In order to efficiently and effectively sample the…
Word similarity has many applications to social science and cultural analytics tasks like measuring meaning change over time and making sense of contested terms. Yet traditional similarity methods based on cosine similarity between word…
The Jaccard similarity index has often been employed in science and technology as a means to quantify the similarity between two sets. When modified to operate on real-valued values, the Jaccard similarity index can be applied to compare…
We propose a general method for predicting potentially good folders from a given number of amino acid sequences. Our approach is based on the calculation of the rate of convergence of each amino acid chain towards the native structure using…
Results obtained with stochastic methods have an inherent uncertainty due to the finite number of samples that can be achieved in practice. In lattice QCD this problem is particularly salient in some observables like, for instance,…
The time taken for gene expression varies not least because proteins vary in length considerably. This paper uses an abstract, tuneable Boolean regulatory network model to explore gene expression time variation. In particular, it is shown…
Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…
The effects of cooperativity are studied within Go-Lennard-Jones models of proteins by making the contact interactions dependent on the proximity to the native conformation. The kinetic universality classes are found to remain the same as…
Shannon information has, in the past, been applied to quantify the genetic diversity of many natural populations. Here, we apply the Shannon concept to consecutive generations of alleles as they evolve over time. We suppose a genetic system…