Related papers: A Minimum Principle in Codon-Anticodon Interaction
A structure prediction method is presented based on the Minima Hopping method. Optimized moves on the configurational enthalpy surface are performed to escape local minima using variable cell shape molecular dynamics by aligning the initial…
Why is the genetic code the way it is? The most successful theory states that the codon assignments minimise the effects of errors arising in primordial living systems. Here a transversion is reported that leaves invariant degeneracy in the…
A method based on mapping a symbolic sequence into a set of patterns (strings resulting from the sequence parsing) is proposed as a tool for the reconstruction of ancestral sequences. The set union of patterns comprises all the patterns…
Determining the kinetic bottlenecks that make transitions between metastable states difficult is key to understanding important physical problems like crystallization, chemical reactions, or protein folding. In all these phenomena, the…
Currently, the only worldwide source of low-energy antiprotons is the AD/ELENA facility located at CERN. To date, all precision measurements on single antiprotons have been conducted at this facility and provide stringent tests of the…
In this paper we consider the problem of characterizing the minimum energy configurations of a finite system of particles interacting between them due to attracting or repulsive forces given by a certain inter molecular potential. We limit…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
The structure of the genetic code is discussed in formal terms. A rectangular table of the code ("the code matrix"), whose properties reveal its arithmetical content tagged with the information symbols in several notations. New parameters…
Finding an optimal match between two different crystal structures underpins many important materials science problems, including describing solid-solid phase transitions, developing models for interface and grain boundary structures. In…
Prions are misfolded proteins that transmit their structural arrangement to neighboring proteins. In biological systems, prion dynamics can produce a variety of complex functional outcomes. Yet, an understanding of prionic causes has been…
Using the shape space of codons and tRNAs we give a physical description of the genetic code evolution on the basis of the codon capture and ambiguous intermediate scenarios in a consistent manner. In the lowest dimensional version of our…
Given an assignment of real weights to the ground elements of a matroid, the min-max weight of a ground element $e$ is the minimum, over all circuits containing $e$, of the maximum weight of an element in that circuit with the element $e$…
Motivated by recent findings, we discuss the existence of a direct and robust mechanism providing discontinuous absorbing transitions in short range systems with single species, with no extra symmetries or conservation laws. We consider…
We propose a unified framework for dealing with matching rules of quasiperiodic patterns, relevant for both tiling models and real world quasicrystals. The approach is intended for extraction and validation of a minimal set of matching…
Essential genes constitute the core of genes which cannot be mutated too much nor lost along the evolutionary history of a species. Natural selection is expected to be stricter on essential genes and on conserved (highly shared) genes, than…
This is about the Minimum Description Length (MDL) principle applied to pattern mining. The length of this description is kept to the minimum. Mining patterns is a core task in data analysis and, beyond issues of efficient enumeration, the…
It is argued that, for strongly non-linear behaviors, a fully deterministic position can hardly be maintained in the micro-macro transitions. This is due to the lack of information on the relevant boundary conditions, and to the tendency of…
The infrastructure upon which the functioning of society depends is composed of complex ecosystems of systems. Consequently, we must reason about the properties of such ecosystems, which requires that we construct models of them. There are…
We describe the conditions under which a set of continuous variables or characters can be described as an X-tree or a split network. A distance matrix corresponds exactly to a split network or a valued X-tree if, after ordering of the taxa,…