Related papers: A Minimum Principle in Codon-Anticodon Interaction
Thermodynamic cost of communication is a major factor in the thermodynamic cost of real-world computers, both biological and digital. Despite its importance, the fundamental principles underlying this cost remain poorly understood. This…
The macro-to-micro transition in a heterogeneous material is envisaged as the selection of a probability distribution by the Principle of Maximum Entropy (MAXENT). The material is made of constituents, e.g. given crystal orientations. Each…
This document gives a specification for the model used in [1]. It presents a simple way of optimizing mutual information between some input and the attractors of a (noisy) network, using a genetic algorithm. The nodes of this network are…
We propose a novel method for the determination of the effective interaction potential between the amino acids of a protein. The strategy is based on the combination of a new optimization procedure and a geometrical argument, which also…
Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are…
We propose a heuristic explanation for the numerous non-close-packed crystal structures observed in various colloidal systems. By developing an analogy between soap froths and the soft coronas of fuzzy colloids, we provide a geometrical…
Given a sequence composed of a limit number of characters, we try to "read" it as a "text". This involves to segment the sequence into "words". The difficulty is to distinguish good segmentation from enormous number of random ones.Aiming at…
We study a class of minimal geometric partial differential equations that serves as a framework to understand the evolution of boundaries between states in different pattern forming systems. The framework combines normal growth, curvature…
The thermodynamics of the lattice model of intercalation of ions in crystals is considered in the mean field approximation. Pseudospin formalism is used for the description of interaction of electrons with ions and the possibility of…
Measuring similarities/dissimilarities between atomic structures is important for the exploration of potential energy landscapes. However, the cell vectors together with the coordinates of the atoms, which are generally used to describe…
The physiology of voltage gated ion channels is complex and insights into their gating mechanism is incomplete. Their function is best represented by Markov models with relatively large number of distinct states that are connected by…
Degeneracy is a salient feature of genetic codes, because there are more codons than amino acids. The conventional table for genetic codes suffers from an inability of illustrating a symmetrical nature among genetic base codes. In fact,…
Sampling minimum energy grain boundary (GB) structures in the five-dimensional crystallographic phase space can provide much-needed insight into how GB crystallography affects various interfacial properties. However, the complexity and…
One of the major challenges of bottom-up synthetic biology is rebuilding a minimal division machinery. The animal cell division apparatus is mechanically the simplest, in which an actin-based ring constricts the membrane, as compared to…
Several technological applications require the translation of a protein into a nucleic acid that codes for it (``backtranslation''). The degeneracy of the genetic code makes this translation ambiguous; moreover, not every translation is…
We have developed an efficient and reliable methodology for crystal structure prediction, merging ab initio total-energy calculations and a specifically devised evolutionary algorithm. This method allows one to predict the most stable…
We derive generalisations of the Weingarten--Witten QCD mass inequalities for particular multi-hadron systems. For systems of any number of identical pseudo-scalar mesons of maximal isospin, these inequalities prove that interactions…
A non perturbative renormalization scheme for Nucleon-Nucleon interaction based on boundary conditions at short distances is presented and applied to the One Pion Exchange Potential. It is free of off-shell ambiguities and ultraviolet…
The genetic code maps the sixty-four nucleotide triplets (codons) to twenty amino-acids. Some argue that the specific form of the code with its twenty amino-acids might be a 'frozen accident' because of the overwhelming effects of any…
This paper formalizes a widely used dynamical class--replicator-mutator dynamics and Price-style selection-and-transmission--and makes explicit the modeling choices (scale, atomic unit, interaction topology, transmission kernel) that…