Mahler Measuring the Genetic Code of Amoebae

The mapping between biological genotypes and phenotypes is central to the study of biological evolution. Here we introduce a rich, intuitive, and biologically realistic genotype-phenotype (GP) map, that serves as a model of self-assembling biological structures, such as protein complexes, and remains computationally and analytically tractable. Our GP map arises naturally from the self-assembly of polyomino structures on a 2D lattice and exhibits a number of properties: $\text...

Some of the basic concepts of topology are explored through known physics problems. This helps us in two ways, one, in motivating the definitions and the concepts, and two, in showing that topological analysis leads to a clearer understanding of the problem. The problems discussed are taken from classical mechanics, quantum mechanics, statistical mechanics, solid state physics, and biology (DNA), to emphasize some unity in diverse areas of physics. It is the real Euclidean sp...

We use machine learning to predict the dimension of a lattice polytope directly from its Ehrhart series. This is highly effective, achieving almost 100% accuracy. We also use machine learning to recover the volume of a lattice polytope from its Ehrhart series, and to recover the dimension, volume, and quasi-period of a rational polytope from its Ehrhart series. In each case we achieve very high accuracy, and we propose mathematical explanations for why this should be so.

We show that the recent derivation that triangleland's topology and geometry is $S^2$ from Heron's formula does not extend to quadrilaterals by considering Brahmagupta, Bretschneider and Coolidge's area formulae. That $N$-a-gonland is more generally $CP^{N - 2}$ (with $CP^1 = S^2$ recovering the triangleland sphere) follows from Kendall's extremization that is habitually used in Shape Theory, or the generalized Hopf map. We further explain our observation of non-extension in ...

These are the proceedings of the workshop "Math in the Black Forest", which brought together researchers in shape analysis to discuss promising new directions. Shape analysis is an inter-disciplinary area of research with theoretical foundations in infinite-dimensional Riemannian geometry, geometric statistics, and geometric stochastics, and with applications in medical imaging, evolutionary development, and fluid dynamics. The workshop is the 6th instance of a series of work...

At present, there is a great deal of confusion regarding complexity and its measures (reviews on complexity measures are found in, e.g. Lloyd, 2001 and Shalizi, 2006 and more references therein). Moreover, there is also confusion regarding the nature of life. In this situation, it seems the task of determining the fundamental complexity measures of life is especially difficult. Yet this task is just part of a greater task: obtaining substantial insights into the nature of bio...

A representation of the genetic code as a six-dimensional Boolean hypercube is described. This structure is the result of the hierarchical order of the interaction energies of the bases in codon-anticodon recognition. In this paper it is applied to study molecular evolution in vivo and in vitro. In the first case we compared aligned positions in homologous protein sequences and found two different behaviors: a) There are sites in which the different amino acids may be explain...

Many standard structural quantities, such as order parameters and correlation functions, exist for common condensed matter systems, such as spherical and rod-like particles. However, these structural quantities are often insufficient for characterizing the unique and highly complex structures often encountered in the emerging field of nano and microscale self-assembly, or other disciplines involving complex structures such as computational biology. Computer science algorithms...

The systematics of indices of physico-chemical properties of codons and amino acids across the genetic code are examined. Using a simple numerical labelling scheme for nucleic acid bases, data can be fitted as low-order polynomials of the 6 coordinates in the 64-dimensional codon weight space. The work confirms and extends recent studies by Siemion of amino acid conformational parameters. The connections between the present work, and recent studies of the genetic code structu...

This article investigates the Mahler measure of a family of 2-variate polynomials, denoted by $P_d, d\geq 1$, unbounded in both degree and genus. By using a closed formula for the Mahler measure introduced in "Volume function and Mahler measure of exact polynomials" (by Guilloux and March\'e), we are able to compute $m(P_d)$, for arbitrary $d$, as a sum of the values of dilogarithm at special roots of unity. We prove that $m(P_d)$ converges and the limit is proportional to $\...