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

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

How does an external electrical field affect adsorption patterns of thiol and thiolate on the gold substrate ?

The responsive behavior of methanethiol and methylthiolate molecules on the Au(111) surface with an applied electrical potential is studied, and it is shown how the sulfur adsorption site, the S-H bond orientation and the interacting energy change with an external electric field strength. The electron charge density corresponding to an electric field minus that obtained in zero field, with zero-field optimal geometry, is calculated to explain the responsive behavior. The interacting energy for the intact methanethiol adsorption is larger than that for the dissociative one, showing that an external electric field can not make the hydrogen dissociate from the sulfur.Comment: 11 pages, 3 figures, LaTe

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

Cluster pair correlation function of simple fluids: energetic connectivity criteria

We consider the clustering of Lennard-Jones particles by using an energetic connectivity criterion proposed long ago by T.L. Hill [J. Chem. Phys. 32, 617 (1955)] for the bond between pairs of particles. The criterion establishes that two particles are bonded (directly connected) if their relative kinetic energy is less than minus their relative potential energy. Thus, in general, it depends on the direction as well as on the magnitude of the velocities and positions of the particles. An integral equation for the pair connectedness function, proposed by two of the authors [Phys Rev. E 61, R6067 (2000)], is solved for this criterion and the results are compared with those obtained from molecular dynamics simulations and from a connectedness Percus-Yevick like integral equation for a velocity-averaged version of Hill's energetic criterion.Comment: 17 pages, 6 figure

The Role of a Double Molecular Anchor on the Mobility and Self-Assembly of Thiols on Au(111): The Case of Mercaptobenzoic Acid

The dynamics of the self-assembly process of thiol molecules on Au(111) is affected by the interplay between molecule–substrate and molecule–molecule interactions. Therefore, it is interesting to explore the effect of a second anchor to the gold surface, in addition to the S atom, on both the order and the feasibility of phase transitions in self-assembled monolayers. To assess the role of an additional O anchor, we have compared the adsorption of two mercaptobenzoic acid isomers, 2-mercaptobenzoic acid (2-MBA) and 4-mercaptobenzoic acid (4-MBA), on Au(111). Results from scanning tunneling microscopy, X-ray photoelectron spectroscopy, electrochemical techniques, and density functional theory calculations show that the additional O anchor in 2-MBA hinders surface mobility, reducing domain size and impeding the molecular reorganization involved in phase transition to denser phases on the Au(111) substrates. This knowledge can help to predict the range order and molecular density of the thiol SAM depending on the chemical structure of the adsorbate.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada

New insight into the chemical nature of the plasmonic nanostructures synthesized by the reduction of Au(III) with sulfide species

We have studied the products of the controversial synthesis of HAuCl4 with Na2S, which include gold nanostructures (Au NSs) that absorb in the near-infrared (NIR) region and are highly promising for photothermal therapies and other nanomedical applications. From high-resolution transmission electron microscopy, X-ray absorption spectroscopy, and small-angle X-ray scattering, we have found that only metallic Au NSs are formed as a result of this synthesis, with no detectable amount of gold sulfide or other oxidized gold species that could account for the NIR absorption. Different sulfur species are adsorbed on the Au NSs, mainly sulfides (monomeric sulfur) and polysulfides, similar to what is found on the planar gold surfaces, therefore precluding the idea that thiosulfate or other oxidized species are the actual reducing agents for Au(III) ions. The presence of strongly adsorbed S species, which are difficult to remove from the gold surface, is of great importance for their applications as regards toxicity and use of postfunctionalization strategies to anchor biomolecules and/or to increase circulation time after administration.Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicada