Automation on the generation of genome scale metabolic models

Background: Nowadays, the reconstruction of genome scale metabolic models is a non-automatized and interactive process based on decision taking. This lengthy process usually requires a full year of one person's work in order to satisfactory collect, analyze and validate the list of all metabolic reactions present in a specific organism. In order to write this list, one manually has to go through a huge amount of genomic, metabolomic and physiological information. Currently, there is no optimal algorithm that allows one to automatically go through all this information and generate the models taking into account probabilistic criteria of unicity and completeness that a biologist would consider. Results: This work presents the automation of a methodology for the reconstruction of genome scale metabolic models for any organism. The methodology that follows is the automatized version of the steps implemented manually for the reconstruction of the genome scale metabolic model of a photosynthetic organism, {\it Synechocystis sp. PCC6803}. The steps for the reconstruction are implemented in a computational platform (COPABI) that generates the models from the probabilistic algorithms that have been developed. Conclusions: For validation of the developed algorithm robustness, the metabolic models of several organisms generated by the platform have been studied together with published models that have been manually curated. Network properties of the models like connectivity and average shortest mean path of the different models have been compared and analyzed.Comment: 24 pages, 2 figures, 2 table

A real delivery problem dealt with Monte Carlo techniques

[EN] In this paper we use Monte Carlo Techniques to deal with a real world delivery problem of a food company in Valencia (Spain). The problem is modeled as a set of 11 instances of the well known Vehicle Routing Problem, VRP, with additional time constraints. Given that VRP is a NP-hard problem, a heuristic algorithm, based on Monte Carlo techniques, is implemented. The solution proposed by this heuristic algorithm reaches distance and money savings of about 20% and 5% respectively.This research was partially supported by MICINN, Project MTM2013-43540-P and by UPV, Project Programa de Apoyo a la Investigación y Desarrollo de la UPV PAID-06-12.S577181Fernández de Córdoba, P., L.M. García-Raffi and J.M. Sanchis Llopis (1998), A heuristic algorithm based on Monte Carlo methods for the Rural Postman Problem.Computers and Op. Research,25, No. 12, pp. 1097–1106, 1998.Fernández de Córdoba, P. and L.M. García-Raffi, E. Nieto and J.M. Sanchis Llopis (1999a), Aplicación de técnicas Monte Carlo a un problema real de Rutas de Vehículos.Anales de Ingeniería, Colombia. In press.Fernández de Córdoba, P., L.M. García-Raffi and J.M. Sanchis Llopis (1999b), A Constructive Parallel Algorithm based on Monte Carlo techniques for Routing Problems, Submitted toParallel Computers.Laporte, G. (1992), The Vehicle Routing Problem: an overview of exact and approximate algorithms,European Journal of Operations Research,59, 345.Laporte, G., M. Desrochers and Y. Nobert (1985), “Optimal Routing under Capacity and Distance Restrictions.Operations Research,33, pp. 1050–1073.Laporte G. and Y. Nobert (1987), Exact algorithms for The Vehicle Routing Problem,Surveys in Combinatorial Optimization (S. Martello, G. Laporte, M. Minoux and C. Ribeiro Eds.). North-HollandAmsterdamMayado, A. (1998), Organización de los itinerarios de la flota de camiones de reparto de una sociedad cooperativa. Optimización mediante técnicas de simulación Monte Carlo. Proyecto Fin de Carrera. E.T.S.I.I. Universidad Politécnica de Valencia

Coherent pion production in neutrino nucleus collision in the 1 GeV region

We calculate cross sections for coherent pion production in nuclei induced by neutrinos and antineutrinos of the electron and muon type. The analogies and differences between this process and the related ones of coherent pion production induced by photons, or the (p,n) and $(^3 He, t)$ reactions are discussed. The process is one of the several ones occurring for intermediate energy neutrinos, to be considered when detecting atmospheric neutrinos. For this purpose the results shown here can be easily extrapolated to other energies and other nuclei.Comment: 13 pages, LaTex, 8 post-script figures available at [email protected]

Lack of uniqueness for weak solutions of the incompressible porous media equation

In this work we consider weak solutions of the incompressible 2-D porous media equation. By using the approach of De Lellis-Sz\'ekelyhidi we prove non-uniqueness for solutions in $L^\infty$ in space and time.Comment: 23 pages, 2 fugure

Projectile Δ\Delta and target-Roper excitation in the p (d, d')X reaction

In this paper we compare a model that contains the mechanisms of $\Delta$ excitation in the projectile and Roper excitation in the target with experimental data from two (d, d') experiments on a proton target. The agreement of the theory with the experiment is fair for the data taken at T_d = 2.3 GeV. The $\Delta$ excitation in the projectile is predicted close to the observed energy with the correct width. The theory, however, underpredicts by about 40% the cross sections measured at T_d = 1.6 GeV at angles where the cross section has fallen by about two orders of magnitude. The analysis done here allows to extract an approximate strength for the excitation of the Roper [N^*(1440)] excitation and a qualitative agreement with the theoretical predictions is also found.Comment: 8 ps figure

The cosmological constant of emergent spacetime in the Newtonian approximation

[EN] We present a simple quantum-mechanical estimate of the cosmological constant of a Newtonian Universe. We first mimic the dynamics of a Newtonian spacetime by means of a nonrelativistic quantum mechanics for the matter contents of the Universe (baryonic and dark) within a fixed (i.e. nondynamical) Euclidean spacetime. Then we identify an operator that plays, on the matter states, a role analogous to that played by the cosmological constant. Finally, we prove that there exists a quantum state for the matter fields, in which the above-mentioned operator has an expectation value equal to the cosmological constant of the given Newtonian Universe.This research was supported by grant no. RTI2018-102256-B-I00 (Spain).Castro-Palacio, JC.; Fernández De Córdoba, P.; Isidro, J. (2020). The cosmological constant of emergent spacetime in the Newtonian approximation. International Journal of Modern Physics D. 29(13):1-11. https://doi.org/10.1142/S0218271820500935S1112913Susskind, L. (1995). The world as a hologram. Journal of Mathematical Physics, 36(11), 6377-6396. doi:10.1063/1.531249Padmanabhan, T. (2016). The atoms of space, gravity and the cosmological constant. International Journal of Modern Physics D, 25(07), 1630020. doi:10.1142/s0218271816300202Padmanabhan, T. (2017). The atoms of spacetime and the cosmological constant. Journal of Physics: Conference Series, 880, 012008. doi:10.1088/1742-6596/880/1/012008Cabrera, D., & Isidro, J. M. (2017). Boltzmann Entropy of a Newtonian Universe. Entropy, 19(5), 212. doi:10.3390/e19050212Isidro, J. (2018). On the Holographic Bound in Newtonian Cosmology. Entropy, 20(2), 83. doi:10.3390/e20020083Verlinde, E. (2011). On the origin of gravity and the laws of Newton. Journal of High Energy Physics, 2011(4). doi:10.1007/jhep04(2011)029Astashenok, A. V., Elizalde, E., & Yurov, A. V. (2013). The cosmological constant as an eigenvalue of a Sturm-Liouville problem. Astrophysics and Space Science, 349(1), 25-32. doi:10.1007/s10509-013-1606-zBarrow, J. D., & Shaw, D. J. (2011). The value of the cosmological constant. General Relativity and Gravitation, 43(10), 2555-2560. doi:10.1007/s10714-011-1199-1Riess, A. G., Filippenko, A. V., Challis, P., Clocchiatti, A., Diercks, A., Garnavich, P. M., … Tonry, J. (1998). Observational Evidence from Supernovae for an Accelerating Universe and a Cosmological Constant. The Astronomical Journal, 116(3), 1009-1038. doi:10.1086/300499Hubble, E. (1929). A relation between distance and radial velocity among extra-galactic nebulae. Proceedings of the National Academy of Sciences, 15(3), 168-173. doi:10.1073/pnas.15.3.168Madelung, E. (1927). Quantentheorie in hydrodynamischer Form. Zeitschrift f�r Physik, 40(3-4), 322-326. doi:10.1007/bf01400372Cadoni, M., Casadio, R., Giusti, A., Mück, W., & Tuveri, M. (2018). Effective fluid description of the dark universe. Physics Letters B, 776, 242-248. doi:10.1016/j.physletb.2017.11.058Cadoni, M., Casadio, R., Giusti, A., & Tuveri, M. (2018). Emergence of a dark force in corpuscular gravity. Physical Review D, 97(4). doi:10.1103/physrevd.97.044047Elizalde, E., Odintsov, S. D., Romeo, A., Bytsenko, A. A., & Zerbini, S. (1994). Zeta Regularization Techniques with Applications. doi:10.1142/2065Blanchet, L., & Faye, G. (2000). Hadamard regularization. Journal of Mathematical Physics, 41(11), 7675-7714. doi:10.1063/1.1308506Finster, F., & Isidro, J. M. (2017). Lp-spectrum of the Schrödinger operator with inverted harmonic oscillator potential. Journal of Mathematical Physics, 58(9), 092104. doi:10.1063/1.4997418Rajeev, K., Chakraborty, S., & Padmanabhan, T. (2018). Inverting a normal harmonic oscillator: physical interpretation and applications. General Relativity and Gravitation, 50(9). doi:10.1007/s10714-018-2438-

Delta excitation in K^+-nucleus collisions

We present calculations for \Delta excitation in the (K^+,K^+) reaction in nuclei. The background from quasielastic K^+ scattering in the \Delta region is also evaluated and shown to be quite small in some kinematical regions, so as to allow for a clean identification of the \Delta excitation strength. Nuclear effects tied to the \Delta renormalization in the nucleus are considered and the reaction is shown to provide new elements to enrich our knowledge of the \Delta properties in a nuclear medium.Comment: 11 pages, 6 figures, LaTe