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

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

Ultrasound as pretreatment in biogas production from crude glycerol

Air pollution, acid precipitation, ozone depletion and the gaseous emissions to the atmosphere are associated to the petroleum derivate use, currently considered the main energy source used in the world. Renewable energy sources are expected to replace them in order to solve these environmental concerns. Biofuels as biodiesel and biogas are renewable energy produced from natural matter. Studies made suggest that using the principal by-product of biodiesel’s production process, crude glycerol, is possible to obtain biogas. Biogas can be produced from an anaerobic digestion process and enhanced by using pretreatment in substrate. This work tested ultrasound pretreatment on crude glycerol as a substrate in the biogas production. Different times of pretreatment (15 and 30 minutes) were examined, to determinate the best performance and compare it to the untreated substrate. The biogas production was daily measured directly from the reactors. The results showed that ultrasound pretreatment improved methane production. The best result was obtained by using 30 minutes of pretreatment on crude glycerol.info:eu-repo/semantics/publishedVersio

Physicochemical characterization of moringa oleífera’s shells as biosorbent for pharmaceuticals biosorption

Pharmaceuticals as emerging contaminants have become one of the most controversial environmental issues at global scale. Over the years, the presence of antibiotics and antiinflammatory drugs in rivers, lakes, and even in drinking water streams has increased. The waste water treatment plants (WWTPs) lack the necessary technology to remove concentrations within the range ng/l-mg/l and therefore, the need to develop new methods able to remove contaminants in an effective, low cost and environmental friendly way arises. “Biosorption” appears as a possible solution. The present work is focused on studying the potential adsorption capacity of Moringa oleífera (MO) to remove Diclofenac (DCF) and Oxytetracycline (OTC) from wastewater. Through different experiences, it was possible to characterizes the main functional groups of MO and determine the principal responsible of the adsorption process.info:eu-repo/semantics/publishedVersio

Architecture to Support Automatic Grading Processes in Programming Teaching

La calificación automática de tareas de programación es un tema importante dentro del campo de la innovación educativa que se enfoca en mejorar las habilidades de programación de los estudiantes y en optimizar el tiempo que el profesorado dedica a ello. Uno de los principales problemas vigentes está relacionado con la diversidad de criterios para calificar las tareas de programación. El presente trabajo propone e implementa una arquitectura, basada en el concepto de orquestación de servicios, para soportar varios procesos de calificación automática de tareas de programación. Esto es obtenido a través de las características de modularidad, extensibilidad y flexibilidad que la arquitectura provee al proceso de calificación. La arquitectura define como pieza clave un elemento llamado Grading-submodule, el mismo que provee un servicio de evaluación del código fuente considerando un criterio de calificación. La implementación se ha llevado a cabo sobre la herramienta Virtual Programming Lab; y los resultados demuestran la factibilidad de realización, y la utilidad tanto para el profesorado como para los estudiantes. ---------- ABSTRACT---------- Automatic grading of programming assignments is an important topic in academic research. It aims at improving students’ programming skills and optimizing the time of teaching staff. One important gap is related to the diversity of criteria to grade programming assignments. This work proposes and implements an architecture, based on the services orchestration concept, to support many kinds of grading process of programming assignments. It is achieved due architecture’s features including modularity, extensibility, and flexibility. The cornerstone of the architecture is a new software component named Grading-submodule, which provides of an evaluation service for the source code considering a grading criterion. The implementation has been done on Virtual Programming Lab. Results show workability, and uselfulness for teaching staff and students