Chirality in a quaternionic representation of the genetic code

A quaternionic representation of the genetic code, previously reported by the authors, is updated in order to incorporate chirality of nucleotide bases and amino acids. The original representation assigns to each nucleotide base a prime integer quaternion of norm 7 and involves a function that associates with each codon, represented by three of these quaternions, another integer quaternion (amino acid type quaternion) in such a way that the essentials of the standard genetic code (particulaty its degeneration) are preserved. To show the advantages of such a quaternionic representation we have, in turn, associated with each amino acid of a given protein, besides of the type quaternion, another real one according to its order along the protein (order quaternion) and have designed an algorithm to go from the primary to the tertiary structure of the protein by using type and order quaternions. In this context, we incorporate chirality in our representation by observing that the set of eight integer quaternions of norm 7 can be partitioned into a pair of subsets of cardinality four each with their elements mutually conjugates and by putting they in correspondence one to one with the two sets of enantiomers (D and L) of the four nucleotide bases adenine, cytosine, guanine and uracil, respectively. Thus, guided by two diagrams proposed for the codes evolution, we define functions that in each case assign a L- (D-) amino acid type integer quaternion to the triplets of D- (L-) bases. The assignation is such that for a given D-amino acid, the associated integer quaternion is the conjugate of that one corresponding to the enantiomer L. The chiral type quaternions obtained for the amino acids are used, together with a common set of order quaternions, to describe the folding of the two classes, L and D, of homochiral proteins.Comment: 17 pages, 9 figures. arXiv admin note: substantial text overlap with arXiv:1505.0465

Flow rate of polygonal grains through a bottleneck: Interplay between shape and size

We report two-dimensional simulations of circular and polygonal grains passing through an aperture at the bottom of a silo. The mass flow rate for regular polygons is lower than for disks as observed by other authors. We show that both the exit velocity of the grains and the packing fraction are lower for polygons, which leads to the reduced flow rate. We point out the importance of the criteria used to define when two objects of different shape are considered to be of the same size. Depending on this criteria, the mass flow rate may vary significantly for some polygons. Moreover, the particle flow rate is non-trivially related to a combination of mass flow rate, particle shape and particle size. For some polygons, the particle flow rate may be lower or higher than that of the corresponding disks depending on the size comparison criteria.Comment: 9 pages, 8 figure

Quaternionic representation of the genetic code

A heuristic diagram of the evolution of the standard genetic code is presented. It incorporates, in a way that resembles the energy levels of an atom, the physical notion of broken symmetry and it is consistent with original ideas by Crick on the origin and evolution of the code as well as with the chronological order of appearence of the amino acids along the evolution as inferred from work that mixtures known experimental results with theoretical speculations. Suggested by the diagram we propose a Hamilton quaternions based mathematical representation of the code as it stands now-a-days. The central object in the description is a codon function that assigns to each amino acid an integer quaternion in such a way that the observed code degeneration is preserved. We emphasize the advantages of a quaternionic representation of amino acids taking as an example the folding of proteins. With this aim we propose an algorithm to go from the quaternions sequence to the protein three dimensional structure which can be compared with the corresponding experimental one stored at the Protein Data Bank. In our criterion the mathematical representation of the genetic code in terms of quaternions merits to be taken into account because it describes not only most of the known properties of the genetic code but also opens new perspectives that are mainly derived from the close relationship between quaternions and rotations.Comment: 19 pages, 11 figure

Exact predictions from Edwards ensemble vs. realistic simulations of tapped narrow two-dimensional granular columns

We simulate via a Discrete Element Method the tapping of a narrow column of disk under gravity. For frictionless disks, this system has a simple analytic expression for the density of states in the Edwards volume ensemble. We compare the predictions of the ensemble at constant compactivity against the results for the steady states obtained in the simulations. We show that the steady states cannot be properly described since the microstates sampled are not in correspondence with the predicted distributions, suggesting that the postulates of flat measure and ergodicity are, either or both, invalid for this simple realization of a static granular system. However, we show that certain qualitative features of the volume fluctuations difficult to predict from simple arguments are captured by the theory.Comment: 11 pages, 6 figure

Effect of the trabecular bone microstructure on measuring its thermal conductivity: A computer modeling-based study

[EN] The objective of this work is to quantify the relation between the value of the effective thermal conductivity of trabecular bone and its microstructure and marrow content. The thermal conductivity of twenty bovine trabecular bone samples was measured prior to and after defatting at 37, 47, and 57 degrees C. Computer models were built including the microstructure geometry and the gap between the tissue and measurement probe. The thermal conductivity (k) measured was 0.39 +/- 0.06 W m(-1) K-1 at 37 degrees C, with a temperature dependence of + 0.2%degrees C-1. Replacing marrow by phosphate-buffered saline (defatting) increased both the computer simulations and measurement results by 0.04 W m(-1) K-1. The computer simulations showed that k increases by 0.02-0.04 W m(-1) K-1 when the model includes a gap filled by phosphate-buffered saline between the tissue and measurement probe. In the presence of microstructure and fatty red marrow, k varies by +/- 0.01 W m(-1) K-1 compared with the case considering matrix only, which suggests that there are no significant differences between cortical and trabecular bone in terms of k. The computer results showed that the presence of a gap filled by phosphate-buffered saline around the energy applicator changes maximum temperature by < 0.7 degrees C, while including the bone microstructure involved a variation of < 0.2 mm in the isotherm location. Future experimental studies on measuring the value of k involving the insertion of a probe into the bone through a drill hole should consider the bias found in the simulations. Thermal models based on a homogeneous geometry (i.e. ignoring the microstructure) could provide sufficient accuracy.This work was supported by a grant from the "Agencia Nacional de Promocion Cientfica y Tecnologica de Argentina" (Ref. PICT-2016-2303), by the National Scientific and Technical Research Council of Argentina (Grant PIO CONICET-UNAJ 0001), and by the Spanish "Programa Estatal de Investigacion, Desarrollo e Innovacion Orientada a los Retos de la Sociedad" under Grant TEC2014-52383-C3-R (TEC2014-52383-C3-1-R).Fajardo, JE.; Carlevaro, CM.; Vericat, F.; Berjano, E.; Irastorza, RM. (2018). Effect of the trabecular bone microstructure on measuring its thermal conductivity: A computer modeling-based study. Journal of Thermal Biology. 77:131-136. https://doi.org/10.1016/j.jtherbio.2018.08.009S1311367

Nonlinear dynamic analysis of an optimal particle damper

We study the dynamical behavior of a single degree of freedom mechanical system with a particle damper. The particle (granular) damping was optimized for the primary system operating condition by using an appropriate gap size for a prismatic enclosure. The particles absorb the kinetic energy of the vibrating structure and convert it into heat through the inelastic collisions and friction. This results in a highly nonlinear mechanical system. Considering linear signal analysis, state space reconstruction, Poincar\'e sections and the determination of maximal Lyapunov exponents, the motion of the granular system inside the enclosure is characterized for a wide frequency range. With the excitation frequency as control parameter, either regular and chaotic motion of the granular bed are found and their influence on the damping is analyzed.Comment: 18 pages, 8 figures. arXiv admin note: text overlap with arXiv:1105.030

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts